after_merge
stringlengths 28
79.6k
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stringlengths 20
79.6k
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stringlengths 38
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stringlengths 43
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stringclasses 555
values |
|---|---|---|---|---|
def console(self, console):
self._console = console
self.dockConsole.widget = console
self._update_palette()
|
def console(self, console):
self._console = console
self.dockConsole.widget = console
self._update_palette(None)
|
https://github.com/napari/napari/issues/1079
|
Traceback (most recent call last):
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 418, in _toggle_theme
self.theme = theme_names[(cur_theme + 1) % len(theme_names)]
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 130, in theme
self.palette = self.themes[theme]
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 114, in palette
self.events.palette()
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/Users/gbokota/Documents/projekty/napari/napari/_qt/qt_main_window.py", line 99, in <lambda>
lambda event: self._update_palette(event.palette)
AttributeError: 'Event' object has no attribute 'palette'
|
AttributeError
|
def _update_palette(self, event=None):
"""Update the napari GUI theme."""
# template and apply the primary stylesheet
themed_stylesheet = template(self.raw_stylesheet, **self.viewer.palette)
if self._console is not None:
self.console._update_palette(self.viewer.palette, themed_stylesheet)
self.setStyleSheet(themed_stylesheet)
self.canvas.bgcolor = self.viewer.palette["canvas"]
|
def _update_palette(self, event):
"""Update the napari GUI theme."""
# template and apply the primary stylesheet
themed_stylesheet = template(self.raw_stylesheet, **self.viewer.palette)
if self._console is not None:
self.console._update_palette(self.viewer.palette, themed_stylesheet)
self.setStyleSheet(themed_stylesheet)
self.canvas.bgcolor = self.viewer.palette["canvas"]
|
https://github.com/napari/napari/issues/1079
|
Traceback (most recent call last):
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 418, in _toggle_theme
self.theme = theme_names[(cur_theme + 1) % len(theme_names)]
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 130, in theme
self.palette = self.themes[theme]
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 114, in palette
self.events.palette()
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/Users/gbokota/Documents/projekty/napari/napari/_qt/qt_main_window.py", line 99, in <lambda>
lambda event: self._update_palette(event.palette)
AttributeError: 'Event' object has no attribute 'palette'
|
AttributeError
|
def toggle_console_visibility(self, event=None):
"""Toggle console visible and not visible.
Imports the console the first time it is requested.
"""
# force instantiation of console if not already instantiated
_ = self.console
viz = not self.dockConsole.isVisible()
# modulate visibility at the dock widget level as console is docakable
self.dockConsole.setVisible(viz)
if self.dockConsole.isFloating():
self.dockConsole.setFloating(True)
self.viewerButtons.consoleButton.setProperty(
"expanded", self.dockConsole.isVisible()
)
self.viewerButtons.consoleButton.style().unpolish(self.viewerButtons.consoleButton)
self.viewerButtons.consoleButton.style().polish(self.viewerButtons.consoleButton)
|
def toggle_console_visibility(self, event):
"""Toggle console visible and not visible.
Imports the console the first time it is requested.
"""
# force instantiation of console if not already instantiated
_ = self.console
viz = not self.dockConsole.isVisible()
# modulate visibility at the dock widget level as console is docakable
self.dockConsole.setVisible(viz)
if self.dockConsole.isFloating():
self.dockConsole.setFloating(True)
self.viewerButtons.consoleButton.setProperty(
"expanded", self.dockConsole.isVisible()
)
self.viewerButtons.consoleButton.style().unpolish(self.viewerButtons.consoleButton)
self.viewerButtons.consoleButton.style().polish(self.viewerButtons.consoleButton)
|
https://github.com/napari/napari/issues/1079
|
Traceback (most recent call last):
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 418, in _toggle_theme
self.theme = theme_names[(cur_theme + 1) % len(theme_names)]
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 130, in theme
self.palette = self.themes[theme]
File "/Users/gbokota/Documents/projekty/napari/napari/components/viewer_model.py", line 114, in palette
self.events.palette()
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/Users/gbokota/Documents/projekty/napari/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/Users/gbokota/Documents/projekty/napari/napari/_qt/qt_main_window.py", line 99, in <lambda>
lambda event: self._update_palette(event.palette)
AttributeError: 'Event' object has no attribute 'palette'
|
AttributeError
|
def __init__(self, layer):
super().__init__(layer)
self.layer.events.mode.connect(self.set_mode)
self.layer.events.n_dimensional.connect(self._on_n_dim_change)
self.layer.events.symbol.connect(self._on_symbol_change)
self.layer.events.size.connect(self._on_size_change)
self.layer.events.current_edge_color.connect(self._on_edge_color_change)
self.layer.events.current_face_color.connect(self._on_face_color_change)
self.layer.events.editable.connect(self._on_editable_change)
sld = QSlider(Qt.Horizontal)
sld.setFocusPolicy(Qt.NoFocus)
sld.setMinimum(1)
sld.setMaximum(100)
sld.setSingleStep(1)
value = self.layer.current_size
sld.setValue(int(value))
sld.valueChanged.connect(self.changeSize)
self.sizeSlider = sld
face_comboBox = QComboBox()
face_comboBox.addItems(self.layer._colors)
face_comboBox.activated[str].connect(self.changeFaceColor)
self.faceComboBox = face_comboBox
self.faceColorSwatch = QFrame()
self.faceColorSwatch.setObjectName("swatch")
self.faceColorSwatch.setToolTip("Face color swatch")
self._on_face_color_change()
edge_comboBox = QComboBox()
edge_comboBox.addItems(self.layer._colors)
edge_comboBox.activated[str].connect(self.changeEdgeColor)
self.edgeComboBox = edge_comboBox
self.edgeColorSwatch = QFrame()
self.edgeColorSwatch.setObjectName("swatch")
self.edgeColorSwatch.setToolTip("Edge color swatch")
self._on_edge_color_change()
symbol_comboBox = QComboBox()
symbol_comboBox.addItems([str(s) for s in Symbol])
index = symbol_comboBox.findText(self.layer.symbol, Qt.MatchFixedString)
symbol_comboBox.setCurrentIndex(index)
symbol_comboBox.activated[str].connect(self.changeSymbol)
self.symbolComboBox = symbol_comboBox
ndim_cb = QCheckBox()
ndim_cb.setToolTip("N-dimensional points")
ndim_cb.setChecked(self.layer.n_dimensional)
ndim_cb.stateChanged.connect(self.change_ndim)
self.ndimCheckBox = ndim_cb
self.select_button = QtModeRadioButton(
layer, "select_points", Mode.SELECT, tooltip="Select points"
)
self.addition_button = QtModeRadioButton(
layer, "add_points", Mode.ADD, tooltip="Add points"
)
self.panzoom_button = QtModeRadioButton(
layer, "pan_zoom", Mode.PAN_ZOOM, tooltip="Pan/zoom", checked=True
)
self.delete_button = QtModePushButton(
layer,
"delete_shape",
slot=self.layer.remove_selected,
tooltip="Delete selected points",
)
self.button_group = QButtonGroup(self)
self.button_group.addButton(self.select_button)
self.button_group.addButton(self.addition_button)
self.button_group.addButton(self.panzoom_button)
button_row = QHBoxLayout()
button_row.addWidget(self.delete_button)
button_row.addWidget(self.addition_button)
button_row.addWidget(self.select_button)
button_row.addWidget(self.panzoom_button)
button_row.addStretch(1)
button_row.setSpacing(4)
# grid_layout created in QtLayerControls
# addWidget(widget, row, column, [row_span, column_span])
self.grid_layout.addLayout(button_row, 0, 1, 1, 2)
self.grid_layout.addWidget(QLabel("opacity:"), 1, 0)
self.grid_layout.addWidget(self.opacitySlider, 1, 1, 1, 2)
self.grid_layout.addWidget(QLabel("point size:"), 2, 0)
self.grid_layout.addWidget(self.sizeSlider, 2, 1, 1, 2)
self.grid_layout.addWidget(QLabel("blending:"), 3, 0)
self.grid_layout.addWidget(self.blendComboBox, 3, 1, 1, 2)
self.grid_layout.addWidget(QLabel("symbol:"), 4, 0)
self.grid_layout.addWidget(self.symbolComboBox, 4, 1, 1, 2)
self.grid_layout.addWidget(QLabel("face color:"), 5, 0)
self.grid_layout.addWidget(self.faceComboBox, 5, 2)
self.grid_layout.addWidget(self.faceColorSwatch, 5, 1)
self.grid_layout.addWidget(QLabel("edge color:"), 6, 0)
self.grid_layout.addWidget(self.edgeComboBox, 6, 2)
self.grid_layout.addWidget(self.edgeColorSwatch, 6, 1)
self.grid_layout.addWidget(QLabel("n-dim:"), 7, 0)
self.grid_layout.addWidget(self.ndimCheckBox, 7, 1)
self.grid_layout.setRowStretch(8, 1)
self.grid_layout.setColumnStretch(1, 1)
self.grid_layout.setSpacing(4)
|
def __init__(self, layer):
super().__init__(layer)
self.layer.events.mode.connect(self.set_mode)
self.layer.events.n_dimensional.connect(self._on_n_dim_change)
self.layer.events.symbol.connect(self._on_symbol_change)
self.layer.events.size.connect(self._on_size_change)
self.layer.events.edge_color.connect(self._on_edge_color_change)
self.layer.events.face_color.connect(self._on_face_color_change)
self.layer.events.editable.connect(self._on_editable_change)
sld = QSlider(Qt.Horizontal)
sld.setFocusPolicy(Qt.NoFocus)
sld.setMinimum(1)
sld.setMaximum(100)
sld.setSingleStep(1)
value = self.layer.current_size
sld.setValue(int(value))
sld.valueChanged.connect(self.changeSize)
self.sizeSlider = sld
face_comboBox = QComboBox()
face_comboBox.addItems(self.layer._colors)
face_comboBox.activated[str].connect(self.changeFaceColor)
self.faceComboBox = face_comboBox
self.faceColorSwatch = QFrame()
self.faceColorSwatch.setObjectName("swatch")
self.faceColorSwatch.setToolTip("Face color swatch")
self._on_face_color_change()
edge_comboBox = QComboBox()
edge_comboBox.addItems(self.layer._colors)
edge_comboBox.activated[str].connect(self.changeEdgeColor)
self.edgeComboBox = edge_comboBox
self.edgeColorSwatch = QFrame()
self.edgeColorSwatch.setObjectName("swatch")
self.edgeColorSwatch.setToolTip("Edge color swatch")
self._on_edge_color_change()
symbol_comboBox = QComboBox()
symbol_comboBox.addItems([str(s) for s in Symbol])
index = symbol_comboBox.findText(self.layer.symbol, Qt.MatchFixedString)
symbol_comboBox.setCurrentIndex(index)
symbol_comboBox.activated[str].connect(self.changeSymbol)
self.symbolComboBox = symbol_comboBox
ndim_cb = QCheckBox()
ndim_cb.setToolTip("N-dimensional points")
ndim_cb.setChecked(self.layer.n_dimensional)
ndim_cb.stateChanged.connect(self.change_ndim)
self.ndimCheckBox = ndim_cb
self.select_button = QtModeRadioButton(
layer, "select_points", Mode.SELECT, tooltip="Select points"
)
self.addition_button = QtModeRadioButton(
layer, "add_points", Mode.ADD, tooltip="Add points"
)
self.panzoom_button = QtModeRadioButton(
layer, "pan_zoom", Mode.PAN_ZOOM, tooltip="Pan/zoom", checked=True
)
self.delete_button = QtModePushButton(
layer,
"delete_shape",
slot=self.layer.remove_selected,
tooltip="Delete selected points",
)
self.button_group = QButtonGroup(self)
self.button_group.addButton(self.select_button)
self.button_group.addButton(self.addition_button)
self.button_group.addButton(self.panzoom_button)
button_row = QHBoxLayout()
button_row.addWidget(self.delete_button)
button_row.addWidget(self.addition_button)
button_row.addWidget(self.select_button)
button_row.addWidget(self.panzoom_button)
button_row.addStretch(1)
button_row.setSpacing(4)
# grid_layout created in QtLayerControls
# addWidget(widget, row, column, [row_span, column_span])
self.grid_layout.addLayout(button_row, 0, 1, 1, 2)
self.grid_layout.addWidget(QLabel("opacity:"), 1, 0)
self.grid_layout.addWidget(self.opacitySlider, 1, 1, 1, 2)
self.grid_layout.addWidget(QLabel("point size:"), 2, 0)
self.grid_layout.addWidget(self.sizeSlider, 2, 1, 1, 2)
self.grid_layout.addWidget(QLabel("blending:"), 3, 0)
self.grid_layout.addWidget(self.blendComboBox, 3, 1, 1, 2)
self.grid_layout.addWidget(QLabel("symbol:"), 4, 0)
self.grid_layout.addWidget(self.symbolComboBox, 4, 1, 1, 2)
self.grid_layout.addWidget(QLabel("face color:"), 5, 0)
self.grid_layout.addWidget(self.faceComboBox, 5, 2)
self.grid_layout.addWidget(self.faceColorSwatch, 5, 1)
self.grid_layout.addWidget(QLabel("edge color:"), 6, 0)
self.grid_layout.addWidget(self.edgeComboBox, 6, 2)
self.grid_layout.addWidget(self.edgeColorSwatch, 6, 1)
self.grid_layout.addWidget(QLabel("n-dim:"), 7, 0)
self.grid_layout.addWidget(self.ndimCheckBox, 7, 1)
self.grid_layout.setRowStretch(8, 1)
self.grid_layout.setColumnStretch(1, 1)
self.grid_layout.setSpacing(4)
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def _on_display_change(self):
parent = self.node.parent
self.node.transforms = ChainTransform()
self.node.parent = None
if self.layer.dims.ndisplay == 2:
self.node = Compound([Markers(), Markers(), Line()])
else:
self.node = Compound([Markers(), Markers()])
self.node.parent = parent
self._reset_base()
|
def _on_display_change(self):
parent = self.node.parent
self.node.transforms = ChainTransform()
self.node.parent = None
if self.layer.dims.ndisplay == 2:
self.node = Compound([Markers(), Markers(), Line()])
else:
self.node = Markers()
self.node.parent = parent
self._reset_base()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def _on_data_change(self, event=None):
# Check if ndisplay has changed current node type needs updating
if (self.layer.dims.ndisplay == 3 and len(self.node._subvisuals) != 2) or (
self.layer.dims.ndisplay == 2 and len(self.node._subvisuals) != 3
):
self._on_display_change()
self._on_highlight_change()
if len(self.layer._data_view) > 0:
edge_color = self.layer.edge_color[self.layer._indices_view]
face_color = self.layer.face_color[self.layer._indices_view]
else:
edge_color = np.array([[0.0, 0.0, 0.0, 1.0]], dtype=np.float32)
face_color = np.array([[1.0, 1.0, 1.0, 1.0]], dtype=np.float32)
# Set vispy data, noting that the order of the points needs to be
# reversed to make the most recently added point appear on top
# and the rows / columns need to be switch for vispys x / y ordering
if len(self.layer._data_view) == 0:
data = np.zeros((1, self.layer.dims.ndisplay))
size = [0]
else:
data = self.layer._data_view
size = self.layer._size_view
set_data = self.node._subvisuals[0].set_data
set_data(
data[:, ::-1] + 0.5,
size=size,
edge_width=self.layer.edge_width,
symbol=self.layer.symbol,
edge_color=edge_color,
face_color=face_color,
scaling=True,
)
self.node.update()
|
def _on_data_change(self, event=None):
# Check if ndisplay has changed current node type needs updating
if (self.layer.dims.ndisplay == 3 and not isinstance(self.node, Markers)) or (
self.layer.dims.ndisplay == 2 and not isinstance(self.node, Compound)
):
self._on_display_change()
self._on_highlight_change()
if len(self.layer._data_view) > 0:
edge_color = self.layer.edge_color[self.layer._indices_view]
face_color = self.layer.face_color[self.layer._indices_view]
else:
edge_color = np.array([[0.0, 0.0, 0.0, 1.0]], dtype=np.float32)
face_color = np.array([[1.0, 1.0, 1.0, 1.0]], dtype=np.float32)
# Set vispy data, noting that the order of the points needs to be
# reversed to make the most recently added point appear on top
# and the rows / columns need to be switch for vispys x / y ordering
if len(self.layer._data_view) == 0:
data = np.zeros((1, self.layer.dims.ndisplay))
size = [0]
else:
data = self.layer._data_view
size = self.layer._size_view
if self.layer.dims.ndisplay == 2:
set_data = self.node._subvisuals[0].set_data
else:
set_data = self.node.set_data
set_data(
data[:, ::-1] + 0.5,
size=size,
edge_width=self.layer.edge_width,
symbol=self.layer.symbol,
edge_color=edge_color,
face_color=face_color,
scaling=True,
)
self.node.update()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def _on_highlight_change(self, event=None):
if len(self.layer._highlight_index) > 0:
# Color the hovered or selected points
data = self.layer._data_view[self.layer._highlight_index]
if data.ndim == 1:
data = np.expand_dims(data, axis=0)
size = self.layer._size_view[self.layer._highlight_index]
else:
data = np.zeros((1, self.layer.dims.ndisplay))
size = 0
self.node._subvisuals[1].set_data(
data[:, ::-1] + 0.5,
size=size,
edge_width=self._highlight_width,
symbol=self.layer.symbol,
edge_color=self._highlight_color,
face_color=transform_color("transparent"),
scaling=True,
)
# only draw a box in 2D
if self.layer.dims.ndisplay == 2:
if self.layer._highlight_box is None or 0 in self.layer._highlight_box.shape:
pos = np.zeros((1, self.layer.dims.ndisplay))
width = 0
else:
pos = self.layer._highlight_box
width = self._highlight_width
self.node._subvisuals[2].set_data(
pos=pos[:, ::-1] + 0.5,
color=self._highlight_color,
width=width,
)
self.node.update()
|
def _on_highlight_change(self, event=None):
if self.layer.dims.ndisplay == 3:
return
if len(self.layer._highlight_index) > 0:
# Color the hovered or selected points
data = self.layer._data_view[self.layer._highlight_index]
if data.ndim == 1:
data = np.expand_dims(data, axis=0)
size = self.layer._size_view[self.layer._highlight_index]
face_color = self.layer.face_color[
self.layer._indices_view[self.layer._highlight_index]
]
else:
data = np.zeros((1, self.layer.dims.ndisplay))
size = 0
face_color = np.array([[1.0, 1.0, 1.0, 1.0]], dtype=np.float32)
self.node._subvisuals[1].set_data(
data[:, ::-1] + 0.5,
size=size,
edge_width=self._highlight_width,
symbol=self.layer.symbol,
edge_color=self._highlight_color,
face_color=face_color,
scaling=True,
)
if self.layer._highlight_box is None or 0 in self.layer._highlight_box.shape:
pos = np.zeros((1, self.layer.dims.ndisplay))
width = 0
else:
pos = self.layer._highlight_box
width = self._highlight_width
self.node._subvisuals[2].set_data(
pos=pos[:, ::-1] + 0.5, color=self._highlight_color, width=width
)
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def __init__(
self,
data=None,
*,
properties=None,
symbol="o",
size=10,
edge_width=1,
edge_color="black",
edge_color_cycle=None,
edge_colormap="viridis",
edge_contrast_limits=None,
face_color="white",
face_color_cycle=None,
face_colormap="viridis",
face_contrast_limits=None,
n_dimensional=False,
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending="translucent",
visible=True,
):
if data is None:
data = np.empty((0, 2))
else:
data = np.atleast_2d(data)
ndim = data.shape[1]
super().__init__(
ndim,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.events.add(
mode=Event,
size=Event,
edge_width=Event,
face_color=Event,
current_face_color=Event,
edge_color=Event,
current_edge_color=Event,
symbol=Event,
n_dimensional=Event,
highlight=Event,
)
# update highlights when the layer is selected/deselected
self.events.select.connect(self._set_highlight)
self.events.deselect.connect(self._set_highlight)
self._colors = get_color_namelist()
# Save the point coordinates
self._data = np.asarray(data)
self.dims.clip = False
# Save the properties
if properties is None:
properties = {}
elif not isinstance(properties, dict):
properties = dataframe_to_properties(properties)
self._properties = self._validate_properties(properties)
# Save the point style params
self.symbol = symbol
self._n_dimensional = n_dimensional
self.edge_width = edge_width
# The following point properties are for the new points that will
# be added. For any given property, if a list is passed to the
# constructor so each point gets its own value then the default
# value is used when adding new points
if np.isscalar(size):
self._current_size = np.asarray(size)
else:
self._current_size = 10
# Indices of selected points
self._selected_data = []
self._selected_data_stored = []
self._selected_data_history = []
# Indices of selected points within the currently viewed slice
self._selected_view = []
# Index of hovered point
self._value = None
self._value_stored = None
self._mode = Mode.PAN_ZOOM
self._mode_history = self._mode
self._status = self.mode
self._highlight_index = []
self._highlight_box = None
self._drag_start = None
# Nx2 array of points in the currently viewed slice
self._data_view = np.empty((0, 2))
# Sizes of points in the currently viewed slice
self._size_view = 0
# Full data indices of points located in the currently viewed slice
self._indices_view = []
self._drag_box = None
self._drag_box_stored = None
self._is_selecting = False
self._clipboard = {}
with self.block_update_properties():
self.edge_color_property = ""
self.edge_color = edge_color
if edge_color_cycle is None:
edge_color_cycle = DEFAULT_COLOR_CYCLE
self.edge_color_cycle = edge_color_cycle
self.edge_colormap = edge_colormap
self._edge_contrast_limits = edge_contrast_limits
self._face_color_property = ""
self.face_color = face_color
if face_color_cycle is None:
face_color_cycle = DEFAULT_COLOR_CYCLE
self.face_color_cycle = face_color_cycle
self.face_colormap = face_colormap
self._face_contrast_limits = face_contrast_limits
self.refresh_colors()
# set the current_* properties
self._current_edge_color = self.edge_color[-1]
self._current_face_color = self.face_color[-1]
self.size = size
self.current_properties = {
k: np.asarray([v[-1]]) for k, v in self.properties.items()
}
# Trigger generation of view slice and thumbnail
self._update_dims()
|
def __init__(
self,
data=None,
*,
properties=None,
symbol="o",
size=10,
edge_width=1,
edge_color="black",
edge_color_cycle=None,
edge_colormap="viridis",
edge_contrast_limits=None,
face_color="white",
face_color_cycle=None,
face_colormap="viridis",
face_contrast_limits=None,
n_dimensional=False,
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending="translucent",
visible=True,
):
if data is None:
data = np.empty((0, 2))
else:
data = np.atleast_2d(data)
ndim = data.shape[1]
super().__init__(
ndim,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.events.add(
mode=Event,
size=Event,
edge_width=Event,
face_color=Event,
edge_color=Event,
symbol=Event,
n_dimensional=Event,
highlight=Event,
)
self._colors = get_color_namelist()
# Save the point coordinates
self._data = np.asarray(data)
self.dims.clip = False
# Save the properties
if properties is None:
properties = {}
elif not isinstance(properties, dict):
properties = dataframe_to_properties(properties)
self._properties = self._validate_properties(properties)
# Save the point style params
self.symbol = symbol
self._n_dimensional = n_dimensional
self.edge_width = edge_width
# The following point properties are for the new points that will
# be added. For any given property, if a list is passed to the
# constructor so each point gets its own value then the default
# value is used when adding new points
if np.isscalar(size):
self._current_size = np.asarray(size)
else:
self._current_size = 10
# Indices of selected points
self._selected_data = []
self._selected_data_stored = []
self._selected_data_history = []
# Indices of selected points within the currently viewed slice
self._selected_view = []
# Index of hovered point
self._value = None
self._value_stored = None
self._selected_box = None
self._mode = Mode.PAN_ZOOM
self._mode_history = self._mode
self._status = self.mode
self._highlight_index = []
self._highlight_box = None
self._drag_start = None
# Nx2 array of points in the currently viewed slice
self._data_view = np.empty((0, 2))
# Sizes of points in the currently viewed slice
self._size_view = 0
# Full data indices of points located in the currently viewed slice
self._indices_view = []
self._drag_box = None
self._drag_box_stored = None
self._is_selecting = False
self._clipboard = {}
with self.block_update_properties():
self.edge_color_property = ""
self.edge_color = edge_color
if edge_color_cycle is None:
edge_color_cycle = DEFAULT_COLOR_CYCLE
self.edge_color_cycle = edge_color_cycle
self.edge_colormap = edge_colormap
self._edge_contrast_limits = edge_contrast_limits
self._face_color_property = ""
self.face_color = face_color
if face_color_cycle is None:
face_color_cycle = DEFAULT_COLOR_CYCLE
self.face_color_cycle = face_color_cycle
self.face_colormap = face_colormap
self._face_contrast_limits = face_contrast_limits
self.refresh_colors()
# set the current_* properties
self._current_edge_color = self.edge_color[-1]
self._current_face_color = self.face_color[-1]
self.size = size
self.current_properties = {
k: np.asarray([v[-1]]) for k, v in self.properties.items()
}
# Trigger generation of view slice and thumbnail
self._update_dims()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def data(self, data: np.ndarray):
cur_npoints = len(self._data)
self._data = data
# Adjust the size array when the number of points has changed
if len(data) < cur_npoints:
# If there are now fewer points, remove the size and colors of the
# extra ones
with self.events.set_data.blocker():
self._edge_color = self.edge_color[: len(data)]
self._face_color = self.face_color[: len(data)]
self._size = self._size[: len(data)]
for k in self.properties:
self.properties[k] = self.properties[k][: len(data)]
elif len(data) > cur_npoints:
# If there are now more points, add the size and colors of the
# new ones
with self.events.set_data.blocker():
adding = len(data) - cur_npoints
if len(self._size) > 0:
new_size = copy(self._size[-1])
for i in self.dims.displayed:
new_size[i] = self.current_size
else:
# Add the default size, with a value for each dimension
new_size = np.repeat(self.current_size, self._size.shape[1])
size = np.repeat([new_size], adding, axis=0)
for k in self.properties:
new_property = np.repeat(self.current_properties[k], adding, axis=0)
self.properties[k] = np.concatenate(
(self.properties[k], new_property), axis=0
)
# add new edge colors
if self._edge_color_mode == ColorMode.DIRECT:
new_edge_colors = np.tile(self._current_edge_color, (adding, 1))
elif self._edge_color_mode == ColorMode.CYCLE:
edge_color_property = self.current_properties[
self._edge_color_property
][0]
new_edge_colors = np.tile(
self.edge_color_cycle_map[edge_color_property],
(adding, 1),
)
elif self._edge_color_mode == ColorMode.COLORMAP:
edge_color_property_value = self.current_properties[
self._edge_color_property
][0]
ec, _ = map_property(
prop=edge_color_property_value,
colormap=self.edge_colormap[1],
contrast_limits=self._edge_contrast_limits,
)
new_edge_colors = np.tile(ec, (adding, 1))
self._edge_color = np.vstack((self.edge_color, new_edge_colors))
# add new face colors
if self._face_color_mode == ColorMode.DIRECT:
new_face_colors = np.tile(self._current_face_color, (adding, 1))
elif self._face_color_mode == ColorMode.CYCLE:
face_color_property_value = self.current_properties[
self._face_color_property
][0]
new_face_colors = np.tile(
self.face_color_cycle_map[face_color_property_value],
(adding, 1),
)
elif self._face_color_mode == ColorMode.COLORMAP:
face_color_property_value = self.current_properties[
self._face_color_property
][0]
fc, _ = map_property(
prop=face_color_property_value,
colormap=self.face_colormap[1],
contrast_limits=self._face_contrast_limits,
)
new_face_colors = np.tile(fc, (adding, 1))
self._face_color = np.vstack((self.face_color, new_face_colors))
self.size = np.concatenate((self._size, size), axis=0)
self.selected_data = list(np.arange(cur_npoints, len(data)))
self._update_dims()
self.events.data()
|
def data(self, data: np.ndarray):
cur_npoints = len(self._data)
self._data = data
# Adjust the size array when the number of points has changed
if len(data) < cur_npoints:
# If there are now fewer points, remove the size and colors of the
# extra ones
with self.events.set_data.blocker():
self._edge_color = self.edge_color[: len(data)]
self._face_color = self.face_color[: len(data)]
self._size = self._size[: len(data)]
for k in self.properties:
self.properties[k] = self.properties[k][: len(data)]
elif len(data) > cur_npoints:
# If there are now more points, add the size and colors of the
# new ones
with self.events.set_data.blocker():
adding = len(data) - cur_npoints
if len(self._size) > 0:
new_size = copy(self._size[-1])
for i in self.dims.displayed:
new_size[i] = self.current_size
else:
# Add the default size, with a value for each dimension
new_size = np.repeat(self.current_size, self._size.shape[1])
size = np.repeat([new_size], adding, axis=0)
for k in self.properties:
new_property = np.repeat(self.current_properties[k], adding, axis=0)
self.properties[k] = np.concatenate(
(self.properties[k], new_property), axis=0
)
# add new edge colors
if self._edge_color_mode == ColorMode.DIRECT:
new_edge_colors = np.tile(self._current_edge_color, (adding, 1))
elif self._edge_color_mode == ColorMode.CYCLE:
edge_color_property = self.current_properties[
self._edge_color_property
][0]
new_edge_colors = np.tile(
self.edge_color_cycle_map[edge_color_property],
(adding, 1),
)
elif self._edge_color_mode == ColorMode.COLORMAP:
edge_color_property_value = self.current_properties[
self._edge_color_property
][0]
ec, _ = map_property(
prop=edge_color_property_value,
colormap=self.edge_colormap[1],
contrast_limits=self._edge_contrast_limits,
)
new_edge_colors = np.tile(ec, (adding, 1))
self._edge_color = np.vstack((self.edge_color, new_edge_colors))
# add new face colors
if self._face_color_mode == ColorMode.DIRECT:
new_face_colors = np.tile(self._current_face_color, (adding, 1))
elif self._face_color_mode == ColorMode.CYCLE:
face_color_property_value = self.current_properties[
self._face_color_property
][0]
new_face_colors = np.tile(
self.face_color_cycle_map[face_color_property_value],
(adding, 1),
)
elif self._face_color_mode == ColorMode.COLORMAP:
face_color_property_value = self.current_properties[
self._face_color_property
][0]
fc, _ = map_property(
prop=face_color_property_value,
colormap=self.face_colormap[1],
contrast_limits=self._face_contrast_limits,
)
new_face_colors = np.tile(fc, (adding, 1))
self._face_color = np.vstack((self.face_color, new_face_colors))
self.size = np.concatenate((self._size, size), axis=0)
self._update_dims()
self.events.data()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def current_size(self, size: Union[None, float]) -> None:
self._current_size = size
if (
self._update_properties
and len(self.selected_data) > 0
and self._mode != Mode.ADD
):
for i in self.selected_data:
self.size[i, :] = (self.size[i, :] > 0) * size
self.refresh()
self.events.size()
self.status = format_float(self.current_size)
|
def current_size(self, size: Union[None, float]) -> None:
self._current_size = size
if self._update_properties and len(self.selected_data) > 0:
for i in self.selected_data:
self.size[i, :] = (self.size[i, :] > 0) * size
self.refresh()
self.status = format_float(self.current_size)
self.events.size()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def edge_width(self, edge_width: Union[None, float]) -> None:
self._edge_width = edge_width
self.status = format_float(self.edge_width)
self.events.edge_width()
|
def edge_width(self, edge_width: Union[None, float]) -> None:
self._edge_width = edge_width
self.status = format_float(self.edge_width)
self.events.edge_width()
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def edge_color(self, edge_color):
# if the provided face color is a string, first check if it is a key in the properties.
# otherwise, assume it is the name of a color
if self._is_color_mapped(edge_color):
if guess_continuous(self.properties[edge_color]):
self._edge_color_mode = ColorMode.COLORMAP
else:
self._edge_color_mode = ColorMode.CYCLE
self._edge_color_property = edge_color
self.refresh_colors()
else:
transformed_color = transform_color_with_defaults(
num_entries=len(self.data),
colors=edge_color,
elem_name="edge_color",
default="white",
)
self._edge_color = normalize_and_broadcast_colors(
len(self.data), transformed_color
)
self.edge_color_mode = ColorMode.DIRECT
self._edge_color_property = ""
self.events.edge_color()
|
def edge_color(self, edge_color):
# if the provided face color is a string, first check if it is a key in the properties.
# otherwise, assume it is the name of a color
if self._is_color_mapped(edge_color):
if guess_continuous(self.properties[edge_color]):
self._edge_color_mode = ColorMode.COLORMAP
else:
self._edge_color_mode = ColorMode.CYCLE
self._edge_color_property = edge_color
self.refresh_colors()
else:
transformed_color = transform_color_with_defaults(
num_entries=len(self.data),
colors=edge_color,
elem_name="edge_color",
default="white",
)
self._edge_color = normalize_and_broadcast_colors(
len(self.data), transformed_color
)
self.edge_color_mode = ColorMode.DIRECT
self._edge_color_property = ""
self.events.edge_color()
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def current_edge_color(self, edge_color: ColorType) -> None:
self._current_edge_color = transform_color(edge_color)
if (
self._update_properties
and len(self.selected_data) > 0
and self._mode != Mode.ADD
):
cur_colors: np.ndarray = self.edge_color
cur_colors[self.selected_data] = self._current_edge_color
self.edge_color = cur_colors
self.events.current_edge_color()
|
def current_edge_color(self, edge_color: ColorType) -> None:
self._current_edge_color = transform_color(edge_color)
if self._update_properties and len(self.selected_data) > 0:
cur_colors: np.ndarray = self.edge_color
cur_colors[self.selected_data] = self._current_edge_color
self.edge_color = cur_colors
self.events.edge_color()
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def face_color(self, face_color):
# if the provided face color is a string, first check if it is a key in the properties.
# otherwise, assume it is the name of a color
if self._is_color_mapped(face_color):
if guess_continuous(self.properties[face_color]):
self._face_color_mode = ColorMode.COLORMAP
else:
self._face_color_mode = ColorMode.CYCLE
self._face_color_property = face_color
self.refresh_colors()
else:
transformed_color = transform_color_with_defaults(
num_entries=len(self.data),
colors=face_color,
elem_name="face_color",
default="white",
)
self._face_color = normalize_and_broadcast_colors(
len(self.data), transformed_color
)
self.face_color_mode = ColorMode.DIRECT
self.events.face_color()
|
def face_color(self, face_color):
# if the provided face color is a string, first check if it is a key in the properties.
# otherwise, assume it is the name of a color
if self._is_color_mapped(face_color):
if guess_continuous(self.properties[face_color]):
self._face_color_mode = ColorMode.COLORMAP
else:
self._face_color_mode = ColorMode.CYCLE
self._face_color_property = face_color
self.refresh_colors()
else:
transformed_color = transform_color_with_defaults(
num_entries=len(self.data),
colors=face_color,
elem_name="face_color",
default="white",
)
self._face_color = normalize_and_broadcast_colors(
len(self.data), transformed_color
)
self.face_color_mode = ColorMode.DIRECT
self.events.face_color()
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def current_face_color(self, face_color: ColorType) -> None:
self._current_face_color = transform_color(face_color)
if (
self._update_properties
and len(self.selected_data) > 0
and self._mode != Mode.ADD
):
cur_colors: np.ndarray = self.face_color
cur_colors[self.selected_data] = self._current_face_color
self.face_color = cur_colors
self.events.current_face_color()
|
def current_face_color(self, face_color: ColorType) -> None:
self._current_face_color = transform_color(face_color)
if self._update_properties and len(self.selected_data) > 0:
cur_colors: np.ndarray = self.face_color
cur_colors[self.selected_data] = self._current_face_color
self.face_color = cur_colors
self.events.face_color()
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def refresh_colors(self, update_color_mapping: bool = True):
"""Calculate and update face and edge colors if using a cycle or color map
Parameters
----------
update_color_mapping : bool
If set to True, the function will recalculate the color cycle map
or colormap (whichever is being used). If set to False, the function
will use the current color cycle map or color map. For example, if you
are adding/modifying points and want them to be colored with the same
mapping as the other points (i.e., the new points shouldn't affect
the color cycle map or colormap), set update_color_mapping=False.
Default value is True.
"""
if self._update_properties:
if self._face_color_mode == ColorMode.CYCLE:
face_color_properties = self.properties[self._face_color_property]
if update_color_mapping:
self.face_color_cycle_map = {
k: c
for k, c in zip(
np.unique(face_color_properties),
self.face_color_cycle,
)
}
face_colors = np.array(
[self.face_color_cycle_map[x] for x in face_color_properties]
)
self._face_color = face_colors
self.events.face_color()
elif self._face_color_mode == ColorMode.COLORMAP:
face_color_properties = self.properties[self._face_color_property]
if update_color_mapping:
face_colors, contrast_limits = map_property(
prop=face_color_properties,
colormap=self.face_colormap[1],
)
self.face_contrast_limits = contrast_limits
else:
face_colors, _ = map_property(
prop=face_color_properties,
colormap=self.face_colormap[1],
contrast_limits=self.face_contrast_limits,
)
self._face_color = face_colors
if self._edge_color_mode == ColorMode.CYCLE:
edge_color_properties = self.properties[self._edge_color_property]
if update_color_mapping:
self.edge_color_cycle_map = {
k: c
for k, c in zip(
np.unique(edge_color_properties),
self.edge_color_cycle,
)
}
edge_colors = np.array(
[self.edge_color_cycle_map[x] for x in edge_color_properties]
)
self._edge_color = edge_colors
elif self._edge_color_mode == ColorMode.COLORMAP:
edge_color_properties = self.properties[self._edge_color_property]
if update_color_mapping:
edge_colors, contrast_limits = map_property(
prop=edge_color_properties,
colormap=self.edge_colormap[1],
)
self.edge_contrast_limits = contrast_limits
else:
edge_colors, _ = map_property(
prop=edge_color_properties,
colormap=self.edge_colormap[1],
contrast_limits=self.edge_contrast_limits,
)
self._edge_color = edge_colors
self.events.face_color()
self.events.edge_color()
|
def refresh_colors(self, update_color_mapping: bool = True):
"""Calculate and update face and edge colors if using a cycle or color map
Parameters
----------
update_color_mapping : bool
If set to True, the function will recalculate the color cycle map
or colormap (whichever is being used). If set to False, the function
will use the current color cycle map or color map. For example, if you
are adding/modifying points and want them to be colored with the same
mapping as the other points (i.e., the new points shouldn't affect
the color cycle map or colormap), set update_color_mapping=False.
Default value is True.
"""
if self._update_properties:
if self._face_color_mode == ColorMode.CYCLE:
face_color_properties = self.properties[self._face_color_property]
if update_color_mapping:
self.face_color_cycle_map = {
k: c
for k, c in zip(
np.unique(face_color_properties),
self.face_color_cycle,
)
}
face_colors = np.array(
[self.face_color_cycle_map[x] for x in face_color_properties]
)
self._face_color = face_colors
self.events.face_color()
self.events.highlight()
elif self._face_color_mode == ColorMode.COLORMAP:
face_color_properties = self.properties[self._face_color_property]
if update_color_mapping:
face_colors, contrast_limits = map_property(
prop=face_color_properties,
colormap=self.face_colormap[1],
)
self.face_contrast_limits = contrast_limits
else:
face_colors, _ = map_property(
prop=face_color_properties,
colormap=self.face_colormap[1],
contrast_limits=self.face_contrast_limits,
)
self._face_color = face_colors
if self._edge_color_mode == ColorMode.CYCLE:
edge_color_properties = self.properties[self._edge_color_property]
if update_color_mapping:
self.edge_color_cycle_map = {
k: c
for k, c in zip(
np.unique(edge_color_properties),
self.edge_color_cycle,
)
}
edge_colors = np.array(
[self.edge_color_cycle_map[x] for x in edge_color_properties]
)
self._edge_color = edge_colors
elif self._edge_color_mode == ColorMode.COLORMAP:
edge_color_properties = self.properties[self._edge_color_property]
if update_color_mapping:
edge_colors, contrast_limits = map_property(
prop=edge_color_properties,
colormap=self.edge_colormap[1],
)
self.edge_contrast_limits = contrast_limits
else:
edge_colors, _ = map_property(
prop=edge_color_properties,
colormap=self.edge_colormap[1],
contrast_limits=self.edge_contrast_limits,
)
self._edge_color = edge_colors
self.events.face_color()
self.events.edge_color()
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def selected_data(self, selected_data):
self._selected_data = list(selected_data)
selected = []
for c in self._selected_data:
if c in self._indices_view:
ind = list(self._indices_view).index(c)
selected.append(ind)
self._selected_view = selected
# Update properties based on selected points
if len(self._selected_data) == 0:
return
index = self._selected_data
edge_colors = np.unique(self.edge_color[index], axis=0)
if len(edge_colors) == 1:
edge_color = edge_colors[0]
with self.block_update_properties():
self.current_edge_color = edge_color
face_colors = np.unique(self.face_color[index], axis=0)
if len(face_colors) == 1:
face_color = face_colors[0]
with self.block_update_properties():
self.current_face_color = face_color
size = list(set([self.size[i, self.dims.displayed].mean() for i in index]))
if len(size) == 1:
size = size[0]
with self.block_update_properties():
self.current_size = size
properties = {k: np.unique(v[index], axis=0) for k, v in self.properties.items()}
n_unique_properties = np.array([len(v) for v in properties.values()])
if np.all(n_unique_properties == 1):
self.current_properties = properties
|
def selected_data(self, selected_data):
self._selected_data = list(selected_data)
selected = []
for c in self._selected_data:
if c in self._indices_view:
ind = list(self._indices_view).index(c)
selected.append(ind)
self._selected_view = selected
self._selected_box = self.interaction_box(self._selected_view)
# Update properties based on selected points
if len(self._selected_data) == 0:
return
index = self._selected_data
edge_colors = np.unique(self.edge_color[index], axis=0)
if len(edge_colors) == 1:
edge_color = edge_colors[0]
with self.block_update_properties():
self.current_edge_color = edge_color
face_colors = np.unique(self.face_color[index], axis=0)
if len(face_colors) == 1:
face_color = face_colors[0]
with self.block_update_properties():
self.current_face_color = face_color
size = list(set([self.size[i, self.dims.displayed].mean() for i in index]))
if len(size) == 1:
size = size[0]
with self.block_update_properties():
self.current_size = size
properties = {k: np.unique(v[index], axis=0) for k, v in self.properties.items()}
n_unique_properties = np.array([len(v) for v in properties.values()])
if np.all(n_unique_properties == 1):
self.current_properties = properties
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def mode(self, mode):
if isinstance(mode, str):
mode = Mode(mode)
if not self.editable:
mode = Mode.PAN_ZOOM
if mode == self._mode:
return
old_mode = self._mode
if mode == Mode.ADD:
self.cursor = "pointing"
self.interactive = False
self.help = "hold <space> to pan/zoom"
self.selected_data = []
self._set_highlight()
elif mode == Mode.SELECT:
self.cursor = "standard"
self.interactive = False
self.help = "hold <space> to pan/zoom"
elif mode == Mode.PAN_ZOOM:
self.cursor = "standard"
self.interactive = True
self.help = ""
else:
raise ValueError("Mode not recognized")
if not (mode == Mode.SELECT and old_mode == Mode.SELECT):
self._selected_data_stored = []
self.status = str(mode)
self._mode = mode
self._set_highlight()
self.events.mode(mode=mode)
|
def mode(self, mode):
if isinstance(mode, str):
mode = Mode(mode)
if not self.editable:
mode = Mode.PAN_ZOOM
if mode == self._mode:
return
old_mode = self._mode
if mode == Mode.ADD:
self.cursor = "pointing"
self.interactive = False
self.help = "hold <space> to pan/zoom"
elif mode == Mode.SELECT:
self.cursor = "standard"
self.interactive = False
self.help = "hold <space> to pan/zoom"
elif mode == Mode.PAN_ZOOM:
self.cursor = "standard"
self.interactive = True
self.help = ""
else:
raise ValueError("Mode not recognized")
if not (mode == Mode.SELECT and old_mode == Mode.SELECT):
self.selected_data = []
self._set_highlight()
self.status = str(mode)
self._mode = mode
self.events.mode(mode=mode)
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def _set_view_slice(self):
"""Sets the view given the indices to slice with."""
in_slice_data, indices, scale = self._slice_data(self.dims.indices)
# Display points if there are any in this slice
if len(in_slice_data) > 0:
# Get the point sizes
sizes = self.size[np.ix_(indices, self.dims.displayed)].mean(axis=1) * scale
# Update the points node
data = np.array(in_slice_data)
else:
# if no points in this slice send dummy data
data = np.zeros((0, self.dims.ndisplay))
sizes = [0]
self._data_view = data
self._size_view = sizes
self._indices_view = indices
# Make sure if changing planes any selected points not in the current
# plane are removed
selected = []
for c in self.selected_data:
if c in self._indices_view:
ind = list(self._indices_view).index(c)
selected.append(ind)
self._selected_view = selected
self._set_highlight()
|
def _set_view_slice(self):
"""Sets the view given the indices to slice with."""
in_slice_data, indices, scale = self._slice_data(self.dims.indices)
# Display points if there are any in this slice
if len(in_slice_data) > 0:
# Get the point sizes
sizes = self.size[np.ix_(indices, self.dims.displayed)].mean(axis=1) * scale
# Update the points node
data = np.array(in_slice_data)
else:
# if no points in this slice send dummy data
data = np.zeros((0, self.dims.ndisplay))
sizes = [0]
self._data_view = data
self._size_view = sizes
self._indices_view = indices
# Make sure if changing planes any selected points not in the current
# plane are removed
selected = []
for c in self.selected_data:
if c in self._indices_view:
ind = list(self._indices_view).index(c)
selected.append(ind)
self._selected_view = selected
if self.dims.ndisplay == 2:
self._selected_box = self.interaction_box(self._selected_view)
else:
self._selected_box = None
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def _set_highlight(self, force=False):
"""Render highlights of shapes including boundaries, vertices,
interaction boxes, and the drag selection box when appropriate.
Highlighting only occurs in Mode.SELECT.
Parameters
----------
force : bool
Bool that forces a redraw to occur when `True`
"""
# if self._mode == Mode.SELECT:
# Check if any point ids have changed since last call
if self.selected:
if (
self.selected_data == self._selected_data_stored
and self._value == self._value_stored
and np.all(self._drag_box == self._drag_box_stored)
) and not force:
return
self._selected_data_stored = copy(self.selected_data)
self._value_stored = copy(self._value)
self._drag_box_stored = copy(self._drag_box)
if self._value is not None or len(self._selected_view) > 0:
if len(self._selected_view) > 0:
index = copy(self._selected_view)
# highlight the hovered point if not in adding mode
if self._value is not None and self._mode != Mode.ADD:
hover_point = list(self._indices_view).index(self._value)
if hover_point in index:
pass
else:
index.append(hover_point)
index.sort()
else:
# don't highlight hovered points in add mode
if self._mode != Mode.ADD:
hover_point = list(self._indices_view).index(self._value)
index = [hover_point]
else:
index = []
self._highlight_index = index
else:
self._highlight_index = []
# only display dragging selection box in 2D
if self.dims.ndisplay == 2 and self._is_selecting:
pos = create_box(self._drag_box)
pos = pos[list(range(4)) + [0]]
else:
pos = None
self._highlight_box = pos
self.events.highlight()
else:
self._highlight_box = None
self._highlight_index = []
self.events.highlight()
|
def _set_highlight(self, force=False):
"""Render highlights of shapes including boundaries, vertices,
interaction boxes, and the drag selection box when appropriate
Parameters
----------
force : bool
Bool that forces a redraw to occur when `True`
"""
# Check if any point ids have changed since last call
if (
self.selected_data == self._selected_data_stored
and self._value == self._value_stored
and np.all(self._drag_box == self._drag_box_stored)
) and not force:
return
self._selected_data_stored = copy(self.selected_data)
self._value_stored = copy(self._value)
self._drag_box_stored = copy(self._drag_box)
if self._mode == Mode.SELECT and (
self._value is not None or len(self._selected_view) > 0
):
if len(self._selected_view) > 0:
index = copy(self._selected_view)
if self._value is not None:
hover_point = list(self._indices_view).index(self._value)
if hover_point in index:
pass
else:
index.append(hover_point)
index.sort()
else:
hover_point = list(self._indices_view).index(self._value)
index = [hover_point]
self._highlight_index = index
else:
self._highlight_index = []
pos = self._selected_box
if pos is None and not self._is_selecting:
pos = np.zeros((0, 2))
elif self._is_selecting:
pos = create_box(self._drag_box)
pos = pos[list(range(4)) + [0]]
else:
pos = pos[list(range(4)) + [0]]
self._highlight_box = pos
self.events.highlight()
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def add(self, coord):
"""Adds point at coordinate.
Parameters
----------
coord : sequence of indices to add point at
"""
self.data = np.append(self.data, np.atleast_2d(coord), axis=0)
|
def add(self, coord):
"""Adds point at coordinate.
Parameters
----------
coord : sequence of indices to add point at
"""
self.data = np.append(self.data, [coord], axis=0)
|
https://github.com/napari/napari/issues/901
|
WARNING: Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
WARNING:vispy:Traceback (most recent call last):
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1037, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/components/dims.py", line 296, in ndisplay
self.events.ndisplay()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/utils/event.py", line 523, in _invoke_callback
cb(event)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 180, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 383, in _update_dims
self.refresh()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/base/base.py", line 600, in refresh
self._set_view_slice()
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 654, in _set_view_slice
self._selected_box = self.interaction_box(self._selected_view)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 480, in interaction_box
data = points_to_squares(data, size)
File "/home/hagai/.conda/envs/ncd/lib/python3.7/site-packages/napari/layers/points/points.py", line 972, in points_to_squares
points + np.sqrt(2) / 2 * np.array([sizes, sizes]).T,
ValueError: operands could not be broadcast together with shapes (1,3) (1,2)
|
ValueError
|
def on_mouse_press(self, event):
"""Called whenever mouse pressed in canvas.
Parameters
----------
event : Event
Vispy event
"""
if self._mode == Mode.PAN_ZOOM:
# If in pan/zoom mode do nothing
pass
elif self._mode == Mode.PICKER:
self.selected_label = self._value or 0
elif self._mode == Mode.PAINT:
# Start painting with new label
self._save_history()
self._block_saving = True
self.paint(self.coordinates, self.selected_label)
self._last_cursor_coord = copy(self.coordinates)
elif self._mode == Mode.FILL:
# Fill clicked on region with new label
self.fill(self.coordinates, self._value, self.selected_label)
else:
raise ValueError("Mode not recongnized")
|
def on_mouse_press(self, event):
"""Called whenever mouse pressed in canvas.
Parameters
----------
event : Event
Vispy event
"""
if self._mode == Mode.PAN_ZOOM:
# If in pan/zoom mode do nothing
pass
elif self._mode == Mode.PICKER:
self.selected_label = self._value
elif self._mode == Mode.PAINT:
# Start painting with new label
self._save_history()
self._block_saving = True
self.paint(self.coordinates, self.selected_label)
self._last_cursor_coord = copy(self.coordinates)
elif self._mode == Mode.FILL:
# Fill clicked on region with new label
self.fill(self.coordinates, self._value, self.selected_label)
else:
raise ValueError("Mode not recongnized")
|
https://github.com/napari/napari/issues/857
|
Traceback (most recent call last):
File "~/miniconda3/envs/napdev/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 447, in mousePressEvent
modifiers=self._modifiers(ev),
File "~/miniconda3/envs/napdev/lib/python3.7/site-packages/vispy/app/base.py", line 181, in _vispy_mouse_press
ev = self._vispy_canvas.events.mouse_press(**kwargs)
File "~/miniconda3/envs/napdev/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "~/miniconda3/envs/napdev/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
File "~/miniconda3/envs/napdev/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "~/napari/napari/_qt/qt_viewer.py", line 338, in on_mouse_press
self.layer_to_visual[layer].on_mouse_press(event)
File "~/napari/napari/_vispy/vispy_base_layer.py", line 194, in on_mouse_press
self.layer.on_mouse_press(event)
File "~/napari/napari/layers/labels/labels.py", line 542, in on_mouse_press
self.selected_label = self._value
File "~/napari/napari/layers/labels/labels.py", line 270, in selected_label
if selected_label < 0:
TypeError: '<' not supported between instances of 'NoneType' and 'int'
|
TypeError
|
def hold_to_lock_aspect_ratio(layer):
"""Hold to lock aspect ratio when resizing a shape."""
# on key press
layer._fixed_aspect = True
box = layer._selected_box
if box is not None:
size = box[Box.BOTTOM_RIGHT] - box[Box.TOP_LEFT]
if not np.any(size == np.zeros(2)):
layer._aspect_ratio = abs(size[1] / size[0])
else:
layer._aspect_ratio = 1
else:
layer._aspect_ratio = 1
if layer._is_moving:
layer._move([layer.coordinates[i] for i in layer.dims.displayed])
yield
# on key release
layer._fixed_aspect = False
if layer._is_moving:
layer._move([layer.coordinates[i] for i in layer.dims.displayed])
|
def hold_to_lock_aspect_ratio(layer):
"""Hold to lock aspect ratio when resizing a shape."""
# on key press
layer._fixed_aspect = True
box = layer._selected_box
if box is not None:
size = box[Box.BOTTOM_RIGHT] - box[Box.TOP_LEFT]
if not np.any(size == np.zeros(2)):
layer._aspect_ratio = abs(size[1] / size[0])
else:
layer._aspect_ratio = 1
else:
layer._aspect_ratio = 1
if layer._is_moving:
layer._move(layer.coordinates[layer.dims.displayed])
yield
# on key release
layer._fixed_aspect = False
if layer._is_moving:
layer._move(layer.coordinates[layer.dims.displayed])
|
https://github.com/napari/napari/issues/870
|
Traceback (most recent call last):
File "napdev/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 502, in keyPressEvent
self._keyEvent(self._vispy_canvas.events.key_press, ev)
File "napdev/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 551, in _keyEvent
func(native=ev, key=key, text=text_type(ev.text()), modifiers=mod)
File "napdev/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "napdev/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
File "napdev/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "napari/napari/_qt/qt_viewer.py", line 394, in on_key_press
next(gen)
File "napari/napari/layers/shapes/keybindings.py", line 39, in hold_to_lock_aspect_ratio
layer._move(layer.coordinates[layer.dims.displayed])
TypeError: tuple indices must be integers or slices, not list
|
TypeError
|
def show_at(self, position="top", *, width_ratio=0.9):
if not self.parent():
raise NotImplementedError("cannot show_at without parent")
main_window = self.parent().window()
xy = main_window.pos()
if position == "top":
width = main_window.width() * width_ratio
height = self.sizeHint().height()
xy = xy + QPoint(main_window.width() * (1 - width_ratio) / 2, 24)
elif position == "bottom":
width = main_window.width() * width_ratio
height = self.sizeHint().height()
y = main_window.height() - self.height() - 2
xy = xy + QPoint(main_window.width() * (1 - width_ratio) / 2, y)
elif position == "left":
width = self.sizeHint().width()
height = main_window.height() * width_ratio
xy = xy + QPoint(12, main_window.height() * (1 - width_ratio) / 2)
elif position == "right":
width = self.sizeHint().width()
height = main_window.height() * width_ratio
x = main_window.width() - width - 12
xy = xy + QPoint(x, main_window.height() * (1 - width_ratio) / 2)
else:
raise ValueError('position must be one of ["top", "left", "bottom", "right"]')
# necessary for transparent round corners
self.resize(self.sizeHint())
self.setGeometry(xy.x(), xy.y(), max(width, 20), max(height, 20))
self.show()
|
def show_at(self, position="top", *, width_ratio=0.9):
if not self.parent():
raise NotImplementedError("cannot show_at without parent")
main_window = self.parent().window()
xy = main_window.pos()
if position == "top":
width = main_window.width() * width_ratio
height = self.sizeHint().height()
xy = xy + QPoint(main_window.width() * (1 - width_ratio) / 2, 24)
elif position == "bottom":
width = main_window.width() * width_ratio
height = self.sizeHint().height()
y = main_window.height() - self.height() - 2
xy = xy + QPoint(main_window.width() * (1 - width_ratio) / 2, y)
elif position == "left":
width = self.sizeHint().width()
height = main_window.height() * width_ratio
xy = xy + QPoint(12, main_window.height() * (1 - width_ratio) / 2)
elif position == "right":
width = self.sizeHint().width()
height = main_window.height() * width_ratio
x = main_window.width() - width - 12
xy = xy + QPoint(x, main_window.height() * (1 - width_ratio) / 2)
else:
raise ValueError('position must be one of ["top", "left", "bottom", "right"]')
# necessary for transparent round corners
self.resize(self.sizeHint())
self.setGeometry(*xy.toTuple(), max(width, 20), max(height, 20))
self.show()
|
https://github.com/napari/napari/issues/865
|
WARNING: Traceback (most recent call last):
File "c:\users\nico\anaconda3\lib\site-packages\napari\_qt\layers\qt_image_base_layer.py", line 78, in _clim_mousepress
self.clim_pop.show_at('top')
File "c:\users\nico\anaconda3\lib\site-packages\napari\_qt\qt_modal.py", line 72, in show_at
self.setGeometry(*xy.toTuple(), max(width, 20), max(height, 20))
AttributeError: 'QPoint' object has no attribute 'toTuple'
WARNING:vispy:Traceback (most recent call last):
File "c:\users\nico\anaconda3\lib\site-packages\napari\_qt\layers\qt_image_base_layer.py", line 78, in _clim_mousepress
self.clim_pop.show_at('top')
File "c:\users\nico\anaconda3\lib\site-packages\napari\_qt\qt_modal.py", line 72, in show_at
self.setGeometry(*xy.toTuple(), max(width, 20), max(height, 20))
AttributeError: 'QPoint' object has no attribute 'toTuple'
|
AttributeError
|
def __init__(
self,
ndim,
*,
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending="translucent",
visible=True,
):
super().__init__()
self.metadata = metadata or {}
self._opacity = opacity
self._blending = Blending(blending)
self._visible = visible
self._selected = True
self._freeze = False
self._status = "Ready"
self._help = ""
self._cursor = "standard"
self._cursor_size = None
self._interactive = True
self._value = None
self.scale_factor = 1
self.dims = Dims(ndim)
if scale is None:
self._scale = [1] * ndim
else: # covers list and array-like inputs
self._scale = list(scale)
if translate is None:
self._translate = [0] * ndim
else: # covers list and array-like inputs
self._translate = list(translate)
self._scale_view = np.ones(ndim)
self._translate_view = np.zeros(ndim)
self._translate_grid = np.zeros(ndim)
self.coordinates = (0,) * ndim
self._position = (0,) * self.dims.ndisplay
self.is_pyramid = False
self._editable = True
self._thumbnail_shape = (32, 32, 4)
self._thumbnail = np.zeros(self._thumbnail_shape, dtype=np.uint8)
self._update_properties = True
self._name = ""
self.events = EmitterGroup(
source=self,
auto_connect=True,
refresh=Event,
set_data=Event,
blending=Event,
opacity=Event,
visible=Event,
select=Event,
deselect=Event,
scale=Event,
translate=Event,
data=Event,
name=Event,
thumbnail=Event,
status=Event,
help=Event,
interactive=Event,
cursor=Event,
cursor_size=Event,
editable=Event,
)
self.name = name
self.events.data.connect(lambda e: self._set_editable())
self.dims.events.ndisplay.connect(lambda e: self._set_editable())
self.dims.events.order.connect(lambda e: self._set_view_slice())
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
self.dims.events.order.connect(lambda e: self._update_dims())
self.dims.events.axis.connect(lambda e: self._set_view_slice())
self.mouse_move_callbacks = []
self.mouse_drag_callbacks = []
self._persisted_mouse_event = {}
self._mouse_drag_gen = {}
|
def __init__(
self,
ndim,
*,
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending="translucent",
visible=True,
):
super().__init__()
self.metadata = metadata or {}
self._opacity = opacity
self._blending = Blending(blending)
self._visible = visible
self._selected = True
self._freeze = False
self._status = "Ready"
self._help = ""
self._cursor = "standard"
self._cursor_size = None
self._interactive = True
self._value = None
self.scale_factor = 1
self.dims = Dims(ndim)
self._scale = scale or [1] * ndim
self._translate = translate or [0] * ndim
self._scale_view = np.ones(ndim)
self._translate_view = np.zeros(ndim)
self._translate_grid = np.zeros(ndim)
self.coordinates = (0,) * ndim
self._position = (0,) * self.dims.ndisplay
self.is_pyramid = False
self._editable = True
self._thumbnail_shape = (32, 32, 4)
self._thumbnail = np.zeros(self._thumbnail_shape, dtype=np.uint8)
self._update_properties = True
self._name = ""
self.events = EmitterGroup(
source=self,
auto_connect=True,
refresh=Event,
set_data=Event,
blending=Event,
opacity=Event,
visible=Event,
select=Event,
deselect=Event,
scale=Event,
translate=Event,
data=Event,
name=Event,
thumbnail=Event,
status=Event,
help=Event,
interactive=Event,
cursor=Event,
cursor_size=Event,
editable=Event,
)
self.name = name
self.events.data.connect(lambda e: self._set_editable())
self.dims.events.ndisplay.connect(lambda e: self._set_editable())
self.dims.events.order.connect(lambda e: self._set_view_slice())
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
self.dims.events.order.connect(lambda e: self._update_dims())
self.dims.events.axis.connect(lambda e: self._set_view_slice())
self.mouse_move_callbacks = []
self.mouse_drag_callbacks = []
self._persisted_mouse_event = {}
self._mouse_drag_gen = {}
|
https://github.com/napari/napari/issues/751
|
Traceback (most recent call last):
File "test_array_spacing.py", line 9, in <module>
napari.view_image(camera, scale=np.array([1, 1]))
File "/home/jni/projects/napari/napari/view_layers.py", line 130, in view_image
path=path,
File "/home/jni/projects/napari/napari/components/viewer_model.py", line 512, in add_image
visible=visible,
File "/home/jni/projects/napari/napari/layers/image/image.py", line 163, in __init__
visible=visible,
File "/home/jni/projects/napari/napari/layers/base/base.py", line 133, in __init__
self._scale = scale or [1] * ndim
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
|
ValueError
|
def __init__(self, qt_viewer, *, show=True):
self.qt_viewer = qt_viewer
self._qt_window = QMainWindow()
self._qt_window.setUnifiedTitleAndToolBarOnMac(True)
self._qt_center = QWidget()
self._qt_window.setCentralWidget(self._qt_center)
self._qt_window.setWindowTitle(self.qt_viewer.viewer.title)
self._qt_center.setLayout(QHBoxLayout())
self._status_bar = QStatusBar()
self._qt_window.setStatusBar(self._status_bar)
self._qt_window.closeEvent = self.closeEvent
self.close = self._qt_window.close
self._add_menubar()
self._add_file_menu()
self._add_view_menu()
self._add_window_menu()
self._add_help_menu()
self._status_bar.showMessage("Ready")
self._help = QLabel("")
self._status_bar.addPermanentWidget(self._help)
self._qt_center.layout().addWidget(self.qt_viewer)
self._qt_center.layout().setContentsMargins(4, 0, 4, 0)
self._update_palette(qt_viewer.viewer.palette)
self.qt_viewer.viewer.events.status.connect(self._status_changed)
self.qt_viewer.viewer.events.help.connect(self._help_changed)
self.qt_viewer.viewer.events.title.connect(self._title_changed)
self.qt_viewer.viewer.events.palette.connect(
lambda event: self._update_palette(event.palette)
)
if show:
self.show()
|
def __init__(self, qt_viewer, *, show=True):
self.qt_viewer = qt_viewer
self._qt_window = QMainWindow()
self._qt_window.setUnifiedTitleAndToolBarOnMac(True)
self._qt_center = QWidget(self._qt_window)
self._qt_window.setCentralWidget(self._qt_center)
self._qt_window.setWindowTitle(self.qt_viewer.viewer.title)
self._qt_center.setLayout(QHBoxLayout())
self._status_bar = QStatusBar()
self._qt_window.setStatusBar(self._status_bar)
self._qt_window.closeEvent = self.closeEvent
self.close = self._qt_window.close
self._add_menubar()
self._add_file_menu()
self._add_view_menu()
self._add_window_menu()
self._add_help_menu()
self._status_bar.showMessage("Ready")
self._help = QLabel("")
self._status_bar.addPermanentWidget(self._help)
self._qt_center.layout().addWidget(self.qt_viewer)
self._qt_center.layout().setContentsMargins(4, 0, 4, 0)
self._update_palette(qt_viewer.viewer.palette)
if self.qt_viewer.console.shell is not None:
self._add_viewer_dock_widget(self.qt_viewer.dockConsole)
self.qt_viewer.viewer.events.status.connect(self._status_changed)
self.qt_viewer.viewer.events.help.connect(self._help_changed)
self.qt_viewer.viewer.events.title.connect(self._title_changed)
self.qt_viewer.viewer.events.palette.connect(
lambda event: self._update_palette(event.palette)
)
if show:
self.show()
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def show(self):
"""Resize, show, and bring forward the window."""
self._qt_window.resize(self._qt_window.layout().sizeHint())
self._qt_window.show()
|
def show(self):
"""Resize, show, and bring forward the window."""
self._qt_window.resize(self._qt_window.layout().sizeHint())
self._qt_window.show()
# make sure window is not hidden, e.g. by browser window in Jupyter
self._qt_window.raise_()
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def _update_palette(self, palette):
# set window styles which don't use the primary stylesheet
# FIXME: this is a problem with the stylesheet not using properties
self._status_bar.setStyleSheet(
template(
"QStatusBar { background: {{ background }}; color: {{ text }}; }",
**palette,
)
)
self._qt_center.setStyleSheet(
template("QWidget { background: {{ background }}; }", **palette)
)
|
def _update_palette(self, palette):
# set window styles which don't use the primary stylesheet
# FIXME: this is a problem with the stylesheet not using properties
self._status_bar.setStyleSheet(
template(
"QStatusBar { background: {{ background }}; color: {{ text }}; }",
**palette,
)
)
self._qt_center.setStyleSheet(
template("QWidget { background: {{ background }}; }", **palette)
)
self._qt_window.setStyleSheet(template(self.raw_stylesheet, **palette))
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def __init__(self, viewer):
super().__init__()
self.pool = QThreadPool()
QCoreApplication.setAttribute(Qt.AA_UseStyleSheetPropagationInWidgetStyles, True)
self.viewer = viewer
self.dims = QtDims(self.viewer.dims)
self.controls = QtControls(self.viewer)
self.layers = QtLayerList(self.viewer.layers)
self.layerButtons = QtLayerButtons(self.viewer)
self.viewerButtons = QtViewerButtons(self.viewer)
self.console = QtConsole({"viewer": self.viewer})
# This dictionary holds the corresponding vispy visual for each layer
self.layer_to_visual = {}
if self.console.shell is not None:
self.console.style().unpolish(self.console)
self.console.style().polish(self.console)
self.console.hide()
self.viewerButtons.consoleButton.clicked.connect(lambda: self._toggle_console())
else:
self.viewerButtons.consoleButton.setEnabled(False)
self.canvas = SceneCanvas(keys=None, vsync=True)
self.canvas.events.ignore_callback_errors = False
self.canvas.events.draw.connect(self.dims.enable_play)
self.canvas.native.setMinimumSize(QSize(200, 200))
self.canvas.context.set_depth_func("lequal")
self.canvas.connect(self.on_mouse_move)
self.canvas.connect(self.on_mouse_press)
self.canvas.connect(self.on_mouse_release)
self.canvas.connect(self.on_key_press)
self.canvas.connect(self.on_key_release)
self.canvas.connect(self.on_draw)
self.view = self.canvas.central_widget.add_view()
self._update_camera()
main_widget = QWidget()
main_layout = QGridLayout()
main_layout.setContentsMargins(15, 20, 15, 10)
main_layout.addWidget(self.canvas.native, 0, 1, 3, 1)
main_layout.addWidget(self.dims, 3, 1)
main_layout.addWidget(self.controls, 0, 0)
main_layout.addWidget(self.layerButtons, 1, 0)
main_layout.addWidget(self.layers, 2, 0)
main_layout.addWidget(self.viewerButtons, 3, 0)
main_layout.setColumnStretch(1, 1)
main_layout.setSpacing(10)
main_widget.setLayout(main_layout)
self.setOrientation(Qt.Vertical)
self.addWidget(main_widget)
if self.console.shell is not None:
self.addWidget(self.console)
self._last_visited_dir = str(Path.home())
self._cursors = {
"disabled": QCursor(
QPixmap(":/icons/cursor/cursor_disabled.png").scaled(20, 20)
),
"cross": Qt.CrossCursor,
"forbidden": Qt.ForbiddenCursor,
"pointing": Qt.PointingHandCursor,
"standard": QCursor(),
}
self._update_palette(viewer.palette)
self._key_release_generators = {}
self.viewer.events.interactive.connect(self._on_interactive)
self.viewer.events.cursor.connect(self._on_cursor)
self.viewer.events.reset_view.connect(self._on_reset_view)
self.viewer.events.palette.connect(
lambda event: self._update_palette(event.palette)
)
self.viewer.layers.events.reordered.connect(self._reorder_layers)
self.viewer.layers.events.added.connect(self._add_layer)
self.viewer.layers.events.removed.connect(self._remove_layer)
self.viewer.dims.events.camera.connect(lambda event: self._update_camera())
# stop any animations whenever the layers change
self.viewer.events.layers_change.connect(lambda x: self.dims.stop())
self.setAcceptDrops(True)
|
def __init__(self, viewer):
super().__init__()
self.pool = QThreadPool()
QCoreApplication.setAttribute(Qt.AA_UseStyleSheetPropagationInWidgetStyles, True)
self.viewer = viewer
self.dims = QtDims(self.viewer.dims)
self.controls = QtControls(self.viewer)
self.layers = QtLayerList(self.viewer.layers)
self.layerButtons = QtLayerButtons(self.viewer)
self.viewerButtons = QtViewerButtons(self.viewer)
self.console = QtConsole({"viewer": self.viewer})
self.dockConsole = QtViewerDockWidget(self, self.console, name="console")
self.dockConsole.setVisible(False)
# This dictionary holds the corresponding vispy visual for each layer
self.layer_to_visual = {}
if self.console.shell is not None:
self.viewerButtons.consoleButton.clicked.connect(lambda: self.toggle_console())
else:
self.viewerButtons.consoleButton.setEnabled(False)
self.canvas = SceneCanvas(keys=None, vsync=True)
self.canvas.events.ignore_callback_errors = False
self.canvas.events.draw.connect(self.dims.enable_play)
self.canvas.native.setMinimumSize(QSize(200, 200))
self.canvas.context.set_depth_func("lequal")
self.canvas.connect(self.on_mouse_move)
self.canvas.connect(self.on_mouse_press)
self.canvas.connect(self.on_mouse_release)
self.canvas.connect(self.on_key_press)
self.canvas.connect(self.on_key_release)
self.canvas.connect(self.on_draw)
self.view = self.canvas.central_widget.add_view()
self._update_camera()
main_widget = QWidget()
main_layout = QGridLayout()
main_layout.setContentsMargins(15, 20, 15, 10)
main_layout.addWidget(self.canvas.native, 0, 1, 3, 1)
main_layout.addWidget(self.dims, 3, 1)
main_layout.addWidget(self.controls, 0, 0)
main_layout.addWidget(self.layerButtons, 1, 0)
main_layout.addWidget(self.layers, 2, 0)
main_layout.addWidget(self.viewerButtons, 3, 0)
main_layout.setColumnStretch(1, 1)
main_layout.setSpacing(10)
main_widget.setLayout(main_layout)
self.setOrientation(Qt.Vertical)
self.addWidget(main_widget)
self._last_visited_dir = str(Path.home())
self._cursors = {
"disabled": QCursor(
QPixmap(":/icons/cursor/cursor_disabled.png").scaled(20, 20)
),
"cross": Qt.CrossCursor,
"forbidden": Qt.ForbiddenCursor,
"pointing": Qt.PointingHandCursor,
"standard": QCursor(),
}
self._update_palette(viewer.palette)
self._key_release_generators = {}
self.viewer.events.interactive.connect(self._on_interactive)
self.viewer.events.cursor.connect(self._on_cursor)
self.viewer.events.reset_view.connect(self._on_reset_view)
self.viewer.events.palette.connect(
lambda event: self._update_palette(event.palette)
)
self.viewer.layers.events.reordered.connect(self._reorder_layers)
self.viewer.layers.events.added.connect(self._add_layer)
self.viewer.layers.events.removed.connect(self._remove_layer)
self.viewer.dims.events.camera.connect(lambda event: self._update_camera())
# stop any animations whenever the layers change
self.viewer.events.layers_change.connect(lambda x: self.dims.stop())
self.setAcceptDrops(True)
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def _update_camera(self):
if self.viewer.dims.ndisplay == 3:
# Set a 3D camera
if not isinstance(self.view.camera, ArcballCamera):
self.view.camera = ArcballCamera(name="ArcballCamera")
# flip y-axis to have correct alignment
# self.view.camera.flip = (0, 1, 0)
self.view.camera.viewbox_key_event = viewbox_key_event
self.viewer.reset_view()
else:
# Set 2D camera
if not isinstance(self.view.camera, PanZoomCamera):
self.view.camera = PanZoomCamera(aspect=1, name="PanZoomCamera")
# flip y-axis to have correct alignment
self.view.camera.flip = (0, 1, 0)
self.view.camera.viewbox_key_event = viewbox_key_event
self.viewer.reset_view()
|
def _update_camera(self):
if self.viewer.dims.ndisplay == 3:
# Set a 3D camera
if not isinstance(self.view.camera, ArcballCamera):
self.view.camera = ArcballCamera(name="ArcballCamera", fov=0)
# flip y-axis to have correct alignment
# self.view.camera.flip = (0, 1, 0)
self.view.camera.viewbox_key_event = viewbox_key_event
self.viewer.reset_view()
else:
# Set 2D camera
if not isinstance(self.view.camera, PanZoomCamera):
self.view.camera = PanZoomCamera(aspect=1, name="PanZoomCamera")
# flip y-axis to have correct alignment
self.view.camera.flip = (0, 1, 0)
self.view.camera.viewbox_key_event = viewbox_key_event
self.viewer.reset_view()
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def screenshot(self):
"""Take currently displayed screen and convert to an image array.
Returns
-------
image : array
Numpy array of type ubyte and shape (h, w, 4). Index [0, 0] is the
upper-left corner of the rendered region.
"""
img = self.canvas.native.grabFramebuffer()
b = img.constBits()
h, w, c = img.height(), img.width(), 4
# As vispy doesn't use qtpy we need to reconcile the differences
# between the `QImage` API for `PySide2` and `PyQt5` on how to convert
# a QImage to a numpy array.
if API_NAME == "PySide2":
arr = np.array(b).reshape(h, w, c)
else:
b.setsize(h * w * c)
arr = np.frombuffer(b, np.uint8).reshape(h, w, c)
# Format of QImage is ARGB32_Premultiplied, but color channels are
# reversed.
arr = arr[:, :, [2, 1, 0, 3]]
return arr
|
def screenshot(self):
"""Take currently displayed screen and convert to an image array.
Returns
-------
image : array
Numpy array of type ubyte and shape (h, w, 4). Index [0, 0] is the
upper-left corner of the rendered region.
"""
img = self.canvas.native.grabFramebuffer()
return QImg2array(img)
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def _open_images(self):
"""Add image files from the menubar."""
filenames, _ = QFileDialog.getOpenFileNames(
parent=self,
caption="Select image(s)...",
directory=self._last_visited_dir, # home dir by default
)
if filenames is not None:
self._add_files(filenames)
|
def _open_images(self):
"""Add image files from the menubar."""
filenames, _ = QFileDialog.getOpenFileNames(
parent=self,
caption="Select image(s)...",
directory=self._last_visited_dir, # home dir by default
)
if (filenames != []) and (filenames is not None):
self._add_files(filenames)
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def _open_folder(self):
"""Add a folder of files from the menubar."""
folder = QFileDialog.getExistingDirectory(
parent=self,
caption="Select folder...",
directory=self._last_visited_dir, # home dir by default
)
if folder is not None:
self._add_files([folder])
|
def _open_folder(self):
"""Add a folder of files from the menubar."""
folder = QFileDialog.getExistingDirectory(
parent=self,
caption="Select folder...",
directory=self._last_visited_dir, # home dir by default
)
if folder not in {"", None}:
self._add_files([folder])
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def add_image(
self,
data=None,
*,
channel_axis=None,
rgb=None,
is_pyramid=None,
colormap=None,
contrast_limits=None,
gamma=1,
interpolation="nearest",
rendering="mip",
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending=None,
visible=True,
path=None,
):
"""Add an image layer to the layers list.
Parameters
----------
data : array or list of array
Image data. Can be N dimensional. If the last dimension has length
3 or 4 can be interpreted as RGB or RGBA if rgb is `True`. If a
list and arrays are decreasing in shape then the data is treated as
an image pyramid.
channel_axis : int, optional
Axis to expand image along.
rgb : bool
Whether the image is rgb RGB or RGBA. If not specified by user and
the last dimension of the data has length 3 or 4 it will be set as
`True`. If `False` the image is interpreted as a luminance image.
is_pyramid : bool
Whether the data is an image pyramid or not. Pyramid data is
represented by a list of array like image data. If not specified by
the user and if the data is a list of arrays that decrease in shape
then it will be taken to be a pyramid. The first image in the list
should be the largest.
colormap : str, vispy.Color.Colormap, tuple, dict, list
Colormaps to use for luminance images. If a string must be the name
of a supported colormap from vispy or matplotlib. If a tuple the
first value must be a string to assign as a name to a colormap and
the second item must be a Colormap. If a dict the key must be a
string to assign as a name to a colormap and the value must be a
Colormap. If a list then must be same length as the axis that is
being expanded as channels, and each colormap is applied to each
new image layer.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image. If list of lists then must be same length as the axis
that is being expanded and then each colormap is applied to each
image.
gamma : list, float
Gamma correction for determining colormap linearity. Defaults to 1.
If a list then must be same length as the axis that is being
expanded and then each entry in the list is applied to each image.
interpolation : str
Interpolation mode used by vispy. Must be one of our supported
modes.
name : str
Name of the layer.
metadata : dict
Layer metadata.
scale : tuple of float
Scale factors for the layer.
translate : tuple of float
Translation values for the layer.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
blending : str
One of a list of preset blending modes that determines how RGB and
alpha values of the layer visual get mixed. Allowed values are
{'opaque', 'translucent', and 'additive'}.
visible : bool
Whether the layer visual is currently being displayed.
path : str or list of str
Path or list of paths to image data.
Returns
-------
layer : :class:`napari.layers.Image` or list
The newly-created image layer or list of image layers.
"""
if data is None and path is None:
raise ValueError("One of either data or path must be provided")
elif data is not None and path is not None:
raise ValueError("Only one of data or path can be provided")
elif data is None:
data = io.magic_imread(path)
if channel_axis is None:
if colormap is None:
colormap = "gray"
if blending is None:
blending = "translucent"
layer = layers.Image(
data,
rgb=rgb,
is_pyramid=is_pyramid,
colormap=colormap,
contrast_limits=contrast_limits,
gamma=gamma,
interpolation=interpolation,
rendering=rendering,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.add_layer(layer)
return layer
else:
if is_pyramid:
n_channels = data[0].shape[channel_axis]
else:
n_channels = data.shape[channel_axis]
name = ensure_iterable(name)
if blending is None:
blending = "additive"
if colormap is None:
if n_channels < 3:
colormap = colormaps.MAGENTA_GREEN
else:
colormap = itertools.cycle(colormaps.CYMRGB)
else:
colormap = ensure_iterable(colormap)
# If one pair of clim values is passed then need to iterate them to
# all layers.
if contrast_limits is not None and not is_iterable(contrast_limits[0]):
contrast_limits = itertools.repeat(contrast_limits)
else:
contrast_limits = ensure_iterable(contrast_limits)
gamma = ensure_iterable(gamma)
layer_list = []
zipped_args = zip(range(n_channels), colormap, contrast_limits, gamma, name)
for i, cmap, clims, _gamma, name in zipped_args:
if is_pyramid:
image = [data[j].take(i, axis=channel_axis) for j in range(len(data))]
else:
image = data.take(i, axis=channel_axis)
layer = layers.Image(
image,
rgb=rgb,
colormap=cmap,
contrast_limits=clims,
gamma=_gamma,
interpolation=interpolation,
rendering=rendering,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.add_layer(layer)
layer_list.append(layer)
return layer_list
|
def add_image(
self,
data=None,
*,
channel_axis=None,
rgb=None,
is_pyramid=None,
colormap=None,
contrast_limits=None,
gamma=1,
interpolation="nearest",
rendering="mip",
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending=None,
visible=True,
path=None,
):
"""Add an image layer to the layers list.
Parameters
----------
data : array or list of array
Image data. Can be N dimensional. If the last dimension has length
3 or 4 can be interpreted as RGB or RGBA if rgb is `True`. If a
list and arrays are decreasing in shape then the data is treated as
an image pyramid.
channel_axis : int, optional
Axis to expand image along.
rgb : bool
Whether the image is rgb RGB or RGBA. If not specified by user and
the last dimension of the data has length 3 or 4 it will be set as
`True`. If `False` the image is interpreted as a luminance image.
is_pyramid : bool
Whether the data is an image pyramid or not. Pyramid data is
represented by a list of array like image data. If not specified by
the user and if the data is a list of arrays that decrease in shape
then it will be taken to be a pyramid. The first image in the list
should be the largest.
colormap : str, vispy.Color.Colormap, tuple, dict, list
Colormaps to use for luminance images. If a string must be the name
of a supported colormap from vispy or matplotlib. If a tuple the
first value must be a string to assign as a name to a colormap and
the second item must be a Colormap. If a dict the key must be a
string to assign as a name to a colormap and the value must be a
Colormap. If a list then must be same length as the axis that is
being expanded as channels, and each colormap is applied to each
new image layer.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image. If list of lists then must be same length as the axis
that is being expanded and then each colormap is applied to each
image.
gamma : list, float
Gamma correction for determining colormap linearity. Defaults to 1.
If a list then must be same length as the axis that is being
expanded and then each entry in the list is applied to each image.
interpolation : str
Interpolation mode used by vispy. Must be one of our supported
modes.
name : str
Name of the layer.
metadata : dict
Layer metadata.
scale : tuple of float
Scale factors for the layer.
translate : tuple of float
Translation values for the layer.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
blending : str
One of a list of preset blending modes that determines how RGB and
alpha values of the layer visual get mixed. Allowed values are
{'opaque', 'translucent', and 'additive'}.
visible : bool
Whether the layer visual is currently being displayed.
path : str or list of str
Path or list of paths to image data. Paths can be passed as strings
or `pathlib.Path` instances.
Returns
-------
layer : :class:`napari.layers.Image` or list
The newly-created image layer or list of image layers.
"""
if data is None and path is None:
raise ValueError("One of either data or path must be provided")
elif data is not None and path is not None:
raise ValueError("Only one of data or path can be provided")
elif data is None:
data = io.magic_imread(path)
if channel_axis is None:
if colormap is None:
colormap = "gray"
if blending is None:
blending = "translucent"
layer = layers.Image(
data,
rgb=rgb,
is_pyramid=is_pyramid,
colormap=colormap,
contrast_limits=contrast_limits,
gamma=gamma,
interpolation=interpolation,
rendering=rendering,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.add_layer(layer)
return layer
else:
if is_pyramid:
n_channels = data[0].shape[channel_axis]
else:
n_channels = data.shape[channel_axis]
name = ensure_iterable(name)
if blending is None:
blending = "additive"
if colormap is None:
if n_channels < 3:
colormap = colormaps.MAGENTA_GREEN
else:
colormap = itertools.cycle(colormaps.CYMRGB)
else:
colormap = ensure_iterable(colormap)
# If one pair of clim values is passed then need to iterate them to
# all layers.
if contrast_limits is not None and not is_iterable(contrast_limits[0]):
contrast_limits = itertools.repeat(contrast_limits)
else:
contrast_limits = ensure_iterable(contrast_limits)
gamma = ensure_iterable(gamma)
layer_list = []
zipped_args = zip(range(n_channels), colormap, contrast_limits, gamma, name)
for i, cmap, clims, _gamma, name in zipped_args:
if is_pyramid:
image = [
np.take(data[j], i, axis=channel_axis) for j in range(len(data))
]
else:
image = np.take(data, i, axis=channel_axis)
layer = layers.Image(
image,
rgb=rgb,
colormap=cmap,
contrast_limits=clims,
gamma=_gamma,
interpolation=interpolation,
rendering=rendering,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.add_layer(layer)
layer_list.append(layer)
return layer_list
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def magic_imread(filenames, *, use_dask=None, stack=True):
"""Dispatch the appropriate reader given some files.
The files are assumed to all have the same shape.
Parameters
-------
filenames : list
List of filenames or directories to be opened
use_dask : bool
Whether to use dask to create a lazy array, rather than NumPy.
Default of None will resolve to True if filenames contains more than
one image, False otherwise.
stack : bool
Whether to stack the images in multiple files into a single array. If
False, a list of arrays will be returned.
Returns
-------
image : array-like
Array or list of images
"""
if len(filenames) == 0:
return None
if isinstance(filenames, str):
filenames = [filenames] # ensure list
# replace folders with their contents
filenames_expanded = []
for filename in filenames:
ext = os.path.splitext(filename)[-1]
# zarr files are folders, but should be read as 1 file
if os.path.isdir(filename) and not ext == ".zarr":
dir_contents = sorted(
glob(os.path.join(filename, "*.*")), key=alphanumeric_key
)
# remove subdirectories
dir_contents_files = filter(lambda f: not os.path.isdir(f), dir_contents)
filenames_expanded.extend(dir_contents_files)
else:
filenames_expanded.append(filename)
if use_dask is None:
use_dask = len(filenames_expanded) > 1
# then, read in images
images = []
shape = None
for filename in filenames_expanded:
ext = os.path.splitext(filename)[-1]
if ext == ".zarr":
image, zarr_shape = read_zarr_dataset(filename)
if shape is None:
shape = zarr_shape
else:
if shape is None:
image = io.imread(filename)
shape = image.shape
dtype = image.dtype
if use_dask:
image = da.from_delayed(
delayed(io.imread)(filename), shape=shape, dtype=dtype
)
elif len(images) > 0: # not read by shape clause
image = io.imread(filename)
images.append(image)
if len(images) == 1:
image = images[0]
else:
if stack:
if use_dask:
image = da.stack(images)
else:
image = np.stack(images)
else:
image = images # return a list
return image
|
def magic_imread(filenames, *, use_dask=None, stack=True):
"""Dispatch the appropriate reader given some files.
The files are assumed to all have the same shape.
Parameters
-------
filenames : list
List of filenames or directories to be opened.
A list of `pathlib.Path` objects and a single filename or `Path` object
are also accepted.
use_dask : bool
Whether to use dask to create a lazy array, rather than NumPy.
Default of None will resolve to True if filenames contains more than
one image, False otherwise.
stack : bool
Whether to stack the images in multiple files into a single array. If
False, a list of arrays will be returned.
Returns
-------
image : array-like
Array or list of images
"""
# cast Path to string
if isinstance(filenames, Path):
filenames = filenames.as_posix()
if len(filenames) == 0:
return None
if isinstance(filenames, str):
filenames = [filenames] # ensure list
# replace folders with their contents
filenames_expanded = []
for filename in filenames:
ext = os.path.splitext(filename)[-1]
# zarr files are folders, but should be read as 1 file
if os.path.isdir(filename) and not ext == ".zarr":
dir_contents = sorted(
glob(os.path.join(filename, "*.*")), key=alphanumeric_key
)
# remove subdirectories
dir_contents_files = filter(lambda f: not os.path.isdir(f), dir_contents)
filenames_expanded.extend(dir_contents_files)
else:
filenames_expanded.append(filename)
if use_dask is None:
use_dask = len(filenames_expanded) > 1
# then, read in images
images = []
shape = None
for filename in filenames_expanded:
ext = os.path.splitext(filename)[-1]
if ext == ".zarr":
image, zarr_shape = read_zarr_dataset(filename)
if shape is None:
shape = zarr_shape
else:
if shape is None:
image = io.imread(filename)
shape = image.shape
dtype = image.dtype
if use_dask:
image = da.from_delayed(
delayed(io.imread)(filename), shape=shape, dtype=dtype
)
elif len(images) > 0: # not read by shape clause
image = io.imread(filename)
images.append(image)
if len(images) == 1:
image = images[0]
else:
if stack:
if use_dask:
image = da.stack(images)
else:
image = np.stack(images)
else:
image = images # return a list
return image
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def is_pyramid(data):
"""If shape of arrays along first axis is strictly decreasing."""
size = np.array([np.prod(d.shape, dtype=np.uint64) for d in data])
if len(size) > 1:
return np.all(size[:-1] > size[1:])
else:
return False
|
def is_pyramid(data):
"""If shape of arrays along first axis is strictly decreasing."""
size = np.array([np.prod(d.shape) for d in data])
if len(size) > 1:
return np.all(size[:-1] > size[1:])
else:
return False
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def calc_data_range(data):
"""Calculate range of data values. If all values are equal return [0, 1].
Parameters
-------
data : array
Data to calculate range of values over.
Returns
-------
values : list of float
Range of values.
"""
if np.prod(data.shape) > 1e6:
# If data is very large take the average of the top, bottom, and
# middle slices
bottom_plane_idx = (0,) * (data.ndim - 2)
middle_plane_idx = tuple(s // 2 for s in data.shape[:-2])
top_plane_idx = tuple(s - 1 for s in data.shape[:-2])
idxs = [bottom_plane_idx, middle_plane_idx, top_plane_idx]
reduced_data = [
[np.max(data[idx]) for idx in idxs],
[np.min(data[idx]) for idx in idxs],
]
else:
reduced_data = data
min_val = np.min(reduced_data)
max_val = np.max(reduced_data)
if min_val == max_val:
min_val = 0
max_val = 1
return [float(min_val), float(max_val)]
|
def calc_data_range(data):
"""Calculate range of data values. If all values are equal return [0, 1].
Parameters
-------
data : array
Data to calculate range of values over.
Returns
-------
values : list of float
Range of values.
Notes
-----
If the data type is uint8, no calculation is performed, and 0-255 is
returned.
"""
if data.dtype == np.uint8:
return [0, 255]
if np.prod(data.shape) > 1e6:
# If data is very large take the average of the top, bottom, and
# middle slices
bottom_plane_idx = (0,) * (data.ndim - 2)
middle_plane_idx = tuple(s // 2 for s in data.shape[:-2])
top_plane_idx = tuple(s - 1 for s in data.shape[:-2])
idxs = [bottom_plane_idx, middle_plane_idx, top_plane_idx]
reduced_data = [
[np.max(data[idx]) for idx in idxs],
[np.min(data[idx]) for idx in idxs],
]
else:
reduced_data = data
min_val = np.min(reduced_data)
max_val = np.max(reduced_data)
if min_val == max_val:
min_val = 0
max_val = 1
return [float(min_val), float(max_val)]
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def view_image(
data=None,
*,
channel_axis=None,
rgb=None,
is_pyramid=None,
colormap=None,
contrast_limits=None,
gamma=1,
interpolation="nearest",
rendering="mip",
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending=None,
visible=True,
path=None,
title="napari",
ndisplay=2,
order=None,
axis_labels=None,
):
"""Create a viewer and add an image layer.
Parameters
----------
data : array or list of array
Image data. Can be N dimensional. If the last dimension has length
3 or 4 can be interpreted as RGB or RGBA if rgb is `True`. If a
list and arrays are decreasing in shape then the data is treated as
an image pyramid.
channel_axis : int, optional
Axis to expand image along.
rgb : bool
Whether the image is rgb RGB or RGBA. If not specified by user and
the last dimension of the data has length 3 or 4 it will be set as
`True`. If `False` the image is interpreted as a luminance image.
is_pyramid : bool
Whether the data is an image pyramid or not. Pyramid data is
represented by a list of array like image data. If not specified by
the user and if the data is a list of arrays that decrease in shape
then it will be taken to be a pyramid. The first image in the list
should be the largest.
colormap : str, vispy.Color.Colormap, tuple, dict, list
Colormaps to use for luminance images. If a string must be the name
of a supported colormap from vispy or matplotlib. If a tuple the
first value must be a string to assign as a name to a colormap and
the second item must be a Colormap. If a dict the key must be a
string to assign as a name to a colormap and the value must be a
Colormap. If a list then must be same length as the axis that is
being expanded as channels, and each colormap is applied to each new
image layer.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image. If list of lists then must be same length as the axis
that is being expanded and then each colormap is applied to each
image.
gamma : list, float
Gamma correction for determining colormap linearity. Defaults to 1.
If a list then must be same length as the axis that is being expanded
and then each entry in the list is applied to each image.
interpolation : str
Interpolation mode used by vispy. Must be one of our supported
modes.
name : str
Name of the layer.
metadata : dict
Layer metadata.
scale : tuple of float
Scale factors for the layer.
translate : tuple of float
Translation values for the layer.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
blending : str
One of a list of preset blending modes that determines how RGB and
alpha values of the layer visual get mixed. Allowed values are
{'opaque', 'translucent', and 'additive'}.
visible : bool
Whether the layer visual is currently being displayed.
path : str or list of str
Path or list of paths to image data.
title : string
The title of the viewer window.
ndisplay : {2, 3}
Number of displayed dimensions.
order : tuple of int
Order in which dimensions are displayed where the last two or last
three dimensions correspond to row x column or plane x row x column if
ndisplay is 2 or 3.
axis_labels : list of str
Dimension names.
Returns
-------
viewer : :class:`napari.Viewer`
The newly-created viewer.
"""
viewer = Viewer(
title=title, ndisplay=ndisplay, order=order, axis_labels=axis_labels
)
viewer.add_image(
data=data,
channel_axis=channel_axis,
rgb=rgb,
is_pyramid=is_pyramid,
colormap=colormap,
contrast_limits=contrast_limits,
gamma=gamma,
interpolation=interpolation,
rendering=rendering,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
path=path,
)
return viewer
|
def view_image(
data=None,
*,
channel_axis=None,
rgb=None,
is_pyramid=None,
colormap=None,
contrast_limits=None,
gamma=1,
interpolation="nearest",
rendering="mip",
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending=None,
visible=True,
path=None,
title="napari",
ndisplay=2,
order=None,
axis_labels=None,
):
"""Create a viewer and add an image layer.
Parameters
----------
data : array or list of array
Image data. Can be N dimensional. If the last dimension has length
3 or 4 can be interpreted as RGB or RGBA if rgb is `True`. If a
list and arrays are decreasing in shape then the data is treated as
an image pyramid.
channel_axis : int, optional
Axis to expand image along.
rgb : bool
Whether the image is rgb RGB or RGBA. If not specified by user and
the last dimension of the data has length 3 or 4 it will be set as
`True`. If `False` the image is interpreted as a luminance image.
is_pyramid : bool
Whether the data is an image pyramid or not. Pyramid data is
represented by a list of array like image data. If not specified by
the user and if the data is a list of arrays that decrease in shape
then it will be taken to be a pyramid. The first image in the list
should be the largest.
colormap : str, vispy.Color.Colormap, tuple, dict, list
Colormaps to use for luminance images. If a string must be the name
of a supported colormap from vispy or matplotlib. If a tuple the
first value must be a string to assign as a name to a colormap and
the second item must be a Colormap. If a dict the key must be a
string to assign as a name to a colormap and the value must be a
Colormap. If a list then must be same length as the axis that is
being expanded as channels, and each colormap is applied to each new
image layer.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image. If list of lists then must be same length as the axis
that is being expanded and then each colormap is applied to each
image.
gamma : list, float
Gamma correction for determining colormap linearity. Defaults to 1.
If a list then must be same length as the axis that is being expanded
and then each entry in the list is applied to each image.
interpolation : str
Interpolation mode used by vispy. Must be one of our supported
modes.
name : str
Name of the layer.
metadata : dict
Layer metadata.
scale : tuple of float
Scale factors for the layer.
translate : tuple of float
Translation values for the layer.
opacity : float
Opacity of the layer visual, between 0.0 and 1.0.
blending : str
One of a list of preset blending modes that determines how RGB and
alpha values of the layer visual get mixed. Allowed values are
{'opaque', 'translucent', and 'additive'}.
visible : bool
Whether the layer visual is currently being displayed.
path : str or list of str
Path or list of paths to image data. Paths can be passed as strings
or `pathlib.Path` instances.
title : string
The title of the viewer window.
ndisplay : {2, 3}
Number of displayed dimensions.
order : tuple of int
Order in which dimensions are displayed where the last two or last
three dimensions correspond to row x column or plane x row x column if
ndisplay is 2 or 3.
axis_labels : list of str
Dimension names.
Returns
-------
viewer : :class:`napari.Viewer`
The newly-created viewer.
"""
viewer = Viewer(
title=title, ndisplay=ndisplay, order=order, axis_labels=axis_labels
)
viewer.add_image(
data=data,
channel_axis=channel_axis,
rgb=rgb,
is_pyramid=is_pyramid,
colormap=colormap,
contrast_limits=contrast_limits,
gamma=gamma,
interpolation=interpolation,
rendering=rendering,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
path=path,
)
return viewer
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def __init__(self, title="napari", ndisplay=2, order=None, axis_labels=None):
# instance() returns the singleton instance if it exists, or None
app = QApplication.instance()
# if None, raise a RuntimeError with the appropriate message
if app is None:
message = (
"napari requires a Qt event loop to run. To create one, "
"try one of the following: \n"
" - use the `napari.gui_qt()` context manager. See "
"https://github.com/napari/napari/tree/master/examples for"
" usage examples.\n"
" - In IPython or a local Jupyter instance, use the "
"`%gui qt` magic command.\n"
" - Launch IPython with the option `--gui=qt`.\n"
" - (recommended) in your IPython configuration file, add"
" or uncomment the line `c.TerminalIPythonApp.gui = 'qt'`."
" Then, restart IPython."
)
raise RuntimeError(message)
super().__init__(
title=title,
ndisplay=ndisplay,
order=order,
axis_labels=axis_labels,
)
qt_viewer = QtViewer(self)
self.window = Window(qt_viewer)
self.screenshot = self.window.qt_viewer.screenshot
self.update_console = self.window.qt_viewer.console.push
|
def __init__(self, title="napari", ndisplay=2, order=None, axis_labels=None):
# instance() returns the singleton instance if it exists, or None
app = QApplication.instance()
# if None, raise a RuntimeError with the appropriate message
if app is None:
message = (
"napari requires a Qt event loop to run. To create one, "
"try one of the following: \n"
" - use the `napari.gui_qt()` context manager. See "
"https://github.com/napari/napari/tree/master/examples for"
" usage examples.\n"
" - In IPython or a local Jupyter instance, use the "
"`%gui qt` magic command.\n"
" - Launch IPython with the option `--gui=qt`.\n"
" - (recommended) in your IPython configuration file, add"
" or uncomment the line `c.TerminalIPythonApp.gui = 'qt'`."
" Then, restart IPython."
)
raise RuntimeError(message)
super().__init__(
title=title,
ndisplay=ndisplay,
order=order,
axis_labels=axis_labels,
)
qt_viewer = QtViewer(self)
self.window = Window(qt_viewer)
self.update_console = self.window.qt_viewer.console.push
|
https://github.com/napari/napari/issues/691
|
Traceback (most recent call last):
File "<ipython-input-48-ce4a0e063e17>", line 3, in <module>
napari.view_image(pyramid, is_pyramid=True)
File "C:\anaconda3\envs\nap\lib\site-packages\napari\view_layers.py", line 120, in view_image
path=path,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\components\viewer_model.py", line 509, in add_image
visible=visible,
File "C:\anaconda3\envs\nap\lib\site-packages\napari\layers\image\image.py", line 147, in __init__
data, pyramid=is_pyramid, rgb=rgb
File "C:\anaconda3\envs\nap\lib\site-packages\napari\util\misc.py", line 143, in get_pyramid_and_rgb
init_shape = data.shape
AttributeError: 'list' object has no attribute 'shape'
|
AttributeError
|
def _open_images(self):
"""Add image files from the menubar."""
filenames, _ = QFileDialog.getOpenFileNames(
parent=self,
caption="Select image(s)...",
directory=self._last_visited_dir, # home dir by default
)
if (filenames != []) and (filenames is not None):
self._add_files(filenames)
|
def _open_images(self):
"""Add image files from the menubar."""
filenames, _ = QFileDialog.getOpenFileNames(
parent=self,
caption="Select image(s)...",
directory=self._last_visited_dir, # home dir by default
)
if filenames is not None:
self._add_files(filenames)
|
https://github.com/napari/napari/issues/706
|
WARNING: Traceback (most recent call last):
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 233, in _open_folder
self._add_files([folder])
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 247, in _add_files
self.viewer.add_image(path=filenames)
File "/home/jni/projects/napari/napari/components/viewer_model.py", line 485, in add_image
data = io.magic_imread(path)
File "/home/jni/projects/napari/napari/util/io.py", line 71, in magic_imread
image = io.imread(filename)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_io.py", line 48, in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/manage_plugins.py", line 210, in call_plugin
return func(*args, **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_plugins/imageio_plugin.py", line 10, in imread
return np.asarray(imageio_imread(*args, **kwargs))
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 264, in imread
reader = read(uri, format, "i", **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 182, in get_reader
"Could not find a format to read the specified file " "in mode %r" % mode
ValueError: Could not find a format to read the specified file in mode 'i'
WARNING:vispy:Traceback (most recent call last):
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 233, in _open_folder
self._add_files([folder])
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 247, in _add_files
self.viewer.add_image(path=filenames)
File "/home/jni/projects/napari/napari/components/viewer_model.py", line 485, in add_image
data = io.magic_imread(path)
File "/home/jni/projects/napari/napari/util/io.py", line 71, in magic_imread
image = io.imread(filename)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_io.py", line 48, in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/manage_plugins.py", line 210, in call_plugin
return func(*args, **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_plugins/imageio_plugin.py", line 10, in imread
return np.asarray(imageio_imread(*args, **kwargs))
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 264, in imread
reader = read(uri, format, "i", **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 182, in get_reader
"Could not find a format to read the specified file " "in mode %r" % mode
ValueError: Could not find a format to read the specified file in mode 'i'
Aborted (core dumped)
|
ValueError
|
def _open_folder(self):
"""Add a folder of files from the menubar."""
folder = QFileDialog.getExistingDirectory(
parent=self,
caption="Select folder...",
directory=self._last_visited_dir, # home dir by default
)
if folder not in {"", None}:
self._add_files([folder])
|
def _open_folder(self):
"""Add a folder of files from the menubar."""
folder = QFileDialog.getExistingDirectory(
parent=self,
caption="Select folder...",
directory=self._last_visited_dir, # home dir by default
)
if folder is not None:
self._add_files([folder])
|
https://github.com/napari/napari/issues/706
|
WARNING: Traceback (most recent call last):
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 233, in _open_folder
self._add_files([folder])
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 247, in _add_files
self.viewer.add_image(path=filenames)
File "/home/jni/projects/napari/napari/components/viewer_model.py", line 485, in add_image
data = io.magic_imread(path)
File "/home/jni/projects/napari/napari/util/io.py", line 71, in magic_imread
image = io.imread(filename)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_io.py", line 48, in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/manage_plugins.py", line 210, in call_plugin
return func(*args, **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_plugins/imageio_plugin.py", line 10, in imread
return np.asarray(imageio_imread(*args, **kwargs))
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 264, in imread
reader = read(uri, format, "i", **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 182, in get_reader
"Could not find a format to read the specified file " "in mode %r" % mode
ValueError: Could not find a format to read the specified file in mode 'i'
WARNING:vispy:Traceback (most recent call last):
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 233, in _open_folder
self._add_files([folder])
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 247, in _add_files
self.viewer.add_image(path=filenames)
File "/home/jni/projects/napari/napari/components/viewer_model.py", line 485, in add_image
data = io.magic_imread(path)
File "/home/jni/projects/napari/napari/util/io.py", line 71, in magic_imread
image = io.imread(filename)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_io.py", line 48, in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/manage_plugins.py", line 210, in call_plugin
return func(*args, **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/skimage/io/_plugins/imageio_plugin.py", line 10, in imread
return np.asarray(imageio_imread(*args, **kwargs))
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 264, in imread
reader = read(uri, format, "i", **kwargs)
File "/home/jni/miniconda3/envs/f7/lib/python3.7/site-packages/imageio/core/functions.py", line 182, in get_reader
"Could not find a format to read the specified file " "in mode %r" % mode
ValueError: Could not find a format to read the specified file in mode 'i'
Aborted (core dumped)
|
ValueError
|
def __init__(self, layer, node):
super().__init__()
self.layer = layer
self.node = node
self._position = (0,) * self.layer.dims.ndisplay
self.camera = None
self.layer.events.refresh.connect(lambda e: self.node.update())
self.layer.events.set_data.connect(lambda e: self._on_data_change())
self.layer.events.visible.connect(lambda e: self._on_visible_change())
self.layer.events.opacity.connect(lambda e: self._on_opacity_change())
self.layer.events.blending.connect(lambda e: self._on_blending_change())
self.layer.events.scale.connect(lambda e: self._on_scale_change())
self.layer.events.translate.connect(lambda e: self._on_translate_change())
|
def __init__(self, layer, node):
super().__init__()
self.layer = layer
self.node = node
self._position = (0,) * self.layer.ndim
self.camera = None
self.layer.events.refresh.connect(lambda e: self.node.update())
self.layer.events.set_data.connect(lambda e: self._on_data_change())
self.layer.events.visible.connect(lambda e: self._on_visible_change())
self.layer.events.opacity.connect(lambda e: self._on_opacity_change())
self.layer.events.blending.connect(lambda e: self._on_blending_change())
self.layer.events.scale.connect(lambda e: self._on_scale_change())
self.layer.events.translate.connect(lambda e: self._on_translate_change())
|
https://github.com/napari/napari/issues/678
|
(1, 10, 2, 15, 256, 256, 1)
BTCZYX0
(1, 10, 2, 15, 256, 256)
Dim PosT : 1
Dim PosZ : 3
Dim PosC : 2
Scale Factors XYZ: [1, 1, 1, 3.516, 1, 1]
(1, 10, 15, 256, 256)
Adding Channel: AF555
(1, 10, 15, 256, 256)
Adding Channel: AF488
WARNING: Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_qt\qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_qt\qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\dims.py", line 205, in ndisplay
self.events.ndisplay()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 523, in _invoke_callback
cb(event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\viewer_model.py", line 89, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\viewer_model.py", line 1018, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\dims.py", line 205, in ndisplay
self.events.ndisplay()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 523, in _invoke_callback
cb(event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\layers\base\base.py", line 174, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\layers\base\base.py", line 372, in _update_dims
self._set_view_slice()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\layers\image\image.py", line 502, in _set_view_slice
self.events.set_data()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 523, in _invoke_callback
cb(event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_base_layer.py", line 46, in <lambda>
self.layer.events.set_data.connect(lambda e: self._on_data_change())
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 59, in _on_data_change
self._on_display_change()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 48, in _on_display_change
self.reset()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 216, in reset
self._reset_base()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_base_layer.py", line 165, in _reset_base
self._on_scale_change()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 123, in _on_scale_change
self.layer.position = self._transform_position(self._position)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_base_layer.py", line 153, in _transform_position
transform.map(list(position))[: len(self.layer.dims.displayed)]
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\vispy\visuals\transforms\chain.py", line 148, in map
coords = tr.map(coords)
File "<decorator-gen-4>", line 2, in imap
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\vispy\visuals\transforms\_util.py", line 111, in arg_to_vec4
arg = as_vec4(arg)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\vispy\visuals\transforms\_util.py", line 81, in as_vec4
% obj.shape)
TypeError: not all arguments converted during string formatting
WARNING:vispy:Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_qt\qt_viewer_buttons.py", line 173, in <lambda>
lambda state=self: self.change_ndisplay(state)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_qt\qt_viewer_buttons.py", line 178, in change_ndisplay
self.viewer.dims.ndisplay = 3
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\dims.py", line 205, in ndisplay
self.events.ndisplay()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 523, in _invoke_callback
cb(event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\viewer_model.py", line 89, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_layers())
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\viewer_model.py", line 1018, in _update_layers
layer.dims.ndisplay = self.dims.ndisplay
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\components\dims.py", line 205, in ndisplay
self.events.ndisplay()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 523, in _invoke_callback
cb(event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\layers\base\base.py", line 174, in <lambda>
self.dims.events.ndisplay.connect(lambda e: self._update_dims())
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\layers\base\base.py", line 372, in _update_dims
self._set_view_slice()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\layers\image\image.py", line 502, in _set_view_slice
self.events.set_data()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\util\event.py", line 523, in _invoke_callback
cb(event)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_base_layer.py", line 46, in <lambda>
self.layer.events.set_data.connect(lambda e: self._on_data_change())
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 59, in _on_data_change
self._on_display_change()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 48, in _on_display_change
self.reset()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 216, in reset
self._reset_base()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_base_layer.py", line 165, in _reset_base
self._on_scale_change()
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_image_layer.py", line 123, in _on_scale_change
self.layer.position = self._transform_position(self._position)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\napari\_vispy\vispy_base_layer.py", line 153, in _transform_position
transform.map(list(position))[: len(self.layer.dims.displayed)]
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\vispy\visuals\transforms\chain.py", line 148, in map
coords = tr.map(coords)
File "<decorator-gen-4>", line 2, in imap
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\vispy\visuals\transforms\_util.py", line 111, in arg_to_vec4
arg = as_vec4(arg)
File "C:\ProgramData\Anaconda3\envs\imageanalysis\lib\site-packages\vispy\visuals\transforms\_util.py", line 81, in as_vec4
% obj.shape)
TypeError: not all arguments converted during string formatting
|
TypeError
|
def _update_thumbnail(self):
"""Update thumbnail with current image data and colormap."""
if self.dims.ndisplay == 3 and self.dims.ndim > 2:
image = np.max(self._data_thumbnail, axis=0)
else:
image = self._data_thumbnail
# float16 not supported by ndi.zoom
dtype = np.dtype(image.dtype)
if dtype in [np.dtype(np.float16)]:
image = image.astype(np.float32)
raw_zoom_factor = np.divide(self._thumbnail_shape[:2], image.shape[:2]).min()
new_shape = np.clip(
raw_zoom_factor * np.array(image.shape[:2]),
1, # smallest side should be 1 pixel wide
self._thumbnail_shape[:2],
)
zoom_factor = tuple(new_shape / image.shape[:2])
if self.rgb:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(image, zoom_factor + (1,), prefilter=False, order=0)
if image.shape[2] == 4: # image is RGBA
colormapped = np.copy(downsampled)
colormapped[..., 3] = downsampled[..., 3] * self.opacity
if downsampled.dtype == np.uint8:
colormapped = colormapped.astype(np.uint8)
else: # image is RGB
if downsampled.dtype == np.uint8:
alpha = np.full(
downsampled.shape[:2] + (1,),
int(255 * self.opacity),
dtype=np.uint8,
)
else:
alpha = np.full(downsampled.shape[:2] + (1,), self.opacity)
colormapped = np.concatenate([downsampled, alpha], axis=2)
else:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(image, zoom_factor, prefilter=False, order=0)
low, high = self.contrast_limits
downsampled = np.clip(downsampled, low, high)
color_range = high - low
if color_range != 0:
downsampled = (downsampled - low) / color_range
downsampled = downsampled**self.gamma
color_array = self.colormap[1][downsampled.ravel()]
colormapped = color_array.rgba.reshape(downsampled.shape + (4,))
colormapped[..., 3] *= self.opacity
self.thumbnail = colormapped
|
def _update_thumbnail(self):
"""Update thumbnail with current image data and colormap."""
if self.dims.ndisplay == 3 and self.dims.ndim > 2:
image = np.max(self._data_thumbnail, axis=0)
else:
image = self._data_thumbnail
# float16 not supported by ndi.zoom
dtype = np.dtype(image.dtype)
if dtype in [np.dtype(np.float16)]:
image = image.astype(np.float32)
zoom_factor = np.divide(self._thumbnail_shape[:2], image.shape[:2]).min()
if self.rgb:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(
image,
(zoom_factor, zoom_factor, 1),
prefilter=False,
order=0,
)
if image.shape[2] == 4: # image is RGBA
colormapped = np.copy(downsampled)
colormapped[..., 3] = downsampled[..., 3] * self.opacity
if downsampled.dtype == np.uint8:
colormapped = colormapped.astype(np.uint8)
else: # image is RGB
if downsampled.dtype == np.uint8:
alpha = np.full(
downsampled.shape[:2] + (1,),
int(255 * self.opacity),
dtype=np.uint8,
)
else:
alpha = np.full(downsampled.shape[:2] + (1,), self.opacity)
colormapped = np.concatenate([downsampled, alpha], axis=2)
else:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(image, zoom_factor, prefilter=False, order=0)
low, high = self.contrast_limits
downsampled = np.clip(downsampled, low, high)
color_range = high - low
if color_range != 0:
downsampled = (downsampled - low) / color_range
downsampled = downsampled**self.gamma
color_array = self.colormap[1][downsampled.ravel()]
colormapped = color_array.rgba.reshape(downsampled.shape + (4,))
colormapped[..., 3] *= self.opacity
self.thumbnail = colormapped
|
https://github.com/napari/napari/issues/641
|
WARNING: Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 121, in <lambda>
self.clicked.connect(lambda: self.viewer.dims._roll())
File "/usr/lib/python3.7/site-packages/napari/components/dims.py", line 340, in _roll
self.order = np.roll(self.order, 1)
File "/usr/lib/python3.7/site-packages/napari/components/dims.py", line 130, in order
self.events.order()
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 523, in _invoke_callback
cb(event)
File "/usr/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.order.connect(lambda e: self._update_layers())
File "/usr/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1045, in _update_layers
layer.dims.order = order
File "/usr/lib/python3.7/site-packages/napari/components/dims.py", line 130, in order
self.events.order()
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 523, in _invoke_callback
cb(event)
File "/usr/lib/python3.7/site-packages/napari/layers/base/base.py", line 176, in <lambda>
self.dims.events.order.connect(lambda e: self._update_dims())
File "/usr/lib/python3.7/site-packages/napari/layers/base/base.py", line 373, in _update_dims
self._set_view_slice()
File "/usr/lib/python3.7/site-packages/napari/layers/image/image.py", line 477, in _set_view_slice
self._update_thumbnail()
File "/usr/lib/python3.7/site-packages/napari/layers/image/image.py", line 536, in _update_thumbnail
color_array = self.colormap[1][downsampled.ravel()]
File "/usr/lib/python3.7/site-packages/vispy/color/colormap.py", line 293, in __getitem__
return ColorArray(colors)
File "/usr/lib/python3.7/site-packages/vispy/color/color_array.py", line 148, in __init__
rgba = _user_to_rgba(color, clip=clip)
File "/usr/lib/python3.7/site-packages/vispy/color/color_array.py", line 61, in _user_to_rgba
if color.min() < 0 or color.max() > 1:
File "/usr/lib/python3.7/site-packages/numpy/core/_methods.py", line 32, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial)
ValueError: zero-size array to reduction operation minimum which has no identity
WARNING:vispy:Traceback (most recent call last):
File "/usr/lib/python3.7/site-packages/napari/_qt/qt_viewer_buttons.py", line 121, in <lambda>
self.clicked.connect(lambda: self.viewer.dims._roll())
File "/usr/lib/python3.7/site-packages/napari/components/dims.py", line 340, in _roll
self.order = np.roll(self.order, 1)
File "/usr/lib/python3.7/site-packages/napari/components/dims.py", line 130, in order
self.events.order()
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 523, in _invoke_callback
cb(event)
File "/usr/lib/python3.7/site-packages/napari/components/viewer_model.py", line 88, in <lambda>
self.dims.events.order.connect(lambda e: self._update_layers())
File "/usr/lib/python3.7/site-packages/napari/components/viewer_model.py", line 1045, in _update_layers
layer.dims.order = order
File "/usr/lib/python3.7/site-packages/napari/components/dims.py", line 130, in order
self.events.order()
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 508, in __call__
self._invoke_callback(cb, event)
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 529, in _invoke_callback
cb_event=(cb, event),
File "/usr/lib/python3.7/site-packages/napari/util/event.py", line 523, in _invoke_callback
cb(event)
File "/usr/lib/python3.7/site-packages/napari/layers/base/base.py", line 176, in <lambda>
self.dims.events.order.connect(lambda e: self._update_dims())
File "/usr/lib/python3.7/site-packages/napari/layers/base/base.py", line 373, in _update_dims
self._set_view_slice()
File "/usr/lib/python3.7/site-packages/napari/layers/image/image.py", line 477, in _set_view_slice
self._update_thumbnail()
File "/usr/lib/python3.7/site-packages/napari/layers/image/image.py", line 536, in _update_thumbnail
color_array = self.colormap[1][downsampled.ravel()]
File "/usr/lib/python3.7/site-packages/vispy/color/colormap.py", line 293, in __getitem__
return ColorArray(colors)
File "/usr/lib/python3.7/site-packages/vispy/color/color_array.py", line 148, in __init__
rgba = _user_to_rgba(color, clip=clip)
File "/usr/lib/python3.7/site-packages/vispy/color/color_array.py", line 61, in _user_to_rgba
if color.min() < 0 or color.max() > 1:
File "/usr/lib/python3.7/site-packages/numpy/core/_methods.py", line 32, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial)
ValueError: zero-size array to reduction operation minimum which has no identity
[1] 16296 abort (core dumped) napari FITC.tif
|
ValueError
|
def __init__(
self,
data,
*,
rgb=None,
is_pyramid=None,
colormap="gray",
contrast_limits=None,
interpolation="nearest",
rendering="mip",
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending="translucent",
visible=True,
):
if isinstance(data, types.GeneratorType):
data = list(data)
ndim, rgb, is_pyramid, data_pyramid = get_pyramid_and_rgb(
data, pyramid=is_pyramid, rgb=rgb
)
super().__init__(
ndim,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.events.add(
contrast_limits=Event,
colormap=Event,
interpolation=Event,
rendering=Event,
)
# Set data
self.is_pyramid = is_pyramid
self.rgb = rgb
self._data = data
self._data_pyramid = data_pyramid
self._top_left = np.zeros(ndim, dtype=int)
if self.is_pyramid:
self._data_level = len(data_pyramid) - 1
else:
self._data_level = 0
# Intitialize image views and thumbnails with zeros
if self.rgb:
self._data_view = np.zeros((1,) * self.dims.ndisplay + (self.shape[-1],))
else:
self._data_view = np.zeros((1,) * self.dims.ndisplay)
self._data_thumbnail = self._data_view
# Set contrast_limits and colormaps
self._colormap_name = ""
self._contrast_limits_msg = ""
if contrast_limits is None:
if self.is_pyramid:
input_data = self._data_pyramid[-1]
else:
input_data = self.data
self._contrast_limits_range = calc_data_range(input_data)
else:
self._contrast_limits_range = contrast_limits
self._contrast_limits = copy(self._contrast_limits_range)
self.colormap = colormap
self.contrast_limits = self._contrast_limits
self.interpolation = interpolation
self.rendering = rendering
# Trigger generation of view slice and thumbnail
self._update_dims()
|
def __init__(
self,
data,
*,
rgb=None,
is_pyramid=None,
colormap="gray",
contrast_limits=None,
interpolation="nearest",
rendering="mip",
name=None,
metadata=None,
scale=None,
translate=None,
opacity=1,
blending="translucent",
visible=True,
):
ndim, rgb, is_pyramid, data_pyramid = get_pyramid_and_rgb(
data, pyramid=is_pyramid, rgb=rgb
)
super().__init__(
ndim,
name=name,
metadata=metadata,
scale=scale,
translate=translate,
opacity=opacity,
blending=blending,
visible=visible,
)
self.events.add(
contrast_limits=Event,
colormap=Event,
interpolation=Event,
rendering=Event,
)
# Set data
self.is_pyramid = is_pyramid
self.rgb = rgb
self._data = data
self._data_pyramid = data_pyramid
self._top_left = np.zeros(ndim, dtype=int)
if self.is_pyramid:
self._data_level = len(data_pyramid) - 1
else:
self._data_level = 0
# Intitialize image views and thumbnails with zeros
if self.rgb:
self._data_view = np.zeros((1,) * self.dims.ndisplay + (self.shape[-1],))
else:
self._data_view = np.zeros((1,) * self.dims.ndisplay)
self._data_thumbnail = self._data_view
# Set contrast_limits and colormaps
self._colormap_name = ""
self._contrast_limits_msg = ""
if contrast_limits is None:
if self.is_pyramid:
input_data = self._data_pyramid[-1]
else:
input_data = self.data
self._contrast_limits_range = calc_data_range(input_data)
else:
self._contrast_limits_range = contrast_limits
self._contrast_limits = copy(self._contrast_limits_range)
self.colormap = colormap
self.contrast_limits = self._contrast_limits
self.interpolation = interpolation
self.rendering = rendering
# Trigger generation of view slice and thumbnail
self._update_dims()
|
https://github.com/napari/napari/issues/563
|
regions
<xarray.Regions 'array-baa123768d7ef2a6d2cdfa885e8f3eaa' (x_region: 31725, y_region: 51669)>
array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=int16)
Dimensions without coordinates: x_region, y_region
Attributes:
assay: osmFISH
authors: ['Simone Codeluppi', 'Lars E. Borm', 'Amit Zeisel', 'G...
organism: mouse
publication_name: Spatial organization of the somatosensory cortex revea...
publication_url: https://www.nature.com/articles/s41592-018-0175-z
sample_type: somatosensory cortex
year: 2018
pyramid = tuple(pyramid_gaussian(regions), multichannel=False)
[i.shape for i in pyramid]
[(31725, 51669),
(15863, 25835),
(7932, 12918),
(3966, 6459),
(1983, 3230),
(992, 1615),
(496, 808),
(248, 404),
(124, 202),
(62, 101),
(31, 51),
(16, 26),
(8, 13),
(4, 7),
(2, 4),
(1, 2),
(1, 1)]
viewer = napari.Viewer()
viewer.add_image(np.asarray(pyramid), is_pyramid=True)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-35-665dfea0cb05> in <module>
----> 1 viewer.add_image(np.asarray(pyramid), is_pyramid=True)
/usr/local/lib/python3.7/site-packages/napari/components/viewer_model.py in add_image(self, data, rgb, is_pyramid, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
426 opacity=opacity,
427 blending=blending,
--> 428 visible=visible,
429 )
430 self.add_layer(layer)
/usr/local/lib/python3.7/site-packages/napari/layers/image/image.py in __init__(self, data, rgb, is_pyramid, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
185 else:
186 input_data = self.data
--> 187 self._contrast_limits_range = calc_data_range(input_data)
188 else:
189 self._contrast_limits_range = contrast_limits
/usr/local/lib/python3.7/site-packages/napari/util/misc.py in calc_data_range(data)
268 reduced_data = data
269
--> 270 min_val = reduced_data.min()
271 max_val = reduced_data.max()
272
/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py in _amin(a, axis, out, keepdims, initial)
30 def _amin(a, axis=None, out=None, keepdims=False,
31 initial=_NoValue):
---> 32 return umr_minimum(a, axis, None, out, keepdims, initial)
33
34 def _sum(a, axis=None, dtype=None, out=None, keepdims=False,
ValueError: operands could not be broadcast together with shapes (31725,51669) (15863,25835)
|
ValueError
|
def is_pyramid(data):
"""If shape of arrays along first axis is strictly decreasing."""
size = np.array([np.prod(d.shape) for d in data])
if len(size) > 1:
return np.all(size[:-1] > size[1:])
else:
return False
|
def is_pyramid(data):
"""If data is a list of arrays of decreasing size."""
if isinstance(data, list):
size = [np.prod(d.shape) for d in data]
return np.all(size[:-1] > size[1:])
else:
return False
|
https://github.com/napari/napari/issues/563
|
regions
<xarray.Regions 'array-baa123768d7ef2a6d2cdfa885e8f3eaa' (x_region: 31725, y_region: 51669)>
array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=int16)
Dimensions without coordinates: x_region, y_region
Attributes:
assay: osmFISH
authors: ['Simone Codeluppi', 'Lars E. Borm', 'Amit Zeisel', 'G...
organism: mouse
publication_name: Spatial organization of the somatosensory cortex revea...
publication_url: https://www.nature.com/articles/s41592-018-0175-z
sample_type: somatosensory cortex
year: 2018
pyramid = tuple(pyramid_gaussian(regions), multichannel=False)
[i.shape for i in pyramid]
[(31725, 51669),
(15863, 25835),
(7932, 12918),
(3966, 6459),
(1983, 3230),
(992, 1615),
(496, 808),
(248, 404),
(124, 202),
(62, 101),
(31, 51),
(16, 26),
(8, 13),
(4, 7),
(2, 4),
(1, 2),
(1, 1)]
viewer = napari.Viewer()
viewer.add_image(np.asarray(pyramid), is_pyramid=True)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-35-665dfea0cb05> in <module>
----> 1 viewer.add_image(np.asarray(pyramid), is_pyramid=True)
/usr/local/lib/python3.7/site-packages/napari/components/viewer_model.py in add_image(self, data, rgb, is_pyramid, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
426 opacity=opacity,
427 blending=blending,
--> 428 visible=visible,
429 )
430 self.add_layer(layer)
/usr/local/lib/python3.7/site-packages/napari/layers/image/image.py in __init__(self, data, rgb, is_pyramid, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
185 else:
186 input_data = self.data
--> 187 self._contrast_limits_range = calc_data_range(input_data)
188 else:
189 self._contrast_limits_range = contrast_limits
/usr/local/lib/python3.7/site-packages/napari/util/misc.py in calc_data_range(data)
268 reduced_data = data
269
--> 270 min_val = reduced_data.min()
271 max_val = reduced_data.max()
272
/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py in _amin(a, axis, out, keepdims, initial)
30 def _amin(a, axis=None, out=None, keepdims=False,
31 initial=_NoValue):
---> 32 return umr_minimum(a, axis, None, out, keepdims, initial)
33
34 def _sum(a, axis=None, dtype=None, out=None, keepdims=False,
ValueError: operands could not be broadcast together with shapes (31725,51669) (15863,25835)
|
ValueError
|
def get_pyramid_and_rgb(data, pyramid=None, rgb=None):
"""Check if data is or needs to be a pyramid and make one if needed.
Parameters
----------
data : array, list, or tuple
Data to be checked if pyramid or if needs to be turned into a pyramid.
pyramid : bool, optional
Value that can force data to be considered as a pyramid or not,
otherwise computed.
rgb : bool, optional
Value that can force data to be considered as a rgb, otherwise
computed.
Returns
-------
ndim : int
Dimensionality of the data.
rgb : bool
If data is rgb.
pyramid : bool
If data is a pyramid or a pyramid has been generated.
data_pyramid : list or None
If None then data is not and does not need to be a pyramid. Otherwise
is a list of arrays where each array is a level of the pyramid.
"""
# Determine if data currently is a pyramid
currently_pyramid = is_pyramid(data)
if currently_pyramid:
shapes = [d.shape for d in data]
init_shape = shapes[0]
else:
init_shape = data.shape
# Determine if rgb, and determine dimensionality
if rgb is False:
pass
else:
# If rgb is True or None then guess if rgb
# allowed or not, and if allowed set it to be True
rgb_guess = is_rgb(init_shape)
if rgb and rgb_guess is False:
raise ValueError(
"Non rgb or rgba data was passed, but rgb data was requested."
)
else:
rgb = rgb_guess
if rgb:
ndim = len(init_shape) - 1
else:
ndim = len(init_shape)
if pyramid is False:
if currently_pyramid:
raise ValueError(
"Non pyramided data was requested, but pyramid data was passed"
)
else:
data_pyramid = None
else:
if currently_pyramid:
data_pyramid = trim_pyramid(data)
pyramid = True
else:
# Guess if data should be pyramid or if a pyramid was requested
if pyramid:
pyr_axes = [True] * ndim
else:
pyr_axes = should_be_pyramid(data.shape)
if np.any(pyr_axes):
pyramid = True
# Set axes to be downsampled to have a factor of 2
downscale = np.ones(len(data.shape))
downscale[pyr_axes] = 2
largest = np.min(np.array(data.shape)[pyr_axes])
# Determine number of downsample steps needed
max_layer = np.floor(np.log2(largest) - 9).astype(int)
data_pyramid = fast_pyramid(
data, downscale=downscale, max_layer=max_layer
)
data_pyramid = trim_pyramid(data_pyramid)
else:
data_pyramid = None
pyramid = False
return ndim, rgb, pyramid, data_pyramid
|
def get_pyramid_and_rgb(data, pyramid=None, rgb=None):
"""Check if data is or needs to be a pyramid and make one if needed.
Parameters
----------
data : array or list
Data to be checked if pyramid or if needs to be turned into a pyramid.
pyramid : bool, optional
Value that can force data to be considered as a pyramid or not,
otherwise computed.
rgb : bool, optional
Value that can force data to be considered as a rgb, otherwise
computed.
Returns
-------
ndim : int
Dimensionality of the data.
rgb : bool
If data is rgb.
pyramid : bool
If data is a pyramid or a pyramid has been generated.
data_pyramid : list or None
If None then data is not and does not need to be a pyramid. Otherwise
is a list of arrays where each array is a level of the pyramid.
"""
# Determine if data currently is a pyramid
currently_pyramid = is_pyramid(data)
if currently_pyramid:
init_shape = data[0].shape
else:
init_shape = data.shape
# Determine if rgb, and determine dimensionality
if rgb is False:
pass
else:
# If rgb is True or None then guess if rgb
# allowed or not, and if allowed set it to be True
rgb = is_rgb(init_shape)
if rgb:
ndim = len(init_shape) - 1
else:
ndim = len(init_shape)
if pyramid is False:
if currently_pyramid:
raise ValueError(
"""Non pyramided data was requested, but pyramid
data was passed"""
)
else:
data_pyramid = None
else:
if currently_pyramid:
data_pyramid = trim_pyramid(data)
pyramid = True
else:
# Guess if data should be pyramid
pyr_axes = should_be_pyramid(data.shape)
if np.any(pyr_axes):
pyramid = True
# Set axes to be downsampled to have a factor of 2
downscale = np.ones(len(data.shape))
downscale[pyr_axes] = 2
largest = np.min(np.array(data.shape)[pyr_axes])
# Determine number of downsample steps needed
max_layer = np.floor(np.log2(largest) - 9).astype(int)
data_pyramid = fast_pyramid(
data, downscale=downscale, max_layer=max_layer
)
data_pyramid = trim_pyramid(data_pyramid)
else:
data_pyramid = None
pyramid = False
return ndim, rgb, pyramid, data_pyramid
|
https://github.com/napari/napari/issues/563
|
regions
<xarray.Regions 'array-baa123768d7ef2a6d2cdfa885e8f3eaa' (x_region: 31725, y_region: 51669)>
array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=int16)
Dimensions without coordinates: x_region, y_region
Attributes:
assay: osmFISH
authors: ['Simone Codeluppi', 'Lars E. Borm', 'Amit Zeisel', 'G...
organism: mouse
publication_name: Spatial organization of the somatosensory cortex revea...
publication_url: https://www.nature.com/articles/s41592-018-0175-z
sample_type: somatosensory cortex
year: 2018
pyramid = tuple(pyramid_gaussian(regions), multichannel=False)
[i.shape for i in pyramid]
[(31725, 51669),
(15863, 25835),
(7932, 12918),
(3966, 6459),
(1983, 3230),
(992, 1615),
(496, 808),
(248, 404),
(124, 202),
(62, 101),
(31, 51),
(16, 26),
(8, 13),
(4, 7),
(2, 4),
(1, 2),
(1, 1)]
viewer = napari.Viewer()
viewer.add_image(np.asarray(pyramid), is_pyramid=True)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-35-665dfea0cb05> in <module>
----> 1 viewer.add_image(np.asarray(pyramid), is_pyramid=True)
/usr/local/lib/python3.7/site-packages/napari/components/viewer_model.py in add_image(self, data, rgb, is_pyramid, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
426 opacity=opacity,
427 blending=blending,
--> 428 visible=visible,
429 )
430 self.add_layer(layer)
/usr/local/lib/python3.7/site-packages/napari/layers/image/image.py in __init__(self, data, rgb, is_pyramid, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
185 else:
186 input_data = self.data
--> 187 self._contrast_limits_range = calc_data_range(input_data)
188 else:
189 self._contrast_limits_range = contrast_limits
/usr/local/lib/python3.7/site-packages/napari/util/misc.py in calc_data_range(data)
268 reduced_data = data
269
--> 270 min_val = reduced_data.min()
271 max_val = reduced_data.max()
272
/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py in _amin(a, axis, out, keepdims, initial)
30 def _amin(a, axis=None, out=None, keepdims=False,
31 initial=_NoValue):
---> 32 return umr_minimum(a, axis, None, out, keepdims, initial)
33
34 def _sum(a, axis=None, dtype=None, out=None, keepdims=False,
ValueError: operands could not be broadcast together with shapes (31725,51669) (15863,25835)
|
ValueError
|
def _set_view_slice(self):
"""Set the view given the indices to slice with."""
if self.multichannel:
# if multichannel need to keep the final axis fixed during the
# transpose. The index of the final axis depends on how many
# axes are displayed.
order = self.dims.displayed_order + (self.dims.ndisplay,)
else:
order = self.dims.displayed_order
image = np.asarray(self.data[self.dims.indices]).transpose(order)
if self.multichannel and image.dtype.kind == "f":
self._data_view = np.clip(image, 0, 1)
else:
self._data_view = image
self._data_thumbnail = self._data_view
self._update_thumbnail()
self._update_coordinates()
self.events.set_data()
|
def _set_view_slice(self):
"""Set the view given the indices to slice with."""
if self.multichannel:
# if multichannel need to keep the final axis fixed during the
# transpose. The index of the final axis depends on how many
# axes are displayed.
order = self.dims.displayed_order + (self.dims.ndisplay,)
else:
order = self.dims.displayed_order
self._data_view = np.asarray(self.data[self.dims.indices]).transpose(order)
self._data_thumbnail = self._data_view
self._update_thumbnail()
self._update_coordinates()
self.events.set_data()
|
https://github.com/napari/napari/issues/523
|
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-42-5ae500208e78> in <module>
----> 1 napari.view(array)
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/view_function.py in view(title, metadata, multichannel, contrast_limits, *images, **named_images)
51 metadata=metadata,
52 multichannel=multichannel,
---> 53 contrast_limits=contrast_limits,
54 )
55 for name, image in named_images.items():
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/components/viewer_model.py in add_image(self, data, multichannel, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
411 opacity=opacity,
412 blending=blending,
--> 413 visible=visible,
414 )
415 self.add_layer(layer)
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/image/image.py in __init__(self, data, multichannel, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
174
175 # Trigger generation of view slice and thumbnail
--> 176 self._update_dims()
177
178 @property
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/base/base.py in _update_dims(self)
313 self.dims.set_range(i, r)
314
--> 315 self._set_view_slice()
316 self._update_coordinates()
317
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/image/image.py in _set_view_slice(self)
333
334 self._data_thumbnail = self._data_view
--> 335 self._update_thumbnail()
336 self._update_coordinates()
337 self.events.set_data()
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/image/image.py in _update_thumbnail(self)
392 colormapped = colormapped.reshape(downsampled.shape + (4,))
393 colormapped[..., 3] *= self.opacity
--> 394 self.thumbnail = colormapped
395
396 def get_value(self):
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/base/base.py in thumbnail(self, thumbnail)
353 with warnings.catch_warnings():
354 warnings.simplefilter("ignore")
--> 355 thumbnail = img_as_ubyte(thumbnail)
356 self._thumbnail = thumbnail
357 self.events.thumbnail()
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/skimage/util/dtype.py in img_as_ubyte(image, force_copy)
484
485 """
--> 486 return convert(image, np.uint8, force_copy)
487
488
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/skimage/util/dtype.py in convert(image, dtype, force_copy, uniform)
253
254 if np.min(image) < -1.0 or np.max(image) > 1.0:
--> 255 raise ValueError("Images of type float must be between -1 and 1.")
256 # floating point -> integer
257 prec_loss()
ValueError: Images of type float must be between -1 and 1.
|
ValueError
|
def _set_view_slice(self):
"""Set the view given the indices to slice with."""
nd = self.dims.not_displayed
if self.multichannel:
# if multichannel need to keep the final axis fixed during the
# transpose. The index of the final axis depends on how many
# axes are displayed.
order = self.dims.displayed_order + (self.dims.ndisplay,)
else:
order = self.dims.displayed_order
# Slice thumbnail
indices = np.array(self.dims.indices)
downsampled = indices[nd] / self.level_downsamples[-1, nd]
downsampled = np.round(downsampled.astype(float)).astype(int)
downsampled = np.clip(downsampled, 0, self.level_shapes[-1, nd] - 1)
indices[nd] = downsampled
image = np.asarray(self.data[-1][tuple(indices)]).transpose(order)
if self.multichannel and image.dtype.kind == "f":
self._data_thumbnail = np.clip(image, 0, 1)
else:
self._data_thumbnail = image
# Slice currently viewed level
indices = np.array(self.dims.indices)
level = self.data_level
downsampled = indices[nd] / self.level_downsamples[level, nd]
downsampled = np.round(downsampled.astype(float)).astype(int)
downsampled = np.clip(downsampled, 0, self.level_shapes[level, nd] - 1)
indices[nd] = downsampled
disp_shape = self.level_shapes[level, self.dims.displayed]
scale = np.ones(self.ndim)
for d in self.dims.displayed:
scale[d] = self.level_downsamples[self.data_level][d]
self._scale = scale
self.events.scale()
if np.any(disp_shape > self._max_tile_shape):
for d in self.dims.displayed:
indices[d] = slice(
self._top_left[d],
self._top_left[d] + self._max_tile_shape,
1,
)
self.translate = self._top_left * self.scale
else:
self.translate = [0] * self.ndim
image = np.asarray(self.data[level][tuple(indices)]).transpose(order)
if self.multichannel and image.dtype.kind == "f":
self._data_view = np.clip(image, 0, 1)
else:
self._data_view = image
self._update_thumbnail()
self._update_coordinates()
self.events.set_data()
|
def _set_view_slice(self):
"""Set the view given the indices to slice with."""
nd = self.dims.not_displayed
if self.multichannel:
# if multichannel need to keep the final axis fixed during the
# transpose. The index of the final axis depends on how many
# axes are displayed.
order = self.dims.displayed_order + (self.dims.ndisplay,)
else:
order = self.dims.displayed_order
# Slice thumbnail
indices = np.array(self.dims.indices)
downsampled = indices[nd] / self.level_downsamples[-1, nd]
downsampled = np.round(downsampled.astype(float)).astype(int)
downsampled = np.clip(downsampled, 0, self.level_shapes[-1, nd] - 1)
indices[nd] = downsampled
self._data_thumbnail = np.asarray(self.data[-1][tuple(indices)]).transpose(order)
# Slice currently viewed level
indices = np.array(self.dims.indices)
level = self.data_level
downsampled = indices[nd] / self.level_downsamples[level, nd]
downsampled = np.round(downsampled.astype(float)).astype(int)
downsampled = np.clip(downsampled, 0, self.level_shapes[level, nd] - 1)
indices[nd] = downsampled
disp_shape = self.level_shapes[level, self.dims.displayed]
scale = np.ones(self.ndim)
for d in self.dims.displayed:
scale[d] = self.level_downsamples[self.data_level][d]
self._scale = scale
self.events.scale()
if np.any(disp_shape > self._max_tile_shape):
for d in self.dims.displayed:
indices[d] = slice(
self._top_left[d],
self._top_left[d] + self._max_tile_shape,
1,
)
self.translate = self._top_left * self.scale
else:
self.translate = [0] * self.ndim
self._data_view = np.asarray(self.data[level][tuple(indices)]).transpose(order)
self._update_thumbnail()
self._update_coordinates()
self.events.set_data()
|
https://github.com/napari/napari/issues/523
|
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-42-5ae500208e78> in <module>
----> 1 napari.view(array)
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/view_function.py in view(title, metadata, multichannel, contrast_limits, *images, **named_images)
51 metadata=metadata,
52 multichannel=multichannel,
---> 53 contrast_limits=contrast_limits,
54 )
55 for name, image in named_images.items():
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/components/viewer_model.py in add_image(self, data, multichannel, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
411 opacity=opacity,
412 blending=blending,
--> 413 visible=visible,
414 )
415 self.add_layer(layer)
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/image/image.py in __init__(self, data, multichannel, colormap, contrast_limits, interpolation, rendering, name, metadata, scale, translate, opacity, blending, visible)
174
175 # Trigger generation of view slice and thumbnail
--> 176 self._update_dims()
177
178 @property
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/base/base.py in _update_dims(self)
313 self.dims.set_range(i, r)
314
--> 315 self._set_view_slice()
316 self._update_coordinates()
317
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/image/image.py in _set_view_slice(self)
333
334 self._data_thumbnail = self._data_view
--> 335 self._update_thumbnail()
336 self._update_coordinates()
337 self.events.set_data()
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/image/image.py in _update_thumbnail(self)
392 colormapped = colormapped.reshape(downsampled.shape + (4,))
393 colormapped[..., 3] *= self.opacity
--> 394 self.thumbnail = colormapped
395
396 def get_value(self):
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/napari/layers/base/base.py in thumbnail(self, thumbnail)
353 with warnings.catch_warnings():
354 warnings.simplefilter("ignore")
--> 355 thumbnail = img_as_ubyte(thumbnail)
356 self._thumbnail = thumbnail
357 self.events.thumbnail()
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/skimage/util/dtype.py in img_as_ubyte(image, force_copy)
484
485 """
--> 486 return convert(image, np.uint8, force_copy)
487
488
/Applications/anaconda3/envs/chloe/lib/python3.7/site-packages/skimage/util/dtype.py in convert(image, dtype, force_copy, uniform)
253
254 if np.min(image) < -1.0 or np.max(image) > 1.0:
--> 255 raise ValueError("Images of type float must be between -1 and 1.")
256 # floating point -> integer
257 prec_loss()
ValueError: Images of type float must be between -1 and 1.
|
ValueError
|
def _on_data_change(self):
data = self.layer._data_view
dtype = np.dtype(data.dtype)
if dtype not in texture_dtypes:
try:
dtype = dict(i=np.int16, f=np.float32)[dtype.kind]
except KeyError: # not an int or float
raise TypeError(
f"type {dtype} not allowed for texture; must be one of {set(texture_dtypes)}"
)
data = data.astype(dtype)
if self.layer.dims.ndisplay == 3:
self.node.set_data(data, clim=self.layer.contrast_limits)
else:
self.node._need_colortransform_update = True
self.node.set_data(data)
self.node.update()
|
def _on_data_change(self):
if self.layer.dims.ndisplay == 3:
self.node.set_data(
self.layer._data_view,
contrast_limits=self.layer.contrast_limits,
)
else:
self.node._need_colortransform_update = True
self.node.set_data(self.layer._data_view)
self.node.update()
|
https://github.com/napari/napari/issues/447
|
WARNING: Traceback (most recent call last):
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 76, in <module>
demo(astronaut())
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 31, in demo
rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy'
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/contextlib.py", line 119, in __exit__
next(self.gen)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/napari/_qt/event_loop.py", line 31, in gui_qt
app.exec_()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 501, in event
out = super(QtBaseCanvasBackend, self).event(ev)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 818, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/visual.py", line 443, in draw
self._vshare.index_buffer)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 1537, in set_data
raise ValueError("Type %r not allowed for texture" % data.dtype)
ValueError: Type dtype('int64') not allowed for texture
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> for DrawEvent
WARNING: Error drawing visual <Image at 0x133fde5f8>
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> repeat 2
|
ValueError
|
def _on_contrast_limits_change(self):
if self.layer.dims.ndisplay == 3:
self._on_data_change()
else:
self.node.clim = self.layer.contrast_limits
|
def _on_contrast_limits_change(self):
if self.layer.dims.ndisplay == 3:
self.node.set_data(
self.layer._data_view,
contrast_limits=self.layer.contrast_limits,
)
else:
self.node.clim = self.layer.contrast_limits
|
https://github.com/napari/napari/issues/447
|
WARNING: Traceback (most recent call last):
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 76, in <module>
demo(astronaut())
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 31, in demo
rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy'
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/contextlib.py", line 119, in __exit__
next(self.gen)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/napari/_qt/event_loop.py", line 31, in gui_qt
app.exec_()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 501, in event
out = super(QtBaseCanvasBackend, self).event(ev)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 818, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/visual.py", line 443, in draw
self._vshare.index_buffer)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 1537, in set_data
raise ValueError("Type %r not allowed for texture" % data.dtype)
ValueError: Type dtype('int64') not allowed for texture
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> for DrawEvent
WARNING: Error drawing visual <Image at 0x133fde5f8>
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> repeat 2
|
ValueError
|
def _on_data_change(self):
data = self.layer._data_view
dtype = np.dtype(data.dtype)
if dtype not in texture_dtypes:
try:
dtype = dict(i=np.int16, f=np.float64)[dtype.kind]
except KeyError: # not an int or float
raise TypeError(
f"type {dtype} not allowed for texture; must be one of {set(texture_dtypes)}"
)
data = data.astype(dtype)
self.node._need_colortransform_update = True
self.node.set_data(data)
self.node.update()
|
def _on_data_change(self):
self.node._need_colortransform_update = True
self.node.set_data(self.layer._data_view)
self.node.update()
|
https://github.com/napari/napari/issues/447
|
WARNING: Traceback (most recent call last):
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 76, in <module>
demo(astronaut())
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 31, in demo
rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy'
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/contextlib.py", line 119, in __exit__
next(self.gen)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/napari/_qt/event_loop.py", line 31, in gui_qt
app.exec_()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 501, in event
out = super(QtBaseCanvasBackend, self).event(ev)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 818, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/visual.py", line 443, in draw
self._vshare.index_buffer)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 1537, in set_data
raise ValueError("Type %r not allowed for texture" % data.dtype)
ValueError: Type dtype('int64') not allowed for texture
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> for DrawEvent
WARNING: Error drawing visual <Image at 0x133fde5f8>
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> repeat 2
|
ValueError
|
def _update_thumbnail(self):
"""Update thumbnail with current image data and colormap."""
if self.dims.ndisplay == 3:
image = np.max(self._data_thumbnail, axis=0)
else:
image = self._data_thumbnail
# float16 not supported by ndi.zoom
dtype = np.dtype(image.dtype)
if dtype in [np.dtype(np.float16)]:
image = image.astype(np.float32)
zoom_factor = np.divide(self._thumbnail_shape[:2], image.shape[:2]).min()
if self.multichannel:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(
image,
(zoom_factor, zoom_factor, 1),
prefilter=False,
order=0,
)
if image.shape[2] == 4: # image is RGBA
colormapped = np.copy(downsampled)
colormapped[..., 3] = downsampled[..., 3] * self.opacity
if downsampled.dtype == np.uint8:
colormapped = colormapped.astype(np.uint8)
else: # image is RGB
if downsampled.dtype == np.uint8:
alpha = np.full(
downsampled.shape[:2] + (1,),
int(255 * self.opacity),
dtype=np.uint8,
)
else:
alpha = np.full(downsampled.shape[:2] + (1,), self.opacity)
colormapped = np.concatenate([downsampled, alpha], axis=2)
else:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(image, zoom_factor, prefilter=False, order=0)
low, high = self.contrast_limits
downsampled = np.clip(downsampled, low, high)
color_range = high - low
if color_range != 0:
downsampled = (downsampled - low) / color_range
colormapped = self.colormap[1].map(downsampled)
colormapped = colormapped.reshape(downsampled.shape + (4,))
colormapped[..., 3] *= self.opacity
self.thumbnail = colormapped
|
def _update_thumbnail(self):
"""Update thumbnail with current image data and colormap."""
if self.dims.ndisplay == 3:
image = np.max(self._data_thumbnail, axis=0)
else:
image = self._data_thumbnail
zoom_factor = np.divide(self._thumbnail_shape[:2], image.shape[:2]).min()
if self.multichannel:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(
image,
(zoom_factor, zoom_factor, 1),
prefilter=False,
order=0,
)
if image.shape[2] == 4: # image is RGBA
colormapped = np.copy(downsampled)
colormapped[..., 3] = downsampled[..., 3] * self.opacity
if downsampled.dtype == np.uint8:
colormapped = colormapped.astype(np.uint8)
else: # image is RGB
if downsampled.dtype == np.uint8:
alpha = np.full(
downsampled.shape[:2] + (1,),
int(255 * self.opacity),
dtype=np.uint8,
)
else:
alpha = np.full(downsampled.shape[:2] + (1,), self.opacity)
colormapped = np.concatenate([downsampled, alpha], axis=2)
else:
# warning filter can be removed with scipy 1.4
with warnings.catch_warnings():
warnings.simplefilter("ignore")
downsampled = ndi.zoom(image, zoom_factor, prefilter=False, order=0)
low, high = self.contrast_limits
downsampled = np.clip(downsampled, low, high)
color_range = high - low
if color_range != 0:
downsampled = (downsampled - low) / color_range
colormapped = self.colormap[1].map(downsampled)
colormapped = colormapped.reshape(downsampled.shape + (4,))
colormapped[..., 3] *= self.opacity
self.thumbnail = colormapped
|
https://github.com/napari/napari/issues/447
|
WARNING: Traceback (most recent call last):
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 76, in <module>
demo(astronaut())
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 31, in demo
rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy'
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/contextlib.py", line 119, in __exit__
next(self.gen)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/napari/_qt/event_loop.py", line 31, in gui_qt
app.exec_()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 501, in event
out = super(QtBaseCanvasBackend, self).event(ev)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 818, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/visual.py", line 443, in draw
self._vshare.index_buffer)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 1537, in set_data
raise ValueError("Type %r not allowed for texture" % data.dtype)
ValueError: Type dtype('int64') not allowed for texture
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> for DrawEvent
WARNING: Error drawing visual <Image at 0x133fde5f8>
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> repeat 2
|
ValueError
|
def view(
*images,
title="napari",
metadata=None,
multichannel=None,
contrast_limits=None,
**named_images,
):
"""View one or more input images.
Parameters
----------
*images : ndarray
Arrays to render as image layers.
title : string, optional
The title of the viewer window.
meta : dictionary, optional
A dictionary of metadata attributes. If multiple images are provided,
the metadata applies to all of them.
multichannel : bool, optional
Whether to consider the last dimension of the image(s) as channels
rather than spatial attributes. If not provided, napari will attempt
to make an educated guess. If provided, and multiple images are given,
the same value applies to all images.
contrast_limits : list (2,)
Color limits to be used for determining the colormap bounds for
luminance images. If not passed is calculated as the min and max of
the image. Passing a value prevents this calculation which can be useful
when working with very large datasets that are dynamically loaded.
If provided, and multiple images are given, the same value applies to
all images.
**named_images : dict of str -> ndarray, optional
Arrays to render as image layers, keyed by layer name.
Returns
-------
viewer : napari.Viewer
A Viewer widget displaying the images.
Notes
-----
This convenience function is used to view one or few images with identical
parameters (colormap etc). To customize each image layer, either use the
:class:`napari.Viewer` class (preferred), or update the layers directly on
the returned :class:`napari.Viewer` object.
"""
viewer = Viewer(title=title)
for image in images:
viewer.add_image(
image,
metadata=metadata,
multichannel=multichannel,
contrast_limits=contrast_limits,
)
for name, image in named_images.items():
viewer.add_image(
image,
metadata=metadata,
multichannel=multichannel,
contrast_limits=contrast_limits,
name=name,
)
return viewer
|
def view(
*images,
title="napari",
metadata=None,
multichannel=None,
contrast_limits_range=None,
**named_images,
):
"""View one or more input images.
Parameters
----------
*images : ndarray
Arrays to render as image layers.
title : string, optional
The title of the viewer window.
meta : dictionary, optional
A dictionary of metadata attributes. If multiple images are provided,
the metadata applies to all of them.
multichannel : bool, optional
Whether to consider the last dimension of the image(s) as channels
rather than spatial attributes. If not provided, napari will attempt
to make an educated guess. If provided, and multiple images are given,
the same value applies to all images.
contrast_limits_range : list | array | None
Length two list or array with the default color limit range for the
image. If not passed will be calculated as the min and max of the
image. Passing a value prevents this calculation which can be useful
when working with very large datasets that are dynamically loaded.
If provided, and multiple images are given, the same value applies to
all images.
**named_images : dict of str -> ndarray, optional
Arrays to render as image layers, keyed by layer name.
Returns
-------
viewer : napari.Viewer
A Viewer widget displaying the images.
Notes
-----
This convenience function is used to view one or few images with identical
parameters (colormap etc). To customize each image layer, either use the
:class:`napari.Viewer` class (preferred), or update the layers directly on
the returned :class:`napari.Viewer` object.
"""
viewer = Viewer(title=title)
for image in images:
viewer.add_image(
image,
metadata=metadata,
multichannel=multichannel,
contrast_limits_range=contrast_limits_range,
)
for name, image in named_images.items():
viewer.add_image(
image,
metadata=metadata,
multichannel=multichannel,
contrast_limits_range=contrast_limits_range,
name=name,
)
return viewer
|
https://github.com/napari/napari/issues/447
|
WARNING: Traceback (most recent call last):
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 76, in <module>
demo(astronaut())
File "/Users/royer/workspace/python/pitl/pitl/it/demo/demo_it_n2s_gbm_2D_rgb.py", line 31, in demo
rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy'
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/contextlib.py", line 119, in __exit__
next(self.gen)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/napari/_qt/event_loop.py", line 31, in gui_qt
app.exec_()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 501, in event
out = super(QtBaseCanvasBackend, self).event(ev)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 818, in paintGL
self._vispy_canvas.events.draw(region=None)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 217, in on_draw
self._draw_scene()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 266, in _draw_scene
self.draw_visual(self.scene)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/canvas.py", line 304, in draw_visual
node.draw()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/scene/visuals.py", line 99, in draw
self._visual_superclass.draw(self)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/visual.py", line 443, in draw
self._vshare.index_buffer)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/visuals/shaders/program.py", line 101, in draw
Program.draw(self, *args, **kwargs)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/program.py", line 533, in draw
canvas.context.flush_commands()
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/context.py", line 176, in flush_commands
self.glir.flush(self.shared.parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 572, in flush
self._shared.flush(parser)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 494, in flush
parser.parse(self._filter(self.clear(), parser))
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 819, in parse
self._parse(command)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 787, in _parse
ob.set_data(*args)
File "/Users/royer/anaconda3/envs/pitl/lib/python3.7/site-packages/vispy/gloo/glir.py", line 1537, in set_data
raise ValueError("Type %r not allowed for texture" % data.dtype)
ValueError: Type dtype('int64') not allowed for texture
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> for DrawEvent
WARNING: Error drawing visual <Image at 0x133fde5f8>
ERROR: Invoking <bound method SceneCanvas.on_draw of <SceneCanvas (PySide2) at 0x128724438>> repeat 2
|
ValueError
|
def on_key_press(self, event):
"""Called whenever key pressed in canvas."""
if event.native.isAutoRepeat():
return
else:
if event.key == " ":
if self._mode != Mode.PAN_ZOOM:
self._mode_history = self.mode
self._selected_data_history = copy(self.selected_data)
self.mode = Mode.PAN_ZOOM
else:
self._mode_history = Mode.PAN_ZOOM
elif event.key == "Shift":
if self._mode == Mode.ADD:
self.cursor = "forbidden"
elif event.key == "p":
self.mode = Mode.ADD
elif event.key == "s":
self.mode = Mode.SELECT
elif event.key == "z":
self.mode = Mode.PAN_ZOOM
elif event.key == "c" and "Control" in event.modifiers:
if self._mode == Mode.SELECT:
self._copy_data()
elif event.key == "v" and "Control" in event.modifiers:
if self._mode == Mode.SELECT:
self._paste_data()
elif event.key == "a":
if self._mode == Mode.SELECT:
self.selected_data = self._indices_view[: len(self._data_view)]
self._set_highlight()
elif event.key == "Backspace":
if self._mode == Mode.SELECT:
self.remove_selected()
|
def on_key_press(self, event):
"""Called whenever key pressed in canvas."""
if event.native.isAutoRepeat():
return
else:
if event.key == " ":
if self._mode != Mode.PAN_ZOOM:
self._mode_history = self.mode
self._selected_data_history = copy(self.selected_data)
self.mode = Mode.PAN_ZOOM
else:
self._mode_history = Mode.PAN_ZOOM
elif event.key == "Shift":
if self._mode == Mode.ADD:
self.cursor = "forbidden"
elif event.key == "p":
self.mode = Mode.ADD
elif event.key == "s":
self.mode = Mode.SELECT
elif event.key == "z":
self.mode = Mode.PAN_ZOOM
elif event.key == "c" and "Control" in event.modifiers:
if self._mode == Mode.SELECT:
self._copy_data()
elif event.key == "v" and "Control" in event.modifiers:
if self._mode == Mode.SELECT:
self._paste_data()
elif event.key == "a":
if self._mode == Mode.SELECT:
self.selected_data = self._indices_view[
list(range(len(self._data_view)))
]
self._set_highlight()
elif event.key == "Backspace":
if self._mode == Mode.SELECT:
self.remove_selected()
|
https://github.com/napari/napari/issues/417
|
$ python examples/add_image.py
/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/visuals/markers.py:564: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
('a_edgewidth', np.float32, 1)])
/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/visuals/markers.py:564: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
('a_edgewidth', np.float32, 1)])
WARNING: Traceback (most recent call last):
File "examples/add_image.py", line 44, in <module>
layer.interpolation = 'nearest'
File "/home/jni/miniconda3/envs/cf/lib/python3.6/contextlib.py", line 88, in __exit__
next(self.gen)
File "/home/jni/projects/napari/napari/_qt/event_loop.py", line 31, in gui_qt
app.exec_()
File "/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/app/backends/_qt.py", line 501, in event
out = super(QtBaseCanvasBackend, self).event(ev)
File "/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/app/backends/_qt.py", line 495, in keyPressEvent
self._keyEvent(self._vispy_canvas.events.key_press, ev)
File "/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/app/backends/_qt.py", line 544, in _keyEvent
func(native=ev, key=key, text=text_type(ev.text()), modifiers=mod)
File "/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/home/jni/miniconda3/envs/cf/lib/python3.6/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/home/jni/projects/napari/napari/_qt/qt_viewer.py", line 236, in on_key_press
layer.on_key_press(event)
File "/home/jni/projects/napari/napari/layers/points/points.py", line 968, in on_key_press
list(range(len(self._data_view)))
TypeError: list indices must be integers or slices, not list
ERROR: Invoking <bound method QtViewer.on_key_press of <napari._qt.qt_viewer.QtViewer object at 0x7fc1c12c1798>> for KeyEvent
|
TypeError
|
def _remove(event):
"""When a layer is removed, remove its viewer."""
layers = event.source
layer = event.item
layer._order = 0
layer._node.transforms = ChainTransform()
layer._node.parent = None
|
def _remove(event):
"""When a layer is removed, remove its viewer."""
layers = event.source
layer = event.item
layer._order = 0
layer._node.parent = None
|
https://github.com/napari/napari/issues/170
|
In [15]: WARNING: Traceback (most recent call last):
File "/Users/jni/conda/envs/36/bin/ipython", line 11, in <module>
sys.exit(start_ipython())
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/__init__.py", line 125, in start_ipython
return launch_new_instance(argv=argv, **kwargs)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/terminal/ipapp.py", line 356, in start
self.shell.mainloop()
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/terminal/interactiveshell.py", line 480, in mainloop
self.interact()
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/terminal/interactiveshell.py", line 463, in interact
code = self.prompt_for_code()
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/terminal/interactiveshell.py", line 376, in prompt_for_code
pre_run=self.pre_prompt, reset_current_buffer=True)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/prompt_toolkit/interface.py", line 415, in run
self.eventloop.run(self.input, self.create_eventloop_callbacks())
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/prompt_toolkit/eventloop/posix.py", line 102, in run
self._inputhook_context.call_inputhook(ready)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/prompt_toolkit/eventloop/inputhook.py", line 74, in call_inputhook
self.inputhook(self)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/terminal/interactiveshell.py", line 495, in inputhook
self._inputhook(context)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/IPython/terminal/pt_inputhooks/qt.py", line 35, in inputhook
event_loop.exec_()
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/components/_layers_list/model.py", line 182, in remove_selected
self.pop(i)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/util/list/_model.py", line 55, in pop
self.changed.removed(item=obj)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/util/event.py", line 489, in __call__
self._invoke_callback(cb, event)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/util/event.py", line 504, in _invoke_callback
cb(event)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/components/_layers_list/model.py", line 29, in _remove
layer.viewer = None
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/layers/_base_layer/model.py", line 162, in viewer
self._parent = parent
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/layers/_base_layer/_visual_wrapper.py", line 82, in _parent
self._node.parent = parent
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/util/frozen.py", line 17, in __setattr__
object.__setattr__(self, key, value)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/scene/node.py", line 209, in parent
self._update_trsys(None)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/napari/_vispy/scene/visuals.py", line 82, in _update_trsys
self.transforms.scene_transform = scene.node_transform(doc)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/visuals/transforms/transform_system.py", line 276, in scene_transform
self._scene_transform.transforms = tr
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/visuals/transforms/chain.py", line 96, in transforms
self.update()
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/visuals/transforms/base_transform.py", line 153, in update
self.changed(*args)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/visuals/transforms/chain.py", line 212, in _subtr_changed
self.update(ev)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/visuals/transforms/base_transform.py", line 153, in update
self.changed(*args)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/util/event.py", line 455, in __call__
self._invoke_callback(cb, event)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/util/event.py", line 475, in _invoke_callback
self, cb_event=(cb, event))
<< caught exception here: >>
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/util/event.py", line 471, in _invoke_callback
cb(event)
File "/Users/jni/conda/envs/36/lib/python3.6/site-packages/vispy/visuals/transforms/chain.py", line 281, in source_changed
new_tr = [tr[0]]
IndexError: list index out of range
ERROR: Invoking <bound method SimplifiedChainTransform.source_changed of <ChainTransform [<STTransform scale=[1. 1. 1. 1.] translate=[0. 0. 0. 0.] at 0x5071730616>,
<STTransform scale=[2.6181054e+00 2.6181054e+00 1.0000000e-06 1.0000000e+00] translate=[-558.83954 -403.84387 0. 0. ] at 0x5319047544>] at 0x12e27aba8>> for Event
|
IndexError
|
def __init__(self, layers):
super().__init__()
self.layers = layers
self.setWidgetResizable(True)
self.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
scrollWidget = QWidget()
self.setWidget(scrollWidget)
self.vbox_layout = QVBoxLayout(scrollWidget)
self.vbox_layout.addWidget(QtDivider())
self.vbox_layout.addStretch(1)
self.vbox_layout.setContentsMargins(0, 0, 0, 0)
self.centers = []
self.setAcceptDrops(True)
self.setToolTip("Layer list")
self.layers.events.added.connect(self._add)
self.layers.events.removed.connect(self._remove)
self.layers.events.reordered.connect(self._reorder)
self.drag_start_position = np.zeros(2)
self.drag_name = None
|
def __init__(self, layers):
super().__init__()
self.layers = layers
self.setWidgetResizable(True)
self.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
scrollWidget = QWidget()
self.setWidget(scrollWidget)
self.vbox_layout = QVBoxLayout(scrollWidget)
self.vbox_layout.addWidget(QtDivider())
self.vbox_layout.addStretch(1)
self.vbox_layout.setContentsMargins(0, 0, 0, 0)
self.centers = []
self.setAcceptDrops(True)
self.setToolTip("Layer list")
self.layers.events.added.connect(self._add)
self.layers.events.removed.connect(self._remove)
self.layers.events.reordered.connect(self._reorder)
self.drag_start_position = (0, 0)
self.drag_name = None
|
https://github.com/napari/napari/issues/304
|
WARNING: Traceback (most recent call last):
File "/Users/kiraevans/Projects/napari/napari/components/_layers_list/view/main.py", line 115, in mouseMoveEvent
distance = (event.pos() - self.drag_start_position).manhattanLength()
TypeError: unsupported operand type(s) for -: 'QPoint' and 'tuple'
|
TypeError
|
def mousePressEvent(self, event):
# Check if mouse press happens on a layer properties widget or
# a child of such a widget. If not, the press has happended on the
# Layers Widget itself and should be ignored.
widget = self.childAt(event.pos())
layer = (
getattr(widget, "layer", None)
or getattr(widget.parentWidget(), "layer", None)
or getattr(widget.parentWidget().parentWidget(), "layer", None)
)
if layer is not None:
self.drag_start_position = np.array([event.pos().x(), event.pos().y()])
self.drag_name = layer.name
else:
self.drag_name = None
|
def mousePressEvent(self, event):
# Check if mouse press happens on a layer properties widget or
# a child of such a widget. If not, the press has happended on the
# Layers Widget itself and should be ignored.
widget = self.childAt(event.pos())
layer = (
getattr(widget, "layer", None)
or getattr(widget.parentWidget(), "layer", None)
or getattr(widget.parentWidget().parentWidget(), "layer", None)
)
if layer is not None:
self.drag_start_position = event.pos()
self.drag_name = layer.name
else:
self.drag_name = None
|
https://github.com/napari/napari/issues/304
|
WARNING: Traceback (most recent call last):
File "/Users/kiraevans/Projects/napari/napari/components/_layers_list/view/main.py", line 115, in mouseMoveEvent
distance = (event.pos() - self.drag_start_position).manhattanLength()
TypeError: unsupported operand type(s) for -: 'QPoint' and 'tuple'
|
TypeError
|
def mouseMoveEvent(self, event):
position = np.array([event.pos().x(), event.pos().y()])
distance = np.linalg.norm(position - self.drag_start_position)
if distance < QApplication.startDragDistance() or self.drag_name is None:
return
mimeData = QMimeData()
mimeData.setText(self.drag_name)
drag = QDrag(self)
drag.setMimeData(mimeData)
drag.setHotSpot(event.pos() - self.rect().topLeft())
dropAction = drag.exec_()
|
def mouseMoveEvent(self, event):
distance = (event.pos() - self.drag_start_position).manhattanLength()
if distance < QApplication.startDragDistance():
return
mimeData = QMimeData()
mimeData.setText(self.drag_name)
drag = QDrag(self)
drag.setMimeData(mimeData)
drag.setHotSpot(event.pos() - self.rect().topLeft())
dropAction = drag.exec_()
|
https://github.com/napari/napari/issues/304
|
WARNING: Traceback (most recent call last):
File "/Users/kiraevans/Projects/napari/napari/components/_layers_list/view/main.py", line 115, in mouseMoveEvent
distance = (event.pos() - self.drag_start_position).manhattanLength()
TypeError: unsupported operand type(s) for -: 'QPoint' and 'tuple'
|
TypeError
|
def dragEnterEvent(self, event):
if event.source() == self:
event.accept()
divs = []
for i in range(0, self.vbox_layout.count(), 2):
widget = self.vbox_layout.itemAt(i).widget()
divs.append(widget.y() + widget.frameGeometry().height() / 2)
self.centers = [(divs[i + 1] + divs[i]) / 2 for i in range(len(divs) - 1)]
else:
event.ignore()
|
def dragEnterEvent(self, event):
divs = []
for i in range(0, self.vbox_layout.count(), 2):
widget = self.vbox_layout.itemAt(i).widget()
divs.append(widget.y() + widget.frameGeometry().height() / 2)
self.centers = [(divs[i + 1] + divs[i]) / 2 for i in range(len(divs) - 1)]
event.accept()
|
https://github.com/napari/napari/issues/304
|
WARNING: Traceback (most recent call last):
File "/Users/kiraevans/Projects/napari/napari/components/_layers_list/view/main.py", line 115, in mouseMoveEvent
distance = (event.pos() - self.drag_start_position).manhattanLength()
TypeError: unsupported operand type(s) for -: 'QPoint' and 'tuple'
|
TypeError
|
def clim(self, clim):
self._clim_msg = f"{float(clim[0]): 0.3}, {float(clim[1]): 0.3}"
self.status = self._clim_msg
self._node.clim = clim
self.events.clim()
|
def clim(self, clim):
self._clim_msg = f"{clim[0]: 0.3}, {clim[1]: 0.3}"
self.status = self._clim_msg
self._node.clim = clim
self.events.clim()
|
https://github.com/napari/napari/issues/154
|
from napari import Window, Viewer
viewer = Viewer()
window = Window(viewer)
viewer.add_image(data.camera())
viewer.layers[0].clim = [0, 255]
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-7-4d36bc0c2b58> in <module>()
----> 1 viewer.layers[0].clim = [0, 255]
~/Github/napari/napari/layers/_image_layer/model.py in clim(self, clim)
265 @clim.setter
266 def clim(self, clim):
--> 267 self._clim_msg = f'{clim[0]: 0.3}, {clim[1]: 0.3}'
268 self.status = self._clim_msg
269 self._node.clim = clim
ValueError: Precision not allowed in integer format specifier
|
ValueError
|
def screenshot(self, region=None, size=None, bgcolor=None):
"""Render the scene to an offscreen buffer and return the image array.
Parameters
----------
region : tuple | None
Specifies the region of the canvas to render. Format is
(x, y, w, h). By default, the entire canvas is rendered.
size : tuple | None
Specifies the size of the image array to return. If no size is
given, then the size of the *region* is used, multiplied by the
pixel scaling factor of the canvas (see `pixel_scale`). This
argument allows the scene to be rendered at resolutions different
from the native canvas resolution.
bgcolor : instance of Color | None
The background color to use.
Returns
-------
image : array
Numpy array of type ubyte and shape (h, w, 4). Index [0, 0] is the
upper-left corner of the rendered region.
"""
return self._canvas.render(region, size, bgcolor)
|
def screenshot(self, region=None, size=None, bgcolor=None, crop=None):
"""Render the scene to an offscreen buffer and return the image array.
Parameters
----------
region : tuple | None
Specifies the region of the canvas to render. Format is
(x, y, w, h). By default, the entire canvas is rendered.
size : tuple | None
Specifies the size of the image array to return. If no size is
given, then the size of the *region* is used, multiplied by the
pixel scaling factor of the canvas (see `pixel_scale`). This
argument allows the scene to be rendered at resolutions different
from the native canvas resolution.
bgcolor : instance of Color | None
The background color to use.
crop : array-like | None
If specified it determines the pixels read from the framebuffer.
In the format (x, y, w, h), relative to the region being rendered.
Returns
-------
image : array
Numpy array of type ubyte and shape (h, w, 4). Index [0, 0] is the
upper-left corner of the rendered region.
"""
return self._canvas.render(region=None, size=None, bgcolor=None, crop=None)
|
https://github.com/napari/napari/issues/159
|
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-11-1db5616997f4> in <module>()
----> 1 viewer.screenshot()
~/Github/napari/napari/components/_viewer/model.py in screenshot(self, region, size, bgcolor, crop)
156 """
157 return self._canvas.render(region=None, size=None, bgcolor=None,
--> 158 crop=None)
159
160 def add_layer(self, layer):
TypeError: render() got an unexpected keyword argument 'crop'
|
TypeError
|
def use_info_auxv():
lines = pwndbg.info.auxv().splitlines()
if not lines:
return None
auxv = AUXV()
for line in lines:
match = re.match("([0-9]+) .*? (0x[0-9a-f]+|[0-9]+)", line)
if not match:
print("Warning: Skipping auxv entry '{}'".format(line))
continue
const, value = int(match.group(1)), int(match.group(2), 0)
auxv.set(const, value)
return auxv
|
def use_info_auxv():
lines = pwndbg.info.auxv().splitlines()
if not lines:
return None
auxv = AUXV()
for line in lines:
match = re.match("([0-9]+) .* (0x[0-9a-f]+|[0-9]+)", line)
if not match:
print("Warning: Skipping auxv entry '{}'".format(line))
continue
const, value = int(match.group(1)), int(match.group(2), 0)
auxv.set(const, value)
return auxv
|
https://github.com/pwndbg/pwndbg/issues/858
|
$ pwd
/home/user/test/x 01
$ cat test.c
#include <stdio.h>
#include <stdlib.h>
void main()
{
printf("Hello world\n");
getchar();
}
$ gcc -o test test.c
$ gdb test
GNU gdb (Ubuntu 9.2-0ubuntu1~20.04) 9.2
Copyright (C) 2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
pwndbg: loaded 191 commands. Type pwndbg [filter] for a list.
pwndbg: created $rebase, $ida gdb functions (can be used with print/break)
Reading symbols from test...
(No debugging symbols found in test)
pwndbg> r
Starting program: /home/user/test/x 01/test
Hello world
^C
Program received signal SIGINT, Interrupt.
0x00007ffff7ebe142 in __GI___libc_read (fd=0, buf=0x5555555596b0, nbytes=1024) at ../sysdeps/unix/sysv/linux/read.c:26
26 ../sysdeps/unix/sysv/linux/read.c: No such file or directory.
Exception occurred: Error: invalid literal for int() with base 0: '01' (<class 'ValueError'>)
For more info invoke `set exception-verbose on` and rerun the command
or debug it by yourself with `set exception-debugger on`
Python Exception <class 'ValueError'> invalid literal for int() with base 0: '01':
Exception occurred: Error: invalid literal for int() with base 0: '01' (<class 'ValueError'>)
For more info invoke `set exception-verbose on` and rerun the command
or debug it by yourself with `set exception-debugger on`
Python Exception <class 'ValueError'> invalid literal for int() with base 0: '01':
Exception occurred: Error: invalid literal for int() with base 0: '01' (<class 'ValueError'>)
For more info invoke `set exception-verbose on` and rerun the command
or debug it by yourself with `set exception-debugger on`
Python Exception <class 'ValueError'> invalid literal for int() with base 0: '01':
pwndbg> set exception-debugger on
Set whether to debug exceptions raised in Pwndbg commands to True
Traceback (most recent call last):
File "/home/user/pwndbg/pwndbg/pwndbg/events.py", line 165, in caller
func()
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/stack.py", line 79, in update
page = pwndbg.memory.Page(start, stop-start, 6 if not is_executable() else 7, 0, '[stack]')
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/stack.py", line 127, in is_executable
ehdr = pwndbg.elf.exe()
File "/home/user/pwndbg/pwndbg/pwndbg/proc.py", line 71, in wrapper
return func(*a, **kw)
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/elf.py", line 180, in exe
e = entry()
File "/home/user/pwndbg/pwndbg/pwndbg/proc.py", line 71, in wrapper
return func(*a, **kw)
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/elf.py", line 191, in entry
entry = pwndbg.auxv.get().AT_ENTRY
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/auxv.py", line 106, in get
return use_info_auxv() or walk_stack() or AUXV()
File "/home/user/pwndbg/pwndbg/pwndbg/auxv.py", line 121, in use_info_auxv
const, value = int(match.group(1)), int(match.group(2), 0)
ValueError: invalid literal for int() with base 0: '01'
If that is an issue, you can report it on https://github.com/pwndbg/pwndbg/issues
(Please don't forget to search if it hasn't been reported before)
To generate the report and open a browser, you may run `bugreport --run-browser`
PS: Pull requests are welcome
/home/user/pwndbg/pwndbg/pwndbg/auxv.py(121)use_info_auxv()
-> const, value = int(match.group(1)), int(match.group(2), 0)
(Pdb) q
Traceback (most recent call last):
File "/home/user/pwndbg/pwndbg/pwndbg/prompt.py", line 33, in prompt_hook
pwndbg.events.after_reload(start=False)
File "/home/user/pwndbg/pwndbg/pwndbg/events.py", line 216, in after_reload
f()
File "/home/user/pwndbg/pwndbg/pwndbg/events.py", line 169, in caller
raise e
File "/home/user/pwndbg/pwndbg/pwndbg/events.py", line 165, in caller
func()
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/stack.py", line 79, in update
page = pwndbg.memory.Page(start, stop-start, 6 if not is_executable() else 7, 0, '[stack]')
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/stack.py", line 127, in is_executable
ehdr = pwndbg.elf.exe()
File "/home/user/pwndbg/pwndbg/pwndbg/proc.py", line 71, in wrapper
return func(*a, **kw)
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/elf.py", line 180, in exe
e = entry()
File "/home/user/pwndbg/pwndbg/pwndbg/proc.py", line 71, in wrapper
return func(*a, **kw)
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/elf.py", line 191, in entry
entry = pwndbg.auxv.get().AT_ENTRY
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/auxv.py", line 106, in get
return use_info_auxv() or walk_stack() or AUXV()
File "/home/user/pwndbg/pwndbg/pwndbg/auxv.py", line 121, in use_info_auxv
const, value = int(match.group(1)), int(match.group(2), 0)
ValueError: invalid literal for int() with base 0: '01'
pwndbg> info auxv
33 AT_SYSINFO_EHDR System-supplied DSO's ELF header 0x7ffff7fce000
16 AT_HWCAP Machine-dependent CPU capability hints 0xbfebfbff
6 AT_PAGESZ System page size 4096
17 AT_CLKTCK Frequency of times() 100
3 AT_PHDR Program headers for program 0x555555554040
4 AT_PHENT Size of program header entry 56
5 AT_PHNUM Number of program headers 13
7 AT_BASE Base address of interpreter 0x7ffff7fcf000
8 AT_FLAGS Flags 0x0
9 AT_ENTRY Entry point of program 0x555555555080
11 AT_UID Real user ID 1000
12 AT_EUID Effective user ID 1000
13 AT_GID Real group ID 1001
14 AT_EGID Effective group ID 1001
23 AT_SECURE Boolean, was exec setuid-like? 0
25 AT_RANDOM Address of 16 random bytes 0x7fffffffdff9
26 AT_HWCAP2 Extension of AT_HWCAP 0x0
31 AT_EXECFN File name of executable 0x7fffffffefde "/home/user/test/x 01/test"
15 AT_PLATFORM String identifying platform 0x7fffffffe009 "x86_64"
0 AT_NULL End of vector 0x0
Traceback (most recent call last):
File "/home/user/pwndbg/pwndbg/pwndbg/events.py", line 165, in caller
func()
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/stack.py", line 79, in update
page = pwndbg.memory.Page(start, stop-start, 6 if not is_executable() else 7, 0, '[stack]')
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/stack.py", line 127, in is_executable
ehdr = pwndbg.elf.exe()
File "/home/user/pwndbg/pwndbg/pwndbg/proc.py", line 71, in wrapper
return func(*a, **kw)
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/elf.py", line 180, in exe
e = entry()
File "/home/user/pwndbg/pwndbg/pwndbg/proc.py", line 71, in wrapper
return func(*a, **kw)
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/elf.py", line 191, in entry
entry = pwndbg.auxv.get().AT_ENTRY
File "/home/user/pwndbg/pwndbg/pwndbg/memoize.py", line 44, in __call__
value = self.func(*args, **kwargs)
File "/home/user/pwndbg/pwndbg/pwndbg/auxv.py", line 106, in get
return use_info_auxv() or walk_stack() or AUXV()
File "/home/user/pwndbg/pwndbg/pwndbg/auxv.py", line 121, in use_info_auxv
const, value = int(match.group(1)), int(match.group(2), 0)
ValueError: invalid literal for int() with base 0: '01'
/home/user/pwndbg/pwndbg/pwndbg/auxv.py(121)use_info_auxv()
-> const, value = int(match.group(1)), int(match.group(2), 0)
(Pdb)
|
ValueError
|
def malloc_chunk(addr, fake=False, verbose=False, simple=False):
"""Print a malloc_chunk struct's contents."""
# points to the real start of the chunk
cursor = int(addr)
allocator = pwndbg.heap.current
ptr_size = allocator.size_sz
size_field = pwndbg.memory.u(cursor + allocator.chunk_key_offset("size"))
real_size = size_field & ~allocator.malloc_align_mask
headers_to_print = [] # both state (free/allocated) and flags
fields_to_print = set() # in addition to addr and size
out_fields = "Addr: {}\n".format(M.get(cursor))
if fake:
headers_to_print.append(message.on("Fake chunk"))
verbose = True # print all fields for fake chunks
if simple:
chunk = read_chunk(cursor)
if not headers_to_print:
headers_to_print.append(message.hint(M.get(cursor)))
prev_inuse, is_mmapped, non_main_arena = allocator.chunk_flags(
int(chunk["size"])
)
if prev_inuse:
headers_to_print.append(message.hint("PREV_INUSE"))
if is_mmapped:
headers_to_print.append(message.hint("IS_MMAPED"))
if non_main_arena:
headers_to_print.append(message.hint("NON_MAIN_ARENA"))
print(" | ".join(headers_to_print))
for key, val in chunk.items():
print(message.system(key) + ": 0x{:02x}".format(int(val)))
print("")
return
arena = allocator.get_arena_for_chunk(cursor)
arena_address = None
is_top = False
if not fake and arena:
arena_address = arena.address
top_chunk = arena["top"]
if cursor == top_chunk:
headers_to_print.append(message.off("Top chunk"))
is_top = True
if not is_top:
fastbins = allocator.fastbins(arena_address) or {}
smallbins = allocator.smallbins(arena_address) or {}
largebins = allocator.largebins(arena_address) or {}
unsortedbin = allocator.unsortedbin(arena_address) or {}
if allocator.has_tcache():
tcachebins = allocator.tcachebins(None)
if real_size in fastbins.keys() and cursor in fastbins[real_size]:
headers_to_print.append(message.on("Free chunk (fastbins)"))
if not verbose:
fields_to_print.add("fd")
elif real_size in smallbins.keys() and cursor in bin_addrs(
smallbins[real_size], "smallbins"
):
headers_to_print.append(message.on("Free chunk (smallbins)"))
if not verbose:
fields_to_print.update(["fd", "bk"])
elif real_size >= list(largebins.items())[0][0] and cursor in bin_addrs(
largebins[
(list(largebins.items())[allocator.largebin_index(real_size) - 64][0])
],
"largebins",
):
headers_to_print.append(message.on("Free chunk (largebins)"))
if not verbose:
fields_to_print.update(["fd", "bk", "fd_nextsize", "bk_nextsize"])
elif cursor in bin_addrs(unsortedbin["all"], "unsortedbin"):
headers_to_print.append(message.on("Free chunk (unsortedbin)"))
if not verbose:
fields_to_print.update(["fd", "bk"])
elif (
allocator.has_tcache()
and real_size in tcachebins.keys()
and cursor + ptr_size * 2 in bin_addrs(tcachebins[real_size], "tcachebins")
):
headers_to_print.append(message.on("Free chunk (tcache)"))
if not verbose:
fields_to_print.add("fd")
else:
headers_to_print.append(message.hint("Allocated chunk"))
if verbose:
fields_to_print.update(
["prev_size", "size", "fd", "bk", "fd_nextsize", "bk_nextsize"]
)
else:
out_fields += "Size: 0x{:02x}\n".format(size_field)
prev_inuse, is_mmapped, non_main_arena = allocator.chunk_flags(size_field)
if prev_inuse:
headers_to_print.append(message.hint("PREV_INUSE"))
if is_mmapped:
headers_to_print.append(message.hint("IS_MMAPED"))
if non_main_arena:
headers_to_print.append(message.hint("NON_MAIN_ARENA"))
fields_ordered = ["prev_size", "size", "fd", "bk", "fd_nextsize", "bk_nextsize"]
for field_to_print in fields_ordered:
if field_to_print in fields_to_print:
out_fields += message.system(field_to_print) + ": 0x{:02x}\n".format(
pwndbg.memory.u(cursor + allocator.chunk_key_offset(field_to_print))
)
print(" | ".join(headers_to_print) + "\n" + out_fields)
|
def malloc_chunk(addr, fake=False, verbose=False, simple=False):
"""Print a malloc_chunk struct's contents."""
# points to the real start of the chunk
cursor = int(addr)
allocator = pwndbg.heap.current
ptr_size = allocator.size_sz
size_field = pwndbg.memory.u(cursor + allocator.chunk_key_offset("size"))
real_size = size_field & ~allocator.malloc_align_mask
headers_to_print = [] # both state (free/allocated) and flags
fields_to_print = set() # in addition to addr and size
out_fields = "Addr: {}\n".format(M.get(cursor))
arena = allocator.get_arena_for_chunk(cursor)
arena_address = None
if fake:
headers_to_print.append(message.on("Fake chunk"))
verbose = True # print all fields for fake chunks
if simple:
chunk = read_chunk(cursor)
if not headers_to_print:
headers_to_print.append(message.hint(M.get(cursor)))
prev_inuse, is_mmapped, non_main_arena = allocator.chunk_flags(
int(chunk["size"])
)
if prev_inuse:
headers_to_print.append(message.hint("PREV_INUSE"))
if is_mmapped:
headers_to_print.append(message.hint("IS_MMAPED"))
if non_main_arena:
headers_to_print.append(message.hint("NON_MAIN_ARENA"))
print(" | ".join(headers_to_print))
for key, val in chunk.items():
print(message.system(key) + ": 0x{:02x}".format(int(val)))
print("")
return
is_top = False
if arena:
arena_address = arena.address
top_chunk = arena["top"]
if cursor == top_chunk:
headers_to_print.append(message.off("Top chunk"))
is_top = True
if not is_top:
fastbins = allocator.fastbins(arena_address) or {}
smallbins = allocator.smallbins(arena_address) or {}
largebins = allocator.largebins(arena_address) or {}
unsortedbin = allocator.unsortedbin(arena_address) or {}
if allocator.has_tcache():
tcachebins = allocator.tcachebins(None)
if real_size in fastbins.keys() and cursor in fastbins[real_size]:
headers_to_print.append(message.on("Free chunk (fastbins)"))
if not verbose:
fields_to_print.add("fd")
elif real_size in smallbins.keys() and cursor in bin_addrs(
smallbins[real_size], "smallbins"
):
headers_to_print.append(message.on("Free chunk (smallbins)"))
if not verbose:
fields_to_print.update(["fd", "bk"])
elif real_size >= list(largebins.items())[0][0] and cursor in bin_addrs(
largebins[
(list(largebins.items())[allocator.largebin_index(real_size) - 64][0])
],
"largebins",
):
headers_to_print.append(message.on("Free chunk (largebins)"))
if not verbose:
fields_to_print.update(["fd", "bk", "fd_nextsize", "bk_nextsize"])
elif cursor in bin_addrs(unsortedbin["all"], "unsortedbin"):
headers_to_print.append(message.on("Free chunk (unsortedbin)"))
if not verbose:
fields_to_print.update(["fd", "bk"])
elif (
allocator.has_tcache()
and real_size in tcachebins.keys()
and cursor + ptr_size * 2 in bin_addrs(tcachebins[real_size], "tcachebins")
):
headers_to_print.append(message.on("Free chunk (tcache)"))
if not verbose:
fields_to_print.add("fd")
else:
headers_to_print.append(message.hint("Allocated chunk"))
if verbose:
fields_to_print.update(
["prev_size", "size", "fd", "bk", "fd_nextsize", "bk_nextsize"]
)
else:
out_fields += "Size: 0x{:02x}\n".format(size_field)
prev_inuse, is_mmapped, non_main_arena = allocator.chunk_flags(size_field)
if prev_inuse:
headers_to_print.append(message.hint("PREV_INUSE"))
if is_mmapped:
headers_to_print.append(message.hint("IS_MMAPED"))
if non_main_arena:
headers_to_print.append(message.hint("NON_MAIN_ARENA"))
fields_ordered = ["prev_size", "size", "fd", "bk", "fd_nextsize", "bk_nextsize"]
for field_to_print in fields_ordered:
if field_to_print in fields_to_print:
out_fields += message.system(field_to_print) + ": 0x{:02x}\n".format(
pwndbg.memory.u(cursor + allocator.chunk_key_offset(field_to_print))
)
print(" | ".join(headers_to_print) + "\n" + out_fields)
|
https://github.com/pwndbg/pwndbg/issues/781
|
pwndbg> find_fake_fast &__malloc_hook
FAKE CHUNKS
Traceback (most recent call last):
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 136, in __call__
return self.function(*args, **kwargs)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 227, in _OnlyWhenRunning
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 265, in _OnlyWithLibcDebugSyms
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 245, in _OnlyWhenHeapIsInitialized
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/heap.py", line 279, in malloc_chunk
if cursor == top_chunk:
gdb.MemoryError: Cannot access memory at address 0x30d7080900003131
|
gdb.MemoryError
|
def find_fake_fast(addr, size=None):
"""Find candidate fake fast chunks overlapping the specified address."""
psize = pwndbg.arch.ptrsize
allocator = pwndbg.heap.current
align = allocator.malloc_alignment
min_fast = allocator.min_chunk_size
max_fast = allocator.global_max_fast
max_fastbin = allocator.fastbin_index(max_fast)
start = int(addr) - max_fast + psize
if start < 0:
print(
message.warn(
"addr - global_max_fast is negative, if the max_fast is not corrupted, you gave wrong address"
)
)
start = 0 # TODO, maybe some better way to handle case when global_max_fast is overwritten with something large
mem = pwndbg.memory.read(start, max_fast - psize, partial=True)
fmt = {"little": "<", "big": ">"}[pwndbg.arch.endian] + {4: "I", 8: "Q"}[psize]
if size is None:
sizes = range(min_fast, max_fast + 1, align)
else:
sizes = [int(size)]
print(C.banner("FAKE CHUNKS"))
for size in sizes:
fastbin = allocator.fastbin_index(size)
for offset in range((max_fastbin - fastbin) * align, max_fast - align + 1):
candidate = mem[offset : offset + psize]
if len(candidate) == psize:
value = struct.unpack(fmt, candidate)[0]
if allocator.fastbin_index(value) == fastbin:
malloc_chunk(start + offset - psize, fake=True)
|
def find_fake_fast(addr, size=None):
"""Find candidate fake fast chunks overlapping the specified address."""
psize = pwndbg.arch.ptrsize
allocator = pwndbg.heap.current
align = allocator.malloc_alignment
min_fast = allocator.min_chunk_size
max_fast = allocator.global_max_fast
max_fastbin = allocator.fastbin_index(max_fast)
start = int(addr) - max_fast + psize
mem = pwndbg.memory.read(start, max_fast - psize, partial=True)
fmt = {"little": "<", "big": ">"}[pwndbg.arch.endian] + {4: "I", 8: "Q"}[psize]
if size is None:
sizes = range(min_fast, max_fast + 1, align)
else:
sizes = [int(size)]
print(C.banner("FAKE CHUNKS"))
for size in sizes:
fastbin = allocator.fastbin_index(size)
for offset in range((max_fastbin - fastbin) * align, max_fast - align + 1):
candidate = mem[offset : offset + psize]
if len(candidate) == psize:
value = struct.unpack(fmt, candidate)[0]
if allocator.fastbin_index(value) == fastbin:
malloc_chunk(start + offset - psize, fake=True)
|
https://github.com/pwndbg/pwndbg/issues/781
|
pwndbg> find_fake_fast &__malloc_hook
FAKE CHUNKS
Traceback (most recent call last):
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 136, in __call__
return self.function(*args, **kwargs)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 227, in _OnlyWhenRunning
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 265, in _OnlyWithLibcDebugSyms
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 245, in _OnlyWhenHeapIsInitialized
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/heap.py", line 279, in malloc_chunk
if cursor == top_chunk:
gdb.MemoryError: Cannot access memory at address 0x30d7080900003131
|
gdb.MemoryError
|
def get_arena(self, arena_addr=None):
"""Read a malloc_state struct from the specified address, default to
reading the current thread's arena. Return the main arena if the
current thread is not attached to an arena.
"""
if arena_addr is None:
if self.multithreaded:
arena_addr = pwndbg.memory.u(pwndbg.symbol.address("thread_arena"))
if arena_addr != 0:
return pwndbg.memory.poi(self.malloc_state, arena_addr)
return self.main_arena
try:
next(i for i in pwndbg.vmmap.get() if arena_addr in i)
return pwndbg.memory.poi(self.malloc_state, arena_addr)
except (gdb.MemoryError, StopIteration):
# print(message.warn('Bad arena address {}'.format(arena_addr.address)))
return None
|
def get_arena(self, arena_addr=None):
"""Read a malloc_state struct from the specified address, default to
reading the current thread's arena. Return the main arena if the
current thread is not attached to an arena.
"""
if arena_addr is None:
if self.multithreaded:
arena_addr = pwndbg.memory.u(pwndbg.symbol.address("thread_arena"))
if arena_addr != 0:
return pwndbg.memory.poi(self.malloc_state, arena_addr)
return self.main_arena
try:
return pwndbg.memory.poi(self.malloc_state, arena_addr)
except gdb.MemoryError:
# print(message.warn('Bad arena address {}'.format(arena_addr.address)))
return None
|
https://github.com/pwndbg/pwndbg/issues/781
|
pwndbg> find_fake_fast &__malloc_hook
FAKE CHUNKS
Traceback (most recent call last):
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 136, in __call__
return self.function(*args, **kwargs)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 227, in _OnlyWhenRunning
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 265, in _OnlyWithLibcDebugSyms
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/__init__.py", line 245, in _OnlyWhenHeapIsInitialized
return function(*a, **kw)
File "/home/ubuntu/pwndbg/pwndbg/commands/heap.py", line 279, in malloc_chunk
if cursor == top_chunk:
gdb.MemoryError: Cannot access memory at address 0x30d7080900003131
|
gdb.MemoryError
|
def get_containing_segments(elf_filepath, elf_loadaddr, vaddr):
elf = get_elf_info_rebased(elf_filepath, elf_loadaddr)
segments = []
for seg in elf.segments:
# disregard segments which were unable to be named by pyelftools (see #777)
# and non-LOAD segments that are not file-backed (typically STACK)
if isinstance(seg["p_type"], int) or (
"LOAD" not in seg["p_type"] and seg["p_filesz"] == 0
):
continue
# disregard segments not containing vaddr
if vaddr < seg["p_vaddr"] or vaddr >= seg["x_vaddr_mem_end"]:
continue
segments.append(dict(seg))
return segments
|
def get_containing_segments(elf_filepath, elf_loadaddr, vaddr):
elf = get_elf_info_rebased(elf_filepath, elf_loadaddr)
segments = []
for seg in elf.segments:
# disregard non-LOAD segments that are not file-backed (typically STACK)
if "LOAD" not in seg["p_type"] and seg["p_filesz"] == 0:
continue
# disregard segments not containing vaddr
if vaddr < seg["p_vaddr"] or vaddr >= seg["x_vaddr_mem_end"]:
continue
segments.append(dict(seg))
return segments
|
https://github.com/pwndbg/pwndbg/issues/777
|
pwndbg> set exception-verbose on
Set whether to print a full stacktracefor exceptions raised in Pwndbg commands to True
pwndbg> xinfo 0x7ffff7e33e10
Extended information for virtual address 0x7ffff7e33e10:
Containing mapping:
0x7ffff7df4000 0x7ffff7f6c000 r-xp 178000 25000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
Offset information:
Mapped Area 0x7ffff7e33e10 = 0x7ffff7df4000 + 0x3fe10
File (Base) 0x7ffff7e33e10 = 0x7ffff7dcf000 + 0x64e10
'xinfo': Shows offsets of the specified address to useful other locations
Traceback (most recent call last):
File "/opt/pwndbg/pwndbg/commands/__init__.py", line 136, in __call__
return self.function(*args, **kwargs)
File "/opt/pwndbg/pwndbg/commands/__init__.py", line 227, in _OnlyWhenRunning
return function(*a, **kw)
File "/opt/pwndbg/pwndbg/commands/xinfo.py", line 126, in xinfo
xinfo_mmap_file(page, addr)
File "/opt/pwndbg/pwndbg/commands/xinfo.py", line 72, in xinfo_mmap_file
containing_loads = [seg for seg in pwndbg.elf.get_containing_segments(file_name, first.vaddr, addr)
File "/opt/pwndbg/pwndbg/elf.py", line 153, in get_containing_segments
if 'LOAD' not in seg['p_type'] and seg['p_filesz'] == 0:
TypeError: argument of type 'int' is not iterable
|
TypeError
|
def __getattr__(self, attr):
attr = attr.lstrip("$")
try:
# Seriously, gdb? Only accepts uint32.
if "eflags" in attr or "cpsr" in attr:
value = gdb77_get_register(attr)
value = value.cast(pwndbg.typeinfo.uint32)
else:
if attr.lower() == "xpsr":
attr = "xPSR"
value = get_register(attr)
value = value.cast(pwndbg.typeinfo.ptrdiff)
value = int(value)
return value & pwndbg.arch.ptrmask
except (ValueError, gdb.error):
return None
|
def __getattr__(self, attr):
attr = attr.lstrip("$")
try:
# Seriously, gdb? Only accepts uint32.
if "eflags" in attr:
value = gdb77_get_register(attr)
value = value.cast(pwndbg.typeinfo.uint32)
else:
if attr.lower() == "xpsr":
attr = "xPSR"
value = get_register(attr)
value = value.cast(pwndbg.typeinfo.ptrdiff)
value = int(value)
return value & pwndbg.arch.ptrmask
except (ValueError, gdb.error):
return None
|
https://github.com/pwndbg/pwndbg/issues/660
|
0x0000005578b133a4 in memcmp@plt ()
'context': Print out the current register, instruction, and stack context.
Traceback (most recent call last):
File "/root/Pwn/Tools/pwndbg/pwndbg/commands/__init__.py", line 136, in __call__
return self.function(*args, **kwargs)
File "/root/Pwn/Tools/pwndbg/pwndbg/commands/__init__.py", line 227, in _OnlyWhenRunning
return function(*a, **kw)
File "/root/Pwn/Tools/pwndbg/pwndbg/commands/context.py", line 112, in context
result.extend(func())
File "/root/Pwn/Tools/pwndbg/pwndbg/commands/context.py", line 127, in context_regs
return [pwndbg.ui.banner("registers")] + get_regs()
File "/root/Pwn/Tools/pwndbg/pwndbg/commands/context.py", line 176, in get_regs
desc = pwndbg.chain.format(value)
File "/root/Pwn/Tools/pwndbg/pwndbg/chain.py", line 122, in format
enhanced = pwndbg.enhance.enhance(chain[-2] + offset, code=code)
File "/root/Pwn/Tools/pwndbg/pwndbg/enhance.py", line 102, in enhance
instr = pwndbg.disasm.one(value)
File "/root/Pwn/Tools/pwndbg/pwndbg/disasm/__init__.py", line 118, in one
for insn in get(address, 1):
File "/root/Pwn/Tools/pwndbg/pwndbg/disasm/__init__.py", line 138, in get
i = get_one_instruction(address)
File "/root/Pwn/Tools/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/root/Pwn/Tools/pwndbg/pwndbg/disasm/__init__.py", line 106, in get_one_instruction
md = get_disassembler(address)
File "/root/Pwn/Tools/pwndbg/pwndbg/disasm/__init__.py", line 88, in get_disassembler
extra = CS_MODE_THUMB if (pwndbg.regs.cpsr & (1<<5)) else CS_MODE_ARM
TypeError: unsupported operand type(s) for &: 'NoneType' and 'int'
|
TypeError
|
def get_raw_out():
local_path = pwndbg.file.get_file(pwndbg.proc.exe)
try:
version_output = subprocess.check_output(
[get_raw_out.cmd_path, "--version"], stderr=STDOUT
).decode("utf-8")
match = search("checksec v([\\w.]+),", version_output)
if match:
version = tuple(map(int, (match.group(1).split("."))))
if version >= (2, 0):
return pwndbg.wrappers.call_cmd(
[get_raw_out.cmd_path, "--file=" + local_path]
)
except Exception:
pass
return pwndbg.wrappers.call_cmd([get_raw_out.cmd_path, "--file", local_path])
|
def get_raw_out():
local_path = pwndbg.file.get_file(pwndbg.proc.exe)
cmd = [get_raw_out.cmd_path, "--file", local_path]
return pwndbg.wrappers.call_cmd(cmd)
|
https://github.com/pwndbg/pwndbg/issues/662
|
pwndbg> checksec
Traceback (most recent call last):
File "/root/pwndbg/pwndbg/commands/__init__.py", line 109, in __call__
return self.function(*args, **kwargs)
File "/root/pwndbg/pwndbg/commands/__init__.py", line 189, in _OnlyWithFile
return function(*a, **kw)
File "/root/pwndbg/pwndbg/commands/checksec.py", line 16, in checksec
print(pwndbg.wrappers.checksec.get_raw_out())
File "/root/pwndbg/pwndbg/commands/__init__.py", line 189, in _OnlyWithFile
return function(*a, **kw)
File "/root/pwndbg/pwndbg/wrappers/__init__.py", line 28, in _OnlyWithCommand
return function(*a, **kw)
File "/root/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/root/pwndbg/pwndbg/wrappers/checksec.py", line 20, in get_raw_out
return pwndbg.wrappers.call_cmd(cmd)
File "/root/pwndbg/pwndbg/wrappers/__init__.py", line 35, in call_cmd
return subprocess.check_output(cmd, stderr=STDOUT).decode('utf-8')
File "/usr/lib/python3.7/subprocess.py", line 395, in check_output
**kwargs).stdout
File "/usr/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/usr/local/bin/checksec', '--file', '/tmp/forgot']' returned non-zero exit status 2.
|
subprocess.CalledProcessError
|
def exe(self):
return gdb.current_progspace().filename
|
def exe(self):
for obj in gdb.objfiles():
if obj.filename:
return obj.filename
break
if self.alive:
auxv = pwndbg.auxv.get()
return auxv["AT_EXECFN"]
|
https://github.com/pwndbg/pwndbg/issues/623
|
pwndbg> got
Traceback (most recent call last):
File "/home/mzr/sources/pwndbg/pwndbg/commands/__init__.py", line 135,
in __call__
return self.function(*args, **kwargs)
File "/home/mzr/sources/pwndbg/pwndbg/commands/__init__.py", line 226,
in _OnlyWhenRunning
return function(*a, **kw)
File "/home/mzr/sources/pwndbg/pwndbg/commands/got.py", line 28, in got
relro_status = pwndbg.wrappers.checksec.relro_status()
File "/home/mzr/sources/pwndbg/pwndbg/commands/__init__.py", line 215,
in _OnlyWithFile
return function(*a, **kw)
File "/home/mzr/sources/pwndbg/pwndbg/wrappers/__init__.py", line 28, i
n _OnlyWithCommand
return function(*a, **kw)
File "/home/mzr/sources/pwndbg/pwndbg/wrappers/checksec.py", line 25, i
n relro_status
out = get_raw_out()
File "/home/mzr/sources/pwndbg/pwndbg/commands/__init__.py", line 215,
in _OnlyWithFile
return function(*a, **kw)
File "/home/mzr/sources/pwndbg/pwndbg/wrappers/__init__.py", line 28, i
n _OnlyWithCommand
return function(*a, **kw)
File "/home/mzr/sources/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/home/mzr/sources/pwndbg/pwndbg/wrappers/checksec.py", line 18, i
n get_raw_out
local_path = pwndbg.file.get_file(pwndbg.proc.exe)
File "/home/mzr/sources/pwndbg/pwndbg/file.py", line 48, in get_file
"Error: %s" % (path, error))
OSError: Could not download remote file 'target:/lib64/ld-linux-x86-64.so
.2':
Error: Remote I/O error: No such file or directory
|
OSError
|
def iter_phdrs(ehdr):
if not ehdr:
return
phnum, phentsize, phdr = get_phdrs(ehdr.address)
if not phdr:
return
first_phdr = phdr.address
PhdrType = phdr.type
for i in range(0, phnum):
p_phdr = int(first_phdr + (i * phentsize))
p_phdr = read(PhdrType, p_phdr)
yield p_phdr
|
def iter_phdrs(ehdr):
if not ehdr:
raise StopIteration
phnum, phentsize, phdr = get_phdrs(ehdr.address)
if not phdr:
raise StopIteration
first_phdr = phdr.address
PhdrType = phdr.type
for i in range(0, phnum):
p_phdr = int(first_phdr + (i * phentsize))
p_phdr = read(PhdrType, p_phdr)
yield p_phdr
|
https://github.com/pwndbg/pwndbg/issues/570
|
pwndbg> target remote localhost:1234
Remote debugging using localhost:1234
warning: No executable has been specified and target does not support
determining executable automatically. Try using the "file" command.
0x0000000000000000 in ?? ()
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/elf.py", line 318, in iter_phdrs
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/events.py", line 169, in caller
func()
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/stack.py", line 81, in update
page = pwndbg.memory.Page(start, stop-start, 6 if not is_executable() else 7, 0, '[stack]')
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/stack.py", line 131, in is_executable
for phdr in pwndbg.elf.iter_phdrs(ehdr):
RuntimeError: generator raised StopIteration
If that is an issue, you can report it on https://github.com/pwndbg/pwndbg/issues
(Please don't forget to search if it hasn't been reported before)
To generate the report and open a browser, you may run `bugreport --run-browser`
PS: Pull requests are welcome
/usr/share/pwndbg/pwndbg/stack.py(131)is_executable()
-> for phdr in pwndbg.elf.iter_phdrs(ehdr):
(Pdb)
(Pdb) c
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/elf.py", line 318, in iter_phdrs
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/events.py", line 173, in caller
raise e
File "/usr/share/pwndbg/pwndbg/events.py", line 169, in caller
func()
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/stack.py", line 81, in update
page = pwndbg.memory.Page(start, stop-start, 6 if not is_executable() else 7, 0, '[stack]')
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/stack.py", line 131, in is_executable
for phdr in pwndbg.elf.iter_phdrs(ehdr):
RuntimeError: generator raised StopIteration
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/elf.py", line 318, in iter_phdrs
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/events.py", line 169, in caller
func()
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/stack.py", line 131, in is_executable
for phdr in pwndbg.elf.iter_phdrs(ehdr):
RuntimeError: generator raised StopIteration
If that is an issue, you can report it on https://github.com/pwndbg/pwndbg/issues
(Please don't forget to search if it hasn't been reported before)
To generate the report and open a browser, you may run `bugreport --run-browser`
PS: Pull requests are welcome
/usr/share/pwndbg/pwndbg/stack.py(131)is_executable()
-> for phdr in pwndbg.elf.iter_phdrs(ehdr):
(Pdb) c
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/elf.py", line 318, in iter_phdrs
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/events.py", line 173, in caller
raise e
File "/usr/share/pwndbg/pwndbg/events.py", line 169, in caller
func()
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/stack.py", line 131, in is_executable
for phdr in pwndbg.elf.iter_phdrs(ehdr):
RuntimeError: generator raised StopIteration
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/events.py", line 169, in caller
func()
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 116, in explore_registers
find(pwndbg.regs[regname])
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 75, in find
return explore(address)
File "/usr/share/pwndbg/pwndbg/abi.py", line 165, in caller
return func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 105, in explore
page = find_boundaries(address_maybe)
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 366, in find_boundaries
start = pwndbg.memory.find_lower_boundary(addr)
File "/usr/share/pwndbg/pwndbg/memory.py", line 357, in find_lower_boundary
pwndbg.memory.read(addr, 1)
File "/usr/share/pwndbg/pwndbg/memory.py", line 44, in read
result = gdb.selected_inferior().read_memory(addr, count)
gdb.error: Remote connection closed
If that is an issue, you can report it on https://github.com/pwndbg/pwndbg/issues
(Please don't forget to search if it hasn't been reported before)
To generate the report and open a browser, you may run `bugreport --run-browser`
PS: Pull requests are welcome
/usr/share/pwndbg/pwndbg/memory.py(44)read()
-> result = gdb.selected_inferior().read_memory(addr, count)
(Pdb) c
Traceback (most recent call last):
File "/usr/share/pwndbg/pwndbg/events.py", line 173, in caller
raise e
File "/usr/share/pwndbg/pwndbg/events.py", line 169, in caller
func()
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 116, in explore_registers
find(pwndbg.regs[regname])
File "/usr/share/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 75, in find
return explore(address)
File "/usr/share/pwndbg/pwndbg/abi.py", line 165, in caller
return func(*args, **kwargs)
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 105, in explore
page = find_boundaries(address_maybe)
File "/usr/share/pwndbg/pwndbg/vmmap.py", line 366, in find_boundaries
start = pwndbg.memory.find_lower_boundary(addr)
File "/usr/share/pwndbg/pwndbg/memory.py", line 357, in find_lower_boundary
pwndbg.memory.read(addr, 1)
File "/usr/share/pwndbg/pwndbg/memory.py", line 44, in read
result = gdb.selected_inferior().read_memory(addr, count)
gdb.error: Remote connection closed
[1] 7286 segmentation fault (core dumped) aarch64-linux-gnu-gdb
|
RuntimeError
|
def next(self, instruction, call=False):
"""
Architecture-specific hook point for enhance_next.
"""
if CS_GRP_CALL in instruction.groups:
if not call:
return None
elif CS_GRP_JUMP not in instruction.groups:
return None
# At this point, all operands have been resolved.
# Assume only single-operand jumps.
if len(instruction.operands) != 1:
return None
# Memory operands must be dereferenced
op = instruction.operands[0]
addr = op.int
if addr:
addr &= pwndbg.arch.ptrmask
if op.type == CS_OP_MEM:
if addr is None:
addr = self.memory(instruction, op)
# self.memory may return none, so we need to check it here again
if addr is not None:
try:
# fails with gdb.MemoryError if the dereferenced address
# doesn't belong to any of process memory maps
addr = int(pwndbg.memory.poi(pwndbg.typeinfo.ppvoid, addr))
except gdb.MemoryError:
return None
if op.type == CS_OP_REG:
addr = self.register(instruction, op)
# Evidently this can happen?
if addr is None:
return None
return int(addr)
|
def next(self, instruction, call=False):
"""
Architecture-specific hook point for enhance_next.
"""
if CS_GRP_CALL in instruction.groups:
if not call:
return None
elif CS_GRP_JUMP not in instruction.groups:
return None
# At this point, all operands have been resolved.
# Assume only single-operand jumps.
if len(instruction.operands) != 1:
return None
# Memory operands must be dereferenced
op = instruction.operands[0]
addr = op.int
if addr:
addr &= pwndbg.arch.ptrmask
if op.type == CS_OP_MEM:
if addr is None:
addr = self.memory(instruction, op)
# self.memory may return none, so we need to check it here again
if addr is not None:
addr = int(pwndbg.memory.poi(pwndbg.typeinfo.ppvoid, addr))
if op.type == CS_OP_REG:
addr = self.register(instruction, op)
# Evidently this can happen?
if addr is None:
return None
return int(addr)
|
https://github.com/pwndbg/pwndbg/issues/587
|
Traceback (most recent call last):
File "/home/dc/pwndbg/pwndbg/commands/__init__.py", line 135, in __call__
return self.function(*args, **kwargs)
File "/home/dc/pwndbg/pwndbg/commands/__init__.py", line 226, in _OnlyWhenRunning
return function(*a, **kw)
File "/home/dc/pwndbg/pwndbg/commands/context.py", line 88, in context
result.extend(func())
File "/home/dc/pwndbg/pwndbg/commands/context.py", line 100, in context_regs
return [pwndbg.ui.banner("registers")] + get_regs()
File "/home/dc/pwndbg/pwndbg/commands/context.py", line 144, in get_regs
desc = pwndbg.chain.format(value)
File "/home/dc/pwndbg/pwndbg/chain.py", line 122, in format
enhanced = pwndbg.enhance.enhance(chain[-2] + offset, code=code)
File "/home/dc/pwndbg/pwndbg/enhance.py", line 102, in enhance
instr = pwndbg.disasm.one(value)
File "/home/dc/pwndbg/pwndbg/disasm/__init__.py", line 115, in one
for insn in get(address, 1):
File "/home/dc/pwndbg/pwndbg/disasm/__init__.py", line 135, in get
i = get_one_instruction(address)
File "/home/dc/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/home/dc/pwndbg/pwndbg/disasm/__init__.py", line 107, in get_one_instruction
pwndbg.disasm.arch.DisassemblyAssistant.enhance(ins)
File "/home/dc/pwndbg/pwndbg/disasm/arch.py", line 55, in enhance
enhancer.enhance_next(instruction)
File "/home/dc/pwndbg/pwndbg/disasm/arch.py", line 111, in enhance_next
instruction.target = self.next(instruction, call=True)
File "/home/dc/pwndbg/pwndbg/disasm/x86.py", line 112, in next
return super(DisassemblyAssistant, self).next(instruction, call)
File "/home/dc/pwndbg/pwndbg/disasm/arch.py", line 150, in next
addr = int(pwndbg.memory.poi(pwndbg.typeinfo.ppvoid, addr))
File "/home/dc/pwndbg/pwndbg/inthook.py", line 40, in __new__
value = value.cast(pwndbg.typeinfo.ulong)
gdb.MemoryError: Cannot access memory at address 0x30
|
gdb.MemoryError
|
def dump(self, instruction):
"""
Debug-only method.
"""
ins = instruction
rv = []
rv.append("%s %s" % (ins.mnemonic, ins.op_str))
for i, group in enumerate(ins.groups):
rv.append(" groups[%i] = %s" % (i, groups.get(group, group)))
rv.append(" next = %#x" % (ins.next))
rv.append(" condition = %r" % (ins.condition))
for i, op in enumerate(ins.operands):
rv.append(" operands[%i] = %s" % (i, ops.get(op.type, op.type)))
rv.append(" access = %s" % (access.get(op.access, op.access)))
if op.int is not None:
rv.append(" int = %#x" % (op.int))
if op.symbol is not None:
rv.append(" sym = %s" % (op.symbol))
if op.str is not None:
rv.append(" str = %s" % (op.str))
return "\n".join(rv)
|
def dump(self, instruction):
ins = instruction
rv = []
rv.append("%s %s" % (ins.mnemonic, ins.op_str))
for i, group in enumerate(ins.groups):
rv.append(" groups[%i] = %s" % (i, groups.get(group, group)))
rv.append(" next = %#x" % (ins.next))
rv.append(" condition = %r" % (ins.condition))
for i, op in enumerate(ins.operands):
rv.append(" operands[%i] = %s" % (i, ops.get(op.type, op.type)))
rv.append(" access = %s" % (access.get(op.access, op.access)))
if op.int is not None:
rv.append(" int = %#x" % (op.int))
if op.symbol is not None:
rv.append(" sym = %s" % (op.symbol))
if op.str is not None:
rv.append(" str = %s" % (op.str))
return "\n".join(rv)
|
https://github.com/pwndbg/pwndbg/issues/587
|
Traceback (most recent call last):
File "/home/dc/pwndbg/pwndbg/commands/__init__.py", line 135, in __call__
return self.function(*args, **kwargs)
File "/home/dc/pwndbg/pwndbg/commands/__init__.py", line 226, in _OnlyWhenRunning
return function(*a, **kw)
File "/home/dc/pwndbg/pwndbg/commands/context.py", line 88, in context
result.extend(func())
File "/home/dc/pwndbg/pwndbg/commands/context.py", line 100, in context_regs
return [pwndbg.ui.banner("registers")] + get_regs()
File "/home/dc/pwndbg/pwndbg/commands/context.py", line 144, in get_regs
desc = pwndbg.chain.format(value)
File "/home/dc/pwndbg/pwndbg/chain.py", line 122, in format
enhanced = pwndbg.enhance.enhance(chain[-2] + offset, code=code)
File "/home/dc/pwndbg/pwndbg/enhance.py", line 102, in enhance
instr = pwndbg.disasm.one(value)
File "/home/dc/pwndbg/pwndbg/disasm/__init__.py", line 115, in one
for insn in get(address, 1):
File "/home/dc/pwndbg/pwndbg/disasm/__init__.py", line 135, in get
i = get_one_instruction(address)
File "/home/dc/pwndbg/pwndbg/memoize.py", line 48, in __call__
value = self.func(*args, **kwargs)
File "/home/dc/pwndbg/pwndbg/disasm/__init__.py", line 107, in get_one_instruction
pwndbg.disasm.arch.DisassemblyAssistant.enhance(ins)
File "/home/dc/pwndbg/pwndbg/disasm/arch.py", line 55, in enhance
enhancer.enhance_next(instruction)
File "/home/dc/pwndbg/pwndbg/disasm/arch.py", line 111, in enhance_next
instruction.target = self.next(instruction, call=True)
File "/home/dc/pwndbg/pwndbg/disasm/x86.py", line 112, in next
return super(DisassemblyAssistant, self).next(instruction, call)
File "/home/dc/pwndbg/pwndbg/disasm/arch.py", line 150, in next
addr = int(pwndbg.memory.poi(pwndbg.typeinfo.ppvoid, addr))
File "/home/dc/pwndbg/pwndbg/inthook.py", line 40, in __new__
value = value.cast(pwndbg.typeinfo.ulong)
gdb.MemoryError: Cannot access memory at address 0x30
|
gdb.MemoryError
|
def get_set_string(self):
value = self.raw_value
# For string value, convert utf8 byte string to unicode.
if isinstance(value, six.binary_type):
value = codecs.decode(value, "utf-8")
# Remove surrounded ' and " characters
if isinstance(value, six.string_types):
# The first character must be ' or " and ends with the same character.
# See PR #404 for more information
pattern = r"^(?P<quote>[\"'])(?P<content>.*?)(?P=quote)$"
value = re.sub(pattern, r"\g<content>", value)
# Write back to self.value
self.value = value
for trigger in triggers[self.name]:
trigger()
if not pwndbg.decorators.first_prompt:
# Remove the newline that gdb adds automatically
return "\b"
return "Set %s to %r" % (self.docstring, self.value)
|
def get_set_string(self):
value = self.raw_value
# For string value, convert utf8 byte string to unicode.
if isinstance(value, six.binary_type):
value = codecs.decode(value, "utf-8")
# Remove surrounded ' and " characters
if isinstance(value, six.string_types):
# The first character must be ' or " and ends with the same character.
# See PR #404 for more information
pattern = r"^(?P<quote>[\"'])(?P<content>.*?)(?P=quote)$"
value = re.sub(pattern, r"\g<content>", value)
# Write back to self.value
self.value = value
for trigger in triggers[self.name]:
trigger()
return "Set %s to %r" % (self.docstring, self.value)
|
https://github.com/pwndbg/pwndbg/issues/440
|
[!] Ida Pro xmlrpc error
Traceback (most recent call last):
File "/mnt/d/Uni/SS18/exploits/pwndbg/pwndbg/pwndbg/ida.py", line 64, in init_ida_rpc_client
_ida.here()
File "/usr/lib/python3.4/xmlrpc/client.py", line 1098, in __call__
return self.__send(self.__name, args)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1437, in __request
verbose=self.__verbose
File "/usr/lib/python3.4/xmlrpc/client.py", line 1140, in request
return self.single_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1152, in single_request
http_conn = self.send_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1264, in send_request
self.send_content(connection, request_body)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1294, in send_content
connection.endheaders(request_body)
File "/usr/lib/python3.4/http/client.py", line 1121, in endheaders
self._send_output(message_body)
File "/usr/lib/python3.4/http/client.py", line 951, in _send_output
self.send(msg)
File "/usr/lib/python3.4/http/client.py", line 886, in send
self.connect()
File "/usr/lib/python3.4/http/client.py", line 863, in connect
self.timeout, self.source_address)
File "/usr/lib/python3.4/socket.py", line 512, in create_connection
raise err
File "/usr/lib/python3.4/socket.py", line 503, in create_connection
sock.connect(sa)
InterruptedError: [Errno 4] Unterbrechung während des Betriebssystemaufrufs
|
InterruptedError
|
def init_ida_rpc_client():
global _ida, _ida_last_exception, _ida_last_connection_check
if not ida_enabled:
return
now = time.time()
if _ida is None and (now - _ida_last_connection_check) < int(ida_timeout) + 5:
return
addr = "http://{host}:{port}".format(host=ida_rpc_host, port=ida_rpc_port)
_ida = xmlrpclib.ServerProxy(addr)
socket.setdefaulttimeout(int(ida_timeout))
exception = None # (type, value, traceback)
try:
_ida.here()
print(
message.success(
"Pwndbg successfully connected to Ida Pro xmlrpc: %s" % addr
)
)
except socket.error as e:
if e.errno != errno.ECONNREFUSED:
exception = sys.exc_info()
_ida = None
except socket.timeout:
exception = sys.exc_info()
_ida = None
except xmlrpclib.ProtocolError:
exception = sys.exc_info()
_ida = None
if exception:
if (
not isinstance(_ida_last_exception, exception[0])
or _ida_last_exception.args != exception[1].args
):
if (
hasattr(pwndbg.config, "exception_verbose")
and pwndbg.config.exception_verbose
):
print(message.error("[!] Ida Pro xmlrpc error"))
traceback.print_exception(*exception)
else:
exc_type, exc_value, _ = exception
print(
message.error(
"Failed to connect to IDA Pro ({}: {})".format(
exc_type.__qualname__, exc_value
)
)
)
if exc_type is socket.timeout:
print(
message.notice("To increase the time to wait for IDA Pro use `")
+ message.hint("set ida-timeout <new-timeout-in-seconds>")
+ message.notice("`")
)
else:
print(
message.notice("For more info invoke `")
+ message.hint("set exception-verbose on")
+ message.notice("`")
)
print(
message.notice("To disable IDA Pro integration invoke `")
+ message.hint("set ida-enabled off")
+ message.notice("`")
)
_ida_last_exception = exception and exception[1]
_ida_last_connection_check = now
|
def init_ida_rpc_client():
global _ida, _ida_last_exception
addr = "http://{host}:{port}".format(host=ida_rpc_host, port=ida_rpc_port)
_ida = xmlrpclib.ServerProxy(addr)
socket.setdefaulttimeout(3)
exception = None # (type, value, traceback)
try:
_ida.here()
print(
message.success(
"Pwndbg successfully connected to Ida Pro xmlrpc: %s" % addr
)
)
except socket.error as e:
if e.errno != errno.ECONNREFUSED:
exception = sys.exc_info()
_ida = None
except socket.timeout:
exception = sys.exc_info()
_ida = None
except xmlrpclib.ProtocolError:
exception = sys.exc_info()
_ida = None
if exception:
if (
not isinstance(_ida_last_exception, exception[0])
or _ida_last_exception.args != exception[1].args
):
print(message.error("[!] Ida Pro xmlrpc error"))
traceback.print_exception(*exception)
_ida_last_exception = exception and exception[1]
|
https://github.com/pwndbg/pwndbg/issues/440
|
[!] Ida Pro xmlrpc error
Traceback (most recent call last):
File "/mnt/d/Uni/SS18/exploits/pwndbg/pwndbg/pwndbg/ida.py", line 64, in init_ida_rpc_client
_ida.here()
File "/usr/lib/python3.4/xmlrpc/client.py", line 1098, in __call__
return self.__send(self.__name, args)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1437, in __request
verbose=self.__verbose
File "/usr/lib/python3.4/xmlrpc/client.py", line 1140, in request
return self.single_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1152, in single_request
http_conn = self.send_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1264, in send_request
self.send_content(connection, request_body)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1294, in send_content
connection.endheaders(request_body)
File "/usr/lib/python3.4/http/client.py", line 1121, in endheaders
self._send_output(message_body)
File "/usr/lib/python3.4/http/client.py", line 951, in _send_output
self.send(msg)
File "/usr/lib/python3.4/http/client.py", line 886, in send
self.connect()
File "/usr/lib/python3.4/http/client.py", line 863, in connect
self.timeout, self.source_address)
File "/usr/lib/python3.4/socket.py", line 512, in create_connection
raise err
File "/usr/lib/python3.4/socket.py", line 503, in create_connection
sock.connect(sa)
InterruptedError: [Errno 4] Unterbrechung während des Betriebssystemaufrufs
|
InterruptedError
|
def __call__(self, *args, **kwargs):
if _ida is None:
init_ida_rpc_client()
if _ida is not None:
return self.fn(*args, **kwargs)
return None
|
def __call__(self, *args, **kwargs):
if not ida_enabled:
return None
if _ida is None:
init_ida_rpc_client()
if _ida is not None:
return self.fn(*args, **kwargs)
return None
|
https://github.com/pwndbg/pwndbg/issues/440
|
[!] Ida Pro xmlrpc error
Traceback (most recent call last):
File "/mnt/d/Uni/SS18/exploits/pwndbg/pwndbg/pwndbg/ida.py", line 64, in init_ida_rpc_client
_ida.here()
File "/usr/lib/python3.4/xmlrpc/client.py", line 1098, in __call__
return self.__send(self.__name, args)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1437, in __request
verbose=self.__verbose
File "/usr/lib/python3.4/xmlrpc/client.py", line 1140, in request
return self.single_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1152, in single_request
http_conn = self.send_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1264, in send_request
self.send_content(connection, request_body)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1294, in send_content
connection.endheaders(request_body)
File "/usr/lib/python3.4/http/client.py", line 1121, in endheaders
self._send_output(message_body)
File "/usr/lib/python3.4/http/client.py", line 951, in _send_output
self.send(msg)
File "/usr/lib/python3.4/http/client.py", line 886, in send
self.connect()
File "/usr/lib/python3.4/http/client.py", line 863, in connect
self.timeout, self.source_address)
File "/usr/lib/python3.4/socket.py", line 512, in create_connection
raise err
File "/usr/lib/python3.4/socket.py", line 503, in create_connection
sock.connect(sa)
InterruptedError: [Errno 4] Unterbrechung während des Betriebssystemaufrufs
|
InterruptedError
|
def prompt_hook(*a):
global cur
pwndbg.decorators.first_prompt = True
new = (gdb.selected_inferior(), gdb.selected_thread())
if cur != new:
pwndbg.events.after_reload(start=False)
cur = new
if pwndbg.proc.alive and pwndbg.proc.thread_is_stopped:
prompt_hook_on_stop(*a)
|
def prompt_hook(*a):
global cur
new = (gdb.selected_inferior(), gdb.selected_thread())
if cur != new:
pwndbg.events.after_reload(start=False)
cur = new
if pwndbg.proc.alive and pwndbg.proc.thread_is_stopped:
prompt_hook_on_stop(*a)
|
https://github.com/pwndbg/pwndbg/issues/440
|
[!] Ida Pro xmlrpc error
Traceback (most recent call last):
File "/mnt/d/Uni/SS18/exploits/pwndbg/pwndbg/pwndbg/ida.py", line 64, in init_ida_rpc_client
_ida.here()
File "/usr/lib/python3.4/xmlrpc/client.py", line 1098, in __call__
return self.__send(self.__name, args)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1437, in __request
verbose=self.__verbose
File "/usr/lib/python3.4/xmlrpc/client.py", line 1140, in request
return self.single_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1152, in single_request
http_conn = self.send_request(host, handler, request_body, verbose)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1264, in send_request
self.send_content(connection, request_body)
File "/usr/lib/python3.4/xmlrpc/client.py", line 1294, in send_content
connection.endheaders(request_body)
File "/usr/lib/python3.4/http/client.py", line 1121, in endheaders
self._send_output(message_body)
File "/usr/lib/python3.4/http/client.py", line 951, in _send_output
self.send(msg)
File "/usr/lib/python3.4/http/client.py", line 886, in send
self.connect()
File "/usr/lib/python3.4/http/client.py", line 863, in connect
self.timeout, self.source_address)
File "/usr/lib/python3.4/socket.py", line 512, in create_connection
raise err
File "/usr/lib/python3.4/socket.py", line 503, in create_connection
sock.connect(sa)
InterruptedError: [Errno 4] Unterbrechung während des Betriebssystemaufrufs
|
InterruptedError
|
def entry(*a):
"""
Set a breakpoint at the first instruction executed in
the target binary.
"""
global break_on_first_instruction
break_on_first_instruction = True
run = "run " + " ".join(map(shlex.quote, a))
gdb.execute(run, from_tty=False)
|
def entry(*a):
"""
Set a breakpoint at the first instruction executed in
the target binary.
"""
global break_on_first_instruction
break_on_first_instruction = True
run = "run " + " ".join(a)
gdb.execute(run, from_tty=False)
|
https://github.com/pwndbg/pwndbg/issues/362
|
[dc@dc:pwndbg|dev *$%]$ gdb python
Loaded 113 commands. Type pwndbg [filter] for a list.
Reading symbols from python...(no debugging symbols found)...done.
pwndbg> set exception-verbose on
Set whether to print a full stacktracefor exceptions raised in Pwndbg commands to True
pwndbg> run -c "print(1); print(2)"
Starting program: /usr/bin/python -c "print(1); print(2)"
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib/libthread_db.so.1".
1
2
[Inferior 1 (process 20590) exited normally]
pwndbg> entry -c "print(1); print(2)"
('-c', 'print(1); print(2)')
Running '%s' run -c print(1); print(2)
/bin/bash: -c: line 0: syntax error near unexpected token `('
/bin/bash: -c: line 0: `exec /usr/bin/python -c print(1); print(2)'
Traceback (most recent call last):
File "/home/dc/installed/pwndbg/pwndbg/commands/__init__.py", line 100, in __call__
return self.function(*args, **kwargs)
File "/home/dc/installed/pwndbg/pwndbg/commands/__init__.py", line 181, in _OnlyWithFile
return function(*a, **kw)
File "/home/dc/installed/pwndbg/pwndbg/commands/start.py", line 72, in entry
gdb.execute(run, from_tty=False)
gdb.error: During startup program exited with code 1.
If that is an issue, you can report it on https://github.com/pwndbg/pwndbg/issues
(Please don't forget to search if it hasn't been reported before)
PS: Pull requests are welcome
|
gdb.error
|
def dt(name="", addr=None, obj=None):
"""
Dump out a structure type Windbg style.
"""
# Return value is a list of strings.of
# We concatenate at the end.
rv = []
if obj and not name:
t = obj.type
while t.code == (gdb.TYPE_CODE_PTR):
t = t.target()
obj = obj.dereference()
name = str(t)
# Lookup the type name specified by the user
else:
t = pwndbg.typeinfo.load(name)
# If it's not a struct (e.g. int or char*), bail
if t.code not in (gdb.TYPE_CODE_STRUCT, gdb.TYPE_CODE_TYPEDEF, gdb.TYPE_CODE_UNION):
raise Exception("Not a structure: %s" % t)
# If an address was specified, create a Value of the
# specified type at that address.
if addr is not None:
obj = pwndbg.memory.poi(t, addr)
# Header, optionally include the name
header = name
if obj:
header = "%s @ %s" % (header, hex(int(obj.address)))
rv.append(header)
if t.strip_typedefs().code == gdb.TYPE_CODE_ARRAY:
return "Arrays not supported yet"
if t.strip_typedefs().code not in (gdb.TYPE_CODE_STRUCT, gdb.TYPE_CODE_UNION):
t = {name: obj or gdb.Value(0).cast(t)}
for name, field in t.items():
# Offset into the parent structure
o = getattr(field, "bitpos", 0) // 8
b = getattr(field, "bitpos", 0) % 8
extra = str(field.type)
ftype = field.type.strip_typedefs()
if obj and obj.type.strip_typedefs().code in (
gdb.TYPE_CODE_STRUCT,
gdb.TYPE_CODE_UNION,
):
v = obj[name]
if ftype.code == gdb.TYPE_CODE_INT:
v = hex(int(v))
if (
ftype.code in (gdb.TYPE_CODE_PTR, gdb.TYPE_CODE_ARRAY)
and ftype.target() == pwndbg.typeinfo.uchar
):
data = pwndbg.memory.read(v.address, ftype.sizeof)
v = " ".join("%02x" % b for b in data)
extra = v
# Adjust trailing lines in 'extra' to line up
# This is necessary when there are nested structures.
# Ideally we'd expand recursively if the type is complex.
extra_lines = []
for i, line in enumerate(str(extra).splitlines()):
if i == 0:
extra_lines.append(line)
else:
extra_lines.append(35 * " " + line)
extra = "\n".join(extra_lines)
bitpos = "" if not b else (".%i" % b)
line = " +0x%04x%s %-20s : %s" % (o, bitpos, name, extra)
rv.append(line)
return "\n".join(rv)
|
def dt(name="", addr=None, obj=None):
"""
Dump out a structure type Windbg style.
"""
# Return value is a list of strings.of
# We concatenate at the end.
rv = []
if obj and not name:
t = obj.type
while t.code == (gdb.TYPE_CODE_PTR):
t = t.target()
obj = obj.dereference()
name = str(t)
# Lookup the type name specified by the user
else:
t = pwndbg.typeinfo.load(name)
# If it's not a struct (e.g. int or char*), bail
if t.code not in (gdb.TYPE_CODE_STRUCT, gdb.TYPE_CODE_TYPEDEF, gdb.TYPE_CODE_UNION):
raise Exception("Not a structure: %s" % t)
# If an address was specified, create a Value of the
# specified type at that address.
if addr is not None:
obj = pwndbg.memory.poi(t, addr)
# Header, optionally include the name
header = name
if obj:
header = "%s @ %s" % (header, hex(int(obj.address)))
rv.append(header)
if t.strip_typedefs().code == gdb.TYPE_CODE_ARRAY:
return "Arrays not supported yet"
if t.strip_typedefs().code not in (gdb.TYPE_CODE_STRUCT, gdb.TYPE_CODE_UNION):
t = {name: obj or gdb.Value(0).cast(t)}
for name, field in t.items():
# Offset into the parent structure
o = getattr(field, "bitpos", 0) / 8
extra = str(field.type)
ftype = field.type.strip_typedefs()
if obj and obj.type.strip_typedefs().code in (
gdb.TYPE_CODE_STRUCT,
gdb.TYPE_CODE_UNION,
):
v = obj[name]
if ftype.code == gdb.TYPE_CODE_INT:
v = hex(int(v))
if (
ftype.code in (gdb.TYPE_CODE_PTR, gdb.TYPE_CODE_ARRAY)
and ftype.target() == pwndbg.typeinfo.uchar
):
data = pwndbg.memory.read(v.address, ftype.sizeof)
v = " ".join("%02x" % b for b in data)
extra = v
# Adjust trailing lines in 'extra' to line up
# This is necessary when there are nested structures.
# Ideally we'd expand recursively if the type is complex.
extra_lines = []
for i, line in enumerate(str(extra).splitlines()):
if i == 0:
extra_lines.append(line)
else:
extra_lines.append(35 * " " + line)
extra = "\n".join(extra_lines)
line = " +0x%04x %-20s : %s" % (o, name, extra)
rv.append(line)
return "\n".join(rv)
|
https://github.com/pwndbg/pwndbg/issues/362
|
[dc@dc:pwndbg|dev *$%]$ gdb python
Loaded 113 commands. Type pwndbg [filter] for a list.
Reading symbols from python...(no debugging symbols found)...done.
pwndbg> set exception-verbose on
Set whether to print a full stacktracefor exceptions raised in Pwndbg commands to True
pwndbg> run -c "print(1); print(2)"
Starting program: /usr/bin/python -c "print(1); print(2)"
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/usr/lib/libthread_db.so.1".
1
2
[Inferior 1 (process 20590) exited normally]
pwndbg> entry -c "print(1); print(2)"
('-c', 'print(1); print(2)')
Running '%s' run -c print(1); print(2)
/bin/bash: -c: line 0: syntax error near unexpected token `('
/bin/bash: -c: line 0: `exec /usr/bin/python -c print(1); print(2)'
Traceback (most recent call last):
File "/home/dc/installed/pwndbg/pwndbg/commands/__init__.py", line 100, in __call__
return self.function(*args, **kwargs)
File "/home/dc/installed/pwndbg/pwndbg/commands/__init__.py", line 181, in _OnlyWithFile
return function(*a, **kw)
File "/home/dc/installed/pwndbg/pwndbg/commands/start.py", line 72, in entry
gdb.execute(run, from_tty=False)
gdb.error: During startup program exited with code 1.
If that is an issue, you can report it on https://github.com/pwndbg/pwndbg/issues
(Please don't forget to search if it hasn't been reported before)
PS: Pull requests are welcome
|
gdb.error
|
def search(type, hex, string, executable, writable, value, mapping, save, next):
# Adjust pointer sizes to the local architecture
if type == "pointer":
type = {4: "dword", 8: "qword"}[pwndbg.arch.ptrsize]
if save is None:
save = bool(pwndbg.config.auto_save_search)
if hex:
value = codecs.decode(value, "hex")
# Convert to an integer if needed, and pack to bytes
if type not in ("string", "bytes"):
value = pwndbg.commands.fix_int(value)
value &= pwndbg.arch.ptrmask
fmt = {"little": "<", "big": ">"}[pwndbg.arch.endian] + {
"byte": "B",
"short": "H",
"dword": "L",
"qword": "Q",
}[type]
value = struct.pack(fmt, value)
# Null-terminate strings
elif type == "string":
value += b"\x00"
# Prep the saved set if necessary
global saved
if save:
saved = set()
# Perform the search
for address in pwndbg.search.search(
value, mapping=mapping, executable=executable, writable=writable
):
if next and address not in saved:
continue
if save:
saved.add(address)
print_search_hit(address)
|
def search(type, hex, string, executable, writable, value, mapping, save, next):
# Adjust pointer sizes to the local architecture
if type == "pointer":
type = {4: "dword", 8: "qword"}[pwndbg.arch.ptrsize]
if save is None:
save = bool(pwndbg.config.auto_save_search)
if hex:
value = codecs.decode(value, "hex")
# Convert to an integer if needed, and pack to bytes
if type not in ("string", "bytes"):
value = pwndbg.commands.fix_int(value)
fmt = {"little": "<", "big": ">"}[pwndbg.arch.endian] + {
"byte": "B",
"short": "H",
"dword": "L",
"qword": "Q",
}[type]
value = struct.pack(fmt, value)
# Null-terminate strings
elif type == "string":
value += b"\x00"
# Prep the saved set if necessary
global saved
if save:
saved = set()
# Perform the search
for address in pwndbg.search.search(
value, mapping=mapping, executable=executable, writable=writable
):
if next and address not in saved:
continue
if save:
saved.add(address)
print_search_hit(address)
|
https://github.com/pwndbg/pwndbg/issues/123
|
pwndbg> search -4 0xf7eebf83
Traceback (most recent call last):
File "/home/bruce30262/pwndbg/pwndbg/commands/__init__.py", line 57, in __call__
return self.function(*args, **kwargs)
File "/home/bruce30262/pwndbg/pwndbg/commands/__init__.py", line 162, in _ArgparsedCommand
return function(**vars(args))
File "/home/bruce30262/pwndbg/pwndbg/commands/__init__.py", line 115, in _OnlyWhenRunning
return function(*a, **kw)
File "/home/bruce30262/pwndbg/pwndbg/commands/search.py", line 112, in search
value = struct.pack(fmt, value)
struct.error: argument out of range
|
struct.error
|
def _same_modules(source_module, target_module):
"""Compare the filenames associated with the given modules names.
This tries to not actually load the modules.
"""
if not (source_module or target_module):
return False
if target_module == source_module:
return True
def _get_filename(module):
filename = None
try:
if not inspect.ismodule(module):
loader = pkgutil.get_loader(module)
if isinstance(loader, importlib.machinery.SourceFileLoader):
filename = loader.get_filename()
else:
filename = inspect.getfile(module)
except (TypeError, ImportError):
pass
return filename
source_filename = _get_filename(source_module)
target_filename = _get_filename(target_module)
return source_filename and target_filename and source_filename == target_filename
|
def _same_modules(source_module, target_module):
"""Compare the filenames associated with the given modules names.
This tries to not actually load the modules.
"""
if not (source_module or target_module):
return False
if target_module == source_module:
return True
def _get_filename(module):
filename = None
try:
if not inspect.ismodule(module):
loader = pkgutil.get_loader(module)
if loader:
filename = loader.get_filename()
else:
filename = inspect.getfile(module)
except (TypeError, ImportError):
pass
return filename
source_filename = _get_filename(source_module)
target_filename = _get_filename(target_module)
return source_filename and target_filename and source_filename == target_filename
|
https://github.com/hylang/hy/issues/1911
|
$ python
Python 3.7.5 (default, Jun 8 2020, 17:36:22)
[Clang 11.0.3 (clang-1103.0.32.29)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import hy
hy.eval(hy.read_str("(require [hy.contrib.walk [let]])"))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/compiler.py", line 2099, in hy_eval
module.__dict__, locals)
File "<string>", line 1, in <module>
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/macros.py", line 170, in require
if _same_modules(source_module, target_module):
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/macros.py", line 118, in _same_modules
target_filename = _get_filename(target_module)
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/macros.py", line 109, in _get_filename
filename = loader.get_filename()
AttributeError: type object 'BuiltinImporter' has no attribute 'get_filename'
|
AttributeError
|
def _get_filename(module):
filename = None
try:
if not inspect.ismodule(module):
loader = pkgutil.get_loader(module)
if isinstance(loader, importlib.machinery.SourceFileLoader):
filename = loader.get_filename()
else:
filename = inspect.getfile(module)
except (TypeError, ImportError):
pass
return filename
|
def _get_filename(module):
filename = None
try:
if not inspect.ismodule(module):
loader = pkgutil.get_loader(module)
if loader:
filename = loader.get_filename()
else:
filename = inspect.getfile(module)
except (TypeError, ImportError):
pass
return filename
|
https://github.com/hylang/hy/issues/1911
|
$ python
Python 3.7.5 (default, Jun 8 2020, 17:36:22)
[Clang 11.0.3 (clang-1103.0.32.29)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import hy
hy.eval(hy.read_str("(require [hy.contrib.walk [let]])"))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/compiler.py", line 2099, in hy_eval
module.__dict__, locals)
File "<string>", line 1, in <module>
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/macros.py", line 170, in require
if _same_modules(source_module, target_module):
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/macros.py", line 118, in _same_modules
target_filename = _get_filename(target_module)
File "/Users/chris/.pyenv/versions/3.7.5/lib/python3.7/site-packages/hy/macros.py", line 109, in _get_filename
filename = loader.get_filename()
AttributeError: type object 'BuiltinImporter' has no attribute 'get_filename'
|
AttributeError
|
def run_command(source, filename=None):
__main__ = importlib.import_module("__main__")
require("hy.cmdline", __main__, assignments="ALL")
try:
tree = hy_parse(source, filename=filename)
except HyLanguageError:
hy_exc_handler(*sys.exc_info())
return 1
with filtered_hy_exceptions():
hy_eval(tree, __main__.__dict__, __main__, filename=filename, source=source)
return 0
|
def run_command(source, filename=None):
__main__ = importlib.import_module("__main__")
require("hy.cmdline", __main__, assignments="ALL")
try:
tree = hy_parse(source, filename=filename)
except HyLanguageError:
hy_exc_handler(*sys.exc_info())
return 1
with filtered_hy_exceptions():
hy_eval(tree, None, __main__, filename=filename, source=source)
return 0
|
https://github.com/hylang/hy/issues/1879
|
$ CODE='(import math) (print (lfor j [1] (math.sqrt 5)))'
$ hy -c "$CODE"
Traceback (most recent call last):
File "/usr/local/bin/hy", line 8, in <module>
sys.exit(hy_main())
File "<string>", line 1, in <module>
File "<string>", line 1, in <listcomp>
NameError: name 'math' is not defined
$ echo "$CODE" | hy
hy 0.18.0 using CPython(default) 3.7.5 on Linux
=> [2.23606797749979]
=>
now exiting HyREPL...
$ echo "$CODE" > /tmp/foo.hy && hy /tmp/foo.hy
[2.23606797749979]
|
NameError
|
def macroexpand(tree, module, compiler=None, once=False):
"""Expand the toplevel macros for the given Hy AST tree.
Load the macros from the given `module`, then expand the (top-level) macros
in `tree` until we no longer can.
`HyExpression` resulting from macro expansions are assigned the module in
which the macro function is defined (determined using `inspect.getmodule`).
If the resulting `HyExpression` is itself macro expanded, then the
namespace of the assigned module is checked first for a macro corresponding
to the expression's head/car symbol. If the head/car symbol of such a
`HyExpression` is not found among the macros of its assigned module's
namespace, the outer-most namespace--e.g. the one given by the `module`
parameter--is used as a fallback.
Parameters
----------
tree: HyObject or list
Hy AST tree.
module: str or types.ModuleType
Module used to determine the local namespace for macros.
compiler: HyASTCompiler, optional
The compiler object passed to expanded macros.
once: boolean, optional
Only expand the first macro in `tree`.
Returns
------
out: HyObject
Returns a mutated tree with macros expanded.
"""
if not inspect.ismodule(module):
module = importlib.import_module(module)
assert not compiler or compiler.module == module
while isinstance(tree, HyExpression) and tree:
fn = tree[0]
if fn in ("quote", "quasiquote") or not isinstance(fn, HySymbol):
break
fn = mangle(fn)
expr_modules = ([] if not hasattr(tree, "module") else [tree.module]) + [module]
# Choose the first namespace with the macro.
m = next(
(mod.__macros__[fn] for mod in expr_modules if fn in mod.__macros__), None
)
if not m:
break
opts = {}
if m._hy_macro_pass_compiler:
if compiler is None:
from hy.compiler import HyASTCompiler
compiler = HyASTCompiler(module)
opts["compiler"] = compiler
with macro_exceptions(module, tree, compiler):
obj = m(module.__name__, *tree[1:], **opts)
if isinstance(obj, HyExpression):
obj.module = inspect.getmodule(m)
tree = replace_hy_obj(obj, tree)
if once:
break
tree = wrap_value(tree)
return tree
|
def macroexpand(tree, module, compiler=None, once=False):
"""Expand the toplevel macros for the given Hy AST tree.
Load the macros from the given `module`, then expand the (top-level) macros
in `tree` until we no longer can.
`HyExpression` resulting from macro expansions are assigned the module in
which the macro function is defined (determined using `inspect.getmodule`).
If the resulting `HyExpression` is itself macro expanded, then the
namespace of the assigned module is checked first for a macro corresponding
to the expression's head/car symbol. If the head/car symbol of such a
`HyExpression` is not found among the macros of its assigned module's
namespace, the outer-most namespace--e.g. the one given by the `module`
parameter--is used as a fallback.
Parameters
----------
tree: HyObject or list
Hy AST tree.
module: str or types.ModuleType
Module used to determine the local namespace for macros.
compiler: HyASTCompiler, optional
The compiler object passed to expanded macros.
once: boolean, optional
Only expand the first macro in `tree`.
Returns
------
out: HyObject
Returns a mutated tree with macros expanded.
"""
if not inspect.ismodule(module):
module = importlib.import_module(module)
assert not compiler or compiler.module == module
while True:
if not isinstance(tree, HyExpression) or tree == []:
break
fn = tree[0]
if fn in ("quote", "quasiquote") or not isinstance(fn, HySymbol):
break
fn = mangle(fn)
expr_modules = ([] if not hasattr(tree, "module") else [tree.module]) + [module]
# Choose the first namespace with the macro.
m = next(
(mod.__macros__[fn] for mod in expr_modules if fn in mod.__macros__), None
)
if not m:
break
opts = {}
if m._hy_macro_pass_compiler:
if compiler is None:
from hy.compiler import HyASTCompiler
compiler = HyASTCompiler(module)
opts["compiler"] = compiler
with macro_exceptions(module, tree, compiler):
obj = m(module.__name__, *tree[1:], **opts)
if isinstance(obj, HyExpression):
obj.module = inspect.getmodule(m)
tree = replace_hy_obj(obj, tree)
if once:
break
tree = wrap_value(tree)
return tree
|
https://github.com/hylang/hy/issues/1885
|
felix@alienware:~$ hy --version
hy 0.18.0
felix@alienware:~$ echo "()" > foo.hy && hy foo.hy
Traceback (most recent call last):
File "/home/felix/.pyenv/versions/3.8.0/bin/hy", line 8, in <module>
sys.exit(hy_main())
File "/home/felix/.pyenv/versions/3.8.0/lib/python3.8/runpy.py", line 261, in run_path
code, fname = _get_code_from_file(run_name, path_name)
File "<frozen importlib._bootstrap_external>", line 916, in get_code
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ Traceback (most recent call last):
File "/home/felix/.pyenv/versions/3.8.0/lib/python3.8/site-packages/hy/compiler.py", line 433, in compile
ret = self.compile_atom(tree)
File "/home/felix/.pyenv/versions/3.8.0/lib/python3.8/site-packages/hy/compiler.py", line 427, in compile_atom
return Result() + _model_compilers[type(atom)](self, atom)
File "/home/felix/.pyenv/versions/3.8.0/lib/python3.8/site-packages/hy/compiler.py", line 1730, in compile_expression
expr = macroexpand(expr, self.module, self)
File "/home/felix/.pyenv/versions/3.8.0/lib/python3.8/site-packages/hy/macros.py", line 316, in macroexpand
fn = tree[0]
File "/home/felix/.pyenv/versions/3.8.0/lib/python3.8/site-packages/hy/models.py", line 278, in __getitem__
ret = super(HySequence, self).__getitem__(item)
IndexError: tuple index out of range
|
hy.errors.HyCompileError
|
def _format_string(self, string, rest, allow_recursion=True):
values = []
ret = Result()
while True:
# Look for the next replacement field, and get the
# plain text before it.
match = re.search(r"\{\{?|\}\}?", rest)
if match:
literal_chars = rest[: match.start()]
if match.group() == "}":
raise self._syntax_error(string, "f-string: single '}' is not allowed")
if match.group() in ("{{", "}}"):
# Doubled braces just add a single brace to the text.
literal_chars += match.group()[0]
rest = rest[match.end() :]
else:
literal_chars = rest
rest = ""
if literal_chars:
values.append(asty.Str(string, s=literal_chars))
if not rest:
break
if match.group() != "{":
continue
# Look for the end of the replacement field, allowing
# one more level of matched braces, but no deeper, and only
# if we can recurse.
match = re.match(
r"(?: \{ [^{}]* \} | [^{}]+ )* \}" if allow_recursion else r"[^{}]* \}",
rest,
re.VERBOSE,
)
if not match:
raise self._syntax_error(string, "f-string: mismatched braces")
item = rest[: match.end() - 1]
rest = rest[match.end() :]
# Parse the first form.
try:
model, item = parse_one_thing(item)
except (ValueError, LexException) as e:
raise self._syntax_error(string, "f-string: " + str(e))
# Look for a conversion character.
item = item.lstrip()
conversion = None
if item.startswith("!"):
conversion = item[1]
item = item[2:].lstrip()
# Look for a format specifier.
format_spec = None
if item.startswith(":"):
if allow_recursion:
ret += self._format_string(string, item[1:], allow_recursion=False)
format_spec = ret.force_expr
else:
format_spec = asty.Str(string, s=item[1:])
if PY36:
format_spec = asty.JoinedStr(string, values=[format_spec])
elif item:
raise self._syntax_error(string, "f-string: trailing junk in field")
# Now, having finished compiling any recursively included
# forms, we can compile the first form that we parsed.
ret += self.compile(model)
if PY36:
values.append(
asty.FormattedValue(
string,
conversion=-1 if conversion is None else ord(conversion),
format_spec=format_spec,
value=ret.force_expr,
)
)
else:
# Make an expression like:
# "{!r:{}}".format(value, format_spec)
values.append(
asty.Call(
string,
func=asty.Attribute(
string,
value=asty.Str(
string,
s="{" + ("!" + conversion if conversion else "") + ":{}}",
),
attr="format",
ctx=ast.Load(),
),
args=[ret.force_expr, format_spec or asty.Str(string, s="")],
keywords=[],
starargs=None,
kwargs=None,
)
)
return ret + (
asty.JoinedStr(string, values=values)
if PY36
else reduce(
lambda x, y: asty.BinOp(string, left=x, op=ast.Add(), right=y), values
)
)
|
def _format_string(self, string, rest, allow_recursion=True):
values = []
ret = Result()
while True:
# Look for the next replacement field, and get the
# plain text before it.
match = re.search(r"\{\{?|\}\}?", rest)
if match:
literal_chars = rest[: match.start()]
if match.group() == "}":
raise self._syntax_error(string, "f-string: single '}' is not allowed")
if match.group() in ("{{", "}}"):
# Doubled braces just add a single brace to the text.
literal_chars += match.group()[0]
rest = rest[match.end() :]
else:
literal_chars = rest
rest = ""
if literal_chars:
values.append(asty.Str(string, s=literal_chars))
if not rest:
break
if match.group() != "{":
continue
# Look for the end of the replacement field, allowing
# one more level of matched braces, but no deeper, and only
# if we can recurse.
match = re.match(
r"(?: \{ [^{}]* \} | [^{}]+ )* \}" if allow_recursion else r"[^{}]* \}",
rest,
re.VERBOSE,
)
if not match:
raise self._syntax_error(string, "f-string: mismatched braces")
item = rest[: match.end() - 1]
rest = rest[match.end() :]
# Parse the first form.
try:
model, item = parse_one_thing(item)
except (ValueError, LexException) as e:
raise self._syntax_error(string, "f-string: " + str(e))
# Look for a conversion character.
item = item.lstrip()
conversion = None
if item.startswith("!"):
conversion = item[1]
item = item[2:].lstrip()
# Look for a format specifier.
format_spec = asty.Str(string, s="")
if item.startswith(":"):
if allow_recursion:
ret += self._format_string(string, item[1:], allow_recursion=False)
format_spec = ret.force_expr
else:
format_spec = asty.Str(string, s=item[1:])
elif item:
raise self._syntax_error(string, "f-string: trailing junk in field")
# Now, having finished compiling any recursively included
# forms, we can compile the first form that we parsed.
ret += self.compile(model)
if PY36:
values.append(
asty.FormattedValue(
string,
conversion=-1 if conversion is None else ord(conversion),
format_spec=format_spec,
value=ret.force_expr,
)
)
else:
# Make an expression like:
# "{!r:{}}".format(value, format_spec)
values.append(
asty.Call(
string,
func=asty.Attribute(
string,
value=asty.Str(
string,
s="{" + ("!" + conversion if conversion else "") + ":{}}",
),
attr="format",
ctx=ast.Load(),
),
args=[ret.force_expr, format_spec],
keywords=[],
starargs=None,
kwargs=None,
)
)
return ret + (
asty.JoinedStr(string, values=values)
if PY36
else reduce(
lambda x, y: asty.BinOp(string, left=x, op=ast.Add(), right=y), values
)
)
|
https://github.com/hylang/hy/issues/1802
|
(hylearn) # hy2py minor.hy
Traceback (most recent call last):
File "/home/diego/hylearn/bin/hy2py", line 12, in <module>
sys.exit(hy2py_main())
File "/home/diego/hylearn/lib/python3.7/site-packages/hy/cmdline.py", line 690, in hy2py_main
print(astor.code_gen.to_source(_ast))
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 62, in to_source
generator.visit(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/node_util.py", line 143, in visit
return visitor(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 876, in visit_Module
self.write(*node.body)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 177, in write
visit(item)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/node_util.py", line 143, in visit
return visitor(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 370, in visit_If
self.body(node.body)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 225, in body
self.write(*statements)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 177, in write
visit(item)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/node_util.py", line 143, in visit
return visitor(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 334, in visit_FunctionDef
self.body(node.body)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 225, in body
self.write(*statements)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 177, in write
visit(item)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/node_util.py", line 143, in visit
return visitor(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 487, in visit_Return
self.conditional_write(' ', node.value)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 213, in conditional_write
self.write(*stuff)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 177, in write
visit(item)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/node_util.py", line 143, in visit
return visitor(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 532, in visit_Call
write(write_comma, arg)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 177, in write
visit(item)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/node_util.py", line 143, in visit
return visitor(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 564, in visit_JoinedStr
self._handle_string_constant(node, None, is_joined=True)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 620, in _handle_string_constant
recurse(node)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 612, in recurse
recurse(value.format_spec)
File "/home/diego/hylearn/lib/python3.7/site-packages/astor/code_gen.py", line 597, in recurse
for value in node.values:
AttributeError: 'Str' object has no attribute 'values'
|
AttributeError
|
def __init__(self, spy=False, output_fn=None, locals=None, filename="<stdin>"):
# Create a proper module for this REPL so that we can obtain it easily
# (e.g. using `importlib.import_module`).
# We let `InteractiveConsole` initialize `self.locals` when it's
# `None`.
super(HyREPL, self).__init__(locals=locals, filename=filename)
module_name = self.locals.get("__name__", "__console__")
# Make sure our newly created module is properly introduced to
# `sys.modules`, and consistently use its namespace as `self.locals`
# from here on.
self.module = sys.modules.setdefault(module_name, types.ModuleType(module_name))
self.module.__dict__.update(self.locals)
self.locals = self.module.__dict__
# Load cmdline-specific macros.
require("hy.cmdline", self.module, assignments="ALL")
self.hy_compiler = HyASTCompiler(self.module)
self.compile = HyCommandCompiler(self.module, self.ast_callback, self.hy_compiler)
self.spy = spy
self.last_value = None
if output_fn is None:
self.output_fn = repr
elif callable(output_fn):
self.output_fn = output_fn
else:
if "." in output_fn:
parts = [mangle(x) for x in output_fn.split(".")]
module, f = ".".join(parts[:-1]), parts[-1]
self.output_fn = getattr(importlib.import_module(module), f)
else:
self.output_fn = __builtins__[mangle(output_fn)]
# Pre-mangle symbols for repl recent results: *1, *2, *3
self._repl_results_symbols = [mangle("*{}".format(i + 1)) for i in range(3)]
self.locals.update({sym: None for sym in self._repl_results_symbols})
|
def __init__(self, spy=False, output_fn=None, locals=None, filename="<input>"):
super(HyREPL, self).__init__(locals=locals, filename=filename)
# Create a proper module for this REPL so that we can obtain it easily
# (e.g. using `importlib.import_module`).
# Also, make sure it's properly introduced to `sys.modules` and
# consistently use its namespace as `locals` from here on.
module_name = self.locals.get("__name__", "__console__")
self.module = sys.modules.setdefault(module_name, types.ModuleType(module_name))
self.module.__dict__.update(self.locals)
self.locals = self.module.__dict__
# Load cmdline-specific macros.
require("hy.cmdline", module_name, assignments="ALL")
self.hy_compiler = HyASTCompiler(self.module)
self.spy = spy
if output_fn is None:
self.output_fn = repr
elif callable(output_fn):
self.output_fn = output_fn
else:
if "." in output_fn:
parts = [mangle(x) for x in output_fn.split(".")]
module, f = ".".join(parts[:-1]), parts[-1]
self.output_fn = getattr(importlib.import_module(module), f)
else:
self.output_fn = __builtins__[mangle(output_fn)]
# Pre-mangle symbols for repl recent results: *1, *2, *3
self._repl_results_symbols = [mangle("*{}".format(i + 1)) for i in range(3)]
self.locals.update({sym: None for sym in self._repl_results_symbols})
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def ast_callback(self, exec_ast, eval_ast):
if self.spy:
try:
# Mush the two AST chunks into a single module for
# conversion into Python.
new_ast = ast.Module(exec_ast.body + [ast.Expr(eval_ast.body)])
print(astor.to_source(new_ast))
except Exception:
msg = "Exception in AST callback:\n{}\n".format(traceback.format_exc())
self.write(msg)
|
def ast_callback(self, main_ast, expr_ast):
if self.spy:
# Mush the two AST chunks into a single module for
# conversion into Python.
new_ast = ast.Module(main_ast.body + [ast.Expr(expr_ast.body)])
print(astor.to_source(new_ast))
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def runsource(self, source, filename="<stdin>", symbol="exec"):
try:
res = super(HyREPL, self).runsource(source, filename, symbol)
except (HyMacroExpansionError, HyRequireError):
# We need to handle these exceptions ourselves, because the base
# method only handles `OverflowError`, `SyntaxError` and
# `ValueError`.
self.showsyntaxerror(filename)
return False
except HyLanguageError:
# Our compiler will also raise `TypeError`s
self.showtraceback()
return False
# Shift exisitng REPL results
if not res:
next_result = self.last_value
for sym in self._repl_results_symbols:
self.locals[sym], next_result = next_result, self.locals[sym]
# Print the value.
if self.print_last_value:
try:
output = self.output_fn(self.last_value)
except Exception:
self.showtraceback()
return False
print(output)
return res
|
def runsource(self, source, filename="<input>", symbol="single"):
try:
do = hy_parse(source, filename=filename)
except PrematureEndOfInput:
return True
except HySyntaxError as e:
self.showsyntaxerror(filename=filename)
return False
try:
# Our compiler doesn't correspond to a real, fixed source file, so
# we need to [re]set these.
self.hy_compiler.filename = filename
self.hy_compiler.source = source
value = hy_eval(
do,
self.locals,
self.module,
self.ast_callback,
compiler=self.hy_compiler,
filename=filename,
source=source,
)
except SystemExit:
raise
except Exception as e:
self.showtraceback()
return False
if value is not None:
# Shift exisitng REPL results
next_result = value
for sym in self._repl_results_symbols:
self.locals[sym], next_result = next_result, self.locals[sym]
# Print the value.
try:
output = self.output_fn(value)
except Exception:
self.showtraceback()
return False
print(output)
return False
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def run_command(source, filename=None):
__main__ = importlib.import_module("__main__")
require("hy.cmdline", __main__, assignments="ALL")
try:
tree = hy_parse(source, filename=filename)
except HyLanguageError:
hy_exc_handler(*sys.exc_info())
return 1
with filtered_hy_exceptions():
hy_eval(tree, None, __main__, filename=filename, source=source)
return 0
|
def run_command(source, filename=None):
tree = hy_parse(source, filename=filename)
__main__ = importlib.import_module("__main__")
require("hy.cmdline", __main__, assignments="ALL")
with filtered_hy_exceptions():
hy_eval(tree, None, __main__, filename=filename, source=source)
return 0
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def run_icommand(source, **kwargs):
if os.path.exists(source):
# Emulate Python cmdline behavior by setting `sys.path` relative
# to the executed file's location.
if sys.path[0] == "":
sys.path[0] = os.path.realpath(os.path.split(source)[0])
else:
sys.path.insert(0, os.path.split(source)[0])
with io.open(source, "r", encoding="utf-8") as f:
source = f.read()
filename = source
else:
filename = "<string>"
hr = HyREPL(**kwargs)
with filtered_hy_exceptions():
res = hr.runsource(source, filename=filename)
# If the command was prematurely ended, show an error (just like Python
# does).
if res:
hy_exc_handler(sys.last_type, sys.last_value, sys.last_traceback)
return run_repl(hr)
|
def run_icommand(source, **kwargs):
if os.path.exists(source):
# Emulate Python cmdline behavior by setting `sys.path` relative
# to the executed file's location.
if sys.path[0] == "":
sys.path[0] = os.path.realpath(os.path.split(source)[0])
else:
sys.path.insert(0, os.path.split(source)[0])
with io.open(source, "r", encoding="utf-8") as f:
source = f.read()
filename = source
else:
filename = "<input>"
with filtered_hy_exceptions():
hr = HyREPL(**kwargs)
hr.runsource(source, filename=filename, symbol="single")
return run_repl(hr)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def cmdline_handler(scriptname, argv):
parser = argparse.ArgumentParser(
prog="hy",
usage=USAGE,
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=EPILOG,
)
parser.add_argument("-c", dest="command", help="program passed in as a string")
parser.add_argument("-m", dest="mod", help="module to run, passed in as a string")
parser.add_argument(
"-E", action="store_true", help="ignore PYTHON* environment variables"
)
parser.add_argument(
"-B",
action="store_true",
help="don't write .py[co] files on import; also PYTHONDONTWRITEBYTECODE=x",
)
parser.add_argument(
"-i", dest="icommand", help="program passed in as a string, then stay in REPL"
)
parser.add_argument(
"--spy",
action="store_true",
help="print equivalent Python code before executing",
)
parser.add_argument(
"--repl-output-fn",
help="function for printing REPL output (e.g., hy.contrib.hy-repr.hy-repr)",
)
parser.add_argument("-v", "--version", action="version", version=VERSION)
# this will contain the script/program name and any arguments for it.
parser.add_argument("args", nargs=argparse.REMAINDER, help=argparse.SUPPRESS)
# Get the path of the Hy cmdline executable and swap it with
# `sys.executable` (saving the original, just in case).
# XXX: The `__main__` module will also have `__file__` set to the
# entry-point script. Currently, I don't see an immediate problem, but
# that's not how the Python cmdline works.
hy.executable = argv[0]
hy.sys_executable = sys.executable
sys.executable = hy.executable
# Need to split the args. If using "-m" all args after the MOD are sent to
# the module in sys.argv.
module_args = []
if "-m" in argv:
mloc = argv.index("-m")
if len(argv) > mloc + 2:
module_args = argv[mloc + 2 :]
argv = argv[: mloc + 2]
options = parser.parse_args(argv[1:])
if options.E:
# User did "hy -E ..."
_remove_python_envs()
if options.B:
sys.dont_write_bytecode = True
if options.command:
# User did "hy -c ..."
return run_command(options.command, filename="<string>")
if options.mod:
# User did "hy -m ..."
sys.argv = [sys.argv[0]] + options.args + module_args
runpy.run_module(options.mod, run_name="__main__", alter_sys=True)
return 0
if options.icommand:
# User did "hy -i ..."
return run_icommand(
options.icommand, spy=options.spy, output_fn=options.repl_output_fn
)
if options.args:
if options.args[0] == "-":
# Read the program from stdin
return run_command(sys.stdin.read(), filename="<stdin>")
else:
# User did "hy <filename>"
filename = options.args[0]
# Emulate Python cmdline behavior by setting `sys.path` relative
# to the executed file's location.
if sys.path[0] == "":
sys.path[0] = os.path.realpath(os.path.split(filename)[0])
else:
sys.path.insert(0, os.path.split(filename)[0])
try:
sys.argv = options.args
with filtered_hy_exceptions():
runhy.run_path(filename, run_name="__main__")
return 0
except FileNotFoundError as e:
print(
"hy: Can't open file '{0}': [Errno {1}] {2}".format(
e.filename, e.errno, e.strerror
),
file=sys.stderr,
)
sys.exit(e.errno)
except HyLanguageError:
hy_exc_handler(*sys.exc_info())
sys.exit(1)
# User did NOTHING!
return run_repl(spy=options.spy, output_fn=options.repl_output_fn)
|
def cmdline_handler(scriptname, argv):
parser = argparse.ArgumentParser(
prog="hy",
usage=USAGE,
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=EPILOG,
)
parser.add_argument("-c", dest="command", help="program passed in as a string")
parser.add_argument("-m", dest="mod", help="module to run, passed in as a string")
parser.add_argument(
"-E", action="store_true", help="ignore PYTHON* environment variables"
)
parser.add_argument(
"-B",
action="store_true",
help="don't write .py[co] files on import; also PYTHONDONTWRITEBYTECODE=x",
)
parser.add_argument(
"-i", dest="icommand", help="program passed in as a string, then stay in REPL"
)
parser.add_argument(
"--spy",
action="store_true",
help="print equivalent Python code before executing",
)
parser.add_argument(
"--repl-output-fn",
help="function for printing REPL output (e.g., hy.contrib.hy-repr.hy-repr)",
)
parser.add_argument("-v", "--version", action="version", version=VERSION)
# this will contain the script/program name and any arguments for it.
parser.add_argument("args", nargs=argparse.REMAINDER, help=argparse.SUPPRESS)
# Get the path of the Hy cmdline executable and swap it with
# `sys.executable` (saving the original, just in case).
# XXX: The `__main__` module will also have `__file__` set to the
# entry-point script. Currently, I don't see an immediate problem, but
# that's not how the Python cmdline works.
hy.executable = argv[0]
hy.sys_executable = sys.executable
sys.executable = hy.executable
# Need to split the args. If using "-m" all args after the MOD are sent to
# the module in sys.argv.
module_args = []
if "-m" in argv:
mloc = argv.index("-m")
if len(argv) > mloc + 2:
module_args = argv[mloc + 2 :]
argv = argv[: mloc + 2]
options = parser.parse_args(argv[1:])
if options.E:
# User did "hy -E ..."
_remove_python_envs()
if options.B:
sys.dont_write_bytecode = True
if options.command:
# User did "hy -c ..."
return run_command(options.command, filename="<string>")
if options.mod:
# User did "hy -m ..."
sys.argv = [sys.argv[0]] + options.args + module_args
runpy.run_module(options.mod, run_name="__main__", alter_sys=True)
return 0
if options.icommand:
# User did "hy -i ..."
return run_icommand(
options.icommand, spy=options.spy, output_fn=options.repl_output_fn
)
if options.args:
if options.args[0] == "-":
# Read the program from stdin
return run_command(sys.stdin.read(), filename="<stdin>")
else:
# User did "hy <filename>"
filename = options.args[0]
# Emulate Python cmdline behavior by setting `sys.path` relative
# to the executed file's location.
if sys.path[0] == "":
sys.path[0] = os.path.realpath(os.path.split(filename)[0])
else:
sys.path.insert(0, os.path.split(filename)[0])
try:
sys.argv = options.args
with filtered_hy_exceptions():
runhy.run_path(filename, run_name="__main__")
return 0
except FileNotFoundError as e:
print(
"hy: Can't open file '{0}': [Errno {1}] {2}".format(
e.filename, e.errno, e.strerror
),
file=sys.stderr,
)
sys.exit(e.errno)
# User did NOTHING!
return run_repl(spy=options.spy, output_fn=options.repl_output_fn)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def hy2py_main():
import platform
options = dict(
prog="hy2py",
usage="%(prog)s [options] [FILE]",
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser = argparse.ArgumentParser(**options)
parser.add_argument(
"FILE",
type=str,
nargs="?",
help='Input Hy code (use STDIN if "-" or not provided)',
)
parser.add_argument(
"--with-source",
"-s",
action="store_true",
help="Show the parsed source structure",
)
parser.add_argument(
"--with-ast", "-a", action="store_true", help="Show the generated AST"
)
parser.add_argument(
"--without-python",
"-np",
action="store_true",
help=("Do not show the Python code generated from the AST"),
)
options = parser.parse_args(sys.argv[1:])
if options.FILE is None or options.FILE == "-":
filename = "<stdin>"
source = sys.stdin.read()
else:
filename = options.FILE
with io.open(options.FILE, "r", encoding="utf-8") as source_file:
source = source_file.read()
with filtered_hy_exceptions():
hst = hy_parse(source, filename=filename)
if options.with_source:
# need special printing on Windows in case the
# codepage doesn't support utf-8 characters
if PY3 and platform.system() == "Windows":
for h in hst:
try:
print(h)
except:
print(str(h).encode("utf-8"))
else:
print(hst)
print()
print()
with filtered_hy_exceptions():
_ast = hy_compile(hst, "__main__", filename=filename, source=source)
if options.with_ast:
if PY3 and platform.system() == "Windows":
_print_for_windows(astor.dump_tree(_ast))
else:
print(astor.dump_tree(_ast))
print()
print()
if not options.without_python:
if PY3 and platform.system() == "Windows":
_print_for_windows(astor.code_gen.to_source(_ast))
else:
print(astor.code_gen.to_source(_ast))
parser.exit(0)
|
def hy2py_main():
import platform
options = dict(
prog="hy2py",
usage="%(prog)s [options] [FILE]",
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser = argparse.ArgumentParser(**options)
parser.add_argument(
"FILE",
type=str,
nargs="?",
help='Input Hy code (use STDIN if "-" or not provided)',
)
parser.add_argument(
"--with-source",
"-s",
action="store_true",
help="Show the parsed source structure",
)
parser.add_argument(
"--with-ast", "-a", action="store_true", help="Show the generated AST"
)
parser.add_argument(
"--without-python",
"-np",
action="store_true",
help=("Do not show the Python code generated from the AST"),
)
options = parser.parse_args(sys.argv[1:])
if options.FILE is None or options.FILE == "-":
source = sys.stdin.read()
with filtered_hy_exceptions():
hst = hy_parse(source, filename="<stdin>")
else:
with (
filtered_hy_exceptions(),
io.open(options.FILE, "r", encoding="utf-8") as source_file,
):
source = source_file.read()
hst = hy_parse(source, filename=options.FILE)
if options.with_source:
# need special printing on Windows in case the
# codepage doesn't support utf-8 characters
if PY3 and platform.system() == "Windows":
for h in hst:
try:
print(h)
except:
print(str(h).encode("utf-8"))
else:
print(hst)
print()
print()
with filtered_hy_exceptions():
_ast = hy_compile(hst, "__main__")
if options.with_ast:
if PY3 and platform.system() == "Windows":
_print_for_windows(astor.dump_tree(_ast))
else:
print(astor.dump_tree(_ast))
print()
print()
if not options.without_python:
if PY3 and platform.system() == "Windows":
_print_for_windows(astor.code_gen.to_source(_ast))
else:
print(astor.code_gen.to_source(_ast))
parser.exit(0)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def __call__(self, source, filename="<input>", symbol="single"):
try:
hy_ast = hy_parse(source, filename=filename)
root_ast = ast.Interactive if symbol == "single" else ast.Module
# Our compiler doesn't correspond to a real, fixed source file, so
# we need to [re]set these.
self.hy_compiler.filename = filename
self.hy_compiler.source = source
exec_ast, eval_ast = hy_compile(
hy_ast,
self.module,
root=root_ast,
get_expr=True,
compiler=self.hy_compiler,
filename=filename,
source=source,
)
if self.ast_callback:
self.ast_callback(exec_ast, eval_ast)
exec_code = ast_compile(exec_ast, filename, symbol)
eval_code = ast_compile(eval_ast, filename, "eval")
return exec_code, eval_code
except PrematureEndOfInput:
# Save these so that we can reraise/display when an incomplete
# interactive command is given at the prompt.
sys.last_type, sys.last_value, sys.last_traceback = sys.exc_info()
return None
|
def __call__(self, code=None):
try:
sys.stdin.close()
except:
pass
raise SystemExit(code)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def compile(self, tree):
if tree is None:
return Result()
try:
ret = self.compile_atom(tree)
self.update_imports(ret)
return ret
except HyCompileError:
# compile calls compile, so we're going to have multiple raise
# nested; so let's re-raise this exception, let's not wrap it in
# another HyCompileError!
raise
except HyLanguageError as e:
# These are expected errors that should be passed to the user.
reraise(type(e), e, sys.exc_info()[2])
except Exception as e:
# These are unexpected errors that will--hopefully--never be seen
# by the user.
f_exc = traceback.format_exc()
exc_msg = "Internal Compiler Bug 😱\n⤷ {}".format(f_exc)
reraise(HyCompileError, HyCompileError(exc_msg), sys.exc_info()[2])
|
def compile(self, tree):
if tree is None:
return Result()
try:
ret = self.compile_atom(tree)
self.update_imports(ret)
return ret
except HyCompileError:
# compile calls compile, so we're going to have multiple raise
# nested; so let's re-raise this exception, let's not wrap it in
# another HyCompileError!
raise
except HyTypeError as e:
reraise(type(e), e, None)
except Exception as e:
f_exc = traceback.format_exc()
exc_msg = "Internal Compiler Bug 😱\n⤷ {}".format(f_exc)
reraise(HyCompileError, HyCompileError(exc_msg), sys.exc_info()[2])
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def _syntax_error(self, expr, message):
return HySyntaxError(message, expr, self.filename, self.source)
|
def _syntax_error(self, expr, message):
return HyTypeError(message, self.filename, expr, self.source)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def __init__(
self, message, expression=None, filename=None, source=None, lineno=1, colno=1
):
"""
Parameters
----------
message: str
The message to display for this error.
expression: HyObject, optional
The Hy expression generating this error.
filename: str, optional
The filename for the source code generating this error.
Expression-provided information will take precedence of this value.
source: str, optional
The actual source code generating this error. Expression-provided
information will take precedence of this value.
lineno: int, optional
The line number of the error. Expression-provided information will
take precedence of this value.
colno: int, optional
The column number of the error. Expression-provided information
will take precedence of this value.
"""
self.msg = message
self.compute_lineinfo(expression, filename, source, lineno, colno)
if isinstance(self, SyntaxError):
syntax_error_args = (self.filename, self.lineno, self.offset, self.text)
super(HyLanguageError, self).__init__(message, syntax_error_args)
else:
super(HyLanguageError, self).__init__(message)
|
def __init__(self, message, *args):
super(HyLanguageError, self).__init__(message, *args)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def hy_exc_handler(exc_type, exc_value, exc_traceback):
"""A `sys.excepthook` handler that uses `hy_exc_filter` to
remove internal Hy frames from a traceback print-out.
"""
if os.environ.get("HY_DEBUG", False):
return sys.__excepthook__(exc_type, exc_value, exc_traceback)
try:
output = hy_exc_filter(exc_type, exc_value, exc_traceback)
sys.stderr.write(output)
sys.stderr.flush()
except Exception:
sys.__excepthook__(exc_type, exc_value, exc_traceback)
|
def hy_exc_handler(exc_type, exc_value, exc_traceback):
"""Produce exceptions print-outs with all frames originating from the
modules in `_tb_hidden_modules` filtered out.
The frames are actually filtered by each module's filename and only when a
subclass of `HyLanguageError` is emitted.
This does not remove the frames from the actual tracebacks, so debugging
will show everything.
"""
try:
# frame = (filename, line number, function name*, text)
new_tb = [
frame
for frame in traceback.extract_tb(exc_traceback)
if not (
frame[0].replace(".pyc", ".py") in _tb_hidden_modules
or os.path.dirname(frame[0]) in _tb_hidden_modules
)
]
lines = traceback.format_list(new_tb)
if lines:
lines.insert(0, "Traceback (most recent call last):\n")
lines.extend(traceback.format_exception_only(exc_type, exc_value))
output = "".join(lines)
sys.stderr.write(output)
sys.stderr.flush()
except Exception:
sys.__excepthook__(exc_type, exc_value, exc_traceback)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def __init__(
self, message, expression=None, filename=None, source=None, lineno=1, colno=1
):
"""
Parameters
----------
message: str
The message to display for this error.
expression: HyObject, optional
The Hy expression generating this error.
filename: str, optional
The filename for the source code generating this error.
Expression-provided information will take precedence of this value.
source: str, optional
The actual source code generating this error. Expression-provided
information will take precedence of this value.
lineno: int, optional
The line number of the error. Expression-provided information will
take precedence of this value.
colno: int, optional
The column number of the error. Expression-provided information
will take precedence of this value.
"""
self.msg = message
self.compute_lineinfo(expression, filename, source, lineno, colno)
if isinstance(self, SyntaxError):
syntax_error_args = (self.filename, self.lineno, self.offset, self.text)
super(HyLanguageError, self).__init__(message, syntax_error_args)
else:
super(HyLanguageError, self).__init__(message)
|
def __init__(self, message, filename=None, lineno=-1, colno=-1, source=None):
"""
Parameters
----------
message: str
The exception's message.
filename: str, optional
The filename for the source code generating this error.
lineno: int, optional
The line number of the error.
colno: int, optional
The column number of the error.
source: str, optional
The actual source code generating this error.
"""
self.message = message
self.filename = filename
self.lineno = lineno
self.colno = colno
self.source = source
super(HySyntaxError, self).__init__(
message,
# The builtin `SyntaxError` needs a
# tuple.
(filename, lineno, colno, source),
)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def __str__(self):
"""Provide an exception message that includes SyntaxError-like source
line information when available.
"""
global _hy_colored_errors
# Syntax errors are special and annotate the traceback (instead of what
# we would do in the message that follows the traceback).
if isinstance(self, SyntaxError):
return super(HyLanguageError, self).__str__()
# When there isn't extra source information, use the normal message.
if not isinstance(self, SyntaxError) and not self.text:
return super(HyLanguageError, self).__str__()
# Re-purpose Python's builtin syntax error formatting.
output = traceback.format_exception_only(
SyntaxError,
SyntaxError(self.msg, (self.filename, self.lineno, self.offset, self.text)),
)
arrow_idx, _ = next(
((i, x) for i, x in enumerate(output) if x.strip() == "^"), (None, None)
)
if arrow_idx:
msg_idx = arrow_idx + 1
else:
msg_idx, _ = next(
(i, x) for i, x in enumerate(output) if x.startswith("SyntaxError: ")
)
# Get rid of erroneous error-type label.
output[msg_idx] = re.sub("^SyntaxError: ", "", output[msg_idx])
# Extend the text arrow, when given enough source info.
if arrow_idx and self.arrow_offset:
output[arrow_idx] = "{}{}^\n".format(
output[arrow_idx].rstrip("\n"), "-" * (self.arrow_offset - 1)
)
if _hy_colored_errors:
from clint.textui import colored
output[msg_idx:] = [colored.yellow(o) for o in output[msg_idx:]]
if arrow_idx:
output[arrow_idx] = colored.green(output[arrow_idx])
for idx, line in enumerate(output[::msg_idx]):
if line.strip().startswith('File "{}", line'.format(self.filename)):
output[idx] = colored.red(line)
# This resulting string will come after a "<class-name>:" prompt, so
# put it down a line.
output.insert(0, "\n")
# Avoid "...expected str instance, ColoredString found"
return reduce(lambda x, y: x + y, output)
|
def __str__(self):
global _hy_colored_errors
output = traceback.format_exception_only(SyntaxError, SyntaxError(*self.args))
if _hy_colored_errors:
from hy.errors import colored
output[-1] = colored.yellow(output[-1])
if len(self.source) > 0:
output[-2] = colored.green(output[-2])
for line in output[::-2]:
if line.strip().startswith('File "{}", line'.format(self.filename)):
break
output[-3] = colored.red(output[-3])
# Avoid "...expected str instance, ColoredString found"
return reduce(lambda x, y: x + y, output)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def hy_parse(source, filename="<string>"):
"""Parse a Hy source string.
Parameters
----------
source: string
Source code to parse.
filename: string, optional
File name corresponding to source. Defaults to "<string>".
Returns
-------
out : HyExpression
"""
_source = re.sub(r"\A#!.*", "", source)
res = HyExpression([HySymbol("do")] + tokenize(_source + "\n", filename=filename))
res.source = source
res.filename = filename
return res
|
def hy_parse(source, filename="<string>"):
"""Parse a Hy source string.
Parameters
----------
source: string
Source code to parse.
filename: string, optional
File name corresponding to source. Defaults to "<string>".
Returns
-------
out : HyExpression
"""
_source = re.sub(r"\A#!.*", "", source)
try:
res = HyExpression(
[HySymbol("do")] + tokenize(_source + "\n", filename=filename)
)
res.source = source
res.filename = filename
return res
except HySyntaxError as e:
reraise(type(e), e, None)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
def tokenize(source, filename=None):
"""Tokenize a Lisp file or string buffer into internal Hy objects.
Parameters
----------
source: str
The source to tokenize.
filename: str, optional
The filename corresponding to `source`.
"""
from hy.lex.lexer import lexer
from hy.lex.parser import parser
from rply.errors import LexingError
try:
return parser.parse(lexer.lex(source), state=ParserState(source, filename))
except LexingError as e:
pos = e.getsourcepos()
raise LexException(
"Could not identify the next token.",
None,
filename,
source,
max(pos.lineno, 1),
max(pos.colno, 1),
)
except LexException as e:
raise e
|
def tokenize(source, filename=None):
"""Tokenize a Lisp file or string buffer into internal Hy objects.
Parameters
----------
source: str
The source to tokenize.
filename: str, optional
The filename corresponding to `source`.
"""
from hy.lex.lexer import lexer
from hy.lex.parser import parser
from rply.errors import LexingError
try:
return parser.parse(lexer.lex(source), state=ParserState(source, filename))
except LexingError as e:
pos = e.getsourcepos()
raise LexException(
"Could not identify the next token.",
filename,
pos.lineno,
pos.colno,
source,
)
|
https://github.com/hylang/hy/issues/1486
|
Traceback (most recent call last):
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/importer.py", line 180, in hy_eval
_ast, expr = hy_compile(hytree, module_name, get_expr=True)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 2213, in hy_compile
result = compiler.compile(tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 819, in compile_do
return self._compile_branch(expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 873, in compile_try_expression
name)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1002, in _compile_catch_expression
body = self._compile_branch(expr)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in _compile_branch
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 318, in _branch
results = list(results)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 545, in <genexpr>
return _branch(self.compile(expr) for expr in exprs)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 372, in checker
return fn(self, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 858, in compile_try_expression
body += self.compile(expr.pop(0))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 472, in compile
raise_empty(HyCompileError, e, sys.exc_info()[2])
File "<string>", line 1, in raise_empty
hy.errors.HyCompileError: Internal Compiler Bug 😱
⤷ ImportError: cannot require names: [HySymbol('let')]
Compilation traceback:
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 460, in compile
ret = self.compile_atom(_type, tree)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1731, in compile_expression
ret = self.compile_atom(fn, expression)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 447, in compile_atom
else _compile_table[atom_type](self, atom))
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/compiler.py", line 1486, in compile_require
require(module, self.module_name, assignments=assignments)
File "/home/johnzhuang/.virtualenvs/hy/lib/python3.6/site-packages/hy/macros.py", line 106, in require
raise ImportError("cannot require names: " + repr(list(unseen)))
|
hy.errors.HyCompileError
|
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