keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_files_managment.py | .py | 2,381 | 54 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Files input and output.
"""
import os
from pymod... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_elements_loading.py | .py | 31,180 | 656 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Module implementing a series of methods which allo... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_elements_interactions.py | .py | 18,021 | 410 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Methods to manipulate PyMod elements within the pl... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_pymol_interactions.py | .py | 5,827 | 126 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Interactions of PyMod with PyMOL.
"""
import os
f... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_workspaces.py | .py | 8,643 | 218 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
PyMod sessions managment.
"""
import os
import sh... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_main_menu_commands.py | .py | 44,228 | 983 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Commands executed when interacting with the PyMod ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_external.py | .py | 2,083 | 56 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Interactions with external tools.
"""
import os
i... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_main/_development.py | .py | 8,800 | 217 | """
Module for development.
"""
import os
import sys
import urllib.request
import random
import shutil
import importlib
from pymod_lib.pymod_seq.seq_star_alignment import global_pairwise_alignment_cs
class PyMod_development:
"""
Methods used when developing or testing PyMod.
"""
def _launch_develop... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_externals/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_externals/hhsuite/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_externals/hhsuite/hhmakemodel.py | .py | 23,951 | 705 | #!/usr/bin/env python
from pymod_lib.pymod_externals.hhsuite.hh_reader import read_result
from copy import deepcopy
import re, os, sys, tempfile, glob
from operator import itemgetter # hzhu
from itertools import groupby # hzhu
EMPTY = '*'
GAP = '-'
DEBUG_MODE = False
class Gap:
""" A gap is a continuous st... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_externals/hhsuite/hh_reader.py | .py | 7,178 | 205 | #!/usr/bin/env python
"""
Parser for hhr result files created with hhblits|hhsearch|hhalign -o <hhr_file>
"""
import sys
from collections import namedtuple
__author__ = 'Markus Meier (markus.meier@mpibpc.mpg.de)'
__version__ = '1.0'
__license__ = "GPL-3"
hhr_alignment = namedtuple('hhr_alignment', ['query_id', '... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/shared_gui_components_qt.py | .py | 33,063 | 1,010 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Common functions and variables used by the Qt GUI ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/pymod_table.py | .py | 4,840 | 133 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
import csv
import warnings
from pymol.Qt import QtCor... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/specific_gui_components_qt.py | .py | 21,533 | 559 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Classes for PyQt widgets used in specific parts of... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/_header_entry_qt.py | .py | 39,691 | 781 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Module implementing the widgets showed in the left... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/_sequence_text_qt.py | .py | 25,703 | 583 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Module implementing the widgets showing the sequen... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/_main_menu_qt.py | .py | 23,319 | 406 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
A module for building the Qt PyMod main window men... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/main_window_qt.py | .py | 45,008 | 1,076 | # Copyright 2020 by Giacomo Janson, Alessandro Paiardini. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
This module implements the m... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/_element_widgets_qt.py | .py | 17,313 | 456 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Module implementing the "widget group" class for a... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/aqua/qsshelper.py | .py | 921 | 27 | import os
import re
class QSSHelper:
def __init__(self):
pass
@staticmethod
def open_qss(path):
"""
opens a Qt stylesheet with a path relative to the project
Note: it changes the urls in the Qt stylesheet (in memory), and makes these urls relative to the project
W... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_gui/main_window/aqua/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pymod_plot_qt.py | .py | 41,762 | 1,014 | # Copyright 2020 by Giacomo Janson. All rights reserved.
# This code is part of the PyMod package and governed by its license. Please
# see the LICENSE file that should have been included as part of this package
# or the main __init__.py file in the pymod3 folder.
"""
Module for a PyQt window with plots built with the... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/pgcollections.py | .py | 15,679 | 485 | # -*- coding: utf-8 -*-
"""
advancedTypes.py - Basic data structures not included with python
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
Includes:
- OrderedDict - Dictionary which preserves the order of its elements
- BiDict, ReverseDict - Bi-direction... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/SRTTransform.py | .py | 7,960 | 261 | # -*- coding: utf-8 -*-
from .Qt import QtCore, QtGui
from .Point import Point
import numpy as np
class SRTTransform(QtGui.QTransform):
"""Transform that can always be represented as a combination of 3 matrices: scale * rotate * translate
This transform has no shear; angles are always preserved.
"""
d... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/Transform3D.py | .py | 1,867 | 53 | # -*- coding: utf-8 -*-
from .Qt import QtCore, QtGui
from . import functions as fn
from .Vector import Vector
import numpy as np
class Transform3D(QtGui.QMatrix4x4):
"""
Extension of QMatrix4x4 with some helpful methods added.
"""
def __init__(self, *args):
if len(args) == 1:
if i... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/ordereddict.py | .py | 4,532 | 132 | # Copyright (c) 2009 Raymond Hettinger
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish,... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/python2_3.py | .py | 542 | 26 | # -*- coding: utf-8 -*-
"""
Helper functions that smooth out the differences between python 2 and 3.
"""
import sys
def asUnicode(x):
if sys.version_info[0] == 2:
if isinstance(x, unicode):
return x
elif isinstance(x, str):
return x.decode('UTF-8')
else:
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/ptime.py | .py | 1,039 | 38 | # -*- coding: utf-8 -*-
"""
ptime.py - Precision time function made os-independent (should have been taken care of by python)
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
"""
import sys
if sys.version_info[0] < 3:
from time import clock
from time i... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/Qt.py | .py | 10,195 | 349 | # -*- coding: utf-8 -*-
"""
This module exists to smooth out some of the differences between PySide and PyQt4:
* Automatically import either PyQt4 or PySide depending on availability
* Allow to import QtCore/QtGui pyqtgraph.Qt without specifying which Qt wrapper
you want to use.
* Declare QtCore.Signal, .Slot in PyQ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/debug.py | .py | 40,699 | 1,209 | # -*- coding: utf-8 -*-
"""
debug.py - Functions to aid in debugging
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
"""
from __future__ import print_function
import sys, traceback, time, gc, re, types, weakref, inspect, os, cProfile, threading
from . import p... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/units.py | .py | 1,402 | 64 | # -*- coding: utf-8 -*-
## Very simple unit support:
## - creates variable names like 'mV' and 'kHz'
## - the value assigned to the variable corresponds to the scale prefix
## (mV = 0.001)
## - the actual units are purely cosmetic for making code clearer:
##
## x = 20*pA is identical to x = 20*1e-12
#... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/Point.py | .py | 4,633 | 162 | # -*- coding: utf-8 -*-
"""
Point.py - Extension of QPointF which adds a few missing methods.
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
"""
from .Qt import QtCore
import numpy as np
def clip(x, mn, mx):
if x > mx:
return mx
if x < mn:
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exceptionHandling.py | .py | 4,149 | 107 | # -*- coding: utf-8 -*-
"""This module installs a wrapper around sys.excepthook which allows multiple
new exception handlers to be registered.
Optionally, the wrapper also stops exceptions from causing long-term storage
of local stack frames. This has two major effects:
- Unhandled exceptions will no longer cause ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/__init__.py | .py | 18,237 | 473 | # -*- coding: utf-8 -*-
"""
PyQtGraph - Scientific Graphics and GUI Library for Python
www.pyqtgraph.org
"""
__version__ = '0.11.0.dev0'
### import all the goodies and add some helper functions for easy CLI use
## 'Qt' is a local module; it is intended mainly to cover up the differences
## between PyQt4 and PySide.
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/colormap.py | .py | 9,998 | 260 | import numpy as np
from .Qt import QtGui, QtCore
from .python2_3 import basestring
from .functions import mkColor
class ColorMap(object):
"""
A ColorMap defines a relationship between a scalar value and a range of colors.
ColorMaps are commonly used for false-coloring monochromatic images, coloring
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/graphicsWindows.py | .py | 2,738 | 86 | # -*- coding: utf-8 -*-
"""
DEPRECATED: The classes below are convenience classes that create a new window
containting a single, specific widget. These classes are now unnecessary because
it is possible to place any widget into its own window by simply calling its
show() method.
"""
from .Qt import QtCore, QtGui, mkQ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/WidgetGroup.py | .py | 10,004 | 286 | # -*- coding: utf-8 -*-
"""
WidgetGroup.py - WidgetGroup class for easily managing lots of Qt widgets
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
This class addresses the problem of having to save and restore the state
of a large group of widgets.
"""
fro... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/PlotData.py | .py | 1,572 | 56 |
class PlotData(object):
"""
Class used for managing plot data
- allows data sharing between multiple graphics items (curve, scatter, graph..)
- each item may define the columns it needs
- column groupings ('pos' or x, y, z)
- efficiently appendable
- log, fft transformations
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/functions.py | .py | 96,082 | 2,510 | # -*- coding: utf-8 -*-
"""
functions.py - Miscellaneous functions with no other home
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
"""
from __future__ import division
import warnings
import numpy as np
import decimal, re
import ctypes
import sys, struct
from... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/SRTTransform3D.py | .py | 10,879 | 316 | # -*- coding: utf-8 -*-
from .Qt import QtCore, QtGui
from .Vector import Vector
from .Transform3D import Transform3D
from .Vector import Vector
import numpy as np
class SRTTransform3D(Transform3D):
"""4x4 Transform matrix that can always be represented as a combination of 3 matrices: scale * rotate * translate
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/configfile.py | .py | 6,853 | 217 | # -*- coding: utf-8 -*-
"""
configfile.py - Human-readable text configuration file library
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
Used for reading and writing dictionary objects to a python-like configuration
file format. Data structures may be nested ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/Vector.py | .py | 2,932 | 87 | # -*- coding: utf-8 -*-
"""
Vector.py - Extension of QVector3D which adds a few missing methods.
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
"""
from .Qt import QtGui, QtCore, QT_LIB
import numpy as np
class Vector(QtGui.QVector3D):
"""Extension of QVe... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/reload.py | .py | 19,304 | 572 | # -*- coding: utf-8 -*-
"""
Magic Reload Library
Luke Campagnola 2010
Python reload function that actually works (the way you expect it to)
- No re-importing necessary
- Modules can be reloaded in any order
- Replaces functions and methods with their updated code
- Changes instances to use updated classes
- Aut... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/ThreadsafeTimer.py | .py | 1,551 | 41 | from .Qt import QtCore, QtGui
class ThreadsafeTimer(QtCore.QObject):
"""
Thread-safe replacement for QTimer.
"""
timeout = QtCore.Signal()
sigTimerStopRequested = QtCore.Signal()
sigTimerStartRequested = QtCore.Signal(object)
def __init__(self):
QtCore.QObject.__init__(sel... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/frozenSupport.py | .py | 1,830 | 52 | ## Definitions helpful in frozen environments (eg py2exe)
import os, sys, zipfile
def listdir(path):
"""Replacement for os.listdir that works in frozen environments."""
if not hasattr(sys, 'frozen'):
return os.listdir(path)
(zipPath, archivePath) = splitZip(path)
if archivePath is None:
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/SignalProxy.py | .py | 3,854 | 119 | # -*- coding: utf-8 -*-
from .Qt import QtCore
from .ptime import time
from . import ThreadsafeTimer
import weakref
__all__ = ['SignalProxy']
class SignalProxy(QtCore.QObject):
"""Object which collects rapid-fire signals and condenses them
into a single signal or a rate-limited stream of signals.
Used, f... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/template_pyqt5.py | .py | 6,230 | 115 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyqtgraph/console/template.ui'
#
# Created by: PyQt5 UI code generator 5.5.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Form(object):
def setupUi(self, Form):
Fo... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/template_pyside2.py | .py | 6,517 | 114 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'template.ui'
#
# Created: Sun Sep 18 19:19:10 2016
# by: pyside2-uic running on PySide2 2.0.0~alpha0
#
# WARNING! All changes made in this file will be lost!
from PySide2 import QtCore, QtGui, QtWidgets
class Ui_Form(object):
def... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/__init__.py | .py | 34 | 1 | from .Console import ConsoleWidget | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/Console.py | .py | 19,438 | 484 | # -*- coding: utf-8 -*-
import sys, re, os, time, traceback, subprocess
import pickle
from ..Qt import QtCore, QtGui, QT_LIB
from ..python2_3 import basestring
from .. import exceptionHandling as exceptionHandling
from .. import getConfigOption
from ..functions import SignalBlock
if QT_LIB == 'PySide':
from . impo... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/template_pyside.py | .py | 6,793 | 116 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyqtgraph/console/template.ui'
#
# Created: Tue Sep 19 09:45:18 2017
# by: pyside-uic 0.2.15 running on PySide 1.2.2
#
# WARNING! All changes made in this file will be lost!
from PySide import QtCore, QtGui
class Ui_Form(object):
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/CmdInput.py | .py | 1,236 | 41 | from ..Qt import QtCore, QtGui
from ..python2_3 import asUnicode
class CmdInput(QtGui.QLineEdit):
sigExecuteCmd = QtCore.Signal(object)
def __init__(self, parent):
QtGui.QLineEdit.__init__(self, parent)
self.history = [""]
self.ptr = 0
def keyPressEvent(self, ev):
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/console/template_pyqt.py | .py | 6,808 | 128 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyqtgraph/console/template.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/Exporter.py | .py | 5,393 | 140 | from ..widgets.FileDialog import FileDialog
from ..Qt import QtGui, QtCore, QtSvg
from ..python2_3 import asUnicode, basestring
from ..GraphicsScene import GraphicsScene
import os, re
LastExportDirectory = None
class Exporter(object):
"""
Abstract class used for exporting graphics to file / printer / whatever... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/HDF5Exporter.py | .py | 2,396 | 72 | from ..Qt import QtGui, QtCore
from .Exporter import Exporter
from ..parametertree import Parameter
from .. import PlotItem
import numpy
try:
import h5py
HAVE_HDF5 = True
except ImportError:
HAVE_HDF5 = False
__all__ = ['HDF5Exporter']
class HDF5Exporter(Exporter):
Name = "HDF5 Export: plot... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/CSVExporter.py | .py | 2,857 | 85 | # -*- coding: utf-8 -*-
from ..Qt import QtGui, QtCore
from .Exporter import Exporter
from ..parametertree import Parameter
from .. import PlotItem
__all__ = ['CSVExporter']
class CSVExporter(Exporter):
Name = "CSV from plot data"
windows = []
def __init__(self, item):
Exporter.__init__(s... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/SVGExporter.py | .py | 17,482 | 444 | from .Exporter import Exporter
from ..python2_3 import asUnicode
from ..parametertree import Parameter
from ..Qt import QtGui, QtCore, QtSvg, QT_LIB
from .. import debug
from .. import functions as fn
import re
import xml.dom.minidom as xml
import numpy as np
__all__ = ['SVGExporter']
class SVGExporter(Exporter):
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/ImageExporter.py | .py | 4,304 | 109 | from .Exporter import Exporter
from ..parametertree import Parameter
from ..Qt import QtGui, QtCore, QtSvg, QT_LIB
from .. import functions as fn
import numpy as np
__all__ = ['ImageExporter']
class ImageExporter(Exporter):
Name = "Image File (PNG, TIF, JPG, ...)"
allowCopy = True
def __init__(self, ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/__init__.py | .py | 253 | 12 | from .Exporter import Exporter
from .ImageExporter import *
from .SVGExporter import *
from .Matplotlib import *
from .CSVExporter import *
from .PrintExporter import *
from .HDF5Exporter import *
def listExporters():
return Exporter.Exporters[:]
| Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/PrintExporter.py | .py | 2,671 | 69 | from .Exporter import Exporter
from ..parametertree import Parameter
from ..Qt import QtGui, QtCore, QtSvg
import re
__all__ = ['PrintExporter']
#__all__ = [] ## Printer is disabled for now--does not work very well.
class PrintExporter(Exporter):
Name = "Printer"
def __init__(self, item):
Exporter... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/Matplotlib.py | .py | 4,842 | 128 | from ..Qt import QtGui, QtCore
from .Exporter import Exporter
from .. import PlotItem
from .. import functions as fn
__all__ = ['MatplotlibExporter']
"""
It is helpful when using the matplotlib Exporter if your
.matplotlib/matplotlibrc file is configured appropriately.
The following are suggested for getting usable P... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/tests/test_csv.py | .py | 1,704 | 59 | """
CSV export test
"""
from __future__ import division, print_function, absolute_import
import pyqtgraph as pg
import csv
import os
import tempfile
app = pg.mkQApp()
def approxeq(a, b):
return (a-b) <= ((a + b) * 1e-6)
def test_CSVExporter():
tempfilename = tempfile.NamedTemporaryFile(suffix='.csv').name
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/tests/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/tests/test_svg.py | .py | 2,206 | 79 | """
SVG export test
"""
from __future__ import division, print_function, absolute_import
import pyqtgraph as pg
import tempfile
import os
app = pg.mkQApp()
def test_plotscene():
tempfilename = tempfile.NamedTemporaryFile(suffix='.svg').name
print("using %s as a temporary file" % tempfilename)
pg.setConf... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/tests/test_hdf5.py | .py | 2,058 | 72 | # -*- coding: utf-8 -*-
import pytest
import pyqtgraph as pg
from pyqtgraph.exporters import HDF5Exporter
import numpy as np
from numpy.testing import assert_equal
import h5py
import os
@pytest.fixture
def tmp_h5(tmp_path):
yield tmp_path / "data.h5"
@pytest.mark.parametrize("combine", [False, True])
def test_H... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/exporters/tests/test_image.py | .py | 341 | 14 | # -*- coding: utf-8 -*-
import pyqtgraph as pg
from pyqtgraph.exporters import ImageExporter
app = pg.mkQApp()
def test_ImageExporter_filename_dialog():
"""Tests ImageExporter code path that opens a file dialog. Regression test
for pull request 1133."""
p = pg.plot()
exp = ImageExporter(p.getPlotItem... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/garbage_collector.py | .py | 1,599 | 51 | import gc
from ..Qt import QtCore
class GarbageCollector(object):
'''
Disable automatic garbage collection and instead collect manually
on a timer.
This is done to ensure that garbage collection only happens in the GUI
thread, as otherwise Qt can crash.
Credit: Erik Janssens
Source: ht... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/lru_cache.py | .py | 4,236 | 122 | import operator
import sys
import itertools
_IS_PY3 = sys.version_info[0] == 3
class LRUCache(object):
'''
This LRU cache should be reasonable for short collections (until around 100 items), as it does a
sort on the items if the collection would become too big (so, it is very fast for getting and
set... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/cprint.py | .py | 3,028 | 103 | """
Cross-platform color text printing
Based on colorama (see pyqtgraph/util/colorama/README.txt)
"""
import sys, re
from .colorama.winterm import WinTerm, WinColor, WinStyle
from .colorama.win32 import windll
from ..python2_3 import basestring
_WIN = sys.platform.startswith('win')
if windll is not None:
winterm... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/pil_fix.py | .py | 2,053 | 64 | # -*- coding: utf-8 -*-
"""
Importing this module installs support for 16-bit images in PIL.
This works by patching objects in the PIL namespace; no files are
modified.
"""
from PIL import Image
if Image.VERSION == '1.1.7':
Image._MODE_CONV["I;16"] = ('%su2' % Image._ENDIAN, None)
Image._fromarray_typemap[((1... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/get_resolution.py | .py | 527 | 15 | from .. import mkQApp
def test_screenInformation():
qApp = mkQApp()
desktop = qApp.desktop()
resolution = desktop.screenGeometry()
availableResolution = desktop.availableGeometry()
print("Screen resolution: {}x{}".format(resolution.width(), resolution.height()))
print("Available geometry: {}x{}... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/mutex.py | .py | 3,466 | 115 | # -*- coding: utf-8 -*-
import traceback
from ..Qt import QtCore
class Mutex(QtCore.QMutex):
"""
Subclass of QMutex that provides useful debugging information during
deadlocks--tracebacks are printed for both the code location that is
attempting to lock the mutex as well as the location that has alre... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/colorama/winterm.py | .py | 4,205 | 121 | # Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
from . import win32
# from wincon.h
class WinColor(object):
BLACK = 0
BLUE = 1
GREEN = 2
CYAN = 3
RED = 4
MAGENTA = 5
YELLOW = 6
GREY = 7
# from wincon.h
class WinStyle(object):
NORMAL = 0... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/colorama/__init__.py | .py | 0 | 0 | null | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/colorama/win32.py | .py | 4,901 | 138 | # Copyright Jonathan Hartley 2013. BSD 3-Clause license, see LICENSE file.
# from winbase.h
STDOUT = -11
STDERR = -12
try:
from ctypes import windll
from ctypes import wintypes
except ImportError:
windll = None
SetConsoleTextAttribute = lambda *_: None
else:
from ctypes import (
byref, Str... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/util/tests/test_lru_cache.py | .py | 1,191 | 51 | from pyqtgraph.util.lru_cache import LRUCache
def testLRU():
lru = LRUCache(2, 1)
# check twice
checkLru(lru)
checkLru(lru)
def checkLru(lru):
lru[1] = 1
lru[2] = 2
lru[3] = 3
assert len(lru) == 2
assert set([2, 3]) == set(lru.keys())
assert set([2, 3]) == set(lru.values())
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/pixmaps/compile.py | .py | 627 | 20 | # -*- coding: utf-8 -*-
import numpy as np
from PyQt4 import QtGui
import os, pickle, sys
path = os.path.abspath(os.path.split(__file__)[0])
pixmaps = {}
for f in os.listdir(path):
if not f.endswith('.png'):
continue
print(f)
img = QtGui.QImage(os.path.join(path, f))
ptr = img.bits()
ptr.se... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/pixmaps/__init__.py | .py | 803 | 28 | """
Allows easy loading of pixmaps used in UI elements.
Provides support for frozen environments as well.
"""
import os, sys, pickle
from ..functions import makeQImage
from ..Qt import QtGui
from ..python2_3 import basestring
if sys.version_info[0] == 2:
from . import pixmapData_2 as pixmapData
else:
from . i... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/pixmaps/pixmapData_2.py | .py | 65,632 | 1 | import numpy as np; pixmapData={'lock.png': "cnumpy.core.multiarray\n_reconstruct\np0\n(cnumpy\nndarray\np1\n(I0\ntp2\nS'b'\np3\ntp4\nRp5\n(I1\n(I32\nI32\nI4\ntp6\ncnumpy\ndtype\np7\n(S'u1'\np8\nI0\nI1\ntp9\nRp10\n(I3\nS'|'\np11\nNNNI-1\nI-1\nI0\ntp12\nbI00\nS'\\xff\\xff\\xff\\x00\\xff\\xff\\xff\\x00\\xff\\xff\\xff\\x0... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/pixmaps/pixmapData_3.py | .py | 53,111 | 1 | import numpy as np; pixmapData={'lock.png': b'\x80\x03cnumpy.core.multiarray\n_reconstruct\nq\x00cnumpy\nndarray\nq\x01K\x00\x85q\x02C\x01bq\x03\x87q\x04Rq\x05(K\x01K K K\x04\x87q\x06cnumpy\ndtype\nq\x07X\x02\x00\x00\x00u1q\x08K\x00K\x01\x87q\tRq\n(K\x03X\x01\x00\x00\x00|q\x0bNNNJ\xff\xff\xff\xffJ\xff\xff\xff\xffK\x00t... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/__init__.py | .py | 234 | 5 | from .Parameter import Parameter, registerParameterType
from .ParameterTree import ParameterTree
from .ParameterItem import ParameterItem
from .ParameterSystem import ParameterSystem, SystemSolver
from . import parameterTypes as types | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/Parameter.py | .py | 32,590 | 779 | from ..Qt import QtGui, QtCore
import os, weakref, re
from ..pgcollections import OrderedDict
from ..python2_3 import asUnicode, basestring
from .ParameterItem import ParameterItem
PARAM_TYPES = {}
PARAM_NAMES = {}
def registerParameterType(name, cls, override=False):
global PARAM_TYPES
if name in PARAM_TYPES... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/parameterTypes.py | .py | 25,922 | 688 | from ..Qt import QtCore, QtGui
from ..python2_3 import asUnicode
from .Parameter import Parameter, registerParameterType
from .ParameterItem import ParameterItem
from ..widgets.SpinBox import SpinBox
from ..widgets.ColorButton import ColorButton
from ..colormap import ColorMap
#from ..widgets.GradientWidget import Grad... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/ParameterTree.py | .py | 5,662 | 155 | from ..Qt import QtCore, QtGui
from ..widgets.TreeWidget import TreeWidget
import os, weakref, re
from .ParameterItem import ParameterItem
#import functions as fn
class ParameterTree(TreeWidget):
"""Widget used to display or control data from a hierarchy of Parameters"""
def __init__... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/ParameterSystem.py | .py | 4,598 | 128 | from .parameterTypes import GroupParameter
from .. import functions as fn
from .SystemSolver import SystemSolver
class ParameterSystem(GroupParameter):
"""
ParameterSystem is a subclass of GroupParameter that manages a tree of
sub-parameters with a set of interdependencies--changing any one parameter
... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/SystemSolver.py | .py | 17,816 | 425 | from ..pgcollections import OrderedDict
import numpy as np
import copy
class SystemSolver(object):
"""
This abstract class is used to formalize and manage user interaction with a
complex system of equations (related to "constraint satisfaction problems").
It is often the case that devices must be con... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/ParameterItem.py | .py | 6,541 | 172 | from ..Qt import QtGui, QtCore
from ..python2_3 import asUnicode
import os, weakref, re
class ParameterItem(QtGui.QTreeWidgetItem):
"""
Abstract ParameterTree item.
Used to represent the state of a Parameter from within a ParameterTree.
- Sets first column of item to name
- generates context ... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/parametertree/tests/test_parametertypes.py | .py | 4,884 | 134 | # ~*~ coding: utf8 ~*~
import sys
import pytest
from pyqtgraph.Qt import QtGui, QtCore
import pyqtgraph.parametertree as pt
import pyqtgraph as pg
from pyqtgraph.python2_3 import asUnicode
from pyqtgraph.functions import eq
import numpy as np
app = pg.mkQApp()
def _getWidget(param):
return list(param.items.keys()... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/metaarray/__init__.py | .py | 25 | 2 | from .MetaArray import *
| Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/metaarray/MetaArray.py | .py | 57,689 | 1,510 | # -*- coding: utf-8 -*-
"""
MetaArray.py - Class encapsulating ndarray with meta data
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more information.
MetaArray is an array class based on numpy.ndarray that allows storage of per-axis meta data
such as axis values, names, units,... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/metaarray/readMeta.m | .m | 1,752 | 87 | function f = readMeta(file)
info = hdf5info(file);
f = readMetaRecursive(info.GroupHierarchy.Groups(1));
end
function f = readMetaRecursive(root)
typ = 0;
for i = 1:length(root.Attributes)
if strcmp(root.Attributes(i).Shortname, '_metaType_')
typ = root.Attributes(i).Value.Data;
break
end
end
... | MATLAB |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/canvas/TransformGuiTemplate_pyside.py | .py | 2,827 | 56 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyqtgraph/canvas/TransformGuiTemplate.ui'
#
# Created: Wed Nov 9 17:57:16 2016
# by: pyside-uic 0.2.15 running on PySide 1.2.2
#
# WARNING! All changes made in this file will be lost!
from PySide import QtCore, QtGui
class Ui_Form(ob... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/canvas/TransformGuiTemplate_pyqt.py | .py | 2,986 | 69 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyqtgraph/canvas/TransformGuiTemplate.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except Attribute... | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/canvas/__init__.py | .py | 71 | 3 | # -*- coding: utf-8 -*-
from .Canvas import *
from .CanvasItem import * | Python |
3D | pymodproject/pymod | pymod3/pymod_lib/pymod_plot/pyqtgraph/canvas/CanvasTemplate_pyqt.py | .py | 5,347 | 105 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'CanvasTemplate.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf... | Python |
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