JorgeVB/code_unlearning_dataset · Data Studio

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Get the value associated with a name in the current context. The current context could be an dictionary in a list, or a dictionary outside a list. Args: name: name to lookup, e.g. 'foo' or 'foo.bar.baz' Returns: The value, or self.undefined_str Raises: UndefinedVariable if self...
Low level method to expand the template piece by piece. Args: data_dict: The JSON data dictionary. callback: A callback which should be called with each expanded token. group: Dictionary of name -> Template instance (for styles) Example: You can pass 'f.write' as the callback to write direct...
Expands the template with the given data dictionary, returning a string. This is a small wrapper around execute(), and is the most convenient interface. Args: data_dict: The JSON data dictionary. Like the builtin dict() constructor, it can take a single dictionary as a positional argument...
Yields a list of tokens resulting from expansion. This may be useful for WSGI apps. NOTE: In the current implementation, the entire expanded template must be stored memory. NOTE: This is a generator, but JavaScript doesn't have generators. def tokenstream(self, data_dict): """Yields a list of to...
Align an unwrapped phase array to zero-phase All operations are performed in-place. def align_unwrapped(sino): """Align an unwrapped phase array to zero-phase All operations are performed in-place. """ samples = [] if len(sino.shape) == 2: # 2D # take 1D samples at beginning a...
Return divmod with closest result to zero def divmod_neg(a, b): """Return divmod with closest result to zero""" q, r = divmod(a, b) # make sure r is close to zero sr = np.sign(r) if np.abs(r) > b/2: q += sr r -= b * sr return q, r
r"""Compute the phase from a complex wave field sinogram This step is essential when using the ray approximation before computation of the refractive index with the inverse Radon transform. Parameters ---------- uSin: 2d or 3d complex ndarray The background-corrected sinogram of the co...
r"""Convert the complex wave field sinogram to the Rytov phase This method applies the Rytov approximation to the recorded complex wave sinogram. To achieve this, the following filter is applied: .. math:: u_\mathrm{B}(\mathbf{r}) = u_\mathrm{0}(\mathbf{r}) \ln\!\left( ...
Handle more data types than the default JSON encoder. Specifically, it treats a `set` and a `numpy.array` like a `list`. Example usage: ``json.dumps(obj, default=json_encoder_default)`` def json_encoder_default(obj): """Handle more data types than the default JSON encoder. Specifically, it treats a ...
Convert a matplotlib figure to an inline HTML image. :param matplotlib.figure.Figure figure: Figure to display. :param str image_format: png (default) or svg :param int dpi: dots-per-inch for raster graphics. :rtype: str def fig_to_src(figure, image_format='png', dpi=80): """Convert a matplotlib f...
Reset Axis and set default parameters for H-bridge def Reset(self): ' Reset Axis and set default parameters for H-bridge ' spi.SPI_write(self.CS, [0xC0, 0x60]) # reset # spi.SPI_write(self.CS, [0x14, 0x14]) # Stall Treshold setup # spi.SPI_write(self.CS, [0xFF, 0xFF]) # ...
Setup of maximum speed def MaxSpeed(self, speed): ' Setup of maximum speed ' spi.SPI_write(self.CS, [0x07, 0x07]) # Max Speed setup spi.SPI_write(self.CS, [0x00, 0x00]) spi.SPI_write(self.CS, [speed, speed])
Go away from Limit Switch def ReleaseSW(self): ' Go away from Limit Switch ' while self.ReadStatusBit(2) == 1: # is Limit Switch ON ? spi.SPI_write(self.CS, [0x92, 0x92] \| (~self.Dir & 1)) # release SW while self.IsBusy(): pass self.Mov...
Move some distance units from current position def Move(self, units): ' Move some distance units from current position ' steps = units * self.SPU # translate units to steps if steps > 0: # look for direction spi.SPI_write(self.CS, [0x40 \| (...
create a bounding box vector object or shapefile from coordinates and coordinate reference system. The CRS can be in either WKT, EPSG or PROJ4 format Parameters ---------- coordinates: dict a dictionary containing numerical variables with keys `xmin`, `xmax`, `ymin` and `ymax` crs: int,...
dissolve the polygons of a vector file by an attribute field Parameters ---------- infile: str the input vector file outfile: str the output shapefile field: str the field name to merge the polygons by layername: str the name of the output vector layer; If...
create a Vector object from ogr features Parameters ---------- feature: list of :osgeo:class:`ogr.Feature` or :osgeo:class:`ogr.Feature` a single feature or a list of features ref: Vector a reference Vector object to retrieve geo information from layername: str or None the n...
intersect two Vector objects Parameters ---------- obj1: Vector the first vector object; this object is reprojected to the CRS of obj2 if necessary obj2: Vector the second vector object Returns ------- Vector the intersect of obj1 and obj2 def intersect(obj1, obj2)...
add a feature to the vector object from a geometry Parameters ---------- geometry: :osgeo:class:`ogr.Geometry` the geometry to add as a feature fields: dict or None the field names and values to assign to the new feature Returns ------- ...
add a field to the vector layer Parameters ---------- name: str the field name type: int the OGR Field Type (OFT), e.g. ogr.OFTString. See `Module ogr <https://gdal.org/python/osgeo.ogr-module.html>`_. width: int the width of the n...
add a layer to the vector layer Parameters ---------- name: str the layer name srs: int, str or :osgeo:class:`osr.SpatialReference` the spatial reference system. See :func:`spatialist.auxil.crsConvert` for options. geomType: int an OGR well-kn...
add a vector object to the layer of the current Vector object Parameters ---------- vec: Vector the vector object to add merge: bool merge overlapping polygons? Returns ------- def addvector(self, vec): """ add a vector object to...
create a bounding box from the extent of the Vector object Parameters ---------- outname: str or None the name of the vector file to be written; if None, a Vector object is returned format: str the name of the file format to write overwrite: bool ...
export the geometry of each feature as a wkt string Parameters ---------- set3D: bool keep the third (height) dimension? Returns ------- def convert2wkt(self, set3D=True): """ export the geometry of each feature as a wkt string Parameters ...
get features by field attribute Parameters ---------- fieldname: str the name of the queried field attribute: int or str the field value of interest Returns ------- list of :osgeo:class:`ogr.Feature` or :osgeo:class:`ogr.Feature` ...
get features by numerical (positional) index Parameters ---------- index: int the queried index Returns ------- :osgeo:class:`ogr.Feature` the requested feature def getFeatureByIndex(self, index): """ get features by numerical (p...
initialize a layer object Returns ------- def init_layer(self): """ initialize a layer object Returns ------- """ self.layer = self.vector.GetLayer() self.__features = [None] * self.nfeatures
load all feature into memory Returns ------- def load(self): """ load all feature into memory Returns ------- """ self.layer.ResetReading() for i in range(self.nfeatures): if self.__features[i] is None: self.__featur...
in-memory reprojection Parameters ---------- projection: int, str or :osgeo:class:`osr.SpatialReference` the target CRS. See :func:`spatialist.auxil.crsConvert`. Returns ------- def reproject(self, projection): """ in-memory reprojection Pa...
directly reset the spatial reference system of the vector object. This is not going to reproject the Vector object, see :meth:`reproject` instead. Parameters ---------- crs: int, str or :osgeo:class:`osr.SpatialReference` the input CRS Returns ------- ...
write the Vector object to a file Parameters ---------- outfile: the name of the file to write format: str the output file format overwrite: bool overwrite an already existing file? Returns ------- def write(self, outfile, fo...
SMBus Read Byte: i2c_smbus_read_byte_data() ============================================ This reads a single byte from a device, from a designated register. The register is specified through the Comm byte. S Addr Wr [A] Comm [A] S Addr Rd [A] [Data] NA P Functionality flag: I...
SMBus Write Word: i2c_smbus_write_word_data() ============================================== This is the opposite of the Read Word operation. 16 bits of data is written to a device, to the designated register that is specified through the Comm byte. S Addr Wr [A] Comm [A] Data...
SMBus Block Write: i2c_smbus_write_block_data() ================================================ The opposite of the Block Read command, this writes up to 32 bytes to a device, to a designated register that is specified through the Comm byte. The amount of data is specified in the Coun...
SMBus Block Write - Block Read Process Call =========================================== SMBus Block Write - Block Read Process Call was introduced in Revision 2.0 of the specification. This command selects a device register (through the Comm byte), sends 1 to 31 bytes of data t...
I2C block transactions do not limit the number of bytes transferred but the SMBus layer places a limit of 32 bytes. I2C Block Write: i2c_smbus_write_i2c_block_data() ================================================== The opposite of the Block Read command, this writes bytes to ...
I2C block transactions do not limit the number of bytes transferred but the SMBus layer places a limit of 32 bytes. I2C Block Read: i2c_smbus_read_i2c_block_data() ================================================ This command reads a block of bytes from a device, from a design...
Initialize zmq messaging. Listen on sub_port. This port might at some point receive the message to start publishing on a certain port, but until then, no publishing. def _init_zmq(self, port_publish, port_subscribe): """Initialize zmq messaging. Listen on sub_port. This port m...
Executes an process in the analysis with the given message. It also handles the start and stop signals in case an process_id is given. This method is similar to the method in databench.Analysis. def run_process(self, analysis, action_name, message='__nomessagetoken__'): """Executes an...
Event loop. def event_loop(self): """Event loop.""" try: zmq.eventloop.ioloop.IOLoop.current().start() except KeyboardInterrupt: zmq.eventloop.ioloop.IOLoop.current().stop()
Emit signal to main. Args: signal: Name of the signal to be emitted. message: Message to be sent. analysis_id: Identifies the instance of this analysis. def emit(self, signal, message, analysis_id): """Emit signal to main. Args: signal: Name of ...
Writes specified value to the pins defined as output by config_ports() method. Writing to input pins has no effect. def set_ports(self, port0 = 0x00, port1 = 0x00): 'Writes specified value to the pins defined as output by config_ports() method. Writing to input pins has no effect.' self.bus.write_byte_...
Reads logical values at pins. def get_ports(self): 'Reads logical values at pins.' return (self.bus.read_byte_data(self.address, self.STATUS_PORT0), self.bus.read_byte_data(self.address, self.STATUS_PORT1));
Reads logical values at pins. def get_config(self): 'Reads logical values at pins.' return (self.bus.read_byte_data(self.address, self.CONTROL_PORT0), self.bus.read_byte_data(self.address, self.CONTROL_PORT1));
Sets INPUT (1) or OUTPUT (0) direction on pins. Inversion setting is applicable for input pins 1-inverted 0-noninverted input polarity. def set_pullups(self, port0 = 0x00, port1 = 0x00): 'Sets INPUT (1) or OUTPUT (0) direction on pins. Inversion setting is applicable for input pins 1-inverted 0-noninverted i...
Writes specified value to the pins defined as output by method. Writing to input pins has no effect. def set_ports(self, port0 = 0x00, port1 = 0x00): 'Writes specified value to the pins defined as output by method. Writing to input pins has no effect.' self.bus.write_byte_data(self.address, self.CONTRO...
create a gffutils DB def get_gtf_db(gtf, in_memory=False): """ create a gffutils DB """ db_file = gtf + '.db' if gtf.endswith('.gz'): db_file = gtf[:-3] + '.db' if file_exists(db_file): return gffutils.FeatureDB(db_file) db_file = ':memory:' if in_memory else db_file if ...
create a BED file of transcript-level features with attached gene name or gene ids def gtf_to_bed(gtf, alt_out_dir=None): """ create a BED file of transcript-level features with attached gene name or gene ids """ out_file = os.path.splitext(gtf)[0] + '.bed' if file_exists(out_file): ...
write out a file of transcript->gene mappings. use the installed tx2gene.csv if it exists, else write a new one out def tx2genefile(gtf, out_file=None): """ write out a file of transcript->gene mappings. use the installed tx2gene.csv if it exists, else write a new one out """ installed_tx2gene ...
return a dictionary keyed by transcript_id of the associated gene_id def transcript_to_gene(gtf): """ return a dictionary keyed by transcript_id of the associated gene_id """ gene_lookup = {} for feature in complete_features(get_gtf_db(gtf)): gene_id = feature.attributes.get('gene_id', [Non...
Sets new output frequency, required parameters are real current frequency at output and new required frequency. def set_freq(self, fout, freq): """ Sets new output frequency, required parameters are real current frequency at output and new required frequency. """ hsdiv_tuple = (4, 5, 6,...
Detects alignment requirements for binary files with new nn::util::BinaryFileHeader. def _get_file_alignment_for_new_binary_file(self, file: File) -> int: """Detects alignment requirements for binary files with new nn::util::BinaryFileHeader.""" if len(file.data) <= 0x20: return 0 b...
Only checks and asks questions. Nothing is written to disk. def check_folders(name): """Only checks and asks questions. Nothing is written to disk.""" if os.getcwd().endswith('analyses'): correct = input('You are in an analyses folder. This will create ' 'another analyses folde...
Create an analysis with given name and suffix. If it does not exist already, it creates the top level analyses folder and it's __init__.py and index.yaml file. def create_analyses(name, kernel=None): """Create an analysis with given name and suffix. If it does not exist already, it creates the top le...
Create analysis files. def create_analysis(name, kernel, src_dir, scaffold_name): """Create analysis files.""" # analysis folder folder = os.path.join(os.getcwd(), 'analyses', name) if not os.path.exists(folder): os.makedirs(folder) else: log.warning('Analysis folder {} already exi...
convert between different types of spatial references Parameters ---------- crsIn: int, str or :osgeo:class:`osr.SpatialReference` the input CRS crsOut: {'wkt', 'proj4', 'epsg', 'osr', 'opengis' or 'prettyWkt'} the output CRS type Returns ------- int, str or :osgeo:class:`o...
compute the distance in meters between two points in latlon Parameters ---------- lat1: int or float the latitude of point 1 lon1: int or float the longitude of point 1 lat2: int or float the latitude of point 2 lon2: int or float the longitude of point 2 Re...
a simple wrapper for :osgeo:func:`gdal.Warp` Parameters ---------- src: str, :osgeo:class:`ogr.DataSource` or :osgeo:class:`gdal.Dataset` the input data set dst: str the output data set options: dict additional parameters passed to gdal.Warp; see :osgeo:func:`gdal.WarpOption...
a simple wrapper for :osgeo:func:`gdal.BuildVRT` Parameters ---------- src: str, list, :osgeo:class:`ogr.DataSource` or :osgeo:class:`gdal.Dataset` the input data set(s) dst: str the output data set options: dict additional parameters passed to gdal.BuildVRT; see :osgeo:func...
a simple wrapper for `gdal.Translate <https://gdal.org/python/osgeo.gdal-module.html#Translate>`_ Parameters ---------- src: str, :osgeo:class:`ogr.DataSource` or :osgeo:class:`gdal.Dataset` the input data set dst: str the output data set options: dict additional parameters ...
a simple wrapper for gdal.VectorTranslate aka `ogr2ogr <https://www.gdal.org/ogr2ogr.html>`_ Parameters ---------- src: str or :osgeo:class:`ogr.DataSource` the input data set dst: str the output data set options: dict additional parameters passed to gdal.VectorTranslate; ...
a simple wrapper for gdal.Rasterize Parameters ---------- src: str or :osgeo:class:`ogr.DataSource` the input data set dst: str the output data set options: dict additional parameters passed to gdal.Rasterize; see :osgeo:func:`gdal.RasterizeOptions` Returns ------- ...
reproject a coordinate from one CRS to another Parameters ---------- x: int or float the X coordinate component y: int or float the Y coordinate component s_crs: int, str or :osgeo:class:`osr.SpatialReference` the source CRS. See :func:`~spatialist.auxil.crsConvert` for ...
Creates output_dir, work_dir, and sets up log def set_up_dirs(proc_name, output_dir=None, work_dir=None, log_dir=None): """ Creates output_dir, work_dir, and sets up log """ output_dir = safe_mkdir(adjust_path(output_dir or join(os.getcwd(), proc_name)), 'output_dir') debug('Saving results into ' + out...
Generator used to yield 100 KiB chunks for a given response. def _iter_content_generator(response, decode_unicode): """Generator used to yield 100 KiB chunks for a given response.""" for chunk in response.iter_content(100 * 1024, decode_unicode=decode_unicode): if decode_unicode: # Replace ...
Iterates over the response data, one line at a time. When stream=True is set on the request, this avoids reading the content at once into memory for large responses. The function is taken from :meth:`requests.models.Response.iter_lines`, but modified to use our :func:`~spacetrack.base._iter_content_ge...
Raises stored :class:`HTTPError`, if one occurred. This is the :meth:`requests.models.Response.raise_for_status` method, modified to add the response from Space-Track, if given. def _raise_for_status(response): """Raises stored :class:`HTTPError`, if one occurred. This is the :meth:`requests.models.R...
r"""Generic Space-Track query. The request class methods use this method internally; the public API is as follows: .. code-block:: python st.tle_publish(args, kw) st.basicspacedata.tle_publish(args, *kw) st.file(args, **kw) st.fileshare.fi...
Perform get request, handling rate limiting. def _ratelimited_get(self, args, kwargs): """Perform get request, handling rate limiting.""" with self._ratelimiter: resp = self.session.get(args, **kwargs) # It's possible that Space-Track will return HTTP status 500 with a ...
Find first controller that matches given request class. Order is specified by the keys of ``SpaceTrackClient.request_controllers`` (:class:`~collections.OrderedDict`) def _find_controller(self, class_): """Find first controller that matches given request class. Order is specif...
Get raw predicate information for given request class, and cache for subsequent calls. def _download_predicate_data(self, class_, controller): """Get raw predicate information for given request class, and cache for subsequent calls. """ self.authenticate() url = ('{0}{1...
Get full predicate information for given request class, and cache for subsequent calls. def get_predicates(self, class_, controller=None): """Get full predicate information for given request class, and cache for subsequent calls. """ if class_ not in self._predicates: ...
Proxy ``get_predicates`` to client with stored request controller. def get_predicates(self, class_): """Proxy ``get_predicates`` to client with stored request controller. """ return self.client.get_predicates( class_=class_, controller=self.controller)
Add the folding menu to the editor, on install. :param editor: editor instance on which the mode has been installed to. def on_install(self, editor): """ Add the folding menu to the editor, on install. :param editor: editor instance on which the mode has been installed to. """...
Draw the background rectangle using the current style primitive color or foldIndicatorBackground if nativeFoldingIndicator is true. :param rect: The fold zone rect to draw :param painter: The widget's painter. def _draw_rect(self, rect, painter): """ Draw the background rectan...
Gets a system color for drawing the fold scope background. def get_system_bck_color(): """ Gets a system color for drawing the fold scope background. """ def merged_colors(colorA, colorB, factor): maxFactor = 100 colorA = QtGui.QColor(colorA) colorB =...
Draw the fold indicator/trigger (arrow). :param top: Top position :param mouse_over: Whether the mouse is over the indicator :param collapsed: Whether the trigger is collapsed or not. :param painter: QPainter def _draw_fold_indicator(self, top, mouse_over, collapsed, painter): ...
Gets the base scope highlight color (derivated from the editor background) def _get_scope_highlight_color(self): """ Gets the base scope highlight color (derivated from the editor background) """ color = self.editor.background if color.lightness() < 128: ...
Adds a scope decoration that enclose the current scope :param start: Start of the current scope :param end: End of the current scope :param parent_start: Start of the parent scope :param parent_end: End of the parent scope :param base_color: base color for scope decoration ...
Show a scope decoration on the editor widget :param start: Start line :param end: End line def _add_scope_decorations(self, block, start, end): """ Show a scope decoration on the editor widget :param start: Start line :param end: End line """ try: ...
Highlights the scopes surrounding the current fold scope. :param block: Block that starts the current fold scope. def _highlight_surrounding_scopes(self, block): """ Highlights the scopes surrounding the current fold scope. :param block: Block that starts the current fold scope. ...
Removes scope decorations and background from the editor and the panel if highlight_caret_scope, else simply update the scope decorations to match the caret scope. def leaveEvent(self, event): """ Removes scope decorations and background from the editor and the panel if highligh...
Add fold decorations (boxes arround a folded block in the editor widget). def _add_fold_decoration(self, block, region): """ Add fold decorations (boxes arround a folded block in the editor widget). """ deco = TextDecoration(block) deco.signals.clicked.connect(se...
Toggle a fold trigger block (expand or collapse it). :param block: The QTextBlock to expand/collapse def toggle_fold_trigger(self, block): """ Toggle a fold trigger block (expand or collapse it). :param block: The QTextBlock to expand/collapse """ if not TextBlockHelpe...
On state changed we (dis)connect to the cursorPositionChanged signal def on_state_changed(self, state): """ On state changed we (dis)connect to the cursorPositionChanged signal """ if state: self.editor.key_pressed.connect(self._on_key_pressed) if self._highlight...
Override key press to select the current scope if the user wants to deleted a folded scope (without selecting it). def _on_key_pressed(self, event): """ Override key press to select the current scope if the user wants to deleted a folded scope (without selecting it). """ ...
Auto indent if the released key is the return key. :param event: the key event def _on_key_pressed(self, event): """ Auto indent if the released key is the return key. :param event: the key event """ if not event.isAccepted(): if event.key() == Qt.Key_Return ...
Verify that the payload was sent from our GitHub instance. def verify_signature(self, payload, headers): """Verify that the payload was sent from our GitHub instance.""" github_signature = headers.get("x-hub-signature") if not github_signature: json_abort(401, "X-Hub-Signature heade...
Get the options that have been set. Called after the user has added all their own options and is ready to use the variables. def get_options(self): """Get the options that have been set. Called after the user has added all their own options and is ready to use the variables. ...
Check for job definitions in known zuul files. def parse_job_files(self): """Check for job definitions in known zuul files.""" repo_jobs = [] for rel_job_file_path, job_info in self.job_files.items(): LOGGER.debug("Checking for job definitions in %s", rel_job_file_path) ...
Changes the current directory. Change is made by running a "cd" command followed by a "clear" command. :param directory: :return: def change_directory(self, directory): """ Changes the current directory. Change is made by running a "cd" command followed by a "clear" co...
Gets the icon file name. Read-only. def icon(self): """ Gets the icon file name. Read-only. """ if isinstance(self._icon, str): if QtGui.QIcon.hasThemeIcon(self._icon): return QtGui.QIcon.fromTheme(self._icon) else: return QtGui.QI...
Adds the marker to the panel. :param marker: Marker to add :type marker: pyqode.core.modes.Marker def add_marker(self, marker): """ Adds the marker to the panel. :param marker: Marker to add :type marker: pyqode.core.modes.Marker """ self._markers.appen...
Removes a marker from the panel :param marker: Marker to remove :type marker: pyqode.core.Marker def remove_marker(self, marker): """ Removes a marker from the panel :param marker: Marker to remove :type marker: pyqode.core.Marker """ self._markers.remo...
Returns the marker that is displayed at the specified line number if any. :param line: The marker line. :return: Marker of None :rtype: pyqode.core.Marker def marker_for_line(self, line): """ Returns the marker that is displayed at the specified line number if ...
Display tooltip at the specified top position. def _display_tooltip(self, tooltip, top): """ Display tooltip at the specified top position. """ QtWidgets.QToolTip.showText(self.mapToGlobal(QtCore.QPoint( self.sizeHint().width(), top)), tooltip, self)
Search occurrences using str.find instead of regular expressions. :param string: string to parse :param sub: search string :param whole_word: True to select whole words only def finditer_noregex(string, sub, whole_word): """ Search occurrences using str.find instead of regular expressions. :p...
Generator that finds all occurrences of ``sub`` in ``string`` :param string: string to parse :param sub: string to search :param regex: True to search using regex :param case_sensitive: True to match case, False to ignore case :param whole_word: True to returns only whole words :return: def fi...
Worker that finds all occurrences of a given string (or regex) in a given text. :param data: Request data dict:: { 'string': string to search in text 'sub': input text 'regex': True to consider string as a regular expression 'whole_word': True to match wh...
Splits a text in a meaningful list of words based on a list of word separators (define in pyqode.core.settings) :param txt: Text to split :param seps: List of words separators :return: A set of words found in the document (excluding punctuations, numbers, ...) def split...

Get the value associated with a name in the current context. The current context could be an dictionary in a list, or a dictionary outside a list. Args: name: name to lookup, e.g. 'foo' or 'foo.bar.baz' Returns: The value, or self.undefined_str Raises: UndefinedVariable if self...

Low level method to expand the template piece by piece. Args: data_dict: The JSON data dictionary. callback: A callback which should be called with each expanded token. group: Dictionary of name -> Template instance (for styles) Example: You can pass 'f.write' as the callback to write direct...

Expands the template with the given data dictionary, returning a string. This is a small wrapper around execute(), and is the most convenient interface. Args: data_dict: The JSON data dictionary. Like the builtin dict() constructor, it can take a single dictionary as a positional argument...

Yields a list of tokens resulting from expansion. This may be useful for WSGI apps. NOTE: In the current implementation, the entire expanded template must be stored memory. NOTE: This is a generator, but JavaScript doesn't have generators. def tokenstream(self, data_dict): """Yields a list of to...

Align an unwrapped phase array to zero-phase All operations are performed in-place. def align_unwrapped(sino): """Align an unwrapped phase array to zero-phase All operations are performed in-place. """ samples = [] if len(sino.shape) == 2: # 2D # take 1D samples at beginning a...

Return divmod with closest result to zero def divmod_neg(a, b): """Return divmod with closest result to zero""" q, r = divmod(a, b) # make sure r is close to zero sr = np.sign(r) if np.abs(r) > b/2: q += sr r -= b * sr return q, r

r"""Compute the phase from a complex wave field sinogram This step is essential when using the ray approximation before computation of the refractive index with the inverse Radon transform. Parameters ---------- uSin: 2d or 3d complex ndarray The background-corrected sinogram of the co...

r"""Convert the complex wave field sinogram to the Rytov phase This method applies the Rytov approximation to the recorded complex wave sinogram. To achieve this, the following filter is applied: .. math:: u_\mathrm{B}(\mathbf{r}) = u_\mathrm{0}(\mathbf{r}) \ln\!\left( ...

Handle more data types than the default JSON encoder. Specifically, it treats a `set` and a `numpy.array` like a `list`. Example usage: ``json.dumps(obj, default=json_encoder_default)`` def json_encoder_default(obj): """Handle more data types than the default JSON encoder. Specifically, it treats a ...

Convert a matplotlib figure to an inline HTML image. :param matplotlib.figure.Figure figure: Figure to display. :param str image_format: png (default) or svg :param int dpi: dots-per-inch for raster graphics. :rtype: str def fig_to_src(figure, image_format='png', dpi=80): """Convert a matplotlib f...

Reset Axis and set default parameters for H-bridge def Reset(self): ' Reset Axis and set default parameters for H-bridge ' spi.SPI_write(self.CS, [0xC0, 0x60]) # reset # spi.SPI_write(self.CS, [0x14, 0x14]) # Stall Treshold setup # spi.SPI_write(self.CS, [0xFF, 0xFF]) # ...

Setup of maximum speed def MaxSpeed(self, speed): ' Setup of maximum speed ' spi.SPI_write(self.CS, [0x07, 0x07]) # Max Speed setup spi.SPI_write(self.CS, [0x00, 0x00]) spi.SPI_write(self.CS, [speed, speed])

Go away from Limit Switch def ReleaseSW(self): ' Go away from Limit Switch ' while self.ReadStatusBit(2) == 1: # is Limit Switch ON ? spi.SPI_write(self.CS, [0x92, 0x92] | (~self.Dir & 1)) # release SW while self.IsBusy(): pass self.Mov...

Move some distance units from current position def Move(self, units): ' Move some distance units from current position ' steps = units * self.SPU # translate units to steps if steps > 0: # look for direction spi.SPI_write(self.CS, [0x40 | (...

create a bounding box vector object or shapefile from coordinates and coordinate reference system. The CRS can be in either WKT, EPSG or PROJ4 format Parameters ---------- coordinates: dict a dictionary containing numerical variables with keys `xmin`, `xmax`, `ymin` and `ymax` crs: int,...

dissolve the polygons of a vector file by an attribute field Parameters ---------- infile: str the input vector file outfile: str the output shapefile field: str the field name to merge the polygons by layername: str the name of the output vector layer; If...

create a Vector object from ogr features Parameters ---------- feature: list of :osgeo:class:`ogr.Feature` or :osgeo:class:`ogr.Feature` a single feature or a list of features ref: Vector a reference Vector object to retrieve geo information from layername: str or None the n...

intersect two Vector objects Parameters ---------- obj1: Vector the first vector object; this object is reprojected to the CRS of obj2 if necessary obj2: Vector the second vector object Returns ------- Vector the intersect of obj1 and obj2 def intersect(obj1, obj2)...

add a feature to the vector object from a geometry Parameters ---------- geometry: :osgeo:class:`ogr.Geometry` the geometry to add as a feature fields: dict or None the field names and values to assign to the new feature Returns ------- ...

add a field to the vector layer Parameters ---------- name: str the field name type: int the OGR Field Type (OFT), e.g. ogr.OFTString. See `Module ogr <https://gdal.org/python/osgeo.ogr-module.html>`_. width: int the width of the n...

add a layer to the vector layer Parameters ---------- name: str the layer name srs: int, str or :osgeo:class:`osr.SpatialReference` the spatial reference system. See :func:`spatialist.auxil.crsConvert` for options. geomType: int an OGR well-kn...

add a vector object to the layer of the current Vector object Parameters ---------- vec: Vector the vector object to add merge: bool merge overlapping polygons? Returns ------- def addvector(self, vec): """ add a vector object to...

create a bounding box from the extent of the Vector object Parameters ---------- outname: str or None the name of the vector file to be written; if None, a Vector object is returned format: str the name of the file format to write overwrite: bool ...

export the geometry of each feature as a wkt string Parameters ---------- set3D: bool keep the third (height) dimension? Returns ------- def convert2wkt(self, set3D=True): """ export the geometry of each feature as a wkt string Parameters ...

get features by field attribute Parameters ---------- fieldname: str the name of the queried field attribute: int or str the field value of interest Returns ------- list of :osgeo:class:`ogr.Feature` or :osgeo:class:`ogr.Feature` ...

get features by numerical (positional) index Parameters ---------- index: int the queried index Returns ------- :osgeo:class:`ogr.Feature` the requested feature def getFeatureByIndex(self, index): """ get features by numerical (p...

initialize a layer object Returns ------- def init_layer(self): """ initialize a layer object Returns ------- """ self.layer = self.vector.GetLayer() self.__features = [None] * self.nfeatures

load all feature into memory Returns ------- def load(self): """ load all feature into memory Returns ------- """ self.layer.ResetReading() for i in range(self.nfeatures): if self.__features[i] is None: self.__featur...

in-memory reprojection Parameters ---------- projection: int, str or :osgeo:class:`osr.SpatialReference` the target CRS. See :func:`spatialist.auxil.crsConvert`. Returns ------- def reproject(self, projection): """ in-memory reprojection Pa...

directly reset the spatial reference system of the vector object. This is not going to reproject the Vector object, see :meth:`reproject` instead. Parameters ---------- crs: int, str or :osgeo:class:`osr.SpatialReference` the input CRS Returns ------- ...

write the Vector object to a file Parameters ---------- outfile: the name of the file to write format: str the output file format overwrite: bool overwrite an already existing file? Returns ------- def write(self, outfile, fo...

SMBus Read Byte: i2c_smbus_read_byte_data() ============================================ This reads a single byte from a device, from a designated register. The register is specified through the Comm byte. S Addr Wr [A] Comm [A] S Addr Rd [A] [Data] NA P Functionality flag: I...

SMBus Write Word: i2c_smbus_write_word_data() ============================================== This is the opposite of the Read Word operation. 16 bits of data is written to a device, to the designated register that is specified through the Comm byte. S Addr Wr [A] Comm [A] Data...

SMBus Block Write: i2c_smbus_write_block_data() ================================================ The opposite of the Block Read command, this writes up to 32 bytes to a device, to a designated register that is specified through the Comm byte. The amount of data is specified in the Coun...

SMBus Block Write - Block Read Process Call =========================================== SMBus Block Write - Block Read Process Call was introduced in Revision 2.0 of the specification. This command selects a device register (through the Comm byte), sends 1 to 31 bytes of data t...

I2C block transactions do not limit the number of bytes transferred but the SMBus layer places a limit of 32 bytes. I2C Block Write: i2c_smbus_write_i2c_block_data() ================================================== The opposite of the Block Read command, this writes bytes to ...

I2C block transactions do not limit the number of bytes transferred but the SMBus layer places a limit of 32 bytes. I2C Block Read: i2c_smbus_read_i2c_block_data() ================================================ This command reads a block of bytes from a device, from a design...

Initialize zmq messaging. Listen on sub_port. This port might at some point receive the message to start publishing on a certain port, but until then, no publishing. def _init_zmq(self, port_publish, port_subscribe): """Initialize zmq messaging. Listen on sub_port. This port m...

Executes an process in the analysis with the given message. It also handles the start and stop signals in case an process_id is given. This method is similar to the method in databench.Analysis. def run_process(self, analysis, action_name, message='__nomessagetoken__'): """Executes an...

Event loop. def event_loop(self): """Event loop.""" try: zmq.eventloop.ioloop.IOLoop.current().start() except KeyboardInterrupt: zmq.eventloop.ioloop.IOLoop.current().stop()

Emit signal to main. Args: signal: Name of the signal to be emitted. message: Message to be sent. analysis_id: Identifies the instance of this analysis. def emit(self, signal, message, analysis_id): """Emit signal to main. Args: signal: Name of ...

Writes specified value to the pins defined as output by config_ports() method. Writing to input pins has no effect. def set_ports(self, port0 = 0x00, port1 = 0x00): 'Writes specified value to the pins defined as output by config_ports() method. Writing to input pins has no effect.' self.bus.write_byte_...

Reads logical values at pins. def get_ports(self): 'Reads logical values at pins.' return (self.bus.read_byte_data(self.address, self.STATUS_PORT0), self.bus.read_byte_data(self.address, self.STATUS_PORT1));

Reads logical values at pins. def get_config(self): 'Reads logical values at pins.' return (self.bus.read_byte_data(self.address, self.CONTROL_PORT0), self.bus.read_byte_data(self.address, self.CONTROL_PORT1));

Sets INPUT (1) or OUTPUT (0) direction on pins. Inversion setting is applicable for input pins 1-inverted 0-noninverted input polarity. def set_pullups(self, port0 = 0x00, port1 = 0x00): 'Sets INPUT (1) or OUTPUT (0) direction on pins. Inversion setting is applicable for input pins 1-inverted 0-noninverted i...

Writes specified value to the pins defined as output by method. Writing to input pins has no effect. def set_ports(self, port0 = 0x00, port1 = 0x00): 'Writes specified value to the pins defined as output by method. Writing to input pins has no effect.' self.bus.write_byte_data(self.address, self.CONTRO...

create a gffutils DB def get_gtf_db(gtf, in_memory=False): """ create a gffutils DB """ db_file = gtf + '.db' if gtf.endswith('.gz'): db_file = gtf[:-3] + '.db' if file_exists(db_file): return gffutils.FeatureDB(db_file) db_file = ':memory:' if in_memory else db_file if ...

create a BED file of transcript-level features with attached gene name or gene ids def gtf_to_bed(gtf, alt_out_dir=None): """ create a BED file of transcript-level features with attached gene name or gene ids """ out_file = os.path.splitext(gtf)[0] + '.bed' if file_exists(out_file): ...

write out a file of transcript->gene mappings. use the installed tx2gene.csv if it exists, else write a new one out def tx2genefile(gtf, out_file=None): """ write out a file of transcript->gene mappings. use the installed tx2gene.csv if it exists, else write a new one out """ installed_tx2gene ...

return a dictionary keyed by transcript_id of the associated gene_id def transcript_to_gene(gtf): """ return a dictionary keyed by transcript_id of the associated gene_id """ gene_lookup = {} for feature in complete_features(get_gtf_db(gtf)): gene_id = feature.attributes.get('gene_id', [Non...

Sets new output frequency, required parameters are real current frequency at output and new required frequency. def set_freq(self, fout, freq): """ Sets new output frequency, required parameters are real current frequency at output and new required frequency. """ hsdiv_tuple = (4, 5, 6,...

Detects alignment requirements for binary files with new nn::util::BinaryFileHeader. def _get_file_alignment_for_new_binary_file(self, file: File) -> int: """Detects alignment requirements for binary files with new nn::util::BinaryFileHeader.""" if len(file.data) <= 0x20: return 0 b...

Only checks and asks questions. Nothing is written to disk. def check_folders(name): """Only checks and asks questions. Nothing is written to disk.""" if os.getcwd().endswith('analyses'): correct = input('You are in an analyses folder. This will create ' 'another analyses folde...

Create an analysis with given name and suffix. If it does not exist already, it creates the top level analyses folder and it's __init__.py and index.yaml file. def create_analyses(name, kernel=None): """Create an analysis with given name and suffix. If it does not exist already, it creates the top le...

Create analysis files. def create_analysis(name, kernel, src_dir, scaffold_name): """Create analysis files.""" # analysis folder folder = os.path.join(os.getcwd(), 'analyses', name) if not os.path.exists(folder): os.makedirs(folder) else: log.warning('Analysis folder {} already exi...

convert between different types of spatial references Parameters ---------- crsIn: int, str or :osgeo:class:`osr.SpatialReference` the input CRS crsOut: {'wkt', 'proj4', 'epsg', 'osr', 'opengis' or 'prettyWkt'} the output CRS type Returns ------- int, str or :osgeo:class:`o...

compute the distance in meters between two points in latlon Parameters ---------- lat1: int or float the latitude of point 1 lon1: int or float the longitude of point 1 lat2: int or float the latitude of point 2 lon2: int or float the longitude of point 2 Re...

a simple wrapper for :osgeo:func:`gdal.Warp` Parameters ---------- src: str, :osgeo:class:`ogr.DataSource` or :osgeo:class:`gdal.Dataset` the input data set dst: str the output data set options: dict additional parameters passed to gdal.Warp; see :osgeo:func:`gdal.WarpOption...

a simple wrapper for :osgeo:func:`gdal.BuildVRT` Parameters ---------- src: str, list, :osgeo:class:`ogr.DataSource` or :osgeo:class:`gdal.Dataset` the input data set(s) dst: str the output data set options: dict additional parameters passed to gdal.BuildVRT; see :osgeo:func...

a simple wrapper for `gdal.Translate <https://gdal.org/python/osgeo.gdal-module.html#Translate>`_ Parameters ---------- src: str, :osgeo:class:`ogr.DataSource` or :osgeo:class:`gdal.Dataset` the input data set dst: str the output data set options: dict additional parameters ...

a simple wrapper for gdal.VectorTranslate aka `ogr2ogr <https://www.gdal.org/ogr2ogr.html>`_ Parameters ---------- src: str or :osgeo:class:`ogr.DataSource` the input data set dst: str the output data set options: dict additional parameters passed to gdal.VectorTranslate; ...

a simple wrapper for gdal.Rasterize Parameters ---------- src: str or :osgeo:class:`ogr.DataSource` the input data set dst: str the output data set options: dict additional parameters passed to gdal.Rasterize; see :osgeo:func:`gdal.RasterizeOptions` Returns ------- ...

reproject a coordinate from one CRS to another Parameters ---------- x: int or float the X coordinate component y: int or float the Y coordinate component s_crs: int, str or :osgeo:class:`osr.SpatialReference` the source CRS. See :func:`~spatialist.auxil.crsConvert` for ...

Creates output_dir, work_dir, and sets up log def set_up_dirs(proc_name, output_dir=None, work_dir=None, log_dir=None): """ Creates output_dir, work_dir, and sets up log """ output_dir = safe_mkdir(adjust_path(output_dir or join(os.getcwd(), proc_name)), 'output_dir') debug('Saving results into ' + out...

Generator used to yield 100 KiB chunks for a given response. def _iter_content_generator(response, decode_unicode): """Generator used to yield 100 KiB chunks for a given response.""" for chunk in response.iter_content(100 * 1024, decode_unicode=decode_unicode): if decode_unicode: # Replace ...

Iterates over the response data, one line at a time. When stream=True is set on the request, this avoids reading the content at once into memory for large responses. The function is taken from :meth:`requests.models.Response.iter_lines`, but modified to use our :func:`~spacetrack.base._iter_content_ge...

Raises stored :class:`HTTPError`, if one occurred. This is the :meth:`requests.models.Response.raise_for_status` method, modified to add the response from Space-Track, if given. def _raise_for_status(response): """Raises stored :class:`HTTPError`, if one occurred. This is the :meth:`requests.models.R...

r"""Generic Space-Track query. The request class methods use this method internally; the public API is as follows: .. code-block:: python st.tle_publish(*args, **kw) st.basicspacedata.tle_publish(*args, **kw) st.file(*args, **kw) st.fileshare.fi...

Perform get request, handling rate limiting. def _ratelimited_get(self, *args, **kwargs): """Perform get request, handling rate limiting.""" with self._ratelimiter: resp = self.session.get(*args, **kwargs) # It's possible that Space-Track will return HTTP status 500 with a ...

Find first controller that matches given request class. Order is specified by the keys of ``SpaceTrackClient.request_controllers`` (:class:`~collections.OrderedDict`) def _find_controller(self, class_): """Find first controller that matches given request class. Order is specif...

Get raw predicate information for given request class, and cache for subsequent calls. def _download_predicate_data(self, class_, controller): """Get raw predicate information for given request class, and cache for subsequent calls. """ self.authenticate() url = ('{0}{1...

Get full predicate information for given request class, and cache for subsequent calls. def get_predicates(self, class_, controller=None): """Get full predicate information for given request class, and cache for subsequent calls. """ if class_ not in self._predicates: ...

Proxy ``get_predicates`` to client with stored request controller. def get_predicates(self, class_): """Proxy ``get_predicates`` to client with stored request controller. """ return self.client.get_predicates( class_=class_, controller=self.controller)

Add the folding menu to the editor, on install. :param editor: editor instance on which the mode has been installed to. def on_install(self, editor): """ Add the folding menu to the editor, on install. :param editor: editor instance on which the mode has been installed to. """...

Draw the background rectangle using the current style primitive color or foldIndicatorBackground if nativeFoldingIndicator is true. :param rect: The fold zone rect to draw :param painter: The widget's painter. def _draw_rect(self, rect, painter): """ Draw the background rectan...

Gets a system color for drawing the fold scope background. def get_system_bck_color(): """ Gets a system color for drawing the fold scope background. """ def merged_colors(colorA, colorB, factor): maxFactor = 100 colorA = QtGui.QColor(colorA) colorB =...

Draw the fold indicator/trigger (arrow). :param top: Top position :param mouse_over: Whether the mouse is over the indicator :param collapsed: Whether the trigger is collapsed or not. :param painter: QPainter def _draw_fold_indicator(self, top, mouse_over, collapsed, painter): ...

Gets the base scope highlight color (derivated from the editor background) def _get_scope_highlight_color(self): """ Gets the base scope highlight color (derivated from the editor background) """ color = self.editor.background if color.lightness() < 128: ...

Adds a scope decoration that enclose the current scope :param start: Start of the current scope :param end: End of the current scope :param parent_start: Start of the parent scope :param parent_end: End of the parent scope :param base_color: base color for scope decoration ...

Show a scope decoration on the editor widget :param start: Start line :param end: End line def _add_scope_decorations(self, block, start, end): """ Show a scope decoration on the editor widget :param start: Start line :param end: End line """ try: ...

Highlights the scopes surrounding the current fold scope. :param block: Block that starts the current fold scope. def _highlight_surrounding_scopes(self, block): """ Highlights the scopes surrounding the current fold scope. :param block: Block that starts the current fold scope. ...

Removes scope decorations and background from the editor and the panel if highlight_caret_scope, else simply update the scope decorations to match the caret scope. def leaveEvent(self, event): """ Removes scope decorations and background from the editor and the panel if highligh...

Add fold decorations (boxes arround a folded block in the editor widget). def _add_fold_decoration(self, block, region): """ Add fold decorations (boxes arround a folded block in the editor widget). """ deco = TextDecoration(block) deco.signals.clicked.connect(se...

Toggle a fold trigger block (expand or collapse it). :param block: The QTextBlock to expand/collapse def toggle_fold_trigger(self, block): """ Toggle a fold trigger block (expand or collapse it). :param block: The QTextBlock to expand/collapse """ if not TextBlockHelpe...

On state changed we (dis)connect to the cursorPositionChanged signal def on_state_changed(self, state): """ On state changed we (dis)connect to the cursorPositionChanged signal """ if state: self.editor.key_pressed.connect(self._on_key_pressed) if self._highlight...

Override key press to select the current scope if the user wants to deleted a folded scope (without selecting it). def _on_key_pressed(self, event): """ Override key press to select the current scope if the user wants to deleted a folded scope (without selecting it). """ ...

Auto indent if the released key is the return key. :param event: the key event def _on_key_pressed(self, event): """ Auto indent if the released key is the return key. :param event: the key event """ if not event.isAccepted(): if event.key() == Qt.Key_Return ...

Verify that the payload was sent from our GitHub instance. def verify_signature(self, payload, headers): """Verify that the payload was sent from our GitHub instance.""" github_signature = headers.get("x-hub-signature") if not github_signature: json_abort(401, "X-Hub-Signature heade...

Get the options that have been set. Called after the user has added all their own options and is ready to use the variables. def get_options(self): """Get the options that have been set. Called after the user has added all their own options and is ready to use the variables. ...

Check for job definitions in known zuul files. def parse_job_files(self): """Check for job definitions in known zuul files.""" repo_jobs = [] for rel_job_file_path, job_info in self.job_files.items(): LOGGER.debug("Checking for job definitions in %s", rel_job_file_path) ...

Changes the current directory. Change is made by running a "cd" command followed by a "clear" command. :param directory: :return: def change_directory(self, directory): """ Changes the current directory. Change is made by running a "cd" command followed by a "clear" co...

Gets the icon file name. Read-only. def icon(self): """ Gets the icon file name. Read-only. """ if isinstance(self._icon, str): if QtGui.QIcon.hasThemeIcon(self._icon): return QtGui.QIcon.fromTheme(self._icon) else: return QtGui.QI...

Adds the marker to the panel. :param marker: Marker to add :type marker: pyqode.core.modes.Marker def add_marker(self, marker): """ Adds the marker to the panel. :param marker: Marker to add :type marker: pyqode.core.modes.Marker """ self._markers.appen...

Removes a marker from the panel :param marker: Marker to remove :type marker: pyqode.core.Marker def remove_marker(self, marker): """ Removes a marker from the panel :param marker: Marker to remove :type marker: pyqode.core.Marker """ self._markers.remo...

Returns the marker that is displayed at the specified line number if any. :param line: The marker line. :return: Marker of None :rtype: pyqode.core.Marker def marker_for_line(self, line): """ Returns the marker that is displayed at the specified line number if ...

Display tooltip at the specified top position. def _display_tooltip(self, tooltip, top): """ Display tooltip at the specified top position. """ QtWidgets.QToolTip.showText(self.mapToGlobal(QtCore.QPoint( self.sizeHint().width(), top)), tooltip, self)

Search occurrences using str.find instead of regular expressions. :param string: string to parse :param sub: search string :param whole_word: True to select whole words only def finditer_noregex(string, sub, whole_word): """ Search occurrences using str.find instead of regular expressions. :p...

Generator that finds all occurrences of ``sub`` in ``string`` :param string: string to parse :param sub: string to search :param regex: True to search using regex :param case_sensitive: True to match case, False to ignore case :param whole_word: True to returns only whole words :return: def fi...

Worker that finds all occurrences of a given string (or regex) in a given text. :param data: Request data dict:: { 'string': string to search in text 'sub': input text 'regex': True to consider string as a regular expression 'whole_word': True to match wh...

Splits a text in a meaningful list of words based on a list of word separators (define in pyqode.core.settings) :param txt: Text to split :param seps: List of words separators :return: A **set** of words found in the document (excluding punctuations, numbers, ...) def split...