pyroglancer package

Subpackages

Submodules

pyroglancer.createconfig module

Module for creating yaml based configuration files for adding layers in the neuroglancer.

pyroglancer.createconfig.createconfig(configdata, configfileloc=None, overwrite=False)[source]

Create config file in case it is not found.

Parameters

configdata (dict) – different layers to be added in the neuroglancer instance
configfileloc (str) – location of the configuration file
overwrite (bool) – if set to True, then overwrites the existing configuration file

pyroglancer.createconfig.getdefaultconfigdata()[source]: Get neuroglancer layer data from default configuration in case configuration fileit is not found.

pyroglancer.flywire module

pyroglancer.layers module

pyroglancer.loadconfig module

Module contains functions to handle configuratio data fron YAML files.

pyroglancer.loadconfig.getconfigdata(configfileloc=None)[source]

Get the YAML config data from the default location.

Parameters: configfileloc (str) – override the default location if configfileloc is present
Returns: configdata – different layers to be added in the neuroglancer instance
Return type: dict

pyroglancer.localserver module

This code is used to serve local data via http port, so it can be read by neuroglancer.

class pyroglancer.localserver.RequestHandler(*args, directory=None, **kwargs)[source]

Bases: http.server.SimpleHTTPRequestHandler

This class provides support for generic cors access, HTTP ‘Range’ requests In case of the range implementation, the approach is to: - Override send_head to look for ‘Range’ and respond appropriately. - Override copyfile to only transmit a range when requested.

copyfile(source, outputfile)[source]

Copy all data between two file objects.

The SOURCE argument is a file object open for reading (or anything with a read() method) and the DESTINATION argument is a file object open for writing (or anything with a write() method).

The only reason for overriding this would be to change the block size or perhaps to replace newlines by CRLF – note however that this the default server uses this to copy binary data as well.

do_OPTIONS()[source]

end_headers()[source]: Allow responses to be shared with any requester without any credentials.

send_head()[source]

Common code for GET and HEAD commands.

This sends the response code and MIME headers.

Return value is either a file object (which has to be copied to the outputfile by the caller unless the command was HEAD, and must be closed by the caller under all circumstances), or None, in which case the caller has nothing further to do.

class pyroglancer.localserver.Server(server_address)[source]

Bases: http.server.HTTPServer

Class for basic HTTP server.

protocol_version = 'HTTP/1.1'

pyroglancer.localserver.closedataserver(removefiles=True)[source]

Close a already started dataserver.

Parameters: removefiles (flag to remove the created contents in the hosted server) –
Return type: None

pyroglancer.localserver.copy_byte_range(infile, outfile, start=None, stop=None, bufsize=16384)[source]: Like shutil.copyfileobj, but only copy a range of the streams. Both start and stop are inclusive.

pyroglancer.localserver.parse_byte_range(byte_range)[source]: Returns the two numbers in ‘bytes=123-456’ or throws ValueError. The last number or both numbers may be None.

pyroglancer.localserver.startdataserver(address='127.0.0.1', port=8000, directory=None, restart=True)[source]

Start a dataserver thread(return control back) that can host local folder via http.

Parameters

address (str) – ip address to use for the local host server
port (int) – port number to use for the local host server
directory (str) – local directory to be used for hosting
restart (bool) – restart/clean up already running data server

pyroglancer.meshgenerator module

Module contains functions to generate multi-resolution meshes.

class pyroglancer.meshgenerator.Quantize(fragment_origin, fragment_shape, input_origin, quantization_bits)[source]: Bases: object

pyroglancer.meshgenerator.cmp_zorder(lhs, rhs)[source]

Return type: bool

pyroglancer.meshgenerator.decompose_meshes(verts, faces, nodes_per_dim, bits)[source]

pyroglancer.ngspaces module

pyroglancer.ngviewer module

Module contains code to open a neuroglancer viewer.

pyroglancer.ngviewer.closeviewer()[source]: Close a already started ngviewer.

pyroglancer.ngviewer.get_ngscreenshot(ngviewer, viewer_size=[1000, 1000])[source]

Get screenshot of neuroglancer viewing engine. :param ngviewer: object of Neuroglancer viewer class. :type ngviewer: ng.viewer.Viewer :param viewer_size: :type viewer_size: screenshot size

Returns: screenshot
Return type: screenshot image.

pyroglancer.ngviewer.openviewer(ngviewer=None, headless=False)[source]

Open a neuroglancer viewing engine.

Parameters

ngviewer (ng.viewer.Viewer) – object of Neuroglancer viewer class.
headless (bool) – if True, then operating in servers or testcase mode.

Returns

ngviewer – object of Neuroglancer viewer class.

Return type

ng.viewer.Viewer

pyroglancer.ngviewer.setviewerstate(ngviewer=None, axis_lines=True, bounding_box=True, layout=None, zoom_factor=None)[source]

Set state of neuroglancer viewing engine.

Parameters

ngviewer (ng.viewer.Viewer) – object of Neuroglancer viewer class.
axis_lines (bool) – if False, then disable the axis lines.
bounding_box (bool) – if False, then disable the default annotations like bounding box.
layout (string | dict) – possible layout options.
zoom_factor (float) – zoom factor of image.

Returns

ngviewer – object of Neuroglancer viewer class.

Return type

ng.viewer.Viewer

pyroglancer.points module

Module contains functions to handle point data.

pyroglancer.points.annotate_points(ngviewer, dimensions, pointscolor, points_df, layer_name, layer_scale)[source]

Annotate points from a dataframe (defunct do not use..).

Parameters

ngviewer (ng.viewer.Viewer) – object of Neuroglancer viewer class.
dimensions (neuroglancer.CoordinateSpace) – object of neuroglancer coordinate space class.
points_df (dataframe) – should contain ‘x’, ‘y’, ‘z’ columns
layer_scale (int | float) – scaling from voxel to native space in ‘x’, ‘y’, ‘z’

pyroglancer.points.commit_info(pointinfo, path, pointlayername)[source]

Commit the info file created for the points based precomputed format.

Parameters

pointinfo (dict) – info in json format for the points
path (str) – local path of the precomputed hosted layer.
pointlayername (str) – name for the points layer

pyroglancer.points.create_pointinfo(dimensions, path, layer_name)[source]

Create info file for the points based precomputed format.

Parameters

path (str) – local path of the precomputed hosted layer.
layer_name (str) – name for the points layer
dimensions (neuroglancer.CoordinateSpace) – object of neuroglancer coordinate space class.

Returns

path – local path of the precomputed hosted layer.

Return type

str

pyroglancer.points.put_pointfile(path, layer_name, points, pointsscale, pointname)[source]

Put pointfile in the local dataserver.

Parameters

path (str) – local path of the precomputed hosted layer.
layer_name (str) – name for the points layer
points (dataframe) – should contain ‘x’, ‘y’, ‘z’ columns
pointsscale (int | float) – scaling from voxel to native space in ‘x’, ‘y’, ‘z’
pointsname (str) – name for the points (not yet implemented)

pyroglancer.points.upload_points(points_df, path, layer_name, layer_scale)[source]

Upload points from a dataframe.

Parameters

points_df (dataframe) – should contain ‘x’, ‘y’, ‘z’ columns
path (str) – local path of the precomputed hosted layer.
layer_name (str) – name for the points layer
layer_scale (int | float) – scaling from voxel to native space in ‘x’, ‘y’, ‘z’

pyroglancer.skeletons module

pyroglancer.synapses module

Module contains functions to handle synapse data.

pyroglancer.synapses.annotate_synapses(ngviewer, dimensions, x)[source]

Annotate postsynapses of a neuron/neuronlist. (defunct do not use..).

This function annotates synapses of a neuron/neuronlist

Parameters

ngviewer (ng.viewer.Viewer) – object of Neuroglancer viewer class.
dimensions (neuroglancer.CoordinateSpace) – object of neuroglancer coordinate space class.
x (CatmaidNeuron | CatmaidNeuronList or TreeNeuron | NeuronList) – neuron or neuronlist of different formats

Returns

status – annotation status

Return type

bool

pyroglancer.synapses.commit_info(synapseinfo, path, synapsetype)[source]

Commit the info file created for the synapses based on precomputed format.

Parameters

synapseinfo (dict) – info in json format for the synapses
path (str) – local path of the precomputed hosted layer.
synapsetype (str) – pre or postsynapses

pyroglancer.synapses.create_synapseinfo(dimensions, path)[source]

Create info file for the synapse based precomputed format.

Parameters

path (str) – local path of the precomputed hosted layer.
dimensions (neuroglancer.CoordinateSpace) – object of neuroglancer coordinate space class.

pyroglancer.synapses.put_synapsefile(path, synapsetype, synapses, skeletonid)[source]

Put synapse in the local dataserver.

Parameters

path (str) – local path of the precomputed hosted layer.
synapsetype (str) – pre or postsynapses
synapses (dataframe) – contains ‘x’, ‘y’, ‘z’ columns
skeletonid (int) – skeleton id to be associated with the corresponding synapse
pointsname (str) – name for the points (not yet implemented)

pyroglancer.synapses.synapses2nodepoints(x, layer_scale)[source]

Generate nodepoints (point A, point B) from synapses for given neuron(s).

Parameters

x (CatmaidNeuron | CatmaidNeuronList or TreeNeuron | NeuronList) – neuron or neuronlist of different formats
layer_scale (int | float) – scaling from voxel to native space in ‘x’, ‘y’, ‘z’

Returns

synapsepointscollec_df – contains synapse points in point A - point B format used in flywire annotations.

Return type

dataframe

pyroglancer.synapses.upload_synapses(x, path)[source]

Upload synpases from a neuron or neuronlist.

Parameters

x (CatmaidNeuron | CatmaidNeuronList or TreeNeuron | NeuronList) – neuron or neuronlist of different formats
path (str) – local path of the precomputed hosted layer.

pyroglancer.utils module

Module contains utility functions.

pyroglancer.utils.get_alphavalue(layer_kws)[source]: Get alpha values from the interface APIs.

pyroglancer.utils.get_annotationstatetype(layer_kws)[source]: Get alpha values from the interface APIs.

pyroglancer.utils.get_hexcolor(layer_kws)[source]: Convert text based color to hex value.

pyroglancer.utils.get_scalevalue(layer_kws)[source]: Get scale values from the interface APIs.

pyroglancer.utils.obj2pointcloud(objurl=None)[source]

Convert object url to point cloud data in open3d format.

Parameters: objurl (str) – url containing the obj file.
Returns: pcd – point cloud object of open3d PointCloud class.
Return type: o3d.geometry.PointCloud

pyroglancer.utils.pointcloud2meshes(pcd_data, algorithm='rollingball', **kwargs)[source]

Convert point cloud files to volumetric meshes.

Parameters

pcd_data (o3d.geometry.PointCloud or str) – pointcloud object or file location in polygon file format.
algorithm (str) – algorithm of either ‘rollingball’ or ‘marchingcubes’ to convert points to meshes.

Returns

ret_mesh – mesh object of navis volume class.

Return type

navis.Volume

pyroglancer.volumes module

Module contents

Module contains functions to handle init etc.