Files

Tools for loading and processing experimental data.

pyneurotrace.files.load2PData(path, hasLocation=True)

Load Node IDs, positions, and raw data from an EXPT.TXT file.

Parameters:

  • path (string) – Path to the EXPT.TXT file.

  • hasLocation (bool, optional) – Flag indicating if location data is available. Default is True.

Returns:

  • nodeIDs (np.array) – List of node IDs.

  • positions (np.array) – Node positions (if hasLocation is True).

  • rawData (np.array) – Raw trace data.

pyneurotrace.files.loadMetadata(path)

Load stimulus [start, end] sample indices, plus sample rate, from the rscan_metadata .txt file.

Parameters:

path (string) – Path to the metadata file.

Returns:

  • stimIndices (array) – Array of stimulus start and end indices.

  • hz (float) – Sample rate in Hz.

  • xySizeM (float) – XY pixel size in meters

  • zStackLocations (array) – Array of Z stack locations.

pyneurotrace.files.loadTreeStructure(path)

Load Tree structure (branch & parent details) from an interp-neuron-.txt file.

Parameters:

path (string) – Path to the tree structure file.

Returns:

  • rootId (int) – ID of the root node.

  • nodes (dict) – Dictionary of nodes with their details.

pyneurotrace.files.loadNodeXYZ(path)

Load (nodeID, x, y, z) from a file, separate from the traces file. Return as the list of IDs, then the list of positions. This supports having positions for nodes which have no trace recorded.

Parameters:

path (string) – Path to the file containing node XYZ data.

Returns:

  • nodeIDs (array) – List of node IDs.

  • positions (array) – Node positions.

pyneurotrace.files.loadKymograph(path, pxlPerNode=11)

Load kymograph - a big (R x C) matrix with: a) First row is node IDs, every pxlPerNode (the rest being -1) b) The remaining are concatenated blocks of (R - 1) x (pxlPerNode) kymograph intensities This parses them out, and returns as a mapping of node ID -> Kymograph data. Load kymograph data from a file.

Parameters:

  • path (string) – Path to the kymograph file.

  • pxlPerNode (int, optional) – Number of pixels per node. Default is 11.

Returns:

kymoData – Dictionary mapping node IDs to kymograph data.

Return type:

dict

pyneurotrace.files.loadSingleStep(stepPath, metaPath, treePath, xyzsPath, kymoPath, volumeXYZSource, convertXYZtoPx=False, normalizeXYZ=False)

Loads as many of the above as possible for a single step of an experiment.

Parameters:

  • stepPath (string) – Path to EXPT.TXT raw data traces.

  • metaPath (string) – Path to metadata file containing sample rate, stim times, and pixel sizes.

  • treePath (string) – Path to tree structure file.

  • xyzsPath (string, optional) – Path to mapping from ID to x/y/z location of all points in the tree.

  • kymoPath – Path to kymograph intensity time series for all scanned points.

  • volumeXYZSource (array, optional) – Source for position data if not available for all points (e.g., planar scan).

  • convertXYZtoPx (bool, optional) – Flag indicating if XYZ should be converted to pixels. Default is False.

  • normalizeXYZ (bool, optional) – Flag indicating if XYZ should be normalized. Default is False.

Returns:

stepData – Dictionary containing the data for a single step of an experiment.

Return type:

dict

pyneurotrace.files.loadHybrid(rootPath, loadKymoData=False, convertXYZtoPx=False, getPlanarXYZFromVolume=False, normalizeXYZ=False)

Loads an entire hybrid experiment from a folder, containing many scan results.

Parameters:

  • rootPath (string) – Folder to load all the steps from.

  • loadKymoData (bool, optional) – Flag indicating whether to load kymographs. Default is False.

  • convertXYZtoPx (bool, optional) – Flag indicating if XYZ should be converted to pixels. Default is False.

  • getPlanarXYZFromVolume (bool, optional) – Flag indicating if planar XYZ should be obtained from volume. Default is False.

  • normalizeXYZ (bool, optional) – Flag indicating if XYZ should be normalized. Default is False.

Returns:

hybridData – Dictionary containing data for the entire hybrid experiment.

Return type:

dict