morphology_workflows.marker_helper¶

Module to read/write/plot morphology markers.

Attributes¶

logger

Exceptions¶

MarkerHelperError

Exception for Marker helpers.

Classes¶

`MarkerSet`	Container of several markers for a single morphology.
`Marker`	Container of a single marker.

Module Contents¶

morphology_workflows.marker_helper.logger¶

exception morphology_workflows.marker_helper.MarkerHelperError¶

Bases: morphology_workflows.MorphologyWorkflowsError

Exception for Marker helpers.

class morphology_workflows.marker_helper.MarkerSet¶

Container of several markers for a single morphology.

markers = None¶

morph_name = None¶

morph_path = None¶

classmethod from_markers(markers)¶: Load from a list of Marker object.

static check_labels(markers)¶: Ensure label names are different.

classmethod from_file(marker_path)¶: Load maker yaml file.

classmethod from_dicts(markers)¶: Load marker from dict, where markers[“markers”] is a list of dict markers.

plot(filename='markers.html', with_plotly=True, plane='3d', **kwargs)¶: Plot morphology with markers.

to_dicts()¶: Create a list of dicts from marker class.

save(filename=None, mode='a')¶

Save marker data.

Parameters:

filename (str) – if provided, path to marker file
mode (str) – writing mode, ‘a’ or ‘w’

TODO: if data is large, write in an h5/pickle for speedup

class morphology_workflows.marker_helper.Marker(label, marker_type, data, morph_name=None, morph_path=None, plot_style=None, extra_data=None)¶

Container of a single marker.

label¶

marker_type¶

data¶

morph_name¶

morph_path¶

extra_data¶

property list_data¶: Returns data without numpy types.

to_dict()¶: Create a dict from marker class.