visualize ❭ cell_morphology_visualizer ❭ CMVDataParser ❭ _calc_morphology

CMVDataParser._calc_morphology

visualize.cell_morphology_visualizer.CMVDataParser._calc_morphology(cell)

Retrieve cell morphology from cell object.

Retrieves all points of the cell morphology from the cell object. In addition, it keeps track of parent sections. Fills the following attributes:

  • self._morphology_unconnected: a pandas DataFrame containing point information, diameter and section ID WITHOUT duplicated points for branchpoints for connections between sections.

  • self.morphology: a pandas DataFrame containing point information, diameter and section ID WITHOUT duplicated points for branchpoints for connections between sections. Same as above, but publically accessible.

  • self._morphology_connected: a pandas DataFrame containing point information, diameter and section ID WITH duplicated points for branchpoints for connections between sections. Same as above, but with branchpoints connected to the parent section.

  • self.sections: an array of unique section indices.

  • self.n_sections: number of sections in the cell.

  • self.parents: a dictionary that maps sections to their parents. self.parents[10] returns the parent of section 10.

Parameters:

cell – Cell object

Returns:

Nothing. Updates the attributes mentioned above.