write_cell_simulation¶

single_cell_parser.writer.write_cell_simulation(fname=None, cell=None, traces=None, tVec=None, allPoints=False, step_frames=10, selected_index=None)¶

Write Amira SpatialGraph files corresponding to time steps of entire simulation run.

Recorded quantities are passed in tuple traces with strings and recorded in Vectors attached to Sections of cell

Attention

Make sure to have created the cell with allPoints = True.

Attention

Performs interpolation if nseg != nrOfPts for a Section

Parameters:¶

fname : str¶

The name of the file to write to.

cell : single_cell_parser.cell.Cell¶

The cell object.

traces : list¶

A list of strings, each representing a recorded quantity.

tVec : list¶

A list of time points.

allPoints : bool¶

If True, all points of the cell are written to the file.

step_frames : int¶

The number of frames to write.

selected_index : list¶

A list of indices of the sections to write.

Example:

>>> write_cell_simulation(
...     '/output/directory',
...     cell = cell,
...     traces = ['Vm'],
...     tVec = cell.tVec,
...     step_frames = 1,
...     selected_index=[selected_index],
...     allPoints = True)