visualize ❭ cell_morphology_visualizer ❭ CellMorphologyVisualizer ❭ write_video

CellMorphologyVisualizer.write_video

visualize.cell_morphology_visualizer.CellMorphologyVisualizer.write_video(images_path, out_name, overwrite_frames=False, color='grey', show_synapses=False, show_legend=False, client=None, t_start=None, t_stop=None, t_step=None, highlight_section=None, highlight_x=None, quality=5, codec='mpeg4', tpf=20)

Write the individual frames of a neuron during a simulation and merge them into a video.

Creates a set of images of a neuron color-coded with voltage together with synapse activations. The parameters t_start, t_stop and t_step update the times_to_show attribute.

Parameters:

  • images_path (str) – dir where the images for the gif will be generated

  • out_name (str) – path location of the resulting gif.

  • overwrite_frames (bool) – whether to overwrite previously existing frames in the images_path directory.

  • color (str) – color of the cell morphology. Can be a fixed color, or a keyword referring to scalar data of the simulation, such as membrane voltage or ion channel dynamics.

  • show_synapses (bool) – whether to show the synapse activation locations onto the morphology.

  • show_legend (bool) – whether to show the color legend in the plot.

  • client (distributed.client.Client) – dask client for parallelization

  • t_start (float) – start time point of our time series visualization

  • t_stop (float) – last time point of our time series visualization

  • t_step (float) – time between the different time points of our visualization

  • highlight_section (int) – section number of the section that should be highlighted with an arrow.

  • highlight_x (float) – x coordinate of the section that should be highlighted with an arrow.

  • framerate (int) – frames per second

  • quality (int) – quality of the output video. 1 is the highest quality and 31 is the lowest quality. This is ignored if codec is not MPEG* (mpeg4, mpeg2video, mpeg1video, mjpeg, libxvid, msmpeg4).

  • codec (str) – codec to use for the video. Default is mpeg4.

  • tpf (float) – duration of each frame in ms