simple_test_movies_cells_only.py

import sys
import matplotlib.pyplot as plt
sys.path.append(r'../python_imaging')

from image_processing_for_physicell import *

options_for_figure2d = {} # should be the same as 2b and 2c

options_for_figure2d = {"output_plot" : True,
                       "show_plot" : False,
                       "produce_for_panel" : False,
                        "plot_ECM_anisotropy" : False,
                        "plot_ECM_orientation" : False,
                        "retrieve_ECM_data": False,
                        "load_full_physicell_data" : False,
                        "plot_cells_from_SVG" : True,
                        "load_SVG_data": True,
                        'plot_cells_from_physicell_data': False,
                        "produce_for_movie" : True,
                        "quiver_options" : {"scale_quiver": False,
                                          "mask_quiver": False}
                       }

movie_options_for_figure_2d = {}

movie_options_for_figure_2d = {'INCLUDE_ALL_SVGs': True,
                            'INCLUDE_FULL_HISTORY': True
                            }

#### Right now, if you don't have None or the full contour and quiver options, it will break in the plotting ... I wonder if there
#### is a better/more robust way to do it (kwargs???, lots of "trapping"??) but this will be handled later ... and I can ask Randy etc
### What is up with scaling - hum ...

# oof - I got different results on the two runs when I did and didn't scale by anistoropy ... yikes! How do I manage that!!

mf = PhysiCellPlotter()

mf.produce_movie(save_name='simple_test_cells', movie_options=movie_options_for_figure_2d, image_options=options_for_figure2d)

# mf.generic_plotter(starting_index=0, number_of_samples=1, options=options_for_figure2d, file_name='circular_ECM_w_chemical_cue_0')

# image_list_for_figure2d = [150, 417]

# options_for_figure2d['plot_ECM_orientation'] = False
# options_for_figure2d['retrieve_ECM_data'] = False
# options_for_figure2d['load_full_physicell_data'] = False


# mf.produce_movie()

# for number in image_list_for_figure2d:
#     mf.generic_plotter(starting_index=0, number_of_samples=number, options=options_for_figure2d, file_name='circular_ECM_w_chemical_cue_' + str(number))