From b12a652154e6a17ec0adfede289b408ddff07bfb Mon Sep 17 00:00:00 2001 From: jpmetzca Date: Tue, 12 Mar 2024 22:47:26 -0400 Subject: [PATCH] Found a missing config file and two recently added imaging scripts. --- ...lower_model_decreased_remodeling_rates.xml | 419 ++++++++++++++++++ ...story_multilevel_contour_movie_fibrosis.py | 56 +++ ...ilevel_contour_movie_invasive_carcinoma.py | 57 +++ 3 files changed, 532 insertions(+) create mode 100644 config/leader_follower_model_decreased_remodeling_rates.xml create mode 100644 python_imaging/partial_history_multilevel_contour_movie_fibrosis.py create mode 100644 python_imaging/partial_history_multilevel_contour_movie_invasive_carcinoma.py diff --git a/config/leader_follower_model_decreased_remodeling_rates.xml b/config/leader_follower_model_decreased_remodeling_rates.xml new file mode 100644 index 0000000..f3018f0 --- /dev/null +++ b/config/leader_follower_model_decreased_remodeling_rates.xml @@ -0,0 +1,419 @@ + + + + + + + + + + + + + -800 + 800 + -800 + 800 + -10 + 10 + 20 + 20 + 20 + true + + + + 14400.0 + min + micron + 0.01 + 0.1 + 6 + + + + 6 + + + + leader_follower_decreased_remodeling + + 6 + true + + + 6 + true + + oxygen + + + + + + false + + + + + false + true + true + + + + + + 100000.0 + 0.1 + + 0 + 38 + + 38 + 38 + 38 + 38 + 38 + 38 + + + + true + true + + ./config/initial.mat + + + ./config/dirichlet.mat + + + + + + + + + + 0.0 + + + + + 0.0 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 10.0 + 25.0 + 1.25 + + 1.0 + 1.0 + + + 1.8 + 15.12 + + 0.01 + 0.0 + 0.0 + + + 0.5 + 10 + 0.95 + + true + true + + true + oxygen + 1 + + + false + false + + 0.0 + + + + + + + 0 + 38 + 10 + 0 + + + + 0.0 + + 0.0 + 0.0 + + + 0.0 + 0.0 + + 1.0 + + 0.0 + 0.0 + + + + + 0.0 + 0.0 + + + + + 0.0 + 1.0 + 0.5 + 0.5 + 0.05 + 0.0 + 38 + 0.5 + 1.0 + 0 + 0.001 + 1.0 + 1.0 + 0.0 + 1.0 + 1.0 + + + + + + + 0.0 + + + + + 0 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 10.0 + 25.0 + 1.25 + + 1.0 + 1.0 + + + 1.8 + 15.12 + + 0.01 + 0.0 + 0.0 + + + .5 + 10 + 0.05 + + true + true + + true + oxygen + 1 + + + false + false + + 0.0 + + + + + + + 0 + 38 + 10 + 0 + + + + 0.0 + + 0.0 + 0.0 + + + 0.0 + 0.0 + + 1.0 + + 0.0 + 0.0 + + + + + 0.0 + 0.0 + + + + + 0.0 + 1.0 + 0.5 + 0.5 + 1.0 + 1.0 + 38 + 0.5 + 1.0 + 0 + 0.000 + 0.0 + 0.0 + 0.0 + 1.0 + 1.0 + + + + + + + ./config + cells.csv + + + + + 0.0 + 0.5 + lesion + 175 + 0.05 + 10 + 0.5 + 10.0 + 10.0 + 25.0 + 0.95 + 0.004 + 4.0 + 0.5 + 10.0 + 25.0 + 0.05 + 1.0 + 0.0 + 1.0 + 0.5 + 1.0 + true + true + 0.1 + none + 45.0 + random + 20 + 20 + 20 + follower chemotaxis/no follower hysteresis + 1 + 0 + ecm_update_from_cell_motility_vector + false + 10 + false + 0 + 0 + none + true + + \ No newline at end of file diff --git a/python_imaging/partial_history_multilevel_contour_movie_fibrosis.py b/python_imaging/partial_history_multilevel_contour_movie_fibrosis.py new file mode 100644 index 0000000..4582786 --- /dev/null +++ b/python_imaging/partial_history_multilevel_contour_movie_fibrosis.py @@ -0,0 +1,56 @@ +import sys +import matplotlib.pyplot as plt +sys.path.append(r'../python_imaging') + +from image_processing_for_physicell import * + +options_for_figure4_movie = {} + +options_for_figure4_movie = {"output_plot" : True, + "show_plot" : False, + "produce_for_panel" : False, + "plot_ECM_anisotropy" : True, + "plot_ECM_orientation" : False, + "plot_ECM_density" : True, + "retrieve_ECM_data": True, + "load_full_physicell_data" : True, + "plot_cells_from_SVG" : True, + "load_SVG_data": True, + 'plot_cells_from_physicell_data': False, + "produce_for_movie" : True, + "contour_options" : {'lowest_contour': 0.5, ### I woud like this to be cleaner - but it does work!!! + 'upper_contour': 1.0, + 'number_of_levels': 25, + 'color_map_name': 'YlOrRd', + 'color_bar': False + }, + } + +movie_options_for_figure_4 = {} + +movie_options_for_figure_4 = {'INCLUDE_ALL_SVGs': True, + 'INCLUDE_FULL_HISTORY': False + } + +#### Right now, if you don't have None or the full contour and quiver options, it will break in the plotting . + +mf = PhysiCellPlotter() + +mf.produce_movie(save_name='multi_color_movie', trail_length=6, movie_options=movie_options_for_figure_4, image_options=options_for_figure4_movie) + +# generic_plotter (start, intervnal, finish, save_filename, data_path, save_path, options) +# +# All based on options/logic- function +# load_cell_positiondata +# load_uE_data_chemical +# load_uE_data_ECM +# +# process data into plots - functions +# - cell tracks (might be loaded by just be plotted???) +# - cell positions +# - ECM layer +# - chemical layer +# +# complete plot presentaiont and save (maybe functions) +# - title +# - axes \ No newline at end of file diff --git a/python_imaging/partial_history_multilevel_contour_movie_invasive_carcinoma.py b/python_imaging/partial_history_multilevel_contour_movie_invasive_carcinoma.py new file mode 100644 index 0000000..51dad1e --- /dev/null +++ b/python_imaging/partial_history_multilevel_contour_movie_invasive_carcinoma.py @@ -0,0 +1,57 @@ +import sys +import matplotlib.pyplot as plt +sys.path.append(r'../python_imaging') + +from image_processing_for_physicell import * + +options_for_figure4_movie = {} + +options_for_figure4_movie = {"output_plot" : True, + "show_plot" : False, + "produce_for_panel" : False, + "plot_ECM_anisotropy" : True, + "plot_ECM_orientation" : True, + "plot_ECM_density" : True, + "retrieve_ECM_data": True, + "load_full_physicell_data" : True, + "plot_cells_from_SVG" : True, + "load_SVG_data": True, + 'plot_cells_from_physicell_data': False, + "produce_for_movie" : True, + "contour_options" : {'lowest_contour': 0.0, ### I woud like this to be cleaner - but it does work!!! + 'upper_contour': 1.0, + 'number_of_levels': 25, + 'color_map_name': 'YlOrRd', + 'color_bar': True, + 'alpha': 0.5 + }, + } + +movie_options_for_figure_4 = {} + +movie_options_for_figure_4 = {'INCLUDE_ALL_SVGs': True, + 'INCLUDE_FULL_HISTORY': False + } + +#### Right now, if you don't have None or the full contour and quiver options, it will break in the plotting . + +mf = PhysiCellPlotter() + +mf.produce_movie(save_name='multi_color_movie', trail_length=6, movie_options=movie_options_for_figure_4, image_options=options_for_figure4_movie) + +# generic_plotter (start, intervnal, finish, save_filename, data_path, save_path, options) +# +# All based on options/logic- function +# load_cell_positiondata +# load_uE_data_chemical +# load_uE_data_ECM +# +# process data into plots - functions +# - cell tracks (might be loaded by just be plotted???) +# - cell positions +# - ECM layer +# - chemical layer +# +# complete plot presentaiont and save (maybe functions) +# - title +# - axes \ No newline at end of file