Density fig updates #34
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chantelleleveille
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chantelleleveille
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Please fix loading the data from scratch! It is failing so it makes it hard to go through the code and test the workflows.
nuc_morph_analysis/lib/preprocessing/global_dataset_filtering.py
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nuc_morph_analysis/analyses/density/confirm_no_corr_btn_density_and _nuclear_area.py
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nuc_morph_analysis/analyses/density/confirm_no_corr_btn_density_and _nuclear_area.py
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nuc_morph_analysis/analyses/density/figure_watershed_based_density_schematic.py
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nuc_morph_analysis/analyses/density/figure_watershed_based_density_schematic.py
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nuc_morph_analysis/analyses/density/figure_watershed_based_density_schematic.py
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nuc_morph_analysis/analyses/density/figure_watershed_based_density_schematic.py
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| savename = f'{colony}_{track}_{TIMEPOINT}_{full_crop}_res{RESOLUTION_LEVEL}_{cmapstr}' | ||
| savepath = savedir / savename | ||
| print(f'Saved figure to {savepath}') | ||
| save_and_show_plot(str(savepath), |
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The plots are getting cut off in the saved output. Maybe bbox_inches='tight' would fix it!
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they don't look cut off on my machine ...
| watershed_validate.run_validation_and_plot(plot_everything=False) | ||
| from nuc_morph_analysis.analyses.density import effect_of_resolution_level | ||
| from nuc_morph_analysis.analyses.density import pseudocell_based_density_analysis | ||
| # this code runs all workflows in the density folder (not all of these are in the paper) |
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I dont think you have to say this now that we have the figure numbered workflow. But also it begs the question which ones are in the paper?
Maybe we simplify to:
| # this code runs all workflows in the density folder (not all of these are in the paper) | |
| # this code runs all workflows in the density folder |
or maybe remove the run_all_density_workflows and folks can run them individually?
Not sure.
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Yeah with all the new files I'm left confused about where to find all the workflows I should run to test the code, but that points to a larger question of what plots and workflows are we adding that aren't in the paper and are we sure we want/need them? Have we fully edited out all the testing plots that don't really need to be preserved beyond the git history?
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will delete this file and move others to a folder that specifies that they are useful extra code files
nuc_morph_analysis/analyses/density/visualize_filter_for_uncaught_pseudo_cell_artifacts.py
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nuc_morph_analysis/analyses/density/visually_validate_watershed_psuedo_cell_seg_workflow.py
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nuc_morph_analysis/analyses/neighbor_of_X/figure_mitotic_filtering_examples.py
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nuc_morph_analysis/analyses/neighbor_of_X/figure_mitotic_filtering_examples.py
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…d cell_H modifications
…of this workflow and remove old density schematic
Suggested edits to address reviews of Chris' density branch
…t_number_of_uncaught_density_outliers.py remove temp file
…nsity_fig_updates
|
Running tests now! ====== Successes ====== |
main code update to see:
toymodel update:
watershed method illustration figure
filtering neighbors of mitotics figure
Updated density over time figure (after removing colony_depth as criteria in remove_uncaught_pseudo_cell_artifacts filter)
