v2.41.7 - improve error handling parsing older config files

Merge pull request #297 from PhysiCell-Tools/development

error handling for older config files

v2.41.6 - skip missing asym div xml; improve substrate ICs import

Merge pull request #296 from PhysiCell-Tools/development

Development

v2.41.5 - fixes for nanoHUB plots; fix download_binary.py

• various fixes/improvements to population plots (primarily to work with nanoHUB's out of date matplotlib)
• move the legend on population plots to the left
• fix/update the download_binary.py script to be able to download precompiled sample projects

v2.41.4 - redesign Rules layout, new default motility params, etc

• redesign the Rules tab layout to highlight the importance of enabling rules (or not)
• update default params for motility:
  • migration speed: 1 (unchanged)
  • persistence time: 5 min (was 1)
  • bias: 0.5 (was 0)
• update config/template.xml (= PhysiCell_settings.xml) with persistence=5
• minor BIWT fixes
  • ensure spatial_data_found is initialized
  • handle empty text in manual counts
• code cleanup

v2.41.3 - plot cells' spring attachments option

• View -> Plot options now has a toggle option to plot cells' spring attachments. Currently only works when plotting cell scalars (.mat) and not .svg. Thanks Vincent Noel!
• minor tweaks to: increase overall GUI height to avoid Plot widgets top row from being confusingly hidden; button sizes, etc.

v2.41.2 - fix memory leak when plotting cell scalars

• fix memory leak when plotting cell scalars which led to a "maximum recursion depth exceeded" error in matplotlib
• note, however, there still remains a memory leak for Make Movie, regardless of what is being plotted

v2.41.1 - update studio_ecm.py

• fix studio_ecm.py for latest refactored code
• custom Studio used in this PhysiCell ECM model https://doi.org/10.1101/2022.11.21.514608

Example use after installing PhysiCell Studio into that model's directory:

python studio/bin/studio_ecm.py -e AMIGOS-invasion -c config/simple_test1_cell_march.xml
python studio/bin/studio_ecm.py -e AMIGOS-invasion -c config/leader_follower_instant_speed_050.xml

v2.41.0 - asymm cell division, save movie, cell plot filter

v2.41.0 - coordinate with PhysiCell 1.14.1 release

New features:

• Asymmetric cell division sub-tab: Cells Types tab | Cycle | Division Function
  • It also becomes a choice for cell scalars (.mat): Plot tab
  • It also becomes an option in the Behavior dropdown: Rules tab
• Add “damage delivered” as a signal: Rules tab
• Warn when saturation value on wrong side of base: Rules tab
• Generate a movie (requires having ffmpeg installed): Plot tab
• “Filter” button for cell plots (e.g., hide cell types): Plot tab
• Helpful warnings when user edits various rates, e.g. “A {phrase} is instantaneous. May as well set to {max_val}”
• Allow relative path for saving substrate file: ICs tab ( #267)
• Add option to crop 2D plotting axes: View menu -> Plot options

Bug fixes:

• When an invalid behavior name is typed into the dropdown widget in Rules, prevent crash due base_val = float(“??”)
• Prevent numerical noise being displayed in Saturation value: Rules tab
• Fix matplotlib colormap access for newer versions of matplotlib: ICS tab
• Fix voxel sizes for 3D plot slicing planes

Cleaning/refactoring:

• Removed excessive commented out code
• More refactoring: studio_classes.py, cell_def_cycle_tab.py
• Use “phase_element” instead of “rate” variable when parsing XML cycle params

See commit logs for more details. Special thanks to @drbergman and @heberlr !

Known issues:

• A memory leak when plotting cell scalars (.mat) if there are lots of frames. May result in sluggish plotting rate and eventual “RecursionError: maximum recursion depth exceeded”

See release notes for PhysiCell 1.14.1 for its changes:
https://github.com/MathCancer/PhysiCell/releases/tag/1.14.1

v2.40.0 - bug fixes and improvements to GUI and/or code base

• fix saving rules version = 3.0
• fix bugs related to initial parameter distributions of cells (Misc subtab)
• addedd download_binary.py to get project executable (customized version of the one in PhysiCell /beta; thanks @vincent-noel !)
• several helpful warnings, e.g., Interactions rates (hover over red exclamation marks for info)
• improved Mechanics UI for adhesion strength alternatives (equilibrium distances)
• much cleaner code for programmatically processing xml for cell cycle params
• updated several /config files for 1.14 syntax (and removed random_seed in User Params)
• icon for disabled radio buttons

See commit logs for more details. Huge thanks to @drbergman for most of these contributions and to everyone for testing and providing feedback!

v2.39.3 - fix custom radiobuttons for any root dir

Merge pull request #249 from PhysiCell-Tools/development

fix custom radio btns for cwd