I noticed some bugs using v3 updates, and the file format spec is out of date, and also wanted to add the ability to skip frames in PhysiCell reading, like in MCell (this should be a separate PR but I did it at the same time while working with PhysiCell data, sorry!)
Solution
fixed bugs, added nth_timestep_to_read to PhysicellData, updated file format spec.
Type of change
[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] This change requires a documentation update
[ ] This change requires updated or new tests
Change summary:
fixed errors if a geometry block was in a .simularium file being read back in with FileConverter
added the ability to skip frames in PhysiCell reading
updated file format spec
added and updated tests
updated PhysiCell example notebook
Keyfiles:
simulariumio/data_objects/agent_data.py - provide a name to DisplayData constructor to fix bug
simulariumio/data_objects/display_data.py - try to create a DISPLAY_TYPE enum from a string display type, since that's how it is saved in JSON, to fix bug. Also added more descriptive error messages
simulariumio/physicell/physicell_data.py - added nth_timestep_to_read like in McellData, to be able to skip timesteps when there's too much data.
simulariumio/physicell/physicell_converter.py - use nth_timestep_to_read
Problem
I noticed some bugs using v3 updates, and the file format spec is out of date, and also wanted to add the ability to skip frames in PhysiCell reading, like in MCell (this should be a separate PR but I did it at the same time while working with PhysiCell data, sorry!)
Solution
fixed bugs, added
nth_timestep_to_readtoPhysicellData, updated file format spec.Type of change
Change summary:
Keyfiles:
DisplayDataconstructor to fix bugDISPLAY_TYPEenum from a string display type, since that's how it is saved in JSON, to fix bug. Also added more descriptive error messagesnth_timestep_to_readlike inMcellData, to be able to skip timesteps when there's too much data.nth_timestep_to_read