things to fix

[rheiland]

• [ ] IMPORTANT! Verify the default params for a New cell type match those in the C++ code
• [x] for rates|durations: after parsing rates in .xml, compute duration; and vice-versa
• [x] for rates|durations: when editing a rate in the GUI, update its duration; and vice-versa
• [x] for rates|durations: when toggling Fixed checkbox for one, make the other the same
• [x] when creating a new Custom Data param, create it in the dict with a default value
• [ ] setting Chemotaxis for cell type-signal-towards/against is not retained unless user does a Save
• [x] fix DCs checkboxes from .xml (when only some are True); resolve different values from primary
• [x] fix buggy 3D plotting of substrate; axes mismatch boundary DCs
• [ ] fix anomaly with dummy 3D cell generating black rectangle in other tabs
• [ ] have get_cell_type_colors_lut() match legend colors for 3D cell glyphs
• [ ] widgets to control more vis features
• [ ] domain range for 2D
• [ ] bounding box for 3D
• [x] slice planes for 3D substrates
• [ ] isosurfaces for 3D substrates
• [ ] allow coloring of cells in 3D by other than cell type
• [ ] allow for vis with non-equal output intervals?
• [ ] allow for additional analysis plot, possibly user-defined info
• [ ] expand width of QTreeWidget(s) borders via QSplitter
• [ ] make the overall GUI resizeable?
• [x] fix the confusing, mismatched 2D susbstrate mesh vs. voxel center (.mat info)
• [ ] when volume total changes, should nuclear value be auto-updated?
• [ ] fix duplicate(?) death and volume params (relative rupture, calcification rate)
• [ ] add a "motility_vector" or "bias_migration_vector" (= motility.motility_vector[])
• [x] add movable checkbox (=is_movable in *_cell.h); applies to all cells of a Cell Type?
• [ ] is it possible to halt a QProcess instead of/in addition to kill?
• [ ] Help reminder of 3D vis keypresses: j(oystick)/t(rackball), c(amera)/a(ctor), r(eset), 3(stereo), pan, etc
• [x] bundling into self-contained applications
• [x] add a Rules tab
• [ ] documentation: users and devs (->readthedocs work in progress)
• [ ] move Release info out of README into Releases.md
• [ ] renaming a cell type keeps the old name in various internal dicts which get written to .xml
• [ ] retain the state of certain widgets, e.g., min/max colormap ranges for all substrates
• [ ] when the colorbar range is tiny, a scientific notation header is added and obscures the title
• [ ] is there a problem displaying widgets on a very high res screen? (rf. Nicky)
• [x] fix dark mode colors on Mac
• [ ] provide editable units; currently hardcoded, e.g., mmHg in Microenv DCs
• [ ] in the Mechanics subtab, does it make sense to allow setting BOTH relative and absolute equilibrium distance?

[drbergman]

colorbar for .mat coloring of cells seems to be located and sized by pixels, rather than normalized units sometimes causing it to enter the axes:

[rheiland]

I noticed something similar a couple days ago which makes me think recent edits have caused it as it used to display properly. Not sure what may have caused it. One obvious debug is to test with previous releases. Edit: Maybe I was wrong. Maybe this annoyance was always present but it just didn't show up unless one resized the plotting window in various ways.

[rheiland]

In this release, https://github.com/PhysiCell-Tools/PhysiCell-Studio/releases/tag/v2.32.0, we introduced colorbars for cells' discrete scalars. Testing the release just before that (2.31.2), we don't see the weird placement of that lower colorbar. I imagine @vincent-noel is swamped with other things right now (as most of us are), but FYI. Positioning colorbars on resizable windows is tricky, but hopefully there's some "tight" mpl magic that will work.

[rheiland]

and this screenshot shows the situation using the latest release, with discrete scalars colorbar essentiall going out-of-view on a window resize.

[vincent-noel]

Yes, I noticed it too. It's on my todo list, but I couldn't find time yet...

[rheiland]

I've spent a LONG time looking at possible fixes for the colorbars and the discrete scalars legend. If anyone has time to test, it's in https://github.com/PhysiCell-Tools/PhysiCell-Studio/tree/dev-colorbars . I still need to test for physiboss vis... actually, I'm hoping Vincent or Marco can test as they know it best.

[drbergman]

This fixes it for me on my m2 mac!

[vincent-noel]

Thanks Randy ! I'll have a look asap