v8.05.000: Paint bundle load & Count Cells fixes for .tiff

BARCC v8.05.000

Patch release focused on reliability of the new Paint bundle (.barccpaint) workflow — specifically loading painted regions + names onto TIFFs and then running Count Cells — plus related crash and feedback fixes.

Highlights

Fixed "failed to load paint bundle: ufunc 'less' ..." on .tiff

• The error ufunc 'less' did not contain a loop with signature matching types (<class 'numpy.dtypes.UInt8DType'>)->none occurred when loading a .barccpaint (containing strokes.png + zones.png + manifest with named painted regions) onto a .tiff via the left File Browser or Load Paint.
• Root cause: json stringifies dict keys → zone IDs became strings in zone_names/painted_zone_outlines. After load, np.array(zones mask) produced uint8 scalars. _populate_region_list (called from _update_ribbon_selection during bundle load + show_page) did if zid > 0 and zid not in names + sorted(names.items()), causing Python sort / numpy ufunc 'less' to fail on mixed str + np.uint8.
• Fixed by:
  • Normalizing keys with {int(k): v for ...} immediately after loading manifest / legacy sidecar JSON in _load_barccpaint_bundle, legacy paths, and StateManager restore.
  • int(zid) in _populate_region_list, _ensure_zone_has_name, and count lookup paths.
  • Same normalization for painted outlines.
• Painted regions now load with names appearing immediately in the Atlas Manager list and shapes usable for counting.

Fixed silent crash / no feedback on Count Cells after painted bundle load

• After a successful bundle load, clicking Count Cells would sometimes "crash" with no dialog at all and no .xlsx (or _masked.tif) generated.
• Causes addressed:
  • Numpy broadcast error in the cell marker drawing code inside count_cells_in_zones (rgb_img[slice, x] = [255,0,0] etc.) on edge centroids or degenerate (0-length) slices after window-fit scaling of the TIFF. This happened after counts were computed but before df was returned → exception escaped the count path.
  • Progress dialog close timing vs. the "Results Saved" / warning messagebox: leaving the busy Toplevel open while showing the results dialog + closing it afterward could cause event/focus issues on OK.
  • Auto-save block silently skipped (only a log) when tiff_dir / tiff_filename was not set (some direct open vs. browser flows, or state after accessory load). No user-visible indication and no file.
• Fixes:
  • Explicit [:, :] channel indexing + if start < end guards in the cross drawing.
  • Full try/except around non-critical viz blocks in count_cells_in_zones so df / counts / return always succeed (fallback annotated image).
  • Close the busy progress dialog before any final "Results Saved" popup (and perform masked save early).
  • If save paths are missing, still show an info dialog ("Count Complete...") so the user always gets feedback.
  • Added defensive guard for original_background before detection.
• Result: Count Cells after loading a painted bundle on a .tiff now reliably produces the spreadsheet (with your painted region names), the masked image, and dialogs. No more silent failures.

Other robustness for painted + TIFF + count

• Manual add/remove cell masks are now cleared on every new TIFF load (via browser or direct) so stale edits from a previous image don't get resized and OR'd into the current count.
• zone_counters bumped from loaded zone IDs on bundle load (in addition to the ribbon populate path) so future naming doesn't collide.
• All zone ID handling now consistently uses Python int keys.
• The left File Browser accessory flow (double-click paint child) continues to chain TIFF load + bundle restore correctly.

These changes make the "draw or load painted regions with names → Count Cells" workflow on TIFFs (including via .barccpaint bundles that carry both visuals and labeled shapes) production-ready.

Other Notes

• Version string in code and exported settings JSON updated to "8.05.000".
• README.md updated with v8.05.000 section.
• Release notes added (this file).
• BARCC_User_Manual.pdf and generator may be updated in a follow-up if new "What's New" text is desired; core behavior is documented in the code comments and this note.
• No changes to requirements or installation.

Requirements

Unchanged.

Preparing / Installing the Release

• Source, this release note, updated README are in the repository.
• Git tag: v8.05.000 (to be created on push)
• Run py -3.12 barcc.py (or your normal launcher) from the Application directory.