[HazenBabcock]

Summary

Ports storm_analysis/visualizer from PyQt5 to PyQt6 (6.12), and fixes the problems found along the way.

• PyQt6: scoped enums, | for render hints, QMouseEvent.position(), visualizer_ui.py regenerated with pyuic6. The visualizer is now a package, so python -m storm_analysis.visualizer.visualizer works from any directory.

• Click selection: a click selected the localization one pixel down and to the right of the one under the mouse whenever there was one. This dates from the switch to zero-based HDF5 coordinates.

  -dx = self.locs["x"] - px - 0.5
  +dx = self.locs["x"] - (px - 0.5)

• Contrast changes: these no longer clear the scene, so the circles stay put and a click right after a change no longer hits deleted items, which used to abort the program.

   handleRangeChange
  -  displayFrame(False)          # re-read the frame, scene.clear() deletes the circles
  -  start the 100 ms timer       # circles reloaded from the file
  +  movie_view.setContrast()     # redraw the pixmap only

• Errors: a movie or localization file that can't be read is reported in a message box instead of aborting. The program also installs an exception hook for anything else.

• Smaller fixes:

  • The movie file is closed when replaced and on exit.
  • Equal contrast limits threshold the image instead of dividing by zero.
  • Integers of any width are shown as integers.

• Read-only HDF5: localization files are opened read-only (SAH5Reader), so a loaded file no longer locks other programs out. sa_h5py.isSAHDF5() now opens files read-only as well. It used to open them read-write, so it returned False whenever another process had the file open.

• New behavior:

  • The info table shows each file's own fields, for example DECODE's score or ground-truth intensity.
  • A new movie is fitted to the view.
  • Frame Capture asks where to save.
  • The contrast slider runs from 0 to the smallest power of 2 (at least 256) that covers the brightest pixel shown so far and the max setting. It was fixed at 0–100000.

• Docs and packaging:

  • The README and install docs list PyQt6.
  • pyproject.toml gains a gui extra (pip install .[gui]).
  • Dead code is removed.

Evidence

The new tests in storm_analysis/test/test_visualizer.py drive the GUI on Qt's offscreen platform. Most were written before their fix and seen to fail on the ported code:

Test	Before	After
click on a circle center	assert '11.000' == '10.000' (neighbor selected)	pass
click after a contrast change	RuntimeError: wrapped C/C++ object of type MoleculeItem has been deleted	pass
unreadable movie	OSError: only .dax, .spe and .tif are supported (aborts the GUI)	reported, pass
replaced movie closed	fileptr still open	pass
int64 field	'7.000' == '7'	pass
another process reads a loaded file	BlockingIOError: unable to lock file	pass

On test.dax with test_ref.hdf5, 5 of 200 clicks on circle centers selected the wrong localization before the fix.

The full suite gives 306 passed locally. The 12 visualizer tests need PyQt6, and the file is skipped without it. CI doesn't install PyQt6, so CI does not run them. I also checked the window on a real X display, and on the SMLM challenge AS-Exp movies with Spliner, DECODE and ground-truth HDF5 files.

Merge Danger

Door: two-way

Blast Radius: visualizer

The visualizer now requires PyQt6 and no longer runs on PyQt5. multi_plane/mapper.py, which is deprecated, still uses PyQt5 and is unchanged. Outside the visualizer, the only change is that isSAHDF5() opens files read-only. It gives the same answer, except that it now says True for a valid file another process has open, where it used to say False. fitting.py is its only other caller.

🤖 Generated with Claude Code