Fix fixes from experiments

[beniroquai]

This pull request introduces several significant enhancements and fixes to the frontend and coordinate calculation logic, focusing on improving scan efficiency, UI features, and robustness. The most important changes include deduplication of scan points, implementation of area-level scan ordering, addition of 3D viewer and picture-in-picture UI components, and improved handling of Z coordinates in scan computations.

Scan coordinate calculation improvements:

• Deduplicated experimentState.pointList before processing to prevent scanning the same physical location multiple times, improving scan efficiency and avoiding redundant operations.
• Added area-level scan pattern ordering (applyAreaLevelScanPattern) to optimize stage movement across multi-area experiments, grouping areas into rows and applying snake/raster ordering as appropriate. [1] [2]
• Enhanced scan coordinate computations to consistently handle Z coordinates for points, area centers, and neighbor points, ensuring accurate 3D positioning. [1] [2] [3] [4]

Frontend UI enhancements:

• Added a new "3D Twin" tab and integrated the Frame3DViewerPanel component for interactive 3D visualization of the microscope model. [1] [2]
• Introduced a floating picture-in-picture (PiP) live preview overlay with toggle button, improving user experience for live monitoring.

Codebase and configuration updates:

• Updated .vscode/settings.json to specify Python project environment and package manager, improving developer workflow.
• Cleaned up .vscode/launch.json by removing unused configuration blocks. [1] [2]

These changes collectively improve scan accuracy, UI usability, and maintainability of the codebase.

[Copilot]

Pull request overview

This PR updates ImSwitch’s acquisition and UI stack to improve scan efficiency/robustness (dedup + Z handling + illumination workflow changes), expands frontend functionality (3D digital-twin viewer, PiP live preview, richer focus-map UI), and enhances device/firmware tooling (USB flashing options + CAN address assignment), alongside a few dependency/config cleanups.

Changes:

• Scan/acquisition logic: per-point Z origins, focus-map Z integration, illumination “keep on” mode, writer indexing for multi-timepoint experiments, and grid/scan-point deduplication.
• Frontend enhancements: 3D Twin viewer with persisted camera/axis mapping, picture-in-picture live preview, improved experiment designer dimensions/summaries, and focus-map UX upgrades.
• Hardware & tooling: Hik camera high-bit pixel formats, lightsheet writer behavior, and expanded UC2 USB flashing + CAN address assignment flow.

Reviewed changes

Copilot reviewed 53 out of 55 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
uv.lock	Adjusts locked Python deps (aiortc/av versions) and adds av to lock metadata.
pyproject.toml	Adds av==13.1.0 and configures uv to install psygnal from source.
imswitch/imcontrol/view/widgets/__init__.py	Removes StandaStageWidget export/import.
imswitch/imcontrol/view/widgets/StandaStageWidget.py	Removes Standa stage widget implementation.
imswitch/imcontrol/view/guitools/ViewSetupInfo.py	Removes StandaStage widget mention from docs list.
imswitch/imcontrol/view/ImConMainView.py	Removes StandaStage dock entry.
imswitch/imcontrol/model/managers/detectors/HikCamManager.py	Uses hardware exposure units conversion; sets preview max based on pixel format.
imswitch/imcontrol/model/interfaces/picamera2_interface.py	Keeps frames in RGB (and updates mono conversion accordingly).
imswitch/imcontrol/model/interfaces/hikcamera.py	Adds high-bit pixel format constants, tracks active format, and changes buffer dtype/reshape logic.
imswitch/imcontrol/model/focus_map.py	Deduplicates generated focus-map grid points for degenerate bounds.
imswitch/imcontrol/controller/controllers/experiment_controller/experiment_normal_mode.py	Adds continuous-illumination option, Z “single source of truth” workflow, writer offsets, and revised finalization behavior.
imswitch/imcontrol/controller/controllers/UC2ConfigController.py	Adds chip auto-detect + erase/skip-disconnect flash options and CAN address assignment API.
imswitch/imcontrol/controller/controllers/StandaStageController.py	Removes Standa stage controller implementation.
imswitch/imcontrol/controller/controllers/StandaPositionerController.py	Removes Standa positioner controller implementation.
imswitch/imcontrol/controller/controllers/PixelCalibrationController.py	Objective ID resolution via ObjectiveController; preserves affine rotation/flip when updating manual scale calibration.
imswitch/imcontrol/controller/controllers/LiveViewController.py	Converts RGB→BGR before JPEG encoding.
imswitch/imcontrol/controller/controllers/LightsheetController.py	Uses tifffile ImageJ stack writing and moves buffered writes to a background thread.
imswitch/imcontrol/controller/controllers/ExperimentController.py	Adds per-point/per-position Z fields, illumination mode selection, Z-offset semantics, autofocus illumination activation, and return-to-start behavior.
imswitch/imcommon/framework/noqt.py	Adds a more robust psygnal “decompile + reload” guard for pure-Python fallback.
frontend/src/state/store.js	Adds persisted Frame3D viewer slice and nested persist config for focus-map UI.
frontend/src/state/slices/usbFlashSlice.js	Adds chip/erase/skip-disconnect options and CAN assignment wizard step/state.
frontend/src/state/slices/ObjectiveSlice.js	Sets currentObjective initial value to null until first status fetch.
frontend/src/state/slices/Frame3DViewerSlice.js	New slice: axis mapping, camera state, visibility toggles (persisted).
frontend/src/state/slices/FocusMapSlice.js	Persists accordion expansion states for manual/measured points.
frontend/src/state/slices/ExperimentUISlice.js	Adds Objective as an experiment-designer dimension.
frontend/src/state/slices/ExperimentSlice.js	Adds illumination mode parameter and point deduplication on creation; stores point z.
frontend/src/middleware/fetchObjectiveControllerGetStatus.js	Syncs currentObjective into Redux on status fetch.
frontend/src/components/UsbFlashWizard.jsx	Adds chip hints, erase/skip-disconnect options, CAN assignment step, and restart flow.
frontend/src/components/ObjectiveSwitcher.js	Updates objective switching logic and adds “Switch + Z” buttons.
frontend/src/components/HoloController.js	UI layout adjustments for consistent video panel sizing and transforms.
frontend/src/components/Frame3DViewer.jsx	New Three.js GLB viewer that maps stage/turret movement from Redux positions.
frontend/src/components/FRAMESettings/ManualPixelCalibrationTab.js	Adds backlash-compensation step and updates stepper flow.
frontend/src/components/AutofocusController.js	Fixes stop endpoint path (stopAutofocus).
frontend/src/backendapi/apiUC2ConfigControllerSendCanAddress.js	New API wrapper for CAN address assignment.
frontend/src/backendapi/apiUC2ConfigControllerFlashMasterFirmwareUSB.js	Extends flash API wrapper with chip/erase/skip-disconnect params.
frontend/src/axon/experiment-designer/ZFocusDimension.js	Improves Z-stack inputs (supports negative typing) and clarifies relative offsets.
frontend/src/axon/experiment-designer/ObjectiveDimension.js	New experiment-designer panel embedding ObjectiveSwitcher.
frontend/src/axon/experiment-designer/FocusMapDimension.js	Persists accordion state, adds measured-point pagination, and enables heatmap Z moves.
frontend/src/axon/experiment-designer/ExperimentSummary.js	Counts total positions via coordinate calculator; counts enabled channels correctly.
frontend/src/axon/experiment-designer/ExperimentDesigner.js	Adds beforeunload warning and focus-map interrupt on stop.
frontend/src/axon/experiment-designer/DimensionBar.js	Adds Objective to the dimension bar config.
frontend/src/axon/experiment-designer/ChannelsDimension.js	Uses numeric exposure input and adds illumination “keep on” mode UI.
frontend/src/axon/WellSelectorUtils.js	Uses integer grid indices in raster BFS to avoid float-key collisions.
frontend/src/axon/WellSelectorCanvas.js	Stores current Z into created scan points.
frontend/src/axon/PointListEditorComponent.js	Adds Z editing and optional Z move on “Goto”.
frontend/src/axon/PictureInPicture.js	New draggable/resizable PiP overlay for live preview.
frontend/src/axon/OverviewRegistrationWizard.js	Adds explicit speed to stage jog moves.
frontend/src/axon/Frame3DViewerPanel.jsx	New panel for configuring the 3D viewer (mapping/visibility + live readout).
frontend/src/axon/CoordinateCalculator.js	Deduplicates scan areas, adds area-level ordering, and propagates Z through scan model.
frontend/src/axon/AxonTabComponent.js	Adds PiP toggle and a “3D Twin” tab/panel.
frontend/public/assets/frame3d.html	Adds a standalone reference viewer/debug page for the FRAME GLB.
_test_psygnal.py	Adds a local diagnostic script for psygnal compilation state.
.vscode/settings.json	Adds Python env/project settings for VS Code.
.vscode/launch.json	Removes unused whitespace/config blocks.

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[Copilot]

skipZ is a boolean in the backend (ObjectiveController.moveToObjective), but switchTo defaults it to 0 and both the "Switch to" and "Switch + Z" buttons pass falsy values. As a result, both buttons currently behave the same (Z adjustment is never skipped). Consider making the default skipZ a boolean and wiring the buttons so "Switch to" uses skipZ=true (no Z focus move) while "Switch + Z" uses skipZ=false (include Z move).

[Copilot]

_MONO_HIGHBIT_FORMATS includes PixelType_Gvsp_Mono10_Packed / PixelType_Gvsp_Mono12_Packed, but the callback path treats every entry in this set as 2-bytes-per-pixel uint16 and reshapes to (h, w). Packed mono formats are bit-packed (not 16-bit-per-pixel), so this will produce incorrect frames or reshape errors if those formats are ever selected. Either remove packed formats from _MONO_HIGHBIT_FORMATS (if not supported) or add explicit unpack/convert logic for the packed formats before reshaping.

[Copilot]

Finalization currently only calls finalize_current_ome_writer on the last timepoint. In _ome_write_single_tiff mode, a separate writer is created per timepoint (see _setup_ome_writers usage), so intermediate timepoints can leave many writers open until the end of the run, increasing open-file handles and memory usage for long timelapses. Consider finalizing the timepoint writer after each timepoint in single-TIFF mode (e.g. by calling finalize_current_ome_writer(..., time_index=t) or equivalent), and/or remove the unused writer_offset parameter here if it’s not needed.

[Copilot]

This looks like an ad-hoc diagnostic script. Keeping it at repo root makes it easy to ship accidentally and can confuse packaging/test discovery. Consider moving it under a dedicated scripts/ or tools/ directory (or adding it to .gitignore if it’s meant to be local-only), and ensure it’s not picked up by any test runner.

Suggested change

	print("version:", psygnal.__version__)
	print("SignalInstance type:", type(psygnal.SignalInstance))
	# Try subclassing
	try:
	class TestSub(psygnal.SignalInstance): pass
	print("Subclassing SignalInstance: OK")
	except TypeError as e:
	print("Subclassing SignalInstance FAILED:", e)
	# Try decompile
	try:
	psygnal.utils.decompile()
	class TestSub2(psygnal.SignalInstance): pass
	print("After decompile, subclassing SignalInstance: OK")
	except Exception as e:
	print("After decompile:", e)
	# Test direct instantiation (composition approach)
	try:
	inst = psygnal.SignalInstance((int,), name="test")
	print("Direct instantiation: OK, name =", inst.name)
	except Exception as e:
	print("Direct instantiation FAILED:", e)
	def main() -> None:
	print("version:", psygnal.__version__)
	print("SignalInstance type:", type(psygnal.SignalInstance))
	# Try subclassing
	try:
	class TestSub(psygnal.SignalInstance):
	pass
	print("Subclassing SignalInstance: OK")
	except TypeError as e:
	print("Subclassing SignalInstance FAILED:", e)
	# Try decompile
	try:
	psygnal.utils.decompile()
	class TestSub2(psygnal.SignalInstance):
	pass
	print("After decompile, subclassing SignalInstance: OK")
	except Exception as e:
	print("After decompile:", e)
	# Test direct instantiation (composition approach)
	try:
	inst = psygnal.SignalInstance((int,), name="test")
	print("Direct instantiation: OK, name =", inst.name)
	except Exception as e:
	print("Direct instantiation FAILED:", e)
	if __name__ == "__main__":
	main()