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feat: Record + Z-Stack acquisition mode - #564

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hongquanli wants to merge 115 commits into

feat/in-process-zarr-savingfrom

feat/record-zstack-acquisition

Open

feat: Record + Z-Stack acquisition mode#564
hongquanli wants to merge 115 commits into
feat/in-process-zarr-savingfrom
feat/record-zstack-acquisition

Commits on Oct 11, 2026
- feat(camera): add best-effort set_frame_rate hint to AbstractCamera
  
  hongquanli
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  4d94bac
- feat(camera): SimulatedCamera honors set_frame_rate in continuous stream
  
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  e6249e1
- feat(camera): ToupcamCamera.set_frame_rate via PRECISE_FRAMERATE
  
  hongquanli
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  f6ed2b4
- refactor: extract MultiPointWorkerBase (no behavior change)
  
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  dc9b9f6
- refactor: extract create_experiment_dir helper into acquisition_setup.py (no behavior change)
  
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  120ebfd
- feat(streaming): add CountStop + RecordingRouter (pure)
  
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  ed97d39
- feat(streaming): RecordingWriter (bounded queue + thread -> ZarrWriter)
  
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  7c39d53
- fix(streaming): drain thread solely owns ZarrWriter lifecycle (no abort/write race)
  
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  62e90fb
- feat(streaming): ContinuousFrameSource + StreamingCapture orchestrator
  
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  fedf4c3
- fix(streaming): move CameraAcquisitionMode import to top (no real cycle); document stop/finalize assumption
  
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  40ba174
- feat(record-zstack): params + pure planning helpers
  
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  fe12f26
- test(record-zstack): cover validation paths + document epsilon
  
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  8846ea2
- feat(record-zstack): RecordZStackWorker (record + zstack per FOV)
  
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  b77c237
- feat(record-zstack): RecordZStackController + ZarrWriter daemon-thread fix
  
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  02e669c
- feat(record-zstack): RecordZStackMultiPointWidget + validation
  
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  4007b27
- fix(record-zstack): correct laser-AF reference check + dedup zstack row table
  
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  ada2a0f
- feat(record-zstack): inline channel editors, Copy-from-Live, computed labels
  
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  2a04afa
- test(record-zstack): tighten invalid-range plane-label assertion + docstring
  
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  cc5d894
- feat(record-zstack): Start/Stop handoff to RecordZStackController
  
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  a4b2bbb
- feat(record-zstack): add Record + Z-Stack tab to gui_hcs (ENABLE_RECORDING)
  
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  fe5f641
- feat(record-zstack): widget finished/progress slots for gui_hcs wiring
  
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  80cc428
- fix(record-zstack): add recordZStackWidget None sentinel (gui_hcs)
  
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  8eb51af
- fix(record-zstack): illumination, trigger mode, streaming & live-view lifecycle
  
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  366bf19
- fix: harden streaming_capture (fps order, start error path, OOB gating, non-blocking enqueue, abort sealing, partial warning)
  
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  13b3943
- fix(record-zstack): batch-3 correctness, threading, and simplification fixes
  
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  e940571
- refactor: DRY batch 4 — lift _wait_for_outstanding_callback_images to base, extract compute_pixel_size_um, drop redundant _job_runners re-assignments, fix misleading __class__ comment
  
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  a7b3980
- fix: Wire signal_acquisition_started for Record+Z-Stack UI lockout (fix-batch5)
  
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  43772ff
- fix: emit signal_acquisition_started(True) before spawning worker thread
  
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  44a67b7
- refactor: Remove setter shims and duplicate attrs from RecordZStackController
  
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  ce2dbd7
- style(record-zstack): compact widget layout to match WellplateMultiPoint
  
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  1bad106
- feat(record-zstack): wire FOV grid and compact the acquisition widget
  
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  576e679
- fix(record-zstack): release RecordingWriter if drain thread fails to start
  
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  f8b9298
- fix(record-zstack): clear stale FOV regions before re-geometrying + allow sub-0.1um z-step
  
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  af08d88
- test(record-zstack): skip tensorstore-dependent tests when it's absent (CI)
  
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  0e0cda3
- fix(record-zstack): add emit_selected_channels stub + keep well selector on tab
  
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  160c306
- fix(record-zstack): critical review fixes — data loss, deadlock, abort, state restore, fps
  
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  1ec3b92
- fix(record-zstack): medium review fixes — byte cap, per-FOV z, dt pacing, refresh, cleanup, bookkeeping
  
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  1921e15
- fix(record-zstack): round-2 review fixes on the fix commits
  
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  af08841
- fix(record-zstack): data-integrity cluster from completed round-2 verification
  
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  da61d26
- fix(record-zstack): GUI + cleanup findings from completed round-2 verification
  
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  068483a
- feat(multi-plane): params + pure plane-offset/validation helpers
  
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  1f6058d
- feat(multi-plane): extra _squid attrs passthrough on ZarrAcquisitionConfig
  
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  982d542
- feat(multi-plane): per-plane recording loop, paths, and metadata in RecordZStackWorker
  
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  a8735fa
- feat(multi-plane): Bottom Z / Nz / dz recording fields with dz hidden at Nz=1
  
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  c9a5d9f
- fix(multi-plane): move plane-0 Z move before illumination; restore camera/Z on fail-fast path; harden validate-wiring test
  
  hongquanli
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  c0c2a3e
- refactor(multi-plane): compact recording UI — Nz leads FPS/Dur row, dynamic Z-offset caption
  
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  10e31aa
- refactor(multi-plane): single-row recording controls — Nz, Z offset, dz | FPS, Dur
  
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  aa50083
- refactor(multi-plane): integer FPS/Dur spinboxes, drop fps suffix
  
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  0f88316
- feat(multi-plane): show recording Z offset only when Laser AF is enabled; slim spinbox widths
  
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  2674ec6
- feat(record-zstack): XY/Time tabbed row, Select Wells mode, channel seeding, narrower layout
  
  hongquanli
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  d7dd1ef
- feat(record-zstack): add xy_mode/scan_size_mm/overlap_percent to acquisition params
  
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  b452150
- feat(record-zstack): add _build_objective_info helper for acquisition.yaml
  
  hongquanli
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  7605d1b
- feat(record-zstack): write full acquisition.yaml snapshot alongside acquisition_channels.yaml
  
  hongquanli
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  8dda233
- feat(record-zstack): parse record_zstack acquisition.yaml into RecordZStackYAMLData
  
  hongquanli
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  e0db6d6
- refactor(widgets): generalize AcquisitionYAMLDropMixin for a 3rd widget_type
  
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  42be5fd
- fix(record-zstack): match mismatch-dialog display name to actual tab label
  
  hongquanli
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  c175190
- refactor(widgets): extract well-region YAML apply logic into shared functions
  
  hongquanli
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  86d7397
- feat(record-zstack): wire RecordZStackMultiPointWidget into AcquisitionYAMLDropMixin
  
  hongquanli
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  8c506b9
- fix: RecordZStackMultiPointWidget._apply_yaml_settings channel/time bugs
  
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  eb906e0
- fix: refresh Time tab styling in RecordZStackMultiPointWidget YAML load
  
  hongquanli
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  e57ce42
- feat(record-zstack): add Save Settings/Load Settings buttons
  
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  80d00b2
- fix(tests): exercise real save/load chains in record_zstack settings tests
  
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  616b5c7
- test(record-zstack): add full save/load round-trip regression test
  
  hongquanli
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  a4219f9
- test: Add assertions for recording_channel and z-stack channel numeric fields
  
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  3447bfd
- fix(record-zstack): resync xy_controls_frame visibility after YAML load
  
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  e2bce04
- fix(record-zstack): catch _apply_yaml_settings failures in the shared drop mixin
  
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  c2e4072
- fix(record-zstack): let real save-YAML write failures reach the caller
  
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  4bfa53d
- test(record-zstack): cover Nz/dz/bottom-Z fields in the settings round-trip test
  
  hongquanli
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  434db70
- feat(multi-plane): confirm recording plane summary before starting acquisition
  
  hongquanli
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  ee384f7
- refactor(multi-plane): FPS/Duration lead the recording row; Bottom-Z offset moves to its own row
  
  hongquanli
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  ec86a7d
- refactor(multi-plane): align Bottom-Z offset row under Nz via QGridLayout
  
  hongquanli
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  79f2fe3
- refactor: drop dead no-op stubs after master's duck-typing removal (#584)
  
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  93105f0
- refactor(multi-plane): dynamic recording-row reflow with aligned columns
  
  hongquanli
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  cbd64da
- fix(record-zstack): size continuous recording to the camera's true free-run max, not the triggered frame time
  
  Alpaca233
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  26d224f
- refactor(record-zstack): drop dead fallback in _continuous_max_framerate
  
  Alpaca233
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  7b15a17
- feat(record-zstack): Recording phase checked by default; collapse unchecked phases
  
  hongquanli
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  75f043a
- style(record-zstack): replace QGroupBox sections with plain QFrame + dividers
  
  hongquanli
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  9c7515c
- style(record-zstack): flatten Start Acquisition box, hide Save/Load Settings
  
  hongquanli
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  7edab21
- fix(record-zstack): resync Recording/Z-Stack section visibility after YAML load; fix double-indented content
  
  hongquanli
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  59fb917
- fix(record-zstack): remove empty space below recording channel table row
  
  hongquanli
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  e0a7c57
- fix(record-zstack): un-bold channel table headers; copy-from-live used wrong channel
  
  hongquanli
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  93f8e4b
- fix(record-zstack): copy-from-live no longer resets on lookup miss; DRY header/test fixes
  
  hongquanli
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  c990055
- fix(record-zstack): probe frame shape in CONTINUOUS mode so software-trigger live can't break recording
  
  Alpaca233
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  2e7e2ba
- feat(record-zstack): gray out Start Acquisition when neither phase is enabled
  
  hongquanli
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  ee031ea
- style(record-zstack): drop the raised-panel frame on the outer widget
  
  hongquanli
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  4fd6558
- fix(record-zstack): match tab background — QScrollArea was painting its own gray fill
  
  hongquanli
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  d9e19e0
- rebase: restore merge resolutions lost when flattening branch merges
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  26c0c25
- refactor: dedupe shared acquisition machinery, hoist hot-path work (review cleanups)
  
  Alpaca233
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  598866a
- fix: make record-zstack smoke tests machine-independent; inject zarr_writer_info on the in-process job path
  
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  d5db54e
- refactor: remove the Simple Recording widget
  
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  15e4881
- fix(camera): apply the toupcam PRECISE_FRAMERATE hint while the stream is stopped, bound it by exposure
  
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  e26c76d
- perf(recording): pipeline TensorStore writes; route camera-paced recordings sequentially
  
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  ddccdb4
- fix(camera): toupcam precise-framerate range tracks the mode; hint re-applied once the stream runs
  
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  13b5a8a
- feat(record-zstack): throttled display tap in StreamingCapture
  
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  551723c
- feat(record-zstack): thread display callable through controller and worker
  
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  2ddcad3
- feat(record-zstack): live preview signal + display wiring at RECORD_ZSTACK_DISPLAY_FPS
  
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  b914c21
- docs: fix contradictory preview-fps comment and stale hot-path docstrings
  
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  7a81bea
- fix(record-zstack-live-preview): update tests for recording_z_offset_um rename
  
  hongquanli
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  db4e1fc
- fix(recording): stamp the measured t-axis spacing when a paced source runs off its nominal rate; review follow-ups
  
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  f8ca0aa
- fix(recording): no corrupted first frame with a hardware ROI (toupcam live frame-rate write)
  
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  5bad2d6
- feat(record-zstack): warn before starting when the camera cannot reach the requested fps; record requested vs effective fps
  
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  a8afa9e
- feat(record-zstack): resolve the recording fps before the acquisition starts
  
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  90cc309
- rebase: restore merge resolutions lost when flattening the master merge
  
  Alpaca233
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  claude
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  752b71d
- refactor(record-zstack): remove duplication and probing left by the review rounds (no behavior change)
  
  Alpaca233
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  0262f9f
- fix(record-zstack): a collapsed Recording section stays collapsed when Laser AF or Nz changes
  
  Alpaca233
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  d4e2ee4
- fix(record-zstack): every acquisition of a session keeps its z-stack
  
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  3442c90
- test(record-zstack): give the simulated test camera its own CameraConfig
  
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  588503b
- refactor(record-zstack): simplify the in-process z-stack saving commit
  
  Alpaca233
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  ec84e67
- fix(record-zstack): address the Copilot review on the stacked branch
  
  Alpaca233
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  6c36b1a
- refactor(record-zstack): simplify the Copilot-review fixes
  
  Alpaca233
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  claude
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  54eb11c
Commits on Oct 12, 2026

Commits

Commits on Oct 11, 2026

Commits on Oct 12, 2026