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- Add AbstractSystem and AbstractSystemState types to instrument.jl - Export get_state, set_state for system interface - Fix armcamera duplicate method in ThorCamCSC (remove default argument) - Fix CrystaLaser constructor: handle missing NI-DAQ gracefully - Fix VortranLaser constructor: handle missing NI-DAQ gracefully - Both laser constructors now use try-catch and validate device list Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Constructor now validates device index before accessing - All interface methods check for empty channels before use - Warnings instead of crashes when hardware unavailable Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- VortranLaser: wrap all DAQ operations in try-catch, check channel counts - CrystaLaser: wrap all DAQ operations in try-catch, check for empty channels - Shutdown now completes gracefully even when hardware unavailable Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add permutedims after reshape in all camera getdata/getlastframe functions to convert from row-major C buffer to column-major Julia (H, W) arrays - Fix array allocations to use (H, W, N) instead of (W, H, N) - Add HDF5 metadata (dimension_order, dimension_labels, memory_layout) to make convention explicit for downstream readers - Document convention in CLAUDE.md Cameras fixed: DCAM4, SimCamera, ThorCamCSC, ThorCamDCx Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
…MicroscopeControl.jl into fix-camera-permutation
Replace the deprecated NIDAQ.jl package (v0.6) with the locally developed NIDAQmx.jl package which provides better type safety, error handling, and a more complete API. Key changes: - Update Project.toml dependencies (NIDAQ -> NIDAQmx) - Update channelfunctions to use NIDAQmx API (ai_channels, ao_channels, etc.) - Update taskfunctions to use typed task constructors (AITask, AOTask, etc.) - Enhance createtask() to query device voltage ranges for compatibility - Update setvoltage/readvoltage to use write_scalar/read_scalar with auto_start - Add separate method signatures for AOTask/DOTask and AITask/DITask - Update all consumer modules (CrystaLaser, VortranLaser, TransmissionDaq) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- ThorCam DCX: Use IS_CM_MONO8 instead of RGBA8 for grayscale camera - ThorCam DCX: Change buffer type from Cchar to UInt8 for proper 0-255 range - Fix Makie deprecation: resolution -> size in all GUI files - Fix camera display permutation: (H,W) data needs permutedims for Makie - Add exposure time tolerance check to avoid spurious warnings - Update CLAUDE.md with image()/heatmap() display documentation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace manual export propagation with Reexport.jl for cleaner module structure. MicroscopeControl.jl reduced from 79 to 31 lines by removing 50+ manual exports and 15+ using statements. Changes: - Add Reexport.jl dependency - HardwareInterfaces.jl: @reexport all interface modules - HardwareImplementations.jl: @reexport all implementation modules - MicroscopeControl.jl: @reexport both layers, remove manual exports Adding new hardware now requires edits in only one place instead of three. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Package was renamed upstream. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Brings in Reexport.jl to simplify export propagation from submodules. Resolved conflict: keep DAQmx (not old NIDAQ) + add Reexport dep. Fixed CI checkout action back to v6. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Move NIDAQcard include before TCubeLaserControl since it depends on it. Restore DAQmx to Project.toml after it was removed during manifest cleanup. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
DAQmx.jl is not in General registry, so [sources] is needed. [sources] requires Julia 1.11+. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
When the live display window is closed, abort the camera and invoke an optional on_close callback. This lets callers (e.g. MicroscopeAdapt) hook in additional cleanup like turning off lasers and updating GUI. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
NIDAQ.jltoDAQmx.jl(renamed to avoid copyright issues)Reexport.jlto simplifyMicroscopeControl.jlfrom ~80 lines to ~30[sources]for DAQmx since it's not in General registry (requires Julia 1.11+)(H, W, N)convention, ThorCam mono mode, Makie deprecationsAbstractSysteminterface and error handling for laser/DAQ modulesTest plan
Pkg.test()passes with simulated devicesusing MicroscopeControlloads cleanly with Reexport[sources]🤖 Generated with Claude Code