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Pull request overview
This pull request removes dead code and obsolete features from the codebase to reduce maintenance overhead. The changes primarily target unused optional features including image stitching, tracking, classification models, plate readers, spectrometers, displacement measurement, and volumetric imaging.
Key changes include:
- Deletion of 14 complete files containing unused functionality
- Removal of UI widgets and settings related to tracking, recording, and displacement measurement
- Cleanup of unused constants, configuration classes, and method parameters
- Simplification of GUI initialization by removing conditional logic for disabled features
- Documentation update to remove installation instructions for image stitching dependencies
Reviewed changes
Copilot reviewed 25 out of 25 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
software/tools/stitcher.py |
Deleted entire ImageJ-based image stitching implementation |
software/tools/script_stitch_slide.py |
Deleted stitching script and helper functions |
software/tools/script_flip_i_indices.py |
Deleted utility script for inverting image indices |
software/control/widgets_usbspectrometer.py |
Deleted USB spectrometer widgets |
software/control/stitcher.py |
Deleted alternative stitcher implementation with Zarr/OME support |
software/control/spectrometer_oceanoptics.py |
Deleted Ocean Optics spectrometer interface |
software/control/processing_handler.py |
Deleted parallel processing handler |
software/control/tracking.py |
Deleted object tracking implementation |
software/control/utils_/image_processing.py |
Deleted image processing utilities for tracking |
software/control/core_volumetric_imaging.py |
Deleted volumetric imaging stream handlers |
software/control/core_usbspectrometer.py |
Deleted USB spectrometer stream handlers |
software/control/core_platereader.py |
Deleted plate reader controller |
software/control/core_displacement_measurement.py |
Deleted displacement measurement controller |
software/control/core_PDAF.py |
Deleted phase detection autofocus implementation |
software/control/widgets.py |
Removed tracking, recording, and displacement measurement widgets; removed related settings UI |
software/control/microscope.py |
Removed for_displacement_measurement parameter from live controller initialization |
software/control/gui_hcs.py |
Removed tracking, displacement, and recording UI components; simplified napari integration |
software/control/core/core.py |
Removed TrackingController, TrackingWorker, ImageSaver_Tracking, and ImageArrayDisplayWindow classes |
software/control/core/live_controller.py |
Removed for_displacement_measurement parameter and related laser control logic |
software/control/core/multi_point_controller.py |
Removed unused CameraFrame import |
software/control/core/stream_handler.py |
Removed unused cv2 import |
software/control/core/channel_configuration_mananger.py |
Removed save_current_configuration_to_path method |
software/control/_def.py |
Removed configuration constants for volumetric imaging, plate readers, tracking, classification, stitching |
software/README.md |
Removed ImageJ/Maven installation instructions for stitching |
software/tests/control/test_MultiPointController.py |
Renamed test class from TestAcquisitionTracker to AcquisitionTracker |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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This pull request primarily removes unused or obsolete configuration options and code related to optional features (such as image stitching, tracking, and classification) from the codebase and documentation. The goal is to clean up the code, reduce maintenance overhead, and simplify configuration files. No core functionality is affected.
Key changes include:
Configuration and Feature Cleanup:
software/control/_def.py, including those related to image stitching, tracking, plate reader, volumetric imaging, classification models, and legacy features. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]software/README.mddocumentation.Code Simplification and Refactoring:
save_current_configuration_to_pathmethod fromsoftware/control/core/channel_configuration_mananger.py, as it was only used temporarily.for_displacement_measurementparameter and all related logic fromsoftware/control/core/live_controller.py, simplifying the controller's initialization and live control flow. [1] [2] [3] [4]software/control/core/multi_point_controller.pyandsoftware/control/core/stream_handler.pyby removing unused modules. [1] [2]autoto explicit values in theEnumimport in_def.pyfor clarity.