remove dead code

[Alpaca233]

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:

• Removed numerous unused constants and configuration classes from 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]
• Removed the section on optional image stitching dependencies (ImageJ, Java, Maven, etc.) from the software/README.md documentation.

Code Simplification and Refactoring:

• Removed the save_current_configuration_to_path method from software/control/core/channel_configuration_mananger.py, as it was only used temporarily.
• Removed the for_displacement_measurement parameter and all related logic from software/control/core/live_controller.py, simplifying the controller's initialization and live control flow. [1] [2] [3] [4]
• Cleaned up imports in software/control/core/multi_point_controller.py and software/control/core/stream_handler.py by removing unused modules. [1] [2]
• Minor change: switched from auto to explicit values in the Enum import in _def.py for clarity.

[Copilot]

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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