Uv docs #209

beniroquai · 2026-01-14T14:13:10Z

This PR focusses on a simplifcation of the readme (e.g. install via UV).

Copilot

Pull request overview

This PR simplifies the README documentation with a focus on UV (a fast Python package installer) as the primary installation method. The changes also include various code improvements across multiple controller and manager files.

Changes:

Simplified README to emphasize UV-based installation and removed extensive platform-specific documentation
Fixed spelling errors throughout the codebase (corrected "availableIlliminations" to "availableIlluminations")
Refactored illumination parameter handling to use list-based approach instead of individual parameters
Added error handling for camera trigger source configuration
Improved objective position detection logic

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
README.md	Streamlined installation instructions to focus on UV, removed outdated platform-specific guides, fixed typos
ESP32LEDMatrixManager.py	Added channel_index attribute for LED matrix
hikcamera.py	Added error handling for trigger mode/source setting, changed auto_trigger default, upgraded debug to info logging
experiment_performance_mode.py	Refactored illumination parameters from dict to list, added synchronization delays with TODOs
experiment_normal_mode.py	Conditionally add timing workflow step only when n_times > 1
experiment_mode_base.py	Updated illumination parameter preparation to handle LED channel detection
TimelapseController.py	Fixed spelling: availableIlliminations → availableIlluminations
ObjectiveController.py	Added logic to detect current objective position, with position recalibration
MCTController.py / MCTController.py_OLD	Fixed spelling: availableIlliminations → availableIlluminations
ExperimentController.py	Refactored illumination API to use list instead of individual parameters

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Copilot · 2026-01-14T14:21:44Z

imswitch/imcontrol/model/interfaces/hikcamera.py

+                ret = self.camera.MV_CC_SetEnumValue("TriggerMode",  MV_TRIGGER_MODE_ON)
+                if ret != 0:
+                    self.__logger.error(f"Set TriggerMode failed! ret [0x{ret:x}]")
+                    return False
+                ret = self.camera.MV_CC_SetEnumValue("TriggerSource", MV_TRIGGER_SOURCE_SOFTWARE)
+                if ret != 0:
+                    self.__logger.error(f"Set TriggerSource failed! ret [0x{ret:x}]")
+                    return False


The error handling has been added for setting TriggerMode and TriggerSource, but the function returns False on error while it doesn't have an explicit return type declaration. This creates an inconsistent return pattern where success has no explicit return (implicit None) while failure returns False. Consider either returning True on success or making the return type consistent throughout the function.

Copilot · 2026-01-14T14:21:45Z

imswitch/imcontrol/controller/controllers/experiment_controller/experiment_performance_mode.py

            data: Dictionary with completion information
        """
        self._logger.info(f"Stagescan completion signal received: {data}")
+        time.sleep(0.5)  # Small delay to ensure all processing is done # TODO: 


Hard-coded sleep delays (0.5 seconds) are added with TODO comments suggesting uncertainty about the approach. These arbitrary delays can impact performance and suggest potential race conditions or synchronization issues that should be addressed properly rather than with fixed delays. Consider using proper synchronization mechanisms like checking actual completion status or using event-driven approaches instead of fixed sleeps.

Copilot · 2026-01-14T14:21:45Z

README.md

-<a href="https://discord.gg/y4Su9PpEvX">
-<img src="https://cdn.prod.website-files.com/6257adef93867e50d84d30e2/636e0a6918e57475a843f59f_icon_clyde_black_RGB.svg" alt="W3Schools.com" width="100">
-</a>
+It is a fork - that has been detached from the original ImSwitch fork: https://github.com/ImSwitch/ImSwitch


The phrase "has been detached from the original ImSwitch fork" is confusing. If this is a fork, it cannot be "detached from" a fork. Consider rephrasing to something like "This is a fork of the original ImSwitch project" or "This is a fork that has diverged from the original ImSwitch repository".

@copilot open a new pull request to apply changes based on this feedback

Copilot · 2026-01-14T14:21:45Z

README.md

-<a href="https://discord.gg/y4Su9PpEvX">
-<img src="https://cdn.prod.website-files.com/6257adef93867e50d84d30e2/636e0a6918e57475a843f59f_icon_clyde_black_RGB.svg" alt="W3Schools.com" width="100">
-</a>
+It is a fork - that has been detached from the original ImSwitch fork: https://github.com/ImSwitch/ImSwitch


Typo in the phrase "focusses on". The correct spelling is "focuses" (with one 's').

@copilot open a new pull request to apply changes based on this feedback

Copilot · 2026-01-14T14:21:45Z

README.md


-```
-sudo apt-get install libxml2-dev libxslt-dev
+For this, please reffer to the bash files in this repo: https://github.com/openUC2/ImSwitchDockerInstall


Typo in "reffer". The correct spelling is "refer".

@copilot open a new pull request to apply changes based on this feedback

Copilot · 2026-01-14T14:21:47Z

imswitch/imcontrol/controller/controllers/experiment_controller/experiment_performance_mode.py


                # Check if we received all expected frames
                if self._frame_count >= expected_frames:
+                    time.sleep(0.5)  # Small delay to ensure all processing is done # TODO: We should rather count stored frames not camera triggers? 


Another hard-coded 0.5 second sleep with a TODO suggesting it should count stored frames rather than camera triggers. This is the same performance and synchronization issue as line 717. The TODO provides a better alternative approach that should be implemented.

Copilot · 2026-01-14T14:21:47Z

imswitch/imcontrol/model/managers/LEDMatrixs/ESP32LEDMatrixManager.py

        self.I_max = 255
        self.intensity=0
        self.enabled = False
+        self.channel_index = "led"


The channel_index is being set to lowercase "led", but other parts of the codebase (e.g., ESP32LEDLaserManager.py line 96) check for uppercase "LED" using exact string comparison. This inconsistency could cause the LED channel to not be properly recognized. Consider either setting it to uppercase "LED" to match existing code patterns, or ensuring all comparisons are case-insensitive.

@copilot open a new pull request to apply changes based on this feedback

Copilot · 2026-01-14T14:21:47Z

README.md

-<a href="https://discord.gg/y4Su9PpEvX">
-<img src="https://cdn.prod.website-files.com/6257adef93867e50d84d30e2/636e0a6918e57475a843f59f_icon_clyde_black_RGB.svg" alt="W3Schools.com" width="100">
-</a>
+It is a fork - that has been detached from the original ImSwitch fork: https://github.com/ImSwitch/ImSwitch


Typo in "simplifcation". The correct spelling is "simplification".

Copilot · 2026-01-14T14:21:48Z

README.md

-
-
-### Option D: Install from Github (UC2 version)
+This is an outdated version how you can install it through conda.


Grammatical error: "This is an outdated version how you can install it through conda" should be "This is an outdated version of how you can install it through conda" or "This describes an outdated method to install it through conda".

Copilot · 2026-01-14T14:21:48Z

imswitch/imcontrol/controller/controllers/ObjectiveController.py

+                if abs(mPositionObjective - self._objectivePositions[self._currentObjective]) > 500:
+                    self.calibrateObjective()
+                    self._moveMotorToSlot(0)
+                self._currentObjective = 0 # TODO: We should compare the position with the configured positions and decided if in slot 0/1


The code sets self._currentObjective = 0 after all the logic to determine the actual objective position (lines 100-109). This hardcoded assignment at line 110 overwrites the carefully calculated position from the previous logic, making lines 100-109 effectively dead code. Either remove line 110 or remove the position calculation logic above it.

Copilot · 2026-01-14T14:31:10Z

@beniroquai I've opened a new pull request, #210, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot · 2026-01-14T14:31:15Z

@beniroquai I've opened a new pull request, #211, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot · 2026-01-14T14:31:25Z

@beniroquai I've opened a new pull request, #212, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot · 2026-01-14T14:31:50Z

@beniroquai I've opened a new pull request, #213, to work on those changes. Once the pull request is ready, I'll request review from you.

The review comment references a typo "focusses" → "focuses" in README.md:5, but this word does not exist in any tracked files or git history. ## Investigation Results - Searched all markdown files, README.md (current and historical), and entire codebase - Checked commit dcee095 and all ancestors - The word "focusses" only appears in PR #209's description text: "This PR focusses on a simplifcation..." ## Analysis The review bot likely flagged the PR description rather than file content. PR descriptions cannot be modified through code changes. **Awaiting clarification:** Should I address other typos from the review (e.g., "reffer" → "refer" on line 130), or is there a different file/location for the "focusses" typo?  --- 💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more [Copilot coding agent tips](https://gh.io/copilot-coding-agent-tips) in the docs. Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>

The `ESP32LEDMatrixManager` was setting `channel_index = "led"` (lowercase), causing it to fail case-sensitive comparisons for `"LED"` in `ESP32LEDLaserManager.py` and breaking LED channel recognition. ## Changes - Changed `channel_index` from `"led"` to `"LED"` in `ESP32LEDMatrixManager.__init__()` to match: - Case-sensitive equality checks in `ESP32LEDLaserManager.setEnabled()` (line 96) and `setValue()` (line 114) - Uppercase `"LED"` values in configuration files (example_histo_daheng.json, FRAME2b.json, example_uc2.json) ```python # Before self.channel_index = "led" # Would not match == "LED" checks # After self.channel_index = "LED" # Matches case-sensitive comparisons ```  --- 💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more [Copilot coding agent tips](https://gh.io/copilot-coding-agent-tips) in the docs. --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beniroquai <4345528+beniroquai@users.noreply.github.com>

Corrects spelling error in the "Installation of drivers" section of README.md. **Changes:** - Line 130: Changed "reffer" to "refer"  --- 💬 We'd love your input! Share your thoughts on Copilot coding agent in our [2 minute survey](https://gh.io/copilot-coding-agent-survey). --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beniroquai <4345528+beniroquai@users.noreply.github.com>

Addresses review feedback on contradictory phrasing in README.md line 5. ## Changes - Rephrased "It is a fork - that has been detached from the original ImSwitch fork" to "This is a fork that has diverged from the original ImSwitch repository" The original text was logically inconsistent—something cannot be "detached from a fork." The new phrasing clearly states the relationship to the upstream project.  --- 💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more [Copilot coding agent tips](https://gh.io/copilot-coding-agent-tips) in the docs. --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: beniroquai <4345528+beniroquai@users.noreply.github.com>

ethanjli · 2026-01-14T14:50:25Z

While you were working and I was waiting for Docker container images to download on my RPi, I also did a simplification of README.md in #208. I've now merged your changes into that PR, which I will be merging into the master branch soon. So you can go ahead and close/delete this PR; or you can rename it to something else if you don't want to throw away all the non-README.md changes you've made in this PR.

This PR merges https://github.com/openUC2/ImSwitch-ReactAPP into this repository so that we aren't constantly crapping React app build outputs into this repo upon every new commit for the React app. This merger also makes it simpler and less error-prone to commit API changes: a single pull request in this repo would include all changes in both the React app and the backend. This PR also resolves #205 (incorporating changes made in #209).

Simplify Readme

3fb59f4

beniroquai requested review from Copilot and ethanjli January 14, 2026 14:13

beniroquai mentioned this pull request Jan 14, 2026

Need a simpler README.md guide for setting up the dev env #205

Closed

adding psygnal instructions

dcee095

Copilot started reviewing on behalf of beniroquai January 14, 2026 14:16 View session

Copilot AI reviewed Jan 14, 2026

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This was referenced Jan 14, 2026

Fix confusing fork description in README #210

Merged

Unable to locate "focusses" typo referenced in review feedback #211

Merged

Copilot AI mentioned this pull request Jan 14, 2026

Fix typo in README.md: reffer → refer #212

Merged

Copilot AI mentioned this pull request Jan 14, 2026

Fix LED channel case inconsistency in ESP32LEDMatrixManager #213

Merged

Copilot AI and others added 4 commits January 14, 2026 15:43

beniroquai enabled auto-merge January 14, 2026 14:47

ethanjli added a commit that referenced this pull request Jan 14, 2026

Update README.md based on changes in PR #209

36eba77

ethanjli mentioned this pull request Jan 14, 2026

Merge the React frontend in from openUC2/ImSwitch-ReactAPP #208

Merged

Merge branch 'master' into uv-docs

bb8ab91

beniroquai closed this Jan 14, 2026

auto-merge was automatically disabled January 14, 2026 22:28
Pull request was closed



		### Option D: Install from Github (UC2 version)
		This is an outdated version how you can install it through conda.

Uv docs #209

Uv docs #209

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