Performance Diagnostics

[AdvancedImagingUTSW]

This pull request draft introduces a new diagnostics popup feature for performance monitoring, adds supporting infrastructure, and improves logging and documentation.

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@annie-xd-wang - I wanted to see if there were particular points in the code that you were hoping to monitor. If so, we can add the appropriate regular expressions to pull out the time it takes to execute that section of code, and we can populate a histogram or line plot in this popup.

I also wanted to see if there was a better way to capture screenshots of our GUI. Our documentation is increasingly out of date, and I thought it would be nice to automate capturing screenshots. I added a new dependency to do this, but I then realized that PIL provides the basic functionality needed and that additional dependency may not be necessary.

So, don't merge, but I would love your feedback on what we should monitor. The time necessary to save the data is another area that could be valuable.

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New Diagnostics Popup Feature:

• Added the new DiagnosticsPopupController class, which manages a diagnostics popup window for visualizing performance metrics from log files. This includes methods for displaying, updating, and saving diagnostic plots, and is integrated with the application's logging system. (src/navigate/controller/sub_controllers/diagnostics_popup.py)
• Registered DiagnosticsPopupController in the sub-controller initialization and imported the corresponding view class. (src/navigate/controller/sub_controllers/__init__.py, src/navigate/controller/sub_controllers/menus.py) [1] [2] [3]
• Integrated the diagnostics popup into the application menu, adding a "Performance Diagnostics" menu item and the logic to open the popup, ensuring only one instance is active at a time. (src/navigate/controller/sub_controllers/menus.py) [1] [2]

Logging and Diagnostics Improvements:

• Added info-level logging to the histogram population process, recording the time taken to populate histograms for performance diagnostics. (src/navigate/controller/sub_controllers/histogram.py) [1] [2] [3]
• Improved log message clarity when receiving images in the controller. (src/navigate/controller/controller.py)

Documentation and Dependency Updates:

• Added a new example script docs/capture_gui.py to automate capturing screenshots of various GUI windows and tabs. (docs/capture_gui.py)
• Updated pyproject.toml to include the mss package (for screenshot functionality) and fixed formatting in the docs dependencies list. (pyproject.toml) [1] [2]

Minor Code Quality Improvements:

• Minor formatting and style cleanups in controller initialization and thread pool usage. (src/navigate/controller/controller.py) [1] [2]
• Removed unused inner function from log file management. (src/navigate/log_files/log_functions.py)

[codecov]

Codecov Report

❌ Patch coverage is 34.23729% with 194 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.63%. Comparing base (5fb486e) to head (7f1a0b0).

Files with missing lines	Patch %	Lines
...te/controller/sub_controllers/diagnostics_popup.py	19.81%	89 Missing ⚠️
src/navigate/view/popups/diagnostics_popup.py	23.52%	39 Missing ⚠️
src/navigate/log_files/log_functions.py	44.68%	26 Missing ⚠️
src/navigate/tools/gui.py	0.00%	13 Missing ⚠️
src/navigate/model/features/common_features.py	56.52%	10 Missing ⚠️
src/navigate/model/devices/device_types.py	65.21%	8 Missing ⚠️
src/navigate/controller/sub_controllers/menus.py	25.00%	6 Missing ⚠️
src/navigate/model/device_startup_functions.py	33.33%	2 Missing ⚠️
...c/navigate/controller/sub_controllers/histogram.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1128      +/-   ##
===========================================
- Coverage    53.93%   53.63%   -0.30%     
===========================================
  Files          191      194       +3     
  Lines        21953    22198     +245     
===========================================
+ Hits         11840    11906      +66     
- Misses       10113    10292     +179     

Flag	Coverage Δ
unittests	53.63% <34.23%> (-0.30%)	⬇️

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