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@tngo2019 tngo2019 commented Aug 6, 2025

He needs to make his own branch.

He needs to make his own branch.
Updated ConfigurationController to handle all stage axes dynamically instead of a fixed set. Returned stage speed settings to 90% in ASI and MS2000 stage classes. WIll add to the advanced stage popup in next commit.
Introduces home position fields and update buttons to the advanced stage parameters popup, updates controller logic to handle home positions, and adjusts layout to accommodate new controls.

@annie-xd-wang - I may need your help coming up with a proper solution. Right now, when we query the stages, it only does it for the active microscope, and it will only return the stage positions for the standard x, y, z, f, theta stages.

A better solution would be to know which microscope is what, and the query the stage there.
Introduces a new 'query_select_microscope' command to Controller and Model, allowing thread-blocking queries for a specific microscope's stage positions. AdvancedStageParametersController now uses this to update axis limits based on the selected microscope, allowing one to query non-standard stages.
Replaces grid-based column headers with ttk.LabelFrames for each functional area, improving visual grouping and alignment. Widgets for each stage are now placed inside their respective column frames, and row heights are normalized for perfect alignment. Updates widget clearing logic to handle new column frames and row widgets.

Also, to make it easier to find the updated values in the yaml file, this is now sorted alphabetically.
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@annie-xd-wang - This should hopefully be ready to review. While reviewing @tngo2019's code, I realized that the advanced stage settings popup would struggle with non-default stages, so I had to add logic to query a specific stage from a specific microscope instance. In the process, made the popup a bit cleaner by organizing each update category within a common label frame.

Hopefully the tests pass.

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codecov bot commented Aug 12, 2025

Codecov Report

❌ Patch coverage is 27.63158% with 110 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.87%. Comparing base (2646712) to head (887adfd).
⚠️ Report is 12 commits behind head on develop.

Files with missing lines Patch % Lines
src/navigate/view/popups/stages_advanced_popup.py 0.00% 54 Missing ⚠️
...gate/controller/sub_controllers/stages_advanced.py 4.54% 21 Missing ⚠️
src/navigate/controller/controller.py 27.77% 13 Missing ⚠️
src/navigate/model/model.py 30.76% 9 Missing ⚠️
src/navigate/controller/sub_controllers/stages.py 55.55% 4 Missing ⚠️
src/navigate/model/devices/stage/asi.py 25.00% 3 Missing ⚠️
src/navigate/view/custom_widgets/validation.py 25.00% 3 Missing ⚠️
src/navigate/tools/file_functions.py 0.00% 2 Missing ⚠️
src/navigate/view/main_window_content/stage_tab.py 87.50% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1124      +/-   ##
===========================================
- Coverage    54.00%   53.87%   -0.13%     
===========================================
  Files          191      191              
  Lines        21785    21893     +108     
===========================================
+ Hits         11765    11795      +30     
- Misses       10020    10098      +78     
Flag Coverage Δ
unittests 53.87% <27.63%> (-0.13%) ⬇️

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@AdvancedImagingUTSW AdvancedImagingUTSW merged commit 2ec2db1 into develop Aug 12, 2025
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3 participants