TheDeanLab / navigate

navigate - open source light-sheet microscope controls
https://thedeanlab.github.io/navigate/
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3 d volume search #1013

Closed annie-xd-wang closed 1 week ago

annie-xd-wang commented 1 month ago

We can start testing with the feature pipeline: [{"name": ZStackAcquisition,"args": (False,False,"z-stack",True,),},{"name": WaitToContinue,},{"name": VolumeSearch3D,"args": ("Nanoscale","N/A",0,1,0.5,None,),},{"name": WaitToContinue,},{"name": ChangeResolution,"args": ("Nanoscale","N/A",),},{"name": ZStackAcquisition,"args": (False,False,"z-stack",True,),},]. We need to load a custom function to accurately label the images for improved results.

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 28.31169% with 276 lines in your changes missing coverage. Please review.

Project coverage is 53.98%. Comparing base (b7412e9) to head (81c5064). Report is 28 commits behind head on develop.

Files with missing lines Patch % Lines
src/navigate/model/features/update_setting.py 15.53% 87 Missing :warning:
src/navigate/model/features/volume_search.py 8.57% 64 Missing :warning:
src/navigate/model/analysis/boundary_detect.py 8.92% 51 Missing :warning:
...rc/navigate/model/data_sources/tiff_data_source.py 30.76% 36 Missing :warning:
src/navigate/model/features/image_writer.py 68.96% 18 Missing :warning:
...igate/controller/sub_controllers/features_popup.py 8.33% 11 Missing :warning:
src/navigate/model/data_sources/data_source.py 69.23% 4 Missing :warning:
src/navigate/controller/controller.py 57.14% 3 Missing :warning:
src/navigate/model/features/common_features.py 50.00% 1 Missing :warning:
src/navigate/model/model.py 50.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #1013 +/- ## =========================================== - Coverage 54.32% 53.98% -0.34% =========================================== Files 180 181 +1 Lines 20428 20697 +269 =========================================== + Hits 11097 11174 +77 - Misses 9331 9523 +192 ``` | [Flag](https://app.codecov.io/gh/TheDeanLab/navigate/pull/1013/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TheDeanLab) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/TheDeanLab/navigate/pull/1013/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TheDeanLab) | `53.98% <28.31%> (-0.34%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TheDeanLab#carryforward-flags-in-the-pull-request-comment) to find out more.

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AdvancedImagingUTSW commented 1 week ago

Is this ready for review @annie-xd-wang ?

annie-xd-wang commented 1 week ago

Yes, it is ready for review.