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Merged
C-Achard merged 7 commits into from
Jul 13, 2022
Merged

UI API overhaul + several features/fixes #17

C-Achard merged 7 commits into from
Jul 13, 2022

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@C-Achard
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@C-Achard C-Achard commented Jul 7, 2022

  • started cleaning up UI class/functions

  • fixed incorrect plots when using anisotropy correction

  • added anisotropy conversion to utils

  • fixed errors in launching review in new viewer

@C-Achard
UI refactor + aniso convert + fixed review plots
d1f83b2 
- started cleaning up UI class/functions

- fixed incorrect plots when using anisotropy correction

- added anisotropy conversion to utils

- fixed errors in launching review in new viewer
@C-Achard C-Achard added enhancement New feature or request fix Something needs to be or has been fixed labels Jul 7, 2022
@C-Achard C-Achard self-assigned this Jul 7, 2022
@C-Achard C-Achard mentioned this pull request Jul 7, 2022
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codecov-commenter commented Jul 7, 2022 •
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Codecov Report

Merging #17 (debb923) into main (c2eb134) will increase coverage by 0.40%.
The diff coverage is 62.60%.

@@            Coverage Diff             @@
##             main      #17      +/-   ##
==========================================
+ Coverage   37.40%   37.80%   +0.40%     
==========================================
  Files          37       37              
  Lines        3294     3383      +89     
==========================================
+ Hits         1232     1279      +47     
- Misses       2062     2104      +42
Impacted Files Coverage Δ
napari_cellseg3d/plugin_convert.py 0.00% <0.00%> (ø)
napari_cellseg3d/plugin_crop.py 0.00% <0.00%> (ø)
napari_cellseg3d/plugin_helper.py 0.00% <0.00%> (ø)
napari_cellseg3d/plugin_metrics.py 0.00% <0.00%> (ø)
napari_cellseg3d/plugin_model_inference.py 0.00% <0.00%> (ø)
napari_cellseg3d/utils.py 31.57% <25.00%> (-0.07%) ⬇️
napari_cellseg3d/plugin_dock.py 74.56% <66.66%> (-1.37%) ⬇️
napari_cellseg3d/launch_review.py 58.76% <68.75%> (-0.24%) ⬇️
napari_cellseg3d/plugin_review.py 89.33% <80.00%> (ø)
napari_cellseg3d/interface.py 86.39% <83.90%> (-1.28%) ⬇️
... and 4 more

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deprecated-napari-hub-preview-bot bot commented Jul 7, 2022 •
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Preview page for your plugin is ready here:
https://preview.napari-hub.org/AdaptiveMotorControlLab/CellSeg3d/17
Updated: 2022-07-13T13:52:08.973153

vidalmaxime
vidalmaxime suggested changes Jul 7, 2022
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napari_cellseg3d/launch_review.py Outdated

def crop_volume_around_point(points, layer, zoom_factor):
if zoom_factor != [1, 1, 1]:
vol = np.array(layer.data, dtype=np.int16)
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I think the datatypes of all arrays dealt with here should be changed from int16 to uint16

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@C-Achard C-Achard Jul 8, 2022

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I get this with uint16 :
can't convert np.ndarray of type numpy.uint16. The only supported types are: float64, float32, float16, complex64, complex128, int64, int32, int16, int8, uint8, and bool.

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@C-Achard C-Achard Jul 8, 2022

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Most likely due to the way utils.resize works (Uses MONAI, ndimage would be cleaner but MONAI transform is actually faster)

napari_cellseg3d/plugin_convert.py
"Remove in folder", func=self.folder_remove_small
# remove small
self.btn_remove_small_folder = ui.Button(
"Remove small in folder", func=self.folder_remove_small
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Remove small cells ?

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Screenshot 2022-07-07 at 14 50 22

Also, the title shows up cropped here.

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@C-Achard C-Achard Jul 8, 2022

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It removes anything below a certain number of pixels in size, it works only for labels

Do you still have a cropped title ? It might be a Qt version/macOS specific issue

C-Achard added 3 commits July 8, 2022 14:04
@C-Achard
UI API refactor + aniso conversion + docs
b7837be
@C-Achard
Update cropping_module_guide.rst
a1707bd 
Updated docs
@C-Achard
Feedback from PR
61863a7 
- Improved conversion file path handling
- Edit for ambiguous desc in framework model
- Changed training validation dropdown to spinbox
@C-Achard C-Achard requested a review from vidalmaxime July 8, 2022 13:15
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C-Achard commented Jul 8, 2022

Edited with the feedback in mind :) Let me know what you think.

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C-Achard commented Jul 8, 2022 •
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  • Major overhaul to interface.py
  • Added anisotropy conversion to utilities
  • Updated docs
  • Fixed what could be in what was mentioned in the requested changes

@C-Achard C-Achard changed the title [WIP] UI refactor + aniso convert + fixed review plots [WIP] UI API overhaul + several features/fixes Jul 9, 2022
@C-Achard C-Achard marked this pull request as draft July 9, 2022 08:26
@C-Achard C-Achard marked this pull request as ready for review July 13, 2022 13:46
@C-Achard C-Achard merged commit eb33f31 into main Jul 13, 2022
C-Achard added a commit that referenced this pull request Jul 14, 2022
@C-Achard
Revert "[WIP] UI API overhaul + several features/fixes (#17)"
a0e85a5 
This reverts commit eb33f31.
@C-Achard C-Achard mentioned this pull request Jul 14, 2022
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@C-Achard C-Achard deleted the cy/aniso_convert branch July 14, 2022 15:13
@MMathisLab MMathisLab changed the title [WIP] UI API overhaul + several features/fixes UI API overhaul + several features/fixes Jul 17, 2022
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@MMathisLab MMathisLab Awaiting requested review from MMathisLab

@vidalmaxime vidalmaxime Awaiting requested review from vidalmaxime

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