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Feedback fixes #58

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merged 27 commits into from
Dec 5, 2023
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7007cb9
Update plugin_convert.py
C-Achard Nov 15, 2023
d73ed02
Update plugin_convert.py
C-Achard Nov 16, 2023
fe28b45
Update plugin_convert.py
C-Achard Nov 16, 2023
7a4646a
Update napari_cellseg3d_m1.yml
C-Achard Nov 16, 2023
0569a64
Fix memory allocation issue
C-Achard Nov 16, 2023
463c569
Add debug info to stats
C-Achard Nov 16, 2023
e001acb
Add mini-stats test
C-Achard Nov 16, 2023
fc73e5b
TEMP Comment out image stats
C-Achard Nov 16, 2023
4edc20d
Revert "TEMP Comment out image stats"
C-Achard Nov 16, 2023
7264abd
Disable image deletion
C-Achard Nov 16, 2023
22dbf56
Disable sphericity
C-Achard Nov 16, 2023
e567b22
Add sphericity
C-Achard Nov 16, 2023
e478bee
Add *.tiff as valid path everywhere
C-Achard Nov 21, 2023
62b76c8
Fix tests and tif+tiff loading
C-Achard Nov 21, 2023
7a24794
Fix several test issues and inconsistencies
C-Achard Nov 21, 2023
9d896b8
Update .gitignore
C-Achard Nov 21, 2023
3b1cd8d
Move pydensecrf back to main repo
C-Achard Nov 21, 2023
7adc683
Update worker_inference.py
C-Achard Nov 22, 2023
5d5b0a3
Update worker_inference.py
C-Achard Nov 22, 2023
0b03fe7
Update worker_inference.py
C-Achard Nov 22, 2023
b824bfb
Reduce warning spam in stats
C-Achard Nov 22, 2023
c6f6d6a
Update instance_segmentation.py
C-Achard Nov 22, 2023
f2f4b52
Update utils.py
C-Achard Nov 22, 2023
29894c5
Update instance_segmentation.py
C-Achard Nov 22, 2023
7064d95
Fix attr error in inference
C-Achard Nov 25, 2023
9e7d1ab
Add artifact removal (#60)
C-Achard Dec 5, 2023
254d7fd
macOS Silicon install (#59)
C-Achard Dec 5, 2023
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Add debug info to stats
C-Achard committed Nov 16, 2023
commit 463c5692bacedd899b5565f0cd14a929dabd94da
5 changes: 4 additions & 1 deletion napari_cellseg3d/code_plugins/plugin_convert.py
Original file line number Diff line number Diff line change
@@ -674,6 +674,7 @@ def _start(self):
self.folder_choice.isChecked() and len(self.labels_filepaths) != 0
):
for i, image_path in enumerate(self.labels_filepaths):
logger.debug(f"Loading image {i} : {image_path}")
image = imread(image_path)
image_name = Path(image_path).stem
if image.sum() == 0:
@@ -686,13 +687,15 @@ def _start(self):
logger.warning(m)
warn(m, stacklevel=0)
continue
logger.debug(f"Image {i} has shape {image.shape}")
stats = volume_stats(image)
logger.debug("Computing stats")
stats_df = pd.DataFrame(stats.get_dict())
csv_name = (
str(image_name) + "_" + self.csv_name.text() + f"_{i}.csv"
)
logger.info(
f"Saving stats to {Path(self.results_path) / Path(csv_name)}"
f"Saving stats to {(Path(self.results_path) / Path(csv_name)).resolve()}"
)
stats_df.to_csv(
Path(self.results_path) / Path(csv_name), index=False