Automatically install missing packages #43
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…onSelectVolumesFolderButton() method
jcohenadad
commented
Jul 12, 2024
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| segm_data = segm.get_fdata() | ||
| segm_data_dtype = segm.dataobj.dtype | ||
| print(f'infile: {input_path}, dtype: {segm_data.dtype}') | ||
| if segm_data.dtype != np.uint8: | ||
| if segm_data_dtype != np.uint8: | ||
| segm_data = segm_data.astype(np.uint8) | ||
| segm_nii = nib.Nifti1Image(segm_data, segm.affine) | ||
| segm.header.set_data_dtype(np.uint8) | ||
| segm_nii = nib.Nifti1Image(segm_data, segm.affine, segm.header) |
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These changes seem unrelated to package management. For the sake of clarity in the git history, should we do avoid unrelated changes in this PR, and address these changes in another, more specific, PR?
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Yes, sorry, I should have created another issue and PR specific to this, a small bug I found while testing the module. Note: .get_fdata() returns a floating point image so if segm_data.dtype != np.uint8: would always have returned False.
jcohenadad
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Jul 12, 2024
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| modality: 'MRI' # 'CT' or 'MRI' | ||
| modality: 'CT' # 'CT' or 'MRI' | ||
| slice_view_color: 'Red' # 'Red' or 'Yellow' or 'Green' | ||
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| interpolate_value: 0 | ||
| interpolate_value: 1 | ||
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| impose_bids_format: True | ||
| impose_bids_format: False | ||
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| is_classification_requested: True | ||
| is_segmentation_requested: True | ||
| is_semi_automatic_phe_tool_requested: True | ||
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| ct_window_width: 85 | ||
| ct_window_level: 45 |
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Also unrelated to package management
jcohenadad
changed the title
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Tested on fresh Slicer install, and issue related to the missing qt import: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/imp.py", line 169, in load_source
module = _exec(spec, sys.modules[name])
File "<frozen importlib._bootstrap>", line 613, in _exec
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "/Users/julien/code/slicer-manual-annotation/SlicerCART/src/SlicerCART.py", line 67, in <module>
check_and_install_python_packages()
File "/Users/julien/code/slicer-manual-annotation/SlicerCART/src/SlicerCART.py", line 52, in check_and_install_python_packages
response = qt.QMessageBox.question(slicer.util.mainWindow(), 'Install Extensions', msg,
NameError: name 'qt' is not defined
[Qt] loadSourceAsModule - Failed to load file "/Users/julien/code/slicer-manual-annotation/SlicerCART/src/SlicerCART.py" as module "SlicerCART" !
[Qt] Fail to instantiate module "SlicerCART"
[Qt] The following modules failed to be instantiated:
[Qt] SlicerCART
[Qt] Populating font family aliases took 106 ms. Replace uses of missing font family ".AppleSystemUIFont" with one that exists to avoid this cost. Although |
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Example of qt box on Slicer fresh install: 
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This is a branch off of #41
TODO:
TODO in subsequent PRs: