Improved CLI, fixed bug with the GUI and refactored into module #2459
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Now using SCT's module: spinalcordtoolbox.gui.sagittal Fixes #2458
jcohenadad
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enhancement
jcohenadad
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compatibility
Now using SCT's module: spinalcordtoolbox.gui.sagittal Fixes #2458
…rdtoolbox into jca/2458-crop
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Results of |
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Results of on master (commit: 3da4b26): --> slight difference |
jcohenadad
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Dec 18, 2019
* sct_crop_image: Refactored cropping with GUI (WIP) Now using SCT's module: spinalcordtoolbox.gui.sagittal Fixes #2458 * sct_crop_image: Cleanup * sct_crop_image: Cleanup * sct_crop_image: Modify usage (WIP) * sct_crop_image: Refactored cropping with GUI (WIP) Now using SCT's module: spinalcordtoolbox.gui.sagittal Fixes #2458 * sct_crop_image: Cleanup * sct_crop_image: Cleanup * sct_crop_image: Made output filename optional * sct_crop_image: FIxed output filename * spinalcordtoolbox/cropping: Moved ImageCropper into python module * cropping: Replaced printv with logger, cleanup * sct_crop_image: Replaced cropping box param with ?min/?max WIP Fixes #1818 * cropping: Introduced class BoundingBox * cropping: Further work on get_voxel_bbox (WIP) * cropping: Replaced binary isct_crop_image with Python cropping * sct_crop_image: Fixed type of input params * cropping: Refactored to have several functions output bbox * cropping: Implemented get_bbox_from_mask() * sct_crop_image: Updated CLIs with recent changes in cropping * test_sct_crop_image: Updated test * sct_crop_image: Added entry for -ref option * resampling: Now accepting nibabel and Image object * resampling: Added 'mode' input parameter * cropping: Added get_bbox_from_ref() * sct_crop_image: Added entry for -ref option * test_sct_crop_image: Added testing for cropping with ref * cropping: Fixed origin * sct_crop_image: Improved CLI, save output there, display fsleyes syntax * cropping: Updated get_bbox_from_gui, few improvements * cropping: Cleanup * sct_crop_image: Cleanup, removed useless options * sct_crop_image: Added examples to usage * sct_crop_image: Clarified usage, prioritized cropping methods * cropping: Clarified GUI usage * sct_crop_image: Clarified usage * make_binaries.sh: Removed isct_crop_image binary generation * cropping: Removed useless input params * test_sct_crop_image: Updated integrity testing values * sct_apply_transfo: Updated with recent changes in ImageCropper * msct_gmseg_utils: Updated with recent changes in ImageCropper * sct_apply_transfo: Fixed if case typo * resampling: Fixed wrong type for nibabel * Fixed wrong input argument for nib_resampling() * Updated files with recent changes in sct_crop_image CLI * sct_detect_pmj: Fixed syntax for cropping image * sct_crop_image: Re-established flag -b because it is used elsewhere * Re-established sct_crop_image with flag -b * cropping: Fixed index error * sct_apply_transfo: Fixed wrongly commented line * cropping: get_bbox_from_ref() now checking dims for img_in and img_ref * cropping: Fixed wrong array assignment * cropping: Added useful verbose * test_sct_apply_transfo: Made test more sensitive * test_sct_apply_transfo: Now testing for 4D input * sct_apply_transfo: Fixed if cases * make_binaries.sh: removed isct_orientation3d * sct_download_data: Updated links to binaries Former-commit-id: 59da3093cd04609da5b6c0a51efb7ea887b284ea [formerly 88e0d74 [formerly 91beb0b]] Former-commit-id: e5c02a3a33bde11ffa719a6276e7264cc2230cc0 Former-commit-id: 8dfcf40
jcohenadad
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Dec 18, 2019
* sct_crop_image: Refactored cropping with GUI (WIP) Now using SCT's module: spinalcordtoolbox.gui.sagittal Fixes #2458 * sct_crop_image: Cleanup * sct_crop_image: Cleanup * sct_crop_image: Modify usage (WIP) * sct_crop_image: Refactored cropping with GUI (WIP) Now using SCT's module: spinalcordtoolbox.gui.sagittal Fixes #2458 * sct_crop_image: Cleanup * sct_crop_image: Cleanup * sct_crop_image: Made output filename optional * sct_crop_image: FIxed output filename * spinalcordtoolbox/cropping: Moved ImageCropper into python module * cropping: Replaced printv with logger, cleanup * sct_crop_image: Replaced cropping box param with ?min/?max WIP Fixes #1818 * cropping: Introduced class BoundingBox * cropping: Further work on get_voxel_bbox (WIP) * cropping: Replaced binary isct_crop_image with Python cropping * sct_crop_image: Fixed type of input params * cropping: Refactored to have several functions output bbox * cropping: Implemented get_bbox_from_mask() * sct_crop_image: Updated CLIs with recent changes in cropping * test_sct_crop_image: Updated test * sct_crop_image: Added entry for -ref option * resampling: Now accepting nibabel and Image object * resampling: Added 'mode' input parameter * cropping: Added get_bbox_from_ref() * sct_crop_image: Added entry for -ref option * test_sct_crop_image: Added testing for cropping with ref * cropping: Fixed origin * sct_crop_image: Improved CLI, save output there, display fsleyes syntax * cropping: Updated get_bbox_from_gui, few improvements * cropping: Cleanup * sct_crop_image: Cleanup, removed useless options * sct_crop_image: Added examples to usage * sct_crop_image: Clarified usage, prioritized cropping methods * cropping: Clarified GUI usage * sct_crop_image: Clarified usage * make_binaries.sh: Removed isct_crop_image binary generation * cropping: Removed useless input params * test_sct_crop_image: Updated integrity testing values * sct_apply_transfo: Updated with recent changes in ImageCropper * msct_gmseg_utils: Updated with recent changes in ImageCropper * sct_apply_transfo: Fixed if case typo * resampling: Fixed wrong type for nibabel * Fixed wrong input argument for nib_resampling() * Updated files with recent changes in sct_crop_image CLI * sct_detect_pmj: Fixed syntax for cropping image * sct_crop_image: Re-established flag -b because it is used elsewhere * Re-established sct_crop_image with flag -b * cropping: Fixed index error * sct_apply_transfo: Fixed wrongly commented line * cropping: get_bbox_from_ref() now checking dims for img_in and img_ref * cropping: Fixed wrong array assignment * cropping: Added useful verbose * test_sct_apply_transfo: Made test more sensitive * test_sct_apply_transfo: Now testing for 4D input * sct_apply_transfo: Fixed if cases * make_binaries.sh: removed isct_orientation3d * sct_download_data: Updated links to binaries Former-commit-id: 91beb0b
This was referenced Oct 15, 2020
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This PR introduces various improvements the
sct_crop_imagefunction, including:-dim,-startand-endwith the more intuitive-xmin -xmax -ymin -ymax -zmin -zmax. See function usage. Fixes Enhancement sct_crop_image documentation #1818isct_crop_imagewith Python-only cropping method. Fixes replace isct_crop_image with Python (i.e. no binary) #470ImageCropper()from CLI to new Python modulespinalcordtoolbox.cropping-meshand-shiftbecause unused (I think).isct_crop_imageandisct_orientation3d. Fixes Remove binaries isct_crop_image and isct_orientation3d #2460.This PR also deals with the resampling module:
Imageobject (previously only nibabel was allowed).resample_nib()toresample()and passImageobjects instead ofNifti1Images#2461) will take care of related refactoring.The CLIs has changed, hence the compatibility flag.