Removed support for -initc2 flag because there is an alternative approach with sct_label_utils #2125
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User can do sct_label_utils()
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* detect_c2c3: improvements -- postprocessing * keep clusters with correct margin * use normalised margin * use top of the segmentation as anatomical prior * dev/detect_c2c3/train: create qc, nb of sagittal slices avg * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7 sag slices, remove hard coded post processing * Update README.md (#2118) * Expose aggregate_slicewise() API and various improvements (#2115) * sct_extract_metric: Created API: extract_metric * sct_extract_metric: Started refactoring to use aggregate_slicewise * aggregate_slicewise: Started refactoring for accommodating extract_metric - metrics is now ndarray (instead of list) to deal with >1 dim - added mask for computing weighted average, ml, etc. * sct_extract_metric,aggregate_slicewise: Main steps of working API sct_extract_metric now working (in specific scenario) with new APIs. * aggregate_slicewise,sct_extract_metric: Further improvements - Moved Metric() class inside aggregate_slicewise - Now display Mask in output csv - Now display func with metric name (for compatibility with process_seg module) * aggregate_slicewise: Changed variable name * process_seg: Adapted code to fit recent changes in aggregate_slicewise * msct_shape,process_seg: Adapted code to fit changes in aggregate_slicewise Other modifications: - drop features: incremental_length, distance_from_C1, vertebral_level * test_process_seg: Fixed broken compatibility with recent changes * sct_extract_metric,aggregate_slicewise: Refactored to generalize for ML and WA Notably introduced label_struc Class inside sct_extract_metric for simplicity * sct_extract_metric,aggregate_slicewise: Moved extract_metric inside aggregate_slicewise Will enable unit testing * aggregate_slicewise: Generalized to n-dim was breaking compatibility with process_seg * test_aggregate_slicewise: Started to update tests with recent changes * aggregate_slicewise: Generalized to n-dim, added tests * test_aggregate_slicewise: All tests pass * test_aggregate_slicewise: Added test for csv Testing output of extract_metric() Also fixed few issues in aggregate_slicewise.py * aggregate_slicewise: Fixed ordering of column in output csv All tests pass * aggregate_slicewise: Fixed issue with STD and ML method * aggregate_slicewise: Changed the way errors are raised * sct_extract_metric: Added field for appending to csv * utils: Fixed bug in parse_num_list_inv() Number of chars to adapt based on int * aggregate_slicewise: Implemented method=bin and added test * sct_extract_metric: Dropped support for method=wath Not really used... * aggregate_slicewise: Implemented method=max And associated tests and wrapper * sct_process_segmentation: Fixed broken compatibility * msct_shape: Fixed bug when looping across slices * sct_extract_metric: Fixed undeclared variable * aggregate_slicewise: Removed weight in ML for faster estimate Also started to implement MAP * sct_extract_metric: Changed default value for perslice * aggregate_slicewise: Implemented MAP (unfinished) need to pass ml_clusters information to func_ml() * aggregate_slicewise: Refactored for compatibility with MAP * aggregate_slicewise: Fixed bug related to reshaping mask Also added MAX in csv output * aggregate_slicewise: Fixed wrong indentation for try/except * aggregate_slicewise: Fixed duplicated dict key * aggregate_slicewise: Added check for non-finite values * test_sct_extract_metric: Updated test * aggregate_slicewise: Fixed bug introduced with checking for nonfinite * aggregate_slicewise: Fixed wrong reshape of array * batch_processing: Update with recent modifs in API * aggregate_slicewise,sct_process_segmentation: Added TODO * sct_process_segmentation,aggregate_slicewise: Changed default Regarding perslice and perlevel. To be closer to previous behaviour. * template: Now checking for inf in get_slices_from_vertebral_levels * sct_extract_metric: Few improvements - Display output file - Fixed default params * aggregate_slicewise: Created merge_dict() to deal with dict of dict Useful for sct_process_seg with several output metrics, to be able to concatenate them in a single csv * sct_process_segmentation: Now output all metrics in the same csv There's still a bug to solve in merge_dict() * aggregate_slicewise: Fixed small bug in merge_dict * aggregate_slicewise: Now ordering metrics in a friendly way * test_aggregate_slicewise: Fixed bug caused by recent changes * aggregate_slicewise: Forgot to add CSA and Angle * batch_processing: Updated to match recent changes * sct_extract_metric: Fixed deprecated default method wath * test_sct_extract_metric: Updated ground truth value * batch_processing: Fixed verbose bug * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7mm instead of 7slices * scripts/sct_download_data: update download link for c2c3 models * Output volume fraction on csv (#2122) * aggregate_slicewise: Removed VertLevel in agg_metric if not exist * aggregate_slicewise: Now display Label volume fraction Fixes #2121 * aggregate_slicewise: Fixed regression on detection nan * sct_extract_metric: Fixed bug with single mask as input * sct_extract_metric: Now display file name in Label column * test_aggregate_slicewise: Fixed unit test caused by recent changes * sct_label_vertebrae: Removed support for initc2 (#2125) User can do sct_label_utils() * detect_c2c3: improvements -- postprocessing * keep clusters with correct margin * use normalised margin * use top of the segmentation as anatomical prior * dev/detect_c2c3/train: create qc, nb of sagittal slices avg * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7 sag slices, remove hard coded post processing * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7mm instead of 7slices * scripts/sct_download_data: update download link for c2c3 models
jcohenadad
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Dec 18, 2019
User can do sct_label_utils() Former-commit-id: fe30f1b
jcohenadad
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Dec 18, 2019
* detect_c2c3: improvements -- postprocessing * keep clusters with correct margin * use normalised margin * use top of the segmentation as anatomical prior * dev/detect_c2c3/train: create qc, nb of sagittal slices avg * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7 sag slices, remove hard coded post processing * Update README.md (#2118) * Expose aggregate_slicewise() API and various improvements (#2115) * sct_extract_metric: Created API: extract_metric * sct_extract_metric: Started refactoring to use aggregate_slicewise * aggregate_slicewise: Started refactoring for accommodating extract_metric - metrics is now ndarray (instead of list) to deal with >1 dim - added mask for computing weighted average, ml, etc. * sct_extract_metric,aggregate_slicewise: Main steps of working API sct_extract_metric now working (in specific scenario) with new APIs. * aggregate_slicewise,sct_extract_metric: Further improvements - Moved Metric() class inside aggregate_slicewise - Now display Mask in output csv - Now display func with metric name (for compatibility with process_seg module) * aggregate_slicewise: Changed variable name * process_seg: Adapted code to fit recent changes in aggregate_slicewise * msct_shape,process_seg: Adapted code to fit changes in aggregate_slicewise Other modifications: - drop features: incremental_length, distance_from_C1, vertebral_level * test_process_seg: Fixed broken compatibility with recent changes * sct_extract_metric,aggregate_slicewise: Refactored to generalize for ML and WA Notably introduced label_struc Class inside sct_extract_metric for simplicity * sct_extract_metric,aggregate_slicewise: Moved extract_metric inside aggregate_slicewise Will enable unit testing * aggregate_slicewise: Generalized to n-dim was breaking compatibility with process_seg * test_aggregate_slicewise: Started to update tests with recent changes * aggregate_slicewise: Generalized to n-dim, added tests * test_aggregate_slicewise: All tests pass * test_aggregate_slicewise: Added test for csv Testing output of extract_metric() Also fixed few issues in aggregate_slicewise.py * aggregate_slicewise: Fixed ordering of column in output csv All tests pass * aggregate_slicewise: Fixed issue with STD and ML method * aggregate_slicewise: Changed the way errors are raised * sct_extract_metric: Added field for appending to csv * utils: Fixed bug in parse_num_list_inv() Number of chars to adapt based on int * aggregate_slicewise: Implemented method=bin and added test * sct_extract_metric: Dropped support for method=wath Not really used... * aggregate_slicewise: Implemented method=max And associated tests and wrapper * sct_process_segmentation: Fixed broken compatibility * msct_shape: Fixed bug when looping across slices * sct_extract_metric: Fixed undeclared variable * aggregate_slicewise: Removed weight in ML for faster estimate Also started to implement MAP * sct_extract_metric: Changed default value for perslice * aggregate_slicewise: Implemented MAP (unfinished) need to pass ml_clusters information to func_ml() * aggregate_slicewise: Refactored for compatibility with MAP * aggregate_slicewise: Fixed bug related to reshaping mask Also added MAX in csv output * aggregate_slicewise: Fixed wrong indentation for try/except * aggregate_slicewise: Fixed duplicated dict key * aggregate_slicewise: Added check for non-finite values * test_sct_extract_metric: Updated test * aggregate_slicewise: Fixed bug introduced with checking for nonfinite * aggregate_slicewise: Fixed wrong reshape of array * batch_processing: Update with recent modifs in API * aggregate_slicewise,sct_process_segmentation: Added TODO * sct_process_segmentation,aggregate_slicewise: Changed default Regarding perslice and perlevel. To be closer to previous behaviour. * template: Now checking for inf in get_slices_from_vertebral_levels * sct_extract_metric: Few improvements - Display output file - Fixed default params * aggregate_slicewise: Created merge_dict() to deal with dict of dict Useful for sct_process_seg with several output metrics, to be able to concatenate them in a single csv * sct_process_segmentation: Now output all metrics in the same csv There's still a bug to solve in merge_dict() * aggregate_slicewise: Fixed small bug in merge_dict * aggregate_slicewise: Now ordering metrics in a friendly way * test_aggregate_slicewise: Fixed bug caused by recent changes * aggregate_slicewise: Forgot to add CSA and Angle * batch_processing: Updated to match recent changes * sct_extract_metric: Fixed deprecated default method wath * test_sct_extract_metric: Updated ground truth value * batch_processing: Fixed verbose bug * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7mm instead of 7slices * scripts/sct_download_data: update download link for c2c3 models * Output volume fraction on csv (#2122) * aggregate_slicewise: Removed VertLevel in agg_metric if not exist * aggregate_slicewise: Now display Label volume fraction Fixes #2121 * aggregate_slicewise: Fixed regression on detection nan * sct_extract_metric: Fixed bug with single mask as input * sct_extract_metric: Now display file name in Label column * test_aggregate_slicewise: Fixed unit test caused by recent changes * sct_label_vertebrae: Removed support for initc2 (#2125) User can do sct_label_utils() * detect_c2c3: improvements -- postprocessing * keep clusters with correct margin * use normalised margin * use top of the segmentation as anatomical prior * dev/detect_c2c3/train: create qc, nb of sagittal slices avg * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7 sag slices, remove hard coded post processing * spinalcordtoolbox/vertebrae/detect_c2c3: avg 7mm instead of 7slices * scripts/sct_download_data: update download link for c2c3 models Former-commit-id: 9217ece
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Instead, user can create a label with
sct_label_utilsand then runsct_label_vertebraewith flag-initlabel. This decision enables to lighter the code and minimize the number of choices for the user (could be overwhelming).Example:
Fixes #2120