neuropoly / spinalcordtoolbox / 10279
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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

* aggr... (continued)

9968 of 15008 relevant lines covered (66.42%)

1.33 hits per line

Jobs
ID Job ID Ran Files Coverage
1 10279.1 (SCT_MINICONDA=2 MPLBACKEND=Agg) 0
66.42
 Travis Job 10279.1
2 10279.2 (SCT_MINICONDA=2 MPLBACKEND=Agg) 0
66.42
 Travis Job 10279.2
Source Files on build 10279
Detailed source file information is not available for this build.