Save DSC of original vs. new labels when merging segmentations

- Save to file rather than only printing to console
- Use logging

magmap/atlas/edge_seg.py

@@ -15,6 +15,8 @@
 from magmap.io import df_io, libmag, sitk_io
 from magmap.stats import vols
 
+_logger = config.logger.getChild(__name__)
+
 
 def _mirror_imported_labels(labels_img_np, start, mirror_mult, axis):
     # mirror labels that have been imported and transformed may have had
@@ -355,19 +357,24 @@ def edge_aware_segmentation(path_atlas, show=True, atlas=True, suffix=None,
     labels_sitk_seg = sitk_io.replace_sitk_with_numpy(labels_sitk, labels_seg)
 
     # show DSCs for labels
-    print("Measuring overlap of individual original and watershed labels:")
-    atlas_refiner.measure_overlap_labels(labels_sitk, labels_sitk_seg)
-    print("\nMeasuring overlap of combined original and watershed labels:")
-    atlas_refiner.measure_overlap_labels(
+    _logger.info(
+        "\nMeasuring overlap of individual original and watershed labels:")
+    dsc_lbls_comb = atlas_refiner.measure_overlap_labels(
+        labels_sitk, labels_sitk_seg)
+    _logger.info(
+        "\nMeasuring overlap of combined original and watershed labels:")
+    dsc_lbls_indiv = atlas_refiner.measure_overlap_labels(
         atlas_refiner.make_labels_fg(labels_sitk), 
         atlas_refiner.make_labels_fg(labels_sitk_seg))
-    print()
+    _logger.info("")
 
     # measure and save whole atlas metrics
     metrics = {
         config.AtlasMetrics.SAMPLE: [os.path.basename(mod_path)],
         config.AtlasMetrics.REGION: config.REGION_ALL,
         config.AtlasMetrics.CONDITION: "|".join(cond),
+        config.AtlasMetrics.DSC_LABELS_ORIG_NEW_COMBINED: dsc_lbls_comb,
+        config.AtlasMetrics.DSC_LABELS_ORIG_NEW_INDIV: dsc_lbls_indiv,
     }
     df_metrics_path = libmag.combine_paths(
         mod_path, config.PATH_ATLAS_IMPORT_METRICS)

magmap/settings/config.py

@@ -649,6 +649,8 @@ class AtlasMetrics(Enum):
     DSC_ATLAS_SAMPLE = "DSC_atlas_sample"
     DSC_ATLAS_SAMPLE_CUR = "DSC_atlas_sample_curated"
     DSC_SAMPLE_LABELS = "DSC_sample_labels"
+    DSC_LABELS_ORIG_NEW_COMBINED = "DSC_labels_orig_new_combined"
+    DSC_LABELS_ORIG_NEW_INDIV = "DSC_labels_orig_new_individual"
     SIMILARITY_METRIC = "Similarity_metric"
     LAT_UNLBL_VOL = "Lateral_unlabeled_volume"
     LAT_UNLBL_PLANES = "Lateral_unlabeled_planes"