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Save more DSC metrics when in the merge atlas segmentations task #57

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Jun 29, 2021
Merged

Save more DSC metrics when in the merge atlas segmentations task #57

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1d9a3ab
Fix DSC after merging segmentations to compare atlas and new labels
yoda-vid Jun 25, 2021
562ea56
Clarify overlap measures messages for atlas refinement
yoda-vid Jun 25, 2021
1b1d543
Save DSC of original vs. new labels when merging segmentations
yoda-vid Jun 25, 2021
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9 changes: 6 additions & 3 deletions magmap/atlas/atlas_refiner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@
from magmap.settings import config
from magmap.settings import profiles

_logger = config.logger.getChild(__name__)


def _get_bbox(img_np, threshold=10):
"""Get the bounding box for the largest object within an image.
Expand Down Expand Up @@ -1513,8 +1515,9 @@ def measure_atlas_refinement(

"""
# DSC and total volumes of atlas and labels
print("\nDSC after import:")
overlap_meas_add = config.atlas_profile["overlap_meas_add_lbls"]
lbls_msg = f" (plus {overlap_meas_add})" if overlap_meas_add else ""
_logger.info(f"\nMeasuring overlap of atlas and combined labels{lbls_msg}:")
dsc, atlas_mask, labels_mask = measure_overlap_combined_labels(
img_atlas, img_labels, overlap_meas_add, return_masks=True)
metrics[config.AtlasMetrics.DSC_ATLAS_LABELS] = [dsc]
Expand All @@ -1530,7 +1533,7 @@ def measure_atlas_refinement(
thresh_atlas, img_atlas.GetSpacing()[::-1])
metrics[config.SmoothingMetrics.COMPACTNESS] = [compactness]

print("\nWhole atlas stats:")
_logger.info("\nWhole atlas stats:")
df = df_io.dict_to_data_frame(metrics, path, show=" ")
return df

Expand Down Expand Up @@ -1612,7 +1615,7 @@ def measure_overlap_labels(labels_img1, labels_img2):
overlap_filter = sitk.LabelOverlapMeasuresImageFilter()
overlap_filter.Execute(labels_img1, labels_img2)
mean_region_dsc = overlap_filter.GetDiceCoefficient()
print("Mean label-by-label DSC: {}".format(mean_region_dsc))
_logger.info("Mean label overlap DSC: {}".format(mean_region_dsc))
return mean_region_dsc


Expand Down
21 changes: 13 additions & 8 deletions magmap/atlas/edge_seg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -355,26 +357,29 @@ 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("\nMeasuring overlap of atlas and combined watershed labels:")
atlas_refiner.measure_overlap_combined_labels(atlas_sitk, labels_sitk_seg)
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)
atlas_refiner.measure_atlas_refinement(
metrics, atlas_sitk, labels_sitk, df_metrics_path)
metrics, atlas_sitk, labels_sitk_seg, df_metrics_path)

# show and write image to same directory as atlas with appropriate suffix
sitk_io.write_reg_images(
Expand Down
2 changes: 2 additions & 0 deletions magmap/settings/config.py
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Expand Up @@ -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"
Expand Down