added SurfaceThickness with thresholds 3 and 5 mm

Author: Hendrik-code

src/calc_features.py

@@ -9,7 +9,7 @@
 from TPTBox.core import np_utils
 from TPTBox.core.sitk_utils import nii_to_sitk
 
-from calc_label_thickness import calc_label_thickness
+from src.calc_label_thickness import calc_label_thickness
 
 simplefilter("ignore", category=ConvergenceWarning)
 
@@ -35,6 +35,8 @@ class FEATURES(Enum):
     SurfaceThicknessLIST = auto()  # list of thicknesses for each voxel in the label
     SurfaceThickness95Percentile = auto()  # 95th percentile of thicknesses
     SurfaceCoverage = auto()  # percentage of surface voxels in the label
+    SurfaceThickness3mm = auto()  # percentage of surface voxels with a thickness of at least 3mm
+    SurfaceThickness5mm = auto()  # percentage of surface voxels with a thickness of at least 5mm
     #
     SpatialRelation = auto()
     SpatialRelationMerged = auto()  # wenn label + label+8 merged
@@ -146,8 +148,18 @@ def features_from_two_labels(label_s: int, label_v: int, seg_label_s: NII, seg_l
                 features[featurename((label_s, label_v), FEATURES.SurfaceThickness95Percentile)] = float(
                     np.percentile(features[featurename((label_s, label_v), FEATURES.SurfaceThicknessLIST)], 95)
                 )
+                features[featurename((label_s, label_v), FEATURES.SurfaceThickness3mm)] = float(
+                    np.sum(np.array(features[featurename((label_s, label_v), FEATURES.SurfaceThicknessLIST)]) >= 3.0)
+                    / len(features[featurename((label_s, label_v), FEATURES.SurfaceThicknessLIST)])
+                )
+                features[featurename((label_s, label_v), FEATURES.SurfaceThickness5mm)] = float(
+                    np.sum(np.array(features[featurename((label_s, label_v), FEATURES.SurfaceThicknessLIST)]) >= 5.0)
+                    / len(features[featurename((label_s, label_v), FEATURES.SurfaceThicknessLIST)])
+                )
             else:
-                features[featurename((label_s, label_v), FEATURES.SurfaceThickness95Percentile)] = np.nan
+                features[featurename((label_s, label_v), FEATURES.SurfaceThickness95Percentile)] = 0
+                features[featurename((label_s, label_v), FEATURES.SurfaceThickness3mm)] = 0
+                features[featurename((label_s, label_v), FEATURES.SurfaceThickness5mm)] = 0
         else:
             features[featurename((label_s, label_v), FEATURES.SpatialRelation)] = np.nan
             features[featurename((label_s, label_v), FEATURES.SpatialRelationMerged)] = np.nan