Fix calculation of InactiveVolume feature

pyradiomics_radler/myfirstorder.py

@@ -234,7 +234,8 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
         a threshold of 0.01 × (SUVmax)^2 followed by closing and opening morphological operations were used 
         to differentiate active and inactive regions on FDG-PET scans
         
-        - input: 3D array representing the PET volume in SUV format
+        - input: 3D array representing the PET volume in SUV format, with 
+                voxels outside the ROI set to NaNs.
 
         .. note::
         Extracted from PET scans and not used in the CT feature set.
@@ -244,7 +245,8 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
 
         thresh = 0.01 * (numpy.max(ROIPet[~numpy.isnan(ROIPet)]) ** 2)
 
-        mask_inactive = ROIPet > thresh
+        mask_thresholded = ROIPet > thresh
+        mask_inactive = numpy.logical_and(mask_thresholded, mask)
 
         # MORPHOLOGICAL OPERATIONS
         conn = numpy.zeros([5, 5, 5])
@@ -288,6 +290,7 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
                 mask_inactive = oc.imopen(mask_inactive, conn)
                 new_mask = mask_inactive + perimeter
 
+                new_mask[mask == 0] = 10
                 new_mask[new_mask == 1] = 10
                 new_mask[new_mask == 2] = 10
                 new_mask[new_mask == 0] = 1
@@ -298,21 +301,23 @@ class MyRadiomicsFirstOrder(MyRadiomicsFeaturesBase):
                 b = numpy.zeros((1, int(connObjects.NumObjects)))
 
                 for i in range(int(connObjects.NumObjects)):
-                    a = numpy.where(
-                        len(connObjects.PixelIdxList[i]) >= 15
-                    )  # If the number of of pixel forming and object is lower than 15, reject it
-                    if a.size == 0:
-                        b[i] = 0
+                    if isinstance(connObjects.PixelIdxList[0][i], numpy.ndarray):
+                        a = connObjects.PixelIdxList[0][i].shape[0]
+                        # If the number of of pixel forming and object is lower than 15, reject it
+                        if a < 15:
+                            b[:, i] = 0
+                        else:
+                            b[:, i] = 1
                     else:
-                        b[i] = 1
-
-                row, col = numpy.where(b > 0)
-                sumInactive = 0
+                        b[:, i] = 0
 
-                for i in range(len(col)):
-                    sumInactive = sumInactive + len(
-                        connObjects.PixelIdxList[row[i], col[i]]
-                    )
+                rows, cols = numpy.where(b > 0)
+                sumInactive = sum(
+                    [
+                        connObjects.PixelIdxList[rows, cols][i].shape[0]
+                        for i in range(len(cols))
+                    ]
+                )
 
                 sumVolume = numpy.sum(mask)