ACR Object orientation - bugfix

.gitignore

@@ -29,6 +29,8 @@ uploads
 report*
 # TODO: Remove the following if no longer needed
 hazenlib/data
+dump/
+tests/data
 
 # docs
 docs/_build

hazenlib/ACRObject.py

@@ -1,3 +1,4 @@
+import sys
 import cv2
 import scipy
 import skimage
@@ -39,7 +40,9 @@ def sort_dcms(self, dcm_list):
         """
         orientation, positions = determine_orientation(dcm_list)
         if orientation == "unexpected":
-            pass
+            # TODO: error out for now,
+            # in future allow manual override based on optional CLI args
+            sys.exit()
 
         logger.info("image orientation is %s", orientation)
         dcm_stack = [dcm_list[i] for i in np.argsort(positions)]

hazenlib/tasks/uniformity.py

@@ -137,7 +137,6 @@ def get_fractional_uniformity(self, dcm):
             tuple: values of horizontal and vertical fractional uniformity
         """
         arr = dcm.pixel_array
-        print(type(dcm))
         x, y = self.get_object_centre(dcm)
 
         central_roi = arr[(y - 5) : (y + 5), (x - 5) : (x + 5)].flatten()

hazenlib/utils.py

@@ -364,9 +364,9 @@ def determine_orientation(dcm_list):
     # assuming each have a unique position in one of the 3 directions
     expected = len(dcm_list)
     iop = dcm_list[0].ImageOrientationPatient
-    x = np.array([dcm.ImagePositionPatient[0] for dcm in dcm_list])
-    y = np.array([dcm.ImagePositionPatient[1] for dcm in dcm_list])
-    z = np.array([dcm.ImagePositionPatient[2] for dcm in dcm_list])
+    x = np.array([round(dcm.ImagePositionPatient[0]) for dcm in dcm_list])
+    y = np.array([round(dcm.ImagePositionPatient[1]) for dcm in dcm_list])
+    z = np.array([round(dcm.ImagePositionPatient[2]) for dcm in dcm_list])
 
     # Determine phantom orientation based on DICOM header metadata
     # Assume phantom orientation based on ImageOrientationPatient
@@ -382,12 +382,24 @@ def determine_orientation(dcm_list):
         return "axial", z
     else:
         logger.debug("Checking phantom orientation based on ImagePositionPatient")
-        # Assume phantom orientation based on ImagePositionPatient
-        if len(set(x)) == expected and len(set(y)) == 1 and len(set(z)) == 1:
+        # Assume phantom orientation based on the changing value in ImagePositionPatient
+        if (
+            len(set(x)) == expected
+            and len(set(y)) < expected
+            and len(set(z)) < expected
+        ):
             return "sagittal", x
-        elif len(set(x)) == 1 and len(set(y)) == expected and len(set(z)) == 1:
+        elif (
+            len(set(x)) < expected
+            and len(set(y)) == expected
+            and len(set(z)) < expected
+        ):
             return "coronal", y
-        elif len(set(x)) == 1 and len(set(y)) == 1 and len(set(z)) == expected:
+        elif (
+            len(set(x)) < expected
+            and len(set(y)) < expected
+            and len(set(z)) == expected
+        ):
             return "axial", z
         else:
             logger.warning("Unable to determine orientation based on DICOM metadata")