implement changing direction of slice stacking in dicom images

mu_map/file/dicom.py

@@ -98,34 +98,64 @@ def parse_age(patient_age: str) -> int:
     return int(_num)
 
 
-def load_dcm(filename: str) -> Tuple[DICOM, np.ndarray]:
+def load_dcm(filename: str, direction: float = 0.0) -> Tuple[DICOM, np.ndarray]:
     """
     Load a DICOM image, the data as a numpy array and apply normalization of the Siemens SPECT/CT
     Scanner.
 
     :param filename: filename of the DICOM image
+    :param direction: other than 0 changes the stacking order of slices to the desired direction
     :return: the dicom header and the scaled image as a numpy array
     """
     dcm = pydicom.dcmread(filename)
+    image = dcm.pixel_array
+
     if DCM_TAG_PIXEL_SCALE_FACTOR in dcm:
-        image = dcm.pixel_array / dcm[DCM_TAG_PIXEL_SCALE_FACTOR].value
-    else:
-        image = dcm.pixel_array
+        image = image / dcm[DCM_TAG_PIXEL_SCALE_FACTOR].value
+
+    dcm, image = to_direction((dcm, image), direction=direction)
     return dcm, image
 
 
-def load_dcm_img(filename: str) -> np.ndarray:
+def load_dcm_img(
+    filename: str,
+    direction: float = 0.0,
+) -> np.ndarray:
     """
     Load a DICOM image as a numpy array and apply normalization of the Siemens SPECT/CT
     Scanner.
 
     :param filename: filename of the DICOM image
+    :param direction: other than 0 changes the stacking order of slices to the desired direction
     :return: the image scaled and loaded into a numpy array
     """
-    _, image = load_dcm(filename)
+    _, image = load_dcm(filename, direction=direction)
     return image
 
 
+def to_direction(
+    dcm: Tuple[DICOM, np.ndarray], direction: float = 1
+) -> Tuple[DICOM, np.ndarray]:
+    """
+    Change the stacking direction of slices in a DICOM image.
+    The direction is specified by the sign of the [Spacing Between Slices](https://dicom.innolitics.com/ciods/nm-image/nm-reconstruction/00180088) parameter.
+
+    :param dcm: a tuple of a DICOM header and an image
+    :param direction: the desired stacking direction as a float (>0 positive, <0 negative, =0 stay as it is)
+    :return: dicom header (with values updated) and image according to the desired stacking order
+    """
+    dcm, image = dcm
+    spacing_between_slices = float(dcm.SpacingBetweenSlices)
+    if spacing_between_slices * direction < 0:
+        dcm.DetectorInformationSequence[0].ImagePositionPatient[2] *= (
+            image.shape[0] * spacing_between_slices
+        )
+        dcm.SpacingBetweenSlices = -spacing_between_slices
+
+        image = image[::-1]
+    return dcm, image
+
+
 def scale_image(image: np.ndarray, initial_scale=10000000) -> Tuple[np.ndarray, float]:
     """
     For memory efficiency, the Siemens SPECT/CT does not store images as floating point