introduce scaling factor into mu map dataset

mu_map/dataset/default.py

@@ -16,6 +16,15 @@ from mu_map.dataset.transform import Transform
 from mu_map.logging import get_logger
 
 
+"""
+Since DICOM images only allow images stored in short integer format,
+the Siemens scanner software multiplies values by a factor before storing
+so that no precision is lost.
+The scale can be found in this private DICOM tag.
+"""
+DCM_TAG_PIXEL_SCALE_FACTOR = 0x00331038
+
+
 def align_images(image_1: np.ndarray, image_2: np.ndarray) -> np.ndarray:
     """
     Align one image to another on the first axis (z-axis).
@@ -95,7 +104,8 @@ class MuMapDataset(Dataset):
             _id = row["id"]
 
             mu_map_file = os.path.join(self.dir_images, row[headers.file_mu_map])
-            mu_map = pydicom.dcmread(mu_map_file).pixel_array
+            mu_map = pydicom.dcmread(mu_map_file)
+            mu_map = mu_map.pixel_array / mu_map[DCM_TAG_PIXEL_SCALE_FACTOR].value
             if self.discard_mu_map_slices:
                 mu_map = discard_slices(row, mu_map)
             if self.bed_contours:
@@ -104,7 +114,8 @@ class MuMapDataset(Dataset):
                     mu_map[i] = cv.drawContours(mu_map[i], [bed_contour], -1, 0.0, -1)
 
             recon_file = os.path.join(self.dir_images, row[headers.file_recon_nac_nsc])
-            recon = pydicom.dcmread(recon_file).pixel_array
+            recon = pydicom.dcmread(recon_file)
+            recon = recon.pixel_array / recon[DCM_TAG_PIXEL_SCALE_FACTOR].value
             if self.align:
                 recon = align_images(recon, mu_map)