update mu map dataset to load dicom images in same stacking direction

mu_map/dataset/default.py

@@ -17,7 +17,8 @@ from mu_map.data.remove_bed import (
 from mu_map.data.review_mu_map import discard_slices
 from mu_map.data.split import split_csv
 from mu_map.dataset.transform import Transform
-from mu_map.dataset.util import align_images, load_dcm_img
+from mu_map.dataset.util import align_images
+from mu_map.file.dicom import load_dcm_img
 from mu_map.logging import get_logger
 
 
@@ -97,9 +98,13 @@ class MuMapDataset(Dataset):
         _id = row[headers.id]
 
         mu_map_file = os.path.join(self.dir_images, row[headers.file_mu_map])
-        mu_map = load_dcm_img(mu_map_file)
+        mu_map = load_dcm_img(mu_map_file, direction=1)
+
+        recon_file = os.path.join(self.dir_images, row[self.header_recon])
+        recon = load_dcm_img(recon_file, direction=1)
+
         if self.discard_mu_map_slices:
-            mu_map = discard_slices(row, mu_map)
+            mu_map, recon = discard_slices(row, mu_map, recon)
         if self.bed_contours:
             if _id in self.bed_contours:
                 bed_contour = self.bed_contours[_id]
@@ -107,8 +112,6 @@ class MuMapDataset(Dataset):
             else:
                 logger.warning(f"Could not find bed contour for id {_id}")
 
-        recon_file = os.path.join(self.dir_images, row[self.header_recon])
-        recon = load_dcm_img(recon_file)
         if self.align:
             recon, mu_map = align_images(recon, mu_map)