trial and error with the min_overlap 10% to 2%

src/sfransen/load_images.py

@@ -0,0 +1,30 @@
+from typing import List
+import SimpleITK as sitk
+from sfransen.DWI_exp.helpers import *
+
+def load_images_parrallel(
+    image_paths: str,
+    seq: str,
+    target_shape: List[int],
+    target_space = List[float]):
+
+    img_s = sitk.ReadImage(image_paths, sitk.sitkFloat32)
+
+    #resample
+    mri_tra_s = resample(img_s, 
+                        min_shape=target_shape, 
+                        method=sitk.sitkNearestNeighbor, 
+                        new_spacing=target_space)
+
+    #center crop
+    mri_tra_s = center_crop(mri_tra_s, shape=target_shape)
+    #normalize
+    if seq != 'seg':
+        filter = sitk.NormalizeImageFilter()
+        mri_tra_s = filter.Execute(mri_tra_s)
+    else:
+        filter = sitk.BinaryThresholdImageFilter()
+        filter.SetLowerThreshold(1.0)
+        mri_tra_s = filter.Execute(mri_tra_s)
+    
+    return sitk.GetArrayFromImage(mri_tra_s).T