Fix verification of header

scilpy/image/volume_operations.py

@@ -452,7 +452,7 @@ def _interp_code_to_order(interp_code):
     return orders[interp_code]
 
 
-def resample_volume(img, ref=None, res=None, iso_min=False, zoom=None,
+def resample_volume(img, ref_img=None, res=None, iso_min=False, zoom=None,
                     interp='lin', enforce_dimensions=False):
     """
     Function to resample a dataset to match the resolution of another
@@ -463,7 +463,7 @@ def resample_volume(img, ref=None, res=None, iso_min=False, zoom=None,
     ----------
     img: nib.Nifti1Image
         Image to resample.
-    ref: nib.Nifti1Image
+    ref_img: nib.Nifti1Image, optional
         Reference volume to resample to. This method is used only if ref is not
         None. (default: None)
     res: tuple, shape (3,) or int, optional
@@ -492,11 +492,10 @@ def resample_volume(img, ref=None, res=None, iso_min=False, zoom=None,
     affine = img.affine
     original_zooms = img.header.get_zooms()[:3]
 
-    if ref is not None:
+    if ref_img is not None:
         if iso_min or zoom or res:
             raise ValueError('Please only provide one option amongst ref, res '
                              ', zoom or iso_min.')
-        ref_img = nib.load(ref)
         new_zooms = ref_img.header.get_zooms()[:3]
     elif res is not None:
         if iso_min or zoom:

scripts/scil_volume_resample.py

@@ -12,6 +12,7 @@
 import logging
 
 import nibabel as nib
+import numpy as np
 
 from scilpy.io.utils import (add_verbose_arg, add_overwrite_arg,
                              assert_inputs_exist, assert_outputs_exist,
@@ -67,8 +68,6 @@ def main():
     # Checking args
     assert_inputs_exist(parser, args.in_image, args.ref)
     assert_outputs_exist(parser, args, args.out_image)
-    assert_headers_compatible(parser, args.in_image, args.ref)
-    assert_headers_compatible(parser, args.in_image, args.ref)
 
     if args.enforce_dimensions and not args.ref:
         parser.error("Cannot enforce dimensions without a reference image")
@@ -85,8 +84,17 @@ def main():
 
     img = nib.load(args.in_image)
 
+    ref_img = None
+    if args.ref:
+        ref_img = nib.load(args.ref)
+        # Must not verify that headers are compatible. But can verify that, at
+        # least, that the last column of their affine are compatible.
+        if not np.array_equal(img.affine[:, -1], ref_img.affine[:, -1]):
+            parser.error("The --ref image should have the same affine as the "
+                         "input image (but with a different sampling).")
+
     # Resampling volume
-    resampled_img = resample_volume(img, ref=args.ref, res=args.volume_size,
+    resampled_img = resample_volume(img, ref_img=ref_img, res=args.volume_size,
                                     iso_min=args.iso_min, zoom=args.voxel_size,
                                     interp=args.interp,
                                     enforce_dimensions=args.enforce_dimensions)