Merge branch 'master' into dev

scilus · Jan 17, 2025 · 964e629 · 964e629
2 parents 9c7b861 + 2476ec2
commit 964e629
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Showing 4 changed files with 16 additions and 5 deletions.
diff --git a/scilpy/io/utils.py b/scilpy/io/utils.py
@@ -1050,7 +1050,7 @@ def save_matrix_in_any_format(filepath, output_data):
         raise ValueError('Extension {} is not supported'.format(ext))
 
 
-def assert_fsl_options_exist(parser, options_args, command):
+def assert_fsl_options_exist(parser, options_args, command, overwrite=False):
     """
     Assert that all options for topup or eddy exist.
     If not, print parser's usage and exit.
@@ -1063,6 +1063,8 @@ def assert_fsl_options_exist(parser, options_args, command):
         Options for fsl command
     command: string
         Command used (eddy or topup).
+    overwrite: bool
+        If true, will only print a warning if an option is not valid.
     """
     if command == 'eddy':
         fsl_options = eddy_options
@@ -1078,8 +1080,13 @@ def assert_fsl_options_exist(parser, options_args, command):
 
     for nOption in res:
         if nOption not in fsl_options:
-            parser.error('--{} is not a valid option for '
-                         '{} command.'.format(nOption, command))
+            if overwrite:
+                logging.warning('--{} may not be a valid option for '
+                                '{} command depending '
+                                'of its version.'.format(nOption, command))
+            else:
+                parser.error('--{} is not a valid option for '
+                             '{} command.'.format(nOption, command))
 
 
 def parser_color_type(arg):

diff --git a/scripts/scil_NODDI_maps.py b/scripts/scil_NODDI_maps.py
@@ -26,6 +26,7 @@
                              add_verbose_arg,
                              assert_inputs_exist,
                              assert_output_dirs_exist_and_empty,
+                             assert_headers_compatible,
                              redirect_stdout_c, add_tolerance_arg,
                              add_skip_b0_check_arg)
 from scilpy.gradients.bvec_bval_tools import (check_b0_threshold,
@@ -113,6 +114,8 @@ def main():
     assert_output_dirs_exist_and_empty(parser, args, args.out_dir,
                                        optional=args.save_kernels)
 
+    assert_headers_compatible(parser, args.in_dwi, optional=args.mask)
+
     # Generate a scheme file from the bvals and bvecs files
     bvals, _ = read_bvals_bvecs(args.in_bval, args.in_bvec)
     _ = check_b0_threshold(bvals.min(), b0_thr=args.tolerance,

diff --git a/scripts/scil_dwi_prepare_eddy_command.py b/scripts/scil_dwi_prepare_eddy_command.py
@@ -131,7 +131,7 @@ def main():
     required_args = [args.in_dwi, args.in_bvals, args.in_bvecs, args.in_mask]
 
     assert_inputs_exist(parser, required_args)
-    assert_fsl_options_exist(parser, args.eddy_options, 'eddy')
+    assert_fsl_options_exist(parser, args.eddy_options, 'eddy', args.overwrite)
 
     if os.path.splitext(args.out_prefix)[1] != '':
         parser.error('The prefix must not contain any extension.')

diff --git a/scripts/scil_dwi_prepare_topup_command.py b/scripts/scil_dwi_prepare_topup_command.py
@@ -93,7 +93,8 @@ def main():
 
     assert_inputs_exist(parser, required_args)
     assert_outputs_exist(parser, args, [], args.out_b0s)
-    assert_fsl_options_exist(parser, args.topup_options, 'topup')
+    assert_fsl_options_exist(parser, args.topup_options, 'topup',
+                             overwrite=args.overwrite)
 
     if os.path.splitext(args.out_prefix)[1] != '':
         parser.error('The prefix must not contain any extension.')