Update scripts

scilus · Mar 5, 2024 · 14794b7 · 14794b7
1 parent 654466c
commit 14794b7
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/scilpy/io/mti.py b/scilpy/io/mti.py
@@ -125,13 +125,14 @@ def load_and_verify_mti(args, parser, input_maps_lists, extended_dir, affine,
 
     # Set TR and FlipAngle parameters. Required with --in_mtoff_t1, in which
     # case one of --in_aqc_parameters or --in_jsons is set.
-    rep_times, flip_angles = _parse_acquisition_parameters
+    rep_times, flip_angles = _parse_acquisition_parameters(args)
 
     # Fix issue from the presence of invalid value and division by zero
     np.seterr(divide='ignore', invalid='ignore')
 
     # Load B1 image
-    B1_map, flip_angles = _prepare_B1_map(args, flip_angles)
+    B1_map, flip_angles = _prepare_B1_map(args, flip_angles, extended_dir,
+                                          affine)
 
     # Define contrasts maps names
     if args.filtering:

diff --git a/scripts/scil_mti_maps_MT.py b/scripts/scil_mti_maps_MT.py
@@ -84,7 +84,7 @@
 import nibabel as nib
 import numpy as np
 
-from scilpy.io.mti import add_common_args_mti, verifications_and_loading_mti
+from scilpy.io.mti import add_common_args_mti, load_and_verify_mti
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist, add_verbose_arg,
                              assert_output_dirs_exist_and_empty)
@@ -186,8 +186,8 @@ def main():
 
     # Other checks, loading, saving contrast_maps.
     single_echo, flip_angles, rep_times, B1_map, contrast_maps = \
-        verifications_and_loading_mti(args, parser, input_maps_lists,
-                                      extended_dir, affine, contrast_names)
+        load_and_verify_mti(args, parser, input_maps_lists, extended_dir,
+                            affine, contrast_names)
 
     # Compute MTR
     if 'positive' in contrast_names_og and 'negative' in contrast_names_og:

diff --git a/scripts/scil_mti_maps_ihMT.py b/scripts/scil_mti_maps_ihMT.py
@@ -90,7 +90,7 @@
 import nibabel as nib
 import numpy as np
 
-from scilpy.io.mti import add_common_args_mti, verifications_and_loading_mti
+from scilpy.io.mti import add_common_args_mti, load_and_verify_mti
 from scilpy.io.utils import (add_overwrite_arg,
                              assert_inputs_exist, add_verbose_arg,
                              assert_output_dirs_exist_and_empty)
@@ -203,8 +203,8 @@ def main():
 
     # Other checks, loading, saving contrast_maps.
     single_echo, flip_angles, rep_times, B1_map, contrast_maps = \
-        verifications_and_loading_mti(args, parser, input_maps_lists,
-                                      extended_dir, affine, contrast_names)
+        load_and_verify_mti(args, parser, input_maps_lists, extended_dir,
+                            affine, contrast_names)
 
     # Compute ratio maps
     MTR, ihMTR = compute_ratio_map((contrast_maps[2] + contrast_maps[3]) / 2,