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Macatools · Dec 6, 2024 · d163d28 · d163d28
1 parent 61c46c6
commit d163d28
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/macapype/nodes/prepare.py b/macapype/nodes/prepare.py
@@ -472,19 +472,20 @@ def apply_li_thresh(orig_img_file):
     img_lithresh_data[data_orig <= lithresh] = 0
     img_lithresh_data[lithresh < data_orig] = 1
 
-    print("Min/max values after lithresh:", np.min(img_lithresh_data), np.max(img_lithresh_data))
+    print("Min/max values after lithresh:", np.min(img_lithresh_data),
+          np.max(img_lithresh_data))
 
     # saving lithresh image
     fpath, fname, ext = split_f(orig_img_file)
     lithr_img_file = os.path.abspath(fname + "_lithresh" + ext)
-    img_lithresh = nib.Nifti1Image(img_lithresh_data, affine=affine_orig,
-                                     header=header_orig)
+    img_lithresh = nib.Nifti1Image(img_lithresh_data,
+                                   affine=affine_orig,
+                                   header=header_orig)
     nib.save(img_lithresh, lithr_img_file)
 
     return lithr_img_file
 
 
-
 if __name__ == '__main__':
 
     data_path = "/hpc/meca/data/Macaques/Macaque_hiphop/results/ucdavis"

diff --git a/macapype/pipelines/prepare.py b/macapype/pipelines/prepare.py
@@ -71,7 +71,6 @@ def _create_avg_reorient_pipeline(name="avg_reorient_pipe", params={}):
     return reorient_pipe
 
 
-
 ###############################################################################
 # main pipeline: "short_preparation_pipe"
 ###############################################################################

diff --git a/macapype/pipelines/register.py b/macapype/pipelines/register.py
@@ -620,7 +620,7 @@ def create_crop_aladin_pipe(name="crop_aladin_pipe", params={}):
         reg_pipe.connect(reg_T1_on_template2, 'aff_file',
                          compose_transfo, "comp_input")
 
-    ### padding image to have zeros and non nans
+    # padding image to have zeros and non nans
     pad_image_T1 = pe.Node(
         ants.utils.ImageMath(),
         name="pad_image_T1")