Allow creation of empty mask

manual_correction.py

@@ -282,10 +282,13 @@ def create_json(fname_nifti, name_rater):
         outfile.write("\n")
 
 
-def ask_if_modify(fname_label):
+def ask_if_modify(fname_label, fname_seg):
     """
-    Check if file under derivatives already exists. If so, asks user if they want to modify it.
+    Check if the label file under derivatives already exists. If so, asks user if they want to modify it.
+    If the label file under derivatives does not exist, copy it from processed data.
+    If the file under derivatives and the file under processed data do not exist, create a new empty mask.
     :param fname_label: file under derivatives
+    :param fname_seg: file under processed data
     :return:
     """
     # Check if file under derivatives already exists
@@ -302,12 +305,19 @@ def ask_if_modify(fname_label):
                 print("Please answer with 'y' or 'n'")
             # We don't want to copy because we want to modify the existing file
             copy = False
+            create_empty_mask = False
     # If the file under derivatives does not exist, copy it from processed data
-    else:
+    elif not os.path.isfile(fname_label) and os.path.isfile(fname_seg):
         do_labeling = True
         copy = True
+        create_empty_mask = False
+    # If the file under derivatives and the file under processed data do not exist, create a new empty mask
+    else:
+        do_labeling = True
+        copy = False
+        create_empty_mask = True
 
-    return do_labeling, copy
+    return do_labeling, copy, create_empty_mask
 
 
 def generate_qc(fname, fname_label, task, fname_qc, subject, config_file):
@@ -409,13 +419,16 @@ def main():
                 os.makedirs(os.path.join(path_out_deriv, subject, ses, contrast), exist_ok=True)
                 if not args.qc_only:
                     # Check if file under derivatives already exists. If so, asks user if they want to modify it.
-                    do_labeling, copy = ask_if_modify(fname_label)
+                    do_labeling, copy, create_empty_mask = ask_if_modify(fname_label, fname_seg)
                     # Perform labeling (i.e., segmentation correction, labeling correction etc.) for the specific task
                     if do_labeling:
+                        # Copy file to derivatives folder
                         if copy:
-                            # Copy file to derivatives folder
                             shutil.copyfile(fname_seg, fname_label)
                             print(f'Copying: {fname_seg} to {fname_label}')
+                        # Create empty mask in derivatives folder
+                        elif create_empty_mask:
+                            utils.create_empty_mask(fname, fname_label)
                         if task in ['FILES_SEG', 'FILES_GMSEG']:
                             if not args.add_seg_only:
                                 correct_segmentation(fname, fname_label, args.viewer, args.fsl_color)

requirements.txt

@@ -1,3 +1,5 @@
 coloredlogs==15.0.1
 humanfriendly==10.0
 PyYAML==6.0
+numpy~=1.24.2
+nibabel~=5.0.1

utils.py

@@ -16,6 +16,9 @@
 import shutil
 import yaml
 
+import numpy as np
+import nibabel as nib
+
 
 # BIDS utility tool
 def fetch_subject_and_session(filename_path):
@@ -246,3 +249,16 @@ def check_software_installed(list_software=['sct']):
             logging.error("'{}' is not installed. Please install it before using this program.".format(software))
             install_ok = False
     return install_ok
+
+
+def create_empty_mask(fname, fname_label):
+    """
+    Create empty mask from reference image
+    :param fname: absolute path to reference image
+    :param fname_label: absolute path to output mask under derivatives
+    """
+    img = nib.load(fname)
+    data = np.zeros(img.shape)
+    img_mask = nib.Nifti1Image(data, affine=img.affine, header=img.header)
+    nib.save(img_mask, fname_label)
+    print("Empty mask created at: {}".format(fname_label))