Adding the python script for manual labeling

get_BIDS_sub.py

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+import sys
+import os
+import argparse
+import json
+import subprocess
+import nibabel as nib
+import glob
+import numpy
+
+def get_parser():
+    # Mandatory arguments
+    parser = argparse.ArgumentParser(
+        description=" ",
+        epilog="EXAMPLES:\n",
+        add_help=None,
+        prog=os.path.basename(__file__).strip('.py'))
+
+    mandatoryArguments = parser.add_argument_group("\nMANDATORY ARGUMENTS")
+    mandatoryArguments.add_argument(
+        '-path',
+        required=True,
+        help="path to BIDS Data",
+    )
+    mandatoryArguments.add_argument(
+        '-constraint',
+        required=True,
+        help="constraint field. You can use a specific fields from the header or 'orientation'",
+    )
+
+    mandatoryArguments.add_argument(
+        '-value',
+        required=True,
+        help="value of constraint. Number or other. For orientation use capital letters (e.g., RPI) default operation is '==' if you wish to use something else please check the -ope option.",
+    )
+    optional = parser.add_argument_group("\nOPTIONAL ARGUMENTS")
+    optional.add_argument(
+        '-ope',
+        default='==',
+        help=" operation type. You can use '<' or '>'. Don't forget to use quote (Unix will throw EOL error otherwise)")
+
+    optional = parser.add_argument_group("\nOPTIONAL ARGUMENTS")
+    optional.add_argument(
+        '-ofile',
+        help="name of output file (txt file). If the file already exist, the found subject will be added at the end of the file")
+
+    return parser
+
+
+def get_view(im):
+    nifti = nib.load(im)
+    axis = nib.aff2axcodes(nifti.affine)
+    best_res_axis = numpy.where(nifti.header['pixdim'][1:4] == nifti.header['pixdim'][1:4].min())[0]
+    if len(best_res_axis)==3:
+        return 'valid'
+    elif len(best_res_axis)==2:
+        plane_dic={'SA':'sagittal','SP':'sagittal','IA':'sagittal','IP':'sagittal','AS':'sagittal','PS':'sagittal','AI':'sagittal','PI':'sagittal','SR':'coronal','SL':'coronal','IR':'coronal','IL':'coronal','RS':'coronal','LS':'coronal','RI':'coronal','LI':'coronal','AR':'axial','AL':'axial','PR':'axial','PL':'axial','RP':'axial','LP':'axial','RA':'axial','LA':'axial'}
+        best_plane = axis[best_res_axis[0]]+axis[best_res_axis[1]]
+        print (best_plane)
+        return (plane_dic[best_plane])
+
+
+
+def main(args=None):
+    if args is None:
+        args = None if sys.argv[1:] else ['--help']
+    parser = get_parser()
+    arguments = parser.parse_args(args=args)
+    field = arguments.constraint
+    path_data = arguments.path
+    value = arguments.value
+    operation = arguments.ope
+    if arguments.ofile is not None:
+        out = arguments.ofile
+    else:
+        out =  'list-generated'+ field + operation + value 
+    path_images = (glob.glob(path_data+'/sub-*/anat/*.nii.gz')) #grab all subject images path
+
+    to_keep = []
+    for im in path_images:
+
+        if field == 'orientation':
+            #Orientation gets a special case because it is not in the header per se
+            if nib.aff2axcodes(nifti.affine) == (str(value[0]), str(value[1]), str(value[2])):
+                spli = im.rsplit('/',3) #we get the last 3 element
+                subj = spli[-3]+'/'+spli[-2]+'/'+spli[-1]
+                to_keep.append(subj)
+
+        elif field == 'view':
+            #sagittal or axial or coronal. 
+            if get_view(im) == value or get_view(im) == 'valid':
+                spli = im.rsplit('/',3) #we get the last 3 element
+                subj = spli[-3]+'/'+spli[-2]+'/'+spli[-1]
+                to_keep.append(subj)
+
+
+        else:
+            nifti = nib.load(im)
+            if eval(str(nifti.header[field]) + operation + str(value)): #eval() allows to ask the user for '<' or '>'
+                spli = im.rsplit('/',3) #we get the last 3 element
+                subj = spli[-3]+'/'+spli[-2]+'/'+spli[-1]
+                to_keep.append(subj)
+
+    if len(to_keep)>0:
+        f = open(out + '.txt', 'a') # 'a' option allows you to append file to a list. 
+        l1 = map(lambda x: x + '\n', to_keep)
+        f.writelines(l1)
+        f.close()
+    else:
+        print('No file matching your criteria found')
+
+
+if __name__ == "__main__":
+    main()
+
+
+
+
+

manual_labeling.py

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+import sys
+import os
+import argparse
+import json
+import subprocess
+
+
+def get_parser():
+    # Mandatory arguments
+    parser = argparse.ArgumentParser(
+        description=" ",
+        epilog="EXAMPLES:\n",
+        add_help=None,
+        prog=os.path.basename(__file__).strip('.py'))
+
+    mandatoryArguments = parser.add_argument_group("\nMANDATORY ARGUMENTS")
+    mandatoryArguments.add_argument(
+        '-file',
+        required=True,
+        help="Json file containing list of path to image file",
+    )
+    mandatoryArguments.add_argument(
+            '-path',
+            required=True,
+            help="path to bids folder",)
+    mandatoryArguments.add_argument(
+        '-author',
+        required=True,
+        help="Author name for json file",
+    )
+    optional = parser.add_argument_group("\nOPTIONAL ARGUMENTS")
+    optional.add_argument(
+        '-correct',
+        default=0,
+        help=" if this is activated the -ilabel option will be used and therefore existing file will be open")
+    optional.add_argument(
+            '-o',
+            help="output path. if empty it will save in BIDS_path/label/derivatives/sub/anat ")
+
+    return parser
+
+
+def main(args=None):
+    if args is None:
+        args = None if sys.argv[1:] else ['--help']
+    parser = get_parser()
+    arguments = parser.parse_args(args=args)
+    file_path = arguments.file
+    author_name = arguments.author
+    correct = arguments.correct
+    json_content = {"author": author_name, "label": "labels-disc-manual"}
+    list_of_subj = [line.rstrip('\n') for line in open(file_path)]
+    derivatives_base = arguments.path  # file path is BIDS: last 3 elements are /sub-xx/anat/FILENAM
+    derivatives_path = derivatives_base + 'derivatives/labels'
+    if arguments.o is not None:
+        out_path = argument.o
+    else:
+        out_path = derivatives_path
+        i=0
+
+    try:
+        for rel_path in list_of_subj:
+            im_path = arguments.path+rel_path
+            label_base = im_path.rsplit('/', 1)[-1][:-7]  # we remove the last 7 caracters that are .nii.gz
+            subj = im_path.rsplit('/', 3)[-3]
+            label_filename = label_base + '_labels-disc-manual.nii.gz'
+            json_filename = label_base + '_labels-disc-manual.json'
+
+            if os.path.exists( out_path+'/'+ subj + '/anat'):
+                pass
+            else:
+                os.makedirs(out_path +'/'+ subj + '/anat')
+            path_json =  out_path +'/'+ subj +'/anat/' + json_filename
+            path_label = derivatives_path + subj + '/anat/' + label_filename  # retrieving label filename
+            path_out = out_path +'/'+ subj + '/anat/' + label_filename
+
+            if correct:
+                if os.path.exists(path_label):
+                    command = """sct_label_utils -i """ + im_path + """ -create-viewer 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 -ilabel """ + path_label + """ -o """ + path_out
+                else:
+                    command = """sct_label_utils -i """ + im_path + """ -create-viewer 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20 -o """ + path_out
+
+                subprocess.run(command, shell=True)
+                i=i+1
+
+                with open(path_json, 'w') as f:
+                    json.dump(json_content, f)
+            else:
+                if os.path.exists(path_label):
+                    pass
+                else:
+                    command = """sct_label_utils -i """ + im_path + """ -create-viewer 3,4,5,6,7,8,9,10,11,12,13,14,15 -o """ + path_out
+                    subprocess.run(command, shell=True)
+                    i=i+1
+                    with open(path_json, 'w') as f:
+                        json.dump(json_content, f)
+
+    except KeyboardInterrupt:
+            print('saving list')
+            following = list_of_subj[i:]
+            f = open(file_path,'w') # 'a' option allows you to append file to a list.
+            l1 = map(lambda x: x + '\n', following)
+            f.writelines(l1)
+            f.close()
+
+
+if __name__ == "__main__":
+    main()

sop.md

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+this script is made for manual labeling of BIDS folder
+run the script with python
+python manual-labeling/manual_labeling.py -file list_todo_update.txt -author lucas -path Path_to_duke/ \[-correct 1 -o label_tmp\]
+
+- -file: txt file that contains the list of all images inside bids root folder that you want to process separated by '\n'.The format in sub-xx/anat/sub-xxx_xxx.nii.gz. Can be obtained with get_bids_sub.py.
+- -path : Path th Bids root folder (duke) with a '/' at the end
+- -author: Author name that will appear on the .json file 
+- -correct: Boolean. default is 0. If correct is 1, the script will look for existing label and open them with the -ilabel option from sct_label_utils so you can verify/correct existing label.
+- -o: in the output folder given by the 5th argument, you will find in BIDS convention sub-xxx/anat/sub-xxx_labels-disc-manual.nii.gz and sub-xxx/anat/sub-xxx_lables-disc-manual.json" if this is empty this will save under BIDS_PATH/derivatives/labels/sub-xx/anat/xxx
+
+to end : performa keyboard interrupt from the terminal (ctrl+c). This will update the list by deleting the viewed subjects. don't forget to commit and push it on github. 
+Specific:
+possible file suffix to file are _acq-sag_T2w, _T2w, _T1w, _acq-sagcerv_T2w
+suffix to label is labels-disc-manual
+Example image for manual labeling:
+![example](label_disc_capture.png)