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Add options for sub-folder and for func sesssions #88

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merged 3 commits into from
May 18, 2024
Merged

Add options for sub-folder and for func sesssions #88

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7190b39
add options for sub-folder and for func sesssions
sandrinebedard Nov 1, 2023
39acd0f
Merge branch 'main' into sb/fix-func
rohanbanerjee May 18, 2024
687b5d0
Update utils.py
rohanbanerjee May 18, 2024
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126 changes: 126 additions & 0 deletions manual_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,6 +215,12 @@ def get_parser():
type=str,
default=None
)
parser.add_argument( #TODO
'-add-subfolder',
help="Add a subfolder to find labels or segmentation to correct",
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Example(s) should be added here

type=str,
default=None
)
parser.add_argument(
'-qc-only',
help="Only output QC report based on the manually-corrected files already present in the 'derivatives' folder. "
Expand Down Expand Up @@ -584,6 +590,8 @@ def ask_if_modify(fname_out, fname_label, do_labeling_always=False):
create_empty_mask = False

# If the output file does not exist, copy it from label folder
print(os.path.isfile(fname_label))
print('fname_label', fname_label)
Comment on lines +593 to +594
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@rohanbanerjee, these two prints might be removed, right? I guess they were used for debugging.

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I agree, missed on removing them. On it.

elif not os.path.isfile(fname_out) and os.path.isfile(fname_label):
do_labeling = True
copy = True
Expand Down Expand Up @@ -780,6 +788,123 @@ def main():
# TODO: address "none" issue if no file present under a key
# Perform manual corrections
for task, files in dict_yml.items():
# Get the list of segmentation files to add to derivatives, excluding the manually corrected files in -config.
# TODO: probably extend also for other tasks (such as FILES_GMSEG)
if args.add_seg_only and task == 'FILES_SEG':
# Remove the files in the -config list
for file in files:
# Remove the file suffix (e.g., '_RPI_r') to match the list of files in -path-img
file = utils.remove_suffix(file, args.suffix_files_in)
if file in file_list:
file_list.remove(file)
files = file_list # Rename to use those files instead of the ones to exclude
if len(files) > 0:
# Handle regex (i.e., iterate over all subjects)
if '*' in files[0] and len(files) == 1:
subject, ses, filename, contrast = utils.fetch_subject_and_session(files[0])
# Get list of files recursively
files = sorted(glob.glob(os.path.join(path_img, '**', filename),
recursive=True))
# Loop across files
for file in tqdm.tqdm(files, desc="{}".format(task), unit="file"):
# Print empty line to not overlay with tqdm progress bar
time.sleep(0.1)
print("")
# build file names
subject, ses, filename, contrast = utils.fetch_subject_and_session(file)
if args.add_subfolder:
subfolder = args.add_subfolder
else:
subfolder = False
# Construct absolute path to the input file
# For example: '/Users/user/dataset/data_processed/sub-001/anat/sub-001_T2w.nii.gz'
if subfolder:
fname = os.path.join(path_img, subject, ses, contrast, subfolder, filename)
else:
fname = os.path.join(path_img, subject, ses, contrast, filename)
# Construct absolute path to the other contrast file
if args.load_other_contrast:
# Do not include session in the filename
if ses == '':
other_contrast_filename = subject + '_' + args.load_other_contrast + '.nii.gz'
# Include session in the filename
else:
other_contrast_filename = subject + '_' + ses + '_' + args.load_other_contrast + '.nii.gz'
fname_other_contrast = os.path.join(path_img, subject, ses, contrast, other_contrast_filename)
else:
fname_other_contrast = None
# Construct absolute path to the input label (segmentation, labeling etc.) file
# For example: '/Users/user/dataset/data_processed/sub-001/anat/sub-001_T2w_seg.nii.gz'
if subfolder:
fname_label = utils.add_suffix(os.path.join(path_label, subject, ses, contrast, subfolder, filename), suffix_dict[task])
else:
fname_label = utils.add_suffix(os.path.join(path_label, subject, ses, contrast, filename), suffix_dict[task])
# Construct absolute path to the output file (i.e., path where manually corrected file will be saved)
# For example: '/Users/user/dataset/derivatives/labels/sub-001/anat/sub-001_T2w_seg.nii.gz'
# The information regarding the modified data will be stored within the sidecar .json file
fname_out = utils.add_suffix(os.path.join(path_out, subject, ses, contrast, filename), suffix_dict[task])

# Create subject folder in output if they do not exist
os.makedirs(os.path.join(path_out, subject, ses, contrast), exist_ok=True)
if not args.qc_only:
# Check if the output file already exists. If so, asks user if they want to modify it.
do_labeling, copy, create_empty_mask, do_labeling_always = \
ask_if_modify(fname_out=fname_out,
fname_label=fname_label,
do_labeling_always=do_labeling_always)
# Perform labeling (i.e., segmentation correction, labeling correction etc.) for the specific task
if do_labeling:
if args.denoise:
# Denoise the input file
fname = denoise_image(fname)
# Copy file to derivatives folder
if copy:
shutil.copyfile(fname_label, fname_out)
print(f'Copying: {fname_label} to {fname_out}')
# Create empty mask in derivatives folder
elif create_empty_mask:
utils.create_empty_mask(fname, fname_out)

if task in ['FILES_SEG', 'FILES_GMSEG']:
if not args.add_seg_only:
time_one = get_modification_time(fname_out)
correct_segmentation(fname, fname_out, fname_other_contrast, args.viewer, param_fsleyes)
time_two = get_modification_time(fname_out)
elif task == 'FILES_LESION':
time_one = get_modification_time(fname_out)
correct_segmentation(fname, fname_out, fname_other_contrast, args.viewer, param_fsleyes)
time_two = get_modification_time(fname_out)
elif task == 'FILES_LABEL':
time_one = get_modification_time(fname_out)
correct_vertebral_labeling(fname, fname_out, args.label_disc_list)
time_two = get_modification_time(fname_out)
elif task == 'FILES_COMPRESSION':
time_one = get_modification_time(fname_out)
# Note: be aware of possibility to create compression labels also using
# 'sct_label_utils -create-viewer'
# Context: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3984
correct_segmentation(fname, fname_out, fname_other_contrast, 'fsleyes', param_fsleyes)
time_two = get_modification_time(fname_out)
elif task == 'FILES_PMJ':
time_one = get_modification_time(fname_out)
correct_pmj_label(fname, fname_out)
time_two = get_modification_time(fname_out)
elif task == 'FILES_CENTERLINE':
time_one = get_modification_time(fname_out)
correct_centerline(fname, fname_out)
time_two = get_modification_time(fname_out)
else:
sys.exit('Task not recognized from the YAML file: {}'.format(task))
if args.denoise:
# Remove the denoised file (we do not need it anymore)
remove_denoised_file(fname)

# Add segmentation only (skip generating QC report)
if args.add_seg_only:
# We are passing modified=True because we are adding a new segmentation and we want
# to create a JSON file
update_json(fname_out, name_rater, modified=True)
# Generate QC report
if task.startswith('FILES'):
# Check if task is in suffix_dict.keys(), if not, skip it
# Note that this check is done after the task.startswith('FILES') check because the manual-correction
Expand Down Expand Up @@ -897,6 +1022,7 @@ def main():
# a JSON file
update_json(fname_out, name_rater, json_metadata)
# Generate QC report
#generate_qc(fname, fname_out, task, fname_qc, subject, args.config, args.qc_lesion_plane, suffix_dict)
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@rohanbanerjee, I believe that this line was commented on only for debugging the fmri case. In other cases, we want to generate QC. Thus, I believe a condition checking if contrast = 'func' should be added here.

else:
update_json(fname_out, name_rater, json_metadata)
# Generate QC report
Expand Down
12 changes: 9 additions & 3 deletions utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,16 +35,22 @@ def fetch_subject_and_session(filename_path):
_, filename = os.path.split(filename_path) # Get just the filename (i.e., remove the path)
subject = re.search('sub-(.*?)[_/]', filename_path) # [_/] means either underscore or slash
subjectID = subject.group(0)[:-1] if subject else "" # [:-1] removes the last underscore or slash
session = re.findall(r'ses-.*', filename_path)
sessionID = session[0].split('_')[0] if session else "" # Return None if there is no session
if 'dwi' in filename_path:
contrast = 'dwi'
elif 'bold' in filename_path:
contrast = 'func'
else:
contrast = 'anat'


session = re.search('ses-(.*?)[_/]', filename_path) # [_/] means either underscore or slash
sessionID = session.group(0)[:-1] if session else "" # [:-1] removes the last underscore or slash
# REGEX explanation
# . - match any character (except newline)
# *? - match the previous element as few times as possible (zero or more times)

# TODO - add support for func (fMRI)
contrast = 'dwi' if 'dwi' in filename_path else 'anat' # Return contrast (dwi or anat)

return subjectID, sessionID, filename, contrast


Expand Down
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