Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Do not update json sidecar if the label file was not modified #19

Merged
merged 1 commit into from
Mar 2, 2023
Merged

Do not update json sidecar if the label file was not modified #19

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
55 changes: 46 additions & 9 deletions manual_correction.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
#

import argparse
import datetime
import coloredlogs
import glob
import json
Expand Down Expand Up @@ -303,19 +304,45 @@ def correct_pmj_label(fname, fname_label, viewer='sct_label_utils'):
viewer_not_found(viewer)


def create_json(fname_nifti, name_rater):
def get_modification_time(fname):
"""
Get the modification time of a file.
:param fname: file name
:return:
"""
return datetime.datetime.fromtimestamp(os.path.getmtime(fname))


def check_if_modified(time_one, time_two):
"""
Check if the file was modified by the user. Return True if the file was modified, False otherwise.
:param time_one: modification time of the file before viewing
:param time_two: modification time of the file after viewing
:return:
"""
if time_one != time_two:
print("The label file was modified.")
return True
else:
print("The label file was not modified.")
return False


def create_json(fname_nifti, name_rater, modified):
"""
Create json sidecar with meta information
:param fname_nifti: str: File name of the nifti image to associate with the json sidecar
:param name_rater: str: Name of the expert rater
:param modified: bool: True if the file was modified by the user
:return:
"""
metadata = {'Author': name_rater, 'Date': time.strftime('%Y-%m-%d %H:%M:%S')}
fname_json = fname_nifti.rstrip('.nii').rstrip('.nii.gz') + '.json'
with open(fname_json, 'w') as outfile:
json.dump(metadata, outfile, indent=4)
# Add last newline
outfile.write("\n")
if modified:
metadata = {'Author': name_rater, 'Date': time.strftime('%Y-%m-%d %H:%M:%S')}
fname_json = fname_nifti.rstrip('.nii').rstrip('.nii.gz') + '.json'
with open(fname_json, 'w') as outfile:
json.dump(metadata, outfile, indent=4)
# Add last newline
outfile.write("\n")


def ask_if_modify(fname_label, fname_seg):
Expand Down Expand Up @@ -504,13 +531,21 @@ def main():

if task in ['FILES_SEG', 'FILES_GMSEG']:
if not args.add_seg_only:
time_one = get_modification_time(fname_label)
correct_segmentation(fname, fname_other_contrast, fname_label, args.viewer, args.fsl_color)
time_two = get_modification_time(fname_label)
elif task == 'FILES_LESION':
time_one = get_modification_time(fname_label)
correct_segmentation(fname, fname_other_contrast, fname_label, args.viewer, args.fsl_color)
time_two = get_modification_time(fname_label)
elif task == 'FILES_LABEL':
time_one = get_modification_time(fname_label)
correct_vertebral_labeling(fname, fname_label, args.label_disc_list)
time_two = get_modification_time(fname_label)
elif task == 'FILES_PMJ':
time_one = get_modification_time(fname_label)
correct_pmj_label(fname, fname_label)
time_two = get_modification_time(fname_label)
else:
sys.exit('Task not recognized from yml file: {}'.format(task))
if args.denoise:
Expand All @@ -519,11 +554,13 @@ def main():

if task == 'FILES_LESION':
# create json sidecar with the name of the expert rater
create_json(fname_label, name_rater)
modified = check_if_modified(time_one, time_two)
create_json(fname_label, name_rater, modified)
# NOTE: QC for lesion segmentation does not exist or not implemented yet
else:
# create json sidecar with the name of the expert rater
create_json(fname_label, name_rater)
modified = check_if_modified(time_one, time_two)
create_json(fname_label, name_rater, modified)
# Generate QC report
generate_qc(fname, fname_label, task, fname_qc, subject, args.config)

Expand Down