Add "Name" and "SpatialReference" key-value pair to JSON sidecar, remove check_if_modified

manual_correction.py

@@ -483,50 +483,44 @@ def get_modification_time(fname):
  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 update_json(fname_nifti, name_rater, modified):
+def update_json(fname_nifti, name_rater):
  """
  Create/update 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:
  """
  fname_json = fname_nifti.replace('.gz', '').replace('.nii', '.json')
- if modified:
- if os.path.exists(fname_json):
- # Read already existing json file
- with open(fname_json, "r") as outfile: # r to read
- json_dict = json.load(outfile)
-
- # Special check to fix all of our current json files (Might be deleted later)
- if 'GeneratedBy' not in json_dict.keys():
- json_dict = {'GeneratedBy': [json_dict]}
- else:
- # Init new json dict
- json_dict = {'GeneratedBy': []}
-
- # Add new author with time and date
- json_dict['GeneratedBy'].append({'Author': name_rater, 'Date': time.strftime('%Y-%m-%d %H:%M:%S')})
- with open(fname_json, 'w') as outfile: # w to overwrite the file
- json.dump(json_dict, outfile, indent=4)
- # Add last newline
- outfile.write("\n")
- print("JSON sidecar was updated: {}".format(fname_json))
+
+ # Check if the json file already exists, if so, open it
+ if os.path.exists(fname_json):
+ # Read already existing json file
+ with open(fname_json, "r") as outfile: # r to read
+ json_dict = json.load(outfile)
+
+ # Special checks to fix all of our current json files (Might be deleted later)
+ if 'GeneratedBy' not in json_dict.keys():
+ json_dict = {'GeneratedBy': [json_dict]}
+ if 'SpatialReference' not in json_dict.keys():
+ json_dict['SpatialReference'] = 'orig'
+
+ # If the json file does not exist, initialize a new one
+ else:
+ # Init new json dict
+ json_dict = {'SpatialReference': 'orig',
+ 'GeneratedBy': []}
+
+ # If the label was modified or just checked, add "Name": "Manual" to the JSON sidecar
+ json_dict['GeneratedBy'].append({'Name': 'Manual',
+ 'Author': name_rater,
+ 'Date': time.strftime('%Y-%m-%d %H:%M:%S')})
+
+ # Write the data to the JSON file
+ with open(fname_json, 'w') as outfile: # w to overwrite the file
+ json.dump(json_dict, outfile, indent=4)
+ # Add last newline
+ outfile.write("\n")
+ print("JSON sidecar was updated: {}".format(fname_json))
 
 
 def ask_if_modify(fname_out, fname_label, do_labeling_always=False):
@@ -882,11 +876,10 @@ def main():
  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)
+ update_json(fname_out, name_rater)
  # Generate QC report
  else:
- modified = check_if_modified(time_one, time_two)
- update_json(fname_out, name_rater, modified)
+ update_json(fname_out, name_rater)
  # Generate QC report
  generate_qc(fname, fname_out, task, fname_qc, subject, args.config, args.qc_lesion_plane, suffix_dict)
 

tests/test_create_json.py

@@ -13,18 +13,21 @@
 
 def test_create_json(tmp_path):
  """
- Test that the function update_json() creates a JSON file with the expected metadata if modified=True.
+ Test that the function update_json() creates a JSON file with the expected metadata
  """
  # Create a temporary file for testing
  fname_label = "sub-001_ses-01_T1w_seg-manual.nii.gz"
  nifti_file = tmp_path / fname_label
  nifti_file.touch()
 
  # Call the function with modified=True
- update_json(str(nifti_file), "Test Rater", modified=True)
+ update_json(str(nifti_file), "Test Rater")
 
  # Check that the JSON file was created and contains the expected metadata
- expected_metadata = {'GeneratedBy': [{'Author': "Test Rater", 'Date': time.strftime('%Y-%m-%d %H:%M:%S')}]}
+ expected_metadata = {'SpatialReference': 'orig',
+ 'GeneratedBy': [{'Name': 'Manual',
+ 'Author': "Test Rater",
+ 'Date': time.strftime('%Y-%m-%d %H:%M:%S')}]}
  json_file = tmp_path / fname_label.replace(".nii.gz", ".json")
  assert json_file.exists()
  with open(str(json_file), "r") as f:
@@ -34,7 +37,7 @@ def test_create_json(tmp_path):
 
 def test_update_json(tmp_path):
  """
- Test that the function update_json() updates (appends to) the JSON file with the expected metadata if modified=True.
+ Test that the function update_json() updates (appends to) the JSON file with the expected metadata.
  """
  # Create a temporary file for testing
  fname_label = "sub-001_ses-01_T1w_seg-manual.nii.gz"
@@ -43,14 +46,22 @@ def test_update_json(tmp_path):
  # Create JSON file with some metadata
  json_file = tmp_path / fname_label.replace(".nii.gz", ".json")
  with open(str(json_file), "w") as f:
- json.dump({'GeneratedBy': [{'Author': "Test Rater 1", 'Date': "2023-01-01 00:00:00"}]}, f)
+ json.dump({'SpatialReference': 'orig',
+ 'GeneratedBy': [{'Name': 'Manual',
+ 'Author': "Test Rater 1",
+ 'Date': "2023-01-01 00:00:00"}]}, f)
 
  # Call the function with modified=True
- update_json(str(nifti_file), "Test Rater 2", modified=True)
+ update_json(str(nifti_file), "Test Rater 2")
 
  # Check that the JSON file was created and contains the expected metadata
- expected_metadata = {'GeneratedBy': [{'Author': "Test Rater 1", 'Date': "2023-01-01 00:00:00"},
- {'Author': "Test Rater 2", 'Date': time.strftime('%Y-%m-%d %H:%M:%S')}]}
+ expected_metadata = {'SpatialReference': 'orig',
+ 'GeneratedBy': [{'Name': 'Manual',
+ 'Author': "Test Rater 1",
+ 'Date': "2023-01-01 00:00:00"},
+ {'Name': 'Manual',
+ 'Author': "Test Rater 2",
+ 'Date': time.strftime('%Y-%m-%d %H:%M:%S')}]}
  json_file = tmp_path / fname_label.replace(".nii.gz", ".json")
  assert json_file.exists()
  with open(str(json_file), "r") as f: