import os
import json
import argparse
def get_parser():
parser = argparse.ArgumentParser(
description="Adds spatial reference information to json sidecars." )
parser.add_argument('-d',
required=True, help='Directory to process JSON files in')
parser.add_argument('-r',
default='0.8x0.8x0.8',
help='Resampling factor to add to SpatialReference')
return parser
def create_json_file(nii_gz_files, resampling_factor):
"""Creates a JSON file listing all .nii.gz files and includes the resampling factor.
Args:
nii_gz_files (list): A list of paths to .nii.gz files.
"""
data = {
#"SpatialReference": {
# "Orientation": "RPI",
# "Resampling": resampling_factor,
# },
"GeneratedBy":[
{
"Name": "sct_dmri_moco",
"Version": "SCT v6.1",
#"Author": "Paul Bautin",
#"Date": "2020-07-30 11:57:54",
"Description": "Mean image across directions after motion correction"
}]
}
for file in nii_gz_files:
output_path = file.replace('.nii.gz', '.json')
with open(output_path, 'w', encoding='utf-8') as file:
json.dump(data, file, indent=4)
def add_spatial_reference(file_path, resampling_factor):
"""Adds the SpatialReference field to a JSON file.
Args:
file_path (str): The path to the JSON file.
"""
with open(file_path, 'r+', encoding='utf-8') as file:
# Load the existing data
data = json.load(file)
# Add the "SpatialReference" field
data["SpatialReference"] = {
"Resampling": resampling_factor,
"Reorientation": "RPI",
"Other": "root-mean square across 4th dimension (if it exists)"
}
# Reset file pointer to the beginning and truncate the file
file.seek(0)
file.truncate()
# Write the modified data back to the file
json.dump(data, file, indent=4)
def find_nii_gz_files(directory):
"""Finds all .nii.gz files in a directory and its subdirectories.
Args:
directory (str): The root directory to start the search from.
Returns:
list: A list of paths to the .nii.gz files found.
"""
nii_gz_files = []
for root, _, files in os.walk(directory):
for file in files:
if ('rec-average_dwi.nii.gz' in file):
nii_gz_files.append(os.path.join(root, file))
return nii_gz_files
def process_directory(directory, resampling_factor):
"""Recursively processes directories to find and update JSON files.
Args:
directory (str): The root directory to start the search from.
"""
for root, _, files in os.walk(directory):
for file in files:
if ('T2w' in file) and ('.json' in file):
file_path = os.path.join(root, file)
add_spatial_reference(file_path, resampling_factor)
print(f"Updated {file_path}")
def main():
parser = get_parser()
args = parser.parse_args()
#process_directory(args.d, args.r)
nii_gz_files = find_nii_gz_files(args.d)
create_json_file(nii_gz_files, args.r)
if __name__ == "__main__":
main()
