Feature/prepare json yaml files

README.md

@@ -1,10 +1,10 @@
 
-## :mega: Repository No Longer Being Maintained :mega:
+## :mega: Repository No Longer Being Maintained by DCAN-Labs :mega:
 
-**We have adopted a new process for storing and sharing ABCD data and will therefore no longer be maintaining this repository!**
+**DCAN-Labs has adopted a new process for storing and sharing ABCD data and will therefore no longer be maintaining this repository!**
 
 
-# Welcome to the DCAN Labs NDA BIDS Upload Repository
+# Welcome to the NDA BIDS Upload Repository
 
 This repository is for taking data as BIDS and uploading it to an NDA collection.
 

json_yaml_files/prepare_files.py

@@ -0,0 +1,184 @@
+from bids import BIDSLayout
+import bids
+from collections import defaultdict
+import re
+import json
+import sys
+import yaml
+import argparse
+from pathlib import Path
+
+
+class BIDStoNDAConfigGenerator:
+    def __init__(self):
+        # Set BIDS configuration
+        bids.config.set_option('extension_initial_dot', True)
+
+        # Parse command-line arguments
+        parser = argparse.ArgumentParser(description='Generate YAML and JSON files for a BIDS dataset.')
+        parser.add_argument('-s', '--source', type=str, required=True, help='Path to the BIDS dataset directory')
+        parser.add_argument('-d', '--destination', type=str, required=True, help='Path to save the generated YAML and JSON files')
+        args = parser.parse_args()
+        self.source_path = args.source
+        self.destination_path = Path(args.destination)
+
+        # Initialize BIDS layout
+        self.layout = BIDSLayout(self.source_path, derivatives=True)
+
+        # Define constants
+        self.A = 'image03'
+        self.pattern = r'^(?P<A>[^_]+)_(?P<X>[^.]+)\.(?P<Y>[^.]+)\.(?P<Z>[^.]+)\..+$'
+        self.scan_type = {
+            'anat': {
+                'mprage': 'MR structural (MPRAGE)',
+                't1w': 'MR structural (T1)',
+                'pd': 'MR structural (PD)',
+                'fspgr': 'MR structural (FSPGR)',
+                'fsip': 'MR structural (FISP)',
+                't2w': 'MR structural (T2)',
+                'pd_t2': 'MR structural (PD, T2)',
+                'b0_map': 'MR structural (B0 map)',
+                'b1_map': 'MR structural (B1 map)',
+                'flash': 'MR structural (FLASH)',
+                'mp2rage': 'MR structural (MP2RAGE)',
+                'tse': 'MR structural (TSE)',
+                't1w_t2w': 'MR structural (T1, T2)',
+                'mpnrage': 'MR structural (MPnRAGE)'
+            },
+            'pet': {
+                'pet': 'PET'
+            }
+        }
+        self.image_modality = {
+            'pet': 'PET',
+            'anat': 'MRI',
+            'func': 'MRI',
+            'dwi': 'MRI',
+            'fmap': 'MRI'
+        }
+
+        # Set output directories
+        self.json_dir = self.destination_path / 'prepared_jsons'
+        self.yaml_dir = self.destination_path / 'prepared_yamls'
+        self.json_dir.mkdir(parents=True, exist_ok=True)
+        self.yaml_dir.mkdir(parents=True, exist_ok=True)
+
+    def extract_file_name_components(self, file_name):
+        match = re.match(self.pattern, file_name)
+        return match.groups() if match else (None, None, None, None)
+
+
+    def prepare_json_contents(self, file_name, files):
+        json_contents = {}
+        _, X, _, _ = self.extract_file_name_components(file_name)
+
+        sub_path_prefix = {
+            'derivatives': 'derivatives',
+            'inputs': 'sub-'
+        }
+
+        for file_path in files:
+            sub_path = file_path[file_path.find(sub_path_prefix.get(X, '')):] if X in sub_path_prefix else file_path
+            entities = self.layout.parse_file_entities(sub_path)
+            subject, session = entities.get('subject'), entities.get('session')
+            sub_path = self._replace_placeholders(sub_path, subject, session)
+            json_contents[sub_path] = sub_path
+
+        output_file = self.json_dir / file_name
+        self._write_to_file(output_file, json_contents)
+
+
+    def fetch_scan_type(self, Y, Z):
+        if Z.lower() in self.scan_type.get(Y, {}):
+            return self.scan_type[Y][Z.lower()]
+        if '_' in Z:
+            prefix = Z.split('_')[0]
+            if prefix.lower() in self.scan_type.get(Y, {}):
+                return self.scan_type[Y][prefix.lower()]
+        return self.scan_type.get(Y, {}).get(Y, '')
+
+
+    def prepare_yaml_contents(self, file_name):
+        _, _, Y, Z = self.extract_file_name_components(file_name)
+
+        yaml_contents = {
+            "scan_type": self.fetch_scan_type(Y, Z),
+            "scan_object": 'Live',
+            "image_file_format": 'NIFTI',
+            "image_modality": self.image_modality[Y],
+            "transformation_performed": 'No'
+        }
+        output_file = self.yaml_dir / file_name
+        self._write_to_file(output_file, yaml_contents, file_format='yaml')
+
+
+    def fetch_Z_value(self, files):
+        Z = set()
+        ignore_list = ['desc', 'subject', 'session', 'extension', 'suffix', 'datatype']
+
+        for file in files:
+            entities = self.layout.parse_file_entities(file)
+            filtered_entities = {k: v for k, v in entities.items() if k not in ignore_list}
+
+            for key, value in filtered_entities.items():
+                z = f"{key}-{value}" if key != 'space' else value
+                if entities.get('suffix') and entities.get('suffix') != entities.get('datatype'):
+                    z = f"{z}_{entities['suffix']}" if z else entities['suffix']
+                if z:
+                    Z.add(z) 
+            if not Z and entities['suffix'] != entities['datatype']:
+                Z.add(entities['suffix'])
+
+        return list(Z)
+
+    def prepare_file_names(self, X, Y, Z):
+        file_base = f"{self.A}_{X}.{Y}."
+        return {
+            'json': [f"{file_base}{z}.json" for z in Z],
+            'yaml': [f"{file_base}{z}.yaml" for z in Z]
+        }
+
+
+    def _replace_placeholders(self, path, subject, session):
+        if subject:
+            path = path.replace(subject, '{SUBJECT}')
+        if session:
+            path = path.replace(session, '{SESSION}')
+        return re.sub(r'-\d', '-{#}', path)
+
+    def _write_to_file(self, output_file, contents, file_format='json'):
+        with open(output_file, 'w') as f:
+            if file_format == 'yaml':
+                yaml.dump(contents, f)
+            else:
+                json.dump(contents, f, indent=2)
+
+
+    def run(self): 
+        scopes = {
+            'raw': 'inputs',
+            'derivatives': 'derivatives',
+            'sourcedata': 'sourcedata'
+        }
+        X = [name for scope, name in scopes.items() if self.layout.get(scope=scope)]
+        Y_types = self.layout.get_datatypes()
+
+        for x in X:
+            for y in Y_types:
+                files = self.layout.get(
+                    scope=x if x != 'inputs' else 'raw', datatype=y, return_type='file')
+
+                Z = self.fetch_Z_value(files)
+                file_names = self.prepare_file_names(X=x, Y=y, Z=Z)
+
+                for file_name in file_names['json']:
+                    self.prepare_json_contents(file_name, files)
+                for file_name in file_names['yaml']:
+                    self.prepare_yaml_contents(file_name)
+
+        print(f"\nJSON files: {self.json_dir}")
+        print(f"YAML files: {self.yaml_dir}\n")
+
+if __name__ == "__main__":
+    generator = BIDStoNDAConfigGenerator()
+    generator.run()