20210927-waxholm-v4/code/generate-parc-metadata.py

import os
import json

url_root='https://neuroglancer.humanbrainproject.eu/precomputed/data-repo-ng-bot'
path_to_input_dir='./neuroglancer-scripts-input'

def assemble_segmentation(seg_name):

  cwd=os.getcwd()
  reponame=os.path.basename(cwd)

  with open(f'{path_to_input_dir}/metadata/{seg_name}.json', 'r') as fp:
    meta=json.load(fp)

  with open(f'./output/precomputed/segmentations/{seg_name}/transform.json', 'r') as fp:
    transform=json.load(fp)

  new_dataset={
			"@type": "fzj/tmp/volume_type/v0.0.1",
			"@id": f"fzj/tmp/volume_type/v0.0.1/{seg_name}",
			"name": "Untitled segment",
			"volume_type": "neuroglancer/precomputed",
			"url": f"{url_root}/{reponame}/precomputed/{seg_name}",
			"detail": {
				"neuroglancer/precomputed": {
					"transform": transform
				}
			},
      "space_id": None,
			"map_type": "labelled"
  }

  meta['datasets']=meta.get('datasets', [])
  dss=[ds for ds in meta.get('datasets') if ds.get('name') == seg_name]
  if len(dss) > 1:
    raise Exception(f'Expected no more than one dataset with name {seg_name}. Instead, found {len(dss)}.')
  
  meta['datasets'] = [ds for ds in meta['datasets'] if ds.get('name') != seg_name]
  append_ds = {**new_dataset, **dss[0]} if len(dss) == 1 else new_dataset
  meta['datasets'].append(append_ds)

  with open(f'./output/metadata/{seg_name}.regions.json', 'r') as fp:
    regions=json.load(fp)

  meta['regions']=regions
  
  with open(f'./output/metadata/{seg_name}.full.json', 'w') as fp:
    json.dump(meta, fp, indent=2)

def main():
  path_to_segs='./output/precomputed/segmentations'
  for seg_name in os.listdir(path_to_segs):
    assemble_segmentation(seg_name)

  pass

if __name__ == "__main__":
  main()