20210927-waxholm-v4/code/parse-ilf.py

import xml.etree.ElementTree as ET
import os
import re

path_to_input_meta='./neuroglancer-scripts-input/metadata'
path_to_metadata='./output/metadata'

os.makedirs(path_to_metadata,exist_ok=True)

def get_rgb_from_hex(hex=None):
  if hex is None:
    return None
  r=hex[1:3]
  g=hex[3:5]
  b=hex[5:7]
  return [int(r, 16), int(g, 16), int(b, 16)]

def process_label(label, parent=None):
  name=label.attrib.get('name')
  color=label.attrib.get('color')
  abbreviation=label.attrib.get('abbreviation')
  id=int(label.attrib.get('id'))
  node={
    'name': name,
    'rgb': get_rgb_from_hex(color),
    'labelIndex': id,
    '_': {
      'abbreviation': abbreviation,
    },
    'children': []
  }
  if parent is not None:
    parent['children'].append(node)
  
  for l in label:
    process_label(l, node)

def process_ilf_file(filename):
  stripped_name=re.sub(r'.ilf$', '', filename)
  path_to_ifl=f'{path_to_input_meta}/{filename}'
  ilf=ET.parse(path_to_ifl)

  root_node={
    'name': 'Root',
    'rgb': None,
    'labelIndex': None,
    'children': []
  }

  structure=ilf.find('structure')
  for label in structure:
    process_label(label, root_node)

  path_to_region=f"{path_to_metadata}/{stripped_name}.regions.json"
  with open(path_to_region, 'w') as fp:
    import json
    json.dump(root_node, fp, indent=2)
  pass  

def main():
  is_ilf = re.compile(r'.ilf$')
  for f in [f for f in os.listdir(path_to_input_meta) if is_ilf.search(f)]:
    process_ilf_file(f)

if __name__ == '__main__':
  main()