auto_mindcontrol.py

#! python
import argparse
from pathlib import Path
import json
from bids.grabbids import BIDSLayout
import subprocess
import os
import shutil

parser = argparse.ArgumentParser(description='Autogenerate mindcontrol settings from a BIDS directory')
parser.add_argument('--server', action = 'store_true', 
                    help='Start a simple file server in the bids directory.')
parser.add_argument('--meteor', action = 'store_true', 
                    help='Start the meteor server that will serve mindcontrol.')
parser.add_argument('bids_dir', help='The directory with the input dataset '
                    'formatted according to the BIDS standard.')

args = parser.parse_args()
bids_dir = args.bids_dir
file_server = "http://127.0.0.1:3002/"

# Default settings for each module
default_module = {
"fields": [
  {
    "function_name": "get_qc_viewer",
    "id": "name",
    "name": "Image File"
  },
  {
    "function_name": "get_qc_ave_field",
    "id": "average_vote",
    "name": "QC vote"
  },
  {
    "function_name": None,
    "id": "num_votes",
    "name": "# votes"
  },
  {
    "function_name": None,
    "id": "quality_check.notes_QC",
    "name": "Notes"
  }
],
"metric_names": None,
"graph_type": None,
"staticURL": file_server,
"usePeerJS": False,
"logPainter": False,
"logContours": False,
"logPoints": True,
"qc_options": {"pass": 1, "fail": 1, "needs_edits": 0, "edited": 0, "assignTo": 0, "notes": 1, "confidence": 1}}

layout = BIDSLayout(bids_dir)

# Loop through files, adding them to the manifest
# add entity types to a set to be used to populate the
# autogenerated settings
manifest = []
entry_types = set()
for img in layout.get(extensions = ".nii.gz"):
    img_dict = {}
    img_dict["check_masks"] = [img.filename.replace(bids_dir,"")]
    entry_types.add(img.type)
    img_dict["entry_type"] = img.type
    img_dict["metrics"] = {}
    img_dict["name"] = os.path.split(img.filename)[1].split('.')[0]
    img_dict["subject"] = 'sub-' + img.subject
    img_dict["session"] = 'ses-' + img.session
    manifest.append(img_dict)

# Populate modules list
modules = []
for et in entry_types:
    et_module = default_module.copy()
    et_module["name"] = et
    et_module["entry_type"] = et
    modules.append(et_module)

# autogenerated settings files
pub_set = {"startup_json": file_server+"startup.auto.json",
           "load_if_empty": True,
           "use_custom": True,
           "needs_consent": False,
           "modules": modules}
settings = {"public": pub_set}

# Write out file list to bids directory
with open(os.path.join(bids_dir,"startup.auto.json"), "w") as h:
    json.dump(manifest,h)
# Write out the settings file to the mindcontrol directory
with open("settings.auto.json", "w") as h:
    json.dump(settings,h)

if args.server:
    shutil.copy2("start_static_server.py",bids_dir)
    subprocess.Popen("python start_static_server.py", cwd = bids_dir, shell = True)
if args.meteor:
    meteor = subprocess.Popen("meteor --settings settings.auto.json".split(' '))
    meteor.wait()