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Minor change to auto_mindcontrol #30

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Minor change to auto_mindcontrol #30

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18 changes: 9 additions & 9 deletions auto_mindcontrol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@
import shutil

parser = argparse.ArgumentParser(description='Autogenerate mindcontrol settings from a BIDS directory')
parser.add_argument('--server', action = 'store_true',
parser.add_argument('--server', action = 'store_true',
help='Start a simple file server in the bids directory.')
parser.add_argument('--meteor', action = 'store_true',
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.')
Expand Down Expand Up @@ -61,7 +61,7 @@
entry_types = set()
for img in layout.get(extensions = ".nii.gz"):
img_dict = {}
img_dict["check_masks"] = [img.filename.replace(bids_dir,"")]
img_dict["check_masks"] = [os.path.relpath(img.filename, start=bids_dir)]
entry_types.add(img.type)
img_dict["entry_type"] = img.type
img_dict["metrics"] = {}
Expand All @@ -87,15 +87,15 @@
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)
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)
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)
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()
meteor.wait()