def main():
parser = argparse.ArgumentParser(
description="command line or server tool to view or compare nidm results.")
parser.add_argument("ttl", help="List of comma separated ttl files to parse.", type=str)
parser.add_argument("--base", help="base image (standard brain map) to use for the viewer background.",type=str)
parser.add_argument("--port", help="PORT to use to serve nidmviewer (default 8088).",type=int)
parser.add_argument("--columns_to_remove", help="Comma separated list of columns to remove from viewer.",type=str,default="statmap_filename,excsetmap_location,statmap_type")
try:
args = parser.parse_args()
except:
parser.print_help()
sys.exit(0)
print "Starting up the nidmviewer!"
nidm_files = args.ttl.split(",")
if args.columns_to_remove != None:
args.columns_to_remove = [x.strip(" ") for x in args.columns_to_remove.split(",")]
nidm_files = [os.path.abspath(f) for f in nidm_files]
if args.base != None:
standard_brain = os.path.abspath(args.base)
else:
standard_brain = None
httpd = generate(ttl_files=nidm_files,
base_image=standard_brain,
columns_to_remove=args.columns_to_remove,
view_in_browser=True,
port=args.port)
def view_nidm_results(request, collection_cid, nidm_name):
collection = get_collection(collection_cid,request)
nidmr = get_object_or_404(NIDMResults, collection=collection,name=nidm_name)
if request.method == "POST":
if not request.user.has_perm("statmaps.change_nidmresults", nidmr):
return HttpResponseForbidden()
form = NIDMResultsForm(request.POST, request.FILES, instance=nidmr)
if form.is_valid():
instance = form.save(commit=False)
instance.save()
form.save_nidm()
form.save_m2m()
return HttpResponseRedirect(collection.get_absolute_url())
else:
if owner_or_contrib(request,collection):
form = NIDMResultsForm(instance=nidmr)
else:
form = NIDMViewForm(instance=nidmr)
# Generate viewer for nidm result
nidm_files = [nidmr.ttl_file.path.encode("utf-8")]
standard_brain = "/static/images/MNI152.nii.gz"
# We will remove these scripts
remove_resources = ["BOOTSTRAPCSS","ROBOTOFONT"]
# We will remove these columns
columns_to_remove = ["statmap_location","statmap",
"statmap_type","coordinate_id"]
html_snippet = generate(nidm_files,
base_image=standard_brain,
remove_scripts=remove_resources,
columns_to_remove=columns_to_remove,
template_choice="embed")
context = {"form": form,"nidm_viewer":html_snippet}
return render(request, "statmaps/edit_nidm_results.html", context)
#!/usr/bin/python
from nidmviewer.viewer import generate
from glob import glob
import os
# These examples are for generating code for the viewer from within python. You can achieve
# the local browser version by running from the command line:
# nidmviewer fsl/nidm.ttl
# nidmviewer fsl/nidm1.ttl,nidm2.ttl
# HTML FOR EMBEDDING #####################################################
# Here are images that we want to see, these should be relative to your web server
# Each ttl file must be matched with a provn file, in the case of different versions
ttl_files = glob("fsl/*.ttl")
html_snippet = generate(ttl_files=ttl_files)
