def testFEAT_NIDM(self):
# test feat parsing
for fname, info in self.testfiles.items():
info['found_feat'] = False
for root, dirs, files in os.walk(info['dir']):
if detect_feat_directory(root):
print 'Found FEAT directory at {}.'.format(root)
info['found_feat'] = True
try:
fslnidm = FSLtoNIDMExporter(feat_dir=root, version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
ttl_file = os.path.join(export_dir,'nidm.ttl')
except:
print("Unable to parse the FEAT directory: \n{0}.".format(get_traceback()))
# confirm results path and existence
self.assertTrue(os.path.exists(export_dir))
self.assertEquals(os.path.join(info['dir'],info['export_dir']),export_dir)
# incomplete ttl = failure in processing
self.assertGreaterEqual(os.path.getsize(ttl_file),info['ttl_fsize'])
# test upload nidm
for fname, info in self.testfiles.items():
nidm_zpath = os.path.join(self.tmpdir,'{}.nidm.zip'.format(fname.replace('.zip','')))
nidm_zip = zipfile.ZipFile(nidm_zpath, 'w')
for root, dirs, files in os.walk(os.path.join(info['dir'],info['export_dir'])):
for nfile in files:
nidm_zip.write(os.path.join(root, nfile))
nidm_zip.close()
zname = os.path.basename(nidm_zip.filename)
post_dict = {
'name': zname,
'description':'{0} upload test'.format(zname),
'collection':self.coll.pk,
}
file_dict = {'zip_file': SimpleUploadedFile(zname, open(nidm_zpath,'r').read())}
form = NIDMResultsForm(post_dict, file_dict)
# validate NIDM Results
self.assertEqual(form.errors, {})
nidm = form.save()
statmaps = nidm.nidmresultstatisticmap_set.all()
self.assertEquals(len(statmaps),info['num_statmaps'])
map_types = [v.map_type for v in statmaps]
self.assertEquals(sorted(map_types), sorted(info['map_types']))
names = [v.name for v in statmaps]
self.assertEquals(sorted(names), sorted(info['names']))
def testFEAT_NIDM(self):
# test feat parsing
for fname, info in self.testfiles.items():
info['found_feat'] = False
for root, dirs, files in os.walk(info['dir']):
if detect_feat_directory(root):
print 'Found FEAT directory at {}.'.format(root)
info['found_feat'] = True
fslnidm = FSLtoNIDMExporter(feat_dir=root, version="1.2.0")
fslnidm.parse()
info['nidm_file'] = fslnidm.export()
# confirm results path and existence
self.assertTrue(os.path.exists(info['nidm_file']))
# test upload nidm
for fname, info in self.testfiles.items():
zname = os.path.basename(info['nidm_file'])
post_dict = {
'name': zname,
'description': '{0} upload test'.format(zname),
'collection': self.coll.pk,
}
file_dict = {'zip_file': SimpleUploadedFile(zname, open(info['nidm_file'],'r').read())}
form = NIDMResultsForm(post_dict, file_dict)
# validate NIDM Results
self.assertEqual(form.errors, {})
nidm = form.save()
statmaps = nidm.nidmresultstatisticmap_set.all()
self.assertEquals(len(statmaps),info['num_statmaps'])
map_types = [v.map_type for v in statmaps]
self.assertEquals(sorted(map_types), sorted(info['map_types']))
names = [v.name for v in statmaps]
self.assertEquals(sorted(names), sorted(info['names']))
def testFEAT_NIDM(self):
# test feat parsing
for fname, info in self.testfiles.items():
info['found_feat'] = False
for root, dirs, files in os.walk(info['dir']):
if detect_feat_directory(root):
print 'Found FEAT directory at {}.'.format(root)
info['found_feat'] = True
try:
fslnidm = FSLtoNIDMExporter(feat_dir=root,
version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
ttl_file = os.path.join(export_dir, 'nidm.ttl')
except:
print("Unable to parse the FEAT directory: \n{0}.".
format(get_traceback()))
# confirm results path and existence
self.assertTrue(os.path.exists(export_dir))
self.assertEquals(
os.path.join(info['dir'], info['export_dir']),
export_dir)
# incomplete ttl = failure in processing
self.assertEquals(os.path.getsize(ttl_file),
info['ttl_fsize'])
# test upload nidm
for fname, info in self.testfiles.items():
nidm_zpath = os.path.join(
self.tmpdir, '{}.nidm.zip'.format(fname.replace('.zip', '')))
nidm_zip = zipfile.ZipFile(nidm_zpath, 'w')
for root, dirs, files in os.walk(
os.path.join(info['dir'], info['export_dir'])):
for nfile in files:
nidm_zip.write(os.path.join(root, nfile))
nidm_zip.close()
zname = os.path.basename(nidm_zip.filename)
post_dict = {
'name': zname,
'description': '{0} upload test'.format(zname),
'collection': self.coll.pk,
}
file_dict = {
'zip_file': SimpleUploadedFile(zname,
open(nidm_zpath, 'r').read())
}
form = NIDMResultsForm(post_dict, file_dict)
# validate NIDM Results
self.assertTrue(form.is_valid())
nidm = form.save()
statmaps = nidm.nidmresultstatisticmap_set.all()
self.assertEquals(len(statmaps), info['num_statmaps'])
map_types = [v.map_type for v in statmaps]
self.assertEquals(sorted(map_types), sorted(info['map_types']))
names = [v.name for v in statmaps]
self.assertEquals(sorted(names), sorted(info['names']))
def upload_folder(request, collection_cid):
collection = get_collection(collection_cid, request)
allowed_extensions = ['.nii', '.img', '.nii.gz']
niftiFiles = []
if request.method == 'POST':
print request.POST
print request.FILES
form = UploadFileForm(request.POST, request.FILES)
if form.is_valid():
tmp_directory = tempfile.mkdtemp()
print tmp_directory
try:
# Save archive (.zip or .tar.gz) to disk
if "file" in request.FILES:
archive_name = request.FILES['file'].name
if fnmatch(archive_name, '*.nidm.zip'):
populate_nidm_results(request, collection)
return HttpResponseRedirect(
collection.get_absolute_url())
_, archive_ext = os.path.splitext(archive_name)
if archive_ext == '.zip':
compressed = zipfile.ZipFile(request.FILES['file'])
elif archive_ext == '.gz':
django_file = request.FILES['file']
django_file.open()
compressed = tarfile.TarFile(fileobj=gzip.GzipFile(
fileobj=django_file.file, mode='r'),
mode='r')
else:
raise Exception("Unsupported archive type %s." %
archive_name)
compressed.extractall(path=tmp_directory)
elif "file_input[]" in request.FILES:
for f, path in zip(request.FILES.getlist("file_input[]"),
request.POST.getlist("paths[]")):
if fnmatch(f.name, '*.nidm.zip'):
request.FILES['file'] = f
populate_nidm_results(request, collection)
continue
new_path, _ = os.path.split(
os.path.join(tmp_directory, path))
mkdir_p(new_path)
filename = os.path.join(new_path, f.name)
tmp_file = open(filename, 'w')
tmp_file.write(f.read())
tmp_file.close()
else:
raise Exception("Unable to find uploaded files.")
atlases = {}
for root, subdirs, filenames in os.walk(tmp_directory):
if detect_feat_directory(root):
populate_feat_directory(request, collection, root)
del (subdirs)
filenames = []
# .gfeat parent dir under cope*.feat should not be added as statmaps
# this may be affected by future nidm-results_fsl parsing changes
if root.endswith('.gfeat'):
filenames = []
filenames = [f for f in filenames if not f[0] == '.']
for fname in sorted(filenames):
name, ext = splitext_nii_gz(fname)
nii_path = os.path.join(root, fname)
if ext == '.xml':
print "found xml"
dom = minidom.parse(os.path.join(root, fname))
for atlas in dom.getElementsByTagName(
"summaryimagefile"):
print "found atlas"
path, base = os.path.split(
atlas.lastChild.nodeValue)
nifti_name = os.path.join(path, base)
atlases[str(os.path.join(
root, nifti_name[1:]))] = os.path.join(
root, fname)
if ext in allowed_extensions:
nii = nib.load(nii_path)
if detect_afni4D(nii):
niftiFiles.extend(split_afni4D_to_3D(nii))
else:
niftiFiles.append((fname, nii_path))
for label, fpath in niftiFiles:
# Read nifti file information
nii = nib.load(fpath)
if len(nii.get_shape()) > 3 and nii.get_shape()[3] > 1:
print "skipping wrong size"
continue
hdr = nii.get_header()
raw_hdr = hdr.structarr
# SPM only !!!
# Check if filename corresponds to a T-map
Tregexp = re.compile('spmT.*')
# Fregexp = re.compile('spmF.*')
if Tregexp.search(fpath) is not None:
map_type = StatisticMap.T
else:
# Check if filename corresponds to a F-map
if Tregexp.search(fpath) is not None:
map_type = StatisticMap.F
else:
map_type = StatisticMap.OTHER
path, name, ext = split_filename(fpath)
dname = name + ".nii.gz"
spaced_name = name.replace('_', ' ').replace('-', ' ')
if ext.lower() != ".nii.gz":
new_file_tmp_dir = tempfile.mkdtemp()
new_file_tmp = os.path.join(new_file_tmp_dir,
name) + '.nii.gz'
nib.save(nii, new_file_tmp)
f = ContentFile(open(new_file_tmp).read(), name=dname)
shutil.rmtree(new_file_tmp_dir)
label += " (old ext: %s)" % ext
else:
f = ContentFile(open(fpath).read(), name=dname)
collection = get_collection(collection_cid, request)
if os.path.join(path, name) in atlases:
new_image = Atlas(name=spaced_name,
description=raw_hdr['descrip'],
collection=collection)
new_image.label_description_file = ContentFile(
open(atlases[os.path.join(path, name)]).read(),
name=name + ".xml")
else:
new_image = StatisticMap(name=spaced_name,
description=raw_hdr['descrip']
or label,
collection=collection)
new_image.map_type = map_type
new_image.file = f
new_image.save()
except:
raise
error = traceback.format_exc().splitlines()[-1]
msg = "An error occurred with this upload: {}".format(error)
messages.warning(request, msg)
return HttpResponseRedirect(collection.get_absolute_url())
finally:
shutil.rmtree(tmp_directory)
return HttpResponseRedirect(collection.get_absolute_url())
else:
form = UploadFileForm()
return render_to_response("statmaps/upload_folder.html", {'form': form},
RequestContext(request))
def upload_folder(request, collection_cid):
collection = get_collection(collection_cid,request)
allowed_extensions = ['.nii', '.img', '.nii.gz']
niftiFiles = []
if request.method == 'POST':
print request.POST
print request.FILES
form = UploadFileForm(request.POST, request.FILES)
if form.is_valid():
tmp_directory = tempfile.mkdtemp()
print tmp_directory
try:
# Save archive (.zip or .tar.gz) to disk
if "file" in request.FILES:
archive_name = request.FILES['file'].name
if fnmatch(archive_name,'*.nidm.zip'):
form = populate_nidm_results(request,collection)
if not form:
messages.warning(request, "Invalid NIDM-Results file.")
return HttpResponseRedirect(collection.get_absolute_url())
_, archive_ext = os.path.splitext(archive_name)
if archive_ext == '.zip':
compressed = zipfile.ZipFile(request.FILES['file'])
elif archive_ext == '.gz':
django_file = request.FILES['file']
django_file.open()
compressed = tarfile.TarFile(fileobj=gzip.GzipFile(fileobj=django_file.file, mode='r'), mode='r')
else:
raise Exception("Unsupported archive type %s."%archive_name)
compressed.extractall(path=tmp_directory)
elif "file_input[]" in request.FILES:
for f, path in zip(request.FILES.getlist(
"file_input[]"), request.POST.getlist("paths[]")):
if fnmatch(f.name,'*.nidm.zip'):
request.FILES['file'] = f
populate_nidm_results(request,collection)
continue
new_path, _ = os.path.split(os.path.join(tmp_directory, path))
mkdir_p(new_path)
filename = os.path.join(new_path,f.name)
tmp_file = open(filename, 'w')
tmp_file.write(f.read())
tmp_file.close()
else:
raise Exception("Unable to find uploaded files.")
atlases = {}
for root, subdirs, filenames in os.walk(tmp_directory):
if detect_feat_directory(root):
populate_feat_directory(request,collection,root)
del(subdirs)
filenames = []
# .gfeat parent dir under cope*.feat should not be added as statmaps
# this may be affected by future nidm-results_fsl parsing changes
if root.endswith('.gfeat'):
filenames = []
filenames = [f for f in filenames if not f[0] == '.']
for fname in sorted(filenames):
name, ext = splitext_nii_gz(fname)
nii_path = os.path.join(root, fname)
if ext == '.xml':
print "found xml"
dom = minidom.parse(os.path.join(root, fname))
for atlas in dom.getElementsByTagName("summaryimagefile"):
print "found atlas"
path, base = os.path.split(atlas.lastChild.nodeValue)
nifti_name = os.path.join(path, base)
atlases[str(os.path.join(root,
nifti_name[1:]))] = os.path.join(root, fname)
if ext in allowed_extensions:
nii = nib.load(nii_path)
if detect_4D(nii):
niftiFiles.extend(split_4D_to_3D(nii))
else:
niftiFiles.append((fname,nii_path))
for label,fpath in niftiFiles:
# Read nifti file information
nii = nib.load(fpath)
if len(nii.get_shape()) > 3 and nii.get_shape()[3] > 1:
messages.warning(request, "Skipping %s - not a 3D file."%label)
continue
hdr = nii.get_header()
raw_hdr = hdr.structarr
# SPM only !!!
# Check if filename corresponds to a T-map
Tregexp = re.compile('spmT.*')
# Fregexp = re.compile('spmF.*')
if Tregexp.search(fpath) is not None:
map_type = StatisticMap.T
else:
# Check if filename corresponds to a F-map
if Tregexp.search(fpath) is not None:
map_type = StatisticMap.F
else:
map_type = StatisticMap.OTHER
path, name, ext = split_filename(fpath)
dname = name + ".nii.gz"
spaced_name = name.replace('_',' ').replace('-',' ')
if ext.lower() != ".nii.gz":
new_file_tmp_dir = tempfile.mkdtemp()
new_file_tmp = os.path.join(new_file_tmp_dir, name) + '.nii.gz'
nib.save(nii, new_file_tmp)
f = ContentFile(open(new_file_tmp).read(), name=dname)
shutil.rmtree(new_file_tmp_dir)
label += " (old ext: %s)" % ext
else:
f = ContentFile(open(fpath).read(), name=dname)
collection = get_collection(collection_cid,request)
if os.path.join(path, name) in atlases:
new_image = Atlas(name=spaced_name,
description=raw_hdr['descrip'], collection=collection)
new_image.label_description_file = ContentFile(
open(atlases[os.path.join(path,name)]).read(),
name=name + ".xml")
else:
new_image = StatisticMap(name=spaced_name,
description=raw_hdr['descrip'] or label, collection=collection)
new_image.map_type = map_type
new_image.file = f
new_image.save()
except:
error = traceback.format_exc().splitlines()[-1]
msg = "An error occurred with this upload: {}".format(error)
messages.warning(request, msg)
return HttpResponseRedirect(collection.get_absolute_url())
finally:
shutil.rmtree(tmp_directory)
if not niftiFiles:
messages.warning(request, "No NIFTI files (.nii, .nii.gz, .img/.hdr) found in the upload.")
return HttpResponseRedirect(collection.get_absolute_url())
else:
form = UploadFileForm()
return render_to_response("statmaps/upload_folder.html",
{'form': form}, RequestContext(request))
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "neurovault.settings")
django.setup()
from nidmfsl.fsl_exporter.fsl_exporter import FSLtoNIDMExporter
from neurovault.apps.statmaps.utils import detect_feat_directory, get_traceback
if __name__ == '__main__':
feat_dirs_path = raw_input("Enter location of test data:") or '/vagrant/FEAT'
find = 0
parse = 0
fail = 0
for root, dirs, files in os.walk(feat_dirs_path, topdown=False):
if detect_feat_directory(root):
if '.files' in dirs:
call(["rm", "-rf",os.path.join(root,'.files')])
tmpdir = tempfile.mkdtemp()
feat_dir = os.path.join(tmpdir,os.path.basename(root))
shutil.copytree(root, feat_dir)
print 'found feat directory at {0}'.format(root)
print 'testing {0}'.format(feat_dir)
find += 1
try:
fslnidm = FSLtoNIDMExporter(feat_dir=feat_dir, version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
parse += 1
except:
fail += 1
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "neurovault.settings")
django.setup()
from nidmfsl.fsl_exporter.fsl_exporter import FSLtoNIDMExporter
from neurovault.apps.statmaps.utils import detect_feat_directory, get_traceback
if __name__ == '__main__':
feat_dirs_path = raw_input(
"Enter location of test data:") or '/vagrant/FEAT'
find = 0
parse = 0
fail = 0
for root, dirs, files in os.walk(feat_dirs_path, topdown=False):
if detect_feat_directory(root):
if '.files' in dirs:
call(["rm", "-rf", os.path.join(root, '.files')])
tmpdir = tempfile.mkdtemp()
feat_dir = os.path.join(tmpdir, os.path.basename(root))
shutil.copytree(root, feat_dir)
print 'found feat directory at {0}'.format(root)
print 'testing {0}'.format(feat_dir)
find += 1
try:
fslnidm = FSLtoNIDMExporter(feat_dir=feat_dir, version="0.2.0")
fslnidm.parse()
export_dir = fslnidm.export()
parse += 1
except:
fail += 1
