def clean_and_validate(self, cleaned_data):
print "enter clean_and_validate"
file = cleaned_data.get('file')
surface_left_file = cleaned_data.get('surface_left_file')
surface_right_file = cleaned_data.get('surface_right_file')
if surface_left_file and surface_right_file and not file:
if "file" in self._errors.keys():
del self._errors["file"]
cleaned_data["data_origin"] = 'surface'
tmp_dir = tempfile.mkdtemp()
try:
new_name = cleaned_data["name"] + ".nii.gz"
ribbon_projection_file = os.path.join(tmp_dir, new_name)
inputs_dict = {"lh": "surface_left_file",
"rh": "surface_right_file"}
intent_dict = {"lh": "CortexLeft",
"rh": "CortexRight"}
for hemi in ["lh", "rh"]:
print hemi
surface_file = cleaned_data.get(inputs_dict[hemi])
_, ext = splitext_nii_gz(surface_file.name)
if not ext.lower() in [".mgh", ".curv", ".gii", ".nii", ".nii.gz"]:
self._errors[inputs_dict[hemi]] = self.error_class(
["Doesn't have proper extension"]
)
del cleaned_data[inputs_dict[hemi]]
return cleaned_data
infile = os.path.join(tmp_dir, hemi + ext)
print "write " + hemi
print surface_file.file
surface_file.open()
surface_file = StringIO(surface_file.read())
with open(infile, 'w') as fd:
surface_file.seek(0)
shutil.copyfileobj(surface_file, fd)
try:
if ext.lower() != ".gii":
out_gii = os.path.join(tmp_dir, hemi + '.gii')
subprocess.check_output(
[os.path.join(os.environ['FREESURFER_HOME'],
"bin", "mris_convert"),
"-c", infile,
os.path.join(os.environ['FREESURFER_HOME'],
"subjects", "fsaverage", "surf",
hemi + ".white"),
out_gii])
else:
out_gii = infile
gii = nb.load(out_gii)
if gii.darrays[0].dims != [163842]:
self._errors[inputs_dict[hemi]] = self.error_class(
["Doesn't have proper dimensions - are you sure it's fsaverage?"]
)
del cleaned_data[inputs_dict[hemi]]
return cleaned_data
# fix intent
old_dict = gii.meta.metadata
old_dict['AnatomicalStructurePrimary'] = intent_dict[hemi]
gii.meta = gii.meta.from_dict(old_dict)
gii.to_filename(os.path.join(tmp_dir, hemi + '.gii'))
subprocess.check_output(
[os.path.join(os.environ['FREESURFER_HOME'],
"bin", "mri_surf2surf"),
"--s", "fsaverage",
"--hemi", hemi,
"--srcsurfval",
os.path.join(tmp_dir, hemi+'.gii'),
"--trgsubject", "ICBM2009c_asym_nlin",
"--trgsurfval",
os.path.join(tmp_dir, hemi+'.MNI.gii')])
except CalledProcessError, e:
raise RuntimeError(str(e.cmd) + " returned code " +
str(e.returncode) + " with output " + e.output)
cleaned_data['surface_left_file'] = memory_uploadfile(
os.path.join(tmp_dir, 'lh.gii'),
new_name[:-7] + ".fsaverage.lh.func.gii", None)
cleaned_data['surface_right_file'] = memory_uploadfile(
os.path.join(tmp_dir, 'rh.gii'),
new_name[:-7] + ".fsaverage.rh.func.gii", None)
print "surf2vol"
try:
subprocess.check_output(
[os.path.join(os.environ['FREESURFER_HOME'],
"bin", "mri_surf2vol"),
"--subject", "ICBM2009c_asym_nlin",
"--o",
ribbon_projection_file[:-3],
"--so",
os.path.join(os.environ['FREESURFER_HOME'],
"subjects", "ICBM2009c_asym_nlin", "surf", "lh.white"),
os.path.join(tmp_dir, 'lh.MNI.gii'),
"--so",
os.path.join(os.environ['FREESURFER_HOME'],
"subjects", "ICBM2009c_asym_nlin", "surf", "rh.white"),
os.path.join(tmp_dir, 'rh.MNI.gii')])
except CalledProcessError, e:
raise RuntimeError(str(e.cmd) + " returned code " +
str(e.returncode) + " with output " + e.output)
#fix one voxel offset
nii = nb.load(ribbon_projection_file[:-3])
affine = nii.affine
affine[0, 3] -= 1
nb.Nifti1Image(nii.get_data(), affine).to_filename(ribbon_projection_file)
cleaned_data['file'] = memory_uploadfile(
ribbon_projection_file, new_name, None)
def clean_and_validate(self, cleaned_data):
print "enter clean_and_validate"
file = cleaned_data.get('file')
surface_left_file = cleaned_data.get('surface_left_file')
surface_right_file = cleaned_data.get('surface_right_file')
if surface_left_file and surface_right_file and not file:
if "file" in self._errors.keys():
del self._errors["file"]
cleaned_data["data_origin"] = 'surface'
tmp_dir = tempfile.mkdtemp()
try:
new_name = cleaned_data["name"] + ".nii.gz"
ribbon_projection_file = os.path.join(tmp_dir, new_name)
inputs_dict = {"lh": "surface_left_file",
"rh": "surface_right_file"}
intent_dict = {"lh": "CortexLeft",
"rh": "CortexRight"}
for hemi in ["lh", "rh"]:
print hemi
surface_file = cleaned_data.get(inputs_dict[hemi])
_, ext = splitext_nii_gz(surface_file.name)
if not ext.lower() in [".mgh", ".curv", ".gii", ".nii", ".nii.gz"]:
self._errors[inputs_dict[hemi]] = self.error_class(
["Doesn't have proper extension"]
)
del cleaned_data[inputs_dict[hemi]]
return cleaned_data
infile = os.path.join(tmp_dir, hemi + ext)
print "write " + hemi
print surface_file.file
surface_file.open()
surface_file = StringIO(surface_file.read())
with open(infile, 'w') as fd:
surface_file.seek(0)
shutil.copyfileobj(surface_file, fd)
try:
if ext.lower() != ".gii":
out_gii = os.path.join(tmp_dir, hemi + '.gii')
subprocess.check_output(
[os.path.join(os.environ['FREESURFER_HOME'],
"bin", "mris_convert"),
"-c", infile,
os.path.join(os.environ['FREESURFER_HOME'],
"subjects", "fsaverage", "surf",
hemi + ".white"),
out_gii])
else:
out_gii = infile
gii = nb.load(out_gii)
if gii.darrays[0].dims != [163842]:
self._errors[inputs_dict[hemi]] = self.error_class(
["Doesn't have proper dimensions - are you sure it's fsaverage?"]
)
del cleaned_data[inputs_dict[hemi]]
return cleaned_data
# fix intent
old_dict = gii.meta.metadata
old_dict['AnatomicalStructurePrimary'] = intent_dict[hemi]
gii.meta = gii.meta.from_dict(old_dict)
gii.to_filename(os.path.join(tmp_dir, hemi + '.gii'))
subprocess.check_output(
[os.path.join(os.environ['FREESURFER_HOME'],
"bin", "mri_surf2surf"),
"--s", "fsaverage",
"--hemi", hemi,
"--srcsurfval",
os.path.join(tmp_dir, hemi+'.gii'),
"--trgsubject", "ICBM2009c_asym_nlin",
"--trgsurfval",
os.path.join(tmp_dir, hemi+'.MNI.gii')])
except CalledProcessError, e:
raise RuntimeError(str(e.cmd) + " returned code " +
str(e.returncode) + " with output " + e.output)
cleaned_data['surface_left_file'] = memory_uploadfile(
os.path.join(tmp_dir, 'lh.gii'),
new_name[:-7] + ".fsaverage.lh.func.gii", None)
cleaned_data['surface_right_file'] = memory_uploadfile(
os.path.join(tmp_dir, 'rh.gii'),
new_name[:-7] + ".fsaverage.rh.func.gii", None)
print "surf2vol"
try:
subprocess.check_output(
[os.path.join(os.environ['FREESURFER_HOME'],
"bin", "mri_surf2vol"),
"--subject", "ICBM2009c_asym_nlin",
"--o",
ribbon_projection_file[:-3],
"--so",
os.path.join(os.environ['FREESURFER_HOME'],
"subjects", "ICBM2009c_asym_nlin", "surf", "lh.white"),
os.path.join(tmp_dir, 'lh.MNI.gii'),
"--so",
os.path.join(os.environ['FREESURFER_HOME'],
"subjects", "ICBM2009c_asym_nlin", "surf", "rh.white"),
os.path.join(tmp_dir, 'rh.MNI.gii')])
except CalledProcessError, e:
raise RuntimeError(str(e.cmd) + " returned code " +
str(e.returncode) + " with output " + e.output)
#fix one voxel offset
nii = nb.load(ribbon_projection_file[:-3])
affine = nii.affine
affine[0, 3] -= 1
nb.Nifti1Image(nii.get_data(), affine).to_filename(ribbon_projection_file)
cleaned_data['file'] = memory_uploadfile(
ribbon_projection_file, new_name, None)
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))
