def view_image_with_pycortex(request, pk, collection_cid=None):
image = get_image(pk,collection_cid,request)
base, fname, _ = split_filename(image.file.path)
pycortex_dir = os.path.join(base, fname + "_pycortex")
if not os.path.exists(pycortex_dir):
volume = generate_pycortex_volume(image)
generate_pycortex_static({image.name: volume}, pycortex_dir)
_, _, ext = split_filename(image.file.url)
pycortex_url = image.file.url[:-len(ext)] + "_pycortex/index.html"
return redirect(pycortex_url)
def view_image_with_pycortex(request, pk, collection_cid=None):
image = get_image(pk, collection_cid, request)
base, fname, _ = split_filename(image.file.path)
pycortex_dir = os.path.join(base, fname + "_pycortex")
if not os.path.exists(pycortex_dir):
volume = generate_pycortex_volume(image)
generate_pycortex_static({image.name: volume}, pycortex_dir)
_, _, ext = split_filename(image.file.url)
pycortex_url = image.file.url[:-len(ext)] + "_pycortex/index.html"
return redirect(pycortex_url)
def forwards(self, orm):
"Write your forwards methods here."
# Note: Don't use "from appname.models import ModelName".
# Use orm.ModelName to refer to models in this application,
# and orm['appname.ModelName'] for models in other applications.
for image in orm.Image.objects.all():
if not image.file.name.endswith("nii.gz"):
nii = nb.load(os.path.join(MEDIA_ROOT, image.file.name))
tmp_directory = tempfile.mkdtemp()
path, name, ext = split_filename(image.file.name)
name += ".nii.gz"
new_path = os.path.join(tmp_directory, name)
nb.save(nii, new_path)
print new_path
image.file = ContentFile(open(new_path).read(), name=os.path.join(path, name))
image.save()
shutil.rmtree(tmp_directory)
#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)
finally:
shutil.rmtree(tmp_dir)
elif file:
# check extension of the data file
_, fname, ext = split_filename(file.name)
if not ext.lower() in [".nii.gz", ".nii", ".img"]:
self._errors["file"] = self.error_class(
["Doesn't have proper extension"]
)
del cleaned_data["file"]
return cleaned_data
# prepare file to loading into memory
file.open()
fileobj = file.file
if file.name.lower().endswith(".gz"):
fileobj = GzipFile(filename=file.name, mode='rb',
fileobj=fileobj)
file_map = {'image': nb.FileHolder(file.name, fileobj)}
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 clean_and_validate(self, cleaned_data):
file = cleaned_data.get('file')
if file:
# check extension of the data file
_, fname, ext = split_filename(file.name)
if not ext.lower() in [".nii.gz", ".nii", ".img"]:
self._errors["file"] = self.error_class(
["Doesn't have proper extension"])
del cleaned_data["file"]
return cleaned_data
# prepare file to loading into memory
file.open()
fileobj = file.file
if file.name.lower().endswith(".gz"):
fileobj = GzipFile(filename=file.name,
mode='rb',
fileobj=fileobj)
file_map = {'image': nb.FileHolder(file.name, fileobj)}
try:
tmp_dir = tempfile.mkdtemp()
if ext.lower() == ".img":
hdr_file = cleaned_data.get('hdr_file')
if hdr_file:
# check extension of the hdr file
_, _, hdr_ext = split_filename(hdr_file.name)
if not hdr_ext.lower() in [".hdr"]:
self._errors["hdr_file"] = self.error_class(
["Doesn't have proper extension"])
del cleaned_data["hdr_file"]
return cleaned_data
else:
hdr_file.open()
file_map["header"] = nb.FileHolder(
hdr_file.name, hdr_file.file)
else:
self._errors["hdr_file"] = self.error_class(
[".img file requires .hdr file"])
del cleaned_data["hdr_file"]
return cleaned_data
# check if it is really nifti
try:
print file_map
if "header" in file_map:
nii = nb.Nifti1Pair.from_file_map(file_map)
else:
nii = nb.Nifti1Image.from_file_map(file_map)
except Exception as e:
raise
# detect AFNI 4D files and prepare 3D slices
if nii is not None and detect_4D(nii):
self.afni_subbricks = split_4D_to_3D(nii, tmp_dir=tmp_dir)
else:
squeezable_dimensions = len(
filter(lambda a: a not in [0, 1], nii.shape))
if squeezable_dimensions != 3:
self._errors["file"] = self.error_class([
"4D files are not supported.\n "
"If it's multiple maps in one "
"file please split them and "
"upload separately"
])
del cleaned_data["file"]
return cleaned_data
# convert to nii.gz if needed
if (ext.lower() != ".nii.gz"
or squeezable_dimensions < len(nii.shape)):
# convert pseudo 4D to 3D
if squeezable_dimensions < len(nii.shape):
new_data = np.squeeze(nii.get_data())
nii = nb.Nifti1Image(new_data, nii.get_affine(),
nii.get_header())
# Papaya does not handle float64, but by converting
# files we loose precision
# if nii.get_data_dtype() == np.float64:
# ii.set_data_dtype(np.float32)
new_name = fname + ".nii.gz"
nii_tmp = os.path.join(tmp_dir, new_name)
nb.save(nii, nii_tmp)
print "updating file in cleaned_data"
cleaned_data['file'] = memory_uploadfile(
nii_tmp, new_name, cleaned_data['file'])
finally:
try:
if self.afni_subbricks:
# keep temp dir for AFNI slicing
self.afni_tmp = tmp_dir
else:
print "removing %s" % tmp_dir
shutil.rmtree(tmp_dir)
except OSError as exc:
if exc.errno != 2: # code 2 - no such file or directory
raise # re-raise exception
elif not getattr(self, 'partial', False):
# Skip validation error if this is a partial update from the API
raise ValidationError("Couldn't read uploaded file")
return cleaned_data
def clean_and_validate(self, cleaned_data):
file = cleaned_data.get('file')
if file:
# check extension of the data file
_, fname, ext = split_filename(file.name)
if not ext.lower() in [".nii.gz", ".nii", ".img"]:
self._errors["file"] = self.error_class(
["Doesn't have proper extension"]
)
del cleaned_data["file"]
return cleaned_data
# prepare file to loading into memory
file.open()
fileobj = file.file
if file.name.lower().endswith(".gz"):
fileobj = GzipFile(filename=file.name, mode='rb',
fileobj=fileobj)
file_map = {'image': nb.FileHolder(file.name, fileobj)}
try:
tmp_dir = tempfile.mkdtemp()
if ext.lower() == ".img":
hdr_file = cleaned_data.get('hdr_file')
if hdr_file:
# check extension of the hdr file
_, _, hdr_ext = split_filename(hdr_file.name)
if not hdr_ext.lower() in [".hdr"]:
self._errors["hdr_file"] = self.error_class(
["Doesn't have proper extension"])
del cleaned_data["hdr_file"]
return cleaned_data
else:
hdr_file.open()
file_map["header"] = nb.FileHolder(hdr_file.name,
hdr_file.file)
else:
self._errors["hdr_file"] = self.error_class(
[".img file requires .hdr file"]
)
del cleaned_data["hdr_file"]
return cleaned_data
# check if it is really nifti
try:
print file_map
if "header" in file_map:
nii = nb.Nifti1Pair.from_file_map(file_map)
else:
nii = nb.Nifti1Image.from_file_map(file_map)
except Exception as e:
raise
# detect AFNI 4D files and prepare 3D slices
if nii is not None and detect_4D(nii):
self.afni_subbricks = split_4D_to_3D(nii, tmp_dir=tmp_dir)
else:
squeezable_dimensions = len(
filter(lambda a: a not in [0, 1], nii.shape)
)
if squeezable_dimensions != 3:
self._errors["file"] = self.error_class(
["4D files are not supported.\n "
"If it's multiple maps in one "
"file please split them and "
"upload separately"])
del cleaned_data["file"]
return cleaned_data
# convert to nii.gz if needed
if (ext.lower() != ".nii.gz"
or squeezable_dimensions < len(nii.shape)):
# convert pseudo 4D to 3D
if squeezable_dimensions < len(nii.shape):
new_data = np.squeeze(nii.get_data())
nii = nb.Nifti1Image(new_data, nii.get_affine(),
nii.get_header())
# Papaya does not handle float64, but by converting
# files we loose precision
# if nii.get_data_dtype() == np.float64:
# ii.set_data_dtype(np.float32)
new_name = fname + ".nii.gz"
nii_tmp = os.path.join(tmp_dir, new_name)
nb.save(nii, nii_tmp)
print "updating file in cleaned_data"
cleaned_data['file'] = memory_uploadfile(
nii_tmp, new_name, cleaned_data['file']
)
finally:
try:
if self.afni_subbricks:
# keep temp dir for AFNI slicing
self.afni_tmp = tmp_dir
else:
print "removing %s"%tmp_dir
shutil.rmtree(tmp_dir)
except OSError as exc:
if exc.errno != 2: # code 2 - no such file or directory
raise # re-raise exception
elif not getattr(self, 'partial', False):
# Skip validation error if this is a partial update from the API
raise ValidationError("Couldn't read uploaded file")
return cleaned_data
#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)
finally:
shutil.rmtree(tmp_dir)
elif file:
# check extension of the data file
_, fname, ext = split_filename(file.name)
if not ext.lower() in [".nii.gz", ".nii", ".img"]:
self._errors["file"] = self.error_class(
["Doesn't have proper extension"]
)
del cleaned_data["file"]
return cleaned_data
# prepare file to loading into memory
file.open()
fileobj = file.file
if file.name.lower().endswith(".gz"):
fileobj = GzipFile(filename=file.name, mode='rb',
fileobj=fileobj)
file_map = {'image': nb.FileHolder(file.name, fileobj)}
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))
def upload_folder(request, collection_pk):
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
_, archive_ext = os.path.splitext(archive_name)
if archive_ext == '.zip':
compressed = zipfile.ZipFile(request.FILES['file'])
else:
compressed = tarfile.TarFile(fileobj=gzip.open(request.FILES['file']))
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[]")):
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
for root, _, filenames in os.walk(tmp_directory, topdown=False):
filenames = [f for f in filenames if not f[0] == '.']
for fname in filenames:
_, ext = splitext_nii_gz(fname)
if ext in allowed_extensions:
niftiFiles.append(os.path.join(root, fname))
for fname in niftiFiles:
# Read nifti file information
nii = nib.load(fname)
if len(nii.get_shape()) > 3 and nii.get_shape()[3] > 1:
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(fname) is not None:
map_type = Image.T;
else:
# Check if filename corresponds to a F-map
if Tregexp.search(fname) is not None:
map_type = Image.F;
else:
map_type = Image.OTHER;
path, name, ext = split_filename(fname)
name += ".nii.gz"
db_name = os.path.join(path.replace(tmp_directory,""), name)
db_name = os.path.sep.join(db_name.split(os.path.sep)[2:])
if ext.lower() != ".nii.gz":
new_file_tmp_directory = tempfile.mkdtemp()
nib.save(nii, os.path.join(new_file_tmp_directory, name))
f = ContentFile(open(os.path.join(new_file_tmp_directory, name)).read(), name=name)
shutil.rmtree(new_file_tmp_directory)
db_name += " (old ext: %s)"%ext
else:
f = ContentFile(open(fname).read(), name=name)
collection = Collection.objects.get(pk=collection_pk)
new_image = Image(name=db_name, description=raw_hdr['descrip'], collection=collection)
new_image.file = f
new_image.map_type = map_type
new_image.save()
finally:
shutil.rmtree(tmp_directory)
return HttpResponseRedirect('editimages');
else:
form = UploadFileForm()
return render_to_response("statmaps/upload_folder.html", {'form': form}, RequestContext(request))
def clean(self):
cleaned_data = super(ImageForm, self).clean()
file = cleaned_data.get("file")
if file:
# check extension of the data filr
_, fname, ext = split_filename(file.name)
if not ext.lower() in [".nii.gz", ".nii", ".img"]:
self._errors["file"] = self.error_class(["Doesn't have proper extension"])
del cleaned_data["file"]
return cleaned_data
try:
tmp_dir = tempfile.mkdtemp()
if ext.lower() == ".img":
hdr_file = cleaned_data.get('hdr_file')
if hdr_file:
# check extension of the hdr file
_, _, hdr_ext = split_filename(hdr_file.name)
if not hdr_ext.lower() in [".hdr"]:
self._errors["hdr_file"] = self.error_class(
["Doesn't have proper extension"])
del cleaned_data["hdr_file"]
return cleaned_data
else:
# write the header file to a temporary directory
hf = open(os.path.join(tmp_dir, fname + ".hdr"), "wb")
hf.write(hdr_file.file.read())
hf.close()
else:
self._errors["hdr_file"] = self.error_class([".img files require .hdr"])
del cleaned_data["hdr_file"]
return cleaned_data
# write the data file to a temporary directory
f = open(os.path.join(tmp_dir,fname + ext), "wb")
f.write(file.file.read())
f.close()
# check if it is really nifti
try:
nii = nb.load(os.path.join(tmp_dir,fname + ext))
except Exception as e:
self._errors["file"] = self.error_class([str(e)])
del cleaned_data["file"]
return cleaned_data
# convert to nii.gz if needed
if ext.lower() != ".nii.gz":
#Papaya does not handle flaot64, but by converting files we loose precision
# if nii.get_data_dtype() == np.float64:
# nii.set_data_dtype(np.float32)
nb.save(nii, os.path.join(tmp_dir,fname + ".nii.gz"))
f = ContentFile(open(os.path.join(tmp_dir,fname + ".nii.gz")).read())
print cleaned_data["file"].__class__.__name__
cleaned_data["file"] = InMemoryUploadedFile(f, "file", fname + ".nii.gz",
cleaned_data["file"].content_type, f.size, cleaned_data["file"].charset)
finally:
try:
shutil.rmtree(tmp_dir) # delete directory
except OSError as exc:
if exc.errno != 2: # code 2 - no such file or directory
raise # re-raise exception
else:
raise ValidationError("Couldn't read uploaded file")
return cleaned_data
def clean(self, **kwargs):
cleaned_data = super(ImageForm, self).clean()
file = cleaned_data.get("file")
if file:
# check extension of the data filr
_, fname, ext = split_filename(file.name)
if not ext.lower() in [".nii.gz", ".nii", ".img"]:
self._errors["file"] = self.error_class(["Doesn't have proper extension"])
del cleaned_data["file"]
return cleaned_data
try:
tmp_dir = tempfile.mkdtemp()
if ext.lower() == ".img":
hdr_file = cleaned_data.get('hdr_file')
if hdr_file:
# check extension of the hdr file
_, _, hdr_ext = split_filename(hdr_file.name)
if not hdr_ext.lower() in [".hdr"]:
self._errors["hdr_file"] = self.error_class(
["Doesn't have proper extension"])
del cleaned_data["hdr_file"]
return cleaned_data
else:
# write the header file to a temporary directory
hf = open(os.path.join(tmp_dir, fname + ".hdr"), "wb")
hf.write(hdr_file.file.read())
hf.close()
else:
self._errors["hdr_file"] = self.error_class([".img files require .hdr"])
del cleaned_data["hdr_file"]
return cleaned_data
# write the data file to a temporary directory
nii_tmp = os.path.join(tmp_dir, fname + ext)
f = open(nii_tmp, "wb")
f.write(file.file.read())
f.close()
# check if it is really nifti
try:
nii = nb.load(nii_tmp)
except Exception as e:
self._errors["file"] = self.error_class([str(e)])
del cleaned_data["file"]
return cleaned_data
# convert to nii.gz if needed
if ext.lower() != ".nii.gz":
#Papaya does not handle float64, but by converting files we loose precision
#if nii.get_data_dtype() == np.float64:
#ii.set_data_dtype(np.float32)
new_name = fname + ".nii.gz"
nii_tmp = os.path.join(tmp_dir, new_name)
nb.save(nii, nii_tmp)
cleaned_data['file'] = memory_uploadfile(nii_tmp, new_name,
cleaned_data['file'])
# detect AFNI 4D files and prepare 3D slices
if nii_tmp is not None and detect_afni4D(nii_tmp):
self.afni_subbricks = split_afni4D_to_3D(nii_tmp)
finally:
try:
if self.afni_subbricks:
self.afni_tmp = tmp_dir # keep temp dir for AFNI slicing
else:
shutil.rmtree(tmp_dir)
except OSError as exc:
if exc.errno != 2: # code 2 - no such file or directory
raise # re-raise exception
else:
raise ValidationError("Couldn't read uploaded file")
return cleaned_data
