def save_afni_slices(self, commit):
try:
orig_img = self.instance
for n, (label, brick) in enumerate(self.afni_subbricks):
brick_fname = os.path.split(brick)[-1]
mfile = memory_uploadfile(brick, brick_fname, orig_img.file)
brick_img = StatisticMap(name='%s - %s' %
(orig_img.name, label),
collection=orig_img.collection,
file=mfile)
for field in set(self.Meta.fields) - set(
['file', 'hdr_file', 'name', 'collection']):
if field in self.cleaned_data:
setattr(brick_img, field, self.cleaned_data[field])
brick_img.save()
return orig_img.collection
finally:
try:
shutil.rmtree(self.afni_tmp)
except OSError as exc:
if exc.errno != 2:
raise
def populate_afni(image):
try:
orig_name = image.name
tmpdir = tempfile.mkdtemp()
bricks = split_4D_to_3D(image.file.path, tmp_dir=tmpdir)
for label, brick in bricks:
brick_fname = os.path.split(brick)[-1]
mfile = memory_uploadfile(brick, brick_fname, image.file)
brick_img = Image(name='%s - %s' % (orig_name, label), file=mfile)
for field in ['collection', 'description', 'map_type', 'tags']:
setattr(brick_img, field, getattr(image, field))
if image.tags.exists():
brick_img.save() # generate PK before copying tags
for tag in image.tags.all():
tagobj = ValueTaggedItem(content_object=brick_img, tag=tag)
tagobj.save()
brick_img.save()
finally:
print 'converted afni4d %s to %s sub-brick images.' % (orig_name,
len(bricks))
shutil.rmtree(tmpdir)
os.remove(image.file.path)
image.delete()
def save_afni_slices(self,form,commit):
try:
orig_img = form.instance
first_img = None
for n,(label,brick) in enumerate(form.afni_subbricks):
brick_fname = os.path.split(brick)[-1]
mfile = memory_uploadfile(brick, brick_fname, orig_img.file)
brick_img = StatisticMap(name='%s - %s' % (orig_img.name, label), file=mfile)
for field in ['collection','description']:
setattr(brick_img, field, form.cleaned_data[field])
setattr(brick_img, 'map_type', form.data['%s-map_type' % form.prefix])
if n == 0:
form.instance = brick_img
first_img = form.save()
else:
brick_img.save()
for tag in first_img.tags.all():
tagobj = ValueTaggedItem(content_object=brick_img,tag=tag)
tagobj.save()
finally:
shutil.rmtree(form.afni_tmp)
return form
def populate_afni(image):
try:
orig_name = image.name
tmpdir = tempfile.mkdtemp()
bricks = split_4D_to_3D(image.file.path,tmp_dir=tmpdir)
for label,brick in bricks:
brick_fname = os.path.split(brick)[-1]
mfile = memory_uploadfile(brick, brick_fname, image.file)
brick_img = Image(name='%s - %s' % (orig_name, label), file=mfile)
for field in ['collection','description','map_type','tags']:
setattr(brick_img, field, getattr(image,field))
if image.tags.exists():
brick_img.save() # generate PK before copying tags
for tag in image.tags.all():
tagobj = ValueTaggedItem(content_object=brick_img,tag=tag)
tagobj.save()
brick_img.save()
finally:
print 'converted afni4d %s to %s sub-brick images.' % (orig_name,len(bricks))
shutil.rmtree(tmpdir)
os.remove(image.file.path)
image.delete()
def save_afni_slices(self,form,commit):
try:
orig_img = form.instance
first_img = None
for n,(label,brick) in enumerate(form.afni_subbricks):
brick_fname = os.path.split(brick)[-1]
mfile = memory_uploadfile(brick, brick_fname, orig_img.file)
brick_img = StatisticMap(name='%s - %s' % (orig_img.name, label), file=mfile)
for field in ['collection','description']:
setattr(brick_img, field, form.cleaned_data[field])
setattr(brick_img, 'map_type', form.data['%s-map_type' % form.prefix])
if n == 0:
form.instance = brick_img
first_img = form.save()
else:
brick_img.save()
for tag in first_img.tags.all():
tagobj = ValueTaggedItem(content_object=brick_img,tag=tag)
tagobj.save()
finally:
shutil.rmtree(form.afni_tmp)
return form
def save_afni_slices(self, commit):
try:
orig_img = self.instance
for n, (label, brick) in enumerate(self.afni_subbricks):
brick_fname = os.path.split(brick)[-1]
mfile = memory_uploadfile(brick, brick_fname, orig_img.file)
brick_img = StatisticMap(name='%s - %s' % (orig_img.name, label), collection=orig_img.collection,
file=mfile)
for field in set(self.Meta.fields) - set(['file', 'hdr_file', 'name', 'collection']):
if field in self.cleaned_data:
setattr(brick_img, field, self.cleaned_data[field])
brick_img.save()
return orig_img.collection
finally:
try:
shutil.rmtree(self.afni_tmp)
except OSError as exc:
if exc.errno != 2:
raise
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)
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:
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")
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
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)
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:
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")
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
