def _run_module_cmd(cls, *args):
if 'MODULESHOME' in os.environ:
try:
modulecmd = sp.check_output('which modulecmd',
shell=True).strip()
except sp.CalledProcessError:
modulecmd = False
if not modulecmd:
modulecmd = '{}/bin/modulecmd'.format(
os.environ['MODULESHOME'])
if not os.path.exists(modulecmd):
raise ArcanaError(
"Cannot find 'modulecmd' on path or in MODULESHOME.")
logger.debug("Running modules command '{}'".format(' '.join(args)))
try:
output, error = sp.Popen(
[modulecmd, 'python'] + list(args),
stdout=sp.PIPE, stderr=sp.PIPE).communicate()
except (sp.CalledProcessError, OSError) as e:
raise ArcanaError(
"Call to subprocess `{}` threw an error: {}".format(
' '.join([modulecmd, 'python'] + list(args)), e))
exec(output)
if PY3:
error = error.decode('utf-8')
return error
else:
raise ArcanaModulesNotInstalledException('MODULESHOME')
def _run_interface(self, runtime):
loaded_modules = ModulesEnvironment.preloaded()
if first_req.name not in loaded_modules:
raise ArcanaError("Mrtrix module was not loaded in Node")
if second_req.name not in loaded_modules:
raise ArcanaError("Dcm2niix module was not loaded in Node")
return runtime
def assertField(self, name, ref_value, from_study, subject=None,
visit=None, frequency='per_session',
to_places=None):
esc_name = from_study + '_' + name
output_dir = self.get_session_dir(subject, visit, frequency)
try:
with open(op.join(output_dir,
DirectoryRepository.FIELDS_FNAME)) as f:
fields = json.load(f, 'rb')
except IOError as e:
if e.errno == errno.ENOENT:
raise ArcanaError(
"No fields were created by pipeline in study '{}'"
.format(from_study))
try:
value = fields[esc_name]
except KeyError:
raise ArcanaError(
"Field '{}' was not created by pipeline in study '{}'. "
"Created fields were ('{}')"
.format(esc_name, from_study, "', '".join(fields)))
msg = ("Field value '{}' for study '{}', {}, does not match "
"reference value ({})".format(name, from_study, value,
ref_value))
if to_places is not None:
self.assertAlmostEqual(
value, ref_value, to_places,
'{} to {} decimal places'.format(msg, to_places))
else:
self.assertEqual(value, ref_value, msg)
def __init__(self,
work_dir,
partition=None,
account=None,
email=None,
mail_on=('FAIL', ),
generic_resources=None,
ntasks_per_node=None,
cpus_per_task=None,
**kwargs):
if email is None:
try:
email = os.environ['EMAIL']
except KeyError:
raise ArcanaError(
"'email' kwarg needs to be provided for SlurmProcessor"
" if 'EMAIL' environment variable not set")
self._email = email
self._mail_on = mail_on
self._account = account
self._partition = partition
self._ntasks_per_node = ntasks_per_node
self._cpus_per_task = cpus_per_task
self._generic_resources = generic_resources
super(SlurmProcessor, self).__init__(work_dir, **kwargs)
def add_session(self, filesets=None, fields=None, project_dir=None,
subject=None, visit=None):
if project_dir is None:
project_dir = self.project_dir
if filesets is None:
filesets = {}
if subject is None:
subject = self.SUBJECT
if visit is None:
visit = self.VISIT
session_dir = op.join(project_dir, subject, visit)
os.makedirs(session_dir)
for name, fileset in list(filesets.items()):
if isinstance(fileset, Fileset):
dst_path = op.join(session_dir,
name + fileset.format.ext_str)
if fileset.format.directory:
shutil.copytree(fileset.path, dst_path)
else:
shutil.copy(fileset.path, dst_path)
elif isinstance(fileset, basestring):
# Write string as text file
with open(op.join(session_dir,
name + '.txt'), 'w') as f:
f.write(fileset)
else:
raise ArcanaError(
"Unrecognised fileset ({}) in {} test setup. Can "
"be either a Fileset or basestring object"
.format(fileset, self))
if fields is not None:
with open(op.join(session_dir,
DirectoryRepository.FIELDS_FNAME), 'w',
**JSON_ENCODING) as f:
json.dump(fields, f)
def _run_interface(self, runtime):
dirname = self.out_dir
os.makedirs(dirname)
ext = self.inputs.extension
if isdefined(self.inputs.file_names):
if len(self.inputs.file_names) != len(self.inputs.in_files):
raise ArcanaError(
"Number of provided filenames ({}) does not match number "
"of provided files ({})".format(
len(self.inputs.file_names),
len(self.inputs.in_files)))
for i, f in enumerate(self.inputs.in_files):
if isdefined(self.inputs.file_names):
path = op.join(self.out_dir,
op.basename(self.inputs.file_names[i]))
if op.isdir(f):
shutil.copytree(f, path)
else:
shutil.copy(f, path)
else:
# Not quite sure what is going on here, probably should
# ask Francesco what this logic is for
if op.isdir(f):
out_name = f.split('/')[-1]
if ext:
out_name = '{0}_{1}'.format(out_name,
ext + str(i).zfill(3))
shutil.copytree(f, dirname + '/{}'.format(out_name))
elif op.isfile(f):
if ext == '.dcm':
fname = op.join(dirname, str(i).zfill(4)) + ext
else:
fname = dirname
shutil.copy(f, fname)
return runtime
def path(self):
if self._path is None:
if self.repository is not None:
self._path = self.repository.get_fileset(self)
else:
raise ArcanaError(
"Neither path nor repository has been set for Fileset("
"'{}')".format(self.name))
return self._path
def value(self):
if self._value is None:
if self.repository is not None:
self._value = self.repository.get_field(self)
else:
raise ArcanaError(
"Neither value nor repository has been set for Field("
"'{}')".format(self.name))
return self._value
def pipeline(self):
if self.pipeline_name is None:
raise ArcanaUsageError(
"{} is an acquired data spec so doesn't have a pipeline".
format(self))
try:
getter = getattr(self.study, self.pipeline_name)
except AttributeError:
raise ArcanaError(
"There is no pipeline method named '{}' in present in "
"'{}' study".format(self.pipeline_name, self.study))
# Set up study to record which parameters
# referenced during the pipeline generation
self.study._pipeline_to_generate = self.pipeline_name
self.study._referenced_parameters = set()
try:
pipeline = getter()
if pipeline is None:
raise ArcanaDesignError(
"'{}' pipeline constructor in {} is missing return "
"statement (should return a Pipeline object)".format(
self.pipeline_name, self.study))
# Copy referenced parameters to pipeline
pipeline._referenced_parameters = (
self.study._referenced_parameters)
except AttributeError as e:
# Need to capture this as exception to avoid it getting
# confused with specs that don't have pipelines
raise ArcanaError("AttributeError was thrown attempting to "
"construct '{}': {}".format(
self.pipeline_name, e))
finally:
# Reset referenced parameters after generating pipeline
self.study._pipeline_to_generate = None
self.study._referenced_parameters = None
if self.name not in pipeline.output_names:
raise ArcanaOutputNotProducedException(
"'{}' is not produced by {} pipeline in {} class given the "
"provided switches ({}) and the missing inputs ('{}')".format(
self.name, pipeline.name, self.study.__class__.__name__,
', '.join('{}={}'.format(s.name, s.value)
for s in self.study.switches),
"', '".join(self.study.missing_inputs)))
return pipeline
def __init__(self, root_dir, depth=None):
super(DirectoryRepository, self).__init__()
if not op.exists(root_dir):
raise ArcanaError(
"Base directory for DirectoryRepository '{}' does not exist".
format(root_dir))
self._root_dir = op.abspath(root_dir)
if depth is None:
depth = self.guess_depth(root_dir)
self._depth = depth
def get_atlas_path(name, dataset='brain', resolution='1mm'):
"""
Returns the path to the atlas (or atlas mask) in the arcana repository
Parameters
----------
name : str
Name of the Atlas, can be one of ('mni_nl6')
atlas_type : str
Whether to return the brain mask or the full atlas, can be one of
'image', 'mask'
"""
if name == 'MNI152':
# MNI ICBM 152 non-linear 6th Generation Symmetric Average Brain
# Stereotaxic Registration Model (http://nist.mni.mcgill.ca/?p=858)
if resolution not in ['0.5mm', '1mm', '2mm']:
raise ArcanaError(
"Invalid resolution for MNI152, '{}', can be one of '0.5mm', "
"'1mm' or '2mm'".format(resolution))
if dataset == 'image':
path = os.path.join(get_fsl_reference_path(),
'MNI152_T1_{}.nii.gz'.format(resolution))
elif dataset == 'mask':
path = os.path.join(
get_fsl_reference_path(),
'MNI152_T1_{}_brain_mask.nii.gz'.format(resolution))
elif dataset == 'mask_dilated':
if resolution != '2mm':
raise ArcanaError(
"Dilated MNI masks are not available for {} resolution ".
format(resolution))
path = os.path.join(
get_fsl_reference_path(),
'MNI152_T1_{}_brain_mask_dil.nii.gz'.format(resolution))
elif dataset == 'brain':
path = os.path.join(get_fsl_reference_path(),
'MNI152_T1_{}_brain.nii.gz'.format(resolution))
else:
raise ArcanaError("Unrecognised dataset '{}'".format(dataset))
else:
raise ArcanaError("Unrecognised atlas name '{}'".format(name))
return os.path.abspath(path)
def _gen_outfilename(self):
if isdefined(self.inputs.out_file):
if not self.inputs.out_file.endswith('.mat'):
raise ArcanaError(
"Output NODDI ROI should be saved with '.mat' extension "
"(provided '{}')".format(self.inputs.out_file))
out_name = self.inputs.out_file
else:
base, _ = split_extension(os.path.basename(self.inputs.in_file))
out_name = os.path.join(os.getcwd(), "{}_ROI.mat".format(base))
return out_name
def later_or_equal_version(cls, version, reference):
for v_part, r_part in zip_longest(version, reference, fillvalue=0):
if type(v_part) != type(r_part):
raise ArcanaError(
"Type of version part {} (of '{}'), {}, does not match "
"type of reference part {}, {}".format(
v_part, version, type(v_part), r_part, type(r_part)))
if v_part > r_part:
return True
elif v_part < r_part:
return False
return True
def _get_resource(cls, xfileset, fileset):
for resource_name in fileset.format.xnat_resource_names:
try:
return xfileset.resources[resource_name]
except KeyError:
continue
raise ArcanaError(
"'{}' fileset is not available in '{}' format(s), "
"available resources are '{}'".format(
fileset.name, "', '".join(fileset.format.xnat_resource_names),
"', '".join(r.label
for r in list(fileset.resources.values()))))
def _create_project(self, project_name=None):
if project_name is None:
project_name = self.project
if SERVER == 'https://mbi-xnat.erc.monash.edu.au':
raise ArcanaError(
"Shouldn't be creating projects on the production "
"server")
with xnat.connect(SERVER) as login:
uri = '/data/archive/projects/{}'.format(project_name)
query = {'xsiType': 'xnat:projectData', 'req_format': 'qa'}
response = login.put(uri, query=query)
if response.ok:
logger.info("Created test project '{}'".format(project_name))
def _get_digests(cls, resource):
"""
Downloads the MD5 digests associated with the files in a resource.
These are saved with the downloaded files in the cache and used to
check if the files have been updated on the server
"""
result = resource.xnat_session.get(resource.uri + '/files')
if result.status_code != 200:
raise ArcanaError(
"Could not download metadata for resource {}".format(
resource.id))
return dict((r['Name'], r['digest'])
for r in result.json()['ResultSet']['Result'])
def _extract_ids(self, name):
parts = name.split('_')
if len(parts) < 3:
raise ArcanaError(
"'{}' in multi-subject test session '{}' needs to be "
"prepended with subject and session IDs (delimited by "
"'_')".format(name, self.xnat_session_name))
subj_id, visit_id = parts[:2]
if subj_id.lower() == SUMMARY_NAME.lower():
subj_id = SUMMARY_NAME
if visit_id.lower() == SUMMARY_NAME.lower():
visit_id = SUMMARY_NAME
basename = '_'.join(parts[2:])
return subj_id, visit_id, basename
def download_dataset(download_path,
server,
user,
password,
session_id,
dataset_name,
file_format=None):
"""
Downloads a single dataset from an XNAT server
"""
with xnat.connect(server, user=user, password=password) as xnat_login:
try:
session = xnat_login.experiments[session_id]
except KeyError:
raise ArcanaError("Didn't find session matching '{}' on {}".format(
session_id, server))
try:
dataset = session.scans[dataset_name]
except KeyError:
raise ArcanaError("Didn't find dataset matching '{}' in {}".format(
dataset_name, session_id))
if file_format is None:
file_format = guess_file_format(dataset)
download_resource(download_path, dataset, file_format, session.label)
def __init__(self, name, min_version, max_version=None,
version_split=split_version, references=None,
website=None):
self._name = name.lower()
self._min_ver = tuple(min_version)
if max_version is not None:
self._max_ver = tuple(max_version)
if not self.later_or_equal_version(self._max_ver, self._min_ver):
raise ArcanaError(
"Supplied max version ({}) is not greater than min "
" version ({})".format(self._min_ver, self._max_ver))
else:
self._max_ver = None
self._version_split = version_split
self._references = references if references is not None else []
self._website = website
def outputnode(self, frequency):
"""
Generates an output node for the given frequency. It also adds implicit
file format conversion nodes to the pipeline.
Parameters
----------
frequency : str
The frequency (i.e. 'per_session', 'per_visit', 'per_subject' or
'per_study') of the output node to retrieve
"""
# Check to see whether there are any outputs for the given frequency
outputs = list(self.frequency_outputs(frequency))
if not outputs:
raise ArcanaError(
"No outputs to '{}' pipeline for requested freqency '{}'".
format(self.name, frequency))
# Get list of output names for the requested frequency, addding fields
# to hold iterator IDs
output_names = [o.name for o in outputs]
# Generate output node and connect it to appropriate nodes
outputnode = self.add('{}_outputnode'.format(frequency),
IdentityInterface(fields=output_names))
# Loop through list of nodes connected to study data specs and
# connect them to the newly created output node
for output in outputs: # @ReservedAssignment
conv_cache = {}
(node, node_out, format, conv_kwargs) = self._output_conns[
output.name] # @ReservedAssignment @IgnorePep8
# If fileset formats differ between study and pipeline
# outputs create converter node (if one hasn't been already)
# and connect output to that before connecting to outputnode
if self.requires_conversion(output, format):
if format.name not in conv_cache:
conv_cache[format.name] = output.format.converter_from(
format, **conv_kwargs)
(conv_node, conv_in,
conv_out) = conv_cache[format.name].get_node(
'{}_{}_{}_to_{}_conversion'.format(
self.name, output.name, output.format.name,
format.name))
self.connect(node, node_out, conv_node, conv_in)
self.connect(conv_node, conv_out, outputnode, output.name)
else:
self.connect(node, node_out, outputnode, output.name)
return outputnode
def _upload_datset(self, xnat_login, fileset, xsession):
if self._is_derived(fileset):
type_name = self._derived_name(fileset)
else:
type_name = fileset.name
xfileset = xnat_login.classes.MrScanData(type=type_name,
parent=xsession)
xresource = xfileset.create_resource(fileset.format.name.upper())
if fileset.format.directory:
for fname in os.listdir(fileset.path):
fpath = op.join(fileset.path, fname)
xresource.upload(fpath, fname)
else:
if not op.exists(fileset.path):
raise ArcanaError("Cannot upload fileset {} as path ({}) does "
"not exist".format(fileset, fpath))
xresource.upload(fileset.path, op.basename(fileset.path))
def _download_fileset(cls, tmp_dir, xresource, xfileset, fileset,
session_label, cache_path):
# Download resource to zip file
zip_path = op.join(tmp_dir, 'download.zip')
with open(zip_path, 'wb') as f:
xresource.xnat_session.download_stream(xresource.uri + '/files',
f,
format='zip',
verbose=True)
digests = cls._get_digests(xresource)
# Extract downloaded zip file
expanded_dir = op.join(tmp_dir, 'expanded')
try:
with ZipFile(zip_path) as zip_file:
zip_file.extractall(expanded_dir)
except BadZipfile as e:
raise ArcanaError("Could not unzip file '{}' ({})".format(
xresource.id, e))
data_path = op.join(
expanded_dir, session_label, 'scans',
(xfileset.id + '-' + special_char_re.sub('_', xfileset.type)),
'resources', xresource.label, 'files')
if not fileset.format.directory:
# If the dataformat is not a directory (e.g. DICOM),
# attempt to locate a single file within the resource
# directory with the appropriate filename and add that
# to be the complete data path.
fnames = os.listdir(data_path)
match_fnames = [
f for f in fnames if (lower(split_extension(f)[-1]) == lower(
fileset.format.extension))
]
if len(match_fnames) == 1:
data_path = op.join(data_path, match_fnames[0])
else:
raise ArcanaMissingDataException(
"Did not find single file with extension '{}' "
"(found '{}') in resource '{}'".format(
fileset.format.extension, "', '".join(fnames),
data_path))
shutil.move(data_path, cache_path)
with open(cache_path + XnatRepository.MD5_SUFFIX, 'w',
**JSON_ENCODING) as f:
json.dump(digests, f)
shutil.rmtree(tmp_dir)
def best_requirement(cls, possible_requirements, available_modules,
preloaded_modules=None):
if preloaded_modules is None:
preloaded_modules = {}
# If possible reqs is a singleton, wrap it in a list for
# iterating
if isinstance(possible_requirements, Requirement):
possible_requirements = [possible_requirements]
# Loop through all parameters for a given requirement and see
# if at least one can be satisfied.
logger.debug(
"Searching for one of {}".format(
', '.join(str(r) for r in possible_requirements)))
ver_exceptions = [] # Will hold all version error messages
for req in possible_requirements:
try:
version = preloaded_modules[req.name]
logger.debug("Found preloaded version {} of module '{}'"
.format(version, req.name))
if req.valid_version(req.split_version(version)):
return req.name, version
else:
raise ArcanaError(
"Incompatible module version already loaded {}/{},"
" (valid {}->{}) please unload before running "
"pipeline"
.format(
req.name, version, req.min_version,
(req.max_version if req.max_version is not None
else '')))
except KeyError:
try:
best_version = req.best_version(
available_modules[req.name])
logger.debug("Found best version '{}' of module '{}' for"
" requirement {}".format(best_version,
req.name, req))
return req.name, best_version
except ArcanaRequirementVersionException as e:
ver_exceptions.append(e)
# If no parameters can be satisfied, otherwise raise exception with
# combined messages from all parameters.
raise ArcanaRequirementVersionException(
' and '.join(str(e) for e in ver_exceptions))
def _list_outputs(self):
if (not isdefined(self.inputs.compression)
or (self.inputs.compression == 'y'
or self.inputs.compression == 'i')):
im_ext = '.nii.gz'
else:
im_ext = '.nii'
outputs = self._outputs().get()
# As Dcm2niix sometimes prepends a prefix onto the filenames to avoid
# name clashes with multiple echos, we need to check the output folder
# for all filenames that end with the "generated filename".
out_dir = self._gen_filename('out_dir')
fname = self._gen_filename('filename') + im_ext
base, ext = split_extension(fname)
match_re = re.compile(r'(_e\d+)?{}(_(?:e|c)\d+)?{}'.format(
base, ext if ext is not None else ''))
products = [
os.path.join(out_dir, f) for f in os.listdir(out_dir)
if match_re.match(f) is not None
]
if len(products) == 1:
converted = products[0]
elif len(products) > 1 and self.inputs.multifile_concat:
ex_file = nib.load(products[0])
data = ex_file.get_data()
merged_file = np.zeros(
(data.shape[0], data.shape[1], data.shape[2], len(products)))
for i, el in enumerate(products):
f = nib.load(el)
merged_file[:, :, :, i] = f.get_data()
im2save = nib.Nifti1Image(merged_file, ex_file.affine)
nib.save(im2save, out_dir + fname)
converted = out_dir + fname
elif len(products) > 1 and not self.inputs.multifile_concat:
converted = products[-1]
else:
raise ArcanaError("No products produced by dcm2niix ({})".format(
', '.join(os.listdir(out_dir))))
outputs['converted'] = converted
return outputs
def get_session_dir(self,
subject=None,
visit=None,
frequency='per_session',
derived=False):
if subject is None and frequency in ('per_session', 'per_subject'):
subject = self.SUBJECT
if visit is None and frequency in ('per_session', 'per_visit'):
visit = self.VISIT
if frequency == 'per_session':
assert subject is not None
assert visit is not None
parts = [self.project, subject, visit]
elif frequency == 'per_subject':
assert subject is not None
assert visit is None
parts = [self.project, subject, XnatRepository.SUMMARY_NAME]
elif frequency == 'per_visit':
assert visit is not None
assert subject is None
parts = [self.project, XnatRepository.SUMMARY_NAME, visit]
elif frequency == 'per_study':
assert subject is None
assert visit is None
parts = [
self.project, XnatRepository.SUMMARY_NAME,
XnatRepository.SUMMARY_NAME
]
else:
assert False
session_id = '_'.join(parts)
if derived:
session_id += XnatRepository.PROCESSED_SUFFIX
session_path = op.join(self.output_cache_dir, session_id)
if not op.exists(session_path):
raise ArcanaError(
"Session path '{}' does not exist".format(session_path))
return session_path
def bind(self, study):
"""
Returns a copy of the Spec bound to the given study
Parameters
----------
study : Study
A study to bind the fileset spec to (should happen in the
study __init__)
"""
if self._study is not None:
# Avoid rebinding specs in sub-studies that have already
# been bound to MultiStudy
bound = self
else:
bound = copy(self)
bound._study = study
if not hasattr(study, self.pipeline_name):
raise ArcanaError(
"{} does not have a method named '{}' required to "
"derive {}".format(study, self.pipeline_name, self))
bound._bind_tree(study.tree)
return bound
def download_resource(download_path, dataset, file_format, session_label):
xresource = None
for resource_name in file_format.xnat_resource_names:
try:
xresource = dataset.resources[resource_name]
break
except KeyError:
logger.debug("Did not find resource corresponding to '{}' for {}, "
"will try alternatives if available".format(
resource_name, dataset))
continue
if xresource is None:
raise ArcanaError(
"Didn't find '{}' resource(s) in {} dataset matching "
"'{}' in {}".format("', '".join(file_format.xnat_resource_names),
dataset.type))
tmp_dir = download_path + '.download'
xresource.download_dir(tmp_dir)
dataset_label = dataset.id + '-' + special_char_re.sub('_', dataset.type)
src_path = os.path.join(tmp_dir, session_label, 'scans', dataset_label,
'resources', xresource.label, 'files')
if not file_format.directory:
fnames = os.listdir(src_path)
match_fnames = [
f for f in fnames
if lower(split_extension(f)[-1]) == lower(file_format.extension)
]
if len(match_fnames) == 1:
src_path = os.path.join(src_path, match_fnames[0])
else:
raise ArcanaMissingDataException(
"Did not find single file with extension '{}' "
"(found '{}') in resource '{}'".format(file_format.extension,
"', '".join(fnames),
src_path))
shutil.move(src_path, download_path)
shutil.rmtree(tmp_dir)
def __init__(
self,
name,
valid_formats,
frequency='per_session', # @ReservedAssignment @IgnorePep8
desc=None,
optional=False,
default=None):
# Ensure allowed formats is a list
try:
valid_formats = sorted(valid_formats, key=attrgetter('name'))
except TypeError:
valid_formats = [valid_formats]
else:
if not valid_formats:
raise ArcanaError(
"'{}' spec doesn't have any allowed formats".format(name))
self._valid_formats = valid_formats
BaseFileset.__init__(self, name, valid_formats[0], frequency)
BaseAcquiredSpec.__init__(self,
name,
desc,
optional=optional,
default=default)
def bind(self, study):
"""
Returns a copy of the AcquiredSpec bound to the given study
Parameters
----------
study : Study
A study to bind the fileset spec to (should happen in the
study __init__)
"""
if self.default is None:
raise ArcanaError(
"Attempted to bind '{}' to {} but only acquired specs with "
"a default value should be bound to studies{})".format(
self.name, study))
if self._study is not None:
# This avoids rebinding specs to sub-studies that have already
# been bound to the multi-study
bound = self
else:
bound = copy(self)
bound._study = study
bound._default = bound.default.bind(study)
return bound
def output_file_path(self,
fname,
from_study,
subject=None,
visit=None,
frequency='per_session'):
try:
acq_path = self.BASE_CLASS.output_file_path(self,
fname,
from_study,
subject=subject,
visit=visit,
frequency=frequency,
derived=False)
except KeyError:
acq_path = None
try:
proc_path = self.BASE_CLASS.output_file_path(self,
fname,
from_study,
subject=subject,
visit=visit,
frequency=frequency,
derived=True)
except KeyError:
proc_path = None
if acq_path is not None and op.exists(acq_path):
if op.exists(proc_path):
raise ArcanaError(
"Both acquired and derived paths were found for "
"'{}_{}' ({} and {})".format(from_study, fname, acq_path,
proc_path))
path = acq_path
else:
path = proc_path
return path