def _formatRegistration(self):
retval = []
for ii in range(len(self.inputs.transforms)):
retval.append('--transform %s' % (self._formatTransform(ii)))
for metric in self._formatMetric(ii):
retval.append('--metric %s' % metric)
retval.append('--convergence %s' % self._formatConvergence(ii))
if isdefined(self.inputs.sigma_units):
retval.append(
'--smoothing-sigmas %s%s' %
(self._antsJoinList(self.inputs.smoothing_sigmas[ii]),
self.inputs.sigma_units[ii]))
else:
retval.append(
'--smoothing-sigmas %s' %
self._antsJoinList(self.inputs.smoothing_sigmas[ii]))
retval.append('--shrink-factors %s' %
self._antsJoinList(self.inputs.shrink_factors[ii]))
if isdefined(self.inputs.use_estimate_learning_rate_once):
retval.append('--use-estimate-learning-rate-once %d' %
self.inputs.use_estimate_learning_rate_once[ii])
if isdefined(self.inputs.use_histogram_matching):
# use_histogram_matching is either a common flag for all transforms
# or a list of transform-specific flags
if isinstance(self.inputs.use_histogram_matching, bool):
histval = self.inputs.use_histogram_matching
else:
histval = self.inputs.use_histogram_matching[ii]
retval.append('--use-histogram-matching %d' % histval)
return " ".join(retval)
def _format_arg(self, opt, spec, val):
if opt == 'moving_image_mask':
return '--masks [ %s, %s ]' % (self.inputs.fixed_image_mask, self.inputs.moving_image_mask)
elif opt == 'transforms':
return self._formatRegistration()
elif opt == 'initial_moving_transform':
if self.inputs.invert_initial_moving_transform:
return '--initial-moving-transform [ %s, 1 ]' % self.inputs.initial_moving_transform
else:
return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
elif opt == 'interpolation':
# TODO: handle multilabel, gaussian, and bspline options
return '--interpolation %s' % self.inputs.interpolation
elif opt == 'output_transform_prefix':
if isdefined(self.inputs.output_inverse_warped_image) and self.inputs.output_inverse_warped_image:
return '--output [ %s, %s, %s ]' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image, self.inputs.output_inverse_warped_image)
elif isdefined(self.inputs.output_warped_image) and self.inputs.output_warped_image:
return '--output [ %s, %s ]' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image)
else:
return '--output %s' % self.inputs.output_transform_prefix
elif opt == 'winsorize_upper_quantile' or opt == 'winsorize_lower_quantile':
if not self._quantilesDone:
return self._formatWinsorizeImageIntensities()
return '' # Must return something for argstr!
elif opt == 'collapse_linear_transforms_to_fixed_image_header':
return self._formatCollapseLinearTransformsToFixedImageHeader()
return super(Registration, self)._format_arg(opt, spec, val)
def _clean_container(self, object, undefinedval=None, skipundefined=False):
"""Convert a traited obejct into a pure python representation.
"""
if isinstance(object, TraitDictObject) or isinstance(object, dict):
out = {}
for key, val in object.items():
if isdefined(val):
out[key] = self._clean_container(val, undefinedval)
else:
if not skipundefined:
out[key] = undefinedval
elif isinstance(object, TraitListObject) or isinstance(object, list) or isinstance(object, tuple):
out = []
for val in object:
if isdefined(val):
out.append(self._clean_container(val, undefinedval))
else:
if not skipundefined:
out.append(undefinedval)
else:
out.append(None)
if isinstance(object, tuple):
out = tuple(out)
else:
if isdefined(object):
out = object
else:
if not skipundefined:
out = undefinedval
return out
def _format_arg(self, opt, spec, val):
if opt == 'moving_image_mask':
return '--masks [ %s, %s ]' % (self.inputs.fixed_image_mask,
self.inputs.moving_image_mask)
elif opt == 'transforms':
self.numberOfTransforms = len(self.inputs.transforms)
return self._formatRegistration()
elif opt == 'initial_moving_transform':
if self.inputs.invert_initial_moving_transform:
return '--initial-moving-transform [ %s, 1 ]' % self.inputs.initial_moving_transform
else:
return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
elif opt == 'interpolation':
# TODO: handle multilabel, gaussian, and bspline options
return '--interpolation %s' % self.inputs.interpolation
elif opt == 'output_transform_prefix':
if isdefined(self.inputs.output_inverse_warped_image
) and self.inputs.output_inverse_warped_image:
return '--output [ %s, %s, %s ]' % (
self.inputs.output_transform_prefix,
self.inputs.output_warped_image,
self.inputs.output_inverse_warped_image)
elif isdefined(self.inputs.output_warped_image
) and self.inputs.output_warped_image:
return '--output [ %s, %s ]' % (
self.inputs.output_transform_prefix,
self.inputs.output_warped_image)
else:
return '--output %s' % self.inputs.output_transform_prefix
return super(Registration, self)._format_arg(opt, spec, val)
def _formatRegistration(self):
retval = []
for ii in range(len(self.inputs.transforms)):
retval.append('--transform %s' % (self._formatTransform(ii)))
for metric in self._formatMetric(ii):
retval.append('--metric %s' % metric)
retval.append('--convergence %s' % self._formatConvergence(ii))
if isdefined(self.inputs.sigma_units):
retval.append('--smoothing-sigmas %s%s' %
(self._antsJoinList(self.inputs.smoothing_sigmas[
ii]),
self.inputs.sigma_units[ii]))
else:
retval.append('--smoothing-sigmas %s' %
self._antsJoinList(self.inputs.smoothing_sigmas[ii]))
retval.append('--shrink-factors %s' %
self._antsJoinList(self.inputs.shrink_factors[ii]))
if isdefined(self.inputs.use_estimate_learning_rate_once):
retval.append('--use-estimate-learning-rate-once %d' %
self.inputs.use_estimate_learning_rate_once[ii])
if isdefined(self.inputs.use_histogram_matching):
# use_histogram_matching is either a common flag for all transforms
# or a list of transform-specific flags
if isinstance(self.inputs.use_histogram_matching, bool):
histval = self.inputs.use_histogram_matching
else:
histval = self.inputs.use_histogram_matching[ii]
retval.append('--use-histogram-matching %d' % histval)
return " ".join(retval)
def _get_sorteddict(self, object, dictwithhash=False, hash_method=None, hash_files=True):
if isinstance(object, dict):
out = {}
for key, val in sorted(object.items()):
if isdefined(val):
out[key] = self._get_sorteddict(val, dictwithhash, hash_method=hash_method, hash_files=hash_files)
elif isinstance(object, (list, tuple)):
out = []
for val in object:
if isdefined(val):
out.append(self._get_sorteddict(val, dictwithhash, hash_method=hash_method, hash_files=hash_files))
if isinstance(object, tuple):
out = tuple(out)
else:
if isdefined(object):
if hash_files and isinstance(object, str) and os.path.isfile(object):
if hash_method == None:
hash_method = config.get("execution", "hash_method")
if hash_method.lower() == "timestamp":
hash = hash_timestamp(object)
elif hash_method.lower() == "content":
hash = hash_infile(object)
else:
raise Exception("Unknown hash method: %s" % hash_method)
if dictwithhash:
out = (object, hash)
else:
out = hash
elif isinstance(object, float):
out = "%.10f" % object
else:
out = object
return out
def _format_arg(self, opt, spec, val):
if opt == 'moving_image_mask':
return '--masks [ %s, %s ]' % (self.inputs.fixed_image_mask,
self.inputs.moving_image_mask)
elif opt == 'transforms':
return self._formatRegistration()
elif opt == 'initial_moving_transform':
if self.inputs.invert_initial_moving_transform:
return '--initial-moving-transform [ %s, 1 ]' % self.inputs.initial_moving_transform
else:
return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
elif opt == 'interpolation':
# TODO: handle multilabel, gaussian, and bspline options
return '--interpolation %s' % self.inputs.interpolation
elif opt == 'output_transform_prefix':
if isdefined(self.inputs.output_inverse_warped_image
) and self.inputs.output_inverse_warped_image:
return '--output [ %s, %s, %s ]' % (
self.inputs.output_transform_prefix,
self.inputs.output_warped_image,
self.inputs.output_inverse_warped_image)
elif isdefined(self.inputs.output_warped_image
) and self.inputs.output_warped_image:
return '--output [ %s, %s ]' % (
self.inputs.output_transform_prefix,
self.inputs.output_warped_image)
else:
return '--output %s' % self.inputs.output_transform_prefix
elif opt == 'winsorize_upper_quantile' or opt == 'winsorize_lower_quantile':
if not self._quantilesDone:
return self._formatWinsorizeImageIntensities()
return '' # Must return something for argstr!
elif opt == 'collapse_linear_transforms_to_fixed_image_header':
return self._formatCollapseLinearTransformsToFixedImageHeader()
return super(Registration, self)._format_arg(opt, spec, val)
def _list_outputs(self):
outputs = self._outputs().get()
outputs["forward_transforms"] = []
outputs["forward_invert_flags"] = []
outputs["reverse_transforms"] = []
outputs["reverse_invert_flags"] = []
if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
outputs["forward_transforms"].append(self.inputs.initial_moving_transform)
outputs["forward_invert_flags"].append(self.inputs.invert_initial_moving_transform)
outputs["reverse_transforms"].insert(0, self.inputs.initial_moving_transform)
outputs["reverse_invert_flags"].insert(0, not self.inputs.invert_initial_moving_transform) # Prepend
transformCount += 1
elif isdefined(self.inputs.initial_moving_transform_com):
# forwardFileName, _ = self._outputFileNames(self.inputs.output_transform_prefix,
# transformCount,
# 'Initial')
# outputs['forward_transforms'].append(forwardFileName)
transformCount += 1
for count in range(len(self.inputs.transforms)):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount, self.inputs.transforms[count]
)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount, self.inputs.transforms[count], True
)
outputs["forward_transforms"].append(os.path.abspath(forwardFileName))
outputs["forward_invert_flags"].append(forwardInverseMode)
outputs["reverse_transforms"].insert(0, os.path.abspath(reverseFileName))
outputs["reverse_invert_flags"].insert(0, reverseInverseMode)
transformCount += 1
else:
transformCount = 0
for transform in ["GenericAffine", "SyN"]: # Only files returned by collapse_output_transforms
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount, transform
)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount, transform, True
)
outputs["forward_transforms"].append(os.path.abspath(forwardFileName))
outputs["forward_invert_flags"].append(forwardInverseMode)
outputs["reverse_transforms"].append(os.path.abspath(reverseFileName))
outputs["reverse_invert_flags"].append(reverseInverseMode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + "Composite.h5"
outputs["composite_transform"] = [os.path.abspath(fileName)]
fileName = self.inputs.output_transform_prefix + "InverseComposite.h5"
outputs["inverse_composite_transform"] = [os.path.abspath(fileName)]
out_filename = self._get_outputfilenames(inverse=False)
inv_out_filename = self._get_outputfilenames(inverse=True)
if out_filename:
outputs["warped_image"] = os.path.abspath(out_filename)
if inv_out_filename:
outputs["inverse_warped_image"] = os.path.abspath(inv_out_filename)
return outputs
def _format_arg(self, name, spec, value):
if name == 'use_histogram_matching':
if isdefined(self.inputs.use_histogram_matching):
return spec.argstr % {False: '0', True: '1'}[value]
elif name == 'precision_type':
if isdefined(self.inputs.precision_type):
return spec.argstr % {'float': 'f', 'double': 'd'}[value]
return super(RegistrationSynQuick, self)._format_arg(name, spec, value)
def _parse_stdout(self, stdout):
import re
import os
files = []
reoriented_files = []
reoriented_and_cropped_files = []
bvecs = []
bvals = []
skip = False
last_added_file = None
for line in stdout.split("\n"):
if not skip:
file = None
if line.startswith("Saving "):
file = line[len("Saving "):]
elif line.startswith("GZip..."):
#for gzipped outpus files are not absolute
if isdefined(self.inputs.output_dir):
output_dir = self.inputs.output_dir
else:
output_dir = self._gen_filename('output_dir')
file = os.path.abspath(os.path.join(output_dir,
line[len("GZip..."):]))
elif line.startswith("Number of diffusion directions "):
if last_added_file:
base, filename, ext = split_filename(last_added_file)
bvecs.append(os.path.join(base,filename + ".bvec"))
bvals.append(os.path.join(base,filename + ".bval"))
elif re.search('.*->(.*)', line):
val = re.search('.*->(.*)', line)
val = val.groups()[0]
if isdefined(self.inputs.output_dir):
output_dir = self.inputs.output_dir
else:
output_dir = self._gen_filename('output_dir')
val = os.path.join(output_dir, val)
file = val
if file:
if last_added_file and os.path.exists(file) and not last_added_file in file:
files.append(file)
last_added_file = file
continue
if line.startswith("Reorienting as "):
reoriented_files.append(line[len("Reorienting as "):])
skip = True
continue
elif line.startswith("Cropping NIfTI/Analyze image "):
base, filename = os.path.split(line[len("Cropping NIfTI/Analyze image "):])
filename = "c" + filename
reoriented_and_cropped_files.append(os.path.join(base, filename))
skip = True
continue
skip = False
return files, reoriented_files, reoriented_and_cropped_files, bvecs, bvals
def _check_xor(self, spec, name, value):
""" check if mutually exclusive inputs are satisfied
"""
if spec.xor:
values = [isdefined(getattr(self.inputs, field)) for field in spec.xor]
if not any(values) and not isdefined(value):
msg = "%s requires a value for one of the inputs '%s'. " \
"For a list of required inputs, see %s.help()" % \
(self.__class__.__name__, ', '.join(spec.xor),
self.__class__.__name__)
raise ValueError(msg)
def _check_requires(self, spec, name, value):
""" check if required inputs are satisfied
"""
if spec.requires:
values = [not isdefined(getattr(self.inputs, field)) for field in spec.requires]
if any(values) and isdefined(value):
msg = "%s requires a value for input '%s' because one of %s is set. " \
"For a list of required inputs, see %s.help()" % \
(self.__class__.__name__, name,
', '.join(spec.requires), self.__class__.__name__)
raise ValueError(msg)
def _formatMetric(self, index):
"""
Format the antsRegistration -m metric argument(s).
Parameters
----------
index: the stage index
"""
# The common fixed image.
fixed = self.inputs.fixed_image[0]
# The common moving image.
moving = self.inputs.moving_image[0]
# The metric name input for the current stage.
name_input = self.inputs.metric[index]
# The stage-specific input dictionary.
stage_inputs = dict(
metric=name_input,
weight=self.inputs.metric_weight[index],
radius_or_bins=self.inputs.radius_or_number_of_bins[index],
optional=self.inputs.radius_or_number_of_bins[index])
# The optional sampling strategy and percentage.
if (isdefined(self.inputs.sampling_strategy)
and self.inputs.sampling_strategy):
sampling_strategy = self.inputs.sampling_strategy[index]
if sampling_strategy:
stage_inputs['sampling_strategy'] = sampling_strategy
sampling_percentage = self.inputs.sampling_percentage
if (isdefined(self.inputs.sampling_percentage)
and self.inputs.sampling_percentage):
sampling_percentage = self.inputs.sampling_percentage[index]
if sampling_percentage:
stage_inputs['sampling_percentage'] = sampling_percentage
# Make a list of metric specifications, one per -m command line
# argument for the current stage.
# If there are multiple inputs for this stage, then convert the
# dictionary of list inputs into a list of metric specifications.
# Otherwise, make a singleton list of the metric specification
# from the non-list inputs.
if isinstance(name_input, list):
items = stage_inputs.items()
indexes = range(0, len(name_input))
# dict-comprehension only works with python 2.7 and up
# specs = [{k: v[i] for k, v in items} for i in indexes]
specs = [dict([(k, v[i]) for k, v in items]) for i in indexes]
else:
specs = [stage_inputs]
# Format the --metric command line metric arguments, one per
# specification.
return [
self._formatMetricArgument(fixed, moving, **spec) for spec in specs
]
def _formatRegistration(self):
retval = []
for ii in range(len(self.inputs.transforms)):
retval.append('--transform %s' % (self._formatTransform(ii)))
retval.append('--metric %s' % self._formatMetric(ii))
retval.append('--convergence %s' % self._formatConvergence(ii))
retval.append('--smoothing-sigmas %s' % self._antsJoinList(self.inputs.smoothing_sigmas[ii]))
retval.append('--shrink-factors %s' % self._antsJoinList(self.inputs.shrink_factors[ii]))
if isdefined(self.inputs.use_estimate_learning_rate_once):
retval.append('--use-estimate-learning-rate-once %d' % self.inputs.use_estimate_learning_rate_once[ii])
if isdefined(self.inputs.use_histogram_matching):
retval.append('--use-histogram-matching %d' % self.inputs.use_histogram_matching[ii])
return " ".join(retval)
def _formatMetric(self, index):
"""
Format the antsRegistration -m metric argument(s).
Parameters
----------
index: the stage index
"""
# The common fixed image.
fixed = self.inputs.fixed_image[0]
# The common moving image.
moving = self.inputs.moving_image[0]
# The metric name input for the current stage.
name_input = self.inputs.metric[index]
# The stage-specific input dictionary.
stage_inputs = dict(
metric=name_input,
weight=self.inputs.metric_weight[index],
radius_or_bins=self.inputs.radius_or_number_of_bins[index],
optional=self.inputs.radius_or_number_of_bins[index]
)
# The optional sampling strategy and percentage.
if (isdefined(self.inputs.sampling_strategy) and self.inputs.sampling_strategy):
sampling_strategy = self.inputs.sampling_strategy[index]
if sampling_strategy:
stage_inputs['sampling_strategy'] = sampling_strategy
sampling_percentage = self.inputs.sampling_percentage
if (isdefined(self.inputs.sampling_percentage) and self.inputs.sampling_percentage):
sampling_percentage = self.inputs.sampling_percentage[index]
if sampling_percentage:
stage_inputs['sampling_percentage'] = sampling_percentage
# Make a list of metric specifications, one per -m command line
# argument for the current stage.
# If there are multiple inputs for this stage, then convert the
# dictionary of list inputs into a list of metric specifications.
# Otherwise, make a singleton list of the metric specification
# from the non-list inputs.
if isinstance(name_input, list):
items = stage_inputs.items()
indexes = range(0, len(name_input))
# dict-comprehension only works with python 2.7 and up
#specs = [{k: v[i] for k, v in items} for i in indexes]
specs = [dict([(k, v[i]) for k, v in items]) for i in indexes]
else:
specs = [stage_inputs]
# Format the --metric command line metric arguments, one per
# specification.
return [self._formatMetricArgument(fixed, moving, **spec) for spec in specs]
def _list_outputs(self):
outputs = self.output_spec().get()
if isdefined(self.inputs.trained_wts_filestem):
outputs['trained_wts_file'] = os.path.abspath(self.inputs.trained_wts_filestem + '.RData')
else:
outputs['trained_wts_file'] = os.path.abspath('trained_wts_file.RData')
return outputs
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = op.abspath(self.inputs.out_file)
if isdefined(self.inputs.out_sf):
outputs['out_sf'] = op.abspath(self.inputs.out_sf)
return outputs
def _xor_warn(self, obj, name, old, new):
""" Generates warnings for xor traits
"""
if isdefined(new):
trait_spec = self.traits()[name]
# for each xor, set to default_value
for trait_name in trait_spec.xor:
if trait_name == name:
# skip ourself
continue
if isdefined(getattr(self, trait_name)):
self.trait_set(trait_change_notify=False, **{'%s' % name: Undefined})
msg = 'Input "%s" is mutually exclusive with input "%s", ' \
'which is already set' \
% (name, trait_name)
raise IOError(msg)
def _check_mandatory_inputs(self):
""" Raises an exception if a mandatory input is Undefined
"""
for name, spec in self.inputs.traits(mandatory=True).items():
value = getattr(self.inputs, name)
self._check_xor(spec, name, value)
if not isdefined(value) and spec.xor is None:
msg = "%s requires a value for input '%s'. " \
"For a list of required inputs, see %s.help()" % \
(self.__class__.__name__, name, self.__class__.__name__)
raise ValueError(msg)
if isdefined(value):
self._check_requires(spec, name, value)
for name, spec in self.inputs.traits(mandatory=None,
transient=None).items():
self._check_requires(spec, name, getattr(self.inputs, name))
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = op.abspath(self.inputs.out_file)
if isdefined(self.inputs.out_sf):
outputs['out_sf'] = op.abspath(self.inputs.out_sf)
return outputs
def get_hashval(self, hash_method=None):
"""Return a dictionary of our items with hashes for each file.
Searches through dictionary items and if an item is a file, it
calculates the md5 hash of the file contents and stores the
file name and hash value as the new key value.
However, the overall bunch hash is calculated only on the hash
value of a file. The path and name of the file are not used in
the overall hash calculation.
Returns
-------
dict_withhash : dict
Copy of our dictionary with the new file hashes included
with each file.
hashvalue : str
The md5 hash value of the traited spec
"""
dict_withhash = {}
dict_nofilename = {}
for name, val in sorted(self.get().items()):
if isdefined(val):
trait = self.trait(name)
hash_files = not has_metadata(trait.trait_type, "hash_files", False)
dict_nofilename[name] = self._get_sorteddict(val, hash_method=hash_method, hash_files=hash_files)
dict_withhash[name] = self._get_sorteddict(val, True, hash_method=hash_method, hash_files=hash_files)
return (dict_withhash, md5(str(dict_nofilename)).hexdigest())
def run(self, **inputs):
"""Execute this interface.
This interface will not raise an exception if runtime.returncode is
non-zero.
Parameters
----------
inputs : allows the interface settings to be updated
Returns
-------
results : an InterfaceResult object containing a copy of the instance
that was executed, provenance information and, if successful, results
"""
self.inputs.set(**inputs)
self._check_mandatory_inputs()
interface = self.__class__
# initialize provenance tracking
env = deepcopy(os.environ.data)
runtime = Bunch(cwd=os.getcwd(),
returncode=None,
duration=None,
environ=env,
hostname=gethostname())
t = time()
try:
runtime = self._run_interface(runtime)
runtime.duration = time() - t
results = InterfaceResult(interface, runtime,
inputs=self.inputs.get_traitsfree())
results.outputs = self.aggregate_outputs(results.runtime)
except Exception, e:
if len(e.args) == 0:
e.args = ("")
message = "\nInterface %s failed to run." % self.__class__.__name__
if config.has_option('logging', 'interface_level') and config.get('logging', 'interface_level').lower() == 'debug':
inputs_str = "Inputs:" + str(self.inputs) + "\n"
else:
inputs_str = ''
if len(e.args) == 1 and isinstance(e.args[0], str):
e.args = (e.args[0] + " ".join([message, inputs_str]),)
else:
e.args += (message, )
if inputs_str != '':
e.args += (inputs_str, )
#exception raising inhibition for special cases
if hasattr(self.inputs, 'ignore_exception') and \
isdefined(self.inputs.ignore_exception) and \
self.inputs.ignore_exception:
import traceback
runtime.traceback = traceback.format_exc()
runtime.traceback_args = e.args
return InterfaceResult(interface, runtime)
else:
raise
def _list_outputs(self):
outputs = self.output_spec().get()
if isdefined(self.inputs.output_directory):
outputs['output_directory'] = Directory(exists=False, value=self.inputs.output_directory)
else:
outputs['output_directory'] = Directory(exists=False, value='accuracy_test')
return outputs
def _list_outputs(self):
outputs = self._outputs().get()
outputs['forward_transforms'] = []
outputs['forward_invert_flags'] = []
outputs['reverse_transforms'] = []
outputs['reverse_invert_flags'] = []
if not self.inputs.collapse_output_transforms:
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
self.inputs.invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(
0,
not self.inputs.invert_initial_moving_transform) # Prepend
transformCount = 1
for count in range(self._numberOfOutputTransforms):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count])
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].insert(
0, reverseInverseMode)
transformCount += 1
else:
transformCount = 0
for transform in [
'GenericAffine', 'SyN'
]: # Only files returned by collapse_output_transforms
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
transform)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
transform, True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].append(
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].append(reverseInverseMode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = [os.path.abspath(fileName)]
fileName = self.inputs.output_transform_prefix + \
'InverseComposite.h5'
outputs['inverse_composite_transform'] = [
os.path.abspath(fileName)
]
return outputs
def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True):
"""Manipulates path and name of input filename
Parameters
----------
fname : string
A filename (may or may not include path)
prefix : string
Characters to prepend to the filename
suffix : string
Characters to append to the filename
newpath : string
Path to replace the path of the input fname
use_ext : boolean
If True (default), appends the extension of the original file
to the output name.
Returns
-------
Absolute path of the modified filename
>>> from nipype.utils.filemanip import fname_presuffix
>>> fname = 'foo.nii.gz'
>>> fname_presuffix(fname,'pre','post','/tmp')
'/tmp/prefoopost.nii.gz'
"""
pth, fname, ext = split_filename(fname)
if not use_ext:
ext = ''
if newpath and isdefined(newpath):
pth = os.path.abspath(newpath)
return os.path.join(pth, prefix+fname+suffix+ext)
def _list_outputs(self):
outputs = self.output_spec().get()
if isdefined(self.inputs.output_directory):
outputs['output_directory'] = Directory(exists=False, value=self.inputs.output_directory)
else:
outputs['output_directory'] = Directory(exists=False, value='accuracy_test')
return outputs
def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True):
"""Manipulates path and name of input filename
Parameters
----------
fname : string
A filename (may or may not include path)
prefix : string
Characters to prepend to the filename
suffix : string
Characters to append to the filename
newpath : string
Path to replace the path of the input fname
use_ext : boolean
If True (default), appends the extension of the original file
to the output name.
Returns
-------
Absolute path of the modified filename
>>> from nipype.utils.filemanip import fname_presuffix
>>> fname = 'foo.nii.gz'
>>> fname_presuffix(fname,'pre','post','/tmp')
'/tmp/prefoopost.nii.gz'
"""
pth, fname, ext = split_filename(fname)
if not use_ext:
ext = ''
if newpath and isdefined(newpath):
pth = os.path.abspath(newpath)
return os.path.join(pth, prefix + fname + suffix + ext)
def _list_outputs(self):
outputs = self.output_spec().get()
if isdefined(self.inputs.trained_wts_filestem):
outputs['trained_wts_file'] = os.path.abspath(self.inputs.trained_wts_filestem + '.RData')
else:
outputs['trained_wts_file'] = os.path.abspath('trained_wts_file.RData')
return outputs
def _list_outputs(self):
outputs = self._outputs().get()
transformCount = 0
outputs['forward_transforms'] = []
outputs['forward_invert_flags'] = []
outputs['reverse_transforms'] = []
outputs['reverse_invert_flags'] = []
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(self.inputs.invert_initial_moving_transform)
outputs['reverse_transforms'].insert(0,self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(0,not self.inputs.invert_initial_moving_transform) ## Prepend
transformCount += 1
for count in range(self.numberOfTransforms):
forward_fileName, forward_inverse_mode = self._outputFileNames(self.inputs.output_transform_prefix,
transformCount,
self.inputs.transforms[count],False)
reverse_fileName, reverse_inverse_mode = self._outputFileNames(self.inputs.output_transform_prefix,
transformCount,
self.inputs.transforms[count],True)
outputs['forward_transforms'].append(os.path.abspath(forward_fileName))
outputs['forward_invert_flags'].append(forward_inverse_mode)
outputs['reverse_transforms'].insert(0,os.path.abspath(reverse_fileName))
outputs['reverse_invert_flags'].insert(0,reverse_inverse_mode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = [os.path.abspath(fileName)]
fileName = self.inputs.output_transform_prefix + 'InverseComposite.h5'
outputs['inverse_composite_transform'] = [os.path.abspath(fileName)]
return outputs
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['tract_image'] = self.inputs.out_filename
if not isdefined(outputs['tract_image']):
outputs['tract_image'] = op.abspath(self._gen_outfilename())
else:
outputs['tract_image'] = os.path.abspath(outputs['tract_image'])
return outputs
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['tract_image'] = self.inputs.out_filename
if not isdefined(outputs['tract_image']):
outputs['tract_image'] = op.abspath(self._gen_outfilename())
else:
outputs['tract_image'] = os.path.abspath(outputs['tract_image'])
return outputs
def _list_outputs(self):
outputs = self.output_spec().get()
for k in outputs.keys():
if isdefined(getattr(self.inputs, k)):
outputs[k] = op.abspath(getattr(self.inputs, k))
return outputs
def _formatRegistration(self):
retval = []
for ii in range(len(self.inputs.transforms)):
retval.append('--transform %s' % (self._formatTransform(ii)))
retval.append('--metric %s' % self._formatMetric(ii))
retval.append('--convergence %s' % self._formatConvergence(ii))
retval.append('--smoothing-sigmas %s' %
self._antsJoinList(self.inputs.smoothing_sigmas[ii]))
retval.append('--shrink-factors %s' %
self._antsJoinList(self.inputs.shrink_factors[ii]))
if isdefined(self.inputs.use_estimate_learning_rate_once):
retval.append('--use-estimate-learning-rate-once %d' %
self.inputs.use_estimate_learning_rate_once[ii])
if isdefined(self.inputs.use_histogram_matching):
retval.append('--use-histogram-matching %d' %
self.inputs.use_histogram_matching[ii])
return " ".join(retval)
def _get_outputfilenames(self, inverse=False):
output_filename = None
if not inverse:
if isdefined(self.inputs.output_warped_image) and self.inputs.output_warped_image:
output_filename = self.inputs.output_warped_image
if isinstance(output_filename, bool):
output_filename = "%s_Warped.nii.gz" % self.inputs.output_transform_prefix
else:
output_filename = output_filename
return output_filename
inv_output_filename = None
if isdefined(self.inputs.output_inverse_warped_image) and self.inputs.output_inverse_warped_image:
inv_output_filename = self.inputs.output_inverse_warped_image
if isinstance(inv_output_filename, bool):
inv_output_filename = "%s_InverseWarped.nii.gz" % self.inputs.output_transform_prefix
else:
inv_output_filename = inv_output_filename
return inv_output_filename
def _optionalMetricParameters(self, index):
if (len(self.inputs.sampling_strategy) > index) and (self.inputs.sampling_strategy[index] is not None):
if self.inputs.sampling_strategy[index] == "Dense":
return '' # The default when nothing is specified
if isdefined(self.inputs.sampling_percentage) and (self.inputs.sampling_percentage is not None):
return ',%s,%g' % (self.inputs.sampling_strategy[index], self.inputs.sampling_percentage[index])
else:
return ',%s' % self.inputs.sampling_strategy[index]
return ''
def _parse_inputs(self, skip=None):
if skip is None:
skip = []
try:
if (isdefined(self.inputs.grad_file) or
isdefined(self.inputs.grad_fsl)):
skip += ['in_bvec', 'in_bval']
is_bvec = isdefined(self.inputs.in_bvec)
is_bval = isdefined(self.inputs.in_bval)
if is_bvec or is_bval:
if not is_bvec or not is_bval:
raise RuntimeError('If using bvecs and bvals inputs, both'
'should be defined')
skip += ['in_bval']
except AttributeError:
pass
return super(MRTrix3Base, self)._parse_inputs(skip=skip)
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
include_regexes = dcmstack.default_key_incl_res
if isdefined(self.inputs.include_regexes):
include_regexes += self.inputs.include_regexes
exclude_regexes = dcmstack.default_key_excl_res
if isdefined(self.inputs.exclude_regexes):
exclude_regexes += self.inputs.exclude_regexes
meta_filter = dcmstack.make_key_regex_filter(exclude_regexes, include_regexes)
stack = dcmstack.DicomStack(meta_filter=meta_filter)
for src_path in src_paths:
src_dcm = dicom.read_file(src_path, force=True)
stack.add_dcm(src_dcm)
nii = stack.to_nifti(embed_meta=True)
nw = NiftiWrapper(nii)
self.out_path = self._get_out_path(nw.meta_ext.get_class_dict(("global", "const")))
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nii, self.out_path)
return runtime
def _run_interface(self, runtime):
if isdefined(self.inputs.pattern_file):
from pylab import imread
pattern = imread(self.inputs.pattern_file)[:, :, 0:1]
pattern *= self.inputs.SNR
else:
pattern = self._gen_pattern()
noisy_sequence = self._gen_noisy_sequence(pattern)
nim_tmap = nifti.Nifti1Image(noisy_sequence, np.diag([1, 1, 1, 1]))
nifti.save(nim_tmap, "simulated_sequence.nii")
return runtime
def _parse_inputs(self, skip=None):
if skip is None:
skip = []
try:
if (isdefined(self.inputs.grad_file)
or isdefined(self.inputs.grad_fsl)):
skip += ['in_bvec', 'in_bval']
is_bvec = isdefined(self.inputs.in_bvec)
is_bval = isdefined(self.inputs.in_bval)
if is_bvec or is_bval:
if not is_bvec or not is_bval:
raise RuntimeError('If using bvecs and bvals inputs, both'
'should be defined')
skip += ['in_bval']
except AttributeError:
pass
return super(MRTrix3Base, self)._parse_inputs(skip=skip)
def _run_interface(self, runtime):
if isdefined(self.inputs.pattern_file):
from pylab import imread
pattern = imread(self.inputs.pattern_file)[:, :, 0:1]
pattern *= self.inputs.SNR
else:
pattern = self._gen_pattern()
noisy_sequence = self._gen_noisy_sequence(pattern)
nim_tmap = nifti.Nifti1Image(noisy_sequence, np.diag([1, 1, 1, 1]))
nifti.save(nim_tmap, "simulated_sequence.nii")
return runtime
def _get_outputfilenames(self, inverse=False):
output_filename = None
if not inverse:
if isdefined(self.inputs.output_warped_image) and \
self.inputs.output_warped_image:
output_filename = self.inputs.output_warped_image
if isinstance(output_filename, bool):
output_filename = '%s_Warped.nii.gz' % self.inputs.output_transform_prefix
else:
output_filename = output_filename
return output_filename
inv_output_filename = None
if isdefined(self.inputs.output_inverse_warped_image) and \
self.inputs.output_inverse_warped_image:
inv_output_filename = self.inputs.output_inverse_warped_image
if isinstance(inv_output_filename, bool):
inv_output_filename = '%s_InverseWarped.nii.gz' % self.inputs.output_transform_prefix
else:
inv_output_filename = inv_output_filename
return inv_output_filename
def _requires_warn(self, obj, name, old, new):
"""Part of the xor behavior
"""
if new:
trait_spec = self.traits()[name]
msg = None
for trait_name in trait_spec.requires:
if not isdefined(getattr(self, trait_name)):
if not msg:
msg = "Input %s requires inputs: %s" % (name, ", ".join(trait_spec.requires))
if msg:
warn(msg)
def _optionalMetricParameters(self, index):
if (len(self.inputs.sampling_strategy) >
index) and (self.inputs.sampling_strategy[index] is not None):
if self.inputs.sampling_strategy[index] == "Dense":
return '' # The default when nothing is specified
if isdefined(self.inputs.sampling_percentage) and (
self.inputs.sampling_percentage is not None):
return ',%s,%g' % (self.inputs.sampling_strategy[index],
self.inputs.sampling_percentage[index])
else:
return ',%s' % self.inputs.sampling_strategy[index]
return ''
def _format_arg(self, opt, spec, val):
if opt == 'moving_image_mask':
return '--masks [ %s, %s ]' % (self.inputs.fixed_image_mask, self.inputs.moving_image_mask)
elif opt == 'transforms':
self.numberOfTransforms = len(self.inputs.transforms)
return self._formatRegistration()
elif opt == 'initial_moving_transform':
if self.inputs.invert_initial_moving_transform:
return '--initial-moving-transform [ %s, 1 ]' % self.inputs.initial_moving_transform
else:
return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
elif opt == 'interpolation':
# TODO: handle multilabel, gaussian, and bspline options
return '--interpolation %s' % self.inputs.interpolation
elif opt == 'output_transform_prefix':
if isdefined(self.inputs.output_inverse_warped_image) and self.inputs.output_inverse_warped_image:
return '--output [ %s, %s, %s ]' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image, self.inputs.output_inverse_warped_image )
elif isdefined(self.inputs.output_warped_image) and self.inputs.output_warped_image:
return '--output [ %s, %s ]' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image )
else:
return '--output %s' % self.inputs.output_transform_prefix
return super(Registration, self)._format_arg(opt, spec, val)
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
include_regexes = dcmstack.default_key_incl_res
if isdefined(self.inputs.include_regexes):
include_regexes += self.inputs.include_regexes
exclude_regexes = dcmstack.default_key_excl_res
if isdefined(self.inputs.exclude_regexes):
exclude_regexes += self.inputs.exclude_regexes
meta_filter = dcmstack.make_key_regex_filter(exclude_regexes,
include_regexes)
stack = dcmstack.DicomStack(meta_filter=meta_filter)
for src_path in src_paths:
src_dcm = dicom.read_file(src_path, force=True)
stack.add_dcm(src_dcm)
nii = stack.to_nifti(embed_meta=True)
nw = NiftiWrapper(nii)
self.out_path = \
self._get_out_path(nw.meta_ext.get_class_dict(('global', 'const')))
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nii, self.out_path)
return runtime
def _list_outputs(self):
outputs = self._outputs().get()
outputs['forward_transforms'] = []
outputs['forward_invert_flags'] = []
outputs['reverse_transforms'] = []
outputs['reverse_invert_flags'] = []
if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
self.inputs.invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(0, not self.inputs.invert_initial_moving_transform) # Prepend
transformCount += 1
for count in range(len(self.inputs.transforms)):
forwardFileName, forwardInverseMode = self._outputFileNames(self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count])
reverseFileName, reverseInverseMode = self._outputFileNames(self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs[
'reverse_invert_flags'].insert(0, reverseInverseMode)
transformCount += 1
else:
transformCount = 0
for transform in ['GenericAffine', 'SyN']: # Only files returned by collapse_output_transforms
forwardFileName, forwardInverseMode = self._outputFileNames(self.inputs.output_transform_prefix, transformCount, transform)
reverseFileName, reverseInverseMode = self._outputFileNames(self.inputs.output_transform_prefix, transformCount, transform, True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].append(
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].append(reverseInverseMode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = [os.path.abspath(fileName)]
fileName = self.inputs.output_transform_prefix + \
'InverseComposite.h5'
outputs['inverse_composite_transform'] = [
os.path.abspath(fileName)]
return outputs
def _format_arg(self, opt, spec, val):
if opt == 'fixed_image_mask':
if isdefined(self.inputs.moving_image_mask):
return '--masks [ %s, %s ]' % (self.inputs.fixed_image_mask,
self.inputs.moving_image_mask)
else:
return '--masks %s' % self.inputs.fixed_image_mask
elif opt == 'transforms':
return self._formatRegistration()
elif opt == 'initial_moving_transform':
try:
doInvertTransform = int(
self.inputs.invert_initial_moving_transform)
except:
doInvertTransform = 0 # Just do the default behavior
return '--initial-moving-transform [ %s, %d ]' % (
self.inputs.initial_moving_transform, doInvertTransform)
elif opt == 'initial_moving_transform_com':
try:
doCenterOfMassInit = int(
self.inputs.initial_moving_transform_com)
except:
doCenterOfMassInit = 0 # Just do the default behavior
return '--initial-moving-transform [ %s, %s, %d ]' % (
self.inputs.fixed_image[0], self.inputs.moving_image[0],
doCenterOfMassInit)
elif opt == 'interpolation':
# TODO: handle multilabel, gaussian, and bspline options
return '--interpolation %s' % self.inputs.interpolation
elif opt == 'output_transform_prefix':
out_filename = self._get_outputfilenames(inverse=False)
inv_out_filename = self._get_outputfilenames(inverse=True)
if out_filename and inv_out_filename:
return '--output [ %s, %s, %s ]' % (
self.inputs.output_transform_prefix, out_filename,
inv_out_filename)
elif out_filename:
return '--output [ %s, %s ]' % (
self.inputs.output_transform_prefix, out_filename)
else:
return '--output %s' % self.inputs.output_transform_prefix
elif opt == 'winsorize_upper_quantile' or opt == 'winsorize_lower_quantile':
if not self._quantilesDone:
return self._formatWinsorizeImageIntensities()
return '' # Must return something for argstr!
# This feature was removed from recent versions of antsRegistration due to corrupt outputs.
# elif opt == 'collapse_linear_transforms_to_fixed_image_header':
# return self._formatCollapseLinearTransformsToFixedImageHeader()
return super(Registration, self)._format_arg(opt, spec, val)
def _parse_inputs(self, skip=None):
if skip is None:
skip = []
if not isdefined(self.inputs.in_config):
from distutils.spawn import find_executable
path = find_executable(self._cmd)
if path is None:
path = os.getenv(MRTRIX3_HOME, '/opt/mrtrix3')
else:
path = op.dirname(op.dirname(path))
self.inputs.in_config = op.join(
path, 'src/dwi/tractography/connectomics/'
'example_configs/fs_default.txt')
return super(LabelConfig, self)._parse_inputs(skip=skip)
def get_form(config,mwf):
from nipype.interfaces.traits_extension import isdefined
if not isdefined(mwf.html_view):
schema = colander.Schema()
all_traits = config.trait_names()
all_traits.remove('trait_added')
all_traits.remove('trait_modified')
for tr in all_traits:
_type = type(config.trait(tr).trait_type)
col_type = getNode(_type,tr,config)
schema.add(col_type)
form = Form(schema,buttons = ('submit',),action='')
return form.render(appstruct=config.get())
else:
form = Form(mwf.html_view(),buttons = ('submit',),action='')
return form.render()
def _list_outputs(self):
outputs = self._outputs().get()
transformCount = 0
outputs['forward_transforms'] = []
outputs['forward_invert_flags'] = []
outputs['reverse_transforms'] = []
outputs['reverse_invert_flags'] = []
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
self.inputs.invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(
0, not self.inputs.invert_initial_moving_transform) ## Prepend
transformCount += 1
for count in range(self.numberOfTransforms):
forward_fileName, forward_inverse_mode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], False)
reverse_fileName, reverse_inverse_mode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forward_fileName))
outputs['forward_invert_flags'].append(forward_inverse_mode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverse_fileName))
outputs['reverse_invert_flags'].insert(0, reverse_inverse_mode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = [os.path.abspath(fileName)]
fileName = self.inputs.output_transform_prefix + 'InverseComposite.h5'
outputs['inverse_composite_transform'] = [
os.path.abspath(fileName)
]
return outputs
def _run_interface(self, runtime):
phase_filename_list=self.inputs.phase
json_filename_list=self.inputs.json
truncate_echo=self.inputs.truncate_echo
if not truncate_echo:
truncate_echo=None
mask_filename=self.inputs.mask
freq_filename=self._list_outputs()['freq_filename']
if isdefined(self.inputs.weight):
weight_filename=self.inputs.weight
weight=nib.load(weight_filename).get_data()
else:
weight=None
ne=len(phase_filename_list)
ph_img_obj=nib.load(phase_filename_list[0])
shape=ph_img_obj.get_shape()
voxel_size=ph_img_obj.header['pixdim'][1:4]
ph_img=np.empty(shape+(ne,))
if weight is None:
weight=np.ones(shape+(ne,))
count=0
phase_filename_list.sort()
json_filename_list.sort()
te=np.empty(ne)
for imgloc,jsonloc in zip(phase_filename_list,json_filename_list):
#assert os.path.splitext(jsonloc)[0] in os.path.splitext(imgloc)[0]
ph_img[...,count]=nib.load(imgloc).get_data()
with open(jsonloc) as f:
te[count]=float(json.load(f)['EchoTime'])
count+=1
eps = np.sqrt(sys.float_info.min)
ph_img = ph_img + eps
mask=nib.load(mask_filename).get_data()
freq=pyQSM.frequencyEstimate.estimateFrequencyFromWrappedPhase(ph_img,voxel_size,te,mask,weight,truncateEcho=truncate_echo)
niftifile=nib.Nifti1Pair(freq,ph_img_obj.affine)
nib.save(niftifile,freq_filename)
return runtime
def _get_out_path(self, meta, idx=None):
'''Return the output path for the gernerated Nifti.'''
if self.inputs.out_format:
out_fmt = self.inputs.out_format
else:
#If no out_format is specified, use a sane default that will work
#with the provided meta data.
out_fmt = []
if not idx is None:
out_fmt.append('%03d' % idx)
if 'SeriesNumber' in meta:
out_fmt.append('%(SeriesNumber)03d')
if 'ProtocolName' in meta:
out_fmt.append('%(ProtocolName)s')
elif 'SeriesDescription' in meta:
out_fmt.append('%(SeriesDescription)s')
else:
out_fmt.append('sequence')
out_fmt = '-'.join(out_fmt)
out_fn = (out_fmt % meta) + self.inputs.out_ext
out_fn = sanitize_path_comp(out_fn)
out_path = os.getcwd()
if isdefined(self.inputs.out_path):
out_path = op.abspath(self.inputs.out_path)
# now, mkdir -p $out_path
try:
os.makedirs(out_path)
except OSError as exc: # Python >2.5
if exc.errno == errno.EEXIST and op.isdir(out_path):
pass
else:
raise
return op.join(out_path, out_fn)
class NiiWrangler(BaseInterface):
input_spec = NiiWranglerInputSpec
output_spec = NiiWranglerOutputSpec
def __init__(self, *args, **kwargs):
super(NiiWrangler, self).__init__(*args, **kwargs)
self.t1_files = []
self.rsfmri_files = []
self.dwi_files = []
self.dwi_ap_files = []
self.dwi_pa_files = []
self.flair_files = []
self.fieldmap_mag = []
self.fieldmap_ph = []
self.bval = []
self.bvec = []
self.ep_TR = None
self.fieldmap_mag_delta_te = "NONE"
self.t1_sample_spacing = 0.
self.ep_dwi_echo_spacings = None
self.ep_rsfmri_echo_spacings = None
self.ep_unwarp_dirs = None
def _run_interface(self, runtime):
import re
import operator
print "starting NII wrangler"
nii_files = self.inputs.nii_files
smap = self.inputs.series_map
dinfo = self.inputs.dicom_info
#block_averaging = self.inputs.block_struct_averaging
s_num_reg = re.compile(
".*s(\d+)a(?!.*/)"
) # sux to use filename. make more robust if needed.
nii_by_series = {}
fails = []
extras = []
for fn in nii_files:
try:
# we only want the first nii for each series
# TODO: find out what those others (A/B) are all about. fix this as needed.
sn = int(s_num_reg.match(fn).groups()[0])
if sn in nii_by_series:
extras.append(fn)
continue
nii_by_series[sn] = fn
except Exception, e:
fails.append(fn)
if fails:
raise ValueError(
"Could not derive series number from file names: %s." %
str(fails))
if extras:
print >> sys.stderr, "\nWARNING: Ignoring extra niftis: %s\n" % str(
extras)
# add nifti names to the dicts
m_count = 0
for sn, fn in nii_by_series.iteritems():
m = filter(lambda x: x.get("series_num", -1) == sn, dinfo)
if not m:
continue
m_count += 1
m[0]["nifti_file"] = fn
if not m_count == len(dinfo):
raise ValueError(
"incorrect number of nifti->series matches (%d/%d)" %
(m_count, len(dinfo)))
# time for some data wrangling
nf = "nifti_file"
sd = "series_desc"
it = "image_type"
t1fs = [
d for d in filter(
lambda x: sd in x and x[sd] in smap.get("t1", []), dinfo)
if nf in d
]
#if block_averaging:
# t1fs = [t1fs[0]]
# t2fs = [t2fs[0]]
self.t1_files = [d[nf] for d in t1fs]
#get rsfmri, if no "resting state return default file"
bs = [
d for d in filter(
lambda x: sd in x and x[sd] in smap.get("rsfmri", []), dinfo)
if nf in d
]
self.rsfmri_files = [d[nf] for d in bs]
#get dwi
dwi = [
d for d in filter(
lambda x: sd in x and x[sd] in smap.get("dwi", []), dinfo)
if nf in d
]
if len(dwi) == 0:
print "no DTI acquired"
self.dwi_files = ['nothing to proceed']
self.dwi_pa_files = ['nothing to proceed']
self.dwi_ap_files = ['nothing to proceed']
else:
self.dwi_files = [d[nf] for d in dwi]
dwi_pa = [
d for d in filter(
lambda x: sd in x and x[sd] in smap.get("fieldmap_pa", []),
dinfo) if nf in d
]
self.dwi_pa_files = [d[nf] for d in dwi_pa]
dwi_ap = [
d for d in filter(
lambda x: sd in x and x[sd] in smap.get("fieldmap_ap", []),
dinfo) if nf in d
]
self.dwi_ap_files = [d[nf] for d in dwi_ap]
flair = [
d for d in filter(
lambda x: sd in x and x[sd] in smap.get("flair", []), dinfo)
if nf in d
]
if len(flair) == 0:
print "no FLAIR acquired"
self.flair_files = ['nothing to proceed']
else:
self.flair_files = [d[nf] for d in flair]
# we have to do some extra looking at the headers for the mag and phase fieldmaps too
mag_fs = filter(lambda x: sd in x and x[sd] in smap.get(
"fieldmap_magnitude", []) and it in x and isinstance(x[it], list)
and len(x[it]) > 2 and x[it][2].strip().lower() == "m",
dinfo) # we want the 3rd field of image type to be 'm'
phase_fs = filter(
lambda x: sd in x and x[sd] in smap.get("fieldmap_phase", [
]) and it in x and isinstance(x[it], list) and len(x[
it]) > 2 and x[it][2].strip().lower() == "p",
dinfo) # we want the 3rd field of image type to be 'p'
self.fieldmap_mag = [d[nf] for d in mag_fs if nf in d]
self.fieldmap_ph = [d[nf] for d in phase_fs if nf in d]
# calculate echo spacing for rsfmri:
#if more than one resting state scan was acquired:
ep_rsfmri_echo_fail = False
ep_TR_fail = False
if len(bs) > 1:
print "two or more resting-state scans"
if isdefined(self.inputs.ep_rsfmri_echo_spacings):
self.ep_rsfmri_echo_spacings = [
self.inputs.ep_rsfmri_echo_spacings
for n in self.rsfmri_files
]
elif bs and any([
"bw_per_pix_phase_encode" in d and "acq_matrix_n" in d
for d in bs
]):
if not all([
"bw_per_pix_phase_encode" in d and "acq_matrix_n" in d
for d in bs
]):
ep_rsfmri_echo_fail = True
else:
self.ep_rsfmri_echo_spacings = [
1 / (d["bw_per_pix_phase_encode"] * d["acq_matrix_n"])
for d in bs
]
else:
self.ep_rsfmri_echo_spacings = [
"NONE" for n in self.rsfmri_files
]
if isdefined(self.inputs.ep_TR):
self.ep_TR = [self.inputs.ep_TR for n in self.rsfmri_files]
elif bs and any(["TR" in d for d in bs]):
if not all(["TR" in d for d in bs]):
ep_TR_fail = True
else:
self.ep_TR = [d["TR"] for d in bs]
else:
self.ep_TR = ["NONE" for n in self.rsfmri_files]
else:
print "one resting-state scan"
if isdefined(self.inputs.ep_rsfmri_echo_spacings):
self.ep_rsfmri_echo_spacings = self.inputs.ep_rsfmri_echo_spacings
elif bs and "bw_per_pix_phase_encode" in bs[
0] and "acq_matrix_n" in bs[0]:
if not "bw_per_pix_phase_encode" in bs[
0] and "acq_matrix_n" in bs[0]:
ep_rsfmri_echo_fail = True
else:
self.ep_rsfmri_echo_spacings = 1 / (
bs[0]["bw_per_pix_phase_encode"] *
bs[0]["acq_matrix_n"])
else:
self.ep_rsfmri_echo_spacings = "NONE"
if isdefined(self.inputs.ep_TR):
self.ep_TR = self.inputs.ep_TR
elif bs and "TR" in bs[0]:
if not "TR" in bs[0]:
ep_TR_fail = True
else:
self.ep_TR = bs[0]["TR"]
else:
self.ep_TR = "NONE"
ep_dwi_echo_fail = False
if len(dwi) > 1:
print "more than one dwi scan"
if isdefined(self.inputs.ep_dwi_echo_spacings):
self.ep_dwi_echo_spacings = [
self.inputs.ep_dwi_echo_spacings for n in self.dwi_files
]
elif bs and any([
"bw_per_pix_phase_encode" in d and "acq_matrix_n" in d
for d in dwi
]):
if not all([
"bw_per_pix_phase_encode" in d and "acq_matrix_n" in d
for d in dwi
]):
ep_dwi_echo_fail = True
else:
self.ep_dwi_echo_spacings = [
1 / (d["bw_per_pix_phase_encode"] * d["acq_matrix_n"])
for d in dwi
]
else:
self.ep_dwi_echo_spacings = ["NONE" for n in self.dwi_files]
else:
print "one dwi scan"
if isdefined(self.inputs.ep_dwi_echo_spacings):
self.ep_dwi_echo_spacings = self.inputs.ep_dwi_echo_spacings
elif bs and "bw_per_pix_phase_encode" in bs[
0] and "acq_matrix_n" in bs[0]:
if not "bw_per_pix_phase_encode" in bs[
0] and "acq_matrix_n" in bs[0]:
ep_dwi_echo_fail = True
else:
self.ep_dwi_echo_spacings = 1 / (
bs[0]["bw_per_pix_phase_encode"] *
bs[0]["acq_matrix_n"])
else:
self.ep_dwi_echo_spacings = "NONE"
# output delta te for magnitude fieldmap if available
if mag_fs and self.fieldmap_mag and self.fieldmap_ph:
self.fieldmap_mag_delta_te = mag_fs[0].get("delta_te", "NONE")
else:
self.fieldmap_mag_delta_te = "NONE"
# # a BOLD image by any other name...
# self.bold_names = ["bold_%d" % n for n in xrange(len(self.bolds))]
# # we'll derive the ep unwarp dir in the future... for now, just set it in config
if isdefined(self.inputs.ep_unwarp_dir):
self.ep_unwarp_dirs = [
self.inputs.ep_unwarp_dir for n in self.rsfmri_files
]
# if you have any polarity swapped series, apply that now
pswaps = smap.get("polarity_swapped", [])
if pswaps:
for b_idx, uw_dir in enumerate(self.ep_unwarp_dirs):
if bs[b_idx].get("series_desc", None) in pswaps:
raw_dir = uw_dir.replace("-", "")
self.ep_unwarp_dirs[
b_idx] = "-" + raw_dir if not "-" in uw_dir else raw_dir
else:
# fail. we can do better!
raise ValueError(
"We can't derive ep_unwarp_dir yet. Please set it in the nii wrangler config section."
)
### and let's do some sanity checking
# warn if you're going to ignore field or magnitude phase maps
if not (len(self.fieldmap_mag) and len(self.fieldmap_ph)):
print >> sys.stderr, "\nWARNING: found %d magnitude fieldmaps and %d phase fieldmaps.\n" % (
len(self.fieldmap_mag), len(self.fieldmap_ph))
### derive the derived values
# t1_sample_spacing
if t1fs and "RealDwellTime" in t1fs[0].keys():
self.t1_sample_spacing = t1fs[0]["RealDwellTime"] * math.pow(
10, -9)
else:
self.t1_sample_spacing = "NONE"
# don't continue if there was screwiness around calculating ep echo spacing
if ep_rsfmri_echo_fail:
raise ValueError(
"Unabel to calculate fmri ep echo spacing. Try specifying manually in nii wrangler config section."
)
if ep_dwi_echo_fail:
raise ValueError(
"Unabel to calculate dwi ep echo spacing. Try specifying manually in nii wrangler config section."
)
if ep_TR_fail:
raise ValueError(
"Unabel to derive TR. Try specifying manually in nii wrangler config section."
)
return runtime
class NiiWrangler(BaseInterface):
input_spec = NiiWranglerInputSpec
output_spec = NiiWranglerOutputSpec
def __init__(self, *args, **kwargs):
super(NiiWrangler, self).__init__(*args, **kwargs)
self.t1_files = []
self.t2_files = []
self.bolds = []
self.bold_names = []
self.sbrefs = []
self.fieldmap_pos = []
self.fieldmap_neg = []
self.fieldmap_mag = []
self.fieldmap_ph = []
self.fieldmap_mag_delta_te = "NONE"
self.t1_sample_spacing = 0.
self.t2_sample_spacing = 0.
self.ep_e_spaces = None
self.ep_unwarp_dirs = None
def _run_interface(self, runtime):
import re
import operator
nii_files = self.inputs.nii_files
smap = self.inputs.series_map
dinfo = self.inputs.dicom_info
block_averaging = self.inputs.block_struct_averaging
s_num_reg = re.compile(".*s(\d+)a(?!.*/)") # sux to use filename. make more robust if needed.
nii_by_series = {}
fails = []
extras = []
for fn in nii_files:
try:
# we only want the first nii for each series
# TODO: find out what those others (A/B) are all about. fix this as needed.
sn = int(s_num_reg.match(fn).groups()[0])
if sn in nii_by_series:
extras.append(fn)
continue
nii_by_series[sn] = fn
except Exception, e:
fails.append(fn)
if fails:
raise ValueError("Could not derive series number from file names: %s." % str(fails))
if extras:
print >> sys.stderr, "\nWARNING: Ignoring extra niftis: %s\n" % str(extras)
# add nifti names to the dicts
m_count = 0
for sn, fn in nii_by_series.iteritems():
m = filter(lambda x: x.get("series_num",-1) == sn, dinfo)
if not m:
continue
m_count += 1
m[0]["nifti_file"] = fn
if not m_count == len(dinfo):
raise ValueError("incorrect number of nifti->series matches (%d/%d)" % (m_count, len(dinfo)))
# time for some data wrangling
nf = "nifti_file"
sd = "series_desc"
it = "image_type"
t1fs = [d for d in filter(lambda x: sd in x and x[sd] in smap.get("t1",[]), dinfo) if nf in d]
t2fs = [d for d in filter(lambda x: sd in x and x[sd] in smap.get("t2",[]), dinfo) if nf in d]
if block_averaging:
t1fs = [t1fs[0]]
t2fs = [t2fs[0]]
self.t1_files = [d[nf] for d in t1fs]
self.t2_files = [d[nf] for d in t2fs]
bs = [d for d in filter(lambda x: sd in x and x[sd] in smap.get("bold",[]), dinfo) if nf in d]
self.bolds = [d[nf] for d in bs]
self.sbrefs = [d[nf] for d in filter(lambda x: sd in x and x[sd] in smap.get("bold_sbref",[]), dinfo) if nf in d]
# for now, we only support one se fieldmap pair. In the future, we'll implement
# a more flexible policy here. This is actually really crappy... but the user can always
# flip the unwarpdir through config :/
s_policy = self.inputs.ep_fieldmap_selection
pos_types = reduce(operator.add, [smap.get(k, []) for k in POS_FIELDMAPS])
neg_types = reduce(operator.add, [smap.get(k, []) for k in NEG_FIELDMAPS])
pos = [d for d in filter(lambda x: sd in x and x[sd] in pos_types, dinfo) if nf in d]
neg = [d for d in filter(lambda x: sd in x and x[sd] in neg_types, dinfo) if nf in d]
both = zip(pos,neg)
if s_policy == "most_recent":
pfs = []
nfs = []
for bold in bs:
sn = bold["series_num"]
# we want the last of the images with a lower sn, or the firs tof the images with a higher sn
earlier = filter(lambda x: x[0]["series_num"] < sn and x[1]["series_num"] < sn, both)
later = filter(lambda x: x[0]["series_num"] < sn and x[1]["series_num"] < sn, both)
if earlier:
pfs.append(earlier[-1][0][nf])
nfs.append(earlier[-1][1][nf])
elif later:
pfs.append(later[0][0][nf])
nfs.append(later[0][1][nf])
else:
print "This... should never happen."
self.fieldmaps_pos = pfs
self.fieldmaps_neg = nfs
else: # default to "first"
self.fieldmaps_pos = [pos[0][nf] for n in self.bolds] if pos else []
self.fieldmaps_neg = [neg[0][nf] for n in self.bolds] if pos else []
# we have to do some extra looking at the headers for the mag and phase fieldmaps too
mag_fs = filter(lambda x: sd in x and
x[sd] in smap.get("fieldmap_magnitude",[]) and
it in x and
isinstance(x[it], list) and
len(x[it]) > 2 and
x[it][2].strip().lower() == "m", dinfo) # we want the 3rd field of image type to be 'm'
phase_fs = filter(lambda x: sd in x and
x[sd] in smap.get("fieldmap_phase",[]) and
it in x and
isinstance(x[it], list) and
len(x[it]) > 2 and
x[it][2].strip().lower() == "p", dinfo) # we want the 3rd field of image type to be 'p'
self.fieldmap_mag = [d[nf] for d in mag_fs if nf in d]
self.fieldmap_ph = [d[nf] for d in phase_fs if nf in d]
# calculate echo spacing for each of the bold images
ep_calc_fail = False
if isdefined(self.inputs.ep_echo_spacing):
self.ep_e_spaces = [self.inputs.ep_echo_spacing for n in self.bolds]
elif bs and any(["bw_per_pix_phase_encode" in d and "acq_matrix_n" in d for d in bs]):
if not all(["bw_per_pix_phase_encode" in d and "acq_matrix_n" in d for d in bs]):
ep_calc_fail = True
else:
self.ep_e_spaces = [1/(d["bw_per_pix_phase_encode"] * d["acq_matrix_n"]) for d in bs]
else:
self.ep_e_spaces = ["NONE" for n in self.bolds]
# output delta te for magnitude fieldmap if available
if mag_fs and self.fieldmap_mag and self.fieldmap_ph:
self.fieldmap_mag_delta_te = mag_fs[0].get("delta_te","NONE")
else:
self.fieldmap_mag_delta_te = "NONE"
# a BOLD image by any other name...
self.bold_names = ["bold_%d" % n for n in xrange(len(self.bolds))]
# we'll derive the ep unwarp dir in the future... for now, just set it in config
if isdefined(self.inputs.ep_unwarp_dir):
self.ep_unwarp_dirs = [self.inputs.ep_unwarp_dir for n in self.bolds]
# if you have any polarity swapped series, apply that now
pswaps = smap.get("polarity_swapped", [])
if pswaps:
for b_idx, uw_dir in enumerate(self.ep_unwarp_dirs):
if bs[b_idx].get("series_desc",None) in pswaps:
raw_dir = uw_dir.replace("-","")
self.ep_unwarp_dirs[b_idx] = "-"+raw_dir if not "-" in uw_dir else raw_dir
else:
# fail. we can do better!
raise ValueError("We can't derive ep_unwarp_dir yet. Please set it in the nii wrangler config section.")
### and let's do some sanity checking
# warn if you're going to ignore field or magnitude phase maps
if not (len(self.fieldmap_mag) and len(self.fieldmap_ph)):
print >> sys.stderr, "\nWARNING: found %d magnitude fieldmaps and %d phase fieldmaps.\n" % (len(self.fieldmap_mag), len(self.fieldmap_ph))
# if we have any sbrefs, we should have one for each bold
if self.sbrefs and len(self.sbrefs) != len(self.bolds):
raise ValueError("Had %d bolds, but %d SBRefs. If there are any SBRefs, there must be one for each BOLD image"
% (len(self.bolds), len(self.sbrefs)))
# and if we DON'T have any, then we need a list full of NONE
if not self.sbrefs:
self.sbrefs = ["NONE" for n in self.bolds]
# we should have the same number of positive and negative fieldmaps
if len(self.fieldmaps_pos) != len(self.fieldmaps_neg):
raise ValueError("Mismatched number of pos and neg fieldmaps (%d/%d)" % (len(self.fieldmaps_pos), len(self.fieldmaps_neg)))
# we also need the same number of pos/neg se fieldmaps as bold images
if len(self.fieldmaps_pos) != len(self.bolds):
raise ValueError("Mismatched number of pos/neg fieldmaps and bolds (%d/%d)" % (len(self.fieldmaps_pos), len(self.bolds)))
### derive the derived values
# t1_sample_spacing
if t1fs and "RealDwellTime" in t1fs[0].keys():
self.t1_sample_spacing = t1fs[0]["RealDwellTime"] * math.pow(10,-9)
else:
self.t1_sample_spacing = "NONE"
# t2_sample_spacing
if t2fs and "RealDwellTime" in t2fs[0].keys():
self.t2_sample_spacing = t2fs[0]["RealDwellTime"] * math.pow(10,-9)
else:
self.t2_sample_spacing = "NONE"
# don't continue if there was screwiness around calculating ep echo spacing
if ep_calc_fail:
raise ValueError("Unabel to calculate ep echo spacing. Try specifying manually in nii wrangler config section.")
return runtime
def _list_outputs(self):
outputs = self._outputs().get()
outputs['forward_transforms'] = []
outputs['forward_invert_flags'] = []
outputs['reverse_transforms'] = []
outputs['reverse_invert_flags'] = []
# invert_initial_moving_transform should be always defined, even if
# there's no initial transform
invert_initial_moving_transform = False
if isdefined(self.inputs.invert_initial_moving_transform):
invert_initial_moving_transform = self.inputs.invert_initial_moving_transform
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = os.path.abspath(fileName)
fileName = self.inputs.output_transform_prefix + \
'InverseComposite.h5'
outputs['inverse_composite_transform'] = os.path.abspath(fileName)
else: # If composite transforms are written, then individuals are not written (as of 2014-10-26
if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(
0, not invert_initial_moving_transform) # Prepend
transformCount += 1
elif isdefined(self.inputs.initial_moving_transform_com):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
'Initial')
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
'Initial', True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(False)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].insert(0, True)
transformCount += 1
for count in range(len(self.inputs.transforms)):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count])
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].insert(
0, reverseInverseMode)
transformCount += 1
else:
transformCount = 0
isLinear = [
any(self._linear_transform_names == t)
for t in self.inputs.transforms
]
collapse_list = []
if isdefined(self.inputs.initial_moving_transform) or \
isdefined(self.inputs.initial_moving_transform_com):
isLinear.insert(0, True)
# Only files returned by collapse_output_transforms
if any(isLinear):
collapse_list.append('GenericAffine')
if not all(isLinear):
collapse_list.append('SyN')
for transform in collapse_list:
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
transform,
inverse=False)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
transform,
inverse=True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].append(
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].append(reverseInverseMode)
transformCount += 1
out_filename = self._get_outputfilenames(inverse=False)
inv_out_filename = self._get_outputfilenames(inverse=True)
if out_filename:
outputs['warped_image'] = os.path.abspath(out_filename)
if inv_out_filename:
outputs['inverse_warped_image'] = os.path.abspath(inv_out_filename)
if len(self.inputs.save_state):
outputs['save_state'] = os.path.abspath(self.inputs.save_state)
return outputs
def _list_outputs(self):
outputs = self._outputs().get()
outputs['forward_transforms'] = []
outputs['forward_invert_flags'] = []
outputs['reverse_transforms'] = []
outputs['reverse_invert_flags'] = []
if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
self.inputs.invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(
0,
not self.inputs.invert_initial_moving_transform) # Prepend
transformCount += 1
elif isdefined(self.inputs.initial_moving_transform_com):
#forwardFileName, _ = self._outputFileNames(self.inputs.output_transform_prefix,
# transformCount,
# 'Initial')
#outputs['forward_transforms'].append(forwardFileName)
transformCount += 1
for count in range(len(self.inputs.transforms)):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count])
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].insert(0, reverseInverseMode)
transformCount += 1
else:
transformCount = 0
for transform in [
'GenericAffine', 'SyN'
]: # Only files returned by collapse_output_transforms
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
transform)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
transform, True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].append(
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].append(reverseInverseMode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = [os.path.abspath(fileName)]
fileName = self.inputs.output_transform_prefix + \
'InverseComposite.h5'
outputs['inverse_composite_transform'] = [
os.path.abspath(fileName)
]
out_filename = self._get_outputfilenames(inverse=False)
inv_out_filename = self._get_outputfilenames(inverse=True)
if out_filename:
outputs['warped_image'] = os.path.abspath(out_filename)
if inv_out_filename:
outputs['inverse_warped_image'] = os.path.abspath(inv_out_filename)
return outputs
