class _DerivativesDataSinkInputSpec(DynamicTraitedSpec,
BaseInterfaceInputSpec):
base_directory = traits.Directory(
desc="Path to the base directory for storing data.")
check_hdr = traits.Bool(True,
usedefault=True,
desc="fix headers of NIfTI outputs")
compress = InputMultiObject(
traits.Either(None, traits.Bool),
usedefault=True,
desc=
"whether ``in_file`` should be compressed (True), uncompressed (False) "
"or left unmodified (None, default).",
)
data_dtype = Str(
desc="NumPy datatype to coerce NIfTI data to, or `source` to"
"match the input file dtype")
dismiss_entities = InputMultiObject(
traits.Either(None, Str),
usedefault=True,
desc="a list entities that will not be propagated from the source file",
)
in_file = InputMultiObject(File(exists=True),
mandatory=True,
desc="the object to be saved")
meta_dict = traits.DictStrAny(
desc="an input dictionary containing metadata")
source_file = InputMultiObject(
File(exists=False),
mandatory=True,
desc="the source file(s) to extract entities from")
class _DerivativesDataSinkInputSpec(DynamicTraitedSpec,
BaseInterfaceInputSpec):
base_directory = traits.Directory(
desc='Path to the base directory for storing data.')
check_hdr = traits.Bool(True,
usedefault=True,
desc='fix headers of NIfTI outputs')
compress = traits.Bool(
desc="force compression (True) or uncompression (False)"
" of the output file (default: same as input)")
desc = Str('', usedefault=True, desc='Label for description field')
extra_values = traits.List(Str)
in_file = InputMultiObject(File(exists=True),
mandatory=True,
desc='the object to be saved')
keep_dtype = traits.Bool(False,
usedefault=True,
desc='keep datatype suffix')
meta_dict = traits.DictStrAny(
desc='an input dictionary containing metadata')
source_file = File(exists=False,
mandatory=True,
desc='the input func file')
space = Str('', usedefault=True, desc='Label for space field')
suffix = Str('', usedefault=True, desc='suffix appended to source_file')
class _TemplateFlowSelectInputSpec(BaseInterfaceInputSpec):
template = traits.Enum(*tf.templates(), mandatory=True, desc='Template ID')
atlas = InputMultiObject(traits.Str, desc='Specify an atlas')
resolution = InputMultiObject(traits.Int,
desc='Specify a template resolution index')
template_spec = traits.DictStrAny({'atlas': None},
usedefault=True,
desc='Template specifications')
class WriteBIDSFileInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='input file')
out_dir = Directory(exists=True, mandatory=True, desc='output directory (bids root)')
labelinfo = traits.List(desc=':py:obj:`list` of :py:obj:`dict`. If specified, will be written '
'to a tsv file corresponding to the output bids file using '
':py:func:`utils.write_labels`')
bidsparams = traits.DictStrAny(mandatory=True,
desc='Bids parameters to be passed to :py:meth:`BIDSLayout.build_path`. '
'Must not include "extension", which will be determined from :py:obj:`in_file`')
class CombineStatsInputSpec(BaseInterfaceInputSpec):
bids_dir = traits.Directory(exists=True, mandatory=True)
validate = traits.Bool(default=True, usedefault=True)
row_keys = traits.ListStr(mandatory=True)
invariants = traits.DictStrAny()
strict = traits.Bool(default=True, usedefault=True)
index = traits.Str()
ignore = traits.Either(traits.ListStr,
traits.Set(trait=traits.Str),
traits.Tuple(trait=traits.Str))
class _TemplateFlowSelectInputSpec(BaseInterfaceInputSpec):
template = traits.Str("MNI152NLin2009cAsym", mandatory=True, desc="Template ID")
atlas = InputMultiObject(traits.Str, desc="Specify an atlas")
cohort = InputMultiObject(
traits.Either(traits.Str, traits.Int), desc="Specify a cohort"
)
resolution = InputMultiObject(
traits.Int, desc="Specify a template resolution index"
)
template_spec = traits.DictStrAny(
{"atlas": None, "cohort": None}, usedefault=True, desc="Template specifications"
)
class _TemplateFlowSelectInputSpec(BaseInterfaceInputSpec):
template = traits.Str('MNI152NLin2009cAsym',
mandatory=True,
desc='Template ID')
atlas = InputMultiObject(traits.Str, desc='Specify an atlas')
cohort = InputMultiObject(traits.Either(traits.Str, traits.Int),
desc='Specify a cohort')
resolution = InputMultiObject(traits.Int,
desc='Specify a template resolution index')
template_spec = traits.DictStrAny({
'atlas': None,
'cohort': None
},
usedefault=True,
desc='Template specifications')
class _RobustMNINormalizationInputSpec(BaseInterfaceInputSpec):
# Enable deprecation
package_version = niworkflows_version
# Moving image.
moving_image = File(exists=True,
mandatory=True,
desc="image to apply transformation to")
# Reference image (optional).
reference_image = File(exists=True, desc="override the reference image")
# Moving mask (optional).
moving_mask = File(exists=True, desc="moving image mask")
# Reference mask (optional).
reference_mask = File(exists=True, desc="reference image mask")
# Lesion mask (optional).
lesion_mask = File(exists=True, desc="lesion mask image")
# Number of threads to use for ANTs/ITK processes.
num_threads = traits.Int(cpu_count(),
usedefault=True,
nohash=True,
desc="Number of ITK threads to use")
# ANTs parameter set to use.
flavor = traits.Enum(
"precise",
"testing",
"fast",
usedefault=True,
desc="registration settings parameter set",
)
# Template orientation.
orientation = traits.Enum(
"RAS",
"LAS",
mandatory=True,
usedefault=True,
desc="modify template orientation (should match input image)",
)
# Modality of the reference image.
reference = traits.Enum(
"T1w",
"T2w",
"boldref",
"PDw",
mandatory=True,
usedefault=True,
desc="set the reference modality for registration",
)
# T1 or EPI registration?
moving = traits.Enum("T1w",
"boldref",
usedefault=True,
mandatory=True,
desc="registration type")
# Template to use as the default reference image.
template = traits.Str("MNI152NLin2009cAsym",
usedefault=True,
desc="define the template to be used")
# Load other settings from file.
settings = traits.List(File(exists=True),
desc="pass on the list of settings files")
# Resolution of the default template.
template_spec = traits.DictStrAny(desc="template specifications")
template_resolution = traits.Enum(1,
2,
None,
desc="(DEPRECATED) template resolution")
# Use explicit masking?
explicit_masking = traits.Bool(
True,
usedefault=True,
desc="""\
Set voxels outside the masks to zero thus creating an artificial border
that can drive the registration. Requires reliable and accurate masks.
See https://sourceforge.net/p/advants/discussion/840261/thread/27216e69/#c7ba\
""",
)
initial_moving_transform = File(exists=True,
desc="transform for initialization")
float = traits.Bool(False,
usedefault=True,
desc="use single precision calculations")
