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")