xcp_d.interfaces.ants.CompositeInvTransformUtil

class xcp_d.interfaces.ants.CompositeInvTransformUtil(**inputs)[source]

Wrapped executable: CompositeTransformUtil.

Wrapper for the ANTS CompositeTransformUtil command.

ANTs utility which can combine or break apart transform files into their individual constituent components.

Examples

>>> from nipype.interfaces.ants import CompositeInvTransformUtil
>>> tran = CompositeInvTransformUtil()
>>> tran.inputs.process = 'disassemble'
>>> tran.inputs.in_file = 'output_Composite.h5'
>>> tran.cmdline
'CompositeTransformUtil --disassemble output_Composite.h5 transform'
>>> tran.run()  
example for assembling transformation files
>>> from nipype.interfaces.ants import CompositeInvTransformUtil
>>> tran = CompositeInvTransformUtil()
>>> tran.inputs.process = 'assemble'
>>> tran.inputs.out_file = 'my.h5'
>>> tran.inputs.in_file = ['AffineTransform.mat', 'DisplacementFieldTransform.nii.gz']
>>> tran.cmdline
'CompositeTransformUtil --assemble my.h5 AffineTransform.mat
 DisplacementFieldTransform.nii.gz '
>>> tran.run()
Mandatory Inputs:

in_file (a list of items which are a pathlike object or string representing an existing file) – Input transform file(s). Maps to a command-line argument: %s... (position: 3).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • num_threads (an integer) – Number of ITK threads to use. (Nipype default value: 1)

  • out_file (a pathlike object or string representing a file) – Output file path (only used for disassembly). Maps to a command-line argument: %s (position: 2).

  • output_prefix (a string) – A prefix that is prepended to all output files (only used for assembly). Maps to a command-line argument: %s (position: 4). (Nipype default value: transform)

  • process (‘assemble’ or ‘disassemble’) – What to do with the transform inputs (assemble or disassemble). Maps to a command-line argument: --%s (position: 1). (Nipype default value: assemble)

Outputs:

  • affine_transform (a pathlike object or string representing a file) – Affine transform component.

  • displacement_field (a pathlike object or string representing a file) – Displacement field component.

  • out_file (a pathlike object or string representing a file) – Compound transformation file.

__init__(**inputs)[source]

Subclasses must implement __init__

Methods

__init__(**inputs)

Subclasses must implement __init__

aggregate_outputs([runtime, needed_outputs])

Collate expected outputs and apply output traits validation.

help([returnhelp])

Prints class help

load_inputs_from_json(json_file[, overwrite])

A convenient way to load pre-set inputs from a JSON file.

raise_exception(runtime)

run([cwd, ignore_exception])

Execute this interface.

save_inputs_to_json(json_file)

A convenient way to save current inputs to a JSON file.

set_default_num_threads(num_threads)

Set the default number of threads for ITK calls

set_default_terminal_output(output_type)

Set the default terminal output for CommandLine Interfaces.

version_from_command([flag, cmd])

Attributes

always_run

Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.

can_resume

Defines if the interface can reuse partial results after interruption.

cmd

sets base command, immutable

cmdline

command plus any arguments (args) validates arguments and generates command line

resource_monitor

terminal_output

version

interfaces should implement a version property

write_cmdline