xcp_d.interfaces.workbench.ApplyAffine

class xcp_d.interfaces.workbench.ApplyAffine(command=None, terminal_output=None, write_cmdline=False, **inputs)

Wrapped executable: wb_command -surface-apply-affine.

Interface for wb_command’s -surface-apply-affine command.

wb_command -surface-apply-affine
    <in-surf> - the surface to transform
    <affine> - the affine file
    <out-surf> - output - the output transformed surface

    [-flirt] - MUST be used if affine is a flirt affine
        <source-volume> - the source volume used when generating the affine
        <target-volume> - the target volume used when generating the affine

For flirt matrices, you must use the -flirt option, because flirt matrices are not a complete description of the coordinate transform they represent. If the -flirt option is not present, the affine must be a nifti ‘world’ affine, which can be obtained with the -convert-affine command, or aff_conv from the 4dfp suite.

Mandatory Inputs:

• affine (a pathlike object or string representing an existing file) – The affine file. Maps to a command-line argument: %s (position: 1).

• in_file (a pathlike object or string representing an existing file) – The input file. Maps to a command-line argument: %s (position: 0).

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: {})

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

Outputs:

out_file (a pathlike object or string representing an existing file) – Output file.

__init__(command=None, terminal_output=None, write_cmdline=False, **inputs)

Subclasses must implement __init__

Methods

__init__([command, terminal_output, ...])	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_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