xcp_d.interfaces.workbench.SurfaceAverage

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

Wrapped executable: wb_command -surface-average.

Average surface files together.

wb_command -surface-average
    <surface-out> - output - the output averaged surface
    [-stddev] - compute 3D sample standard deviation
        <stddev-metric-out> - output - the output metric for 3D sample standard deviation
    [-uncertainty] - compute caret5 'uncertainty'
        <uncert-metric-out> - output - the output metric for uncertainty
    [-surf] - repeatable - specify a surface to include in the average
        <surface> - a surface file to average
    [-weight] - specify a weighted average
        <weight> - the weight to use (default 1)

The 3D sample standard deviation is computed as ‘sqrt(sum(squaredlength(xyz - mean(xyz)))/(n - 1))’.

Uncertainty is a legacy measure used in caret5, and is computed as ‘sum(length(xyz - mean(xyz)))/n’.

When weights are used, the 3D sample standard deviation treats them as reliability weights.

Mandatory Inputs:

• surface_in1 (a pathlike object or string representing an existing file) – Specify a surface to include in the average. Maps to a command-line argument: -surf %s (position: 1).

• surface_in2 (a pathlike object or string representing an existing file) – Specify a surface to include in the average. Maps to a command-line argument: -surf %s (position: 2).

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) – Output - the output averaged surface. Maps to a command-line argument: %s (position: 0).

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