niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/responsemean.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RESPONSEMEAN_METADATA = Metadata(
+    id="e6c56f5745cf6a8cbb9c9387ca97dbcce3e44b95.boutiques",
+    name="responsemean",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+ResponsemeanParameters = typing.TypedDict('ResponsemeanParameters', {
+    "__STYX_TYPE__": typing.Literal["responsemean"],
+    "input_response": list[InputPathType],
+    "output_response": str,
+    "legacy": bool,
+    "nocleanup": bool,
+    "scratch_dir": typing.NotRequired[InputPathType | None],
+    "continue_scratch_dir": typing.NotRequired[list[InputPathType] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[float | None],
+    "config": typing.NotRequired[list[str] | None],
+    "help": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "responsemean": responsemean_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "responsemean": responsemean_outputs,
+    }.get(t)
+
+
+class ResponsemeanOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `responsemean(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_response_file: OutputPathType
+    """File containing the averaged tissue response function"""
+
+
+def responsemean_params(
+    input_response: list[InputPathType],
+    output_response: str,
+    legacy: bool = False,
+    nocleanup: bool = False,
+    scratch_dir: InputPathType | None = None,
+    continue_scratch_dir: list[InputPathType] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: float | None = None,
+    config: list[str] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> ResponsemeanParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_response: Input response functions.
+        output_response: Output mean response function.
+        legacy: Calculate the mean response function from a set of text files.
+        nocleanup: Do not delete intermediate files during script execution,\
+            and do not delete scratch directory at script completion.
+        scratch_dir: Manually specify the path in which to generate the scratch\
+            directory.
+        continue_scratch_dir: Continue the script from a previous execution;\
+            must provide the scratch directory path.
+        info: Display information messages.
+        quiet: Do not display information messages or progress status.
+        debug: Display debugging messages.
+        force: Force overwrite of output files.
+        nthreads: Use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: Temporarily set the value of an MRtrix config file entry.
+        help_: Display help information and exit.
+        version: Display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "responsemean",
+        "input_response": input_response,
+        "output_response": output_response,
+        "legacy": legacy,
+        "nocleanup": nocleanup,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+    }
+    if scratch_dir is not None:
+        params["scratch_dir"] = scratch_dir
+    if continue_scratch_dir is not None:
+        params["continue_scratch_dir"] = continue_scratch_dir
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def responsemean_cargs(
+    params: ResponsemeanParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("responsemean")
+    cargs.extend([execution.input_file(f) for f in params.get("input_response")])
+    cargs.append(params.get("output_response"))
+    if params.get("legacy"):
+        cargs.append("-legacy")
+    if params.get("nocleanup"):
+        cargs.append("-nocleanup")
+    if params.get("scratch_dir") is not None:
+        cargs.extend([
+            "-scratch",
+            execution.input_file(params.get("scratch_dir"))
+        ])
+    if params.get("continue_scratch_dir") is not None:
+        cargs.extend([
+            "-continue",
+            *[execution.input_file(f) for f in params.get("continue_scratch_dir")]
+        ])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([
+            "-config",
+            *params.get("config")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    return cargs
+
+
+def responsemean_outputs(
+    params: ResponsemeanParameters,
+    execution: Execution,
+) -> ResponsemeanOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = ResponsemeanOutputs(
+        root=execution.output_file("."),
+        output_response_file=execution.output_file(params.get("output_response")),
+    )
+    return ret
+
+
+def responsemean_execute(
+    params: ResponsemeanParameters,
+    execution: Execution,
+) -> ResponsemeanOutputs:
+    """
+    Calculate the mean response function from a set of text files.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ResponsemeanOutputs`).
+    """
+    params = execution.params(params)
+    cargs = responsemean_cargs(params, execution)
+    ret = responsemean_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def responsemean(
+    input_response: list[InputPathType],
+    output_response: str,
+    legacy: bool = False,
+    nocleanup: bool = False,
+    scratch_dir: InputPathType | None = None,
+    continue_scratch_dir: list[InputPathType] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: float | None = None,
+    config: list[str] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> ResponsemeanOutputs:
+    """
+    Calculate the mean response function from a set of text files.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_response: Input response functions.
+        output_response: Output mean response function.
+        legacy: Calculate the mean response function from a set of text files.
+        nocleanup: Do not delete intermediate files during script execution,\
+            and do not delete scratch directory at script completion.
+        scratch_dir: Manually specify the path in which to generate the scratch\
+            directory.
+        continue_scratch_dir: Continue the script from a previous execution;\
+            must provide the scratch directory path.
+        info: Display information messages.
+        quiet: Do not display information messages or progress status.
+        debug: Display debugging messages.
+        force: Force overwrite of output files.
+        nthreads: Use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: Temporarily set the value of an MRtrix config file entry.
+        help_: Display help information and exit.
+        version: Display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ResponsemeanOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RESPONSEMEAN_METADATA)
+    params = responsemean_params(
+        input_response=input_response,
+        output_response=output_response,
+        legacy=legacy,
+        nocleanup=nocleanup,
+        scratch_dir=scratch_dir,
+        continue_scratch_dir=continue_scratch_dir,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+    )
+    return responsemean_execute(params, execution)
+
+
+__all__ = [
+    "RESPONSEMEAN_METADATA",
+    "ResponsemeanOutputs",
+    "ResponsemeanParameters",
+    "responsemean",
+    "responsemean_params",
+]