niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/responsemean.py

@@ -0,0 +1,385 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RESPONSEMEAN_METADATA = Metadata(
+    id="580e677d66de76d497b1d37c93d76dd82a169d45.boutiques",
+    name="responsemean",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_ResponsemeanParamsDictNoTag = typing.TypedDict('_ResponsemeanParamsDictNoTag', {
+    "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,
+})
+ResponsemeanParamsDictTagged = typing.TypedDict('ResponsemeanParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/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,
+})
+ResponsemeanParamsDict = _ResponsemeanParamsDictNoTag | ResponsemeanParamsDictTagged
+
+
+class ResponsemeanOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ResponsemeanParamsDict(...)`.
+    """
+    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,
+) -> ResponsemeanParamsDictTagged:
+    """
+    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 = {
+        "@type": "mrtrix/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_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `ResponsemeanParamsDict` object.
+    
+    Args:
+        params: The parameters object to validate.
+    """
+    if params is None or not isinstance(params, dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
+    if params.get("input_response", None) is None:
+        raise StyxValidationError("`input_response` must not be None")
+    if not isinstance(params["input_response"], list):
+        raise StyxValidationError(f'`input_response` has the wrong type: Received `{type(params.get("input_response", None))}` expected `list[InputPathType]`')
+    for e in params["input_response"]:
+        if not isinstance(e, (pathlib.Path, str)):
+            raise StyxValidationError(f'`input_response` has the wrong type: Received `{type(params.get("input_response", None))}` expected `list[InputPathType]`')
+    if params.get("output_response", None) is None:
+        raise StyxValidationError("`output_response` must not be None")
+    if not isinstance(params["output_response"], str):
+        raise StyxValidationError(f'`output_response` has the wrong type: Received `{type(params.get("output_response", None))}` expected `str`')
+    if params.get("legacy", False) is None:
+        raise StyxValidationError("`legacy` must not be None")
+    if not isinstance(params["legacy"], bool):
+        raise StyxValidationError(f'`legacy` has the wrong type: Received `{type(params.get("legacy", False))}` expected `bool`')
+    if params.get("nocleanup", False) is None:
+        raise StyxValidationError("`nocleanup` must not be None")
+    if not isinstance(params["nocleanup"], bool):
+        raise StyxValidationError(f'`nocleanup` has the wrong type: Received `{type(params.get("nocleanup", False))}` expected `bool`')
+    if params.get("scratch_dir", None) is not None:
+        if not isinstance(params["scratch_dir"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`scratch_dir` has the wrong type: Received `{type(params.get("scratch_dir", None))}` expected `InputPathType | None`')
+    if params.get("continue_scratch_dir", None) is not None:
+        if not isinstance(params["continue_scratch_dir"], list):
+            raise StyxValidationError(f'`continue_scratch_dir` has the wrong type: Received `{type(params.get("continue_scratch_dir", None))}` expected `list[InputPathType] | None`')
+        if len(params["continue_scratch_dir"]) != 2:
+            raise StyxValidationError("Parameter `continue_scratch_dir` must contain exactly 2 elements")
+        for e in params["continue_scratch_dir"]:
+            if not isinstance(e, (pathlib.Path, str)):
+                raise StyxValidationError(f'`continue_scratch_dir` has the wrong type: Received `{type(params.get("continue_scratch_dir", None))}` expected `list[InputPathType] | None`')
+    if params.get("info", False) is None:
+        raise StyxValidationError("`info` must not be None")
+    if not isinstance(params["info"], bool):
+        raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
+    if params.get("quiet", False) is None:
+        raise StyxValidationError("`quiet` must not be None")
+    if not isinstance(params["quiet"], bool):
+        raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
+    if params.get("debug", False) is None:
+        raise StyxValidationError("`debug` must not be None")
+    if not isinstance(params["debug"], bool):
+        raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
+    if params.get("force", False) is None:
+        raise StyxValidationError("`force` must not be None")
+    if not isinstance(params["force"], bool):
+        raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
+    if params.get("nthreads", None) is not None:
+        if not isinstance(params["nthreads"], (float, int)):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `float | None`')
+    if params.get("config", None) is not None:
+        if not isinstance(params["config"], list):
+            raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[str] | None`')
+        for e in params["config"]:
+            if not isinstance(e, str):
+                raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[str] | None`')
+    if params.get("help", False) is None:
+        raise StyxValidationError("`help` must not be None")
+    if not isinstance(params["help"], bool):
+        raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
+    if params.get("version", False) is None:
+        raise StyxValidationError("`version` must not be None")
+    if not isinstance(params["version"], bool):
+        raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
+
+
+def responsemean_cargs(
+    params: ResponsemeanParamsDict,
+    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", None)])
+    cargs.append(params.get("output_response", None))
+    if params.get("legacy", False):
+        cargs.append("-legacy")
+    if params.get("nocleanup", False):
+        cargs.append("-nocleanup")
+    if params.get("scratch_dir", None) is not None:
+        cargs.extend([
+            "-scratch",
+            execution.input_file(params.get("scratch_dir", None))
+        ])
+    if params.get("continue_scratch_dir", None) is not None:
+        cargs.extend([
+            "-continue",
+            *[execution.input_file(f) for f in params.get("continue_scratch_dir", None)]
+        ])
+    if params.get("info", False):
+        cargs.append("-info")
+    if params.get("quiet", False):
+        cargs.append("-quiet")
+    if params.get("debug", False):
+        cargs.append("-debug")
+    if params.get("force", False):
+        cargs.append("-force")
+    if params.get("nthreads", None) is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads", None))
+        ])
+    if params.get("config", None) is not None:
+        cargs.extend([
+            "-config",
+            *params.get("config", None)
+        ])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    return cargs
+
+
+def responsemean_outputs(
+    params: ResponsemeanParamsDict,
+    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", None)),
+    )
+    return ret
+
+
+def responsemean_execute(
+    params: ResponsemeanParamsDict,
+    runner: Runner | None = None,
+) -> ResponsemeanOutputs:
+    """
+    responsemean
+    
+    Calculate the mean response function from a set of text files.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ResponsemeanOutputs`).
+    """
+    responsemean_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RESPONSEMEAN_METADATA)
+    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:
+    """
+    responsemean
+    
+    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`).
+    """
+    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, runner)
+
+
+__all__ = [
+    "RESPONSEMEAN_METADATA",
+    "ResponsemeanOutputs",
+    "ResponsemeanParamsDict",
+    "ResponsemeanParamsDictTagged",
+    "responsemean",
+    "responsemean_execute",
+    "responsemean_params",
+]