niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixel2peaks.py

@@ -0,0 +1,613 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXEL2PEAKS_METADATA = Metadata(
+    id="0d92be2b2e1ceff15fcfee87e64154e86fddb5a8.boutiques",
+    name="fixel2peaks",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Fixel2peaksConfigParamsDictNoTag = typing.TypedDict('_Fixel2peaksConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Fixel2peaksConfigParamsDictTagged = typing.TypedDict('Fixel2peaksConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Fixel2peaksConfigParamsDict = _Fixel2peaksConfigParamsDictNoTag | Fixel2peaksConfigParamsDictTagged
+
+
+_Fixel2peaksVariousStringParamsDictNoTag = typing.TypedDict('_Fixel2peaksVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+Fixel2peaksVariousStringParamsDictTagged = typing.TypedDict('Fixel2peaksVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+Fixel2peaksVariousStringParamsDict = _Fixel2peaksVariousStringParamsDictNoTag | Fixel2peaksVariousStringParamsDictTagged
+
+
+_Fixel2peaksVariousFileParamsDictNoTag = typing.TypedDict('_Fixel2peaksVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+Fixel2peaksVariousFileParamsDictTagged = typing.TypedDict('Fixel2peaksVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+Fixel2peaksVariousFileParamsDict = _Fixel2peaksVariousFileParamsDictNoTag | Fixel2peaksVariousFileParamsDictTagged
+
+
+_Fixel2peaksParamsDictNoTag = typing.TypedDict('_Fixel2peaksParamsDictNoTag', {
+    "number": typing.NotRequired[int | None],
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2peaksConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": typing.Union[Fixel2peaksVariousStringParamsDictTagged, Fixel2peaksVariousFileParamsDictTagged],
+    "out": str,
+})
+Fixel2peaksParamsDictTagged = typing.TypedDict('Fixel2peaksParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fixel2peaks"],
+    "number": typing.NotRequired[int | None],
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fixel2peaksConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": typing.Union[Fixel2peaksVariousStringParamsDictTagged, Fixel2peaksVariousFileParamsDictTagged],
+    "out": str,
+})
+Fixel2peaksParamsDict = _Fixel2peaksParamsDictNoTag | Fixel2peaksParamsDictTagged
+
+
+def fixel2peaks_in_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": fixel2peaks_various_string_cargs,
+        "VariousFile": fixel2peaks_various_file_cargs,
+    }.get(t)
+
+
+def fixel2peaks_in_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": fixel2peaks_various_string_validate,
+        "VariousFile": fixel2peaks_various_file_validate,
+    }.get(t)
+
+
+def fixel2peaks_config(
+    key: str,
+    value: str,
+) -> Fixel2peaksConfigParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def fixel2peaks_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fixel2peaksConfigParamsDict` 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("key", None) is None:
+        raise StyxValidationError("`key` must not be None")
+    if not isinstance(params["key"], str):
+        raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
+    if params.get("value", None) is None:
+        raise StyxValidationError("`value` must not be None")
+    if not isinstance(params["value"], str):
+        raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
+
+
+def fixel2peaks_config_cargs(
+    params: Fixel2peaksConfigParamsDict,
+    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("-config")
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
+    return cargs
+
+
+def fixel2peaks_various_string(
+    obj: str,
+) -> Fixel2peaksVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def fixel2peaks_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fixel2peaksVariousStringParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], str):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `str`')
+
+
+def fixel2peaks_various_string_cargs(
+    params: Fixel2peaksVariousStringParamsDict,
+    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(params.get("obj", None))
+    return cargs
+
+
+def fixel2peaks_various_file(
+    obj: InputPathType,
+) -> Fixel2peaksVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def fixel2peaks_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fixel2peaksVariousFileParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `InputPathType`')
+
+
+def fixel2peaks_various_file_cargs(
+    params: Fixel2peaksVariousFileParamsDict,
+    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(execution.input_file(params.get("obj", None)))
+    return cargs
+
+
+class Fixel2peaksOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Fixel2peaksParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output peaks image"""
+
+
+def fixel2peaks_params(
+    in_: typing.Union[Fixel2peaksVariousStringParamsDictTagged, Fixel2peaksVariousFileParamsDictTagged],
+    out: str,
+    number: int | None = None,
+    nan: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2peaksConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Fixel2peaksParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input fixel information.
+        out: the output peaks image.
+        number: maximum number of fixels in each voxel (default: based on input\
+            data).
+        nan: fill excess peak data with NaNs rather than zeroes.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        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 this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "mrtrix/fixel2peaks",
+        "nan": nan,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+        "out": out,
+    }
+    if number is not None:
+        params["number"] = number
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixel2peaks_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Fixel2peaksParamsDict` 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("number", None) is not None:
+        if not isinstance(params["number"], int):
+            raise StyxValidationError(f'`number` has the wrong type: Received `{type(params.get("number", None))}` expected `int | None`')
+    if params.get("nan", False) is None:
+        raise StyxValidationError("`nan` must not be None")
+    if not isinstance(params["nan"], bool):
+        raise StyxValidationError(f'`nan` has the wrong type: Received `{type(params.get("nan", False))}` expected `bool`')
+    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"], int):
+            raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | 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[Fixel2peaksConfigParamsDict] | None`')
+        for e in params["config"]:
+            fixel2peaks_config_validate(e)
+    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`')
+    if params.get("in", None) is None:
+        raise StyxValidationError("`in` must not be None")
+    if not isinstance(params["in"], dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params["in"])}\'')
+    if "@type" not in params["in"]:
+        raise StyxValidationError("Params object is missing `@type`")
+    if params["in"]["@type"] not in ["VariousString", "VariousFile"]:
+        raise StyxValidationError("Parameter `in`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+    fixel2peaks_in_validate_dyn_fn(params["in"]["@type"])(params["in"])
+    if params.get("out", None) is None:
+        raise StyxValidationError("`out` must not be None")
+    if not isinstance(params["out"], str):
+        raise StyxValidationError(f'`out` has the wrong type: Received `{type(params.get("out", None))}` expected `str`')
+
+
+def fixel2peaks_cargs(
+    params: Fixel2peaksParamsDict,
+    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("fixel2peaks")
+    if params.get("number", None) is not None:
+        cargs.extend([
+            "-number",
+            str(params.get("number", None))
+        ])
+    if params.get("nan", False):
+        cargs.append("-nan")
+    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([a for c in [fixel2peaks_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
+        cargs.append("-help")
+    if params.get("version", False):
+        cargs.append("-version")
+    cargs.extend(fixel2peaks_in_cargs_dyn_fn(params.get("in", None)["@type"])(params.get("in", None), execution))
+    cargs.append(params.get("out", None))
+    return cargs
+
+
+def fixel2peaks_outputs(
+    params: Fixel2peaksParamsDict,
+    execution: Execution,
+) -> Fixel2peaksOutputs:
+    """
+    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 = Fixel2peaksOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out", None)),
+    )
+    return ret
+
+
+def fixel2peaks_execute(
+    params: Fixel2peaksParamsDict,
+    runner: Runner | None = None,
+) -> Fixel2peaksOutputs:
+    """
+    fixel2peaks
+    
+    Convert data in the fixel directory format into a 4D image of 3-vectors.
+    
+    If a fixel data file is provided as input, then the 3-vectors in the output
+    image will be scaled based on the data in that file. If the input is instead
+    the fixel directory, or the index or directions file, then all output
+    3-vectors will possess unit norm.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Fixel2peaksOutputs`).
+    """
+    fixel2peaks_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXEL2PEAKS_METADATA)
+    params = execution.params(params)
+    cargs = fixel2peaks_cargs(params, execution)
+    ret = fixel2peaks_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixel2peaks(
+    in_: typing.Union[Fixel2peaksVariousStringParamsDictTagged, Fixel2peaksVariousFileParamsDictTagged],
+    out: str,
+    number: int | None = None,
+    nan: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Fixel2peaksConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Fixel2peaksOutputs:
+    """
+    fixel2peaks
+    
+    Convert data in the fixel directory format into a 4D image of 3-vectors.
+    
+    If a fixel data file is provided as input, then the 3-vectors in the output
+    image will be scaled based on the data in that file. If the input is instead
+    the fixel directory, or the index or directions file, then all output
+    3-vectors will possess unit norm.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input fixel information.
+        out: the output peaks image.
+        number: maximum number of fixels in each voxel (default: based on input\
+            data).
+        nan: fill excess peak data with NaNs rather than zeroes.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        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 this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Fixel2peaksOutputs`).
+    """
+    params = fixel2peaks_params(
+        number=number,
+        nan=nan,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+        out=out,
+    )
+    return fixel2peaks_execute(params, runner)
+
+
+__all__ = [
+    "FIXEL2PEAKS_METADATA",
+    "Fixel2peaksConfigParamsDict",
+    "Fixel2peaksConfigParamsDictTagged",
+    "Fixel2peaksOutputs",
+    "Fixel2peaksParamsDict",
+    "Fixel2peaksParamsDictTagged",
+    "Fixel2peaksVariousFileParamsDict",
+    "Fixel2peaksVariousFileParamsDictTagged",
+    "Fixel2peaksVariousStringParamsDict",
+    "Fixel2peaksVariousStringParamsDictTagged",
+    "fixel2peaks",
+    "fixel2peaks_config",
+    "fixel2peaks_execute",
+    "fixel2peaks_params",
+    "fixel2peaks_various_file",
+    "fixel2peaks_various_string",
+]