niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelfilter.py

@@ -0,0 +1,882 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELFILTER_METADATA = Metadata(
+    id="b5e8a361d7de5f948949260328ab5131eb18a9b7.boutiques",
+    name="fixelfilter",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_FixelfilterConfigParamsDictNoTag = typing.TypedDict('_FixelfilterConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+FixelfilterConfigParamsDictTagged = typing.TypedDict('FixelfilterConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+FixelfilterConfigParamsDict = _FixelfilterConfigParamsDictNoTag | FixelfilterConfigParamsDictTagged
+
+
+_FixelfilterVariousStringParamsDictNoTag = typing.TypedDict('_FixelfilterVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+FixelfilterVariousStringParamsDictTagged = typing.TypedDict('FixelfilterVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+FixelfilterVariousStringParamsDict = _FixelfilterVariousStringParamsDictNoTag | FixelfilterVariousStringParamsDictTagged
+
+
+_FixelfilterVariousFileParamsDictNoTag = typing.TypedDict('_FixelfilterVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+FixelfilterVariousFileParamsDictTagged = typing.TypedDict('FixelfilterVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+FixelfilterVariousFileParamsDict = _FixelfilterVariousFileParamsDictNoTag | FixelfilterVariousFileParamsDictTagged
+
+
+_FixelfilterVariousString1ParamsDictNoTag = typing.TypedDict('_FixelfilterVariousString1ParamsDictNoTag', {
+    "obj": str,
+})
+FixelfilterVariousString1ParamsDictTagged = typing.TypedDict('FixelfilterVariousString1ParamsDictTagged', {
+    "@type": typing.Literal["VariousString_1"],
+    "obj": str,
+})
+FixelfilterVariousString1ParamsDict = _FixelfilterVariousString1ParamsDictNoTag | FixelfilterVariousString1ParamsDictTagged
+
+
+_FixelfilterVariousFile1ParamsDictNoTag = typing.TypedDict('_FixelfilterVariousFile1ParamsDictNoTag', {
+    "obj": InputPathType,
+})
+FixelfilterVariousFile1ParamsDictTagged = typing.TypedDict('FixelfilterVariousFile1ParamsDictTagged', {
+    "@type": typing.Literal["VariousFile_1"],
+    "obj": InputPathType,
+})
+FixelfilterVariousFile1ParamsDict = _FixelfilterVariousFile1ParamsDictNoTag | FixelfilterVariousFile1ParamsDictTagged
+
+
+_FixelfilterParamsDictNoTag = typing.TypedDict('_FixelfilterParamsDictNoTag', {
+    "matrix": InputPathType,
+    "threshold_value": typing.NotRequired[float | None],
+    "threshold_connectivity": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "minweight": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelfilterConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": typing.Union[FixelfilterVariousStringParamsDictTagged, FixelfilterVariousFileParamsDictTagged],
+    "filter": str,
+    "output": typing.Union[FixelfilterVariousString1ParamsDictTagged, FixelfilterVariousFile1ParamsDictTagged],
+})
+FixelfilterParamsDictTagged = typing.TypedDict('FixelfilterParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fixelfilter"],
+    "matrix": InputPathType,
+    "threshold_value": typing.NotRequired[float | None],
+    "threshold_connectivity": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "minweight": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelfilterConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": typing.Union[FixelfilterVariousStringParamsDictTagged, FixelfilterVariousFileParamsDictTagged],
+    "filter": str,
+    "output": typing.Union[FixelfilterVariousString1ParamsDictTagged, FixelfilterVariousFile1ParamsDictTagged],
+})
+FixelfilterParamsDict = _FixelfilterParamsDictNoTag | FixelfilterParamsDictTagged
+
+
+def fixelfilter_input_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": fixelfilter_various_string_cargs,
+        "VariousFile": fixelfilter_various_file_cargs,
+    }.get(t)
+
+
+def fixelfilter_input_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": fixelfilter_various_string_validate,
+        "VariousFile": fixelfilter_various_file_validate,
+    }.get(t)
+
+
+def fixelfilter_output_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString_1": fixelfilter_various_string_1_cargs,
+        "VariousFile_1": fixelfilter_various_file_1_cargs,
+    }.get(t)
+
+
+def fixelfilter_output_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString_1": fixelfilter_various_string_1_validate,
+        "VariousFile_1": fixelfilter_various_file_1_validate,
+    }.get(t)
+
+
+def fixelfilter_config(
+    key: str,
+    value: str,
+) -> FixelfilterConfigParamsDictTagged:
+    """
+    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 fixelfilter_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelfilterConfigParamsDict` 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 fixelfilter_config_cargs(
+    params: FixelfilterConfigParamsDict,
+    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 fixelfilter_various_string(
+    obj: str,
+) -> FixelfilterVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelfilterVariousStringParamsDict` 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 fixelfilter_various_string_cargs(
+    params: FixelfilterVariousStringParamsDict,
+    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 fixelfilter_various_file(
+    obj: InputPathType,
+) -> FixelfilterVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelfilterVariousFileParamsDict` 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 fixelfilter_various_file_cargs(
+    params: FixelfilterVariousFileParamsDict,
+    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
+
+
+def fixelfilter_various_string_1(
+    obj: str,
+) -> FixelfilterVariousString1ParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString_1",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_string_1_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelfilterVariousString1ParamsDict` 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 fixelfilter_various_string_1_cargs(
+    params: FixelfilterVariousString1ParamsDict,
+    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 fixelfilter_various_file_1(
+    obj: InputPathType,
+) -> FixelfilterVariousFile1ParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile_1",
+        "obj": obj,
+    }
+    return params
+
+
+def fixelfilter_various_file_1_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelfilterVariousFile1ParamsDict` 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 fixelfilter_various_file_1_cargs(
+    params: FixelfilterVariousFile1ParamsDict,
+    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 FixelfilterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `FixelfilterParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def fixelfilter_params(
+    matrix: InputPathType,
+    input_: typing.Union[FixelfilterVariousStringParamsDictTagged, FixelfilterVariousFileParamsDictTagged],
+    filter_: str,
+    output: typing.Union[FixelfilterVariousString1ParamsDictTagged, FixelfilterVariousFile1ParamsDictTagged],
+    threshold_value: float | None = None,
+    threshold_connectivity: float | None = None,
+    fwhm: float | None = None,
+    minweight: float | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelfilterConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelfilterParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        matrix: provide a fixel-fixel connectivity matrix for filtering\
+            operations that require it.
+        input_: the input: either a fixel data file, or a fixel directory (see\
+            Description).
+        filter_: the filtering operation to perform; options are: connect,\
+            smooth.
+        output: the output: either a fixel data file, or a fixel directory (see\
+            Description).
+        threshold_value: specify a threshold for the input fixel data file\
+            values (default = 0.5).
+        threshold_connectivity: specify a fixel-fixel connectivity threshold\
+            for connected-component analysis (default = 0.10000000000000001).
+        fwhm: the full-width half-maximum (FWHM) of the spatial component of\
+            the smoothing filter (default = 10mm).
+        minweight: apply a minimum threshold to smoothing weights (default =\
+            0.01).
+        mask: only perform smoothing within a specified binary fixel mask.
+        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/fixelfilter",
+        "matrix": matrix,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "filter": filter_,
+        "output": output,
+    }
+    if threshold_value is not None:
+        params["threshold_value"] = threshold_value
+    if threshold_connectivity is not None:
+        params["threshold_connectivity"] = threshold_connectivity
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if minweight is not None:
+        params["minweight"] = minweight
+    if mask is not None:
+        params["mask"] = mask
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelfilter_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelfilterParamsDict` 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("matrix", None) is None:
+        raise StyxValidationError("`matrix` must not be None")
+    if not isinstance(params["matrix"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`matrix` has the wrong type: Received `{type(params.get("matrix", None))}` expected `InputPathType`')
+    if params.get("threshold_value", None) is not None:
+        if not isinstance(params["threshold_value"], (float, int)):
+            raise StyxValidationError(f'`threshold_value` has the wrong type: Received `{type(params.get("threshold_value", None))}` expected `float | None`')
+    if params.get("threshold_connectivity", None) is not None:
+        if not isinstance(params["threshold_connectivity"], (float, int)):
+            raise StyxValidationError(f'`threshold_connectivity` has the wrong type: Received `{type(params.get("threshold_connectivity", None))}` expected `float | None`')
+    if params.get("fwhm", None) is not None:
+        if not isinstance(params["fwhm"], (float, int)):
+            raise StyxValidationError(f'`fwhm` has the wrong type: Received `{type(params.get("fwhm", None))}` expected `float | None`')
+    if params.get("minweight", None) is not None:
+        if not isinstance(params["minweight"], (float, int)):
+            raise StyxValidationError(f'`minweight` has the wrong type: Received `{type(params.get("minweight", None))}` expected `float | None`')
+    if params.get("mask", None) is not None:
+        if not isinstance(params["mask"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `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"], 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[FixelfilterConfigParamsDict] | None`')
+        for e in params["config"]:
+            fixelfilter_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("input", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params["input"])}\'')
+    if "@type" not in params["input"]:
+        raise StyxValidationError("Params object is missing `@type`")
+    if params["input"]["@type"] not in ["VariousString", "VariousFile"]:
+        raise StyxValidationError("Parameter `input`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+    fixelfilter_input_validate_dyn_fn(params["input"]["@type"])(params["input"])
+    if params.get("filter", None) is None:
+        raise StyxValidationError("`filter` must not be None")
+    if not isinstance(params["filter"], str):
+        raise StyxValidationError(f'`filter` has the wrong type: Received `{type(params.get("filter", None))}` expected `str`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params["output"])}\'')
+    if "@type" not in params["output"]:
+        raise StyxValidationError("Params object is missing `@type`")
+    if params["output"]["@type"] not in ["VariousString_1", "VariousFile_1"]:
+        raise StyxValidationError("Parameter `output`s `@type` must be one of [\"VariousString_1\", \"VariousFile_1\"]")
+    fixelfilter_output_validate_dyn_fn(params["output"]["@type"])(params["output"])
+
+
+def fixelfilter_cargs(
+    params: FixelfilterParamsDict,
+    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("fixelfilter")
+    cargs.extend([
+        "-matrix",
+        execution.input_file(params.get("matrix", None))
+    ])
+    if params.get("threshold_value", None) is not None:
+        cargs.extend([
+            "-threshold_value",
+            str(params.get("threshold_value", None))
+        ])
+    if params.get("threshold_connectivity", None) is not None:
+        cargs.extend([
+            "-threshold_connectivity",
+            str(params.get("threshold_connectivity", None))
+        ])
+    if params.get("fwhm", None) is not None:
+        cargs.extend([
+            "-fwhm",
+            str(params.get("fwhm", None))
+        ])
+    if params.get("minweight", None) is not None:
+        cargs.extend([
+            "-minweight",
+            str(params.get("minweight", None))
+        ])
+    if params.get("mask", None) is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask", 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([a for c in [fixelfilter_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(fixelfilter_input_cargs_dyn_fn(params.get("input", None)["@type"])(params.get("input", None), execution))
+    cargs.append(params.get("filter", None))
+    cargs.extend(fixelfilter_output_cargs_dyn_fn(params.get("output", None)["@type"])(params.get("output", None), execution))
+    return cargs
+
+
+def fixelfilter_outputs(
+    params: FixelfilterParamsDict,
+    execution: Execution,
+) -> FixelfilterOutputs:
+    """
+    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 = FixelfilterOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def fixelfilter_execute(
+    params: FixelfilterParamsDict,
+    runner: Runner | None = None,
+) -> FixelfilterOutputs:
+    """
+    fixelfilter
+    
+    Perform filtering operations on fixel-based data.
+    
+    If the first input to the command is a specific fixel data file, then a
+    filtered version of only that file will be generated by the command.
+    Alternatively, if the input is the location of a fixel directory, then the
+    command will create a duplicate of the fixel directory, and apply the
+    specified filter operation to all fixel data files within the directory.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FixelfilterOutputs`).
+    """
+    fixelfilter_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELFILTER_METADATA)
+    params = execution.params(params)
+    cargs = fixelfilter_cargs(params, execution)
+    ret = fixelfilter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelfilter(
+    matrix: InputPathType,
+    input_: typing.Union[FixelfilterVariousStringParamsDictTagged, FixelfilterVariousFileParamsDictTagged],
+    filter_: str,
+    output: typing.Union[FixelfilterVariousString1ParamsDictTagged, FixelfilterVariousFile1ParamsDictTagged],
+    threshold_value: float | None = None,
+    threshold_connectivity: float | None = None,
+    fwhm: float | None = None,
+    minweight: float | None = None,
+    mask: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelfilterConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelfilterOutputs:
+    """
+    fixelfilter
+    
+    Perform filtering operations on fixel-based data.
+    
+    If the first input to the command is a specific fixel data file, then a
+    filtered version of only that file will be generated by the command.
+    Alternatively, if the input is the location of a fixel directory, then the
+    command will create a duplicate of the fixel directory, and apply the
+    specified filter operation to all fixel data files within the directory.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        matrix: provide a fixel-fixel connectivity matrix for filtering\
+            operations that require it.
+        input_: the input: either a fixel data file, or a fixel directory (see\
+            Description).
+        filter_: the filtering operation to perform; options are: connect,\
+            smooth.
+        output: the output: either a fixel data file, or a fixel directory (see\
+            Description).
+        threshold_value: specify a threshold for the input fixel data file\
+            values (default = 0.5).
+        threshold_connectivity: specify a fixel-fixel connectivity threshold\
+            for connected-component analysis (default = 0.10000000000000001).
+        fwhm: the full-width half-maximum (FWHM) of the spatial component of\
+            the smoothing filter (default = 10mm).
+        minweight: apply a minimum threshold to smoothing weights (default =\
+            0.01).
+        mask: only perform smoothing within a specified binary fixel mask.
+        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 `FixelfilterOutputs`).
+    """
+    params = fixelfilter_params(
+        matrix=matrix,
+        threshold_value=threshold_value,
+        threshold_connectivity=threshold_connectivity,
+        fwhm=fwhm,
+        minweight=minweight,
+        mask=mask,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        filter_=filter_,
+        output=output,
+    )
+    return fixelfilter_execute(params, runner)
+
+
+__all__ = [
+    "FIXELFILTER_METADATA",
+    "FixelfilterConfigParamsDict",
+    "FixelfilterConfigParamsDictTagged",
+    "FixelfilterOutputs",
+    "FixelfilterParamsDict",
+    "FixelfilterParamsDictTagged",
+    "FixelfilterVariousFile1ParamsDict",
+    "FixelfilterVariousFile1ParamsDictTagged",
+    "FixelfilterVariousFileParamsDict",
+    "FixelfilterVariousFileParamsDictTagged",
+    "FixelfilterVariousString1ParamsDict",
+    "FixelfilterVariousString1ParamsDictTagged",
+    "FixelfilterVariousStringParamsDict",
+    "FixelfilterVariousStringParamsDictTagged",
+    "fixelfilter",
+    "fixelfilter_config",
+    "fixelfilter_execute",
+    "fixelfilter_params",
+    "fixelfilter_various_file",
+    "fixelfilter_various_file_1",
+    "fixelfilter_various_string",
+    "fixelfilter_various_string_1",
+]