niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tckmap.py

@@ -0,0 +1,1004 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKMAP_METADATA = Metadata(
+    id="6c3a1a0072e37f35d493f0f168ff70a6ce77b20d.boutiques",
+    name="tckmap",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_TckmapVariousStringParamsDictNoTag = typing.TypedDict('_TckmapVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+TckmapVariousStringParamsDictTagged = typing.TypedDict('TckmapVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+TckmapVariousStringParamsDict = _TckmapVariousStringParamsDictNoTag | TckmapVariousStringParamsDictTagged
+
+
+_TckmapVariousFileParamsDictNoTag = typing.TypedDict('_TckmapVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+TckmapVariousFileParamsDictTagged = typing.TypedDict('TckmapVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+TckmapVariousFileParamsDict = _TckmapVariousFileParamsDictNoTag | TckmapVariousFileParamsDictTagged
+
+
+_TckmapConfigParamsDictNoTag = typing.TypedDict('_TckmapConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+TckmapConfigParamsDictTagged = typing.TypedDict('TckmapConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+TckmapConfigParamsDict = _TckmapConfigParamsDictNoTag | TckmapConfigParamsDictTagged
+
+
+_TckmapParamsDictNoTag = typing.TypedDict('_TckmapParamsDictNoTag', {
+    "template": typing.NotRequired[InputPathType | None],
+    "vox": typing.NotRequired[list[float] | None],
+    "datatype": typing.NotRequired[str | None],
+    "dec": bool,
+    "dixel": typing.NotRequired[typing.Union[TckmapVariousStringParamsDictTagged, TckmapVariousFileParamsDictTagged] | None],
+    "tod": typing.NotRequired[int | None],
+    "contrast": typing.NotRequired[str | None],
+    "image": typing.NotRequired[InputPathType | None],
+    "vector_file": typing.NotRequired[InputPathType | None],
+    "stat_vox": typing.NotRequired[str | None],
+    "stat_tck": typing.NotRequired[str | None],
+    "fwhm_tck": typing.NotRequired[float | None],
+    "map_zero": bool,
+    "backtrack": bool,
+    "upsample": typing.NotRequired[int | None],
+    "precise": bool,
+    "ends_only": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckmapConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "output": str,
+})
+TckmapParamsDictTagged = typing.TypedDict('TckmapParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/tckmap"],
+    "template": typing.NotRequired[InputPathType | None],
+    "vox": typing.NotRequired[list[float] | None],
+    "datatype": typing.NotRequired[str | None],
+    "dec": bool,
+    "dixel": typing.NotRequired[typing.Union[TckmapVariousStringParamsDictTagged, TckmapVariousFileParamsDictTagged] | None],
+    "tod": typing.NotRequired[int | None],
+    "contrast": typing.NotRequired[str | None],
+    "image": typing.NotRequired[InputPathType | None],
+    "vector_file": typing.NotRequired[InputPathType | None],
+    "stat_vox": typing.NotRequired[str | None],
+    "stat_tck": typing.NotRequired[str | None],
+    "fwhm_tck": typing.NotRequired[float | None],
+    "map_zero": bool,
+    "backtrack": bool,
+    "upsample": typing.NotRequired[int | None],
+    "precise": bool,
+    "ends_only": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckmapConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "tracks": InputPathType,
+    "output": str,
+})
+TckmapParamsDict = _TckmapParamsDictNoTag | TckmapParamsDictTagged
+
+
+def tckmap_dixel_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": tckmap_various_string_cargs,
+        "VariousFile": tckmap_various_file_cargs,
+    }.get(t)
+
+
+def tckmap_dixel_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": tckmap_various_string_validate,
+        "VariousFile": tckmap_various_file_validate,
+    }.get(t)
+
+
+def tckmap_various_string(
+    obj: str,
+) -> TckmapVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def tckmap_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckmapVariousStringParamsDict` 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 tckmap_various_string_cargs(
+    params: TckmapVariousStringParamsDict,
+    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 tckmap_various_file(
+    obj: InputPathType,
+) -> TckmapVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def tckmap_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckmapVariousFileParamsDict` 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 tckmap_various_file_cargs(
+    params: TckmapVariousFileParamsDict,
+    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 tckmap_config(
+    key: str,
+    value: str,
+) -> TckmapConfigParamsDictTagged:
+    """
+    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 tckmap_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckmapConfigParamsDict` 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 tckmap_config_cargs(
+    params: TckmapConfigParamsDict,
+    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
+
+
+class TckmapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `TckmapParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output track-weighted image"""
+
+
+def tckmap_params(
+    tracks: InputPathType,
+    output: str,
+    template: InputPathType | None = None,
+    vox: list[float] | None = None,
+    datatype: str | None = None,
+    dec: bool = False,
+    dixel: typing.Union[TckmapVariousStringParamsDictTagged, TckmapVariousFileParamsDictTagged] | None = None,
+    tod: int | None = None,
+    contrast: str | None = None,
+    image: InputPathType | None = None,
+    vector_file: InputPathType | None = None,
+    stat_vox: str | None = None,
+    stat_tck: str | None = None,
+    fwhm_tck: float | None = None,
+    map_zero: bool = False,
+    backtrack: bool = False,
+    upsample: int | None = None,
+    precise: bool = False,
+    ends_only: bool = False,
+    tck_weights_in: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckmapConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TckmapParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        tracks: the input track file.
+        output: the output track-weighted image.
+        template: an image file to be used as a template for the output (the\
+            output image will have the same transform and field of view).
+        vox: provide either an isotropic voxel size (in mm), or comma-separated\
+            list of 3 voxel dimensions.
+        datatype: specify output image data type.
+        dec: perform track mapping in directionally-encoded colour (DEC) space.
+        dixel: map streamlines to dixels within each voxel; requires either a\
+            number of dixels (references an internal direction set), or a path to a\
+            text file containing a set of directions stored as azimuth/elevation\
+            pairs.
+        tod: generate a Track Orientation Distribution (TOD) in each voxel;\
+            need to specify the maximum spherical harmonic degree lmax to use when\
+            generating Apodised Point Spread Functions.
+        contrast: define the desired form of contrast for the output image\
+            Options are: tdi, length, invlength, scalar_map, scalar_map_count,\
+            fod_amp, curvature, vector_file (default: tdi).
+        image: provide the scalar image map for generating images with\
+            'scalar_map' / 'scalar_map_count' contrast, or the spherical harmonics\
+            image for 'fod_amp' contrast.
+        vector_file: provide the vector data file for generating images with\
+            'vector_file' contrast.
+        stat_vox: define the statistic for choosing the final voxel intensities\
+            for a given contrast type given the individual values from the tracks\
+            passing through each voxel.\
+            Options are: sum, min, mean, max (default: sum).
+        stat_tck: define the statistic for choosing the contribution to be made\
+            by each streamline as a function of the samples taken along their\
+            lengths.\
+            Only has an effect for 'scalar_map', 'fod_amp' and 'curvature'\
+            contrast types.\
+            Options are: sum, min, mean, max, median, mean_nonzero, gaussian,\
+            ends_min, ends_mean, ends_max, ends_prod (default: mean).
+        fwhm_tck: when using gaussian-smoothed per-track statistic, specify the\
+            desired full-width half-maximum of the Gaussian smoothing kernel (in\
+            mm).
+        map_zero: if a streamline has zero contribution based on the contrast &\
+            statistic, typically it is not mapped; use this option to still\
+            contribute to the map even if this is the case (these non-contributing\
+            voxels can then influence the mean value in each voxel of the map).
+        backtrack: when using -stat_tck ends_*, if the streamline endpoint is\
+            outside the FoV, backtrack along the streamline trajectory until an\
+            appropriate point is found.
+        upsample: upsample the tracks by some ratio using Hermite interpolation\
+            before mappping\
+            (If omitted, an appropriate ratio will be determined automatically).
+        precise: use a more precise streamline mapping strategy, that\
+            accurately quantifies the length through each voxel (these lengths are\
+            then taken into account during TWI calculation).
+        ends_only: only map the streamline endpoints to the image.
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        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/tckmap",
+        "dec": dec,
+        "map_zero": map_zero,
+        "backtrack": backtrack,
+        "precise": precise,
+        "ends_only": ends_only,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "tracks": tracks,
+        "output": output,
+    }
+    if template is not None:
+        params["template"] = template
+    if vox is not None:
+        params["vox"] = vox
+    if datatype is not None:
+        params["datatype"] = datatype
+    if dixel is not None:
+        params["dixel"] = dixel
+    if tod is not None:
+        params["tod"] = tod
+    if contrast is not None:
+        params["contrast"] = contrast
+    if image is not None:
+        params["image"] = image
+    if vector_file is not None:
+        params["vector_file"] = vector_file
+    if stat_vox is not None:
+        params["stat_vox"] = stat_vox
+    if stat_tck is not None:
+        params["stat_tck"] = stat_tck
+    if fwhm_tck is not None:
+        params["fwhm_tck"] = fwhm_tck
+    if upsample is not None:
+        params["upsample"] = upsample
+    if tck_weights_in is not None:
+        params["tck_weights_in"] = tck_weights_in
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tckmap_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TckmapParamsDict` 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("template", None) is not None:
+        if not isinstance(params["template"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`template` has the wrong type: Received `{type(params.get("template", None))}` expected `InputPathType | None`')
+    if params.get("vox", None) is not None:
+        if not isinstance(params["vox"], list):
+            raise StyxValidationError(f'`vox` has the wrong type: Received `{type(params.get("vox", None))}` expected `list[float] | None`')
+        for e in params["vox"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`vox` has the wrong type: Received `{type(params.get("vox", None))}` expected `list[float] | None`')
+    if params.get("datatype", None) is not None:
+        if not isinstance(params["datatype"], str):
+            raise StyxValidationError(f'`datatype` has the wrong type: Received `{type(params.get("datatype", None))}` expected `str | None`')
+    if params.get("dec", False) is None:
+        raise StyxValidationError("`dec` must not be None")
+    if not isinstance(params["dec"], bool):
+        raise StyxValidationError(f'`dec` has the wrong type: Received `{type(params.get("dec", False))}` expected `bool`')
+    if params.get("dixel", None) is not None:
+        if not isinstance(params["dixel"], dict):
+            raise StyxValidationError(f'Params object has the wrong type \'{type(params["dixel"])}\'')
+        if "@type" not in params["dixel"]:
+            raise StyxValidationError("Params object is missing `@type`")
+        if params["dixel"]["@type"] not in ["VariousString", "VariousFile"]:
+            raise StyxValidationError("Parameter `dixel`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+        tckmap_dixel_validate_dyn_fn(params["dixel"]["@type"])(params["dixel"])
+    if params.get("tod", None) is not None:
+        if not isinstance(params["tod"], int):
+            raise StyxValidationError(f'`tod` has the wrong type: Received `{type(params.get("tod", None))}` expected `int | None`')
+    if params.get("contrast", None) is not None:
+        if not isinstance(params["contrast"], str):
+            raise StyxValidationError(f'`contrast` has the wrong type: Received `{type(params.get("contrast", None))}` expected `str | None`')
+    if params.get("image", None) is not None:
+        if not isinstance(params["image"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`image` has the wrong type: Received `{type(params.get("image", None))}` expected `InputPathType | None`')
+    if params.get("vector_file", None) is not None:
+        if not isinstance(params["vector_file"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`vector_file` has the wrong type: Received `{type(params.get("vector_file", None))}` expected `InputPathType | None`')
+    if params.get("stat_vox", None) is not None:
+        if not isinstance(params["stat_vox"], str):
+            raise StyxValidationError(f'`stat_vox` has the wrong type: Received `{type(params.get("stat_vox", None))}` expected `str | None`')
+    if params.get("stat_tck", None) is not None:
+        if not isinstance(params["stat_tck"], str):
+            raise StyxValidationError(f'`stat_tck` has the wrong type: Received `{type(params.get("stat_tck", None))}` expected `str | None`')
+    if params.get("fwhm_tck", None) is not None:
+        if not isinstance(params["fwhm_tck"], (float, int)):
+            raise StyxValidationError(f'`fwhm_tck` has the wrong type: Received `{type(params.get("fwhm_tck", None))}` expected `float | None`')
+    if params.get("map_zero", False) is None:
+        raise StyxValidationError("`map_zero` must not be None")
+    if not isinstance(params["map_zero"], bool):
+        raise StyxValidationError(f'`map_zero` has the wrong type: Received `{type(params.get("map_zero", False))}` expected `bool`')
+    if params.get("backtrack", False) is None:
+        raise StyxValidationError("`backtrack` must not be None")
+    if not isinstance(params["backtrack"], bool):
+        raise StyxValidationError(f'`backtrack` has the wrong type: Received `{type(params.get("backtrack", False))}` expected `bool`')
+    if params.get("upsample", None) is not None:
+        if not isinstance(params["upsample"], int):
+            raise StyxValidationError(f'`upsample` has the wrong type: Received `{type(params.get("upsample", None))}` expected `int | None`')
+    if params.get("precise", False) is None:
+        raise StyxValidationError("`precise` must not be None")
+    if not isinstance(params["precise"], bool):
+        raise StyxValidationError(f'`precise` has the wrong type: Received `{type(params.get("precise", False))}` expected `bool`')
+    if params.get("ends_only", False) is None:
+        raise StyxValidationError("`ends_only` must not be None")
+    if not isinstance(params["ends_only"], bool):
+        raise StyxValidationError(f'`ends_only` has the wrong type: Received `{type(params.get("ends_only", False))}` expected `bool`')
+    if params.get("tck_weights_in", None) is not None:
+        if not isinstance(params["tck_weights_in"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`tck_weights_in` has the wrong type: Received `{type(params.get("tck_weights_in", 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[TckmapConfigParamsDict] | None`')
+        for e in params["config"]:
+            tckmap_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("tracks", None) is None:
+        raise StyxValidationError("`tracks` must not be None")
+    if not isinstance(params["tracks"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`tracks` has the wrong type: Received `{type(params.get("tracks", None))}` expected `InputPathType`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def tckmap_cargs(
+    params: TckmapParamsDict,
+    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("tckmap")
+    if params.get("template", None) is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template", None))
+        ])
+    if params.get("vox", None) is not None:
+        cargs.extend([
+            "-vox",
+            ",".join(map(str, params.get("vox", None)))
+        ])
+    if params.get("datatype", None) is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype", None)
+        ])
+    if params.get("dec", False):
+        cargs.append("-dec")
+    if params.get("dixel", None) is not None:
+        cargs.extend([
+            "-dixel",
+            *tckmap_dixel_cargs_dyn_fn(params.get("dixel", None)["@type"])(params.get("dixel", None), execution)
+        ])
+    if params.get("tod", None) is not None:
+        cargs.extend([
+            "-tod",
+            str(params.get("tod", None))
+        ])
+    if params.get("contrast", None) is not None:
+        cargs.extend([
+            "-contrast",
+            params.get("contrast", None)
+        ])
+    if params.get("image", None) is not None:
+        cargs.extend([
+            "-image",
+            execution.input_file(params.get("image", None))
+        ])
+    if params.get("vector_file", None) is not None:
+        cargs.extend([
+            "-vector_file",
+            execution.input_file(params.get("vector_file", None))
+        ])
+    if params.get("stat_vox", None) is not None:
+        cargs.extend([
+            "-stat_vox",
+            params.get("stat_vox", None)
+        ])
+    if params.get("stat_tck", None) is not None:
+        cargs.extend([
+            "-stat_tck",
+            params.get("stat_tck", None)
+        ])
+    if params.get("fwhm_tck", None) is not None:
+        cargs.extend([
+            "-fwhm_tck",
+            str(params.get("fwhm_tck", None))
+        ])
+    if params.get("map_zero", False):
+        cargs.append("-map_zero")
+    if params.get("backtrack", False):
+        cargs.append("-backtrack")
+    if params.get("upsample", None) is not None:
+        cargs.extend([
+            "-upsample",
+            str(params.get("upsample", None))
+        ])
+    if params.get("precise", False):
+        cargs.append("-precise")
+    if params.get("ends_only", False):
+        cargs.append("-ends_only")
+    if params.get("tck_weights_in", None) is not None:
+        cargs.extend([
+            "-tck_weights_in",
+            execution.input_file(params.get("tck_weights_in", 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 [tckmap_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.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def tckmap_outputs(
+    params: TckmapParamsDict,
+    execution: Execution,
+) -> TckmapOutputs:
+    """
+    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 = TckmapOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def tckmap_execute(
+    params: TckmapParamsDict,
+    runner: Runner | None = None,
+) -> TckmapOutputs:
+    """
+    tckmap
+    
+    Use track data as a form of contrast for producing a high-resolution image.
+    
+    Note: if you run into limitations with RAM usage, make sure you output the
+    results to a .mif file or .mih / .dat file pair - this will avoid the
+    allocation of an additional buffer to store the output for write-out.
+    
+    References:
+    
+    * For TDI or DEC TDI:
+    Calamante, F.; Tournier, J.-D.; Jackson, G. D. & Connelly, A. Track-density
+    imaging (TDI): Super-resolution white matter imaging using whole-brain
+    track-density mapping. NeuroImage, 2010, 53, 1233-1243
+    
+    * If using -contrast length and -stat_vox mean:
+    Pannek, K.; Mathias, J. L.; Bigler, E. D.; Brown, G.; Taylor, J. D. & Rose,
+    S. E. The average pathlength map: A diffusion MRI tractography-derived index
+    for studying brain pathology. NeuroImage, 2011, 55, 133-141
+    
+    * If using -dixel option with TDI contrast only:
+    Smith, R.E., Tournier, J-D., Calamante, F., Connelly, A. A novel paradigm
+    for automated segmentation of very large whole-brain probabilistic
+    tractography data sets. In proc. ISMRM, 2011, 19, 673
+    
+    * If using -dixel option with any other contrast:
+    Pannek, K., Raffelt, D., Salvado, O., Rose, S. Incorporating directional
+    information in diffusion tractography derived maps: angular track imaging
+    (ATI). In Proc. ISMRM, 2012, 20, 1912
+    
+    * If using -tod option:
+    Dhollander, T., Emsell, L., Van Hecke, W., Maes, F., Sunaert, S., Suetens,
+    P. Track Orientation Density Imaging (TODI) and Track Orientation
+    Distribution (TOD) based tractography. NeuroImage, 2014, 94, 312-336
+    
+    * If using other contrasts / statistics:
+    Calamante, F.; Tournier, J.-D.; Smith, R. E. & Connelly, A. A generalised
+    framework for super-resolution track-weighted imaging. NeuroImage, 2012, 59,
+    2494-2503
+    
+    * If using -precise mapping option:
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT:
+    Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013,
+    67, 298-312 (Appendix 3).
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TckmapOutputs`).
+    """
+    tckmap_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKMAP_METADATA)
+    params = execution.params(params)
+    cargs = tckmap_cargs(params, execution)
+    ret = tckmap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tckmap(
+    tracks: InputPathType,
+    output: str,
+    template: InputPathType | None = None,
+    vox: list[float] | None = None,
+    datatype: str | None = None,
+    dec: bool = False,
+    dixel: typing.Union[TckmapVariousStringParamsDictTagged, TckmapVariousFileParamsDictTagged] | None = None,
+    tod: int | None = None,
+    contrast: str | None = None,
+    image: InputPathType | None = None,
+    vector_file: InputPathType | None = None,
+    stat_vox: str | None = None,
+    stat_tck: str | None = None,
+    fwhm_tck: float | None = None,
+    map_zero: bool = False,
+    backtrack: bool = False,
+    upsample: int | None = None,
+    precise: bool = False,
+    ends_only: bool = False,
+    tck_weights_in: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckmapConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TckmapOutputs:
+    """
+    tckmap
+    
+    Use track data as a form of contrast for producing a high-resolution image.
+    
+    Note: if you run into limitations with RAM usage, make sure you output the
+    results to a .mif file or .mih / .dat file pair - this will avoid the
+    allocation of an additional buffer to store the output for write-out.
+    
+    References:
+    
+    * For TDI or DEC TDI:
+    Calamante, F.; Tournier, J.-D.; Jackson, G. D. & Connelly, A. Track-density
+    imaging (TDI): Super-resolution white matter imaging using whole-brain
+    track-density mapping. NeuroImage, 2010, 53, 1233-1243
+    
+    * If using -contrast length and -stat_vox mean:
+    Pannek, K.; Mathias, J. L.; Bigler, E. D.; Brown, G.; Taylor, J. D. & Rose,
+    S. E. The average pathlength map: A diffusion MRI tractography-derived index
+    for studying brain pathology. NeuroImage, 2011, 55, 133-141
+    
+    * If using -dixel option with TDI contrast only:
+    Smith, R.E., Tournier, J-D., Calamante, F., Connelly, A. A novel paradigm
+    for automated segmentation of very large whole-brain probabilistic
+    tractography data sets. In proc. ISMRM, 2011, 19, 673
+    
+    * If using -dixel option with any other contrast:
+    Pannek, K., Raffelt, D., Salvado, O., Rose, S. Incorporating directional
+    information in diffusion tractography derived maps: angular track imaging
+    (ATI). In Proc. ISMRM, 2012, 20, 1912
+    
+    * If using -tod option:
+    Dhollander, T., Emsell, L., Van Hecke, W., Maes, F., Sunaert, S., Suetens,
+    P. Track Orientation Density Imaging (TODI) and Track Orientation
+    Distribution (TOD) based tractography. NeuroImage, 2014, 94, 312-336
+    
+    * If using other contrasts / statistics:
+    Calamante, F.; Tournier, J.-D.; Smith, R. E. & Connelly, A. A generalised
+    framework for super-resolution track-weighted imaging. NeuroImage, 2012, 59,
+    2494-2503
+    
+    * If using -precise mapping option:
+    Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. SIFT:
+    Spherical-deconvolution informed filtering of tractograms. NeuroImage, 2013,
+    67, 298-312 (Appendix 3).
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        tracks: the input track file.
+        output: the output track-weighted image.
+        template: an image file to be used as a template for the output (the\
+            output image will have the same transform and field of view).
+        vox: provide either an isotropic voxel size (in mm), or comma-separated\
+            list of 3 voxel dimensions.
+        datatype: specify output image data type.
+        dec: perform track mapping in directionally-encoded colour (DEC) space.
+        dixel: map streamlines to dixels within each voxel; requires either a\
+            number of dixels (references an internal direction set), or a path to a\
+            text file containing a set of directions stored as azimuth/elevation\
+            pairs.
+        tod: generate a Track Orientation Distribution (TOD) in each voxel;\
+            need to specify the maximum spherical harmonic degree lmax to use when\
+            generating Apodised Point Spread Functions.
+        contrast: define the desired form of contrast for the output image\
+            Options are: tdi, length, invlength, scalar_map, scalar_map_count,\
+            fod_amp, curvature, vector_file (default: tdi).
+        image: provide the scalar image map for generating images with\
+            'scalar_map' / 'scalar_map_count' contrast, or the spherical harmonics\
+            image for 'fod_amp' contrast.
+        vector_file: provide the vector data file for generating images with\
+            'vector_file' contrast.
+        stat_vox: define the statistic for choosing the final voxel intensities\
+            for a given contrast type given the individual values from the tracks\
+            passing through each voxel.\
+            Options are: sum, min, mean, max (default: sum).
+        stat_tck: define the statistic for choosing the contribution to be made\
+            by each streamline as a function of the samples taken along their\
+            lengths.\
+            Only has an effect for 'scalar_map', 'fod_amp' and 'curvature'\
+            contrast types.\
+            Options are: sum, min, mean, max, median, mean_nonzero, gaussian,\
+            ends_min, ends_mean, ends_max, ends_prod (default: mean).
+        fwhm_tck: when using gaussian-smoothed per-track statistic, specify the\
+            desired full-width half-maximum of the Gaussian smoothing kernel (in\
+            mm).
+        map_zero: if a streamline has zero contribution based on the contrast &\
+            statistic, typically it is not mapped; use this option to still\
+            contribute to the map even if this is the case (these non-contributing\
+            voxels can then influence the mean value in each voxel of the map).
+        backtrack: when using -stat_tck ends_*, if the streamline endpoint is\
+            outside the FoV, backtrack along the streamline trajectory until an\
+            appropriate point is found.
+        upsample: upsample the tracks by some ratio using Hermite interpolation\
+            before mappping\
+            (If omitted, an appropriate ratio will be determined automatically).
+        precise: use a more precise streamline mapping strategy, that\
+            accurately quantifies the length through each voxel (these lengths are\
+            then taken into account during TWI calculation).
+        ends_only: only map the streamline endpoints to the image.
+        tck_weights_in: specify a text scalar file containing the streamline\
+            weights.
+        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 `TckmapOutputs`).
+    """
+    params = tckmap_params(
+        template=template,
+        vox=vox,
+        datatype=datatype,
+        dec=dec,
+        dixel=dixel,
+        tod=tod,
+        contrast=contrast,
+        image=image,
+        vector_file=vector_file,
+        stat_vox=stat_vox,
+        stat_tck=stat_tck,
+        fwhm_tck=fwhm_tck,
+        map_zero=map_zero,
+        backtrack=backtrack,
+        upsample=upsample,
+        precise=precise,
+        ends_only=ends_only,
+        tck_weights_in=tck_weights_in,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        tracks=tracks,
+        output=output,
+    )
+    return tckmap_execute(params, runner)
+
+
+__all__ = [
+    "TCKMAP_METADATA",
+    "TckmapConfigParamsDict",
+    "TckmapConfigParamsDictTagged",
+    "TckmapOutputs",
+    "TckmapParamsDict",
+    "TckmapParamsDictTagged",
+    "TckmapVariousFileParamsDict",
+    "TckmapVariousFileParamsDictTagged",
+    "TckmapVariousStringParamsDict",
+    "TckmapVariousStringParamsDictTagged",
+    "tckmap",
+    "tckmap_config",
+    "tckmap_execute",
+    "tckmap_params",
+    "tckmap_various_file",
+    "tckmap_various_string",
+]