niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/amp2sh.py

@@ -0,0 +1,870 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AMP2SH_METADATA = Metadata(
+    id="b1deae186542fe482c4a2e51622f124fe000c4fc.boutiques",
+    name="amp2sh",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Amp2shFslgradParamsDictNoTag = typing.TypedDict('_Amp2shFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Amp2shFslgradParamsDictTagged = typing.TypedDict('Amp2shFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Amp2shFslgradParamsDict = _Amp2shFslgradParamsDictNoTag | Amp2shFslgradParamsDictTagged
+
+
+_Amp2shVariousStringParamsDictNoTag = typing.TypedDict('_Amp2shVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+Amp2shVariousStringParamsDictTagged = typing.TypedDict('Amp2shVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+Amp2shVariousStringParamsDict = _Amp2shVariousStringParamsDictNoTag | Amp2shVariousStringParamsDictTagged
+
+
+_Amp2shVariousFileParamsDictNoTag = typing.TypedDict('_Amp2shVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+Amp2shVariousFileParamsDictTagged = typing.TypedDict('Amp2shVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+Amp2shVariousFileParamsDict = _Amp2shVariousFileParamsDictNoTag | Amp2shVariousFileParamsDictTagged
+
+
+_Amp2shConfigParamsDictNoTag = typing.TypedDict('_Amp2shConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Amp2shConfigParamsDictTagged = typing.TypedDict('Amp2shConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Amp2shConfigParamsDict = _Amp2shConfigParamsDictNoTag | Amp2shConfigParamsDictTagged
+
+
+_Amp2shParamsDictNoTag = typing.TypedDict('_Amp2shParamsDictNoTag', {
+    "lmax": typing.NotRequired[int | None],
+    "normalise": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "rician": typing.NotRequired[InputPathType | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Amp2shFslgradParamsDict | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "strides": typing.NotRequired[typing.Union[Amp2shVariousStringParamsDictTagged, Amp2shVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2shConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "amp": InputPathType,
+    "SH": str,
+})
+Amp2shParamsDictTagged = typing.TypedDict('Amp2shParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/amp2sh"],
+    "lmax": typing.NotRequired[int | None],
+    "normalise": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "rician": typing.NotRequired[InputPathType | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Amp2shFslgradParamsDict | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "strides": typing.NotRequired[typing.Union[Amp2shVariousStringParamsDictTagged, Amp2shVariousFileParamsDictTagged] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2shConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "amp": InputPathType,
+    "SH": str,
+})
+Amp2shParamsDict = _Amp2shParamsDictNoTag | Amp2shParamsDictTagged
+
+
+def amp2sh_strides_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": amp2sh_various_string_cargs,
+        "VariousFile": amp2sh_various_file_cargs,
+    }.get(t)
+
+
+def amp2sh_strides_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": amp2sh_various_string_validate,
+        "VariousFile": amp2sh_various_file_validate,
+    }.get(t)
+
+
+def amp2sh_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Amp2shFslgradParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        bvecs: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        bvals: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "fslgrad",
+        "bvecs": bvecs,
+        "bvals": bvals,
+    }
+    return params
+
+
+def amp2sh_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2shFslgradParamsDict` 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("bvecs", None) is None:
+        raise StyxValidationError("`bvecs` must not be None")
+    if not isinstance(params["bvecs"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvecs` has the wrong type: Received `{type(params.get("bvecs", None))}` expected `InputPathType`')
+    if params.get("bvals", None) is None:
+        raise StyxValidationError("`bvals` must not be None")
+    if not isinstance(params["bvals"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`bvals` has the wrong type: Received `{type(params.get("bvals", None))}` expected `InputPathType`')
+
+
+def amp2sh_fslgrad_cargs(
+    params: Amp2shFslgradParamsDict,
+    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("-fslgrad")
+    cargs.append(execution.input_file(params.get("bvecs", None)))
+    cargs.append(execution.input_file(params.get("bvals", None)))
+    return cargs
+
+
+def amp2sh_various_string(
+    obj: str,
+) -> Amp2shVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def amp2sh_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2shVariousStringParamsDict` 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 amp2sh_various_string_cargs(
+    params: Amp2shVariousStringParamsDict,
+    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 amp2sh_various_file(
+    obj: InputPathType,
+) -> Amp2shVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def amp2sh_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2shVariousFileParamsDict` 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 amp2sh_various_file_cargs(
+    params: Amp2shVariousFileParamsDict,
+    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 amp2sh_config(
+    key: str,
+    value: str,
+) -> Amp2shConfigParamsDictTagged:
+    """
+    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 amp2sh_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2shConfigParamsDict` 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 amp2sh_config_cargs(
+    params: Amp2shConfigParamsDict,
+    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 Amp2shOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Amp2shParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    sh: OutputPathType
+    """the output spherical harmonics coefficients image."""
+
+
+def amp2sh_params(
+    amp: InputPathType,
+    sh: str,
+    lmax: int | None = None,
+    normalise: bool = False,
+    directions: InputPathType | None = None,
+    rician: InputPathType | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Amp2shFslgradParamsDict | None = None,
+    shells: list[float] | None = None,
+    strides: typing.Union[Amp2shVariousStringParamsDictTagged, Amp2shVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2shConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Amp2shParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        amp: the input amplitude image.
+        sh: the output spherical harmonics coefficients image.
+        lmax: set the maximum harmonic order for the output series. By default,\
+            the program will use the highest possible lmax given the number of\
+            diffusion-weighted images, up to a maximum of 8.
+        normalise: normalise the DW signal to the b=0 image.
+        directions: the directions corresponding to the input amplitude image\
+            used to sample AFD. By default this option is not required providing\
+            the direction set is supplied in the amplitude image. This should be\
+            supplied as a list of directions [az el], as generated using the dirgen\
+            command, or as a list of [ x y z ] Cartesian coordinates.
+        rician: correct for Rician noise induced bias, using noise map supplied.
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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/amp2sh",
+        "normalise": normalise,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "amp": amp,
+        "SH": sh,
+    }
+    if lmax is not None:
+        params["lmax"] = lmax
+    if directions is not None:
+        params["directions"] = directions
+    if rician is not None:
+        params["rician"] = rician
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if shells is not None:
+        params["shells"] = shells
+    if strides is not None:
+        params["strides"] = strides
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def amp2sh_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2shParamsDict` 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("lmax", None) is not None:
+        if not isinstance(params["lmax"], int):
+            raise StyxValidationError(f'`lmax` has the wrong type: Received `{type(params.get("lmax", None))}` expected `int | None`')
+    if params.get("normalise", False) is None:
+        raise StyxValidationError("`normalise` must not be None")
+    if not isinstance(params["normalise"], bool):
+        raise StyxValidationError(f'`normalise` has the wrong type: Received `{type(params.get("normalise", False))}` expected `bool`')
+    if params.get("directions", None) is not None:
+        if not isinstance(params["directions"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`directions` has the wrong type: Received `{type(params.get("directions", None))}` expected `InputPathType | None`')
+    if params.get("rician", None) is not None:
+        if not isinstance(params["rician"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`rician` has the wrong type: Received `{type(params.get("rician", None))}` expected `InputPathType | None`')
+    if params.get("grad", None) is not None:
+        if not isinstance(params["grad"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`grad` has the wrong type: Received `{type(params.get("grad", None))}` expected `InputPathType | None`')
+    if params.get("fslgrad", None) is not None:
+        amp2sh_fslgrad_validate(params["fslgrad"])
+    if params.get("shells", None) is not None:
+        if not isinstance(params["shells"], list):
+            raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+        for e in params["shells"]:
+            if not isinstance(e, (float, int)):
+                raise StyxValidationError(f'`shells` has the wrong type: Received `{type(params.get("shells", None))}` expected `list[float] | None`')
+    if params.get("strides", None) is not None:
+        if not isinstance(params["strides"], dict):
+            raise StyxValidationError(f'Params object has the wrong type \'{type(params["strides"])}\'')
+        if "@type" not in params["strides"]:
+            raise StyxValidationError("Params object is missing `@type`")
+        if params["strides"]["@type"] not in ["VariousString", "VariousFile"]:
+            raise StyxValidationError("Parameter `strides`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+        amp2sh_strides_validate_dyn_fn(params["strides"]["@type"])(params["strides"])
+    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[Amp2shConfigParamsDict] | None`')
+        for e in params["config"]:
+            amp2sh_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("amp", None) is None:
+        raise StyxValidationError("`amp` must not be None")
+    if not isinstance(params["amp"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`amp` has the wrong type: Received `{type(params.get("amp", None))}` expected `InputPathType`')
+    if params.get("SH", None) is None:
+        raise StyxValidationError("`SH` must not be None")
+    if not isinstance(params["SH"], str):
+        raise StyxValidationError(f'`SH` has the wrong type: Received `{type(params.get("SH", None))}` expected `str`')
+
+
+def amp2sh_cargs(
+    params: Amp2shParamsDict,
+    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("amp2sh")
+    if params.get("lmax", None) is not None:
+        cargs.extend([
+            "-lmax",
+            str(params.get("lmax", None))
+        ])
+    if params.get("normalise", False):
+        cargs.append("-normalise")
+    if params.get("directions", None) is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions", None))
+        ])
+    if params.get("rician", None) is not None:
+        cargs.extend([
+            "-rician",
+            execution.input_file(params.get("rician", None))
+        ])
+    if params.get("grad", None) is not None:
+        cargs.extend([
+            "-grad",
+            execution.input_file(params.get("grad", None))
+        ])
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(amp2sh_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("shells", None) is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells", None)))
+        ])
+    if params.get("strides", None) is not None:
+        cargs.extend([
+            "-strides",
+            *amp2sh_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
+        ])
+    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 [amp2sh_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("amp", None)))
+    cargs.append(params.get("SH", None))
+    return cargs
+
+
+def amp2sh_outputs(
+    params: Amp2shParamsDict,
+    execution: Execution,
+) -> Amp2shOutputs:
+    """
+    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 = Amp2shOutputs(
+        root=execution.output_file("."),
+        sh=execution.output_file(params.get("SH", None)),
+    )
+    return ret
+
+
+def amp2sh_execute(
+    params: Amp2shParamsDict,
+    runner: Runner | None = None,
+) -> Amp2shOutputs:
+    """
+    amp2sh
+    
+    Convert a set of amplitudes (defined along a set of corresponding
+    directions) to their spherical harmonic representation.
+    
+    The spherical harmonic decomposition is calculated by least-squares linear
+    fitting to the amplitude data.
+    
+    The directions can be defined either as a DW gradient scheme (for example to
+    compute the SH representation of the DW signal), a set of [az el] pairs as
+    output by the dirgen command, or a set of [ x y z ] directions in Cartesian
+    coordinates. The DW gradient scheme or direction set can be supplied within
+    the input image header or using the -gradient or -directions option. Note
+    that if a direction set and DW gradient scheme can be found, the direction
+    set will be used by default.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Amp2shOutputs`).
+    """
+    amp2sh_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AMP2SH_METADATA)
+    params = execution.params(params)
+    cargs = amp2sh_cargs(params, execution)
+    ret = amp2sh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def amp2sh(
+    amp: InputPathType,
+    sh: str,
+    lmax: int | None = None,
+    normalise: bool = False,
+    directions: InputPathType | None = None,
+    rician: InputPathType | None = None,
+    grad: InputPathType | None = None,
+    fslgrad: Amp2shFslgradParamsDict | None = None,
+    shells: list[float] | None = None,
+    strides: typing.Union[Amp2shVariousStringParamsDictTagged, Amp2shVariousFileParamsDictTagged] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2shConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Amp2shOutputs:
+    """
+    amp2sh
+    
+    Convert a set of amplitudes (defined along a set of corresponding
+    directions) to their spherical harmonic representation.
+    
+    The spherical harmonic decomposition is calculated by least-squares linear
+    fitting to the amplitude data.
+    
+    The directions can be defined either as a DW gradient scheme (for example to
+    compute the SH representation of the DW signal), a set of [az el] pairs as
+    output by the dirgen command, or a set of [ x y z ] directions in Cartesian
+    coordinates. The DW gradient scheme or direction set can be supplied within
+    the input image header or using the -gradient or -directions option. Note
+    that if a direction set and DW gradient scheme can be found, the direction
+    set will be used by default.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        amp: the input amplitude image.
+        sh: the output spherical harmonics coefficients image.
+        lmax: set the maximum harmonic order for the output series. By default,\
+            the program will use the highest possible lmax given the number of\
+            diffusion-weighted images, up to a maximum of 8.
+        normalise: normalise the DW signal to the b=0 image.
+        directions: the directions corresponding to the input amplitude image\
+            used to sample AFD. By default this option is not required providing\
+            the direction set is supplied in the amplitude image. This should be\
+            supplied as a list of directions [az el], as generated using the dirgen\
+            command, or as a list of [ x y z ] Cartesian coordinates.
+        rician: correct for Rician noise induced bias, using noise map supplied.
+        grad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in a text file. This should be supplied as a 4xN text file\
+            with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
+            the direction of the applied gradient, and b gives the b-value in units\
+            of s/mm^2. If a diffusion gradient scheme is present in the input image\
+            header, the data provided with this option will be instead used.
+        fslgrad: Provide the diffusion-weighted gradient scheme used in the\
+            acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
+            scheme is present in the input image header, the data provided with\
+            this option will be instead used.
+        shells: specify one or more b-values to use during processing, as a\
+            comma-separated list of the desired approximate b-values (b-values are\
+            clustered to allow for small deviations). Note that some commands are\
+            incompatible with multiple b-values, and will report an error if more\
+            than one b-value is provided.\
+            WARNING: note that, even though the b=0 volumes are never referred\
+            to as shells in the literature, they still have to be explicitly\
+            included in the list of b-values as provided to the -shell option!\
+            Several algorithms which include the b=0 volumes in their\
+            computations may otherwise return an undesired result.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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 `Amp2shOutputs`).
+    """
+    params = amp2sh_params(
+        lmax=lmax,
+        normalise=normalise,
+        directions=directions,
+        rician=rician,
+        grad=grad,
+        fslgrad=fslgrad,
+        shells=shells,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        amp=amp,
+        sh=sh,
+    )
+    return amp2sh_execute(params, runner)
+
+
+__all__ = [
+    "AMP2SH_METADATA",
+    "Amp2shConfigParamsDict",
+    "Amp2shConfigParamsDictTagged",
+    "Amp2shFslgradParamsDict",
+    "Amp2shFslgradParamsDictTagged",
+    "Amp2shOutputs",
+    "Amp2shParamsDict",
+    "Amp2shParamsDictTagged",
+    "Amp2shVariousFileParamsDict",
+    "Amp2shVariousFileParamsDictTagged",
+    "Amp2shVariousStringParamsDict",
+    "Amp2shVariousStringParamsDictTagged",
+    "amp2sh",
+    "amp2sh_config",
+    "amp2sh_execute",
+    "amp2sh_fslgrad",
+    "amp2sh_params",
+    "amp2sh_various_file",
+    "amp2sh_various_string",
+]