niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/sh2amp.py

@@ -0,0 +1,844 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SH2AMP_METADATA = Metadata(
+    id="845bbdcb825f577d4f4e931e8e0dd0e1f1f2de94.boutiques",
+    name="sh2amp",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Sh2ampFslgradParamsDictNoTag = typing.TypedDict('_Sh2ampFslgradParamsDictNoTag', {
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Sh2ampFslgradParamsDictTagged = typing.TypedDict('Sh2ampFslgradParamsDictTagged', {
+    "@type": typing.Literal["fslgrad"],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+Sh2ampFslgradParamsDict = _Sh2ampFslgradParamsDictNoTag | Sh2ampFslgradParamsDictTagged
+
+
+_Sh2ampVariousStringParamsDictNoTag = typing.TypedDict('_Sh2ampVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+Sh2ampVariousStringParamsDictTagged = typing.TypedDict('Sh2ampVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+Sh2ampVariousStringParamsDict = _Sh2ampVariousStringParamsDictNoTag | Sh2ampVariousStringParamsDictTagged
+
+
+_Sh2ampVariousFileParamsDictNoTag = typing.TypedDict('_Sh2ampVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+Sh2ampVariousFileParamsDictTagged = typing.TypedDict('Sh2ampVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+Sh2ampVariousFileParamsDict = _Sh2ampVariousFileParamsDictNoTag | Sh2ampVariousFileParamsDictTagged
+
+
+_Sh2ampConfigParamsDictNoTag = typing.TypedDict('_Sh2ampConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Sh2ampConfigParamsDictTagged = typing.TypedDict('Sh2ampConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Sh2ampConfigParamsDict = _Sh2ampConfigParamsDictNoTag | Sh2ampConfigParamsDictTagged
+
+
+_Sh2ampParamsDictNoTag = typing.TypedDict('_Sh2ampParamsDictNoTag', {
+    "nonnegative": bool,
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Sh2ampFslgradParamsDict | None],
+    "strides": typing.NotRequired[typing.Union[Sh2ampVariousStringParamsDictTagged, Sh2ampVariousFileParamsDictTagged] | None],
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2ampConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "directions": InputPathType,
+    "output": str,
+})
+Sh2ampParamsDictTagged = typing.TypedDict('Sh2ampParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/sh2amp"],
+    "nonnegative": bool,
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[Sh2ampFslgradParamsDict | None],
+    "strides": typing.NotRequired[typing.Union[Sh2ampVariousStringParamsDictTagged, Sh2ampVariousFileParamsDictTagged] | None],
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2ampConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "directions": InputPathType,
+    "output": str,
+})
+Sh2ampParamsDict = _Sh2ampParamsDictNoTag | Sh2ampParamsDictTagged
+
+
+def sh2amp_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": sh2amp_various_string_cargs,
+        "VariousFile": sh2amp_various_file_cargs,
+    }.get(t)
+
+
+def sh2amp_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": sh2amp_various_string_validate,
+        "VariousFile": sh2amp_various_file_validate,
+    }.get(t)
+
+
+def sh2amp_fslgrad(
+    bvecs: InputPathType,
+    bvals: InputPathType,
+) -> Sh2ampFslgradParamsDictTagged:
+    """
+    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 sh2amp_fslgrad_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2ampFslgradParamsDict` 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 sh2amp_fslgrad_cargs(
+    params: Sh2ampFslgradParamsDict,
+    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 sh2amp_various_string(
+    obj: str,
+) -> Sh2ampVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def sh2amp_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2ampVariousStringParamsDict` 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 sh2amp_various_string_cargs(
+    params: Sh2ampVariousStringParamsDict,
+    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 sh2amp_various_file(
+    obj: InputPathType,
+) -> Sh2ampVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def sh2amp_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2ampVariousFileParamsDict` 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 sh2amp_various_file_cargs(
+    params: Sh2ampVariousFileParamsDict,
+    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 sh2amp_config(
+    key: str,
+    value: str,
+) -> Sh2ampConfigParamsDictTagged:
+    """
+    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 sh2amp_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2ampConfigParamsDict` 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 sh2amp_config_cargs(
+    params: Sh2ampConfigParamsDict,
+    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 Sh2ampOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Sh2ampParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image consisting of the amplitude of the SH functions along
+    the specified directions."""
+
+
+def sh2amp_params(
+    input_: InputPathType,
+    directions: InputPathType,
+    output: str,
+    nonnegative: bool = False,
+    grad: InputPathType | None = None,
+    fslgrad: Sh2ampFslgradParamsDict | None = None,
+    strides: typing.Union[Sh2ampVariousStringParamsDictTagged, Sh2ampVariousFileParamsDictTagged] | None = None,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Sh2ampConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Sh2ampParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image consisting of spherical harmonic (SH)\
+            coefficients.
+        directions: the list of directions along which the SH functions will be\
+            sampled, generated using the dirgen command.
+        output: the output image consisting of the amplitude of the SH\
+            functions along the specified directions.
+        nonnegative: cap all negative amplitudes to zero.
+        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.
+        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.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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/sh2amp",
+        "nonnegative": nonnegative,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "directions": directions,
+        "output": output,
+    }
+    if grad is not None:
+        params["grad"] = grad
+    if fslgrad is not None:
+        params["fslgrad"] = fslgrad
+    if strides is not None:
+        params["strides"] = strides
+    if datatype is not None:
+        params["datatype"] = datatype
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def sh2amp_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Sh2ampParamsDict` 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("nonnegative", False) is None:
+        raise StyxValidationError("`nonnegative` must not be None")
+    if not isinstance(params["nonnegative"], bool):
+        raise StyxValidationError(f'`nonnegative` has the wrong type: Received `{type(params.get("nonnegative", False))}` expected `bool`')
+    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:
+        sh2amp_fslgrad_validate(params["fslgrad"])
+    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\"]")
+        sh2amp_strides_validate_dyn_fn(params["strides"]["@type"])(params["strides"])
+    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("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[Sh2ampConfigParamsDict] | None`')
+        for e in params["config"]:
+            sh2amp_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"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `InputPathType`')
+    if params.get("directions", None) is None:
+        raise StyxValidationError("`directions` must not be 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`')
+    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 sh2amp_cargs(
+    params: Sh2ampParamsDict,
+    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("sh2amp")
+    if params.get("nonnegative", False):
+        cargs.append("-nonnegative")
+    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(sh2amp_fslgrad_cargs(params.get("fslgrad", None), execution))
+    if params.get("strides", None) is not None:
+        cargs.extend([
+            "-strides",
+            *sh2amp_strides_cargs_dyn_fn(params.get("strides", None)["@type"])(params.get("strides", None), execution)
+        ])
+    if params.get("datatype", None) is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype", 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 [sh2amp_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("input", None)))
+    cargs.append(execution.input_file(params.get("directions", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def sh2amp_outputs(
+    params: Sh2ampParamsDict,
+    execution: Execution,
+) -> Sh2ampOutputs:
+    """
+    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 = Sh2ampOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def sh2amp_execute(
+    params: Sh2ampParamsDict,
+    runner: Runner | None = None,
+) -> Sh2ampOutputs:
+    """
+    sh2amp
+    
+    Evaluate the amplitude of an image of spherical harmonic functions along
+    specified directions.
+    
+    The input image should consist of a 4D or 5D image, with SH coefficients
+    along the 4th dimension according to the convention below. If 4D (or size 1
+    along the 5th dimension), the program expects to be provided with a single
+    shell of directions. If 5D, each set of coefficients along the 5th dimension
+    is understood to correspond to a different shell.
+    
+    The directions can be provided as:
+    - a 2-column ASCII text file contained azimuth / elevation pairs (as
+    produced by dirgen)
+    - a 3-column ASCII text file containing x, y, z Cartesian direction vectors
+    (as produced by dirgen -cart)
+    - a 4-column ASCII text file containing the x, y, z, b components of a full
+    DW encoding scheme (in MRtrix format, see main documentation for details).
+    - an image file whose header contains a valid DW encoding scheme
+    
+    If a full DW encoding is provided, the number of shells needs to match those
+    found in the input image of coefficients (i.e. its size along the 5th
+    dimension). If needed, the -shell option can be used to pick out the
+    specific shell(s) of interest.
+    
+    If the input image contains multiple shells (its size along the 5th
+    dimension is greater than one), the program will expect the direction set to
+    contain multiple shells, which can only be provided as a full DW encodings
+    (the last two options in the list above).
+    
+    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 `Sh2ampOutputs`).
+    """
+    sh2amp_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SH2AMP_METADATA)
+    params = execution.params(params)
+    cargs = sh2amp_cargs(params, execution)
+    ret = sh2amp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def sh2amp(
+    input_: InputPathType,
+    directions: InputPathType,
+    output: str,
+    nonnegative: bool = False,
+    grad: InputPathType | None = None,
+    fslgrad: Sh2ampFslgradParamsDict | None = None,
+    strides: typing.Union[Sh2ampVariousStringParamsDictTagged, Sh2ampVariousFileParamsDictTagged] | None = None,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Sh2ampConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Sh2ampOutputs:
+    """
+    sh2amp
+    
+    Evaluate the amplitude of an image of spherical harmonic functions along
+    specified directions.
+    
+    The input image should consist of a 4D or 5D image, with SH coefficients
+    along the 4th dimension according to the convention below. If 4D (or size 1
+    along the 5th dimension), the program expects to be provided with a single
+    shell of directions. If 5D, each set of coefficients along the 5th dimension
+    is understood to correspond to a different shell.
+    
+    The directions can be provided as:
+    - a 2-column ASCII text file contained azimuth / elevation pairs (as
+    produced by dirgen)
+    - a 3-column ASCII text file containing x, y, z Cartesian direction vectors
+    (as produced by dirgen -cart)
+    - a 4-column ASCII text file containing the x, y, z, b components of a full
+    DW encoding scheme (in MRtrix format, see main documentation for details).
+    - an image file whose header contains a valid DW encoding scheme
+    
+    If a full DW encoding is provided, the number of shells needs to match those
+    found in the input image of coefficients (i.e. its size along the 5th
+    dimension). If needed, the -shell option can be used to pick out the
+    specific shell(s) of interest.
+    
+    If the input image contains multiple shells (its size along the 5th
+    dimension is greater than one), the program will expect the direction set to
+    contain multiple shells, which can only be provided as a full DW encodings
+    (the last two options in the list above).
+    
+    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:
+        input_: the input image consisting of spherical harmonic (SH)\
+            coefficients.
+        directions: the list of directions along which the SH functions will be\
+            sampled, generated using the dirgen command.
+        output: the output image consisting of the amplitude of the SH\
+            functions along the specified directions.
+        nonnegative: cap all negative amplitudes to zero.
+        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.
+        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.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        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 `Sh2ampOutputs`).
+    """
+    params = sh2amp_params(
+        nonnegative=nonnegative,
+        grad=grad,
+        fslgrad=fslgrad,
+        strides=strides,
+        datatype=datatype,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        directions=directions,
+        output=output,
+    )
+    return sh2amp_execute(params, runner)
+
+
+__all__ = [
+    "SH2AMP_METADATA",
+    "Sh2ampConfigParamsDict",
+    "Sh2ampConfigParamsDictTagged",
+    "Sh2ampFslgradParamsDict",
+    "Sh2ampFslgradParamsDictTagged",
+    "Sh2ampOutputs",
+    "Sh2ampParamsDict",
+    "Sh2ampParamsDictTagged",
+    "Sh2ampVariousFileParamsDict",
+    "Sh2ampVariousFileParamsDictTagged",
+    "Sh2ampVariousStringParamsDict",
+    "Sh2ampVariousStringParamsDictTagged",
+    "sh2amp",
+    "sh2amp_config",
+    "sh2amp_execute",
+    "sh2amp_fslgrad",
+    "sh2amp_params",
+    "sh2amp_various_file",
+    "sh2amp_various_string",
+]