niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/amp2response.py

@@ -0,0 +1,560 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+AMP2RESPONSE_METADATA = Metadata(
+    id="f0088602c41a6ff20ec7c430ad21aee73ff1f3e4.boutiques",
+    name="amp2response",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_Amp2responseConfigParamsDictNoTag = typing.TypedDict('_Amp2responseConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+Amp2responseConfigParamsDictTagged = typing.TypedDict('Amp2responseConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+Amp2responseConfigParamsDict = _Amp2responseConfigParamsDictNoTag | Amp2responseConfigParamsDictTagged
+
+
+_Amp2responseParamsDictNoTag = typing.TypedDict('_Amp2responseParamsDictNoTag', {
+    "isotropic": bool,
+    "noconstraint": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "lmax": typing.NotRequired[list[int] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2responseConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "amps": InputPathType,
+    "mask": InputPathType,
+    "directions_1": InputPathType,
+    "response": str,
+})
+Amp2responseParamsDictTagged = typing.TypedDict('Amp2responseParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/amp2response"],
+    "isotropic": bool,
+    "noconstraint": bool,
+    "directions": typing.NotRequired[InputPathType | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "lmax": typing.NotRequired[list[int] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Amp2responseConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "amps": InputPathType,
+    "mask": InputPathType,
+    "directions_1": InputPathType,
+    "response": str,
+})
+Amp2responseParamsDict = _Amp2responseParamsDictNoTag | Amp2responseParamsDictTagged
+
+
+def amp2response_config(
+    key: str,
+    value: str,
+) -> Amp2responseConfigParamsDictTagged:
+    """
+    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 amp2response_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2responseConfigParamsDict` 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 amp2response_config_cargs(
+    params: Amp2responseConfigParamsDict,
+    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 Amp2responseOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `Amp2responseParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    response: OutputPathType
+    """the output zonal spherical harmonic coefficients"""
+
+
+def amp2response_params(
+    amps: InputPathType,
+    mask: InputPathType,
+    directions_1: InputPathType,
+    response: str,
+    isotropic: bool = False,
+    noconstraint: bool = False,
+    directions: InputPathType | None = None,
+    shells: list[float] | None = None,
+    lmax: list[int] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2responseConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Amp2responseParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        amps: the amplitudes image.
+        mask: the mask containing the voxels from which to estimate the\
+            response function.
+        directions_1: a 4D image containing the estimated fibre directions.
+        response: the output zonal spherical harmonic coefficients.
+        isotropic: estimate an isotropic response function (lmax=0 for all\
+            shells).
+        noconstraint: disable the non-negativity and monotonicity constraints.
+        directions: provide an external text file containing the directions\
+            along which the amplitudes are sampled.
+        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.
+        lmax: specify the maximum harmonic degree of the response function to\
+            estimate (can be a comma-separated list for multi-shell data).
+        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/amp2response",
+        "isotropic": isotropic,
+        "noconstraint": noconstraint,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "amps": amps,
+        "mask": mask,
+        "directions_1": directions_1,
+        "response": response,
+    }
+    if directions is not None:
+        params["directions"] = directions
+    if shells is not None:
+        params["shells"] = shells
+    if lmax is not None:
+        params["lmax"] = lmax
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def amp2response_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `Amp2responseParamsDict` 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("isotropic", False) is None:
+        raise StyxValidationError("`isotropic` must not be None")
+    if not isinstance(params["isotropic"], bool):
+        raise StyxValidationError(f'`isotropic` has the wrong type: Received `{type(params.get("isotropic", False))}` expected `bool`')
+    if params.get("noconstraint", False) is None:
+        raise StyxValidationError("`noconstraint` must not be None")
+    if not isinstance(params["noconstraint"], bool):
+        raise StyxValidationError(f'`noconstraint` has the wrong type: Received `{type(params.get("noconstraint", 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("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("lmax", None) is not None:
+        if not isinstance(params["lmax"], list):
+            raise StyxValidationError(f'`lmax` has the wrong type: Received `{type(params.get("lmax", None))}` expected `list[int] | None`')
+        for e in params["lmax"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`lmax` has the wrong type: Received `{type(params.get("lmax", None))}` expected `list[int] | 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[Amp2responseConfigParamsDict] | None`')
+        for e in params["config"]:
+            amp2response_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("amps", None) is None:
+        raise StyxValidationError("`amps` must not be None")
+    if not isinstance(params["amps"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`amps` has the wrong type: Received `{type(params.get("amps", None))}` expected `InputPathType`')
+    if params.get("mask", None) is None:
+        raise StyxValidationError("`mask` must not be None")
+    if not isinstance(params["mask"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType`')
+    if params.get("directions_1", None) is None:
+        raise StyxValidationError("`directions_1` must not be None")
+    if not isinstance(params["directions_1"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`directions_1` has the wrong type: Received `{type(params.get("directions_1", None))}` expected `InputPathType`')
+    if params.get("response", None) is None:
+        raise StyxValidationError("`response` must not be None")
+    if not isinstance(params["response"], str):
+        raise StyxValidationError(f'`response` has the wrong type: Received `{type(params.get("response", None))}` expected `str`')
+
+
+def amp2response_cargs(
+    params: Amp2responseParamsDict,
+    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("amp2response")
+    if params.get("isotropic", False):
+        cargs.append("-isotropic")
+    if params.get("noconstraint", False):
+        cargs.append("-noconstraint")
+    if params.get("directions", None) is not None:
+        cargs.extend([
+            "-directions",
+            execution.input_file(params.get("directions", None))
+        ])
+    if params.get("shells", None) is not None:
+        cargs.extend([
+            "-shells",
+            ",".join(map(str, params.get("shells", None)))
+        ])
+    if params.get("lmax", None) is not None:
+        cargs.extend([
+            "-lmax",
+            ",".join(map(str, params.get("lmax", 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 [amp2response_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("amps", None)))
+    cargs.append(execution.input_file(params.get("mask", None)))
+    cargs.append(execution.input_file(params.get("directions_1", None)))
+    cargs.append(params.get("response", None))
+    return cargs
+
+
+def amp2response_outputs(
+    params: Amp2responseParamsDict,
+    execution: Execution,
+) -> Amp2responseOutputs:
+    """
+    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 = Amp2responseOutputs(
+        root=execution.output_file("."),
+        response=execution.output_file(params.get("response", None)),
+    )
+    return ret
+
+
+def amp2response_execute(
+    params: Amp2responseParamsDict,
+    runner: Runner | None = None,
+) -> Amp2responseOutputs:
+    """
+    amp2response
+    
+    Estimate response function coefficients based on the DWI signal in
+    single-fibre voxels.
+    
+    This command uses the image data from all selected single-fibre voxels
+    concurrently, rather than simply averaging their individual spherical
+    harmonic coefficients. It also ensures that the response function is
+    non-negative, and monotonic (i.e. its amplitude must increase from the fibre
+    direction out to the orthogonal plane).
+    
+    If multi-shell data are provided, and one or more b-value shells are not
+    explicitly requested, the command will generate a response function for
+    every b-value shell (including b=0 if present).
+    
+    References:
+    
+    Smith, R. E.; Dhollander, T. & Connelly, A. Constrained linear least squares
+    estimation of anisotropic response function for spherical deconvolution.
+    ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 23.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Amp2responseOutputs`).
+    """
+    amp2response_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AMP2RESPONSE_METADATA)
+    params = execution.params(params)
+    cargs = amp2response_cargs(params, execution)
+    ret = amp2response_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def amp2response(
+    amps: InputPathType,
+    mask: InputPathType,
+    directions_1: InputPathType,
+    response: str,
+    isotropic: bool = False,
+    noconstraint: bool = False,
+    directions: InputPathType | None = None,
+    shells: list[float] | None = None,
+    lmax: list[int] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Amp2responseConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Amp2responseOutputs:
+    """
+    amp2response
+    
+    Estimate response function coefficients based on the DWI signal in
+    single-fibre voxels.
+    
+    This command uses the image data from all selected single-fibre voxels
+    concurrently, rather than simply averaging their individual spherical
+    harmonic coefficients. It also ensures that the response function is
+    non-negative, and monotonic (i.e. its amplitude must increase from the fibre
+    direction out to the orthogonal plane).
+    
+    If multi-shell data are provided, and one or more b-value shells are not
+    explicitly requested, the command will generate a response function for
+    every b-value shell (including b=0 if present).
+    
+    References:
+    
+    Smith, R. E.; Dhollander, T. & Connelly, A. Constrained linear least squares
+    estimation of anisotropic response function for spherical deconvolution.
+    ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 23.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        amps: the amplitudes image.
+        mask: the mask containing the voxels from which to estimate the\
+            response function.
+        directions_1: a 4D image containing the estimated fibre directions.
+        response: the output zonal spherical harmonic coefficients.
+        isotropic: estimate an isotropic response function (lmax=0 for all\
+            shells).
+        noconstraint: disable the non-negativity and monotonicity constraints.
+        directions: provide an external text file containing the directions\
+            along which the amplitudes are sampled.
+        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.
+        lmax: specify the maximum harmonic degree of the response function to\
+            estimate (can be a comma-separated list for multi-shell data).
+        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 `Amp2responseOutputs`).
+    """
+    params = amp2response_params(
+        isotropic=isotropic,
+        noconstraint=noconstraint,
+        directions=directions,
+        shells=shells,
+        lmax=lmax,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        amps=amps,
+        mask=mask,
+        directions_1=directions_1,
+        response=response,
+    )
+    return amp2response_execute(params, runner)
+
+
+__all__ = [
+    "AMP2RESPONSE_METADATA",
+    "Amp2responseConfigParamsDict",
+    "Amp2responseConfigParamsDictTagged",
+    "Amp2responseOutputs",
+    "Amp2responseParamsDict",
+    "Amp2responseParamsDictTagged",
+    "amp2response",
+    "amp2response_config",
+    "amp2response_execute",
+    "amp2response_params",
+]