# This file was auto generated by Styx.
# Do not edit this file directly.

import typing
import pathlib
from styxdefs import *

WARPCORRECT_METADATA = Metadata(
    id="d93e432b2c126575958a3ff19d36f91ad4461c2e.boutiques",
    name="warpcorrect",
    package="mrtrix",
    container_image_tag="mrtrix3/mrtrix3:3.0.4",
)


_WarpcorrectConfigParamsDictNoTag = typing.TypedDict('_WarpcorrectConfigParamsDictNoTag', {
    "key": str,
    "value": str,
})
WarpcorrectConfigParamsDictTagged = typing.TypedDict('WarpcorrectConfigParamsDictTagged', {
    "@type": typing.Literal["config"],
    "key": str,
    "value": str,
})
WarpcorrectConfigParamsDict = _WarpcorrectConfigParamsDictNoTag | WarpcorrectConfigParamsDictTagged


_WarpcorrectParamsDictNoTag = typing.TypedDict('_WarpcorrectParamsDictNoTag', {
    "marker": typing.NotRequired[list[float] | None],
    "tolerance": typing.NotRequired[float | None],
    "info": bool,
    "quiet": bool,
    "debug": bool,
    "force": bool,
    "nthreads": typing.NotRequired[int | None],
    "config": typing.NotRequired[list[WarpcorrectConfigParamsDict] | None],
    "help": bool,
    "version": bool,
    "in": InputPathType,
    "out": str,
})
WarpcorrectParamsDictTagged = typing.TypedDict('WarpcorrectParamsDictTagged', {
    "@type": typing.Literal["mrtrix/warpcorrect"],
    "marker": typing.NotRequired[list[float] | None],
    "tolerance": typing.NotRequired[float | None],
    "info": bool,
    "quiet": bool,
    "debug": bool,
    "force": bool,
    "nthreads": typing.NotRequired[int | None],
    "config": typing.NotRequired[list[WarpcorrectConfigParamsDict] | None],
    "help": bool,
    "version": bool,
    "in": InputPathType,
    "out": str,
})
WarpcorrectParamsDict = _WarpcorrectParamsDictNoTag | WarpcorrectParamsDictTagged


def warpcorrect_config(
    key: str,
    value: str,
) -> WarpcorrectConfigParamsDictTagged:
    """
    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 warpcorrect_config_validate(
    params: typing.Any,
) -> None:
    """
    Validate parameters. Throws an error if `params` is not a valid
    `WarpcorrectConfigParamsDict` 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 warpcorrect_config_cargs(
    params: WarpcorrectConfigParamsDict,
    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 WarpcorrectOutputs(typing.NamedTuple):
    """
    Output object returned when calling `WarpcorrectParamsDict(...)`.
    """
    root: OutputPathType
    """Output root folder. This is the root folder for all outputs."""
    out: OutputPathType
    """the output warp image."""


def warpcorrect_params(
    in_: InputPathType,
    out: str,
    marker: list[float] | None = None,
    tolerance: float | None = None,
    info: bool = False,
    quiet: bool = False,
    debug: bool = False,
    force: bool = False,
    nthreads: int | None = None,
    config: list[WarpcorrectConfigParamsDict] | None = None,
    help_: bool = False,
    version: bool = False,
) -> WarpcorrectParamsDictTagged:
    """
    Build parameters.
    
    Args:
        in_: the input warp image.
        out: the output warp image.
        marker: single value or a comma separated list of values that define\
            out of bounds voxels in the input warp image. Default: (0,0,0).
        tolerance: numerical precision used for L2 matrix norm comparison.\
            Default: 9.99999975e-06.
        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/warpcorrect",
        "info": info,
        "quiet": quiet,
        "debug": debug,
        "force": force,
        "help": help_,
        "version": version,
        "in": in_,
        "out": out,
    }
    if marker is not None:
        params["marker"] = marker
    if tolerance is not None:
        params["tolerance"] = tolerance
    if nthreads is not None:
        params["nthreads"] = nthreads
    if config is not None:
        params["config"] = config
    return params


def warpcorrect_validate(
    params: typing.Any,
) -> None:
    """
    Validate parameters. Throws an error if `params` is not a valid
    `WarpcorrectParamsDict` 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("marker", None) is not None:
        if not isinstance(params["marker"], list):
            raise StyxValidationError(f'`marker` has the wrong type: Received `{type(params.get("marker", None))}` expected `list[float] | None`')
        for e in params["marker"]:
            if not isinstance(e, (float, int)):
                raise StyxValidationError(f'`marker` has the wrong type: Received `{type(params.get("marker", None))}` expected `list[float] | None`')
    if params.get("tolerance", None) is not None:
        if not isinstance(params["tolerance"], (float, int)):
            raise StyxValidationError(f'`tolerance` has the wrong type: Received `{type(params.get("tolerance", None))}` expected `float | 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[WarpcorrectConfigParamsDict] | None`')
        for e in params["config"]:
            warpcorrect_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("in", None) is None:
        raise StyxValidationError("`in` must not be None")
    if not isinstance(params["in"], (pathlib.Path, str)):
        raise StyxValidationError(f'`in` has the wrong type: Received `{type(params.get("in", None))}` expected `InputPathType`')
    if params.get("out", None) is None:
        raise StyxValidationError("`out` must not be None")
    if not isinstance(params["out"], str):
        raise StyxValidationError(f'`out` has the wrong type: Received `{type(params.get("out", None))}` expected `str`')


def warpcorrect_cargs(
    params: WarpcorrectParamsDict,
    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("warpcorrect")
    if params.get("marker", None) is not None:
        cargs.extend([
            "-marker",
            *map(str, params.get("marker", None))
        ])
    if params.get("tolerance", None) is not None:
        cargs.extend([
            "-tolerance",
            str(params.get("tolerance", 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 [warpcorrect_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("in", None)))
    cargs.append(params.get("out", None))
    return cargs


def warpcorrect_outputs(
    params: WarpcorrectParamsDict,
    execution: Execution,
) -> WarpcorrectOutputs:
    """
    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 = WarpcorrectOutputs(
        root=execution.output_file("."),
        out=execution.output_file(params.get("out", None)),
    )
    return ret


def warpcorrect_execute(
    params: WarpcorrectParamsDict,
    runner: Runner | None = None,
) -> WarpcorrectOutputs:
    """
    warpcorrect
    
    Replaces voxels in a deformation field that point to a specific out of
    bounds location with nan,nan,nan.
    
    This can be used in conjunction with the warpinit command to compute a
    MRtrix compatible deformation field from non-linear transformations
    generated by any other registration package.
    
    References:
    
    .
    
    Author: MRTrix3 Developers
    
    URL: https://www.mrtrix.org/
    
    Args:
        params: The parameters.
        runner: Command runner.
    Returns:
        NamedTuple of outputs (described in `WarpcorrectOutputs`).
    """
    warpcorrect_validate(params)
    runner = runner or get_global_runner()
    execution = runner.start_execution(WARPCORRECT_METADATA)
    params = execution.params(params)
    cargs = warpcorrect_cargs(params, execution)
    ret = warpcorrect_outputs(params, execution)
    execution.run(cargs)
    return ret


def warpcorrect(
    in_: InputPathType,
    out: str,
    marker: list[float] | None = None,
    tolerance: float | None = None,
    info: bool = False,
    quiet: bool = False,
    debug: bool = False,
    force: bool = False,
    nthreads: int | None = None,
    config: list[WarpcorrectConfigParamsDict] | None = None,
    help_: bool = False,
    version: bool = False,
    runner: Runner | None = None,
) -> WarpcorrectOutputs:
    """
    warpcorrect
    
    Replaces voxels in a deformation field that point to a specific out of
    bounds location with nan,nan,nan.
    
    This can be used in conjunction with the warpinit command to compute a
    MRtrix compatible deformation field from non-linear transformations
    generated by any other registration package.
    
    References:
    
    .
    
    Author: MRTrix3 Developers
    
    URL: https://www.mrtrix.org/
    
    Args:
        in_: the input warp image.
        out: the output warp image.
        marker: single value or a comma separated list of values that define\
            out of bounds voxels in the input warp image. Default: (0,0,0).
        tolerance: numerical precision used for L2 matrix norm comparison.\
            Default: 9.99999975e-06.
        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 `WarpcorrectOutputs`).
    """
    params = warpcorrect_params(
        marker=marker,
        tolerance=tolerance,
        info=info,
        quiet=quiet,
        debug=debug,
        force=force,
        nthreads=nthreads,
        config=config,
        help_=help_,
        version=version,
        in_=in_,
        out=out,
    )
    return warpcorrect_execute(params, runner)


__all__ = [
    "WARPCORRECT_METADATA",
    "WarpcorrectConfigParamsDict",
    "WarpcorrectConfigParamsDictTagged",
    "WarpcorrectOutputs",
    "WarpcorrectParamsDict",
    "WarpcorrectParamsDictTagged",
    "warpcorrect",
    "warpcorrect_config",
    "warpcorrect_execute",
    "warpcorrect_params",
]
