niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warpcorrect.py

@@ -0,0 +1,448 @@
+# 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",
+]