niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelreorient.py

@@ -0,0 +1,435 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELREORIENT_METADATA = Metadata(
+    id="c2bf37ec8d7ea2da68c628776a8974d1b5351f66.boutiques",
+    name="fixelreorient",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_FixelreorientConfigParamsDictNoTag = typing.TypedDict('_FixelreorientConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+FixelreorientConfigParamsDictTagged = typing.TypedDict('FixelreorientConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+FixelreorientConfigParamsDict = _FixelreorientConfigParamsDictNoTag | FixelreorientConfigParamsDictTagged
+
+
+_FixelreorientParamsDictNoTag = typing.TypedDict('_FixelreorientParamsDictNoTag', {
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelreorientConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "warp": InputPathType,
+    "fixel_out": str,
+})
+FixelreorientParamsDictTagged = typing.TypedDict('FixelreorientParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/fixelreorient"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelreorientConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_in": InputPathType,
+    "warp": InputPathType,
+    "fixel_out": str,
+})
+FixelreorientParamsDict = _FixelreorientParamsDictNoTag | FixelreorientParamsDictTagged
+
+
+def fixelreorient_config(
+    key: str,
+    value: str,
+) -> FixelreorientConfigParamsDictTagged:
+    """
+    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 fixelreorient_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelreorientConfigParamsDict` 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 fixelreorient_config_cargs(
+    params: FixelreorientConfigParamsDict,
+    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 FixelreorientOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `FixelreorientParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fixel_out: OutputPathType
+    """the output fixel directory. If the the input and output directories are
+    the same, the existing directions file will be replaced (providing the
+    -force option is supplied). If a new directory is supplied then the fixel
+    directions and all other fixel data will be copied to the new directory."""
+
+
+def fixelreorient_params(
+    fixel_in: InputPathType,
+    warp: InputPathType,
+    fixel_out: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelreorientConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelreorientParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        fixel_in: the input fixel directory.
+        warp: a 4D deformation field used to perform reorientation.\
+            Reorientation is performed by applying the Jacobian affine transform in\
+            each voxel in the warp, then re-normalising the vector representing the\
+            fixel direction.
+        fixel_out: the output fixel directory. If the the input and output\
+            directories are the same, the existing directions file will be replaced\
+            (providing the -force option is supplied). If a new directory is\
+            supplied then the fixel directions and all other fixel data will be\
+            copied to the new directory.
+        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/fixelreorient",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "fixel_in": fixel_in,
+        "warp": warp,
+        "fixel_out": fixel_out,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelreorient_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `FixelreorientParamsDict` 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("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[FixelreorientConfigParamsDict] | None`')
+        for e in params["config"]:
+            fixelreorient_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("fixel_in", None) is None:
+        raise StyxValidationError("`fixel_in` must not be None")
+    if not isinstance(params["fixel_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`fixel_in` has the wrong type: Received `{type(params.get("fixel_in", None))}` expected `InputPathType`')
+    if params.get("warp", None) is None:
+        raise StyxValidationError("`warp` must not be None")
+    if not isinstance(params["warp"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`warp` has the wrong type: Received `{type(params.get("warp", None))}` expected `InputPathType`')
+    if params.get("fixel_out", None) is None:
+        raise StyxValidationError("`fixel_out` must not be None")
+    if not isinstance(params["fixel_out"], str):
+        raise StyxValidationError(f'`fixel_out` has the wrong type: Received `{type(params.get("fixel_out", None))}` expected `str`')
+
+
+def fixelreorient_cargs(
+    params: FixelreorientParamsDict,
+    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("fixelreorient")
+    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 [fixelreorient_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("fixel_in", None)))
+    cargs.append(execution.input_file(params.get("warp", None)))
+    cargs.append(params.get("fixel_out", None))
+    return cargs
+
+
+def fixelreorient_outputs(
+    params: FixelreorientParamsDict,
+    execution: Execution,
+) -> FixelreorientOutputs:
+    """
+    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 = FixelreorientOutputs(
+        root=execution.output_file("."),
+        fixel_out=execution.output_file(params.get("fixel_out", None)),
+    )
+    return ret
+
+
+def fixelreorient_execute(
+    params: FixelreorientParamsDict,
+    runner: Runner | None = None,
+) -> FixelreorientOutputs:
+    """
+    fixelreorient
+    
+    Reorient fixel directions.
+    
+    Reorientation is performed by transforming the vector representing the fixel
+    direction with the Jacobian (local affine transform) computed at each voxel
+    in the warp, then re-normalising the vector.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FixelreorientOutputs`).
+    """
+    fixelreorient_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELREORIENT_METADATA)
+    params = execution.params(params)
+    cargs = fixelreorient_cargs(params, execution)
+    ret = fixelreorient_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelreorient(
+    fixel_in: InputPathType,
+    warp: InputPathType,
+    fixel_out: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelreorientConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelreorientOutputs:
+    """
+    fixelreorient
+    
+    Reorient fixel directions.
+    
+    Reorientation is performed by transforming the vector representing the fixel
+    direction with the Jacobian (local affine transform) computed at each voxel
+    in the warp, then re-normalising the vector.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        fixel_in: the input fixel directory.
+        warp: a 4D deformation field used to perform reorientation.\
+            Reorientation is performed by applying the Jacobian affine transform in\
+            each voxel in the warp, then re-normalising the vector representing the\
+            fixel direction.
+        fixel_out: the output fixel directory. If the the input and output\
+            directories are the same, the existing directions file will be replaced\
+            (providing the -force option is supplied). If a new directory is\
+            supplied then the fixel directions and all other fixel data will be\
+            copied to the new directory.
+        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 `FixelreorientOutputs`).
+    """
+    params = fixelreorient_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        fixel_in=fixel_in,
+        warp=warp,
+        fixel_out=fixel_out,
+    )
+    return fixelreorient_execute(params, runner)
+
+
+__all__ = [
+    "FIXELREORIENT_METADATA",
+    "FixelreorientConfigParamsDict",
+    "FixelreorientConfigParamsDictTagged",
+    "FixelreorientOutputs",
+    "FixelreorientParamsDict",
+    "FixelreorientParamsDictTagged",
+    "fixelreorient",
+    "fixelreorient_config",
+    "fixelreorient_execute",
+    "fixelreorient_params",
+]