niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrdegibbs.py

@@ -0,0 +1,535 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRDEGIBBS_METADATA = Metadata(
+    id="832d935b5fa8fdff97b78ecd355cb0d26be8033a.boutiques",
+    name="mrdegibbs",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_MrdegibbsConfigParamsDictNoTag = typing.TypedDict('_MrdegibbsConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+MrdegibbsConfigParamsDictTagged = typing.TypedDict('MrdegibbsConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+MrdegibbsConfigParamsDict = _MrdegibbsConfigParamsDictNoTag | MrdegibbsConfigParamsDictTagged
+
+
+_MrdegibbsParamsDictNoTag = typing.TypedDict('_MrdegibbsParamsDictNoTag', {
+    "axes": typing.NotRequired[list[int] | None],
+    "nshifts": typing.NotRequired[int | None],
+    "minW": typing.NotRequired[int | None],
+    "maxW": typing.NotRequired[int | None],
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrdegibbsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "out": str,
+})
+MrdegibbsParamsDictTagged = typing.TypedDict('MrdegibbsParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/mrdegibbs"],
+    "axes": typing.NotRequired[list[int] | None],
+    "nshifts": typing.NotRequired[int | None],
+    "minW": typing.NotRequired[int | None],
+    "maxW": typing.NotRequired[int | None],
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrdegibbsConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "out": str,
+})
+MrdegibbsParamsDict = _MrdegibbsParamsDictNoTag | MrdegibbsParamsDictTagged
+
+
+def mrdegibbs_config(
+    key: str,
+    value: str,
+) -> MrdegibbsConfigParamsDictTagged:
+    """
+    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 mrdegibbs_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrdegibbsConfigParamsDict` 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 mrdegibbs_config_cargs(
+    params: MrdegibbsConfigParamsDict,
+    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 MrdegibbsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `MrdegibbsParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output image."""
+
+
+def mrdegibbs_params(
+    in_: InputPathType,
+    out: str,
+    axes: list[int] | None = None,
+    nshifts: int | None = None,
+    min_w: int | None = None,
+    max_w: int | None = None,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrdegibbsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrdegibbsParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input image.
+        out: the output image.
+        axes: select the slice axes (default: 0,1 - i.e. x-y).
+        nshifts: discretization of subpixel spacing (default: 20).
+        min_w: left border of window used for TV computation (default: 1).
+        max_w: right border of window used for TV computation (default: 3).
+        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/mrdegibbs",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+        "out": out,
+    }
+    if axes is not None:
+        params["axes"] = axes
+    if nshifts is not None:
+        params["nshifts"] = nshifts
+    if min_w is not None:
+        params["minW"] = min_w
+    if max_w is not None:
+        params["maxW"] = max_w
+    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 mrdegibbs_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `MrdegibbsParamsDict` 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("axes", None) is not None:
+        if not isinstance(params["axes"], list):
+            raise StyxValidationError(f'`axes` has the wrong type: Received `{type(params.get("axes", None))}` expected `list[int] | None`')
+        for e in params["axes"]:
+            if not isinstance(e, int):
+                raise StyxValidationError(f'`axes` has the wrong type: Received `{type(params.get("axes", None))}` expected `list[int] | None`')
+    if params.get("nshifts", None) is not None:
+        if not isinstance(params["nshifts"], int):
+            raise StyxValidationError(f'`nshifts` has the wrong type: Received `{type(params.get("nshifts", None))}` expected `int | None`')
+    if params.get("minW", None) is not None:
+        if not isinstance(params["minW"], int):
+            raise StyxValidationError(f'`minW` has the wrong type: Received `{type(params.get("minW", None))}` expected `int | None`')
+    if params.get("maxW", None) is not None:
+        if not isinstance(params["maxW"], int):
+            raise StyxValidationError(f'`maxW` has the wrong type: Received `{type(params.get("maxW", None))}` expected `int | None`')
+    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[MrdegibbsConfigParamsDict] | None`')
+        for e in params["config"]:
+            mrdegibbs_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 mrdegibbs_cargs(
+    params: MrdegibbsParamsDict,
+    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("mrdegibbs")
+    if params.get("axes", None) is not None:
+        cargs.extend([
+            "-axes",
+            *map(str, params.get("axes", None))
+        ])
+    if params.get("nshifts", None) is not None:
+        cargs.extend([
+            "-nshifts",
+            str(params.get("nshifts", None))
+        ])
+    if params.get("minW", None) is not None:
+        cargs.extend([
+            "-minW",
+            str(params.get("minW", None))
+        ])
+    if params.get("maxW", None) is not None:
+        cargs.extend([
+            "-maxW",
+            str(params.get("maxW", None))
+        ])
+    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 [mrdegibbs_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 mrdegibbs_outputs(
+    params: MrdegibbsParamsDict,
+    execution: Execution,
+) -> MrdegibbsOutputs:
+    """
+    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 = MrdegibbsOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out", None)),
+    )
+    return ret
+
+
+def mrdegibbs_execute(
+    params: MrdegibbsParamsDict,
+    runner: Runner | None = None,
+) -> MrdegibbsOutputs:
+    """
+    mrdegibbs
+    
+    Remove Gibbs Ringing Artifacts.
+    
+    This application attempts to remove Gibbs ringing artefacts from MRI images
+    using the method of local subvoxel-shifts proposed by Kellner et al. (see
+    reference below for details).
+    
+    This command is designed to run on data directly after it has been
+    reconstructed by the scanner, before any interpolation of any kind has taken
+    place. You should not run this command after any form of motion correction
+    (e.g. not after dwifslpreproc). Similarly, if you intend running dwidenoise,
+    you should run denoising before this command to not alter the noise
+    structure, which would impact on dwidenoise's performance.
+    
+    Note that this method is designed to work on images acquired with full
+    k-space coverage. Running this method on partial Fourier ('half-scan') data
+    may lead to suboptimal and/or biased results, as noted in the original
+    reference below. There is currently no means of dealing with this; users
+    should exercise caution when using this method on partial Fourier data, and
+    inspect its output for any obvious artefacts.
+    
+    References:
+    
+    Kellner, E; Dhital, B; Kiselev, V.G & Reisert, M. Gibbs-ringing artifact
+    removal based on local subvoxel-shifts. Magnetic Resonance in Medicine,
+    2016, 76, 1574–1581.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrdegibbsOutputs`).
+    """
+    mrdegibbs_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRDEGIBBS_METADATA)
+    params = execution.params(params)
+    cargs = mrdegibbs_cargs(params, execution)
+    ret = mrdegibbs_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrdegibbs(
+    in_: InputPathType,
+    out: str,
+    axes: list[int] | None = None,
+    nshifts: int | None = None,
+    min_w: int | None = None,
+    max_w: int | None = None,
+    datatype: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrdegibbsConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrdegibbsOutputs:
+    """
+    mrdegibbs
+    
+    Remove Gibbs Ringing Artifacts.
+    
+    This application attempts to remove Gibbs ringing artefacts from MRI images
+    using the method of local subvoxel-shifts proposed by Kellner et al. (see
+    reference below for details).
+    
+    This command is designed to run on data directly after it has been
+    reconstructed by the scanner, before any interpolation of any kind has taken
+    place. You should not run this command after any form of motion correction
+    (e.g. not after dwifslpreproc). Similarly, if you intend running dwidenoise,
+    you should run denoising before this command to not alter the noise
+    structure, which would impact on dwidenoise's performance.
+    
+    Note that this method is designed to work on images acquired with full
+    k-space coverage. Running this method on partial Fourier ('half-scan') data
+    may lead to suboptimal and/or biased results, as noted in the original
+    reference below. There is currently no means of dealing with this; users
+    should exercise caution when using this method on partial Fourier data, and
+    inspect its output for any obvious artefacts.
+    
+    References:
+    
+    Kellner, E; Dhital, B; Kiselev, V.G & Reisert, M. Gibbs-ringing artifact
+    removal based on local subvoxel-shifts. Magnetic Resonance in Medicine,
+    2016, 76, 1574–1581.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input image.
+        out: the output image.
+        axes: select the slice axes (default: 0,1 - i.e. x-y).
+        nshifts: discretization of subpixel spacing (default: 20).
+        min_w: left border of window used for TV computation (default: 1).
+        max_w: right border of window used for TV computation (default: 3).
+        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 `MrdegibbsOutputs`).
+    """
+    params = mrdegibbs_params(
+        axes=axes,
+        nshifts=nshifts,
+        min_w=min_w,
+        max_w=max_w,
+        datatype=datatype,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+        out=out,
+    )
+    return mrdegibbs_execute(params, runner)
+
+
+__all__ = [
+    "MRDEGIBBS_METADATA",
+    "MrdegibbsConfigParamsDict",
+    "MrdegibbsConfigParamsDictTagged",
+    "MrdegibbsOutputs",
+    "MrdegibbsParamsDict",
+    "MrdegibbsParamsDictTagged",
+    "mrdegibbs",
+    "mrdegibbs_config",
+    "mrdegibbs_execute",
+    "mrdegibbs_params",
+]