niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warpconvert.py

@@ -0,0 +1,498 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARPCONVERT_METADATA = Metadata(
+    id="7468f4768b6e008e092ad5508a8d2b4875bab30a.boutiques",
+    name="warpconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_WarpconvertConfigParamsDictNoTag = typing.TypedDict('_WarpconvertConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+WarpconvertConfigParamsDictTagged = typing.TypedDict('WarpconvertConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+WarpconvertConfigParamsDict = _WarpconvertConfigParamsDictNoTag | WarpconvertConfigParamsDictTagged
+
+
+_WarpconvertParamsDictNoTag = typing.TypedDict('_WarpconvertParamsDictNoTag', {
+    "template": typing.NotRequired[InputPathType | None],
+    "midway_space": bool,
+    "from": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpconvertConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "type": str,
+    "out": str,
+})
+WarpconvertParamsDictTagged = typing.TypedDict('WarpconvertParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/warpconvert"],
+    "template": typing.NotRequired[InputPathType | None],
+    "midway_space": bool,
+    "from": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpconvertConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "type": str,
+    "out": str,
+})
+WarpconvertParamsDict = _WarpconvertParamsDictNoTag | WarpconvertParamsDictTagged
+
+
+def warpconvert_config(
+    key: str,
+    value: str,
+) -> WarpconvertConfigParamsDictTagged:
+    """
+    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 warpconvert_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `WarpconvertConfigParamsDict` 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 warpconvert_config_cargs(
+    params: WarpconvertConfigParamsDict,
+    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 WarpconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `WarpconvertParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output warp image."""
+
+
+def warpconvert_params(
+    in_: InputPathType,
+    type_: str,
+    out: str,
+    template: InputPathType | None = None,
+    midway_space: bool = False,
+    from_: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpconvertConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> WarpconvertParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input warp image.
+        type_: the conversion type required. Valid choices are:\
+            deformation2displacement, displacement2deformation,\
+            warpfull2deformation, warpfull2displacement.
+        out: the output warp image.
+        template: define a template image when converting a warpfull file\
+            (which is defined on a grid in the midway space between image 1 & 2).\
+            For example to generate the deformation field that maps image1 to\
+            image2, then supply image2 as the template image.
+        midway_space: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. The output will only contain\
+            the non-linear warp to map an input image to the midway space (defined\
+            by the warpfull grid). If a linear transform exists in the warpfull\
+            file header then it will be composed and included in the output.
+        from_: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. Used to define the direction of\
+            the desired output field.Use -from 1 to obtain the image1->image2 field\
+            and from 2 for image2->image1. Can be used in combination with the\
+            -midway_space option to produce a field that only maps to midway space.
+        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/warpconvert",
+        "midway_space": midway_space,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+        "type": type_,
+        "out": out,
+    }
+    if template is not None:
+        params["template"] = template
+    if from_ is not None:
+        params["from"] = from_
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warpconvert_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `WarpconvertParamsDict` 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("template", None) is not None:
+        if not isinstance(params["template"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`template` has the wrong type: Received `{type(params.get("template", None))}` expected `InputPathType | None`')
+    if params.get("midway_space", False) is None:
+        raise StyxValidationError("`midway_space` must not be None")
+    if not isinstance(params["midway_space"], bool):
+        raise StyxValidationError(f'`midway_space` has the wrong type: Received `{type(params.get("midway_space", False))}` expected `bool`')
+    if params.get("from", None) is not None:
+        if not isinstance(params["from"], int):
+            raise StyxValidationError(f'`from` has the wrong type: Received `{type(params.get("from", None))}` expected `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[WarpconvertConfigParamsDict] | None`')
+        for e in params["config"]:
+            warpconvert_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("type", None) is None:
+        raise StyxValidationError("`type` must not be None")
+    if not isinstance(params["type"], str):
+        raise StyxValidationError(f'`type` has the wrong type: Received `{type(params.get("type", None))}` expected `str`')
+    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 warpconvert_cargs(
+    params: WarpconvertParamsDict,
+    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("warpconvert")
+    if params.get("template", None) is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template", None))
+        ])
+    if params.get("midway_space", False):
+        cargs.append("-midway_space")
+    if params.get("from", None) is not None:
+        cargs.extend([
+            "-from",
+            str(params.get("from", 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 [warpconvert_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("type", None))
+    cargs.append(params.get("out", None))
+    return cargs
+
+
+def warpconvert_outputs(
+    params: WarpconvertParamsDict,
+    execution: Execution,
+) -> WarpconvertOutputs:
+    """
+    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 = WarpconvertOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out", None)),
+    )
+    return ret
+
+
+def warpconvert_execute(
+    params: WarpconvertParamsDict,
+    runner: Runner | None = None,
+) -> WarpconvertOutputs:
+    """
+    warpconvert
+    
+    Convert between different representations of a non-linear warp.
+    
+    A deformation field is defined as an image where each voxel defines the
+    corresponding position in the other image (in scanner space coordinates). A
+    displacement field stores the displacements (in mm) to the other image from
+    the each voxel's position (in scanner space). The warpfull file is the 5D
+    format output from mrregister -nl_warp_full, which contains linear
+    transforms, warps and their inverses that map each image to a midway space.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `WarpconvertOutputs`).
+    """
+    warpconvert_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPCONVERT_METADATA)
+    params = execution.params(params)
+    cargs = warpconvert_cargs(params, execution)
+    ret = warpconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warpconvert(
+    in_: InputPathType,
+    type_: str,
+    out: str,
+    template: InputPathType | None = None,
+    midway_space: bool = False,
+    from_: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpconvertConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> WarpconvertOutputs:
+    """
+    warpconvert
+    
+    Convert between different representations of a non-linear warp.
+    
+    A deformation field is defined as an image where each voxel defines the
+    corresponding position in the other image (in scanner space coordinates). A
+    displacement field stores the displacements (in mm) to the other image from
+    the each voxel's position (in scanner space). The warpfull file is the 5D
+    format output from mrregister -nl_warp_full, which contains linear
+    transforms, warps and their inverses that map each image to a midway space.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input warp image.
+        type_: the conversion type required. Valid choices are:\
+            deformation2displacement, displacement2deformation,\
+            warpfull2deformation, warpfull2displacement.
+        out: the output warp image.
+        template: define a template image when converting a warpfull file\
+            (which is defined on a grid in the midway space between image 1 & 2).\
+            For example to generate the deformation field that maps image1 to\
+            image2, then supply image2 as the template image.
+        midway_space: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. The output will only contain\
+            the non-linear warp to map an input image to the midway space (defined\
+            by the warpfull grid). If a linear transform exists in the warpfull\
+            file header then it will be composed and included in the output.
+        from_: to be used only with warpfull2deformation and\
+            warpfull2displacement conversion types. Used to define the direction of\
+            the desired output field.Use -from 1 to obtain the image1->image2 field\
+            and from 2 for image2->image1. Can be used in combination with the\
+            -midway_space option to produce a field that only maps to midway space.
+        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 `WarpconvertOutputs`).
+    """
+    params = warpconvert_params(
+        template=template,
+        midway_space=midway_space,
+        from_=from_,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+        type_=type_,
+        out=out,
+    )
+    return warpconvert_execute(params, runner)
+
+
+__all__ = [
+    "WARPCONVERT_METADATA",
+    "WarpconvertConfigParamsDict",
+    "WarpconvertConfigParamsDictTagged",
+    "WarpconvertOutputs",
+    "WarpconvertParamsDict",
+    "WarpconvertParamsDictTagged",
+    "warpconvert",
+    "warpconvert_config",
+    "warpconvert_execute",
+    "warpconvert_params",
+]