niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/transformcompose.py

@@ -0,0 +1,625 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TRANSFORMCOMPOSE_METADATA = Metadata(
+    id="00dff5d1cb74f969e2ad40f5dbeaedf75a029491.boutiques",
+    name="transformcompose",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_TransformcomposeConfigParamsDictNoTag = typing.TypedDict('_TransformcomposeConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+TransformcomposeConfigParamsDictTagged = typing.TypedDict('TransformcomposeConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+TransformcomposeConfigParamsDict = _TransformcomposeConfigParamsDictNoTag | TransformcomposeConfigParamsDictTagged
+
+
+_TransformcomposeVariousStringParamsDictNoTag = typing.TypedDict('_TransformcomposeVariousStringParamsDictNoTag', {
+    "obj": str,
+})
+TransformcomposeVariousStringParamsDictTagged = typing.TypedDict('TransformcomposeVariousStringParamsDictTagged', {
+    "@type": typing.Literal["VariousString"],
+    "obj": str,
+})
+TransformcomposeVariousStringParamsDict = _TransformcomposeVariousStringParamsDictNoTag | TransformcomposeVariousStringParamsDictTagged
+
+
+_TransformcomposeVariousFileParamsDictNoTag = typing.TypedDict('_TransformcomposeVariousFileParamsDictNoTag', {
+    "obj": InputPathType,
+})
+TransformcomposeVariousFileParamsDictTagged = typing.TypedDict('TransformcomposeVariousFileParamsDictTagged', {
+    "@type": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+TransformcomposeVariousFileParamsDict = _TransformcomposeVariousFileParamsDictNoTag | TransformcomposeVariousFileParamsDictTagged
+
+
+_TransformcomposeParamsDictNoTag = typing.TypedDict('_TransformcomposeParamsDictNoTag', {
+    "template": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TransformcomposeConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "output": typing.Union[TransformcomposeVariousStringParamsDictTagged, TransformcomposeVariousFileParamsDictTagged],
+})
+TransformcomposeParamsDictTagged = typing.TypedDict('TransformcomposeParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/transformcompose"],
+    "template": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TransformcomposeConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+    "output": typing.Union[TransformcomposeVariousStringParamsDictTagged, TransformcomposeVariousFileParamsDictTagged],
+})
+TransformcomposeParamsDict = _TransformcomposeParamsDictNoTag | TransformcomposeParamsDictTagged
+
+
+def transformcompose_output_cargs_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "VariousString": transformcompose_various_string_cargs,
+        "VariousFile": transformcompose_various_file_cargs,
+    }.get(t)
+
+
+def transformcompose_output_validate_dyn_fn(
+    t: str,
+) -> typing.Any:
+    """
+    Get validate params function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Validate params function.
+    """
+    return {
+        "VariousString": transformcompose_various_string_validate,
+        "VariousFile": transformcompose_various_file_validate,
+    }.get(t)
+
+
+def transformcompose_config(
+    key: str,
+    value: str,
+) -> TransformcomposeConfigParamsDictTagged:
+    """
+    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 transformcompose_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TransformcomposeConfigParamsDict` 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 transformcompose_config_cargs(
+    params: TransformcomposeConfigParamsDict,
+    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
+
+
+def transformcompose_various_string(
+    obj: str,
+) -> TransformcomposeVariousStringParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def transformcompose_various_string_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TransformcomposeVariousStringParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], str):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `str`')
+
+
+def transformcompose_various_string_cargs(
+    params: TransformcomposeVariousStringParamsDict,
+    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(params.get("obj", None))
+    return cargs
+
+
+def transformcompose_various_file(
+    obj: InputPathType,
+) -> TransformcomposeVariousFileParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "@type": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def transformcompose_various_file_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TransformcomposeVariousFileParamsDict` 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("obj", None) is None:
+        raise StyxValidationError("`obj` must not be None")
+    if not isinstance(params["obj"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`obj` has the wrong type: Received `{type(params.get("obj", None))}` expected `InputPathType`')
+
+
+def transformcompose_various_file_cargs(
+    params: TransformcomposeVariousFileParamsDict,
+    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(execution.input_file(params.get("obj", None)))
+    return cargs
+
+
+class TransformcomposeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `TransformcomposeParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def transformcompose_params(
+    input_: list[InputPathType],
+    output: typing.Union[TransformcomposeVariousStringParamsDictTagged, TransformcomposeVariousFileParamsDictTagged],
+    template: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TransformcomposeConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TransformcomposeParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input transforms (either linear or non-linear warps).
+        output: the output file (may be a linear transformation text file, or a\
+            deformation warp field image, depending on usage).
+        template: define the output grid defined by a template image.
+        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/transformcompose",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if template is not None:
+        params["template"] = template
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def transformcompose_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `TransformcomposeParamsDict` 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("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[TransformcomposeConfigParamsDict] | None`')
+        for e in params["config"]:
+            transformcompose_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("input", None) is None:
+        raise StyxValidationError("`input` must not be None")
+    if not isinstance(params["input"], list):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `list[InputPathType]`')
+    for e in params["input"]:
+        if not isinstance(e, (pathlib.Path, str)):
+            raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `list[InputPathType]`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], dict):
+        raise StyxValidationError(f'Params object has the wrong type \'{type(params["output"])}\'')
+    if "@type" not in params["output"]:
+        raise StyxValidationError("Params object is missing `@type`")
+    if params["output"]["@type"] not in ["VariousString", "VariousFile"]:
+        raise StyxValidationError("Parameter `output`s `@type` must be one of [\"VariousString\", \"VariousFile\"]")
+    transformcompose_output_validate_dyn_fn(params["output"]["@type"])(params["output"])
+
+
+def transformcompose_cargs(
+    params: TransformcomposeParamsDict,
+    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("transformcompose")
+    if params.get("template", None) is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template", 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 [transformcompose_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.extend([execution.input_file(f) for f in params.get("input", None)])
+    cargs.extend(transformcompose_output_cargs_dyn_fn(params.get("output", None)["@type"])(params.get("output", None), execution))
+    return cargs
+
+
+def transformcompose_outputs(
+    params: TransformcomposeParamsDict,
+    execution: Execution,
+) -> TransformcomposeOutputs:
+    """
+    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 = TransformcomposeOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def transformcompose_execute(
+    params: TransformcomposeParamsDict,
+    runner: Runner | None = None,
+) -> TransformcomposeOutputs:
+    """
+    transformcompose
+    
+    Compose any number of linear transformations and/or warps into a single
+    transformation.
+    
+    Any linear transforms must be supplied as a 4x4 matrix in a text file (e.g.
+    as per the output of mrregister). Any warp fields must be supplied as a 4D
+    image representing a deformation field (e.g. as output from mrrregister
+    -nl_warp).
+    
+    Input transformations should be provided to the command in the order in
+    which they would be applied to an image if they were to be applied
+    individually.
+    
+    If all input transformations are linear, and the -template option is not
+    provided, then the file output by the command will also be a linear
+    transformation saved as a 4x4 matrix in a text file. If a template image is
+    supplied, then the output will always be a deformation field. If at least
+    one of the inputs is a warp field, then the output will be a deformation
+    field, which will be defined on the grid of the last input warp image
+    supplied if the -template option is not used.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TransformcomposeOutputs`).
+    """
+    transformcompose_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRANSFORMCOMPOSE_METADATA)
+    params = execution.params(params)
+    cargs = transformcompose_cargs(params, execution)
+    ret = transformcompose_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def transformcompose(
+    input_: list[InputPathType],
+    output: typing.Union[TransformcomposeVariousStringParamsDictTagged, TransformcomposeVariousFileParamsDictTagged],
+    template: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TransformcomposeConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TransformcomposeOutputs:
+    """
+    transformcompose
+    
+    Compose any number of linear transformations and/or warps into a single
+    transformation.
+    
+    Any linear transforms must be supplied as a 4x4 matrix in a text file (e.g.
+    as per the output of mrregister). Any warp fields must be supplied as a 4D
+    image representing a deformation field (e.g. as output from mrrregister
+    -nl_warp).
+    
+    Input transformations should be provided to the command in the order in
+    which they would be applied to an image if they were to be applied
+    individually.
+    
+    If all input transformations are linear, and the -template option is not
+    provided, then the file output by the command will also be a linear
+    transformation saved as a 4x4 matrix in a text file. If a template image is
+    supplied, then the output will always be a deformation field. If at least
+    one of the inputs is a warp field, then the output will be a deformation
+    field, which will be defined on the grid of the last input warp image
+    supplied if the -template option is not used.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input transforms (either linear or non-linear warps).
+        output: the output file (may be a linear transformation text file, or a\
+            deformation warp field image, depending on usage).
+        template: define the output grid defined by a template image.
+        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 `TransformcomposeOutputs`).
+    """
+    params = transformcompose_params(
+        template=template,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return transformcompose_execute(params, runner)
+
+
+__all__ = [
+    "TRANSFORMCOMPOSE_METADATA",
+    "TransformcomposeConfigParamsDict",
+    "TransformcomposeConfigParamsDictTagged",
+    "TransformcomposeOutputs",
+    "TransformcomposeParamsDict",
+    "TransformcomposeParamsDictTagged",
+    "TransformcomposeVariousFileParamsDict",
+    "TransformcomposeVariousFileParamsDictTagged",
+    "TransformcomposeVariousStringParamsDict",
+    "TransformcomposeVariousStringParamsDictTagged",
+    "transformcompose",
+    "transformcompose_config",
+    "transformcompose_execute",
+    "transformcompose_params",
+    "transformcompose_various_file",
+    "transformcompose_various_string",
+]