niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/labelconvert.py

@@ -0,0 +1,460 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+LABELCONVERT_METADATA = Metadata(
+    id="5aa09ff9ec4b21693b7d07b8329c2bc641669b7c.boutiques",
+    name="labelconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_LabelconvertConfigParamsDictNoTag = typing.TypedDict('_LabelconvertConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+LabelconvertConfigParamsDictTagged = typing.TypedDict('LabelconvertConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+LabelconvertConfigParamsDict = _LabelconvertConfigParamsDictNoTag | LabelconvertConfigParamsDictTagged
+
+
+_LabelconvertParamsDictNoTag = typing.TypedDict('_LabelconvertParamsDictNoTag', {
+    "spine": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[LabelconvertConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "path_in": InputPathType,
+    "lut_in": InputPathType,
+    "lut_out": InputPathType,
+    "image_out": str,
+})
+LabelconvertParamsDictTagged = typing.TypedDict('LabelconvertParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/labelconvert"],
+    "spine": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[LabelconvertConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "path_in": InputPathType,
+    "lut_in": InputPathType,
+    "lut_out": InputPathType,
+    "image_out": str,
+})
+LabelconvertParamsDict = _LabelconvertParamsDictNoTag | LabelconvertParamsDictTagged
+
+
+def labelconvert_config(
+    key: str,
+    value: str,
+) -> LabelconvertConfigParamsDictTagged:
+    """
+    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 labelconvert_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `LabelconvertConfigParamsDict` 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 labelconvert_config_cargs(
+    params: LabelconvertConfigParamsDict,
+    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 LabelconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `LabelconvertParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    image_out: OutputPathType
+    """the output image"""
+
+
+def labelconvert_params(
+    path_in: InputPathType,
+    lut_in: InputPathType,
+    lut_out: InputPathType,
+    image_out: str,
+    spine: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[LabelconvertConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> LabelconvertParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        path_in: the input image.
+        lut_in: the connectome lookup table corresponding to the input image.
+        lut_out: the target connectome lookup table for the output image.
+        image_out: the output image.
+        spine: provide a manually-defined segmentation of the base of the spine\
+            where the streamlines terminate, so that this can become a node in the\
+            connection matrix.
+        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/labelconvert",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "path_in": path_in,
+        "lut_in": lut_in,
+        "lut_out": lut_out,
+        "image_out": image_out,
+    }
+    if spine is not None:
+        params["spine"] = spine
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def labelconvert_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `LabelconvertParamsDict` 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("spine", None) is not None:
+        if not isinstance(params["spine"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`spine` has the wrong type: Received `{type(params.get("spine", 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[LabelconvertConfigParamsDict] | None`')
+        for e in params["config"]:
+            labelconvert_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("path_in", None) is None:
+        raise StyxValidationError("`path_in` must not be None")
+    if not isinstance(params["path_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`path_in` has the wrong type: Received `{type(params.get("path_in", None))}` expected `InputPathType`')
+    if params.get("lut_in", None) is None:
+        raise StyxValidationError("`lut_in` must not be None")
+    if not isinstance(params["lut_in"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`lut_in` has the wrong type: Received `{type(params.get("lut_in", None))}` expected `InputPathType`')
+    if params.get("lut_out", None) is None:
+        raise StyxValidationError("`lut_out` must not be None")
+    if not isinstance(params["lut_out"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`lut_out` has the wrong type: Received `{type(params.get("lut_out", None))}` expected `InputPathType`')
+    if params.get("image_out", None) is None:
+        raise StyxValidationError("`image_out` must not be None")
+    if not isinstance(params["image_out"], str):
+        raise StyxValidationError(f'`image_out` has the wrong type: Received `{type(params.get("image_out", None))}` expected `str`')
+
+
+def labelconvert_cargs(
+    params: LabelconvertParamsDict,
+    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("labelconvert")
+    if params.get("spine", None) is not None:
+        cargs.extend([
+            "-spine",
+            execution.input_file(params.get("spine", 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 [labelconvert_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("path_in", None)))
+    cargs.append(execution.input_file(params.get("lut_in", None)))
+    cargs.append(execution.input_file(params.get("lut_out", None)))
+    cargs.append(params.get("image_out", None))
+    return cargs
+
+
+def labelconvert_outputs(
+    params: LabelconvertParamsDict,
+    execution: Execution,
+) -> LabelconvertOutputs:
+    """
+    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 = LabelconvertOutputs(
+        root=execution.output_file("."),
+        image_out=execution.output_file(params.get("image_out", None)),
+    )
+    return ret
+
+
+def labelconvert_execute(
+    params: LabelconvertParamsDict,
+    runner: Runner | None = None,
+) -> LabelconvertOutputs:
+    """
+    labelconvert
+    
+    Convert a connectome node image from one lookup table to another.
+    
+    Typical usage is to convert a parcellation image provided by some other
+    software, based on the lookup table provided by that software, to conform to
+    a new lookup table, particularly one where the node indices increment from
+    1, in preparation for connectome construction; examples of such target
+    lookup table files are provided in share//mrtrix3//labelconvert//, but can
+    be created by the user to provide the desired node set // ordering //
+    colours.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `LabelconvertOutputs`).
+    """
+    labelconvert_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABELCONVERT_METADATA)
+    params = execution.params(params)
+    cargs = labelconvert_cargs(params, execution)
+    ret = labelconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def labelconvert(
+    path_in: InputPathType,
+    lut_in: InputPathType,
+    lut_out: InputPathType,
+    image_out: str,
+    spine: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[LabelconvertConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> LabelconvertOutputs:
+    """
+    labelconvert
+    
+    Convert a connectome node image from one lookup table to another.
+    
+    Typical usage is to convert a parcellation image provided by some other
+    software, based on the lookup table provided by that software, to conform to
+    a new lookup table, particularly one where the node indices increment from
+    1, in preparation for connectome construction; examples of such target
+    lookup table files are provided in share//mrtrix3//labelconvert//, but can
+    be created by the user to provide the desired node set // ordering //
+    colours.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        path_in: the input image.
+        lut_in: the connectome lookup table corresponding to the input image.
+        lut_out: the target connectome lookup table for the output image.
+        image_out: the output image.
+        spine: provide a manually-defined segmentation of the base of the spine\
+            where the streamlines terminate, so that this can become a node in the\
+            connection matrix.
+        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 `LabelconvertOutputs`).
+    """
+    params = labelconvert_params(
+        spine=spine,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        path_in=path_in,
+        lut_in=lut_in,
+        lut_out=lut_out,
+        image_out=image_out,
+    )
+    return labelconvert_execute(params, runner)
+
+
+__all__ = [
+    "LABELCONVERT_METADATA",
+    "LabelconvertConfigParamsDict",
+    "LabelconvertConfigParamsDictTagged",
+    "LabelconvertOutputs",
+    "LabelconvertParamsDict",
+    "LabelconvertParamsDictTagged",
+    "labelconvert",
+    "labelconvert_config",
+    "labelconvert_execute",
+    "labelconvert_params",
+]