niwrap-mrtrix 0.8.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/v_5ttedit.py

@@ -0,0 +1,513 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_5TTEDIT_METADATA = Metadata(
+    id="600cbbcfcf2cf74592c61897ae8adbd5df0e6fdd.boutiques",
+    name="5ttedit",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+_V5tteditConfigParamsDictNoTag = typing.TypedDict('_V5tteditConfigParamsDictNoTag', {
+    "key": str,
+    "value": str,
+})
+V5tteditConfigParamsDictTagged = typing.TypedDict('V5tteditConfigParamsDictTagged', {
+    "@type": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+V5tteditConfigParamsDict = _V5tteditConfigParamsDictNoTag | V5tteditConfigParamsDictTagged
+
+
+_V5tteditParamsDictNoTag = typing.TypedDict('_V5tteditParamsDictNoTag', {
+    "cgm": typing.NotRequired[InputPathType | None],
+    "sgm": typing.NotRequired[InputPathType | None],
+    "wm": typing.NotRequired[InputPathType | None],
+    "csf": typing.NotRequired[InputPathType | None],
+    "path": typing.NotRequired[InputPathType | None],
+    "none": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5tteditConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+V5tteditParamsDictTagged = typing.TypedDict('V5tteditParamsDictTagged', {
+    "@type": typing.Literal["mrtrix/5ttedit"],
+    "cgm": typing.NotRequired[InputPathType | None],
+    "sgm": typing.NotRequired[InputPathType | None],
+    "wm": typing.NotRequired[InputPathType | None],
+    "csf": typing.NotRequired[InputPathType | None],
+    "path": typing.NotRequired[InputPathType | None],
+    "none": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5tteditConfigParamsDict] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+V5tteditParamsDict = _V5tteditParamsDictNoTag | V5tteditParamsDictTagged
+
+
+def v_5ttedit_config(
+    key: str,
+    value: str,
+) -> V5tteditConfigParamsDictTagged:
+    """
+    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 v_5ttedit_config_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5tteditConfigParamsDict` 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 v_5ttedit_config_cargs(
+    params: V5tteditConfigParamsDict,
+    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 V5tteditOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `V5tteditParamsDict(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output modified 5TT image"""
+
+
+def v_5ttedit_params(
+    input_: InputPathType,
+    output: str,
+    cgm: InputPathType | None = None,
+    sgm: InputPathType | None = None,
+    wm: InputPathType | None = None,
+    csf: InputPathType | None = None,
+    path: InputPathType | None = None,
+    none: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[V5tteditConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> V5tteditParamsDictTagged:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the 5TT image to be modified.
+        output: the output modified 5TT image.
+        cgm: provide a mask of voxels that should be set to cortical grey\
+            matter.
+        sgm: provide a mask of voxels that should be set to sub-cortical grey\
+            matter.
+        wm: provide a mask of voxels that should be set to white matter.
+        csf: provide a mask of voxels that should be set to CSF.
+        path: provide a mask of voxels that should be set to pathological\
+            tissue.
+        none: provide a mask of voxels that should be cleared (i.e. are\
+            non-brain); note that this will supersede all other provided masks.
+        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/5ttedit",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if cgm is not None:
+        params["cgm"] = cgm
+    if sgm is not None:
+        params["sgm"] = sgm
+    if wm is not None:
+        params["wm"] = wm
+    if csf is not None:
+        params["csf"] = csf
+    if path is not None:
+        params["path"] = path
+    if none is not None:
+        params["none"] = none
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def v_5ttedit_validate(
+    params: typing.Any,
+) -> None:
+    """
+    Validate parameters. Throws an error if `params` is not a valid
+    `V5tteditParamsDict` 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("cgm", None) is not None:
+        if not isinstance(params["cgm"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`cgm` has the wrong type: Received `{type(params.get("cgm", None))}` expected `InputPathType | None`')
+    if params.get("sgm", None) is not None:
+        if not isinstance(params["sgm"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`sgm` has the wrong type: Received `{type(params.get("sgm", None))}` expected `InputPathType | None`')
+    if params.get("wm", None) is not None:
+        if not isinstance(params["wm"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`wm` has the wrong type: Received `{type(params.get("wm", None))}` expected `InputPathType | None`')
+    if params.get("csf", None) is not None:
+        if not isinstance(params["csf"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`csf` has the wrong type: Received `{type(params.get("csf", None))}` expected `InputPathType | None`')
+    if params.get("path", None) is not None:
+        if not isinstance(params["path"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`path` has the wrong type: Received `{type(params.get("path", None))}` expected `InputPathType | None`')
+    if params.get("none", None) is not None:
+        if not isinstance(params["none"], (pathlib.Path, str)):
+            raise StyxValidationError(f'`none` has the wrong type: Received `{type(params.get("none", 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[V5tteditConfigParamsDict] | None`')
+        for e in params["config"]:
+            v_5ttedit_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"], (pathlib.Path, str)):
+        raise StyxValidationError(f'`input` has the wrong type: Received `{type(params.get("input", None))}` expected `InputPathType`')
+    if params.get("output", None) is None:
+        raise StyxValidationError("`output` must not be None")
+    if not isinstance(params["output"], str):
+        raise StyxValidationError(f'`output` has the wrong type: Received `{type(params.get("output", None))}` expected `str`')
+
+
+def v_5ttedit_cargs(
+    params: V5tteditParamsDict,
+    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("5ttedit")
+    if params.get("cgm", None) is not None:
+        cargs.extend([
+            "-cgm",
+            execution.input_file(params.get("cgm", None))
+        ])
+    if params.get("sgm", None) is not None:
+        cargs.extend([
+            "-sgm",
+            execution.input_file(params.get("sgm", None))
+        ])
+    if params.get("wm", None) is not None:
+        cargs.extend([
+            "-wm",
+            execution.input_file(params.get("wm", None))
+        ])
+    if params.get("csf", None) is not None:
+        cargs.extend([
+            "-csf",
+            execution.input_file(params.get("csf", None))
+        ])
+    if params.get("path", None) is not None:
+        cargs.extend([
+            "-path",
+            execution.input_file(params.get("path", None))
+        ])
+    if params.get("none", None) is not None:
+        cargs.extend([
+            "-none",
+            execution.input_file(params.get("none", 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 [v_5ttedit_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("input", None)))
+    cargs.append(params.get("output", None))
+    return cargs
+
+
+def v_5ttedit_outputs(
+    params: V5tteditParamsDict,
+    execution: Execution,
+) -> V5tteditOutputs:
+    """
+    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 = V5tteditOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output", None)),
+    )
+    return ret
+
+
+def v_5ttedit_execute(
+    params: V5tteditParamsDict,
+    runner: Runner | None = None,
+) -> V5tteditOutputs:
+    """
+    5ttedit
+    
+    Manually set the partial volume fractions in an ACT five-tissue-type (5TT)
+    image using mask images.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V5tteditOutputs`).
+    """
+    v_5ttedit_validate(params)
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TTEDIT_METADATA)
+    params = execution.params(params)
+    cargs = v_5ttedit_cargs(params, execution)
+    ret = v_5ttedit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_5ttedit(
+    input_: InputPathType,
+    output: str,
+    cgm: InputPathType | None = None,
+    sgm: InputPathType | None = None,
+    wm: InputPathType | None = None,
+    csf: InputPathType | None = None,
+    path: InputPathType | None = None,
+    none: InputPathType | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[V5tteditConfigParamsDict] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> V5tteditOutputs:
+    """
+    5ttedit
+    
+    Manually set the partial volume fractions in an ACT five-tissue-type (5TT)
+    image using mask images.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the 5TT image to be modified.
+        output: the output modified 5TT image.
+        cgm: provide a mask of voxels that should be set to cortical grey\
+            matter.
+        sgm: provide a mask of voxels that should be set to sub-cortical grey\
+            matter.
+        wm: provide a mask of voxels that should be set to white matter.
+        csf: provide a mask of voxels that should be set to CSF.
+        path: provide a mask of voxels that should be set to pathological\
+            tissue.
+        none: provide a mask of voxels that should be cleared (i.e. are\
+            non-brain); note that this will supersede all other provided masks.
+        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 `V5tteditOutputs`).
+    """
+    params = v_5ttedit_params(
+        cgm=cgm,
+        sgm=sgm,
+        wm=wm,
+        csf=csf,
+        path=path,
+        none=none,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return v_5ttedit_execute(params, runner)
+
+
+__all__ = [
+    "V5tteditConfigParamsDict",
+    "V5tteditConfigParamsDictTagged",
+    "V5tteditOutputs",
+    "V5tteditParamsDict",
+    "V5tteditParamsDictTagged",
+    "V_5TTEDIT_METADATA",
+    "v_5ttedit",
+    "v_5ttedit_config",
+    "v_5ttedit_execute",
+    "v_5ttedit_params",
+]