niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/v_5ttedit.py

@@ -0,0 +1,420 @@
+# 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="5adde2b592e9e0431b8a338ae66dce3c82eee77e.boutiques",
+    name="5ttedit",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+V5tteditConfigParameters = typing.TypedDict('V5tteditConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+V5tteditParameters = typing.TypedDict('V5tteditParameters', {
+    "__STYX_TYPE__": typing.Literal["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[V5tteditConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "5ttedit": v_5ttedit_cargs,
+        "config": v_5ttedit_config_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "5ttedit": v_5ttedit_outputs,
+    }.get(t)
+
+
+def v_5ttedit_config_params(
+    key: str,
+    value: str,
+) -> V5tteditConfigParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def v_5ttedit_config_cargs(
+    params: V5tteditConfigParameters,
+    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"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class V5tteditOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_5ttedit(...)`.
+    """
+    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[V5tteditConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> V5tteditParameters:
+    """
+    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 = {
+        "__STYXTYPE__": "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_cargs(
+    params: V5tteditParameters,
+    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") is not None:
+        cargs.extend([
+            "-cgm",
+            execution.input_file(params.get("cgm"))
+        ])
+    if params.get("sgm") is not None:
+        cargs.extend([
+            "-sgm",
+            execution.input_file(params.get("sgm"))
+        ])
+    if params.get("wm") is not None:
+        cargs.extend([
+            "-wm",
+            execution.input_file(params.get("wm"))
+        ])
+    if params.get("csf") is not None:
+        cargs.extend([
+            "-csf",
+            execution.input_file(params.get("csf"))
+        ])
+    if params.get("path") is not None:
+        cargs.extend([
+            "-path",
+            execution.input_file(params.get("path"))
+        ])
+    if params.get("none") is not None:
+        cargs.extend([
+            "-none",
+            execution.input_file(params.get("none"))
+        ])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def v_5ttedit_outputs(
+    params: V5tteditParameters,
+    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")),
+    )
+    return ret
+
+
+def v_5ttedit_execute(
+    params: V5tteditParameters,
+    execution: Execution,
+) -> V5tteditOutputs:
+    """
+    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.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V5tteditOutputs`).
+    """
+    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[V5tteditConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> V5tteditOutputs:
+    """
+    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`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TTEDIT_METADATA)
+    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, execution)
+
+
+__all__ = [
+    "V5tteditConfigParameters",
+    "V5tteditOutputs",
+    "V5tteditParameters",
+    "V_5TTEDIT_METADATA",
+    "v_5ttedit",
+    "v_5ttedit_config_params",
+    "v_5ttedit_params",
+]