niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/maskfilter.py

@@ -0,0 +1,537 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MASKFILTER_METADATA = Metadata(
+    id="0f58b29a006fb07347957237ea8b1bd75f33ff41.boutiques",
+    name="maskfilter",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MaskfilterVariousStringParameters = typing.TypedDict('MaskfilterVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+MaskfilterVariousFileParameters = typing.TypedDict('MaskfilterVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+MaskfilterConfigParameters = typing.TypedDict('MaskfilterConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MaskfilterParameters = typing.TypedDict('MaskfilterParameters', {
+    "__STYX_TYPE__": typing.Literal["maskfilter"],
+    "scale": typing.NotRequired[int | None],
+    "axes": typing.NotRequired[list[int] | None],
+    "largest": bool,
+    "connectivity": bool,
+    "npass": typing.NotRequired[int | None],
+    "extent": typing.NotRequired[list[int] | None],
+    "strides": typing.NotRequired[typing.Union[MaskfilterVariousStringParameters, MaskfilterVariousFileParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MaskfilterConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "filter": str,
+    "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 {
+        "maskfilter": maskfilter_cargs,
+        "VariousString": maskfilter_various_string_cargs,
+        "VariousFile": maskfilter_various_file_cargs,
+        "config": maskfilter_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 {
+        "maskfilter": maskfilter_outputs,
+    }.get(t)
+
+
+def maskfilter_various_string_params(
+    obj: str,
+) -> MaskfilterVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def maskfilter_various_string_cargs(
+    params: MaskfilterVariousStringParameters,
+    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"))
+    return cargs
+
+
+def maskfilter_various_file_params(
+    obj: InputPathType,
+) -> MaskfilterVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def maskfilter_various_file_cargs(
+    params: MaskfilterVariousFileParameters,
+    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")))
+    return cargs
+
+
+def maskfilter_config_params(
+    key: str,
+    value: str,
+) -> MaskfilterConfigParameters:
+    """
+    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 maskfilter_config_cargs(
+    params: MaskfilterConfigParameters,
+    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 MaskfilterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `maskfilter(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image."""
+
+
+def maskfilter_params(
+    input_: InputPathType,
+    filter_: str,
+    output: str,
+    scale: int | None = None,
+    axes: list[int] | None = None,
+    largest: bool = False,
+    connectivity: bool = False,
+    npass: int | None = None,
+    extent: list[int] | None = None,
+    strides: typing.Union[MaskfilterVariousStringParameters, MaskfilterVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MaskfilterConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MaskfilterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image.
+        filter_: the type of filter to be applied (clean, connect, dilate,\
+            erode, median).
+        output: the output image.
+        scale: the maximum scale used to cut bridges. A certain maximum scale\
+            cuts bridges up to a width (in voxels) of 2x the provided scale.\
+            (Default: 2).
+        axes: specify which axes should be included in the connected\
+            components. By default only the first 3 axes are included. The axes\
+            should be provided as a comma-separated list of values.
+        largest: only retain the largest connected component.
+        connectivity: use 26-voxel-neighbourhood connectivity (Default: 6).
+        npass: the number of times to repeatedly apply the filter.
+        extent: specify the extent (width) of kernel size in voxels. This can\
+            be specified either as a single value to be used for all axes, or as a\
+            comma-separated list of the extent for each axis. The default is 3x3x3.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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__": "maskfilter",
+        "largest": largest,
+        "connectivity": connectivity,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "filter": filter_,
+        "output": output,
+    }
+    if scale is not None:
+        params["scale"] = scale
+    if axes is not None:
+        params["axes"] = axes
+    if npass is not None:
+        params["npass"] = npass
+    if extent is not None:
+        params["extent"] = extent
+    if strides is not None:
+        params["strides"] = strides
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def maskfilter_cargs(
+    params: MaskfilterParameters,
+    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("maskfilter")
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-scale",
+            str(params.get("scale"))
+        ])
+    if params.get("axes") is not None:
+        cargs.extend([
+            "-axes",
+            ",".join(map(str, params.get("axes")))
+        ])
+    if params.get("largest"):
+        cargs.append("-largest")
+    if params.get("connectivity"):
+        cargs.append("-connectivity")
+    if params.get("npass") is not None:
+        cargs.extend([
+            "-npass",
+            str(params.get("npass"))
+        ])
+    if params.get("extent") is not None:
+        cargs.extend([
+            "-extent",
+            ",".join(map(str, params.get("extent")))
+        ])
+    if params.get("strides") is not None:
+        cargs.extend([
+            "-strides",
+            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+        ])
+    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("filter"))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def maskfilter_outputs(
+    params: MaskfilterParameters,
+    execution: Execution,
+) -> MaskfilterOutputs:
+    """
+    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 = MaskfilterOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def maskfilter_execute(
+    params: MaskfilterParameters,
+    execution: Execution,
+) -> MaskfilterOutputs:
+    """
+    Perform filtering operations on 3D / 4D mask images.
+    
+    The available filters are: clean, connect, dilate, erode, median.
+    
+    Each filter has its own unique set of optional parameters.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MaskfilterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = maskfilter_cargs(params, execution)
+    ret = maskfilter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def maskfilter(
+    input_: InputPathType,
+    filter_: str,
+    output: str,
+    scale: int | None = None,
+    axes: list[int] | None = None,
+    largest: bool = False,
+    connectivity: bool = False,
+    npass: int | None = None,
+    extent: list[int] | None = None,
+    strides: typing.Union[MaskfilterVariousStringParameters, MaskfilterVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MaskfilterConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MaskfilterOutputs:
+    """
+    Perform filtering operations on 3D / 4D mask images.
+    
+    The available filters are: clean, connect, dilate, erode, median.
+    
+    Each filter has its own unique set of optional parameters.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image.
+        filter_: the type of filter to be applied (clean, connect, dilate,\
+            erode, median).
+        output: the output image.
+        scale: the maximum scale used to cut bridges. A certain maximum scale\
+            cuts bridges up to a width (in voxels) of 2x the provided scale.\
+            (Default: 2).
+        axes: specify which axes should be included in the connected\
+            components. By default only the first 3 axes are included. The axes\
+            should be provided as a comma-separated list of values.
+        largest: only retain the largest connected component.
+        connectivity: use 26-voxel-neighbourhood connectivity (Default: 6).
+        npass: the number of times to repeatedly apply the filter.
+        extent: specify the extent (width) of kernel size in voxels. This can\
+            be specified either as a single value to be used for all axes, or as a\
+            comma-separated list of the extent for each axis. The default is 3x3x3.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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 `MaskfilterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MASKFILTER_METADATA)
+    params = maskfilter_params(
+        scale=scale,
+        axes=axes,
+        largest=largest,
+        connectivity=connectivity,
+        npass=npass,
+        extent=extent,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        filter_=filter_,
+        output=output,
+    )
+    return maskfilter_execute(params, execution)
+
+
+__all__ = [
+    "MASKFILTER_METADATA",
+    "MaskfilterConfigParameters",
+    "MaskfilterOutputs",
+    "MaskfilterParameters",
+    "MaskfilterVariousFileParameters",
+    "MaskfilterVariousStringParameters",
+    "maskfilter",
+    "maskfilter_config_params",
+    "maskfilter_params",
+    "maskfilter_various_file_params",
+    "maskfilter_various_string_params",
+]