niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrfilter.py

@@ -0,0 +1,716 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRFILTER_METADATA = Metadata(
+    id="3bb2ab8375a99185acaeac0f9e608829bff091ac.boutiques",
+    name="mrfilter",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrfilterVariousStringParameters = typing.TypedDict('MrfilterVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+MrfilterVariousFileParameters = typing.TypedDict('MrfilterVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+MrfilterConfigParameters = typing.TypedDict('MrfilterConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrfilterParameters = typing.TypedDict('MrfilterParameters', {
+    "__STYX_TYPE__": typing.Literal["mrfilter"],
+    "axes": typing.NotRequired[list[int] | None],
+    "inverse": bool,
+    "magnitude": bool,
+    "centre_zero": bool,
+    "stdev": typing.NotRequired[list[float] | None],
+    "magnitude_1": bool,
+    "scanner": bool,
+    "extent": typing.NotRequired[list[int] | None],
+    "extent_1": typing.NotRequired[list[int] | None],
+    "stdev_1": typing.NotRequired[list[float] | None],
+    "fwhm": typing.NotRequired[list[float] | None],
+    "extent_2": typing.NotRequired[list[int] | None],
+    "zupper": typing.NotRequired[float | None],
+    "zlower": typing.NotRequired[float | None],
+    "bridge": typing.NotRequired[int | None],
+    "maskin": typing.NotRequired[InputPathType | None],
+    "maskout": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[MrfilterVariousStringParameters, MrfilterVariousFileParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrfilterConfigParameters] | 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 {
+        "mrfilter": mrfilter_cargs,
+        "VariousString": mrfilter_various_string_cargs,
+        "VariousFile": mrfilter_various_file_cargs,
+        "config": mrfilter_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 {
+        "mrfilter": mrfilter_outputs,
+    }.get(t)
+
+
+def mrfilter_various_string_params(
+    obj: str,
+) -> MrfilterVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def mrfilter_various_string_cargs(
+    params: MrfilterVariousStringParameters,
+    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 mrfilter_various_file_params(
+    obj: InputPathType,
+) -> MrfilterVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def mrfilter_various_file_cargs(
+    params: MrfilterVariousFileParameters,
+    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 mrfilter_config_params(
+    key: str,
+    value: str,
+) -> MrfilterConfigParameters:
+    """
+    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 mrfilter_config_cargs(
+    params: MrfilterConfigParameters,
+    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 MrfilterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrfilter(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output image."""
+    maskout: OutputPathType | None
+    """Output a refined mask based on a spatially coherent region with normal
+    intensity range. """
+
+
+def mrfilter_params(
+    input_: InputPathType,
+    filter_: str,
+    output: str,
+    axes: list[int] | None = None,
+    inverse: bool = False,
+    magnitude: bool = False,
+    centre_zero: bool = False,
+    stdev: list[float] | None = None,
+    magnitude_1: bool = False,
+    scanner: bool = False,
+    extent: list[int] | None = None,
+    extent_1: list[int] | None = None,
+    stdev_1: list[float] | None = None,
+    fwhm: list[float] | None = None,
+    extent_2: list[int] | None = None,
+    zupper: float | None = None,
+    zlower: float | None = None,
+    bridge: int | None = None,
+    maskin: InputPathType | None = None,
+    maskout: str | None = None,
+    strides: typing.Union[MrfilterVariousStringParameters, MrfilterVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrfilterConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> MrfilterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image.
+        filter_: the type of filter to be applied.
+        output: the output image.
+        axes: the axes along which to apply the Fourier Transform. By default,\
+            the transform is applied along the three spatial axes. Provide as a\
+            comma-separate list of axis indices.
+        inverse: apply the inverse FFT.
+        magnitude: output a magnitude image rather than a complex-valued image.
+        centre_zero: re-arrange the FFT results so that the zero-frequency\
+            component appears in the centre of the image, rather than at the edges.
+        stdev: the standard deviation of the Gaussian kernel used to smooth the\
+            input image (in mm). The image is smoothed to reduced large spurious\
+            gradients caused by noise. Use this option to override the default\
+            stdev of 1 voxel. This can be specified either as a single value to be\
+            used for all 3 axes, or as a comma-separated list of 3 values, one for\
+            each axis.
+        magnitude_1: output the gradient magnitude, rather than the default\
+            x,y,z components.
+        scanner: define the gradient with respect to the scanner coordinate\
+            frame of reference.
+        extent: specify extent of median filtering neighbourhood in voxels.\
+            This can be specified either as a single value to be used for all 3\
+            axes, or as a comma-separated list of 3 values, one for each axis\
+            (default: 3x3x3).
+        extent_1: specify extent of normalisation filtering neighbourhood in\
+            voxels. This can be specified either as a single value to be used for\
+            all 3 axes, or as a comma-separated list of 3 values, one for each axis\
+            (default: 3x3x3).
+        stdev_1: apply Gaussian smoothing with the specified standard\
+            deviation. The standard deviation is defined in mm (Default 1 voxel).\
+            This can be specified either as a single value to be used for all axes,\
+            or as a comma-separated list of the stdev for each axis.
+        fwhm: apply Gaussian smoothing with the specified full-width half\
+            maximum. The FWHM is defined in mm (Default 1 voxel * 2.3548). This can\
+            be specified either as a single value to be used for all axes, or as a\
+            comma-separated list of the FWHM for each axis.
+        extent_2: 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 extent is\
+            2 * ceil(2.5 * stdev / voxel_size) - 1.
+        zupper: define high intensity outliers: default: 2.5.
+        zlower: define low intensity outliers: default: 2.5.
+        bridge: number of voxels to gap to fill holes in mask: default: 4.
+        maskin: initial mask that defines the maximum spatial extent and the\
+            region from which to smaple the intensity range.
+        maskout: Output a refined mask based on a spatially coherent region\
+            with normal intensity range.
+        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__": "mrfilter",
+        "inverse": inverse,
+        "magnitude": magnitude,
+        "centre_zero": centre_zero,
+        "magnitude_1": magnitude_1,
+        "scanner": scanner,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "filter": filter_,
+        "output": output,
+    }
+    if axes is not None:
+        params["axes"] = axes
+    if stdev is not None:
+        params["stdev"] = stdev
+    if extent is not None:
+        params["extent"] = extent
+    if extent_1 is not None:
+        params["extent_1"] = extent_1
+    if stdev_1 is not None:
+        params["stdev_1"] = stdev_1
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if extent_2 is not None:
+        params["extent_2"] = extent_2
+    if zupper is not None:
+        params["zupper"] = zupper
+    if zlower is not None:
+        params["zlower"] = zlower
+    if bridge is not None:
+        params["bridge"] = bridge
+    if maskin is not None:
+        params["maskin"] = maskin
+    if maskout is not None:
+        params["maskout"] = maskout
+    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 mrfilter_cargs(
+    params: MrfilterParameters,
+    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("mrfilter")
+    if params.get("axes") is not None:
+        cargs.extend([
+            "-axes",
+            *map(str, params.get("axes"))
+        ])
+    if params.get("inverse"):
+        cargs.append("-inverse")
+    if params.get("magnitude"):
+        cargs.append("-magnitude")
+    if params.get("centre_zero"):
+        cargs.append("-centre_zero")
+    if params.get("stdev") is not None:
+        cargs.extend([
+            "-stdev",
+            ",".join(map(str, params.get("stdev")))
+        ])
+    if params.get("magnitude_1"):
+        cargs.append("-magnitude")
+    if params.get("scanner"):
+        cargs.append("-scanner")
+    if params.get("extent") is not None:
+        cargs.extend([
+            "-extent",
+            ",".join(map(str, params.get("extent")))
+        ])
+    if params.get("extent_1") is not None:
+        cargs.extend([
+            "-extent",
+            ",".join(map(str, params.get("extent_1")))
+        ])
+    if params.get("stdev_1") is not None:
+        cargs.extend([
+            "-stdev",
+            ",".join(map(str, params.get("stdev_1")))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "-fwhm",
+            ",".join(map(str, params.get("fwhm")))
+        ])
+    if params.get("extent_2") is not None:
+        cargs.extend([
+            "-extent",
+            ",".join(map(str, params.get("extent_2")))
+        ])
+    if params.get("zupper") is not None:
+        cargs.extend([
+            "-zupper",
+            str(params.get("zupper"))
+        ])
+    if params.get("zlower") is not None:
+        cargs.extend([
+            "-zlower",
+            str(params.get("zlower"))
+        ])
+    if params.get("bridge") is not None:
+        cargs.extend([
+            "-bridge",
+            str(params.get("bridge"))
+        ])
+    if params.get("maskin") is not None:
+        cargs.extend([
+            "-maskin",
+            execution.input_file(params.get("maskin"))
+        ])
+    if params.get("maskout") is not None:
+        cargs.extend([
+            "-maskout",
+            params.get("maskout")
+        ])
+    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 mrfilter_outputs(
+    params: MrfilterParameters,
+    execution: Execution,
+) -> MrfilterOutputs:
+    """
+    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 = MrfilterOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+        maskout=execution.output_file(params.get("maskout")) if (params.get("maskout") is not None) else None,
+    )
+    return ret
+
+
+def mrfilter_execute(
+    params: MrfilterParameters,
+    execution: Execution,
+) -> MrfilterOutputs:
+    """
+    Perform filtering operations on 3D / 4D MR images.
+    
+    The available filters are: fft, gradient, median, smooth, normalise, zclean.
+    
+    Each filter has its own unique set of optional parameters.
+    
+    For 4D images, each 3D volume is processed independently.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrfilterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrfilter_cargs(params, execution)
+    ret = mrfilter_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrfilter(
+    input_: InputPathType,
+    filter_: str,
+    output: str,
+    axes: list[int] | None = None,
+    inverse: bool = False,
+    magnitude: bool = False,
+    centre_zero: bool = False,
+    stdev: list[float] | None = None,
+    magnitude_1: bool = False,
+    scanner: bool = False,
+    extent: list[int] | None = None,
+    extent_1: list[int] | None = None,
+    stdev_1: list[float] | None = None,
+    fwhm: list[float] | None = None,
+    extent_2: list[int] | None = None,
+    zupper: float | None = None,
+    zlower: float | None = None,
+    bridge: int | None = None,
+    maskin: InputPathType | None = None,
+    maskout: str | None = None,
+    strides: typing.Union[MrfilterVariousStringParameters, MrfilterVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrfilterConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> MrfilterOutputs:
+    """
+    Perform filtering operations on 3D / 4D MR images.
+    
+    The available filters are: fft, gradient, median, smooth, normalise, zclean.
+    
+    Each filter has its own unique set of optional parameters.
+    
+    For 4D images, each 3D volume is processed independently.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image.
+        filter_: the type of filter to be applied.
+        output: the output image.
+        axes: the axes along which to apply the Fourier Transform. By default,\
+            the transform is applied along the three spatial axes. Provide as a\
+            comma-separate list of axis indices.
+        inverse: apply the inverse FFT.
+        magnitude: output a magnitude image rather than a complex-valued image.
+        centre_zero: re-arrange the FFT results so that the zero-frequency\
+            component appears in the centre of the image, rather than at the edges.
+        stdev: the standard deviation of the Gaussian kernel used to smooth the\
+            input image (in mm). The image is smoothed to reduced large spurious\
+            gradients caused by noise. Use this option to override the default\
+            stdev of 1 voxel. This can be specified either as a single value to be\
+            used for all 3 axes, or as a comma-separated list of 3 values, one for\
+            each axis.
+        magnitude_1: output the gradient magnitude, rather than the default\
+            x,y,z components.
+        scanner: define the gradient with respect to the scanner coordinate\
+            frame of reference.
+        extent: specify extent of median filtering neighbourhood in voxels.\
+            This can be specified either as a single value to be used for all 3\
+            axes, or as a comma-separated list of 3 values, one for each axis\
+            (default: 3x3x3).
+        extent_1: specify extent of normalisation filtering neighbourhood in\
+            voxels. This can be specified either as a single value to be used for\
+            all 3 axes, or as a comma-separated list of 3 values, one for each axis\
+            (default: 3x3x3).
+        stdev_1: apply Gaussian smoothing with the specified standard\
+            deviation. The standard deviation is defined in mm (Default 1 voxel).\
+            This can be specified either as a single value to be used for all axes,\
+            or as a comma-separated list of the stdev for each axis.
+        fwhm: apply Gaussian smoothing with the specified full-width half\
+            maximum. The FWHM is defined in mm (Default 1 voxel * 2.3548). This can\
+            be specified either as a single value to be used for all axes, or as a\
+            comma-separated list of the FWHM for each axis.
+        extent_2: 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 extent is\
+            2 * ceil(2.5 * stdev / voxel_size) - 1.
+        zupper: define high intensity outliers: default: 2.5.
+        zlower: define low intensity outliers: default: 2.5.
+        bridge: number of voxels to gap to fill holes in mask: default: 4.
+        maskin: initial mask that defines the maximum spatial extent and the\
+            region from which to smaple the intensity range.
+        maskout: Output a refined mask based on a spatially coherent region\
+            with normal intensity range.
+        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 `MrfilterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRFILTER_METADATA)
+    params = mrfilter_params(
+        axes=axes,
+        inverse=inverse,
+        magnitude=magnitude,
+        centre_zero=centre_zero,
+        stdev=stdev,
+        magnitude_1=magnitude_1,
+        scanner=scanner,
+        extent=extent,
+        extent_1=extent_1,
+        stdev_1=stdev_1,
+        fwhm=fwhm,
+        extent_2=extent_2,
+        zupper=zupper,
+        zlower=zlower,
+        bridge=bridge,
+        maskin=maskin,
+        maskout=maskout,
+        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 mrfilter_execute(params, execution)
+
+
+__all__ = [
+    "MRFILTER_METADATA",
+    "MrfilterConfigParameters",
+    "MrfilterOutputs",
+    "MrfilterParameters",
+    "MrfilterVariousFileParameters",
+    "MrfilterVariousStringParameters",
+    "mrfilter",
+    "mrfilter_config_params",
+    "mrfilter_params",
+    "mrfilter_various_file_params",
+    "mrfilter_various_string_params",
+]