niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/mrthreshold.py

@@ -0,0 +1,549 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRTHRESHOLD_METADATA = Metadata(
+    id="5f0e00d650d7ff4c22350347b81985e0b496eddf.boutiques",
+    name="mrthreshold",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+MrthresholdConfigParameters = typing.TypedDict('MrthresholdConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+MrthresholdParameters = typing.TypedDict('MrthresholdParameters', {
+    "__STYX_TYPE__": typing.Literal["mrthreshold"],
+    "abs": typing.NotRequired[float | None],
+    "percentile": typing.NotRequired[float | None],
+    "top": typing.NotRequired[int | None],
+    "bottom": typing.NotRequired[int | None],
+    "allvolumes": bool,
+    "ignorezero": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "comparison": typing.NotRequired[str | None],
+    "invert": bool,
+    "out_masked": bool,
+    "nan": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrthresholdConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mrthreshold": mrthreshold_cargs,
+        "config": mrthreshold_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 {
+        "mrthreshold": mrthreshold_outputs,
+    }.get(t)
+
+
+def mrthreshold_config_params(
+    key: str,
+    value: str,
+) -> MrthresholdConfigParameters:
+    """
+    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 mrthreshold_config_cargs(
+    params: MrthresholdConfigParameters,
+    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 MrthresholdOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mrthreshold(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType | None
+    """the (optional) output binary image mask"""
+
+
+def mrthreshold_params(
+    input_: InputPathType,
+    abs_: float | None = None,
+    percentile: float | None = None,
+    top: int | None = None,
+    bottom: int | None = None,
+    allvolumes: bool = False,
+    ignorezero: bool = False,
+    mask: InputPathType | None = None,
+    comparison: str | None = None,
+    invert: bool = False,
+    out_masked: bool = False,
+    nan: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrthresholdConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    output: str | None = None,
+) -> MrthresholdParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input image to be thresholded.
+        abs_: specify threshold value as absolute intensity.
+        percentile: determine threshold based on some percentile of the image\
+            intensity distribution.
+        top: determine threshold that will result in selection of some number\
+            of top-valued voxels.
+        bottom: determine & apply threshold resulting in selection of some\
+            number of bottom-valued voxels (note: implies threshold application\
+            operator of "le" unless otherwise specified).
+        allvolumes: compute a single threshold for all image volumes, rather\
+            than an individual threshold per volume.
+        ignorezero: ignore zero-valued input values during threshold\
+            determination.
+        mask: compute the threshold based only on values within an input mask\
+            image.
+        comparison: comparison operator to use when applying the threshold;\
+            options are: lt,le,ge,gt (default = "le" for -bottom; "ge" otherwise).
+        invert: invert the output binary mask (equivalent to flipping the\
+            operator; provided for backwards compatibility).
+        out_masked: mask the output image based on the provided input mask\
+            image.
+        nan: set voxels that fail the threshold to NaN rather than zero (output\
+            image will be floating-point rather than binary).
+        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.
+        output: the (optional) output binary image mask.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mrthreshold",
+        "allvolumes": allvolumes,
+        "ignorezero": ignorezero,
+        "invert": invert,
+        "out_masked": out_masked,
+        "nan": nan,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+    }
+    if abs_ is not None:
+        params["abs"] = abs_
+    if percentile is not None:
+        params["percentile"] = percentile
+    if top is not None:
+        params["top"] = top
+    if bottom is not None:
+        params["bottom"] = bottom
+    if mask is not None:
+        params["mask"] = mask
+    if comparison is not None:
+        params["comparison"] = comparison
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    if output is not None:
+        params["output"] = output
+    return params
+
+
+def mrthreshold_cargs(
+    params: MrthresholdParameters,
+    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("mrthreshold")
+    if params.get("abs") is not None:
+        cargs.extend([
+            "-abs",
+            str(params.get("abs"))
+        ])
+    if params.get("percentile") is not None:
+        cargs.extend([
+            "-percentile",
+            str(params.get("percentile"))
+        ])
+    if params.get("top") is not None:
+        cargs.extend([
+            "-top",
+            str(params.get("top"))
+        ])
+    if params.get("bottom") is not None:
+        cargs.extend([
+            "-bottom",
+            str(params.get("bottom"))
+        ])
+    if params.get("allvolumes"):
+        cargs.append("-allvolumes")
+    if params.get("ignorezero"):
+        cargs.append("-ignorezero")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("comparison") is not None:
+        cargs.extend([
+            "-comparison",
+            params.get("comparison")
+        ])
+    if params.get("invert"):
+        cargs.append("-invert")
+    if params.get("out_masked"):
+        cargs.append("-out_masked")
+    if params.get("nan"):
+        cargs.append("-nan")
+    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")))
+    if params.get("output") is not None:
+        cargs.append(params.get("output"))
+    return cargs
+
+
+def mrthreshold_outputs(
+    params: MrthresholdParameters,
+    execution: Execution,
+) -> MrthresholdOutputs:
+    """
+    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 = MrthresholdOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
+    )
+    return ret
+
+
+def mrthreshold_execute(
+    params: MrthresholdParameters,
+    execution: Execution,
+) -> MrthresholdOutputs:
+    """
+    Create bitwise image by thresholding image intensity.
+    
+    The threshold value to be applied can be determined in one of a number of
+    ways:
+    
+    - If no relevant command-line option is used, the command will automatically
+    determine an optimal threshold;
+    
+    - The -abs option provides the threshold value explicitly;
+    
+    - The -percentile, -top and -bottom options enable more fine-grained control
+    over how the threshold value is determined.
+    
+    The -mask option only influences those image values that contribute toward
+    the determination of the threshold value; once the threshold is determined,
+    it is applied to the entire image, irrespective of use of the -mask option.
+    If you wish for the voxels outside of the specified mask to additionally be
+    excluded from the output mask, this can be achieved by providing the
+    -out_masked option.
+    
+    The four operators available through the "-comparison" option ("lt", "le",
+    "ge" and "gt") correspond to "less-than" (<), "less-than-or-equal" (<=),
+    "greater-than-or-equal" (>=) and "greater-than" (>). This offers
+    fine-grained control over how the thresholding operation will behave in the
+    presence of values equivalent to the threshold. By default, the command will
+    select voxels with values greater than or equal to the determined threshold
+    ("ge"); unless the -bottom option is used, in which case after a threshold
+    is determined from the relevant lowest-valued image voxels, those voxels
+    with values less than or equal to that threshold ("le") are selected. This
+    provides more fine-grained control than the -invert option; the latter is
+    provided for backwards compatibility, but is equivalent to selection of the
+    opposite comparison within this selection.
+    
+    If no output image path is specified, the command will instead write to
+    standard output the determined threshold value.
+    
+    References:
+    
+    * If not using any explicit thresholding mechanism:
+    Ridgway, G. R.; Omar, R.; Ourselin, S.; Hill, D. L.; Warren, J. D. & Fox, N.
+    C. Issues with threshold masking in voxel-based morphometry of atrophied
+    brains. NeuroImage, 2009, 44, 99-111.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MrthresholdOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mrthreshold_cargs(params, execution)
+    ret = mrthreshold_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mrthreshold(
+    input_: InputPathType,
+    abs_: float | None = None,
+    percentile: float | None = None,
+    top: int | None = None,
+    bottom: int | None = None,
+    allvolumes: bool = False,
+    ignorezero: bool = False,
+    mask: InputPathType | None = None,
+    comparison: str | None = None,
+    invert: bool = False,
+    out_masked: bool = False,
+    nan: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[MrthresholdConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    output: str | None = None,
+    runner: Runner | None = None,
+) -> MrthresholdOutputs:
+    """
+    Create bitwise image by thresholding image intensity.
+    
+    The threshold value to be applied can be determined in one of a number of
+    ways:
+    
+    - If no relevant command-line option is used, the command will automatically
+    determine an optimal threshold;
+    
+    - The -abs option provides the threshold value explicitly;
+    
+    - The -percentile, -top and -bottom options enable more fine-grained control
+    over how the threshold value is determined.
+    
+    The -mask option only influences those image values that contribute toward
+    the determination of the threshold value; once the threshold is determined,
+    it is applied to the entire image, irrespective of use of the -mask option.
+    If you wish for the voxels outside of the specified mask to additionally be
+    excluded from the output mask, this can be achieved by providing the
+    -out_masked option.
+    
+    The four operators available through the "-comparison" option ("lt", "le",
+    "ge" and "gt") correspond to "less-than" (<), "less-than-or-equal" (<=),
+    "greater-than-or-equal" (>=) and "greater-than" (>). This offers
+    fine-grained control over how the thresholding operation will behave in the
+    presence of values equivalent to the threshold. By default, the command will
+    select voxels with values greater than or equal to the determined threshold
+    ("ge"); unless the -bottom option is used, in which case after a threshold
+    is determined from the relevant lowest-valued image voxels, those voxels
+    with values less than or equal to that threshold ("le") are selected. This
+    provides more fine-grained control than the -invert option; the latter is
+    provided for backwards compatibility, but is equivalent to selection of the
+    opposite comparison within this selection.
+    
+    If no output image path is specified, the command will instead write to
+    standard output the determined threshold value.
+    
+    References:
+    
+    * If not using any explicit thresholding mechanism:
+    Ridgway, G. R.; Omar, R.; Ourselin, S.; Hill, D. L.; Warren, J. D. & Fox, N.
+    C. Issues with threshold masking in voxel-based morphometry of atrophied
+    brains. NeuroImage, 2009, 44, 99-111.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input image to be thresholded.
+        abs_: specify threshold value as absolute intensity.
+        percentile: determine threshold based on some percentile of the image\
+            intensity distribution.
+        top: determine threshold that will result in selection of some number\
+            of top-valued voxels.
+        bottom: determine & apply threshold resulting in selection of some\
+            number of bottom-valued voxels (note: implies threshold application\
+            operator of "le" unless otherwise specified).
+        allvolumes: compute a single threshold for all image volumes, rather\
+            than an individual threshold per volume.
+        ignorezero: ignore zero-valued input values during threshold\
+            determination.
+        mask: compute the threshold based only on values within an input mask\
+            image.
+        comparison: comparison operator to use when applying the threshold;\
+            options are: lt,le,ge,gt (default = "le" for -bottom; "ge" otherwise).
+        invert: invert the output binary mask (equivalent to flipping the\
+            operator; provided for backwards compatibility).
+        out_masked: mask the output image based on the provided input mask\
+            image.
+        nan: set voxels that fail the threshold to NaN rather than zero (output\
+            image will be floating-point rather than binary).
+        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.
+        output: the (optional) output binary image mask.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MrthresholdOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRTHRESHOLD_METADATA)
+    params = mrthreshold_params(
+        abs_=abs_,
+        percentile=percentile,
+        top=top,
+        bottom=bottom,
+        allvolumes=allvolumes,
+        ignorezero=ignorezero,
+        mask=mask,
+        comparison=comparison,
+        invert=invert,
+        out_masked=out_masked,
+        nan=nan,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return mrthreshold_execute(params, execution)
+
+
+__all__ = [
+    "MRTHRESHOLD_METADATA",
+    "MrthresholdConfigParameters",
+    "MrthresholdOutputs",
+    "MrthresholdParameters",
+    "mrthreshold",
+    "mrthreshold_config_params",
+    "mrthreshold_params",
+]