niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_local_unifize.py

@@ -0,0 +1,286 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LOCAL_UNIFIZE_METADATA = Metadata(
+    id="15f1fc4af844d2f3848e6e3527f1534179ded986.boutiques",
+    name="3dLocalUnifize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLocalUnifizeParameters = typing.TypedDict('V3dLocalUnifizeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLocalUnifize"],
+    "input": InputPathType,
+    "output": str,
+    "working_dir": typing.NotRequired[str | None],
+    "echo": bool,
+    "no_clean": bool,
+    "local_rad": typing.NotRequired[float | None],
+    "local_perc": typing.NotRequired[float | None],
+    "local_mask": typing.NotRequired[str | None],
+    "filter_thr": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dLocalUnifize": v_3d_local_unifize_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 {
+        "3dLocalUnifize": v_3d_local_unifize_outputs,
+    }.get(t)
+
+
+class V3dLocalUnifizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_local_unifize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output dataset file"""
+
+
+def v_3d_local_unifize_params(
+    input_: InputPathType,
+    output: str,
+    working_dir: str | None = None,
+    echo: bool = False,
+    no_clean: bool = False,
+    local_rad: float | None = None,
+    local_perc: float | None = None,
+    local_mask: str | None = None,
+    filter_thr: float | None = None,
+) -> V3dLocalUnifizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input dataset.
+        output: Output dataset name, including path.
+        working_dir: Name of temporary working directory (def:\
+            __wdir_LocalUni_, plus a random alphanumeric str).
+        echo: Run this program very verbosely (default: false).
+        no_clean: Do not remove the working directory (default: remove it).
+        local_rad: The spherical neighborhood's radius for the 3dLocalStat step\
+            (default: -3).
+        local_perc: The percentile used in the 3dLocalStat step, generating the\
+            scaling volume (default: 50).
+        local_mask: Provide the masking option for the 3dLocalStat step; to\
+            remove any masking, put 'None' as the option value (default:\
+            "-automask").
+        filter_thr: Ceiling on values in the final, scaled dataset; values <=0\
+            turn off this final filtering (default: 1.5).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLocalUnifize",
+        "input": input_,
+        "output": output,
+        "echo": echo,
+        "no_clean": no_clean,
+    }
+    if working_dir is not None:
+        params["working_dir"] = working_dir
+    if local_rad is not None:
+        params["local_rad"] = local_rad
+    if local_perc is not None:
+        params["local_perc"] = local_perc
+    if local_mask is not None:
+        params["local_mask"] = local_mask
+    if filter_thr is not None:
+        params["filter_thr"] = filter_thr
+    return params
+
+
+def v_3d_local_unifize_cargs(
+    params: V3dLocalUnifizeParameters,
+    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("3dLocalUnifize")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.extend([
+        "-prefix",
+        params.get("output")
+    ])
+    if params.get("working_dir") is not None:
+        cargs.extend([
+            "-wdir_name",
+            params.get("working_dir")
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("local_rad") is not None:
+        cargs.extend([
+            "-local_rad",
+            str(params.get("local_rad"))
+        ])
+    if params.get("local_perc") is not None:
+        cargs.extend([
+            "-local_perc",
+            str(params.get("local_perc"))
+        ])
+    if params.get("local_mask") is not None:
+        cargs.extend([
+            "-local_mask",
+            params.get("local_mask")
+        ])
+    if params.get("filter_thr") is not None:
+        cargs.extend([
+            "-filter_thr",
+            str(params.get("filter_thr"))
+        ])
+    return cargs
+
+
+def v_3d_local_unifize_outputs(
+    params: V3dLocalUnifizeParameters,
+    execution: Execution,
+) -> V3dLocalUnifizeOutputs:
+    """
+    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 = V3dLocalUnifizeOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def v_3d_local_unifize_execute(
+    params: V3dLocalUnifizeParameters,
+    execution: Execution,
+) -> V3dLocalUnifizeOutputs:
+    """
+    This program generates a 'unifized' output volume by estimating the median in
+    the local neighborhood of each voxel and using that to scale each voxel's
+    brightness.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalUnifizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_local_unifize_cargs(params, execution)
+    ret = v_3d_local_unifize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_local_unifize(
+    input_: InputPathType,
+    output: str,
+    working_dir: str | None = None,
+    echo: bool = False,
+    no_clean: bool = False,
+    local_rad: float | None = None,
+    local_perc: float | None = None,
+    local_mask: str | None = None,
+    filter_thr: float | None = None,
+    runner: Runner | None = None,
+) -> V3dLocalUnifizeOutputs:
+    """
+    This program generates a 'unifized' output volume by estimating the median in
+    the local neighborhood of each voxel and using that to scale each voxel's
+    brightness.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input dataset.
+        output: Output dataset name, including path.
+        working_dir: Name of temporary working directory (def:\
+            __wdir_LocalUni_, plus a random alphanumeric str).
+        echo: Run this program very verbosely (default: false).
+        no_clean: Do not remove the working directory (default: remove it).
+        local_rad: The spherical neighborhood's radius for the 3dLocalStat step\
+            (default: -3).
+        local_perc: The percentile used in the 3dLocalStat step, generating the\
+            scaling volume (default: 50).
+        local_mask: Provide the masking option for the 3dLocalStat step; to\
+            remove any masking, put 'None' as the option value (default:\
+            "-automask").
+        filter_thr: Ceiling on values in the final, scaled dataset; values <=0\
+            turn off this final filtering (default: 1.5).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalUnifizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_UNIFIZE_METADATA)
+    params = v_3d_local_unifize_params(
+        input_=input_,
+        output=output,
+        working_dir=working_dir,
+        echo=echo,
+        no_clean=no_clean,
+        local_rad=local_rad,
+        local_perc=local_perc,
+        local_mask=local_mask,
+        filter_thr=filter_thr,
+    )
+    return v_3d_local_unifize_execute(params, execution)
+
+
+__all__ = [
+    "V3dLocalUnifizeOutputs",
+    "V3dLocalUnifizeParameters",
+    "V_3D_LOCAL_UNIFIZE_METADATA",
+    "v_3d_local_unifize",
+    "v_3d_local_unifize_params",
+]

niwrap_afni/afni/v_3d_localstat.py

@@ -0,0 +1,427 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LOCALSTAT_METADATA = Metadata(
+    id="f927c9d4ad8b0ef0fa566fe0b9648789d0b3eb44.boutiques",
+    name="3dLocalstat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLocalstatParameters = typing.TypedDict('V3dLocalstatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLocalstat"],
+    "dataset": InputPathType,
+    "nbhd": str,
+    "stat": typing.NotRequired[list[str] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "use_nonmask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "label_ext": typing.NotRequired[str | None],
+    "reduce_grid": typing.NotRequired[list[float] | None],
+    "reduce_restore_grid": typing.NotRequired[list[float] | None],
+    "reduce_max_vox": typing.NotRequired[float | None],
+    "grid_rmode": typing.NotRequired[str | None],
+    "quiet": bool,
+    "verbose": bool,
+    "proceed_small_N": bool,
+    "fillvalue": typing.NotRequired[float | None],
+    "unfillvalue": typing.NotRequired[float | None],
+    "maskvalue": typing.NotRequired[float | None],
+    "maskvalue2": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dLocalstat": v_3d_localstat_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 {
+        "3dLocalstat": v_3d_localstat_outputs,
+    }.get(t)
+
+
+class V3dLocalstatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_localstat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """Output dataset"""
+
+
+def v_3d_localstat_params(
+    dataset: InputPathType,
+    nbhd: str,
+    stat_: list[str] | None = None,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    use_nonmask: bool = False,
+    prefix: str | None = None,
+    datum: str | None = None,
+    label_ext: str | None = None,
+    reduce_grid: list[float] | None = None,
+    reduce_restore_grid: list[float] | None = None,
+    reduce_max_vox: float | None = None,
+    grid_rmode: str | None = None,
+    quiet: bool = False,
+    verbose: bool = False,
+    proceed_small_n: bool = False,
+    fillvalue: float | None = None,
+    unfillvalue: float | None = None,
+    maskvalue: float | None = None,
+    maskvalue2: float | None = None,
+) -> V3dLocalstatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        nbhd: The region around each voxel that will be extracted for the\
+            statistics calculation.
+        stat_: Compute the specified statistic on the values extracted from the\
+            neighborhood.
+        mask: Read in dataset 'mset' and use the nonzero voxels therein as a\
+            mask.
+        automask: Compute the mask as in program 3dAutomask (mutually exclusive\
+            with -mask).
+        use_nonmask: Compute local statistics from all voxels in the\
+            neighborhood that are in the mask, even if the central voxel is not in\
+            the mask.
+        prefix: Use the given string as the prefix for the output dataset.
+        datum: Coerce the output data to be stored as the given type (byte,\
+            short, float).
+        label_ext: Append given label to each sub-brick label.
+        reduce_grid: Compute output on a grid that is reduced by the given\
+            factor in X, Y, and Z directions of the input dataset.
+        reduce_restore_grid: Resample the output back to input grid after\
+            reducing the grid.
+        reduce_max_vox: Automatically set Rx Ry Rz so that the computation grid\
+            is at a resolution of nbhd/MAX_VOX voxels.
+        grid_rmode: Interpolant to use when resampling the output with\
+            reduce_restore_grid option.
+        quiet: Stop the highly informative progress reports.
+        verbose: A little more verbose output.
+        proceed_small_n: Do not crash if neighborhood is too small for certain\
+            estimates.
+        fillvalue: Value used for filled statistic, default=1.
+        unfillvalue: Value used for unfilled statistic, default=1.
+        maskvalue: Value searched for with has_mask option.
+        maskvalue2: Alternate value for has_mask2 option.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLocalstat",
+        "dataset": dataset,
+        "nbhd": nbhd,
+        "automask": automask,
+        "use_nonmask": use_nonmask,
+        "quiet": quiet,
+        "verbose": verbose,
+        "proceed_small_N": proceed_small_n,
+    }
+    if stat_ is not None:
+        params["stat"] = stat_
+    if mask is not None:
+        params["mask"] = mask
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum is not None:
+        params["datum"] = datum
+    if label_ext is not None:
+        params["label_ext"] = label_ext
+    if reduce_grid is not None:
+        params["reduce_grid"] = reduce_grid
+    if reduce_restore_grid is not None:
+        params["reduce_restore_grid"] = reduce_restore_grid
+    if reduce_max_vox is not None:
+        params["reduce_max_vox"] = reduce_max_vox
+    if grid_rmode is not None:
+        params["grid_rmode"] = grid_rmode
+    if fillvalue is not None:
+        params["fillvalue"] = fillvalue
+    if unfillvalue is not None:
+        params["unfillvalue"] = unfillvalue
+    if maskvalue is not None:
+        params["maskvalue"] = maskvalue
+    if maskvalue2 is not None:
+        params["maskvalue2"] = maskvalue2
+    return params
+
+
+def v_3d_localstat_cargs(
+    params: V3dLocalstatParameters,
+    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("3dLocalstat")
+    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.extend([
+        "-nbhd",
+        params.get("nbhd")
+    ])
+    if params.get("stat") is not None:
+        cargs.extend([
+            "-stat",
+            *params.get("stat")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("use_nonmask"):
+        cargs.append("-use_nonmask")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("label_ext") is not None:
+        cargs.extend([
+            "-label_ext",
+            params.get("label_ext")
+        ])
+    if params.get("reduce_grid") is not None:
+        cargs.extend([
+            "-reduce_grid",
+            *map(str, params.get("reduce_grid"))
+        ])
+    if params.get("reduce_restore_grid") is not None:
+        cargs.extend([
+            "-reduce_restore_grid",
+            *map(str, params.get("reduce_restore_grid"))
+        ])
+    if params.get("reduce_max_vox") is not None:
+        cargs.extend([
+            "-reduce_max_vox",
+            str(params.get("reduce_max_vox"))
+        ])
+    if params.get("grid_rmode") is not None:
+        cargs.extend([
+            "-grid_rmode",
+            params.get("grid_rmode")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("proceed_small_N"):
+        cargs.append("-proceed_small_N")
+    if params.get("fillvalue") is not None:
+        cargs.extend([
+            "-fillvalue",
+            str(params.get("fillvalue"))
+        ])
+    if params.get("unfillvalue") is not None:
+        cargs.extend([
+            "-unfillvalue",
+            str(params.get("unfillvalue"))
+        ])
+    if params.get("maskvalue") is not None:
+        cargs.extend([
+            "-maskvalue",
+            str(params.get("maskvalue"))
+        ])
+    if params.get("maskvalue2") is not None:
+        cargs.extend([
+            "-maskvalue2",
+            str(params.get("maskvalue2"))
+        ])
+    return cargs
+
+
+def v_3d_localstat_outputs(
+    params: V3dLocalstatParameters,
+    execution: Execution,
+) -> V3dLocalstatOutputs:
+    """
+    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 = V3dLocalstatOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_localstat_execute(
+    params: V3dLocalstatParameters,
+    execution: Execution,
+) -> V3dLocalstatOutputs:
+    """
+    This program computes statistics at each voxel, based on a local neighborhood of
+    that voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalstatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_localstat_cargs(params, execution)
+    ret = v_3d_localstat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_localstat(
+    dataset: InputPathType,
+    nbhd: str,
+    stat_: list[str] | None = None,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    use_nonmask: bool = False,
+    prefix: str | None = None,
+    datum: str | None = None,
+    label_ext: str | None = None,
+    reduce_grid: list[float] | None = None,
+    reduce_restore_grid: list[float] | None = None,
+    reduce_max_vox: float | None = None,
+    grid_rmode: str | None = None,
+    quiet: bool = False,
+    verbose: bool = False,
+    proceed_small_n: bool = False,
+    fillvalue: float | None = None,
+    unfillvalue: float | None = None,
+    maskvalue: float | None = None,
+    maskvalue2: float | None = None,
+    runner: Runner | None = None,
+) -> V3dLocalstatOutputs:
+    """
+    This program computes statistics at each voxel, based on a local neighborhood of
+    that voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        nbhd: The region around each voxel that will be extracted for the\
+            statistics calculation.
+        stat_: Compute the specified statistic on the values extracted from the\
+            neighborhood.
+        mask: Read in dataset 'mset' and use the nonzero voxels therein as a\
+            mask.
+        automask: Compute the mask as in program 3dAutomask (mutually exclusive\
+            with -mask).
+        use_nonmask: Compute local statistics from all voxels in the\
+            neighborhood that are in the mask, even if the central voxel is not in\
+            the mask.
+        prefix: Use the given string as the prefix for the output dataset.
+        datum: Coerce the output data to be stored as the given type (byte,\
+            short, float).
+        label_ext: Append given label to each sub-brick label.
+        reduce_grid: Compute output on a grid that is reduced by the given\
+            factor in X, Y, and Z directions of the input dataset.
+        reduce_restore_grid: Resample the output back to input grid after\
+            reducing the grid.
+        reduce_max_vox: Automatically set Rx Ry Rz so that the computation grid\
+            is at a resolution of nbhd/MAX_VOX voxels.
+        grid_rmode: Interpolant to use when resampling the output with\
+            reduce_restore_grid option.
+        quiet: Stop the highly informative progress reports.
+        verbose: A little more verbose output.
+        proceed_small_n: Do not crash if neighborhood is too small for certain\
+            estimates.
+        fillvalue: Value used for filled statistic, default=1.
+        unfillvalue: Value used for unfilled statistic, default=1.
+        maskvalue: Value searched for with has_mask option.
+        maskvalue2: Alternate value for has_mask2 option.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalstatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCALSTAT_METADATA)
+    params = v_3d_localstat_params(
+        dataset=dataset,
+        nbhd=nbhd,
+        stat_=stat_,
+        mask=mask,
+        automask=automask,
+        use_nonmask=use_nonmask,
+        prefix=prefix,
+        datum=datum,
+        label_ext=label_ext,
+        reduce_grid=reduce_grid,
+        reduce_restore_grid=reduce_restore_grid,
+        reduce_max_vox=reduce_max_vox,
+        grid_rmode=grid_rmode,
+        quiet=quiet,
+        verbose=verbose,
+        proceed_small_n=proceed_small_n,
+        fillvalue=fillvalue,
+        unfillvalue=unfillvalue,
+        maskvalue=maskvalue,
+        maskvalue2=maskvalue2,
+    )
+    return v_3d_localstat_execute(params, execution)
+
+
+__all__ = [
+    "V3dLocalstatOutputs",
+    "V3dLocalstatParameters",
+    "V_3D_LOCALSTAT_METADATA",
+    "v_3d_localstat",
+    "v_3d_localstat_params",
+]