niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_wilcoxon.py

@@ -0,0 +1,231 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_WILCOXON_METADATA = Metadata(
+    id="463bd0c7f172cd1b8be0a6f1adaeefb51a0010ea.boutiques",
+    name="3dWilcoxon",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dWilcoxonParameters = typing.TypedDict('V3dWilcoxonParameters', {
+    "__STYX_TYPE__": typing.Literal["3dWilcoxon"],
+    "workmem": typing.NotRequired[float | None],
+    "voxel": typing.NotRequired[float | None],
+    "dset1_x": list[InputPathType],
+    "dset2_y": list[InputPathType],
+    "output_prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dWilcoxon": v_3d_wilcoxon_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 {
+        "3dWilcoxon": v_3d_wilcoxon_outputs,
+    }.get(t)
+
+
+class V3dWilcoxonOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_wilcoxon(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Estimated population delta and Wilcoxon signed-rank statistics"""
+
+
+def v_3d_wilcoxon_params(
+    dset1_x: list[InputPathType],
+    dset2_y: list[InputPathType],
+    output_prefix: str,
+    workmem: float | None = None,
+    voxel: float | None = None,
+) -> V3dWilcoxonParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset1_x: Data set for X observations. The user must specify 1 and only\
+            1 sub-brick with each -dset command.
+        dset2_y: Data set for Y observations. The user must specify 1 and only\
+            1 sub-brick with each -dset command.
+        output_prefix: Estimated population delta and Wilcoxon signed-rank\
+            statistics are written to file.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel: Screen output for voxel # num.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dWilcoxon",
+        "dset1_x": dset1_x,
+        "dset2_y": dset2_y,
+        "output_prefix": output_prefix,
+    }
+    if workmem is not None:
+        params["workmem"] = workmem
+    if voxel is not None:
+        params["voxel"] = voxel
+    return params
+
+
+def v_3d_wilcoxon_cargs(
+    params: V3dWilcoxonParameters,
+    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("3dWilcoxon")
+    if params.get("workmem") is not None:
+        cargs.extend([
+            "-workmem",
+            str(params.get("workmem"))
+        ])
+    if params.get("voxel") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel"))
+        ])
+    cargs.append("-dset")
+    cargs.append("1")
+    cargs.extend([execution.input_file(f) for f in params.get("dset1_x")])
+    cargs.append("-dset")
+    cargs.append("2")
+    cargs.extend([execution.input_file(f) for f in params.get("dset2_y")])
+    cargs.extend([
+        "-out",
+        params.get("output_prefix")
+    ])
+    return cargs
+
+
+def v_3d_wilcoxon_outputs(
+    params: V3dWilcoxonParameters,
+    execution: Execution,
+) -> V3dWilcoxonOutputs:
+    """
+    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 = V3dWilcoxonOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix")),
+    )
+    return ret
+
+
+def v_3d_wilcoxon_execute(
+    params: V3dWilcoxonParameters,
+    execution: Execution,
+) -> V3dWilcoxonOutputs:
+    """
+    Nonparametric Wilcoxon signed-rank test for paired comparisons of two samples.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dWilcoxonOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_wilcoxon_cargs(params, execution)
+    ret = v_3d_wilcoxon_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_wilcoxon(
+    dset1_x: list[InputPathType],
+    dset2_y: list[InputPathType],
+    output_prefix: str,
+    workmem: float | None = None,
+    voxel: float | None = None,
+    runner: Runner | None = None,
+) -> V3dWilcoxonOutputs:
+    """
+    Nonparametric Wilcoxon signed-rank test for paired comparisons of two samples.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset1_x: Data set for X observations. The user must specify 1 and only\
+            1 sub-brick with each -dset command.
+        dset2_y: Data set for Y observations. The user must specify 1 and only\
+            1 sub-brick with each -dset command.
+        output_prefix: Estimated population delta and Wilcoxon signed-rank\
+            statistics are written to file.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel: Screen output for voxel # num.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dWilcoxonOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WILCOXON_METADATA)
+    params = v_3d_wilcoxon_params(
+        workmem=workmem,
+        voxel=voxel,
+        dset1_x=dset1_x,
+        dset2_y=dset2_y,
+        output_prefix=output_prefix,
+    )
+    return v_3d_wilcoxon_execute(params, execution)
+
+
+__all__ = [
+    "V3dWilcoxonOutputs",
+    "V3dWilcoxonParameters",
+    "V_3D_WILCOXON_METADATA",
+    "v_3d_wilcoxon",
+    "v_3d_wilcoxon_params",
+]

niwrap_afni/afni/v_3d_winsor.py

@@ -0,0 +1,287 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_WINSOR_METADATA = Metadata(
+    id="5b03e02998e8591af14134792670004ae23adb4e.boutiques",
+    name="3dWinsor",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dWinsorParameters = typing.TypedDict('V3dWinsorParameters', {
+    "__STYX_TYPE__": typing.Literal["3dWinsor"],
+    "irad": typing.NotRequired[float | None],
+    "cbot": typing.NotRequired[float | None],
+    "ctop": typing.NotRequired[float | None],
+    "nrep": typing.NotRequired[float | None],
+    "keepzero": bool,
+    "clip": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dWinsor": v_3d_winsor_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 {
+        "3dWinsor": v_3d_winsor_outputs,
+    }.get(t)
+
+
+class V3dWinsorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_winsor(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile_head: OutputPathType | None
+    """Output dataset with Winsorizing filter applied."""
+    outfile_brik: OutputPathType | None
+    """Output dataset with Winsorizing filter applied."""
+
+
+def v_3d_winsor_params(
+    dataset: InputPathType,
+    irad: float | None = None,
+    cbot: float | None = None,
+    ctop: float | None = None,
+    nrep: float | None = None,
+    keepzero: bool = False,
+    clip: float | None = None,
+    prefix: str | None = None,
+    mask: InputPathType | None = None,
+) -> V3dWinsorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset to apply the filter on.
+        irad: Include all points within 'distance' rr in the operation, where\
+            distance is defined as sqrt(i*i+j*j+k*k), and (i,j,k) are voxel index\
+            offsets.
+        cbot: Set bottom clip index to bb.
+        ctop: Set top clip index to tt.
+        nrep: Repeat filter nn times. If nn < 0, means to repeat filter until\
+            less than abs(n) voxels change.
+        keepzero: Don't filter voxels that are zero.
+        clip: Set voxels at or below 'xx' to zero.
+        prefix: Use 'pp' as the prefix for the output dataset.
+        mask: Use 'mmm' as a mask dataset - voxels NOT in the mask won't be\
+            filtered.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dWinsor",
+        "keepzero": keepzero,
+        "dataset": dataset,
+    }
+    if irad is not None:
+        params["irad"] = irad
+    if cbot is not None:
+        params["cbot"] = cbot
+    if ctop is not None:
+        params["ctop"] = ctop
+    if nrep is not None:
+        params["nrep"] = nrep
+    if clip is not None:
+        params["clip"] = clip
+    if prefix is not None:
+        params["prefix"] = prefix
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_winsor_cargs(
+    params: V3dWinsorParameters,
+    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("3dWinsor")
+    if params.get("irad") is not None:
+        cargs.extend([
+            "-irad",
+            str(params.get("irad"))
+        ])
+    if params.get("cbot") is not None:
+        cargs.extend([
+            "-cbot",
+            str(params.get("cbot"))
+        ])
+    if params.get("ctop") is not None:
+        cargs.extend([
+            "-ctop",
+            str(params.get("ctop"))
+        ])
+    if params.get("nrep") is not None:
+        cargs.extend([
+            "-nrep",
+            str(params.get("nrep"))
+        ])
+    if params.get("keepzero"):
+        cargs.append("-keepzero")
+    if params.get("clip") is not None:
+        cargs.extend([
+            "-clip",
+            str(params.get("clip"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_winsor_outputs(
+    params: V3dWinsorParameters,
+    execution: Execution,
+) -> V3dWinsorOutputs:
+    """
+    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 = V3dWinsorOutputs(
+        root=execution.output_file("."),
+        outfile_head=execution.output_file(params.get("prefix") + "+*.HEAD") if (params.get("prefix") is not None) else None,
+        outfile_brik=execution.output_file(params.get("prefix") + "+*.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_winsor_execute(
+    params: V3dWinsorParameters,
+    execution: Execution,
+) -> V3dWinsorOutputs:
+    """
+    Apply a 3D 'Winsorizing' filter to a short-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dWinsorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_winsor_cargs(params, execution)
+    ret = v_3d_winsor_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_winsor(
+    dataset: InputPathType,
+    irad: float | None = None,
+    cbot: float | None = None,
+    ctop: float | None = None,
+    nrep: float | None = None,
+    keepzero: bool = False,
+    clip: float | None = None,
+    prefix: str | None = None,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dWinsorOutputs:
+    """
+    Apply a 3D 'Winsorizing' filter to a short-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset to apply the filter on.
+        irad: Include all points within 'distance' rr in the operation, where\
+            distance is defined as sqrt(i*i+j*j+k*k), and (i,j,k) are voxel index\
+            offsets.
+        cbot: Set bottom clip index to bb.
+        ctop: Set top clip index to tt.
+        nrep: Repeat filter nn times. If nn < 0, means to repeat filter until\
+            less than abs(n) voxels change.
+        keepzero: Don't filter voxels that are zero.
+        clip: Set voxels at or below 'xx' to zero.
+        prefix: Use 'pp' as the prefix for the output dataset.
+        mask: Use 'mmm' as a mask dataset - voxels NOT in the mask won't be\
+            filtered.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dWinsorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WINSOR_METADATA)
+    params = v_3d_winsor_params(
+        irad=irad,
+        cbot=cbot,
+        ctop=ctop,
+        nrep=nrep,
+        keepzero=keepzero,
+        clip=clip,
+        prefix=prefix,
+        mask=mask,
+        dataset=dataset,
+    )
+    return v_3d_winsor_execute(params, execution)
+
+
+__all__ = [
+    "V3dWinsorOutputs",
+    "V3dWinsorParameters",
+    "V_3D_WINSOR_METADATA",
+    "v_3d_winsor",
+    "v_3d_winsor_params",
+]