niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_clusterize.py

@@ -0,0 +1,448 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CLUSTERIZE_METADATA = Metadata(
+    id="246ae39c1ef3384b86a60550a94fbf5baade053a.boutiques",
+    name="3dClusterize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dClusterizeParameters = typing.TypedDict('V3dClusterizeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dClusterize"],
+    "inset": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_from_hdr": bool,
+    "out_mask": typing.NotRequired[str | None],
+    "ithr": str,
+    "idat": typing.NotRequired[str | None],
+    "onesided": typing.NotRequired[str | None],
+    "twosided": typing.NotRequired[str | None],
+    "bisided": typing.NotRequired[str | None],
+    "within_range": typing.NotRequired[str | None],
+    "nn": int,
+    "clust_nvox": typing.NotRequired[int | None],
+    "clust_vol": typing.NotRequired[int | None],
+    "pref_map": typing.NotRequired[str | None],
+    "pref_dat": typing.NotRequired[str | None],
+    "one_d_format": bool,
+    "no_one_d_format": bool,
+    "summarize": bool,
+    "nosum": bool,
+    "quiet": bool,
+    "outvol_if_no_clust": bool,
+    "orient": typing.NotRequired[str | None],
+    "abs_table_data": bool,
+    "binary": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dClusterize": v_3d_clusterize_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 {
+        "3dClusterize": v_3d_clusterize_outputs,
+    }.get(t)
+
+
+class V3dClusterizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_clusterize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_map_file: OutputPathType | None
+    """Output map of cluster ROIs"""
+    out_data_file: OutputPathType | None
+    """Cluster-masked version of the data volume"""
+    out_mask_file: OutputPathType | None
+    """Utilized mask dataset"""
+
+
+def v_3d_clusterize_params(
+    inset: InputPathType,
+    ithr: str,
+    nn: int,
+    mask: InputPathType | None = None,
+    mask_from_hdr: bool = False,
+    out_mask: str | None = None,
+    idat: str | None = None,
+    onesided: str | None = None,
+    twosided: str | None = None,
+    bisided: str | None = None,
+    within_range: str | None = None,
+    clust_nvox: int | None = None,
+    clust_vol: int | None = None,
+    pref_map: str | None = None,
+    pref_dat: str | None = None,
+    one_d_format: bool = False,
+    no_one_d_format: bool = False,
+    summarize: bool = False,
+    nosum: bool = False,
+    quiet: bool = False,
+    outvol_if_no_clust: bool = False,
+    orient: str | None = None,
+    abs_table_data: bool = False,
+    binary: bool = False,
+) -> V3dClusterizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset: Load in a dataset for thresholding and clusterizing.
+        ithr: Specify the sub-brick to use as the threshold source.
+        nn: Specify the number of voxel neighbors (1: 6, 2: 18, 3: 26).
+        mask: Load in a dataset to use as a mask.
+        mask_from_hdr: Use internal mask from dataset header.
+        out_mask: Specify to dump the utilized mask as a dataset.
+        idat: Specify the sub-brick to use as the data source.
+        onesided: Perform one-sided testing.
+        twosided: Perform two-sided testing.
+        bisided: Perform bisided testing.
+        within_range: Keep values within the range [AA, BB].
+        clust_nvox: Specify the minimum cluster size in terms of number of\
+            voxels.
+        clust_vol: Specify the minimum cluster size by volume in microliters.
+        pref_map: Prefix/filename of the output map of cluster ROIs.
+        pref_dat: Output a cluster-masked version of the data volume.
+        one_d_format: Write output in 1D format.
+        no_one_d_format: Do not write output in 1D format.
+        summarize: Write out only the total nonzero voxel count and volume for\
+            each dataset.
+        nosum: Suppress printout of the totals.
+        quiet: Suppress all non-essential output.
+        outvol_if_no_clust: Output an empty volume if no clusters are found.
+        orient: Coordinate order in the output report table (default: RAI).
+        abs_table_data: Use absolute values for mean and SEM in report table.
+        binary: Turn output map of cluster ROIs into a binary mask.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dClusterize",
+        "inset": inset,
+        "mask_from_hdr": mask_from_hdr,
+        "ithr": ithr,
+        "nn": nn,
+        "one_d_format": one_d_format,
+        "no_one_d_format": no_one_d_format,
+        "summarize": summarize,
+        "nosum": nosum,
+        "quiet": quiet,
+        "outvol_if_no_clust": outvol_if_no_clust,
+        "abs_table_data": abs_table_data,
+        "binary": binary,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if out_mask is not None:
+        params["out_mask"] = out_mask
+    if idat is not None:
+        params["idat"] = idat
+    if onesided is not None:
+        params["onesided"] = onesided
+    if twosided is not None:
+        params["twosided"] = twosided
+    if bisided is not None:
+        params["bisided"] = bisided
+    if within_range is not None:
+        params["within_range"] = within_range
+    if clust_nvox is not None:
+        params["clust_nvox"] = clust_nvox
+    if clust_vol is not None:
+        params["clust_vol"] = clust_vol
+    if pref_map is not None:
+        params["pref_map"] = pref_map
+    if pref_dat is not None:
+        params["pref_dat"] = pref_dat
+    if orient is not None:
+        params["orient"] = orient
+    return params
+
+
+def v_3d_clusterize_cargs(
+    params: V3dClusterizeParameters,
+    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("3dClusterize")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("inset"))
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_from_hdr"):
+        cargs.append("-mask_from_hdr")
+    if params.get("out_mask") is not None:
+        cargs.extend([
+            "-out_mask",
+            params.get("out_mask")
+        ])
+    cargs.extend([
+        "-ithr",
+        params.get("ithr")
+    ])
+    if params.get("idat") is not None:
+        cargs.extend([
+            "-idat",
+            params.get("idat")
+        ])
+    if params.get("onesided") is not None:
+        cargs.extend([
+            "-1sided",
+            params.get("onesided")
+        ])
+    if params.get("twosided") is not None:
+        cargs.extend([
+            "-2sided",
+            params.get("twosided")
+        ])
+    if params.get("bisided") is not None:
+        cargs.extend([
+            "-bisided",
+            params.get("bisided")
+        ])
+    if params.get("within_range") is not None:
+        cargs.extend([
+            "-within_range",
+            params.get("within_range")
+        ])
+    cargs.extend([
+        "-NN",
+        str(params.get("nn"))
+    ])
+    if params.get("clust_nvox") is not None:
+        cargs.extend([
+            "-clust_nvox",
+            str(params.get("clust_nvox"))
+        ])
+    if params.get("clust_vol") is not None:
+        cargs.extend([
+            "-clust_vol",
+            str(params.get("clust_vol"))
+        ])
+    if params.get("pref_map") is not None:
+        cargs.extend([
+            "-pref_map",
+            params.get("pref_map")
+        ])
+    if params.get("pref_dat") is not None:
+        cargs.extend([
+            "-pref_dat",
+            params.get("pref_dat")
+        ])
+    if params.get("one_d_format"):
+        cargs.append("-1Dformat")
+    if params.get("no_one_d_format"):
+        cargs.append("-no_1Dformat")
+    if params.get("summarize"):
+        cargs.append("-summarize")
+    if params.get("nosum"):
+        cargs.append("-nosum")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("outvol_if_no_clust"):
+        cargs.append("-outvol_if_no_clust")
+    if params.get("orient") is not None:
+        cargs.extend([
+            "-orient",
+            params.get("orient")
+        ])
+    if params.get("abs_table_data"):
+        cargs.append("-abs_table_data")
+    if params.get("binary"):
+        cargs.append("-binary")
+    return cargs
+
+
+def v_3d_clusterize_outputs(
+    params: V3dClusterizeParameters,
+    execution: Execution,
+) -> V3dClusterizeOutputs:
+    """
+    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 = V3dClusterizeOutputs(
+        root=execution.output_file("."),
+        out_map_file=execution.output_file(params.get("pref_map") + "+orig.HEAD") if (params.get("pref_map") is not None) else None,
+        out_data_file=execution.output_file(params.get("pref_dat") + "+orig.HEAD") if (params.get("pref_dat") is not None) else None,
+        out_mask_file=execution.output_file(params.get("out_mask") + "+orig.HEAD") if (params.get("out_mask") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_clusterize_execute(
+    params: V3dClusterizeParameters,
+    execution: Execution,
+) -> V3dClusterizeOutputs:
+    """
+    A tool for voxelwise thresholding and clusterizing of datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dClusterizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_clusterize_cargs(params, execution)
+    ret = v_3d_clusterize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_clusterize(
+    inset: InputPathType,
+    ithr: str,
+    nn: int,
+    mask: InputPathType | None = None,
+    mask_from_hdr: bool = False,
+    out_mask: str | None = None,
+    idat: str | None = None,
+    onesided: str | None = None,
+    twosided: str | None = None,
+    bisided: str | None = None,
+    within_range: str | None = None,
+    clust_nvox: int | None = None,
+    clust_vol: int | None = None,
+    pref_map: str | None = None,
+    pref_dat: str | None = None,
+    one_d_format: bool = False,
+    no_one_d_format: bool = False,
+    summarize: bool = False,
+    nosum: bool = False,
+    quiet: bool = False,
+    outvol_if_no_clust: bool = False,
+    orient: str | None = None,
+    abs_table_data: bool = False,
+    binary: bool = False,
+    runner: Runner | None = None,
+) -> V3dClusterizeOutputs:
+    """
+    A tool for voxelwise thresholding and clusterizing of datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset: Load in a dataset for thresholding and clusterizing.
+        ithr: Specify the sub-brick to use as the threshold source.
+        nn: Specify the number of voxel neighbors (1: 6, 2: 18, 3: 26).
+        mask: Load in a dataset to use as a mask.
+        mask_from_hdr: Use internal mask from dataset header.
+        out_mask: Specify to dump the utilized mask as a dataset.
+        idat: Specify the sub-brick to use as the data source.
+        onesided: Perform one-sided testing.
+        twosided: Perform two-sided testing.
+        bisided: Perform bisided testing.
+        within_range: Keep values within the range [AA, BB].
+        clust_nvox: Specify the minimum cluster size in terms of number of\
+            voxels.
+        clust_vol: Specify the minimum cluster size by volume in microliters.
+        pref_map: Prefix/filename of the output map of cluster ROIs.
+        pref_dat: Output a cluster-masked version of the data volume.
+        one_d_format: Write output in 1D format.
+        no_one_d_format: Do not write output in 1D format.
+        summarize: Write out only the total nonzero voxel count and volume for\
+            each dataset.
+        nosum: Suppress printout of the totals.
+        quiet: Suppress all non-essential output.
+        outvol_if_no_clust: Output an empty volume if no clusters are found.
+        orient: Coordinate order in the output report table (default: RAI).
+        abs_table_data: Use absolute values for mean and SEM in report table.
+        binary: Turn output map of cluster ROIs into a binary mask.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dClusterizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLUSTERIZE_METADATA)
+    params = v_3d_clusterize_params(
+        inset=inset,
+        mask=mask,
+        mask_from_hdr=mask_from_hdr,
+        out_mask=out_mask,
+        ithr=ithr,
+        idat=idat,
+        onesided=onesided,
+        twosided=twosided,
+        bisided=bisided,
+        within_range=within_range,
+        nn=nn,
+        clust_nvox=clust_nvox,
+        clust_vol=clust_vol,
+        pref_map=pref_map,
+        pref_dat=pref_dat,
+        one_d_format=one_d_format,
+        no_one_d_format=no_one_d_format,
+        summarize=summarize,
+        nosum=nosum,
+        quiet=quiet,
+        outvol_if_no_clust=outvol_if_no_clust,
+        orient=orient,
+        abs_table_data=abs_table_data,
+        binary=binary,
+    )
+    return v_3d_clusterize_execute(params, execution)
+
+
+__all__ = [
+    "V3dClusterizeOutputs",
+    "V3dClusterizeParameters",
+    "V_3D_CLUSTERIZE_METADATA",
+    "v_3d_clusterize",
+    "v_3d_clusterize_params",
+]

niwrap_afni/afni/v_3d_cm.py

@@ -0,0 +1,177 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CM_METADATA = Metadata(
+    id="b067b12b1032c8b1f441c220e6f5349f1cfe1370.boutiques",
+    name="3dCM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dCmParameters = typing.TypedDict('V3dCmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dCM"],
+    "dset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dCM": v_3d_cm_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 {
+        "3dCM": v_3d_cm_outputs,
+    }.get(t)
+
+
+class V3dCmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_cm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    center_of_mass: OutputPathType
+    """Center of mass of the dataset."""
+
+
+def v_3d_cm_params(
+    dset: InputPathType,
+) -> V3dCmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Input dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dCM",
+        "dset": dset,
+    }
+    return params
+
+
+def v_3d_cm_cargs(
+    params: V3dCmParameters,
+    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("3dCM")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("dset")))
+    return cargs
+
+
+def v_3d_cm_outputs(
+    params: V3dCmParameters,
+    execution: Execution,
+) -> V3dCmOutputs:
+    """
+    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 = V3dCmOutputs(
+        root=execution.output_file("."),
+        center_of_mass=execution.output_file("<stdout>"),
+    )
+    return ret
+
+
+def v_3d_cm_execute(
+    params: V3dCmParameters,
+    execution: Execution,
+) -> V3dCmOutputs:
+    """
+    Tool for computing the center of mass of a dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dCmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_cm_cargs(params, execution)
+    ret = v_3d_cm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_cm(
+    dset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dCmOutputs:
+    """
+    Tool for computing the center of mass of a dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Input dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dCmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CM_METADATA)
+    params = v_3d_cm_params(
+        dset=dset,
+    )
+    return v_3d_cm_execute(params, execution)
+
+
+__all__ = [
+    "V3dCmOutputs",
+    "V3dCmParameters",
+    "V_3D_CM_METADATA",
+    "v_3d_cm",
+    "v_3d_cm_params",
+]