niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_degree_centrality.py

@@ -0,0 +1,270 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DEGREE_CENTRALITY_METADATA = Metadata(
+    id="b52b7e118f9973ad723c05506b8d75f114f296f2.boutiques",
+    name="3dDegreeCentrality",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDegreeCentralityParameters = typing.TypedDict('V3dDegreeCentralityParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDegreeCentrality"],
+    "autoclip": bool,
+    "automask": bool,
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "oned_file": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[int | None],
+    "sparsity": typing.NotRequired[float | None],
+    "thresh": 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 {
+        "3dDegreeCentrality": v_3d_degree_centrality_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 {
+        "3dDegreeCentrality": v_3d_degree_centrality_outputs,
+    }.get(t)
+
+
+class V3dDegreeCentralityOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_degree_centrality(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+    oned_file_outfile: OutputPathType | None
+    """The text output of the similarity matrix computed after thresholding with
+    one-dimensional and ijk voxel indices, correlations, image extents, and
+    affine matrix."""
+
+
+def v_3d_degree_centrality_params(
+    in_file: InputPathType,
+    autoclip: bool = False,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    oned_file: str | None = None,
+    polort: int | None = None,
+    sparsity: float | None = None,
+    thresh: float | None = None,
+) -> V3dDegreeCentralityParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3ddegreecentrality.
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Mask the dataset to target brain-only voxels.
+        mask: Mask file to mask input data.
+        oned_file: Output filepath to text dump of correlation matrix.
+        polort: No description provided.
+        sparsity: Only take the top percent of connections.
+        thresh: Threshold to exclude connections where corr <= thresh.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDegreeCentrality",
+        "autoclip": autoclip,
+        "automask": automask,
+        "in_file": in_file,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if oned_file is not None:
+        params["oned_file"] = oned_file
+    if polort is not None:
+        params["polort"] = polort
+    if sparsity is not None:
+        params["sparsity"] = sparsity
+    if thresh is not None:
+        params["thresh"] = thresh
+    return params
+
+
+def v_3d_degree_centrality_cargs(
+    params: V3dDegreeCentralityParameters,
+    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("3dDegreeCentrality")
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("oned_file") is not None:
+        cargs.extend([
+            "-out1D",
+            params.get("oned_file")
+        ])
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("sparsity") is not None:
+        cargs.extend([
+            "-sparsity",
+            str(params.get("sparsity"))
+        ])
+    if params.get("thresh") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("thresh"))
+        ])
+    return cargs
+
+
+def v_3d_degree_centrality_outputs(
+    params: V3dDegreeCentralityParameters,
+    execution: Execution,
+) -> V3dDegreeCentralityOutputs:
+    """
+    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 = V3dDegreeCentralityOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name),
+        oned_file_outfile=execution.output_file(params.get("oned_file")) if (params.get("oned_file") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_degree_centrality_execute(
+    params: V3dDegreeCentralityParameters,
+    execution: Execution,
+) -> V3dDegreeCentralityOutputs:
+    """
+    Computes voxelwise weighted and binary degree centrality and stores the result
+    in a new 3D bucket dataset as floats to preserve their values. Degree centrality
+    reflects the strength and extent of the correlation of a voxel with every other
+    voxel in the brain. .
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDegreeCentralityOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_degree_centrality_cargs(params, execution)
+    ret = v_3d_degree_centrality_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_degree_centrality(
+    in_file: InputPathType,
+    autoclip: bool = False,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    oned_file: str | None = None,
+    polort: int | None = None,
+    sparsity: float | None = None,
+    thresh: float | None = None,
+    runner: Runner | None = None,
+) -> V3dDegreeCentralityOutputs:
+    """
+    Computes voxelwise weighted and binary degree centrality and stores the result
+    in a new 3D bucket dataset as floats to preserve their values. Degree centrality
+    reflects the strength and extent of the correlation of a voxel with every other
+    voxel in the brain. .
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3ddegreecentrality.
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Mask the dataset to target brain-only voxels.
+        mask: Mask file to mask input data.
+        oned_file: Output filepath to text dump of correlation matrix.
+        polort: No description provided.
+        sparsity: Only take the top percent of connections.
+        thresh: Threshold to exclude connections where corr <= thresh.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDegreeCentralityOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DEGREE_CENTRALITY_METADATA)
+    params = v_3d_degree_centrality_params(
+        autoclip=autoclip,
+        automask=automask,
+        in_file=in_file,
+        mask=mask,
+        oned_file=oned_file,
+        polort=polort,
+        sparsity=sparsity,
+        thresh=thresh,
+    )
+    return v_3d_degree_centrality_execute(params, execution)
+
+
+__all__ = [
+    "V3dDegreeCentralityOutputs",
+    "V3dDegreeCentralityParameters",
+    "V_3D_DEGREE_CENTRALITY_METADATA",
+    "v_3d_degree_centrality",
+    "v_3d_degree_centrality_params",
+]

niwrap_afni/afni/v_3d_depth_map.py

@@ -0,0 +1,317 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DEPTH_MAP_METADATA = Metadata(
+    id="4a6704d8156d9e0a414515196af7b7f69ca298eb.boutiques",
+    name="3dDepthMap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDepthMapParameters = typing.TypedDict('V3dDepthMapParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDepthMap"],
+    "input_dataset": InputPathType,
+    "output_prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "dist_squared": bool,
+    "ignore_voxdims": bool,
+    "rimify": typing.NotRequired[float | None],
+    "zeros_are_zero": bool,
+    "zeros_are_neg": bool,
+    "nz_are_neg": bool,
+    "bounds_are_not_zero": bool,
+    "only2D": typing.NotRequired[str | None],
+    "binary_only": bool,
+    "verbosity": 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 {
+        "3dDepthMap": v_3d_depth_map_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 {
+        "3dDepthMap": v_3d_depth_map_outputs,
+    }.get(t)
+
+
+class V3dDepthMapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_depth_map(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Main output file"""
+
+
+def v_3d_depth_map_params(
+    input_dataset: InputPathType,
+    output_prefix: str,
+    mask: InputPathType | None = None,
+    dist_squared: bool = False,
+    ignore_voxdims: bool = False,
+    rimify: float | None = None,
+    zeros_are_zero: bool = False,
+    zeros_are_neg: bool = False,
+    nz_are_neg: bool = False,
+    bounds_are_not_zero: bool = False,
+    only2_d: str | None = None,
+    binary_only: bool = False,
+    verbosity: float | None = None,
+) -> V3dDepthMapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset.
+        output_prefix: Output prefix name.
+        mask: Mask dataset, applied after the EDT has been calculated.
+        dist_squared: Output EDT values as distance squared.
+        ignore_voxdims: Ignore voxel dimensions, producing outputs as if each\
+            voxel dimension was unity.
+        rimify: Output a map of each ROI's boundary layer up to thickness RIM.
+        zeros_are_zero: EDT values only reported within nonzero locations of\
+            the input dataset.
+        zeros_are_neg: EDT values in the zero/background regions will be\
+            negative.
+        nz_are_neg: EDT values in the nonzero ROI regions will be negative.
+        bounds_are_not_zero: Treat FOV boundaries for nonzero ROIs as open\
+            (i.e., continue infinitely).
+        only2_d: Run EDT in 2D along the specified plane (axi|cor|sag).
+        binary_only: Treat the input as a binary mask for a faster calculation.
+        verbosity: Manage verbosity when running code (default: 1).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDepthMap",
+        "input_dataset": input_dataset,
+        "output_prefix": output_prefix,
+        "dist_squared": dist_squared,
+        "ignore_voxdims": ignore_voxdims,
+        "zeros_are_zero": zeros_are_zero,
+        "zeros_are_neg": zeros_are_neg,
+        "nz_are_neg": nz_are_neg,
+        "bounds_are_not_zero": bounds_are_not_zero,
+        "binary_only": binary_only,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if rimify is not None:
+        params["rimify"] = rimify
+    if only2_d is not None:
+        params["only2D"] = only2_d
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def v_3d_depth_map_cargs(
+    params: V3dDepthMapParameters,
+    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("3dDepthMap")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("dist_squared"):
+        cargs.append("-dist_sq")
+    if params.get("ignore_voxdims"):
+        cargs.append("-ignore_voxdims")
+    if params.get("rimify") is not None:
+        cargs.extend([
+            "-rimify",
+            str(params.get("rimify"))
+        ])
+    if params.get("zeros_are_zero"):
+        cargs.append("-zeros_are_zero")
+    if params.get("zeros_are_neg"):
+        cargs.append("-zeros_are_neg")
+    if params.get("nz_are_neg"):
+        cargs.append("-nz_are_neg")
+    if params.get("bounds_are_not_zero"):
+        cargs.append("-bounds_are_not_zero")
+    if params.get("only2D") is not None:
+        cargs.extend([
+            "-only2D",
+            params.get("only2D")
+        ])
+    if params.get("binary_only"):
+        cargs.append("-binary_only")
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    return cargs
+
+
+def v_3d_depth_map_outputs(
+    params: V3dDepthMapParameters,
+    execution: Execution,
+) -> V3dDepthMapOutputs:
+    """
+    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 = V3dDepthMapOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v_3d_depth_map_execute(
+    params: V3dDepthMapParameters,
+    execution: Execution,
+) -> V3dDepthMapOutputs:
+    """
+    Calculates the Euclidean Distance Transform (EDT) for 3D volumes, allowing
+    computation of ROI depth maps and applying various adjustments like masking and
+    rimification.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDepthMapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_depth_map_cargs(params, execution)
+    ret = v_3d_depth_map_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_depth_map(
+    input_dataset: InputPathType,
+    output_prefix: str,
+    mask: InputPathType | None = None,
+    dist_squared: bool = False,
+    ignore_voxdims: bool = False,
+    rimify: float | None = None,
+    zeros_are_zero: bool = False,
+    zeros_are_neg: bool = False,
+    nz_are_neg: bool = False,
+    bounds_are_not_zero: bool = False,
+    only2_d: str | None = None,
+    binary_only: bool = False,
+    verbosity: float | None = None,
+    runner: Runner | None = None,
+) -> V3dDepthMapOutputs:
+    """
+    Calculates the Euclidean Distance Transform (EDT) for 3D volumes, allowing
+    computation of ROI depth maps and applying various adjustments like masking and
+    rimification.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset.
+        output_prefix: Output prefix name.
+        mask: Mask dataset, applied after the EDT has been calculated.
+        dist_squared: Output EDT values as distance squared.
+        ignore_voxdims: Ignore voxel dimensions, producing outputs as if each\
+            voxel dimension was unity.
+        rimify: Output a map of each ROI's boundary layer up to thickness RIM.
+        zeros_are_zero: EDT values only reported within nonzero locations of\
+            the input dataset.
+        zeros_are_neg: EDT values in the zero/background regions will be\
+            negative.
+        nz_are_neg: EDT values in the nonzero ROI regions will be negative.
+        bounds_are_not_zero: Treat FOV boundaries for nonzero ROIs as open\
+            (i.e., continue infinitely).
+        only2_d: Run EDT in 2D along the specified plane (axi|cor|sag).
+        binary_only: Treat the input as a binary mask for a faster calculation.
+        verbosity: Manage verbosity when running code (default: 1).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDepthMapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DEPTH_MAP_METADATA)
+    params = v_3d_depth_map_params(
+        input_dataset=input_dataset,
+        output_prefix=output_prefix,
+        mask=mask,
+        dist_squared=dist_squared,
+        ignore_voxdims=ignore_voxdims,
+        rimify=rimify,
+        zeros_are_zero=zeros_are_zero,
+        zeros_are_neg=zeros_are_neg,
+        nz_are_neg=nz_are_neg,
+        bounds_are_not_zero=bounds_are_not_zero,
+        only2_d=only2_d,
+        binary_only=binary_only,
+        verbosity=verbosity,
+    )
+    return v_3d_depth_map_execute(params, execution)
+
+
+__all__ = [
+    "V3dDepthMapOutputs",
+    "V3dDepthMapParameters",
+    "V_3D_DEPTH_MAP_METADATA",
+    "v_3d_depth_map",
+    "v_3d_depth_map_params",
+]