niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/qhull.py

@@ -0,0 +1,376 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+QHULL_METADATA = Metadata(
+    id="d25dad9388d53afd5a2f6019c508abe651c2e611.boutiques",
+    name="qhull",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+QhullParameters = typing.TypedDict('QhullParameters', {
+    "__STYX_TYPE__": typing.Literal["qhull"],
+    "input_coords": str,
+    "delaunay": bool,
+    "furthest_delaunay": bool,
+    "voronoi": bool,
+    "furthest_voronoi": bool,
+    "halfspace_intersection": bool,
+    "triangulated_output": bool,
+    "joggled_input": bool,
+    "verify": bool,
+    "summary": bool,
+    "vertices_incident": bool,
+    "normals": bool,
+    "vertex_coordinates": bool,
+    "halfspace_intersections": bool,
+    "extreme_points": bool,
+    "total_area_volume": bool,
+    "off_format": bool,
+    "geomview_output": bool,
+    "mathematica_output": bool,
+    "print_facets": typing.NotRequired[str | None],
+    "output_file": 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 {
+        "qhull": qhull_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 {
+        "qhull": qhull_outputs,
+    }.get(t)
+
+
+class QhullOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `qhull(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_results: OutputPathType | None
+    """Output file with the specified results."""
+
+
+def qhull_params(
+    input_coords: str,
+    delaunay: bool = False,
+    furthest_delaunay: bool = False,
+    voronoi: bool = False,
+    furthest_voronoi: bool = False,
+    halfspace_intersection: bool = False,
+    triangulated_output: bool = False,
+    joggled_input: bool = False,
+    verify: bool = False,
+    summary: bool = False,
+    vertices_incident: bool = False,
+    normals: bool = False,
+    vertex_coordinates: bool = False,
+    halfspace_intersections: bool = False,
+    extreme_points: bool = False,
+    total_area_volume: bool = False,
+    off_format: bool = False,
+    geomview_output: bool = False,
+    mathematica_output: bool = False,
+    print_facets: str | None = None,
+    output_file: str | None = None,
+) -> QhullParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_coords: Dimension, number of points, and point coordinates\
+            provided via stdin.
+        delaunay: Compute Delaunay triangulation by lifting points to a\
+            paraboloid.
+        furthest_delaunay: Compute furthest-site Delaunay triangulation (upper\
+            convex hull).
+        voronoi: Compute Voronoi diagram as the dual of the Delaunay\
+            triangulation.
+        furthest_voronoi: Compute furthest-site Voronoi diagram.
+        halfspace_intersection: Compute halfspace intersection about\
+            [1,1,0,...] via polar duality.
+        triangulated_output: Triangulated output.
+        joggled_input: Joggled input instead of merged facets.
+        verify: Verify result: structure, convexity, and point inclusion.
+        summary: Summary of results.
+        vertices_incident: Vertices incident to each facet.
+        normals: Normals with offsets.
+        vertex_coordinates: Vertex coordinates (if 'Qc', includes coplanar\
+            points). If 'v', Voronoi vertices.
+        halfspace_intersections: Halfspace intersections.
+        extreme_points: Extreme points (convex hull vertices).
+        total_area_volume: Compute total area and volume.
+        off_format: OFF format (if 'v', outputs Voronoi regions).
+        geomview_output: Geomview output (2-d, 3-d and 4-d).
+        mathematica_output: Mathematica output (2-d and 3-d).
+        print_facets: Print facets that include point n, -n if not.
+        output_file: Output results to file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "qhull",
+        "input_coords": input_coords,
+        "delaunay": delaunay,
+        "furthest_delaunay": furthest_delaunay,
+        "voronoi": voronoi,
+        "furthest_voronoi": furthest_voronoi,
+        "halfspace_intersection": halfspace_intersection,
+        "triangulated_output": triangulated_output,
+        "joggled_input": joggled_input,
+        "verify": verify,
+        "summary": summary,
+        "vertices_incident": vertices_incident,
+        "normals": normals,
+        "vertex_coordinates": vertex_coordinates,
+        "halfspace_intersections": halfspace_intersections,
+        "extreme_points": extreme_points,
+        "total_area_volume": total_area_volume,
+        "off_format": off_format,
+        "geomview_output": geomview_output,
+        "mathematica_output": mathematica_output,
+    }
+    if print_facets is not None:
+        params["print_facets"] = print_facets
+    if output_file is not None:
+        params["output_file"] = output_file
+    return params
+
+
+def qhull_cargs(
+    params: QhullParameters,
+    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("qhull")
+    cargs.append(params.get("input_coords"))
+    if params.get("delaunay"):
+        cargs.append("d")
+    if params.get("furthest_delaunay"):
+        cargs.append("d Qu")
+    if params.get("voronoi"):
+        cargs.append("v")
+    if params.get("furthest_voronoi"):
+        cargs.append("v Qu")
+    if params.get("halfspace_intersection"):
+        cargs.append("H1,1")
+    if params.get("triangulated_output"):
+        cargs.append("Qt")
+    if params.get("joggled_input"):
+        cargs.append("QJ")
+    if params.get("verify"):
+        cargs.append("Tv")
+    if params.get("summary"):
+        cargs.append("s")
+    if params.get("vertices_incident"):
+        cargs.append("i")
+    if params.get("normals"):
+        cargs.append("n")
+    if params.get("vertex_coordinates"):
+        cargs.append("p")
+    if params.get("halfspace_intersections"):
+        cargs.append("Fp")
+    if params.get("extreme_points"):
+        cargs.append("Fx")
+    if params.get("total_area_volume"):
+        cargs.append("FA")
+    if params.get("off_format"):
+        cargs.append("o")
+    if params.get("geomview_output"):
+        cargs.append("G")
+    if params.get("mathematica_output"):
+        cargs.append("m")
+    if params.get("print_facets") is not None:
+        cargs.extend([
+            "QVn",
+            params.get("print_facets")
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "TO",
+            params.get("output_file")
+        ])
+    return cargs
+
+
+def qhull_outputs(
+    params: QhullParameters,
+    execution: Execution,
+) -> QhullOutputs:
+    """
+    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 = QhullOutputs(
+        root=execution.output_file("."),
+        output_results=execution.output_file(params.get("output_file") + ".txt") if (params.get("output_file") is not None) else None,
+    )
+    return ret
+
+
+def qhull_execute(
+    params: QhullParameters,
+    execution: Execution,
+) -> QhullOutputs:
+    """
+    Tool to compute convex hulls and related structures.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `QhullOutputs`).
+    """
+    params = execution.params(params)
+    cargs = qhull_cargs(params, execution)
+    ret = qhull_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def qhull(
+    input_coords: str,
+    delaunay: bool = False,
+    furthest_delaunay: bool = False,
+    voronoi: bool = False,
+    furthest_voronoi: bool = False,
+    halfspace_intersection: bool = False,
+    triangulated_output: bool = False,
+    joggled_input: bool = False,
+    verify: bool = False,
+    summary: bool = False,
+    vertices_incident: bool = False,
+    normals: bool = False,
+    vertex_coordinates: bool = False,
+    halfspace_intersections: bool = False,
+    extreme_points: bool = False,
+    total_area_volume: bool = False,
+    off_format: bool = False,
+    geomview_output: bool = False,
+    mathematica_output: bool = False,
+    print_facets: str | None = None,
+    output_file: str | None = None,
+    runner: Runner | None = None,
+) -> QhullOutputs:
+    """
+    Tool to compute convex hulls and related structures.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_coords: Dimension, number of points, and point coordinates\
+            provided via stdin.
+        delaunay: Compute Delaunay triangulation by lifting points to a\
+            paraboloid.
+        furthest_delaunay: Compute furthest-site Delaunay triangulation (upper\
+            convex hull).
+        voronoi: Compute Voronoi diagram as the dual of the Delaunay\
+            triangulation.
+        furthest_voronoi: Compute furthest-site Voronoi diagram.
+        halfspace_intersection: Compute halfspace intersection about\
+            [1,1,0,...] via polar duality.
+        triangulated_output: Triangulated output.
+        joggled_input: Joggled input instead of merged facets.
+        verify: Verify result: structure, convexity, and point inclusion.
+        summary: Summary of results.
+        vertices_incident: Vertices incident to each facet.
+        normals: Normals with offsets.
+        vertex_coordinates: Vertex coordinates (if 'Qc', includes coplanar\
+            points). If 'v', Voronoi vertices.
+        halfspace_intersections: Halfspace intersections.
+        extreme_points: Extreme points (convex hull vertices).
+        total_area_volume: Compute total area and volume.
+        off_format: OFF format (if 'v', outputs Voronoi regions).
+        geomview_output: Geomview output (2-d, 3-d and 4-d).
+        mathematica_output: Mathematica output (2-d and 3-d).
+        print_facets: Print facets that include point n, -n if not.
+        output_file: Output results to file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `QhullOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QHULL_METADATA)
+    params = qhull_params(
+        input_coords=input_coords,
+        delaunay=delaunay,
+        furthest_delaunay=furthest_delaunay,
+        voronoi=voronoi,
+        furthest_voronoi=furthest_voronoi,
+        halfspace_intersection=halfspace_intersection,
+        triangulated_output=triangulated_output,
+        joggled_input=joggled_input,
+        verify=verify,
+        summary=summary,
+        vertices_incident=vertices_incident,
+        normals=normals,
+        vertex_coordinates=vertex_coordinates,
+        halfspace_intersections=halfspace_intersections,
+        extreme_points=extreme_points,
+        total_area_volume=total_area_volume,
+        off_format=off_format,
+        geomview_output=geomview_output,
+        mathematica_output=mathematica_output,
+        print_facets=print_facets,
+        output_file=output_file,
+    )
+    return qhull_execute(params, execution)
+
+
+__all__ = [
+    "QHULL_METADATA",
+    "QhullOutputs",
+    "QhullParameters",
+    "qhull",
+    "qhull_params",
+]

niwrap_afni/afni/quick_alpha_vals_py.py

@@ -0,0 +1,189 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+QUICK_ALPHA_VALS_PY_METADATA = Metadata(
+    id="467c10597885378ee65e5261792a6d6f5203efb5.boutiques",
+    name="quick.alpha.vals.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+QuickAlphaValsPyParameters = typing.TypedDict('QuickAlphaValsPyParameters', {
+    "__STYX_TYPE__": typing.Literal["quick.alpha.vals.py"],
+    "niter": typing.NotRequired[int | None],
+    "max_file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "quick.alpha.vals.py": quick_alpha_vals_py_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 {
+        "quick.alpha.vals.py": quick_alpha_vals_py_outputs,
+    }.get(t)
+
+
+class QuickAlphaValsPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `quick_alpha_vals_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    alpha_table: OutputPathType
+    """Generated alpha table file"""
+
+
+def quick_alpha_vals_py_params(
+    max_file: InputPathType,
+    niter: int | None = None,
+) -> QuickAlphaValsPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        max_file: File containing maximum z values.
+        niter: Number of iterations that should be in the z file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "quick.alpha.vals.py",
+        "max_file": max_file,
+    }
+    if niter is not None:
+        params["niter"] = niter
+    return params
+
+
+def quick_alpha_vals_py_cargs(
+    params: QuickAlphaValsPyParameters,
+    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("quick.alpha.vals.py")
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter"))
+        ])
+    cargs.append(execution.input_file(params.get("max_file")))
+    return cargs
+
+
+def quick_alpha_vals_py_outputs(
+    params: QuickAlphaValsPyParameters,
+    execution: Execution,
+) -> QuickAlphaValsPyOutputs:
+    """
+    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 = QuickAlphaValsPyOutputs(
+        root=execution.output_file("."),
+        alpha_table=execution.output_file("alpha_table.txt"),
+    )
+    return ret
+
+
+def quick_alpha_vals_py_execute(
+    params: QuickAlphaValsPyParameters,
+    execution: Execution,
+) -> QuickAlphaValsPyOutputs:
+    """
+    Generate an alpha table from slow_surf_clustsim.py results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `QuickAlphaValsPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = quick_alpha_vals_py_cargs(params, execution)
+    ret = quick_alpha_vals_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def quick_alpha_vals_py(
+    max_file: InputPathType,
+    niter: int | None = None,
+    runner: Runner | None = None,
+) -> QuickAlphaValsPyOutputs:
+    """
+    Generate an alpha table from slow_surf_clustsim.py results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        max_file: File containing maximum z values.
+        niter: Number of iterations that should be in the z file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `QuickAlphaValsPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUICK_ALPHA_VALS_PY_METADATA)
+    params = quick_alpha_vals_py_params(
+        niter=niter,
+        max_file=max_file,
+    )
+    return quick_alpha_vals_py_execute(params, execution)
+
+
+__all__ = [
+    "QUICK_ALPHA_VALS_PY_METADATA",
+    "QuickAlphaValsPyOutputs",
+    "QuickAlphaValsPyParameters",
+    "quick_alpha_vals_py",
+    "quick_alpha_vals_py_params",
+]