niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/qdelaunay.py

@@ -0,0 +1,534 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+QDELAUNAY_METADATA = Metadata(
+    id="6ffd24be5e49d65ad58c48581dbc1c38e779c71c.boutiques",
+    name="qdelaunay",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+QdelaunayParameters = typing.TypedDict('QdelaunayParameters', {
+    "__STYX_TYPE__": typing.Literal["qdelaunay"],
+    "input_file": InputPathType,
+    "furthest_site": bool,
+    "triangulated_output": bool,
+    "joggled_input": bool,
+    "joggle_range": typing.NotRequired[float | None],
+    "search_simplex": bool,
+    "point_infinity": bool,
+    "delaunay_visible": typing.NotRequired[str | None],
+    "delaunay_regions": typing.NotRequired[str | None],
+    "trace_level": typing.NotRequired[float | None],
+    "check": bool,
+    "statistics": bool,
+    "verify": bool,
+    "output_stdout": bool,
+    "facets_summary": typing.NotRequired[float | None],
+    "input_file_option": typing.NotRequired[InputPathType | None],
+    "output_file_option": typing.NotRequired[InputPathType | None],
+    "trace_point": typing.NotRequired[float | None],
+    "trace_merge": typing.NotRequired[float | None],
+    "trace_merge_width": typing.NotRequired[float | None],
+    "stop_point": typing.NotRequired[float | None],
+    "stop_cone_point": typing.NotRequired[float | None],
+    "centrum_radius": typing.NotRequired[float | None],
+    "max_angle_cosine": typing.NotRequired[float | None],
+    "perturb_factor": typing.NotRequired[float | None],
+    "min_facet_width": typing.NotRequired[float | None],
+    "facet_dump": bool,
+    "geomview": bool,
+    "vertices_incident": bool,
+    "mathematica": bool,
+    "off_format": bool,
+    "point_coordinates": bool,
+    "summary": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "qdelaunay": qdelaunay_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 {
+    }.get(t)
+
+
+class QdelaunayOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `qdelaunay(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def qdelaunay_params(
+    input_file: InputPathType,
+    furthest_site: bool = False,
+    triangulated_output: bool = False,
+    joggled_input: bool = False,
+    joggle_range: float | None = None,
+    search_simplex: bool = False,
+    point_infinity: bool = False,
+    delaunay_visible: str | None = None,
+    delaunay_regions: str | None = None,
+    trace_level: float | None = None,
+    check: bool = False,
+    statistics_: bool = False,
+    verify: bool = False,
+    output_stdout: bool = False,
+    facets_summary: float | None = None,
+    input_file_option: InputPathType | None = None,
+    output_file_option: InputPathType | None = None,
+    trace_point: float | None = None,
+    trace_merge: float | None = None,
+    trace_merge_width: float | None = None,
+    stop_point: float | None = None,
+    stop_cone_point: float | None = None,
+    centrum_radius: float | None = None,
+    max_angle_cosine: float | None = None,
+    perturb_factor: float | None = None,
+    min_facet_width: float | None = None,
+    facet_dump: bool = False,
+    geomview: bool = False,
+    vertices_incident: bool = False,
+    mathematica: bool = False,
+    off_format: bool = False,
+    point_coordinates: bool = False,
+    summary: bool = False,
+) -> QdelaunayParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input file containing point coordinates.
+        furthest_site: Compute furthest-site Delaunay triangulation.
+        triangulated_output: Triangulated output.
+        joggled_input: Joggled input instead of merged facets.
+        joggle_range: Randomly joggle input in range [-n,n].
+        search_simplex: Search all points for the initial simplex.
+        point_infinity: Add point-at-infinity to Delaunay triangulation.
+        delaunay_visible: Print Delaunay region if visible from point n, -n if\
+            not.
+        delaunay_regions: Print Delaunay regions that include point n, -n if\
+            not.
+        trace_level: Trace at level n, 4=all, 5=mem/gauss, -1= events.
+        check: Check frequently during execution.
+        statistics_: Print statistics.
+        verify: Verify result: structure, convexity, and in-circle test.
+        output_stdout: Send all output to stdout.
+        facets_summary: Report summary when n or more facets created.
+        input_file_option: Input data from file, no spaces or single quotes.
+        output_file_option: Output results to file, may be enclosed in single\
+            quotes.
+        trace_point: Turn on tracing when point n added to hull.
+        trace_merge: Turn on tracing at merge n.
+        trace_merge_width: Trace merge facets when width > n.
+        stop_point: Stop Qhull after adding point n, -n for before.
+        stop_cone_point: Stop Qhull after building cone for point n.
+        centrum_radius: Radius of centrum (roundoff added). Merge facets if\
+            non-convex.
+        max_angle_cosine: Cosine of maximum angle. Merge facets if cosine > n\
+            or non-convex.
+        perturb_factor: Randomly perturb computations by a factor of [1-n,1+n].
+        min_facet_width: Min facet width for outside point (before roundoff).
+        facet_dump: Facet dump.
+        geomview: Geomview output.
+        vertices_incident: Vertices incident to each Delaunay region.
+        mathematica: Mathematica output (2-d only, lifted to a paraboloid).
+        off_format: OFF format (dim, points, and facets as a paraboloid).
+        point_coordinates: Point coordinates (lifted to a paraboloid).
+        summary: Summary (stderr).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "qdelaunay",
+        "input_file": input_file,
+        "furthest_site": furthest_site,
+        "triangulated_output": triangulated_output,
+        "joggled_input": joggled_input,
+        "search_simplex": search_simplex,
+        "point_infinity": point_infinity,
+        "check": check,
+        "statistics": statistics_,
+        "verify": verify,
+        "output_stdout": output_stdout,
+        "facet_dump": facet_dump,
+        "geomview": geomview,
+        "vertices_incident": vertices_incident,
+        "mathematica": mathematica,
+        "off_format": off_format,
+        "point_coordinates": point_coordinates,
+        "summary": summary,
+    }
+    if joggle_range is not None:
+        params["joggle_range"] = joggle_range
+    if delaunay_visible is not None:
+        params["delaunay_visible"] = delaunay_visible
+    if delaunay_regions is not None:
+        params["delaunay_regions"] = delaunay_regions
+    if trace_level is not None:
+        params["trace_level"] = trace_level
+    if facets_summary is not None:
+        params["facets_summary"] = facets_summary
+    if input_file_option is not None:
+        params["input_file_option"] = input_file_option
+    if output_file_option is not None:
+        params["output_file_option"] = output_file_option
+    if trace_point is not None:
+        params["trace_point"] = trace_point
+    if trace_merge is not None:
+        params["trace_merge"] = trace_merge
+    if trace_merge_width is not None:
+        params["trace_merge_width"] = trace_merge_width
+    if stop_point is not None:
+        params["stop_point"] = stop_point
+    if stop_cone_point is not None:
+        params["stop_cone_point"] = stop_cone_point
+    if centrum_radius is not None:
+        params["centrum_radius"] = centrum_radius
+    if max_angle_cosine is not None:
+        params["max_angle_cosine"] = max_angle_cosine
+    if perturb_factor is not None:
+        params["perturb_factor"] = perturb_factor
+    if min_facet_width is not None:
+        params["min_facet_width"] = min_facet_width
+    return params
+
+
+def qdelaunay_cargs(
+    params: QdelaunayParameters,
+    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("qdelaunay")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("furthest_site"):
+        cargs.append("Qu")
+    if params.get("triangulated_output"):
+        cargs.append("Qt")
+    if params.get("joggled_input"):
+        cargs.append("QJ")
+    if params.get("joggle_range") is not None:
+        cargs.extend([
+            "QJn",
+            str(params.get("joggle_range"))
+        ])
+    if params.get("search_simplex"):
+        cargs.append("Qs")
+    if params.get("point_infinity"):
+        cargs.append("Qz")
+    if params.get("delaunay_visible") is not None:
+        cargs.extend([
+            "QGn",
+            params.get("delaunay_visible")
+        ])
+    if params.get("delaunay_regions") is not None:
+        cargs.extend([
+            "QVn",
+            params.get("delaunay_regions")
+        ])
+    if params.get("trace_level") is not None:
+        cargs.extend([
+            "T4",
+            str(params.get("trace_level"))
+        ])
+    if params.get("check"):
+        cargs.append("Tc")
+    if params.get("statistics"):
+        cargs.append("Ts")
+    if params.get("verify"):
+        cargs.append("Tv")
+    if params.get("output_stdout"):
+        cargs.append("Tz")
+    if params.get("facets_summary") is not None:
+        cargs.extend([
+            "TFn",
+            str(params.get("facets_summary"))
+        ])
+    if params.get("input_file_option") is not None:
+        cargs.extend([
+            "TI",
+            execution.input_file(params.get("input_file_option"))
+        ])
+    if params.get("output_file_option") is not None:
+        cargs.extend([
+            "TO",
+            execution.input_file(params.get("output_file_option"))
+        ])
+    if params.get("trace_point") is not None:
+        cargs.extend([
+            "TPn",
+            str(params.get("trace_point"))
+        ])
+    if params.get("trace_merge") is not None:
+        cargs.extend([
+            "TMn",
+            str(params.get("trace_merge"))
+        ])
+    if params.get("trace_merge_width") is not None:
+        cargs.extend([
+            "TWn",
+            str(params.get("trace_merge_width"))
+        ])
+    if params.get("stop_point") is not None:
+        cargs.extend([
+            "TVn",
+            str(params.get("stop_point"))
+        ])
+    if params.get("stop_cone_point") is not None:
+        cargs.extend([
+            "TCn",
+            str(params.get("stop_cone_point"))
+        ])
+    if params.get("centrum_radius") is not None:
+        cargs.extend([
+            "Cn",
+            str(params.get("centrum_radius"))
+        ])
+    if params.get("max_angle_cosine") is not None:
+        cargs.extend([
+            "An",
+            str(params.get("max_angle_cosine"))
+        ])
+    if params.get("perturb_factor") is not None:
+        cargs.extend([
+            "Rn",
+            str(params.get("perturb_factor"))
+        ])
+    if params.get("min_facet_width") is not None:
+        cargs.extend([
+            "Wn",
+            str(params.get("min_facet_width"))
+        ])
+    if params.get("facet_dump"):
+        cargs.append("f")
+    if params.get("geomview"):
+        cargs.append("G")
+    if params.get("vertices_incident"):
+        cargs.append("i")
+    if params.get("mathematica"):
+        cargs.append("m")
+    if params.get("off_format"):
+        cargs.append("o")
+    if params.get("point_coordinates"):
+        cargs.append("p")
+    if params.get("summary"):
+        cargs.append("s")
+    return cargs
+
+
+def qdelaunay_outputs(
+    params: QdelaunayParameters,
+    execution: Execution,
+) -> QdelaunayOutputs:
+    """
+    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 = QdelaunayOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def qdelaunay_execute(
+    params: QdelaunayParameters,
+    execution: Execution,
+) -> QdelaunayOutputs:
+    """
+    Compute the Delaunay triangulation using Qhull.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `QdelaunayOutputs`).
+    """
+    params = execution.params(params)
+    cargs = qdelaunay_cargs(params, execution)
+    ret = qdelaunay_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def qdelaunay(
+    input_file: InputPathType,
+    furthest_site: bool = False,
+    triangulated_output: bool = False,
+    joggled_input: bool = False,
+    joggle_range: float | None = None,
+    search_simplex: bool = False,
+    point_infinity: bool = False,
+    delaunay_visible: str | None = None,
+    delaunay_regions: str | None = None,
+    trace_level: float | None = None,
+    check: bool = False,
+    statistics_: bool = False,
+    verify: bool = False,
+    output_stdout: bool = False,
+    facets_summary: float | None = None,
+    input_file_option: InputPathType | None = None,
+    output_file_option: InputPathType | None = None,
+    trace_point: float | None = None,
+    trace_merge: float | None = None,
+    trace_merge_width: float | None = None,
+    stop_point: float | None = None,
+    stop_cone_point: float | None = None,
+    centrum_radius: float | None = None,
+    max_angle_cosine: float | None = None,
+    perturb_factor: float | None = None,
+    min_facet_width: float | None = None,
+    facet_dump: bool = False,
+    geomview: bool = False,
+    vertices_incident: bool = False,
+    mathematica: bool = False,
+    off_format: bool = False,
+    point_coordinates: bool = False,
+    summary: bool = False,
+    runner: Runner | None = None,
+) -> QdelaunayOutputs:
+    """
+    Compute the Delaunay triangulation using Qhull.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input file containing point coordinates.
+        furthest_site: Compute furthest-site Delaunay triangulation.
+        triangulated_output: Triangulated output.
+        joggled_input: Joggled input instead of merged facets.
+        joggle_range: Randomly joggle input in range [-n,n].
+        search_simplex: Search all points for the initial simplex.
+        point_infinity: Add point-at-infinity to Delaunay triangulation.
+        delaunay_visible: Print Delaunay region if visible from point n, -n if\
+            not.
+        delaunay_regions: Print Delaunay regions that include point n, -n if\
+            not.
+        trace_level: Trace at level n, 4=all, 5=mem/gauss, -1= events.
+        check: Check frequently during execution.
+        statistics_: Print statistics.
+        verify: Verify result: structure, convexity, and in-circle test.
+        output_stdout: Send all output to stdout.
+        facets_summary: Report summary when n or more facets created.
+        input_file_option: Input data from file, no spaces or single quotes.
+        output_file_option: Output results to file, may be enclosed in single\
+            quotes.
+        trace_point: Turn on tracing when point n added to hull.
+        trace_merge: Turn on tracing at merge n.
+        trace_merge_width: Trace merge facets when width > n.
+        stop_point: Stop Qhull after adding point n, -n for before.
+        stop_cone_point: Stop Qhull after building cone for point n.
+        centrum_radius: Radius of centrum (roundoff added). Merge facets if\
+            non-convex.
+        max_angle_cosine: Cosine of maximum angle. Merge facets if cosine > n\
+            or non-convex.
+        perturb_factor: Randomly perturb computations by a factor of [1-n,1+n].
+        min_facet_width: Min facet width for outside point (before roundoff).
+        facet_dump: Facet dump.
+        geomview: Geomview output.
+        vertices_incident: Vertices incident to each Delaunay region.
+        mathematica: Mathematica output (2-d only, lifted to a paraboloid).
+        off_format: OFF format (dim, points, and facets as a paraboloid).
+        point_coordinates: Point coordinates (lifted to a paraboloid).
+        summary: Summary (stderr).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `QdelaunayOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QDELAUNAY_METADATA)
+    params = qdelaunay_params(
+        input_file=input_file,
+        furthest_site=furthest_site,
+        triangulated_output=triangulated_output,
+        joggled_input=joggled_input,
+        joggle_range=joggle_range,
+        search_simplex=search_simplex,
+        point_infinity=point_infinity,
+        delaunay_visible=delaunay_visible,
+        delaunay_regions=delaunay_regions,
+        trace_level=trace_level,
+        check=check,
+        statistics_=statistics_,
+        verify=verify,
+        output_stdout=output_stdout,
+        facets_summary=facets_summary,
+        input_file_option=input_file_option,
+        output_file_option=output_file_option,
+        trace_point=trace_point,
+        trace_merge=trace_merge,
+        trace_merge_width=trace_merge_width,
+        stop_point=stop_point,
+        stop_cone_point=stop_cone_point,
+        centrum_radius=centrum_radius,
+        max_angle_cosine=max_angle_cosine,
+        perturb_factor=perturb_factor,
+        min_facet_width=min_facet_width,
+        facet_dump=facet_dump,
+        geomview=geomview,
+        vertices_incident=vertices_incident,
+        mathematica=mathematica,
+        off_format=off_format,
+        point_coordinates=point_coordinates,
+        summary=summary,
+    )
+    return qdelaunay_execute(params, execution)
+
+
+__all__ = [
+    "QDELAUNAY_METADATA",
+    "QdelaunayOutputs",
+    "QdelaunayParameters",
+    "qdelaunay",
+    "qdelaunay_params",
+]