niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_mesh.py

@@ -0,0 +1,256 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_MESH_METADATA = Metadata(
+    id="aba9dc7cdd5795dd83c2c7deb8fe8088d1965d12.boutiques",
+    name="SurfMesh",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfMeshParameters = typing.TypedDict('SurfMeshParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfMesh"],
+    "input_surface": str,
+    "output_surface": str,
+    "edge_fraction": float,
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "one_state": bool,
+    "anatomical_label": bool,
+    "no_volume_registration": bool,
+    "set_env": 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 {
+        "SurfMesh": surf_mesh_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 {
+        "SurfMesh": surf_mesh_outputs,
+    }.get(t)
+
+
+class SurfMeshOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_mesh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_surface_file: OutputPathType
+    """Output surface file"""
+
+
+def surf_mesh_params(
+    input_surface: str,
+    output_surface: str,
+    edge_fraction: float,
+    surface_volume: InputPathType | None = None,
+    one_state: bool = False,
+    anatomical_label: bool = False,
+    no_volume_registration: bool = False,
+    set_env: str | None = None,
+) -> SurfMeshParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Input surface file with specified type.
+        output_surface: Output surface file with specified type.
+        edge_fraction: Fraction of edges to simplify the surface.
+        surface_volume: Surface volume file.
+        one_state: Make all input surfaces have the same state.
+        anatomical_label: Label all input surfaces as anatomically correct.
+        no_volume_registration: Ignore any Rotate, Volreg, Tagalign, or\
+            WarpDrive transformations present in the Surface Volume.
+        set_env: Set environment variable.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfMesh",
+        "input_surface": input_surface,
+        "output_surface": output_surface,
+        "edge_fraction": edge_fraction,
+        "one_state": one_state,
+        "anatomical_label": anatomical_label,
+        "no_volume_registration": no_volume_registration,
+    }
+    if surface_volume is not None:
+        params["surface_volume"] = surface_volume
+    if set_env is not None:
+        params["set_env"] = set_env
+    return params
+
+
+def surf_mesh_cargs(
+    params: SurfMeshParameters,
+    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("SurfMesh")
+    cargs.extend([
+        "-i_TYPE",
+        params.get("input_surface")
+    ])
+    cargs.extend([
+        "-o_TYPE",
+        params.get("output_surface")
+    ])
+    cargs.extend([
+        "-edges",
+        str(params.get("edge_fraction"))
+    ])
+    if params.get("surface_volume") is not None:
+        cargs.extend([
+            "-sv",
+            execution.input_file(params.get("surface_volume"))
+        ])
+    if params.get("one_state"):
+        cargs.append("-onestate")
+    if params.get("anatomical_label"):
+        cargs.append("-anatomical")
+    if params.get("no_volume_registration"):
+        cargs.append("-novolreg")
+    if params.get("set_env") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("set_env")
+        ])
+    return cargs
+
+
+def surf_mesh_outputs(
+    params: SurfMeshParameters,
+    execution: Execution,
+) -> SurfMeshOutputs:
+    """
+    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 = SurfMeshOutputs(
+        root=execution.output_file("."),
+        output_surface_file=execution.output_file(params.get("output_surface") + ".surface"),
+    )
+    return ret
+
+
+def surf_mesh_execute(
+    params: SurfMeshParameters,
+    execution: Execution,
+) -> SurfMeshOutputs:
+    """
+    Surface mesh manipulation tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfMeshOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_mesh_cargs(params, execution)
+    ret = surf_mesh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_mesh(
+    input_surface: str,
+    output_surface: str,
+    edge_fraction: float,
+    surface_volume: InputPathType | None = None,
+    one_state: bool = False,
+    anatomical_label: bool = False,
+    no_volume_registration: bool = False,
+    set_env: str | None = None,
+    runner: Runner | None = None,
+) -> SurfMeshOutputs:
+    """
+    Surface mesh manipulation tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_surface: Input surface file with specified type.
+        output_surface: Output surface file with specified type.
+        edge_fraction: Fraction of edges to simplify the surface.
+        surface_volume: Surface volume file.
+        one_state: Make all input surfaces have the same state.
+        anatomical_label: Label all input surfaces as anatomically correct.
+        no_volume_registration: Ignore any Rotate, Volreg, Tagalign, or\
+            WarpDrive transformations present in the Surface Volume.
+        set_env: Set environment variable.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfMeshOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_MESH_METADATA)
+    params = surf_mesh_params(
+        input_surface=input_surface,
+        output_surface=output_surface,
+        edge_fraction=edge_fraction,
+        surface_volume=surface_volume,
+        one_state=one_state,
+        anatomical_label=anatomical_label,
+        no_volume_registration=no_volume_registration,
+        set_env=set_env,
+    )
+    return surf_mesh_execute(params, execution)
+
+
+__all__ = [
+    "SURF_MESH_METADATA",
+    "SurfMeshOutputs",
+    "SurfMeshParameters",
+    "surf_mesh",
+    "surf_mesh_params",
+]

niwrap_afni/afni/surf_patch.py

@@ -0,0 +1,412 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_PATCH_METADATA = Metadata(
+    id="1b9f54ccf622083c532013b3e22205e01ab00c46.boutiques",
+    name="SurfPatch",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfPatchParameters = typing.TypedDict('SurfPatchParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfPatch"],
+    "spec_file": InputPathType,
+    "surf_A": InputPathType,
+    "surf_B": InputPathType,
+    "nodefile": InputPathType,
+    "inode": float,
+    "ilabel": float,
+    "prefix": str,
+    "hits": typing.NotRequired[float | None],
+    "masklabel": typing.NotRequired[str | None],
+    "vol": bool,
+    "vol_only": bool,
+    "patch2surf": bool,
+    "coord_gain": typing.NotRequired[float | None],
+    "check_bowtie": bool,
+    "fix_bowtie": bool,
+    "ok_bowtie": bool,
+    "adjust_contour": bool,
+    "do_not_adjust_contour": bool,
+    "stitched_surface": typing.NotRequired[InputPathType | None],
+    "flip_orientation": 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 {
+        "SurfPatch": surf_patch_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 {
+        "SurfPatch": surf_patch_outputs,
+    }.get(t)
+
+
+class SurfPatchOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_patch(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outpatch_a: OutputPathType
+    """Output patch for surface A"""
+    outpatch_b: OutputPathType
+    """Output patch for surface B"""
+    out_stitched_surface: OutputPathType
+    """Stitched surface file"""
+
+
+def surf_patch_params(
+    spec_file: InputPathType,
+    surf_a: InputPathType,
+    surf_b: InputPathType,
+    nodefile: InputPathType,
+    inode: float,
+    ilabel: float,
+    prefix: str,
+    hits: float | None = None,
+    masklabel: str | None = None,
+    vol: bool = False,
+    vol_only: bool = False,
+    patch2surf: bool = False,
+    coord_gain: float | None = None,
+    check_bowtie: bool = False,
+    fix_bowtie: bool = False,
+    ok_bowtie: bool = False,
+    adjust_contour: bool = False,
+    do_not_adjust_contour: bool = False,
+    stitched_surface: InputPathType | None = None,
+    flip_orientation: bool = False,
+    verbosity: float | None = None,
+) -> SurfPatchParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: Spec file containing input surfaces.
+        surf_a: Input surface A.
+        surf_b: Input surface B.
+        nodefile: File containing nodes defining the patch.
+        inode: Index of the column containing the nodes.
+        ilabel: Index of the column containing labels of the nodes in column\
+            inode.
+        prefix: Prefix of output patch.
+        hits: Minimum number of nodes specified for a triangle to be made a\
+            part of the patch (1 <= min_hits <= 3); default is 2.
+        masklabel: Only nodes that are labeled with this label are considered\
+            for the patch.
+        vol: Calculate the volume formed by the patch on surf_A and surf_B.\
+            Requires only two surfaces specified with surf_A and surf_B.
+        vol_only: Only calculate the volume, don't write out patches.
+        patch2surf: Turn surface patch into a surface where only nodes used in\
+            forming the mesh are preserved.
+        coord_gain: Multiply node coordinates by a gain. Useful for enlarging\
+            tiny patches for easier viewing in SUMA.
+        check_bowtie: Check if the patch has a section hanging by one node to\
+            the rest of the mesh. Default when -vol or -vol_only are used.
+        fix_bowtie: Modify patch to eliminate bowties.
+        ok_bowtie: Do not check for, or fix bowties. Default when -vol* are not\
+            used.
+        adjust_contour: Shrink patch contours at nodes that were not in\
+            nodefile.
+        do_not_adjust_contour: Do not adjust contours. This is the default.
+        stitched_surface: Write out the stitched surface used to calculate the\
+            volume.
+        flip_orientation: Change orientation of triangles before writing\
+            surfaces.
+        verbosity: Set verbosity level, 1 is the default.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfPatch",
+        "spec_file": spec_file,
+        "surf_A": surf_a,
+        "surf_B": surf_b,
+        "nodefile": nodefile,
+        "inode": inode,
+        "ilabel": ilabel,
+        "prefix": prefix,
+        "vol": vol,
+        "vol_only": vol_only,
+        "patch2surf": patch2surf,
+        "check_bowtie": check_bowtie,
+        "fix_bowtie": fix_bowtie,
+        "ok_bowtie": ok_bowtie,
+        "adjust_contour": adjust_contour,
+        "do_not_adjust_contour": do_not_adjust_contour,
+        "flip_orientation": flip_orientation,
+    }
+    if hits is not None:
+        params["hits"] = hits
+    if masklabel is not None:
+        params["masklabel"] = masklabel
+    if coord_gain is not None:
+        params["coord_gain"] = coord_gain
+    if stitched_surface is not None:
+        params["stitched_surface"] = stitched_surface
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def surf_patch_cargs(
+    params: SurfPatchParameters,
+    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("SurfPatch")
+    cargs.append(execution.input_file(params.get("spec_file")))
+    cargs.extend([
+        "-surf_A",
+        execution.input_file(params.get("surf_A"))
+    ])
+    cargs.extend([
+        "-surf_B",
+        execution.input_file(params.get("surf_B"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("nodefile"))
+    ])
+    cargs.append(str(params.get("inode")))
+    cargs.append(str(params.get("ilabel")))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("hits") is not None:
+        cargs.extend([
+            "-hits",
+            str(params.get("hits"))
+        ])
+    if params.get("masklabel") is not None:
+        cargs.extend([
+            "-masklabel",
+            params.get("masklabel")
+        ])
+    if params.get("vol"):
+        cargs.append("-vol")
+    if params.get("vol_only"):
+        cargs.append("-vol_only")
+    if params.get("patch2surf"):
+        cargs.append("-patch2surf")
+    if params.get("coord_gain") is not None:
+        cargs.extend([
+            "-coord_gain",
+            str(params.get("coord_gain"))
+        ])
+    if params.get("check_bowtie"):
+        cargs.append("-check_bowtie")
+    if params.get("fix_bowtie"):
+        cargs.append("-fix_bowtie")
+    if params.get("ok_bowtie"):
+        cargs.append("-ok_bowtie")
+    if params.get("adjust_contour"):
+        cargs.append("-adjust_contour")
+    if params.get("do_not_adjust_contour"):
+        cargs.append("-do-not-adjust_contour")
+    if params.get("stitched_surface") is not None:
+        cargs.extend([
+            "-stitched_surface",
+            execution.input_file(params.get("stitched_surface"))
+        ])
+    if params.get("flip_orientation"):
+        cargs.append("-flip_orientation")
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    return cargs
+
+
+def surf_patch_outputs(
+    params: SurfPatchParameters,
+    execution: Execution,
+) -> SurfPatchOutputs:
+    """
+    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 = SurfPatchOutputs(
+        root=execution.output_file("."),
+        outpatch_a=execution.output_file(params.get("prefix") + "_A"),
+        outpatch_b=execution.output_file(params.get("prefix") + "_B"),
+        out_stitched_surface=execution.output_file(params.get("prefix") + "_stitched"),
+    )
+    return ret
+
+
+def surf_patch_execute(
+    params: SurfPatchParameters,
+    execution: Execution,
+) -> SurfPatchOutputs:
+    """
+    Creates a patch of surface formed by nodes in a nodefile and optionally
+    calculates the volume between the same patch on two isotopic surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfPatchOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_patch_cargs(params, execution)
+    ret = surf_patch_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_patch(
+    spec_file: InputPathType,
+    surf_a: InputPathType,
+    surf_b: InputPathType,
+    nodefile: InputPathType,
+    inode: float,
+    ilabel: float,
+    prefix: str,
+    hits: float | None = None,
+    masklabel: str | None = None,
+    vol: bool = False,
+    vol_only: bool = False,
+    patch2surf: bool = False,
+    coord_gain: float | None = None,
+    check_bowtie: bool = False,
+    fix_bowtie: bool = False,
+    ok_bowtie: bool = False,
+    adjust_contour: bool = False,
+    do_not_adjust_contour: bool = False,
+    stitched_surface: InputPathType | None = None,
+    flip_orientation: bool = False,
+    verbosity: float | None = None,
+    runner: Runner | None = None,
+) -> SurfPatchOutputs:
+    """
+    Creates a patch of surface formed by nodes in a nodefile and optionally
+    calculates the volume between the same patch on two isotopic surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: Spec file containing input surfaces.
+        surf_a: Input surface A.
+        surf_b: Input surface B.
+        nodefile: File containing nodes defining the patch.
+        inode: Index of the column containing the nodes.
+        ilabel: Index of the column containing labels of the nodes in column\
+            inode.
+        prefix: Prefix of output patch.
+        hits: Minimum number of nodes specified for a triangle to be made a\
+            part of the patch (1 <= min_hits <= 3); default is 2.
+        masklabel: Only nodes that are labeled with this label are considered\
+            for the patch.
+        vol: Calculate the volume formed by the patch on surf_A and surf_B.\
+            Requires only two surfaces specified with surf_A and surf_B.
+        vol_only: Only calculate the volume, don't write out patches.
+        patch2surf: Turn surface patch into a surface where only nodes used in\
+            forming the mesh are preserved.
+        coord_gain: Multiply node coordinates by a gain. Useful for enlarging\
+            tiny patches for easier viewing in SUMA.
+        check_bowtie: Check if the patch has a section hanging by one node to\
+            the rest of the mesh. Default when -vol or -vol_only are used.
+        fix_bowtie: Modify patch to eliminate bowties.
+        ok_bowtie: Do not check for, or fix bowties. Default when -vol* are not\
+            used.
+        adjust_contour: Shrink patch contours at nodes that were not in\
+            nodefile.
+        do_not_adjust_contour: Do not adjust contours. This is the default.
+        stitched_surface: Write out the stitched surface used to calculate the\
+            volume.
+        flip_orientation: Change orientation of triangles before writing\
+            surfaces.
+        verbosity: Set verbosity level, 1 is the default.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfPatchOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_PATCH_METADATA)
+    params = surf_patch_params(
+        spec_file=spec_file,
+        surf_a=surf_a,
+        surf_b=surf_b,
+        nodefile=nodefile,
+        inode=inode,
+        ilabel=ilabel,
+        prefix=prefix,
+        hits=hits,
+        masklabel=masklabel,
+        vol=vol,
+        vol_only=vol_only,
+        patch2surf=patch2surf,
+        coord_gain=coord_gain,
+        check_bowtie=check_bowtie,
+        fix_bowtie=fix_bowtie,
+        ok_bowtie=ok_bowtie,
+        adjust_contour=adjust_contour,
+        do_not_adjust_contour=do_not_adjust_contour,
+        stitched_surface=stitched_surface,
+        flip_orientation=flip_orientation,
+        verbosity=verbosity,
+    )
+    return surf_patch_execute(params, execution)
+
+
+__all__ = [
+    "SURF_PATCH_METADATA",
+    "SurfPatchOutputs",
+    "SurfPatchParameters",
+    "surf_patch",
+    "surf_patch_params",
+]