# -*- coding: utf-8 -*-
#
from __future__ import print_function

import os
import subprocess
import tempfile

import numpy

import meshio


def rotation_matrix(u, theta):
    """Return matrix that implements the rotation around the vector :math:`u`
    by the angle :math:`\\theta`, cf.
    https://en.wikipedia.org/wiki/Rotation_matrix#Rotation_matrix_from_axis_and_angle.

    :param u: rotation vector
    :param theta: rotation angle
    """
    assert numpy.isclose(numpy.inner(u, u), 1.0), "the rotation axis must be unitary"

    # Cross-product matrix.
    cpm = numpy.array([[0.0, -u[2], u[1]], [u[2], 0.0, -u[0]], [-u[1], u[0], 0.0]])
    c = numpy.cos(theta)
    s = numpy.sin(theta)
    R = numpy.eye(3) * c + s * cpm + (1.0 - c) * numpy.outer(u, u)
    return R


def _is_string(obj):
    try:
        # Python 2
        return isinstance(obj, basestring)
    except NameError:
        # Python 3
        return isinstance(obj, str)


def _get_gmsh_exe():
    macos_gmsh_location = "/Applications/Gmsh.app/Contents/MacOS/gmsh"
    return macos_gmsh_location if os.path.isfile(macos_gmsh_location) else "gmsh"


def get_gmsh_major_version(gmsh_exe=_get_gmsh_exe()):
    out = (
        subprocess.check_output([gmsh_exe, "--version"], stderr=subprocess.STDOUT)
        .strip()
        .decode("utf8")
    )
    ex = out.split(".")
    return int(ex[0])


def generate_mesh(
    geo_object,
    verbose=True,
    dim=3,
    prune_vertices=True,
    prune_z_0=False,
    remove_faces=False,
    gmsh_path=None,
    extra_gmsh_arguments=None,
    # for debugging purposes:
    geo_filename=None,
    msh_filename=None,
    mesh_file_type="msh",
):
    """Return a meshio.Mesh, storing the mesh points, cells, and data,
    generated by Gmsh from the `geo_object`, written to a temporary file,
    and reread by `meshio`.

    Gmsh's native "msh" format is ill-suited to fast I/O.  This can
    greatly reduce the performance of pygmsh.  As alternatives, try
    `mesh_file_type=`:

    - "vtk"`, though Gmsh doesn't write the physical tags
    to VTK <https://gitlab.onelab.info/gmsh/gmsh/issues/389> or

    - `"mesh"`, though this only supports a few basic elements - "line",
    "triangle", "quad", "tetra", "hexahedron" - and doesn't preserve
    the `$PhysicalNames`, just the `int` tags.

    """
    if extra_gmsh_arguments is None:
        extra_gmsh_arguments = []

    # For format "mesh", ask Gmsh to save the physical tags
    # http://gmsh.info/doc/texinfo/gmsh.html#index-Mesh_002eSaveElementTagType
    if mesh_file_type == "mesh":
        extra_gmsh_arguments += ["-string", "Mesh.SaveElementTagType=2;"]

    preserve_geo = geo_filename is not None
    if geo_filename is None:
        with tempfile.NamedTemporaryFile(suffix=".geo") as f:
            geo_filename = f.name

    with open(geo_filename, "w") as f:
        f.write(geo_object.get_code())

    # As of Gmsh 4.1.3, the mesh format options are
    # ```
    # auto, msh1, msh2, msh3, msh4, msh, unv, vtk, wrl, mail, stl, p3d, mesh, bdf, cgns,
    # med, diff, ir3, inp, ply2, celum, su2, x3d, dat, neu, m, key
    # ```
    # Pick the correct filename suffix.
    filename_suffix = "msh" if mesh_file_type[:3] == "msh" else mesh_file_type

    preserve_msh = msh_filename is not None
    if msh_filename is None:
        with tempfile.NamedTemporaryFile(suffix="." + filename_suffix) as handle:
            msh_filename = handle.name

    gmsh_executable = gmsh_path if gmsh_path is not None else _get_gmsh_exe()

    args = [
        "-{}".format(dim),
        geo_filename,
        "-format",
        mesh_file_type,
        "-bin",
        "-o",
        msh_filename,
    ] + extra_gmsh_arguments

    # https://stackoverflow.com/a/803421/353337
    try:
        p = subprocess.Popen(
            [gmsh_executable] + args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
        )
    except FileNotFoundError:
        print("Is gmsh installed?")
        raise

    if verbose:
        while True:
            line = p.stdout.readline()
            if not line:
                break
            print(line.decode("utf-8"), end="")

    p.communicate()
    assert p.returncode == 0, "Gmsh exited with error (return code {}).".format(
        p.returncode
    )

    mesh = meshio.read(msh_filename)

    if remove_faces:
        # Only keep the cells of highest topological dimension; discard faces
        # and such.
        two_d_cells = set(["triangle", "quad"])
        three_d_cells = set(
            ["tetra", "hexahedron", "wedge", "pyramid", "penta_prism", "hexa_prism"]
        )
        if any(k in mesh.cells for k in three_d_cells):
            keep_keys = three_d_cells.intersection(mesh.cells.keys())
        elif any(k in mesh.cells for k in two_d_cells):
            keep_keys = two_d_cells.intersection(mesh.cells.keys())
        else:
            keep_keys = mesh.cells.keys()

        mesh.cells = {key: mesh.cells[key] for key in keep_keys}
        mesh.cell_data = {key: mesh.cell_data[key] for key in keep_keys}

    if prune_vertices:
        # Make sure to include only those vertices which belong to a cell.
        ncells = numpy.concatenate([numpy.concatenate(c) for c in mesh.cells.values()])
        uvertices, uidx = numpy.unique(ncells, return_inverse=True)

        k = 0
        for key in mesh.cells.keys():
            n = numpy.prod(mesh.cells[key].shape)
            mesh.cells[key] = uidx[k : k + n].reshape(mesh.cells[key].shape)
            k += n

        mesh.points = mesh.points[uvertices]
        for key in mesh.point_data:
            mesh.point_data[key] = mesh.point_data[key][uvertices]

    # clean up
    if preserve_msh:
        print("\nmsh file: {}".format(msh_filename))
    else:
        os.remove(msh_filename)
    if preserve_geo:
        print("\ngeo file: {}".format(geo_filename))
    else:
        os.remove(geo_filename)

    if (
        prune_z_0
        and mesh.points.shape[1] == 3
        and numpy.all(numpy.abs(mesh.points[:, 2]) < 1.0e-13)
    ):
        mesh.points = mesh.points[:, :2]

    return mesh

@@ -1379,16 +1379,30 @@
 te_mesh(
+  # noqa: C901
 %0A    geo

noqa 901