# Source code for pysph.tools.gmsh

    """Utility module to read input mesh files.  This is primarily for meshes
    generated using Gmsh.  This module also provides some simple classes
    that allow one to create extruded 3D surfaces by generating a gmsh file
    in Python.

    There is also a function to read VTK dataset and produce points from them.
    This is very useful as Gmsh can generate VTK datasets from its meshes and thus
    the meshes can be imported as point clouds that may be used in an SPH
    simulation.
    """
    # Copyright (c) 2015 Prabhu Ramachandran

    import gzip
    import json

    import numpy as np
    import subprocess

    import tempfile
    from tvtk.api import tvtk

    import os
    from os.path import exists, expanduser, join
    import sys

    def _read_vtk_file(fname):
        """Given a .vtk file (or .vtk.gz), read it and return the output.
        """
        if fname.endswith('.vtk.gz'):
            tmpfname = tempfile.mktemp(suffix='.vtk')
            with open(tmpfname, 'wb') as tmpf:
                data = gzip.open(fname).read()
                tmpf.write(data)
            r = tvtk.DataSetReader(file_name=tmpfname)
        else:
            tmpfname = None
            r = tvtk.DataSetReader(file_name=fname)
        r.update()
        if tmpfname is not None:
            os.remove(tmpfname)
        return r.output

    def _convert_to_points(dataset, vertices=True, cell_centers=True):
        """Given a VTK dataset, convert it to a set of points that can be used
        for simulation with SPH.

        Parameters
        ----------

        dataset : tvtk.DataSet
        vertices: bool
            If True, it converts the vertices to points.
        cell_centers: bool
            If True, converts the cell centers to points.

        Returns
        -------

        x, y, z of the points.
        """
        pts = np.array([], dtype=float)
        if vertices:
            pts = np.append(pts, dataset.points.to_array())
        if cell_centers:
            cell_centers = tvtk.CellCenters(input=dataset)
            cell_centers.update()
            p = cell_centers.output.points.to_array()
            pts = np.append(pts, p)
        pts.shape = len(pts)//3, 3
        x, y, z = pts.T
        return x, y, z

    def vtk_file_to_points(fname, vertices=True, cell_centers=True):
        """Given a file containing a VTK dataset (currently only an old style .vtk
        file), convert it to a set of points that can be used for simulation with
        SPH.

        Parameters
        ----------

        fname : str
            File name.
        vertices: bool
            If True, it converts the vertices to points.
        cell_centers: bool
            If True, converts the cell centers to points.

        Returns
        -------

        x, y, z of the points.
        """
        dataset = _read_vtk_file(fname)
        return _convert_to_points(dataset, vertices, cell_centers)

    def transform_points(x, y, z, transform):
        """Given the coordinates, x, y, z and the TVTK transform instance,
        return the transformed coordinates.
        """
        assert isinstance(transform, tvtk.Transform)

        m = transform.matrix.to_array()
        xt, yt, zt, wt = np.dot(m, np.array((x, y, z, np.ones_like(x))))
        return xt, yt, zt

    class Loop(object):
        """Create a Line Loop in Gmsh parlance but using a turtle-graphics like
        approach.

        Use this to create a 2D closed surface.  The surface is always in the x-y
        plane.

        Examples
        --------

        Here is a simple example::

          >>> l1 = Loop((0.0, 0.0), mesh_size=0.1)
          >>> l1.move(1.0).turn(90).move(1.0).turn(90).move(1.0).turn(90).move(1.0)

        This will create a square shape.

        """

        def __init__(self, start, mesh_size=0.1):
            self.mesh_size = mesh_size
            self.points = [start]
            self.elems = []
            self.tolerance = 1e-12
            self._last_angle = 0.0
            self._last_position = start
            self._index = 1

        ### Public Protocol ###################################

        def turn(self, angle):
            """Turn by angle (in degrees).
            """
            self._last_angle += angle
            return self

        def move(self, dist):
            """Move by given distance at the current angle.
            """
            x0, y0 = self._last_position
            angle = self._last_angle
            rad = np.pi*angle/180.
            x = x0 + dist*np.cos(rad)
            y = y0 + dist*np.sin(rad)
            p1 = self._index
            p2 = self._add_point(x, y)
            self._add_elem('line', (p1, p2))
            return self

        def arc(self, radius, angle=180):
            """Create a circular arc given the radius and for an angle as
            specified.
            """
            x0, y0 = self._last_position
            last_angle = self._last_angle
            rad = np.pi*last_angle/180.
            last = complex(x0, y0)
            dz = complex(np.cos(rad), np.sin(rad))
            cen = last + radius*dz
            rad = np.pi*angle/180.
            end = cen + (last - cen)*complex(np.cos(rad), np.sin(rad))
            s_idx = self._index
            c_idx = self._add_point(cen.real, cen.imag)
            e_idx = self._add_point(end.real, end.imag)
            self._add_elem('circle', (s_idx, c_idx, e_idx))
            return self

        def write(self, fp, point_id_base=0, elem_id_base=0):
            """Write data to given file object `fp`.
            """
            points = self.points
            for i in range(len(points)):
                idx = point_id_base + i + 1
                self._write_point(fp, points[i], idx)

            elems = self.elems
            idx = 0
            loop = []
            for i in range(len(elems)):
                elem = elems[i]
                idx = elem_id_base + i + 1
                loop.append(str(idx))
                kind, data = elem[0], elem[1]
                if kind == 'line':
                    self._write_line(fp, data, idx, point_id_base)
                elif kind == 'circle':
                    self._write_circle(fp, data, idx, point_id_base)
            idx += 1
            ids = ', '.join(loop)
            s = 'Line Loop({idx}) = {{{ids}}};\n'.format(idx=idx, ids=ids)
            fp.write(s)
            return len(points), len(elems) + 1

        ### Private Protocol #################################
        def _add_elem(self, kind, data):
            self.elems.append((kind, data))

        def _check_for_existing_point(self, x, y):
            tol = self.tolerance
            for i, (xi, yi) in enumerate(self.points):
                if abs(xi - x) < tol and abs(yi - y) < tol:
                    return i + 1

        def _add_point(self, x, y):
            last_x, last_y = self._last_position
            pnt = (x, y)
            existing = self._check_for_existing_point(x, y)
            if existing is None:
                self.points.append(pnt)
                self._index += 1
                index = self._index
            else:
                index = existing
                pnt = self.points[existing]
            self._last_position = pnt
            return index

        def _write_point(self, fp, pnt, idx):
            fp.write('Point({idx}) = {{{x}, {y}, 0.0, {mesh_size}}};\n'.\
                format(x=pnt[0], y=pnt[1], idx=idx, mesh_size=self.mesh_size))

        def _write_line(self, fp, data, e_idx, p_idx):
            s = 'Line({idx}) = {{{p1}, {p2}}};\n'.format(
                idx=e_idx, p1=data[0]+p_idx, p2=data[1] +p_idx
            )
            fp.write(s)

        def _write_circle(self, fp, data, e_idx, p_idx):
            s = 'Circle({idx}) = {{{start}, {cen}, {end}}};\n'.format(
                idx=e_idx, start=data[0]+p_idx, cen=data[1]+p_idx, end=data[2] +p_idx
            )
            fp.write(s)

    class Surface(object):
        def __init__(self, *loops):
            """Constructor.

            Parameters
            ----------

            loops : tuple(Loop)
                Any additional positional arguments are treated as loop objects.
            """
            self.loops = list(loops)
            self.idx = 0

        def write(self, fp, point_id_base=0, elem_id_base=0):
            pid_base = point_id_base
            eid_base = elem_id_base
            loop_ids = []
            for loop in self.loops:
                np, ne = loop.write(fp, pid_base, eid_base)
                pid_base += np
                eid_base += ne
                loop_ids.append(str(eid_base))
            idx = eid_base + 1
            loop_str = ', '.join(loop_ids)
            fp.write('Plane Surface({idx}) = {{{loop_str}}};\n'.format(
                    idx=idx, loop_str=loop_str))
            self.idx = idx
            return pid_base, eid_base

    class Extrude(object):
        def __init__(self, dx=0.0, dy=0.0, dz=1.0, surfaces=None):
            """Extrude a given set of surfaces by the displacements given
            along each directions.

            Parameters
            ----------

            dx : float
                Extrusion along x.
            dy : float
                Extrusion along y.
            dz : float
                Extrusion along z.
            surfaces: list
                List of surfaces to extrude.

            """
            self.dx, self.dy, self.dz = dx, dy, dz
            if surfaces is None:
                self.surfaces = []
            else:
                self.surfaces = list(surfaces)

        def write(self, fp, point_id_base=0, elem_id_base=0):
            pid_base = point_id_base
            eid_base = elem_id_base
            surf_ids = []
            for surf in self.surfaces:
                np, ne = surf.write(fp, pid_base, eid_base)
                pid_base += np
                eid_base += ne
                surf_ids.append(str(surf.idx))

            s_ids = ', '.join(surf_ids)
            fp.write(
                'Extrude {{{dx}, {dy}, {dz}}} {{\n'
                '    Surface{{{s_ids}}};\n}}\n'.format(
                dx=self.dx, dy=self.dy, dz=self.dz, s_ids=s_ids
                )
            )
            return pid_base, eid_base

    class Gmsh(object):
        def __init__(self, gmsh=None):
            """Construct a Gmsh helper object that can be used to mesh objects.

            Parameters
            ----------

            gmsh: str
                Path to gmsh executable.
            """
            self.config = expanduser(join('~', '.pysph', 'gmsh.json'))
            if gmsh is None:
                if exists(self.config):
                    self._read_config()
                else:
                    gmsh = self._ask_user_for_gmsh()
                    self._set_gmsh(gmsh)
            else:
                self._set_gmsh(gmsh)

        #### Public Protocol ##################################

        def write_geo(self, entities, fp):
            """Write a list of given entities to the given file pointer.
            """
            p_count, e_count = 0, 0
            for entity in entities:
                np, ne = entity.write(fp, p_count, e_count)
                p_count += np
                e_count += ne

        def write_vtk_mesh(self, entities, fname):
            """Write a list of given entities to the given file name.
            """
            tmp_geo = tempfile.mktemp(suffix='.geo')
            try:
                self.write_geo(entities, open(tmp_geo, 'w'))
                self._call_gmsh('-3', tmp_geo, '-o', fname)
            finally:
                os.remove(tmp_geo)

        def get_points(self, entities, vertices=True, cell_centers=False):
            """Given a list of entities, return x, y, z arrays for the position.

            Parameters
            ----------

            entities : list
                List of entities.
            vertices: bool
                If True, it converts the vertices to points.
            cell_centers: bool
                If True, converts the cell centers to points.

            """
            tmp_vtk = tempfile.mktemp(suffix='.vtk')
            try:
                self.write_vtk_mesh(entities, tmp_vtk)
                x, y, z = vtk_file_to_points(
                    tmp_vtk, vertices=vertices, cell_centers=cell_centers
                )
                return x, y, z
            finally:
                os.remove(tmp_vtk)

        def get_points_from_geo(self, geo_file_name, vertices=True,
                                cell_centers=False):
            """Given a .geo file, generate a mesh and get the points from the mesh.

            Parameters
            ----------

            geo_file_name: str
                Filename of the .geo file.
            vertices: bool
                If True, it converts the vertices to points.
            cell_centers: bool
                If True, converts the cell centers to points.

            """
            tmp_vtk = tempfile.mktemp(suffix='.vtk')
            try:
                self._call_gmsh('-3', geo_file_name, '-o', tmp_vtk)
                return vtk_file_to_points(
                    tmp_vtk, vertices=vertices, cell_centers=cell_centers
                )
            finally:
                os.remove(tmp_vtk)

        #### Private Protocol #################################
        def _ask_user_for_gmsh(self):
            gmsh = input('Please provide the path to gmsh executable: ')
            return gmsh

        def _read_config(self):
            if exists(self.config):
                data = json.load(open(self.config))
                self.gmsh = data['path']

        def _set_gmsh(self, gmsh):
            self.gmsh = gmsh
            data = dict(path=gmsh)
            json.dump(data, open(self.config, 'w'))

        def _call_gmsh(self, *args):
            if self.gmsh is None:
                raise RuntimeError('Gmsh is not configured, set the gmsh path.')
            cmd = [self.gmsh] + list(args)
            subprocess.check_call(cmd)

    def example_3d_p(fp=sys.stdout):
        """Creates a 3D "P" with a hole inside it.
        """
        # The exterior of the "P"
        l1 = Loop((0.0, 0.0), mesh_size=0.1)
        l1.turn(-90).move(1.0).turn(90).move(0.2).turn(90).move(0.5)\
           .arc(0.25, -180).turn(90).move(0.2)
        # The inner loop for the hole in the middle.
        l2 = Loop((0.1, -0.25))
        l2.arc(0.1, 90).turn(90).arc(0.1, 90).turn(90)\
          .arc(0.1, 90).turn(90).arc(0.1, 90)
        s = Surface(l1, l2)
        ex = Extrude(0.0, 0.0, 1.0, surfaces=[s])
        ex.write(fp)
        return ex

    def example_cube(fp=sys.stdout):
        """Simple example of a cube.
        """
        l1 = Loop((0.0, 0.0), mesh_size=0.1)
        l1.move(1.0).turn(90).move(1.0).turn(90).move(1.0).turn(90).move(1.0)
        s = Surface(l1)
        ex = Extrude(0.0, 0.0, 1.0, surfaces=[s])
        ex.write(fp)
        return ex

    def example_plot_3d_p(gmsh):
        """Note: this will only work if you have gmsh installed.
        """
        import io
        fp = io.StringIO()
        ex = example_3d_p(fp)
        g = Gmsh(gmsh)
        x, y, z = g.get_points([ex])
        from mayavi import mlab
        mlab.points3d(x, y, z, color=(1, 0, 0))