def _main(): f = viscid.load_file("$WORK/xi_fte_001/*.3d.[4050f].xdmf") mp = get_mp_info(f['pp'], f['b'], f['j'], f['e_cc'], fit='mp_xloc', slc="x=6.5f:10.5f, y=-4f:4f, z=-4.8f:3f", cache=False) y, z = mp['pp_max_xloc'].meshgrid_flat(prune=True) x = mp['pp_max_xloc'].data.reshape(-1) Y, Z = mp['pp_max_xloc'].meshgrid(prune=True) x2 = paraboloid(Y, Z, *mp['paraboloid'][0]) skip = 117 n = paraboloid_normal(Y, Z, *mp['paraboloid'][0]).reshape(3, -1)[:, ::skip] minvar_y = Y.reshape(-1)[::skip] minvar_z = Z.reshape(-1)[::skip] minvar_n = np.zeros([3, len(minvar_y)]) for i in range(minvar_n.shape[0]): p0 = [0.0, minvar_y[i], minvar_z[i]] p0[0] = mp['pp_max_xloc']['y={0[0]}f, z={0[1]}f'.format(p0)] minvar_n[:, i] = viscid.find_minvar_lmn_around(f['b'], p0, l=2.0, n=64)[2, :] # 2d plots, normals don't look normal in the matplotlib projection if False: # pylint: disable=using-constant-test from viscid.plot import mpl normals = paraboloid_normal(Y, Z, *mp['paraboloid'][0]) p0 = np.array([x2, Y, Z]).reshape(3, -1) p1 = p0 + normals.reshape(3, -1) mpl.scatter_3d(np.vstack([x, y, z])[:, ::skip], equal=True) for i in range(0, p0.shape[1], skip): mpl.plt.gca().plot([p0[0, i], p1[0, i]], [p0[1, i], p1[1, i]], [p0[2, i], p1[2, i]], color='c') # z2 = _ellipsiod(X, Y, *popt) mpl.plt.gca().plot_surface(Y, Z, x2, color='r') mpl.show() # mayavi 3d plots, normals look better here if True: # pylint: disable=using-constant-test from viscid.plot import mvi mvi.points3d(x[::skip], y[::skip], z[::skip], scale_factor=0.25, color=(0.0, 0.0, 1.0)) mp_width = mp['mp_width']['x=0'] mp_sheath_edge = mp['mp_sheath_edge']['x=0'] mp_sphere_edge = mp_sheath_edge - mp_width mvi.mesh(x2, Y, Z, scalars=mp_width.data) mvi.mesh(mp_sheath_edge.data, Y, Z, opacity=0.75, color=(0.75, ) * 3) mvi.mesh(mp_sphere_edge.data, Y, Z, opacity=0.75, color=(0.75, ) * 3) n = paraboloid_normal(Y, Z, *mp['paraboloid'][0]).reshape(3, -1)[:, ::skip] mvi.quiver3d(x2.reshape(-1)[::skip], Y.reshape(-1)[::skip], Z.reshape(-1)[::skip], n[0], n[1], n[2], color=(1, 0, 0)) mvi.quiver3d(x2.reshape(-1)[::skip], Y.reshape(-1)[::skip], Z.reshape(-1)[::skip], minvar_n[0], minvar_n[1], minvar_n[2], color=(0, 0, 1)) mvi.show()
def _get_sep_pts_bisect( fld, seed, trace_opts=None, min_depth=3, max_depth=7, plot=False, perimeter_check=perimeter_check_bitwise_or, make_3d=True, start_uneven=False, _base_quadrent="", _uneven_mask=0, _first_recurse=True, ): if len(_base_quadrent) == max_depth: return [_base_quadrent] # causes pylint to complain if trace_opts is None: trace_opts = dict() nx, ny = seed.uv_shape (xlim, ylim) = seed.uv_extent if _first_recurse and start_uneven: _uneven_mask = UNEVEN_MASK if _first_recurse and plot: from viscid.plot import mvi from viscid.plot import mpl mpl.clf() _, all_topo = viscid.calc_streamlines(fld, seed, **trace_opts) mpl.plot(np.bitwise_and(all_topo, 15), show=False) verts, arr = seed.wrap_mesh(all_topo.data) mvi.mesh(verts[0], verts[1], verts[2], scalars=arr, opacity=0.75) # quadrents and lines are indexed as follows... # directions are counter clackwise around the quadrent with # lower index (which matters for lines which are shared among # more than one quadrent, aka, lines 1,2,6,7). Notice that even # numbered lines are horizontal, like the interstate system :) # -<--10-----<-8--- # | ^ ^ # 11 2 9 3 7 # \/ | | # --<-2-----<-6---- # | ^ ^ # 3 0 1 1 5 # \/ | | # ----0->-----4->-- # find low(left), mid(center), and high(right) crds in x and y low_quad = "{0}{1:x}".format(_base_quadrent, 0 | _uneven_mask) high_quad = "{0}{1:x}".format(_base_quadrent, 3 | _uneven_mask) xl, xm, yl, ym = _quadrent_limits(low_quad, xlim, ylim) _, xh, _, yh = _quadrent_limits(high_quad, xlim, ylim) segsx, segsy = [None] * 12, [None] * 12 topo = [None] * 12 nxm, nym = nx // 2, ny // 2 # make all the line segments segsx[0], segsy[0] = np.linspace(xl, xm, nxm), np.linspace(yl, yl, nxm) segsx[1], segsy[1] = np.linspace(xm, xm, nym), np.linspace(yl, ym, nym) segsx[2], segsy[2] = np.linspace(xm, xl, nxm), np.linspace(ym, ym, nxm) segsx[3], segsy[3] = np.linspace(xl, xl, nym), np.linspace(ym, yl, nym) segsx[4], segsy[4] = np.linspace(xm, xh, nxm), np.linspace(yl, yl, nxm) segsx[5], segsy[5] = np.linspace(xh, xh, nym), np.linspace(yl, ym, nym) segsx[6], segsy[6] = np.linspace(xh, xm, nxm), np.linspace(ym, ym, nxm) segsx[7], segsy[7] = np.linspace(xh, xh, nym), np.linspace(ym, yh, nym) segsx[8], segsy[8] = np.linspace(xh, xm, nxm), np.linspace(yh, yh, nxm) segsx[9], segsy[9] = np.linspace(xm, xm, nym), np.linspace(ym, yh, nym) segsx[10], segsy[10] = np.linspace(xm, xl, nxm), np.linspace(yh, yh, nxm) segsx[11], segsy[11] = np.linspace(xl, xl, nym), np.linspace(yh, ym, nym) allx = np.concatenate(segsx) ally = np.concatenate(segsy) # print("plot::", _base_quadrent, '|', _uneven_mask, '|', len(allx), len(ally)) pts3d = seed.to_3d(seed.uv_to_local(np.array([allx, ally]))) _, all_topo = viscid.calc_streamlines(fld, pts3d, **trace_opts) topo[0] = all_topo[: len(segsx[0])] cnt = len(topo[0]) for i, segx in zip(count(1), segsx[1:]): topo[i] = all_topo[cnt : cnt + len(segx)] # print("??", i, cnt, cnt + len(segx), np.bitwise_and.reduce(topo[i])) cnt += len(topo[i]) # assemble the lines into the four quadrents quad_topo = [None] * 4 # all arrays snip off the last element since those are # duplicated by the next line... reversed arrays do the # snipping with -1:0:-1 quad_topo[0] = np.concatenate([topo[0][:-1], topo[1][:-1], topo[2][:-1], topo[3][:-1]]) quad_topo[1] = np.concatenate([topo[4][:-1], topo[5][:-1], topo[6][:-1], topo[1][-1:0:-1]]) quad_topo[2] = np.concatenate([topo[2][-1:0:-1], topo[9][:-1], topo[10][:-1], topo[11][:-1]]) quad_topo[3] = np.concatenate([topo[6][-1:0:-1], topo[7][:-1], topo[8][:-1], topo[9][-1:0:-1]]) # now that the quad arrays are populated, decide which quadrents # still contain the separator (could be > 1) required_uneven_subquads = False ret = [] for i in range(4): if perimeter_check(quad_topo[i]): next_quad = "{0}{1:x}".format(_base_quadrent, i | _uneven_mask) subquads = _get_sep_pts_bisect( fld, seed, trace_opts=trace_opts, min_depth=min_depth, max_depth=max_depth, plot=plot, _base_quadrent=next_quad, _uneven_mask=0, _first_recurse=False, ) ret += subquads if len(ret) == 0: perimeter = np.concatenate( [ topo[0][::-1], topo[4][::-1], topo[5][::-1], topo[7][::-1], topo[8][::-1], topo[10][::-1], topo[11][::-1], topo[3][::-1], ] ) if _uneven_mask: if len(_base_quadrent) > min_depth: print("sep trace issue, but min depth reached: {0} > {1}" "".format(len(_base_quadrent), min_depth)) ret = [_base_quadrent] else: print("sep trace issue, the separator ended prematurely") elif perimeter_check(perimeter): ret = _get_sep_pts_bisect( fld, seed, trace_opts=trace_opts, min_depth=min_depth, max_depth=max_depth, plot=plot, _base_quadrent=_base_quadrent, _uneven_mask=UNEVEN_MASK, _first_recurse=False, ) required_uneven_subquads = True if plot and not required_uneven_subquads: from viscid.plot import mvi from viscid.plot import mpl _pts3d = seed.to_3d(seed.uv_to_local(np.array([allx, ally]))) mvi.points3d(_pts3d[0], _pts3d[1], _pts3d[2], all_topo.data.reshape(-1), scale_mode="none", scale_factor=0.02) mpl.plt.scatter( allx, ally, color=np.bitwise_and(all_topo, 15), vmin=0, vmax=15, marker="o", edgecolor="y", s=40 ) if _first_recurse: # turn quadrent strings into locations xc = np.empty(len(ret)) yc = np.empty(len(ret)) for i, r in enumerate(ret): xc[i], yc[i] = _quadrent_center(r, xlim, ylim) pts_uv = np.array([xc, yc]) if plot: from viscid.plot import mvi from viscid.plot import mpl mpl.plt.plot(pts_uv[0], pts_uv[1], "y*", ms=20, markeredgecolor="k", markeredgewidth=1.0) mpl.show(block=False) mvi.show(stop=True) # return seed.to_3d(seed.uv_to_local(pts_uv)) # if pts_uv.size == 0: # return None if make_3d: return seed.uv_to_3d(pts_uv) else: return pts_uv else: return ret