def _main(): parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("--show", "--plot", action="store_true") args = viscid.vutil.common_argparse(parser, default_verb=0) img = np.load(os.path.join(viscid.sample_dir, "logo.npy")) x = np.linspace(-1, 1, img.shape[0]) y = np.linspace(-1, 1, img.shape[1]) z = np.linspace(-1, 1, img.shape[2]) logo = viscid.arrays2field([x, y, z], img) seeds = viscid.Volume([-0.8, -0.8, 0.0], [0.8, 0.8, 0.0], n=[64, 64, 1]) run_test(logo, seeds, "Nearest", show=args.show) run_test(logo, seeds, "Trilinear", show=args.show) return 0
def _main(): parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("--notwo", dest='notwo', action="store_true") parser.add_argument("--nothree", dest='nothree', action="store_true") parser.add_argument("--show", "--plot", action="store_true") args = viscid.vutil.common_argparse(parser, default_verb=0) plot2d = not args.notwo plot3d = not args.nothree # plot2d = True # plot3d = True # args.show = True img = np.load(os.path.join(sample_dir, "logo.npy")) x = np.linspace(-1, 1, img.shape[0]) y = np.linspace(-1, 1, img.shape[1]) z = np.linspace(-1, 1, img.shape[2]) logo = viscid.arrays2field([x, y, z], img) if 1: viscid.logger.info('Testing Point with custom local coordinates...') pts = np.vstack([[-1, -0.5, 0, 0.5, 1], [-1, -0.5, 0, 0.5, 1], [ 0, 0.5, 1, 1.5, 2]]) local_crds = viscid.asarray_datetime64([0, 60, 120, 180, 240], conservative=True) seeds = viscid.Point(pts, local_crds=local_crds) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Line...') seeds = viscid.Line([-1, -1, 0], [1, 1, 2], n=5) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Plane...') seeds = viscid.Plane([0.0, 0.0, 0.0], [1, 1, 1], [1, 0, 0], 2, 2, nl=160, nm=170, NL_are_vectors=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Volume...') seeds = viscid.Volume([-0.8, -0.8, -0.8], [0.8, 0.8, 0.8], n=[64, 64, 3]) # note: can't make a 2d plot of the volume w/o a slice run_test(logo, seeds, plot2d=False, plot3d=plot3d, add_title="3d", show=args.show) if 1: viscid.logger.info('Testing Volume (with ignorable dim)...') seeds = viscid.Volume([-0.8, -0.8, 0.0], [0.8, 0.8, 0.0], n=[64, 64, 1]) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="2d", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (phi, theta)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (theta, phi)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (phi, theta)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (theta, phi)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Patch...') seeds = viscid.SphericalPatch(p0=[0, 0, 0], p1=[0, -0, -1], max_alpha=30.0, max_beta=59.9, nalpha=65, nbeta=80, r=0.5, roll=45.0) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: # this spline test is very custom viscid.logger.info('Testing Spline...') try: import scipy.interpolate as interpolate except ImportError: msg = "XFail: ImportError (is scipy installed?)" if plot2d: try: from viscid.plot import vpyplot as vlt from matplotlib import pyplot as plt plt.clf() plt.annotate(msg, xy=(0.3, 0.4), xycoords='axes fraction') plt.savefig(next_plot_fname(__file__, series='2d')) plt.savefig(next_plot_fname(__file__, series='2d')) plt.savefig(next_plot_fname(__file__, series='3d')) if args.show: plt.show() except ImportError: pass else: knots = np.array([[ 0.2, 0.5, 0.0], [-0.2, 0.5, 0.2], [-0.2, 0.0, 0.4], [ 0.2, 0.0, 0.2], [ 0.2, -0.5, 0.0], [-0.2, -0.5, 0.2]]).T seed_name = "Spline" fld = logo seeds = viscid.Spline(knots) seed_pts = seeds.get_points() interp_fld = viscid.interp_trilin(fld, seeds) if plot2d: try: from viscid.plot import vpyplot as vlt from matplotlib import pyplot as plt plt.clf() vlt.plot(interp_fld) plt.title(seed_name) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: plt.show() plt.clf() from matplotlib import rcParams _ms = rcParams['lines.markersize'] plt.gca().scatter(knots[0, :], knots[1, :], s=(2 * _ms)**2, marker='^', color='y') plt.gca().scatter(seed_pts[0, :], seed_pts[1, :], s=(1.5 * _ms)**2, marker='o', color='k') vlt.plot2d_line(seed_pts, scalars=interp_fld.flat_data, symdir='z') plt.title(seed_name) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: plt.show() except ImportError: pass if plot3d: try: from viscid.plot import vlab _ = get_mvi_fig(offscreen=not args.show) vlab.points3d(knots[0], knots[1], knots[2], color=(1.0, 1.0, 0), scale_mode='none', scale_factor=0.04) p = vlab.points3d(seed_pts[0], seed_pts[1], seed_pts[2], color=(0, 0, 0), scale_mode='none', scale_factor=0.03) vlab.plot_line(seed_pts, scalars=interp_fld.flat_data, tube_radius=0.01) vlab.axes(p) vlab.title(seed_name) vlab.mlab.roll(-90.0) vlab.savefig(next_plot_fname(__file__, series='3d')) if args.show: vlab.show(stop=True) except ImportError: pass if 1: viscid.logger.info('Testing RectilinearMeshPoints...') f = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[-1].xdmf')) slc = 'x=-40j:12j, y=-10j:10j, z=-10j:10j' b = f['b'][slc] z = b.get_crd('z') sheet_iz = np.argmin(b['x']**2, axis=2) sheet_pts = b['z=0:1'].get_points() sheet_pts[2, :] = z[sheet_iz].reshape(-1) isphere_mask = np.sum(sheet_pts[:2, :]**2, axis=0) < 5**2 day_mask = sheet_pts[0:1, :] > -1.0 sheet_pts[2, :] = np.choose(isphere_mask, [sheet_pts[2, :], 0]) sheet_pts[2, :] = np.choose(day_mask, [sheet_pts[2, :], 0]) nx, ny, _ = b.sshape sheet_seed = viscid.RectilinearMeshPoints(sheet_pts.reshape(3, nx, ny)) vx_sheet = viscid.interp_nearest(f['vx'], sheet_seed) try: if not plot2d: raise ImportError from viscid.plot import vpyplot as vlt from matplotlib import pyplot as plt vlt.clf() vlt.plot(vx_sheet, symmetric=True) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: vlt.show() except ImportError: pass try: if not plot3d: raise ImportError from viscid.plot import vlab _ = get_mvi_fig(offscreen=not args.show) mesh = vlab.mesh_from_seeds(sheet_seed, scalars=vx_sheet, clim=(-400, 400)) vlab.plot_earth_3d(crd_system=b) vlab.view(azimuth=+90.0 + 45.0, elevation=90.0 - 25.0, distance=30.0, focalpoint=(-10.0, +1.0, +1.0)) vlab.title("RectilinearMeshPoints") vlab.savefig(next_plot_fname(__file__, series='3d')) if args.show: vlab.show(stop=True) except ImportError: pass # prevent weird xorg bad-instructions on tear down if 'figure' in _global_ns and _global_ns['figure'] is not None: from viscid.plot import vlab vlab.mlab.close(_global_ns['figure']) return 0
def _main(): global offscreen_vlab parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("--notwo", dest='notwo', action="store_true") parser.add_argument("--nothree", dest='nothree', action="store_true") parser.add_argument("--show", "--plot", action="store_true") args = viscid.vutil.common_argparse(parser, default_verb=0) plot2d = not args.notwo plot3d = not args.nothree # plot2d = True # plot3d = True # args.show = True offscreen_vlab = not args.show img = np.load(os.path.join(sample_dir, "logo.npy")) x = np.linspace(-1, 1, img.shape[0]) y = np.linspace(-1, 1, img.shape[1]) z = np.linspace(-1, 1, img.shape[2]) logo = viscid.arrays2field([x, y, z], img) if 1: viscid.logger.info('Testing Point with custom local coordinates...') pts = np.vstack([[-1, -0.5, 0, 0.5, 1], [-1, -0.5, 0, 0.5, 1], [ 0, 0.5, 1, 1.5, 2]]) local_crds = viscid.asarray_datetime64([0, 60, 120, 180, 240], conservative=True) seeds = viscid.Point(pts, local_crds=local_crds) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Line...') seeds = viscid.Line([-1, -1, 0], [1, 1, 2], n=5) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Plane...') seeds = viscid.Plane([0.0, 0.0, 0.0], [1, 1, 1], [1, 0, 0], 2, 2, nl=160, nm=170, NL_are_vectors=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Volume...') seeds = viscid.Volume([-0.8, -0.8, -0.8], [0.8, 0.8, 0.8], n=[64, 64, 3]) # note: can't make a 2d plot of the volume w/o a slice run_test(logo, seeds, plot2d=False, plot3d=plot3d, add_title="3d", show=args.show) if 1: viscid.logger.info('Testing Volume (with ignorable dim)...') seeds = viscid.Volume([-0.8, -0.8, 0.0], [0.8, 0.8, 0.0], n=[64, 64, 1]) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="2d", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (phi, theta)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (theta, phi)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (phi, theta)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (theta, phi)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Patch...') seeds = viscid.SphericalPatch(p0=[0, 0, 0], p1=[0, -0, -1], max_alpha=30.0, max_beta=59.9, nalpha=65, nbeta=80, r=0.5, roll=45.0) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: # this spline test is very custom viscid.logger.info('Testing Spline...') try: import scipy.interpolate as interpolate except ImportError: msg = "XFail: ImportError (is scipy installed?)" if plot2d: try: from viscid.plot import vpyplot as vlt from matplotlib import pyplot as plt plt.clf() plt.annotate(msg, xy=(0.3, 0.4), xycoords='axes fraction') plt.savefig(next_plot_fname(__file__, series='2d')) plt.savefig(next_plot_fname(__file__, series='2d')) plt.savefig(next_plot_fname(__file__, series='3d')) if args.show: plt.show() except ImportError: pass else: knots = np.array([[ 0.2, 0.5, 0.0], [-0.2, 0.5, 0.2], [-0.2, 0.0, 0.4], [ 0.2, 0.0, 0.2], [ 0.2, -0.5, 0.0], [-0.2, -0.5, 0.2]]).T seed_name = "Spline" fld = logo seeds = viscid.Spline(knots) seed_pts = seeds.get_points() interp_fld = viscid.interp_trilin(fld, seeds) if plot2d: try: from viscid.plot import vpyplot as vlt from matplotlib import pyplot as plt plt.clf() vlt.plot(interp_fld) plt.title(seed_name) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: plt.show() plt.clf() from matplotlib import rcParams _ms = rcParams['lines.markersize'] plt.gca().scatter(knots[0, :], knots[1, :], s=(2 * _ms)**2, marker='^', color='y') plt.gca().scatter(seed_pts[0, :], seed_pts[1, :], s=(1.5 * _ms)**2, marker='o', color='k') vlt.plot2d_line(seed_pts, scalars=interp_fld.flat_data, symdir='z') plt.title(seed_name) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: plt.show() except ImportError: pass if plot3d: try: vlab, _ = get_mvi_fig() vlab.points3d(knots[0], knots[1], knots[2], color=(1.0, 1.0, 0), scale_mode='none', scale_factor=0.04) p = vlab.points3d(seed_pts[0], seed_pts[1], seed_pts[2], color=(0, 0, 0), scale_mode='none', scale_factor=0.03) vlab.plot_line(seed_pts, scalars=interp_fld.flat_data, tube_radius=0.01) vlab.axes(p) vlab.title(seed_name) vlab.mlab.roll(-90.0) vlab.savefig(next_plot_fname(__file__, series='3d')) if args.show: vlab.show(stop=True) except ImportError: pass if 1: viscid.logger.info('Testing RectilinearMeshPoints...') f = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[-1].xdmf')) slc = 'x=-40j:12j, y=-10j:10j, z=-10j:10j' b = f['b'][slc] z = b.get_crd('z') sheet_iz = np.argmin(b['x']**2, axis=2) sheet_pts = b['z=0:1'].get_points() sheet_pts[2, :] = z[sheet_iz].reshape(-1) isphere_mask = np.sum(sheet_pts[:2, :]**2, axis=0) < 5**2 day_mask = sheet_pts[0:1, :] > -1.0 sheet_pts[2, :] = np.choose(isphere_mask, [sheet_pts[2, :], 0]) sheet_pts[2, :] = np.choose(day_mask, [sheet_pts[2, :], 0]) nx, ny, _ = b.sshape sheet_seed = viscid.RectilinearMeshPoints(sheet_pts.reshape(3, nx, ny)) vx_sheet = viscid.interp_nearest(f['vx'], sheet_seed) try: if not plot2d: raise ImportError from viscid.plot import vpyplot as vlt from matplotlib import pyplot as plt vlt.clf() vlt.plot(vx_sheet, symmetric=True) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: vlt.show() except ImportError: pass try: if not plot3d: raise ImportError vlab, _ = get_mvi_fig() mesh = vlab.mesh_from_seeds(sheet_seed, scalars=vx_sheet, clim=(-400, 400)) vlab.plot_earth_3d(crd_system=b) vlab.view(azimuth=+90.0 + 45.0, elevation=90.0 - 25.0, distance=30.0, focalpoint=(-10.0, +1.0, +1.0)) vlab.title("RectilinearMeshPoints") vlab.savefig(next_plot_fname(__file__, series='3d')) if args.show: vlab.show(stop=True) except ImportError: pass # prevent weird xorg bad-instructions on tear down if 'figure' in _global_ns and _global_ns['figure'] is not None: from viscid.plot import vlab vlab.mlab.close(_global_ns['figure']) return 0
def topology_bitor_clusters(fld, min_depth=1, max_depth=10, multiple=True, plot=False, sep_val=streamline.TOPOLOGY_MS_SEPARATOR, mask_limit=0b1111, periodic="00", pt_bnds=()): """Find separator as intersection of all global topologies Neighbors are bitwise ORed until at least one value matches `sep_val` which is presumably (Close | Open N | Open S | SW). This happens between min_depth and max_depth times, where the resolution of each iteration is reduced by a factor of two, ie, worst case 2**(max_depth). Args: fld (Field): Topology (bitmask) as a field min_depth (int): Iterate at least this many times max_depth (int): Iterate at most this many times multiple (bool): passed to :py:func:`viscid.cluster` sep_val (int): Value of bitmask that indicates a separator plot (bool): Make a 2D plot of Fld and the sep candidates mask_limit (int): if > 0, then bitmask fld with mask_limit, i.e., fld = fld & mask_limit (bitwise and) periodic (sequence): indicate whether that direction is periodic, and if so, whether the coordinate arrays are overlapped or not. Values can be True, False, or '+'. '+' indicates that x[0] and x[-1] are not colocated, so assume they're dx apart where dx = x[-1] - x[-2]. pt_bnd (sequence): Boundaries that come to a point, i.e., all values along that boundary are neighbors such as the poles of a sphere. Specified like "0-" for lower boundary of dimension 0 or "1+" for the upper boundary of dimension 1. Returns: ndarray: 2xN for N clusters of separator points in the same coordinates as `fld` """ pd = [False if pi == "0" else bool(pi) for pi in periodic] fld = fld.slice_reduce(":") if mask_limit: fld = np.bitwise_and(fld, mask_limit) a = fld.data x, y = fld.get_crds() for i in range(max_depth): if pd[0]: a[(0, -1), :] |= a[(-1, 0), :] if pd[1]: a[:, (0, -1)] |= a[:, (-1, 0)] a = ( a[:-1, :-1] | a[:-1, 1:] | # pylint: disable=bad-whitespace a[1:, :-1] | a[1:, 1:]) # pylint: disable=bad-whitespace x = 0.5 * (x[1:] + x[:-1]) y = 0.5 * (y[1:] + y[:-1]) # bitwise_or an entire bounary if all points are neighbors, like # at the poles of a sphere for bnd in pt_bnds: slc = [slice(None), slice(None)] slc[int(bnd[0])] = -1 if bnd[1] == "+" else 0 a[slc] = np.bitwise_or.reduce(a[slc]) indx, indy = np.where(a == sep_val) if i + 1 >= min_depth and len(indx): break pts = viscid.cluster(indx, indy, x, y, multiple=multiple, periodic=periodic) if plot: from matplotlib import pyplot as plt from viscid.plot import vpyplot as vlt vlt.clf() ax0 = vlt.subplot(121) vlt.plot(fld, title=True) vlt.subplot(122, sharex=ax0, sharey=ax0) or_fld = viscid.arrays2field((x, y), a, name="OR") vlt.plot(or_fld, title=True) _x, _y = or_fld.get_crds() plt.plot(_x[indx], _y[indy], 'ko') plt.plot(pts[0], pts[1], 'y^') plt.show() return pts
def _main(): parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("--notwo", dest='notwo', action="store_true") parser.add_argument("--nothree", dest='nothree', action="store_true") parser.add_argument("--show", "--plot", action="store_true") args = viscid.vutil.common_argparse(parser, default_verb=0) plot2d = not args.notwo plot3d = not args.nothree # plot2d = True # plot3d = True # args.show = True img = np.load(os.path.join(sample_dir, "logo.npy")) x = np.linspace(-1, 1, img.shape[0]) y = np.linspace(-1, 1, img.shape[1]) z = np.linspace(-1, 1, img.shape[2]) logo = viscid.arrays2field([x, y, z], img) if 1: viscid.logger.info('Testing Line...') seeds = viscid.Line([-1, -1, 0], [1, 1, 2], n=5) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Plane...') seeds = viscid.Plane([0.0, 0.0, 0.0], [1, 1, 1], [1, 0, 0], 2, 2, nl=160, nm=170, NL_are_vectors=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Volume...') seeds = viscid.Volume([-0.8, -0.8, -0.8], [0.8, 0.8, 0.8], n=[64, 64, 3]) # note: can't make a 2d plot of the volume w/o a slice run_test(logo, seeds, plot2d=False, plot3d=plot3d, add_title="3d", show=args.show) if 1: viscid.logger.info('Testing Volume (with ignorable dim)...') seeds = viscid.Volume([-0.8, -0.8, 0.0], [0.8, 0.8, 0.0], n=[64, 64, 1]) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="2d", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (phi, theta)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (theta, phi)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (phi, theta)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (theta, phi)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Patch...') seeds = viscid.SphericalPatch(p0=[0, 0, 0], p1=[0, -0, -1], max_alpha=30.0, max_beta=59.9, nalpha=65, nbeta=80, r=0.5, roll=45.0) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing RectilinearMeshPoints...') f = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[-1].xdmf')) slc = 'x=-40f:12f, y=-10f:10f, z=-10f:10f' b = f['b'][slc] z = b.get_crd('z') sheet_iz = np.argmin(b['x']**2, axis=2) sheet_pts = b['z=0:1'].get_points() sheet_pts[2, :] = z[sheet_iz].reshape(-1) isphere_mask = np.sum(sheet_pts[:2, :]**2, axis=0) < 5**2 day_mask = sheet_pts[0:1, :] > -1.0 sheet_pts[2, :] = np.choose(isphere_mask, [sheet_pts[2, :], 0]) sheet_pts[2, :] = np.choose(day_mask, [sheet_pts[2, :], 0]) nx, ny, _ = b.sshape sheet_seed = viscid.RectilinearMeshPoints(sheet_pts.reshape(3, nx, ny)) vx_sheet = viscid.interp_nearest(f['vx'], sheet_seed) try: if not plot2d: raise ImportError from matplotlib import pyplot as plt from viscid.plot import vpyplot as vlt vlt.clf() vlt.plot(vx_sheet, symmetric=True) plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: vlt.show() except ImportError: pass try: if not plot3d: raise ImportError from viscid.plot import vlab vlab.clf() mesh = vlab.mesh_from_seeds(sheet_seed, scalars=vx_sheet, clim=(-400, 400)) vlab.plot_earth_3d(crd_system=b) vlab.view(azimuth=+90.0 + 45.0, elevation=90.0 - 25.0, distance=30.0, focalpoint=(-10.0, +1.0, +1.0)) vlab.title("RectilinearMeshPoints") vlab.savefig(next_plot_fname(__file__, series='3d')) if args.show: vlab.show() except ImportError: pass # prevent weird xorg bad-instructions on tear down if 'figure' in _global_ns and _global_ns['figure'] is not None: from viscid.plot import vlab vlab.mlab.close(_global_ns['figure']) return 0
def main(): parser = argparse.ArgumentParser() parser.add_argument("--notwo", dest='notwo', action="store_true") parser.add_argument("--nothree", dest='nothree', action="store_true") parser.add_argument("--show", "--plot", action="store_true") args = viscid.vutil.common_argparse(parser, default_verb=0) plot2d = not args.notwo plot3d = not args.nothree # plot2d = True # plot3d = True # args.show = True img = np.load(sample_dir + "/logo.npy") x = np.linspace(-1, 1, img.shape[0]) y = np.linspace(-1, 1, img.shape[1]) z = np.linspace(-1, 1, img.shape[2]) logo = viscid.arrays2field(img, [x, y, z]) if 1: viscid.logger.info('Testing Line...') seeds = viscid.Line([-1, -1, 0], [1, 1, 2], n=5) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Plane...') seeds = viscid.Plane([0.0, 0.0, 0.0], [1, 1, 1], [1, 0, 0], 2, 2, nl=160, nm=170, NL_are_vectors=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing Volume...') seeds = viscid.Volume([-0.8, -0.8, -0.8], [0.8, 0.8, 0.8], n=[64, 64, 3]) # note: can't make a 2d plot of the volume w/o a slice run_test(logo, seeds, plot2d=False, plot3d=plot3d, add_title="3d", show=args.show) if 1: viscid.logger.info('Testing Volume (with ignorable dim)...') seeds = viscid.Volume([-0.8, -0.8, 0.0], [0.8, 0.8, 0.0], n=[64, 64, 1]) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="2d", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (phi, theta)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", show=args.show) if 1: viscid.logger.info('Testing Spherical Sphere (theta, phi)...') seeds = viscid.Sphere([0, 0, 0], r=1.0, ntheta=160, nphi=170, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (phi, theta)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=False) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="PT", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Cap (theta, phi)...') seeds = viscid.SphericalCap(p0=[0, 0, 0], r=1.0, ntheta=64, nphi=80, pole=[-1, -1, -1], theta_phi=True) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, add_title="TP", view_kwargs=dict(azimuth=180, elevation=180), show=args.show) if 1: viscid.logger.info('Testing Spherical Patch...') seeds = viscid.SphericalPatch(p0=[0, 0, 0], p1=[0, -0, -1], max_alpha=30.0, max_beta=59.9, nalpha=65, nbeta=80, r=0.5, roll=45.0) run_test(logo, seeds, plot2d=plot2d, plot3d=plot3d, show=args.show) if 1: viscid.logger.info('Testing RectilinearMeshPoints...') f = viscid.load_file(sample_dir + '/sample_xdmf.3d.[-1].xdmf') slc = 'x=-40f:12f, y=-10f:10f, z=-10f:10f' b = f['b'][slc] z = b.get_crd('z') sheet_iz = np.argmin(b['x']**2, axis=2) sheet_pts = b['z=0:1'].get_points() sheet_pts[2, :] = z[sheet_iz].reshape(-1) isphere_mask = np.sum(sheet_pts[:2, :]**2, axis=0) < 5**2 day_mask = sheet_pts[0:1, :] > -1.0 sheet_pts[2, :] = np.choose(isphere_mask, [sheet_pts[2, :], 0]) sheet_pts[2, :] = np.choose(day_mask, [sheet_pts[2, :], 0]) nx, ny, _ = b.sshape sheet_seed = viscid.RectilinearMeshPoints(sheet_pts.reshape(3, nx, ny)) vx_sheet = viscid.interp_nearest(f['vx'], sheet_seed) try: if not plot2d: raise ImportError from viscid.plot import mpl mpl.clf() mpl.plot(vx_sheet, symmetric=True) mpl.plt.savefig(next_plot_fname(__file__, series='2d')) if args.show: mpl.show() except ImportError: pass try: if not plot3d: raise ImportError from viscid.plot import mvi mvi.clf() mesh = mvi.mesh_from_seeds(sheet_seed, scalars=vx_sheet, clim=(-400, 400)) mvi.plot_earth_3d(crd_system=b) mvi.view(azimuth=+90.0 + 45.0, elevation=90.0 - 25.0, distance=30.0, focalpoint=(-10.0, +1.0, +1.0)) mvi.title("RectilinearMeshPoints") mvi.savefig(next_plot_fname(__file__, series='3d')) if args.show: mvi.show() except ImportError: pass return 0
def topology_bitor_clusters( fld, min_depth=1, max_depth=10, multiple=True, plot=False, sep_val=streamline.TOPOLOGY_MS_SEPARATOR, mask_limit=0b1111, periodic="00", pt_bnds=(), ): """Find separator as intersection of all global topologies Neighbors are bitwise ORed until at least one value matches `sep_val` which is presumably (Close | Open N | Open S | SW). This happens between min_depth and max_depth times, where the resolution of each iteration is reduced by a factor of two, ie, worst case 2**(max_depth). Args: fld (Field): Topology (bitmask) as a field min_depth (int): Iterate at least this many times max_depth (int): Iterate at most this many times multiple (bool): passed to :py:func:`viscid.cluster` sep_val (int): Value of bitmask that indicates a separator plot (bool): Make a 2D plot of Fld and the sep candidates mask_limit (int): if > 0, then bitmask fld with mask_limit, i.e., fld = fld & mask_limit (bitwise and) periodic (sequence): indicate whether that direction is periodic, and if so, whether the coordinate arrays are overlapped or not. Values can be True, False, or '+'. '+' indicates that x[0] and x[-1] are not colocated, so assume they're dx apart where dx = x[-1] - x[-2]. pt_bnd (sequence): Boundaries that come to a point, i.e., all values along that boundary are neighbors such as the poles of a sphere. Specified like "0-" for lower boundary of dimension 0 or "1+" for the upper boundary of dimension 1. Returns: ndarray: 2xN for N clusters of separator points in the same coordinates as `fld` """ pd = [False if pi == "0" else bool(pi) for pi in periodic] fld = fld.slice_reduce(":") if mask_limit: fld = np.bitwise_and(fld, mask_limit) a = fld.data x, y = fld.get_crds() for i in range(max_depth): if pd[0]: a[(0, -1), :] |= a[(-1, 0), :] if pd[1]: a[:, (0, -1)] |= a[:, (-1, 0)] a = ( a[:-1, :-1] | a[:-1, 1:] | a[1:, :-1] | a[1:, 1:] # pylint: disable=bad-whitespace ) # pylint: disable=bad-whitespace x = 0.5 * (x[1:] + x[:-1]) y = 0.5 * (y[1:] + y[:-1]) # bitwise_or an entire bounary if all points are neighbors, like # at the poles of a sphere for bnd in pt_bnds: slc = [slice(None), slice(None)] slc[int(bnd[0])] = -1 if bnd[1] == "+" else 0 a[slc] = np.bitwise_or.reduce(a[slc]) indx, indy = np.where(a == sep_val) if i + 1 >= min_depth and len(indx): break pts = viscid.cluster(indx, indy, x, y, multiple=multiple, periodic=periodic) if plot: from viscid.plot import mpl mpl.clf() ax0 = mpl.subplot(121) mpl.plot(fld, title=True) mpl.subplot(122, sharex=ax0, sharey=ax0) or_fld = viscid.arrays2field(a, (x, y), name="OR") mpl.plot(or_fld, title=True) _x, _y = or_fld.get_crds() mpl.plt.plot(_x[indx], _y[indy], "ko") mpl.plt.plot(pts[0], pts[1], "y^") mpl.plt.show() return pts