def main():
parser = argparse.ArgumentParser(description="Test quasi potential")
parser.add_argument("--show", "--plot", action="store_true")
args = vutil.common_argparse(parser)
b, e = make_arcade(8.0, N=[64, 64, 64])
epar = viscid.project(e, b)
epar.pretty_name = "E parallel"
###############
# Calculate Xi
seeds = viscid.Volume(xl=[-10, 0.0, -10], xh=[10, 0.0, 10],
n=[64, 1, 64])
b_lines, _ = viscid.calc_streamlines(b, seeds)
xi_dat = viscid.integrate_along_lines(b_lines, e, reduction='dot')
xi = seeds.wrap_field(xi_dat, name='xi', pretty_name=r"$\Xi$")
################################
# Make 2D Matplotlib plot of Xi
mpl.plot(xi, x=(-10, 10), y=(-10, 10), style='contourf', levels=256,
lin=(2e-4, 1.5718))
mpl.plot(xi, x=(-10, 10), y=(-10, 10), style='contour', colors='grey',
levels=[0.5, 1.0])
mpl.savefig(next_plot_fname(__file__))
if args.show:
mpl.show()
############################################################
# Make 3D mayavi plot of Xi and the 'brightest' field lines
# as well as some other field lines for context
try:
from viscid.plot import mvi
except ImportError:
xfail("Mayavi not installed")
mvi.figure(size=[1200, 800], offscreen=not args.show)
inds = np.argsort(xi_dat)[-64:]
inds = np.concatenate([inds, np.arange(len(xi_dat))[::71]])
s = mvi.plot_lines(b_lines[inds], scalars=epar, cmap='viridis')
mvi.mesh_from_seeds(seeds, scalars=xi, cmap='inferno')
mvi.colorbar(s, orientation='horizontal', title=epar.pretty_name)
# mvi.streamline(b, scalars=e, seedtype='sphere', seed_resolution=4,
# integration_direction='both')
oa = mvi.orientation_axes()
oa.marker.set_viewport(0.75, 0.75, 1.0, 1.0)
mvi.view(roll=0, azimuth=90, elevation=25, distance=30.0,
focalpoint=[0, 2, 0])
mvi.savefig(next_plot_fname(__file__))
if args.show:
mvi.show()
def run_test(fld, seeds, plot2d=True, plot3d=True, add_title="",
view_kwargs=None, show=False):
interpolated_fld = viscid.interp_trilin(fld, seeds)
seed_name = seeds.__class__.__name__
if add_title:
seed_name += " " + add_title
try:
if not plot2d:
raise ImportError
from viscid.plot import mpl
mpl.plt.clf()
# mpl.plt.plot(seeds.get_points()[2, :], fld)
mpl_plot_kwargs = dict()
if interpolated_fld.is_spherical():
mpl_plot_kwargs['hemisphere'] = 'north'
mpl.plot(interpolated_fld, **mpl_plot_kwargs)
mpl.plt.title(seed_name)
mpl.plt.savefig(next_plot_fname(__file__, series='2d'))
if show:
mpl.plt.show()
except ImportError:
pass
try:
if not plot3d:
raise ImportError
from viscid.plot import mvi
try:
fig = _global_ns['figure']
mvi.clf()
except KeyError:
fig = mvi.figure(size=[1200, 800], offscreen=not show)
_global_ns['figure'] = fig
try:
mesh = mvi.mesh_from_seeds(seeds, scalars=interpolated_fld)
mesh.actor.property.backface_culling = True
except RuntimeError:
pass
pts = seeds.get_points()
p = mvi.points3d(pts[0], pts[1], pts[2], interpolated_fld.flat_data,
scale_mode='none', scale_factor=0.02)
mvi.axes(p)
mvi.title(seed_name)
if view_kwargs:
mvi.view(**view_kwargs)
mvi.savefig(next_plot_fname(__file__, series='3d'))
if show:
mvi.show()
except ImportError:
pass
def run_test(_fld, _seeds, plot2d=True, plot3d=True, title="", show=False, **kwargs):
lines, topo = viscid.calc_streamlines(_fld, _seeds, **kwargs)
topo_color = viscid.topology2color(topo)
# downsample lines for plotting
lines = [line[:, ::8] for line in lines]
try:
if not plot2d:
raise ImportError
from viscid.plot import mpl
mpl.plt.clf()
mpl.plot2d_lines(lines, scalars=topo_color, symdir="y", marker="^")
if title:
mpl.plt.title(title)
mpl.plt.savefig(next_plot_fname(__file__, series="2d"))
if show:
mpl.plt.show()
except ImportError:
pass
try:
if not plot3d:
raise ImportError
from viscid.plot import mvi
try:
fig = _global_ns["figure"]
mvi.clf()
except KeyError:
fig = mvi.figure(size=[1200, 800], offscreen=not show)
_global_ns["figure"] = fig
fld_mag = np.log(viscid.magnitude(_fld))
try:
# note: mayavi.mlab.mesh can't take color tuples as scalars
# so one can't use topo_color on a mesh surface. This
# is a limitation of mayavi. To actually plot a specific
# set of colors on a mesh, one must use a texture
mesh = mvi.mesh_from_seeds(_seeds, scalars=topo, opacity=0.6)
mesh.actor.property.backface_culling = True
except RuntimeError:
pass
mvi.plot_lines(lines, scalars=fld_mag, tube_radius=0.01, cmap="viridis")
if title:
mvi.title(title)
mvi.savefig(next_plot_fname(__file__, series="3d"))
if show:
mvi.show()
except ImportError:
pass
def _main():
"""This _main is a faux unit-test of cotr
It makes 3d plots using both Viscid and Mayavi
"""
plot_mpl = True
plot_mvi = True
crd_system = 'gse'
dtfmt = "%Y-%m-%d %H:%M"
t = "2010-06-23T00:00:00.0"
print("Dipole Moment at {0},".format(format_datetime(t, dtfmt)))
print(" - mhd:", get_dipole_moment(t, crd_system='gse', strength=1.0))
print(" - gse:", get_dipole_moment(t, crd_system='mhd', strength=1.0))
if plot_mpl:
from matplotlib import pyplot as plt
import matplotlib.dates as mdates
try:
from viscid.plot import mpl
except ImportError:
pass
times = linspace_datetime64("2010-01-01T00:00:00.0",
"2010-06-21T00:00:00.0", n=(365//2*24))
# times = linspace_datetime64("1952-01-01T00:00:00.0",
# "1956-01-01T00:00:00.0", n=(4*365*24*2))
t_dt = as_datetime(times).tolist()
m_gse = np.empty((len(times), 3), dtype='f8')
m_sm = np.empty((len(times), 3), dtype='f8')
psi = np.empty((len(times), ), dtype='f8')
mu = np.empty((len(times), ), dtype='f8')
message_cadence = len(times) // 20
for i, t in enumerate(times):
if i % message_cadence == 0:
print("Getting moment for: {0} {1} ({2:.0f}% complete)"
"".format(i, t, 100 * i / len(times)))
c = Cotr(t)
m_gse[i, :] = c.get_dipole_moment(crd_system='gse', strength=1)
m_sm[i, :] = c.get_dipole_moment(crd_system='sm', strength=1)
mu[i], psi[i] = c.get_dipole_angles()
dip_angle = np.rad2deg(np.arccos(np.sum(m_gse * m_sm, axis=1)))
i_smallest_diptilt = np.argmin(np.abs(mu))
i_largest_diptilt = np.argmax(np.abs(mu))
i_smallest_dipangle = np.argmin(np.abs(dip_angle))
i_largest_dipangle = np.argmax(np.abs(dip_angle))
print()
print("Dipole info between {0} and {1},"
"".format(format_datetime(times[0], dtfmt),
format_datetime(times[-1], dtfmt)))
print(" - Smallest dipole tilt angle: {1:.03g} deg @ {0}"
"".format(format_datetime(times[i_smallest_diptilt], dtfmt),
mu[i_smallest_diptilt]))
print(" - Largest dipole tilt angle: {1:.03g} deg @ {0}"
"".format(format_datetime(times[i_largest_diptilt], dtfmt),
mu[i_largest_diptilt]))
print(" - Smallest angle between dip and GSE-Z: {1:.03g} deg @ {0}"
"".format(format_datetime(times[i_smallest_dipangle], dtfmt),
dip_angle[i_smallest_dipangle]))
print(" - Largest angle between dip and GSE-Z: {1:.03g} deg @ {0}"
"".format(format_datetime(times[i_largest_dipangle], dtfmt),
dip_angle[i_largest_dipangle]))
plt.clf()
ax0 = plt.subplot(211)
plt.plot(t_dt, psi, label='GSM Angle')
plt.plot(t_dt, mu, label='DIP Tilt Angle')
plt.gca().get_xaxis().set_visible(False)
plt.legend(loc=0)
plt.subplot(212, sharex=ax0)
plt.plot(t_dt, dip_angle, label='Angle between dip and GSE-Z')
# plt.ylim(11.62, 11.73) # to see knee on 1954-12-14 @ 17:05
dateFmt = mdates.DateFormatter(dtfmt)
plt.gca().xaxis.set_major_formatter(dateFmt)
plt.gcf().autofmt_xdate()
plt.legend(loc=0)
plt.subplots_adjust(left=0.15, right=0.98, top=0.97)
plt.show()
# m = m_gse
# plt.clf()
# plt.subplot(311)
# plt.plot(times, m[:, 0], label='M$_{0}$')
# plt.subplot(312)
# plt.plot(times, m[:, 1], label='M$_{1}$')
# plt.subplot(313)
# plt.plot(times, m[:, 2], label='M$_{2}$')
# plt.show()
if plot_mvi:
import os
import viscid
from viscid.plot import mvi
mvi.figure(size=(768, 768), fgcolor=(0, 0, 0), bgcolor=(1, 1, 1),
offscreen=True)
def _plot_time_range(times, figname):
for i, t in enumerate(times):
mvi.clf()
cotr = Cotr(t)
mvi.plot_blue_marble(r=1.0, rotate=t, crd_system=crd_system,
nphi=256, ntheta=128, res=4, lines=True)
mvi.plot_earth_3d(radius=1.005, crd_system=crd_system,
night_only=True, opacity=0.5)
mag_north = cotr.transform('sm', crd_system, [0, 0, 1.0])
mvi.mlab.points3d(*mag_north, scale_factor=0.05, mode='sphere',
color=(0.992, 0.455, 0.0), resolution=32)
mvi.orientation_axes(line_width=4.0)
mvi.mlab.text(0.325, 0.95, viscid.format_datetime(t))
mvi.view(azimuth=0.0, elevation=90.0, distance=5.0,
focalpoint=[0, 0, 0])
mvi.savefig("{0}_eq_{1:06d}.png".format(figname, i))
mvi.view(azimuth=0.0, elevation=0.0, distance=5.0,
focalpoint=[0, 0, 0])
mvi.savefig("{0}_pole_{1:06d}.png".format(figname, i))
path = os.path.expanduser("~/Desktop/day/{0}/".format(crd_system))
if not os.path.exists(path):
os.makedirs(path)
print()
print("Writing 3D images in:", path)
# summer solstice (earth-sun line @ tropic of cancer)
print()
print("Making a movie for the June solstice")
solstice_times = linspace_datetime64("2010-06-21T00:00:00.0",
"2010-06-22T00:00:00.0", n=49)
_plot_time_range(solstice_times, path + "solstice")
pfx = path + "solstice_eq"
viscid.vutil.make_animation(pfx + '.mp4', pfx, framerate=23.976, yes=1)
pfx = path + "solstice_pole"
viscid.vutil.make_animation(pfx + '.mp4', pfx, framerate=23.976, yes=1)
# autumnal equinox (earth-sun line @ equator)
print()
print("Making a movie for the September equinox")
equinox_times = linspace_datetime64("2010-09-23T00:00:00.0",
"2010-09-24T00:00:00.0", n=49)
_plot_time_range(equinox_times, path + "equinox")
pfx = path + "equinox_eq"
viscid.vutil.make_animation(pfx + '.mp4', pfx, framerate=23.976, yes=1)
pfx = path + "equinox_pole"
viscid.vutil.make_animation(pfx + '.mp4', pfx, framerate=23.976, yes=1)
# Watching the magnetic pole move year-by-year
print()
print("Making a movie to show magnetic pole motion")
years = range(1950, 2016, 1)
times = [as_datetime64("{0:04d}-06-21".format(y)) for y in years]
_plot_time_range(times, path + "year")
pfx = path + "year_eq"
viscid.vutil.make_animation(pfx + '.mp4', pfx, yes=1, framerate=8)
pfx = path + "year_pole"
viscid.vutil.make_animation(pfx + '.mp4', pfx, yes=1, framerate=8)
def main():
parser = argparse.ArgumentParser(description="Test calc")
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument("--interact", "-i", action="store_true")
args = vutil.common_argparse(parser)
f3d = viscid.load_file(sample_dir + '/sample_xdmf.3d.[0].xdmf')
f_iono = viscid.load_file(sample_dir + "/sample_xdmf.iof.[0].xdmf")
b = f3d["b"]
v = f3d["v"]
pp = f3d["pp"]
e = f3d["e_cc"]
mvi.figure(size=(1200, 800), offscreen=not args.show)
##########################################################
# make b a dipole inside 3.1Re and set e = 0 inside 4.0Re
cotr = viscid.Cotr(dip_tilt=0.0) # pylint: disable=not-callable
moment = cotr.get_dipole_moment(crd_system=b)
isphere_mask = viscid.make_spherical_mask(b, rmax=3.1)
viscid.fill_dipole(b, m=moment, mask=isphere_mask)
e_mask = viscid.make_spherical_mask(b, rmax=4.0)
viscid.set_in_region(e, 0.0, alpha=0.0, mask=e_mask, out=e)
######################################
# plot a scalar cut plane of pressure
pp_src = mvi.field2source(pp, center='node')
scp = mvi.scalar_cut_plane(pp_src, plane_orientation='z_axes', opacity=0.5,
transparent=True, view_controls=False,
cmap="inferno", logscale=True)
scp.implicit_plane.normal = [0, 0, -1]
scp.implicit_plane.origin = [0, 0, 0]
cbar = mvi.colorbar(scp, title=pp.name, orientation='vertical')
######################################
# plot a vector cut plane of the flow
vcp = mvi.vector_cut_plane(v, scalars=pp_src, plane_orientation='z_axes',
view_controls=False, mode='arrow',
cmap='Greens_r')
vcp.implicit_plane.normal = [0, 0, -1]
vcp.implicit_plane.origin = [0, 0, 0]
##############################
# plot very faint isosurfaces
iso = mvi.iso_surface(pp_src, contours=5, opacity=0.1, cmap=False)
##############################################################
# calculate B field lines && topology in Viscid and plot them
seeds = viscid.SphericalPatch([0, 0, 0], [2, 0, 1], 30, 15, r=5.0,
nalpha=5, nbeta=5)
b_lines, topo = viscid.calc_streamlines(b, seeds, ibound=3.5,
obound0=[-25, -20, -20],
obound1=[15, 20, 20], wrap=True)
mvi.plot_lines(b_lines, scalars=viscid.topology2color(topo))
######################################################################
# plot a random circle at geosynchronus orbit with scalars colored
# by the Matplotlib viridis color map, just because we can; this is
# a useful toy for debugging
circle = viscid.Circle(p0=[0, 0, 0], r=6.618, n=128, endpoint=True)
scalar = np.sin(circle.as_local_coordinates().get_crd('phi'))
surf = mvi.plot_line(circle.get_points(), scalars=scalar, clim=0.8,
cmap="Spectral_r")
######################################################################
# Use Mayavi (VTK) to calculate field lines using an interactive seed
# These field lines are colored by E parallel
epar = viscid.project(e, b)
epar.name = "Epar"
bsl2 = mvi.streamline(b, epar, seedtype='sphere', seed_resolution=4,
integration_direction='both', clim=(-0.05, 0.05))
# now tweak the VTK streamlines
bsl2.stream_tracer.maximum_propagation = 20.
bsl2.seed.widget.center = [-11, 0, 0]
bsl2.seed.widget.radius = 1.0
bsl2.streamline_type = 'tube'
bsl2.tube_filter.radius = 0.03
bsl2.stop() # this stop/start was a hack to get something to update
bsl2.start()
bsl2.seed.widget.enabled = False
cbar = mvi.colorbar(bsl2, title=epar.name, orientation='horizontal')
cbar.scalar_bar_representation.position = (0.2, 0.01)
cbar.scalar_bar_representation.position2 = (0.6, 0.14)
###############################################################
# Make a contour at the open-closed boundary in the ionosphere
seeds_iono = viscid.Sphere(r=1.063, pole=-moment, ntheta=256, nphi=256,
thetalim=(0, 180), philim=(0, 360), crd_system=b)
_, topo_iono = viscid.calc_streamlines(b, seeds_iono, ibound=1.0,
nr_procs='all',
output=viscid.OUTPUT_TOPOLOGY)
topo_iono = np.log2(topo_iono)
m = mvi.mesh_from_seeds(seeds_iono, scalars=topo_iono, opacity=1.0,
clim=(0, 3), color=(0.992, 0.445, 0.0))
m.enable_contours = True
####################################################################
# Plot the ionosphere, note that the sample data has the ionosphere
# at a different time, so the open-closed boundary found above
# will not be consistant with the field aligned currents
fac_tot = 1e9 * f_iono['fac_tot']
m = mvi.plot_ionosphere(fac_tot, bounding_lat=30.0, vmin=-300, vmax=300,
opacity=0.75, rotate=cotr, crd_system=b)
m.actor.property.backface_culling = True
########################################################################
# Add some markers for earth, i.e., real earth, and dayside / nightside
# representation
mvi.plot_blue_marble(r=1.0, lines=False, ntheta=64, nphi=128,
rotate=cotr, crd_system=b)
# now shade the night side with a transparent black hemisphere
mvi.plot_earth_3d(radius=1.01, night_only=True, opacity=0.5, crd_system=b)
####################
# Finishing Touches
# mvi.axes(pp_src, nb_labels=5)
oa = mvi.orientation_axes()
oa.marker.set_viewport(0.75, 0.75, 1.0, 1.0)
# note that resize won't work if the current figure has the
# off_screen_rendering flag set
# mvi.resize([1200, 800])
mvi.view(azimuth=45, elevation=70, distance=35.0, focalpoint=[-2, 0, 0])
##############
# Save Figure
# print("saving png")
# mvi.savefig('mayavi_msphere_sample.png')
# print("saving x3d")
# # x3d files can be turned into COLLADA files with meshlab, and
# # COLLADA (.dae) files can be opened in OS X's preview
# #
# # IMPORTANT: for some reason, using bounding_lat in mvi.plot_ionosphere
# # causes a segfault when saving x3d files
# #
# mvi.savefig('mayavi_msphere_sample.x3d')
# print("done")
mvi.savefig(next_plot_fname(__file__))
###########################
# Interact Programatically
if args.interact:
mvi.interact()
#######################
# Interact Graphically
if args.show:
mvi.show()
