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 _test(_p1, _p2, r1=None, r2=None, color=(0.8, 0.8, 0.8)):
if r1 is not None:
_p1 = r1 * np.asarray(_p1) / np.linalg.norm(_p1)
if r2 is not None:
_p2 = r2 * np.asarray(_p2) / np.linalg.norm(_p2)
circ = great_circle(_p1, _p2)
if not np.all(np.isclose(circ[:, 0], _p1)):
print("!! great circle error P1:", _p1, ", P2:", _p2)
print(" first_point:", circ[:, 0], "!= P1")
if not np.all(np.isclose(circ[:, -1], _p2)):
print("!! great circle error P1:", _p1, ", P2:", _p2)
print(" last_point:", circ[:, -1], "!= P2")
if _HAS_MVI:
mvi.plot_lines([circ], tube_radius=0.02, color=color)
def run_test(_fld, _seeds, plot2d=True, plot3d=True, show=False, **kwargs):
lines, topo = viscid.calc_streamlines(_fld, _seeds, **kwargs)
topo_fld = _seeds.wrap_field(topo)
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 show:
mpl.plt.show()
except ImportError:
pass
try:
if not plot3d:
raise ImportError
from viscid.plot import mvi
mvi.clf()
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
vertices, scalars = _seeds.wrap_mesh(topo_fld.data)
mesh = mvi.mlab.mesh(vertices[0], vertices[1], vertices[2], scalars=scalars, opacity=0.5)
mesh.actor.property.backface_culling = True
except RuntimeError:
pass
mvi.plot_lines(lines, scalars=fld_mag, tube_radius=0.005)
if show:
mvi.show()
except ImportError:
pass
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 main():
parser = argparse.ArgumentParser(description="Test calc")
parser.add_argument("--show", "--plot", action="store_true")
args = vutil.common_argparse(parser)
f3d = viscid.load_file(_viscid_root + '/../sample/sample.3df.[0].xdmf')
f_iono = viscid.load_file(_viscid_root + "/../sample/*.iof.[0].xdmf")
b = f3d["b"]
pp = f3d["pp"]
# plot a scalar cut plane of pressure
pp_src = mvi.field2source(pp, center='node')
scp = mlab.pipeline.scalar_cut_plane(pp_src, plane_orientation='z_axes',
transparent=True, opacity=0.5,
view_controls=False)
scp.implicit_plane.normal = [0, 0, -1]
scp.implicit_plane.origin = [0, 0, 0]
# i don't know why this log10 doesn't seem to work
scp.module_manager.scalar_lut_manager.lut.scale = 'log10'
scp.module_manager.scalar_lut_manager.lut_mode = 'Reds'
scp.module_manager.scalar_lut_manager.reverse_lut = True
scp.module_manager.scalar_lut_manager.show_scalar_bar = True
# 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])
mvi.plot_lines(b_lines, scalars=viscid.topology2color(topo))
# Use Mayavi (VTK) to calculate field lines using an interactive seed
b_src = mvi.field2source(b, center='node')
bsl2 = mlab.pipeline.streamline(b_src, seedtype='sphere',
integration_direction='both',
seed_resolution=4)
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 work?
bsl2.start()
bsl2.seed.widget.enabled = True
# Plot the ionosphere too
fac_tot = 1e9 * f_iono['fac_tot']
crd_system = 'gse'
m = mvi.plot_ionosphere(fac_tot, crd_system=crd_system, bounding_lat=30.0,
vmin=-300, vmax=300, opacity=0.75)
m.module_manager.scalar_lut_manager.lut_mode = 'RdBu'
m.module_manager.scalar_lut_manager.reverse_lut = True
mvi.plot_blue_marble(r=1.0, orientation=(0, 21.5, -45.0))
# now shade the night side with a transparent black hemisphere
mvi.plot_earth_3d(radius=1.01, crd_system="gse", night_only=True,
opacity=0.5)
mlab.axes(pp_src, nb_labels=5)
mlab.orientation_axes()
mvi.resize([1200, 800])
mlab.view(azimuth=40, elevation=70, distance=35.0, focalpoint=[-3, 0, 0])
# # Save Figure
# print("saving png")
# mvi.mlab.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.mlab.savefig('mayavi_msphere_sample.x3d')
# print("done")
if args.show:
mlab.show()
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()
def main():
mhd_type = "C"
make_plots = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C",):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 2e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
do_fill_dipole = True
gslc = "x=-21.2f:12f, y=-11f:11f, z=-11f:11f"
b = f['b_cc'][gslc]
b1 = f['b_fc'][gslc]
e_cc = f['e_cc'][gslc]
e_ec = f['e_ec'][gslc]
if do_fill_dipole:
mask = viscid.make_spherical_mask(b, rmax=3.5)
viscid.fill_dipole(b, mask=mask)
mask = viscid.make_spherical_mask(b1, rmax=3.5)
viscid.fill_dipole(b1, mask=mask)
mask = None
# seeds = viscid.SphericalCap(r=1.02, ntheta=64, nphi=32, angle0=17, angle=20,
# philim=(100, 260), roll=-180.0)
# seeds = viscid.SphericalCap(r=1.02, ntheta=64, nphi=32, angle0=17, angle=20,
# philim=(0, 10), roll=0.0)
seedsN = viscid.Sphere(r=1.02, ntheta=16, nphi=16, thetalim=(15, 25),
philim=(0, 300), crd_system=b)
seedsS = viscid.Sphere(r=1.02, ntheta=16, nphi=16, thetalim=(155, 165),
philim=(0, 300), crd_system=b)
bl_kwargs = dict(ibound=0.9, obound0=(-20, -10, -10), obound1=(11, 10, 10))
# blines_cc, topo_cc = viscid.streamlines(b, seeds, **bl_kwargs)
blinesN_fc, topoN_fc = viscid.streamlines(b1, seedsN, **bl_kwargs)
_, topoS_fc = viscid.streamlines(b1, seedsS, output=viscid.OUTPUT_TOPOLOGY,
**bl_kwargs)
if True:
from viscid.plot import mvi
mesh = mvi.mesh_from_seeds(seedsN, scalars=topoN_fc)
mesh.actor.property.backface_culling = True
# mvi.plot_lines(blines_cc, scalars="#000000", tube_radius=0.03)
mvi.plot_lines(blinesN_fc, scalars=viscid.topology2color(topoN_fc),
opacity=0.7)
mvi.plot_blue_marble(r=1.0)
mvi.plot_earth_3d(radius=1.01, crd_system=b, night_only=True,
opacity=0.5)
mvi.show()
if True:
mpl.subplot(121, projection='polar')
mpl.plot(topoN_fc)
mpl.subplot(122, projection='polar')
mpl.plot(topoS_fc)
mpl.show()
return 0