def run_mag_test(fld, title="", show=False):
vx, vy, vz = fld.component_views() # pylint: disable=W0612
vx, vy, vz = fld.component_fields()
try:
t0 = time()
mag_ne = viscid.magnitude(fld, preferred="numexpr", only=False)
t1 = time()
logger.info("numexpr mag runtime: %g", t1 - t0)
except viscid.verror.BackendNotFound:
xfail("Numexpr is not installed")
planes = ["z=0", "y=0"]
nrows = 4
ncols = len(planes)
_, axes = plt.subplots(nrows, ncols, sharex=True, sharey=True, squeeze=False)
for ind, p in enumerate(planes):
vlt.plot(vx, p, ax=axes[0, ind], show=False)
vlt.plot(vy, p, ax=axes[1, ind], show=False)
vlt.plot(vz, p, ax=axes[2, ind], show=False)
vlt.plot(mag_ne, p, ax=axes[3, ind], show=False)
plt.suptitle(title)
vlt.auto_adjust_subplots(subplot_params=dict(top=0.9, right=0.9))
plt.gcf().set_size_inches(6, 7)
plt.savefig(next_plot_fname(__file__))
if show:
vlt.mplshow()
def run_mag_test(fld, title="", show=False):
vx, vy, vz = fld.component_views() # pylint: disable=W0612
vx, vy, vz = fld.component_fields()
try:
t0 = time()
mag_ne = viscid.magnitude(fld, preferred="numexpr", only=False)
t1 = time()
logger.info("numexpr mag runtime: %g", t1 - t0)
except viscid.verror.BackendNotFound:
xfail("Numexpr is not installed")
planes = ["z=0", "y=0"]
nrows = 4
ncols = len(planes)
ax = plt.subplot2grid((nrows, ncols), (0, 0))
ax.axis("equal")
for ind, p in enumerate(planes):
plt.subplot2grid((nrows, ncols), (0, ind), sharex=ax, sharey=ax)
mpl.plot(vx, p, show=False)
plt.subplot2grid((nrows, ncols), (1, ind), sharex=ax, sharey=ax)
mpl.plot(vy, p, show=False)
plt.subplot2grid((nrows, ncols), (2, ind), sharex=ax, sharey=ax)
mpl.plot(vz, p, show=False)
plt.subplot2grid((nrows, ncols), (3, ind), sharex=ax, sharey=ax)
mpl.plot(mag_ne, p, show=False)
mpl.plt.suptitle(title)
mpl.auto_adjust_subplots(subplot_params=dict(top=0.9))
mpl.plt.gcf().set_size_inches(6, 7)
mpl.plt.savefig(next_plot_fname(__file__))
if show:
mpl.mplshow()
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=__doc__)
_ = vutil.common_argparse(parser)
if _HAS_SCIPY:
warnings.filterwarnings("ignore", category=OptimizeWarning)
f = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[0].xdmf'))
mp = viscid.get_mp_info(f['pp'],
f['b'],
f['j'],
f['e_cc'],
fit='mp_xloc',
slc="x=7f:12.0f, y=-6f:6f, z=-6f:6f",
cache=False)
Y, Z = mp['pp_max_xloc'].meshgrid(prune=True)
# # get normals from paraboloid surface
if isinstance(mp['paraboloid'], viscid.DeferredImportError):
xfail("Scipy not installed; paraboloid curve fitting not tested")
else:
parab_n = viscid.paraboloid_normal(Y, Z, *mp['paraboloid'][0])
parab_n = parab_n.reshape(3, -1)
# get normals from minvar
minvar_y = Y.reshape(-1)
minvar_z = Z.reshape(-1)
minvar_n = np.zeros([3, len(minvar_y)])
for i in range(minvar_n.shape[1]):
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)]
lmn = viscid.find_minvar_lmn_around(f['b'], p0, l=2.0, n=64)
minvar_n[:, i] = lmn[2, :]
theta = (180 / np.pi) * np.arccos(np.sum(parab_n * minvar_n, axis=0))
# make sure paraboloid normals and minvar normals are closeish
# this is a poor check, but at least it's something
assert np.min(theta) < 3.0
assert np.average(theta) < 20.0
assert np.median(theta) < 20.0
assert np.max(theta) < 70.0
return 0
def _main():
parser = argparse.ArgumentParser(description=__doc__)
_ = vutil.common_argparse(parser)
if _HAS_SCIPY:
warnings.filterwarnings("ignore", category=OptimizeWarning)
f = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[0].xdmf'))
mp = viscid.get_mp_info(f['pp'], f['b'], f['j'], f['e_cc'], fit='mp_xloc',
slc="x=7j:12.0j, y=-6j:6j, z=-6j:6j",
cache=False)
Y, Z = mp['pp_max_xloc'].meshgrid(prune=True)
# # get normals from paraboloid surface
if isinstance(mp['paraboloid'], viscid.DeferredImportError):
xfail("Scipy not installed; paraboloid curve fitting not tested")
else:
parab_n = viscid.paraboloid_normal(Y, Z, *mp['paraboloid'][0])
parab_n = parab_n.reshape(3, -1)
# get normals from minvar
minvar_y = Y.reshape(-1)
minvar_z = Z.reshape(-1)
minvar_n = np.zeros([3, len(minvar_y)])
for i in range(minvar_n.shape[1]):
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)]
lmn = viscid.find_minvar_lmn_around(f['b'], p0, l=2.0, n=64)
minvar_n[:, i] = lmn[2, :]
theta = (180 / np.pi) * np.arccos(np.sum(parab_n * minvar_n, axis=0))
# make sure paraboloid normals and minvar normals are closeish
# this is a poor check, but at least it's something
assert np.min(theta) < 3.0
assert np.average(theta) < 20.0
assert np.median(theta) < 20.0
assert np.max(theta) < 70.0
return 0
from __future__ import print_function
import argparse
import os
import sys
from viscid_test_common import next_plot_fname, xfail
import numpy as np
import viscid
from viscid import sample_dir
from viscid import vutil
try:
from viscid.plot import vlab
except ImportError:
xfail("Mayavi not installed")
# In this test, the OpenGGCM reader needs to read the log file
# in order to determine the crds when doing the cotr transformation.
# In general, this flag is useful to put in your viscidrc file, see
# the corresponding page in the tutorial for more information.
viscid.readers.openggcm.GGCMFile.read_log_file = True
viscid.readers.openggcm.GGCMGrid.mhd_to_gse_on_read = "auto"
def _main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument("--interact", "-i", action="store_true")
args = vutil.common_argparse(parser)
def _main():
parser = argparse.ArgumentParser(description=__doc__)
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
vlt.plot(xi,
x=(-10, 10),
y=(-10, 10),
style='contourf',
levels=256,
lin=(2e-4, 1.5718))
vlt.plot(xi,
x=(-10, 10),
y=(-10, 10),
style='contour',
colors='grey',
levels=[0.5, 1.0])
vlt.savefig(next_plot_fname(__file__))
if args.show:
vlt.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 vlab
except ImportError:
xfail("Mayavi not installed")
vlab.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 = vlab.plot_lines(b_lines[inds], scalars=epar, cmap='viridis')
vlab.mesh_from_seeds(seeds, scalars=xi, cmap='inferno')
vlab.colorbar(s, orientation='horizontal', title=epar.pretty_name)
# vlab.streamline(b, scalars=e, seedtype='sphere', seed_resolution=4,
# integration_direction='both')
oa = vlab.orientation_axes()
oa.marker.set_viewport(0.75, 0.75, 1.0, 1.0)
vlab.view(roll=0,
azimuth=90,
elevation=25,
distance=30.0,
focalpoint=[0, 2, 0])
vlab.savefig(next_plot_fname(__file__))
if args.show:
vlab.show()
try:
vlab.mlab.close()
except AttributeError:
pass
return 0
from __future__ import print_function
import argparse
import os
import sys
from viscid_test_common import next_plot_fname, xfail
import numpy as np
import viscid
from viscid import sample_dir
from viscid import vutil
try:
from viscid.plot import vlab
except ImportError:
xfail("Mayavi not installed")
# In this test, the OpenGGCM reader needs to read the log file
# in order to determine the crds when doing the cotr transformation.
# In general, this flag is useful to put in your viscidrc file, see
# the corresponding page in the tutorial for more information.
viscid.readers.openggcm.GGCMFile.read_log_file = True
viscid.readers.openggcm.GGCMGrid.mhd_to_gse_on_read = "auto"
def _main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument("--interact", "-i", action="store_true")
args = vutil.common_argparse(parser)
