def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
args = vutil.common_argparse(parser)
iono_file = viscid.load_file(_viscid_root + '/../sample/jrrle_sample.iof.*')
fac_tot = 1e9 * iono_file["fac_tot"]
plot_args = dict(projection="polar",
lin=[-4e3, 3e3],
bounding_lat=35.0,
drawcoastlines=True, # for basemap only, probably will never be used
title="Total FAC\n", # make a title, or if a string, use the string as title
gridec='gray',
label_lat=True,
label_mlt=True,
colorbar=dict(pad=0.1) # pad the colorbar away from the plot
)
ax1 = plt.subplot(121, projection='polar')
mpl.plot(fac_tot, ax=ax1, hemisphere='north', **plot_args)
ax1.annotate('(a)', xy=(0, 0), textcoords="axes fraction",
xytext=(-0.1, 1.0), fontsize=18)
ax2 = plt.subplot(122, projection='polar')
plot_args['gridec'] = False
mpl.plot(fac_tot, ax=ax2, hemisphere="south", style="contourf",
levels=50, extend="both", **plot_args)
ax2.annotate('(b)', xy=(0, 0), textcoords="axes fraction",
xytext=(-0.1, 1.0), fontsize=18)
if args.show:
mpl.mplshow()
def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
args = vutil.common_argparse(parser)
f3d = viscid.load_file(_viscid_root + '/../sample/sample.3df.xdmf',
grid_type=MyGGCMGrid)
pp = f3d['pp']
rr = f3d['rr']
T = f3d['T']
# bmag = timeit(lambda: f3d['bmag'])
bmag = f3d["bmag"]
plt.subplot(141)
mpl.plot(pp, "y=0f,x=-20f:10f", plot_opts="log", earth=True, show=False)
plt.subplot(142)
mpl.plot(rr, "y=0f,x=-20f:10f", plot_opts="log", earth=True, show=False)
plt.subplot(143)
mpl.plot(T, "y=0f,x=-20f:10f", plot_opts="log", earth=True, show=False)
plt.subplot(144)
mpl.plot(bmag, "y=0f,x=-20f:10f", plot_opts="log", earth=True, show=False)
if args.show:
mpl.mplshow()
def run_mag_test(fld, show=False):
vx, vy, vz = fld.component_views() #pylint: disable=W0612
vx, vy, vz = fld.component_fields()
t0 = time()
mag_ne = viscid.magnitude(fld, preferred="numexpr", only=True)
t1 = time()
logger.info("numexpr mag runtime: %g", t1 - t0)
t0 = time()
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)
if show:
mpl.mplshow()
def run_test_iof(f, main__file__, show=False):
mpl.clf()
fac_tot = 1e9 * f["fac_tot"]
plot_args = dict(projection="polar",
lin=[-300, 300],
bounding_lat=35.0,
drawcoastlines=True, # for basemap only
title="Total FAC\n",
gridec='gray',
label_lat=True,
label_mlt=True,
colorbar=dict(pad=0.1) # pad the colorbar away from the plot
)
ax1 = mpl.subplot(121, projection='polar')
mpl.plot(fac_tot, ax=ax1, hemisphere='north', **plot_args)
ax1.annotate('(a)', xy=(0, 0), textcoords="axes fraction",
xytext=(-0.1, 1.0), fontsize=18)
ax2 = mpl.subplot(122, projection='polar')
plot_args['gridec'] = False
mpl.plot(fac_tot, ax=ax2, hemisphere="south", style="contourf",
levels=50, extend="both", **plot_args)
ax2.annotate('(b)', xy=(0, 0), textcoords="axes fraction",
xytext=(-0.1, 1.0), fontsize=18)
mpl.auto_adjust_subplots(subplot_params=dict())
mpl.plt.gcf().set_size_inches(8, 4)
mpl.plt.savefig(next_plot_fname(main__file__))
if show:
mpl.mplshow()
def run_mpl_testB(show=False):
logger.info("3D node centered tests")
x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
z = np.array(np.linspace(-10, 10, 140), dtype=dtype)
fld_s = viscid.empty([x, y, z], center='node')
X, Y, Z = fld_s.get_crds_nc(shaped=True) # pylint: disable=W0612
fld_s[:, :, :] = np.sin(X) + np.cos(Y) - np.cos(Z)
# print("shape: ", fld_s.data.shape)
nrows = 4
ncols = 1
plt.subplot2grid((nrows, ncols), (0, 0))
mpl.plot(fld_s, "z=0,x=:30", earth=True, plot_opts="lin_0")
plt.subplot2grid((nrows, ncols), (1, 0))
mpl.plot(fld_s, "z=0.75f,x=-4:-1,y=-3f:3f", earth=True)
plt.subplot2grid((nrows, ncols), (2, 0))
mpl.plot(fld_s, "x=-0.5f:,y=-3f:3f,z=0f", earth=True)
plt.subplot2grid((nrows, ncols), (3, 0))
mpl.plot(fld_s, "x=0.0f,y=-5.0f:5.0f", earth=True, plot_opts="log,g")
mpl.plt.suptitle("3d node centered")
mpl.auto_adjust_subplots()
mpl.plt.savefig(next_plot_fname(__file__))
if show:
mpl.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 run_mpl_testA(show=False):
logger.info("2D cell centered tests")
x = np.array(np.linspace(-10, 10, 100), dtype=dtype)
y = np.array(np.linspace(-10, 10, 120), dtype=dtype)
z = np.array(np.linspace(-1, 1, 2), dtype=dtype)
fld_s = viscid.empty([x, y, z], center='cell')
Xcc, Ycc, Zcc = fld_s.get_crds_cc(shaped=True) # pylint: disable=unused-variable
fld_s[:, :, :] = np.sin(Xcc) + np.cos(Ycc)
nrows = 4
ncols = 1
plt.subplot2grid((nrows, ncols), (0, 0))
mpl.plot(fld_s, "y=20f", show=False, plot_opts="lin_0")
plt.subplot2grid((nrows, ncols), (1, 0))
mpl.plot(fld_s, "x=0f:20f,y=0f:5f", earth=True, show=False,
plot_opts="x_-10_0,y_0_7")
plt.subplot2grid((nrows, ncols), (2, 0))
mpl.plot(fld_s, "y=0f", show=False, plot_opts="lin_-1_1")
plt.subplot2grid((nrows, ncols), (3, 0))
mpl.plot(fld_s, "z=0f,x=-20f:0f", earth=True, show=False, plot_opts="lin_-5_5")
mpl.plt.suptitle("2d cell centered")
mpl.auto_adjust_subplots()
mpl.plt.savefig(next_plot_fname(__file__))
if show:
mpl.mplshow()
def run_div_test(fld, exact, show=False, ignore_inexact=False):
t0 = time()
result_numexpr = viscid.div(fld, preferred="numexpr", only=True)
t1 = time()
logger.info("numexpr magnitude runtime: %g", t1 - t0)
result_diff = viscid.diff(result_numexpr, exact[1:-1, 1:-1, 1:-1])
if not ignore_inexact and not (result_diff.data < 5e-5).all():
logger.warn("numexpr result is far from the exact result")
logger.info("min/max(abs(numexpr - exact)): %g / %g",
np.min(result_diff.data), np.max(result_diff.data))
planes = ["y=0f", "z=0f"]
nrows = 2
ncols = len(planes)
ax = plt.subplot2grid((nrows, ncols), (0, 0))
ax.axis("equal")
for i, p in enumerate(planes):
plt.subplot2grid((nrows, ncols), (0, i), sharex=ax, sharey=ax)
mpl.plot(result_numexpr, p, show=False)
plt.subplot2grid((nrows, ncols), (1, i), sharex=ax, sharey=ax)
mpl.plot(result_diff, p, show=False)
if show:
mpl.mplshow()
def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
args = vutil.common_argparse(parser)
####### test binary files
f_bin = viscid.load_file(_viscid_root + "/../sample/ath_sample.*.bin")
for i, grid in enumerate(f_bin.iter_times(":")):
plt.subplot2grid((2, 2), (0, i))
mpl.plot(grid["bx"])
plt.subplot2grid((2, 2), (1, i))
mpl.plot(grid["by"])
if args.show:
mpl.tighten()
mpl.mplshow()
plt.clf()
####### test ascii files
f_tab = viscid.load_file(_viscid_root + "/../sample/ath_sample.*.tab")
for i, grid in enumerate(f_tab.iter_times(":")):
plt.subplot2grid((2, 2), (0, i))
mpl.plot(grid["bx"])
plt.subplot2grid((2, 2), (1, i))
mpl.plot(grid["by"])
if args.show:
mpl.tighten()
mpl.mplshow()
plt.clf()
def run_div_test(fld, exact, title='', show=False, ignore_inexact=False):
t0 = time()
result_numexpr = viscid.div(fld, preferred="numexpr", only=False)
t1 = time()
logger.info("numexpr magnitude runtime: %g", t1 - t0)
result_diff = viscid.diff(result_numexpr, exact)['x=1:-1, y=1:-1, z=1:-1']
if not ignore_inexact and not (result_diff.data < 5e-5).all():
logger.warn("numexpr result is far from the exact result")
logger.info("min/max(abs(numexpr - exact)): %g / %g",
np.min(result_diff.data), np.max(result_diff.data))
planes = ["y=0f", "z=0f"]
nrows = 2
ncols = len(planes)
ax = plt.subplot2grid((nrows, ncols), (0, 0))
ax.axis("equal")
for i, p in enumerate(planes):
plt.subplot2grid((nrows, ncols), (0, i), sharex=ax, sharey=ax)
mpl.plot(result_numexpr, p, show=False)
plt.subplot2grid((nrows, ncols), (1, i), sharex=ax, sharey=ax)
mpl.plot(result_diff, p, show=False)
mpl.plt.suptitle(title)
mpl.auto_adjust_subplots(subplot_params=dict(top=0.9))
mpl.plt.savefig(next_plot_fname(__file__))
if show:
mpl.mplshow()
def main():
parser = argparse.ArgumentParser(description="Test xdmf")
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument('file', nargs="?", default=None)
args = vutil.common_argparse(parser)
# f3d = readers.load_file(_viscid_root + '/../../sample/sample.3df.xdmf')
# b3d = f3d['b']
# bx, by, bz = b3d.component_fields() # pylint: disable=W0612
if args.file is None:
args.file = "/Users/kmaynard/dev/work/cen4000/cen4000.3d.xdmf"
f3d = readers.load_file(args.file)
bx = f3d["bx"]
by = f3d["by"]
bz = f3d["bz"]
B = field.scalar_fields_to_vector([bx, by, bz], name="B_cc",
_force_layout=field.LAYOUT_INTERLACED)
t0 = time()
lines_single, topo = trace_cython(B, nr_procs=1)
t1 = time()
topo_single = vol.wrap_field(topo, name="CyTopo1")
print("single proc:", t1 - t0, "s")
nr_procs_list = np.array([1, 2, 3])
# nr_procs_list = np.array([1, 2, 3, 4, 5, 6, 7, 8])
times = np.empty_like(nr_procs_list, dtype="float")
print("always parallel overhead now...")
for i, nr_procs in enumerate(nr_procs_list):
t0 = time()
lines, topo = trace_cython(B, nr_procs=nr_procs, force_subprocess=True)
t1 = time()
fld = vol.wrap_field(topo, name="CyTopo")
same_topo = (fld.data == topo_single.data).all()
same_lines = True
for j, line in enumerate(lines):
same_lines = same_lines and (line == lines_single[j]).all()
print("nr_procs:", nr_procs, "time:", t1 - t0, "s",
"same topo:", same_topo, "same lines:", same_lines)
times[i] = t1 - t0
plt.plot(nr_procs_list, times, 'k^')
plt.plot(nr_procs_list, times[0] / nr_procs_list, 'b--')
plt.xscale("log")
plt.yscale("log")
plt.show()
if False:
cmap = plt.get_cmap('spectral')
levels = [4, 5, 6, 7, 8, 13, 14, 16, 17]
norm = BoundaryNorm(levels, cmap.N)
mpl.plot(topo_flds[-1], "y=0", cmap=cmap, norm=norm, show=False)
#mpl.plot_streamlines2d(lines[::5], "y", topology=topo[::5], show=False)
#mpl.plot_streamlines(lines, topology=topo, show=False)
mpl.mplshow()
def run_test_timeseries(f, main__file__, show=False):
mpl.clf()
ntimes = f.nr_times()
t = [None] * ntimes
pressure = np.zeros((ntimes,), dtype='f4')
for i, grid in enumerate(f.iter_times()):
t[i] = grid.time_as_datetime()
pressure[i] = grid['pp']['x=10.0f, y=0.0f, z=0.0f']
mpl.plt.plot(t, pressure)
mpl.plt.ylabel('Pressure')
dateFmt = mdates.DateFormatter('%H:%M:%S')
mpl.plt.gca().xaxis.set_major_formatter(dateFmt)
mpl.plt.gcf().autofmt_xdate()
mpl.plt.gca().grid(True)
mpl.plt.gcf().set_size_inches(8, 4)
mpl.plt.savefig(next_plot_fname(main__file__))
if show:
mpl.mplshow()
def main():
parser = argparse.ArgumentParser(description="Test xdmf")
parser.add_argument("--show", "--plot", action="store_true")
args = vutil.common_argparse(parser)
f2d = viscid.load_file(_viscid_root + '/../sample/sample.py_0.xdmf')
b2d = viscid.scalar_fields_to_vector([f2d['bx'], f2d['by'], f2d['bz']],
name="b")
bx2d, by2d, bz2d = b2d.component_fields() #pylint: disable=W0612
f3d = viscid.load_file(_viscid_root + '/../sample/sample.3df.xdmf')
b3d = f3d['b']
bx, by, bz = b3d.component_fields() #pylint: disable=W0612
nrows = 4
ncols = 2
plt.subplot2grid((nrows, ncols), (0, 0))
mpl.plot(bx, "z=0,x=:30", earth=True, show=False)
plt.subplot2grid((nrows, ncols), (1, 0))
mpl.plot(bx, "z=0.5f,x=0:2,y=-100.0f:100.0f", earth=True, show=False)
plt.subplot2grid((nrows, ncols), (2, 0))
mpl.plot(bx, "z=-1,x=-10.0f:,y=-100.0f:100.0f", earth=True, show=False)
plt.subplot2grid((nrows, ncols), (3, 0))
mpl.plot(bx, "x=0.0f,y=-5.0f:5.0f,z=-5.0f:5.0f", earth=True, show=False)
plt.subplot2grid((nrows, ncols), (0, 1))
mpl.plot(bx2d, "y=20.0f,z=-100.0f:100.0f", earth=True, show=False)
plt.subplot2grid((nrows, ncols), (1, 1))
mpl.plot(bx2d, "x=0f:20:-1,y=0.0f,z=0.0f", show=False)
plt.subplot2grid((nrows, ncols), (2, 1))
mpl.plot(bx2d, earth=True, show=False)
plt.subplot2grid((nrows, ncols), (3, 1))
mpl.plot(bx2d, "z=0.0f,x=-20.0f:0.0f", show=False)
if args.show:
mpl.mplshow()
