def main(filename, start, count, output, write_start):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['ux','uz']
scale = 2.5
dpi = 300
title_func = lambda sim_time: r'$t = {:.3f}$'.format(sim_time)
# savename_func = lambda write: 'yubo_{:06}.png'.format(write+write_start)
def savename_func(write):
# regex parse out filename number, 10 writes per file
num_per_file = 10
write_num = (write - 1) % num_per_file
filenum = int(re.match('.*s([\d]+)\.h5', filename)[1])
suffix_num = (filenum - 1) * num_per_file + write_num
if suffix_num > 201:
suffix_num -= 9 # hard coded, one of the restores is misnumbered
print(suffix_num)
return 'yubo_{:06}.png'.format(suffix_num)
# Layout
nrows, ncols = 1, 2
image = plot_tools.Box(1, 2)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start+count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
if n==0: #ux
clim = [-0.25, 0.25]
title = r'$u_x$'
elif n==1: #uz
clim = [-0.1, 0.1]
title = r'$\Upsilon$'
plot_tools.plot_bot_3d(dset, 0, index, axes=axes, title=title, even_scale=True,clim=clim)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, y=title_height)
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def midplane(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
#tasks = ['phi','w','n','phi2','w2','n2']
tasks = ['phi', 'w', 'n', 'phi ZF', 'w ZF', 'n ZF']
scale = 2.5
dpi = 100
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'mid_{:06}.png'.format(write)
# Layout
nrows, ncols = 2, 3
image = plot_tools.Box(1, 1)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start + count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call plotting helper (dset axes: [t, x, y, z])
dset = file['tasks'][task]
logger.info('dset %s length %s' % (dset, len(dset.shape)))
#if (n > 1):
#dset = np.log10(np.absolute(dset))
#dset = file.create_dataset('log_%d' %n, data=dset)
# image_axes = (2, 1)
# data_slices = (index, slice(None), slice(None), 0)
plot_tools.plot_bot_3d(dset,
0,
index,
axes=axes,
title=task,
even_scale=True)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def main(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['uphi', 'ur', 'vorticity', 'b']
scale = 2.5
dpi = 200
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'write_{:06}.png'.format(write)
# Layout
nrows, ncols = 2, 2
image = plot_tools.Box(1, 1)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Function
def func(phimesh, rmesh, data):
xmesh = rmesh * np.cos(phimesh)
ymesh = rmesh * np.sin(phimesh)
return xmesh, ymesh, data
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start + count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
plot_tools.plot_bot_3d(dset,
0,
index,
axes=axes,
title=task,
even_scale=True,
func=func)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def main(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['p', 'b', 'u', 'w']
scale = 2
dpi = 80
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'write_{:06}.png'.format(write)
# Layout
nrows, ncols = 1, 4
image = plot_tools.Box(1, 2)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
logmag = lambda xmesh, ymesh, data: (xmesh, ymesh, np.log10(np.abs(data)))
clim = [-20, 0]
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start + count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
plot_tools.plot_bot_3d(dset,
0,
index,
axes=axes,
title=task,
func=logmag,
clim=clim)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def main(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['b', 'u', 'w']
scale = 2.5
dpi = 100
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'write_{:06}.png'.format(write)
# Layout
nrows, ncols = 3, 1
image = plot_tools.Box(4, 1)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start+count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
# if (task == 'b'):
# print('task: ' + str(task))
# print(str(dset.shape))
# plt.plot(dset[0][0])
# plt.plot(dset[0][1])
# plt.plot(dset[0][2])
# plt.plot(dset[0][3])
# plt.show()
plot_tools.plot_bot_3d(dset, 0, index, axes=axes, title=task, even_scale=True)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def midplane(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
#tasks = ['phi','w','n','phi2','w2','n2']
tasks = ['phi','w','n','phi ZF','w ZF','n ZF']
scale = 2.5
dpi = 100
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'mid_{:06}.png'.format(write)
# Layout
nrows, ncols = 2, 3
image = plot_tools.Box(1, 1)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start+count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call plotting helper (dset axes: [t, x, y, z])
dset = file['tasks'][task]
logger.info('dset %s length %s' %(dset,len(dset.shape)))
#if (n > 1):
#dset = np.log10(np.absolute(dset))
#dset = file.create_dataset('log_%d' %n, data=dset)
# image_axes = (2, 1)
# data_slices = (index, slice(None), slice(None), 0)
plot_tools.plot_bot_3d(dset,0, index, axes=axes, title=task, even_scale=True)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def main(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['vorticity']
cmap = plt.cm.RdBu_r
savename_func = lambda write: 'write_{:06}.png'.format(write)
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
dpi = 200
func = lambda phi, r, data: (r * np.cos(phi), r * np.sin(phi), data)
# Layout
nrows, ncols = 1, 1
image = plot_tools.Box(1, 1)
pad = plot_tools.Frame(0, 0, 0, 0)
margin = plot_tools.Frame(0.1, 0.1, 0.1, 0.1)
scale = 3
# Create figure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plotting loop
with h5py.File(filename, mode='r') as file:
for index in range(start, start + count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
paxes, caxes = plot_tools.plot_bot_3d(dset,
0,
index,
axes=axes,
title=task,
even_scale=True,
visible_axes=False,
func=func,
cmap=cmap)
paxes.axis('off')
caxes.cla()
caxes.axis('off')
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.4, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def main(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
#tasks = ['invRi']
tasks = ['v']
scale = 2.5
dpi = 100
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'write_{:06}.png'.format(write)
# Layout
nrows, ncols = 1, 1
image = plot_tools.Box(2,1)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start+count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
# plot_tools.plot_bot_3d(dset, 0, index, axes=axes, clim=(0,0.01),title='Inverse Richardson', even_scale=True)
plot_tools.plot_bot_3d(dset, 0, index, axes=axes, clim=(-0.2,0.2),title='Meridional Velocity (kmhr^(-1))', even_scale=True)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def main(filename, start, count, output):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['b', 'p', 'u', 'w']
scale = 2.5
dpi = 100
title_func = lambda sim_time: 't = {:.3f}'.format(sim_time)
savename_func = lambda write: 'write_{:06}.png'.format(write)
# Layout
nrows, ncols = 4, 1
image = plot_tools.Box(4, 1)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.3, 0.2, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as file:
for index in range(start, start+count):
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = file['tasks'][task]
plot_tools.plot_bot_3d(dset, 0, index, axes=axes, title=task, even_scale=True)
# Add time title
title = title_func(file['scales/sim_time'][index])
title_height = 1 - 0.5 * mfig.margin.top / mfig.fig.y
fig.suptitle(title, x=0.48, y=title_height, ha='left')
# Save figure
savename = savename_func(file['scales/write_number'][index])
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
fig.clear()
plt.close(fig)
def make_plot(axs, solver, u_op, v_op, nz=16, nx=32, scale=4):
# Plot solution
ψ = solver.state['ψ']
ψ.require_grid_space()
u = u_op.evaluate()
u.set_scales(scale)
u.require_grid_space()
v = v_op.evaluate()
v.set_scales(scale)
v.require_grid_space()
plt.sca(axs[0, 0])
plt.cla()
plot_tools.plot_bot_3d(u,
"z",
scale * nz - 1,
axes=axs[0, 0],
even_scale=True)
plt.sca(axs[0, 1])
plt.cla()
plot_tools.plot_bot_3d(v,
"z",
scale * nz - 1,
axes=axs[0, 1],
even_scale=True)
plt.sca(axs[1, 0])
plt.cla()
plot_tools.plot_bot_3d(u,
"y",
int(scale * nx / 2),
axes=axs[1, 0],
even_scale=True)
plt.sca(axs[1, 1])
plt.cla()
plot_tools.plot_bot_3d(u,
"x",
int(scale * nx / 2),
axes=axs[1, 1],
even_scale=True)
plt.pause(0.1)
def main(filename, start, count, output, write_start):
"""Save plot of specified tasks for given range of analysis writes."""
# Plot settings
tasks = ['ux', 'uz']
scale = 2.5
dpi = 300
# savename_func = lambda write: 'yubo_{:06}.png'.format(write+write_start)
def savename_func(suffix_num):
return 'yubo_{:06}'.format(suffix_num)
# Layout
nrows, ncols = 1, 2
image = plot_tools.Box(1, 2)
pad = plot_tools.Frame(0.2, 0.2, 0.1, 0.1)
margin = plot_tools.Frame(0.15, 0.15, 0.1, 0.1)
# Create multifigure
mfig = plot_tools.MultiFigure(nrows, ncols, image, pad, margin, scale)
fig = mfig.figure
# Plot writes
with h5py.File(filename, mode='r') as f:
for index in range(start, start + count):
paxes0 = None # use this to overplot text
for n, task in enumerate(tasks):
# Build subfigure axes
i, j = divmod(n, ncols)
axes = mfig.add_axes(i, j, [0, 0, 1, 1])
# Call 3D plotting helper, slicing in time
dset = f['tasks'][task]
if n == 0: #ux
clim = [-1.3, 1.3]
title = r'$u_x / \overline{U}_c$'
func = lambda xmesh, ymesh, data: (xmesh, ymesh, data /
UX_C)
elif n == 1: #U
clim = [-0.1, 0.1]
title = r'$\Upsilon \equiv \ln (\rho / \overline{\rho})$'
func = None
paxes, _ = plot_tools.plot_bot_3d(dset,
0,
index,
axes=axes,
title=title,
even_scale=True,
clim=clim,
func=func)
if paxes0 is None:
paxes0 = paxes
# shade in forcing + damping zones
x = paxes.get_xlim()
plot_zbot, plot_ztop = paxes.get_ylim()
paxes.fill_between(x, [plot_zbot, plot_zbot], [Z_BOT, Z_BOT],
alpha=0.3,
color='grey')
paxes.fill_between(x, [Z_TOP, Z_TOP], [plot_ztop, plot_ztop],
alpha=0.3,
color='grey')
paxes.fill_between(x, [Z0 + 3 * SIGMA, Z0 + 3 * SIGMA],
[Z0 - 3 * SIGMA, Z0 - 3 * SIGMA],
alpha=0.5,
color='g')
# Add time annotation
sim_time = f['scales/sim_time'][index]
time_str = '$t=%.1f/N$' % sim_time
annotation = paxes0.text(0.1, 10.8, time_str, fontsize=14)
# regex parse out filename number, 10 writes per f
num_per_file = 10
write = f['scales/write_number'][index]
write_num = (write - 1) % num_per_file
filenum = int(re.match('.*s([\d]+)\.h5', filename)[1])
suffix_num = (filenum - 1) * num_per_file + write_num
if suffix_num > 201:
suffix_num -= 9 # hard coded, one of the restores is misnumbered
print(suffix_num)
# Save figure
savename = savename_func(suffix_num)
savepath = output.joinpath(savename)
fig.savefig(str(savepath), dpi=dpi)
# if in PLOT_IDXS, change overplotted text and plot separately
try:
fig_idx = PLOT_IDXS.index(suffix_num)
annotation.remove()
print('Adding extra annotation', suffix_num)
overlay = '%s %s' % (PLOT_PREFIXES[fig_idx], time_str)
paxes0.text(0.1, 10.8, overlay, fontsize=14)
except ValueError:
# suffix_num not in PLOT_IDXS, continue
continue
fig.savefig(str(savepath) + '_labeled', dpi=dpi)
fig.clear()
plt.close(fig)
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import h5py
import numpy as np
plt.style.use('ggplot')
mpl.rcParams['font.size'] = 18
import dedalus.extras.plot_tools as dpt
from docopt import docopt
# parse arguments
args = docopt(__doc__)
var = args['--var']
datadir = args['<datapath>']
integrals = h5py.File(datadir + "/integrals/integrals.h5", "r")
fig = plt.figure(figsize=(14, 8))
st_ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
data = integrals['tasks/{}'.format(var)]
dpt.plot_bot_3d(data, 2, 0, axes=st_ax)
savefilename = datadir.rstrip('/')
savefilename = savefilename.split('/')[1]
fig.savefig('../figs/{}_var_{}_spacetime.png'.format(savefilename, var))
z = domain.grid(2, scales=scale)
X, Y = np.meshgrid(x, y)
u_surface_op = de.operators.interpolate(u, z=0)
v_surface_op = de.operators.interpolate(v, z=0)
u_surface = u_surface_op.evaluate()
u_surface.set_scales(scale)
plt.sca(axs[0, 0])
plt.pcolormesh(X, Y, u_surface['g'][:, :, -1])
#plot_tools.plot_bot_3d(u, "z", scale*nz-1, axes=axs[0, 0], even_scale=True)
plt.sca(axs[0, 1])
plot_tools.plot_bot_3d(v, "z", scale * nz - 1, axes=axs[0, 1], even_scale=True)
plt.sca(axs[1, 0])
plot_tools.plot_bot_3d(u,
"y",
int(scale * nx / 2),
axes=axs[1, 0],
even_scale=True)
plt.sca(axs[1, 1])
plot_tools.plot_bot_3d(u,
"x",
int(scale * nx / 2),
axes=axs[1, 1],
even_scale=True)
