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#!/usr/bin/env python
The first form produces surfaces for each named DATASET in the summary H5FILE.
The second form plots DATASET1 - DATASET2*DATASET3 which can show fluctuations.
-c CSTRIDE Downsample by providing cstride=CSTRIDE to plot_surface
-f Plot fluctuating quantities using the second invocation type
-F Fluctuations as above but instantaneous NOT ensemble means
-h Display this help message and exit
-l LINEWIDTH Set a non-zero linewidth=LINEWIDTH to plot_surface
-o OUTSUFFIX Save the output file DATASET.OUTSUFFIX instead of displaying
-r RSTRIDE Downsample by providing rstride=RSTRIDE to plot_surface
-t TITLE Set the specified plot title
-C LEVELS Instead of drawing surfaces, plot LEVELS contours.
-T LO,HI Limit plot extents to /t in [LO, HI]
-Y LO,HI Limit plot extents to /y in [LO, HI]
-Z LO,HI Limit plot extents to data values in [LO, HI]
File H5FILE must have 1D /y and /t datasets to provide the meshgrid.
Each DATASET must have extents matching the /y and /t dataset sizes.
from __future__ import print_function
import getopt
import h5py
import matplotlib
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d
import numpy as np
import sys
class Usage(Exception):
def __init__(self, msg):
self.msg = msg
def surface(x, y, xyplane, kwargs={}):
fig = plt.figure()
ax = fig.gca(projection='3d')
X, Y = np.meshgrid(x, y)
plot = ax.plot_surface(X, Y, xyplane,
vmin=np.min(xyplane), vmax=np.max(xyplane),
if 'cmap' in kwargs:
cbar = fig.colorbar(plot)
cbar = None
return (fig, ax, plot, cbar)
def contour(x, y, xyplane, levels, kwargs={}):
fig = plt.figure()
ax = fig.gca()
X, Y = np.meshgrid(x, y)
plot = ax.contourf(X, Y, xyplane, levels, **kwargs)
if 'cmap' in kwargs:
cbar = fig.colorbar(plot)
cbar = None
return (fig, ax, plot, cbar)
def main(argv=None):
# Permit interactive use
if argv is None:
argv = sys.argv
# Parse and check incoming command line arguments
cstride = 1
fluct = 0
linewidth = 0
outsuffix = None
rstride = 1
levels = 0
title = None
textents = (-np.inf, np.inf)
yextents = (-np.inf, np.inf)
zextents = None
opts, args = getopt.getopt(argv[1:],
"c:fhl:o:r:t:C:FT:Y:Z:", ["help"])
except getopt.error as msg:
raise Usage(msg)
for o, a in opts:
if o == "-c":
cstride = int(a)
if o == "-f":
fluct = 1
elif o in ("-h", "--help"):
return 0
elif o == "-l":
linewidth = int(a)
elif o == "-o":
outsuffix = a
elif o == "-r":
rstride = int(a)
elif o == "-t":
title = a
elif o == "-C":
levels = int(a)
if o == "-F":
fluct = 2
elif o == "-T":
textents = tuple(float(r) for r in a.split(','))
elif o == "-Y":
yextents = tuple(float(r) for r in a.split(','))
elif o == "-Z":
zextents = tuple(float(r) for r in a.split(','))
if fluct:
if len(args) != 4:
print("Incorrect argument count. See --help.", file=sys.stderr)
return 1
if len(args) < 2:
print("Too few arguments. See --help.", file=sys.stderr)
return 1
except Usage as err:
print(err.msg, file=sys.stderr)
return 2
# Push interactive mode off (in case we get used from IPython)
was_interactive = plt.isinteractive()
# Open the HDF5 file and read extent information
# (Attempting to trim loaded data to be as small as possible)
h5file = h5py.File(args[0], 'r')
y = h5file['/y'][()]
yb = np.nonzero(y > yextents[0])[0][ 0]
ye = np.nonzero(y < yextents[1])[0][-1]
y = y[yb:ye+1]
t = h5file['/t'][()]
tb = np.nonzero(t > textents[0])[0][ 0]
te = np.nonzero(t < textents[1])[0][-1]
t = t[tb:te+1]
# Load everything, truncating any irrelevant range or values
data, name = [], []
for arg in args[1:]:
data.append(h5file[arg][tb:te+1, yb:ye+1])
if zextents:
data[-1][data[-1] < zextents[0]] = np.nan
data[-1][data[-1] > zextents[1]] = np.nan
# Compute derived fluctuating dataset, if requested
# Notice the ensemble average of the latter two is performed
if fluct:
data3, name3 = data.pop(), name.pop()
if fluct == 1: # Ensemble means
data2, name2 = np.mean(data.pop(),0), name.pop()
data1, name1 = np.mean(data.pop(),0), name.pop()
elif fluct == 2: # Instantaneous means
data2, name2 = data.pop(), name.pop()
data1, name1 = data.pop(), name.pop()
assert False, "sanity error on fluct = %d" % fluct
assert len(data) == 0
assert len(name) == 0
data.append(data1 - data2*data3)
name.append("%s-%s*%s" % (name1, name2, name3))
# Plot each dataset, annotating, and possibly saving
for dataname, dataset in zip(name, data):
if (levels == 0):
fig, ax, plot, cbar = surface(y, t, dataset, {
'cstride' : cstride
, 'rstride' : rstride
, 'cmap' :
, 'linewidth': linewidth
ax.set_xlabel('Wall-normal distance')
ax.set_ylabel('Simulation time')
fig, ax, plot, cbar = contour(t, y, dataset.transpose(), levels, {
'cmap' :
, 'linewidth': linewidth
ax.set_xlabel('Simulation time')
ax.set_ylabel('Wall-normal distance')
if title:
if outsuffix:
# If not saving, then display.
if not outsuffix:
# Pop interactive mode
if __name__ == "__main__":