def _getData(self):
ret = {}
if (self.dm == 2):
# Loop over all components
for cmpstr in self.comps:
tmpdat = numpy.array([[0.0] * self.ny] * self.nx)
tmpdat = [[0.0] * self.nx, [0.0] * self.ny]
(tmpdat, ierr) = fsnapshot.fplotfile_get_data_2d(
self.name, cmpstr, tmpdat)
if (ierr != 0):
sys.exit(2)
ret[cmpstr] = tmpdat
return ret
elif (self.dm == 3):
# Loop over all components
for cmpstr in self.comps:
tmpdat = numpy.array([[[0.0] * self.nz] * self.ny] * self.nx)
(tmpdat, ierr) = fsnapshot.fplotfile_get_data_3d(
self.name, cmpstr, tmpdat)
if (ierr != 0):
sys.exit(2)
ret[cmpstr] = tmpdat
return ret
else:
print('ERROR! Invalid dimension in BLPlotfile._getData()')
sys.exit(2)
def _getData(self):
ret = {}
if(self.dm == 2):
#Loop over all components
for cmpstr in self.comps:
tmpdat = numpy.array([[0.0]*self.ny]*self.nx)
tmpdat = [[0.0]*self.nx, [0.0]*self.ny]
(tmpdat, ierr) = fsnapshot.fplotfile_get_data_2d(self.name, cmpstr, tmpdat)
if(ierr != 0): sys.exit(2)
ret[cmpstr] = tmpdat
return ret
elif(self.dm == 3):
#Loop over all components
for cmpstr in self.comps:
tmpdat = numpy.array([[[0.0]*self.nz]*self.ny]*self.nx)
(tmpdat, ierr) = fsnapshot.fplotfile_get_data_3d(self.name, cmpstr, tmpdat)
if(ierr != 0): sys.exit(2)
ret[cmpstr] = tmpdat
return ret
else:
print('ERROR! Invalid dimension in BLPlotfile._getData()')
sys.exit(2)
def do_plot(plotfile, component, component2, outFile, log,
minval, maxval, minval2, maxval2, eps, dpi, origin,
annotation, particles, time_ind):
# plotfile plotfile to read data from
# component first variable to plot
# component2 optional second variable to plot
# outFile save plot as "outFile"
# log (= 1,0) plot log (base 10) of the data
# minval (float) specify minimum data range for plot
# maxval (float) specify maximum data range for plot
# eps (= 1,0) make an EPS plot instead of PNG
# dpi (int) (PNG only) make the plot with dpi value
# origin (= 1,0) (3-d only) slice through origin (0,0,0)
# annotation (2-d only) add annotation string under time
# particles (2-d only) particle data
# time_ind array index of time cooresponding to plotfile
#----------------------
# check incoming values:
#-----------------------
if (plotfile == ""):
print "\n---ERROR: plotfile not specified---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if (component == ""):
print "\n---ERROR: no component specified---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if ((log != 1) and (log != 0)):
print "\n---ERROR: invalid value for log (= 1,0)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if ((eps != 1) and (eps != 0)):
print "\n---ERROR: invalid value for eps (= 1,0)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if (minval != None):
try: minval = float(minval)
except ValueError:
print "\n---ERROR: invalid value for minval (= float)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if (maxval != None):
try: maxval = float(maxval)
except ValueError:
print "\n---ERROR: invalid value for maxval (= float)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if (minval2 != None):
try: minval2 = float(minval2)
except ValueError:
print "\n---ERROR: invalid value for minval2 (= float)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if (maxval2 != None):
try: maxval2 = float(maxval2)
except ValueError:
print "\n---ERROR: invalid value for maxval2 (= float)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if ((origin != 1) and (origin != 0)):
print "\n---ERROR: invalid value for origin (= 1,0)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
if (dpi != None):
try: dpi = int(dpi)
except ValueError:
print "\n---ERROR: invalid value for dpi (= int)---"
print " (plotsinglevar_parts.py)\n"
usage()
sys.exit(2)
#--------------------------------------------------------------------------
# construct the output file name
#--------------------------------------------------------------------------
if (outFile == ""):
outFile = os.path.normpath(plotfile) + "_" + component
if (not component2 == ""): outFile += "_" + component2
if (not eps):
outFile += ".png"
else:
outFile += ".eps"
else:
# make sure the proper extension is used
if (not eps):
if (not string.rfind(outFile, ".png") > 0):
outFile = outFile + ".png"
else:
if (not string.rfind(outFile, ".eps") > 0):
outFile = outFile + ".eps"
#--------------------------------------------------------------------------
# read in the meta-data from the plotfile
#--------------------------------------------------------------------------
(nx, ny, nz) = fsnapshot.fplotfile_get_size(plotfile)
time = fsnapshot.fplotfile_get_time(plotfile)
(xmin, xmax, ymin, ymax, zmin, zmax) = \
fsnapshot.fplotfile_get_limits(plotfile)
x = xmin + numpy.arange( (nx), dtype=numpy.float64 )*(xmax - xmin)/nx
y = ymin + numpy.arange( (ny), dtype=numpy.float64 )*(ymax - ymin)/ny
if (nz > 0):
z = zmin + numpy.arange( (nz), dtype=numpy.float64 )*(zmax - zmin)/nz
if (nz == -1):
#----------------------------------------------------------------------
# 2-d plots
#----------------------------------------------------------------------
extent = xmin, xmax, ymin, ymax
# read in the main component
data = numpy.zeros( (nx, ny), dtype=numpy.float64)
(data, err) = fsnapshot.fplotfile_get_data_2d(plotfile, component, data)
if (not err == 0):
sys.exit(2)
data = numpy.transpose(data)
if (minval == None): minval = numpy.min(data)
if (maxval == None): maxval = numpy.max(data)
# read in the component #2, if present
if (not component2 == ""):
data2 = numpy.zeros( (nx, ny), dtype=numpy.float64)
(data2, err) = fsnapshot.fplotfile_get_data_2d(plotfile, component2, data2)
if (not err == 0):
sys.exit(2)
data2 = numpy.transpose(data2)
if (minval2 == None): minval2 = numpy.min(data2)
if (maxval2 == None): maxval2 = numpy.max(data2)
if log:
data = numpy.log10(data)
if (not component2 == ""):
data2 = numpy.log10(data2)
minval2 = math.log10(minval2)
maxval2 = math.log10(maxval2)
minval = math.log10(minval)
maxval = math.log10(maxval)
#----------------------------------------------------------------------
# plot main component
#----------------------------------------------------------------------
if (not component2 == ""):
ax = pylab.subplot(1,2,1)
pylab.subplots_adjust(wspace=0.5)
else:
ax = pylab.subplot(1,1,1)
divider = mpl_toolkits.axes_grid1.make_axes_locatable(ax)
im=pylab.imshow(data,origin='lower', extent=extent, vmin=minval, vmax=maxval)
#----------------------------------------------------------------------
# plot the particle data
#----------------------------------------------------------------------
n=0
while(n < len(particles)):
# sometimes the length of particle history is larger than index
if (time_ind < len(particles[n].history)):
pylab.scatter(particles[n].history[time_ind].xyz[0],
particles[n].history[time_ind].xyz[1],
s=0.5,c='black',marker='o')
n += 1
pylab.title(component)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
# make space for a colorbar -- getting it the same size as the
# vertical extent of the plot is surprisingly tricky. See
# http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#colorbar-whose-height-or-width-in-sync-with-the-master-axes
ax_cb = divider.new_horizontal(size="10%", pad=0.1)
fig1 = ax.get_figure()
fig1.add_axes(ax_cb)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cb = pylab.colorbar(im, format=formatter, cax=ax_cb)
# make the font size for the colorbar axis labels small. Note
#----------------------------------------------------------------------
# plot component #2
#----------------------------------------------------------------------
if (not component2 == ""):
ax = pylab.subplot(1,2,2)
divider = mpl_toolkits.axes_grid1.make_axes_locatable(ax)
im = pylab.imshow(data2, origin='lower', extent=extent,
vmin=minval2, vmax=maxval2)
#----------------------------------------------------------------
# plot the particle data
#----------------------------------------------------------------
n=0
while(n < len(particles)):
# sometimes the length of particle history is larger than index
if (time_ind < len(particles[n].history)):
pylab.scatter(particles[n].history[time_ind].xyz[0],
particles[n].history[time_ind].xyz[1],
s=0.5,c='black',marker='o')
n += 1
pylab.title(component2)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
# make space for a colorbar -- getting it the same size as
# the vertical extent of the plot is surprisingly tricky.
# See
# http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#colorbar-whose-height-or-width-in-sync-with-the-master-axes
ax_cb = divider.new_horizontal(size="10%", pad=0.1)
fig1 = ax.get_figure()
fig1.add_axes(ax_cb)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cb = pylab.colorbar(im, format=formatter, cax=ax_cb)
# make the font size for the colorbar axis labels small. Note the
# offsetText is the 10^N that appears at the top of the y-axis.
cl = pylab.getp(cb.ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cb.ax.yaxis.offsetText.set_fontsize("small")
#ax_cb.yaxis.tick_right()
else:
#----------------------------------------------------------------------
# 3-d plot
#----------------------------------------------------------------------
###################################
# NOT SUPPORTED YET
###################################
print "\n\n--- ERROR: 3-d not yet implemented ---"
print " (plotsinglevar_parts.py)\n"
sys.exit(2)
# figure out the maximum width -- we will plot xy, xz, and yz
w1 = xmax - xmin # also w2
w3 = ymax - ymin
if (w3 > w1):
scale = w3
else:
scale = w1
# starting points for the figure positions
# assume that the width of the plotting area is 0.05 to 0.95,
# leaving 0.9 to be split amongst the 3 plots. So each has a
# width of 0.3
# for the height, we will assume that the colorbar at the
# bottom gets 0.15, and that we go until 0.95, leaving 0.8 of
# height for the plots.
pos1 = [0.05, 0.15, 0.3, 0.8]
pos2 = [0.35, 0.15, 0.3, 0.8]
pos3 = [0.65, 0.15, 0.3, 0.8]
fig = pylab.figure()
# x-y
extent = xmin, xmax, ymin, ymax
# read in the main component
data = numpy.zeros( (nx, ny), dtype=numpy.float64)
indir = 3
(data, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, indir, origin, data)
if (not err == 0):
sys.exit(2)
data = numpy.transpose(data)
if log:
data = numpy.log10(data)
if (not minval == None): minval = math.log10(minval)
if (not maxval == None): maxval = math.log10(maxval)
ax = pylab.subplot(1,3,1)
pylab.subplots_adjust(wspace=0.4)
#fig.add_axes(pos1)
im=pylab.imshow(data,origin='lower', extent=extent,
vmin=minval, vmax=maxval, axes=pos1)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# do a fixed offset in pixels from the (xmin,ymin) data point
fig1 = ax.get_figure()
trans=matplotlib.transforms.offset_copy(ax.transData, x=0, y=-0.5,
fig=fig1, units='inches')
pylab.text(xmin, ymin, "time = %7.3g s" % (time),
verticalalignment="bottom", transform = trans,
clip_on=False, fontsize=10)
# x-z
extent = xmin, xmax, zmin, zmax
# read in the main component
data = numpy.zeros( (nx, nz), dtype=numpy.float64)
(data, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, 2, origin, data)
if (not err == 0):
sys.exit(2)
data = numpy.transpose(data)
if log:
data = numpy.log10(data)
if (not minval == None): minval = math.log10(minval)
if (not maxval == None): maxval = math.log10(maxval)
ax = pylab.subplot(1,3,2)
#fig.add_axes(pos2)
im=pylab.imshow(data,origin='lower', extent=extent,
vmin=minval, vmax=maxval, axes=pos2)
pylab.xlabel("x")
pylab.ylabel("z")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# y-z
extent = ymin, ymax, zmin, zmax
# read in the main component
data = numpy.zeros( (ny, nz), dtype=numpy.float64)
(data, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, 1, origin, data)
if (not err == 0):
sys.exit(2)
data = numpy.transpose(data)
if log:
data = numpy.log10(data)
if (not minval == None): minval = math.log10(minval)
if (not maxval == None): maxval = math.log10(maxval)
ax = pylab.subplot(1,3,3)
#fig.add_axes(pos3)
im=pylab.imshow(data,origin='lower', extent=extent,
vmin=minval, vmax=maxval, axes=pos3)
pylab.xlabel("y")
pylab.ylabel("z")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# colorbar
pylab.subplots_adjust(bottom=0.1, left=0.05, right=0.95)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cax = pylab.axes([0.05, 0.06, 0.9, 0.04])
pylab.colorbar(orientation="horizontal", cax=cax, format=formatter)
pylab.title(component)
#--------------------------------------------------------------------------
# save the figure
#--------------------------------------------------------------------------
if (not eps):
pylab.savefig(outFile, bbox_inches='tight', dpi=dpi, pad_inches=0.33)
else:
pylab.savefig(outFile, bbox_inches='tight', pad_inches=0.33)
def do_plot(plotfile, component, component2, outFile, log, minval, maxval,
minval2, maxval2, eps, dpi, origin, annotation, xmin_pass,
ymin_pass, zmin_pass, xmax_pass, ymax_pass, zmax_pass):
pylab.rc("font", size=9)
#--------------------------------------------------------------------------
# construct the output file name
#--------------------------------------------------------------------------
if (outFile == ""):
outFile = os.path.normpath(plotfile) + "_" + component
if (not component2 == ""): outFile += "_" + component2
if (not eps):
outFile += ".png"
else:
outFile += ".eps"
else:
# make sure the proper extension is used
if (not eps):
if (not string.rfind(outFile, ".png") > 0):
outFile = outFile + ".png"
else:
if (not string.rfind(outFile, ".eps") > 0):
outFile = outFile + ".eps"
#--------------------------------------------------------------------------
# read in the meta-data from the plotfile
#--------------------------------------------------------------------------
(nx, ny, nz) = fsnapshot.fplotfile_get_size(plotfile)
time = fsnapshot.fplotfile_get_time(plotfile)
(xmin, xmax, ymin, ymax, zmin, zmax) = \
fsnapshot.fplotfile_get_limits(plotfile)
dx = (xmax - xmin) / nx
x = xmin + numpy.arange((nx), dtype=numpy.float64) * dx
dy = (ymax - ymin) / ny
y = ymin + numpy.arange((ny), dtype=numpy.float64) * dy
if (nz > 0):
dz = (zmax - zmin) / nz
z = zmin + numpy.arange((nz), dtype=numpy.float64) * dz
if (nz == -1):
#----------------------------------------------------------------------
# 2-d plots
#----------------------------------------------------------------------
extent = [xmin, xmax, ymin, ymax]
ix0 = 0
ix = nx
iy0 = 0
iy = ny
if (not xmin_pass == None):
extent[0] = xmin_pass
ix0 = int((xmin_pass - xmin) / dx)
if (not ymin_pass == None):
extent[2] = ymin_pass
iy0 = int((ymin_pass - ymin) / dy)
if (not xmax_pass == None):
extent[1] = xmax_pass
ix = int((xmax_pass - xmin) / dx)
if (not ymax_pass == None):
extent[3] = ymax_pass
iy = int((ymax_pass - ymin) / dy)
sparseX = 0
if (ny >= 3 * nx):
sparseX = 1
# read in the main component
data = numpy.zeros((nx, ny), dtype=numpy.float64)
(data, err) = fsnapshot.fplotfile_get_data_2d(plotfile, component,
data)
if (not err == 0):
sys.exit(2)
data = numpy.transpose(data)
# read in the component #2, if present
if (not component2 == ""):
data2 = numpy.zeros((nx, ny), dtype=numpy.float64)
(data2,
err) = fsnapshot.fplotfile_get_data_2d(plotfile, component2,
data2)
if (not err == 0):
sys.exit(2)
data2 = numpy.transpose(data2)
# log?
if log:
if (numpy.min(data) < 0):
data = numpy.log10(numpy.abs(data))
else:
data = numpy.log10(data)
if (not component2 == ""):
if (numpy.min(data2) < 0.0):
data2 = numpy.log10(numpy.abs(data2))
else:
data2 = numpy.log10(data2)
if (not minval == None): minval = math.log10(minval)
if (not maxval == None): maxval = math.log10(maxval)
if (not minval2 == None): minval2 = math.log10(minval2)
if (not maxval2 == None): maxval2 = math.log10(maxval2)
#----------------------------------------------------------------------
# plot main component
#----------------------------------------------------------------------
if (not component2 == ""):
ax = pylab.subplot(1, 2, 1)
pylab.subplots_adjust(wspace=0.5)
else:
ax = pylab.subplot(1, 1, 1)
divider = mpl_toolkits.axes_grid1.make_axes_locatable(ax)
im = pylab.imshow(data[iy0:iy, ix0:ix],
origin='lower',
extent=extent,
vmin=minval,
vmax=maxval)
pylab.title(component)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
if (sparseX):
ax.xaxis.set_major_locator(pylab.MaxNLocator(3))
# make space for a colorbar -- getting it the same size as the
# vertical extent of the plot is surprisingly tricky. See
# http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#colorbar-whose-height-or-width-in-sync-with-the-master-axes
ax_cb = divider.new_horizontal(size="10%", pad=0.1)
fig1 = ax.get_figure()
fig1.add_axes(ax_cb)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cb = pylab.colorbar(im, format=formatter, cax=ax_cb)
# make the font size for the colorbar axis labels small. Note
# the offsetText is the 10^N that appears at the top of the
# y-axis.
cl = pylab.getp(cb.ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cb.ax.yaxis.offsetText.set_fontsize("small")
# do a fixed offset in pixels from the (xmin,ymin) data point
trans = matplotlib.transforms.offset_copy(ax.transData,
x=0,
y=-0.5,
fig=fig1,
units='inches')
pylab.text(xmin,
ymin,
"time = %7.3g s" % (time),
verticalalignment="bottom",
transform=trans,
clip_on=False,
fontsize=10)
if (not annotation == ""):
trans = matplotlib.transforms.offset_copy(ax.transData,
x=0,
y=-0.65,
fig=fig1,
units='inches')
pylab.text(xmin,
ymin,
"%s" % (annotation),
verticalalignment="bottom",
transform=trans,
clip_on=False,
fontsize=10)
#----------------------------------------------------------------------
# plot component #2
#----------------------------------------------------------------------
if (not component2 == ""):
ax = pylab.subplot(1, 2, 2)
divider = mpl_toolkits.axes_grid1.make_axes_locatable(ax)
im = pylab.imshow(data2[iy0:iy, ix0:ix],
origin='lower',
extent=extent,
vmin=minval2,
vmax=maxval2)
pylab.title(component2)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax.xaxis.set_major_formatter(
pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(
pylab.ScalarFormatter(useMathText=True))
if (sparseX):
ax.xaxis.set_major_locator(pylab.MaxNLocator(3))
# make space for a colorbar -- getting it the same size as
# the vertical extent of the plot is surprisingly tricky.
# See
# http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#colorbar-whose-height-or-width-in-sync-with-the-master-axes
ax_cb = divider.new_horizontal(size="10%", pad=0.1)
fig1 = ax.get_figure()
fig1.add_axes(ax_cb)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cb = pylab.colorbar(im, format=formatter, cax=ax_cb)
# make the font size for the colorbar axis labels small. Note the
# offsetText is the 10^N that appears at the top of the y-axis.
cl = pylab.getp(cb.ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cb.ax.yaxis.offsetText.set_fontsize("small")
#ax_cb.yaxis.tick_right()
else:
#----------------------------------------------------------------------
# 3-d plot
#----------------------------------------------------------------------
# starting points for the figure positions
# assume that the width of the plotting area is 0.05 to 0.95,
# leaving 0.9 to be split amongst the 3 plots. So each has a
# width of 0.3
# for the height, we will assume that the colorbar at the
# bottom gets 0.15, and that we go until 0.95, leaving 0.8 of
# height for the plots.
pos1 = [0.05, 0.15, 0.3, 0.8]
pos2 = [0.35, 0.15, 0.3, 0.8]
pos3 = [0.65, 0.15, 0.3, 0.8]
fig = pylab.figure()
# read in the slices
# x-y
data_xy = numpy.zeros((nx, ny), dtype=numpy.float64)
indir = 3
(data_xy, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, indir,
origin, data_xy)
if (not err == 0):
sys.exit(2)
data_xy = numpy.transpose(data_xy)
if log:
if (numpy.min(data_xy) < 0):
data_xy = numpy.log10(numpy.abs(data_xy))
else:
data_xy = numpy.log10(data_xy)
# x-z
data_xz = numpy.zeros((nx, nz), dtype=numpy.float64)
(data_xz, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, 2,
origin, data_xz)
if (not err == 0):
sys.exit(2)
data_xz = numpy.transpose(data_xz)
if log:
if (numpy.min(data_xz) < 0):
data_xz = numpy.log10(numpy.abs(data_xz))
else:
data_xz = numpy.log10(data_xz)
# y-z
data_yz = numpy.zeros((ny, nz), dtype=numpy.float64)
(data_yz, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, 1,
origin, data_yz)
if (not err == 0):
sys.exit(2)
data_yz = numpy.transpose(data_yz)
if log:
if (numpy.min(data_yz) < 0):
data_yz = numpy.log10(numpy.abs(data_yz))
else:
data_yz = numpy.log10(data_yz)
if (not minval == None):
if (log):
minval = math.log10(minval)
else:
minval = numpy.min(data_xy)
minval = min(minval, numpy.min(data_xz))
minval = min(minval, numpy.min(data_yz))
if (not maxval == None):
if (log):
maxval = math.log10(maxval)
else:
maxval = numpy.max(data_xy)
maxval = max(maxval, numpy.max(data_xz))
maxval = max(maxval, numpy.max(data_yz))
# x-y
extent = [xmin, xmax, ymin, ymax]
ix0 = 0
ix = nx
iy0 = 0
iy = ny
if (not xmin_pass == None):
extent[0] = xmin_pass
ix0 = int((xmin_pass - xmin) / dx)
if (not ymin_pass == None):
extent[2] = ymin_pass
iy0 = int((ymin_pass - ymin) / dy)
if (not xmax_pass == None):
extent[1] = xmax_pass
ix = int((xmax_pass - xmin) / dx)
if (not ymax_pass == None):
extent[3] = ymax_pass
iy = int((ymax_pass - ymin) / dy)
ax = pylab.subplot(1, 3, 1)
pylab.subplots_adjust(wspace=0.4)
#fig.add_axes(pos1)
im = pylab.imshow(data_xy[iy0:iy, ix0:ix],
origin='lower',
extent=extent,
vmin=minval,
vmax=maxval,
axes=pos1)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# do a fixed offset in pixels from the (xmin,ymin) data point
fig1 = ax.get_figure()
trans = matplotlib.transforms.offset_copy(ax.transData,
x=0,
y=-0.5,
fig=fig1,
units='inches')
# pylab.text(xmin_pass, ymin_pass, "time = %7.3g s" % (time),
# verticalalignment="bottom", transform = trans,
# clip_on=False, fontsize=10)
# x-z
extent = [xmin, xmax, zmin, zmax]
ix0 = 0
ix = nx
iz0 = 0
iz = nz
if (not xmin_pass == None):
extent[0] = xmin_pass
ix0 = int((xmin_pass - xmin) / dx)
if (not zmin_pass == None):
extent[2] = zmin_pass
iz0 = int((zmin_pass - zmin) / dz)
if (not xmax_pass == None):
extent[1] = xmax_pass
ix = int((xmax_pass - xmin) / dx)
if (not zmax_pass == None):
extent[3] = zmax_pass
iz = int((zmax_pass - zmin) / dz)
ax = pylab.subplot(1, 3, 2)
#fig.add_axes(pos2)
im = pylab.imshow(data_xz[iz0:iz, ix0:ix],
origin='lower',
extent=extent,
vmin=minval,
vmax=maxval,
axes=pos2)
pylab.xlabel("x")
pylab.ylabel("z")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# y-z
extent = [ymin, ymax, zmin, zmax]
iy0 = 0
iy = ny
iz0 = 0
iz = nz
if (not ymin_pass == None):
extent[0] = ymin_pass
iy0 = int((ymin_pass - ymin) / dy)
if (not zmin_pass == None):
extent[2] = zmin_pass
iz0 = int((zmin_pass - zmin) / dz)
if (not ymax_pass == None):
extent[1] = ymax_pass
iy = int((ymax_pass - ymin) / dy)
if (not zmax_pass == None):
extent[3] = zmax_pass
iz = int((zmax_pass - zmin) / dz)
ax = pylab.subplot(1, 3, 3)
#fig.add_axes(pos3)
im = pylab.imshow(data_yz[iz0:iz, iy0:iy],
origin='lower',
extent=extent,
vmin=minval,
vmax=maxval,
axes=pos3)
pylab.xlabel("y")
pylab.ylabel("z")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# colorbar
pylab.subplots_adjust(bottom=0.1, left=0.05, right=0.95)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cax = pylab.axes([0.05, 0.06, 0.9, 0.04])
pylab.colorbar(orientation="horizontal", cax=cax, format=formatter)
pylab.title(component)
#--------------------------------------------------------------------------
# save the figure
#--------------------------------------------------------------------------
# try: pylab.tight_layout() # requires matplotlib >= 1.1
# except:
# pass
if (not eps):
pylab.savefig(outFile, bbox_inches='tight', dpi=dpi, pad_inches=0.33)
else:
pylab.savefig(outFile) #, bbox_inches='tight', pad_inches=0.33)
def do_plot(plotfile, component, component2, outFile, log,
minval, maxval, minval2, maxval2, eps, dpi, origin, annotation,
xmin_pass, ymin_pass, zmin_pass, xmax_pass, ymax_pass, zmax_pass):
pylab.rc("font", size=9)
#--------------------------------------------------------------------------
# construct the output file name
#--------------------------------------------------------------------------
if (outFile == ""):
outFile = os.path.normpath(plotfile) + "_" + component
if (not component2 == ""): outFile += "_" + component2
if (not eps):
outFile += ".png"
else:
outFile += ".eps"
else:
# make sure the proper extension is used
if (not eps):
if (not string.rfind(outFile, ".png") > 0):
outFile = outFile + ".png"
else:
if (not string.rfind(outFile, ".eps") > 0):
outFile = outFile + ".eps"
#--------------------------------------------------------------------------
# read in the meta-data from the plotfile
#--------------------------------------------------------------------------
(nx, ny, nz) = fsnapshot.fplotfile_get_size(plotfile)
time = fsnapshot.fplotfile_get_time(plotfile)
(xmin, xmax, ymin, ymax, zmin, zmax) = \
fsnapshot.fplotfile_get_limits(plotfile)
dx = (xmax - xmin)/nx
x = xmin + numpy.arange( (nx), dtype=numpy.float64 )*dx
dy = (ymax - ymin)/ny
y = ymin + numpy.arange( (ny), dtype=numpy.float64 )*dy
if (nz > 0):
dz = (zmax - zmin)/nz
z = zmin + numpy.arange( (nz), dtype=numpy.float64 )*dz
if (nz == -1):
#----------------------------------------------------------------------
# 2-d plots
#----------------------------------------------------------------------
extent = [xmin, xmax, ymin, ymax]
ix0 = 0
ix = nx
iy0 = 0
iy = ny
if (not xmin_pass == None):
extent[0] = xmin_pass
ix0 = int((xmin_pass - xmin)/dx)
if (not ymin_pass == None):
extent[2] = ymin_pass
iy0 = int((ymin_pass - ymin)/dy)
if (not xmax_pass == None):
extent[1] = xmax_pass
ix = int((xmax_pass - xmin)/dx)
if (not ymax_pass == None):
extent[3] = ymax_pass
iy = int((ymax_pass - ymin)/dy)
sparseX = 0
if (ny >= 3*nx):
sparseX = 1
# read in the main component
data = numpy.zeros( (nx, ny), dtype=numpy.float64)
(data, err) = fsnapshot.fplotfile_get_data_2d(plotfile, component, data)
if (not err == 0):
sys.exit(2)
data = numpy.transpose(data)
# read in the component #2, if present
if (not component2 == ""):
data2 = numpy.zeros( (nx, ny), dtype=numpy.float64)
(data2, err) = fsnapshot.fplotfile_get_data_2d(plotfile, component2, data2)
if (not err == 0):
sys.exit(2)
data2 = numpy.transpose(data2)
# log?
if log:
if (numpy.min(data) < 0):
data = numpy.log10(numpy.abs(data))
else:
data = numpy.log10(data)
if (not component2 == ""):
if (numpy.min(data2) < 0.0):
data2 = numpy.log10(numpy.abs(data2))
else:
data2 = numpy.log10(data2)
if (not minval == None): minval = math.log10(minval)
if (not maxval == None): maxval = math.log10(maxval)
if (not minval2 == None): minval2 = math.log10(minval2)
if (not maxval2 == None): maxval2 = math.log10(maxval2)
#----------------------------------------------------------------------
# plot main component
#----------------------------------------------------------------------
if (not component2 == ""):
ax = pylab.subplot(1,2,1)
pylab.subplots_adjust(wspace=0.5)
else:
ax = pylab.subplot(1,1,1)
divider = mpl_toolkits.axes_grid1.make_axes_locatable(ax)
im=pylab.imshow(data[iy0:iy,ix0:ix],origin='lower', extent=extent, vmin=minval, vmax=maxval)
pylab.title(component)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
if (sparseX):
ax.xaxis.set_major_locator(pylab.MaxNLocator(3))
# make space for a colorbar -- getting it the same size as the
# vertical extent of the plot is surprisingly tricky. See
# http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#colorbar-whose-height-or-width-in-sync-with-the-master-axes
ax_cb = divider.new_horizontal(size="10%", pad=0.1)
fig1 = ax.get_figure()
fig1.add_axes(ax_cb)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cb = pylab.colorbar(im, format=formatter, cax=ax_cb)
# make the font size for the colorbar axis labels small. Note
# the offsetText is the 10^N that appears at the top of the
# y-axis.
cl = pylab.getp(cb.ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cb.ax.yaxis.offsetText.set_fontsize("small")
# do a fixed offset in pixels from the (xmin,ymin) data point
trans=matplotlib.transforms.offset_copy(ax.transData, x=0, y=-0.5,
fig=fig1, units='inches')
pylab.text(xmin, ymin, "time = %7.3g s" % (time),
verticalalignment="bottom", transform = trans,
clip_on=False, fontsize=10)
if (not annotation == ""):
trans=matplotlib.transforms.offset_copy(ax.transData, x=0, y=-0.65,
fig=fig1, units='inches')
pylab.text(xmin, ymin, "%s" % (annotation),
verticalalignment="bottom", transform = trans,
clip_on=False, fontsize=10)
#----------------------------------------------------------------------
# plot component #2
#----------------------------------------------------------------------
if (not component2 == ""):
ax = pylab.subplot(1,2,2)
divider = mpl_toolkits.axes_grid1.make_axes_locatable(ax)
im = pylab.imshow(data2[iy0:iy,ix0:ix], origin='lower', extent=extent,
vmin=minval2, vmax=maxval2)
pylab.title(component2)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
if (sparseX):
ax.xaxis.set_major_locator(pylab.MaxNLocator(3))
# make space for a colorbar -- getting it the same size as
# the vertical extent of the plot is surprisingly tricky.
# See
# http://matplotlib.sourceforge.net/mpl_toolkits/axes_grid/users/overview.html#colorbar-whose-height-or-width-in-sync-with-the-master-axes
ax_cb = divider.new_horizontal(size="10%", pad=0.1)
fig1 = ax.get_figure()
fig1.add_axes(ax_cb)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cb = pylab.colorbar(im, format=formatter, cax=ax_cb)
# make the font size for the colorbar axis labels small. Note the
# offsetText is the 10^N that appears at the top of the y-axis.
cl = pylab.getp(cb.ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cb.ax.yaxis.offsetText.set_fontsize("small")
#ax_cb.yaxis.tick_right()
else:
#----------------------------------------------------------------------
# 3-d plot
#----------------------------------------------------------------------
# starting points for the figure positions
# assume that the width of the plotting area is 0.05 to 0.95,
# leaving 0.9 to be split amongst the 3 plots. So each has a
# width of 0.3
# for the height, we will assume that the colorbar at the
# bottom gets 0.15, and that we go until 0.95, leaving 0.8 of
# height for the plots.
pos1 = [0.05, 0.15, 0.3, 0.8]
pos2 = [0.35, 0.15, 0.3, 0.8]
pos3 = [0.65, 0.15, 0.3, 0.8]
fig = pylab.figure()
# read in the slices
# x-y
data_xy = numpy.zeros( (nx, ny), dtype=numpy.float64)
indir = 3
(data_xy, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, indir,
origin, data_xy)
if (not err == 0):
sys.exit(2)
data_xy = numpy.transpose(data_xy)
if log:
if (numpy.min(data_xy) < 0):
data_xy = numpy.log10(numpy.abs(data_xy))
else:
data_xy = numpy.log10(data_xy)
# x-z
data_xz = numpy.zeros( (nx, nz), dtype=numpy.float64)
(data_xz, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, 2,
origin, data_xz)
if (not err == 0):
sys.exit(2)
data_xz = numpy.transpose(data_xz)
if log:
if (numpy.min(data_xz) < 0):
data_xz = numpy.log10(numpy.abs(data_xz))
else:
data_xz = numpy.log10(data_xz)
# y-z
data_yz = numpy.zeros( (ny, nz), dtype=numpy.float64)
(data_yz, err) = \
fsnapshot.fplotfile_get_data_3d(plotfile, component, 1,
origin, data_yz)
if (not err == 0):
sys.exit(2)
data_yz = numpy.transpose(data_yz)
if log:
if (numpy.min(data_yz) < 0):
data_yz = numpy.log10(numpy.abs(data_yz))
else:
data_yz = numpy.log10(data_yz)
if (not minval == None):
if (log):
minval = math.log10(minval)
else:
minval = numpy.min(data_xy)
minval = min(minval,numpy.min(data_xz))
minval = min(minval,numpy.min(data_yz))
if (not maxval == None):
if (log):
maxval = math.log10(maxval)
else:
maxval = numpy.max(data_xy)
maxval = max(maxval,numpy.max(data_xz))
maxval = max(maxval,numpy.max(data_yz))
# x-y
extent = [xmin, xmax, ymin, ymax]
ix0 = 0
ix = nx
iy0 = 0
iy = ny
if (not xmin_pass == None):
extent[0] = xmin_pass
ix0 = int((xmin_pass - xmin)/dx)
if (not ymin_pass == None):
extent[2] = ymin_pass
iy0 = int((ymin_pass - ymin)/dy)
if (not xmax_pass == None):
extent[1] = xmax_pass
ix = int((xmax_pass - xmin)/dx)
if (not ymax_pass == None):
extent[3] = ymax_pass
iy = int((ymax_pass - ymin)/dy)
ax = pylab.subplot(1,3,1)
pylab.subplots_adjust(wspace=0.4)
#fig.add_axes(pos1)
im=pylab.imshow(data_xy[iy0:iy,ix0:ix],origin='lower', extent=extent,
vmin=minval, vmax=maxval, axes=pos1)
pylab.xlabel("x")
pylab.ylabel("y")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# do a fixed offset in pixels from the (xmin,ymin) data point
fig1 = ax.get_figure()
trans=matplotlib.transforms.offset_copy(ax.transData, x=0, y=-0.5,
fig=fig1, units='inches')
# pylab.text(xmin_pass, ymin_pass, "time = %7.3g s" % (time),
# verticalalignment="bottom", transform = trans,
# clip_on=False, fontsize=10)
# x-z
extent = [xmin, xmax, zmin, zmax]
ix0 = 0
ix = nx
iz0 = 0
iz = nz
if (not xmin_pass == None):
extent[0] = xmin_pass
ix0 = int((xmin_pass - xmin)/dx)
if (not zmin_pass == None):
extent[2] = zmin_pass
iz0 = int((zmin_pass - zmin)/dz)
if (not xmax_pass == None):
extent[1] = xmax_pass
ix = int((xmax_pass - xmin)/dx)
if (not zmax_pass == None):
extent[3] = zmax_pass
iz = int((zmax_pass - zmin)/dz)
ax = pylab.subplot(1,3,2)
#fig.add_axes(pos2)
im=pylab.imshow(data_xz[iz0:iz,ix0:ix],origin='lower', extent=extent,
vmin=minval, vmax=maxval, axes=pos2)
pylab.xlabel("x")
pylab.ylabel("z")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# y-z
extent = [ymin, ymax, zmin, zmax]
iy0 = 0
iy = ny
iz0 = 0
iz = nz
if (not ymin_pass == None):
extent[0] = ymin_pass
iy0 = int((ymin_pass - ymin)/dy)
if (not zmin_pass == None):
extent[2] = zmin_pass
iz0 = int((zmin_pass - zmin)/dz)
if (not ymax_pass == None):
extent[1] = ymax_pass
iy = int((ymax_pass - ymin)/dy)
if (not zmax_pass == None):
extent[3] = zmax_pass
iz = int((zmax_pass - zmin)/dz)
ax = pylab.subplot(1,3,3)
#fig.add_axes(pos3)
im=pylab.imshow(data_yz[iz0:iz,iy0:iy],origin='lower', extent=extent,
vmin=minval, vmax=maxval, axes=pos3)
pylab.xlabel("y")
pylab.ylabel("z")
# axis labels in scientific notation with LaTeX
ax = pylab.gca()
ax.xaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.yaxis.set_major_formatter(pylab.ScalarFormatter(useMathText=True))
ax.xaxis.offsetText.set_fontsize("small")
ax.yaxis.offsetText.set_fontsize("small")
cl = pylab.getp(ax, 'ymajorticklabels')
pylab.setp(cl, fontsize=10)
cl = pylab.getp(ax, 'xmajorticklabels')
pylab.setp(cl, fontsize=10)
# colorbar
pylab.subplots_adjust(bottom=0.1, left=0.05, right=0.95)
formatter = matplotlib.ticker.ScalarFormatter(useMathText=True)
cax = pylab.axes([0.05, 0.06, 0.9, 0.04])
pylab.colorbar(orientation="horizontal", cax=cax, format=formatter)
pylab.title(component)
#--------------------------------------------------------------------------
# save the figure
#--------------------------------------------------------------------------
# try: pylab.tight_layout() # requires matplotlib >= 1.1
# except:
# pass
if (not eps):
pylab.savefig(outFile, bbox_inches='tight', dpi=dpi, pad_inches=0.33)
else:
pylab.savefig(outFile)#, bbox_inches='tight', pad_inches=0.33)