def plot1d(data, var='rho', direction='x', xpos=None, ypos=None, zpos=None \
, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=None \
, physUnit=True, physTick=True, log=False, save=False \
, *args, **kwargs):
"""plot1d function to plot variables in a 1D DUMSES-Hybrid simulation
Usage:
plot1d(data [, var, direction, xpos, ypos, zpos, xmin, xmax, xmin, xmax, zmin, zmax, physUnit, physTick, log, save, *args, **kwargs])
With:
data a DumsesData object
var a variable or list of variables to plot
direction direction in which to plot, in {'x', 'y', 'z'}
xpos position of the slice in the x-direction. Default: None
ypos position of the slice in the y-direction. Default: None
zpos position of the slice in the z-direction. Default: None
xmin lower x-boundary of the plot
xmax upper x-boundary of the plot
ymin lower y-boundary of the plot
ymax upper y-boundary of the plot
zmin lower z-boundary of the plot
zmax upper z-boundary of the plot
physUnit if True, use physical units for positions and boundaries
physTick if True, use physical units for plotting
log if True, plot in logscale
save if True, save the plot in PNG, PDF and EPS
"""
# Ensure that data is a DumsesData object
try:
assert (isinstance(data, dp.DumsesData))
except AssertionError:
print("Error: 'data' must be a DumsesData object!")
sys.exit(42)
dictDat = dp.dictionarize(data)
if var == "all":
var = dictDat.keys()
if "Brx" in var:
var.remove("Brx")
var.remove("Bry")
var.remove("Brz")
if not isinstance(var, list): var = [var]
try:
assert (direction in ['x', 'y', 'z'])
except AssertionError:
print("Error: direction must be in {'x', 'y', 'z'}")
sys.exit(42)
# Determine the position, the boundaries and the labels of the plot
if direction == "x":
xdir = True
ydir = False
zdir = False
elif direction == "y":
xdir = False
ydir = True
zdir = False
else:
xdir = False
ydir = False
zdir = True
if xdir:
try:
assert (data.nx > 1)
except AssertionError:
print(
'Error: you should specify another direction for your plot (xdim = 1)'
)
sys.exit(42)
try:
assert (xpos == None)
except AssertionError:
print(
"Error: you cannot specify 'xpos' in a plot in the x-direction"
)
sys.exit(42)
if physUnit:
if xmin: xmin = findPosition(xmin, data.x)
if xmax: xmax = findPosition(xmax, data.x)
if not xmin: xmin = 0
if not xmax: xmax = dictDat[dictDat.keys()[0]].shape[0]
if physTick:
xlab = "x/H"
xlim = (data.x[xmin], data.x[xmax - 1])
xplot = data.x[xmin:xmax]
else:
xlab = "x"
xlim = (xmin, xmax - 1)
else:
xmin = 0
xmax = 1
if ydir:
try:
assert (data.ny > 1)
except AssertionError:
print(
'Error: you should specify another direction for your plot (ydim = 1)'
)
sys.exit(42)
try:
assert (ypos == None)
except AssertionError:
print(
"Error: you cannot specify 'ypos' in a plot in the y-direction"
)
sys.exit(42)
if physUnit:
if ymin: ymin = findPosition(ymin, data.y)
if ymax: ymax = findPosition(ymax, data.y)
if not ymin: ymin = 0
if not ymax: ymax = dictDat[dictDat.keys()[0]].shape[1]
if physTick:
xlab = "y/H"
xlim = (data.y[ymin], data.y[ymax - 1])
xplot = data.y[ymin:ymax]
else:
xlab = "y"
xlim = (ymin, ymax - 1)
else:
ymin = 0
ymax = 1
if zdir:
try:
assert (data.nz > 1)
except AssertionError:
print(
'Error: you should specify another direction for your plot (zdim = 1)'
)
sys.exit(42)
try:
assert (zpos == None)
except AssertionError:
print(
"Error: you cannot specify 'zpos' in a plot in the z-direction"
)
sys.exit(42)
if physUnit:
if zmin: zmin = findPosition(zmin, data.z)
if zmax: zmax = findPosition(zmax, data.z)
if not zmin: zmin = 0
if not zmax: zmax = dictDat[dictDat.keys()[0]].shape[2]
if physTick:
xlab = "z/H"
xlim = (data.z[zmin], data.z[zmin - 1])
xplot = data.z[zmin:zmax]
else:
xlab = "z"
xlim = (zmin, zmax - 1)
else:
zmin = 0
zmax = 1
ldim = np.array([xmax - xmin, ymax - ymin, zmax - zmin])
ldim = ldim[ldim > 1]
try:
assert (ldim.size == 1)
except AssertionError:
print('Error: Wrong dimensions! Check your {x,y,z} boundaries.')
sys.exit(42)
if xpos:
if physUnit:
xmin = findPosition(xpos, data.x)
else:
xmin = xpos
xmax = xmin + 1
if ypos:
if physUnit:
ymin = findPosition(ypos, data.y)
else:
ymin = ypos
ymax = ymin + 1
if zpos:
if physUnit:
zmin = findPosition(zpos, data.z)
else:
zmin = zpos
zmax = zmin + 1
try:
assert (xmax <= data.x.shape[0])
except AssertionError:
print('Error: the position provided does not fit the data')
print('xmax > dimx(data)')
sys.exit(42)
try:
assert (ymax <= data.y.shape[0])
except AssertionError:
print('Error: the position provided does not fit the data')
print('ymax > dimy(data)')
sys.exit(42)
try:
assert (zmax <= data.z.shape[0])
except AssertionError:
print('Error: the position provided does not fit the data')
print('zmax > dimz(data)')
sys.exit(42)
# Define array of figure
fig, ax = pl.subplots(len(var), 1, figsize=(6, 3.5 * len(var)))
if not isinstance(ax, np.ndarray): ax = np.array([ax])
for i, cvar in enumerate(var):
if cvar == "rho":
title = r"$\rho$"
elif "rhou" in cvar:
title = r"$\rho v_" + cvar[-1] + "$"
elif "B" in cvar:
title = "B$_" + cvar[-1] + "$"
else:
title = cvar
if log: title = "log(" + title + ")"
ax[i].set_title(title)
if (i == len(var) - 1): ax[i].set_xlabel(xlab)
datPlot = dictDat[cvar][xmin:xmax, ymin:ymax, zmin:zmax].reshape(ldim)
if physTick:
if log:
ax[i].semilogy(xplot, datPlot, *args, **kwargs)
else:
ax[i].plot(xplot, datPlot, *args, **kwargs)
else:
if log:
ax[i].semilogy(datPlot, *args, **kwargs)
else:
ax[i].plot(datPlot, *args, **kwargs)
ax[i].set_xlim(xlim)
ax[i].xaxis.set_major_locator(mp.ticker.MaxNLocator(5))
ax[i].yaxis.set_major_locator(mp.ticker.MaxNLocator(4))
fig.tight_layout()
if save:
basename = "snapshot_"
for format_ in ['png', 'pdf', 'eps']:
pl.savefig(basename + "".join(name[:3].title() for name in var) \
+ "." + format_)
else:
pl.show()
def comp(ndump, var="rho", dir1="old/", dir2="new/", xmin=None, xmax=None \
, ymin=None, ymax=None, zmin=0, zmax=1, ratio=False, save=False \
, *args, **kwargs):
"""Compare two outputs from two different DUMSES runs.
Usage:
comp(ndump, [var=var, dir1=dir1, dir2=dir2, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax, zmin=zmin, zmax=zmax, ratio=ratio])
With:
ndump index of the output to read
var name (or list of names) of variable to plot. Use the keyword 'all' to plot all the fields. Default: 'rho'
dir1 directory of the first DUMSES output to read. Default: 'old/'
dir2 directory of the second DUMSES output to read. Default: 'new/'
xmin, xmax boundaries of the domain to plot in the x-direction. Default: None
ymin, ymax boundaries of the domain to plot in the y-direction. Default: None
zmin, zmax boundaries of the domain to plot in the x-direction. Default: 0, 1
ratio set to 'True' to plot the ratio of each field. Default: False
save set to 'True' to save the plot in PNG, PDF and EPS formats
Examples:
comp(42)
comp(42, 'all', dir1="ot/oacc/", dir2="ot/ompi/")
comp(42, ['rho', 'Bx', 'E'], xmin=0, xmax=1, zmin=0, zmax=16)
"""
do = dp.DumsesData()
do.load(ndump, dir1)
dn = dp.DumsesData()
dn.load(ndump, dir2)
dod = dp.dictionarize(do)
dnd = dp.dictionarize(dn)
if var == "all":
var = dod.keys()
if "Brx" in var:
var.remove("Brx")
var.remove("Bry")
var.remove("Brz")
if not isinstance(var, list): var = [var]
if not xmin: xmin = 0
if not xmax: xmax = dod[dod.keys()[0]].shape[0]
if not ymin: ymin = 0
if not ymax: ymax = dod[dod.keys()[0]].shape[1]
if not zmin: zmin = 0
if not zmax: zmax = dod[dod.keys()[0]].shape[2]
ldim = np.array([xmax - xmin, ymax - ymin, zmax - zmin])
ldim = ldim[ldim > 1]
try:
assert(ldim.size == 2)
except AssertionError:
print('Error: Wrong dimensions! Check your {x,y,z} boundaries.')
sys.exit(42)
xdim, ydim = ldim
if zmax - zmin == 1:
xlab = "x"
ylab = "y"
if ymax - ymin == 1:
xlab = "x"
ylab = "z"
if xmax - xmin == 1:
xlab = "y"
ylab = "z"
if ratio:
fig, ax = pl.subplots(3, len(var), figsize=(3.5*len(var),6))
else:
fig, ax = pl.subplots(2, len(var), figsize=(4.*len(var),6))
pl.subplots_adjust(hspace=0.5)
if len(ax.shape) == 1: ax = ax[:, np.newaxis]
for i, cvar in enumerate(var):
if cvar == "rho":
title = r"$\rho$"
elif "rhou" in cvar:
title = r"$\rho v_" + cvar[-1] + "$"
elif "B" in cvar:
title = "B$_" + cvar[-1] + "$"
else:
title = cvar
dop = dod[cvar][xmin:xmax,ymin:ymax,zmin:zmax].reshape((xdim, ydim))
ax[0,i].set_title(title)
if i == 0: ax[0,i].set_ylabel(ylab)
map1 = ax[0,i].imshow(dop, origin='lower', *args, **kwargs)
ax[0,i].xaxis.set_major_locator(mp.ticker.MaxNLocator(4))
ax[0,i].yaxis.set_major_locator(mp.ticker.MaxNLocator(4))
fig.colorbar(map1, ax=ax[0,i])
dnp = dnd[cvar][xmin:xmax,ymin:ymax,zmin:zmax].reshape((xdim, ydim))
if i == 0: ax[1,i].set_ylabel(ylab)
map2 = ax[1,i].imshow(dnp, origin='lower', *args, **kwargs)
ax[1,i].xaxis.set_major_locator(mp.ticker.MaxNLocator(4))
ax[1,i].yaxis.set_major_locator(mp.ticker.MaxNLocator(4))
fig.colorbar(map2, ax=ax[1,i])
if ratio:
if i == 0: ax[2,i].set_ylabel(ylab)
ax[2,i].set_xlabel(xlab)
map3 = ax[2,i].imshow(dnp/dop, origin='lower', *args, **kwargs)
ax[2,i].xaxis.set_major_locator(mp.ticker.MaxNLocator(4))
ax[2,i].yaxis.set_major_locator(mp.ticker.MaxNLocator(4))
fig.colorbar(map3, ax=ax[2,i])
else:
ax[1,i].set_xlabel(xlab)
if save:
for format_ in ['png', 'pdf', 'eps']:
pl.savefig("comp_" + "".join(name[:3].title() for name in var) \
+ "." + format_)
else:
pl.show()
def plot2d(data, var='rho', xpos=None, ypos=None, zpos=0 \
, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=None \
, physUnit=True, physTick=True, polar=False, log=False, save=False \
, cm=None, showTitle=True, *args, **kwargs):
"""plot2d function to plot a slice in a DUMSES-Hybrid simulation
Usage:
plot2d(data [, var, xpos, ypos, zpos, xmin, xmax, xmin, xmax, zmin, zmax, physUnit, physTick, polar, log, save, cm, *args, **kwargs])
With:
data a DumsesData object
var a variable or list of variables to plot. Variables can be a combination of ['rho', 'rhou{x,y,z}', 'E', 'B{x,y,z}'] and any simple mathematical operations. Default: 'rho'
xpos position of the slice in the x-direction. Default: None
ypos position of the slice in the y-direction. Default: None
zpos position of the slice in the z-direction. Default: 0
xmin lower x-boundary of the slice. Default: None
xmax upper x-boundary of the slice. Default: None
ymin lower y-boundary of the slice. Default: None
ymax upper y-boundary of the slice. Default: None
zmin lower z-boundary of the slice. Default: None
zmax upper z-boundary of the slice. Default: None
physUnit if True, use physical units for positions and boundaries. Default: True
physTick if True, use physical units for plotting. Default: True
polar if True, plot in polar coordinates. Default: False
log if True, plot in logscale. Default: False
save if True, save the plot in PNG, PDF and EPS. Default: False
cm colormap. Default: None
showTitle if True, display title for each plot. Default: True
"""
# Ensure that data is a DumsesData object
try:
assert (isinstance(data, dp.DumsesData))
except AssertionError:
print("Error: 'data' must be a DumsesData object!")
sys.exit(42)
dictDat = dp.dictionarize(data)
if var == "all":
var = dictDat.keys()
if "Brx" in var:
var.remove("Brx")
var.remove("Bry")
var.remove("Brz")
if not isinstance(var, list): var = [var]
# Parse the variables
vname = re.compile(r'(?!\d)([\w_]+)')
code = []
for cvar in var:
st = parser.expr(vname.sub(r"dictDat['\1']", cvar))
code.append(st.compile())
# Determine the position and the boundaries of the slice to plot
if xpos != None: zpos = None
if ypos != None: zpos = None
try:
assert ([xpos, ypos, zpos].count(None) == 2)
except AssertionError:
print(
'Error: you have to specify one (and only one) direction and its position where to cut for the snapshot.'
)
sys.exit(42)
if polar and (xpos != None or ypos != None):
print(
"Warning: you probably want to make your polar plot in a z-plane")
if xpos == None:
if physUnit:
if xmin: xmin = findPosition(xmin, data.x)
if xmax: xmax = findPosition(xmax, data.x)
if not xmin: xmin = 0
if not xmax: xmax = dictDat[list(dictDat.keys())[0]].shape[0]
else:
if physUnit:
xmin = findPosition(xpos, data.x)
xmax = xmin + 1
else:
xmin = xpos
xmax = xpos + 1
if ypos == None:
if physUnit:
if ymin: ymin = findPosition(ymin, data.y)
if ymax: ymax = findPosition(ymax, data.y)
if not ymin: ymin = 0
if not ymax: ymax = dictDat[list(dictDat.keys())[0]].shape[1]
else:
if physUnit:
ymin = findPosition(ypos, data.y)
ymax = ymin + 1
else:
ymin = ypos
ymax = ypos + 1
if zpos == None:
if physUnit:
if zmin: zmin = findPosition(zmin, data.z)
if zmax: zmax = findPosition(zmax, data.z)
if not zmin: zmin = 0
if not zmax: zmax = dictDat[list(dictDat.keys())[0]].shape[2]
else:
if physUnit:
zmin = findPosition(zpos, data.z)
zmax = zmin + 1
else:
zmin = zpos
zmax = zpos + 1
ldim = np.array([xmax - xmin, ymax - ymin, zmax - zmin])
ldim = ldim[ldim > 1]
try:
assert (ldim.size == 2)
except AssertionError:
print('Error: Wrong dimensions! Check your {x,y,z} boundaries.')
sys.exit(42)
xdim, ydim = ldim
# Define labels and extent of the plot
if zmax - zmin == 1:
xlab = "x"
ylab = "y"
if physTick:
extent = [data.x[xmin], data.x[xmax-1], data.y[ymin] \
, data.y[ymax-1]]
else:
extent = [xmin, xmax - 1, ymin, ymax - 1]
if ymax - ymin == 1:
xlab = "x"
ylab = "z"
if physTick:
extent = [data.x[xmin], data.x[xmax-1], data.z[zmin] \
, data.z[zmax-1]]
else:
extent = [xmin, xmax - 1, zmin, zmax - 1]
if xmax - xmin == 1:
xlab = "y"
ylab = "z"
if physTick:
extent = [data.y[ymin], data.y[ymax-1], data.z[zmin] \
, data.z[zmax-1]]
else:
extent = [ymin, ymax - 1, zmin, zmax - 1]
if polar:
xlab = "R"
ylab = ""
if not physTick:
print(
"Warning: you probably want to make your polar plot in physical units"
)
# Define array of figures
fig, ax = pl.subplots(1, len(var), figsize=(6. * len(var), 4.))
pl.subplots_adjust(bottom=0.15, left=0.15, wspace=0.5)
if not isinstance(ax, np.ndarray): ax = np.array([ax])
for i, cvar in enumerate(var):
# Use SymPy to simplify and TeXify the title
if "sympy" in sys.modules:
title = sympy.simplify(
cvar.replace('rhou', 'rho*v').replace('S', 'S_'))
title = sympy.latex(title)
title = '$' + title.replace('x', r'_x').replace(
'y', r'_y').replace('z', r'_z').replace('S_', 'S') + '$'
else:
if cvar == "rho":
title = r"$\rho$"
elif "rhou" in cvar and len(cvar) == 5:
title = r"$\rho v_" + cvar[-1] + "$"
elif "B" in cvar and len(cvar) == 2:
title = "B$_" + cvar[-1] + "$"
else:
title = cvar
if log: title = "log(" + title + ")"
# Compute the actual variable to plot
res = eval(code[i])
datPlot = res[xmin:xmax, ymin:ymax, zmin:zmax].reshape((xdim, ydim))
if not polar:
datPlot = datPlot.transpose()
if showTitle:
ax[i].set_title(title)
if i == 0: ax[i].set_ylabel(ylab)
ax[i].set_xlabel(xlab)
# if polar, defines plot coordinates
if polar:
ax[i].yaxis.set_ticks_position('none')
ax[i].set_yticks(())
rtile = np.ones(ydim)
ttile = np.ones(xdim)
dtheta = (extent[3] - extent[2]) / ydim
r = np.linspace(extent[0], extent[1], xdim)
theta = np.linspace(extent[2] - dtheta/2., extent[3] + dtheta/2. \
, ydim)
r = r[:, np.newaxis] * rtile
theta = theta * ttile[:, np.newaxis]
xp = r * np.cos(theta)
yp = r * np.sin(theta)
# if in logscale, hatched negative regions
if log:
if polar:
map1 = ax[i].pcolormesh(xp, yp, np.log10(abs(datPlot)) \
, cmap=cm, *args, **kwargs)
cs = ax[i].contourf(xp, yp, np.where(datPlot > 0, 1, -1), 2 \
, hatches=['//', ''], alpha=0.)
else:
map1 = ax[i].imshow(np.log10(abs(datPlot)), extent=extent \
, origin='lower', cmap=cm, *args, **kwargs)
cs = ax[i].contourf(np.where(datPlot > 0, 1, -1), 2 \
, extent=extent, hatches=['//', ''], alpha=0.)
else:
if polar:
map1 = ax[i].pcolormesh(xp, yp, datPlot, cmap=cm \
, *args, **kwargs)
else:
map1 = ax[i].imshow(datPlot, extent=extent, origin='lower' \
, cmap=cm, *args, **kwargs)
ax[i].xaxis.set_major_locator(mp.ticker.MaxNLocator(4))
if not polar:
ax[i].yaxis.set_major_locator(mp.ticker.MaxNLocator(4))
fig.colorbar(map1, ax=ax[i])
if log:
pl.suptitle('hatched where $<$ 0', fontsize=10, x=0.2)
if save:
basename = "snapshot_" + ("polar_" if polar else "")
for format_ in ['png', 'pdf', 'eps']:
pl.savefig(basename + "_".join(name[:3].title() \
if name in dictDat.keys() else name.translate(None, ' +-*/()') \
for name in var) + "." + format_)
pl.clf()
else:
pl.show()