def loadData(field, extension):
global data
# check if data has already been loaded
if (field+extension in data.loaded) == False:
data.slices[field+extension], data.t = pc.read_slices(datadir = 'data', field = field, extension = extension, proc = -1)
data.dim[field+extension] = pc.read_dim() # system dimensions
data.param[field+extension] = pc.read_param(quiet=True) # system parameters
data.loaded.add(field+extension)
def slices2vtk(
variables=["rho"],
extensions=["xy", "xy2", "xz", "yz"],
datadir="data/",
destination="slices",
proc=-1,
format="native",
):
"""
Convert slices from PencilCode format to vtk.
call signature::
slices2vtk(variables = ['rho'], extensions = ['xy', 'xy2', 'xz', 'yz'],
datadir = 'data/', destination = 'slices', proc = -1,
format = 'native'):
Read slice files specified by *variables* and convert
them into vtk format for the specified extensions.
Write the result in *destination*.
NB: You need to have called src/read_videofiles.x before using this script.
Keyword arguments:
*variables*:
All allowed fields which can be written as slice files, e.g. b2, uu1, lnrho, ...
See the pencil code manual for more (chapter: "List of parameters for `video.in'").
*extensions*:
List of slice positions.
*datadir*:
Directory where the data is stored.
*destination*:
Destination files.
*proc*:
Processor which should be read. Set to -1 for all processors.
*format*:
Endian, one of little, big, or native (default)
"""
# this should correct for the case the user types only one variable
if len(variables) > 0:
if len(variables[0]) == 1:
variables = [variables]
# this should correct for the case the user types only one extension
if len(extensions) > 0:
if len(extensions[0]) == 1:
extensions = [extensions]
# read the grid dimensions
grid = pc.read_grid(datadir=datadir, proc=proc, trim=True, quiet=True)
# read the user given parameters for the slice positions
params = pc.read_param(param2=True, quiet=True)
# run through all specified variables
for field in variables:
# run through all specified extensions
for ext in extensions:
print("read ", field, " ", ext)
slices, t = pc.read_slices(field=field, datadir=datadir, proc=proc, extension=ext, format=format)
dim_p = slices.shape[2]
dim_q = slices.shape[1]
if ext[0] == "x":
d_p = (np.max(grid.x) - np.min(grid.x)) / (dim_p)
else:
d_p = (np.max(grid.y) - np.min(grid.y)) / (dim_p)
if ext[1] == "y":
d_q = (np.max(grid.y) - np.min(grid.y)) / (dim_q)
else:
d_q = (np.max(grid.z) - np.min(grid.z)) / (dim_q)
if params.ix != -1:
x0 = grid.x[params.ix]
elif params.slice_position == "m":
x0 = grid.x[len(grid.x) / 2]
if params.iy != -1:
y0 = grid.y[params.iy]
elif params.slice_position == "m":
y0 = grid.y[len(grid.y) / 2]
if params.iz != -1:
z0 = grid.z[params.iz]
elif params.slice_position == "m":
z0 = grid.z[len(grid.z) / 2]
for i in range(slices.shape[0]):
# open the destination file for writing
fd = open(destination + "_" + field + "_" + ext + "_" + str(i) + ".vtk", "wb")
# write the header
fd.write("# vtk DataFile Version 2.0\n")
fd.write(field + "_" + ext + "\n")
fd.write("BINARY\n")
fd.write("DATASET STRUCTURED_POINTS\n")
if ext[0:2] == "xy":
x0 = grid.x[0]
y0 = grid.y[0]
fd.write("DIMENSIONS {0:9} {1:9} {2:9}\n".format(dim_p, dim_q, 1))
fd.write("ORIGIN {0:8.12} {1:8.12} {2:8.12}\n".format(x0, y0, z0))
fd.write("SPACING {0:8.12} {1:8.12} {2:8.12}\n".format(grid.dx, grid.dy, 1.0))
elif ext[0:2] == "xz":
x0 = grid.x[0]
z0 = grid.z[0]
fd.write("DIMENSIONS {0:9} {1:9} {2:9}\n".format(dim_p, 1, dim_q))
fd.write("ORIGIN {0:8.12} {1:8.12} {2:8.12}\n".format(x0, y0, z0))
fd.write("SPACING {0:8.12} {1:8.12} {2:8.12}\n".format(grid.dx, 1.0, grid.dy))
elif ext[0:2] == "yz":
y0 = grid.y[0]
z0 = grid.z[0]
fd.write("DIMENSIONS {0:9} {1:9} {2:9}\n".format(1, dim_p, dim_q))
fd.write("ORIGIN {0:8.12} {1:8.12} {2:8.12}\n".format(x0, y0, z0))
fd.write("SPACING {0:8.12} {1:8.12} {2:8.12}\n".format(1.0, grid.dy, grid.dy))
fd.write("POINT_DATA {0:9}\n".format(dim_p * dim_q))
fd.write("SCALARS " + field + "_" + ext + " float\n")
fd.write("LOOKUP_TABLE default\n")
for j in range(dim_q):
for k in range(dim_p):
fd.write(struct.pack(">f", slices[i, j, k]))
fd.close()
#!/usr/bin/env python
#
# $Id: fourier.py,v 1.3 2009-04-27 10:29:47 dintrans Exp $
# Fourier diagram of the vertical velocity
#
import numpy as N
import pylab as P
import pencil as pc
from scipy.integrate import simps
from theory import *
uz, t = pc.read_slices(field='uu3', proc=0)
dim = pc.read_dim()
par = pc.read_param(quiet=True)
par2 = pc.read_param(quiet=True, param2=True)
grid = pc.read_grid(param=par, quiet=True, trim=True)
nt = len(t)
uz = uz.reshape(nt, dim.nz, dim.nx)
w1 = N.empty((nt, dim.nz, dim.nx), dtype='Complex64')
for i in range(dim.nz):
w1[:, i, :] = N.fft.fft2(uz[:, i, :]) / nt / dim.nx
w2 = N.abs(w1[1:nt / 2 + 1, ...])
dw = 2 * N.pi / (t[-1] - t[0])
w = dw * N.arange(nt)
w = w[1:nt / 2 + 1]
kmax = 5
def slices2vtk(variables=['rho'],
extensions=['xy', 'xy2', 'xz', 'yz'],
datadir='data/',
destination='slices',
proc=-1,
format='native'):
"""
Convert slices from PencilCode format to vtk.
call signature::
slices2vtk(variables = ['rho'], extensions = ['xy', 'xy2', 'xz', 'yz'],
datadir = 'data/', destination = 'slices', proc = -1,
format = 'native'):
Read slice files specified by *variables* and convert
them into vtk format for the specified extensions.
Write the result in *destination*.
NB: You need to have called src/read_videofiles.x before using this script.
Keyword arguments:
*variables*:
All allowed fields which can be written as slice files, e.g. b2, uu1, lnrho, ...
See the pencil code manual for more (chapter: "List of parameters for `video.in'").
*extensions*:
List of slice positions.
*datadir*:
Directory where the data is stored.
*destination*:
Destination files.
*proc*:
Processor which should be read. Set to -1 for all processors.
*format*:
Endian, one of little, big, or native (default)
"""
# this should correct for the case the user types only one variable
if (len(variables) > 0):
if (len(variables[0]) == 1):
variables = [variables]
# this should correct for the case the user types only one extension
if (len(extensions) > 0):
if (len(extensions[0]) == 1):
extensions = [extensions]
# read the grid dimensions
grid = pc.read_grid(datadir=datadir, proc=proc, trim=True, quiet=True)
# read the user given parameters for the slice positions
params = pc.read_param(param2=True, quiet=True)
# run through all specified variables
for field in variables:
# run through all specified extensions
for ext in extensions:
print("read " + field + ' ' + ext)
slices, t = pc.read_slices(field=field,
datadir=datadir,
proc=proc,
extension=ext,
format=format)
dim_p = slices.shape[2]
dim_q = slices.shape[1]
if ext[0] == 'x':
d_p = (np.max(grid.x) - np.min(grid.x)) / (dim_p)
else:
d_p = (np.max(grid.y) - np.min(grid.y)) / (dim_p)
if ext[1] == 'y':
d_q = (np.max(grid.y) - np.min(grid.y)) / (dim_q)
else:
d_q = (np.max(grid.z) - np.min(grid.z)) / (dim_q)
if params.ix != -1:
x0 = grid.x[params.ix]
elif params.slice_position == 'm':
x0 = grid.x[int(len(grid.x) / 2)]
if params.iy != -1:
y0 = grid.y[params.iy]
elif params.slice_position == 'm':
y0 = grid.y[int(len(grid.y) / 2)]
if params.iz != -1:
z0 = grid.z[params.iz]
elif params.slice_position == 'm':
z0 = grid.z[int(len(grid.z) / 2)]
for i in range(slices.shape[0]):
# open the destination file for writing
fd = open(
destination + '_' + field + '_' + ext + '_' + str(i) +
'.vtk', 'wb')
# write the header
fd.write('# vtk DataFile Version 2.0\n')
fd.write(field + '_' + ext + '\n')
fd.write('BINARY\n')
fd.write('DATASET STRUCTURED_POINTS\n')
if ext[0:2] == 'xy':
x0 = grid.x[0]
y0 = grid.y[0]
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(
dim_p, dim_q, 1))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
x0, y0, z0))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
grid.dx, grid.dy, 1.))
elif ext[0:2] == 'xz':
x0 = grid.x[0]
z0 = grid.z[0]
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(
dim_p, 1, dim_q))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
x0, y0, z0))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
grid.dx, 1., grid.dy))
elif ext[0:2] == 'yz':
y0 = grid.y[0]
z0 = grid.z[0]
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(
1, dim_p, dim_q))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
x0, y0, z0))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
1., grid.dy, grid.dy))
fd.write('POINT_DATA {0:9}\n'.format(dim_p * dim_q))
fd.write('SCALARS ' + field + '_' + ext + ' float\n')
fd.write('LOOKUP_TABLE default\n')
for j in range(dim_q):
for k in range(dim_p):
fd.write(struct.pack(">f", slices[i, j, k]))
fd.close()
#!/usr/bin/python
# $Id$
import numpy as N
import pylab as P
import pencil as pc
from os import system
system('cat video.in')
field=raw_input('which field? ')
f, t = pc.read_slices(field=field, proc=0, extension='xy')
dim=pc.read_dim()
grid=pc.read_grid(trim=True)
nt=len(t)
ff=f.reshape(nt, dim.nx)
P.ion()
P.subplot(211)
line, = P.plot(grid.x, ff[0, :])
P.xlim(grid.x[0], grid.x[-1])
P.ylim(ymin=ff.min(), ymax=ff.max())
P.title(field)
st=P.figtext(0.2, 0.85, 't=%.1f'%t[0])
for i in range(1, nt):
line.set_ydata(ff[i, :])
st.set_text('t=%.1f'%t[i])
P.draw()
#!/usr/bin/python
# $Id: pvid2D.py,v 1.1.1.1 2009-12-16 17:37:16 dintrans Exp $
import numpy as N
import pylab as P
import pencil as pc
from os import system
system('cat video.in')
field=raw_input('which field? ')
f, t = pc.read_slices(field=field, proc=0, extension='xz')
ux, t = pc.read_slices(field='uu1', proc=0, extension='xz')
uz, t = pc.read_slices(field='uu3', proc=0, extension='xz')
dim=pc.read_dim()
grid=pc.read_grid(trim=True)
param=pc.read_param(quiet=True)
nt=len(t)
f=f.reshape(nt, dim.nz, dim.nx)
ux=ux.reshape(nt, dim.nz, dim.nx)
uz=uz.reshape(nt, dim.nz, dim.nx)
P.ion()
frame=param.xyz0[0],param.xyz1[0],param.xyz0[2],param.xyz1[2]
qs1=N.random.random_integers(0,dim.nx-1, 1000)
qs2=N.random.random_integers(0,dim.nz-1, 1000)
xx,zz=P.meshgrid(grid.x, grid.z)
im=P.imshow(f[0,...], extent=frame, origin='lower', aspect='auto')
a=ux[0, qs2, qs1]**2+uz[0, qs2, qs1]**2 ; norm=N.sqrt(a.max())
#!/usr/bin/python
# $Id: pvid2D.py,v 1.1.1.1 2009-12-16 17:37:16 dintrans Exp $
import numpy as N
import pylab as P
import pencil as pc
from os import system
system('cat video.in')
field = raw_input('which field? ')
f, t = pc.read_slices(field=field, proc=0, extension='xz')
ux, t = pc.read_slices(field='uu1', proc=0, extension='xz')
uz, t = pc.read_slices(field='uu3', proc=0, extension='xz')
dim = pc.read_dim()
grid = pc.read_grid(trim=True)
param = pc.read_param(quiet=True)
nt = len(t)
f = f.reshape(nt, dim.nz, dim.nx)
ux = ux.reshape(nt, dim.nz, dim.nx)
uz = uz.reshape(nt, dim.nz, dim.nx)
P.ion()
frame = param.xyz0[0], param.xyz1[0], param.xyz0[2], param.xyz1[2]
qs1 = N.random.random_integers(0, dim.nx - 1, 1000)
qs2 = N.random.random_integers(0, dim.nz - 1, 1000)
xx, zz = P.meshgrid(grid.x, grid.z)
im = P.imshow(f[0, ...], extent=frame, origin='lower', aspect='auto')
a = ux[0, qs2, qs1]**2 + uz[0, qs2, qs1]**2
#!/usr/bin/env python # # $Id: pvid.py,v 1.5 2009-08-27 08:11:08 dintrans Exp $ # Animate the entropy snapshots with the velocity field superimposed # import numpy as N import pylab as P import pencil as pc ss, t = pc.read_slices(field='ss', proc=0) ux, t = pc.read_slices(field='uu1', proc=0) uz, t = pc.read_slices(field='uu3', proc=0) dim=pc.read_dim() par=pc.read_param(quiet=True) par2=pc.read_param(quiet=True, param2=True) grid=pc.read_grid(param=par, quiet=True, trim=True) nt=len(t) ss=ss.reshape(nt, dim.nz, dim.nx) ux=ux.reshape(nt, dim.nz, dim.nx) uz=uz.reshape(nt, dim.nz, dim.nx) qs1=N.random.random_integers(0,dim.nx-1, 1000) qs2=N.random.random_integers(0,dim.nz-1, 1000) xx,zz=P.meshgrid(grid.x, grid.z) frame=par.xyz0[0],par.xyz1[0],par.xyz0[2],par.xyz1[2] P.ion() im=P.imshow(ss[0,...], extent=frame, origin='lower', aspect='auto')
#!/usr/bin/python
# $Id$
import numpy as N
import pylab as P
import pencil as pc
from os import system
system('cat video.in')
field = raw_input('which field? ')
f, t = pc.read_slices(field=field, proc=0, extension='xy')
dim = pc.read_dim()
grid = pc.read_grid(trim=True)
nt = len(t)
ff = f.reshape(nt, dim.nx)
P.ion()
P.subplot(211)
line, = P.plot(grid.x, ff[0, :])
P.xlim(grid.x[0], grid.x[-1])
P.ylim(ymin=ff.min(), ymax=ff.max())
P.title(field)
st = P.figtext(0.2, 0.85, 't=%.1f' % t[0])
for i in range(1, nt):
line.set_ydata(ff[i, :])
st.set_text('t=%.1f' % t[i])
P.draw()
