Hi
I have four-dimensional data stored in a netcdf file and want to create
an isosurface visualization for each time step in the file (>100 times)
and save the resulting image as a PNG-file.
The problem is that after a few iterations I run out of memory. How do I
correctly destroy the tvtk and mayavi objects which I have created
before entering into the next iteration?
I'm using scene.children.remove() to remove data sources and using del
to delete all the objects which I have created. What am I missing?
Thanks,
Juerg
#!/usr/bin/env mayavi2
"""This script demonstrates how to create a numpy array data and
visualize it as image data using a few modules.
"""
# The following *optional* two lines allow a user to call this script
# as either `python script.py` or `mayavi2 script.py`. These two
# lines must be placed before any other mayavi imports.
from enthought.mayavi.scripts import mayavi2
mayavi2.standalone(globals())
# Standard library imports
import enthought.util.scipyx as scipy
import Nio
import numpy
from numpy import newaxis, gradient
# Enthought library imports
from enthought.mayavi.sources.array_source import ArraySource
from enthought.mayavi.sources.vtk_data_source import VTKDataSource
from enthought.mayavi.modules.outline import Outline
from enthought.mayavi.modules.axes import Axes
from enthought.mayavi.modules.grid_plane import GridPlane
from enthought.mayavi.modules.contour_grid_plane import ContourGridPlane
from enthought.mayavi.modules.scalar_cut_plane import ScalarCutPlane
from enthought.mayavi.modules.image_plane_widget import ImagePlaneWidget
from enthought.mayavi.modules.iso_surface import IsoSurface
from enthought.tvtk.api import tvtk
def get_points(file):
f = Nio.open_file(file)
ix = slice(200); iy = slice(None); iz = slice(40)
z = f.variables['ZP'][iz,iy,ix].astype('f')/500.
(nz,ny,nx) = z.shape
x = numpy.zeros(z.shape)
y = numpy.zeros(z.shape)
xc = f.variables['xc'][ix].astype('f')/1000.
yc = f.variables['yc'][iy].astype('f')/1000.
x[:,:,:] = xc[newaxis,newaxis,:]
y[:,:,:] = yc[newaxis,:,newaxis]
f.close()
z.shape = (-1,)
y.shape = (-1,)
x.shape = (-1,)
pts = numpy.array([x,y,z]).T
return pts
def get_data(file, varname, itime, pts):
f = Nio.open_file(file)
ix = slice(200); iy = slice(None); iz = slice(40)
if varname == 'DIV':
u = f.variables['U'][itime,iz,iy,ix].astype('f')
v = f.variables['V'][itime,iz,iy,ix].astype('f')
fld = gradient(u)[2]+gradient(v)[1]
else:
fld = f.variables['W'][itime,iz,iy,ix].astype('f')
f.close()
(nz,ny,nx) = fld.shape
fld.shape = (-1,)
sg = tvtk.StructuredGrid(dimensions=(nx,ny,nz))
sg.point_data.scalars = fld
sg.point_data.scalars.name = varname
sg.points = pts
return sg
def make_fig(file, itime, figname, pts):
# visualize DIV
sg = get_data(file, 'DIV', itime, pts)
src = VTKDataSource(data=sg)
mayavi.add_source(src)
c1 = ContourGridPlane()
mayavi.add_module(c1)
c1.grid_plane.axis='z'
c1.contour.filled_contours = True
c1.contour.auto_contours = True
c1.contour.minimum_contour = -1.5
c1.contour.maximum_contour = 1.5
c1.contour.number_of_contours = 10
c1.module_manager.scalar_lut_manager.lut_mode = 'hsv'
# visualize W
sg2 = get_data(file, 'W', itime, pts)
src2 = VTKDataSource(data=sg2)
mayavi.add_source(src2)
c2 = ContourGridPlane()
mayavi.add_module(c2)
c2.grid_plane.axis='y'
c2.contour.filled_contours = True
c2.contour.auto_contours = True
c2.contour.minimum_contour = -2.0
c2.contour.maximum_contour = 2.0
c2.contour.number_of_contours = 5
c2.module_manager.scalar_lut_manager.lut_mode = 'black-white'
c3 = ContourGridPlane()
mayavi.add_module(c3)
c3.grid_plane.axis='x'
c3.contour.filled_contours = True
c3.contour.minimum_contour = -2.0
c3.contour.maximum_contour = 2.0
c3.contour.number_of_contours = 5
c3.module_manager.scalar_lut_manager.lut_mode = 'black-white'
i1 = IsoSurface()
mayavi.add_module(i1)
i1.module_manager.scalar_lut_manager.lut_mode = 'black-white'
i1.contour.contours[0] = 1.0
i1.scene.isometric_view()
figname = figname + str(itime).zfill(6) + '.png'
i1.scene.save(figname, size=(900,750))
s = mayavi.engine.current_scene
s.children.remove(src)
s.children.remove(src2)
del(src)
del(src2)
del(c1); del(c2); del(c3); del(i1)
del(sg); del(sg2)
if __name__ == '__main__':
mayavi.new_scene()
file = 'dat/arps/bv_vles_tcst02/ncdf/arps_vles_tcst02_30s.nc'
pts = get_points(file)
for itime in range(121):
make_fig(file, itime, 'fig/isosrf_vles_tcst02_t', pts)
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