Scripts: readvol.2.py

#
# Example opening volume file and accessing data size, xyz coordinates, and
# data values.
#
# Volume grid data object is defined in Chimera file
#
#  chimera/share/VolumeData/griddata.py
#
from chimera import openModels
v = openModels.open('/usr/local/src/chimera-demos/volume/examples/1a0m.omap')[0]

d = v.data
print 'read map', d.name

isize, jsize, ksize = d.size
print 'data size', isize, jsize, ksize

istep, jstep, kstep = d.step
print 'voxel size', istep, jstep, kstep
print 'voxel volume', istep*jstep*kstep

i,j,k = 15,7,13
x,y,z = d.ijk_to_xyz((i,j,k))
print 'xyz for index', i, j, k, 'is', x, y, z

m = d.matrix()
print 'data value at ijk', i, j, k, 'is', m[k,j,i]

from numpy import float32
print 'sum of all data values', m.sum(dtype = float32)

nz = len(m.nonzero()[0])
print 'number of non-zero values', nz, 'of', m.size

print 'volume occupied by non-zero values', nz * istep * jstep * kstep