def __init__(self, filename, xdim, ydim, zdim, voxel_width):
'''Assumes cubic voxels'''
self.phantom = EGSPhant(None, xdim, ydim, zdim)
# TODO: don't overwrite pre-existing file
self.phantom.phantfilename = filename
self.phantom.nmaterials = 6
self.phantom.materials = []
self.phantom.materials.append('AIR700ICRU')
#self.phantom.materials.append('H2O700ICRU')
self.phantom.materials.append('LUNG700ICRU')
self.phantom.materials.append('ICRUTISSUE700ICRU')
self.phantom.materials.append('ICRPBONE700ICRU')
self.phantom.materials.append('ECLIPSE')
self.phantom.materials.append('CERAMCOC3')
self.phantom.estepe = ones(self.phantom.nmaterials, type=Float32)
self.phantom.xedges = zeros(self.phantom.dimensions[0]+1, type=Float32)
self.phantom.yedges = zeros(self.phantom.dimensions[1]+1, type=Float32)
self.phantom.zedges = zeros(self.phantom.dimensions[2]+1, type=Float32)
# make the x-y slices center on (x=0, y=0)
x_start = self.phantom.dimensions[0] * voxel_width / 2.
y_start = self.phantom.dimensions[1] * voxel_width / 2.
for i in range(self.phantom.dimensions[0]+1):
self.phantom.xedges[i] = -x_start + i * voxel_width
for i in range(self.phantom.dimensions[1]+1):
self.phantom.yedges[i] = -y_start + i * voxel_width
for i in range(self.phantom.dimensions[2]+1):
self.phantom.zedges[i] = i * voxel_width
self.phantom.materialscan = zeros([self.phantom.dimensions[2],self.phantom.dimensions[1],
self.phantom.dimensions[0]], type=Int32)
# set all slices to be tissue
self.phantom.materialscan[:,:,:] = self.phantom.materialscan[:,:,:] + 3 * ones((self.phantom.dimensions[2], self.phantom.dimensions[1], self.phantom.dimensions[0]), type=Int32)
self.phantom.densityscan = zeros([self.phantom.dimensions[2],self.phantom.dimensions[1],
self.phantom.dimensions[0]], type=Float32)
# fix only the artificial materials
self.phantom.fix_density()
class BlankPhant:
def __init__(self, filename, xdim, ydim, zdim, voxel_width):
'''Assumes cubic voxels'''
self.phantom = EGSPhant(None, xdim, ydim, zdim)
# TODO: don't overwrite pre-existing file
self.phantom.phantfilename = filename
self.phantom.nmaterials = 6
self.phantom.materials = []
self.phantom.materials.append('AIR700ICRU')
#self.phantom.materials.append('H2O700ICRU')
self.phantom.materials.append('LUNG700ICRU')
self.phantom.materials.append('ICRUTISSUE700ICRU')
self.phantom.materials.append('ICRPBONE700ICRU')
self.phantom.materials.append('ECLIPSE')
self.phantom.materials.append('CERAMCOC3')
self.phantom.estepe = ones(self.phantom.nmaterials, type=Float32)
self.phantom.xedges = zeros(self.phantom.dimensions[0]+1, type=Float32)
self.phantom.yedges = zeros(self.phantom.dimensions[1]+1, type=Float32)
self.phantom.zedges = zeros(self.phantom.dimensions[2]+1, type=Float32)
# make the x-y slices center on (x=0, y=0)
x_start = self.phantom.dimensions[0] * voxel_width / 2.
y_start = self.phantom.dimensions[1] * voxel_width / 2.
for i in range(self.phantom.dimensions[0]+1):
self.phantom.xedges[i] = -x_start + i * voxel_width
for i in range(self.phantom.dimensions[1]+1):
self.phantom.yedges[i] = -y_start + i * voxel_width
for i in range(self.phantom.dimensions[2]+1):
self.phantom.zedges[i] = i * voxel_width
self.phantom.materialscan = zeros([self.phantom.dimensions[2],self.phantom.dimensions[1],
self.phantom.dimensions[0]], type=Int32)
# set all slices to be tissue
self.phantom.materialscan[:,:,:] = self.phantom.materialscan[:,:,:] + 3 * ones((self.phantom.dimensions[2], self.phantom.dimensions[1], self.phantom.dimensions[0]), type=Int32)
self.phantom.densityscan = zeros([self.phantom.dimensions[2],self.phantom.dimensions[1],
self.phantom.dimensions[0]], type=Float32)
# fix only the artificial materials
self.phantom.fix_density()
def fix_all_density(self):
'''Fixes up the density scan'''
# if tissue, want density to be 1.0
# otherwise, set to the mean density for that material
# (to be accurate, only "mean" in the sense of middle of the
# range of possible densities.)
for k in range(self.phantom.dimensions[2]):
for j in range(self.phantom.dimensions[1]):
for i in range(self.phantom.dimensions[0]):
mat = self.phantom.material(self.phantom.materialscan[k,j,i])
if not self.phantom.density_correct_p(k,j,i):
mat = self.phantom.material(self.phantom.materialscan[k,j,i])
self.phantom.debug_print(mat)
if mat == 'ICRUTISSUE700ICRU':
proper_dens = 1.0
else:
proper_dens = 0.5 (self.phantom.density[mat][0] + self.phantom.density[mat][1])
self.phantom.densityscan[k,j,i] = proper_dens
def save(self):
self.phantom.save(self.phantom.phantfilename)
#!/usr/bin/env python2.4
# $Id: pickle_these.py 86 2007-11-12 22:11:40Z dwchin $
import os
import pickle
from EGSPhant import *
from MCDose import *
# loop over all egsphant and 3ddose file, and pickle them
for o in sys.argv:
if o.endswith('3ddose'):
d = MCDose(o)
picklename = o.split('.3ddose')[0] + '_3ddose.pickle'
f = open(picklename, 'wo')
pickle.dump(d, f)
f.close()
elif o.endswith('egsphant'):
p = EGSPhant(o)
picklename = o.split('.egsphant')[0] + '_egsphant.pickle'
f = open(picklename, 'wo')
pickle.dump(p, f)
f.close()
else:
pass
#!/usr/bin/env python2.4
from EGSPhant import *
if len(sys.argv) == 1:
print 'Need name of egsphant file'
sys.exit(1)
p = EGSPhant(sys.argv[1])
# set the density for tissue and bone voxels
for k in range(p.dimensions[2]):
for j in range(p.dimensions[1]):
for i in range(p.dimensions[0]):
mat = p.material(p.materialscan[k, j, i])
if mat == 'ICRPBONE700ICRU':
print '%s, %f g/cc' % (mat, p.densityscan[k, j, i])
#!/usr/bin/env python2.4
import sys
from EGSPhant import *
if len(sys.argv) == 1:
print "Need one argument, name of phantom file to fix"
else:
try:
phant = EGSPhant(sys.argv[1])
except IOError:
raise
suffix = '.egsphant'
phant.fix_density()
basename = sys.argv[1].split(suffix)[0]
newname = basename + '_fixed' + suffix
phant.save(newname)
#!/usr/bin/env python
from EGSPhant import *
from MCDose import *
from pylab import *
d = MCDose('block_amalgam.3ddose')
d.make_absolute('6MV', 100)
p = EGSPhant('block_amalgam.egsphant')
X, Y = meshgrid(d.x, d.y)
Z = d.dose[11, :, :]
CS = contourf(X, Y, p.densityscan[11, :, :], cmap=cm.bone, origin='lower')
#CS2 = contourf(X, Y, Z, 10, cmap=cm.jet, origin='lower', alpha='0.5')
CS2 = imshow(X, Y, Z, 10, cmap=cm.jet, origin='lower', alpha='0.5')
title('Example isodose plot')
xlabel('X (cm)')
ylabel('Y (cm)')
#CS2 = contour(X, Y, Z, CS.levels, colors='white', origin='lower', hold='on')
ax_cbar = colorbar(CS, tickfmt='%1.2f')
ax_cbar.set_ylabel('dose (foo units)')
show()
#!/usr/bin/env python2.4
import sys
from EGSPhant import *
if len(sys.argv) == 1:
print "Need one argument, name of phantom file to fix"
else:
try:
phant = EGSPhant(sys.argv[1])
except IOError:
raise
suffix = '.egsphant'
phant.fix_density()
basename = sys.argv[1].split(suffix)[0]
newname = basename + '_fixed' + suffix
phant.save(newname)