def __init__(self, filename=None):
self.debug_p = False
self.phantfilename = filename
# all measurements are in cm
self.height = 5.
self.radius = 10.
self.width = 2. * self.radius
self.depth = 30.
# voxel size
self.dx = 0.05
self.dy = 0.05
self.dz = 0.25
# compute dimensions of phantom, i.e. number of
# voxels in each direction
self.dimensions = (int(self.width / self.dx), \
int((self.height + self.radius) / self.dy), \
int(self.depth / self.dz))
# print self.dimensions
# make a blank phantom
self.phantom = EGSPhant.EGSPhant(None, self.dimensions[0],
self.dimensions[1],
self.dimensions[2])
self.phantom.phantfilename = self.phantfilename
# phantom is just air and water
self.phantom.nmaterials = 2
self.phantom.materials = ('AIR700ICRU', 'H2O700ICRU')
self.phantom.estepe = ones(self.phantom.nmaterials, type=Float32)
# set the voxel edges
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)
for i in range(self.phantom.dimensions[0] + 1):
self.phantom.xedges[i] = -10. + i * self.dx
for i in range(self.phantom.dimensions[1] + 1):
self.phantom.yedges[i] = -10. + i * self.dy
for i in range(self.phantom.dimensions[2] + 1):
self.phantom.zedges[i] = -15. + i * self.dz
self.phantom.edges_to_centers()
#!/usr/bin/env python2.4
import sys
from egsnrc import EGSPhant
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
# encoding: utf-8
"""
phant_info.py
Created by David Chin on 2006-07-11.
Copyright (c) 2006 Brigham & Women's Hospital. All rights reserved.
"""
import sys
from egsnrc.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
phant.print_info()
#!/usr/bin/env python2.4
# $Id: fix_phantom_tissue.py 86 2007-11-12 22:11:40Z dwchin $
from egsnrc.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 == 'ICRUTISSUE700ICRU':
proper_dens = 1.0
p.densityscan[k,j,i] = proper_dens
elif mat == 'ICRPBONE700ICRU': # set to mid-range value
proper_dens = 0.5 * (p.density[mat][0] + p.density[mat][1])
p.densityscan[k,j,i] = proper_dens
new_filename = p.phantfilename.split('.egsphant')[0] + '_fixed.egsphant'
p.save(new_filename)
#!/usr/bin/env python2.4
import sys
from egsnrc import EGSPhant
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 python2.4
# $Id: fix_phantom_tissue.py 86 2007-11-12 22:11:40Z dwchin $
from egsnrc.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 == 'ICRUTISSUE700ICRU':
proper_dens = 1.0
p.densityscan[k, j, i] = proper_dens
elif mat == 'ICRPBONE700ICRU': # set to mid-range value
proper_dens = 0.5 * (p.density[mat][0] + p.density[mat][1])
p.densityscan[k, j, i] = proper_dens
new_filename = p.phantfilename.split('.egsphant')[0] + '_fixed.egsphant'
p.save(new_filename)
