def bowtie_filter(cfg):
'''
Apply the transmittance of bowtie filter, dim: [Ebin, totalNumCells]
'''
if not cfg.protocol.bowtie:
return cfg
# find bowtie file
bowtieFile = cfg.protocol.bowtie
if not os.path.isfile(bowtieFile):
bowtiePath = get_path().bowtie + "/"
if os.path.isfile(bowtieFile + ".dat"):
bowtieFile += ".dat"
elif os.path.isfile(bowtiePath + bowtieFile):
bowtieFile = bowtiePath + bowtieFile
elif os.path.isfile(bowtiePath + bowtieFile + ".dat"):
bowtieFile = bowtiePath + bowtieFile + ".dat"
else:
raise Exception("Cannot find bowtie file: %s or %s.dat" %
(bowtieFile, bowtieFile))
# read bowtie file
data = np.loadtxt(bowtieFile, dtype=np.single, comments=['#', '%'])
gammas0 = data[:, 0]
t0 = data[:, 1:] # thickness in cm
bowtieMaterials = ['al', 'graphite', 'cu', 'ti']
Evec = cfg.spec.Evec
gammas1 = cfg.det.gammas
muT = 0
for i in range(len(bowtieMaterials)):
mu = GetMu(bowtieMaterials[i], Evec)
f = interpolate.interp1d(gammas0,
t0[:, i],
kind='linear',
fill_value='extrapolate')
t1 = f(gammas1) / cfg.det.cosAlphas
muT += t1 @ mu.reshape(1, len(mu))
trans = np.exp(-muT)
cfg.src.filterTrans *= trans
return cfg
def flat_filter(cfg):
'''
Apply the transmittance of flat filter at source side, dim: [Ebin, totalNumCells]
'''
cosineFactors = 1/cfg.det.cosGammas/cfg.det.cosAlphas
Evec = cfg.sim.Evec
trans = np.ones([cfg.det.totalNumCells, cfg.spec.nEbin], dtype = np.single)
if hasattr(cfg.protocol, "flatFilter"):
for ii in range(0, round(len(cfg.protocol.flatFilter)/2)):
material = cfg.protocol.flatFilter[2*ii]
depth = cfg.protocol.flatFilter[2*ii+1]
mu = GetMu(material, Evec)
trans *= np.exp(-depth*0.1*cosineFactors @ mu.reshape(1, mu.size))
cfg.src.filterTrans *= trans
return cfg
def set_material(cfg, materialList):
Evec = cfg.spec.Evec
nMat = len(materialList)
Mus = np.zeros([Evec.size, nMat], dtype=np.single)
for i in range(nMat):
Mus[:, i] = GetMu(materialList[i], Evec) / 10 # cm^-1 --> mm^-1
# the C func wants data order: materialIndex -> Ebin, so the dim is [Ebin, materialIndex]
fun = cfg.clib.set_material_info_vox
fun.argtypes = [c_int, c_int, ndpointer(c_float)]
fun.restype = None
fun(nMat, Evec.size, Mus)
def Detection_EI(cfg, viewId, subViewId):
Evec = cfg.sim.Evec
# detection efficiency
if viewId == cfg.sim.startViewId and subViewId == 0:
# detector prefilter
Wvec = feval(cfg.physics.prefilterCallback, cfg)
# detector absorption
detectorMu = GetMu(cfg.scanner.detectorMaterial, Evec)
detEff = 1-np.exp(-0.1*cfg.scanner.detectorDepth/cfg.det.cosBetas*detectorMu)
cfg.sim.Wvec = Wvec*detEff
# Apply energy-dependent detection efficiency
thisSubView = cfg.thisSubView*cfg.sim.Wvec
# scatter cross-talk
if cfg.physics.crosstalkCallback:
thisSubView = feval(cfg.physics.crosstalkCallback, thisSubView, cfg)
# quantum noise
if cfg.sim.enableQuantumNoise:
thisSubView = randpf(thisSubView)
# merge energies
thisSubView = thisSubView.dot(Evec)
# lag
if cfg.physics.lagCallback:
thisSubView = feval(cfg.physics.lagCallback, thisSubView, cfg)
# accumulate subviews
if subViewId == 0:
cfg.thisView = thisSubView
else:
cfg.thisView += thisSubView
# for final subview
if subViewId == cfg.sim.subViewCount-1:
# optical cross-talk
if cfg.physics.opticalCrosstalkCallback:
cfg.thisView = feval(cfg.physics.opticalCrosstalkCallback, cfg.thisView, cfg)
# DAS
cfg.thisView = feval(cfg.physics.DASCallback, cfg.thisView, cfg)
return cfg
def Detection_prefilter(cfg):
# Wvec dim: [pixel, Ebin] ([col, row, Ebin])
Evec = cfg.sim.Evec
Wvec = np.ones(Evec.shape, dtype=np.single)
if hasattr(cfg.scanner, "detectorPrefilter"):
for ii in range(round(len(cfg.scanner.detectorPrefilter) / 2)):
material = cfg.scanner.detectorPrefilter[2 * ii]
depth = cfg.scanner.detectorPrefilter[2 * ii + 1]
mu = GetMu(material, Evec)
Wvec = Wvec * np.exp(-mu * depth * 0.1)
Wvec = nm.repmat(Wvec, cfg.det.totalNumCells, 1)
return Wvec
# Copyright 2020, General Electric Company. All rights reserved. See https://github.com/xcist/code/blob/master/LICENSE
import numpy as np
from catsim.GetMu import GetMu
Mu = []
Mu.append(GetMu('water', 70))
Mu.append(GetMu('water', 70.0))
Mu.append(GetMu('bone', (30, 50, 70)))
Mu.append(GetMu('bone', [30, 50, 70]))
Mu.append(GetMu('al', range(10, 60, 10)))
types = ['int', 'float', 'tuple', 'list', 'range']
for mu in Mu:
print()
for ii in range(len(mu)):
print(mu[ii], end="\n")
print()
Evec = np.array([(20, 30, 40), (50, 60, 70)], dtype=np.single)
mu = GetMu('water', Evec)
print(mu, type(mu))