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Commit 19bc6d4d authored by Pilar Cossio's avatar Pilar Cossio
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Tutorial Corr

parent 16384bca
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Tutorial_BioEM/MODEL_COMPARISION/Param_Input_ModelComparision
View file @ 19bc6d4d
......@@ -2,16 +2,13 @@
NUMBER_PIXELS 224
PIXEL_SIZE 1.32
###### Sincs its a full atom structure #####
NO_PROJECT_RADIUS
##### Quaterion grid points: #######
USE_QUATERNIONS
##### Constrast transfer integration: #######
CTF_B_FACTOR 100.0 300.5 8
CTF_B_ENV 100.0 300.5 8
CTF_DEFOCUS 1.0 6.0 5
CTF_AMPLITUDE 0.1 0.1 1
CTF_AMPLITUDE 0.01 0.5 3
##### Center displacement: #######
DISPLACE_CENTER 10 2
Tutorial_BioEM/MODEL_COMPARISION/subtract_LogP.sh 0 → 100644
View file @ 19bc6d4d
paste $1 $2 | grep LogProb: | awk 'BEGIN{cum=0;dif=0}{if($1=="RefMap:"){dif=$4-$10;cum+=dif;printf"MapNum: %6d Mod1: %10.5f Mod2: %10.5f Dif: %10.5f Cum: %10.5f\n",$2,$4,$10,dif,cum}}'
bioem_algorithm.h
View file @ 19bc6d4d
......@@ -85,13 +85,23 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
return(logpro);
}
__device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, myfloat_t value, int disx, int disy, bioem_Probability& pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
__device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myfloat_t amp, myfloat_t pha, myfloat_t env, myfloat_t sumC, myfloat_t sumsquareC, myfloat_t value, int disx, int disy, bioem_Probability& pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
{
// ********************************************************
// *********** Calculates the BioEM probability ***********
// ********************************************************
const myfloat_t logpro = calc_logpro(param, sumC, sumsquareC, value, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
myfloat_t logpro = calc_logpro(param, sumC, sumsquareC, value, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
//Adding Gaussian Prior to envelope parameter
if(not param.tousepsf){
logpro = logpro - env * env / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf ;
} else {
myfloat_t envF;
envF = 4.* M_PI * M_PI * env / ( env * env + pha * pha) ;
logpro = logpro - envF * envF / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf ;
}
//GCC is too stupid to inline properly, so the code is copied here
......@@ -115,9 +125,12 @@ __device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myflo
pProbMap.Total += exp(logpro - pProbMap.Constoadd);
if(param.debugterm){
// printf("Separate Ptot: %f Const: %f logProb %f %f %f \n",pProbMap.Total,pProbMap.Constoadd,logpro,pProbMap.max.max_prob_norm,pProbMap.max.max_prob_mu);
printf("Separate Ptot: %f Const: %f logProb %f %f %f \n",pProbMap.Total,pProbMap.Constoadd,logpro,pProbMap.max.max_prob_norm,pProbMap.max.max_prob_mu);
}
// printf("Separate Ptot: %f Const: %f logProb %f %f %f \n",amp,pha,env,logpro,param.sigmaPriorbctf);
// cout << amp,pha,env,logpro,sumC;
if (param.writeAngles)
{
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
......@@ -135,28 +148,28 @@ __device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myflo
}
__device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient, const int iConv, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability& pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
__device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient, const int iConv, const myfloat_t amp, const myfloat_t pha, const myfloat_t env, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability& pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
{
for (int cent_x = 0; cent_x <= param.maxDisplaceCenter; cent_x = cent_x + param.GridSpaceCenter)
{
for (int cent_y = 0; cent_y <= param.maxDisplaceCenter; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y, pProb, param, RefMap);
}
for (int cent_y = param.NumberPixels - param.maxDisplaceCenter; cent_y < param.NumberPixels; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y - param.NumberPixels, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv,amp, pha, env, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x, cent_y - param.NumberPixels, pProb, param, RefMap);
}
}
for (int cent_x = param.NumberPixels - param.maxDisplaceCenter; cent_x < param.NumberPixels; cent_x = cent_x + param.GridSpaceCenter)
{
for (int cent_y = 0; cent_y < param.maxDisplaceCenter; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x - param.NumberPixels, cent_y, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv,amp, pha, env, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x - param.NumberPixels, cent_y, pProb, param, RefMap);
}
for (int cent_y = param.NumberPixels - param.maxDisplaceCenter; cent_y <= param.NumberPixels; cent_y = cent_y + param.GridSpaceCenter)
{
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x - param.NumberPixels, cent_y - param.NumberPixels, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), cent_x - param.NumberPixels, cent_y - param.NumberPixels, pProb, param, RefMap);
}
}
// printf("HERE!!!");
......
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