Skip to content

GitLab

B
BioEM
Commit 65ca8537 authored by David Rohr's avatar David Rohr
Browse files
Options

convert indent spaces to tabs, unify indentation

parent a30096fc
Hide whitespace changes
Inline Side-by-side
Showing with 324 additions and 324 deletions
bioem.cpp
View file @ 65ca8537
......@@ -54,9 +54,9 @@ int bioem::configure(int ac, char* av[])
/*************************************************************************************/
/*** Inizialzing default variables ***/
std::string infile,modelfile,mapfile;
Model.readPDB=false;
param.writeAngles=false;
std::string infile, modelfile, mapfile;
Model.readPDB = false;
param.writeAngles = false;
param.dumpMap = false;
param.loadMap = false;
......@@ -104,20 +104,20 @@ int bioem::configure(int ac, char* av[])
if (vm.count("Inputfile"))
{
cout << "Input file is: ";
cout << vm["Inputfile"].as< std::string >()<< "\n";
infile=vm["Inputfile"].as< std::string >();
cout << vm["Inputfile"].as< std::string >() << "\n";
infile = vm["Inputfile"].as< std::string >();
}
if (vm.count("Modelfile"))
{
cout << "Model file is: "
<< vm["Modelfile"].as< std::string >() << "\n";
modelfile=vm["Modelfile"].as< std::string >();
modelfile = vm["Modelfile"].as< std::string >();
}
if (vm.count("ReadPDB"))
{
cout << "Reading model file in PDB format.\n";
Model.readPDB=true;
Model.readPDB = true;
}
if (vm.count("DumpMaps"))
......@@ -136,7 +136,7 @@ int bioem::configure(int ac, char* av[])
{
cout << "Paricle file is: "
<< vm["Particlesfile"].as< std::string >() << "\n";
mapfile=vm["Particlesfile"].as< std::string >();
mapfile = vm["Particlesfile"].as< std::string >();
}
}
catch(std::exception& e)
......@@ -184,15 +184,15 @@ int bioem::precalculate()
// Generating Grids of orientations
param.CalculateGridsParam();
myfloat_t sum,sumsquare;
myfloat_t sum, sumsquare;
//Precalculating cross-correlations of maps
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap ; iRefMap++)
{
calcross_cor(RefMap.getmap(iRefMap),sum,sumsquare);
calcross_cor(RefMap.getmap(iRefMap), sum, sumsquare);
//Storing Crosscorrelations in Map class
RefMap.sum_RefMap[iRefMap]=sum;
RefMap.sumsquare_RefMap[iRefMap]=sumsquare;
RefMap.sum_RefMap[iRefMap] = sum;
RefMap.sumsquare_RefMap[iRefMap] = sumsquare;
}
// Precalculating CTF Kernels stored in class Param
......@@ -219,13 +219,13 @@ int bioem::run()
// Inizialzing Probabilites to zero and constant to -Infinity
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
pProb[iRefMap].Total=0.0;
pProb[iRefMap].Constoadd=-9999999;
pProb[iRefMap].max_prob=-9999999;
pProb[iRefMap].Total = 0.0;
pProb[iRefMap].Constoadd = -9999999;
pProb[iRefMap].max_prob = -9999999;
for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
{
pProb[iRefMap].forAngles[iOrient]=0.0;
pProb[iRefMap].ConstAngle[iOrient]=-99999999;
pProb[iRefMap].forAngles[iOrient] = 0.0;
pProb[iRefMap].ConstAngle[iOrient] = -99999999;
}
}
/**************************************************************************************/
......@@ -237,11 +237,11 @@ int bioem::run()
mycomplex_t* proj_mapFFT;
myfloat_t* conv_map = new myfloat_t[param.param_device.NumberPixels * param.param_device.NumberPixels];
mycomplex_t* conv_mapFFT;
myfloat_t sumCONV,sumsquareCONV;
myfloat_t sumCONV, sumsquareCONV;
//allocating fftw_complex vector
proj_mapFFT= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels*param.param_device.NumberFFTPixels1D);
conv_mapFFT= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels*param.param_device.NumberFFTPixels1D);
proj_mapFFT = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
conv_mapFFT = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
HighResTimer timer;
......@@ -304,7 +304,7 @@ int bioem::run()
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
/**** Total Probability ***/
outputProbFile << "RefMap " << iRefMap << " Probability " << log(pProb[iRefMap].Total)+pProb[iRefMap].Constoadd+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " Constant " << pProb[iRefMap].Constoadd << "\n";
outputProbFile << "RefMap " << iRefMap << " Probability " << log(pProb[iRefMap].Total) + pProb[iRefMap].Constoadd + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5)*(log(2 * M_PI) + 1) + log(param.param_device.volu) << " Constant " << pProb[iRefMap].Constoadd << "\n";
outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";
......@@ -326,7 +326,7 @@ int bioem::run()
{
for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
{
angProbfile << " " << iRefMap << " " << param.angles[iProjectionOut].pos[0] << " " << param.angles[iProjectionOut].pos[1] << " " << param.angles[iProjectionOut].pos[2] << " " << log(pProb[iRefMap].forAngles[iProjectionOut])+pProb[iRefMap].ConstAngle[iProjectionOut]+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " " << log(param.param_device.volu) << "\n";
angProbfile << " " << iRefMap << " " << param.angles[iProjectionOut].pos[0] << " " << param.angles[iProjectionOut].pos[1] << " " << param.angles[iProjectionOut].pos[2] << " " << log(pProb[iRefMap].forAngles[iProjectionOut]) + pProb[iRefMap].ConstAngle[iProjectionOut] + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5)*(log(2 * M_PI) + 1) + log(param.param_device.volu) << " " << log(param.param_device.volu) << "\n";
}
}
......@@ -346,7 +346,7 @@ int bioem::run()
if (param.refCTF)
{
delete[] param.refCTF;
param.refCTF =NULL;
param.refCTF = NULL;
}
RefMap.freePointers();
......@@ -357,12 +357,12 @@ int bioem::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_m
{
if (FFTAlgo)
{
#pragma omp parallel
#pragma omp parallel
{
mycomplex_t *localCCT;
myfloat_t *lCC;
localCCT= (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) *param.param_device.NumberPixels*param.param_device.NumberFFTPixels1D);
lCC= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
localCCT = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
lCC = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
const int num_threads = omp_get_num_threads();
const int thread_id = omp_get_thread_num();
......@@ -372,7 +372,7 @@ int bioem::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_m
for (int iRefMap = iStart; iRefMap < iEnd; iRefMap ++)
{
calculateCCFFT(iRefMap,iProjectionOut, iConv, sumC, sumsquareC, localmultFFT, localCCT,lCC);
calculateCCFFT(iRefMap, iProjectionOut, iConv, sumC, sumsquareC, localmultFFT, localCCT, lCC);
}
myfftw_free(localCCT);
myfftw_free(lCC);
......@@ -380,30 +380,30 @@ int bioem::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_m
}
else
{
#pragma omp parallel for
#pragma omp parallel for
for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
compareRefMapShifted < -1 > (iRefMap, iProjectionOut, iConv, conv_map, pProb, param.param_device, RefMap);
}
}
return(0);
}
inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC,myfloat_t sumsquareC, mycomplex_t* localConvFFT,mycomplex_t* localCCT,myfloat_t* lCC)
inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC)
{
const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.FFTMapSize];
for(int i = 0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
{
localCCT[i][0] = localConvFFT[i][0] * RefMapFFT[i][0] + localConvFFT[i][1] * RefMapFFT[i][1];
localCCT[i][1] = localConvFFT[i][1] * RefMapFFT[i][0] - localConvFFT[i][0] * RefMapFFT[i][1];
}
myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,localCCT,lCC);
myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, localCCT, lCC);
doRefMapFFT(iRefMap, iOrient, iConv, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
}
int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
{
/**************************************************************************************/
/**** BioEM Create Projection routine in Euler angle predefined grid****************
......@@ -412,43 +412,43 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
myfloat3_t RotatedPointsModel[Model.nPointsModel];
myfloat_t rotmat[3][3];
myfloat_t alpha, gam,beta;
myfloat_t alpha, gam, beta;
myfloat_t* localproj;
localproj= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) *param.param_device.NumberPixels*param.param_device.NumberPixels);
memset(localproj,0,param.param_device.NumberPixels*param.param_device.NumberPixels*sizeof(*localproj));
localproj = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
memset(localproj, 0, param.param_device.NumberPixels * param.param_device.NumberPixels * sizeof(*localproj));
alpha=param.angles[iMap].pos[0];
beta=param.angles[iMap].pos[1];
gam=param.angles[iMap].pos[2];
alpha = param.angles[iMap].pos[0];
beta = param.angles[iMap].pos[1];
gam = param.angles[iMap].pos[2];
/**** To see how things are going: cout << "Id " << omp_get_thread_num() << " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***/
/********** Creat Rotation with pre-defiend grid of orientations**********/
rotmat[0][0]=cos(gam)*cos(alpha)-cos(beta)*sin(alpha)*sin(gam);
rotmat[0][1]=cos(gam)*sin(alpha)+cos(beta)*cos(alpha)*sin(gam);
rotmat[0][2]=sin(gam)*sin(beta);
rotmat[1][0]=-sin(gam)*cos(alpha)-cos(beta)*sin(alpha)*cos(gam);
rotmat[1][1]=-sin(gam)*sin(alpha)+cos(beta)*cos(alpha)*cos(gam);
rotmat[1][2]=cos(gam)*sin(beta);
rotmat[2][0]=sin(beta)*sin(alpha);
rotmat[2][1]=-sin(beta)*cos(alpha);
rotmat[2][2]=cos(beta);
for(int n=0; n< Model.nPointsModel; n++)
rotmat[0][0] = cos(gam) * cos(alpha) - cos(beta) * sin(alpha) * sin(gam);
rotmat[0][1] = cos(gam) * sin(alpha) + cos(beta) * cos(alpha) * sin(gam);
rotmat[0][2] = sin(gam) * sin(beta);
rotmat[1][0] = -sin(gam) * cos(alpha) - cos(beta) * sin(alpha) * cos(gam);
rotmat[1][1] = -sin(gam) * sin(alpha) + cos(beta) * cos(alpha) * cos(gam);
rotmat[1][2] = cos(gam) * sin(beta);
rotmat[2][0] = sin(beta) * sin(alpha);
rotmat[2][1] = -sin(beta) * cos(alpha);
rotmat[2][2] = cos(beta);
for(int n = 0; n < Model.nPointsModel; n++)
{
RotatedPointsModel[n].pos[0]=0.0;
RotatedPointsModel[n].pos[1]=0.0;
RotatedPointsModel[n].pos[2]=0.0;
RotatedPointsModel[n].pos[0] = 0.0;
RotatedPointsModel[n].pos[1] = 0.0;
RotatedPointsModel[n].pos[2] = 0.0;
}
for(int n=0; n< Model.nPointsModel; n++)
for(int n = 0; n < Model.nPointsModel; n++)
{
for(int k=0; k< 3; k++)
for(int k = 0; k < 3; k++)
{
for(int j=0; j< 3; j++)
for(int j = 0; j < 3; j++)
{
RotatedPointsModel[n].pos[k]+=rotmat[k][j]*Model.PointsModel[n].pos[j];
RotatedPointsModel[n].pos[k] += rotmat[k][j] * Model.PointsModel[n].pos[j];
}
}
}
......@@ -456,41 +456,41 @@ int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
int i, j;
/************ Projection over the Z axis********************/
for(int n=0; n< Model.nPointsModel; n++)
for(int n = 0; n < Model.nPointsModel; n++)
{
//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
i=floor(RotatedPointsModel[n].pos[0]/param.pixelSize+ (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
j=floor(RotatedPointsModel[n].pos[1]/param.pixelSize+ (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
i = floor(RotatedPointsModel[n].pos[0] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
j = floor(RotatedPointsModel[n].pos[1] / param.pixelSize + (myfloat_t) param.param_device.NumberPixels / 2.0f + 0.5f);
localproj[i*param.param_device.NumberPixels+j]+=Model.densityPointsModel[n]/Model.NormDen;
localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
}
/**** Output Just to check****/
if(iMap==10)
if(iMap == 10)
{
ofstream myexamplemap;
ofstream myexampleRot;
myexamplemap.open ("MAP_i10");
myexampleRot.open ("Rot_i10");
myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
for(int k=0; k<param.param_device.NumberPixels; k++)
for(int k = 0; k < param.param_device.NumberPixels; k++)
{
for(int j=0; j<param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*param.param_device.NumberPixels+j];
for(int j = 0; j < param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j << " " << localproj[k * param.param_device.NumberPixels + j];
}
myexamplemap << " \n";
for(int n=0; n< Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
for(int n = 0; n < Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
myexamplemap.close();
myexampleRot.close();
}
/***** Converting projection to Fourier Space for Convolution later with kernel****/
/********** Omp Critical is necessary with FFTW*******/
myfftw_execute_dft_r2c(param.fft_plan_r2c_forward,localproj,mapFFT);
myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
return(0);
}
int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
{
/**************************************************************************************/
/**** BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
......@@ -499,14 +499,14 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,m
/**************************************************************************************/
myfloat_t* localconvFFT;
localconvFFT= (myfloat_t *) myfftw_malloc(sizeof(myfloat_t)*param.param_device.NumberPixels*param.param_device.NumberPixels);
localconvFFT = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
mycomplex_t* tmp;
tmp = (mycomplex_t*) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
/**** Multiplying FFTmap with corresponding kernel ****/
const mycomplex_t* refCTF = &param.refCTF[iConv * param.FFTMapSize];
for(int i=0;i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D;i++)
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
{
localmultFFT[i][0] = lproj[i][0] * refCTF[i][0] + lproj[i][1] * refCTF[i][1];
localmultFFT[i][1] = lproj[i][1] * refCTF[i][0] - lproj[i][0] * refCTF[i][1];
......@@ -517,20 +517,20 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,m
memcpy(tmp, localmultFFT, sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
/**** Bringing convoluted Map to real Space ****/
myfftw_execute_dft_c2r(param.fft_plan_c2r_backward,tmp,localconvFFT);
myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, localconvFFT);
/****Asigning convolution fftw_complex to bioem_map ****/
for(int i=0; i < param.param_device.NumberPixels ; i++ )
for(int i = 0; i < param.param_device.NumberPixels ; i++ )
{
for(int j=0; j < param.param_device.NumberPixels ; j++ )
for(int j = 0; j < param.param_device.NumberPixels ; j++ )
{
Mapconv[i*param.param_device.NumberPixels+j] = localconvFFT[i*param.param_device.NumberPixels+j];
Mapconv[i * param.param_device.NumberPixels + j] = localconvFFT[i * param.param_device.NumberPixels + j];
}
}
/*** Calculating Cross-correlations of cal-convoluted map with its self *****/
sumC=0;
sumsquareC=0;
sumC = 0;
sumsquareC = 0;
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
{
sumC += localconvFFT[i];
......@@ -550,20 +550,20 @@ int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,m
return(0);
}
int bioem::calcross_cor(myfloat_t* localmap,myfloat_t& sum,myfloat_t& sumsquare)
int bioem::calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare)
{
/*********************** Routine to calculate Cross correlations***********************/
sum=0.0;
sumsquare=0.0;
sum = 0.0;
sumsquare = 0.0;
for (int i = 0; i < param.param_device.NumberPixels; i++)
{
for (int j = 0; j < param.param_device.NumberPixels; j++)
{
// Calculate Sum of pixels
sum += localmap[i*param.param_device.NumberPixels+j];
sum += localmap[i * param.param_device.NumberPixels + j];
// Calculate Sum of pixels squared
sumsquare += localmap[i*param.param_device.NumberPixels+j] * localmap[i*param.param_device.NumberPixels+j];
sumsquare += localmap[i * param.param_device.NumberPixels + j] * localmap[i * param.param_device.NumberPixels + j];
}
}
return(0);
......
bioem_algorithm.h
View file @ 65ca8537
......@@ -61,8 +61,8 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
const myfloat_t ForLogProb = (sumsquare * param.Ntotpi - sum * sum);
// Products of different cross-correlations (first element in formula)
const myfloat_t firstele = param.Ntotpi * (sumsquareref * sumsquare-crossproMapConv * crossproMapConv) +
2 * sumref * sum * crossproMapConv - sumsquareref * sum * sum - sumref * sumref * sumsquare;
const myfloat_t firstele = param.Ntotpi * (sumsquareref * sumsquare - crossproMapConv * crossproMapConv) +
2 * sumref * sum * crossproMapConv - sumsquareref * sum * sum - sumref * sumref * sumsquare;
//******* Calculating log of Prob*********/
// As in fortran code: logpro=(3-Ntotpi)*0.5*log(firstele/pConvMap[iOrient].ForLogProbfromConv[iConv])+(Ntotpi*0.5-2)*log(Ntotpi-2)-0.5*log(pConvMap[iOrient].ForLogProbfromConv[iConv])+0.5*log(PI)+(1-Ntotpi*0.5)*(log(2*PI)+1);
......@@ -70,7 +70,7 @@ __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, float 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 sumC, myfloat_t sumsquareC, float value, int disx, int disy, bioem_Probability* pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
{
/********************************************************/
/*********** Calculates the BioEM probability ***********/
......@@ -80,8 +80,8 @@ __device__ static inline void calProb(int iRefMap,int iOrient, int iConv,myfloat
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb);
//GCC is too stupid to inline properly, so the code is copied here
if(pProb[iRefMap].Constoadd < logpro)
{
if(pProb[iRefMap].Constoadd < logpro)
{
pProb[iRefMap].Total = pProb[iRefMap].Total * exp(-logpro + pProb[iRefMap].Constoadd);
pProb[iRefMap].Constoadd = logpro;
}
......@@ -106,33 +106,33 @@ __device__ static inline void calProb(int iRefMap,int iOrient, int iConv,myfloat
__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)
{
for (int cent_x = 0; cent_x <= param.maxDisplaceCenter; cent_x=cent_x+param.GridSpaceCenter)
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)
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, 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)
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, pProb, param, RefMap);
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);
}
}
for (int cent_x = param.NumberPixels-param.maxDisplaceCenter; cent_x < param.NumberPixels; cent_x=cent_x+param.GridSpaceCenter)
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)
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), param.NumberPixels-cent_x, cent_y, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * 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)
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), param.NumberPixels-cent_x, param.NumberPixels-cent_y, pProb, param, RefMap);
calProb(iRefMap, iOrient, iConv, sumC, sumsquareC, (myfloat_t) lCC[cent_x * param.NumberPixels + cent_y] / (myfloat_t) (param.NumberPixels * param.NumberPixels), param.NumberPixels - cent_x, param.NumberPixels - cent_y, pProb, param, RefMap);
}
}
}
template <int GPUAlgo, class RefT>
__device__ static inline void compareRefMap(const int iRefMap, const int iOrient, const int iConv, const myfloat_t* Mapconv, bioem_Probability* pProb, const bioem_param_device& param, const RefT& RefMap,
const int cent_x, const int cent_y, const int myShift = 0, const int nShifts2 = 0, const int myRef = 0, const bool threadActive = true)
const int cent_x, const int cent_y, const int myShift = 0, const int nShifts2 = 0, const int myRef = 0, const bool threadActive = true)
{
// ********************** Calculating BioEM Probability ********************************
......@@ -145,9 +145,9 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
myfloat_t sum, sumsquare, crossproMapConv;
__m128 sum_v = _mm_setzero_ps(), sumsquare_v = _mm_setzero_ps(), cross_v = _mm_setzero_ps(), d1, d2;
#else
myfloat_t sum=0.0;
myfloat_t sumsquare=0.0;
myfloat_t crossproMapConv=0.0;
myfloat_t sum = 0.0;
myfloat_t sumsquare = 0.0;
myfloat_t crossproMapConv = 0.0;
#endif
// Loop over Pixels to calculate dot product and cross-correlations of displaced Ref Conv. Map
myfloat_t logpro;
......@@ -182,7 +182,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
const float* ptr2 = RefMap.getp(iRefMap, i, jStart);
int j;
const int count = jEnd - jStart;
for (j = 0;j <= count - 4;j += 4)
for (j = 0; j <= count - 4; j += 4)
{
d1 = _mm_loadu_ps(ptr1);
d2 = _mm_loadu_ps(ptr2);
......@@ -201,7 +201,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
// Crosscorrelation of calculated displaced map
sum += pointMap;
// Calculate Sum of pixels squared
sumsquare += pointMap*pointMap;
sumsquare += pointMap * pointMap;
}
#endif
}
......@@ -380,18 +380,18 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
else
#endif
// Summing & Storing total/Orientation Probabilites for each map
// Summing & Storing total/Orientation Probabilites for each map
{
update_prob<-1>(logpro, iRefMap, iOrient, iConv, cent_x, cent_y, pProb);
update_prob < -1 > (logpro, iRefMap, iOrient, iConv, cent_x, cent_y, pProb);
}
}
template <int GPUAlgo, class RefT>
__device__ static inline void compareRefMapShifted(const int iRefMap, const int iOrient, const int iConv, const myfloat_t* Mapconv, bioem_Probability* pProb, const bioem_param_device& param, const RefT& RefMap)
{
for (int cent_x = -param.maxDisplaceCenter; cent_x <= param.maxDisplaceCenter; cent_x=cent_x+param.GridSpaceCenter)
for (int cent_x = -param.maxDisplaceCenter; cent_x <= param.maxDisplaceCenter; cent_x = cent_x + param.GridSpaceCenter)
{
for (int cent_y = -param.maxDisplaceCenter; cent_y <= param.maxDisplaceCenter; cent_y=cent_y+param.GridSpaceCenter)
for (int cent_y = -param.maxDisplaceCenter; cent_y <= param.maxDisplaceCenter; cent_y = cent_y + param.GridSpaceCenter)
{
compareRefMap<GPUAlgo>(iRefMap, iOrient, iConv, Mapconv, pProb, param, RefMap, cent_x, cent_y);
}
......
bioem_cuda.cu
View file @ 65ca8537
......@@ -37,7 +37,7 @@ __global__ void compareRefMap_kernel(const int iOrient, const int iConv, const m
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < maxRef)
{
compareRefMap<0>(iRefMap,iOrient,iConv, pMap, pProb, param, *RefMap, cent_x, cent_y);
compareRefMap<0>(iRefMap, iOrient, iConv, pMap, pProb, param, *RefMap, cent_x, cent_y);
}
}
......@@ -46,7 +46,7 @@ __global__ void compareRefMapShifted_kernel(const int iOrient, const int iConv,
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < maxRef)
{
compareRefMapShifted<1>(iRefMap,iOrient,iConv, pMap, pProb, param, *RefMap);
compareRefMapShifted<1>(iRefMap, iOrient, iConv, pMap, pProb, param, *RefMap);
}
}
......@@ -56,7 +56,7 @@ __global__ void cudaZeroMem(void* ptr, size_t size)
int mysize = size / sizeof(int);
int myid = myBlockDimX * myBlockIdxX + myThreadIdxX;
int mygrid = myBlockDimX * myGridDimX;
for (int i = myid;i < mysize;i += mygrid) myptr[i] = 0;
for (int i = myid; i < mysize; i += mygrid) myptr[i] = 0;
}
__global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iConv, const myfloat_t* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap RefMap, const int blockoffset, const int nShifts, const int nShiftBits, const int maxRef)
......@@ -72,7 +72,7 @@ __global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iCon
const bool threadActive = myShiftIdx < nShifts && myShiftIdy < nShifts && iRefMap < maxRef;
compareRefMap<2>(iRefMap,iOrient,iConv, pMap, pProb, param, RefMap, cent_x, cent_y, myShift, nShifts * nShifts, myRef, threadActive);
compareRefMap<2>(iRefMap, iOrient, iConv, pMap, pProb, param, RefMap, cent_x, cent_y, myShift, nShifts * nShifts, myRef, threadActive);
}
__global__ void multComplexMap(const mycomplex_t* convmap, const mycomplex_t* refmap, mycuComplex_t* out, const int NumberPixelsTotal, const int MapSize, const int NumberMaps, const int Offset)
......@@ -80,7 +80,7 @@ __global__ void multComplexMap(const mycomplex_t* convmap, const mycomplex_t* re
if (myBlockIdxX >= NumberMaps) return;
const mycomplex_t* myin = &refmap[myBlockIdxX * MapSize + Offset];
mycuComplex_t* myout = &out[(myBlockIdxX * MapSize)];
for(int i = myThreadIdxX;i < NumberPixelsTotal;i += myBlockDimX)
for(int i = myThreadIdxX; i < NumberPixelsTotal; i += myBlockDimX)
{
myout[i].x = convmap[i][0] * myin[i][0] + convmap[i][1] * myin[i][1];
myout[i].y = convmap[i][1] * myin[i][0] - convmap[i][0] * myin[i][1];
......@@ -123,7 +123,7 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* c
if (FFTAlgo)
{
checkCudaErrors(cudaMemcpyAsync(&pConvMapFFT[(iConv & 1) * param.FFTMapSize], localmultFFT, param.FFTMapSize * sizeof(mycomplex_t), cudaMemcpyHostToDevice, cudaStream));
for (int i = 0;i < maxRef;i += CUDA_FFTS_AT_ONCE)
for (int i = 0; i < maxRef; i += CUDA_FFTS_AT_ONCE)
{
const int num = min(CUDA_FFTS_AT_ONCE, maxRef - i);
multComplexMap<<<num, CUDA_THREAD_COUNT, 0, cudaStream>>>(&pConvMapFFT[(iConv & 1) * param.FFTMapSize], pRefMapsFFT, pFFTtmp2, param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D, param.FFTMapSize, num, i);
......@@ -161,24 +161,24 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* c
const int nShiftBits = ilog2(nShifts);
size_t totalBlocks = divup((size_t) maxRef * (size_t) nShifts * (size_t) nShifts, (size_t) CUDA_THREAD_COUNT);
size_t nBlocks = CUDA_BLOCK_COUNT;
for (size_t i = 0;i < totalBlocks;i += nBlocks)
for (size_t i = 0; i < totalBlocks; i += nBlocks)
{
compareRefMapLoopShifts_kernel <<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *gpumap, i, nShifts, nShiftBits, maxRef);
compareRefMapLoopShifts_kernel<<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream >>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *gpumap, i, nShifts, nShiftBits, maxRef);