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Commit 9582b044 authored by David Rohr's avatar David Rohr
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fix comment style

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bioem.cpp
View file @ 9582b044
......@@ -47,13 +47,13 @@ bioem::~bioem()
int bioem::configure(int ac, char* av[])
{
//**************************************************************************************
//**** Configuration Routine using boost for extracting parameters, models and maps ****
//**************************************************************************************
//****** And Precalculating necessary grids, map crosscorrelations and kernels ********
//*************************************************************************************
// **************************************************************************************
// **** Configuration Routine using boost for extracting parameters, models and maps ****
// **************************************************************************************
// ****** And Precalculating necessary grids, map crosscorrelations and kernels ********
// *************************************************************************************
/*** Inizialzing default variables ***/
// *** Inizialzing default variables ***
std::string infile, modelfile, mapfile;
Model.readPDB = false;
param.writeAngles = false;
......@@ -63,11 +63,11 @@ int bioem::configure(int ac, char* av[])
RefMap.readMultMRC = false;
//*************************************************************************************
// *************************************************************************************
cout << "+++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
//*************************************************************************************
// *************************************************************************************
//********************* Command line reading input with BOOST ************************
// ********************* Command line reading input with BOOST ************************
try {
po::options_description desc("Command line inputs");
......@@ -164,23 +164,23 @@ int bioem::configure(int ac, char* av[])
return 1;
}
//********************* Reading Parameter Input ***************************
// ********************* Reading Parameter Input ***************************
// copying inputfile to param class
param.fileinput = infile.c_str();
param.readParameters();
//********************* Reading Model Input ******************************
// ********************* Reading Model Input ******************************
// copying modelfile to model class
Model.filemodel = modelfile.c_str();
Model.readModel();
//********************* Reading Particle Maps Input **********************
//********* HERE: PROBLEM if maps dont fit on the memory!! ***************
// ********************* Reading Particle Maps Input **********************
// ********* HERE: PROBLEM if maps dont fit on the memory!! ***************
// copying mapfile to ref map class
RefMap.filemap = mapfile.c_str();
RefMap.readRefMaps(param);
//****************** Precalculating Necessary Stuff *********************
// ****************** Precalculating Necessary Stuff *********************
precalculate();
if (getenv("BIOEM_DEBUG_BREAK"))
......@@ -196,9 +196,9 @@ int bioem::configure(int ac, char* av[])
int bioem::precalculate()
{
//**************************************************************************************
// **************************************************************************************
//* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels *
//**************************************************************************************
// **************************************************************************************
// Generating Grids of orientations
param.CalculateGridsParam();
......@@ -226,12 +226,12 @@ int bioem::precalculate()
int bioem::run()
{
//**************************************************************************************
//**** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
//**************************************************************************************
// **************************************************************************************
// **** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****
// **************************************************************************************
//**** If we want to control the number of threads -> omp_set_num_threads(XX); ******
//****************** Declarying class of Probability Pointer *************************
// **** If we want to control the number of threads -> omp_set_num_threads(XX); ******
// ****************** Declarying class of Probability Pointer *************************
pProb = new bioem_Probability[RefMap.ntotRefMap];
printf("\tInitializing\n");
......@@ -247,12 +247,12 @@ int bioem::run()
pProb[iRefMap].ConstAngle[iOrient] = -99999999;
}
}
//**************************************************************************************
// **************************************************************************************
deviceStartRun();
//******************************** MAIN CYCLE ******************************************
// ******************************** MAIN CYCLE ******************************************
//*** Declaring Private variables for each thread *****
// *** Declaring Private variables for each thread *****
mycomplex_t* proj_mapFFT;
bioem_map conv_map;
mycomplex_t* conv_mapFFT;
......@@ -268,25 +268,25 @@ int bioem::run()
printf("\tInner Loop Count (%d %d %d) %lld\n", param.param_device.maxDisplaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, (long long int) (param.param_device.NumberPixels * param.param_device.NumberPixels * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1) * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1)));
for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
{
//***************************************************************************************
//***** Creating Projection for given orientation and transforming to Fourier space *****
// ***************************************************************************************
// ***** Creating Projection for given orientation and transforming to Fourier space *****
timer.ResetStart();
createProjection(iProjectionOut, proj_mapFFT);
printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime());
//***************************************************************************************
//***** **** Internal Loop over convolutions **** *****
// ***************************************************************************************
// ***** **** Internal Loop over convolutions **** *****
for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
{
printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
//*** Calculating convolutions of projection map and crosscorrelations ***
// *** Calculating convolutions of projection map and crosscorrelations ***
timer.ResetStart();
createConvolutedProjectionMap(iProjectionOut, iConv, proj_mapFFT, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());
//***************************************************************************************
//*** Comparing each calculated convoluted map with all experimental maps ***
// ***************************************************************************************
// *** Comparing each calculated convoluted map with all experimental maps ***
timer.ResetStart();
compareRefMaps(iProjectionOut, iConv, conv_map, conv_mapFFT, sumCONV, sumsquareCONV);
......@@ -307,9 +307,9 @@ int bioem::run()
deviceFinishRun();
//************* Writing Out Probabilities ***************
// ************* Writing Out Probabilities ***************
//*** Angular Probability ***
// *** Angular Probability ***
// if(param.writeAngles){
ofstream angProbfile;
......@@ -321,12 +321,12 @@ int bioem::run()
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
//**** Total Probability ***
// **** 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 << " Maximizing Param: ";
//*** Param that maximize probability****
// *** Param that maximize probability****
outputProbFile << (pProb[iRefMap].max_prob + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " ";
outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[0] << " ";
outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[1] << " ";
......@@ -338,7 +338,7 @@ int bioem::run()
outputProbFile << pProb[iRefMap].max_prob_cent_y;
outputProbFile << "\n";
//*** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
if(param.writeAngles)
{
......@@ -378,8 +378,8 @@ int bioem::run()
int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
{
//***************************************************************************************
//***** BioEM routine for comparing reference maps to convoluted maps *****
// ***************************************************************************************
// ***** BioEM routine for comparing reference maps to convoluted maps *****
if (FFTAlgo) //IF using the fft algorithm
{
......@@ -418,8 +418,8 @@ int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_m
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)
{
//***************************************************************************************
//***** Calculating cross correlation in FFTALGOrithm *****
// ***************************************************************************************
// ***** Calculating cross correlation in FFTALGOrithm *****
const mycomplex_t* RefMapFFT = &RefMap.RefMapsFFT[iRefMap * param.RefMapSize];
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
......@@ -435,10 +435,10 @@ inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_t
int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
{
//**************************************************************************************
//**** BioEM Create Projection routine in Euler angle predefined grid****************
//********************* and turns projection into Fourier space **********************
//**************************************************************************************
// **************************************************************************************
// **** BioEM Create Projection routine in Euler angle predefined grid****************
// ********************* and turns projection into Fourier space **********************
// **************************************************************************************
myfloat3_t RotatedPointsModel[Model.nPointsModel];
myfloat_t rotmat[3][3];
......@@ -452,9 +452,9 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
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"; ***
// **** 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**********
// ********** 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);
......@@ -485,7 +485,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
int i, j;
//************ Projection over the Z axis********************
// ************ Projection over the Z axis********************
for(int n = 0; n < Model.nPointsModel; n++)
{
//Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
......@@ -495,7 +495,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
localproj[i * param.param_device.NumberPixels + j] += Model.densityPointsModel[n] / Model.NormDen;
}
//**** Output Just to check****
// **** Output Just to check****
if(iMap == 10)
{
ofstream myexamplemap;
......@@ -513,8 +513,8 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
myexampleRot.close();
}
//***** Converting projection to Fourier Space for Convolution later with kernel****
//********** Omp Critical is necessary with FFTW*******
// ***** 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);
return(0);
......@@ -522,18 +522,18 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj, bioem_map& Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC)
{
//**************************************************************************************
//**** BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
//**************** calculated Projection with convoluted precalculated Kernel**********
//*************** and Backtransforming it to real Space ******************************
//**************************************************************************************
// **************************************************************************************
// **** BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
// **************** calculated Projection with convoluted precalculated Kernel**********
// *************** and Backtransforming it to real Space ******************************
// **************************************************************************************
myfloat_t* localconvFFT;
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 ****
// **** Multiplying FFTmap with corresponding kernel ****
const mycomplex_t* refCTF = &param.refCTF[iConv * param.RefMapSize];
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D; i++)
......@@ -546,10 +546,10 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
//FFTW_C2R will destroy the input array, so we have to work on a copy here
memcpy(tmp, localmultFFT, sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
//**** Bringing convoluted Map to real Space ****
// **** Bringing convoluted Map to real Space ****
myfftw_execute_dft_c2r(param.fft_plan_c2r_backward, tmp, localconvFFT);
//****Asigning convolution fftw_complex to bioem_map ****
// ****Asigning convolution fftw_complex to bioem_map ****
for(int i = 0; i < param.param_device.NumberPixels ; i++ )
{
for(int j = 0; j < param.param_device.NumberPixels ; j++ )
......@@ -558,7 +558,7 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
}
}
//*** Calculating Cross-correlations of cal-convoluted map with its self *****
// *** Calculating Cross-correlations of cal-convoluted map with its self *****
sumC = 0;
sumsquareC = 0;
for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberPixels; i++)
......@@ -566,14 +566,14 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
sumC += localconvFFT[i];
sumsquareC += localconvFFT[i] * localconvFFT[i];
}
//*** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
// *** The DTF gives an unnormalized value so have to divded by the total number of pixels in Fourier ***
// Normalizing
myfloat_t norm2 = (myfloat_t) (param.param_device.NumberPixels * param.param_device.NumberPixels);
myfloat_t norm4 = norm2 * norm2;
sumC = sumC / norm2;
sumsquareC = sumsquareC / norm4;
//**** Freeing fftw_complex created (dont know if omp critical is necessary) ****
// **** Freeing fftw_complex created (dont know if omp critical is necessary) ****
myfftw_free(localconvFFT);
myfftw_free(tmp);
......@@ -582,7 +582,7 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
int bioem::calcross_cor(bioem_map& localmap, myfloat_t& sum, myfloat_t& sumsquare)
{
//*********************** Routine to calculate Cross correlations***********************
// *********************** Routine to calculate Cross correlations***********************
sum = 0.0;
sumsquare = 0.0;
......
bioem_algorithm.h
View file @ 9582b044
......@@ -14,8 +14,8 @@
template <int GPUAlgo>
__device__ static inline void update_prob(const myfloat_t logpro, const int iRefMap, const int iOrient, const int iConv, const int cent_x, const int cent_y, bioem_Probability* pProb, myfloat_t* buf3 = NULL, int* bufint = NULL)
{
/******* Summing total Probabilities *************/
/******* Need a constant because of numerical divergence*****/
// ******* Summing total Probabilities *************
// ******* Need a constant because of numerical divergence*****
if(pProb[iRefMap].Constoadd < logpro)
{
pProb[iRefMap].Total = pProb[iRefMap].Total * exp(-logpro + pProb[iRefMap].Constoadd);
......@@ -35,7 +35,7 @@ __device__ static inline void update_prob(const myfloat_t logpro, const int iRef
pProb[iRefMap].forAngles[iOrient] += exp(logpro - pProb[iRefMap].ConstAngle[iOrient]);
}
/********** Getting parameters that maximize the probability ***********/
// ********** Getting parameters that maximize the probability ***********
if(pProb[iRefMap].max_prob < logpro)
{
pProb[iRefMap].max_prob = logpro;
......@@ -64,7 +64,7 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
const myfloat_t firstele = param.Ntotpi * (sumsquareref * sumsquare - crossproMapConv * crossproMapConv) +
2 * sumref * sum * crossproMapConv - sumsquareref * sum * sum - sumref * sumref * sumsquare;
//******* Calculating log of Prob*********/
// ******* 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);
const myfloat_t logpro = (3 - param.Ntotpi) * 0.5 * log(firstele) + (param.Ntotpi * 0.5 - 2) * log((param.Ntotpi - 2) * ForLogProb);
return(logpro);
......@@ -72,9 +72,9 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
__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 ***********/
/********************************************************/
// ********************************************************
// *********** Calculates the BioEM probability ***********
// ********************************************************
const myfloat_t logpro = calc_logpro(param, sumC, sumsquareC, value, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
......@@ -134,13 +134,13 @@ template <int GPUAlgo, class RefT>
__device__ static inline void compareRefMap(const int iRefMap, const int iOrient, const int iConv, const bioem_map& 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)
{
/**************************************************************************************/
/********************** Calculating BioEM Probability ********************************/
/************************* Loop of center displacement here ***************************/
// **************************************************************************************
// ********************** Calculating BioEM Probability ********************************
// ************************* Loop of center displacement here ***************************
// Taking into account the center displacement
/*** Inizialzing crosscorrelations of calculated projected convolutions ***/
// *** Inizialzing crosscorrelations of calculated projected convolutions ***
#ifdef SSECODE
myfloat_t sum, sumsquare, crossproMapConv;
__m128 sum_v = _mm_setzero_ps(), sumsquare_v = _mm_setzero_ps(), cross_v = _mm_setzero_ps(), d1, d2;
......@@ -149,7 +149,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
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***/
// ****** Loop over Pixels to calculate dot product and cross-correlations of displaced Ref Conv. Map***
myfloat_t logpro;
if (GPUAlgo != 2 || threadActive)
{
......@@ -217,7 +217,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
crossproMapConv = _mm_cvtss_f32(cross_v);
#endif
/********** Calculating elements in BioEM Probability formula ********/
// ********** Calculating elements in BioEM Probability formula ********
logpro = calc_logpro(param, sum, sumsquare, crossproMapConv, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
}
else
......@@ -380,7 +380,7 @@ __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);
}
......
main.cpp
View file @ 9582b044
......@@ -21,9 +21,9 @@
int main(int argc, char* argv[])
{
//*************************************************************************************
//********************************* Main BioEM code **********************************
//*************************************************************************************
// *************************************************************************************
// ********************************* Main BioEM code **********************************
// *************************************************************************************
#ifdef _MM_SET_DENORMALS_ZERO_MODE
#pragma omp parallel
......@@ -45,17 +45,17 @@ int main(int argc, char* argv[])
bio = new bioem;
}
//************ Configuration and Pre-calculating necessary objects *********************
// ************ Configuration and Pre-calculating necessary objects *********************
printf("Configuring\n");
bio->configure(argc, argv);
//******************************* Run BioEM routine ************************************
// ******************************* Run BioEM routine ************************************
printf("Running\n");
timer.Start();
bio->run();
timer.Stop();
//************************************ End ***********************************************
// ************************************ End ***********************************************
printf ("The code ran for %f seconds.\n", timer.GetElapsedTime());
delete bio;
......
map.cpp
View file @ 9582b044
......@@ -13,9 +13,9 @@ using namespace std;
int bioem_RefMap::readRefMaps(bioem_param& param)
{
//**************************************************************************************
//***********************Reading reference Particle Maps************************
//**************************************************************************************
// **************************************************************************************
// ***********************Reading reference Particle Maps************************
// **************************************************************************************
if (loadMap)
{
FILE* fp = fopen("maps.dump", "rb");
......@@ -187,9 +187,9 @@ int bioem_RefMap::readRefMaps(bioem_param& param)
int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
{
//**************************************************************************************
//********** Routine that pre-calculates Kernels for Convolution ***********************
//**************************************************************************************
// **************************************************************************************
// ********** Routine that pre-calculates Kernels for Convolution ***********************
// **************************************************************************************
myfloat_t* localMap;
......
model.cpp
View file @ 9582b044
......@@ -11,9 +11,9 @@ using namespace std;
int bioem_model::readModel()
{
//**************************************************************************************
//***************Reading reference Models either PDB or x,y,z,r,d format****************
//**************************************************************************************
// **************************************************************************************
// ***************Reading reference Models either PDB or x,y,z,r,d format****************
// **************************************************************************************
ofstream exampleReadCoor;
exampleReadCoor.open ("COORDREAD");
......@@ -173,7 +173,7 @@ int bioem_model::readModel()
myfloat_t bioem_model::getAminoAcidRad(char *name)
{
//************** Function that gets the radius for each amino acid ****************
// ************** Function that gets the radius for each amino acid ****************
myfloat_t iaa = 0;
if(std::strcmp(name, "CYS") == 0)iaa = 2.75;
......@@ -208,7 +208,7 @@ myfloat_t bioem_model::getAminoAcidRad(char *name)
myfloat_t bioem_model::getAminoAcidDensity(char *name)
{
//************** Function that gets the number of electrons for each amino acid ****************
// ************** Function that gets the number of electrons for each amino acid ****************
myfloat_t iaa = 0.0;
if(std::strcmp(name, "CYS") == 0)iaa = 64.0;
......
param.cpp
View file @ 9582b044
......@@ -25,7 +25,7 @@ bioem_param::bioem_param()
numberGridPointsCTF_amp = 0;
numberGridPointsCTF_phase = 0;
//****center displacement paramters Equal in both directions***
// ****center displacement paramters Equal in both directions***
param_device.maxDisplaceCenter = 0;
numberGridPointsDisplaceCenter = 0;
......@@ -37,9 +37,9 @@ bioem_param::bioem_param()
int bioem_param::readParameters()
{
//**************************************************************************************
//***************************** Reading Input Parameters ******************************
//**************************************************************************************
// **************************************************************************************
// ***************************** Reading Input Parameters ******************************
// **************************************************************************************
// Control for Parameters
bool yesPixSi = false;
......@@ -369,9 +369,9 @@ void bioem_param::releaseFFTPlans()
int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
{
//************************************************************************************
//**************** Routine that pre-calculates Euler angle grids *********************
//************************************************************************************
// ************************************************************************************
// **************** Routine that pre-calculates Euler angle grids *********************
// ************************************************************************************
myfloat_t grid_alpha, cos_grid_beta;
int n = 0;
......@@ -397,13 +397,13 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
}
nTotGridAngles = n;
//********** Calculating normalized volumen element *********
// ********** Calculating normalized volumen element *********
param_device.volu = grid_alpha * grid_alpha * cos_grid_beta * (myfloat_t) param_device.GridSpaceCenter * pixelSize * (myfloat_t) param_device.GridSpaceCenter * pixelSize
* gridCTF_phase * gridCTF_amp * gridEnvelop / (2.f * M_PI) / (2.f * M_PI) / 2.f / (2.f * (myfloat_t) param_device.maxDisplaceCenter) / (2.f * (myfloat_t) param_device.maxDisplaceCenter) / ((myfloat_t) numberGridPointsCTF_amp * gridCTF_amp + startGridCTF_amp)
/ ((myfloat_t) numberGridPointsCTF_phase * gridCTF_phase + startGridCTF_phase) / ((myfloat_t) numberGridPointsEnvelop * gridEnvelop + startGridEnvelop);
//*** Number of total pixels***
// *** Number of total pixels***
param_device.Ntotpi = (myfloat_t) (param_device.NumberPixels * param_device.NumberPixels);
param_device.NtotDist = (2 * (int) (param_device.maxDisplaceCenter / param_device.GridSpaceCenter) + 1 ) * (2 * (int) (param_device.maxDisplaceCenter / param_device.GridSpaceCenter) + 1);
......@@ -414,9 +414,9 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
int bioem_param::CalculateRefCTF()
{
//************************************************************************************
//********** Routine that pre-calculates Kernels for Convolution *********************
//************************************************************************************
// ************************************************************************************
// ********** Routine that pre-calculates Kernels for Convolution *********************
// ************************************************************************************
myfloat_t amp, env, phase, ctf, radsq;
myfloat_t* localCTF;
......
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