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CMakeLists.txt 0 → 100755
View file @ aada7e38
CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
PROJECT( BioEM )
FIND_PACKAGE(CUDA)
SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -march=native -fopenmp -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb" )
SET( CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};-gencode arch=compute_35,code=sm_35;--use_fast_math;-ftz=true;-O4;-Xptxas -O4" )
INCLUDE_DIRECTORIES( include $HOME/usr/include )
CUDA_ADD_EXECUTABLE( bioEM bioem.cpp main.cpp map.cpp model.cpp param.cpp cmodules/timer.cpp bioem_cuda.cu )
SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x -Wall -Wno-vla -Wno-unused-result -pedantic" )
TARGET_LINK_LIBRARIES( bioEM -lfftw3 -fopenmp -lboost_program_options )
\ No newline at end of file
README 0 → 100755
View file @ aada7e38
********************************************************
BioEM: Bayesian inference of Electron Microscopy
********************************************************
Requisites:
**** FFTW libraries: http://www.fftw.org/
**** BOOST libraries: http://www.boost.org/
**** OpenMP: http://openmp.org/
Optional:
**** CMake: http://www.cmake.org/
for compliation with CMakeLists.txt file.
**********************************************************
bioem.cpp 0 → 100755
View file @ aada7e38
#include <fstream>
#include <boost/program_options.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <cmath>
#include <omp.h>
#include <fftw3.h>
#include <math.h>
#include "cmodules/timer.h"
#include "param.h"
#include "bioem.h"
#include "model.h"
#include "map.h"
#include "bioem_algorithm.h"
using namespace boost;
namespace po = boost::program_options;
using namespace std;
// A helper function of Boost
template<class T>
ostream& operator<<(ostream& os, const vector<T>& v)
{
copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
return os;
}
bioem::bioem()
{
}
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 ********/
/*************************************************************************************/
/*** Inizialzing default variables ***/
std::string infile,modelfile,mapfile;
Model.readPDB=false;
param.writeAngles=false;
RefMap.dumpMap = false;
RefMap.loadMap = false;
/*************************************************************************************/
cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
/*************************************************************************************/
/********************* Command line reading input with BOOST ************************/
try {
po::options_description desc("Command line inputs");
desc.add_options()
("Inputfile", po::value<std::string>(), "Name of input parameter file")
("Modelfile", po::value< std::string>() , "Name of model file")
("Particlesfile", po::value< std::string>(), "Name of paricles file")
("ReadPDB", "(Optional) If reading model file in PDB format")
("DumpMaps", "(Optional) Dump maps after they were red from maps file")
("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
("help", "(Optional) Produce help message")
;
po::positional_options_description p;
p.add("Inputfile", -1);
p.add("Modelfile", -1);
p.add("Particlesfile", -1);
p.add("ReadPDB", -1);
p.add("DumpMaps", -1);
p.add("LoadMapDump", -1);
po::variables_map vm;
po::store(po::command_line_parser(ac, av).
options(desc).positional(p).run(), vm);
po::notify(vm);
if((ac < 6)) {
std::cout << desc << std::endl;
return 0;
}
if (vm.count("help")) {
cout << "Usage: options_description [options]\n";
cout << desc;
return 0;
}
if (vm.count("Inputfile"))
{
cout << "Input file is: ";
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 >();
}
if (vm.count("ReadPDB"))
{
cout << "Reading model file in PDB format.\n";
Model.readPDB=true;
}
if (vm.count("DumpMaps"))
{
cout << "Dumping Maps after reading from file.\n";
RefMap.dumpMap = true;
}
if (vm.count("LoadMapDump"))
{
cout << "Loading Map dump.\n";
RefMap.loadMap = true;
}
if (vm.count("Particlesfile"))
{
cout << "Paricle file is: "
<< vm["Particlesfile"].as< std::string >() << "\n";
mapfile=vm["Particlesfile"].as< std::string >();
}
}
catch(std::exception& e)
{
cout << e.what() << "\n";
return 1;
}
/********************* Reading Parameter Input ***************************/
// copying inputfile to param class
param.fileinput = infile.c_str();
param.readParameters();
/********************* 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!! ***************/
// copying mapfile to ref map class
RefMap.filemap = mapfile.c_str();
RefMap.readRefMaps();
/****************** Precalculating Necessary Stuff *********************/
precalculate();
param.nTotGridAngles = 10;
param.nTotCTFs = 10;
//param.param_device.maxDisplaceCenter = 0;
deviceInit();
return(0);
}
int bioem::precalculate()
{
/**************************************************************************************/
/* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels */
/**************************************************************************************/
// Generating Grids of orientations
param.CalculateGridsParam();
//Inizialzing crosscorrelations of Maps
memset(RefMap.sum_RefMap, 0, BIOEM_MAX_MAPS * sizeof(*RefMap.sum_RefMap));
memset(RefMap.sumsquare_RefMap, 0, BIOEM_MAX_MAPS * sizeof(*RefMap.sum_RefMap));
myfloat_t sum,sumsquare;
//Precalculating cross-correlations of maps
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap ; iRefMap++)
{
calcross_cor(RefMap.Ref[iRefMap],sum,sumsquare);
//Storing Crosscorrelations in Map class
RefMap.sum_RefMap[iRefMap]=sum;
RefMap.sumsquare_RefMap[iRefMap]=sumsquare;
}
// Precalculating CTF Kernels stored in class Param
param.CalculateRefCTF();
return(0);
}
int bioem::run()
{
/**************************************************************************************/
/**** 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 *************************/
pProb = new bioem_Probability[RefMap.ntotRefMap];
printf("\tInitializing\n");
// 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;
for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
{
pProb[iRefMap].forAngles[iOrient]=0.0;
pProb[iRefMap].ConstAngle[iOrient]=-99999999;
}
}
/**************************************************************************************/
deviceStartRun();
/******************************** MAIN CYCLE ******************************************/
/*** Declaring Private variables for each thread *****/
mycomplex_t* proj_mapFFT;
bioem_map conv_map;
//allocating fftw_complex vector
proj_mapFFT= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t) *4*param.param_device.NumberPixels*param.param_device.NumberPixels);
HighResTimer timer;
printf("\tMain Loop (GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)²), Pixels %d²\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels);
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)));
//#pragma omp parallel for
for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
{
/***************************************************************************************/
/***** 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 **** *****/
for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
{
printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
/*** Calculating convolutions of projection map and crosscorrelations ***/
timer.ResetStart();
createConvolutedProjectionMap(iProjectionOut,iConv,proj_mapFFT,conv_map);
printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());
/***************************************************************************************/
/*** Comparing each calculated convoluted map with all experimental maps ***/
timer.ResetStart();
compareRefMaps(iProjectionOut, iConv, conv_map);
printf("Time Comparison %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());
}
}
//deallocating fftw_complex vector
fftw_free(proj_mapFFT);
deviceFinishRun();
/************* Writing Out Probabilities ***************/
/*** Angular Probability ***/
// if(param.writeAngles){
ofstream angProbfile;
angProbfile.open ("ANG_PROB_iRefMap");
// }
ofstream outputProbFile;
outputProbFile.open ("Output_Probabilities");
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 << " Maximizing Param: ";
/*** 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] << " ";
outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[2] << " ";
outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[0] << " ";
outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[1] << " ";
outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[2] << " ";
outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
outputProbFile << pProb[iRefMap].max_prob_cent_y;
outputProbFile << "\n";
/*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);
if(param.writeAngles)
{
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.close();
outputProbFile.close();
//Deleting allocated pointers
if (pProb)
{
delete[] pProb;
pProb = NULL;
}
if (param.refCTF)
{
delete[] param.refCTF;
param.refCTF =NULL;
}
return(0);
}
int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map)
{
#pragma omp parallel for
for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
}
return(0);
}
int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
{
/**************************************************************************************/
/**** 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];
myfloat_t alpha, gam,beta;
fftw_plan plan;
mycomplex_t* localproj;
int totnumPixFFT=2*param.param_device.NumberPixels;
localproj= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t) *4*param.param_device.NumberPixels*param.param_device.NumberPixels);
memset(localproj,0,4*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];
/**** 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++)
{
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 k=0; k< 3; k++)
{
for(int j=0; j< 3; j++)
{
RotatedPointsModel[n].pos[k]+=rotmat[k][j]*Model.PointsModel[n].pos[j];
}
}
}
int i, j;
/************ 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 )
i=floor(RotatedPointsModel[n].pos[0]/(*param.pixelSize)+float(param.param_device.NumberPixels)/2.0+0.5);
j=floor(RotatedPointsModel[n].pos[1]/(*param.pixelSize)+float(param.param_device.NumberPixels)/2.0+0.5);
localproj[i*2*param.param_device.NumberPixels+j+param.param_device.NumberPixels*param.param_device.NumberPixels+int(param.param_device.NumberPixels/2.0)][0]+=Model.densityPointsModel[n];
}
/**** Output Just to check****/
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<2*param.param_device.NumberPixels; k++)
{
for(int j=0; j<2*param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*2*param.param_device.NumberPixels+j][0];
}
myexamplemap << " \n";
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*******/
//#pragma omp critical
{
plan = fftw_plan_dft_2d(totnumPixFFT,totnumPixFFT,localproj,mapFFT,FFTW_FORWARD,FFTW_ESTIMATE);
fftw_execute(plan);
fftw_destroy_plan(plan);
fftw_free(localproj);
}
return(0);
}
int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv)
{
/**************************************************************************************/
/**** BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
**************** calculated Projection with convoluted precalculated Kernel**********
*************** and Backtransforming it to real Space ******************************/
/**************************************************************************************/
fftw_plan plan;
mycomplex_t* localmultFFT;
mycomplex_t* localconvFFT;
int totnumPixFFT=2*param.param_device.NumberPixels;
localmultFFT= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t)*totnumPixFFT*totnumPixFFT);
localconvFFT= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t)*totnumPixFFT*totnumPixFFT);
/**** Multiplying FFTmap with corresponding kernel ****/
for(int i=0; i < 2*param.param_device.NumberPixels ; i++ )
{
for(int j=0; j < 2*param.param_device.NumberPixels ; j++ )
{ //Projection*CONJ(KERNEL)
localmultFFT[i*2*param.param_device.NumberPixels+j][0]=lproj[i*2*param.param_device.NumberPixels+j][0]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][0]+lproj[i*2*param.param_device.NumberPixels+j][1]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][1];
localmultFFT[i*2*param.param_device.NumberPixels+j][1]=lproj[i*2*param.param_device.NumberPixels+j][1]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][0]-lproj[i*2*param.param_device.NumberPixels+j][0]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][1];
// cout << "GG " << i << " " << j << " " << param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][0] << " " <<param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][1] <<" " <<lproj[i*2*param.param_device.NumberPixels+j][0] <<" " <<lproj[i*2*param.param_device.NumberPixels+j][1] << "\n";
}
}
/**** Bringing convoluted Map to real Space ****/
//#pragma omp critical
{
plan = fftw_plan_dft_2d(totnumPixFFT,totnumPixFFT,localmultFFT,localconvFFT,FFTW_BACKWARD,FFTW_ESTIMATE);
fftw_execute(plan);
}
/****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++ )
{
Mapconv.points[i][j]=localconvFFT[i*2*param.param_device.NumberPixels+j+param.param_device.NumberPixels*param.param_device.NumberPixels+int(param.param_device.NumberPixels/2.0)][0];
}
}
/**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
//#pragma omp critical
{
fftw_destroy_plan(plan);
fftw_free(localconvFFT);
fftw_free(localmultFFT);
}
return(0);
}
int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{
/*********************** Routine to calculate Cross correlations***********************/
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.points[i][j];
// Calculate Sum of pixels squared
sumsquare += localmap.points[i][j]*localmap.points[i][j];
}
}
return(0);
}
int bioem::deviceInit()
{
return(0);
}
int bioem::deviceStartRun()
{
return(0);
}
int bioem::deviceFinishRun()
{
return(0);
}
bioem_algorithm.h 0 → 100644
View file @ aada7e38
#ifndef BIOEM_ALGORITHM_H
#define BIOEM_ALGORITHM_H
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)
{
/**************************************************************************************/
/********************** Calculating BioEM Probability ********************************/
/************************* Loop of center displacement here ***************************/
// Taking into account the center displacement
/*** Inizialzing crosscorrelations of calculated projected convolutions ***/
myfloat_t sum=0.0;
myfloat_t sumsquare=0.0;
myfloat_t crossproMapConv=0.0;
/****** Loop over Pixels to calculate dot product and cross-correlations of displaced Ref Conv. Map***/
if (GPUAlgo != 2 || iRefMap < RefMap.ntotRefMap)
{
int iStart, jStart, iEnd, jEnd;
if (cent_x < 0)
{
iStart = -cent_x;
iEnd = param.NumberPixels;
}
else
{
iStart = 0;
iEnd = param.NumberPixels - cent_x;