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BioEM
Commit 01a19a3d authored by Pilar Cossio-Tejada's avatar Pilar Cossio-Tejada
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Polishing & including priors without FFTALGO

parent 470535fe
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CMakeLists.txt
View file @ 01a19a3d
......@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
project(BioEM)
###Set up options
option (INCLUDE_CUDA "Build BioEM with CUDA support" ON)
option (INCLUDE_CUDA "Build BioEM with CUDA support" OFF)
option (INCLUDE_OPENMP "Build BioEM with OpenMP support" ON)
option (INCLUDE_MPI "Build BioEM with MPI support" ON)
option (PRINT_CMAKE_VARIABLES "List all CMAKE Variables" OFF)
......@@ -23,7 +23,7 @@ else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_GCC_FLAGS}")
endif()
set (BIOEM_SOURCE_FILES "bioem.cpp" "main.cpp" "map.cpp" "model.cpp" "param.cpp" "cmodules/timer.cpp")
set (BIOEM_SOURCE_FILES "bioem.cpp" "main.cpp" "map.cpp" "model.cpp" "param.cpp" "timer.cpp")
###Find Required Packages
find_package(PkgConfig)
......
License.txt
View file @ 01a19a3d
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr and Gerhard Hummer
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
......
Manual/BioEM_Manual.tex
View file @ 01a19a3d
This diff is collapsed.
Tutorial_BioEM/MODEL_COMPARISION/Param_Input_ModelComparision
View file @ 01a19a3d
......@@ -6,14 +6,14 @@ PIXEL_SIZE 1.32
USE_QUATERNIONS
##### Constrast transfer integration: #######
CTF_B_ENV 10.0 500. 5
CTF_B_ENV 2.0 300. 4
CTF_DEFOCUS 0.5 4.5 8
CTF_AMPLITUDE 0.01 0.601 5
SIGMA_PRIOR_B_CTF 50.
SIGMA_PRIOR_DEFOCUS 0.4
PRIOR_DEFOCUS_CENTER 2.7
PRIOR_DEFOCUS_CENTER 2.8
##### Center displacement: #######
......
Tutorial_BioEM/Param_Input_Priors
View file @ 01a19a3d
......@@ -17,3 +17,8 @@ DISPLACE_CENTER 10 2
####### Priors ###############
PRIOR_MODEL 0.005
PRIOR_ANGLES
SIGMA_PRIOR_DEFOCUS 0.4
PRIOR_DEFOCUS_CENTER 1.8
SIGMA_PRIOR_B_CTF 10.
Tutorial_BioEM/Param_ProRun
View file @ 01a19a3d
......@@ -6,9 +6,9 @@ PIXEL_SIZE 1.77
USE_QUATERNIONS
##### Constrast transfer integration: #######
CTF_B_ENV 10.0 500. 5.
CTF_B_ENV 2.0 300. 4.
CTF_DEFOCUS 0.5 4.5 8.
CTF_AMPLITUDE 0.01 0.401 4.
CTF_AMPLITUDE 0.01 0.601 5.
## Gaussian width of Prior of b-parameter
SIGMA_PRIOR_B_CTF 50.
......
bioem.cpp
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr and Gerhard Hummer.
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
......@@ -35,7 +36,7 @@
#include <fftw3.h>
#include <math.h>
#include "cmodules/timer.h"
#include "timer.h"
#include "param.h"
#include "bioem.h"
......@@ -816,8 +817,8 @@ int bioem::run()
else{outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << " [1/A²] ";}
outputProbFile << pProbMap.max.max_prob_cent_x << " [pix] ";
outputProbFile << pProbMap.max.max_prob_cent_y << " [pix] " ;
outputProbFile << pProbMap.max.max_prob_norm << " [] " ;
outputProbFile << pProbMap.max.max_prob_mu << " [] ";
if(FFTAlgo){outputProbFile << pProbMap.max.max_prob_norm << " [] " ;}else{outputProbFile << "N.A." << " [] ";}
if(FFTAlgo){outputProbFile << pProbMap.max.max_prob_mu << " [] ";}else{outputProbFile << "N.A." << " [] ";}
outputProbFile << "\n";
// Writing out CTF parameters if requiered
......@@ -827,8 +828,6 @@ int bioem::run()
denomi = param.CtfParam[pProbMap.max.max_prob_conv].pos[1] * param.CtfParam[pProbMap.max.max_prob_conv].pos[1] +
param.CtfParam[pProbMap.max.max_prob_conv].pos[2] * param.CtfParam[pProbMap.max.max_prob_conv].pos[2];
outputProbFile << "RefMap: " << iRefMap << " CTFMaxParam: ";
// outputProbFile << 2*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[1]/denomi/param.elecwavel << " [micro-m]; ";
// outputProbFile << param.CtfParam[pProbMap.max.max_prob_conv].pos[1] << param.CtfParam[pProbMap.max.max_prob_conv].pos[2] << denomi ;
outputProbFile << 2*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[1]/denomi/param.elecwavel*0.0001 << " [micro-m] ";
outputProbFile << 4*M_PI*M_PI*param.CtfParam[pProbMap.max.max_prob_conv].pos[2]/denomi << " [A²] \n";
}
......@@ -867,6 +866,7 @@ int bioem::run()
}
//************* Writing Cross-Correlations if requiered
//************* This is currently not in the manual *****
if(param.param_device.writeCC){
int cc=0;
......@@ -981,6 +981,7 @@ int bioem::compareRefMaps(int iOrient, int iConv, myfloat_t amp, myfloat_t pha,
//***************************************************************************************
//***** BioEM routine for comparing reference maps to convoluted maps *****
//***************************************************************************************
if (FFTAlgo)
{
//With FFT Algorithm
......@@ -997,7 +998,7 @@ int bioem::compareRefMaps(int iOrient, int iConv, myfloat_t amp, myfloat_t pha,
#pragma omp parallel for schedule(dynamic, 1)
for (int iRefMap = startMap; iRefMap < RefMap.ntotRefMap; iRefMap ++)
{
compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, conv_map, pProb, param.param_device, RefMap);
compareRefMapShifted < -1 > (iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, conv_map, pProb, param.param_device, RefMap);
}
}
return(0);
......@@ -1066,46 +1067,13 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
if(param.doquater){
myfloat_t quater[4];
// myfloat_t cq[4],temp[4];
// myfloat_t a[4];
//quaternion
/* quater[1]=param.angles[iMap].pos[1];
quater[2]=param.angles[iMap].pos[2];
quater[3]=param.angles[iMap].pos[0];
quater[0]=param.angles[iMap].quat4;*/
quater[0]=param.angles[iMap].pos[0];
quater[1]=param.angles[iMap].pos[1];
quater[2]=param.angles[iMap].pos[2];
quater[3]=param.angles[iMap].quat4;
// its conjugate
/* cq[0]=quater[0];
cq[1]=-quater[1];
cq[2]=-quater[2];
cq[3]=-quater[3];
for(int n = 0; n < Model.nPointsModel; n++)
{
//Rotation with quaterion
// Initial coords
a[0]=0.;
a[1]=Model.points[n].point.pos[0];
a[2]=Model.points[n].point.pos[1];
a[3]=Model.points[n].point.pos[2];
temp[0]=a[0]*cq[0]-a[1]*cq[1]-a[2]*cq[2]-a[3]*cq[3];
temp[1]=a[0]*cq[1]+a[1]*cq[0]+a[2]*cq[3]-a[3]*cq[2];
temp[2]=a[0]*cq[2]-a[1]*cq[3]+a[2]*cq[0]+a[3]*cq[1];
temp[3]=a[0]*cq[3]+a[1]*cq[2]-a[2]*cq[1]+a[3]*cq[0];
// First coordinate is zero Going back to real space
RotatedPointsModel[n].pos[0] = quater[0]*temp[1]+quater[1]*temp[0]+quater[2]*temp[3]-quater[3]*temp[2];
RotatedPointsModel[n].pos[1] = quater[0]*temp[2]-quater[1]*temp[3]+quater[2]*temp[0]+quater[3]*temp[1];
RotatedPointsModel[n].pos[2] = quater[0]*temp[3]+quater[1]*temp[2]-quater[2]*temp[1]+quater[3]*temp[0];
}*/
//Rotation Matrix for Quaterions (wikipeda)
//Rotation Matrix for Quaterions (wikipeda)
rotmat[0][0] = 1- 2 * quater[1] * quater[1] - 2 * quater[2] * quater[2];
rotmat[1][0] = 2 * ( quater[0] * quater[1] - quater[2] * quater[3]);
rotmat[2][0] = 2 * ( quater[0] * quater[2] + quater[1] * quater[3]);
......@@ -1117,10 +1085,6 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
rotmat[2][2] = 1- 2 * quater[0] * quater[0] - 2 * quater[1] * quater[1];
/*Debug for(int i =0; i <3 ; i++){
for(int j =0; j <3 ; j++){cout << "MAT "<< i << " " << j << " " << rotmat[i][j] << "\n";
} } */
} else{
//*************** Euler Angles****************************
......@@ -1249,7 +1213,6 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
localproj[ i * param.param_device.NumberPixels + j] *= ratioDen;
}
}
// cout << "HERE " << tempden << " " << Model.NormDen << " \n";
// **** Output Just to check****
#ifdef DEBUG
......
bioem_algorithm.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
......@@ -24,7 +25,8 @@ 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, bool doAngle, myfloat_t* buf3 = NULL, int* bufint = NULL)
{
//**************** Routine to perform the numerical BioEM intergal ***********
// *********** Not using FFT ALGORITHM ******************
//*********** Routine to perform the numerical BioEM intergal ***********
// ******* Summing total Probabilities *************
......@@ -49,8 +51,8 @@ __device__ static inline void update_prob(const myfloat_t logpro, const int iRef
}
pProbMap.max.max_prob_orient = iOrient;
pProbMap.max.max_prob_conv = iConv;
// pProbMap.max.max_prob_norm = - ( -sumC * RefMap.sum_RefMap[iRefMap] + param.Ntotpi * value ) / ( sumC * sumC - sumsquareC * param.Ntotpi);
// pProbMap.max.max_prob_mu = - ( -sumC * value + sumsquareC * RefMap.sum_RefMap[iRefMap] ) / ( sumC * sumC - sumsquareC * param.Ntotpi);
// pProbMap.max.max_prob_norm = - ( -sumC * RefMap.sum_RefMap[iRefMap] + param.Ntotpi * value ) / ( sumC * sumC - sumsquareC * param.Ntotpi);
// pProbMap.max.max_prob_mu = - ( -sumC * value + sumsquareC * RefMap.sum_RefMap[iRefMap] ) / ( sumC * sumC - sumsquareC * param.Ntotpi);
}
if (GPUAlgo != 2) pProbMap.Total += exp(logpro - pProbMap.Constoadd);
......@@ -69,11 +71,11 @@ __device__ static inline void update_prob(const myfloat_t logpro, const int iRef
}
}
__device__ static inline myfloat_t calc_logpro(const bioem_param_device& param, const myfloat_t sum, const myfloat_t sumsquare, const myfloat_t crossproMapConv, const myfloat_t sumref, const myfloat_t sumsquareref)
__device__ static inline myfloat_t calc_logpro(const bioem_param_device& param, const myfloat_t amp, const myfloat_t pha, const myfloat_t env, const myfloat_t sum, const myfloat_t sumsquare, const myfloat_t crossproMapConv, const myfloat_t sumref, const myfloat_t sumsquareref)
{
// ********** Routine to calculate the log posterior of Eq. of Pmw in SI of JSB paper
//*** MAIN ROUTINE TO CALCULATE THE LOGPRO FOR ALL KERNELS*************//
// **** calculate the log posterior of Eq. of Pmw in SI of JSB paper ***//
// Related to Reference calculated Projection
const myfloat_t ForLogProb = (sumsquare * param.Ntotpi - sum * sum);
......@@ -84,34 +86,32 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
/// ******* 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);
// if(param.debugterm){
// printf("Separate cc: %f c: %f oo: %f o: %f co: %f logP: %f\n",sumsquare,sum,sumsquareref,sumref,crossproMapConv, logpro );
// }
myfloat_t logpro = (3 - param.Ntotpi) * 0.5 * log(firstele) + (param.Ntotpi * 0.5 - 2) * log((param.Ntotpi - 2) * ForLogProb);
//*************Adding Gaussian Prior to envelope & Defocus parameter******************
if(not param.tousepsf){
logpro = logpro - env * env / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf -
(pha - param.Priordefcent ) * (pha - param.Priordefcent ) / 2. / param.sigmaPriordefo / param.sigmaPriordefo ;
} else {
myfloat_t envF,phaF;
envF = 4.* M_PI * M_PI * env / ( env * env + pha * pha) ;
phaF = 4.* M_PI * M_PI * pha / ( env * env + pha * pha);
logpro = logpro - envF * envF / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf - (phaF - param.Priordefcent ) * (phaF - param.Priordefcent ) / 2. / param.sigmaPriordefo / param.sigmaPriordefo ;
}
return(logpro);
}
__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)
{
// MOST IMPORTANT ROUTINE
// IMPORTANT ROUTINE Summation of LogProb using FFTALGO
// ********************************************************
// *********** Calculates the BioEM probability ***********
// ********************************************************
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 - (pha - param.Priordefcent ) * (pha - param.Priordefcent ) / 2. / param.sigmaPriordefo / param.sigmaPriordefo ;
} else {
myfloat_t envF,phaF;
envF = 4.* M_PI * M_PI * env / ( env * env + pha * pha) ;
phaF = 4.* M_PI * M_PI * pha / ( env * env + pha * pha);
logpro = logpro - envF * envF / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf - (phaF - param.Priordefcent ) * (phaF - param.Priordefcent ) / 2. / param.sigmaPriordefo / param.sigmaPriordefo ;
}
myfloat_t logpro = calc_logpro(param, amp, pha, env, sumC, sumsquareC, value, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
//GCC is too stupid to inline properly, so the code is copied here
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb, param.writeAngles);
......@@ -153,6 +153,7 @@ __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 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)
{
//******************** Using FFT algorithm **************************
//******************* Get cross-crollation of Ical to Iobs *******************
//*********** Routine to get the Cross-Corellation from lCC for the interested center displacement *************
......@@ -180,6 +181,7 @@ __device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient,
}
}
//************ The following if is not in the manual***********
if (param.writeCC)
{
// If the Cross-correlation is to be written out and stored using Bayesian analysis
......@@ -226,7 +228,8 @@ __device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient,
}
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,
__device__ static inline void compareRefMap(const int iRefMap, const int iOrient, const int iConv, const myfloat_t amp, const myfloat_t pha, const myfloat_t env, const myfloat_t sumC,
const myfloat_t sumsquareC, 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)
{
......@@ -314,7 +317,7 @@ template <int GPUAlgo, class RefT>
#endif
// Calculating elements in BioEM Probability formula
logpro = calc_logpro(param, sum, sumsquare, crossproMapConv, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
logpro = calc_logpro(param, amp, pha, env, sum, sumsquare, crossproMapConv, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
}
else
{
......@@ -485,13 +488,13 @@ template <int GPUAlgo, class RefT>
}
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)
__device__ static inline void compareRefMapShifted(const int iRefMap, const int iOrient, const int iConv, const myfloat_t amp, const myfloat_t pha, const myfloat_t env, const myfloat_t sumC, const myfloat_t sumsquareC, 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_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);
compareRefMap<GPUAlgo>(iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, Mapconv, pProb, param, RefMap, cent_x, cent_y);
}
}
}
......
bioem_cuda.cu
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
......@@ -80,21 +81,23 @@ bioem_cuda::~bioem_cuda()
deviceExit();
}
__global__ void compareRefMap_kernel(const int iOrient, const int iConv, const myfloat_t* pMap, bioem_Probability pProb, const bioem_param_device param, const bioem_RefMap_Mod RefMap, const int cent_x, const int cent_y, const int maxRef)
__global__ void compareRefMap_kernel(const int iOrient, const int iConv, const myfloat_t amp, const myfloat_t pha, const myfloat_t env, const myfloat_t sumC,
const myfloat_t sumsquareC, const myfloat_t* pMap, bioem_Probability pProb,
const bioem_param_device param, const bioem_RefMap_Mod RefMap, const int cent_x, const int cent_y, const int maxRef)
{
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, amp, pha, env, sumC, sumsquareC, pMap, pProb, param, RefMap, cent_x, cent_y);
}
}
__global__ void compareRefMapShifted_kernel(const int iOrient, const int iConv, const myfloat_t* pMap, bioem_Probability pProb, const bioem_param_device param, const bioem_RefMap_Mod RefMap, const int maxRef)
__global__ void compareRefMapShifted_kernel(const int iOrient, const int iConv, const myfloat_t amp, const myfloat_t pha, const myfloat_t env, const myfloat_t sumC, const myfloat_t sumsquareC, nst myfloat_t* pMap, bioem_Probability pProb, const bioem_param_device param, const bioem_RefMap_Mod RefMap, const int maxRef)
{
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX;
if (iRefMap < maxRef)
{
compareRefMapShifted<1>(iRefMap, iOrient, iConv, pMap, pProb, param, RefMap);
compareRefMapShifted<1>(iRefMap, iOrient, iConv, amp, pha, env, sumC, sumsquareC, pMap, pProb, param, RefMap);
}
}
......@@ -250,7 +253,7 @@ int bioem_cuda::compareRefMaps(int iOrient, int iConv, myfloat_t amp, myfloat_t
}
else if (GPUAlgo == 0) //All shifts in one kernel
{
compareRefMapShifted_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream[0]>>> (iOrient, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *pRefMap_device_Mod, maxRef);
compareRefMapShifted_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream[0]>>> (iOrient, iConv, amp, pha, env, sumC, sumsquareC, pConvMap_device[iConv & 1], pProb_device, param.param_device, *pRefMap_device_Mod, maxRef);
}
else
{
......
include/bioem.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_H
#define BIOEM_H
......
include/bioem_cuda.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_CUDA_H
#define BIOEM_CUDA_H
......
include/bioem_cuda_internal.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_CUDA_INTERNAL_H
#define BIOEM_CUDA_INTERNAL_H
......
include/defs.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_DEFS_H
#define BIOEM_DEFS_H
......
include/map.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_MAP_H
#define BIOEM_MAP_H
......
include/model.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_MODEL_H
#define BIOEM_MODEL_H
......
include/param.h
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef BIOEM_PARAM_H
#define BIOEM_PARAM_H
......@@ -61,6 +71,7 @@ public:
bool notnormmap;
bool usepsf;
bool ignorepointsout;
bool ignorePDB;
myfloat_t elecwavel;
......
include/timer.h 0 → 100644
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifndef TIMER_H
#define TIMER_H
class HighResTimer {
public:
HighResTimer();
~HighResTimer();
void Start();
void Stop();
void Reset();
void ResetStart();
double GetElapsedTime();
double GetCurrentElapsedTime();
private:
static double Frequency;
static double GetFrequency();
double ElapsedTime;
double StartTime;
int running;
};
#endif
main.cpp
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifdef WITH_MPI
#include <mpi.h>
......@@ -37,7 +47,7 @@ int mpi_rank = 0;
int mpi_size = 1;
#endif
#include "cmodules/timer.h"
#include "timer.h"
int main(int argc, char* argv[])
{
......
map.cpp
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
......
model.cpp
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
......@@ -169,6 +170,8 @@ int bioem_model::readModel(bioem_param& param, const char* filemodel)
if(foundpos < endpos){
cout << "Warining:::: .pdb dectected in file name whilst using text read \n";
cout << "Warining:::: Are you sure you do not need --ReadPDB? \n";
cout << "If so then you must include the keyword IGNORE_PDB in inputfile\n";
if(not param.ignorePDB)exit(1);
}
FILE *file = fopen ( filemodel , "r" );
......
param.cpp
View file @ 01a19a3d
/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
Volker Lindenstruth and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
See license statement for terms of distribution.
......@@ -93,6 +94,7 @@ int bioem_param::readParameters(const char* fileinput)
yespriorAngles=false;
ignorepointsout=false;
printrotmod=false;
ignorePDB=false;
NotUn_angles=0;
priorMod=1; //Default
......@@ -334,6 +336,11 @@ int bioem_param::readParameters(const char* fileinput)
ignoreCCoff = true;
cout << "Ignoring Cross-Correlation offset \n";
}
else if (strcmp(token, "IGNORE_PDB") == 0) //Ignore PDB extension
{
ignorePDB = true;
cout << "Ignoring PDB extension in model file \n";
}
else if (strcmp(token, "NO_PROJECT_RADIUS") == 0) //If projecting CA with amino-acid radius
{
doaaradius = false;
......
timer.cpp 0 → 100644
View file @ 01a19a3d
#include "timer.h"
#ifdef _WIN32
#include <windows.h>
#include <winbase.h>
#else
#include <time.h>
#endif
HighResTimer::HighResTimer()
{
ElapsedTime = 0;
running = 0;
}
HighResTimer::~HighResTimer() {}
void HighResTimer::Start()
{
#ifdef _WIN32
__int64 istart;
QueryPerformanceCounter((LARGE_INTEGER*)&istart);
StartTime = (double) istart;
#else
timespec tv;
clock_gettime(CLOCK_REALTIME, &tv);
StartTime = (double) tv.tv_sec * 1.0E9 + (double) tv.tv_nsec;
#endif
running = 1;
}
void HighResTimer::ResetStart()
{