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Commit ba7aae45 authored by Pilar Cossio's avatar Pilar Cossio
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Prior on defocus

parent af0a4c90
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Showing with 55 additions and 19 deletions
bioem.cpp
View file @ ba7aae45
......@@ -6,7 +6,7 @@
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
#ifdef WITH_MPI
#include <mpi.h>
#define MPI_CHK(expr) \
......@@ -14,9 +14,13 @@
{ \
fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
}
#endif
#include <fstream>
#include <boost/program_options.hpp>
#include <boost/random/normal_distribution.hpp>
#include <boost/random/uniform_int_distribution.hpp>
#include <boost/random/mersenne_twister.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
......@@ -67,6 +71,7 @@ const int num_colors = sizeof(colors)/sizeof(colors[0]);
using namespace boost;
namespace po = boost::program_options;
namespace bran= boost::random;
using namespace std;
......@@ -104,6 +109,8 @@ int bioem::configure(int ac, char* av[])
HighResTimer timer;
std::string infile, modelfile, mapfile,Inputanglefile,Inputbestmap;
if (mpi_rank == 0)
{
......@@ -309,7 +316,7 @@ int bioem::configure(int ac, char* av[])
if (mpi_rank != 0)param.angles = (myfloat3_t*) mallocchk(param.nTotGridAngles * sizeof (myfloat3_t));
MPI_Bcast(param.angles, param.nTotGridAngles * sizeof (myfloat3_t),MPI_BYTE, 0, MPI_COMM_WORLD);
#ifdef PILAR_DEBUG
#ifdef DEBUG
for(int n=0;n<param.nTotGridAngles;n++){
cout << "CHECK: Angle orient " << mpi_rank << " "<< n << " " << param.angles[n].pos[0] << " " << param.angles[n].pos[1] << " " << param.angles[n].pos[2] << " " << param.angles[n].quat4 << " " << "\n";}
......@@ -614,7 +621,7 @@ int bioem::run()
for (int i = 0;i < RefMap.ntotRefMap;i++)
{
bioem_Probability_map& pProbMap = pProb.getProbMap(i);
#ifdef PILAR_DEBUG
#ifdef DEBUG
cout << "Reduction " << mpi_rank << " Map " << i << " Prob " << pProbMap.Total << " Const " << pProbMap.Constoadd << "\n";
#endif
tmp1[i] = pProbMap.Total * exp(pProbMap.Constoadd - tmp2[i]);
......@@ -1021,7 +1028,7 @@ inline void bioem::calculateCCFFT(int iRefMap, int iOrient, int iConv, myfloat_
doRefMapFFT(iRefMap, iOrient, iConv, amp, pha, env, lCC, sumC, sumsquareC, pProb, param.param_device, RefMap);
#ifdef PILAR_DEBUG
#ifdef DEBUG
if (param.param_device.writeCC)
{ int cc=0;
for (int cent_x = 0; cent_x < param.param_device.NumberPixels ; cent_x = cent_x + param.param_device.CCdisplace)
......@@ -1105,7 +1112,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
gam = param.angles[iMap].pos[2];
//*** To see how things are going:
#ifdef PILAR_DEBUG
#ifdef DEBUG
cout << "Id " << omp_get_thread_num() << " Angs: " << alpha << " " << beta << " " << gam << "\n";
#endif
// ********** Creat Rotation with pre-defiend grid of orientations**********
......@@ -1151,7 +1158,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
for(int n = 0; n < Model.nPointsModel; n++)
{
if(Model.points[n].radius < param.pixelSize){
if(Model.points[n].radius <= param.pixelSize){
// cout << "Radius less than Pixel size: use keyword NO_PROJECT_RADIUS in inputfile\n";
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);
......@@ -1207,7 +1214,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
// **** Output Just to check****
#ifdef PILAR_DEBUG
#ifdef DEBUG
// if(iMap == 0)
{
ofstream myexamplemap;
......@@ -1317,7 +1324,14 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
if (mpi_rank == 0 && param.printModel)
{
MTRand mtr;
// MTRand mtr;
bran::mt19937 gen;
//Generating random seed so the maps do not have correlated Noise
gen.seed(static_cast<unsigned int>(std::time(0)));
//Uniform Noise: bran::uniform_int_distribution<> dist(1, 6);
//Gaussian noise
bran::normal_distribution <> distn(0.0,param.stnoise);
memcpy(tmp, localmultFFT, sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
......@@ -1334,7 +1348,8 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
if(!param.withnoise){
myexamplemap << "\nMAP " << k+param.ddx << " " << j+param.ddy << " " << Mapconv[k * param.param_device.NumberPixels + j] / norm2 *param.bestnorm +param.bestoff ;
} else {
myexamplemap << "\nMAP " << k+param.ddx << " " << j+param.ddy << " " << Mapconv[k * param.param_device.NumberPixels + j] / norm2 *param.bestnorm +param.bestoff+ mtr.randNorm(0.0,param.stnoise);
myexamplemap << "\nMAP " << k+param.ddx << " " << j+param.ddy << " " << Mapconv[k * param.param_device.NumberPixels + j] / norm2 *param.bestnorm +param.bestoff+distn(gen);
// cout << distn(gen) << "CHECK\n";
}
}
myexamplemap << " \n";
......
bioem_algorithm.h
View file @ ba7aae45
......@@ -105,11 +105,12 @@ __device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myflo
//Adding Gaussian Prior to envelope parameter
if(not param.tousepsf){
logpro = logpro - env * env / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf ;
logpro = logpro - env * env / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf - (pha - param.Priordefcent ) * (pha - param.Priordefcent ) / 2. / param.sigmaPriordefo / param.sigmaPriordefo ;
} else {
myfloat_t envF;
myfloat_t envF,phaF;
envF = 4.* M_PI * M_PI * env / ( env * env + pha * pha) ;
logpro = logpro - envF * envF / 2. / param.sigmaPriorbctf / param.sigmaPriorbctf ;
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 ;
}
//GCC is too stupid to inline properly, so the code is copied here
......
include/param.h
View file @ ba7aae45
......@@ -22,6 +22,9 @@ public:
myfloat_t Ntotpi;
myfloat_t volu;
myfloat_t sigmaPriorbctf;
myfloat_t sigmaPriordefo;
myfloat_t Priordefcent;
// If to write Probabilities of Angles from Model
bool writeAngles;
......
main.cpp
View file @ ba7aae45
#ifdef WITH_MPI
#include <mpi.h>
#define MPI_CHK(expr) \
......@@ -5,6 +6,7 @@
{ \
fprintf(stderr, "Error in MPI function %s: %d\n", __FILE__, __LINE__); \
}
#endif
#include <stdio.h>
#include <stdlib.h>
......
param.cpp
View file @ ba7aae45
......@@ -83,7 +83,7 @@ int bioem_param::readParameters(const char* fileinput)
writeCTF=false;
elecwavel=0.019866;
ignoreCCoff=false;
doquater= false;
doquater=false;
nocentermass=false;
printrotmod=false;
readquatlist=false;
......@@ -98,7 +98,8 @@ int bioem_param::readParameters(const char* fileinput)
shiftX=0;
shiftY=0;
param_device.sigmaPriorbctf=100.;
param_device.sigmaPriordefo=1.0;
param_device.Priordefcent=3.0;
ifstream input(fileinput);
if (!input.good())
......@@ -390,8 +391,21 @@ int bioem_param::readParameters(const char* fileinput)
{
token = strtok(NULL, " ");
param_device.sigmaPriorbctf=atof(token);
cout << "Chainging Gaussian width in Prior of Envelope b parameter" << param_device.sigmaPriorbctf << "\n";
cout << "Chainging Gaussian width in Prior of Envelope b parameter: " << param_device.sigmaPriorbctf << "\n";
}
else if (strcmp(token, "SIGMA_PRIOR_DEFOCUS") == 0)
{
token = strtok(NULL, " ");
param_device.sigmaPriordefo=atof(token);
cout << "Gaussian Width in Prior of defocus parameter: " << param_device.sigmaPriordefo << "\n";
}
else if (strcmp(token, "PRIOR_DEFOCUS_CENTER") == 0)
{
token = strtok(NULL, " ");
param_device.Priordefcent=atof(token);
cout << "Gaussian Center in Prior of defocus parameter: " << param_device.Priordefcent << "\n";
}
else if (strcmp(token, "IGNORE_POINTSOUT") == 0)
{
ignorepointsout=true;
......@@ -437,6 +451,8 @@ int bioem_param::readParameters(const char* fileinput)
//Asigning values of envelope according to b-envelope (not b-factor)
startGridEnvelop = startBfactor ;// 2.f;
endGridEnvelop = endBfactor ; // / 2.f;
param_device.Priordefcent *= M_PI * 2.f * 10000 * elecwavel ;
param_device.sigmaPriordefo *= M_PI * 2.f * 10000 * elecwavel ;
}
if(elecwavel==0.019688)cout << "Using default electron wave length: 0.019688 (A) of 300kV microscope\n";
......@@ -469,12 +485,11 @@ int bioem_param::forprintBest(const char* fileinput)
writeCTF=false;
elecwavel=0.019866;
ignoreCCoff=false;
doquater= false;
doquater=false;
nocentermass=false;
printrotmod=false;
readquatlist=false;
doaaradius=true;
doquater=true;
shiftX=0;
shiftY=0;
......@@ -890,7 +905,7 @@ int bioem_param::CalculateGridsParam(const char* fileangles) //TO DO FOR QUATERN
angles[n].pos[1] = (myfloat_t) b;
angles[n].pos[2] = (myfloat_t) g;
angles[n].quat4 =0.0;//just to be sure */
#ifdef PILAR_DEBUG
#ifdef DEBUG
if(yespriorAngles) cout << "check orient: " << n << " " << " " << angles[n].pos[0] << " " << angles[n].pos[1] << " " << angles[n].pos[2] << " prior: " << angprior[n]<< "\n";
#endif
}
......@@ -1049,7 +1064,7 @@ int bioem_param::CalculateGridsParam(const char* fileangles) //TO DO FOR QUATERN
sscanf (tmpVals, "%f", &pp);
if(pp <0.0000001)cout << "Sure you're input is correct? Very small prior.\n";
angprior[n] = pp;
#ifdef PILAR_DEBUG
#ifdef DEBUG
if(yespriorAngles) cout << "check orient: " << n << " " << angles[n].pos[0] << " " << angles[n].pos[1] << " " << angles[n].pos[2] << " prior: " << angprior[n] << "\n";
#endif
}
......
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