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BioEM
Commit 860031e3 authored by David Rohr's avatar David Rohr
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create angular probabilites only if writeAngles set

parent 88c93497
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Showing with 58 additions and 44 deletions
bioem.cpp
View file @ 860031e3
......@@ -92,7 +92,7 @@ int bioem::configure(int ac, char* av[])
// *** Inizialzing default variables ***
std::string infile, modelfile, mapfile;
Model.readPDB = false;
param.writeAngles = false;
param.param_device.writeAngles = false;
param.dumpMap = false;
param.loadMap = false;
RefMap.readMRC = false;
......@@ -280,6 +280,8 @@ int bioem::run()
pProbMap.Total = 0.0;
pProbMap.Constoadd = -9999999;
pProbMap.max_prob = -9999999;
if (param.param_device.writeAngles)
{
for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
{
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
......@@ -288,6 +290,7 @@ int bioem::run()
pProbAngle.ConstAngle = -99999999;
}
}
}
// **************************************************************************************
deviceStartRun();
{
......@@ -377,7 +380,7 @@ int bioem::run()
// *** Angular Probability ***
ofstream angProbfile;
if(param.writeAngles)
if(param.param_device.writeAngles)
{
angProbfile.open ("ANG_PROB");
}
......@@ -407,7 +410,7 @@ int bioem::run()
// *** For individual files*** //angProbfile.open ("ANG_PROB_"iRefMap);
if(param.writeAngles)
if(param.param_device.writeAngles)
{
for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient++)
{
......@@ -418,7 +421,7 @@ int bioem::run()
}
}
if(param.writeAngles)
if(param.param_device.writeAngles)
{
angProbfile.close();
}
......@@ -540,6 +543,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
}
// **** Output Just to check****
#ifdef PILAR_DEBUG
if(iMap == 10)
{
ofstream myexamplemap;
......@@ -556,6 +560,7 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
myexamplemap.close();
myexampleRot.close();
}
#endif
// ***** Converting projection to Fourier Space for Convolution later with kernel****
// ********** Omp Critical is necessary with FFTW*******
......
bioem_algorithm.h
View file @ 860031e3
......@@ -21,18 +21,21 @@
#endif
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)
__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)
{
// ******* Summing total Probabilities *************
// ******* Need a constant because of numerical divergence*****
bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
if(pProbMap.Constoadd < logpro)
{
pProbMap.Total = pProbMap.Total * exp(-logpro + pProbMap.Constoadd);
pProbMap.Constoadd = logpro;
}
if (GPUAlgo != 2) pProbMap.Total += exp(logpro - pProbMap.Constoadd);
if (doAngle)
{
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
//Summing probabilities for each orientation
if(pProbAngle.ConstAngle < logpro)
......@@ -41,10 +44,7 @@ __device__ static inline void update_prob(const myfloat_t logpro, const int iRef
pProbAngle.ConstAngle = logpro;
}
if (GPUAlgo != 2)
{
pProbMap.Total += exp(logpro - pProbMap.Constoadd);
pProbAngle.forAngles += exp(logpro - pProbAngle.ConstAngle);
if (GPUAlgo != 2) pProbAngle.forAngles += exp(logpro - pProbAngle.ConstAngle);
}
// ********** Getting parameters that maximize the probability ***********
......@@ -90,11 +90,9 @@ __device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myflo
const myfloat_t logpro = calc_logpro(param, sumC, sumsquareC, value, RefMap.sum_RefMap[iRefMap], RefMap.sumsquare_RefMap[iRefMap]);
bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
//GCC is too stupid to inline properly, so the code is copied here
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb);
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb, param.writeAngles);
bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
if(pProbMap.Constoadd < logpro)
{
pProbMap.Total = pProbMap.Total * exp(-logpro + pProbMap.Constoadd);
......@@ -102,12 +100,17 @@ __device__ static inline void calProb(int iRefMap, int iOrient, int iConv, myflo
}
pProbMap.Total += exp(logpro - pProbMap.Constoadd);
if (param.writeAngles)
{
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
if(pProbAngle.ConstAngle < logpro)
{
pProbAngle.forAngles = pProbAngle.forAngles * exp(-logpro + pProbAngle.ConstAngle);
pProbAngle.ConstAngle = logpro;
}
pProbAngle.forAngles += exp(logpro - pProbAngle.ConstAngle);
}
if(pProbMap.max_prob < logpro)
{
......@@ -291,7 +294,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
if (myShift == 0 && iRefMap < RefMap.ntotRefMap)
{
const myfloat_t logpro_max = vbuf[myThreadIdxX];
update_prob<GPUAlgo>(logpro_max, iRefMap, iOrient, iConv, -1, -1, pProb, buf3, bufint);
update_prob<GPUAlgo>(logpro_max, iRefMap, iOrient, iConv, -1, -1, pProb, param.writeAngles, buf3, bufint);
}
}
......@@ -399,7 +402,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
else
#endif
{
update_prob < -1 > (logpro, iRefMap, iOrient, iConv, cent_x, cent_y, pProb);
update_prob < -1 > (logpro, iRefMap, iOrient, iConv, cent_x, cent_y, pProb, param.writeAngles);
}
}
......
bioem_cuda.cu
View file @ 860031e3
......@@ -374,7 +374,7 @@ int bioem_cuda::deviceInit()
gpumap->sum_RefMap = sum;
gpumap->sumsquare_RefMap = sumsquare;
checkCudaErrors(cudaMalloc(&pProb_memory, pProb_device.get_size(RefMap.ntotRefMap, param.nTotGridAngles)));
checkCudaErrors(cudaMalloc(&pProb_memory, pProb_device.get_size(RefMap.ntotRefMap, param.nTotGridAngles, param.param_device.writeAngles)));
for (int i = 0; i < 2; i++)
{
checkCudaErrors(cudaStreamCreate(&cudaStream[i]));
......@@ -466,7 +466,7 @@ int bioem_cuda::deviceStartRun()
pProb_device = *pProb_host;
pProb_device.ptr = pProb_memory;
pProb_device.set_pointers();
checkCudaErrors(cudaMemcpyAsync(pProb_device.ptr, pProb_host->ptr, pProb_host->get_size(maxRef, param.nTotGridAngles), cudaMemcpyHostToDevice, cudaStream[0]));
checkCudaErrors(cudaMemcpyAsync(pProb_device.ptr, pProb_host->ptr, pProb_host->get_size(maxRef, param.nTotGridAngles, param.param_device.writeAngles), cudaMemcpyHostToDevice, cudaStream[0]));
if (FFTAlgo)
{
......@@ -501,7 +501,7 @@ int bioem_cuda::deviceStartRun()
int bioem_cuda::deviceFinishRun()
{
if (GPUAsync) cudaStreamSynchronize(cudaStream[0]);
checkCudaErrors(cudaMemcpyAsync(pProb_host->ptr, pProb_device.ptr, pProb_host->get_size(maxRef, param.nTotGridAngles), cudaMemcpyDeviceToHost, cudaStream[0]));
checkCudaErrors(cudaMemcpyAsync(pProb_host->ptr, pProb_device.ptr, pProb_host->get_size(maxRef, param.nTotGridAngles, param.param_device.writeAngles), cudaMemcpyDeviceToHost, cudaStream[0]));
if (FFTAlgo)
{
......
include/map.h
View file @ 860031e3
......@@ -2,6 +2,7 @@
#define BIOEM_MAP_H
#include "defs.h"
#include "param.h"
#include <complex>
#include <math.h>
......@@ -107,9 +108,11 @@ public:
bioem_Probability_map* ptr_map;
bioem_Probability_angle* ptr_angle;
static size_t get_size(size_t maps, size_t angles)
static size_t get_size(size_t maps, size_t angles, bool writeAngles)
{
return(maps * (angles * sizeof(bioem_Probability_angle) + sizeof(bioem_Probability_map)));
size_t size = sizeof(bioem_Probability_map);
if (writeAngles) size += angles * sizeof(bioem_Probability_angle);
return(maps * size);
}
void init(size_t maps, size_t angles, bioem& bio);
......
include/param.h
View file @ 860031e3
......@@ -18,6 +18,8 @@ public:
int NtotDist;
myfloat_t Ntotpi;
myfloat_t volu;
// If to write Probabilities of Angles from Model
bool writeAngles;
};
class bioem_param
......@@ -38,8 +40,6 @@ public:
mycomplex_t* refCTF;
myfloat3_t* CtfParam;
// If to write Probabilities of Angles from Model
bool writeAngles;
myfloat_t pixelSize;
// Grid Points in Euler angles, assuming uniform sampling d_alpha=d_gamma (in 2pi) & cos(beta)=-1,1
int angleGridPointsAlpha;
......
map.cpp
View file @ 860031e3
......@@ -276,7 +276,7 @@ void bioem_Probability::init(size_t maps, size_t angles, bioem& bio)
{
nMaps = maps;
nAngles = angles;
ptr = bio.malloc_device_host(get_size(maps, angles));
ptr = bio.malloc_device_host(get_size(maps, angles, bio.param.param_device.writeAngles));
set_pointers();
}
......@@ -286,12 +286,15 @@ void bioem_Probability::copyFrom(bioem_Probability* from, bioem& bio)
bioem_Probability_map& pProbMapFrom = from->getProbMap(0);
memcpy(&pProbMap, &pProbMapFrom, from->nMaps * sizeof(bioem_Probability_map));
if (bio.param.param_device.writeAngles)
{
for (int iOrient = 0; iOrient < bio.param.nTotGridAngles; iOrient ++)
{
bioem_Probability_angle& pProbAngle = getProbAngle(0, iOrient);
bioem_Probability_angle& pProbAngleFrom = from->getProbAngle(0, iOrient);
memcpy(&pProbAngle, &pProbAngleFrom, from->nMaps * sizeof(bioem_Probability_angle));
}
}
}
int bioem_RefMap::read_MRC(const char* filename,bioem_param& param)
......
param.cpp
View file @ 860031e3
......@@ -209,7 +209,7 @@ int bioem_param::readParameters(const char* fileinput)
}
else if (strcmp(token, "WRITE_PROB_ANGLES") == 0)
{
writeAngles = true;
param_device.writeAngles = true;
cout << "Writing Probabilies of each angle \n";
}
}
......
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