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BioEM
Commit a65e74a6 authored by David Rohr's avatar David Rohr
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Fix allocation of FFTW scratch space, move deallocation of memory allocated in... 

Fix allocation of FFTW scratch space, move deallocation of memory allocated in configuration to cleanup function, get rid of MAX_ORIENT constant
parent 6b401955
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Showing with 214 additions and 152 deletions
bioem.cpp
View file @ a65e74a6
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bioem_algorithm.h
View file @ a65e74a6
......@@ -12,33 +12,36 @@
#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, myfloat_t* buf3 = NULL, int* bufint = NULL)
{
// ******* Summing total Probabilities *************
// ******* Need a constant because of numerical divergence*****
if(pProb[iRefMap].Constoadd < logpro)
bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
if(pProbMap.Constoadd < logpro)
{
pProb[iRefMap].Total = pProb[iRefMap].Total * exp(-logpro + pProb[iRefMap].Constoadd);
pProb[iRefMap].Constoadd = logpro;
pProbMap.Total = pProbMap.Total * exp(-logpro + pProbMap.Constoadd);
pProbMap.Constoadd = logpro;
}
//Summing probabilities for each orientation
if(pProb[iRefMap].ConstAngle[iOrient] < logpro)
if(pProbAngle.ConstAngle < logpro)
{
pProb[iRefMap].forAngles[iOrient] = pProb[iRefMap].forAngles[iOrient] * exp(-logpro + pProb[iRefMap].ConstAngle[iOrient]);
pProb[iRefMap].ConstAngle[iOrient] = logpro;
pProbAngle.forAngles = pProbAngle.forAngles * exp(-logpro + pProbAngle.ConstAngle);
pProbAngle.ConstAngle = logpro;
}
if (GPUAlgo != 2)
{
pProb[iRefMap].Total += exp(logpro - pProb[iRefMap].Constoadd);
pProb[iRefMap].forAngles[iOrient] += exp(logpro - pProb[iRefMap].ConstAngle[iOrient]);
pProbMap.Total += exp(logpro - pProbMap.Constoadd);
pProbAngle.forAngles += exp(logpro - pProbAngle.ConstAngle);
}
// ********** Getting parameters that maximize the probability ***********
if(pProb[iRefMap].max_prob < logpro)
if(pProbMap.max_prob < logpro)
{
pProb[iRefMap].max_prob = logpro;
pProbMap.max_prob = logpro;
if (GPUAlgo == 2)
{
......@@ -47,11 +50,11 @@ __device__ static inline void update_prob(const myfloat_t logpro, const int iRef
}
else
{
pProb[iRefMap].max_prob_cent_x = cent_x;
pProb[iRefMap].max_prob_cent_y = cent_y;
pProbMap.max_prob_cent_x = cent_x;
pProbMap.max_prob_cent_y = cent_y;
}
pProb[iRefMap].max_prob_orient = iOrient;
pProb[iRefMap].max_prob_conv = iConv;
pProbMap.max_prob_orient = iOrient;
pProbMap.max_prob_conv = iConv;
}
}
......@@ -70,7 +73,7 @@ __device__ static inline myfloat_t calc_logpro(const bioem_param_device& param,
return(logpro);
}
__device__ static inline void calProb(int iRefMap, int iOrient, int iConv, 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)
__device__ static inline void calProb(int iRefMap, int iOrient, int iConv, 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)
{
// ********************************************************
// *********** Calculates the BioEM probability ***********
......@@ -78,33 +81,36 @@ __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]);
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb);
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
if(pProb[iRefMap].Constoadd < logpro)
//update_prob<-1>(logpro, iRefMap, iOrient, iConv, disx, disy, pProb);
if(pProbMap.Constoadd < logpro)
{
pProb[iRefMap].Total = pProb[iRefMap].Total * exp(-logpro + pProb[iRefMap].Constoadd);
pProb[iRefMap].Constoadd = logpro;
pProbMap.Total = pProbMap.Total * exp(-logpro + pProbMap.Constoadd);
pProbMap.Constoadd = logpro;
}
pProb[iRefMap].Total += exp(logpro - pProb[iRefMap].Constoadd);
pProbMap.Total += exp(logpro - pProbMap.Constoadd);
if(pProb[iRefMap].ConstAngle[iOrient] < logpro)
if(pProbAngle.ConstAngle < logpro)
{
pProb[iRefMap].forAngles[iOrient] = pProb[iRefMap].forAngles[iOrient] * exp(-logpro + pProb[iRefMap].ConstAngle[iOrient]);
pProb[iRefMap].ConstAngle[iOrient] = logpro;
pProbAngle.forAngles = pProbAngle.forAngles * exp(-logpro + pProbAngle.ConstAngle);
pProbAngle.ConstAngle = logpro;
}
pProb[iRefMap].forAngles[iOrient] += exp(logpro - pProb[iRefMap].ConstAngle[iOrient]);
pProbAngle.forAngles += exp(logpro - pProbAngle.ConstAngle);
if(pProb[iRefMap].max_prob < logpro)
if(pProbMap.max_prob < logpro)
{
pProb[iRefMap].max_prob = logpro;
pProb[iRefMap].max_prob_cent_x = disx;
pProb[iRefMap].max_prob_cent_y = disy;
pProb[iRefMap].max_prob_orient = iOrient;
pProb[iRefMap].max_prob_conv = iConv;
pProbMap.max_prob = logpro;
pProbMap.max_prob_cent_x = disx;
pProbMap.max_prob_cent_y = disy;
pProbMap.max_prob_orient = iOrient;
pProbMap.max_prob_conv = iConv;
}
}
__device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient, const int iConv, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability* pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
__device__ static inline void doRefMapFFT(const int iRefMap, const int iOrient, const int iConv, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability& pProb, const bioem_param_device& param, const bioem_RefMap& RefMap)
{
for (int cent_x = 0; cent_x <= param.maxDisplaceCenter; cent_x = cent_x + param.GridSpaceCenter)
{
......@@ -131,7 +137,7 @@ __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* 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)
{
......@@ -281,18 +287,22 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
}
__syncthreads();
bioem_Probability_map& pProbMap = pProb.getProbMap(iRefMap);
bioem_Probability_angle& pProbAngle = pProb.getProbAngle(iRefMap, iOrient);
if (bufint[0] == 1 && buf3[1] == logpro && iRefMap < RefMap.ntotRefMap && atomicAdd(&bufint[0], 1) == 1)
{
pProb[iRefMap].max_prob_cent_x = cent_x;
pProb[iRefMap].max_prob_cent_y = cent_y;
pProbMap.max_prob_cent_x = cent_x;
pProbMap.max_prob_cent_y = cent_y;
}
__syncthreads();
if (iRefMap < RefMap.ntotRefMap)
{
buf[myThreadIdxX] = exp(logpro - pProb[iRefMap].Constoadd);
buf2[myThreadIdxX] = exp(logpro - pProb[iRefMap].ConstAngle[iOrient]);
buf[myThreadIdxX] = exp(logpro - pProbMap.Constoadd);
buf2[myThreadIdxX] = exp(logpro - pProbAngle.ConstAngle);
}
__syncthreads();
......@@ -372,8 +382,8 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
}
if (myShift == 0 && iRefMap < RefMap.ntotRefMap)
{
pProb[iRefMap].Total += vbuf[myThreadIdxX];
pProb[iRefMap].forAngles[iOrient] += vbuf2[myThreadIdxX];
pProbMap.Total += vbuf[myThreadIdxX];
pProbAngle.forAngles += vbuf2[myThreadIdxX];
}
}
}
......@@ -385,7 +395,7 @@ __device__ static inline void compareRefMap(const int iRefMap, const int iOrient
}
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* 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)
{
......
bioem_cuda.cu
View file @ a65e74a6
......@@ -69,7 +69,7 @@ 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* 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)
......@@ -78,7 +78,7 @@ __global__ void compareRefMap_kernel(const int iOrient, const int iConv, const m
}
}
__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* 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)
......@@ -96,7 +96,7 @@ __global__ void cudaZeroMem(void* ptr, size_t size)
for (int i = myid; i < mysize; i += mygrid) myptr[i] = 0;
}
__global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iConv, const myfloat_t* pMap, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap RefMap, const int blockoffset, const int nShifts, const int nShiftBits, const int maxRef)
__global__ void compareRefMapLoopShifts_kernel(const int iOrient, const int iConv, const myfloat_t* pMap, bioem_Probability pProb, const bioem_param_device param, const bioem_RefMap RefMap, const int blockoffset, const int nShifts, const int nShiftBits, const int maxRef)
{
const size_t myid = (myBlockIdxX + blockoffset) * myBlockDimX + myThreadIdxX;
const int iRefMap = myid >> (nShiftBits << 1);
......@@ -124,7 +124,7 @@ __global__ void multComplexMap(const mycomplex_t* convmap, const mycomplex_t* re
}
}
__global__ void cuDoRefMapsFFT(const int iOrient, const int iConv, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability* pProb, const bioem_param_device param, const bioem_RefMap RefMap, const int maxRef, const int Offset)
__global__ void cuDoRefMapsFFT(const int iOrient, const int iConv, const myfloat_t* lCC, const myfloat_t sumC, const myfloat_t sumsquareC, bioem_Probability pProb, const bioem_param_device param, const bioem_RefMap RefMap, const int maxRef, const int Offset)
{
const int iRefMap = myBlockIdxX * myBlockDimX + myThreadIdxX + Offset;
const myfloat_t* mylCC = &lCC[(myBlockIdxX * myBlockDimX + myThreadIdxX) * param.NumberPixels * param.NumberPixels];
......@@ -145,7 +145,7 @@ static inline int ilog2 (int value)
static inline int ilog2(int value) {return 31 - __builtin_clz(value);}
#endif
int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
int bioem_cuda::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap)
{
if (startMap)
{
......@@ -170,7 +170,7 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* c
cout << "Error running CUFFT " << cufftGetErrorStrung(err) << "\n";
exit(1);
}
cuDoRefMapsFFT<<<divup(num, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>>(iProjectionOut, iConv, pFFTtmp, sumC, sumsquareC, pProb_device, param.param_device, *gpumap, num, i);
cuDoRefMapsFFT<<<divup(num, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>>(iOrient, iConv, pFFTtmp, sumC, sumsquareC, pProb_device, param.param_device, *gpumap, num, i);
}
checkCudaErrors(cudaGetLastError());
}
......@@ -201,7 +201,7 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* c
size_t nBlocks = CUDA_BLOCK_COUNT;
for (size_t i = 0; i < totalBlocks; i += nBlocks)
{
compareRefMapLoopShifts_kernel<<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream >>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *gpumap, i, nShifts, nShiftBits, maxRef);
compareRefMapLoopShifts_kernel<<<min(nBlocks, totalBlocks - i), CUDA_THREAD_COUNT, (CUDA_THREAD_COUNT * 2 + CUDA_THREAD_COUNT / (nShifts * nShifts) * 4) * sizeof(myfloat_t), cudaStream >>> (iOrient, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *gpumap, i, nShifts, nShiftBits, maxRef);
}
}
else if (GPUAlgo == 1) //Split shifts in multiple kernels
......@@ -210,13 +210,13 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* c
{
for (int cent_y = -param.param_device.maxDisplaceCenter; cent_y <= param.param_device.maxDisplaceCenter; cent_y = cent_y + param.param_device.GridSpaceCenter)
{
compareRefMap_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *pRefMap_device_Mod, cent_x, cent_y, maxRef);
compareRefMap_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iOrient, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *pRefMap_device_Mod, cent_x, cent_y, maxRef);
}
}
}
else if (GPUAlgo == 0) //All shifts in one kernel
{
compareRefMapShifted_kernel<<<divup(maxRef, CUDA_THREAD_COUNT), CUDA_THREAD_COUNT, 0, cudaStream>>> (iProjectionOut, 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>>> (iOrient, iConv, pConvMap_device[iConv & 1], pProb_device, param.param_device, *pRefMap_device_Mod, maxRef);
}
else
{
......@@ -226,7 +226,7 @@ int bioem_cuda::compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* c
}
if (GPUWorkload < 100)
{
bioem::compareRefMaps(iProjectionOut, iConv, conv_map, localmultFFT, sumC, sumsquareC, maxRef);
bioem::compareRefMaps(iOrient, iConv, conv_map, localmultFFT, sumC, sumsquareC, maxRef);
}
if (GPUAsync)
{
......@@ -273,7 +273,9 @@ int bioem_cuda::deviceInit()
gpumap->sumsquare_RefMap = sumsquare;
checkCudaErrors(cudaStreamCreate(&cudaStream));
checkCudaErrors(cudaMalloc(&pProb_device, sizeof(bioem_Probability) * RefMap.ntotRefMap));
pProb_device = pProb;
checkCudaErrors(cudaMalloc(&pProb_device.ptr, pProb_device.get_size(RefMap.ntotRefMap, param.nTotGridAngles)));
pProb_device.set_pointers();
for (int i = 0; i < 2; i++)
{
checkCudaErrors(cudaEventCreate(&cudaEvent[i]));
......@@ -298,7 +300,7 @@ int bioem_cuda::deviceExit()
if (deviceInitialized == 0) return(0);
cudaStreamDestroy(cudaStream);
cudaFree(pProb_device);
cudaFree(pProb_device.ptr);
cudaFree(sum);
cudaFree(sumsquare);
for (int i = 0; i < 2; i++)
......@@ -332,7 +334,7 @@ int bioem_cuda::deviceStartRun()
{
maxRef = GPUWorkload >= 100 ? RefMap.ntotRefMap : ((size_t) RefMap.ntotRefMap * (size_t) GPUWorkload / 100);
cudaMemcpy(pProb_device, pProb, sizeof(bioem_Probability) * maxRef, cudaMemcpyHostToDevice);
cudaMemcpy(pProb_device.ptr, pProb.ptr, pProb.get_size(RefMap.ntotRefMap, param.nTotGridAngles), cudaMemcpyHostToDevice);
if (FFTAlgo)
{
......@@ -362,7 +364,7 @@ int bioem_cuda::deviceStartRun()
int bioem_cuda::deviceFinishRun()
{
if (GPUAsync) cudaStreamSynchronize(cudaStream);
cudaMemcpy(pProb, pProb_device, sizeof(bioem_Probability) * maxRef, cudaMemcpyDeviceToHost);
cudaMemcpy(pProb.ptr, pProb_device.ptr, pProb.get_size(RefMap.ntotRefMap, param.nTotGridAngles), cudaMemcpyDeviceToHost);
if (FFTAlgo)
{
......
include/bioem.h
View file @ a65e74a6
......@@ -12,24 +12,28 @@
class bioem
{
friend class bioem_RefMap;
public:
bioem();
virtual ~bioem();
int configure(int ac, char* av[]);
void cleanup(); //Cleanup everything happening during configure
int precalculate(); // Is it better to pass directly the input File names?
int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
int run();
int doProjections(int iMap);
int createConvolutedProjectionMap(int iOreint, int iMap, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC);
virtual int compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
virtual int compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
int createProjection(int iMap, mycomplex_t* map);
int calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare);
void calculateCCFFT(int iMap, int iOrient, int iConv, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC);
bioem_Probability* pProb;
bioem_Probability pProb;
protected:
virtual int deviceInit();
......
include/bioem_cuda_internal.h
View file @ a65e74a6
......@@ -17,7 +17,7 @@ public:
bioem_cuda();
virtual ~bioem_cuda();
virtual int compareRefMaps(int iProjectionOut, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
virtual int compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
protected:
virtual int deviceInit();
......@@ -31,7 +31,7 @@ protected:
cudaEvent_t cudaEvent[2];
bioem_RefMap_Mod* pRefMap_device_Mod;
bioem_RefMap* gpumap;
bioem_Probability* pProb_device;
bioem_Probability pProb_device;
myfloat_t* pConvMap_device[2];
mycomplex_t* pRefMapsFFT;
......
include/defs.h
View file @ a65e74a6
......@@ -40,7 +40,6 @@ typedef myfloat_t mycomplex_t[2];
#define BIOEM_FLOAT_3_PHYSICAL_SIZE 3 //Possible set to 4 for GPU
#define BIOEM_MODEL_SIZE 120000
#define MAX_ORIENT 20000
struct myfloat3_t
{
......
include/map.h
View file @ a65e74a6
......@@ -6,6 +6,7 @@
#include <math.h>
class bioem_param;
class bioem;
class bioem_RefMap
{
......@@ -30,6 +31,7 @@ public:
RefMapsFFT = NULL;
}
int readRefMaps(bioem_param& param);
int precalculate(bioem_param& param, bioem& bio);
int PreCalculateMapsFFT(bioem_param& param);
mycomplex_t* RefMapsFFT;
......@@ -68,15 +70,52 @@ public:
}
};
class bioem_Probability
class bioem_Probability_map
{
public:
myfloat_t forAngles[MAX_ORIENT];
myfloat_t Total;
myfloat_t Constoadd;
myfloat_t ConstAngle[MAX_ORIENT];
myfloat_t max_prob;
int max_prob_cent_x, max_prob_cent_y, max_prob_orient, max_prob_conv;
};
class bioem_Probability_angle
{
public:
myfloat_t forAngles;
myfloat_t ConstAngle;
};
class bioem_Probability
{
public:
int nMaps;
int nAngles;
__device__ __host__ bioem_Probability_map& getProbMap(int map) {return(ptr_map[map]);}
__device__ __host__ bioem_Probability_angle& getProbAngle(int map, int angle) {return(ptr_angle[angle * nMaps + map]);}
void* ptr;
bioem_Probability_map* ptr_map;
bioem_Probability_angle* ptr_angle;
size_t get_size(size_t maps, size_t angles)
{
return(maps * (angles * sizeof(bioem_Probability_angle) + sizeof(bioem_Probability_map)));
}
void init(size_t maps, size_t angles)
{
nMaps = maps;
nAngles = angles;
ptr = mallocchk(get_size(maps, angles));
set_pointers();
}
void set_pointers()
{
ptr_map = (bioem_Probability_map*) ptr;
ptr_angle = (bioem_Probability_angle*) (&ptr_map[nMaps]);
}
};
#endif
main.cpp
View file @ a65e74a6
......@@ -55,6 +55,7 @@ int main(int argc, char* argv[])
// ************************************ End **********************************
printf ("The code ran for %f seconds.\n", timer.GetElapsedTime());
bio->cleanup();
delete bio;
return(0);
......
map.cpp
View file @ a65e74a6
......@@ -8,6 +8,7 @@
#include "map.h"
#include "param.h"
#include "bioem.h"
using namespace std;
......@@ -178,3 +179,31 @@ int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
return(0);
}
int bioem_RefMap::precalculate(bioem_param& param, bioem& bio)
{
// **************************************************************************************
// *******************************Precalculating Routine for Maps************************
// **************************************************************************************
myfloat_t sum, sumsquare;
//Precalculating cross-correlations of maps
for (int iRefMap = 0; iRefMap < ntotRefMap ; iRefMap++)
{
bio.calcross_cor(getmap(iRefMap), sum, sumsquare);
//Storing Crosscorrelations in Map class
sum_RefMap[iRefMap] = sum;
sumsquare_RefMap[iRefMap] = sumsquare;
}
// Precalculating Maps in Fourier space
if (bio.FFTAlgo)
{
PreCalculateMapsFFT(param);
free(maps);
maps = NULL;
}
return(0);
}
param.cpp
View file @ a65e74a6
......@@ -246,6 +246,7 @@ int bioem_param::CalculateGridsParam() //TO DO FOR QUATERNIONS
cos_grid_beta = 2.f / (myfloat_t) angleGridPointsBeta;
// Euler Angle Array
delete[] angles;
angles = new myfloat3_t[angleGridPointsAlpha * angleGridPointsBeta * angleGridPointsAlpha];
for (int ialpha = 0; ialpha < angleGridPointsAlpha; ialpha ++)
{
......
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