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feat: fix all TEST and add DICOM export TEST

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kradchen
2024-09-19 15:37:02 +08:00
parent 4c4ab3794e
commit 01210045bc
10 changed files with 287 additions and 377 deletions
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137
src/reflectionReconstruction/startReflectionReconstruction.cpp.orig
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@@ -1,137 +0,0 @@
#include "startReflectionReconstruction.h"
#include "Function.h"
#include "Function2D.h"
#include "Function3D.h"
#include "Matrix.h"
#include "MatlabWriter.h"
#include "common/getGeometryInfo.h"
#include "common/precalculateChannelList.h"
#include "common/dataBlockCreation/getAScanBlockPreprocessed.h"
#include "common/dataBlockCreation/removeDataFromArrays.h"
#include "log/notify.h"
#include "reflectionReconstruction/preprocessData/determineOptimalPulse.h"
#include "reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.h"
#include "src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h"
#include "config/config.h"
#include "log/log.h"
#include "CudaEnvInit.h"
#include <cstdio>
#include <iostream>
#include <queue>
#include <thread>
#include <vector>
using namespace Aurora;
using namespace Recon;
namespace
{
std::queue<preprocessAScanRResult> PRODUCER_PROCESSDATAS;
std::queue<AscanBlockPreprocessed> PRODUCER_BLOCKDATAS;
std::mutex PRODUCER_MUTEX;
std::condition_variable PRODUCER_CONDITION;
std::mutex CUSTOMER_MUTEX;
std::condition_variable CUSTOMER_CONDITION;
}
void producerThread( Parser* aParser, const Aurora::Matrix& aMotorPos,
const Aurora::Matrix& aSlList, const Aurora::Matrix& aSnList,
const Aurora::Matrix& aRlList, const Aurora::Matrix& aRnList,
GeometryInfo& aGeom, MeasurementInfo& aExpInfo, PreComputes& aPreComputes)
{
if(reflectParams::useOptPulse==1 && reflectParams::runReflectionReco)
{
aPreComputes.sincPeak_ft = determineOptimalPulse(aPreComputes.timeInterval, aExpInfo.expectedAScanLength);
}
printf(" - channel list");
auto channelList = precalculateChannelList(aRlList, aRnList, aExpInfo, aPreComputes);
size_t numScans = aMotorPos.getDataSize() * aSlList.getDataSize() *
aSnList.getDataSize() * aRlList.getDataSize() *
aRnList.getDataSize();
int numTakenScans = 0,numProcessedScans = 0,numPossibleScans = 0;
for(int i=0; i<aMotorPos.getDataSize(); ++i)
{
//#pragma omp parallel for num_threads(24)
for(int j=0; j<aSlList.getDataSize() / transParams::senderTASSize; ++j)
{
for(int k=0; k<aSnList.getDataSize() / transParams::senderElementSize; ++k)
{
Matrix mp = aMotorPos(i).toMatrix();
Matrix sl = aSlList.block(0, transParams::senderTASSize*j, transParams::senderTASSize*j+transParams::senderTASSize - 1);
Matrix sn = aSnList.block(0, transParams::senderElementSize*k, transParams::senderElementSize*k+transParams::senderElementSize - 1);
auto blockData = getAscanBlockPreprocessed(aParser, mp, sl, sn, aRlList, aRnList, aGeom, aExpInfo, true, false);
float* channelListSizeData = Aurora::malloc(2);
channelListSizeData[0] = channelList.getDimSize(0);
channelListSizeData[1] = channelList.getDimSize(1);
Matrix channelListSize = Matrix::New(channelListSizeData, 2, 1);
Matrix ind = sub2ind(channelListSize, {blockData.rlBlock, blockData.rnBlock});
size_t channelBlockSize = ind.getDataSize();
float* channelBlockData = Aurora::malloc(channelBlockSize);
for(size_t i=0; i<channelBlockSize; ++i)
{
channelBlockData[i] = channelList[ind[i] - 1];
}
Matrix channelBlock = Matrix::New(channelBlockData, 1, channelBlockSize);
RECON_INFO("start cpu---------preprocessAScanBlockForReflection");
auto preprocessData = preprocessAScanBlockForReflection(blockData.ascanBlockPreprocessed, blockData.mpBlock, blockData.slBlock,
blockData.snBlock, blockData.rlBlock, blockData.rnBlock, blockData.senderPositionBlock,
blockData.receiverPositionBlock, blockData.gainBlock, channelBlock, aExpInfo, aPreComputes);
PRODUCER_BLOCKDATAS.push(blockData);
PRODUCER_PROCESSDATAS.push(preprocessData);
}
}
}
}
Aurora::Matrix Recon::startReflectionReconstruction( Parser* aParser, int aSAFT_mode, const Aurora::Matrix& aMotorPos,
const Aurora::Matrix& aSlList, const Aurora::Matrix& aSnList,
const Aurora::Matrix& aRlList, const Aurora::Matrix& aRnList,
GeometryInfo& aGeom, TransRecos& aTransRecos,
MeasurementInfo& aExpInfo, PreComputes& aPreComputes)
{
printf("Reflection reconstruction is carried out.");
printf("Preperations for reconstructions.");
printf(" - reset GPUs");
for (size_t i = 0; i < reflectParams::gpuSelectionList.getDataSize(); i++)
{
std::string msg;
if (!resetGPUDevice((int)reflectParams::gpuSelectionList[i],msg))
{
std::cerr<<msg<<std::endl;
}
}
std::thread thread = std::thread(producerThread, aParser, aMotorPos, aSlList, aSnList, aRlList, aRnList, aGeom, aExpInfo, aPreComputes);
Matrix Env = Aurora::zeros((int)reflectParams::imageXYZ[0],(int)reflectParams::imageXYZ[1],(int)reflectParams::imageXYZ[2]);
for(int i=0; i<aMotorPos.getDataSize(); ++i)
{
//#pragma omp parallel for num_threads(24)
for(int j=0; j<aSlList.getDataSize() / transParams::senderTASSize; ++j)
{
for(int k=0; k<aSnList.getDataSize() / transParams::senderElementSize; ++k)
{
RECON_INFO("start gpu---------recontructSAFT");
Env = recontructSAFT(removeDataFromArrays(preprocessData.AscanBlock, preprocessData.usedData),
removeDataFromArrays(blockData.senderPositionBlock, preprocessData.usedData),
removeDataFromArrays(blockData.receiverPositionBlock, preprocessData.usedData),
removeDataFromArrays(blockData.mpBlock, preprocessData.usedData),
aSAFT_mode, aTransRecos, Env);
std::cout<<Env[0]<<"-" << Env[1] <<"-" << Env[2] <<"-" << Env[3]<<std::endl;
RECON_INFO("Reflection Reconstructon: " + std::to_string(j));
}
//Recon::notifyProgress(25+73*((j*i)/(aMotorPos.getDataSize() * aSlList.getDataSize())));
}
}
return Env;
}