Update startReflectionReconstruction.
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sunwen
@@ -1,60 +1,99 @@
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#include "startReflectionReconstruction.h"
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#include "Function.h"
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#include "Function2D.h"
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#include "Function3D.h"
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#include "Matrix.h"
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#include "MatlabWriter.h"
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#include "common/getGeometryInfo.h"
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#include "common/precalculateChannelList.h"
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#include "common/dataBlockCreation/getAScanBlockPreprocessed.h"
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#include "common/dataBlockCreation/removeDataFromArrays.h"
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#include "reflectionReconstruction/preprocessData/determineOptimalPulse.h"
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#include "reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.h"
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#include "src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h"
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#include "config/config.h"
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#include "CudaEnvInit.h"
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#include <cstdio>
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#include <iostream>
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namespace Recon
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{
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Aurora::Matrix startReflectionReconstruction(Parser* aParser, int SAFT_mode, const Aurora::Matrix &motorPos,
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const Aurora::Matrix &slList, const Aurora::Matrix &snList,
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const Aurora::Matrix &rlList, const Aurora::Matrix &rnList,
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const Aurora::Matrix &geom, MeasurementInfo expInfo, PreComputes preComputes)
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using namespace Aurora;
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using namespace Recon;
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Aurora::Matrix Recon::startReflectionReconstruction( Parser* aParser, int aSAFT_mode, const Aurora::Matrix& aMotorPos,
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const Aurora::Matrix& aSlList, const Aurora::Matrix& aSnList,
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const Aurora::Matrix& aRlList, const Aurora::Matrix& aRnList,
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GeometryInfo& aGeom, TransRecos& aTransRecos,
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MeasurementInfo& aExpInfo, PreComputes& aPreComputes)
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{
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printf("Reflection reconstruction is carried out.");
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printf("Preperations for reconstructions.");
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printf(" - reset GPUs");
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for (size_t i = 0; i < reconParams::gpuSelectionList.getDataSize(); i++)
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for (size_t i = 0; i < reflectParams::gpuSelectionList.getDataSize(); i++)
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{
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std::string msg;
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if (!resetGPUDevice((int)transParams::gpuSelectionList[i],msg))
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if (!resetGPUDevice((int)reflectParams::gpuSelectionList[i],msg))
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{
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std::cerr<<msg<<std::endl;
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}
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}
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printf(" - optimal pulse");
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if(reflectParams::useOptPulse==1 && reflectParams::runReflectionReco){
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preComputes.sincPeak_ft = determineOptimalPulse(preComputes.timeInterval ,expInfo.expectedAScanLength);
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if(reflectParams::useOptPulse==1 && reflectParams::runReflectionReco)
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{
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aPreComputes.sincPeak_ft = determineOptimalPulse(aPreComputes.timeInterval, aExpInfo.expectedAScanLength);
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}
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printf(" - channel list");
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auto channelList = precalculateChannelList(rlList, rnList, expInfo, preComputes);
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size_t numScans = motorPos.getDataSize() * slList.getDataSize() *
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snList.getDataSize() * rlList.getDataSize() *
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rnList.getDataSize();
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auto channelList = precalculateChannelList(aRlList, aRnList, aExpInfo, aPreComputes);
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size_t numScans = aMotorPos.getDataSize() * aSlList.getDataSize() *
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aSnList.getDataSize() * aRlList.getDataSize() *
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aRnList.getDataSize();
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printf(" - blocking");
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auto Env = Aurora::zeros((int)reflectParams::imageXYZ[0],(int)reflectParams::imageXYZ[1],(int)reflectParams::imageXYZ[2]);
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Matrix Env = Aurora::zeros((int)reflectParams::imageXYZ[0],(int)reflectParams::imageXYZ[1],(int)reflectParams::imageXYZ[2]);
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int numTakenScans = 0,numProcessedScans = 0,numPossibleScans = 0;
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for(int i=0; i<motorPos.getDataSize(); ++i)
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for(int i=0; i<aMotorPos.getDataSize(); ++i)
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{
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#pragma omp parallel for num_threads(24)
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for(int j=0; j<slList.getDataSize() / transParams::senderTASSize; ++j)
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//#pragma omp parallel for num_threads(24)
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for(int j=0; j<aSlList.getDataSize() / transParams::senderTASSize; ++j)
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{
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for(int k=0; k<snList.getDataSize() / transParams::senderElementSize; ++k)
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for(int k=0; k<aSnList.getDataSize() / transParams::senderElementSize; ++k)
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{
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Aurora::Matrix mp = motorPos(i).toMatrix();
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Matrix mp = aMotorPos(i).toMatrix();
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Matrix sl = aSlList.block(0, transParams::senderTASSize*j, transParams::senderTASSize*j+transParams::senderTASSize - 1);
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Matrix sn = aSnList.block(0, transParams::senderElementSize*k, transParams::senderElementSize*k+transParams::senderElementSize - 1);
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auto blockData = getAscanBlockPreprocessed(aParser, mp, sl, sn, aRlList, aRnList, aGeom, aExpInfo, true, false);
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double* channelListSizeData = Aurora::malloc(2);
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channelListSizeData[0] = channelList.getDimSize(0);
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channelListSizeData[1] = channelList.getDimSize(1);
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Matrix channelListSize = Matrix::New(channelListSizeData, 2, 1);
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Matrix ind = sub2ind(channelListSize, {blockData.rlBlock, blockData.rnBlock});
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size_t channelBlockSize = ind.getDataSize();
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double* channelBlockData = Aurora::malloc(channelBlockSize);
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for(size_t i=0; i<channelBlockSize; ++i)
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{
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channelBlockData[i] = channelList[ind[i] - 1];
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}
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Matrix channelBlock = Matrix::New(channelBlockData, 1, channelBlockSize);
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auto preprocessData = preprocessAScanBlockForReflection(blockData.ascanBlockPreprocessed, blockData.mpBlock, blockData.slBlock,
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blockData.snBlock, blockData.rlBlock, blockData.rnBlock, blockData.senderPositionBlock,
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blockData.receiverPositionBlock, blockData.gainBlock, channelBlock, aExpInfo, aPreComputes);
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Env = recontructSAFT(removeDataFromArrays(preprocessData.AscanBlock, preprocessData.usedData),
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removeDataFromArrays(blockData.senderPositionBlock, preprocessData.usedData),
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removeDataFromArrays(blockData.receiverPositionBlock, preprocessData.usedData),
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removeDataFromArrays(blockData.mpBlock, preprocessData.usedData),
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aSAFT_mode, aTransRecos, Env);
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}
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}
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}
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MatlabWriter m("/home/sun/Reflect.mat");
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m.write(Env, "reflect");
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return Aurora::Matrix();
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}
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}
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@@ -1,6 +1,7 @@
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#ifndef __STARTREFLECTIONRECONSTRUCTION_H__
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#define __STARTREFLECTIONRECONSTRUCTION_H__
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#include "Matrix.h"
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#include "common/getGeometryInfo.h"
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#include "transmissionReconstruction/detection/getTransmissionData.h"
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#include "reconstructionSAFT/reconstructionSAFT.h"
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namespace Recon {
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@@ -8,7 +9,7 @@ Aurora::Matrix startReflectionReconstruction(
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Parser* aParser, int SAFT_mode, const Aurora::Matrix& motorPos,
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const Aurora::Matrix& slList, const Aurora::Matrix& snList,
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const Aurora::Matrix& rlList, const Aurora::Matrix& rnList,
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const Aurora::Matrix &geom,TransRecosParams &transRecos,
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MeasurementInfo expInfo, PreComputes preComputes);
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GeometryInfo& geom, TransRecos& transRecos,
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MeasurementInfo& expInfo, PreComputes& preComputes);
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}
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#endif // __STARTREFLECTIONRECONSTRUCTION_H__
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