Add start Refelection Reconstruction
This commit is contained in:
kradchen
@@ -64,6 +64,7 @@ namespace Recon
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bool measuredCEUsed;
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bool measuredCEUsed;
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Aurora::Matrix measuredCE_TASIndices;
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Aurora::Matrix measuredCE_TASIndices;
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Aurora::Matrix measuredCE_receiverIndices;
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Aurora::Matrix measuredCE_receiverIndices;
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Aurora::Matrix sincPeak_ft;
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double offset;
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double offset;
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};
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};
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@@ -0,0 +1,329 @@
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#include "reconstructionSAFT.h"
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#include "Function1D.h"
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#include "Function3D.h"
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#include "Matrix.h"
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#include "SAFTStructs.h"
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#include "SAFT_ATT.h"
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#include "SAFT_TOFI.h"
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#include "config/config.h"
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#include <algorithm>
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#include <cstddef>
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#include <cstdlib>
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#include <iostream>
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#include <sys/types.h>
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#include <vector>
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namespace Recon {
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int compareColumn(const Aurora::Matrix &aMatrix, int colCount,
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const Aurora::Matrix &aOther, int col2) {
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for (size_t j = 0; j < colCount; j++) {
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size_t i = 0;
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for (; i < aMatrix.getDimSize(0); i++) {
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if (aMatrix[j * aMatrix.getDimSize(0) + 1] !=
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aOther[col2 * aOther.getDimSize(0) + i])
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break;
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}
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if (i == aMatrix.getDimSize(0))
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return j;
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}
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return -1;
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}
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Aurora::Matrix callSAFT(const Aurora::Matrix &AScans,
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const Aurora::Matrix &receiverIndex,
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const Aurora::Matrix &senderIndex,
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const Aurora::Matrix &receiverPosGeom,
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const Aurora::Matrix &senderPosGeom,
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int SAFT_mode, double TimeInterval,
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TransRecosParams transRecos,
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const Aurora::Matrix &Env)
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{
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if (reflectParams::useAscanIndex == 0) {
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if (reflectParams::soundSpeedCorrection == 0) {
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std::cerr
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<< "reconstruction without sound speed correction not allowed!!!!"
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<< std::endl;
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return Aurora::Matrix();
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}
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}
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std::vector<Matrix_t> params;
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Matrix_t AScan{nullptr,
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(size_t)AScans.getDims(),
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{(size_t)AScans.getDimSize(0), (size_t)AScans.getDimSize(1),
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(size_t)AScans.getDimSize(2)},
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AScans.getDataSize()};
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float *ASdata = new float[AScans.getDataSize()]{0};
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std::copy(AScans.getData(), AScans.getData() + AScans.getDataSize(),
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ASdata);
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AScan.Data = ASdata;
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params.push_back(AScan);
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Matrix_t imageStartpoint{nullptr, 2, {1, 3}, 3};
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imageStartpoint.Data =
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new float[3]{(float)reflectParams::imageStartpoint[0],
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(float)reflectParams::imageStartpoint[1],
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(float)reflectParams::imageStartpoint[2]};
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params.push_back(imageStartpoint);
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Matrix_t receiverIdx{nullptr,
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2,
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{1, receiverIndex.getDataSize(), 1},
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receiverIndex.getDataSize()};
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unsigned short *temp1 = new unsigned short[receiverIndex.getDataSize()];
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std::copy(receiverIndex.getData(),
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receiverIndex.getData() + receiverIndex.getDataSize(), temp1);
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receiverIdx.Data = temp1;
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params.push_back(receiverIdx);
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Matrix_t senderIdx{nullptr,
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2,
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{1, senderIndex.getDataSize(), 1},
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senderIndex.getDataSize()};
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temp1 = new unsigned short[senderIndex.getDataSize()];
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std::copy(senderIndex.getData(),
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senderIndex.getData() + senderIndex.getDataSize(), temp1);
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senderIdx.Data = temp1;
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params.push_back(senderIdx);
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Matrix_t receiverGeom{nullptr,
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(size_t)receiverPosGeom.getDims(),
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{(size_t)receiverPosGeom.getDimSize(0),
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(size_t)receiverPosGeom.getDimSize(1),
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(size_t)receiverPosGeom.getDimSize(2)},
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receiverPosGeom.getDataSize()};
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float *fdata = new float[receiverPosGeom.getDataSize()]{0};
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std::copy(receiverPosGeom.getData(),
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receiverPosGeom.getData() + receiverPosGeom.getDataSize(), fdata);
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receiverGeom.Data = fdata;
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params.push_back(receiverGeom);
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Matrix_t senderGeom{nullptr,
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(size_t)senderPosGeom.getDims(),
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{(size_t)senderPosGeom.getDimSize(0),
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(size_t)senderPosGeom.getDimSize(1),
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(size_t)senderPosGeom.getDimSize(2)},
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senderPosGeom.getDataSize()};
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fdata = new float[senderPosGeom.getDataSize()]{0};
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std::copy(senderPosGeom.getData(),
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senderPosGeom.getData() + senderPosGeom.getDataSize(), fdata);
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senderGeom.Data = fdata;
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params.push_back(senderGeom);
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Matrix_t _SAFT_mode{&SAFT_mode, 1, {1, 1, 1}, 1};
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params.push_back(_SAFT_mode);
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int saftVariant_v[3]{(int)reflectParams::saftVariant[0],(int)reflectParams::saftVariant[1],(int)reflectParams::saftVariant[2]};
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Matrix_t saftVariant{saftVariant_v,2,{1,3,1},3};
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params.push_back(saftVariant);
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Matrix_t SpeedMap3D{nullptr,
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(size_t)transRecos.SpeedMap3D.getDims(),
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{(size_t)transRecos.SpeedMap3D.getDimSize(0),
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(size_t)transRecos.SpeedMap3D.getDimSize(1),
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(size_t)transRecos.SpeedMap3D.getDimSize(2)},
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transRecos.SpeedMap3D.getDataSize()};
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fdata = new float[transRecos.SpeedMap3D.getDataSize()]{0};
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std::copy(transRecos.SpeedMap3D.getData(),
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transRecos.SpeedMap3D.getData() + transRecos.SpeedMap3D.getDataSize(), fdata);
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SpeedMap3D.Data = fdata;
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params.push_back(SpeedMap3D);
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Matrix_t BeginTransMap{nullptr,
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(size_t)transRecos.BeginTransMap.getDims(),
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{(size_t)transRecos.BeginTransMap.getDimSize(0),
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(size_t)transRecos.BeginTransMap.getDimSize(1),
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(size_t)transRecos.BeginTransMap.getDimSize(2)},
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transRecos.BeginTransMap.getDataSize()};
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fdata = new float[transRecos.BeginTransMap.getDataSize()]{0};
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std::copy(transRecos.BeginTransMap.getData(),
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transRecos.BeginTransMap.getData() + transRecos.BeginTransMap.getDataSize(), fdata);
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BeginTransMap.Data = fdata;
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params.push_back(BeginTransMap);
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Matrix_t DeltaTransMap{nullptr,
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(size_t)transRecos.DeltaTransMap.getDims(),
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{(size_t)transRecos.DeltaTransMap.getDimSize(0),
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(size_t)transRecos.DeltaTransMap.getDimSize(1),
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(size_t)transRecos.DeltaTransMap.getDimSize(2)},
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transRecos.DeltaTransMap.getDataSize()};
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fdata = new float[transRecos.DeltaTransMap.getDataSize()]{0};
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std::copy(transRecos.DeltaTransMap.getData(),
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transRecos.DeltaTransMap.getData() + transRecos.DeltaTransMap.getDataSize(), fdata);
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DeltaTransMap.Data = fdata;
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params.push_back(DeltaTransMap);
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Matrix_t AttenuationMap3D{nullptr,
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(size_t)transRecos.AttenuationMap3D.getDims(),
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{(size_t)transRecos.AttenuationMap3D.getDimSize(0),
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(size_t)transRecos.AttenuationMap3D.getDimSize(1),
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(size_t)transRecos.AttenuationMap3D.getDimSize(2)},
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transRecos.AttenuationMap3D.getDataSize()};
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fdata = new float[transRecos.AttenuationMap3D.getDataSize()]{0};
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std::copy(transRecos.AttenuationMap3D.getData(),
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transRecos.AttenuationMap3D.getData() + transRecos.AttenuationMap3D.getDataSize(), fdata);
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AttenuationMap3D.Data = fdata;
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params.push_back(AttenuationMap3D);
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float imageResolution_v = (float)reflectParams::imageResolution;
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Matrix_t imageResolution{&imageResolution_v, 1, {1, 1, 1}, 1};
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params.push_back(imageResolution);
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float TimeInterval_v = (float)TimeInterval;
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Matrix_t _TimeInterval{&TimeInterval_v, 1, {1, 1, 1}, 1};
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params.push_back(_TimeInterval);
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int imageXYZ_v[3]{(int)reflectParams::imageXYZ[0],(int)reflectParams::imageXYZ[1],(int)reflectParams::imageXYZ[2]};
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Matrix_t imageXYZ{imageXYZ_v,2,{1,3,1},3};
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params.push_back(imageXYZ);
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Matrix_t _Env{nullptr,
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(size_t)Env.getDims(),
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{(size_t)Env.getDimSize(0), (size_t)Env.getDimSize(1),
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(size_t)Env.getDimSize(2)},
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Env.getDataSize()};
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float *Envdata = new float[Env.getDataSize()]{0};
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std::copy(Env.getData(), Env.getData() + Env.getDataSize(),
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Envdata);
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_Env.Data = Envdata;
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params.push_back(_Env);
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int blockXYZ_v[3]{(int)reflectParams::blockDimXYZ[0],(int)reflectParams::blockDimXYZ[1],(int)reflectParams::blockDimXYZ[2]};
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Matrix_t blockXYZ{blockXYZ_v,2,{1,3,1},3};
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params.push_back(blockXYZ);
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Matrix_t gpus{nullptr,
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(size_t)reconParams::gpuSelectionList.getDims(),
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{(size_t)reconParams::gpuSelectionList.getDimSize(0), (size_t)reconParams::gpuSelectionList.getDimSize(1),
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(size_t)reconParams::gpuSelectionList.getDimSize(2)},
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reconParams::gpuSelectionList.getDataSize()};
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int *gdata = new int[reconParams::gpuSelectionList.getDataSize()]{0};
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std::copy(reconParams::gpuSelectionList.getData(), reconParams::gpuSelectionList.getData() + reconParams::gpuSelectionList.getDataSize(),
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gdata);
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gpus.Data = gdata;
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params.push_back(gpus);
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if (reflectParams::useAscanIndex == 0){
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Matrix_t medianWindowSize{&reflectParams::medianWindowSize,1,{1,1,1},1};
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}
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int other[2]={reflectParams::debugMode, reflectParams::attenuationCorrectionLimit} ;
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Matrix_t otherP{other,2,{1,2,1},2};
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params.push_back(otherP);
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if (reflectParams::useAscanIndex == 0) {
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auto result = SAFT_ATT(params);
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return Aurora::Matrix::fromRawData((double *)result.Data, result.Dims[0],
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result.Dims[1], result.Dims[2]);
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} else {
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auto result = SAFT_TOFI(params);
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return Aurora::Matrix::fromRawData((double *)result.Data, result.Dims[0],
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result.Dims[1], result.Dims[2]);
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}
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}
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Aurora::Matrix
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recontructSAFT(const Aurora::Matrix &AScans, const Aurora::Matrix &senderPos,
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const Aurora::Matrix &receiverPos, const Aurora::Matrix &mpIndex,
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int SAFT_mode, TransRecosParams &transRecos, Aurora::Matrix &Env) {
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auto TimeInterval = 1 / (reflectParams::aScanReconstructionFrequency);
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std::vector<int> motorPosAvailable;
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std::unique_copy(mpIndex.getData(), mpIndex.getData() + mpIndex.getDataSize(),
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motorPosAvailable.begin());
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for (auto mp : motorPosAvailable) {
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std::vector<int> mpIdxs;
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for (size_t i = 0; i < mpIndex.getDataSize(); i++) {
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if (mpIndex[i] == mp)
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mpIdxs.push_back(i);
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}
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auto senderPosGeom = Aurora::zeros(senderPos.getDimSize(0), mpIdxs.size());
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auto receiverPosGeom =
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Aurora::zeros(receiverPos.getDimSize(0), mpIdxs.size());
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std::vector<int> idsSender;
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std::vector<int> idsReceiver;
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int addCount_s = 0;
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int addCount_r = 0;
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for (auto mpIdx : mpIdxs) {
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int flag = compareColumn(senderPosGeom, addCount_s, senderPos, mpIdx);
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// old one, add ids
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if (flag >= 0) {
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idsSender.push_back(flag);
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}
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// found new unique one
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else {
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senderPosGeom(addCount_s, Aurora::$) = senderPos(mpIdx, Aurora::$);
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idsSender.push_back(addCount_s++);
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}
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int flag2 =
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compareColumn(receiverPosGeom, addCount_r, receiverPos, mpIdx);
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// old one, add ids
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if (flag2 >= 0) {
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idsReceiver.push_back(flag2);
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}
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// found new unique one
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else {
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receiverPosGeom(addCount_r, Aurora::$) = receiverPos(mpIdx, Aurora::$);
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idsReceiver.push_back(addCount_r++);
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}
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}
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auto numUsedData = mpIdxs.size();
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int count = numUsedData / reflectParams::blockSizeReco;
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auto blockIdxs = Aurora::zeros(1, count + 2);
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for (size_t i = 0; i < count + 1; i++) {
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blockIdxs[i] = i * reflectParams::blockSizeReco;
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}
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blockIdxs[count + 1] = numUsedData;
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for (size_t i = 0; i < count + 1; i++) {
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size_t length = blockIdxs[i + 1] - blockIdxs[i];
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size_t begin = blockIdxs[i];
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size_t end = blockIdxs[i + 1];
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auto _AScans = Aurora::zeros(AScans.getDimSize(0), length);
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auto receiverIndex = Aurora::zeros(1, length);
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auto senderIndex = Aurora::zeros(1, length);
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for (size_t j = begin, k = 0; j < end; j++, k++) {
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_AScans(Aurora::$, k) = AScans(Aurora::$, mpIdxs[j]);
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receiverIndex[k] = idsReceiver[j];
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senderIndex[k] = idsSender[j];
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}
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Env = callSAFT(_AScans, receiverIndex, senderIndex, receiverPosGeom,
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senderPosGeom, SAFT_mode, TimeInterval, transRecos, Env);
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}
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}
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return Env;
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}
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//TODO:untested
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Aurora::Matrix polyvaln(PolyModel polymodel, const Aurora::Matrix &indepvar)
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{
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auto np = Aurora::size(indepvar);
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int n = (int)np[0];
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int p = (int)np[1];
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Aurora::Matrix _indepvar = indepvar;
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if (n == 1 && polymodel.ModelTerms.getDimSize(1) == 1){
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_indepvar = Aurora::transpose(indepvar);
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np = Aurora::size(indepvar);
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n = (int)np[0];
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p = (int)np[1];
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}
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else if(polymodel.ModelTerms.getDimSize(1) != p){
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std::cerr<<"Size of indepvar array and this model are inconsistent."<<std::endl;
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return Aurora::Matrix();
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}
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size_t nt = Aurora::size(polymodel.ModelTerms,1);
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auto ypred = Aurora::zeros(n,1);
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for (size_t i = 0; i < nt; i++)
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{
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auto t = Aurora::ones(n,1);
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for (size_t j = 0; j < p; j++)
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{
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||||||
|
t = (t*(_indepvar(Aurora::$,j).toMatrix()^polymodel.Coefficients(i,j).toMatrix().getScalar()));
|
||||||
|
}
|
||||||
|
ypred = ypred+t*polymodel.Coefficients[i];
|
||||||
|
}
|
||||||
|
return ypred;
|
||||||
|
}
|
||||||
|
} // namespace Recon
|
||||||
@@ -0,0 +1,26 @@
|
|||||||
|
#ifndef __RECONSTRUCTIONSAFT_H__
|
||||||
|
#define __RECONSTRUCTIONSAFT_H__
|
||||||
|
#include "Matrix.h"
|
||||||
|
namespace Recon {
|
||||||
|
|
||||||
|
struct TransRecosParams{
|
||||||
|
Aurora::Matrix SpeedMap3D;
|
||||||
|
Aurora::Matrix AttenuationMap3D;
|
||||||
|
Aurora::Matrix BeginTransMap;
|
||||||
|
Aurora::Matrix DeltaTransMap;
|
||||||
|
};
|
||||||
|
|
||||||
|
struct PolyModel{
|
||||||
|
Aurora::Matrix ModelTerms;
|
||||||
|
Aurora::Matrix Coefficients;
|
||||||
|
};
|
||||||
|
|
||||||
|
Aurora::Matrix
|
||||||
|
recontructSAFT(const Aurora::Matrix &AScans, const Aurora::Matrix &senderPos,
|
||||||
|
const Aurora::Matrix &receiverPos, const Aurora::Matrix &mpIndex,
|
||||||
|
int SAFT_mode, TransRecosParams &transRecos, Aurora::Matrix &Env);
|
||||||
|
|
||||||
|
Aurora::Matrix polyvaln(PolyModel polymodel, const Aurora::Matrix &indepvar);
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif // __RECONSTRUCTIONSAFT_H__
|
||||||
@@ -0,0 +1,60 @@
|
|||||||
|
#include "startReflectionReconstruction.h"
|
||||||
|
#include "Function3D.h"
|
||||||
|
#include "Matrix.h"
|
||||||
|
|
||||||
|
#include "common/precalculateChannelList.h"
|
||||||
|
#include "common/dataBlockCreation/getAScanBlockPreprocessed.h"
|
||||||
|
#include "reflectionReconstruction/preprocessData/determineOptimalPulse.h"
|
||||||
|
#include "config/config.h"
|
||||||
|
|
||||||
|
#include "CudaEnvInit.h"
|
||||||
|
|
||||||
|
#include <cstdio>
|
||||||
|
#include <iostream>
|
||||||
|
namespace Recon
|
||||||
|
{
|
||||||
|
Aurora::Matrix startReflectionReconstruction(Parser* aParser, int SAFT_mode, const Aurora::Matrix &motorPos,
|
||||||
|
const Aurora::Matrix &slList, const Aurora::Matrix &snList,
|
||||||
|
const Aurora::Matrix &rlList, const Aurora::Matrix &rnList,
|
||||||
|
const Aurora::Matrix &geom, MeasurementInfo expInfo, PreComputes preComputes)
|
||||||
|
{
|
||||||
|
printf("Reflection reconstruction is carried out.");
|
||||||
|
|
||||||
|
printf("Preperations for reconstructions.");
|
||||||
|
|
||||||
|
printf(" - reset GPUs");
|
||||||
|
for (size_t i = 0; i < reconParams::gpuSelectionList.getDataSize(); i++)
|
||||||
|
{
|
||||||
|
std::string msg;
|
||||||
|
if (!resetGPUDevice((int)transParams::gpuSelectionList[i],msg))
|
||||||
|
{
|
||||||
|
std::cerr<<msg<<std::endl;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
printf(" - optimal pulse");
|
||||||
|
if(reflectParams::useOptPulse==1 && reflectParams::runReflectionReco){
|
||||||
|
preComputes.sincPeak_ft = determineOptimalPulse(preComputes.timeInterval ,expInfo.expectedAScanLength);
|
||||||
|
}
|
||||||
|
printf(" - channel list");
|
||||||
|
auto channelList = precalculateChannelList(rlList, rnList, expInfo, preComputes);
|
||||||
|
size_t numScans = motorPos.getDataSize() * slList.getDataSize() *
|
||||||
|
snList.getDataSize() * rlList.getDataSize() *
|
||||||
|
rnList.getDataSize();
|
||||||
|
printf(" - blocking");
|
||||||
|
auto Env = Aurora::zeros((int)reflectParams::imageXYZ[0],(int)reflectParams::imageXYZ[1],(int)reflectParams::imageXYZ[2]);
|
||||||
|
|
||||||
|
int numTakenScans = 0,numProcessedScans = 0,numPossibleScans = 0;
|
||||||
|
for(int i=0; i<motorPos.getDataSize(); ++i)
|
||||||
|
{
|
||||||
|
#pragma omp parallel for num_threads(24)
|
||||||
|
for(int j=0; j<slList.getDataSize() / transParams::senderTASSize; ++j)
|
||||||
|
{
|
||||||
|
for(int k=0; k<snList.getDataSize() / transParams::senderElementSize; ++k)
|
||||||
|
{
|
||||||
|
Aurora::Matrix mp = motorPos(i).toMatrix();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return Aurora::Matrix();
|
||||||
|
}
|
||||||
|
}
|
||||||
14
src/reflectionReconstruction/startReflectionReconstruction.h
Normal file
14
src/reflectionReconstruction/startReflectionReconstruction.h
Normal file
@@ -0,0 +1,14 @@
|
|||||||
|
#ifndef __STARTREFLECTIONRECONSTRUCTION_H__
|
||||||
|
#define __STARTREFLECTIONRECONSTRUCTION_H__
|
||||||
|
#include "Matrix.h"
|
||||||
|
#include "transmissionReconstruction/detection/getTransmissionData.h"
|
||||||
|
#include "reconstructionSAFT/reconstructionSAFT.h"
|
||||||
|
namespace Recon {
|
||||||
|
Aurora::Matrix startReflectionReconstruction(
|
||||||
|
Parser* aParser, int SAFT_mode, const Aurora::Matrix &motorPos,
|
||||||
|
const Aurora::Matrix &slList, const Aurora::Matrix &snList,
|
||||||
|
const Aurora::Matrix &rlList, const Aurora::Matrix &rnList,
|
||||||
|
const Aurora::Matrix &geom,TransRecosParams &transRecos,
|
||||||
|
MeasurementInfo expInfo, PreComputes preComputes);
|
||||||
|
}
|
||||||
|
#endif // __STARTREFLECTIONRECONSTRUCTION_H__
|
||||||
Reference in New Issue
Block a user