Update geometry info , measrementInfo for startReconstruction.

src/common/estimatePulseLength.cpp

@@ -0,0 +1,22 @@
+#include "estimatePulseLength.h"
+#include "Function1D.h"
+#include "Function2D.h"
+#include <cstddef>
+#include <vector>
+
+using namespace Aurora;
+
+double Recon::estimatePulseLength(const CeEstimatePulseLength& aCe, double aSampleFreq)
+{
+    Matrix value1 = abs(hilbert(aCe.ce));
+    double value2 = 0.05 * max(abs(hilbert(aCe.ce)),All)[0];
+    std::vector<size_t> t;
+    for(size_t i=0; i<value1.getDataSize(); ++i)
+    {
+        if(value1[i] > value2)
+        {
+            t.push_back(i);
+        }
+    }
+    return (t[t.size()-1] - t[0]) / aCe.ce_sf * aSampleFreq;
+}

src/common/estimatePulseLength.h

@@ -0,0 +1,17 @@
+#ifndef ESTIMATE_PULSE_LENGTH_H
+#define ESTIMATE_PULSE_LENGTH_H
+
+#include "Matrix.h"
+
+namespace Recon
+{
+    struct CeEstimatePulseLength
+    {
+        Aurora::Matrix ce;
+        double ce_sf;
+    };
+
+    double estimatePulseLength(const CeEstimatePulseLength& aCe, double aSampleFreq);
+}
+
+#endif

src/common/getGeometryInfo.cpp

@@ -192,13 +192,13 @@ void getApertureBoundingBox(GeometryInfo& aOutput)
 }
 }
 
-GeometryInfo Recon::getGeometryInfo(const Matrix& aMotorPos, const Matrix& aTransformationMatricesRef,
+GeometryInfo Recon::getGeometryInfo(const Matrix& aMotorPos, const Matrix& aTransformationMatrices,
                                     const Matrix aRlList, const Matrix aRnList, const Matrix aSlList, const Matrix aSnList)
 {
     GeometryInfo result;
     result.headTable = Recon::HEAD_TABLE;
     result.sensChar = loadSensitivity();
-    transformGeometry(aMotorPos, aTransformationMatricesRef, aRlList, aRnList, aSlList, aSnList, result);
+    transformGeometry(aMotorPos, aTransformationMatrices, aRlList, aRnList, aSlList, aSnList, result);
     getApertureBoundingBox(result);
     result.maxSL = emitterPositions.size();
     result.maxSN = emitterPositions[0].getDimSize(0);

src/common/getGeometryInfo.h

@@ -26,7 +26,7 @@ namespace Recon
         std::vector<Aurora::Matrix> receiverPositions;
     };
 
-    GeometryInfo getGeometryInfo(const Aurora::Matrix& aMotorPos, const Aurora::Matrix& aTransformationMatricesRef,
+    GeometryInfo getGeometryInfo(const Aurora::Matrix& aMotorPos, const Aurora::Matrix& aTransformationMatrices,
                                  const Aurora::Matrix aRlList, const Aurora::Matrix aRnList, const Aurora::Matrix aSlList, const Aurora::Matrix aSnList);
 }
 

src/common/getMeasurementMetaData.cpp

@@ -53,6 +53,8 @@ MeasurementInfo Recon::loadMeasurementInfos(Parser* aParser)
     result.Wavelength = 3;
     result.expectedAScanLength = result.numberSamples;
     result.rootMeasUniqueID = metaData.getMeasurementID();
+    result.dacDelay = metaData.getDacDelay();
+    result.filterByPass = metaData.getFilterByPass();
     if(result.Bandpassundersampling)
     {
         result.expectedAScanLength = reflectParams::aScanReconstructionFrequency / result.sampleRate * result.expectedAScanLength;

src/common/getMeasurementMetaData.h

@@ -20,6 +20,9 @@ namespace Recon
         int Wavelength;
         unsigned int expectedAScanLength;
         std::string rootMeasUniqueID;
+        double dacDelay;
+        double filterByPass;
+        Aurora::Matrix matchedFilter;
     };
 
     struct CEInfo

src/config/config.h

@@ -10,25 +10,25 @@ namespace Recon
     {
         //reconParams.measurementInfo.ce
         static bool useCEMeasured = true;
-        static int removeOutliersFromCEMeasured = 1;
+        static bool removeOutliersFromCEMeasured = true;
         static double offsetFilterEnabled = 6.9e-6;
         static double offsetFilterDisabled = 1.2e-6;
         //reconParams.measurementInfo.temp
         static bool useTASTempComp = true;
         static bool correctTASTemp = 1;
-        static //reconParams.hardwareSelection
+        //reconParams.hardwareSelection
-        int gpuSelectionList[8] = {0,1,2,3,4,5,6,7};
+        static Aurora::Matrix gpuSelectionList = Aurora::Matrix::fromRawData(new double[8]{0,1,2,3,4,5,6,7},8);
-        static //reconParams.dataInfo
+        //reconParams.dataInfo
-        int expectedAScanDataLength = 4000;
+        static int expectedAScanDataLength = 4000;
     }
 
     namespace reflectParams
     {
         //reflectParams.dataSelection
-        static double senderTasList[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128};//1~128
+        static Aurora::Matrix senderTasList = Aurora::Matrix::fromRawData(new double[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128},128);//1~128
-        static double senderElementList[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18};//1~18
+        static Aurora::Matrix senderElementList = Aurora::Matrix::fromRawData(new double[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18},18);//1~18
-        static double receiverTasList[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128};//1~128
+        static Aurora::Matrix receiverTasList = Aurora::Matrix::fromRawData(new double[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128},128);//1~128
-        static double receiverElementList[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18};//1~18
+        static Aurora::Matrix receiverElementList = Aurora::Matrix::fromRawData(new double[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18},18);//1~18
         static Aurora::Matrix motorPos = Aurora::Matrix::fromRawData(new double[2]{1,2}, 2);
         static int constricReflectionAngles = 1;
         static int angleLowerLimit = 45;
@@ -64,7 +64,7 @@ namespace Recon
         static int suppressSameHead = 1;
         static int suppressSameHeadLength = 1500;
         static int useCorrelation = 1;
-        static int matchedFilterCeAScan = 1;
+        static bool matchedFilterCeAScan = true;
         static int windowLength = 10;
         static int numThreads = 30;
         static int expectedUSSpeedRange[2] = {1420,1600};
@@ -89,15 +89,16 @@ namespace Recon
 
     namespace transParams
     {
+        static Aurora::Matrix gpuSelectionList;
         //transParams.dataSelection
         static int verbose = 1;
         static int saveRecon = 1;
         static int saveDebugInfomation = 1;
         //transParams.dataSelection
-        static double senderTasList[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128};//1~128
+        static Aurora::Matrix senderTasList = Aurora::Matrix::fromRawData(new double[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128},128);//1~128
-        static double senderElementList[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18};//1~18
+        static Aurora::Matrix senderElementList = Aurora::Matrix::fromRawData(new double[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18},18);//1~18
-        static double receiverTasList[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128};//1~128
+        static Aurora::Matrix receiverTasList = Aurora::Matrix::fromRawData(new double[128]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128},128);//1~128
-        static double receiverElementList[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18};//1~18
+        static Aurora::Matrix receiverElementList = Aurora::Matrix::fromRawData(new double[18]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18},18);//1~18
         static Aurora::Matrix motorPos = Aurora::Matrix::fromRawData(new double[2]{1,2}, 2);
         static int filterSensitivity = 1;
         static double sensFilter = 0.3;
@@ -134,6 +135,8 @@ namespace Recon
         static int maxSpeedOfSound = 1550;
         static int detectionWindowSOS = 1;
         static int detectionWindowATT = 50;
+        static double pulseLengthSamples = 0;
+        static double pulseLengthRefSamples = 0;
         //transParams.rayTracing
         static int bentReconstruction = 0;
         static int bresenham = 1;

src/reflectionReconstruction/preprocessData/estimateOffset.cpp

@@ -0,0 +1,93 @@
+#include "estimateOffset.h"
+#include "../../common/ceMatchedFilterHandling.h"
+#include "Function.h"
+#include "Function1D.h"
+#include "Function2D.h"
+#include "Matrix.h"
+#include "src/config/config.h"
+#include <cstddef>
+
+using namespace Recon;
+using namespace Aurora;
+
+double Recon::estimateOffset(const MeasurementInfo aExpInfo, const CEInfo& aCe, const Aurora::Matrix& aMatchedFilter)
+{
+    double offset = 0;
+    Matrix ce = aCe.ceRef;
+    double ceOffSet = aCe.ceRefOffSet;
+    Matrix ceMeasured;
+    if(aCe.measuredCEAvailable)
+    {
+        if(aCe.measuredCEUsed)
+        {
+            ceMeasured = real(ifft(aMatchedFilter));
+        }
+        else
+        {
+            ceMeasured = real(ifft(reviseMatchedFilter(aCe.ce, true)));
+        }
+    }
+
+    offset = offset + reflectParams::offsetElectronic;
+    if(!aCe.measuredCEUsed)
+    {
+        if(aCe.measuredCEAvailable && aCe.ceAvailable)
+        {
+            size_t column = ceMeasured.getDimSize(1);
+            size_t ceRows = ce.getDimSize(0);
+            double* offsetCEMeasuredData = Aurora::malloc(column);
+            for(int i=0; i<column; ++i)
+            {
+                Matrix corrCE = xcorr(ceMeasured($,i).toMatrix(), ce);
+                long row,column;
+                max(corrCE, FunctionDirection::All,row,column);
+                offsetCEMeasuredData[i] = row + 1;
+                offsetCEMeasuredData[i] = offsetCEMeasuredData[i] - ceRows;
+            }
+            Matrix offsetCEMeasured = Matrix::New(offsetCEMeasuredData, column);
+            offset = offset + median(offsetCEMeasured)[0] / reflectParams::aScanReconstructionFrequency;
+            // 2代
+            // if strcmpi(info.Hardware,'USCT3Dv2')
+            // offset = offset - CEOffset;
+            // CEOffset = 0;
+            // end
+        }
+        else
+        {
+            double dacDelay = aExpInfo.dacDelay;
+            double filterDisabled = aExpInfo.filterByPass;
+            double dacDelayInS = dacDelay / 10000000;
+            if(filterDisabled == 1)
+            {
+                offset += aCe.offsetFilterDisabled + dacDelayInS;
+            }
+            else
+            {
+                offset += aCe.offsetFilterEnabled + dacDelayInS;
+            }
+        }
+    }
+
+    //只对三代处理，Digitalfilterdelay为0；
+    // if (strcmp(info.Hardware,'USCT3Dv2')==1 && info.Bandpassundersampling==1) %%%3.3MHz Filter 208 Tabs
+    //     Digitalfilterdelay=-(0.8e-6);
+    // %seconds
+    // elseif(strcmp(info.Hardware,'USCT3Dv2')==1) %%%%10 MHz  32 Tabs
+    // Digitalfilterdelay=-(4.67e-6 + 0.8e-6);
+    // %seconds
+    // elseif(strcmp(info.Hardware,'USCT3Dv3')==1)
+    double digitalfilterdelay = 0;
+    // else
+    //     Digitalfilterdelay = 0;
+    // end
+
+    if (!aCe.measuredCEUsed)
+    {
+        offset += digitalfilterdelay;
+        offset += ceOffSet;
+    }
+
+    offset -= aExpInfo.EOffset;
+
+    return offset;
+}

src/reflectionReconstruction/preprocessData/estimateOffset.h

@@ -0,0 +1,11 @@
+#ifndef ESTIMATE_OFFSET_H
+#define ESTIMATE_OFFSET_H
+
+#include "../../common/getMeasurementMetaData.h"
+
+namespace Recon
+{
+    double estimateOffset(const MeasurementInfo aExpInfo, const CEInfo& aCe, const Aurora::Matrix& aMatchedFilter);
+}
+
+#endif