feat: arrange include headers

2024-12-19 11:24:56 +08:00
parent e475edd243
commit 8032cb5c3f
56 changed files with 240 additions and 215 deletions
--- a/src/Aurora.cu
+++ b/src/Aurora.cu
@@ -1,16 +1,17 @@
-#include "/usr/local/cuda-10.1/targets/x86_64-linux/include/cufft.h"
-#include </usr/local/cuda-10.1/targets/x86_64-linux/include/cuda_runtime.h>
+#include <iostream>
+
+#include <cuda_texture_types.h>
+#include <cufft.h>
+#include <cuda_runtime.h>
 #include <cstdio>
 #include <thrust/device_vector.h>
 #include <thrust/execution_policy.h>
 #include <thrust/sort.h>

 #include "Aurora.h"
-#include "AuroraDefs.h"
 #include "CudaMatrix.h"
-#include <iostream>
+
 #include "log/log.h"
-#include <cuda_texture_types.h>

 __global__ void doubleToComplexKernel(const double* input, cufftDoubleComplex* output, int size)
 {
--- a/src/Aurora.h
+++ b/src/Aurora.h
@@ -1,7 +1,7 @@
 #ifndef SUM_MATRIX_CU_H
 #define SUM_MATRIX_CU_H
-#include "/usr/local/cuda-10.1/targets/x86_64-linux/include/cufft.h"
-#include </usr/local/cuda-10.1/targets/x86_64-linux/include/cuda_runtime.h>
+#include <cufft.h>
+#include <cuda_runtime.h>

 #include "Matrix.h"
 namespace Aurora
--- a/src/common/DICOMExporter.cpp
+++ b/src/common/DICOMExporter.cpp
@@ -1,18 +1,18 @@
 #include "DICOMExporter.h"

-#include "fileHelper.h"
-#include "config/config.h"
-#include "log/log.h"
-
 #include <cstddef>
 #include <cstdio>
+#include <string>
+#include <sys/types.h>
 #include <dcmtk/dcmdata/dcdeftag.h>
 #include <dcmtk/dcmdata/dcfilefo.h>
 #include <dcmtk/dcmdata/dcuid.h>
 #include <dcmtk/ofstd/offile.h>
-#include <string>
-#include <sys/types.h>
-#include "dcmtk/dcmdata/dctk.h"
+#include <dcmtk/dcmdata/dctk.h>
+
+#include "fileHelper.h"
+#include "config/config.h"
+#include "log/log.h"

 using namespace std;
 namespace  {
--- a/src/common/ceMatchedFilterHandling.cpp
+++ b/src/common/ceMatchedFilterHandling.cpp
@@ -1,13 +1,15 @@
 #include "ceMatchedFilterHandling.h"
-#include "Function.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "Function3D.h"
+
 #include <cstdio>
 #include <iostream>
 #include <mkl_vml_defines.h>
 #include <mkl_vml_functions.h>

+#include "Function.h"
+#include "Function2D.h"
+#include "Function3D.h"
+
+
 Aurora::Matrix Recon::adaptFrequency(Aurora::Matrix &aCE, float ceSampleFrequency, float requiredFrequency)
 {
    if (requiredFrequency < ceSampleFrequency){
--- a/src/common/dataBlockCreation/blockingGeometryInfo.h
+++ b/src/common/dataBlockCreation/blockingGeometryInfo.h
@@ -2,7 +2,7 @@
 #define BLOCKING_GEOMETRYINFO_H

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
+#include "common/getGeometryInfo.h"

 namespace Recon
 {
--- a/src/common/dataBlockCreation/getAScanBlockPreprocessed.cpp
+++ b/src/common/dataBlockCreation/getAScanBlockPreprocessed.cpp
@@ -1,14 +1,13 @@
 #include "getAScanBlockPreprocessed.h"

-#include "Matrix.h"
 #include "blockingGeometryInfo.h"
 #include "removeDataFromArrays.h"
 #include "getAscanBlock.h"
-#include "src/config/config.h"
-#include "src/common/getGeometryInfo.h"
-#include "src/common/preprocessAscanBlock.h"
-#include "src/transmissionReconstruction/dataFilter/dataFilter.h"
-#include "src/reflectionReconstruction/dataFilter.h"
+#include "config/config.h"
+#include "common/getGeometryInfo.h"
+#include "common/preprocessAscanBlock.h"
+#include "transmissionReconstruction/dataFilter/dataFilter.h"
+#include "reflectionReconstruction/dataFilter.h"

 using namespace Aurora;
 using namespace Recon;
--- a/src/common/dataBlockCreation/getAScanBlockPreprocessed.h
+++ b/src/common/dataBlockCreation/getAScanBlockPreprocessed.h
@@ -2,8 +2,8 @@
 #define GETASCANBLOCK_PREPROCESSED_H

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
-#include "src/common/getMeasurementMetaData.h"
+#include "common/getGeometryInfo.h"
+#include "common/getMeasurementMetaData.h"

 class Parser;

--- a/src/common/dataBlockCreation/getAscanBlock.cpp
+++ b/src/common/dataBlockCreation/getAscanBlock.cpp
@@ -1,5 +1,9 @@
 #include "getAscanBlock.h"

+#include <algorithm>
+#include <cstddef>
+#include <vector>
+
 #include "Function.h"
 #include "Matrix.h"
 #include "Parser.h"
@@ -11,9 +15,7 @@
 #include "Data/ElectricIndex.h"
 #include "Data/MetaData.h"
 #include "ShotList/ShotList.h"
-#include <algorithm>
-#include <cstddef>
-#include <vector>
+

 using namespace Recon;
 using namespace Aurora;
--- a/src/common/dataBlockCreation/getAscanBlock.h
+++ b/src/common/dataBlockCreation/getAscanBlock.h
@@ -2,7 +2,7 @@
 #define GET_ASCAN_BLOCK_H

 #include "Matrix.h"
-#include "src/common/getMeasurementMetaData.h"
+#include "common/getMeasurementMetaData.h"

 class Parser;

--- a/src/common/dataBlockCreation/removeDataFromArrays.cpp
+++ b/src/common/dataBlockCreation/removeDataFromArrays.cpp
@@ -1,12 +1,13 @@
 #include "removeDataFromArrays.h"
-#include "Function.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "Matrix.h"
+
 #include <cstddef>
 #include <mkl_cblas.h>
 #include <vector>

+#include "Function.h"
+#include "Function2D.h"
+
+
 using namespace Recon;
 using namespace Aurora;

--- a/src/common/estimatePulseLength.cpp
+++ b/src/common/estimatePulseLength.cpp
@@ -1,9 +1,12 @@
 #include "estimatePulseLength.h"
-#include "Function1D.h"
-#include "Function2D.h"
+
 #include <cstddef>
 #include <vector>

+#include "Function1D.h"
+#include "Function2D.h"
+
+
 using namespace Aurora;

 float Recon::estimatePulseLength(const CeEstimatePulseLength& aCe, float aSampleFreq)
--- a/src/common/getGeometryInfo.cpp
+++ b/src/common/getGeometryInfo.cpp
@@ -1,17 +1,17 @@
 #include "getGeometryInfo.h"
-#include "../config/geometryConfig.h"
-#include "Function1D.h"
-#include "Function.h"
-#include "Function2D.h"
-#include "Function3D.h"
-#include "Matrix.h"
-#include "src/common/getMeasurementMetaData.h"

 #include <algorithm>
 #include <cstddef>
 #include <type_traits>
 #include <vector>

+#include "Function.h"
+#include "Function2D.h"
+#include "Function3D.h"
+
+#include "config/geometryConfig.h"
+#include "common/getMeasurementMetaData.h"
+
 using namespace Recon;
 using namespace Aurora;

--- a/src/common/getMeasurementMetaData.cpp
+++ b/src/common/getMeasurementMetaData.cpp
@@ -1,8 +1,11 @@
 #include "getMeasurementMetaData.h"
-#include "Matrix.h"
-#include "ceMatchedFilterHandling.h"

-#include "ShotList/ShotList.h"
+#include <algorithm>
+#include <mkl.h>
+
+#include "Function.h"
+#include "Function2D.h"
+
 #include "Parser.h"
 #include "Data/MetaData.h"
 #include "Data/MovementData.h"
@@ -10,14 +13,10 @@
 #include "Data/CEMeasuredData.h"
 #include "Data/CEData.h"

-#include "Function.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "AuroraDefs.h"
-#include "mkl.h"
+#include "ceMatchedFilterHandling.h"
+#include "ShotList/ShotList.h"
+#include "config/config.h"

-#include "../config/config.h"
-#include <algorithm>

 using namespace Recon;
 using namespace Aurora;
--- a/src/common/getMeasurementMetaData.h
+++ b/src/common/getMeasurementMetaData.h
@@ -1,8 +1,8 @@
 #ifndef GET_MEASUREMENT_METADATA_H
 #define GET_MEASUREMENT_METADATA_H

-#include "Data/TemperatureData.h"
 #include "Matrix.h"
+#include "Data/TemperatureData.h"

 class Parser;

--- a/src/common/meshgrid.cpp
+++ b/src/common/meshgrid.cpp
@@ -1,6 +1,6 @@
 #include "meshgrid.h"
+
 #include "Function1D.h"
-#include "Matrix.h"

 using namespace Aurora;
 using namespace Recon;
--- a/src/common/precalculateChannelList.h
+++ b/src/common/precalculateChannelList.h
@@ -2,7 +2,7 @@
 #define PRECALCULATE_CHANNELLIST_H

 #include "Matrix.h"
-#include "src/common/getMeasurementMetaData.h"
+#include "common/getMeasurementMetaData.h"

 namespace Recon
 {
--- a/src/common/preprocessAscanBlock.cpp
+++ b/src/common/preprocessAscanBlock.cpp
@@ -1,7 +1,9 @@
 #include "preprocessAscanBlock.h"
+
+#include <cstddef>
+
 #include "Function1D.h"
 #include "Function1D.cuh"
-#include <cstddef>

 Aurora::Matrix Recon::preprocessAscanBlock(const Aurora::Matrix& aAscans, const MeasurementInfo& aMeasInfo)
 {
--- a/src/config/config.cpp
+++ b/src/config/config.cpp
@@ -1,11 +1,13 @@
-#include "Function2D.h"
-#include "Matrix.h"
-#include <vector>
 #define GLOBLE_CONFIG
-#include "config.h"
-#include "src/log/log.h"
-#include "json.hpp"
+
+#include <vector>
 #include <fstream>
+#include "Function2D.h"
+
+
+#include "config.h"
+#include "log/log.h"
+#include "json.hpp"

 namespace Recon
 {
--- a/src/main.cxx
+++ b/src/main.cxx
@@ -1,13 +1,14 @@
 #include "Parser.h"
 #include "Parser.h"
-#include "config/config.h"
 #include <cstdio>
 #include <vector>
 #define EIGEN_USE_MKL_ALL

-#include "src/common/fileHelper.h"
+#include "common/fileHelper.h"
 #include "startReconstructions.h"
 #include "log/log.h"
+#include "config/config.h"
+
 /* 0 is data path.
    1 is dataRef path.
    2 is output path.
--- a/src/reflectionReconstruction/dataFilter.cpp
+++ b/src/reflectionReconstruction/dataFilter.cpp
@@ -1,9 +1,9 @@
 #include "dataFilter.h"
-#include "Function1D.h"
+
 #include "Function2D.h"
 #include "Function3D.h"

-#include "src/config/config.h"
+#include "config/config.h"

 #define PI 3.141592653589793238462
 using namespace Aurora;
--- a/src/reflectionReconstruction/preprocessData/determineOptimalPulse.cpp
+++ b/src/reflectionReconstruction/preprocessData/determineOptimalPulse.cpp
@@ -1,13 +1,15 @@
 #include "determineOptimalPulse.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "Function3D.h"
-#include "config/config.h"
+
 #include <algorithm>
 #include <cmath>
 #include <cstddef>
 #include <cstring>
 #include <omp.h>
+
+#include "Function2D.h"
+#include "Function3D.h"
+#include "config/config.h"
+
 namespace Recon {

    Aurora::Matrix determineOptimalPulse(float timeInterval, size_t expectedAScanLength)
--- a/src/reflectionReconstruction/preprocessData/estimateOffset.cpp
+++ b/src/reflectionReconstruction/preprocessData/estimateOffset.cpp
@@ -1,11 +1,13 @@
 #include "estimateOffset.h"
-#include "../../common/ceMatchedFilterHandling.h"
+
+#include <cstddef>
+
 #include "Function.h"
 #include "Function1D.h"
 #include "Function2D.h"
-#include "Matrix.h"
-#include "src/config/config.h"
-#include <cstddef>
+
+#include "config/config.h"
+#include "common/ceMatchedFilterHandling.h"

 using namespace Recon;
 using namespace Aurora;
--- a/src/reflectionReconstruction/preprocessData/estimateOffset.h
+++ b/src/reflectionReconstruction/preprocessData/estimateOffset.h
@@ -1,7 +1,7 @@
 #ifndef ESTIMATE_OFFSET_H
 #define ESTIMATE_OFFSET_H

-#include "../../common/getMeasurementMetaData.h"
+#include "common/getMeasurementMetaData.h"

 namespace Recon
 {
--- a/src/reflectionReconstruction/preprocessData/imageExtrapolation.cpp
+++ b/src/reflectionReconstruction/preprocessData/imageExtrapolation.cpp
@@ -1,9 +1,11 @@
 #include "imageExtrapolation.h"
-#include "Function1D.h"
-#include "Function2D.h"
+
 #include <cstddef>
 #include <vector>

+#include "Function2D.h"
+
+
 using namespace Recon;
 using namespace Aurora;

--- a/src/reflectionReconstruction/preprocessData/precalcImageParameters.cpp
+++ b/src/reflectionReconstruction/preprocessData/precalcImageParameters.cpp
@@ -1,11 +1,12 @@
 #include "precalcImageParameters.h"
-#include "Matrix.h"
-#include "common/getGeometryInfo.h"
-#include "src/config/config.h"
+
+#include <cmath>

 #include "Function.h"
 #include "Function2D.h"
-#include <cmath>
+
+#include "common/getGeometryInfo.h"
+#include "config/config.h"

 using namespace Recon;
 using namespace Aurora;
--- a/src/reflectionReconstruction/preprocessData/precalcImageParameters.h
+++ b/src/reflectionReconstruction/preprocessData/precalcImageParameters.h
@@ -2,7 +2,7 @@
 #define PRECALC_IMAGE_PARAMETERS_H

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
+#include "common/getGeometryInfo.h"

 namespace Recon
 {
--- a/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.cpp
+++ b/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.cpp
@@ -1,12 +1,5 @@
 #include "preprocessAScanBlockForReflection.h"

-#include "Function.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "Function3D.h"
-#include "Matrix.h"
-#include "common/dataBlockCreation/removeDataFromArrays.h"
-#include "config/config.h"
 #include <algorithm>
 #include <cmath>
 #include <cstddef>
@@ -16,6 +9,14 @@
 #include <mkl_cblas.h>
 #include <mkl_vml_functions.h>
 #include <vector>
+
+#include "Function.h"
+#include "Function2D.h"
+#include "Function3D.h"
+
+#include "common/dataBlockCreation/removeDataFromArrays.h"
+#include "config/config.h"
+
 namespace Recon {

    Aurora::Matrix _createDiffVector(const Aurora::Matrix & aMatrix, float beginValue,float endValue){
--- a/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h
+++ b/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h
@@ -1,8 +1,10 @@
 #ifndef __PREPROCESSASCANBLOCKFORREFLECTION_H__
 #define __PREPROCESSASCANBLOCKFORREFLECTION_H__
+#include <cstddef>
+
 #include "Matrix.h"
 #include "common/getMeasurementMetaData.h"
-#include <cstddef>
+
 namespace Recon {
    struct preprocessAScanRResult {
    Aurora::Matrix AscanBlock;
--- a/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.cpp
+++ b/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.cpp
@@ -1,15 +1,18 @@
 #include "preprocessTransmissionReconstructionForReflection.h"
-#include "Function1D.h"
-#include "Function3D.h"
-#include "Function2D.h"
-#include "Matrix.h"
-#include "reflectionReconstruction/preprocessData/resampleTransmissionVolume.h"
-#include "src/config/config.h"

 #include <algorithm>
 #include <iostream>
 #include <cstddef>

+
+#include "Function3D.h"
+#include "Function2D.h"
+
+#include "reflectionReconstruction/preprocessData/resampleTransmissionVolume.h"
+#include "config/config.h"
+
+
+
 using namespace Aurora;
 using namespace Recon;

--- a/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h
+++ b/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h
@@ -2,8 +2,8 @@
 #define PREPROCESS_TRANSMISSION_RECONSTRUCTION_FOR_REFLECTION

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
-#include "src/common/getMeasurementMetaData.h"
+#include "common/getGeometryInfo.h"
+#include "common/getMeasurementMetaData.h"

 namespace Recon
 {
--- a/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.cpp
+++ b/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.cpp
@@ -1,15 +1,15 @@
 #include "resampleTransmissionVolume.h"
-#include "imageExtrapolation.h"
-#include "config/config.h"
-#include "src/common/meshgrid.h"

-#include "Matrix.h"
-#include "Function2D.h"
-#include "Function1D.h"
-#include "Function3D.h"
 #include <cstddef>
 #include <vector>

+#include "Function2D.h"
+#include "Function3D.h"
+
+#include "imageExtrapolation.h"
+#include "config/config.h"
+#include "common/meshgrid.h"
+
 using namespace Aurora;
 using namespace Recon;

--- a/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.h
+++ b/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.h
@@ -2,7 +2,7 @@
 #define RESAMPLETRANSMISSIONVOLUME_H

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
+#include "common/getGeometryInfo.h"

 namespace Recon
 {
--- a/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.cpp
+++ b/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.cpp
@@ -1,15 +1,5 @@
 #include "reconstructionSAFT.h"

-#include "Function1D.h"
-#include "Function2D.h"
-#include "Function3D.h"
-#include "Matrix.h"
-#include "SAFTStructs.h"
-// #include "SAFT_ATT.h"
-#include "SAFT_TOFI.h"
-#include "common/dataBlockCreation/removeDataFromArrays.h"
-#include "config/config.h"
-
 #include <algorithm>
 #include <cstddef>
 #include <cstdlib>
@@ -18,6 +8,16 @@
 #include <sys/types.h>
 #include <vector>

+#include "Function2D.h"
+#include "Function3D.h"
+
+#include "common/dataBlockCreation/removeDataFromArrays.h"
+#include "config/config.h"
+
+#include "SAFTStructs.h"
+// #include "SAFT_ATT.h"
+#include "SAFT_TOFI.h"
+
 namespace Recon {

    int compareColumn(const Aurora::Matrix &aMatrix, int colCount,
--- a/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.h
+++ b/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.h
@@ -1,7 +1,7 @@
 #ifndef __RECONSTRUCTIONSAFT_H__
 #define __RECONSTRUCTIONSAFT_H__
 #include "Matrix.h"
-#include "src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h"
+#include "reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h"
 namespace Recon {

 struct PolyModel{
--- a/src/reflectionReconstruction/startReflectionReconstruction.cpp
+++ b/src/reflectionReconstruction/startReflectionReconstruction.cpp
@@ -1,8 +1,13 @@
 #include "startReflectionReconstruction.h"
+
+#include <cstdio>
+#include <iostream>
+#include <queue>
+#include <thread>
+
 #include "Function.h"
 #include "Function2D.h"
 #include "Function3D.h"
-#include "Matrix.h"
 #include "MatlabWriter.h"

 #include "common/getGeometryInfo.h"
@@ -17,10 +22,6 @@

 #include "CudaEnvInit.h"

-#include <cstdio>
-#include <iostream>
-#include <queue>
-#include <thread>

 using namespace Aurora;
 using namespace Recon;
--- a/src/startReconstructions.cpp
+++ b/src/startReconstructions.cpp
@@ -1,30 +1,29 @@
 #include "startReconstructions.h"
-#include "Data/TemperatureData.h"
+#include <string>
+#include <iostream>
+
 #include "Function.h"
+#include "Function2D.h"
+#include "MatlabReader.h"
 #include "MatlabWriter.h"
+
+#include "Parser/Parser.h"
+#include "Parser/Data/MetaData.h"
+#include "Parser/ShotList/ShotList.h"
+
+#include "Data/TemperatureData.h"
 #include "config/config.h"
 #include "log/log.h"
 #include "common/DICOMExporter.h"
 #include "common/getMeasurementMetaData.h"
 #include "common/getGeometryInfo.h"
 #include "common/estimatePulseLength.h"
+#include "common/ceMatchedFilterHandling.h"
 #include "transmissionReconstruction/startTransmissionReconstruction.h"
-
-#include <string>
-#include <iostream>
-#include "Parser/Parser.h"
-#include "Parser/Data/MetaData.h"
-#include "Parser/ShotList/ShotList.h"
-
-#include "Matrix.h"
-#include "MatlabReader.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "src/common/ceMatchedFilterHandling.h"
-#include "src/reflectionReconstruction/preprocessData/estimateOffset.h"
-#include "src/reflectionReconstruction/preprocessData/precalcImageParameters.h"
-#include "src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h"
-#include "src/reflectionReconstruction/startReflectionReconstruction.h"
+#include "reflectionReconstruction/preprocessData/estimateOffset.h"
+#include "reflectionReconstruction/preprocessData/precalcImageParameters.h"
+#include "reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h"
+#include "reflectionReconstruction/startReflectionReconstruction.h"


 using namespace Recon;
--- a/src/transmissionReconstruction/dataFilter/dataFilter.cpp
+++ b/src/transmissionReconstruction/dataFilter/dataFilter.cpp
@@ -6,10 +6,10 @@
 #include <iostream>

 #include "Function.h"
-#include "Function1D.h"
+
 #include "Function2D.h"
 #include "Function3D.h"
-#include "Matrix.h"
+

 using namespace Aurora;
 namespace Recon {
--- a/src/transmissionReconstruction/dataFilter/dataFilter.h
+++ b/src/transmissionReconstruction/dataFilter/dataFilter.h
@@ -1,8 +1,10 @@
 #ifndef __DATAFILTER_H__
 #define __DATAFILTER_H__
-#include "Matrix.h"
 #include <vector>

+
+#include "Matrix.h"
+
 namespace Recon {
 Aurora::Matrix calculateSnr(const Aurora::Matrix &aMDataBlock,
                            float aReferenceNoise);
--- a/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.cpp
+++ b/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.cpp
@@ -1,6 +1,6 @@
 #include "estimateNoiseValueFromAScans.h"
-#include "src/common/dataBlockCreation/getAScanBlockPreprocessed.h"
-#include "src/config/config.h"
+#include "common/dataBlockCreation/getAScanBlockPreprocessed.h"
+#include "config/config.h"

 #include "Function2D.h"

--- a/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.h
+++ b/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.h
@@ -2,8 +2,8 @@
 #define ESTIMATENOISEVALUE_FROM_ASCAN_H

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
-#include "src/common/getMeasurementMetaData.h"
+#include "common/getGeometryInfo.h"
+#include "common/getMeasurementMetaData.h"

 class Parser;

--- a/src/transmissionReconstruction/dataFilter/sensitivityCalculations.cpp
+++ b/src/transmissionReconstruction/dataFilter/sensitivityCalculations.cpp
@@ -1,13 +1,14 @@
 #include "sensitivityCalculations.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "Function3D.h"

 #include <cmath>
 #include <cstddef>
 #include <iostream>
 #include <omp.h>

+
+#include "Function2D.h"
+#include "Function3D.h"
+
 namespace {
 inline void cross(float *aVA, float *aVB, float *aVOut, int aIncX = 1) {
  if (!aVA || !aVB || !aVOut)
--- a/src/transmissionReconstruction/dataFilter/sensitivityCalculations.h
+++ b/src/transmissionReconstruction/dataFilter/sensitivityCalculations.h
@@ -3,7 +3,7 @@
 #include <vector>

 #include "Matrix.h"
-#include "src/common/getGeometryInfo.h"
+#include "common/getGeometryInfo.h"

 namespace Recon {

--- a/src/transmissionReconstruction/dataPreperation.cpp
+++ b/src/transmissionReconstruction/dataPreperation.cpp
@@ -1,8 +1,8 @@
 #include "dataPreperation.h"
-#include "Function1D.h"
+#include <cstddef>
+
 #include "Function2D.h"
 #include "Function3D.h"
-#include <cstddef>


 namespace Recon
--- a/src/transmissionReconstruction/detection/detection.cpp
+++ b/src/transmissionReconstruction/detection/detection.cpp
@@ -5,10 +5,8 @@
 #include <sys/types.h>

 #include "Function.h"
-#include "Function1D.h"
 #include "Function2D.h"
 #include "Function3D.h"
-#include "Matrix.h"

 #include "common/getMeasurementMetaData.h"
 #include "config/config.h"
--- a/src/transmissionReconstruction/detection/detection.cu
+++ b/src/transmissionReconstruction/detection/detection.cu
@@ -3,6 +3,7 @@
 #include <math.h>
 #include <thrust/transform.h>
 #include <thrust/execution_policy.h>
+
 #include "Function1D.cuh"
 #include "Function2D.cuh"
 #include "Function3D.h"
--- a/src/transmissionReconstruction/detection/getTransmissionData.cpp
+++ b/src/transmissionReconstruction/detection/getTransmissionData.cpp
@@ -1,32 +1,33 @@
 #include "getTransmissionData.h"
-#include "Function.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "common/dataBlockCreation/removeDataFromArrays.h"
-#include "src//config/config.h"
-#include "src/common/getGeometryInfo.h"
-#include "src/common/temperatureCalculation/extractTasTemperature.h"
-#include "src/common/dataBlockCreation/getAScanBlockPreprocessed.h"
-#include "src/common/precalculateChannelList.h"
-#include "src/transmissionReconstruction/dataFilter/sensitivityCalculations.h"
-#include "src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.h"

-#include "Matrix.h"
-#include "Function3D.h"
-#include "transmissionReconstruction/dataFilter/dataFilter.h"
-#include "transmissionReconstruction/dataPreperation.h"
-#include "transmissionReconstruction/detection/detection.h"
 #include <cstddef>
-#include <mkl_cblas.h>
-
 #include <iostream>
-#include <mkl_vml_functions.h>
 #include <map>
 #include <string>
 #include <thread>
 #include <mutex>
 #include <condition_variable>

+#include <mkl_cblas.h>
+#include <mkl_vml_functions.h>
+
+#include "Function.h"
+#include "Function2D.h"
+#include "Function3D.h"
+
+#include "config/config.h"
+#include "common/dataBlockCreation/removeDataFromArrays.h"
+#include "common/getGeometryInfo.h"
+#include "common/temperatureCalculation/extractTasTemperature.h"
+#include "common/dataBlockCreation/getAScanBlockPreprocessed.h"
+#include "common/precalculateChannelList.h"
+#include "transmissionReconstruction/dataFilter/sensitivityCalculations.h"
+#include "transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.h"
+#include "transmissionReconstruction/dataFilter/dataFilter.h"
+#include "transmissionReconstruction/dataPreperation.h"
+#include "transmissionReconstruction/detection/detection.h"
+
+
 using namespace Recon;
 using namespace Aurora;

--- a/src/transmissionReconstruction/detection/getTransmissionData.cu
+++ b/src/transmissionReconstruction/detection/getTransmissionData.cu
@@ -1,4 +1,3 @@
-#include "AuroraDefs.h"
 #include "getTransmissionData.cuh"

 #include <cstdio>
--- a/src/transmissionReconstruction/detection/getTransmissionData.h
+++ b/src/transmissionReconstruction/detection/getTransmissionData.h
@@ -2,8 +2,8 @@
 #define GET_TRANSMISSION_DATA_H

 #include "Matrix.h"
-#include "../../common/getMeasurementMetaData.h"
-#include "src/common/getGeometryInfo.h"
+#include "common/getMeasurementMetaData.h"
+#include "common/getGeometryInfo.h"

 class Parser;
 namespace Recon
--- a/src/transmissionReconstruction/reconstruction/buildMatrix/FMM.cpp
+++ b/src/transmissionReconstruction/reconstruction/buildMatrix/FMM.cpp
@@ -10,7 +10,6 @@

 #include "Function2D.h"
 #include "Function3D.h"
-#include "Matrix.h"
 #include "Bresenham.h"
 #include "DGradient.h"

--- a/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cpp
+++ b/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cpp
@@ -7,13 +7,13 @@
 #include <ostream>
 #include <sys/types.h>

-#include "Function1D.h"
+
 #include "Function2D.h"
-#include "Bresenham.h"
 #include "Function3D.h"
-#include "FMM.h"
-#include "Matrix.h"
+
 #include "Sparse.h"
+#include "Bresenham.h"
+#include "FMM.h"
 #include "common/common.h"
 #include "config/config.h"

--- a/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cu
+++ b/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cu
@@ -1,5 +1,4 @@
-#include "Function2D.cuh"
-
+#include "buildMatrix.cuh"

 #include <cstdio>
 #include <thrust/reduce.h>
@@ -8,8 +7,9 @@
 #include <math.h>

 #include "CudaMatrix.h"
-#include "buildMatrix.cuh"
 #include "Sparse.h"
+#include "Function2D.cuh"
+


 namespace  {
--- a/src/transmissionReconstruction/reconstruction/reconstruction.cpp
+++ b/src/transmissionReconstruction/reconstruction/reconstruction.cpp
@@ -1,19 +1,20 @@
 #include "reconstruction.h"
-#include "Function.h"
-#include "Function1D.h"
-#include "Function2D.h"
-#include "Function3D.h"
-#include "Matrix.h"
-#include "config/config.h"
-
-#include "CudaEnvInit.h"
-#include "transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.h"
-#include "src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.h"

 #include <algorithm>
 #include <cmath>
 #include <iostream>
 #include <vector>
+
+#include "Function.h"
+#include "Function2D.h"
+#include "Function3D.h"
+
+#include "config/config.h"
+#include "transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.h"
+#include "transmissionReconstruction/reconstruction/solvingEquationSystem/solve.h"
+
+#include "CudaEnvInit.h"
+
 using namespace Aurora;
 namespace Recon {
    Aurora::Matrix calculateMinimalMaximalTransducerPositions(
--- a/src/transmissionReconstruction/reconstruction/solvingEquationSystem/TVAL/TVAL.cpp
+++ b/src/transmissionReconstruction/reconstruction/solvingEquationSystem/TVAL/TVAL.cpp
@@ -1,16 +1,17 @@
 #include "TVAL.h"

 #include "Function2D.h"
-#include "Matrix.h"
 #include "tval3gpu3d.h"

-#include "mkl_spblas.h"
-#include "mkl_solvers_ee.h"
+
 #include <algorithm>
 #include <cstddef>
 #include <iostream>
 #include <vector>
+#include <sys/time.h>

+#include <mkl_spblas.h>
+#include <mkl_solvers_ee.h>
 #include <Eigen/Sparse>
 #include <Spectra/GenEigsSolver.h>
 #include <Spectra/MatOp/SparseGenMatProd.h>
@@ -18,7 +19,6 @@
 #include <Eigen/SparseCore>
 #include <Eigen/Eigenvalues>

-#include <sys/time.h>
 namespace Recon
 {
    bool isEigsFinished = false;
--- a/src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.cpp
+++ b/src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.cpp
@@ -3,11 +3,10 @@
 #include <cstddef>

 #include "Function3D.h"
-#include "Matrix.h"

 #include "config/config.h"
-
 #include "transmissionReconstruction/reconstruction/solvingEquationSystem/TVAL/TVAL.h"
+
 #include "tvalstruct.h"

 namespace Recon
--- a/src/transmissionReconstruction/startTransmissionReconstruction.cpp
+++ b/src/transmissionReconstruction/startTransmissionReconstruction.cpp
@@ -1,19 +1,18 @@
 #include "startTransmissionReconstruction.h"
-#include "./detection/getTransmissionData.h"
-#include "Matrix.h"
-#include "log/log.h"
-#include "common/dataBlockCreation/removeDataFromArrays.h"
-#include "src/transmissionReconstruction/dataFilter/dataFilter.h"
-#include "src/transmissionReconstruction/dataPreperation.h"
-#include "src/common/getMeasurementMetaData.h"
-#include "src/common/qualityReview.h"
-#include "src/transmissionReconstruction/reconstruction/reconstruction.h"
-#include "src/config/config.h"

 #include "Function2D.h"
-
 #include "MatlabWriter.h"

+#include "detection/getTransmissionData.h"
+#include "log/log.h"
+#include "config/config.h"
+#include "common/getMeasurementMetaData.h"
+#include "common/qualityReview.h"
+#include "common/dataBlockCreation/removeDataFromArrays.h"
+#include "transmissionReconstruction/dataFilter/dataFilter.h"
+#include "transmissionReconstruction/dataPreperation.h"
+#include "transmissionReconstruction/reconstruction/reconstruction.h"
+
 using namespace Aurora;
 using namespace Recon;

--- a/src/transmissionReconstruction/startTransmissionReconstruction.h
+++ b/src/transmissionReconstruction/startTransmissionReconstruction.h
@@ -2,8 +2,8 @@
 #define START_TRANSMISSION_RECONSTRUCTION_H

 #include "Matrix.h"
-#include "../common/getMeasurementMetaData.h"
-#include "../common/getGeometryInfo.h"
+#include "common/getMeasurementMetaData.h"
+#include "common/getGeometryInfo.h"
 #include "transmissionReconstruction/detection/getTransmissionData.h"

 class Parser;