From 8032cb5c3f579bd7d36960f1ca130db8c22810ad Mon Sep 17 00:00:00 2001 From: kradchen Date: Thu, 19 Dec 2024 11:24:56 +0800 Subject: [PATCH] feat: arrange include headers --- src/Aurora.cu | 11 +++--- src/Aurora.h | 4 +- src/common/DICOMExporter.cpp | 14 +++---- src/common/ceMatchedFilterHandling.cpp | 10 +++-- .../dataBlockCreation/blockingGeometryInfo.h | 2 +- .../getAScanBlockPreprocessed.cpp | 11 +++--- .../getAScanBlockPreprocessed.h | 4 +- .../dataBlockCreation/getAscanBlock.cpp | 8 ++-- src/common/dataBlockCreation/getAscanBlock.h | 2 +- .../removeDataFromArrays.cpp | 9 +++-- src/common/estimatePulseLength.cpp | 7 +++- src/common/getGeometryInfo.cpp | 14 +++---- src/common/getMeasurementMetaData.cpp | 19 +++++---- src/common/getMeasurementMetaData.h | 2 +- src/common/meshgrid.cpp | 2 +- src/common/precalculateChannelList.h | 2 +- src/common/preprocessAscanBlock.cpp | 4 +- src/config/config.cpp | 14 ++++--- src/main.cxx | 5 ++- src/reflectionReconstruction/dataFilter.cpp | 4 +- .../preprocessData/determineOptimalPulse.cpp | 10 +++-- .../preprocessData/estimateOffset.cpp | 10 +++-- .../preprocessData/estimateOffset.h | 2 +- .../preprocessData/imageExtrapolation.cpp | 6 ++- .../preprocessData/precalcImageParameters.cpp | 9 +++-- .../preprocessData/precalcImageParameters.h | 2 +- .../preprocessAScanBlockForReflection.cpp | 15 +++---- .../preprocessAScanBlockForReflection.h | 4 +- ...ransmissionReconstructionForReflection.cpp | 15 ++++--- ...sTransmissionReconstructionForReflection.h | 4 +- .../resampleTransmissionVolume.cpp | 14 +++---- .../resampleTransmissionVolume.h | 2 +- .../reconstructionSAFT/reconstructionSAFT.cpp | 20 +++++----- .../reconstructionSAFT/reconstructionSAFT.h | 2 +- .../startReflectionReconstruction.cpp | 11 +++--- src/startReconstructions.cpp | 33 ++++++++-------- .../dataFilter/dataFilter.cpp | 4 +- .../dataFilter/dataFilter.h | 4 +- .../estimateNoiseValueFromAScans.cpp | 4 +- .../dataFilter/estimateNoiseValueFromAScans.h | 4 +- .../dataFilter/sensitivityCalculations.cpp | 7 ++-- .../dataFilter/sensitivityCalculations.h | 2 +- .../dataPreperation.cpp | 4 +- .../detection/detection.cpp | 2 - .../detection/detection.cu | 1 + .../detection/getTransmissionData.cpp | 39 ++++++++++--------- .../detection/getTransmissionData.cu | 1 - .../detection/getTransmissionData.h | 4 +- .../reconstruction/buildMatrix/FMM.cpp | 1 - .../buildMatrix/buildMatrix.cpp | 8 ++-- .../reconstruction/buildMatrix/buildMatrix.cu | 6 +-- .../reconstruction/reconstruction.cpp | 21 +++++----- .../solvingEquationSystem/TVAL/TVAL.cpp | 8 ++-- .../solvingEquationSystem/solve.cpp | 3 +- .../startTransmissionReconstruction.cpp | 21 +++++----- .../startTransmissionReconstruction.h | 4 +- 56 files changed, 240 insertions(+), 215 deletions(-) diff --git a/src/Aurora.cu b/src/Aurora.cu index 792a10c..27818b3 100644 --- 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 +#include + +#include +#include +#include #include #include #include #include #include "Aurora.h" -#include "AuroraDefs.h" #include "CudaMatrix.h" -#include + #include "log/log.h" -#include __global__ void doubleToComplexKernel(const double* input, cufftDoubleComplex* output, int size) { diff --git a/src/Aurora.h b/src/Aurora.h index 995bcbc..1d0ce02 100644 --- 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 +#include +#include #include "Matrix.h" namespace Aurora diff --git a/src/common/DICOMExporter.cpp b/src/common/DICOMExporter.cpp index cde631d..73f790b 100644 --- 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 #include +#include +#include #include #include #include #include -#include -#include -#include "dcmtk/dcmdata/dctk.h" +#include + +#include "fileHelper.h" +#include "config/config.h" +#include "log/log.h" using namespace std; namespace { diff --git a/src/common/ceMatchedFilterHandling.cpp b/src/common/ceMatchedFilterHandling.cpp index 63d7175..89cc014 100644 --- 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 #include #include #include +#include "Function.h" +#include "Function2D.h" +#include "Function3D.h" + + Aurora::Matrix Recon::adaptFrequency(Aurora::Matrix &aCE, float ceSampleFrequency, float requiredFrequency) { if (requiredFrequency < ceSampleFrequency){ diff --git a/src/common/dataBlockCreation/blockingGeometryInfo.h b/src/common/dataBlockCreation/blockingGeometryInfo.h index 8572623..7857ba8 100644 --- 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 { diff --git a/src/common/dataBlockCreation/getAScanBlockPreprocessed.cpp b/src/common/dataBlockCreation/getAScanBlockPreprocessed.cpp index 4f37937..a4779e1 100644 --- 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; diff --git a/src/common/dataBlockCreation/getAScanBlockPreprocessed.h b/src/common/dataBlockCreation/getAScanBlockPreprocessed.h index 7285e1c..a07f05f 100644 --- 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; diff --git a/src/common/dataBlockCreation/getAscanBlock.cpp b/src/common/dataBlockCreation/getAscanBlock.cpp index dd43f31..a36a71c 100644 --- a/src/common/dataBlockCreation/getAscanBlock.cpp +++ b/src/common/dataBlockCreation/getAscanBlock.cpp @@ -1,5 +1,9 @@ #include "getAscanBlock.h" +#include +#include +#include + #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 -#include -#include + using namespace Recon; using namespace Aurora; diff --git a/src/common/dataBlockCreation/getAscanBlock.h b/src/common/dataBlockCreation/getAscanBlock.h index 8787d9b..fdebb60 100644 --- 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; diff --git a/src/common/dataBlockCreation/removeDataFromArrays.cpp b/src/common/dataBlockCreation/removeDataFromArrays.cpp index 0b92937..127568a 100644 --- 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 #include #include +#include "Function.h" +#include "Function2D.h" + + using namespace Recon; using namespace Aurora; diff --git a/src/common/estimatePulseLength.cpp b/src/common/estimatePulseLength.cpp index f9395e6..fb08a35 100644 --- a/src/common/estimatePulseLength.cpp +++ b/src/common/estimatePulseLength.cpp @@ -1,9 +1,12 @@ #include "estimatePulseLength.h" -#include "Function1D.h" -#include "Function2D.h" + #include #include +#include "Function1D.h" +#include "Function2D.h" + + using namespace Aurora; float Recon::estimatePulseLength(const CeEstimatePulseLength& aCe, float aSampleFreq) diff --git a/src/common/getGeometryInfo.cpp b/src/common/getGeometryInfo.cpp index cc8b503..ccc4aaf 100644 --- 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 #include #include #include +#include "Function.h" +#include "Function2D.h" +#include "Function3D.h" + +#include "config/geometryConfig.h" +#include "common/getMeasurementMetaData.h" + using namespace Recon; using namespace Aurora; diff --git a/src/common/getMeasurementMetaData.cpp b/src/common/getMeasurementMetaData.cpp index c5d4942..df9ab3f 100644 --- 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 +#include + +#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 using namespace Recon; using namespace Aurora; diff --git a/src/common/getMeasurementMetaData.h b/src/common/getMeasurementMetaData.h index 36c7809..ff1f17e 100644 --- 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; diff --git a/src/common/meshgrid.cpp b/src/common/meshgrid.cpp index 1097891..18fea18 100644 --- 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; diff --git a/src/common/precalculateChannelList.h b/src/common/precalculateChannelList.h index 1f67fac..eb8e907 100644 --- 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 { diff --git a/src/common/preprocessAscanBlock.cpp b/src/common/preprocessAscanBlock.cpp index aad0f5e..899f46e 100644 --- a/src/common/preprocessAscanBlock.cpp +++ b/src/common/preprocessAscanBlock.cpp @@ -1,7 +1,9 @@ #include "preprocessAscanBlock.h" + +#include + #include "Function1D.h" #include "Function1D.cuh" -#include Aurora::Matrix Recon::preprocessAscanBlock(const Aurora::Matrix& aAscans, const MeasurementInfo& aMeasInfo) { diff --git a/src/config/config.cpp b/src/config/config.cpp index dd89991..46b8fdd 100644 --- a/src/config/config.cpp +++ b/src/config/config.cpp @@ -1,11 +1,13 @@ -#include "Function2D.h" -#include "Matrix.h" -#include #define GLOBLE_CONFIG -#include "config.h" -#include "src/log/log.h" -#include "json.hpp" + +#include #include +#include "Function2D.h" + + +#include "config.h" +#include "log/log.h" +#include "json.hpp" namespace Recon { diff --git a/src/main.cxx b/src/main.cxx index b51631c..074e550 100644 --- a/src/main.cxx +++ b/src/main.cxx @@ -1,13 +1,14 @@ #include "Parser.h" #include "Parser.h" -#include "config/config.h" #include #include #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. diff --git a/src/reflectionReconstruction/dataFilter.cpp b/src/reflectionReconstruction/dataFilter.cpp index 9762df4..9fe67b4 100644 --- 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; diff --git a/src/reflectionReconstruction/preprocessData/determineOptimalPulse.cpp b/src/reflectionReconstruction/preprocessData/determineOptimalPulse.cpp index 04546b8..98af4f1 100644 --- 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 #include #include #include #include + +#include "Function2D.h" +#include "Function3D.h" +#include "config/config.h" + namespace Recon { Aurora::Matrix determineOptimalPulse(float timeInterval, size_t expectedAScanLength) diff --git a/src/reflectionReconstruction/preprocessData/estimateOffset.cpp b/src/reflectionReconstruction/preprocessData/estimateOffset.cpp index 209ce3e..92d5148 100644 --- a/src/reflectionReconstruction/preprocessData/estimateOffset.cpp +++ b/src/reflectionReconstruction/preprocessData/estimateOffset.cpp @@ -1,11 +1,13 @@ #include "estimateOffset.h" -#include "../../common/ceMatchedFilterHandling.h" + +#include + #include "Function.h" #include "Function1D.h" #include "Function2D.h" -#include "Matrix.h" -#include "src/config/config.h" -#include + +#include "config/config.h" +#include "common/ceMatchedFilterHandling.h" using namespace Recon; using namespace Aurora; diff --git a/src/reflectionReconstruction/preprocessData/estimateOffset.h b/src/reflectionReconstruction/preprocessData/estimateOffset.h index 43754bc..cf0c2e0 100644 --- 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 { diff --git a/src/reflectionReconstruction/preprocessData/imageExtrapolation.cpp b/src/reflectionReconstruction/preprocessData/imageExtrapolation.cpp index a4f8db8..b59f1ca 100644 --- 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 #include +#include "Function2D.h" + + using namespace Recon; using namespace Aurora; diff --git a/src/reflectionReconstruction/preprocessData/precalcImageParameters.cpp b/src/reflectionReconstruction/preprocessData/precalcImageParameters.cpp index ab1e238..0ce31b5 100644 --- 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 #include "Function.h" #include "Function2D.h" -#include + +#include "common/getGeometryInfo.h" +#include "config/config.h" using namespace Recon; using namespace Aurora; diff --git a/src/reflectionReconstruction/preprocessData/precalcImageParameters.h b/src/reflectionReconstruction/preprocessData/precalcImageParameters.h index 00c2256..037acac 100644 --- 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 { diff --git a/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.cpp b/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.cpp index bbc49a8..e7ec41d 100644 --- 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 #include #include @@ -16,6 +9,14 @@ #include #include #include + +#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){ diff --git a/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h b/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h index 2283d79..47f78e9 100644 --- a/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h +++ b/src/reflectionReconstruction/preprocessData/preprocessAScanBlockForReflection.h @@ -1,8 +1,10 @@ #ifndef __PREPROCESSASCANBLOCKFORREFLECTION_H__ #define __PREPROCESSASCANBLOCKFORREFLECTION_H__ +#include + #include "Matrix.h" #include "common/getMeasurementMetaData.h" -#include + namespace Recon { struct preprocessAScanRResult { Aurora::Matrix AscanBlock; diff --git a/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.cpp b/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.cpp index 56a18e8..805bb06 100644 --- 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 #include #include + +#include "Function3D.h" +#include "Function2D.h" + +#include "reflectionReconstruction/preprocessData/resampleTransmissionVolume.h" +#include "config/config.h" + + + using namespace Aurora; using namespace Recon; diff --git a/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h b/src/reflectionReconstruction/preprocessData/preprocessTransmissionReconstructionForReflection.h index 71718dd..a180461 100644 --- 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 { diff --git a/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.cpp b/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.cpp index a1e5db3..21a1e8c 100644 --- 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 #include +#include "Function2D.h" +#include "Function3D.h" + +#include "imageExtrapolation.h" +#include "config/config.h" +#include "common/meshgrid.h" + using namespace Aurora; using namespace Recon; diff --git a/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.h b/src/reflectionReconstruction/preprocessData/resampleTransmissionVolume.h index 37323eb..e82ddb7 100644 --- 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 { diff --git a/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.cpp b/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.cpp index 17da3fb..f7d8802 100644 --- 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 #include #include @@ -18,6 +8,16 @@ #include #include +#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, diff --git a/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.h b/src/reflectionReconstruction/reconstructionSAFT/reconstructionSAFT.h index d9e3d00..de8c3aa 100644 --- 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{ diff --git a/src/reflectionReconstruction/startReflectionReconstruction.cpp b/src/reflectionReconstruction/startReflectionReconstruction.cpp index 97f84ec..575952a 100644 --- a/src/reflectionReconstruction/startReflectionReconstruction.cpp +++ b/src/reflectionReconstruction/startReflectionReconstruction.cpp @@ -1,8 +1,13 @@ #include "startReflectionReconstruction.h" + +#include +#include +#include +#include + #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 -#include -#include -#include using namespace Aurora; using namespace Recon; diff --git a/src/startReconstructions.cpp b/src/startReconstructions.cpp index ace1bdc..ced7469 100644 --- a/src/startReconstructions.cpp +++ b/src/startReconstructions.cpp @@ -1,30 +1,29 @@ #include "startReconstructions.h" -#include "Data/TemperatureData.h" +#include +#include + #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 -#include -#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; diff --git a/src/transmissionReconstruction/dataFilter/dataFilter.cpp b/src/transmissionReconstruction/dataFilter/dataFilter.cpp index 6200894..9530916 100644 --- a/src/transmissionReconstruction/dataFilter/dataFilter.cpp +++ b/src/transmissionReconstruction/dataFilter/dataFilter.cpp @@ -6,10 +6,10 @@ #include #include "Function.h" -#include "Function1D.h" + #include "Function2D.h" #include "Function3D.h" -#include "Matrix.h" + using namespace Aurora; namespace Recon { diff --git a/src/transmissionReconstruction/dataFilter/dataFilter.h b/src/transmissionReconstruction/dataFilter/dataFilter.h index 44b5e81..7ee9b76 100644 --- 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 + +#include "Matrix.h" + namespace Recon { Aurora::Matrix calculateSnr(const Aurora::Matrix &aMDataBlock, float aReferenceNoise); diff --git a/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.cpp b/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.cpp index 5affdc2..84df9e4 100644 --- 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" diff --git a/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.h b/src/transmissionReconstruction/dataFilter/estimateNoiseValueFromAScans.h index 4f6ae6b..5aa4bf3 100644 --- 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; diff --git a/src/transmissionReconstruction/dataFilter/sensitivityCalculations.cpp b/src/transmissionReconstruction/dataFilter/sensitivityCalculations.cpp index aa6217e..5c63970 100644 --- 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 #include #include #include + +#include "Function2D.h" +#include "Function3D.h" + namespace { inline void cross(float *aVA, float *aVB, float *aVOut, int aIncX = 1) { if (!aVA || !aVB || !aVOut) diff --git a/src/transmissionReconstruction/dataFilter/sensitivityCalculations.h b/src/transmissionReconstruction/dataFilter/sensitivityCalculations.h index b53e7aa..a3822d8 100644 --- a/src/transmissionReconstruction/dataFilter/sensitivityCalculations.h +++ b/src/transmissionReconstruction/dataFilter/sensitivityCalculations.h @@ -3,7 +3,7 @@ #include #include "Matrix.h" -#include "src/common/getGeometryInfo.h" +#include "common/getGeometryInfo.h" namespace Recon { diff --git a/src/transmissionReconstruction/dataPreperation.cpp b/src/transmissionReconstruction/dataPreperation.cpp index ca2738d..37a3ffa 100644 --- a/src/transmissionReconstruction/dataPreperation.cpp +++ b/src/transmissionReconstruction/dataPreperation.cpp @@ -1,8 +1,8 @@ #include "dataPreperation.h" -#include "Function1D.h" +#include + #include "Function2D.h" #include "Function3D.h" -#include namespace Recon diff --git a/src/transmissionReconstruction/detection/detection.cpp b/src/transmissionReconstruction/detection/detection.cpp index 5261e3a..beed361 100644 --- a/src/transmissionReconstruction/detection/detection.cpp +++ b/src/transmissionReconstruction/detection/detection.cpp @@ -5,10 +5,8 @@ #include #include "Function.h" -#include "Function1D.h" #include "Function2D.h" #include "Function3D.h" -#include "Matrix.h" #include "common/getMeasurementMetaData.h" #include "config/config.h" diff --git a/src/transmissionReconstruction/detection/detection.cu b/src/transmissionReconstruction/detection/detection.cu index b82501c..8b52570 100644 --- a/src/transmissionReconstruction/detection/detection.cu +++ b/src/transmissionReconstruction/detection/detection.cu @@ -3,6 +3,7 @@ #include #include #include + #include "Function1D.cuh" #include "Function2D.cuh" #include "Function3D.h" diff --git a/src/transmissionReconstruction/detection/getTransmissionData.cpp b/src/transmissionReconstruction/detection/getTransmissionData.cpp index 2d206e6..9e8e96b 100644 --- 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 -#include - #include -#include #include #include #include #include #include +#include +#include + +#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; diff --git a/src/transmissionReconstruction/detection/getTransmissionData.cu b/src/transmissionReconstruction/detection/getTransmissionData.cu index f893995..abf0c46 100644 --- a/src/transmissionReconstruction/detection/getTransmissionData.cu +++ b/src/transmissionReconstruction/detection/getTransmissionData.cu @@ -1,4 +1,3 @@ -#include "AuroraDefs.h" #include "getTransmissionData.cuh" #include diff --git a/src/transmissionReconstruction/detection/getTransmissionData.h b/src/transmissionReconstruction/detection/getTransmissionData.h index 55bd665..46c3a1d 100644 --- 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 diff --git a/src/transmissionReconstruction/reconstruction/buildMatrix/FMM.cpp b/src/transmissionReconstruction/reconstruction/buildMatrix/FMM.cpp index e1e74c7..e343595 100644 --- 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" diff --git a/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cpp b/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cpp index ea94b01..db52329 100644 --- a/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cpp +++ b/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cpp @@ -7,13 +7,13 @@ #include #include -#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" diff --git a/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cu b/src/transmissionReconstruction/reconstruction/buildMatrix/buildMatrix.cu index 4807c0f..3aad02f 100644 --- 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 #include @@ -8,8 +7,9 @@ #include #include "CudaMatrix.h" -#include "buildMatrix.cuh" #include "Sparse.h" +#include "Function2D.cuh" + namespace { diff --git a/src/transmissionReconstruction/reconstruction/reconstruction.cpp b/src/transmissionReconstruction/reconstruction/reconstruction.cpp index d6b7a5a..0a57737 100644 --- 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 #include #include #include + +#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( diff --git a/src/transmissionReconstruction/reconstruction/solvingEquationSystem/TVAL/TVAL.cpp b/src/transmissionReconstruction/reconstruction/solvingEquationSystem/TVAL/TVAL.cpp index 9fd82a2..93b5ea7 100644 --- 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 #include #include #include +#include +#include +#include #include #include #include @@ -18,7 +19,6 @@ #include #include -#include namespace Recon { bool isEigsFinished = false; diff --git a/src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.cpp b/src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.cpp index d447210..6796a76 100644 --- a/src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.cpp +++ b/src/transmissionReconstruction/reconstruction/solvingEquationSystem/solve.cpp @@ -3,11 +3,10 @@ #include #include "Function3D.h" -#include "Matrix.h" #include "config/config.h" - #include "transmissionReconstruction/reconstruction/solvingEquationSystem/TVAL/TVAL.h" + #include "tvalstruct.h" namespace Recon diff --git a/src/transmissionReconstruction/startTransmissionReconstruction.cpp b/src/transmissionReconstruction/startTransmissionReconstruction.cpp index b49ed73..688b4bf 100644 --- 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; diff --git a/src/transmissionReconstruction/startTransmissionReconstruction.h b/src/transmissionReconstruction/startTransmissionReconstruction.h index 57c8c66..1a5c8fd 100644 --- 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;