diff --git a/src/common/DICOMExporter.cpp b/src/common/DICOMExporter.cpp index 73f790b..0ef2013 100644 --- a/src/common/DICOMExporter.cpp +++ b/src/common/DICOMExporter.cpp @@ -11,6 +11,7 @@ #include #include "fileHelper.h" +#include "Function1D.h" #include "config/config.h" #include "log/log.h" @@ -20,35 +21,67 @@ namespace { return (endPoint[index]-startPoint[index])/(float)(imageXYZ[index])*1000.0; } - void initialDicomFile(DcmDataset* aDataset,DcmMetaInfo* aMetaInfo) + Aurora::Matrix flipHorizontal(const Aurora::Matrix& aImage) { - aMetaInfo->putAndInsertString(DCM_MediaStorageSOPClassUID, - UID_CTImageStorage); - aDataset->putAndInsertString(DCM_SOPClassUID, UID_CTImageStorage); - - aDataset->putAndInsertString(DCM_TransferSyntaxUID, - UID_LittleEndianImplicitTransferSyntax); - aDataset->putAndInsertString(DCM_ImageType, "ORIGINAL\\PRIMARY"); - - aDataset->putAndInsertString(DCM_Manufacturer, "EQ9"); - aDataset->putAndInsertString(DCM_PatientOrientation, "L\\H"); - aDataset->putAndInsertString(DCM_PatientPosition, "HFP"); - - aDataset->putAndInsertString(DCM_ImageOrientationPatient, "1\\0\\0\\0\\0\\1"); - - aDataset->putAndInsertString(DCM_StudyDescription, "USCT BREAST"); - aDataset->putAndInsertString(DCM_ManufacturerModelVersion, "USCT3DV3"); - - aDataset->putAndInsertString(DCM_SamplesPerPixel, "1"); - aDataset->putAndInsertString(DCM_PixelRepresentation, "0"); - aDataset->putAndInsertString(DCM_BitsAllocated, "16"); - aDataset->putAndInsertString(DCM_BitsStored, "16"); - aDataset->putAndInsertString(DCM_HighBit, "15"); - aDataset->putAndInsertString(DCM_PhotometricInterpretation, "MONOCHROME2"); - - aDataset->putAndInsertString(DCM_KVP, "0"); - + int row = aImage.getDimSize(0); + int column = aImage.getDimSize(1); + Aurora::Matrix result = Aurora::Matrix::fromRawData(new float[row*column], row, column); + for (int c = 0; c < column; ++c) + { + const int mirrorC = column - 1 - c; + + for (int r = 0; r < row; ++r) + { + const int originalIndex = c * row + r; + const int newIndex = mirrorC * row + r; + result[newIndex] = aImage[originalIndex]; + } + } + return result; } + + Aurora::Matrix rotate90Clock2D(const Aurora::Matrix& aImage) + { + int row = aImage.getDimSize(0); + int column = aImage.getDimSize(1); + Aurora::Matrix result = Aurora::Matrix::fromRawData(new float[row*column], column, row); + const int originalRow = row; + const int originalCol = column; + + const int newRow = originalCol; + const int newCol = originalRow; + for (int newColIndex = 0; newColIndex < newCol; ++newColIndex) + { + for (int newRowIndex = 0; newRowIndex < newRow; ++newRowIndex) + { + const int oldColindex = newRowIndex; + const int oldRowindex = originalRow - 1 - newColIndex; + + const int oldPos = oldColindex * originalRow + oldRowindex; + const int newPos = newColIndex * newRow + newRowIndex; + + result[newPos] = aImage[oldPos]; + } + } + return result; + } + + Aurora::Matrix transferToDicomType(const Aurora::Matrix& aImage, Recon::DICOMExporter::ImageType aType) + { + switch (aType) + { + case Recon::DICOMExporter::REFL: + case Recon::DICOMExporter::CoronalPositioning: + return Aurora::transpose(flipHorizontal(aImage)); + case Recon::DICOMExporter::SagittalPositioning: + return Aurora::transpose(aImage); + case Recon::DICOMExporter::TransversePositioning: + return Aurora::transpose(rotate90Clock2D(aImage)); + default: + return aImage; + } + } + void initialDate(DcmDataset* aDataset,const std::string& aStudyDate ) { aDataset->putAndInsertString(DCM_StudyDate, aStudyDate.data()); @@ -71,7 +104,7 @@ namespace { aDataset->putAndInsertString(DCM_AcquisitionTime, aStudyTime.data()); aDataset->putAndInsertString(DCM_ContentTime, time.data()); } - const char* SeriesDescriptions[3]={"REFL","SOS","ATT"}; + const char* SeriesDescriptions[6]={"REFL","SOS","ATT","CoronalPositioning","SagittalPositioning","TransversePositioning"}; const char* getSeriesDescription(int type){ return SeriesDescriptions[type]; } @@ -83,6 +116,7 @@ namespace Recon DICOMExporter::DICOMExporter(const PatientData& aPatientData, const MetaData& aMetaData) { mPatientData = aPatientData; + mDicomFile = new DcmFileFormat(); //prepare Study if (aPatientData.getStudyUID().empty()){ char tempStr [100] = {0}; @@ -93,7 +127,7 @@ namespace Recon mStudyInstanceUID = aPatientData.getStudyUID(); } std::string measurementID = aMetaData.getMeasurementID(); - + mLaterality = mPatientData.getLaterality().empty() ? "L" : mPatientData.getLaterality(); unsigned long dateIndex = measurementID.find('_'); unsigned long timeIndex = measurementID.find('T'); OFDateTime currentDateTime; @@ -116,10 +150,12 @@ namespace Recon else{ mStudyTime = measurementID.substr(timeIndex+1,6); } + initialDicomFile(); } DICOMExporter::DICOMExporter() { + mDicomFile = new DcmFileFormat(); //prepare Study char tempStr [100] = {0}; dcmGenerateUniqueIdentifier(tempStr,SITE_STUDY_UID_ROOT); @@ -133,44 +169,48 @@ namespace Recon currentDateTime.getTime().getISOFormattedTime(time,true,false,false,false); mStudyDate = date.data(); mStudyTime = time.data(); + initialDicomFile(); } DICOMExporter::~DICOMExporter() { + delete mDicomFile; } void DICOMExporter::setExportBasePath(const std::string & path) { mBasePath = path; } - void DICOMExporter::exportDICOM(Aurora::Matrix aMatrix, ImageType type){ - int XYZ [3] = {aMatrix.getDimSize(0),aMatrix.getDimSize(1), aMatrix.getDimSize(2)}; - string path = mBasePath+"/"+::getSeriesDescription(type)+"/"; - if (!exists(path)){ - if(!mkdir(path)){ - RECON_ERROR("Fail to create dir with path {0}\r\n",path); - } - } - exportDCM(path, reflectParams::imageStartpoint.getData(), - reflectParams::imageEndpoint.getData(), XYZ, aMatrix.getData(), type); - RECON_INFO("Save DICOM to Path:{0}, type:{1}==================>",path,(int)type); - } - - void DICOMExporter::exportDCM(string path, float * startPoint, float* endPoint, int* imageXYZ,float* data, int type) + void DICOMExporter::initialDicomFile() { - long Rows = imageXYZ[1], Cols = imageXYZ[0] ,Slices = imageXYZ[2]; - DcmFileFormat dcmFile; - DcmDataset* dataset = dcmFile.getDataset(); - DcmMetaInfo* metaInfo = dcmFile.getMetaInfo(); + DcmDataset* dataset = mDicomFile->getDataset(); + DcmMetaInfo* metaInfo = mDicomFile->getMetaInfo(); + metaInfo->putAndInsertString(DCM_MediaStorageSOPClassUID, + UID_CTImageStorage); + dataset->putAndInsertString(DCM_SOPClassUID, UID_CTImageStorage); + dataset->putAndInsertString(DCM_ImageType, "ORIGINAL\\PRIMARY"); + + dataset->putAndInsertString(DCM_Manufacturer, "EQ9"); + dataset->putAndInsertString(DCM_PatientOrientation, "L\\H"); + dataset->putAndInsertString(DCM_PatientPosition, "HFP"); + + dataset->putAndInsertString(DCM_StudyDescription, "USCT BREAST"); + dataset->putAndInsertString(DCM_ManufacturerModelVersion, "USCT3DV3"); + + dataset->putAndInsertString(DCM_SamplesPerPixel, "1"); + dataset->putAndInsertString(DCM_PixelRepresentation, "0"); + dataset->putAndInsertString(DCM_BitsAllocated, "16"); + dataset->putAndInsertString(DCM_BitsStored, "16"); + dataset->putAndInsertString(DCM_HighBit, "15"); + dataset->putAndInsertString(DCM_PhotometricInterpretation, "MONOCHROME2"); + dataset->putAndInsertString(DCM_KVP, "0"); - initialDicomFile(dataset,metaInfo); dataset->putAndInsertString(DCM_SpecificCharacterSet, "ISO_IR 192"); dataset->putAndInsertString(DCM_StudyInstanceUID, mStudyInstanceUID.data()); - dcmGenerateUniqueIdentifier(mSeriesInstanceUID,SITE_SERIES_UID_ROOT); - dataset->putAndInsertString(DCM_SeriesInstanceUID, mSeriesInstanceUID); - dataset->putAndInsertString(DCM_FrameOfReferenceUID, mSeriesInstanceUID); + dcmGenerateUniqueIdentifier(mFrameOfReferenceUID,SITE_SERIES_UID_ROOT); + dataset->putAndInsertString(DCM_FrameOfReferenceUID, mFrameOfReferenceUID); ::initialDate(dataset, mStudyDate); @@ -179,7 +219,7 @@ namespace Recon ::initialSeriesTime(dataset, mStudyTime); dataset->putAndInsertString(DCM_Modality, mPatientData.getModality().empty()? - "CT":mPatientData.getModality().data()); + "CT":mPatientData.getModality().data()); dataset->putAndInsertString(DCM_InstitutionName, mPatientData.getInstituationName().empty()? "":mPatientData.getInstituationName().data()); @@ -196,32 +236,148 @@ namespace Recon dataset->putAndInsertString(DCM_Laterality, mPatientData.getLaterality().data()); dataset->putAndInsertString(DCM_StudyID, mStudyTime.data()); - dataset->putAndInsertString(DCM_SeriesNumber, to_string(type).data()); - dataset->putAndInsertString(DCM_SeriesDescription, ::getSeriesDescription(type)); - // dataset->putAndInsertString(DCM_ProtocolName, "?"); + } + void DICOMExporter::initImageOrientation(ImageType aType) + { + DcmDataset* dataset = mDicomFile->getDataset(); + DcmMetaInfo* metaInfo = mDicomFile->getMetaInfo(); + dataset->putAndInsertString(DCM_ImageOrientationPatient, getImageOrientationPatient(aType).c_str()); + dataset->putAndInsertString(DCM_SeriesNumber, to_string(aType).data()); + dataset->putAndInsertString(DCM_SeriesDescription, std::string(std::string(::getSeriesDescription(aType)) + "-" + mLaterality).c_str()); + } + + std::string DICOMExporter::getImageOrientationPatient(ImageType aType) + { + switch (aType) + { + case REFL: + return "1\\0\\0\\0\\0\\-1"; + case SOS: + return "1\\0\\0\\0\\0\\-1"; + case ATT: + return "1\\0\\0\\0\\0\\-1"; + case CoronalPositioning: + return "1\\0\\0\\0\\0\\-1"; + case SagittalPositioning: + return "0\\1\\0\\0\\0\\-1"; + case TransversePositioning: + return "1\\0\\0\\0\\1\\0"; + } + } + + void DICOMExporter::initOriginPosition(ImageType aType, float* aOriginPosition, float* aPoint, int* aXYZ, float* aSpacing) + { + switch (aType) + { + case REFL: + case SOS: + case ATT: + aOriginPosition[0] = aPoint[1]*(float)1000.0; + aOriginPosition[1] = aPoint[2]*(float)1000.0; + aOriginPosition[2] = aPoint[0]*(float)1000.0; + break; + case CoronalPositioning: + aOriginPosition[0] = aPoint[1]*(float)1000.0; + aOriginPosition[1] = aPoint[2]*(float)1000.0 + (aXYZ[2] / 2 - 1) * aSpacing[2]; + aOriginPosition[2] = aPoint[0]*(float)1000.0; + break; + case SagittalPositioning: + aOriginPosition[0] = aPoint[1]*(float)1000.0 + (aXYZ[1] / 2 - 1)* aSpacing[1]; + aOriginPosition[1] = aPoint[2]*(float)1000.0; + aOriginPosition[2] = aPoint[0]*(float)1000.0; + break; + case TransversePositioning: + aOriginPosition[0] = aPoint[1]*(float)1000.0; + aOriginPosition[1] = aPoint[2]*(float)1000.0; + aOriginPosition[2] = aPoint[0]*(float)1000.0 - (aXYZ[0] / 2 - 1) * aSpacing[0]; + break; + default: + break; + } + } + + void DICOMExporter::initPixelSpacing(ImageType aType, float* aSpacing, int aRow, int aColumn) + { + DcmDataset* dataset = mDicomFile->getDataset(); + DcmMetaInfo* metaInfo = mDicomFile->getMetaInfo(); + string spacingsBP; + switch (aType) + { + case REFL: + case SOS: + case ATT: + case CoronalPositioning: + dataset->putAndInsertString(DCM_SliceThickness, to_string(aSpacing[2]).data()); + dataset->putAndInsertUint16(DCM_Rows, aRow); + dataset->putAndInsertUint16(DCM_Columns, aColumn); + spacingsBP = to_string(aSpacing[1])+"\\"+to_string(aSpacing[0]); + dataset->putAndInsertString(DCM_PixelSpacing, spacingsBP.data()); + break; + case SagittalPositioning: + dataset->putAndInsertString(DCM_SliceThickness, to_string(aSpacing[1]).data()); + dataset->putAndInsertUint16(DCM_Rows, aRow); + dataset->putAndInsertUint16(DCM_Columns, aColumn); + spacingsBP = to_string(aSpacing[2])+"\\"+to_string(aSpacing[0]); + dataset->putAndInsertString(DCM_PixelSpacing, spacingsBP.data()); + break; + case TransversePositioning: + dataset->putAndInsertString(DCM_SliceThickness, to_string(aSpacing[0]).data()); + dataset->putAndInsertUint16(DCM_Rows, aColumn);//因为旋转，必须交换row和column + dataset->putAndInsertUint16(DCM_Columns, aRow); + spacingsBP = to_string(aSpacing[1])+"\\"+to_string(aSpacing[2]); + dataset->putAndInsertString(DCM_PixelSpacing, spacingsBP.data()); + break; + } + } + + void DICOMExporter::exportDICOM(Aurora::Matrix aMatrix, ImageType type){ + int XYZ [3] = {aMatrix.getDimSize(0),aMatrix.getDimSize(1), aMatrix.getDimSize(2)}; + string path = mBasePath+"/"+::getSeriesDescription(type)+"/"; + if (!exists(path)){ + if(!mkdir(path)){ + RECON_ERROR("Fail to create dir with path {0}\r\n",path); + } + } + exportDCM(path, reflectParams::imageStartpoint.getData(), + reflectParams::imageEndpoint.getData(), XYZ, aMatrix.getData(), type, XYZ); + RECON_INFO("Save DICOM to Path:{0}, type:{1}==================>",path,(int)type); + } + + void DICOMExporter::exportDICOM(Aurora::Matrix aMatrix, const Aurora::Matrix& aOriginMatrix, ImageType type) + { + int XYZ [3] = {aMatrix.getDimSize(0),aMatrix.getDimSize(1), aMatrix.getDimSize(2)}; + int originXYZ[3] = {aOriginMatrix.getDimSize(0),aOriginMatrix.getDimSize(1), aOriginMatrix.getDimSize(2)}; + string path = mBasePath+"/"+::getSeriesDescription(type)+"/"; + if (!exists(path)){ + if(!mkdir(path)){ + RECON_ERROR("Fail to create dir with path {0}\r\n",path); + } + } + exportDCM(path, reflectParams::imageStartpoint.getData(), + reflectParams::imageEndpoint.getData(), XYZ, aMatrix.getData(), type, originXYZ); + RECON_INFO("Save DICOM to Path:{0}, type:{1}==================>",path,(int)type); + } + + void DICOMExporter::exportDCM(string path, float * startPoint, float* endPoint, int* imageXYZ,float* data, ImageType type, int* aOriginXYZ) + { + long Cols = imageXYZ[1], Rows = imageXYZ[0] ,Slices = imageXYZ[2]; + // dataset->putAndInsertString(DCM_ProtocolName, "?"); + DcmDataset* dataset = mDicomFile->getDataset(); + DcmMetaInfo* metaInfo = mDicomFile->getMetaInfo(); // initial spacing and position float spacing[3]{.0,.0,.0}; - spacing[0] = getSpacing(startPoint,endPoint,imageXYZ,0); - spacing[1] = getSpacing(startPoint,endPoint,imageXYZ,1); - spacing[2] = getSpacing(startPoint,endPoint,imageXYZ,2); - - float originPosition[3] = { - endPoint[1]*(float)1000.0, - endPoint[2]*(float)1000.0, - endPoint[0]*(float)1000.0, - }; + spacing[0] = getSpacing(startPoint,endPoint,aOriginXYZ,0); + spacing[1] = getSpacing(startPoint,endPoint,aOriginXYZ,1); + spacing[2] = getSpacing(startPoint,endPoint,aOriginXYZ,2); + float originPosition[3]; + initOriginPosition(type, originPosition, endPoint, aOriginXYZ, spacing); + initPixelSpacing(type, spacing, Rows, Cols); float originLocation =-endPoint[2]*1000.0; - dataset->putAndInsertString(DCM_SliceThickness, to_string(spacing[2]).data()); - dataset->putAndInsertUint16(DCM_Rows, Rows); - dataset->putAndInsertUint16(DCM_Columns, Cols); - string spacingsBP = to_string(spacing[0])+"\\"+to_string(spacing[1]); - dataset->putAndInsertString(DCM_PixelSpacing, spacingsBP.data()); // initial data, wwwl , Slope,Intercept float Slope = 1, Intercept = 0 ; size_t size = Rows*Cols*Slices; - ushort* udata = new ushort[size]{0}; float min = data[0]; float max = data[0]; for (size_t i = 0; i < size; i++) @@ -234,10 +390,6 @@ namespace Recon long windowCenter = min + (max-min)/2, windowWidth = max-min; float dSlope = 1.0/(pow(2,16)/windowWidth); float dIntercept = min; - for (size_t i = 0; i < size; i++) - { - udata[i] = (ushort)((data[i] - min)/dSlope); - } if (type !=0){ Slope = dSlope; Intercept = dIntercept; @@ -246,19 +398,29 @@ namespace Recon windowCenter = (windowCenter-min)/dSlope; windowWidth = (windowWidth-min)/dSlope; } + initImageOrientation(type); + dcmGenerateUniqueIdentifier(mSeriesInstanceUID,SITE_SERIES_UID_ROOT); + dataset->putAndInsertString(DCM_SeriesInstanceUID, mSeriesInstanceUID); dataset->putAndInsertString(DCM_WindowCenter, to_string(windowCenter).data()); dataset->putAndInsertString(DCM_WindowWidth, to_string(windowWidth).data()); dataset->putAndInsertString(DCM_RescaleSlope, to_string(Slope).data()); dataset->putAndInsertString(DCM_RescaleIntercept, to_string(Intercept).data()); size_t sliceSize = Rows*Cols; + ushort* udata = new ushort[sliceSize]{0}; for (size_t i = 0; i < Slices; i++) { + Aurora::Matrix image = Aurora::Matrix::copyFromRawData(data + i * sliceSize, Rows, Cols); + Aurora::Matrix dicomImage = transferToDicomType(image, type); + for (size_t i = 0; i < sliceSize; i++) + { + udata[i] = (ushort)((dicomImage[i] - min)/dSlope); + } dataset->putAndInsertString(DCM_AccessionNumber, mPatientData.getAccessionNumber().data()); dataset->putAndInsertString(DCM_InstanceNumber, to_string(i).data()); - string pos = to_string(originPosition[1] ) + "\\" + - to_string(originPosition[2]+ i * spacing[2]) + "\\" + - to_string(originPosition[0]); + string pos = to_string(originPosition[0] ) + "\\" + + to_string(originPosition[1]+ i * spacing[2]) + "\\" + + to_string(originPosition[2]); dataset->putAndInsertString(DCM_ImagePositionPatient, pos.data()); string loc = to_string(originLocation + i * spacing[2]); dataset->putAndInsertString(DCM_SliceLocation, loc.data()); @@ -268,13 +430,13 @@ namespace Recon dcmGenerateUniqueIdentifier(SOP_UID, SITE_INSTANCE_UID_ROOT); metaInfo->putAndInsertString(DCM_MediaStorageSOPInstanceUID, SOP_UID); dataset->putAndInsertString(DCM_SOPInstanceUID, SOP_UID); - - dataset->putAndInsertUint16Array(DCM_PixelData, udata + sliceSize * i, + + dataset->putAndInsertUint16Array(DCM_PixelData, udata, sliceSize); string path2 = path+to_string(i)+".dcm"; OFFilename file ; file = path2.data(); - auto status =dcmFile.saveFile(file, EXS_LittleEndianExplicit); + auto status =mDicomFile->saveFile(file, EXS_LittleEndianExplicit); if(status.bad()) { RECON_ERROR("Save dicom file {0} fail, beacuse of {1}\r\n",path2.data(),status.text()); @@ -283,5 +445,6 @@ namespace Recon RECON_INFO("Save dicom file {0} \r\n",path2.data()); } } + delete udata; } } \ No newline at end of file diff --git a/src/common/DICOMExporter.h b/src/common/DICOMExporter.h index 80d0567..ae74470 100644 --- a/src/common/DICOMExporter.h +++ b/src/common/DICOMExporter.h @@ -7,6 +7,10 @@ #include "Parser/Data/PatientData.h" #include "Parser/Data/MetaData.h" +class DcmDataset; +class DcmMetaInfo; +class DcmFileFormat; + namespace Recon { class DICOMExporter @@ -15,7 +19,10 @@ public: enum ImageType{ REFL, SOS, - ATT + ATT, + CoronalPositioning, + SagittalPositioning, + TransversePositioning }; explicit DICOMExporter(const PatientData& aPatientData, const MetaData& aMetaData); //仅仅用于测试！！！ @@ -27,14 +34,25 @@ public: ~DICOMExporter(); void setExportBasePath(const std::string & path); void exportDICOM(Aurora::Matrix aMatrix, ImageType type); + void exportDICOM(Aurora::Matrix aMatrix, const Aurora::Matrix& aOriginMatrix, ImageType type); + private: std::string mBasePath; std::string mStudyDate; std::string mStudyTime; std::string mStudyInstanceUID; + std::string mLaterality; + char mFrameOfReferenceUID[100]={0}; char mSeriesInstanceUID[100]={0}; PatientData mPatientData; - void exportDCM(std::string path, float * startPoint, float* endPoint, int* imageXYZ,float* data, int type); + DcmFileFormat* mDicomFile; + void exportDCM(std::string path, float * startPoint, float* endPoint, int* imageXYZ,float* data, ImageType type, int* aOriginXYZ); + std::string getImageOrientationPatient(DICOMExporter::ImageType aType); + void initialDicomFile(); + void initImageOrientation(ImageType aType); + void initOriginPosition(ImageType aType, float* aOriginPosition, float* aPoint, int* aXYZ, float* aSpacing); + void initPixelSpacing(ImageType aType, float* aSpacing, int aRow, int aColumn); + };