287 lines
12 KiB
C++
287 lines
12 KiB
C++
#include "DICOMExporter.h"
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#include <cstddef>
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#include <cstdio>
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#include <string>
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#include <sys/types.h>
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#include <dcmtk/dcmdata/dcdeftag.h>
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#include <dcmtk/dcmdata/dcfilefo.h>
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#include <dcmtk/dcmdata/dcuid.h>
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#include <dcmtk/ofstd/offile.h>
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#include <dcmtk/dcmdata/dctk.h>
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#include "fileHelper.h"
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#include "config/config.h"
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#include "log/log.h"
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using namespace std;
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namespace {
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float getSpacing(float * startPoint, float* endPoint, int* imageXYZ, int index){
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return (endPoint[index]-startPoint[index])/(float)(imageXYZ[index])*1000.0;
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}
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void initialDicomFile(DcmDataset* aDataset,DcmMetaInfo* aMetaInfo)
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{
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aMetaInfo->putAndInsertString(DCM_MediaStorageSOPClassUID,
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UID_CTImageStorage);
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aDataset->putAndInsertString(DCM_SOPClassUID, UID_CTImageStorage);
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aDataset->putAndInsertString(DCM_TransferSyntaxUID,
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UID_LittleEndianImplicitTransferSyntax);
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aDataset->putAndInsertString(DCM_ImageType, "ORIGINAL\\PRIMARY");
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aDataset->putAndInsertString(DCM_Manufacturer, "EQ9");
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aDataset->putAndInsertString(DCM_PatientOrientation, "L\\H");
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aDataset->putAndInsertString(DCM_PatientPosition, "HFP");
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aDataset->putAndInsertString(DCM_ImageOrientationPatient, "1\\0\\0\\0\\0\\1");
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aDataset->putAndInsertString(DCM_StudyDescription, "USCT BREAST");
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aDataset->putAndInsertString(DCM_ManufacturerModelVersion, "USCT3DV3");
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aDataset->putAndInsertString(DCM_SamplesPerPixel, "1");
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aDataset->putAndInsertString(DCM_PixelRepresentation, "0");
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aDataset->putAndInsertString(DCM_BitsAllocated, "16");
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aDataset->putAndInsertString(DCM_BitsStored, "16");
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aDataset->putAndInsertString(DCM_HighBit, "15");
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aDataset->putAndInsertString(DCM_PhotometricInterpretation, "MONOCHROME2");
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aDataset->putAndInsertString(DCM_KVP, "0");
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}
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void initialDate(DcmDataset* aDataset,const std::string& aStudyDate )
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{
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aDataset->putAndInsertString(DCM_StudyDate, aStudyDate.data());
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OFDateTime currentDateTime;
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currentDateTime.setCurrentDateTime();
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OFString date;
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currentDateTime.getDate().getISOFormattedDate(date,false);
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aDataset->putAndInsertString(DCM_SeriesDate, aStudyDate.data());
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aDataset->putAndInsertString(DCM_AcquisitionDate, aStudyDate.data());
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aDataset->putAndInsertString(DCM_ContentDate, date.data());
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}
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void initialSeriesTime(DcmDataset* aDataset,const std::string& aStudyTime){
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// 获取当前日期和时间（UTC时间）
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OFDateTime currentDateTime;
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currentDateTime.setCurrentDateTime();
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OFString time;
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currentDateTime.getTime().getISOFormattedTime(time,true,false,false,false);
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aDataset->putAndInsertString(DCM_SeriesTime, aStudyTime.data());
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aDataset->putAndInsertString(DCM_AcquisitionTime, aStudyTime.data());
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aDataset->putAndInsertString(DCM_ContentTime, time.data());
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}
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const char* SeriesDescriptions[3]={"REFL","SOS","ATT"};
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const char* getSeriesDescription(int type){
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return SeriesDescriptions[type];
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}
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}
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namespace Recon
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{
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DICOMExporter::DICOMExporter(const PatientData& aPatientData, const MetaData& aMetaData)
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{
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mPatientData = aPatientData;
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//prepare Study
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if (aPatientData.getStudyUID().empty()){
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char tempStr [100] = {0};
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dcmGenerateUniqueIdentifier(tempStr,SITE_STUDY_UID_ROOT);
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mStudyInstanceUID.append(tempStr);
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}
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else{
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mStudyInstanceUID = aPatientData.getStudyUID();
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}
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std::string measurementID = aMetaData.getMeasurementID();
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unsigned long dateIndex = measurementID.find('_');
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unsigned long timeIndex = measurementID.find('T');
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OFDateTime currentDateTime;
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currentDateTime.setCurrentDateTime();
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if(dateIndex== std::string::npos || measurementID.length()-dateIndex<=8){
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OFString date;
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currentDateTime.getDate().getISOFormattedDate(date,false);
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mStudyDate = date.data();
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}
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else{
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mStudyDate = measurementID.substr(dateIndex+1,8);
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}
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if(timeIndex== std::string::npos || measurementID.length()-timeIndex<=6){
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OFString time;
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currentDateTime.getTime().getISOFormattedTime(time,true,false,false,false);
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mStudyTime = time.data();
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}
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else{
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mStudyTime = measurementID.substr(timeIndex+1,6);
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}
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}
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DICOMExporter::DICOMExporter()
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{
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//prepare Study
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char tempStr [100] = {0};
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dcmGenerateUniqueIdentifier(tempStr,SITE_STUDY_UID_ROOT);
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mStudyInstanceUID.append(tempStr);
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OFDateTime currentDateTime;
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currentDateTime.setCurrentDateTime();
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OFString date;
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currentDateTime.getDate().getISOFormattedDate(date,false);
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OFString time;
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currentDateTime.getTime().getISOFormattedTime(time,true,false,false,false);
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mStudyDate = date.data();
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mStudyTime = time.data();
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}
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DICOMExporter::~DICOMExporter()
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{
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}
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void DICOMExporter::setExportBasePath(const std::string & path)
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{
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mBasePath = path;
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}
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void DICOMExporter::exportDICOM(Aurora::Matrix aMatrix, ImageType type){
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int XYZ [3] = {aMatrix.getDimSize(0),aMatrix.getDimSize(1), aMatrix.getDimSize(2)};
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string path = mBasePath+"/"+::getSeriesDescription(type)+"/";
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if (!exists(path)){
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if(!mkdir(path)){
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RECON_ERROR("Fail to create dir with path {0}\r\n",path);
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}
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}
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exportDCM(path, reflectParams::imageStartpoint.getData(),
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reflectParams::imageEndpoint.getData(), XYZ, aMatrix.getData(), type);
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RECON_INFO("Save DICOM to Path:{0}, type:{1}==================>",path,(int)type);
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}
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void DICOMExporter::exportDCM(string path, float * startPoint, float* endPoint, int* imageXYZ,float* data, int type)
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{
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long Rows = imageXYZ[1], Cols = imageXYZ[0] ,Slices = imageXYZ[2];
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DcmFileFormat dcmFile;
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DcmDataset* dataset = dcmFile.getDataset();
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DcmMetaInfo* metaInfo = dcmFile.getMetaInfo();
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initialDicomFile(dataset,metaInfo);
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dataset->putAndInsertString(DCM_SpecificCharacterSet, "ISO_IR 192");
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dataset->putAndInsertString(DCM_StudyInstanceUID, mStudyInstanceUID.data());
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dcmGenerateUniqueIdentifier(mSeriesInstanceUID,SITE_SERIES_UID_ROOT);
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dataset->putAndInsertString(DCM_SeriesInstanceUID, mSeriesInstanceUID);
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dataset->putAndInsertString(DCM_FrameOfReferenceUID, mSeriesInstanceUID);
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::initialDate(dataset, mStudyDate);
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dataset->putAndInsertString(DCM_StudyTime, mStudyTime.data());
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::initialSeriesTime(dataset, mStudyTime);
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dataset->putAndInsertString(DCM_Modality, mPatientData.getModality().empty()?
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"CT":mPatientData.getModality().data());
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dataset->putAndInsertString(DCM_InstitutionName, mPatientData.getInstituationName().empty()?
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"":mPatientData.getInstituationName().data());
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dataset->putAndInsertString(DCM_InstitutionAddress, mPatientData.getInstituationAddress().empty()?
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"":mPatientData.getInstituationAddress().data());
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dataset->putAndInsertString(DCM_ReferringPhysicianName,mPatientData.getReferringPhysicianName().empty()?
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"": mPatientData.getReferringPhysicianName().data());
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dataset->putAndInsertString(DCM_PatientName, mPatientData.getPatientName().empty()?
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"TestPatient":mPatientData.getPatientName().data());
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dataset->putAndInsertString(DCM_PatientSex, mPatientData.getPatientSex().data());
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dataset->putAndInsertString(DCM_PatientBirthDate, mPatientData.getPatientBirthDate().data());
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dataset->putAndInsertString(DCM_PatientID, mPatientData.getPatientID().empty()?
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"TestPatID":mPatientData.getPatientID().data());
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dataset->putAndInsertString(DCM_Laterality, mPatientData.getLaterality().data());
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dataset->putAndInsertString(DCM_StudyID, mStudyTime.data());
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dataset->putAndInsertString(DCM_SeriesNumber, to_string(type).data());
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dataset->putAndInsertString(DCM_SeriesDescription, ::getSeriesDescription(type));
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// dataset->putAndInsertString(DCM_ProtocolName, "?");
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// initial spacing and position
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float spacing[3]{.0,.0,.0};
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spacing[0] = getSpacing(startPoint,endPoint,imageXYZ,0);
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spacing[1] = getSpacing(startPoint,endPoint,imageXYZ,1);
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spacing[2] = getSpacing(startPoint,endPoint,imageXYZ,2);
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float originPosition[3] = {
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endPoint[1]*(float)1000.0,
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endPoint[2]*(float)1000.0,
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endPoint[0]*(float)1000.0,
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};
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float originLocation =-endPoint[2]*1000.0;
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dataset->putAndInsertString(DCM_SliceThickness, to_string(spacing[2]).data());
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dataset->putAndInsertUint16(DCM_Rows, Rows);
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dataset->putAndInsertUint16(DCM_Columns, Cols);
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string spacingsBP = to_string(spacing[0])+"\\"+to_string(spacing[1]);
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dataset->putAndInsertString(DCM_PixelSpacing, spacingsBP.data());
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// initial data, wwwl , Slope,Intercept
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float Slope = 1, Intercept = 0 ;
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size_t size = Rows*Cols*Slices;
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ushort* udata = new ushort[size]{0};
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float min = data[0];
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float max = data[0];
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for (size_t i = 0; i < size; i++)
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{
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if (type == 0) data[i] = 1000*data[i];
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if (min > data[i]) min = data[i];
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if (max < data[i]) max = data[i];
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}
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long windowCenter = min + (max-min)/2, windowWidth = max-min;
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float dSlope = 1.0/(pow(2,16)/windowWidth);
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float dIntercept = min;
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for (size_t i = 0; i < size; i++)
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{
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udata[i] = (ushort)((data[i] - min)/dSlope);
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}
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if (type !=0){
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Slope = dSlope;
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Intercept = dIntercept;
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}
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else{
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windowCenter = (windowCenter-min)/dSlope;
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windowWidth = (windowWidth-min)/dSlope;
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}
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dataset->putAndInsertString(DCM_WindowCenter, to_string(windowCenter).data());
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dataset->putAndInsertString(DCM_WindowWidth, to_string(windowWidth).data());
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dataset->putAndInsertString(DCM_RescaleSlope, to_string(Slope).data());
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dataset->putAndInsertString(DCM_RescaleIntercept, to_string(Intercept).data());
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size_t sliceSize = Rows*Cols;
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for (size_t i = 0; i < Slices; i++)
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{
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dataset->putAndInsertString(DCM_AccessionNumber, mPatientData.getAccessionNumber().data());
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dataset->putAndInsertString(DCM_InstanceNumber, to_string(i).data());
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string pos = to_string(originPosition[1] ) + "\\" +
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to_string(originPosition[2]+ i * spacing[2]) + "\\" +
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to_string(originPosition[0]);
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dataset->putAndInsertString(DCM_ImagePositionPatient, pos.data());
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string loc = to_string(originLocation + i * spacing[2]);
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dataset->putAndInsertString(DCM_SliceLocation, loc.data());
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// set SOPInstanceUID
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char SOP_UID[100] = {0};
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dcmGenerateUniqueIdentifier(SOP_UID, SITE_INSTANCE_UID_ROOT);
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metaInfo->putAndInsertString(DCM_MediaStorageSOPInstanceUID, SOP_UID);
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dataset->putAndInsertString(DCM_SOPInstanceUID, SOP_UID);
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dataset->putAndInsertUint16Array(DCM_PixelData, udata + sliceSize * i,
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sliceSize);
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string path2 = path+to_string(i)+".dcm";
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OFFilename file ;
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file = path2.data();
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auto status =dcmFile.saveFile(file, EXS_LittleEndianExplicit);
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if(status.bad())
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{
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RECON_ERROR("Save dicom file {0} fail, beacuse of {1}\r\n",path2.data(),status.text());
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}
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else{
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RECON_INFO("Save dicom file {0} \r\n",path2.data());
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}
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}
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}
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} |