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// Author: Yuan Li
#ifndef DATA_HDF_HDF_SCAN_DATA_WRITER_H_
#define DATA_HDF_HDF_SCAN_DATA_WRITER_H_
#include <iostream>
#include <string>
#include <pbdata/Enumerations.h>
#include <hdf/HDFAtom.hpp>
#include <hdf/HDFFile.hpp>
#include <hdf/HDFGroup.hpp>
#include <pbdata/reads/AcqParams.hpp>
#include <pbdata/reads/ScanData.hpp>
class HDFScanDataWriter
{
private:
HDFGroup* rootGroupPtr;
HDFGroup scanDataGroup;
HDFGroup acqParamsGroup;
HDFGroup dyeSetGroup;
HDFGroup runInfoGroup;
HDFAtom<std::string> whenStartedAtom;
HDFAtom<float> frameRateAtom;
HDFAtom<unsigned int> numFramesAtom;
HDFAtom<std::string> baseMapAtom;
HDFAtom<uint16_t> numAnalogAtom;
HDFAtom<std::string> movieNameAtom;
HDFAtom<std::string> runCodeAtom;
HDFAtom<std::string> bindingKitAtom;
HDFAtom<std::string> sequencingKitAtom;
HDFAtom<unsigned int> platformIdAtom;
HDFAtom<std::string> platformNameAtom;
HDFAtom<std::string> instrumentNameAtom;
void CreateAcqParamsGroup();
void CreateDyeSetGroup();
void CreateRunInfoGroup();
public:
HDFScanDataWriter(HDFFile& _outFile);
HDFScanDataWriter(HDFGroup& _rootGroup);
~HDFScanDataWriter();
int Initialize(HDFGroup& _rootGroup);
void Write(const ScanData& scanData);
void Write(const ScanData& scanData, const AcqParams& acqParam);
void WriteFrameRate(const float frameRate);
void WriteNumFrames(const unsigned int numFrames);
void WriteWhenStarted(const std::string whenStarted);
void Close();
private:
void WriteBaseMap(const std::string baseMapStr);
void WriteNumAnalog(const uint16_t numAnalog);
void WritePlatformId(const PlatformId id);
void WriteMovieName(const std::string movieName);
void WriteRunCode(const std::string runCode);
void WriteBindingKit(const std::string& bindingKit);
void WriteSequencingKit(const std::string& sequencingKit);
private:
/// Write attributes to /ScanData/AcqParams
void _WriteAcqParams(const AcqParams& acqParams);
void _WriteAduGain(const float aduGain);
void _WriteCameraGain(const float cameraGain);
void _WriteCameraType(const int cameraType);
void _WriteHotStartFrame(const UInt hotStartFrame);
void _WriteLaserOnFrame(const UInt laserOnFrame);
};
#endif
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