// Author: Yuan Li

#include <hdf/HDFScanDataWriter.hpp>

void HDFScanDataWriter::CreateAcqParamsGroup()
{
    if (acqParamsGroup.Initialize(scanDataGroup, "AcqParams") == 0) {
        std::cout << "ERROR could not create /ScanData/AcqParams." << std::endl;
        std::exit(EXIT_FAILURE);
    }
    frameRateAtom.Create(acqParamsGroup.group, "FrameRate");
    numFramesAtom.Create(acqParamsGroup.group, "NumFrames");
    whenStartedAtom.Create(acqParamsGroup.group, "WhenStarted");
}

void HDFScanDataWriter::CreateDyeSetGroup()
{
    if (dyeSetGroup.Initialize(scanDataGroup, "DyeSet") == 0) {
        std::cout << "ERROR could not create /ScanData/DyeSet." << std::endl;
        std::exit(EXIT_FAILURE);
    }
    baseMapAtom.Create(dyeSetGroup.group, PacBio::AttributeNames::ScanData::DyeSet::basemap);
    numAnalogAtom.Create(dyeSetGroup.group, "NumAnalog");
}

void HDFScanDataWriter::CreateRunInfoGroup()
{
    if (runInfoGroup.Initialize(scanDataGroup, "RunInfo") == 0) {
        std::cout << "ERROR, could not create /ScanDta/RunInfo." << std::endl;
        std::exit(EXIT_FAILURE);
    }
    movieNameAtom.Create(runInfoGroup.group, "MovieName");
    platformIdAtom.Create(runInfoGroup.group, "PlatformId");
    platformNameAtom.Create(runInfoGroup.group, "PlatformName");
    instrumentNameAtom.Create(runInfoGroup.group, "InstrumentName");
    runCodeAtom.Create(runInfoGroup.group, "RunCode");
    bindingKitAtom.Create(runInfoGroup.group, "BindingKit");
    sequencingKitAtom.Create(runInfoGroup.group, "SequencingKit");
}

HDFScanDataWriter::HDFScanDataWriter(HDFFile& _outFile) { Initialize(_outFile.rootGroup); }

HDFScanDataWriter::HDFScanDataWriter(HDFGroup& _rootGroup) { Initialize(_rootGroup); }

HDFScanDataWriter::~HDFScanDataWriter() { this->Close(); }

int HDFScanDataWriter::Initialize(HDFGroup& _rootGroup)
{
    rootGroupPtr = &(_rootGroup);
    rootGroupPtr->AddGroup("ScanData");
    if (scanDataGroup.Initialize(*(rootGroupPtr), "ScanData") == 0) {
        std::cout << "ERROR, could not create /ScanData group." << std::endl;
        std::exit(EXIT_FAILURE);
    }
    scanDataGroup.AddGroup("AcqParams");
    scanDataGroup.AddGroup("DyeSet");
    scanDataGroup.AddGroup("RunInfo");

    CreateAcqParamsGroup();
    CreateDyeSetGroup();
    CreateRunInfoGroup();

    return 1;
}

void HDFScanDataWriter::Write(const ScanData& scanData)
{
    const float DEFAULT_FRAMERATE = 75.0;
    const unsigned int DEFAULT_NUMFRAMES = 1000000;
    const std::string DEFAULT_DATE = "2013-01-01T01:01:01";
    const uint16_t DEFAULT_NUMANALOG = 4;
    const std::string DEFAULT_MOVIENAME = "simulated_movie";
    const std::string DEFAULT_RUNCODE = "simulated_runcode";

    WriteFrameRate((scanData.frameRate == 0) ? (DEFAULT_FRAMERATE) : (scanData.frameRate));
    WriteNumFrames((scanData.numFrames == 0) ? (DEFAULT_NUMFRAMES) : (scanData.numFrames));
    WriteWhenStarted((scanData.whenStarted.empty()) ? (DEFAULT_DATE) : (scanData.whenStarted));

    // Base map is VITAL, must be specified
    if (scanData.BaseMapStr().empty()) {
        assert("ScanData/DyeSet attribute BaseMap MUST be specified." == 0);
    }
    WriteBaseMap(scanData.BaseMapStr());
    WriteNumAnalog(DEFAULT_NUMANALOG);

    WriteMovieName((scanData.movieName.empty() ? (DEFAULT_MOVIENAME) : scanData.movieName));
    WriteRunCode((scanData.runCode.empty()) ? (DEFAULT_RUNCODE) : (scanData.runCode));
    WritePlatformId((scanData.platformId == NoPlatform) ? (Springfield) : (scanData.platformId));

    WriteBindingKit(scanData.BindingKit());
    WriteSequencingKit(scanData.SequencingKit());
    _WriteAcqParams(scanData.GetAcqParams());
}

void HDFScanDataWriter::_WriteAcqParams(const AcqParams& acqParams)
{
    _WriteAduGain(acqParams.aduGain_);
    _WriteCameraGain(acqParams.cameraGain_);
    _WriteCameraType(acqParams.cameraType_);
    _WriteHotStartFrame(acqParams.hotStartFrame_);
    _WriteLaserOnFrame(acqParams.laserOnFrame_);
}

void HDFScanDataWriter::WriteFrameRate(const float frameRate)
{
    // Write /ScanData/AcqParams/FrameRate attribute.
    frameRateAtom.Write(frameRate);
}

void HDFScanDataWriter::WriteNumFrames(const unsigned int numFrames)
{
    // Write /ScanData/AcqParams/NumFrames attribute.
    numFramesAtom.Write(numFrames);
}

void HDFScanDataWriter::WriteWhenStarted(const std::string whenStarted)
{
    // Write /ScanData/AcqParams/WhenStarted attribute.
    whenStartedAtom.Write(whenStarted);
}

void HDFScanDataWriter::_WriteAduGain(const float aduGain)
{
    HDFAtom<float> aduGainAtom;
    aduGainAtom.Create(acqParamsGroup.group, "AduGain");
    aduGainAtom.Write(aduGain);
    aduGainAtom.Close();
}

void HDFScanDataWriter::_WriteCameraGain(const float cameraGain)
{
    HDFAtom<float> cameraGainAtom;
    cameraGainAtom.Create(acqParamsGroup.group, "CameraGain");
    cameraGainAtom.Write(cameraGain);
    cameraGainAtom.Close();
}

void HDFScanDataWriter::_WriteCameraType(const int cameraType)
{
    HDFAtom<int> cameraTypeAtom;
    cameraTypeAtom.Create(acqParamsGroup.group, "CameraType");
    cameraTypeAtom.Write(cameraType);
    cameraTypeAtom.Close();
}

void HDFScanDataWriter::_WriteHotStartFrame(const UInt hotStartFrame)
{
    HDFAtom<UInt> hotStartFrameAtom;
    hotStartFrameAtom.Create(acqParamsGroup.group, "HotStartFrame");
    hotStartFrameAtom.Write(hotStartFrame);
    hotStartFrameAtom.Close();
}

void HDFScanDataWriter::_WriteLaserOnFrame(const UInt laserOnFrame)
{
    HDFAtom<UInt> laserOnFrameAtom;
    laserOnFrameAtom.Create(acqParamsGroup.group, "LaserOnFrame");
    laserOnFrameAtom.Write(laserOnFrame);
    laserOnFrameAtom.Close();
}

void HDFScanDataWriter::WriteBaseMap(const std::string baseMapStr)
{
    //Write /ScanData/DyeSet/BaseMap attribute.
    baseMapAtom.Write(baseMapStr);
}

void HDFScanDataWriter::WriteNumAnalog(const uint16_t numAnalog)
{
    //Write /ScanData/DyeSet/NumAnalog attribute.
    numAnalogAtom.Write(numAnalog);
}

void HDFScanDataWriter::WritePlatformId(const PlatformId id)
{
    //Write /ScanData/RunInfo/Platform attribute.
    std::string name, instrumentName;
    if (id == Springfield) {
        name = "Springfield";
        instrumentName = name;
    } else if (id == Sequel) {
        name = "SequelAlpha";
        instrumentName = "sequel";
    } else if (id == Astro) {
        name = "Astro";
        instrumentName = name;
    } else {
        name = "Unknown";
    }
    platformIdAtom.Write(id);
    platformNameAtom.Write(name);
    instrumentNameAtom.Write(instrumentName);
}

void HDFScanDataWriter::WriteMovieName(const std::string movieName)
{
    //Write /ScanData/RunInfo/MovieName attribute.
    movieNameAtom.Write(movieName);
}

void HDFScanDataWriter::WriteRunCode(const std::string runCode)
{
    //Write /ScanData/RunInfo/MovieName attribute.
    runCodeAtom.Write(runCode);
}

void HDFScanDataWriter::WriteBindingKit(const std::string& bindingKit)
{
    bindingKitAtom.Write(bindingKit);
}

void HDFScanDataWriter::WriteSequencingKit(const std::string& sequencingKit)
{
    sequencingKitAtom.Write(sequencingKit);
}

void HDFScanDataWriter::Close()
{
    // Close /ScanData/AcqParams attributes.
    whenStartedAtom.Close();
    frameRateAtom.Close();
    numFramesAtom.Close();

    // Close /ScanData/DyeSet attributes.
    baseMapAtom.Close();

    // Close /ScanData/RunInfo attributes.
    movieNameAtom.Close();
    runCodeAtom.Close();
    platformIdAtom.Close();
    platformNameAtom.Close();
    instrumentNameAtom.Close();
    bindingKitAtom.Close();
    sequencingKitAtom.Close();

    // Close /ScanData/AcqParams|DyeSet|RunInfo.
    acqParamsGroup.Close();
    dyeSetGroup.Close();
    runInfoGroup.Close();

    // Close /ScanData
    scanDataGroup.Close();
}