cxUsReconstructionFileMaker.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.
                 
Copyright (c) SINTEF Department of Medical Technology.
All rights reserved.
                 
CustusX is released under a BSD 3-Clause license.
                 
See Lisence.txt (https://github.com/SINTEFMedtek/CustusX/blob/master/License.txt) for details.
=========================================================================*/

#include "cxUsReconstructionFileMaker.h"

#include <QTextStream>
#include <QDir>
#include <QFile>
#include <QFileInfo>
#include <vtkImageChangeInformation.h>
#include <vtkImageData.h>
#include "vtkImageAppend.h"
#include "vtkMetaImageWriter.h"
#include "cxTypeConversions.h"
#include "cxLogger.h"
#include "cxSettings.h"
#include "cxXmlOptionItem.h"
#include "cxTimeKeeper.h"
#include "cxDataReaderWriter.h"
#include "cxUSFrameData.h"
#include "cxSavingVideoRecorder.h"
#include "cxImageDataContainer.h"
#include "cxUSReconstructInputDataAlgoritms.h"
#include "cxCustomMetaImage.h"
#include "cxErrorObserver.h"


typedef vtkSmartPointer<vtkImageAppend> vtkImageAppendPtr;

namespace cx
{

UsReconstructionFileMaker::UsReconstructionFileMaker(QString sessionDescription) :
    mSessionDescription(sessionDescription)
{
}

UsReconstructionFileMaker::~UsReconstructionFileMaker()
{
}

USReconstructInputData UsReconstructionFileMaker::getReconstructData()
{
        return mReconstructData;
}

USReconstructInputData UsReconstructionFileMaker::getReconstructData(ImageDataContainerPtr imageData,
                                                                                                                                         std::vector<TimeInfo> imageTimestamps,
                                                                                                                                         TimedTransformMap trackerRecordedData,
                                                                                                                                         std::map<double, ToolPositionMetadata> trackerRecordedMetadata,
                                                                                                                                         std::map<double, ToolPositionMetadata> referenceRecordedMetadata,
                                                                                                                                         ToolPtr tool, QString streamUid,
                                                                                                                                         bool writeColor, Transform3D rMpr)
{
        if(trackerRecordedData.empty())
                reportWarning("No tracking data for writing to reconstruction file.");

        USReconstructInputData retval;

        retval.mFilename = mSessionDescription; // not saved yet - no filename
        retval.mUsRaw = USFrameData::create(mSessionDescription, imageData);
        retval.rMpr = rMpr;
        retval.mTrackerRecordedMetadata = trackerRecordedMetadata;
        retval.mReferenceRecordedMetadata = referenceRecordedMetadata;

        for (TimedTransformMap::iterator it = trackerRecordedData.begin(); it != trackerRecordedData.end(); ++it)
        {
                TimedPosition current;
                current.mTime = it->first;
                current.mTimeInfo.setAcquisitionTime(it->first);
                current.mPos = it->second;
                retval.mPositions.push_back(current);
        }

        std::vector<TimeInfo> fts = imageTimestamps;
        for (unsigned i=0; i<fts.size(); ++i)
        {
                TimedPosition current;
                current.mTimeInfo = fts[i];
                current.mTime = current.mTimeInfo.getAcquisitionTime();
                current.mPos = Transform3D::Identity();
                // current.mPos = not written - will be found from track positions during reconstruction.
                retval.mFrames.push_back(current);
        }

        if (tool && tool->getProbe())
        {
                retval.mProbeDefinition.setData(tool->getProbe()->getProbeDefinition(streamUid));
        }

        if (tool)
                retval.mProbeUid = tool->getUid();

        this->fillFramePositions(&retval);

        return retval;
}

void UsReconstructionFileMaker::fillFramePositions(USReconstructInputData* data) const
{
        cx::USReconstructInputDataAlgorithm::interpolateFramePositionsFromTracking(data);
        cx::USReconstructInputDataAlgorithm::transformFramePositionsTo_rMu(data);
}

bool UsReconstructionFileMaker::writeTrackerTimestamps(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
{
        return this->writeTimestamps(reconstructionFolder+"/"+session+".tts",
                                                                 ts, "tracking timestamps");
}

bool UsReconstructionFileMaker::writeUSTimestamps(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
{
        bool retval = true;

        retval = this->writeTimestamps(reconstructionFolder+"/"+session+".fts",
                                                                 ts, "frame timestamps", Modified);

        retval &= this->writeTimestamps(reconstructionFolder+"/"+session+".scanner.frameTimestamps",
                                                                 ts, "frame scanner timestamps", Scanner);

        retval &= this->writeTimestamps(reconstructionFolder+"/"+session+".softwareArrive.frameTimestamps",
                                                                 ts, "frame arrive in software timestamps", SoftwareArrive);
        return retval;
}

bool UsReconstructionFileMaker::writeTimestamps(QString filename, std::vector<TimedPosition> ts, QString type, TimeStampType timeStampType)
{
        bool success = false;

        QFile file(filename);
        if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
        {
                reportError("Cannot open "+file.fileName());
                return success;
        }
        QTextStream stream(&file);

        for (unsigned i=0; i<ts.size(); ++i)
        {
                switch(timeStampType)
                {
                case Modified:
                        stream << qstring_cast(ts[i].mTimeInfo.getAcquisitionTime());
                        break;
                case SoftwareArrive:
                        stream << qstring_cast(ts[i].mTimeInfo.getSoftwareAcquisitionTime());
                        break;
                case Scanner:
                        stream << qstring_cast(ts[i].mTimeInfo.getScannerAcquisitionTime());
                        break;
                default:
                        stream << qstring_cast(ts[i].mTime); // Is the same as mTimeInfo.getAcquisitionTime()
                        break;
                }
                stream << endl;
        }
        file.close();
        success = true;

        QFileInfo info(file);
        mReport << QString("%1, %2 bytes, %3 %4.")
                           .arg(info.fileName())
                           .arg(info.size())
                           .arg(ts.size())
                           .arg(type);
//      mReport << info.fileName()+", "+qstring_cast(info.size())+" bytes, "+qstring_cast(ts.size())+" frame timestamps.";

        return success;
}

bool UsReconstructionFileMaker::writeUSTransforms(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
{
        return this->writeTransforms(reconstructionFolder+"/"+session+".fp", ts, "frame transforms rMu");
}

bool UsReconstructionFileMaker::writeTrackerMetadata(QString reconstructionFolder, QString session, const std::map<double, ToolPositionMetadata>& ts)
{
        QString filename = reconstructionFolder+"/"+session+".probe.toolmeta";
        return this->writeMetadata(filename, ts, "tracker metadata");
}

bool UsReconstructionFileMaker::writeReferenceMetadata(QString reconstructionFolder, QString session, const std::map<double, ToolPositionMetadata>& ts)
{
        QString filename = reconstructionFolder+"/"+session+".ref.toolmeta";
        return this->writeMetadata(filename, ts, "tracker metadata");
}

bool UsReconstructionFileMaker::writeMetadata(QString filename, const std::map<double, ToolPositionMetadata>& ts, QString type)
{
        bool success = false;
        QFile file(filename);
        if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
        {
                reportError("Cannot open "+file.fileName());
                return success;
        }
        QTextStream stream(&file);

        for (std::map<double, ToolPositionMetadata>::const_iterator i=ts.begin(); i!=ts.end(); ++i)
        {
                stream << i->second.toString() << endl;
        }
        file.close();
        success = true;

        QFileInfo info(file);
        mReport << info.fileName()+", "+qstring_cast(info.size())+" bytes, "+qstring_cast(ts.size())+" " + type + ".";

        return success;
}

bool UsReconstructionFileMaker::writeTrackerTransforms(QString reconstructionFolder, QString session, std::vector<TimedPosition> ts)
{
        return this->writeTransforms(reconstructionFolder+"/"+session+".tp", ts, "tracking transforms prMt");
}

bool UsReconstructionFileMaker::writeTransforms(QString filename, std::vector<TimedPosition> ts, QString type)
{
        bool success = false;
        QFile file(filename);
        if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
        {
                reportError("Cannot open "+file.fileName());
                return success;
        }
        QTextStream stream(&file);

        for (unsigned i=0; i<ts.size(); ++i)
        {
                Transform3D transform = ts[i].mPos;
                stream << transform(0,0) << " ";
                stream << transform(0,1) << " ";
                stream << transform(0,2) << " ";
                stream << transform(0,3);
                stream << endl;
                stream << transform(1,0) << " ";
                stream << transform(1,1) << " ";
                stream << transform(1,2) << " ";
                stream << transform(1,3);
                stream << endl;
                stream << transform(2,0) << " ";
                stream << transform(2,1) << " ";
                stream << transform(2,2) << " ";
                stream << transform(2,3);
                stream << endl;
        }
        file.close();
        success = true;

        QFileInfo info(file);
        mReport << info.fileName()+", "+qstring_cast(info.size())+" bytes, "+qstring_cast(ts.size())+" " + type + ".";

        return success;
}

void UsReconstructionFileMaker::writeProbeConfiguration(QString reconstructionFolder, QString session, ProbeDefinition data, QString uid)
{
        XmlOptionFile file = XmlOptionFile(reconstructionFolder + "/" + session + ".probedata.xml");
        data.addXml(file.getElement("configuration"));
        file.getElement("tool").toElement().setAttribute("toolID", uid);
        file.save();
}

QString UsReconstructionFileMaker::createUniqueFolder(QString patientFolder, QString sessionDescription)
{
        QString retval("");
        QDir patientDir(patientFolder + "/US_Acq");

        QString subfolder = sessionDescription;
        QString subfolderAbsolutePath = patientDir.absolutePath()+"/"+subfolder;
        QString newPathName = subfolderAbsolutePath;
        int i=1;
        while(!findNewSubfolder(newPathName))
        {
                newPathName = subfolderAbsolutePath+"_"+QString::number(i++);
        }
        patientDir.mkpath(newPathName);
        patientDir.cd(newPathName);

        retval = patientDir.absolutePath();
        return retval;
}

QString UsReconstructionFileMaker::createFolder(QString patientFolder, QString sessionDescription)
{
        QString retval("");
        QDir patientDir(patientFolder + "/US_Acq");

        QString subfolder = sessionDescription;
        QString subfolderAbsolutePath = patientDir.absolutePath()+"/"+subfolder;
        QString newPathName = subfolderAbsolutePath;
        patientDir.mkpath(newPathName);
        patientDir.cd(newPathName);

        retval = patientDir.absolutePath();
        return retval;
}

bool UsReconstructionFileMaker::findNewSubfolder(QString subfolderAbsolutePath)
{
        QDir dir;
        if(dir.exists(subfolderAbsolutePath))
                return false;

        return true;
}

void UsReconstructionFileMaker::report()
{
        foreach(QString string, mReport)
        {
                reportSuccess(string);
        }
}

void UsReconstructionFileMaker::writeUSImages(QString path, ImageDataContainerPtr images, bool compression, std::vector<TimedPosition> pos)
{
        CX_ASSERT(images->size()==pos.size());
        vtkMetaImageWriterPtr writer = vtkMetaImageWriterPtr::New();

        for (unsigned i=0; i<images->size(); ++i)
        {
                vtkImageDataPtr currentImage = images->get(i);
                QString filename = QString("%1/%2_%3.mhd").arg(path).arg(mSessionDescription).arg(i);

                writer->SetInputData(currentImage);
                writer->SetFileName(cstring_cast(filename));
                writer->SetCompression(compression);
                {
                        StaticMutexVtkLocker lock;
                        writer->Write();
                }

                CustomMetaImagePtr customReader = CustomMetaImage::create(filename);
                customReader->setTransform(pos[i].mPos);
                customReader->setModality("US");
                customReader->setImageType(mSessionDescription);
        }
}

void UsReconstructionFileMaker::writeMask(QString path, QString session, vtkImageDataPtr mask)
{
        QString filename = QString("%1/%2.mask.mhd").arg(path).arg(session);
        if (!mask)
        {
                reportWarning(QString("No mask found, ignoring write to %1").arg(filename));
                return;
        }

        vtkMetaImageWriterPtr writer = vtkMetaImageWriterPtr::New();
        writer->SetInputData(mask);
        writer->SetFileName(cstring_cast(filename));
        writer->SetCompression(false);
        writer->Write();
}


void UsReconstructionFileMaker::writeREADMEFile(QString reconstructionFolder, QString session)
{
        QString text = ""
"* ==== Format description                                                                                              \n"
"* Refer to                                                                                                                                                 \n"
"*              http://custusx.org/uploads/developer_doc/nightly/org_custusx_acquisition.html   \n"
"* for a description of the files.                                                      \n"
"*/                                                                                                                                             \n";

        QFile file(reconstructionFolder+"/"+session+".README.txt");
        if(!file.open(QIODevice::WriteOnly | QIODevice::Truncate))
        {
                reportError("Cannot open "+file.fileName());
                return;
        }
        QTextStream stream(&file);
        stream << text;
        file.close();
}

QString UsReconstructionFileMaker::writeToNewFolder(QString path, bool compression)
{
        TimeKeeper timer;
        mReconstructData.mFilename = path+"/"+mSessionDescription+".fts"; // use fts since this is a single unique file.

        mReport.clear();
        mReport << "Made reconstruction folder: " + path;
        QString session = mSessionDescription;

        this->writeTrackerMetadata(path, session, mReconstructData.mTrackerRecordedMetadata);
        this->writeReferenceMetadata(path, session, mReconstructData.mReferenceRecordedMetadata);
        this->writeTrackerTimestamps(path, session, mReconstructData.mPositions);
        this->writeTrackerTransforms(path, session, mReconstructData.mPositions);
        this->writeUSTimestamps(path, session, mReconstructData.mFrames);
        this->writeUSTransforms(path, session, mReconstructData.mFrames);
        this->writeProbeConfiguration(path, session, mReconstructData.mProbeDefinition.mData, mReconstructData.mProbeUid);
        this->writeMask(path, session, mReconstructData.getMask());
        this->writeREADMEFile(path, session);

        ImageDataContainerPtr imageData = mReconstructData.mUsRaw->getImageContainer();
        if (imageData)
                this->writeUSImages(path, imageData, compression, mReconstructData.mFrames);
        else
                mReport << "failed to find frame data, save failed.";

        int time = std::max(1, timer.getElapsedms());
        mReport << QString("Completed save to %1. Spent %2s, %3fps").arg(mSessionDescription).arg(time/1000).arg(imageData->size()*1000/time);

        this->report();
        mReport.clear();

        return mReconstructData.mFilename;
}



}//namespace cx