cxUsReconstructionFileMaker.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.

Copyright (c) 2008-2014, SINTEF Department of Medical Technology
All rights reserved.

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modification, are permitted provided that the following conditions are met:

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   may be used to endorse or promote products derived from this software 
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#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"


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<double> imageTimestamps,
                                                                          TimedTransformMap trackerRecordedData,
                                                                          ToolPtr tool,
                                                                          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;

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

        std::vector<double> fts = imageTimestamps;
        for (unsigned i=0; i<fts.size(); ++i)
        {
                TimedPosition current;
                current.mTime = fts[i];
                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.mProbeData.setData(tool->getProbe()->getProbeData());
        }

        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)
{
        bool success = false;

        QFile file(reconstructionFolder+"/"+session+".tts");
        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)
        {
                stream << qstring_cast(ts[i].mTime);
                stream << endl;
        }

        file.close();
        success = true;

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

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

        QFile file(reconstructionFolder+"/"+session+".fts");
        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)
        {
                stream << qstring_cast(ts[i].mTime);
                stream << endl;
        }
        file.close();
        success = true;

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

        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"
"*                                                                                                                                              \n"
"* All files describing one acquisition lie the same folder.  The files all have                \n"
"* the name format US-Acq_<index>_<TS><stream>.<type>,                                  \n"
"* where                                                                                                                                \n"
"*  - <index> is a running index, for convenience.                                              \n"
"*  - <TS> is a timestamp                                                                                               \n"
"*  - <stream> is the uid of the video stream. Not used prior to cx3.5.0.                               \n"
"*  - <type> is the format of that specific file.                                                                               \n"
"*                                                                                                                                              \n"
"* Together, the files contains information about the us images and their                               \n"
"* timestamps, the tracking positions and their timestamps, and the probe                               \n"
"* calibration.                                                                                                                 \n"
"*                                                                                                                                              \n"
"* In the following, we use <filebase> = US-Acq_<index>_<TS><stream>.   \n"
"*                                                                                                                                              \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.mhd (obsolete)                                                                               \n"
"*                                                                                                                                              \n"
"* Used prior to version cx3.4.0.                                                                               \n"
"* A file in the metaheader file format containing the uncompressed image data.                 \n"
"* the z-direction is the time axis, i.e. the z dim is the number of us frames.                 \n"
"* See http://www.itk.org/Wiki/MetaIO/Documentation for more.                                                   \n"
"*                                                                                                                                              \n"
"* Two extra tags are added:                                                                                    \n"
"*                                                                                                                                              \n"
"ConfigurationID = <path:inside:ProbeCalibConfigs.xml>                                  \n"
"ProbeCalibration = <not used>                                                                                  \n"
"*                                                                                                                                              \n"
"* The ConfigurationID refers to a specific configuration within                \n"
"* ProbeCalibConfigs.xml, using colon separators.                                               \n"
"*                                                                                                                                              \n"
"* ==== <filebase>_<index>.mhd                                                                                  \n"
"*                                                                                                                                              \n"
"* A sequence of files in the metaheader file format containing the image data, one file\n"
"* for each frame. The frame index is given by the index in the file name.                              \n"
"* See http://www.itk.org/Wiki/MetaIO/Documentation for more.                                                   \n"
"* Replaces single image files.                                                                                 \n"
"*                                                                                                                                              \n"
"* ==== ProbeCalibConfigs.xml (obsolete)                                                                \n"
"*                                                                                                                                              \n"
"* This file contains the probe definition, and is copied from the              \n"
"* config/tool/Tools folder                                                                                             \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.probedata.xml                                                                                \n"
"*                                                                                                                                              \n"
"* This file contains the probe definition. Replaces ProbeCalibConfigs.xml.                             \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.fts                                                                                                  \n"
"*                                                                                                                                              \n"
"* This file contains the frame timestamps. This is a sequence of                                               \n"
"* newline-separated floating-point numbers in milliceconds. The starting point                 \n"
"* is irrelevant. The number of timestamps must equal the number of us frames.                  \n"
"                                                                                                                                               \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.tp                                                                                                   \n"
"*                                                                                                                                              \n"
"* This file contains the tracking positions. This is a newline-separated                               \n"
"* sequence of matrices, one for each tracking sample. Each matrix is the prMt,                 \n"
"* i.e. the transform from tool to patient reference.                                   \n"
"* The last line of the matrix (always containing 0 0 0 1) is omitted. The matrix               \n"
"* numbers is whitespace-separated with newline between rows. Thus the number of                \n"
"* lines in this file is (# tracking positions) x 3.                                                                    \n"
"*                                                                                                                                              \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.tts                                                                                                  \n"
"*                                                                                                                                              \n"
"* This file contains the tracking timestamps. The format equals .fts ,                                 \n"
"* but the number of timestamps equals the number of tracking positions.                                \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.fp                                                                                                   \n"
"*                                                                                                                                              \n"
"* This file contains the frame positions. This is a newline-separated                                  \n"
"* sequence of matrices, one for each US frame. Each matrix is the rMu,                                 \n"
"* i.e. the transform from lower-left centered image space to                                                   \n"
"* global reference.                                                                                                    \n"
"* The last line of the matrix (always containing 0 0 0 1) is omitted. The matrix               \n"
"* numbers is whitespace-separated with newline between rows. Thus the number of                \n"
"* lines in this file is (# tracking positions) x 3.                                                                    \n"
"*                                                                                                                                              \n"
"* ==== <filebase>.mask.mhd                                                                                             \n"
"*                                                                                                                                              \n"
"* This file contains the image mask. The binary image shows what parts \n"
"* of the frame images contain valid US data. This file is only written,\n"
"* not read. It can be constructed from the probe data.                                 \n"
"*                                                                                                                                              \n"
"*                                                                                                                                              \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->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.mProbeData.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