cxUSFrameData.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 "cxUSFrameData.h"

#include <vtkImageData.h>
#include <vtkImageLuminance.h>
#include <vtkImageClip.h>
#include <vtkImageAppend.h>
#include <vtkMetaImageWriter.h>
#include <vtkImageImport.h>
#include "cxTypeConversions.h"
#include <QFileInfo>
#include "cxTimeKeeper.h"
#include "cxImageDataContainer.h"
#include "cxVolumeHelpers.h"
#include "cxLogger.h"
#include "cxFileManagerService.h"
#include "cxImage.h"


typedef vtkSmartPointer<vtkImageAppend> vtkImageAppendPtr;

namespace cx
{

ProcessedUSInputData::ProcessedUSInputData(std::vector<vtkImageDataPtr> frames, std::vector<TimedPosition> pos, vtkImageDataPtr mask, QString path, QString uid) :
        mProcessedImage(frames),
        mFrames(pos),
        mMask(mask),
        mPath(path),
        mUid(uid)
{
        this->validate();
}

bool ProcessedUSInputData::validate() const
{
        std::vector<TimedPosition> frameInfo = this->getFrames();
        Eigen::Array3i inputDims = this->getDimensions();

        if (inputDims[2] != static_cast<int>(frameInfo.size()))
        {
                QString msg("Mismatch in US input data: inputDims[2] != frameInfo.size() : %1 != %2");
                reportWarning(msg.arg(inputDims[2]).arg(frameInfo.size()));
                return false;
        }

        if (inputDims[2]==0)
        {
                reportWarning("Empty US input data");
                return false;
        }

        return true;
}

unsigned char* ProcessedUSInputData::getFrame(unsigned int index) const
{
        CX_ASSERT(index < mProcessedImage.size());

        // Raw data pointer
        unsigned char *inputPointer = static_cast<unsigned char*> (mProcessedImage[index]->GetScalarPointer());
        return inputPointer;
}

Eigen::Array3i ProcessedUSInputData::getDimensions() const
{
        Eigen::Array3i retval;
        retval[0] = mProcessedImage[0]->GetDimensions()[0];
        retval[1] = mProcessedImage[0]->GetDimensions()[1];
        retval[2] = mProcessedImage.size();
        return retval;
}

Vector3D ProcessedUSInputData::getSpacing() const
{
        Vector3D retval = Vector3D(mProcessedImage[0]->GetSpacing());
        retval[2] = retval[0]; // set z-spacing to arbitrary value.
        return retval;
}

std::vector<TimedPosition> ProcessedUSInputData::getFrames() const
{
        return mFrames;
}

vtkImageDataPtr ProcessedUSInputData::getMask()
{
        return mMask;
}

QString ProcessedUSInputData::getFilePath()
{
        return mPath;
}

QString ProcessedUSInputData::getUid()
{
        return mUid;
}



USFrameDataPtr USFrameData::create(ImagePtr inputFrameData)
{
        USFrameDataPtr retval(new USFrameData());

        retval->mName = QFileInfo(inputFrameData->getName()).completeBaseName();
        retval->mImageContainer.reset(new cx::SplitFramesContainer(inputFrameData->getBaseVtkImageData()));
        retval->resetRemovedFrames();

        return retval;
}

USFrameDataPtr USFrameData::create(QString inputFilename, FileManagerServicePtr fileManager)
{
        QFileInfo info(inputFilename);

        TimeKeeper timer;
        QString mhdSingleFile = info.absolutePath()+"/"+info.completeBaseName()+".mhd";

        if (QFileInfo(mhdSingleFile).exists())
        {
                vtkImageDataPtr image = fileManager->loadVtkImageData(mhdSingleFile);
                // load from single file
                USFrameDataPtr retval = USFrameData::create(ImagePtr(new Image(mhdSingleFile, image)));
                retval->mName = QFileInfo(mhdSingleFile).completeBaseName();
                timer.printElapsedms(QString("Loading single %1").arg(inputFilename));
                return retval;
        }
        else
        {
                USFrameDataPtr retval(new USFrameData());
                retval->mName = QFileInfo(inputFilename).completeBaseName();
                retval->mImageContainer.reset(new cx::CachedImageDataContainer(inputFilename, -1, fileManager));
                retval->resetRemovedFrames();
                return retval;
        }
}

USFrameDataPtr USFrameData::create(QString name, cx::ImageDataContainerPtr images)
{
        if (!images)
                return USFrameDataPtr();
        USFrameDataPtr retval(new USFrameData());
        retval->mName = name;
        retval->mImageContainer = images;
        retval->resetRemovedFrames();

        return retval;
}

USFrameDataPtr USFrameData::create(QString name, std::vector<vtkImageDataPtr> frames)
{
        cx::ImageDataContainerPtr container;
        container.reset(new cx::FramesDataContainer(frames));
        return create(name, container);
}


USFrameData::USFrameData() :
                mCropbox(0,0,0,0,0,0), mPurgeInput(true)
{
}

void USFrameData::resetRemovedFrames()
{
        if (mImageContainer->empty())
                return;

        mReducedToFull.clear();
        for (unsigned i=0; i<mImageContainer->size(); ++i)
                mReducedToFull.push_back(i);
}

USFrameData::~USFrameData()
{
        mImageContainer.reset();
}

void USFrameData::removeFrame(unsigned int index)
{
        CX_ASSERT(index < mReducedToFull.size());
        mReducedToFull.erase(mReducedToFull.begin()+index);
}

Eigen::Array3i USFrameData::getDimensions() const
{
        vtkImageDataPtr image = mImageContainer->get(0);
        if(!image)
                return Eigen::Array3i(0);
        Eigen::Array3i retval(image->GetDimensions());

        if (mCropbox.range()[0]!=0)
        {
                // WARNING: cannot use dimensions from the cropImage function - it uses extent,
                // which may be larger. We need the real size, given by wholeextent/updateextent.
                vtkImageDataPtr sample = this->cropImageExtent(mImageContainer->get(0), mCropbox);
//              Eigen::Array<int, 6, 1> extent(sample->GetWholeExtent());
                Eigen::Array<int, 6, 1> extent(sample->GetExtent());
                retval[0] = extent[1]-extent[0]+1;
                retval[1] = extent[3]-extent[2]+1;
//              std::cout << "extent dim: " << retval[0] << " " << retval[1] << std::endl;
        }

        retval[2] = mReducedToFull.size();
        return retval;
}


Vector3D USFrameData::getSpacing() const
{
        Vector3D retval(1,1,1);
        if (!mImageContainer->empty() && mImageContainer->get(0))
                retval = Vector3D(mImageContainer->get(0)->GetSpacing());
        retval[2] = retval[0]; // set z-spacing to arbitrary value.
        return retval;
}

void USFrameData::setCropBox(IntBoundingBox3D cropbox)
{
        // ensure clip never happens in z dir.
        cropbox[4] = -100000;
        cropbox[5] =  100000;
        mCropbox = cropbox;
}

vtkImageDataPtr USFrameData::cropImageExtent(vtkImageDataPtr input, IntBoundingBox3D cropbox) const
{
  vtkImageClipPtr clip = vtkImageClipPtr::New();
  clip->SetInputData(input);
  clip->SetOutputWholeExtent(cropbox.begin());
//  clip->ClipDataOn(); // this line sets wholeextent==extent, but uses lots of time (~6ms/frame)
  clip->Update();
  vtkImageDataPtr rawResult = clip->GetOutput();
//  rawResult->Update();
        rawResult->Crop(cropbox.begin()); // moved in from toGrayscaleAndEffectuateCropping when VTK5->6
  return rawResult;
}

vtkImageDataPtr USFrameData::to8bitGrayscaleAndEffectuateCropping(vtkImageDataPtr input) const
{
        vtkImageDataPtr grayScaleData;

        if (input->GetNumberOfScalarComponents() == 1) // already gray
        {
                // crop (slow)
                grayScaleData = input;
//              outData->Crop();
        }
        else
        {
                // convert and crop as side effect (optimization)
                grayScaleData = convertImageDataToGrayScale(input);
        }

        vtkImageDataPtr outData = this->convertTo8bit(grayScaleData);

        vtkImageDataPtr copy = vtkImageDataPtr::New();
        copy->DeepCopy(outData);
        return copy;
}

vtkImageDataPtr USFrameData::convertTo8bit(vtkImageDataPtr input) const
{
        vtkImageDataPtr retval = input;
        if (input->GetScalarSize() > 1)
        {
                ImagePtr tempImage = cx::ImagePtr(new cx::Image("tempImage", input, "tempImage"));
                tempImage->resetTransferFunctions();
                retval = tempImage->get8bitGrayScaleVtkImageData();
        }
        return retval;
}

// for testing
//void printStuff(QString text, vtkImageDataPtr data)
//{
//      std::cout << text << std::endl;
//      Eigen::Array<int, 6, 1> wholeExtent(data->GetWholeExtent());
//      Eigen::Array<int, 6, 1> extent(data->GetExtent());
//      Eigen::Array<int, 6, 1> updateExtent(data->GetUpdateExtent());
//      std::cout << "\t whole ext " <<  wholeExtent << std::endl;
//      std::cout << "\tupdate ext " <<  updateExtent << std::endl;
//      std::cout << "\t       ext " <<  extent << std::endl;

//      Eigen::Array<vtkIdType,3,1> hinc;
//      data->GetContinuousIncrements(data->GetWholeExtent(), hinc[0], hinc[1], hinc[2]);
//      std::cout << "\t whole inc " <<  hinc << std::endl;

//      Eigen::Array<vtkIdType,3,1> uinc;
//      data->GetContinuousIncrements(data->GetUpdateExtent(), uinc[0], uinc[1], uinc[2]);
//      std::cout << "\t      uinc " <<  uinc << std::endl;

//      Eigen::Array<vtkIdType,3,1> inc;
//      data->GetContinuousIncrements(data->GetExtent(), inc[0], inc[1], inc[2]);
//      std::cout << "\t       inc " <<  inc << std::endl;

//      Eigen::Array3i dim(data->GetDimensions());
//      std::cout << "\t       dim " <<  dim << std::endl;

//      Eigen::Array3i max(wholeExtent[1] - wholeExtent[0], wholeExtent[3] - wholeExtent[2], wholeExtent[5] - wholeExtent[4]);
//      std::cout << "\t       max " <<  max << std::endl;
//}

vtkImageDataPtr USFrameData::useAngio(vtkImageDataPtr inData, vtkImageDataPtr grayFrame, int frameNum) const
{
        // Some of the code here is borrowed from the vtk examples:
        // http://public.kitware.com/cgi-bin/viewcvs.cgi/*checkout*/Examples/Build/vtkMy/Imaging/vtkImageFoo.cxx?root=VTK&content-type=text/plain

        if (inData->GetNumberOfScalarComponents() != 3)
        {
                if(frameNum == 0) //Only report warning once
                        reportWarning("Angio requested for grayscale ultrasound");
                return grayFrame;
        }

        vtkImageDataPtr outData = vtkImageDataPtr::New();
        outData->DeepCopy(grayFrame);
//      outData->Update(); // updates whole extent.

//      printStuff("Clipped color in", inData);
//      printStuff("Grayscale in", outData);

//      int* inExt = inData->GetWholeExtent();
        int* outExt = outData->GetExtent();

        // Remember that the input might (and do due to vtkImageClip) contain leaps.
        // This means that the wholeextent might be larger than the extent, thus
        // we must use a startoffset and leaps between lines.

        unsigned char *inPtr = static_cast<unsigned char*> (inData->GetScalarPointerForExtent(inData->GetExtent()));
        unsigned char *outPtr = static_cast<unsigned char*> (outData->GetScalarPointerForExtent(outData->GetExtent()));

        int maxX = outExt[1] - outExt[0];
        int maxY = outExt[3] - outExt[2];
        int maxZ = outExt[5] - outExt[4];

        Eigen::Array<vtkIdType,3,1> inInc;
        inData->GetContinuousIncrements(inData->GetExtent(), inInc[0], inInc[1], inInc[2]);
        CX_ASSERT(inInc[0]==0);
        // we assume (wholeextent == extent) for the outData in the algorithm below. assert here.
        Eigen::Array<vtkIdType,3,1> outInc;
        outData->GetContinuousIncrements(outData->GetExtent(), outInc[0], outInc[1], outInc[2]);
        CX_ASSERT(outInc[0]==0);
        CX_ASSERT(outInc[1]==0);
        CX_ASSERT(outInc[2]==0);

        for (int z=0; z<=maxZ; z++)
        {
                for (int y=0; y<=maxY; y++)
                {
                        for (int x=0; x<=maxX; x++)
                        {
                                //Look at 3 scalar components at the same time (RGB),
                                //if color is grayscale or close to grayscale: set to zero.

                                if (((*inPtr) == (*(inPtr + 1))) && ((*inPtr) == (*(inPtr + 2))))
                                {
                                        (*outPtr) = 0;
                                }
                                else
                                {
                                        // strong check: look for near-gray values and remove them.
                                        double r = inPtr[0];
                                        double g = inPtr[1];
                                        double b = inPtr[2];
                                        int metric = (fabs(r-g) + fabs(r-b) + fabs(g-b)) / 3; // average absolute diff must be less than or equal to this
//                                      std::cout << QString("  %1,%2,%3 \t %4, %5 -- %6").arg(int(inPtr[0])).arg(int(inPtr[1])).arg(int(inPtr[2])).arg(idxR).arg(idxY).arg(metric) << std::endl;
                                        if (metric <= 3)
                                                (*outPtr) = 0;

                                }
                                //Assume the outVolume is treated with the luminance filter first
                                outPtr++;
                                inPtr += 3;
                        }
                        inPtr += inInc[1];
                }
                inPtr += inInc[2];
        }

        return outData;
}

void USFrameData::setPurgeInputDataAfterInitialize(bool value)
{
        mPurgeInput = value;
}

std::vector<std::vector<vtkImageDataPtr> > USFrameData::initializeFrames(std::vector<bool> angio)
{

        std::vector<std::vector<vtkImageDataPtr> > raw(angio.size());

        for (unsigned i=0; i<raw.size(); ++i)
        {
                raw[i].resize(mReducedToFull.size());
        }

        // apply cropping and angio
        for (unsigned i=0; i<mReducedToFull.size(); ++i)
        {
                CX_ASSERT(mImageContainer->size() > mReducedToFull[i]);
                vtkImageDataPtr current = mImageContainer->get(mReducedToFull[i]);

                if (mCropbox.range()[0]!=0)
                        current = this->cropImageExtent(current, mCropbox);

                // optimization: grayFrame is used in both calculations: compute once
                vtkImageDataPtr grayFrame = this->to8bitGrayscaleAndEffectuateCropping(current);

                for (unsigned j=0; j<angio.size(); ++j)
                {

                        if (angio[j])
                        {
                                vtkImageDataPtr angioFrame = this->useAngio(current, grayFrame, i);
                                raw[j][i] = angioFrame;
                        }
                        else
                        {
                                raw[j][i] = grayFrame;
                        }
                }

                if (mPurgeInput)
                        mImageContainer->purge(mReducedToFull[i]);
        }

        if (mPurgeInput)
                mImageContainer->purgeAll();

        return raw;
}

void USFrameData::purgeAll()
{
        mImageContainer->purgeAll();
}

USFrameDataPtr USFrameData::copy()
{
        USFrameDataPtr retval(new USFrameData(*this));
        this->resetRemovedFrames();
        return retval;
}

QString USFrameData::getName() const
{
        return QFileInfo(mName).completeBaseName();
}

unsigned USFrameData::getNumImages()
{
        return mImageContainer->size();
}

void USFrameData::fillImageImport(vtkImageImportPtr import, int index)
{
        TimeKeeper timer;
        vtkImageDataPtr source = mImageContainer->get(index);

//       use this test code to display angio output:
//      vtkImageDataPtr current = mImageContainer->get(index);
//      current = this->cropImage(current, IntBoundingBox3D(157, 747, 68, 680, 0, 0));
//      vtkImageDataPtr grayFrame = this->toGrayscale(current);
//      static vtkImageDataPtr source;
//      source = this->useAngio(current, grayFrame);

//      source->Update(); // VTK5->6

        import->SetImportVoidPointer(source->GetScalarPointer());
        import->SetDataScalarType(source->GetScalarType());
        import->SetDataSpacing(source->GetSpacing());
        import->SetNumberOfScalarComponents(source->GetNumberOfScalarComponents());
        import->SetWholeExtent(source->GetExtent());
        import->SetDataExtentToWholeExtent();
}

bool USFrameData::is4D()
{
        int numberOfFrames = mReducedToFull.size();

        if (numberOfFrames > 0)
        {
                vtkImageDataPtr image = mImageContainer->get(0);
                if(image && image->GetDataDimension() == 3)
                {
                        return true;
                }

        }
        return false;
}

bool USFrameData::is8bit() const
{
        if (mImageContainer->get(0)->GetNumberOfScalarComponents() == 1)
                return true;
        return false;
}

}//namespace cx