#ifndef _vvSegmentationDialog_CXX
#define _vvSegmentationDialog_CXX

/*=========================================================================

Program:   vv
Language:  C++
Author :   David Sarrut (david.sarrut@gmail.com)

Copyright (C) 2008
Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
CREATIS-LRMN http://www.creatis.insa-lyon.fr

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

=========================================================================*/
#include <QtGui>
#include <Qt>

#include "vvSegmentationDialog.h"
#include "vvProgressDialog.h"
#include "vvImageWriter.h"
#include "vvLandmarks.h"
#include "vvInteractorStyleNavigator.h"
#include "vvSlicer.h"

#include "vtkMarchingCubes.h"
#include "vtkMarchingSquares.h"
#include "vtkImageClip.h"
#include "vtkCamera.h"
#include "vtkRenderer.h"
#include "vtkProperty.h"
#include "vtkLookupTable.h"
#include "vtkClipPolyData.h"
#include "vtkImageToPolyDataFilter.h"
#include "vtkLookupTable.h"
#include "vtkDoubleArray.h"
#include "vtkPointData.h"
#include "vtkCellData.h"
#include "vtkImageMapToWindowLevelColors.h"
#include "vtkImageContinuousErode3D.h"
#include "vtkImageContinuousDilate3D.h"
#include "vtkImageLogic.h"
#include "vtkInteractorStyleTrackballCamera.h"
#include "vtkImageSeedConnectivity.h"
#include "vtkConnectivityFilter.h"
#include "vtkPolyData.h"
#include <vtkPolyDataMapper.h>
#include <vtkImageData.h>
#include "vtkInformation.h"
#include "vtkInformationVector.h"
#include "vtkStreamingDemandDrivenPipeline.h"
#include <vtkPolyDataWriter.h>

#include <QMessageBox>

//====================================================================
vvSegmentationDialog::vvSegmentationDialog(QWidget * parent, Qt::WindowFlags f)
        :QDialog(parent,f), Ui::vvSegmentationDialog() {

    // initialization
    setupUi(this);
    mManager = new vvSlicerManager(1);

    mClipper = vtkImageClip::New();
    mSquares1 = vtkMarchingSquares::New();
    mSquaresMapper1 = vtkPolyDataMapper::New();
    mSquaresActor1 = vtkActor::New();

    mSquares2 = vtkMarchingSquares::New();
    mSquaresMapper2 = vtkPolyDataMapper::New();
    mSquaresActor2 = vtkActor::New();

    //m3DMapper = vtkPolyDataMapper::New();
    //m3DActor = vtkActor::New();
    m3DExtractor = vtkMarchingCubes::New();
    m3DMappers.clear();
    m3DActors.clear();

    mBinaireImages.clear();
    mKernelValue = 2;

    connect(clipping1Slider,SIGNAL(valueChanged(int)),this,SLOT(clippingvaluechanged(int)));
    connect(clipping2Slider,SIGNAL(valueChanged(int)),this,SLOT(clippingvaluechanged(int)));
    connect(binaryButton,SIGNAL(clicked()),this,SLOT(BinariseSurface()));
    connect(saveButton,SIGNAL(clicked()),this,SLOT(Save()));
    connect(erodeButton,SIGNAL(clicked()),this,SLOT(Erode()));
    connect(dilateButton,SIGNAL(clicked()),this,SLOT(Dilate()));
    connect(dimButton,SIGNAL(clicked()),this,SLOT(ChangeDimRendering()));
    connect(kernelSpinBox,SIGNAL(valueChanged(int)),this,SLOT(KernelValueChanged(int)));

    binaryButton->setEnabled(0);
    erodeButton->setEnabled(0);
    dilateButton->setEnabled(0);
    infoLabel->setText("Select Up and Down threshold before clicking binarise !");
}

vvSegmentationDialog::~vvSegmentationDialog()
{
    mClipper->Delete();

    mSquaresActor1->Delete();
    mSquaresMapper1->Delete();
    mSquares1->Delete();

    mSquaresActor2->Delete();
    mSquaresMapper2->Delete();
    mSquares2->Delete();

    //m3DMapper->Delete();
    //m3DActor->Delete();
    m3DExtractor->Delete();

    for (unsigned int i = 0; i < mBinaireImages.size(); i++)
        mBinaireImages[i]->Delete();

    for (unsigned int i = 0; i < m3DActors.size(); i++)
        m3DActors[i]->Delete();

    for (unsigned int i = 0; i < m3DMappers.size(); i++)
        m3DMappers[i]->Delete();

    delete mManager;
}

//----------------------------------------------------------------------------
// This templated function executes the filter for any type of data.
// Handles the one input operations
template <class T>
void vvImageBinarize(vtkImageData *in1Data, T *in1Ptr,
                     int outExt[6],int clampMin, int clampMax)
{
    int idxR, idxY, idxZ;
    int maxY, maxZ;
    vtkIdType inIncX, inIncY, inIncZ;
    int rowLength;

    // find the region to loop over
    rowLength =
        (outExt[1] - outExt[0]+1)*in1Data->GetNumberOfScalarComponents();
    // What a pain. Maybe I should just make another filter.

    maxY = outExt[3] - outExt[2];
    maxZ = outExt[5] - outExt[4];

    // Get increments to march through data
    in1Data->GetContinuousIncrements(outExt, inIncX, inIncY, inIncZ);

    for (idxZ = 0; idxZ <= maxZ; idxZ++)
    {
        for (idxY = 0; idxY <= maxY; idxY++)
        {
            for (idxR = 0; idxR < rowLength; idxR++)
            {
                if (static_cast<double>(*in1Ptr) > clampMin && static_cast<double>(*in1Ptr) <= clampMax)
                    *in1Ptr = static_cast<T>(1);
                else
                    *in1Ptr = static_cast<T>(0);
                in1Ptr++;
            }
            in1Ptr += inIncY;
        }
        in1Ptr += inIncZ;
    }
}

void vvSegmentationDialog::SetImage(vvImage::Pointer image)
{

    QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
    mManager->SetImage(image);
    mManager->SetSlicerWindow(0,viewWidget->GetRenderWindow());
    vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
    mManager->SetInteractorStyleNavigator(0,style);
    style->Delete();

    double range[2];
    mManager->GetImage()->GetScalarRange(range);
    mManager->GetSlicer(0)->SetColorWindow(range[1]-range[0]);
    mManager->GetSlicer(0)->SetColorLevel((range[1]+range[0])/2);

    clipping1Slider->setMinimum(range[0]);
    clipping1Slider->setMaximum(range[1]);
    clipping2Slider->setMinimum(range[0]);
    clipping2Slider->setMaximum(range[1]);
    clipping1Slider->setValue(range[0]);
    clipping2Slider->setValue(range[1]);

    mClipper->SetInput(mManager->GetSlicer(0)->GetInput());
    mSquares1->SetValue(0,clipping1Slider->value());
    mSquares2->SetValue(0,clipping2Slider->value());
    mSquares1->SetInput(mClipper->GetOutput());
    mSquares2->SetInput(mClipper->GetOutput());

    mSquaresMapper1->SetInput(mSquares1->GetOutput());
    mSquaresMapper2->SetInput(mSquares2->GetOutput());
    mSquaresMapper1->ScalarVisibilityOff();
    mSquaresMapper2->ScalarVisibilityOff();

    mSquaresActor1->SetMapper(mSquaresMapper1);
    mSquaresActor2->SetMapper(mSquaresMapper2);
    mSquaresActor1->GetProperty()->SetColor(1.0,0,0);
    mSquaresActor2->GetProperty()->SetColor(0,0,1.0);
    mSquaresActor1->SetPickable(0);
    mSquaresActor2->SetPickable(0);

    mManager->GetSlicer(0)->GetRenderer()->AddActor(mSquaresActor1);
    mManager->GetSlicer(0)->GetRenderer()->AddActor(mSquaresActor2);

    mSquares1->Update();
    mSquares2->Update();

    UpdateSlice(0,mManager->GetSlicer(0)->GetSlice());

    connect(mManager,SIGNAL(UpdateTSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
    connect(mManager,SIGNAL(UpdateSlice(int,int)),this,SLOT(UpdateSlice(int, int)));
    connect(mManager,SIGNAL(UpdateSliceRange(int,int,int,int,int)),this,SLOT(UpdateSlice(int, int)));
    connect(mManager,SIGNAL(LandmarkAdded()),this,SLOT(InsertSeed()));
    QApplication::restoreOverrideCursor();
}

void vvSegmentationDialog::UpdateSlice(int slicer,int slices)
{
    int slice = mManager->GetSlicer(0)->GetSlice();
    int tslice = mManager->GetSlicer(0)->GetTSlice();
    mClipper->SetInput(mManager->GetSlicer(0)->GetInput());
    int* extent = mManager->GetSlicer(0)->GetImageActor()->GetDisplayExtent();
    mClipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],extent[3],extent[4],extent[5]);
    int i;
    for (i = 0; i < 6;i = i+2)
    {
        if (extent[i] == extent[i+1])
        {
            break;
        }
    }

    switch (i)
    {
    case 0:
        if (mManager->GetSlicer(0)->GetRenderer()->GetActiveCamera()->GetPosition()[0] > slice)
        {
            mSquaresActor1->SetPosition(1,0,0);
            mSquaresActor2->SetPosition(1,0,0);
        }
        else
        {
            mSquaresActor1->SetPosition(-1,0,0);
            mSquaresActor2->SetPosition(-1,0,0);
        }
        break;
    case 2:
        if (mManager->GetSlicer(0)->GetRenderer()->GetActiveCamera()->GetPosition()[1] > slice)
        {
            mSquaresActor1->SetPosition(0,1,0);
            mSquaresActor2->SetPosition(0,1,0);
        }
        else
        {
            mSquaresActor1->SetPosition(0,-1,0);
            mSquaresActor2->SetPosition(0,-1,0);
        }
        break;
    case 4:
        if (mManager->GetSlicer(0)->GetRenderer()->GetActiveCamera()->GetPosition()[2] > slice)
        {
            mSquaresActor1->SetPosition(0,0,1);
            mSquaresActor2->SetPosition(0,0,1);
        }
        else
        {
            mSquaresActor1->SetPosition(0,0,-1);
            mSquaresActor2->SetPosition(0,0,-1);
        }
        break;
    }
    mSquares1->Update();
    mSquares2->Update();

    if (m3DActors.size())
    {
        for (unsigned int i =0; i < m3DActors.size(); i++)
        {
            if (m3DActors[i]->GetVisibility())
            {
                m3DActors[i]->VisibilityOff();
            }
        }
        std::cout << "display " << tslice << " on " << m3DActors.size()  << std::endl;
        m3DActors[tslice]->VisibilityOn();
    }

    mManager->Render();
}


void vvSegmentationDialog::clippingvaluechanged(int value)
{
    binaryButton->setEnabled(1);
    int min = (clipping1Slider->value() < clipping2Slider->value() ) ?
              clipping1Slider->value():clipping2Slider->value();
    int max = (clipping1Slider->value() > clipping2Slider->value() ) ?
              clipping1Slider->value():clipping2Slider->value();
    mSquares1->SetValue(0,min);
    mSquares2->SetValue(0,max);

    QString textMin = "<b> Min : </b>";
    textMin += QString::number(min);
    QString textMax = "\n <b> Max : </b>";
    textMax += QString::number(max);
    minLabel->setText(textMin);
    maxLabel->setText(textMax);

    if (mSquares1->GetInput())
    {
        mSquares1->Update();
        mSquares2->Update();
        mManager->Render();
    }
}


void vvSegmentationDialog::BinariseSurface()
{
    infoLabel->setText("Click erode then space on desired organ !");

    QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
    int clampMin = (clipping1Slider->value() < clipping2Slider->value() ) ?
                   clipping1Slider->value():clipping2Slider->value();
    int clampMax = (clipping1Slider->value() > clipping2Slider->value() ) ?
                   clipping1Slider->value():clipping2Slider->value();
    vtkImageData* outputImage = vtkImageData::New();

    for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++)
    {
        vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
        int ext[6];
        image->GetWholeExtent(ext);
        void *in1Ptr;
        in1Ptr = image->GetScalarPointerForExtent(ext);

        switch (image->GetScalarType())
        {
            vtkTemplateMacro(
                vvImageBinarize(image, static_cast<VTK_TT *>(in1Ptr),
                                ext,clampMin,clampMax));
        default:
            std::cerr << "Error, unknown pixel format : " << image->GetScalarTypeAsString() << std::endl;
            return;
        }

        outputImage->Initialize();
        outputImage->SetExtent(ext);
        outputImage->SetOrigin(image->GetOrigin());
        outputImage->SetSpacing(image->GetSpacing());
        outputImage->SetScalarTypeToUnsignedChar();
        outputImage->CopyAndCastFrom(image,ext);
        outputImage->Update();

        image->DeepCopy(outputImage);
        image->UpdateInformation();
        image->PropagateUpdateExtent();

        vtkImageData* imageBin = vtkImageData::New();
        imageBin->DeepCopy(image);
        imageBin->Update();
        mBinaireImages.push_back(imageBin);
    }

    outputImage->Delete();
    erodeButton->setEnabled(1);
    QApplication::restoreOverrideCursor();
    mManager->SetColorWindow(2);
    mManager->SetColorLevel(0.5);
    mManager->Render();
}

void vvSegmentationDialog::Erode()
{
    QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
    vtkImageContinuousErode3D* erode = vtkImageContinuousErode3D::New();
    erode->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
    for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++)
    {
        vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
        erode->SetInput(image);
        erode->Update();
        image->DeepCopy(erode->GetOutput());
        image->Update();
    }
    erode->Delete();
    dilateButton->setEnabled(1);
    mManager->Render();
    QApplication::restoreOverrideCursor();
}

void vvSegmentationDialog::Dilate()
{
    QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
    vtkImageContinuousDilate3D* dilate = vtkImageContinuousDilate3D::New();
    vtkImageLogic* And = vtkImageLogic::New();
    And->SetOperationToAnd();
    dilate->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
    for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++)
    {
        vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
        dilate->SetInput(image);
        vtkImageData* mask = mBinaireImages[numImage];
        And->SetInput1(dilate->GetOutput());
        And->SetInput2(mask);
        And->Update();
        image->DeepCopy(And->GetOutput());
        image->Update();
    }
    And->Delete();
    dilate->Delete();
    mManager->Render();
    QApplication::restoreOverrideCursor();
}

void vvSegmentationDialog::InsertSeed()
{
    QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
    int point4D[4];
    point4D[0] = mManager->GetLandmarks()->GetCoordinates(
                     mManager->GetLandmarks()->GetNumberOfPoints()-1)[0];
    point4D[1] = mManager->GetLandmarks()->GetCoordinates(
                     mManager->GetLandmarks()->GetNumberOfPoints()-1)[1];
    point4D[2] = mManager->GetLandmarks()->GetCoordinates(
                     mManager->GetLandmarks()->GetNumberOfPoints()-1)[2];
    point4D[3] = mManager->GetLandmarks()->GetCoordinates(
                     mManager->GetLandmarks()->GetNumberOfPoints()-1)[3];

    point4D[0] = point4D[0]/mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetSpacing()[0];
    point4D[1] = point4D[1]/mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetSpacing()[1];
    point4D[2] = point4D[2]/mManager->GetSlicer(0)->GetImage()->GetVTKImages()[0]->GetSpacing()[2];

    vtkImageSeedConnectivity* seed = vtkImageSeedConnectivity::New();
    seed->SetInputConnectValue(1);
    seed->SetOutputConnectedValue(1);
    seed->SetOutputUnconnectedValue(0);
    seed->AddSeed(point4D[0],point4D[1],point4D[2]);

    for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++)
    {
        vtkImageData* image = mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage];
        seed->SetInput(image);
        seed->Update();
        image->DeepCopy(seed->GetOutput());
        image->Update();
    }

    seed->Delete();
    QApplication::restoreOverrideCursor();
}

void vvSegmentationDialog::ChangeDimRendering()
{
    QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));

    if (dimButton->text() == "3D")
    {
        if (m3DActors.size() == 0)
        {
            m3DExtractor->SetValue(0,0.5);
            for (unsigned int numImage = 0; numImage < mManager->GetSlicer(0)->GetImage()->GetVTKImages().size(); numImage++)
            {
                vtkActor* actor = vtkActor::New();
                m3DExtractor->SetInput(mManager->GetSlicer(0)->GetImage()->GetVTKImages()[numImage]);
                m3DExtractor->Update();

                vtkPolyDataMapper* mapper = vtkPolyDataMapper::New();
                mapper->SetInput(m3DExtractor->GetOutput());
                m3DMappers.push_back(mapper);

                actor->SetMapper(mapper);
                actor->GetProperty()->SetColor(1.0,0.7,0.2);
                actor->VisibilityOff();

                mManager->GetSlicer(0)->GetRenderer()->AddActor(actor);
                m3DActors.push_back(actor);
            }
        }

        mManager->GetSlicer(0)->GetRenderer()->SetBackground(0.5,0.6,0.9);
        m3DActors[0]->VisibilityOn();

        vtkInteractorStyleTrackballCamera* style = vtkInteractorStyleTrackballCamera::New();
        mManager->SetInteractorStyleNavigator(0,style);
        style->Delete();

        mManager->GetSlicer(0)->GetImageActor()->VisibilityOff();
        mSquaresActor1->VisibilityOff();
        mSquaresActor2->VisibilityOff();
        mManager->Render();
        dimButton->setText("2D");
    }
    else
    {
        mManager->GetSlicer(0)->GetRenderer()->SetBackground(0.0,0.0,0.0);
        vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
        mManager->SetInteractorStyleNavigator(0,style);
        style->Delete();

        mManager->GetSlicer(0)->SetSliceOrientation(2);
        m3DActors[mManager->GetSlicer(0)->GetTSlice()]->VisibilityOff();

        mManager->GetSlicer(0)->GetImageActor()->VisibilityOn();
        mSquaresActor1->VisibilityOn();
        mSquaresActor2->VisibilityOn();
        dimButton->setText("3D");
    }
    QApplication::restoreOverrideCursor();
}

void vvSegmentationDialog::KernelValueChanged(int kernel)
{
    mKernelValue = kernel;
}

void vvSegmentationDialog::Save()
{
    if (dimButton->text() == "2D") //If in *3D* mode, save the mesh
    {
        QString fileName = QFileDialog::getSaveFileName(this,
                tr("Save Mesh As"),
                QDir::home().dirName(),
                "Mesh Files (*.vtk *.vtp)");
        if (!fileName.isEmpty())
        {
            vtkSmartPointer<vtkPolyDataWriter> w = vtkSmartPointer<vtkPolyDataWriter>::New();
            w->SetInput(m3DExtractor->GetOutput());
            w->SetFileName(fileName.toStdString().c_str());
            w->Write();
        }
    }
    else {
        QStringList OutputListeFormat;
        OutputListeFormat.clear();
        int dimension = mManager->GetDimension();
        if (dimension == 1)
        {
            OutputListeFormat.push_back(".mhd");
        }
        if (dimension == 2)
        {
            OutputListeFormat.push_back(".bmp");
            OutputListeFormat.push_back(".png");
            OutputListeFormat.push_back(".jpeg");
            OutputListeFormat.push_back(".tif");
            OutputListeFormat.push_back(".mhd");
            OutputListeFormat.push_back(".hdr");
            OutputListeFormat.push_back(".vox");
        }
        else if (dimension == 3)
        {
            OutputListeFormat.push_back(".mhd");
            OutputListeFormat.push_back(".hdr");
            OutputListeFormat.push_back(".vox");
        }
        else if (dimension == 4)
        {
            OutputListeFormat.push_back(".mhd");
        }
        QString Extensions = "AllFiles(*.*)";
        for (int i = 0; i < OutputListeFormat.count(); i++)
        {
            Extensions += ";;Images ( *";
            Extensions += OutputListeFormat[i];
            Extensions += ")";
        }
        QString fileName = QFileDialog::getSaveFileName(this,
                tr("Save As"),
                QDir::home().dirName(),
                Extensions);
        if (!fileName.isEmpty())
        {
            std::string fileformat = vtksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
            if (OutputListeFormat.contains(
                        fileformat.c_str()))
            {
                QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
                vvProgressDialog progress("Saving "+fileName.toStdString());
                qApp->processEvents();
                vvImageWriter *writer = new vvImageWriter;
                writer->SetOutputFileName(fileName.toStdString());
                writer->SetInput(mManager->GetSlicer(0)->GetImage());
                writer->Update(dimension,"unsigned_char");
                QApplication::restoreOverrideCursor();
                if (writer->GetLastError().size())
                {
                    QString error = "Saving did not succeed\n";
                    error += writer->GetLastError().c_str();
                    QMessageBox::information(this,tr("Saving Problem"),error);
                    Save();
                }
            }
            else
            {
                QString error = fileformat.c_str();
                if (error.isEmpty())
                    error += "no file format specified !";
                else
                    error += " format unknown !!!\n";
                QMessageBox::information(this,tr("Saving Problem"),error);
                Save();
            }
        }
    }
}

#endif /* end #define _vvSegmentationDialog_CXX */