/***********************************************************************************
 *                                                                                 *
 * Voreen - The Volume Rendering Engine                                            *
 *                                                                                 *
 * Copyright (C) 2005-2013 University of Muenster, Germany.                        *
 * Visualization and Computer Graphics Group <http://viscg.uni-muenster.de>        *
 * For a list of authors please refer to the file "CREDITS.txt".                   *
 *                                                                                 *
 * This file is part of the Voreen software package. Voreen is free software:      *
 * you can redistribute it and/or modify it under the terms of the GNU General     *
 * Public License version 2 as published by the Free Software Foundation.          *
 *                                                                                 *
 * Voreen 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 in the file   *
 * "LICENSE.txt" along with this file. If not, see <http://www.gnu.org/licenses/>. *
 *                                                                                 *
 * For non-commercial academic use see the license exception specified in the file *
 * "LICENSE-academic.txt". To get information about commercial licensing please    *
 * contact the authors.                                                            *
 *                                                                                 *
 ***********************************************************************************/

#include "isolatedconnectedimagefilter.h"
#include "voreen/core/datastructures/volume/volumeram.h"
#include "voreen/core/datastructures/volume/volume.h"
#include "voreen/core/datastructures/volume/volumeatomic.h"
#include "voreen/core/ports/conditions/portconditionvolumetype.h"
#include "modules/itk/utils/itkwrapper.h"
#include "voreen/core/datastructures/volume/operators/volumeoperatorconvert.h"
#include "itkImage.h"

#include "itkIsolatedConnectedImageFilter.h"

#include <iostream>

namespace voreen {

const std::string IsolatedConnectedImageFilterITK::loggerCat_("voreen.IsolatedConnectedImageFilterITK");

IsolatedConnectedImageFilterITK::IsolatedConnectedImageFilterITK()
    : ITKProcessor(),
    inport1_(Port::INPORT, "InputImage"),
    outport1_(Port::OUTPORT, "OutputImage"),
    seedPointPort1_(Port::INPORT, "seedPointInput1"),
    seedPointPort2_(Port::INPORT, "seedPointInput2"),
    enableProcessing_("enabled", "Enable", false),
    replaceValue_("replaceValue", "ReplaceValue"),
    isolatedValueTolerance_("isolatedValueTolerance", "IsolatedValueTolerance"),
    upper_("upper", "Upper"),
    lower_("lower", "Lower"),
    findUpperThreshold_("findUpperThreshold", "FindUpperThreshold", false)
{
    addPort(inport1_);
    PortConditionLogicalOr* orCondition1 = new PortConditionLogicalOr();
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeUInt8());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeInt8());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeUInt16());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeInt16());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeUInt32());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeInt32());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeFloat());
    orCondition1->addLinkedCondition(new PortConditionVolumeTypeDouble());
    inport1_.addCondition(orCondition1);
    addPort(outport1_);
    addPort(seedPointPort1_);
    addPort(seedPointPort2_);

    addProperty(enableProcessing_);
    addProperty(replaceValue_);
    addProperty(isolatedValueTolerance_);
    addProperty(upper_);
    addProperty(lower_);
    addProperty(findUpperThreshold_);

}

Processor* IsolatedConnectedImageFilterITK::create() const {
    return new IsolatedConnectedImageFilterITK();
}

template<class T>
void IsolatedConnectedImageFilterITK::isolatedConnectedImageFilterITK() {
    replaceValue_.setVolume(inport1_.getData());
    isolatedValueTolerance_.setVolume(inport1_.getData());
    upper_.setVolume(inport1_.getData());
    lower_.setVolume(inport1_.getData());

    if (!enableProcessing_.get()) {
        outport1_.setData(inport1_.getData(), false);
        return;
    }

    typedef itk::Image<T, 3> InputImageType1;
    typedef itk::Image<T, 3> OutputImageType1;

    typename InputImageType1::Pointer p1 = voreenToITK<T>(inport1_.getData());


    //Filter define
    typedef itk::IsolatedConnectedImageFilter<InputImageType1, OutputImageType1> FilterType;
    typename FilterType::Pointer filter = FilterType::New();

    filter->SetInput(p1);


    if (seedPointPort1_.hasChanged()) {
        const PointListGeometry<tgt::vec3>* pointList1 = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort1_.getData());
        if (pointList1) {
            seedPoints1 = pointList1->getData();
        }
    }

    filter->ClearSeeds1();
    typename InputImageType1::IndexType seed1;
    for (size_t i = 0; i < seedPoints1.size(); i++) {
        seed1[0] = seedPoints1[i].x;
        seed1[1] = seedPoints1[i].y;
        seed1[2] = seedPoints1[i].z;
        filter->AddSeed1(seed1);
    }

    if (seedPointPort2_.hasChanged()) {
        const PointListGeometry<tgt::vec3>* pointList2 = dynamic_cast< const PointListGeometry<tgt::vec3>* >(seedPointPort2_.getData());
        if (pointList2) {
            seedPoints2 = pointList2->getData();
        }
    }

    filter->ClearSeeds2();
    typename InputImageType1::IndexType seed2;
    for (size_t i = 0; i < seedPoints2.size(); i++) {
        seed2[0] = seedPoints2[i].x;
        seed2[1] = seedPoints2[i].y;
        seed2[2] = seedPoints2[i].z;
        filter->AddSeed2(seed2);
    }
    filter->SetReplaceValue(replaceValue_.getValue<T>());
    filter->SetIsolatedValueTolerance(isolatedValueTolerance_.getValue<T>());
    filter->SetUpper(upper_.getValue<T>());
    filter->SetLower(lower_.getValue<T>());
    filter->SetFindUpperThreshold(findUpperThreshold_.get());


    observe(filter.GetPointer());

    try
    {
        filter->Update();

    }
    catch (itk::ExceptionObject &e)
    {
        LERROR(e);
    }


    Volume* outputVolume1 = 0;
    outputVolume1 = ITKToVoreenCopy<T>(filter->GetOutput());

    if (outputVolume1) {
        transferRWM(inport1_.getData(), outputVolume1);
        transferTransformation(inport1_.getData(), outputVolume1);
        outport1_.setData(outputVolume1);
    } else
        outport1_.setData(0);



}




void IsolatedConnectedImageFilterITK::process() {
    const VolumeBase* inputHandle1 = inport1_.getData();
    const VolumeRAM* inputVolume1 = inputHandle1->getRepresentation<VolumeRAM>();

    if (dynamic_cast<const VolumeRAM_UInt8*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<uint8_t>();
    }
    else if (dynamic_cast<const VolumeRAM_Int8*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<int8_t>();
    }
    else if (dynamic_cast<const VolumeRAM_UInt16*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<uint16_t>();
    }
    else if (dynamic_cast<const VolumeRAM_Int16*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<int16_t>();
    }
    else if (dynamic_cast<const VolumeRAM_UInt32*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<uint32_t>();
    }
    else if (dynamic_cast<const VolumeRAM_Int32*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<int32_t>();
    }
    else if (dynamic_cast<const VolumeRAM_Float*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<float>();
    }
    else if (dynamic_cast<const VolumeRAM_Double*>(inputVolume1))  {
        isolatedConnectedImageFilterITK<double>();
    }
    else {
        LERROR("Inputformat of Volume 1 is not supported!");
    }

}


}   // namespace
