CPVector AutoCtrlPointCreator::readUpdatedControlPoints(const std::string & file,
                                                    PT::Panorama & pano)
{
    ifstream stream(file.c_str());
    if (! stream.is_open()) {
        DEBUG_ERROR("Could not open autopano output: " << file);
        return CPVector();
    }

    Panorama tmpp;
    PanoramaMemento newPano;
    int ptoVersion = 0;
    newPano.loadPTScript(stream, ptoVersion, "");
    tmpp.setMemento(newPano);

    // create mapping between the panorama images.
    map<unsigned int, unsigned int> imgMapping;
    for (unsigned int ni = 0; ni < tmpp.getNrOfImages(); ni++) {
        std::string nname = stripPath(tmpp.getImage(ni).getFilename());
        for (unsigned int oi=0; oi < pano.getNrOfImages(); oi++) {
            std::string oname = stripPath(pano.getImage(oi).getFilename());
            if (nname == oname) {
                // insert image
                imgMapping[ni] = oi;
                break;
            }
        }
        if (! set_contains(imgMapping, ni)) {
            DEBUG_ERROR("Could not find image " << ni << ", name: " << tmpp.getImage(ni).getFilename() << " in autopano output");
            return CPVector();
        }
    }


    // get control points
    CPVector ctrlPoints = tmpp.getCtrlPoints();
    // make sure they are in correct order
    for (CPVector::iterator it= ctrlPoints.begin(); it != ctrlPoints.end(); ++it) {
        (*it).image1Nr = imgMapping[(*it).image1Nr];
        (*it).image2Nr = imgMapping[(*it).image2Nr];
    }

    return ctrlPoints;
}
void AddControlPointsWithCheck(CPVector &cpv, CPVector &new_cp, Panorama *pano=NULL)
{
    for(unsigned int i=0;i<new_cp.size();i++)
    {
        HuginBase::ControlPoint cp=new_cp[i];
        bool duplicate=false;
        for(unsigned int j=0;j<cpv.size();j++)
        {
            if(cp==cpv[j])
            {
                duplicate=true;
                break;
            }
        };
        if(!duplicate)
        {
            cpv.push_back(cp);
            if(pano!=NULL)
                pano->addCtrlPoint(cp);
        };
    };
};
CPVector AutoCtrlPointCreator::readUpdatedControlPoints(const std::string & file,
                                                    PT::Panorama & pano, const PT::UIntSet & imgs)
{
    ifstream stream(file.c_str());
    if (! stream.is_open()) {
        DEBUG_ERROR("Could not open control point detector output: " << file);
        return CPVector();
    }

    Panorama tmpp;
    PanoramaMemento newPano;
    int ptoVersion = 0;
    newPano.loadPTScript(stream, ptoVersion, "");
    tmpp.setMemento(newPano);

    //check if sizes matches
    if(tmpp.getNrOfImages()!=imgs.size())
    {
        return CPVector();
    };

    // create mapping between the panorama images.
    vector<size_t> imgMapping(imgs.size());
    size_t i=0;
    for(UIntSet::const_iterator it=imgs.begin();it!=imgs.end();it++)
    {
        imgMapping[i++]=*it;
    };

    // get control points
    CPVector ctrlPoints = tmpp.getCtrlPoints();
    // make sure they are in correct order
    for (CPVector::iterator it= ctrlPoints.begin(); it != ctrlPoints.end(); ++it) {
        (*it).image1Nr = imgMapping[(*it).image1Nr];
        (*it).image2Nr = imgMapping[(*it).image2Nr];
    }

    return ctrlPoints;
}
bool PanoDetector::matchMultiRow(PoolExecutor& aExecutor)
{
    //step 1
    std::vector<HuginBase::UIntSet> checkedImagePairs(_panoramaInfo->getNrOfImages());
    std::vector<stack_img> stack_images;
    HuginBase::StandardImageVariableGroups* variable_groups = new HuginBase::StandardImageVariableGroups(*_panoramaInfo);
    for(unsigned int i=0; i<_panoramaInfo->getNrOfImages(); i++)
    {
        unsigned int stack_nr=variable_groups->getStacks().getPartNumber(i);
        //check, if this stack is already in list
        bool found=false;
        unsigned int index=0;
        for(index=0; index<stack_images.size(); index++)
        {
            found=(stack_images[index].layer_nr==stack_nr);
            if(found)
            {
                break;
            };
        };
        if(!found)
        {
            //new stack
            stack_images.resize(stack_images.size()+1);
            index=stack_images.size()-1;
            //add new stack
            stack_images[index].layer_nr=stack_nr;
        };
        //add new image
        unsigned int new_image_index=stack_images[index].images.size();
        stack_images[index].images.resize(new_image_index+1);
        stack_images[index].images[new_image_index].img_nr=i;
        stack_images[index].images[new_image_index].ev=_panoramaInfo->getImage(i).getExposure();
    };
    delete variable_groups;
    //get image with median exposure for search with cp generator
    vector<size_t> images_layer;
    UIntSet images_layer_set;
    for(unsigned int i=0; i<stack_images.size(); i++)
    {
        std::sort(stack_images[i].images.begin(),stack_images[i].images.end(),sort_img_ev);
        unsigned int index=0;
        if(stack_images[i].images[0].ev!=stack_images[i].images[stack_images[i].images.size()-1].ev)
        {
            index=stack_images[i].images.size() / 2;
        };
        images_layer.push_back(stack_images[i].images[index].img_nr);
        images_layer_set.insert(stack_images[i].images[index].img_nr);
        if(stack_images[i].images.size()>1)
        {
            //build match list for stacks
            for(unsigned int j=0; j<stack_images[i].images.size()-1; j++)
            {
                size_t img1=stack_images[i].images[j].img_nr;
                size_t img2=stack_images[i].images[j+1].img_nr;
                _matchesData.push_back(MatchData());
                MatchData& aM=_matchesData.back();
                aM._i1=&(_filesData[img1]);
                aM._i2=&(_filesData[img2]);
                checkedImagePairs[img1].insert(img2);
                checkedImagePairs[img2].insert(img1);
            };
        };
    };
    //build match data list for image pairs
    if(images_layer.size()>1)
    {
        std::sort(images_layer.begin(), images_layer.end());
        for(unsigned int i=0; i<images_layer.size()-1; i++)
        {
            size_t img1=images_layer[i];
            size_t img2=images_layer[i+1];
            _matchesData.push_back(MatchData());
            MatchData& aM = _matchesData.back();
            aM._i1 = &(_filesData[img1]);
            aM._i2 = &(_filesData[img2]);
            checkedImagePairs[img1].insert(img2);
            checkedImagePairs[img2].insert(img1);
        };
    };
    TRACE_INFO(endl<< "--- Find matches ---" << endl);
    try
    {
        BOOST_FOREACH(MatchData& aMD, _matchesData)
        aExecutor.execute(new MatchDataRunnable(aMD, *this));
        aExecutor.wait();
    }
    catch(Synchronization_Exception& e)
    {
        TRACE_ERROR(e.what() << endl);
        return false;
    }

    // Add detected matches to _panoramaInfo
    BOOST_FOREACH(MatchData& aM, _matchesData)
    BOOST_FOREACH(lfeat::PointMatchPtr& aPM, aM._matches)
    _panoramaInfo->addCtrlPoint(ControlPoint(aM._i1->_number, aPM->_img1_x, aPM->_img1_y,
                                aM._i2->_number, aPM->_img2_x, aPM->_img2_y));

    // step 2: connect all image groups
    _matchesData.clear();
    Panorama mediumPano=_panoramaInfo->getSubset(images_layer_set);
    CPGraph graph;
    createCPGraph(mediumPano, graph);
    CPComponents comps;
    unsigned int n = findCPComponents(graph, comps);
    if(n>1)
    {
        vector<unsigned int> ImagesGroups;
        for(unsigned int i=0; i<n; i++)
        {
            ImagesGroups.push_back(images_layer[*(comps[i].begin())]);
            if(comps[i].size()>1)
            {
                ImagesGroups.push_back(images_layer[*(comps[i].rbegin())]);
            }
        };
        for(unsigned int i=0; i<ImagesGroups.size()-1; i++)
        {
            for(unsigned int j=i+1; j<ImagesGroups.size(); j++)
            {
                size_t img1=ImagesGroups[i];
                size_t img2=ImagesGroups[j];
                //skip already checked image pairs
                if(set_contains(checkedImagePairs[img1],img2))
                {
                    continue;
                };
                _matchesData.push_back(MatchData());
                MatchData& aM = _matchesData.back();
                aM._i1 = &(_filesData[img1]);
                aM._i2 = &(_filesData[img2]);
                checkedImagePairs[img1].insert(img2);
                checkedImagePairs[img2].insert(img1);
            };
        };
        TRACE_INFO(endl<< "--- Find matches in images groups ---" << endl);
        try
        {
            BOOST_FOREACH(MatchData& aMD, _matchesData)
            aExecutor.execute(new MatchDataRunnable(aMD, *this));
            aExecutor.wait();
        }
        catch(Synchronization_Exception& e)
        {
            TRACE_ERROR(e.what() << endl);
            return false;
        }
        BOOST_FOREACH(MatchData& aM, _matchesData)
        BOOST_FOREACH(lfeat::PointMatchPtr& aPM, aM._matches)
        _panoramaInfo->addCtrlPoint(ControlPoint(aM._i1->_number, aPM->_img1_x, aPM->_img1_y,
                                    aM._i2->_number, aPM->_img2_x, aPM->_img2_y));
    };
    // step 3: now connect all overlapping images
    _matchesData.clear();
    PT::Panorama optPano=_panoramaInfo->getSubset(images_layer_set);
    createCPGraph(optPano, graph);
    if(findCPComponents(graph, comps)==1)
    {
        if(images_layer.size()>2)
        {
            //reset translation parameters
            VariableMapVector varMapVec=optPano.getVariables();
            for(size_t i=0; i<varMapVec.size(); i++)
            {
                map_get(varMapVec[i], "TrX").setValue(0);
                map_get(varMapVec[i], "TrY").setValue(0);
                map_get(varMapVec[i], "TrZ").setValue(0);
            };
            optPano.updateVariables(varMapVec);
            //next steps happens only when all images are connected;
            //now optimize panorama
            PanoramaOptions opts = optPano.getOptions();
            opts.setProjection(PanoramaOptions::EQUIRECTANGULAR);
            opts.optimizeReferenceImage=0;
            // calculate proper scaling, 1:1 resolution.
            // Otherwise optimizer distances are meaningless.
            opts.setWidth(30000, false);
            opts.setHeight(15000);

            optPano.setOptions(opts);
            int w = optPano.calcOptimalWidth();
            opts.setWidth(w);
            opts.setHeight(w/2);
            optPano.setOptions(opts);

            //generate optimize vector, optimize only yaw and pitch
            OptimizeVector optvars;
            const SrcPanoImage& anchorImage = optPano.getImage(opts.optimizeReferenceImage);
            for (unsigned i=0; i < optPano.getNrOfImages(); i++)
            {
                std::set<std::string> imgopt;
                if(i==opts.optimizeReferenceImage)
                {
                    //optimize only anchors pitch, not yaw
                    imgopt.insert("p");
                }
                else
                {
                    imgopt.insert("p");
                    imgopt.insert("y");
                };
                optvars.push_back(imgopt);
            }
            optPano.setOptimizeVector(optvars);

            // remove vertical and horizontal control points
            CPVector cps = optPano.getCtrlPoints();
            CPVector newCP;
            for (CPVector::const_iterator it = cps.begin(); it != cps.end(); it++)
            {
                if (it->mode == ControlPoint::X_Y)
                {
                    newCP.push_back(*it);
                }
            }
            optPano.setCtrlPoints(newCP);

            if (getVerbose() < 2)
            {
                PT_setProgressFcn(ptProgress);
                PT_setInfoDlgFcn(ptinfoDlg);
            };
            //in a first step do a pairwise optimisation
            HuginBase::AutoOptimise::autoOptimise(optPano, false);
            //now the final optimisation
            HuginBase::PTools::optimize(optPano);
            if (getVerbose() < 2)
            {
                PT_setProgressFcn(NULL);
                PT_setInfoDlgFcn(NULL);
            };

            //now match overlapping images
            if(!matchPrealigned(aExecutor, &optPano, checkedImagePairs, images_layer, false))
            {
                return false;
            };
        };
    }
    else
    {
        if(!match(aExecutor, checkedImagePairs))
        {
            return false;
        };
    };
    return true;
};
CPVector AutoPanoSiftMultiRow::automatch(CPDetectorSetting &setting, Panorama & pano, const UIntSet & imgs,
                                     int nFeatures, int & ret_value, wxWindow *parent)
{
    CPVector cps;
    if (imgs.size() < 2) 
    {
        return cps;
    };
    std::vector<wxString> keyFiles(pano.getNrOfImages());
    //generate cp for every consecutive image pair
    unsigned int counter=0;
    for(UIntSet::const_iterator it = imgs.begin(); it != imgs.end(); )
    {
        if(counter==imgs.size()-1)
            break;
        counter++;
        UIntSet ImagePair;
        ImagePair.clear();
        ImagePair.insert(*it);
        it++;
        ImagePair.insert(*it);
        AutoPanoSift matcher;
        CPVector new_cps;
        new_cps.clear();
        if(setting.IsTwoStepDetector())
            new_cps=matcher.automatch(setting, pano, ImagePair, nFeatures, keyFiles, ret_value, parent);
        else
            new_cps=matcher.automatch(setting, pano, ImagePair, nFeatures, ret_value, parent);
        if(new_cps.size()>0)
            AddControlPointsWithCheck(cps,new_cps);
        if(ret_value!=0)
        {
            Cleanup(setting, pano, imgs, keyFiles, parent);
            return cps;
        };
    };
    // now connect all image groups
    // generate temporary panorama to add all found cps
    UIntSet allImgs;
    fill_set(allImgs, 0, pano.getNrOfImages()-1);
    Panorama optPano=pano.getSubset(allImgs);
    for (CPVector::const_iterator it=cps.begin();it!=cps.end();++it)
        optPano.addCtrlPoint(*it);

    CPGraph graph;
    createCPGraph(optPano, graph);
    CPComponents comps;
    int n = findCPComponents(graph, comps);
    if(n>1)
    {
        UIntSet ImagesGroups;
        for(unsigned int i=0;i<n;i++)
        {
            ImagesGroups.insert(*(comps[i].begin()));
            if(comps[i].size()>1)
                ImagesGroups.insert(*(comps[i].rbegin()));
        };
        AutoPanoSift matcher;
        CPVector new_cps;
        if(setting.IsTwoStepDetector())
            new_cps=matcher.automatch(setting, optPano, ImagesGroups, nFeatures, keyFiles, ret_value, parent);
        else
            new_cps=matcher.automatch(setting, optPano, ImagesGroups, nFeatures, ret_value, parent);
        if(new_cps.size()>0)
            AddControlPointsWithCheck(cps,new_cps,&optPano);
        if(ret_value!=0)
        {
            Cleanup(setting, pano, imgs, keyFiles, parent);
            return cps;
        };
        createCPGraph(optPano,graph);
        n=findCPComponents(graph, comps);
    };
    if(n==1 && setting.GetOption())
    {
        //next steps happens only when all images are connected;
        //now optimize panorama
        PanoramaOptions opts = pano.getOptions();
        opts.setProjection(PanoramaOptions::EQUIRECTANGULAR);
        // calculate proper scaling, 1:1 resolution.
        // Otherwise optimizer distances are meaningless.
        opts.setWidth(30000, false);
        opts.setHeight(15000);

        optPano.setOptions(opts);
        int w = optPano.calcOptimalWidth();
        opts.setWidth(w);
        opts.setHeight(w/2);
        optPano.setOptions(opts);

        //generate optimize vector, optimize only yaw and pitch
        OptimizeVector optvars;
        const SrcPanoImage & anchorImage = optPano.getImage(opts.optimizeReferenceImage);
        for (unsigned i=0; i < optPano.getNrOfImages(); i++) 
        {
            std::set<std::string> imgopt;
            if(i==opts.optimizeReferenceImage)
            {
                //optimize only anchors pitch, not yaw
                imgopt.insert("p");
            }
            else
            {
                // do not optimize anchor image's stack for position.
                if(!optPano.getImage(i).YawisLinkedWith(anchorImage))
                {
                    imgopt.insert("p");
                    imgopt.insert("y");
                };
            };
            optvars.push_back(imgopt);
        }
        optPano.setOptimizeVector(optvars);

        // remove vertical and horizontal control points
        CPVector backupOldCPS = optPano.getCtrlPoints();
        CPVector backupNewCPS;
        for (CPVector::const_iterator it = backupOldCPS.begin(); it != backupOldCPS.end(); it++) {
            if (it->mode == ControlPoint::X_Y)
            {
                backupNewCPS.push_back(*it);
            }
        }
        optPano.setCtrlPoints(backupNewCPS);
        // do a first pairwise optimisation step
        HuginBase::AutoOptimise::autoOptimise(optPano,false);
        HuginBase::PTools::optimize(optPano);
        optPano.setCtrlPoints(backupOldCPS);
        //and find cp on overlapping images
        //work only on image pairs, which are not yet connected
        AutoPanoSiftPreAlign matcher;
        CPDetectorSetting newSetting;
        newSetting.SetProg(setting.GetProg());
        newSetting.SetArgs(setting.GetArgs());
        if(setting.IsTwoStepDetector())
        {
            newSetting.SetProgMatcher(setting.GetProgMatcher());
            newSetting.SetArgsMatcher(setting.GetArgsMatcher());
        };
        newSetting.SetOption(true);
        CPVector new_cps;
        if(setting.IsTwoStepDetector())
            new_cps=matcher.automatch(newSetting, optPano, imgs, nFeatures, keyFiles, ret_value, parent);
        else
            new_cps=matcher.automatch(newSetting, optPano, imgs, nFeatures, ret_value, parent);
        if(new_cps.size()>0)
            AddControlPointsWithCheck(cps,new_cps);
    };
    Cleanup(setting, pano, imgs, keyFiles, parent);
    return cps;
};
CPVector AutoPanoSiftMultiRowStack::automatch(CPDetectorSetting &setting, Panorama & pano, const UIntSet & imgs,
                                     int nFeatures, int & ret_value, wxWindow *parent)
{
    CPVector cps;
    if (imgs.size() == 0) {
        return cps;
    };
    std::vector<stack_img> stack_images;
    HuginBase::StandardImageVariableGroups* variable_groups = new HuginBase::StandardImageVariableGroups(pano);
    for(UIntSet::const_iterator it = imgs.begin(); it != imgs.end(); it++)
    {
        unsigned int stack_nr=variable_groups->getStacks().getPartNumber(*it);
        //check, if this stack is already in list
        bool found=false;
        unsigned int index=0;
        for(index=0;index<stack_images.size();index++)
        {
            found=(stack_images[index].layer_nr==stack_nr);
            if(found)
                break;
        };
        if(!found)
        {
            //new stack
            stack_images.resize(stack_images.size()+1);
            index=stack_images.size()-1;
            //add new stack
            stack_images[index].layer_nr=stack_nr;
        };
        //add new image
        unsigned int new_image_index=stack_images[index].images.size();
        stack_images[index].images.resize(new_image_index+1);
        stack_images[index].images[new_image_index].img_nr=*it;
        stack_images[index].images[new_image_index].ev=pano.getImage(*it).getExposure();
    };
    delete variable_groups;
    //get image with median exposure for search with cp generator
    UIntSet images_layer;
    for(unsigned int i=0;i<stack_images.size();i++)
    {
        std::sort(stack_images[i].images.begin(),stack_images[i].images.end(),sort_img_ev);
        unsigned int index=0;
        if(stack_images[i].images[0].ev!=stack_images[i].images[stack_images[i].images.size()-1].ev)
        {
            index=stack_images[i].images.size() / 2;
        };
        images_layer.insert(stack_images[i].images[index].img_nr);
    };
    ret_value=0;
    //work on all stacks
    if(!setting.GetProgStack().IsEmpty())
    {
        CPDetectorSetting stack_setting;
        stack_setting.SetType(CPDetector_AutoPanoSift);
        stack_setting.SetProg(setting.GetProgStack());
        stack_setting.SetArgs(setting.GetArgsStack());

        for(unsigned int i=0;i<stack_images.size();i++)
        {
            UIntSet images_stack;
            images_stack.clear();
            for(unsigned int j=0;j<stack_images[i].images.size();j++)
                images_stack.insert(stack_images[i].images[j].img_nr);
            if(images_stack.size()>1)
            {
                AutoPanoSift matcher;
                CPVector new_cps=matcher.automatch(stack_setting, pano, images_stack, nFeatures, ret_value, parent);
                if(new_cps.size()>0)
                    AddControlPointsWithCheck(cps,new_cps);
                if(ret_value!=0)
                {
                    std::vector<wxString> emptyKeyfiles;
                    Cleanup(setting, pano, imgs, emptyKeyfiles, parent);
                    return cps;
                };
            };
        };
    }
    //generate cp for median exposure with multi-row algorithm
    if(images_layer.size()>1)
    {
        UIntSet allImgs;
        fill_set(allImgs, 0, pano.getNrOfImages()-1);
        Panorama newPano=pano.getSubset(allImgs);
        if(cps.size()>0)
            for (CPVector::const_iterator it=cps.begin();it!=cps.end();++it)
                newPano.addCtrlPoint(*it);

        AutoPanoSiftMultiRow matcher;
        CPVector new_cps=matcher.automatch(setting, newPano, images_layer, nFeatures, ret_value, parent);
        if(new_cps.size()>0)
            AddControlPointsWithCheck(cps,new_cps);
    };
    return cps;
};