int main(int argc, char* argv[])
{

    // Exit with usage unless filename given as argument
    if (argc < 2)
    {
            usage();
    }

    unsigned int i = 1, mask = 0;
    double threshold = 0.5;
    vector<string> images_to_mask;
    string pto_file = (""),output_pto = ("");
    string mask_format = ("PNG");
    string model_file = ("celeste.model");
    int course_fine = 0;
    int resize_dimension=800;

    // Deal with arguments
    // parse arguments
    int c;
    const char * optstring = "i:o:d:s:t:m:f:r:h";

    while ((c = getopt (argc, argv, optstring)) != -1)
    {
        switch(c)
        {
            case 'h': 
                usage();
                break;
            case 'i':
                pto_file=optarg;
                break;
            case 'o':
                output_pto=optarg;
                break;
            case 't':
                threshold = atof(optarg);
                if(threshold<=0 || threshold>1)
                {
                    cerr << "Invalid parameter: threshold (-t) should be between 0 and 1" << std::endl;
                    return 1;
                };
                break;
            case 'm': 
                mask = atoi(optarg);
                if(mask<0 || mask>1)
                {
                    cerr << "Invalid parameter: mask parameter (-m) can only be 0 or 1" << std::endl;
                    return 1;
                };
                break;
            case 'f': 
                mask_format = optarg; 
                break;
            case 'd':
                model_file = optarg;
                break;
            case 'r': 
                course_fine = atoi(optarg);
                break;
            case 's': 
                resize_dimension = atoi(optarg);
                if(resize_dimension<100)
                {
                    cerr << "Invalid parameter: maximum dimension (-s) should be bigger than 100" << std::endl;
                    return 1;
                };
                break;
            case ':':
                cerr <<"Missing parameter for parameter " << argv[optind] << endl;
                return 1;
                break;
            case '?': /* invalid parameter */
                return 1;
                break;
            default: /* unknown */
                usage();
        };
    };

    while(optind<argc)
    {
        images_to_mask.push_back(argv[optind]);
        optind++;
    };
    
    if(images_to_mask.size()==0 && pto_file.empty())
    {
        cout << "No project file or image files given."<< endl;
        return 1;
    };

    
	// Check model file
	if (!fileexists(model_file)){
	
#if _WINDOWS
        char buffer[MAX_PATH];//always use MAX_PATH for filepaths
        GetModuleFileName(NULL,buffer,sizeof(buffer));
        string working_path=(buffer);
        string install_path_model="";
        //remove filename
        std::string::size_type pos=working_path.rfind("\\");
        if(pos!=std::string::npos)
        {
            working_path.erase(pos);
            //remove last dir: should be bin
            pos=working_path.rfind("\\");
            if(pos!=std::string::npos)
            {
                working_path.erase(pos);
                //append path delimiter and path
                working_path.append("\\share\\hugin\\data\\");
                install_path_model=working_path;
            }
        }
#elif defined MAC_SELF_CONTAINED_BUNDLE
		char path[PATH_MAX + 1];
		uint32_t size = sizeof(path);
		string install_path_model("");
		if (_NSGetExecutablePath(path, &size) == 0)
		{
			install_path_model=dirname(path);
			install_path_model.append("/../Resources/xrc/");
		}
#else
        string install_path_model = (INSTALL_DATA_DIR);
#endif

		install_path_model.append(model_file);
		
		if (!fileexists(install_path_model)){
		
    			cout << endl << "Couldn't open SVM model file " << model_file << endl;
			cout << "Also tried " << install_path_model << endl << endl; 
    			exit(1);

		}else{
		
			model_file = install_path_model;
		
		}
  	}

	// Set output .pto filename if not given
	if (output_pto == ("") && pto_file != ("")){
		output_pto = pto_file.substr(0,pto_file.length()-4).append("_celeste.pto");
	}

	// Convert mask format to upper case
	transform(mask_format.begin(), mask_format.end(), mask_format.begin(),(int(*)(int)) toupper);
	if (mask_format == ("JPG")){
		mask_format = ("JPEG");
	}
	if (mask_format != ("PNG") &&mask_format != ("BMP") && mask_format != ("GIF") && mask_format !=	("JPEG") && mask_format != ("TIFF")){
		mask_format = ("TIFF");
	}

	// Print some stuff out
	cout << endl << "Celeste: Removes cloud-like control points from Hugin project files and creates image masks" << endl;
	cout << "using Support Vector Machines." << endl;
	cout << endl << "Version " << DISPLAY_VERSION << endl << endl;
	cout << "Arguments:" << endl;
	cout << "Input Hugin file:\t" << pto_file << endl;
	cout << "Output Hugin file:\t" << output_pto << endl;
	cout << "SVM model file:\t\t" << model_file << endl;
	cout << "Max dimension:\t\t" << resize_dimension << endl;
	cout << "SVM threshold:\t\t" << threshold << endl;
	cout << "Create PTO masks:\t";
	if (mask){
		cout << "Yes" << endl;
	}else{
		cout << "No" << endl;
	} 
	cout << "Mask format:\t\t" << mask_format << endl;
	cout << "Filter radius:\t\t";

	// Mask resolution
    int radius;
	if (course_fine)
    {
        radius = 10;
        cout << "Small" << endl << endl;
	}
    else
    {
        radius=20;
        cout << "Large" << endl << endl;
	} 
	
	// Convert mask format to lower case
        cout << "Converting mask format to lower case..." << endl;
	transform(mask_format.begin(), mask_format.end(), mask_format.begin(),(int(*)(int)) tolower);

	// Vectors to store SVM responses and PTO file info etc
	vector<string> images,pto_file_top,pto_file_cps,pto_file_end;
	vector<double> svm_responses;

    cout << "Loading SVMmodel..." << endl;
    struct celeste::svm_model* model;
    if(!celeste::loadSVMmodel(model,model_file))
    {
        cerr << "Could not load SVMmodel" << endl;
        return 1;
    };

    // Mask images
	if (images_to_mask.size())
    {
        cout << "Masking images..." << endl << endl;
        for (unsigned int l = 0; l < images_to_mask.size(); l++)
        {
            std::string imagefile=images_to_mask[l];
            try
            {
                cout << "Opening image file:\t" << imagefile << endl;
                // Read image given and convert to UInt16
                vigra::UInt16RGBImage in=loadAndConvertImage(imagefile);
                if(in.width()==0 || in.height()==0)
                {
                    continue;
                };

                // Create mask file name
                string mask_name = generateMaskName(imagefile,mask_format);

                cout << "Generating mask:\t" << mask_name << endl;				
                // Create mask
                vigra::BImage mask=celeste::getCelesteMask(model,in,radius,threshold,resize_dimension);
                exportImage(srcImageRange(mask), vigra::ImageExportInfo(mask_name.c_str()).setPixelType("UINT8"));
            }
            catch (vigra::StdException & e)
            {
                // catch any errors that might have occured and print their reason
                cout << "Unable to open file:\t" << imagefile << endl << endl;
                cout << e.what() << endl << endl;
    		};
        };
	};

    // Process PTO file
    if (pto_file != (""))
    {
  		cout << "Parsing Hugin project file " << pto_file << endl << endl;

        Panorama pano;
        ifstream prjfile(pto_file.c_str());
        if (!prjfile.good())
        {
            cerr << "could not open script : " << pto_file << endl;
            celeste::destroySVMmodel(model);
            return 1;
        }
        pano.setFilePrefix(hugin_utils::getPathPrefix(pto_file));
        DocumentData::ReadWriteError err = pano.readData(prjfile);
        if (err != DocumentData::SUCCESSFUL)
        {
            cerr << "error while parsing panos tool script: " << pto_file << endl;
            cerr << "DocumentData::ReadWriteError code: " << err << endl;
            celeste::destroySVMmodel(model);
            return 1;
        }
	cout << "Done parsing Hugin step 1" << endl;

        for(unsigned int i=0;i<pano.getNrOfImages();i++)
        {
            CPointVector cps=pano.getCtrlPointsVectorForImage(i);
            if(cps.size()>0 || mask)
            {
                try
                {
                    string imagefile=pano.getImage(i).getFilename();
                    vigra::UInt16RGBImage in=loadAndConvertImage(imagefile);
                    if(in.width()==0 || in.height()==0)
                    {
                        continue;
                    };
                    if(cps.size()>0)
                    {
                        UIntSet cloudCP=celeste::getCelesteControlPoints(model,in,cps,radius,threshold,resize_dimension);
                        if(cloudCP.size()>0)
                        {
                            for(UIntSet::reverse_iterator it=cloudCP.rbegin();it!=cloudCP.rend();++it)
                            {
                                pano.removeCtrlPoint(*it);
                            };
                        };
                    };
                    if(mask)
                    {
                        string mask_name = generateMaskName(imagefile,mask_format);
                        // Create mask
                        vigra::BImage mask=celeste::getCelesteMask(model,in,radius,threshold,resize_dimension);
                        exportImage(srcImageRange(mask), vigra::ImageExportInfo(mask_name.c_str()).setPixelType("UINT8"));
                    };
                }
                catch (vigra::StdException & e)
                {
                    // catch any errors that might have occured and print their reason
                    cout << "Unable to open file:\t" << pano.getImage(i).getFilename() << endl << endl;
                    cout << e.what() << endl << endl;
    		    };
            };
        };
        cout << "about to write new pto file" << endl;

		// write new pto file
        ofstream of(output_pto.c_str());
        UIntSet imgs;
	cout << "fill_set..." << endl;
        fill_set(imgs,0, pano.getNrOfImages()-1);
	cout << "printing..." << endl; 
        pano.printPanoramaScript(of, pano.getOptimizeVector(), pano.getOptions(), imgs, false, hugin_utils::getPathPrefix(pto_file));
    
        cout << endl << "Written file " << output_pto << endl << endl;
	}
    celeste::destroySVMmodel(model);
	return(0);
	
}	
int main(int argc, char *argv[])
{
    // parse arguments
    const char * optstring = "o:hn:pws";

    int c;
    string output;
    bool onlyPair = false;
    bool wholePano = false;
    bool skipOptimisation = false;
    double n = 2.0;
    while ((c = getopt (argc, argv, optstring)) != -1)
    {
        switch (c) {
        case 'o':
            output = optarg;
            break;
        case 'h':
            usage(argv[0]);
            return 0;
        case 'n':
            n = atof(optarg);
            if(n==0)
            {
                cerr <<"Invalid parameter: " << optarg << " is not valid real number" << endl;
                return 1;
            };
	        if (n<1.0) 
            {
		        cerr << "Invalid parameter: n must be at least 1" << endl;
		        return 1;
            };
            break;
        case 'p':
            onlyPair= true;
            break;
        case 'w':
            wholePano = true;
            break;
        case 's':
            skipOptimisation = true;
            break;
        case ':':
            cerr <<"Option -n requires a number" << endl;
            return 1;
            break;
        case '?':
            break;
        default:
            abort ();
        }
    }

    if (argc - optind != 1) 
    {
        usage(argv[0]);
        return 1;
    };
    
    if (onlyPair && wholePano)
    {
        cerr << "Options -p and -w can't used together" << endl;
        return 1;
    };

    string input=argv[optind];

    Panorama pano;
    ifstream prjfile(input.c_str());
    if (!prjfile.good()) {
        cerr << "could not open script : " << input << endl;
        return 1;
    }
    pano.setFilePrefix(hugin_utils::getPathPrefix(input));
    DocumentData::ReadWriteError err = pano.readData(prjfile);
    if (err != DocumentData::SUCCESSFUL) {
        cerr << "error while parsing panos tool script: " << input << endl;
        cerr << "DocumentData::ReadWriteError code: " << err << endl;
        return 1;
    }

    size_t nrImg=pano.getNrOfImages();
    if (nrImg < 2) 
    {
        cerr << "Panorama should consist of at least two images" << endl;
        return 1;
    }

    if (pano.getNrOfCtrlPoints() < 3)
    {
        cerr << "Panorama should contain at least 3 control point" << endl;
    };
    
    size_t cpremoved1=0;
    UIntSet CPtoRemove;
    // step 1 with pairwise optimisation
    if(!wholePano)
    {
        CPtoRemove=getCPoutsideLimit_pair(pano,n);
        if (CPtoRemove.size()>0)
            for(UIntSet::reverse_iterator it = CPtoRemove.rbegin(); it != CPtoRemove.rend(); ++it)
                pano.removeCtrlPoint(*it);
        cpremoved1=CPtoRemove.size();
    };

    // step 2 with optimisation of whole panorama
    bool unconnected=false;
    if(!onlyPair)
    {
        //check for unconnected images
        CPGraph graph;
        createCPGraph(pano, graph);
        CPComponents comps;
        int parts=findCPComponents(graph, comps);
        if (parts > 1) 
        {
            unconnected=true;
        }
        else
        {
            CPtoRemove.clear();
            if(skipOptimisation)
            {
                std::cout << endl << "Skipping optimisation, current image positions will be used." << endl;
            };
            CPtoRemove=getCPoutsideLimit(pano,n,skipOptimisation);
            if (CPtoRemove.size()>0)
                for(UIntSet::reverse_iterator it = CPtoRemove.rbegin(); it != CPtoRemove.rend(); ++it)
                    pano.removeCtrlPoint(*it);
        };
    };

    cout << endl;
    if(!wholePano)
        cout << "Removed " << cpremoved1 << " control points in step 1" << endl;
    if(!onlyPair)
        if(unconnected)
            cout <<"Skipped step 2 because of unconnected image pairs" << endl;
        else
            cout << "Removed " << CPtoRemove.size() << " control points in step 2" << endl;

    //write output
    OptimizeVector optvec = pano.getOptimizeVector();
    UIntSet imgs;
    fill_set(imgs,0, pano.getNrOfImages()-1);
 	// Set output .pto filename if not given
	if (output=="")
    {
        output=input.substr(0,input.length()-4).append("_clean.pto");
	}
    ofstream of(output.c_str());
    pano.printPanoramaScript(of, optvec, pano.getOptions(), imgs, false, hugin_utils::getPathPrefix(input));
    
    cout << endl << "Written output to " << output << endl;
    return 0;
}