+ std::string current = argv[i];
+ if (!current.compare(0,1,"-")) { // && !current.compare(0,2,"--")) { //We are parsing an option
+ if (parse_mode == P_SEQUENCE) {//First finish the current sequence
+ open_sequence(window, open_mode, parse_mode, sequence_filenames, n_image_loaded);
+ }
+ else if (parse_mode == P_WINDOW) { // handle negative window values
+ win=current;
+ window.ApplyWindowToSetOfImages(atof(win.c_str()), first_of_wl_set, n_image_loaded-1);
+ parse_mode=P_NORMAL;
+ new_wl_set = false;
+ continue;
+ } else if (parse_mode == P_LEVEL) { // handle negative level values
+ lev=current;
+ window.ApplyLevelToSetOfImages(atof(lev.c_str()), first_of_wl_set, n_image_loaded-1);
+ parse_mode=P_NORMAL;
+ new_wl_set = false;
+ continue;
+ }
+ if ((current=="--help") || (current=="-h")) {
+ std::cout << "vv " << VV_VERSION << ", the 2D, 2D+t, 3D and 3D+t (or 4D) image viewer" << std::endl << std::endl
+ << "Synopsis: vv file(s) [OPTIONS] file(s)" << std::endl << std::endl
+ << "Open file(s) for visualization." << std::endl << std::endl
+ << "OPTIONS may be:" << std::endl
+ << "--help \t Print command line help and exit." << std::endl
+ << "--window number\t Gray scale window width for set of images appearing before in the cmd line (may appear more than once)." << std::endl
+ << "--level number \t Gray scale window level for set of images appearing before in the cmd line (may appear more than once)." << std::endl
+ << "--linkall \t Link pan, zoom and spatial position of crosshair in images." << std::endl
+ << "--log \t Log output messages in vv-log directory." << std::endl
+ << "--state file \t Read display parameters from file." << std::endl
+ << "--sequence file\t Read all file(s) until next option in a single temporal sequence." << std::endl
+ << std::endl
+ << "These last options must follow a file name since they overlay something on an image:" << std::endl
+ << "--vf file \t Overlay the vector field in file." << std::endl
+ << "--overlay file \t Overlay the image in file with complementary colors." << std::endl
+ << "--fusion file \t Overlay the image in file with alpha blending and colormap." << std::endl
+ //<< "--roi file \t Overlay binary mask images. Option may be repeated on a single base image." << std::endl
+ << "--contour file \t Overlay DICOM RT-STRUCT contours." << std::endl
+ << "--landmarks [--sequence] file(s) \t Overlay the landmarks in file(s) (.txt or .pts)." << std::endl;
+ exit(0);
+ } else if (current=="--vf") {
+ if (!n_image_loaded) load_image_first_error();
+ open_mode = O_VF;
+ } else if (current=="--overlay") {
+ if (!n_image_loaded) load_image_first_error();
+ open_mode = O_OVERLAY;
+ } else if (current=="--contour") {
+ if (!n_image_loaded) load_image_first_error();
+ open_mode = O_CONTOUR;
+ } else if (current=="--fusion") {
+ if (!n_image_loaded) load_image_first_error();
+ open_mode = O_FUSION;
+ } else if (current=="--landmarks") {
+ if (!n_image_loaded) load_image_first_error();
+ open_mode = O_LANDMARKS;
+ } else if (current == "--sequence") {
+ if(open_mode==O_BASE) n_image_loaded++; //count only one for the whole sequence
+ parse_mode=P_SEQUENCE;
+ if (!new_wl_set) {
+ new_wl_set = true;
+ first_of_wl_set = n_image_loaded-1;
+ }
+ } else if (current == "--window") {
+ parse_mode=P_WINDOW;
+ } else if (current == "--level") {
+ parse_mode=P_LEVEL;
+ } else if (current == "--linkall") {
+ link_images = true;
+ }
+ else if (current == "--log") {
+ std::string log_dir = QDir::tempPath().toStdString() + std::string("/vv-log");
+
+ if(itksys::SystemTools::FileExists(log_dir.c_str()) &&
+ !itksys::SystemTools::FileIsDirectory(log_dir.c_str())) {
+ std::cerr << "Error creating log directory, file exists and is not a directory." << std::endl;
+ exit(1);
+ } else if(!itksys::SystemTools::MakeDirectory(log_dir.c_str())) {
+ std::cerr << "Error creating log directory." << std::endl;
+ exit(1);
+ }
+
+ std::string log_file = log_dir + "/" + create_timed_string() + ".log";
+
+ itk::SmartPointer<itk::FileOutputWindow> itk_log = itk::FileOutputWindow::New();
+ itk_log->SetFileName(log_file.c_str());
+ itk_log->FlushOn();
+ itk_log->AppendOn();
+ itk::OutputWindow::SetInstance(itk_log);
+
+ vtkSmartPointer<vtkFileOutputWindow> vtk_log = vtkFileOutputWindow::New();
+ vtk_log->SetFileName(log_file.c_str());
+ vtk_log->FlushOn();
+ vtk_log->AppendOn();
+ vtkOutputWindow::SetInstance(vtk_log);
+ } else if (current == "--state") {
+ //window.ReadSavedStateFile(argv[i+1]);
+ vvReadState read_state;
+ read_state.Run(&window, argv[i+1]);
+ n_image_loaded += read_state.GetNumberOfImages();
+ i++;
+ }
+
+ } else if (parse_mode == P_SEQUENCE) {
+ sequence_filenames.push_back(current);
+ } else if (parse_mode == P_WINDOW) {
+ win=current;
+ window.ApplyWindowToSetOfImages(atof(win.c_str()), first_of_wl_set, n_image_loaded-1);
+ parse_mode=P_NORMAL;
+ new_wl_set = false;
+ } else if (parse_mode == P_LEVEL) {
+ lev=current;
+ window.ApplyLevelToSetOfImages(atof(lev.c_str()), first_of_wl_set, n_image_loaded-1);
+ parse_mode=P_NORMAL;
+ new_wl_set = false;
+ } else {
+ std::vector<std::string> image;
+ image.push_back(current);
+ if(open_mode==O_BASE) {
+ window.LoadImages(image, vvImageReader::IMAGE);
+ n_image_loaded++;
+ if (!new_wl_set) {
+ new_wl_set = true;
+ first_of_wl_set = n_image_loaded-1;
+ }
+ }
+ else if (open_mode==O_VF)
+ window.AddField(current.c_str(), n_image_loaded-1);
+ else if (open_mode==O_OVERLAY)
+ window.AddOverlayImage(n_image_loaded-1,image,vvImageReader::IMAGE);
+ else if (open_mode==O_CONTOUR)
+ window.AddDCStructContour(n_image_loaded-1,current.c_str());
+ else if (open_mode==O_FUSION)
+ window.AddFusionImage(n_image_loaded-1,image,vvImageReader::IMAGE);
+ else if (open_mode==O_LANDMARKS)
+ window.AddLandmarks(n_image_loaded-1,image);
+ open_mode = O_BASE;