vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #ifdef VTK_USE_FFMPEG_ENCODER
  72 #  include <vtkFFMPEGWriter.h>
  73 #endif
  74 #ifdef VTK_USE_MPEG2_ENCODER
  75 #  include <vtkMPEG2Writer.h>
  76 #endif
  77 #include <vtkMatrix4x4.h>
  78 #include <vtkTransform.h>
  79
  80 // Standard includes
  81 #include <iostream>
  82 #include <sstream>
  83 #include <iomanip>
  84
  85 #define COLUMN_TREE 0
  86 #define COLUMN_UL_VIEW 1
  87 #define COLUMN_UR_VIEW 2
  88 #define COLUMN_DL_VIEW 3
  89 #define COLUMN_DR_VIEW 4
  90 #define COLUMN_CLOSE_IMAGE 5
  91 #define COLUMN_RELOAD_IMAGE 6
  92 #define COLUMN_IMAGE_NAME 7
  93
  94 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  95
  96 /*Data Tree values
  97   0,Qt::UserRole full filename
  98   1,Qt::CheckStateRole checkbutton UL View
  99   1,Qt::UserRole overlay, fusion or vector
 100   2,Qt::CheckStateRole checkbutton UR View
 101   3,Qt::CheckStateRole checkbutton DL View
 102   4,Qt::CheckStateRole checkbutton DR View
 103   5,0  short filename
 104   5,Qt::UserRole mSlicerManager id*/
 105
 106 //------------------------------------------------------------------------------
 107 vvMainWindow::vvMainWindow():vvMainWindowBase()
 108 {
 109   setupUi(this); // this sets up the GUI
 110
 111   mInputPathName = "";
 112   mMenuTools = menuTools;
 113   //  mMenuSegmentation = menuSegmentation;
 114   mContextMenu = &contextMenu;
 115   mMenuExperimentalTools = menuExperimental;
 116   mMainWidget = this;
 117   mCurrentTime = -1;
 118   mCurrentSelectedImageId = "";
 119   mCurrentPickedImageId = "";
 120   mCurrentPickedImageIndex = 0;
 121
 122   //Init the contextMenu
 123   this->setContextMenuPolicy(Qt::CustomContextMenu);
 124   contextActions.resize(0);
 125   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 126                                   tr("O&pen new Image"));
 127   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 128   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 129   contextActions.push_back(actionOpen_new_image);
 130   contextMenu.addSeparator();
 131
 132   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 133                                tr("Close Current Image"));
 134   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 135   contextActions.push_back(actionClose_Image);
 136
 137   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 138                                 tr("Reload Current Image"));
 139   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 140   contextActions.push_back(actionReload_image);
 141
 142   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 143                               tr("Save Current Image"));
 144   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 145   contextActions.push_back(actionSave_image);
 146
 147   contextMenu.addSeparator();
 148
 149   contextMenu.addAction(actionAdd_VF_to_current_Image);
 150   contextActions.push_back(actionAdd_VF_to_current_Image);
 151
 152   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 153       tr("Add overlay image to current image"));
 154   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 155   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 156
 157   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 158
 159   contextMenu.addAction(actionAdd_fusion_image);
 160   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 161   contextActions.push_back(actionAdd_fusion_image);
 162
 163   // TRIAL DS
 164   /*
 165   QMenu * m = new QMenu(menubar);
 166   m->setTitle("TOTO");
 167   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 168   contextMenu.addMenu(m);
 169   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON"));
 171   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 172                      tr("BIDON2"));
 173   m->addAction(a);
 174   m->addAction(b);
 175   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 176   */
 177
 178   //init the DataTree
 179   mSlicerManagers.resize(0);
 180
 181   QStringList header;
 182   header.append("");
 183   header.append("TL");
 184   header.append("TR");
 185   header.append("BL");
 186   header.append("BR");
 187   header.append("");
 188   header.append("");
 189   header.append("Name");
 190
 191   DataTree->setHeaderLabels(header);
 192   DataTree->resizeColumnToContents(COLUMN_TREE);
 193   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 197   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 199   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 200
 201   viewMode = 1;
 202   documentation = new vvDocumentation();
 203   help_dialog = new vvHelpDialog();
 204   dicomSeriesSelector = new vvDicomSeriesSelector();
 205
 206   inverseButton->setEnabled(0);
 207   actionAdd_Overlay_to_current_Image->setEnabled(0);
 208   actionSave_As->setEnabled(0);
 209   actionAdd_VF_to_current_Image->setEnabled(0);
 210   actionAdd_fusion_image->setEnabled(0);
 211
 212   //init the sliders
 213   verticalSliders.push_back(NOVerticalSlider);
 214   verticalSliders.push_back(NEVerticalSlider);
 215   verticalSliders.push_back(SOVerticalSlider);
 216   verticalSliders.push_back(SEVerticalSlider);
 217
 218   for (int i =0; i < 4; i++)
 219     verticalSliders[i]->hide();
 220
 221   horizontalSliders.push_back(NOHorizontalSlider);
 222   horizontalSliders.push_back(NEHorizontalSlider);
 223   horizontalSliders.push_back(SOHorizontalSlider);
 224   horizontalSliders.push_back(SEHorizontalSlider);
 225
 226   for (int i =0; i < 4; i++)
 227     horizontalSliders[i]->hide();
 228
 229
 230   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 231   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 232   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 233   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 234
 235   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 236   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 237   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 238   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 239
 240   //connect everything
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 250   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 251   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 252   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 253   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 254   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 255   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 256   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 257   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 258
 259   ///////////////////////////////////////////////
 260   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 261   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 262   ///////////////////////////////////////////////
 263
 264   actionNorth_East_Window->setEnabled(0);
 265   actionNorth_West_Window->setEnabled(0);
 266   actionSouth_East_Window->setEnabled(0);
 267   actionSouth_West_Window->setEnabled(0);
 268
 269   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 270   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 271   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 272   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 273
 274   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 275   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 276           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 277
 278   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 279   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 281   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 282   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 283   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 284   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 285
 286
 287   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 288
 289   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 290   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 291   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 292   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 293   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double)),
 294           this,SLOT(SetFusionProperty(int,int,int,double,double)));
 295   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 296
 297   playMode = 0;//pause
 298   mFrameRate = 10;
 299   playButton->setEnabled(0);
 300   frameRateLabel->setEnabled(0);
 301   frameRateSpinBox->setEnabled(0);
 302   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 303   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 304
 305   goToCursorPushButton->setEnabled(0);
 306   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 307
 308   NOViewWidget->hide();
 309   NEViewWidget->hide();
 310   SOViewWidget->hide();
 311   SEViewWidget->hide();
 312
 313   //Recently opened files
 314   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 315   recentlyOpenedFilesMenu=NULL;
 316   if ( !recent_files.empty() ) {
 317     createRecentlyOpenedFilesMenu();
 318     updateRecentlyOpenedFilesMenu(recent_files);
 319   }
 320
 321   // Adding all new tools (insertion in the menu)
 322   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 323   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 324
 325   if (!CLITK_EXPERIMENTAL)
 326     menuExperimental->menuAction()->setVisible(false);
 327
 328
 329   QTimer * timerMemory = new QTimer(this);
 330   //timerMemory->setInterval(5);
 331   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 332   timerMemory->start(2000);
 333 }
 334 //------------------------------------------------------------------------------
 335 void vvMainWindow::show()
 336 {
 337   vvMainWindowBase::show();
 338   PopupRegisterForm(true);
 339 }
 340 //------------------------------------------------------------------------------
 341 void vvMainWindow::UpdateMemoryUsage()
 342 {
 343   //  clitk::PrintMemory(true);
 344   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 345   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 346 }
 347 //------------------------------------------------------------------------------
 348
 349
 350 //------------------------------------------------------------------------------
 351 void vvMainWindow::createRecentlyOpenedFilesMenu()
 352 {
 353   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 354   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 355   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 356   menuFile->insertSeparator(actionOpen_Image_With_Time);
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362
 363 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 364 {
 365   if(recentlyOpenedFilesMenu==NULL) {
 366     createRecentlyOpenedFilesMenu();
 367   } else {
 368     recentlyOpenedFilesMenu->clear();
 369   }
 370   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 371     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 372     recentlyOpenedFilesMenu->addAction(current);
 373     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 374   }
 375 }
 376 //------------------------------------------------------------------------------
 377
 378
 379 //------------------------------------------------------------------------------
 380 void vvMainWindow::ComputeMidPosition()
 381 {
 382   bool ok;
 383   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 384   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 385                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 386   if (ok) {
 387     vvMidPosition midp;
 388     midp.slicer_manager = mSlicerManagers[index];
 389     midp.reference_image_index = ref;
 390     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 391     midp.Update();
 392     if (midp.error)
 393       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 394     else {
 395       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 396       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 397     }
 398     QApplication::restoreOverrideCursor();
 399   }
 400 }
 401 //------------------------------------------------------------------------------
 402
 403
 404 //------------------------------------------------------------------------------
 405 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 406 {
 407   QTreeWidgetItem *item = new QTreeWidgetItem();
 408   item->setData(0,Qt::UserRole,"filename.vtk");
 409   item->setData(1,Qt::UserRole,tr("contour"));
 410   QBrush brush;
 411   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 412   brush.setStyle(Qt::SolidPattern);
 413   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 414   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 415
 416   for (int j = 1; j <= 4; j++)
 417     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 418
 419   QTreePushButton* cButton = new QTreePushButton;
 420   cButton->setItem(item);
 421   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 422   cButton->setToolTip(tr("close image"));
 423   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 424   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 425           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 426
 427   QTreePushButton* rButton = new QTreePushButton;
 428   rButton->setItem(item);
 429   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 430   rButton->setToolTip(tr("reload image"));
 431   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 432   rButton->setEnabled(false);
 433   //Not implemented
 434   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 435   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 436
 437   DataTree->topLevelItem(image_index)->setExpanded(1);
 438   DataTree->topLevelItem(image_index)->addChild(item);
 439   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 440   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 441   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 442   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 443
 444   UpdateTree();
 445   mSlicerManagers[image_index]->AddContour(contour,propagation);
 446   mSlicerManagers[image_index]->Render();
 447 }
 448 //------------------------------------------------------------------------------
 449
 450
 451 //------------------------------------------------------------------------------
 452 void vvMainWindow::OpenVTKContour()
 453 {
 454   if (mSlicerManagers.size() > 0) {
 455     QString Extensions = "Images ( *.vtk *.obj)";
 456     Extensions += ";;All Files (*)";
 457     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 458     if (file.isNull())
 459       return;
 460     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 461     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 462     vvMeshReader reader;
 463     reader.SetImage(mSlicerManagers[index]->GetImage());
 464     reader.SetModeToVTK();
 465     reader.SetFilename(file.toStdString());
 466     reader.Update();
 467     AddContour(index,reader.GetOutput()[0],false);
 468     QApplication::restoreOverrideCursor();
 469   }
 470 }
 471 //------------------------------------------------------------------------------
 472
 473
 474 //------------------------------------------------------------------------------
 475 void vvMainWindow::OpenDCStructContour()
 476 {
 477   if (mSlicerManagers.size() > 0) {
 478     QString Extensions = "Dicom Files ( *.dcm RS*)";
 479     Extensions += ";;All Files (*)";
 480     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 481     if (file.isNull())
 482       return;
 483     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 484     vvMeshReader reader;
 485     reader.SetFilename(file.toStdString());
 486     vvStructSelector selector;
 487     selector.SetStructures(reader.GetROINames());
 488     if (!mSlicerManagers[index]->GetVF().IsNull())
 489       selector.EnablePropagationCheckBox();
 490     if (selector.exec()) {
 491       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 492       reader.SetSelectedItems(selector.getSelectedItems());
 493       reader.SetImage(mSlicerManagers[index]->GetImage());
 494       if (selector.PropagationEnabled())
 495         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 496       reader.Update();
 497       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 498       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 499            i!=contours.end(); i++)
 500         AddContour(index,*i,selector.PropagationEnabled());
 501       QApplication::restoreOverrideCursor();
 502     }
 503   }
 504 }
 505 //------------------------------------------------------------------------------
 506
 507
 508 //------------------------------------------------------------------------------
 509 void vvMainWindow::ComputeDeformableRegistration()
 510 {
 511   if (mSlicerManagers.size() > 0) {
 512     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 513     vvDeformationDialog dialog(index,mSlicerManagers);
 514     if (dialog.exec()) {
 515       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 516       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 517       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 518     } else
 519       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 520   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::WarpImage()
 527 {
 528   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 529   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 530     bool ok;
 531     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 532                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 533     if (ok) {
 534       WarpImage(mSlicerManagers[index],ref);
 535     }
 536   } else
 537     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 538 }
 539 //------------------------------------------------------------------------------
 540
 541
 542 //------------------------------------------------------------------------------
 543 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 544 {
 545   if (!selected_slicer->GetVF().IsNull()) {
 546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 547     QFileInfo info(selected_slicer->GetFileName().c_str());
 548     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 549                      reference_phase,this);
 550     if (warp.ComputeWarpedImage()) {
 551       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 552       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 553       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 554       QApplication::restoreOverrideCursor();
 555     } else {
 556       QApplication::restoreOverrideCursor();
 557       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 558     }
 559   } else
 560     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 561 }
 562 //------------------------------------------------------------------------------
 563
 564
 565 //------------------------------------------------------------------------------
 566 vvMainWindow::~vvMainWindow()
 567 {
 568   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 569     if (mSlicerManagers[i] != NULL)
 570       delete mSlicerManagers[i];
 571   }
 572 }
 573 //------------------------------------------------------------------------------
 574
 575 //------------------------------------------------------------------------------
 576 QTabWidget * vvMainWindow::GetTab()
 577 {
 578   return tabWidget;
 579 }
 580 //------------------------------------------------------------------------------
 581
 582
 583 //------------------------------------------------------------------------------
 584 void vvMainWindow::MergeImages()
 585 {
 586   QString Extensions = EXTENSIONS;
 587   Extensions += ";;All Files (*)";
 588   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 589   if (files.isEmpty())
 590     return;
 591   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 592   std::vector<std::string> vector;
 593
 594   unsigned int currentDim = 0;
 595   std::vector<double> currentSpacing;
 596   std::vector<int> currentSize;
 597   std::vector<double> currentOrigin;
 598
 599   for (int i = 0; i < files.size(); i++) {
 600     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 601                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 602     reader->SetFileName(files[i].toStdString().c_str());
 603     reader->ReadImageInformation();
 604     if (reader)        {
 605       //NOViewWidget->hide();
 606       //NEViewWidget->hide();
 607       //SOViewWidget->hide();
 608       //SEViewWidget->hide();
 609       if (i == 0)
 610         currentDim = reader->GetNumberOfDimensions();
 611       bool IsOk = true;
 612       for (unsigned int j = 0; j < currentDim; j++) {
 613         if (i == 0) {
 614           if (j == 0) {
 615             currentSpacing.resize(currentDim);
 616             currentSize.resize(currentDim);
 617             currentOrigin.resize(currentDim);
 618           }
 619           currentOrigin[j] = reader->GetOrigin(j);
 620           currentSpacing[j] = reader->GetSpacing(j);
 621           currentSize[j] = reader->GetDimensions(j);
 622         } else if (currentDim != reader->GetNumberOfDimensions()
 623                    || currentSpacing[j] != reader->GetSpacing(j)
 624                    || currentSize[j] != (int)reader->GetDimensions(j)
 625                    || currentOrigin[j] != reader->GetOrigin(j)) {
 626           QString error = "Cannot read file (too different from others ";
 627           error += files[i].toStdString().c_str();
 628           QMessageBox::information(this,tr("Reading problem"),error);
 629           IsOk = false;
 630           break;
 631         }
 632       }
 633       if (IsOk)
 634         vector.push_back(files[i].toStdString());
 635     }
 636   }
 637   if (vector.size() > 0)
 638     LoadImages(vector, vvImageReader::MERGED);
 639 }
 640 //------------------------------------------------------------------------------
 641
 642 //------------------------------------------------------------------------------
 643 void vvMainWindow::SliceImages()
 644 {
 645   QString Extensions = EXTENSIONS;
 646   Extensions += ";;All Files (*)";
 647
 648   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 649   if (files.isEmpty())
 650     return;
 651   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 652   std::vector<std::string> vector;
 653   for (int i = 0; i < files.size(); i++)
 654     vector.push_back(files[i].toStdString());
 655   LoadImages(vector, vvImageReader::SLICED);
 656 }
 657 //------------------------------------------------------------------------------
 658
 659 //------------------------------------------------------------------------------
 660 void vvMainWindow::MergeImagesWithTime()
 661 {
 662   QString Extensions = EXTENSIONS;
 663   Extensions += ";;All Files (*)";
 664   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 665   if (files.isEmpty())
 666     return;
 667   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 668   std::vector<std::string> vector;
 669
 670   unsigned int currentDim = 0;
 671   std::vector<double> currentSpacing;
 672   std::vector<int> currentSize;
 673   std::vector<double> currentOrigin;
 674
 675   for (int i = 0; i < files.size(); i++) {
 676     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 677                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 678     if (reader) {
 679       reader->SetFileName(files[i].toStdString().c_str());
 680       reader->ReadImageInformation();
 681       if (i == 0)
 682         currentDim = reader->GetNumberOfDimensions();
 683       bool IsOk = true;
 684       for (unsigned int j = 0; j < currentDim; j++) {
 685         if (i == 0) {
 686           if (j == 0) {
 687             currentSpacing.resize(currentDim);
 688             currentSize.resize(currentDim);
 689             currentOrigin.resize(currentDim);
 690           }
 691           currentOrigin[j] = reader->GetOrigin(j);
 692           currentSpacing[j] = reader->GetSpacing(j);
 693           currentSize[j] = reader->GetDimensions(j);
 694         } else if (currentDim != reader->GetNumberOfDimensions()
 695                    || currentSpacing[j] != reader->GetSpacing(j)
 696                    || currentSize[j] != (int)reader->GetDimensions(j)
 697                    || currentOrigin[j] != reader->GetOrigin(j)) {
 698           QString error = "Cannot read file (too different from others ";
 699           error += files[i].toStdString().c_str();
 700           QMessageBox::information(this,tr("Reading problem"),error);
 701           IsOk = false;
 702           break;
 703         }
 704       }
 705       if (IsOk)
 706         vector.push_back(files[i].toStdString());
 707     } else {
 708       QString error = "Cannot read file info for ";
 709       error += files[i].toStdString().c_str();
 710       error += "\n";
 711       error += "Maybe you're trying to open an image in an unsupported format?\n";
 712       QMessageBox::information(this,tr("Reading problem"),error);
 713     }
 714   }
 715   sort(vector.begin(),vector.end());
 716   if (vector.size() > 1)
 717     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 718   else
 719     QMessageBox::warning(this,tr("Reading problem"),"You need to select at least two images to merge images with time.\nIf you only want to open one image, please use the \"Open Image\" function.");
 720 }
 721 //------------------------------------------------------------------------------
 722
 723
 724 //------------------------------------------------------------------------------
 725 void vvMainWindow::OpenDicom()
 726 {
 727   std::vector<std::string> files;
 728
 729   std::cout << "dicomSeriesSelector " << std::endl;
 730   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 731     files = *(dicomSeriesSelector->GetFilenames());
 732     LoadImages(files, vvImageReader::DICOM);
 733   }
 734 }
 735 //------------------------------------------------------------------------------
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenImages()
 739 {
 740   QString Extensions = EXTENSIONS;
 741   Extensions += ";;All Files (*)";
 742
 743   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 744   if (files.isEmpty())
 745     return;
 746   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 747   std::vector<std::string> vector;
 748   for (int i = 0; i < files.size(); i++)
 749     vector.push_back(files[i].toStdString());
 750   LoadImages(vector, vvImageReader::IMAGE);
 751 }
 752 //------------------------------------------------------------------------------
 753 void vvMainWindow::OpenRecentImage()
 754 {
 755   QAction * caller = qobject_cast<QAction*>(sender());
 756   std::vector<std::string> images;
 757   images.push_back(caller->text().toStdString());
 758   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 759   LoadImages(images, vvImageReader::IMAGE);
 760 }
 761 //------------------------------------------------------------------------------
 762
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::OpenImageWithTime()
 766 {
 767   QString Extensions = EXTENSIONS;
 768   Extensions += ";;All Files (*)";
 769
 770   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 771   if (files.isEmpty())
 772     return;
 773   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 774   std::vector<std::string> vector;
 775   for (int i = 0; i < files.size(); i++) {
 776     vector.push_back(files[i].toStdString());
 777   }
 778   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 779 }
 780 //------------------------------------------------------------------------------
 781
 782
 783 //------------------------------------------------------------------------------
 784 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 785 {
 786   //Separate the way to open images and dicoms
 787   int fileSize;
 788   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 789     fileSize = files.size();
 790   else
 791     fileSize = 1;
 792
 793   // For SLICED, we need the number of slices (ndim and #slices)
 794   std::vector<unsigned int> nSlices;
 795   nSlices.resize(files.size());
 796   std::fill(nSlices.begin(), nSlices.end(), 1);
 797   if (filetype == vvImageReader::SLICED) {
 798     for (int i = 0; i < fileSize; i++) {
 799       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 800       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 801       if (!header) {
 802         nSlices[i] = 0;
 803         QString error = "Cannot open file \n";
 804         error += files[i].c_str();
 805         QMessageBox::information(this,tr("Reading problem"),error);
 806         return;
 807       }
 808       if (header->GetNumberOfDimensions() < 3) {
 809         nSlices[i] = 0;
 810         QString error = "Dimension problem. Cannot slice \n";
 811         error += files[i].c_str();
 812         QMessageBox::information(this,tr("Reading problem"),error);
 813         return;
 814       }
 815       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 816     }
 817   }
 818
 819   //Only add to the list of recently opened files when a single file is opened,
 820   //to avoid polluting the list of recently opened files
 821   if (files.size() == 1) {
 822     QFileInfo finfo=tr(files[0].c_str());
 823     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 824     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 825   }
 826   //init the progress events
 827   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 828   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 829   qApp->processEvents();
 830
 831   int numberofsuccesulreads=0;
 832   //open images as 1 or multiples
 833   for (int i = 0; i < fileSize; i++) {
 834
 835     progress.SetText("Opening " + files[i]);
 836     progress.SetProgress(i,fileSize);
 837     qApp->processEvents();
 838
 839     for (unsigned int j = 0; j < nSlices[i]; j++) {
 840       //read the image and put it in mSlicerManagers
 841       vvSlicerManager* imageManager = new vvSlicerManager(4);
 842       qApp->processEvents();
 843
 844       bool SetImageSucceed=false;
 845
 846       // Change filename if an image with the same already exist
 847       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 848
 849       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 850         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 851       else {
 852         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 853       }
 854       if (!SetImageSucceed) {
 855         QApplication::restoreOverrideCursor();
 856         QString error = "Cannot open file \n";
 857         error += imageManager->GetLastError().c_str();
 858         QMessageBox::information(this,tr("Reading problem"),error);
 859         delete imageManager;
 860       } else {
 861         mSlicerManagers.push_back(imageManager);
 862
 863         //create an item in the tree with good settings
 864         QTreeWidgetItem *item = new QTreeWidgetItem();
 865         item->setData(0,Qt::UserRole,files[i].c_str());
 866         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 867         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 868         item->setData(1,Qt::UserRole,tr("image"));
 869         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 870         qApp->processEvents();
 871
 872         //Create the buttons for reload and close
 873         qApp->processEvents();
 874         QTreePushButton* cButton = new QTreePushButton;
 875         cButton->setItem(item);
 876         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 877         cButton->setToolTip(tr("close image"));
 878         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 879         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 880                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 881
 882         QTreePushButton* rButton = new QTreePushButton;
 883         rButton->setItem(item);
 884         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 885         rButton->setToolTip(tr("reload image"));
 886         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 887         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 888                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 889
 890         DataTree->addTopLevelItem(item);
 891         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 892         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 893
 894         //set the id of the image
 895         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 896         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 897         mSlicerManagers.back()->SetId(id.toStdString());
 898
 899         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 900
 901         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 902                 this,SLOT(CurrentImageChanged(std::string)));
 903         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 904                 this, SLOT(CurrentPickedImageChanged(std::string)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 906                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 907         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 908                 this, SLOT(VectorChanged(int,double,double,double, double)));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 910                 this, SLOT(OverlayChanged(int,double,double)));
 911         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 912                 this, SLOT(FusionChanged(int,double)));
 913         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 914                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 916                 this,SLOT(UpdateSlice(int,int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 918                 this,SLOT(UpdateTSlice(int, int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 920                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 922                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 923         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 924                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 925         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 926                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 927         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 928         InitSlicers();
 929         numberofsuccesulreads++;
 930       }
 931     }
 932   }
 933   if (numberofsuccesulreads) {
 934     NOViewWidget->show();
 935     NEViewWidget->show();
 936     SOViewWidget->show();
 937     SEViewWidget->show();
 938     UpdateTree();
 939     InitDisplay();
 940     ShowLastImage();
 941
 942     // Try to guess default WindowLevel
 943     double range[2];
 944     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 945     if ((range[0] == 0) && (range[1] == 1)) {
 946       presetComboBox->setCurrentIndex(5);// binary
 947     } else {
 948       // TODO
 949     }
 950   }
 951   QApplication::restoreOverrideCursor();
 952 }
 953 //------------------------------------------------------------------------------
 954
 955 //------------------------------------------------------------------------------
 956 void vvMainWindow::UpdateTree()
 957 {
 958   DataTree->resizeColumnToContents(COLUMN_TREE);
 959   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 963   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 964   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 965   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 966 }
 967 //------------------------------------------------------------------------------
 968
 969 //------------------------------------------------------------------------------
 970 void vvMainWindow::CurrentImageChanged(std::string id)
 971 {
 972   if (id == mCurrentSelectedImageId) return; // Do nothing
 973   int selected = 0;
 974   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 975     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 976       selected = i;
 977     } else {
 978       DataTree->topLevelItem(i)->setSelected(0);
 979     }
 980     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 981       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 982
 983   }
 984   DataTree->topLevelItem(selected)->setSelected(1);
 985   mCurrentSelectedImageId = id;
 986   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 987 }
 988 //------------------------------------------------------------------------------
 989
 990 //------------------------------------------------------------------------------
 991 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 992 {
 993   if (id == mCurrentPickedImageId) return; // Do nothing
 994   int selected = 0;
 995   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 996     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 997       selected = i;
 998     } else {
 999       DataTree->topLevelItem(i)->setSelected(0);
1000     }
1001     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1002       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1003
1004   }
1005   DataTree->topLevelItem(selected)->setSelected(1);
1006   mCurrentPickedImageId = id;
1007   mCurrentPickedImageIndex = selected;
1008 }
1009 //------------------------------------------------------------------------------
1010
1011 //------------------------------------------------------------------------------
1012 void vvMainWindow::ImageInfoChanged()
1013 {
1014   contextActions[6]->setEnabled(1);
1015   contextActions[5]->setEnabled(1);
1016   actionSave_As->setEnabled(1);
1017   actionAdd_VF_to_current_Image->setEnabled(1);
1018   actionAdd_fusion_image->setEnabled(1);
1019   actionNorth_East_Window->setEnabled(1);
1020   actionNorth_West_Window->setEnabled(1);
1021   actionSouth_East_Window->setEnabled(1);
1022   actionSouth_West_Window->setEnabled(1);
1023   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1024   inverseButton->setEnabled(1);
1025
1026   goToCursorPushButton->setEnabled(1);
1027
1028   if (DataTree->selectedItems().size()) {
1029     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1030
1031     colorMapComboBox->setEnabled(1);
1032     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1033       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1034           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1035         colorMapComboBox->setEnabled(0);
1036         break;
1037       }
1038     }
1039
1040     std::vector<double> origin;
1041     std::vector<double> inputSpacing;
1042     std::vector<int> inputSize;
1043     std::vector<double> sizeMM;
1044     vtkSmartPointer<vtkMatrix4x4> transformation;
1045     int dimension=0;
1046     QString pixelType;
1047     QString inputSizeInBytes;
1048     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1049
1050     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1051       playButton->setEnabled(1);
1052       frameRateLabel->setEnabled(1);
1053       frameRateSpinBox->setEnabled(1);
1054     } else {
1055       playButton->setEnabled(0);
1056       frameRateLabel->setEnabled(0);
1057       frameRateSpinBox->setEnabled(0);
1058     }
1059
1060     //read image header
1061     int NPixel = 1;
1062
1063     vvImage::Pointer imageSelected;
1064     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1065       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1066     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1067       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1068     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1069       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1070     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1071       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1072     }
1073     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1074       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1075     }
1076     else {
1077       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1078     }
1079
1080     dimension = imageSelected->GetNumberOfDimensions();
1081     origin.resize(dimension);
1082     inputSpacing.resize(dimension);
1083     inputSize.resize(dimension);
1084     sizeMM.resize(dimension);
1085     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1086     for (int i = 0; i < dimension; i++) {
1087       origin[i] = imageSelected->GetOrigin()[i];
1088       inputSpacing[i] = imageSelected->GetSpacing()[i];
1089       inputSize[i] = imageSelected->GetSize()[i];
1090       sizeMM[i] = inputSize[i]*inputSpacing[i];
1091       NPixel *= inputSize[i];
1092     }
1093     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1094
1095     QString dim = QString::number(dimension) + " (";
1096     dim += pixelType + ")";
1097
1098     infoPanel->setFileName(image);
1099     infoPanel->setDimension(dim);
1100     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1101     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1102     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1103     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1104     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1105     transformation = imageSelected->GetTransform()->GetMatrix();
1106     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1107
1108     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1109                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1110     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1111     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1112
1113     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1114     for (int i = 0; i < 4; i++) {
1115       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1116         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1117         break;
1118       }
1119     }
1120     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1121     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1122     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1123     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1124
1125     infoPanel->setFileName(image);
1126     infoPanel->setDimension(dim);
1127     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1128     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1129     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1130     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1131     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1132
1133     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1134                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1135     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1136     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1137
1138     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1139     for (int i = 0; i < 4; i++) {
1140       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1141         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1142         break;
1143       }
1144     }
1145     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1146     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1147     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1148     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1149
1150     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1151       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1152       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1153                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1154                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1155     } else {
1156       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1157       overlayPanel->getVFProperty(-1,-1,-1);
1158     }
1159     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1160       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1161       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1162     } else {
1163       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1164       overlayPanel->getOverlayProperty(-1);
1165     }
1166     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1167       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1168       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1169                                       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1170                                       mSlicerManagers[index]->GetFusionColorMap(),
1171                                       mSlicerManagers[index]->GetFusionWindow(),
1172                                       mSlicerManagers[index]->GetFusionLevel());
1173     } else {
1174       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1175       overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1176     }
1177   }
1178 }
1179 //------------------------------------------------------------------------------
1180
1181 //------------------------------------------------------------------------------
1182 void vvMainWindow::ShowDocumentation()
1183 {
1184   documentation->show();
1185 }
1186 //------------------------------------------------------------------------------
1187
1188 //------------------------------------------------------------------------------
1189 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1190 {
1191   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1192   if(!checkCanPush) {
1193     registerForm->show();
1194   } else {
1195     if(registerForm->canPush()) {
1196       registerForm->show();
1197       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1198     }
1199   }
1200 }
1201 //------------------------------------------------------------------------------
1202
1203 //------------------------------------------------------------------------------
1204 void vvMainWindow::ShowHelpDialog()
1205 {
1206   help_dialog->show();
1207 }
1208 //------------------------------------------------------------------------------
1209
1210 //------------------------------------------------------------------------------
1211 void vvMainWindow::ChangeViewMode()
1212 {
1213   QList<int> size;
1214   if (viewMode == 1) {
1215     viewMode = 0;
1216     size.push_back(1);
1217     size.push_back(0);
1218     splitter_3->setSizes(size);
1219     OSplitter->setSizes(size);
1220     DataTree->setColumnHidden(2,1);
1221     DataTree->setColumnHidden(3,1);
1222     DataTree->setColumnHidden(4,1);
1223   } else {
1224     viewMode = 1;
1225     size.push_back(1);
1226     size.push_back(1);
1227     splitter_3->setSizes(size);
1228     OSplitter->setSizes(size);
1229     DataTree->setColumnHidden(2,0);
1230     DataTree->setColumnHidden(3,0);
1231     DataTree->setColumnHidden(4,0);
1232   }
1233   UpdateRenderWindows();
1234   /*
1235   ** I don't know why but for both resized QVTKWidget we also need to render
1236   ** the associated Slicer to redraw crosses.
1237   */
1238   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1239     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1240       mSlicerManagers[i]->GetSlicer(0)->Render();
1241     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1242       mSlicerManagers[i]->GetSlicer(2)->Render();
1243   }
1244 }
1245 //------------------------------------------------------------------------------
1246
1247 //------------------------------------------------------------------------------
1248 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1249 {
1250   QString result = "";// QString::number(size);
1251   //result += " bytes (";
1252   if (size > 1000000000) {
1253     size /= 1000000000;
1254     result += QString::number(size);
1255     result += "Gb";//)";
1256   } else if (size > 1000000) {
1257     size /= 1000000;
1258     result += QString::number(size);
1259     result += "Mb";//)";
1260   } else if (size > 1000) {
1261     size /= 1000;
1262     result += QString::number(size);
1263     result += "kb";//)";
1264   }
1265   return result;
1266 }
1267 //------------------------------------------------------------------------------
1268
1269 //------------------------------------------------------------------------------
1270 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1271 {
1272   std::ostringstream strmatrix;
1273
1274   for (unsigned int i = 0; i < 4; i++) {
1275     for (unsigned int j = 0; j < 4; j++) {
1276       strmatrix.flags(ios::showpos);
1277       strmatrix.width(10);
1278       strmatrix.precision(3);
1279       strmatrix.setf(ios::fixed,ios::floatfield);
1280       strmatrix.fill(' ');
1281       strmatrix << std::left << matrix->GetElement(i, j);
1282       //strmatrix.width(10);
1283       strmatrix << " ";
1284     }
1285     strmatrix << std::endl;
1286   }
1287   QString result = strmatrix.str().c_str();
1288   return result;
1289 }
1290 //------------------------------------------------------------------------------
1291
1292 //------------------------------------------------------------------------------
1293 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1294 {
1295   QString result;
1296   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1297     if (i != 0)
1298       result += " ";
1299     result += QString::number(vectorDouble[i]);
1300   }
1301   return result;
1302 }
1303 //------------------------------------------------------------------------------
1304
1305 //------------------------------------------------------------------------------
1306 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1307 {
1308   QString result;
1309   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1310     if (i != 0)
1311       result += " ";
1312     result += QString::number(vectorInt[i]);
1313   }
1314   return result;
1315 }
1316 //------------------------------------------------------------------------------
1317
1318 //------------------------------------------------------------------------------
1319 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1320 {
1321   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1322   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1323     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1324       return i;
1325   }
1326   return -1;
1327 }
1328 //------------------------------------------------------------------------------
1329
1330 //------------------------------------------------------------------------------
1331 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1332 {
1333   QString id = sm->GetId().c_str();
1334   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1335     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1336       return DataTree->topLevelItem(i);
1337   }
1338   return NULL;
1339 }
1340 //------------------------------------------------------------------------------
1341
1342 //------------------------------------------------------------------------------
1343 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1344 {
1345   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1346     return;
1347
1348   // Get parent information (might be the same item)
1349   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1350   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1351   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1352
1353   // Go over the complete item tree (only 2 levels, parents and children)
1354   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1355     // Trick to avoid redoing twice the job for a key (sr)
1356     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1357
1358     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1359     if(currentParentItem != clickedParentItem) {
1360       // Not the branch of the clicked item, uncheck all
1361
1362       // Parent
1363       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1364       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1365
1366       // Children
1367       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1368         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1369       }
1370     }
1371     else {
1372       // Branch of the clicked one: get check status from actor visibility in slicer
1373       // and toggle the clicked one
1374
1375       // Parent
1376       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1377       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1378
1379       // Update slicer (after getting visibility)
1380       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1381       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1382       DisplaySliders(slicerManagerIndex, column-1);
1383       if(clickedParentItem == clickedItem) {
1384         // Toggle
1385         vis = !draw || !vis;
1386       }
1387       clickedSlicer->SetActorVisibility("image", 0, vis);
1388       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1389
1390       // Children
1391       std::map<std::string, int> actorTypeCounts;
1392       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1393         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1394         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1395         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1396         if(currentChildItem == clickedItem) {
1397           // Toggle or force visibility if it was not on this branch so far
1398           vis = !draw || !vis;
1399           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1400         }
1401         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1402         actorTypeCounts[actorType]++;
1403       }
1404     }
1405   }
1406
1407   clickedSlicer->Render();
1408 }
1409 //------------------------------------------------------------------------------
1410
1411 void vvMainWindow::InitSlicers()
1412 {
1413   if (mSlicerManagers.size()) {
1414     mSlicerManagers.back()->GenerateDefaultLookupTable();
1415
1416     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1417     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1418     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1419     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1420   }
1421 }
1422
1423 //------------------------------------------------------------------------------
1424 void vvMainWindow::InitDisplay()
1425 {
1426   if (mSlicerManagers.size()) {
1427     //BE CAREFUL : this is absolutely necessary to set the interactor style
1428     //in order to have the same style instanciation for all SlicerManagers in
1429     // a same window
1430     for (int j = 0; j < 4; j++) {
1431       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1432       style->SetAutoAdjustCameraClippingRange(1);
1433       bool AlreadySelected = false;
1434       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1435         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1436
1437         //select the image only if previous are not selected
1438         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1439           mSlicerManagers[i]->UpdateSlicer(j,1);
1440           AlreadySelected = true;
1441         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1442           if (DataTree->selectedItems().size() == 0)
1443             DataTree->topLevelItem(i)->setSelected(1);
1444           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1445           mSlicerManagers[i]->UpdateSlicer(j,1);
1446           DisplaySliders(i,j);
1447         } else {
1448           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1449           mSlicerManagers[i]->UpdateSlicer(j,0);
1450         }
1451       }
1452       style->Delete();
1453     }
1454   }
1455 }
1456 //------------------------------------------------------------------------------
1457
1458 //------------------------------------------------------------------------------
1459 void vvMainWindow::DisplaySliders(int slicer, int window)
1460 {
1461   int range[2];
1462   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1463   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1464
1465   int tRange[2];
1466   tRange[0] = 0;
1467   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1468   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1469   bool showHorizontal = false;
1470   bool showVertical = false;
1471   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1472       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1473           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1474           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1475     showVertical = true;
1476   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1477       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1478       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1479     showHorizontal = true;
1480
1481   if (showVertical)
1482     verticalSliders[window]->show();
1483   else
1484     verticalSliders[window]->hide();
1485   verticalSliders[window]->setRange(range[0],range[1]);
1486   verticalSliders[window]->setValue(position);
1487
1488   if (showHorizontal)
1489     horizontalSliders[window]->show();
1490   else
1491     horizontalSliders[window]->hide();
1492   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1493   horizontalSliders[window]->setValue(tPosition);
1494 }
1495 //------------------------------------------------------------------------------
1496
1497 //------------------------------------------------------------------------------
1498 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1499 {
1500   int index = GetSlicerIndexFromItem(item);
1501
1502   if (DataTree->topLevelItem(index) != item) {
1503     QString warning = "Do you really want to close the overlay : ";
1504     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1505     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1506                        warning, 0, this);
1507     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1508     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1509     if (msgBox.exec() == QMessageBox::AcceptRole) {
1510       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1511       int overlay_index=0;
1512       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1513         if (DataTree->topLevelItem(index)->\
1514             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1515           overlay_index++;
1516         if (DataTree->topLevelItem(index)->child(child) == item) break;
1517       }
1518       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1519       mSlicerManagers[index]->SetColorMap(0);
1520       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1521       mSlicerManagers[index]->Render();
1522     }
1523   } else if (DataTree->topLevelItemCount() <= 1) {
1524     QString warning = "Do you really want to close the image : ";
1525     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1526     warning += "\nThis is the last image, you're about to close vv !!!";
1527     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1528                        warning, 0, this);
1529     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1530     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1531     if (msgBox.exec() == QMessageBox::AcceptRole) {
1532       this->close();
1533     }
1534   } else {
1535     QString warning = "Do you really want to close the image : ";
1536     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1537     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1538                        warning, 0, this);
1539     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1540     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1541     if (msgBox.exec() == QMessageBox::AcceptRole) {
1542
1543       // Tell tools that we close an image
1544       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1545
1546       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1547       DataTree->takeTopLevelItem(index);
1548       for (int i = 0; i < index; i++) {
1549         Manageriter++;
1550       }
1551       linkPanel->removeImage(index);
1552       mSlicerManagers[index]->RemoveActors();
1553       delete mSlicerManagers[index];
1554       mSlicerManagers.erase(Manageriter);
1555
1556       //
1557       InitDisplay();
1558     }
1559   }
1560   ImageInfoChanged();
1561 }
1562 //------------------------------------------------------------------------------
1563
1564 //------------------------------------------------------------------------------
1565 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1566 {
1567   // int index = GetSlicerIndexFromItem(item);
1568   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1569   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1570   //     mSlicerManagers[index]->ReloadVF();
1571   //   else
1572   //     mSlicerManagers[index]->Reload();
1573
1574   //   QApplication::restoreOverrideCursor();
1575   int index = GetSlicerIndexFromItem(item);
1576   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1577   QString role=item->data(1,Qt::UserRole).toString();
1578   if ( role == "vector"){
1579     mSlicerManagers[index]->ReloadVF();
1580   }
1581   else if (role == "overlay"){
1582     mSlicerManagers[index]->ReloadOverlay();
1583   }
1584   else if (role == "fusion"){
1585     mSlicerManagers[index]->ReloadFusion();
1586   }
1587   else{
1588     mSlicerManagers[index]->Reload();
1589   }
1590   // Update view and info
1591   ImageInfoChanged();
1592   mSlicerManagers[index]->Render();
1593   QApplication::restoreOverrideCursor();
1594 }
1595 //------------------------------------------------------------------------------
1596
1597 //------------------------------------------------------------------------------
1598 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1599 {
1600   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1601 }
1602 //------------------------------------------------------------------------------
1603
1604 //------------------------------------------------------------------------------
1605 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1606 {
1607   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1608 }
1609 //------------------------------------------------------------------------------
1610
1611 //------------------------------------------------------------------------------
1612 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1613 {
1614   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1615 }
1616 //------------------------------------------------------------------------------
1617
1618 //------------------------------------------------------------------------------
1619 void vvMainWindow::FusionChanged(int visibility, double value)
1620 {
1621   overlayPanel->getCurrentFusionInfo(visibility,value);
1622 }
1623 //------------------------------------------------------------------------------
1624
1625 //------------------------------------------------------------------------------
1626 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1627 {
1628   windowSpinBox->setValue(window);
1629   levelSpinBox->setValue(level);
1630   colorMapComboBox->setCurrentIndex(colormap);
1631   presetComboBox->setCurrentIndex(preset);
1632 }
1633 //------------------------------------------------------------------------------
1634
1635 //------------------------------------------------------------------------------
1636 void vvMainWindow::WindowLevelEdited()
1637 {
1638   presetComboBox->setCurrentIndex(6);
1639   UpdateWindowLevel();
1640 }
1641 //------------------------------------------------------------------------------
1642
1643 //------------------------------------------------------------------------------
1644 void vvMainWindow::UpdateWindowLevel()
1645 {
1646   if (DataTree->selectedItems().size()) {
1647     if (presetComboBox->currentIndex() == 7) //For ventilation
1648       colorMapComboBox->setCurrentIndex(5);
1649     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1650     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1651     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1652     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1653     mSlicerManagers[index]->Render();
1654     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1655     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1656   }
1657 }
1658 //------------------------------------------------------------------------------
1659
1660 //------------------------------------------------------------------------------
1661 void vvMainWindow::UpdateColorMap()
1662 {
1663   if (DataTree->selectedItems().size()) {
1664     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1665     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1666     mSlicerManagers[index]->Render();
1667   }
1668 }
1669 //------------------------------------------------------------------------------
1670 void vvMainWindow::SwitchWindowLevel()
1671 {
1672   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1673   int window = mSlicerManagers[index]->GetColorWindow();
1674   presetComboBox->setCurrentIndex(6);
1675   windowSpinBox->setValue(-window);
1676   UpdateWindowLevel();
1677 }
1678 //------------------------------------------------------------------------------
1679
1680 //------------------------------------------------------------------------------
1681 void vvMainWindow::ApplyWindowLevelToAllImages()
1682 {
1683   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1684     if (mSlicerManagers[i] == NULL)
1685       continue;
1686     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1687     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1688     mSlicerManagers[i]->SetPreset(6);
1689     mSlicerManagers[i]->Render();
1690   }
1691 }
1692 //------------------------------------------------------------------------------
1693
1694 //------------------------------------------------------------------------------
1695 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1696 {
1697   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1698     if (mSlicerManagers[i]->GetId() == id) {
1699       //mSlicerManagers[i]->SetTSlice(temps);
1700       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1701       mSlicerManagers[i]->UpdateViews(0,slicer);
1702       break;
1703     }
1704   }
1705 }
1706 //------------------------------------------------------------------------------
1707
1708 //------------------------------------------------------------------------------
1709 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1710 {
1711   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1712     if (id == mSlicerManagers[i]->GetId()) {
1713       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1714     }
1715   }
1716 }
1717 //------------------------------------------------------------------------------
1718
1719 //------------------------------------------------------------------------------
1720 void vvMainWindow::ShowContextMenu(QPoint point)
1721 {
1722   if (!DataTree->selectedItems().size()) {
1723     contextActions[1]->setEnabled(0);
1724     contextActions[2]->setEnabled(0);
1725     contextActions[3]->setEnabled(0);
1726     contextActions[4]->setEnabled(0);
1727     contextActions[5]->setEnabled(0);
1728     contextActions[6]->setEnabled(0);
1729   } else {
1730     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1731     contextActions[1]->setEnabled(1);
1732     contextActions[2]->setEnabled(
1733       DataTree->itemWidget(DataTree->selectedItems()[0],
1734                            COLUMN_RELOAD_IMAGE)->isEnabled());
1735     contextActions[3]->setEnabled(1);
1736     contextActions[5]->setEnabled(1);
1737     contextActions[6]->setEnabled(1);
1738
1739     if (mSlicerManagers[index]->GetDimension() < 3)
1740       contextActions[4]->setEnabled(0);
1741     else
1742       contextActions[4]->setEnabled(1);
1743   }
1744   contextMenu.exec(QCursor::pos());
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::CloseImage()
1750 {
1751   CloseImage(DataTree->selectedItems()[0],0);
1752 }
1753 //------------------------------------------------------------------------------
1754
1755 //------------------------------------------------------------------------------
1756 void vvMainWindow::ReloadImage()
1757 {
1758   ReloadImage(DataTree->selectedItems()[0],0);
1759 }
1760 //------------------------------------------------------------------------------
1761
1762 //------------------------------------------------------------------------------
1763 void vvMainWindow::SelectOverlayImage()
1764 {
1765   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1766
1767   //check if one overlay image is added
1768   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1769     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1770       QString error = "Cannot add more than one compared image\n";
1771       error += "Please remove first ";
1772       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1773       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1774       return;
1775     }
1776
1777   QString Extensions = EXTENSIONS;
1778   Extensions += ";;All Files (*)";
1779   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1780   if (!file.isEmpty())
1781     AddOverlayImage(index,file);
1782 }
1783 //------------------------------------------------------------------------------
1784
1785 //------------------------------------------------------------------------------
1786 void vvMainWindow::AddOverlayImage(int index, QString file)
1787 {
1788
1789   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1790   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1791                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1792   reader->SetFileName(file.toStdString().c_str());
1793   reader->ReadImageInformation();
1794   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1795   int dimension = reader->GetNumberOfDimensions();
1796   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1797   vvProgressDialog progress("Opening " + file.toStdString());
1798   qApp->processEvents();
1799
1800   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1801   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1802     //create an item in the tree with good settings
1803     QTreeWidgetItem *item = new QTreeWidgetItem();
1804     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1805     item->setData(1,Qt::UserRole,tr("overlay"));
1806     QFileInfo fileinfo(file); //Do not show the path
1807     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1808     item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1809     qApp->processEvents();
1810
1811     for (int j = 1; j <= 4; j++) {
1812       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1813     }
1814
1815     //Create the buttons for reload and close
1816     qApp->processEvents();
1817     QTreePushButton* cButton = new QTreePushButton;
1818     cButton->setItem(item);
1819     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1820     cButton->setToolTip(tr("close image"));
1821     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1822     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1823             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1824
1825     QTreePushButton* rButton = new QTreePushButton;
1826     rButton->setItem(item);
1827     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1828     rButton->setToolTip(tr("reload image"));
1829     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1830     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1831             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1832
1833     DataTree->topLevelItem(index)->setExpanded(1);
1834     DataTree->topLevelItem(index)->addChild(item);
1835     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1836     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1837
1838     //set the id of the image
1839     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1840     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1841     UpdateTree();
1842     qApp->processEvents();
1843     ImageInfoChanged();
1844     QApplication::restoreOverrideCursor();
1845   } else {
1846     QApplication::restoreOverrideCursor();
1847     QString error = "Cannot import the new image.\n";
1848     error += mSlicerManagers[index]->GetLastError().c_str();
1849     QMessageBox::information(this,tr("Problem reading image !"),error);
1850   }
1851 }
1852 //------------------------------------------------------------------------------
1853
1854
1855 //------------------------------------------------------------------------------
1856 void vvMainWindow::AddROI(int index, QString file)
1857 {
1858   /*
1859   // Get slice manager
1860
1861   // Load image
1862
1863   vvImageReader * mReader = new vvImageReader;
1864   mReader->SetInputFilename(filename.toStdString());
1865   mReader->Update(IMAGE);
1866   if (mReader->GetLastError().size() != 0) {
1867     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1868     QString error = "Cannot open file \n";
1869     error += mReader->GetLastError().c_str();
1870     QMessageBox::information(this,tr("Reading problem"),error);
1871     delete mReader;
1872     return;
1873   }
1874   vvImage::Pointer roi = mReader->GetOutput();
1875
1876   // Create roi in new tool
1877   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1878   */
1879 }
1880 //------------------------------------------------------------------------------
1881
1882 //------------------------------------------------------------------------------
1883 void vvMainWindow::SelectFusionImage()
1884 {
1885   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1886
1887   //check if one fusion image is added
1888   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1889     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1890       QString error = "Cannot add more than one fusion image\n";
1891       error += "Please remove first ";
1892       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1893       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1894       return;
1895     }
1896
1897   QString Extensions = EXTENSIONS;
1898   Extensions += ";;All Files (*)";
1899   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1900   if (!file.isEmpty())
1901     AddFusionImage(index,file);
1902 }
1903 //------------------------------------------------------------------------------
1904
1905 //------------------------------------------------------------------------------
1906 void vvMainWindow::AddFusionImage(int index, QString file)
1907 {
1908   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1909   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1910                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1911   reader->SetFileName(file.toStdString().c_str());
1912   reader->ReadImageInformation();
1913   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1914   if (reader) {
1915     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1916     vvProgressDialog progress("Opening fusion");
1917     qApp->processEvents();
1918
1919     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1920     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1921                                           reader->GetNumberOfDimensions(), component)) {
1922       //create an item in the tree with good settings
1923       QTreeWidgetItem *item = new QTreeWidgetItem();
1924       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1925       item->setData(1,Qt::UserRole,tr("fusion"));
1926       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1927       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1928       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
1929       qApp->processEvents();
1930
1931       for (int j = 1; j <= 4; j++) {
1932         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1933       }
1934
1935       //Create the buttons for reload and close
1936       qApp->processEvents();
1937       QTreePushButton* cButton = new QTreePushButton;
1938       cButton->setItem(item);
1939       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1940       cButton->setToolTip(tr("close image"));
1941       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1942       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1943               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1944
1945       QTreePushButton* rButton = new QTreePushButton;
1946       rButton->setItem(item);
1947       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1948       rButton->setToolTip(tr("reload image"));
1949       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1950       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1951               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1952
1953       DataTree->topLevelItem(index)->setExpanded(1);
1954       DataTree->topLevelItem(index)->addChild(item);
1955       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1956       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1957
1958       //set the id of the image
1959       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1960       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1961       UpdateTree();
1962       qApp->processEvents();
1963       ImageInfoChanged();
1964       QApplication::restoreOverrideCursor();
1965     } else {
1966       QApplication::restoreOverrideCursor();
1967       QString error = "Cannot import the new image.\n";
1968       error += mSlicerManagers[index]->GetLastError().c_str();
1969       QMessageBox::information(this,tr("Problem reading image !"),error);
1970     }
1971   } else {
1972     QString error = "Cannot import the new image.\n";
1973     QMessageBox::information(this,tr("Problem reading image !"),error);
1974   }
1975 }
1976 //------------------------------------------------------------------------------
1977
1978
1979 //------------------------------------------------------------------------------
1980 void vvMainWindow::OpenField()
1981 {
1982   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1983   //check if a vector field has already been added
1984   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1985     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1986       QString error = "Cannot add more than one vector field\n";
1987       error += "Please remove first ";
1988       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1989       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1990       return;
1991     }
1992
1993   QString Extensions = "Images ( *.mhd)";
1994   Extensions += ";;Images ( *.vf)";
1995   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1996   if (!file.isEmpty())
1997     AddField(file,index);
1998 }
1999 //------------------------------------------------------------------------------
2000
2001
2002 //------------------------------------------------------------------------------
2003 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2004 {
2005   //create an item in the tree with good settings
2006   QTreeWidgetItem *item = new QTreeWidgetItem();
2007   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2008   item->setData(1,Qt::UserRole,tr("vector"));
2009   QFileInfo fileinfo(filename); //Do not show the path
2010   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2011   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2012   qApp->processEvents();
2013
2014   for (int j = 1; j <= 4; j++) {
2015     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2016   }
2017
2018   //Create the buttons for reload and close
2019   qApp->processEvents();
2020   QTreePushButton* cButton = new QTreePushButton;
2021   cButton->setItem(item);
2022   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2023   cButton->setToolTip(tr("close vector field"));
2024   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2025   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2026           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2027
2028   QTreePushButton* rButton = new QTreePushButton;
2029   rButton->setItem(item);
2030   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2031   rButton->setToolTip(tr("reload vector field"));
2032   rButton->setEnabled(from_disk);
2033   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2034   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2035           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2036
2037   DataTree->topLevelItem(index)->setExpanded(1);
2038   DataTree->topLevelItem(index)->addChild(item);
2039   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2040   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2041
2042   //set the id of the image
2043   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2044   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2045   UpdateTree();
2046   qApp->processEvents();
2047   ImageInfoChanged();
2048   QApplication::restoreOverrideCursor();
2049 }
2050 //------------------------------------------------------------------------------
2051
2052
2053 //------------------------------------------------------------------------------
2054 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2055 {
2056   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2057   vvSlicerManager* imageManager = mSlicerManagers[index];
2058   if (imageManager->SetVF(vf,file.toStdString())) {
2059     AddFieldEntry(file,index,false);
2060   } else {
2061     QString error = "Cannot import the vector field for this image.\n";
2062     error += imageManager->GetLastError().c_str();
2063     QMessageBox::information(this,tr("Problem reading VF !"),error);
2064   }
2065   QApplication::restoreOverrideCursor();
2066 }
2067 //------------------------------------------------------------------------------
2068
2069
2070 //------------------------------------------------------------------------------
2071 void vvMainWindow::AddField(QString file,int index)
2072 {
2073   if (QFile::exists(file)) {
2074     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2075
2076     //init the progress events
2077     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2078     vvProgressDialog progress("Opening " + file.toStdString());
2079     qApp->processEvents();
2080
2081     //read the vector and put it in the current mSlicerManager
2082     vvSlicerManager* imageManager = mSlicerManagers[index];
2083     qApp->processEvents();
2084
2085     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2086     if (imageManager->SetVF(file.toStdString())) {
2087       imageManager->Render();
2088       AddFieldEntry(file,index,true);
2089     } else {
2090       QApplication::restoreOverrideCursor();
2091       QString error = "Cannot import the vector field for this image.\n";
2092       error += imageManager->GetLastError().c_str();
2093       QMessageBox::information(this,tr("Problem reading VF !"),error);
2094     }
2095   } else
2096     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2097
2098 }
2099 //------------------------------------------------------------------------------
2100
2101
2102 //------------------------------------------------------------------------------
2103 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2104 {
2105   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2106   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2107     for (int i = 0; i < 4; i++) {
2108       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2109       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2110       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2111       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2112       if (log > 0)
2113         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2114       else
2115         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2116     }
2117   }
2118 }
2119 //------------------------------------------------------------------------------
2120
2121
2122 //------------------------------------------------------------------------------
2123 void vvMainWindow::SetOverlayProperty(int color)
2124 {
2125   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2126   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2127     mSlicerManagers[index]->SetOverlayColor(color);
2128     mSlicerManagers[index]->SetColorMap(0);
2129     mSlicerManagers[index]->Render();
2130   }
2131 }
2132 //------------------------------------------------------------------------------
2133
2134 //------------------------------------------------------------------------------
2135 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level)
2136 {
2137   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2138   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2139     mSlicerManagers[index]->SetFusionOpacity(opacity);
2140     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2141     mSlicerManagers[index]->SetFusionColorMap(colormap);
2142     mSlicerManagers[index]->SetFusionWindow(window);
2143     mSlicerManagers[index]->SetFusionLevel(level);
2144     mSlicerManagers[index]->SetColorMap(0);
2145     mSlicerManagers[index]->Render();
2146   }
2147 }
2148 //------------------------------------------------------------------------------
2149
2150 //------------------------------------------------------------------------------
2151 void vvMainWindow::SaveAs()
2152 {
2153   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2154     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2155     return;
2156   }
2157
2158   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2159   int dimension = mSlicerManagers[index]->GetDimension();
2160   QStringList OutputListeFormat;
2161   OutputListeFormat.clear();
2162   if (dimension == 1) {
2163     OutputListeFormat.push_back(".mhd");
2164   }
2165   if (dimension == 2) {
2166     OutputListeFormat.push_back(".bmp");
2167     OutputListeFormat.push_back(".png");
2168     OutputListeFormat.push_back(".jpeg");
2169     OutputListeFormat.push_back(".tif");
2170     OutputListeFormat.push_back(".mhd");
2171     OutputListeFormat.push_back(".hdr");
2172     OutputListeFormat.push_back(".vox");
2173   } else if (dimension == 3) {
2174     OutputListeFormat.push_back(".mhd");
2175     OutputListeFormat.push_back(".hdr");
2176     OutputListeFormat.push_back(".vox");
2177   } else if (dimension == 4) {
2178     OutputListeFormat.push_back(".mhd");
2179   }
2180   QString Extensions = "AllFiles(*.*)";
2181   for (int i = 0; i < OutputListeFormat.count(); i++) {
2182     Extensions += ";;Images ( *";
2183     Extensions += OutputListeFormat[i];
2184     Extensions += ")";
2185   }
2186   QString fileName = QFileDialog::getSaveFileName(this,
2187                      tr("Save As"),
2188                      mSlicerManagers[index]->GetFileName().c_str(),
2189                      Extensions);
2190   if (!fileName.isEmpty()) {
2191     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2192     if (OutputListeFormat.contains(
2193           fileformat.c_str())) {
2194       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2195       std::string action = "Saving";
2196       vvProgressDialog progress("Saving "+fileName.toStdString());
2197       qApp->processEvents();
2198       vvImageWriter::Pointer writer = vvImageWriter::New();
2199       writer->SetOutputFileName(fileName.toStdString());
2200       writer->SetInput(mSlicerManagers[index]->GetImage());
2201       writer->Update();
2202       QApplication::restoreOverrideCursor();
2203       if (writer->GetLastError().size()) {
2204         QString error = "Saving did not succeed\n";
2205         error += writer->GetLastError().c_str();
2206         QMessageBox::information(this,tr("Saving Problem"),error);
2207         SaveAs();
2208       }
2209     } else {
2210       QString error = fileformat.c_str();
2211       if (error.isEmpty())
2212         error += "no file format specified !";
2213       else
2214         error += " format unknown !!!\n";
2215       QMessageBox::information(this,tr("Saving Problem"),error);
2216       SaveAs();
2217     }
2218   }
2219 }
2220 //------------------------------------------------------------------------------
2221
2222
2223 //------------------------------------------------------------------------------
2224 void vvMainWindow::AddLink(QString image1,QString image2)
2225 {
2226   unsigned int sm1 = 0;
2227   unsigned int sm2 = 0;
2228
2229   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2230     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2231       mSlicerManagers[i]->AddLink(image2.toStdString());
2232       sm1 = i;
2233     }
2234     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2235       mSlicerManagers[i]->AddLink(image1.toStdString());
2236       sm2 = i;
2237     }
2238   }
2239
2240   if (linkPanel->isLinkAll())   {
2241     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2242     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2243   } else {
2244     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2245   }
2246 }
2247
2248 //------------------------------------------------------------------------------
2249
2250
2251 //------------------------------------------------------------------------------
2252 void vvMainWindow::RemoveLink(QString image1,QString image2)
2253 {
2254   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2255     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2256       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2257     }
2258     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2259       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2260     }
2261   }
2262 }
2263 //------------------------------------------------------------------------------
2264
2265 //------------------------------------------------------------------------------
2266 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2267 {
2268   int index = 0;
2269   while(sm != mSlicerManagers[index])
2270     index++;
2271   index = (index+offset) % mSlicerManagers.size();
2272
2273   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2274   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2275   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2276   DisplayChanged(item,slicer+1);
2277 }
2278 //------------------------------------------------------------------------------
2279
2280 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2281 {
2282   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2283     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2284       for (int j = 0; j < 4; j++) {
2285         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2286         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2287         //UpdateTSlice(j,value);
2288       }
2289       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2290       break;
2291     }
2292   }
2293 }
2294 //------------------------------------------------------------------------------
2295
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::NOHorizontalSliderMoved()
2299 {
2300   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2301   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2302 //  mCurrentTime = NOHorizontalSlider->value();
2303 }
2304 //------------------------------------------------------------------------------
2305
2306
2307 //------------------------------------------------------------------------------
2308 void vvMainWindow::NEHorizontalSliderMoved()
2309 {
2310   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2311   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2312 //  mCurrentTime = NEHorizontalSlider->value();
2313 }
2314 //------------------------------------------------------------------------------
2315
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::SOHorizontalSliderMoved()
2319 {
2320   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2321   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2322   // mCurrentTime = SOHorizontalSlider->value();
2323 }
2324 //------------------------------------------------------------------------------
2325
2326
2327 //------------------------------------------------------------------------------
2328 void vvMainWindow::SEHorizontalSliderMoved()
2329 {
2330   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2331   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2332   // mCurrentTime = SEHorizontalSlider->value();
2333 }
2334 //------------------------------------------------------------------------------
2335
2336 //------------------------------------------------------------------------------
2337 void vvMainWindow::NOVerticalSliderChanged()
2338 {
2339   static int value=-1;
2340   if (value == NOVerticalSlider->value()) return;
2341   else value = NOVerticalSlider->value();
2342   //  int value = NOVerticalSlider->value();
2343   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2344     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2345       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2346         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2347         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2348
2349         // If nor Update/Render -> slider not work
2350         // only render = ok navigation, but for contour Update needed but slower ?
2351
2352         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2353         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2354       }
2355       break;
2356     }
2357   }
2358 }
2359 //------------------------------------------------------------------------------
2360
2361
2362 //------------------------------------------------------------------------------
2363 void vvMainWindow::NEVerticalSliderChanged()
2364 {
2365   static int value=-1;
2366   if (value == NEVerticalSlider->value()) return;
2367   else value = NEVerticalSlider->value();
2368   //  int value = NEVerticalSlider->value();
2369   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2370     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2371       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2372         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2373         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2374         mSlicerManagers[i]->UpdateSlice(1);
2375         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2376       }
2377       break;
2378     }
2379   }
2380 }
2381 //------------------------------------------------------------------------------
2382
2383
2384 //------------------------------------------------------------------------------
2385 void vvMainWindow::SOVerticalSliderChanged()
2386 {
2387   static int value=-1;
2388   if (value == SOVerticalSlider->value()) return;
2389   else value = SOVerticalSlider->value();
2390   //int value = SOVerticalSlider->value();
2391   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2392     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2393       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2394         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2395         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2396         mSlicerManagers[i]->UpdateSlice(2);
2397         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2398       }
2399       // else { DD("avoid SOVerticalSlider slicer update"); }
2400       break;
2401     }
2402   }
2403 }
2404 //------------------------------------------------------------------------------
2405
2406
2407 //------------------------------------------------------------------------------
2408 void vvMainWindow::SEVerticalSliderChanged()
2409 {
2410   static int value=-1;
2411   if (value == SEVerticalSlider->value()) return;
2412   else value = SEVerticalSlider->value();
2413   // int value = SEVerticalSlider->value();
2414   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2415     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2416       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2417         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2418         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2419         mSlicerManagers[i]->UpdateSlice(3);
2420         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2421       }
2422       break;
2423     }
2424   }
2425 }
2426 //------------------------------------------------------------------------------
2427
2428
2429 //------------------------------------------------------------------------------
2430 void vvMainWindow::UpdateSlice(int slicer, int slice)
2431 {
2432   // DD("vvMainWindow::UpdateSlice");
2433 //   DD(slicer);
2434 //   DD(slice);
2435   if (slicer == 0) {
2436     //    if (slice != NOVerticalSlider->value())
2437     NOVerticalSlider->setValue(slice);
2438   } else {
2439     if (slicer == 1)
2440       NEVerticalSlider->setValue(slice);
2441     else {
2442       if (slicer == 2)
2443         SOVerticalSlider->setValue(slice);
2444       else {
2445         if (slicer == 3)
2446           SEVerticalSlider->setValue(slice);
2447       }
2448     }
2449   }
2450   // DD("vvMainWindow:UpdateSlice END");
2451 }
2452 //------------------------------------------------------------------------------
2453
2454
2455 //------------------------------------------------------------------------------
2456 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2457 {
2458   switch (slicer) {
2459   case 0:
2460     NOHorizontalSlider->setValue(slice);
2461     break;
2462   case 1:
2463     NEHorizontalSlider->setValue(slice);
2464     break;
2465   case 2:
2466     SOHorizontalSlider->setValue(slice);
2467     break;
2468   case 3:
2469     SEHorizontalSlider->setValue(slice);
2470     break;
2471   }
2472 }
2473 //------------------------------------------------------------------------------
2474
2475
2476 //------------------------------------------------------------------------------
2477 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2478 {
2479   int position = int((min+max)/2);
2480   int tPosition = int((tmin+tmax)/2);
2481   if (slicer == 0) {
2482     NOVerticalSlider->setValue(position);
2483     NOVerticalSlider->setRange(min,max);
2484     NOHorizontalSlider->setRange(tmin,tmax);
2485     NOHorizontalSlider->setValue(tPosition);
2486   } else if (slicer == 1) {
2487     NEVerticalSlider->setValue(position);
2488     NEVerticalSlider->setRange(min,max);
2489     NEHorizontalSlider->setRange(tmin,tmax);
2490     NEHorizontalSlider->setValue(tPosition);
2491   } else if (slicer == 2) {
2492     SOVerticalSlider->setValue(position);
2493     SOVerticalSlider->setRange(min,max);
2494     SOHorizontalSlider->setRange(tmin,tmax);
2495     SOHorizontalSlider->setValue(tPosition);
2496   } else if (slicer == 3) {
2497     SEVerticalSlider->setValue(position);
2498     SEVerticalSlider->setRange(min,max);
2499     SEHorizontalSlider->setRange(tmin,tmax);
2500     SEHorizontalSlider->setValue(tPosition);
2501   }
2502 }
2503 //------------------------------------------------------------------------------
2504
2505
2506 //------------------------------------------------------------------------------
2507 void vvMainWindow::SaveNOScreenshot()
2508 {
2509   SaveScreenshot(NOViewWidget);
2510 }
2511 //------------------------------------------------------------------------------
2512
2513
2514 //------------------------------------------------------------------------------
2515 void vvMainWindow::SaveNEScreenshot()
2516 {
2517   SaveScreenshot(NEViewWidget);
2518 }
2519 //------------------------------------------------------------------------------
2520
2521
2522 //------------------------------------------------------------------------------
2523 void vvMainWindow::SaveSOScreenshot()
2524 {
2525   SaveScreenshot(SOViewWidget);
2526 }
2527 //------------------------------------------------------------------------------
2528
2529
2530 //------------------------------------------------------------------------------
2531 void vvMainWindow::SaveSEScreenshot()
2532 {
2533   SaveScreenshot(SEViewWidget);
2534 }
2535 //------------------------------------------------------------------------------
2536
2537
2538 //------------------------------------------------------------------------------
2539 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2540 {
2541   QString Extensions = "Images( *.png);;";
2542   Extensions += "Images( *.jpg);;";
2543   Extensions += "Images( *.bmp);;";
2544   Extensions += "Images( *.tif);;";
2545   Extensions += "Images( *.ppm)";
2546 #ifdef VTK_USE_FFMPEG_ENCODER
2547   Extensions += "Images( *.avi)";
2548 #endif
2549 #ifdef VTK_USE_MPEG2_ENCODER
2550   Extensions += "Images( *.mpg)";
2551 #endif
2552
2553   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2554   QString fileName = QFileDialog::getSaveFileName(this,
2555                      tr("Save As"),
2556                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2557                      Extensions);
2558
2559   if (!fileName.isEmpty()) {
2560     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2561     w2i->SetInput(widget->GetRenderWindow());
2562     w2i->Update();
2563     vtkImageData *image = w2i->GetOutput();
2564
2565     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2566     if (!strcmp(ext, ".bmp")) {
2567       vtkBMPWriter *bmp = vtkBMPWriter::New();
2568       bmp->SetInput(image);
2569       bmp->SetFileName(fileName.toStdString().c_str());
2570       bmp->Write();
2571       bmp->Delete();
2572     } else if (!strcmp(ext, ".tif")) {
2573       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2574       tif->SetInput(image);
2575       tif->SetFileName(fileName.toStdString().c_str());
2576       tif->Write();
2577       tif->Delete();
2578     } else if (!strcmp(ext, ".ppm")) {
2579       vtkPNMWriter *pnm = vtkPNMWriter::New();
2580       pnm->SetInput(image);
2581       pnm->SetFileName(fileName.toStdString().c_str());
2582       pnm->Write();
2583       pnm->Delete();
2584     } else if (!strcmp(ext, ".png")) {
2585       vtkPNGWriter *png = vtkPNGWriter::New();
2586       png->SetInput(image);
2587       png->SetFileName(fileName.toStdString().c_str());
2588       png->Write();
2589       png->Delete();
2590     } else if (!strcmp(ext, ".jpg")) {
2591       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2592       jpg->SetInput(image);
2593       jpg->SetFileName(fileName.toStdString().c_str());
2594       jpg->Write();
2595       jpg->Delete();
2596 #ifdef VTK_USE_FFMPEG_ENCODER
2597     } else if (!strcmp(ext, ".avi")) {
2598       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2599       mpg->SetInput(image);
2600       mpg->SetFileName(fileName.toStdString().c_str());
2601       mpg->SetQuality(2);
2602       mpg->SetRate(5);
2603       mpg->Start();
2604
2605       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2606       int nSlice = vvImg->GetVTKImages().size();
2607       for(int i=0; i<nSlice; i++) {
2608         mSlicerManagers[smIndex]->SetNextTSlice(0);
2609         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2610         w2i->SetInput(widget->GetRenderWindow());
2611         w2i->Update();
2612         mpg->SetInput(w2i->GetOutput());
2613         mpg->Write();
2614       }
2615       mpg->End();
2616       mpg->Delete();
2617 #endif
2618 #ifdef VTK_USE_MPEG2_ENCODER
2619     } else if (!strcmp(ext, ".mpg")) {
2620       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2621       mpg->SetInput(image);
2622       mpg->SetFileName(fileName.toStdString().c_str());
2623       mpg->Start();
2624
2625       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2626       int nSlice = vvImg->GetVTKImages().size();
2627       for(int i=0; i<nSlice; i++) {
2628         mSlicerManagers[smIndex]->SetNextTSlice(0);
2629         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2630         w2i->SetInput(widget->GetRenderWindow());
2631         w2i->Update();
2632         mpg->SetInput(w2i->GetOutput());
2633         mpg->Write();
2634       }
2635       mpg->End();
2636       mpg->Delete();
2637 #endif
2638     } else {
2639       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2640     }
2641   }
2642 }
2643 //------------------------------------------------------------------------------
2644
2645
2646 //------------------------------------------------------------------------------
2647 void vvMainWindow::GoToCursor()
2648 {
2649   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2650   for (int column = 1; column < 5; column++) {
2651     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2652       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2653       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2654         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2655       mSlicerManagers[index]->UpdateViews(1,column-1);
2656       mSlicerManagers[index]->UpdateLinked(column-1);
2657       break;
2658     }
2659   }
2660 }
2661 //------------------------------------------------------------------------------
2662
2663 //------------------------------------------------------------------------------
2664 void vvMainWindow::PlayPause()
2665 {
2666   if (playMode) {
2667     playMode = 0;
2668     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2669     ImageInfoChanged();
2670     return;
2671   } else {
2672     int image_number=DataTree->topLevelItemCount();
2673     bool has_temporal;
2674     for (int i=0; i<image_number; i++)
2675       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2676         has_temporal=true;
2677         break;
2678       }
2679     if (has_temporal) {
2680       playMode = 1;
2681       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2682       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2683     }
2684   }
2685 }
2686 //------------------------------------------------------------------------------
2687
2688 //------------------------------------------------------------------------------
2689 void vvMainWindow::PlayNext()
2690 {
2691   if (playMode && !this->isHidden()) {
2692     int image_number=DataTree->topLevelItemCount();
2693     ///Only play one slicer per SM, and only if the SM is being displayed
2694     for (int i=0; i<image_number; i++)
2695       for (int j=0; j<4; j++)
2696         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2697             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2698           mSlicerManagers[i]->SetNextTSlice(j);
2699           break;
2700         }
2701     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2702   }
2703 }
2704 //------------------------------------------------------------------------------
2705
2706 void vvMainWindow::ShowLastImage()
2707 {
2708   if (mSlicerManagers.size() > 1) {
2709     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2710     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2711     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2712     DisplayChanged(item,1);
2713   }
2714 }
2715
2716 //------------------------------------------------------------------------------
2717 void vvMainWindow::UpdateRenderWindows()
2718 {
2719   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2720   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2721   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2722   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2723 }
2724 //------------------------------------------------------------------------------
2725
2726 //------------------------------------------------------------------------------
2727 void vvMainWindow::SegmentationOnCurrentImage()
2728 {
2729   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2730
2731   vvSegmentationDialog segmentation;
2732   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2733   segmentation.exec();
2734 }
2735 //------------------------------------------------------------------------------
2736
2737 void vvMainWindow::SurfaceViewerLaunch()
2738 {
2739   vvSurfaceViewerDialog surfaceViewer;
2740   surfaceViewer.exec();
2741 }
2742 //------------------------------------------------------------------------------
2743
2744
2745 //------------------------------------------------------------------------------
2746 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2747 {
2748   int number=0;
2749   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2750     vvSlicerManager * v = mSlicerManagers[l];
2751     if (v->GetBaseFileName() ==
2752         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2753       number = std::max(number, v->GetBaseFileNameNumber()+1);
2754     }
2755   }
2756   return number;
2757 }
2758 //------------------------------------------------------------------------------
2759
2760
2761 //------------------------------------------------------------------------------
2762 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2763 {
2764   // Change filename if another image exist with the same name
2765   int number = GetImageDuplicateFilenameNumber(filename);
2766
2767   // Create new SliceManager
2768   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2769   slicer_manager->SetImage(image);//, IMAGE, number);
2770   //  filename = filename+"_"+clitk::toString(number);
2771   slicer_manager->SetFilename(filename, number);
2772   mSlicerManagers.push_back(slicer_manager);
2773
2774   //create an item in the tree with good settings
2775   QTreeWidgetItem *item = new QTreeWidgetItem();
2776   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2777   item->setData(1,Qt::UserRole,tr("image"));
2778   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2779   qApp->processEvents();
2780
2781   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2782
2783   //Create the buttons for reload and close
2784   qApp->processEvents();
2785   QTreePushButton* cButton = new QTreePushButton;
2786   cButton->setItem(item);
2787   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2788   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2789   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2790           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2791
2792   QTreePushButton* rButton = new QTreePushButton;
2793   rButton->setItem(item);
2794   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2795   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2796   rButton->setEnabled(0);
2797   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2798           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2799
2800   DataTree->addTopLevelItem(item);
2801   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2802   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2803
2804   //set the id of the image
2805   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2806   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2807   mSlicerManagers.back()->SetId(id.toStdString());
2808
2809   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2810                       , id.toStdString());
2811
2812   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2813           this, SLOT(CurrentImageChanged(std::string)));
2814   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2815           this, SLOT(CurrentPickedImageChanged(std::string)));
2816   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2817           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2818   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2819           this, SLOT(VectorChanged(int,double,double,double, double)));
2820   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2821           this, SLOT(OverlayChanged(int,double,double)));
2822   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2823           this, SLOT(FusionChanged(int,double)));
2824   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2825           this,SLOT(WindowLevelChanged(double, double, int, int)));
2826   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2827           this,SLOT(UpdateSlice(int,int)));
2828   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2829           this,SLOT(UpdateTSlice(int, int)));
2830   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2831           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2832   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2833           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2834   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2835           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2836   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2837           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2838   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2839   UpdateTree();
2840   qApp->processEvents();
2841   InitSlicers();
2842   ShowLastImage();
2843   InitDisplay();
2844   qApp->processEvents();
2845
2846   // End
2847   ImageInfoChanged();
2848   return slicer_manager;
2849 }
2850 //------------------------------------------------------------------------------
2851
2852
2853 //------------------------------------------------------------------------------
2854 void vvMainWindow::UpdateCurrentSlicer()
2855 {
2856   int index = -1;
2857   if (DataTree->selectedItems().size() > 0) {
2858     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2859   }
2860   mSlicerManagerCurrentIndex = index;
2861 }
2862 //------------------------------------------------------------------------------
2863