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 #include <vtkFFMPEGWriter.h>
  72 #ifdef VTK_USE_MPEG2_ENCODER
  73   #include <vtkMPEG2Writer.h>
  74 #endif
  75 #include <vtkMatrix4x4.h>
  76 #include <vtkTransform.h>
  77
  78 // Standard includes
  79 #include <iostream>
  80 #include <sstream>
  81 #include <iomanip>
  82
  83 #define COLUMN_TREE 0
  84 #define COLUMN_UL_VIEW 1
  85 #define COLUMN_UR_VIEW 2
  86 #define COLUMN_DL_VIEW 3
  87 #define COLUMN_DR_VIEW 4
  88 #define COLUMN_CLOSE_IMAGE 5
  89 #define COLUMN_RELOAD_IMAGE 6
  90 #define COLUMN_IMAGE_NAME 7
  91
  92 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  93
  94 /*Data Tree values
  95   0,Qt::UserRole full filename
  96   1,Qt::CheckStateRole checkbutton UL View
  97   1,Qt::UserRole overlay, fusion or vector
  98   2,Qt::CheckStateRole checkbutton UR View
  99   3,Qt::CheckStateRole checkbutton DL View
 100   4,Qt::CheckStateRole checkbutton DR View
 101   5,0  short filename
 102   5,Qt::UserRole mSlicerManager id*/
 103
 104 //------------------------------------------------------------------------------
 105 vvMainWindow::vvMainWindow():vvMainWindowBase()
 106 {
 107   setupUi(this); // this sets up the GUI
 108
 109   mInputPathName = "";
 110   mMenuTools = menuTools;
 111   //  mMenuSegmentation = menuSegmentation;
 112   mContextMenu = &contextMenu;
 113   mMenuExperimentalTools = menuExperimental;
 114   mMainWidget = this;
 115   mCurrentTime = -1;
 116   mCurrentSelectedImageId = "";
 117   mCurrentPickedImageId = "";
 118   mCurrentPickedImageIndex = 0;
 119
 120   //Init the contextMenu
 121   this->setContextMenuPolicy(Qt::CustomContextMenu);
 122   contextActions.resize(0);
 123   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 124                                   tr("O&pen new Image"));
 125   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 126   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 127   contextActions.push_back(actionOpen_new_image);
 128   contextMenu.addSeparator();
 129
 130   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 131                                tr("Close Current Image"));
 132   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 133   contextActions.push_back(actionClose_Image);
 134
 135   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 136                                 tr("Reload Current Image"));
 137   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 138   contextActions.push_back(actionReload_image);
 139
 140   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 141                               tr("Save Current Image"));
 142   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 143   contextActions.push_back(actionSave_image);
 144
 145   contextMenu.addSeparator();
 146
 147   contextMenu.addAction(actionAdd_VF_to_current_Image);
 148   contextActions.push_back(actionAdd_VF_to_current_Image);
 149
 150   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 151       tr("Add overlay image to current image"));
 152   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 153   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 154
 155   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 156
 157   contextMenu.addAction(actionAdd_fusion_image);
 158   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 159   contextActions.push_back(actionAdd_fusion_image);
 160
 161   // TRIAL DS
 162   /*
 163   QMenu * m = new QMenu(menubar);
 164   m->setTitle("TOTO");
 165   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 166   contextMenu.addMenu(m);
 167   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 168                      tr("BIDON"));
 169   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON2"));
 171   m->addAction(a);
 172   m->addAction(b);
 173   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 174   */
 175
 176   //init the DataTree
 177   mSlicerManagers.resize(0);
 178
 179   QStringList header;
 180   header.append("");
 181   header.append("TL");
 182   header.append("TR");
 183   header.append("BL");
 184   header.append("BR");
 185   header.append("");
 186   header.append("");
 187   header.append("Name");
 188
 189   DataTree->setHeaderLabels(header);
 190   DataTree->resizeColumnToContents(COLUMN_TREE);
 191   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 198
 199   viewMode = 1;
 200   documentation = new vvDocumentation();
 201   help_dialog = new vvHelpDialog();
 202   dicomSeriesSelector = new vvDicomSeriesSelector();
 203
 204   inverseButton->setEnabled(0);
 205   actionAdd_Overlay_to_current_Image->setEnabled(0);
 206   actionSave_As->setEnabled(0);
 207   actionAdd_VF_to_current_Image->setEnabled(0);
 208   actionAdd_fusion_image->setEnabled(0);
 209
 210   //init the sliders
 211   verticalSliders.push_back(NOVerticalSlider);
 212   verticalSliders.push_back(NEVerticalSlider);
 213   verticalSliders.push_back(SOVerticalSlider);
 214   verticalSliders.push_back(SEVerticalSlider);
 215
 216   for (int i =0; i < 4; i++)
 217     verticalSliders[i]->hide();
 218
 219   horizontalSliders.push_back(NOHorizontalSlider);
 220   horizontalSliders.push_back(NEHorizontalSlider);
 221   horizontalSliders.push_back(SOHorizontalSlider);
 222   horizontalSliders.push_back(SEHorizontalSlider);
 223
 224   for (int i =0; i < 4; i++)
 225     horizontalSliders[i]->hide();
 226
 227
 228   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 229   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 230   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 231   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 232
 233   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 234   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 235   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 236   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 237
 238   //connect everything
 239   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 240   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 241   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 242   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 243   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 244   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 245   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 246   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 247   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 248   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 249   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 250   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 251   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 252   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 253   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 254   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 255
 256   ///////////////////////////////////////////////
 257   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 258   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 259   ///////////////////////////////////////////////
 260
 261   actionNorth_East_Window->setEnabled(0);
 262   actionNorth_West_Window->setEnabled(0);
 263   actionSouth_East_Window->setEnabled(0);
 264   actionSouth_West_Window->setEnabled(0);
 265
 266   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 267   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 268   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 269   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 270
 271   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 272   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 273           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 274
 275   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 276   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 277   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 278   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 279   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 280   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 281   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 282
 283
 284   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 285
 286   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 287   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 288   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 289   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 290   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 291           this,SLOT(SetFusionProperty(int,int,double,double)));
 292   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 293
 294   playMode = 0;//pause
 295   mFrameRate = 10;
 296   playButton->setEnabled(0);
 297   frameRateLabel->setEnabled(0);
 298   frameRateSpinBox->setEnabled(0);
 299   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 300   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 301
 302   goToCursorPushButton->setEnabled(0);
 303   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 304
 305   NOViewWidget->hide();
 306   NEViewWidget->hide();
 307   SOViewWidget->hide();
 308   SEViewWidget->hide();
 309
 310   //Recently opened files
 311   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 312   recentlyOpenedFilesMenu=NULL;
 313   if ( !recent_files.empty() ) {
 314     createRecentlyOpenedFilesMenu();
 315     updateRecentlyOpenedFilesMenu(recent_files);
 316   }
 317
 318   // Adding all new tools (insertion in the menu)
 319   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 320
 321   if (!CLITK_EXPERIMENTAL)
 322     menuExperimental->menuAction()->setVisible(false);
 323
 324
 325   QTimer * timerMemory = new QTimer(this);
 326   //timerMemory->setInterval(5);
 327   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 328   timerMemory->start(2000);
 329 }
 330 //------------------------------------------------------------------------------
 331
 332 void vvMainWindow::show(){
 333   vvMainWindowBase::show();
 334   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
 335   if(registerForm->canPush()){
 336     registerForm->show();
 337     registerForm->acquitPushed();//too bad if there is not internet connection anymore.
 338   }
 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->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 869         qApp->processEvents();
 870
 871         //Create the buttons for reload and close
 872         qApp->processEvents();
 873         QTreePushButton* cButton = new QTreePushButton;
 874         cButton->setItem(item);
 875         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 876         cButton->setToolTip(tr("close image"));
 877         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 878         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 879                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 880
 881         QTreePushButton* rButton = new QTreePushButton;
 882         rButton->setItem(item);
 883         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 884         rButton->setToolTip(tr("reload image"));
 885         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 886         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 887                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 888
 889         DataTree->addTopLevelItem(item);
 890         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 891         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 892
 893         //set the id of the image
 894         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 895         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 896         mSlicerManagers.back()->SetId(id.toStdString());
 897
 898         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 899
 900         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 901                 this,SLOT(CurrentImageChanged(std::string)));
 902         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 903                 this, SLOT(CurrentPickedImageChanged(std::string)));
 904         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 905                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 906         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 907                 this, SLOT(VectorChanged(int,double,double,double, double)));
 908         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 909                 this, SLOT(OverlayChanged(int,double,double)));
 910         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 911                 this, SLOT(FusionChanged(int,double)));
 912         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 913                 this,SLOT(WindowsChanged(int, int, int)));
 914         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 915                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 916         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 917                 this,SLOT(UpdateSlice(int,int)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 919                 this,SLOT(UpdateTSlice(int, int)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 921                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 923                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 925                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 926         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 927                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 928         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 929         InitSlicers();
 930         numberofsuccesulreads++;
 931       }
 932     }
 933   }
 934   if (numberofsuccesulreads) {
 935     NOViewWidget->show();
 936     NEViewWidget->show();
 937     SOViewWidget->show();
 938     SEViewWidget->show();
 939     UpdateTree();
 940     InitDisplay();
 941     ShowLastImage();
 942
 943     // Try to guess default WindowLevel
 944     double range[2];
 945     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 946     if ((range[0] == 0) && (range[1] == 1)) {
 947       presetComboBox->setCurrentIndex(5);// binary
 948     } else {
 949       // TODO
 950     }
 951   }
 952   QApplication::restoreOverrideCursor();
 953 }
 954 //------------------------------------------------------------------------------
 955
 956 //------------------------------------------------------------------------------
 957 void vvMainWindow::UpdateTree()
 958 {
 959   DataTree->resizeColumnToContents(COLUMN_TREE);
 960   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 963   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 964   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 965   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 966   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 967 }
 968 //------------------------------------------------------------------------------
 969
 970 //------------------------------------------------------------------------------
 971 void vvMainWindow::CurrentImageChanged(std::string id)
 972 {
 973   if (id == mCurrentSelectedImageId) return; // Do nothing
 974   int selected = 0;
 975   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 976     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 977       selected = i;
 978     } else {
 979       DataTree->topLevelItem(i)->setSelected(0);
 980     }
 981     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 982       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 983
 984   }
 985   DataTree->topLevelItem(selected)->setSelected(1);
 986   mCurrentSelectedImageId = id;
 987   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 988 }
 989 //------------------------------------------------------------------------------
 990
 991 //------------------------------------------------------------------------------
 992 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 993 {
 994   if (id == mCurrentPickedImageId) return; // Do nothing
 995   int selected = 0;
 996   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 997     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 998       selected = i;
 999     } else {
1000       DataTree->topLevelItem(i)->setSelected(0);
1001     }
1002     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1003       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1004
1005   }
1006   DataTree->topLevelItem(selected)->setSelected(1);
1007   mCurrentPickedImageId = id;
1008   mCurrentPickedImageIndex = selected;
1009 }
1010 //------------------------------------------------------------------------------
1011
1012 //------------------------------------------------------------------------------
1013 void vvMainWindow::ImageInfoChanged()
1014 {
1015   contextActions[6]->setEnabled(1);
1016   contextActions[5]->setEnabled(1);
1017   actionSave_As->setEnabled(1);
1018   actionAdd_VF_to_current_Image->setEnabled(1);
1019   actionAdd_fusion_image->setEnabled(1);
1020   actionNorth_East_Window->setEnabled(1);
1021   actionNorth_West_Window->setEnabled(1);
1022   actionSouth_East_Window->setEnabled(1);
1023   actionSouth_West_Window->setEnabled(1);
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       dimension = imageSelected->GetNumberOfDimensions();
1067       origin.resize(dimension);
1068       inputSpacing.resize(dimension);
1069       inputSize.resize(dimension);
1070       sizeMM.resize(dimension);
1071       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1072       for (int i = 0; i < dimension; i++) {
1073         origin[i] = imageSelected->GetOrigin()[i];
1074         inputSpacing[i] = imageSelected->GetSpacing()[i];
1075         inputSize[i] = imageSelected->GetSize()[i];
1076         sizeMM[i] = inputSize[i]*inputSpacing[i];
1077         NPixel *= inputSize[i];
1078       }
1079       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1080     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1081       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1082       dimension = imageSelected->GetNumberOfDimensions();
1083       origin.resize(dimension);
1084       inputSpacing.resize(dimension);
1085       inputSize.resize(dimension);
1086       sizeMM.resize(dimension);
1087       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1088       for (int i = 0; i < dimension; i++) {
1089         origin[i] = imageSelected->GetOrigin()[i];
1090         inputSpacing[i] = imageSelected->GetSpacing()[i];
1091         inputSize[i] = imageSelected->GetSize()[i];
1092         sizeMM[i] = inputSize[i]*inputSpacing[i];
1093         NPixel *= inputSize[i];
1094       }
1095       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1096     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1097       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1098       dimension = imageSelected->GetNumberOfDimensions();
1099       origin.resize(dimension);
1100       inputSpacing.resize(dimension);
1101       inputSize.resize(dimension);
1102       sizeMM.resize(dimension);
1103       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1104       for (int i = 0; i < dimension; i++) {
1105         origin[i] = imageSelected->GetOrigin()[i];
1106         inputSpacing[i] = imageSelected->GetSpacing()[i];
1107         inputSize[i] = imageSelected->GetSize()[i];
1108         sizeMM[i] = inputSize[i]*inputSpacing[i];
1109         NPixel *= inputSize[i];
1110       }
1111       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1112     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1113       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1114       dimension = imageSelected->GetNumberOfDimensions();
1115       origin.resize(dimension);
1116       inputSpacing.resize(dimension);
1117       inputSize.resize(dimension);
1118       sizeMM.resize(dimension);
1119       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1120       for (int i = 0; i < dimension; i++) {
1121         origin[i] = imageSelected->GetOrigin()[i];
1122         inputSpacing[i] = imageSelected->GetSpacing()[i];
1123         inputSize[i] = imageSelected->GetSize()[i];
1124         sizeMM[i] = inputSize[i]*inputSpacing[i];
1125         NPixel *= inputSize[i];
1126       }
1127       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1128     }
1129
1130     QString dim = QString::number(dimension) + " (";
1131     dim += pixelType + ")";
1132
1133     infoPanel->setFileName(image);
1134     infoPanel->setDimension(dim);
1135     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1136     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1137     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1138     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1139     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1140     transformation = imageSelected->GetTransform()->GetMatrix();
1141     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1142
1143     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1144                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1145     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1146     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1147
1148     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1149     for (int i = 0; i < 4; i++) {
1150       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1151         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1152         break;
1153       }
1154     }
1155     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1156     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1157     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1158     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1159
1160     infoPanel->setFileName(image);
1161     infoPanel->setDimension(dim);
1162     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1163     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1164     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1165     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1166     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1167
1168     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1169                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1170     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1171     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1172
1173     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1174     for (int i = 0; i < 4; i++) {
1175       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1176         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1177         break;
1178       }
1179     }
1180     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1181     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1182     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1183     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1184
1185     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1186       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1187       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1188                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1189                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1190     } else {
1191       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1192       overlayPanel->getVFProperty(-1,-1,-1);
1193     }
1194     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1195       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1196       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1197     } else {
1198       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1199       overlayPanel->getOverlayProperty(-1);
1200     }
1201     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1202       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1203       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1204                                       mSlicerManagers[index]->GetFusionColorMap(),
1205                                       mSlicerManagers[index]->GetFusionWindow(),
1206                                       mSlicerManagers[index]->GetFusionLevel());
1207     } else {
1208       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1209       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1210     }
1211   }
1212 }
1213 //------------------------------------------------------------------------------
1214
1215 //------------------------------------------------------------------------------
1216 void vvMainWindow::ShowDocumentation()
1217 {
1218   documentation->show();
1219 }
1220 //------------------------------------------------------------------------------
1221 void vvMainWindow::ShowHelpDialog()
1222 {
1223   help_dialog->show();
1224 }
1225 //------------------------------------------------------------------------------
1226
1227 //------------------------------------------------------------------------------
1228 void vvMainWindow::ChangeViewMode()
1229 {
1230   QListIterator<int> it(splitter_3->sizes());
1231   int max_size = 0;
1232   while (it.hasNext()) {
1233     max_size += it.next();
1234   }
1235   QList<int> size0;
1236   QList<int> size1;
1237   if (viewMode == 1) {
1238     viewMode = 0;
1239     size0.push_back(max_size);
1240     size0.push_back(0);
1241     size1.push_back(max_size + 1);
1242     size1.push_back(0);
1243     splitter_3->setSizes(size0);
1244     OSplitter->setSizes(size1);
1245     DataTree->setColumnHidden(2,1);
1246     DataTree->setColumnHidden(3,1);
1247     DataTree->setColumnHidden(4,1);
1248   } else {
1249     viewMode = 1;
1250     size0.push_back(max_size / 2);
1251     size0.push_back(max_size / 2);
1252     size1.push_back((max_size + 1) / 2);
1253     size1.push_back((max_size + 1) / 2);
1254     splitter_3->setSizes(size0);
1255     OSplitter->setSizes(size1);
1256     DataTree->setColumnHidden(2,0);
1257     DataTree->setColumnHidden(3,0);
1258     DataTree->setColumnHidden(4,0);
1259   }
1260 }
1261 //------------------------------------------------------------------------------
1262
1263 //------------------------------------------------------------------------------
1264 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1265 {
1266   QString result = "";// QString::number(size);
1267   //result += " bytes (";
1268   if (size > 1000000000) {
1269     size /= 1000000000;
1270     result += QString::number(size);
1271     result += "Gb";//)";
1272   } else if (size > 1000000) {
1273     size /= 1000000;
1274     result += QString::number(size);
1275     result += "Mb";//)";
1276   } else if (size > 1000) {
1277     size /= 1000;
1278     result += QString::number(size);
1279     result += "kb";//)";
1280   }
1281   return result;
1282 }
1283 //------------------------------------------------------------------------------
1284
1285 //------------------------------------------------------------------------------
1286 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1287 {
1288   std::ostringstream strmatrix;
1289
1290   for (unsigned int i = 0; i < 4; i++) {
1291     for (unsigned int j = 0; j < 4; j++) {
1292       strmatrix.flags(ios::showpos);
1293       strmatrix.width(10);
1294       strmatrix.precision(3);
1295       strmatrix.setf(ios::fixed,ios::floatfield);
1296       strmatrix.fill(' ');
1297       strmatrix << std::left << matrix->GetElement(i, j);
1298       //strmatrix.width(10);
1299       strmatrix << " ";
1300     }
1301     strmatrix << std::endl;
1302   }
1303   QString result = strmatrix.str().c_str();
1304   return result;
1305 }
1306 //------------------------------------------------------------------------------
1307
1308 //------------------------------------------------------------------------------
1309 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1310 {
1311   QString result;
1312   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1313     if (i != 0)
1314       result += " ";
1315     result += QString::number(vectorDouble[i]);
1316   }
1317   return result;
1318 }
1319 //------------------------------------------------------------------------------
1320
1321 //------------------------------------------------------------------------------
1322 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1323 {
1324   QString result;
1325   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1326     if (i != 0)
1327       result += " ";
1328     result += QString::number(vectorInt[i]);
1329   }
1330   return result;
1331 }
1332 //------------------------------------------------------------------------------
1333
1334 //------------------------------------------------------------------------------
1335 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1336 {
1337   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1338   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1339     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1340       return i;
1341   }
1342   return -1;
1343 }
1344 //------------------------------------------------------------------------------
1345
1346 //------------------------------------------------------------------------------
1347 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1348 {
1349   QString id = sm->GetId().c_str();
1350   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1351     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1352       return DataTree->topLevelItem(i);
1353   }
1354   return NULL;
1355 }
1356 //------------------------------------------------------------------------------
1357
1358 //------------------------------------------------------------------------------
1359 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1360 {
1361   int index = GetSlicerIndexFromItem(clicked_item);
1362   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1363     return;
1364   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1365     //Trick to avoid redoing twice the job for a key (sr)
1366     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1367
1368     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1369     if (DataTree->topLevelItem(index) == current_row) {
1370       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1371       if (current_row == clicked_item) {
1372         //If we just activated a slicer
1373         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1374           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1375           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1376           DisplaySliders(i,column-1);
1377           std::map<std::string,int> overlay_counts;
1378           for (int child = 0; child < current_row->childCount(); child++) {
1379             std::string overlay_type =
1380               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1381             overlay_counts[overlay_type]++;
1382             current_row->child(child)->setData(column,Qt::CheckStateRole,
1383                                                current_row->data(column,Qt::CheckStateRole));
1384             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1385           }
1386         } else { //We don't allow simply desactivating a slicer
1387           clicked_item->setData(column,Qt::CheckStateRole,2);
1388           return;
1389         }
1390       }
1391       //if we clicked on the vector(or overlay) and not the image
1392       else {
1393         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1394           current_row->setData(column,Qt::CheckStateRole,2);
1395           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1396           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1397           DisplaySliders(i,column-1);
1398         }
1399         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1400         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1401         int overlay_index=0;
1402         for (int child = 0; child < current_row->childCount(); child++) {
1403           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1404             overlay_index++;
1405           if (current_row->child(child) == clicked_item) break;
1406         }
1407         clicked_slicer->SetActorVisibility(
1408           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1409       }
1410     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1411       current_row->setData(column,Qt::CheckStateRole,0);
1412       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1413       std::map<std::string,int> overlay_counts;
1414       for (int child = 0; child < current_row->childCount(); child++) {
1415         std::string overlay_type =
1416           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1417         overlay_counts[overlay_type]++;
1418         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1419         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1420         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1421       }
1422     }
1423     //mSlicerManagers[i]->SetColorMap(-1);
1424     mSlicerManagers[i]->SetColorMap();
1425   }
1426   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1427 }
1428 //------------------------------------------------------------------------------
1429
1430 void vvMainWindow::InitSlicers()
1431 {
1432   if (mSlicerManagers.size()) {
1433     mSlicerManagers.back()->GenerateDefaultLookupTable();
1434
1435     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1436     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1437     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1438     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1439   }
1440 }
1441
1442 //------------------------------------------------------------------------------
1443 void vvMainWindow::InitDisplay()
1444 {
1445   if (mSlicerManagers.size()) {
1446     //BE CAREFUL : this is absolutely necessary to set the interactor style
1447     //in order to have the same style instanciation for all SlicerManagers in
1448     // a same window
1449     for (int j = 0; j < 4; j++) {
1450       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1451       style->SetAutoAdjustCameraClippingRange(1);
1452       bool AlreadySelected = false;
1453       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1454         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1455
1456         //select the image only if previous are not selected
1457         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1458           mSlicerManagers[i]->UpdateSlicer(j,1);
1459           AlreadySelected = true;
1460         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1461           if (DataTree->selectedItems().size() == 0)
1462             DataTree->topLevelItem(i)->setSelected(1);
1463           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1464           mSlicerManagers[i]->UpdateSlicer(j,1);
1465           DisplaySliders(i,j);
1466         } else {
1467           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1468           mSlicerManagers[i]->UpdateSlicer(j,0);
1469         }
1470       }
1471       style->Delete();
1472     }
1473   }
1474 }
1475 //------------------------------------------------------------------------------
1476
1477 //------------------------------------------------------------------------------
1478 void vvMainWindow::DisplaySliders(int slicer, int window)
1479 {
1480   int range[2];
1481   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1482   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1483
1484   int tRange[2];
1485   tRange[0] = 0;
1486   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1487   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1488   bool showHorizontal = false;
1489   bool showVertical = false;
1490   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1491       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1492           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1493           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1494     showVertical = true;
1495   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1496       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1497       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1498     showHorizontal = true;
1499
1500   if (showVertical)
1501     verticalSliders[window]->show();
1502   else
1503     verticalSliders[window]->hide();
1504   verticalSliders[window]->setRange(range[0],range[1]);
1505   verticalSliders[window]->setValue(position);
1506
1507   if (showHorizontal)
1508     horizontalSliders[window]->show();
1509   else
1510     horizontalSliders[window]->hide();
1511   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1512   horizontalSliders[window]->setValue(tPosition);
1513 }
1514 //------------------------------------------------------------------------------
1515
1516 //------------------------------------------------------------------------------
1517 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1518 {
1519   int index = GetSlicerIndexFromItem(item);
1520
1521   if (DataTree->topLevelItem(index) != item) {
1522     QString warning = "Do you really want to close the overlay : ";
1523     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1524     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1525                        warning, 0, this);
1526     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1527     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1528     if (msgBox.exec() == QMessageBox::AcceptRole) {
1529       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1530       int overlay_index=0;
1531       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1532         if (DataTree->topLevelItem(index)->\
1533             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1534           overlay_index++;
1535         if (DataTree->topLevelItem(index)->child(child) == item) break;
1536       }
1537       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1538       mSlicerManagers[index]->SetColorMap(0);
1539       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1540       mSlicerManagers[index]->Render();
1541     }
1542   } else if (DataTree->topLevelItemCount() <= 1) {
1543     QString warning = "Do you really want to close the image : ";
1544     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1545     warning += "\nThis is the last image, you're about to close vv !!!";
1546     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1547                        warning, 0, this);
1548     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1549     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1550     if (msgBox.exec() == QMessageBox::AcceptRole) {
1551       this->close();
1552     }
1553   } else {
1554     QString warning = "Do you really want to close the image : ";
1555     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1556     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1557                        warning, 0, this);
1558     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1559     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1560     if (msgBox.exec() == QMessageBox::AcceptRole) {
1561
1562       // Tell tools that we close an image
1563       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1564
1565       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1566       DataTree->takeTopLevelItem(index);
1567       for (int i = 0; i < index; i++) {
1568         Manageriter++;
1569       }
1570       linkPanel->removeImage(index);
1571       mSlicerManagers[index]->RemoveActors();
1572       delete mSlicerManagers[index];
1573       mSlicerManagers.erase(Manageriter);
1574
1575       //
1576       InitDisplay();
1577     }
1578   }
1579   ImageInfoChanged();
1580 }
1581 //------------------------------------------------------------------------------
1582
1583 //------------------------------------------------------------------------------
1584 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1585 {
1586   // int index = GetSlicerIndexFromItem(item);
1587   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1588   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1589   //     mSlicerManagers[index]->ReloadVF();
1590   //   else
1591   //     mSlicerManagers[index]->Reload();
1592
1593   //   QApplication::restoreOverrideCursor();
1594   int index = GetSlicerIndexFromItem(item);
1595   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1596   QString role=item->data(1,Qt::UserRole).toString();
1597   if ( role == "vector")
1598     mSlicerManagers[index]->ReloadVF();
1599   else if (role == "overlay")
1600     mSlicerManagers[index]->ReloadOverlay();
1601   else if (role == "fusion")
1602     mSlicerManagers[index]->ReloadFusion();
1603   else
1604     mSlicerManagers[index]->Reload();
1605
1606   // Update view and info
1607   ImageInfoChanged();
1608   mSlicerManagers[index]->Render();
1609   QApplication::restoreOverrideCursor();
1610 }
1611 //------------------------------------------------------------------------------
1612
1613 //------------------------------------------------------------------------------
1614 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1615 {
1616   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1617 }
1618 //------------------------------------------------------------------------------
1619
1620 //------------------------------------------------------------------------------
1621 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1622 {
1623   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1624 }
1625 //------------------------------------------------------------------------------
1626
1627 //------------------------------------------------------------------------------
1628 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1629 {
1630   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1631 }
1632 //------------------------------------------------------------------------------
1633
1634 //------------------------------------------------------------------------------
1635 void vvMainWindow::FusionChanged(int visibility, double value)
1636 {
1637   overlayPanel->getCurrentFusionInfo(visibility,value);
1638 }
1639 //------------------------------------------------------------------------------
1640
1641 //------------------------------------------------------------------------------
1642 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1643 {
1644   infoPanel->setViews(window, view, slice);
1645 }
1646 //------------------------------------------------------------------------------
1647
1648 //------------------------------------------------------------------------------
1649 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1650 {
1651   windowSpinBox->setValue(window);
1652   levelSpinBox->setValue(level);
1653   colorMapComboBox->setCurrentIndex(colormap);
1654   presetComboBox->setCurrentIndex(preset);
1655 }
1656 //------------------------------------------------------------------------------
1657
1658 //------------------------------------------------------------------------------
1659 void vvMainWindow::WindowLevelEdited()
1660 {
1661   presetComboBox->setCurrentIndex(6);
1662   UpdateWindowLevel();
1663 }
1664 //------------------------------------------------------------------------------
1665
1666 //------------------------------------------------------------------------------
1667 void vvMainWindow::UpdateWindowLevel()
1668 {
1669   if (DataTree->selectedItems().size()) {
1670     if (presetComboBox->currentIndex() == 7) //For ventilation
1671       colorMapComboBox->setCurrentIndex(5);
1672     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1673     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1674     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1675     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1676     mSlicerManagers[index]->Render();
1677     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1678     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1679   }
1680 }
1681 //------------------------------------------------------------------------------
1682
1683 //------------------------------------------------------------------------------
1684 void vvMainWindow::UpdateColorMap()
1685 {
1686   if (DataTree->selectedItems().size()) {
1687     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1688     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1689     mSlicerManagers[index]->Render();
1690   }
1691 }
1692 //------------------------------------------------------------------------------
1693 void vvMainWindow::SwitchWindowLevel()
1694 {
1695   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1696   int window = mSlicerManagers[index]->GetColorWindow();
1697   presetComboBox->setCurrentIndex(6);
1698   windowSpinBox->setValue(-window);
1699   UpdateWindowLevel();
1700 }
1701 //------------------------------------------------------------------------------
1702
1703 //------------------------------------------------------------------------------
1704 void vvMainWindow::ApplyWindowLevelToAllImages()
1705 {
1706   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1707     if (mSlicerManagers[i] == NULL)
1708       continue;
1709     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1710     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1711     mSlicerManagers[i]->SetPreset(6);
1712     mSlicerManagers[i]->Render();
1713   }
1714 }
1715 //------------------------------------------------------------------------------
1716
1717 //------------------------------------------------------------------------------
1718 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1719 {
1720   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1721     if (mSlicerManagers[i]->GetId() == id) {
1722       //mSlicerManagers[i]->SetTSlice(temps);
1723       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1724       mSlicerManagers[i]->UpdateViews(0,slicer);
1725       break;
1726     }
1727   }
1728 }
1729 //------------------------------------------------------------------------------
1730
1731 //------------------------------------------------------------------------------
1732 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1733 {
1734   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1735     if (id == mSlicerManagers[i]->GetId()) {
1736       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1737     }
1738   }
1739 }
1740 //------------------------------------------------------------------------------
1741
1742 //------------------------------------------------------------------------------
1743 void vvMainWindow::ShowContextMenu(QPoint point)
1744 {
1745   if (!DataTree->selectedItems().size()) {
1746     contextActions[1]->setEnabled(0);
1747     contextActions[2]->setEnabled(0);
1748     contextActions[3]->setEnabled(0);
1749     contextActions[4]->setEnabled(0);
1750     contextActions[5]->setEnabled(0);
1751     contextActions[6]->setEnabled(0);
1752   } else {
1753     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1754     contextActions[1]->setEnabled(1);
1755     contextActions[2]->setEnabled(
1756       DataTree->itemWidget(DataTree->selectedItems()[0],
1757                            COLUMN_RELOAD_IMAGE)->isEnabled());
1758     contextActions[3]->setEnabled(1);
1759     contextActions[5]->setEnabled(1);
1760     contextActions[6]->setEnabled(1);
1761
1762     if (mSlicerManagers[index]->GetDimension() < 3)
1763       contextActions[4]->setEnabled(0);
1764     else
1765       contextActions[4]->setEnabled(1);
1766   }
1767   contextMenu.exec(QCursor::pos());
1768 }
1769 //------------------------------------------------------------------------------
1770
1771 //------------------------------------------------------------------------------
1772 void vvMainWindow::CloseImage()
1773 {
1774   CloseImage(DataTree->selectedItems()[0],0);
1775 }
1776 //------------------------------------------------------------------------------
1777
1778 //------------------------------------------------------------------------------
1779 void vvMainWindow::ReloadImage()
1780 {
1781   ReloadImage(DataTree->selectedItems()[0],0);
1782 }
1783 //------------------------------------------------------------------------------
1784
1785 //------------------------------------------------------------------------------
1786 void vvMainWindow::SelectOverlayImage()
1787 {
1788   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1789
1790   //check if one overlay image is added
1791   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1792     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1793       QString error = "Cannot add more than one compared image\n";
1794       error += "Please remove first ";
1795       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1796       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1797       return;
1798     }
1799
1800   QString Extensions = EXTENSIONS;
1801   Extensions += ";;All Files (*)";
1802   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1803   if (!file.isEmpty())
1804     AddOverlayImage(index,file);
1805 }
1806 //------------------------------------------------------------------------------
1807
1808 //------------------------------------------------------------------------------
1809 void vvMainWindow::AddOverlayImage(int index, QString file)
1810 {
1811
1812   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1813   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1814                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1815   reader->SetFileName(file.toStdString().c_str());
1816   reader->ReadImageInformation();
1817   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1818   int dimension = reader->GetNumberOfDimensions();
1819   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1820   vvProgressDialog progress("Opening " + file.toStdString());
1821   qApp->processEvents();
1822
1823   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1824   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1825     //create an item in the tree with good settings
1826     QTreeWidgetItem *item = new QTreeWidgetItem();
1827     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1828     item->setData(1,Qt::UserRole,tr("overlay"));
1829     QFileInfo fileinfo(file); //Do not show the path
1830     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1831     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1832     qApp->processEvents();
1833
1834     for (int j = 1; j <= 4; j++) {
1835       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1836       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1837           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1838     }
1839
1840     //Create the buttons for reload and close
1841     qApp->processEvents();
1842     QTreePushButton* cButton = new QTreePushButton;
1843     cButton->setItem(item);
1844     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1845     cButton->setToolTip(tr("close image"));
1846     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1847     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1848             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1849
1850     QTreePushButton* rButton = new QTreePushButton;
1851     rButton->setItem(item);
1852     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1853     rButton->setToolTip(tr("reload image"));
1854     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1855     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1856             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1857
1858     DataTree->topLevelItem(index)->setExpanded(1);
1859     DataTree->topLevelItem(index)->addChild(item);
1860     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1861     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1862
1863     //set the id of the image
1864     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1865     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1866     UpdateTree();
1867     qApp->processEvents();
1868     ImageInfoChanged();
1869     QApplication::restoreOverrideCursor();
1870   } else {
1871     QApplication::restoreOverrideCursor();
1872     QString error = "Cannot import the new image.\n";
1873     error += mSlicerManagers[index]->GetLastError().c_str();
1874     QMessageBox::information(this,tr("Problem reading image !"),error);
1875   }
1876 }
1877 //------------------------------------------------------------------------------
1878
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::AddROI(int index, QString file)
1882 {
1883   /*
1884   // Get slice manager
1885
1886   // Load image
1887
1888   vvImageReader * mReader = new vvImageReader;
1889   mReader->SetInputFilename(filename.toStdString());
1890   mReader->Update(IMAGE);
1891   if (mReader->GetLastError().size() != 0) {
1892     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1893     QString error = "Cannot open file \n";
1894     error += mReader->GetLastError().c_str();
1895     QMessageBox::information(this,tr("Reading problem"),error);
1896     delete mReader;
1897     return;
1898   }
1899   vvImage::Pointer roi = mReader->GetOutput();
1900
1901   // Create roi in new tool
1902   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1903   */
1904 }
1905 //------------------------------------------------------------------------------
1906
1907 //------------------------------------------------------------------------------
1908 void vvMainWindow::SelectFusionImage()
1909 {
1910   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1911
1912   //check if one fusion image is added
1913   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1914     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1915       QString error = "Cannot add more than one fusion image\n";
1916       error += "Please remove first ";
1917       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1918       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1919       return;
1920     }
1921
1922   QString Extensions = EXTENSIONS;
1923   Extensions += ";;All Files (*)";
1924   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1925   if (!file.isEmpty())
1926     AddFusionImage(index,file);
1927 }
1928 //------------------------------------------------------------------------------
1929
1930 //------------------------------------------------------------------------------
1931 void vvMainWindow::AddFusionImage(int index, QString file)
1932 {
1933   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1934   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1935                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1936   reader->SetFileName(file.toStdString().c_str());
1937   reader->ReadImageInformation();
1938   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1939   if (reader) {
1940     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1941     vvProgressDialog progress("Opening fusion");
1942     qApp->processEvents();
1943
1944     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1945     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1946                                           reader->GetNumberOfDimensions(), component)) {
1947       //create an item in the tree with good settings
1948       QTreeWidgetItem *item = new QTreeWidgetItem();
1949       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1950       item->setData(1,Qt::UserRole,tr("fusion"));
1951       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1952       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1953       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1954       qApp->processEvents();
1955
1956       for (int j = 1; j <= 4; j++) {
1957         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1958         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1959             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1960       }
1961
1962       //Create the buttons for reload and close
1963       qApp->processEvents();
1964       QTreePushButton* cButton = new QTreePushButton;
1965       cButton->setItem(item);
1966       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1967       cButton->setToolTip(tr("close image"));
1968       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1969       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1970               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1971
1972       QTreePushButton* rButton = new QTreePushButton;
1973       rButton->setItem(item);
1974       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1975       rButton->setToolTip(tr("reload image"));
1976       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1977       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1978               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1979
1980       DataTree->topLevelItem(index)->setExpanded(1);
1981       DataTree->topLevelItem(index)->addChild(item);
1982       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1983       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1984
1985       //set the id of the image
1986       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1987       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1988       UpdateTree();
1989       qApp->processEvents();
1990       ImageInfoChanged();
1991       QApplication::restoreOverrideCursor();
1992     } else {
1993       QApplication::restoreOverrideCursor();
1994       QString error = "Cannot import the new image.\n";
1995       error += mSlicerManagers[index]->GetLastError().c_str();
1996       QMessageBox::information(this,tr("Problem reading image !"),error);
1997     }
1998   } else {
1999     QString error = "Cannot import the new image.\n";
2000     QMessageBox::information(this,tr("Problem reading image !"),error);
2001   }
2002 }
2003 //------------------------------------------------------------------------------
2004
2005
2006 //------------------------------------------------------------------------------
2007 void vvMainWindow::OpenField()
2008 {
2009   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2010   //check if a vector field has already been added
2011   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2012     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2013       QString error = "Cannot add more than one vector field\n";
2014       error += "Please remove first ";
2015       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2016       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2017       return;
2018     }
2019
2020   QString Extensions = "Images ( *.mhd)";
2021   Extensions += ";;Images ( *.vf)";
2022   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2023   if (!file.isEmpty())
2024     AddField(file,index);
2025 }
2026 //------------------------------------------------------------------------------
2027
2028
2029 //------------------------------------------------------------------------------
2030 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2031 {
2032   //create an item in the tree with good settings
2033   QTreeWidgetItem *item = new QTreeWidgetItem();
2034   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2035   item->setData(1,Qt::UserRole,tr("vector"));
2036   QFileInfo fileinfo(filename); //Do not show the path
2037   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2038   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2039   qApp->processEvents();
2040
2041   for (int j = 1; j <= 4; j++) {
2042     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2043     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2044         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2045   }
2046
2047   //Create the buttons for reload and close
2048   qApp->processEvents();
2049   QTreePushButton* cButton = new QTreePushButton;
2050   cButton->setItem(item);
2051   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2052   cButton->setToolTip(tr("close vector field"));
2053   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2054   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2055           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2056
2057   QTreePushButton* rButton = new QTreePushButton;
2058   rButton->setItem(item);
2059   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2060   rButton->setToolTip(tr("reload vector field"));
2061   rButton->setEnabled(from_disk);
2062   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2063   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2064           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2065
2066   DataTree->topLevelItem(index)->setExpanded(1);
2067   DataTree->topLevelItem(index)->addChild(item);
2068   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2069   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2070
2071   //set the id of the image
2072   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2073   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2074   UpdateTree();
2075   qApp->processEvents();
2076   ImageInfoChanged();
2077   QApplication::restoreOverrideCursor();
2078 }
2079 //------------------------------------------------------------------------------
2080
2081
2082 //------------------------------------------------------------------------------
2083 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2084 {
2085   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2086   vvSlicerManager* imageManager = mSlicerManagers[index];
2087   if (imageManager->SetVF(vf,file.toStdString())) {
2088     AddFieldEntry(file,index,false);
2089   } else {
2090     QString error = "Cannot import the vector field for this image.\n";
2091     error += imageManager->GetLastError().c_str();
2092     QMessageBox::information(this,tr("Problem reading VF !"),error);
2093   }
2094   QApplication::restoreOverrideCursor();
2095 }
2096 //------------------------------------------------------------------------------
2097
2098
2099 //------------------------------------------------------------------------------
2100 void vvMainWindow::AddField(QString file,int index)
2101 {
2102   if (QFile::exists(file)) {
2103     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2104
2105     //init the progress events
2106     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2107     vvProgressDialog progress("Opening " + file.toStdString());
2108     qApp->processEvents();
2109
2110     //read the vector and put it in the current mSlicerManager
2111     vvSlicerManager* imageManager = mSlicerManagers[index];
2112     qApp->processEvents();
2113
2114     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2115     if (imageManager->SetVF(file.toStdString())) {
2116       imageManager->Render();
2117       AddFieldEntry(file,index,true);
2118     } else {
2119       QApplication::restoreOverrideCursor();
2120       QString error = "Cannot import the vector field for this image.\n";
2121       error += imageManager->GetLastError().c_str();
2122       QMessageBox::information(this,tr("Problem reading VF !"),error);
2123     }
2124   } else
2125     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2126
2127 }
2128 //------------------------------------------------------------------------------
2129
2130
2131 //------------------------------------------------------------------------------
2132 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2133 {
2134   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2135   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2136     for (int i = 0; i < 4; i++) {
2137       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2138       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2139       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2140       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2141       if (log > 0)
2142         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2143       else
2144         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2145     }
2146   }
2147 }
2148 //------------------------------------------------------------------------------
2149
2150
2151 //------------------------------------------------------------------------------
2152 void vvMainWindow::SetOverlayProperty(int color)
2153 {
2154   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2155   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2156     mSlicerManagers[index]->SetOverlayColor(color);
2157     mSlicerManagers[index]->SetColorMap(0);
2158     mSlicerManagers[index]->Render();
2159   }
2160 }
2161 //------------------------------------------------------------------------------
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2165 {
2166   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2167   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2168     mSlicerManagers[index]->SetFusionOpacity(opacity);
2169     mSlicerManagers[index]->SetFusionColorMap(colormap);
2170     mSlicerManagers[index]->SetFusionWindow(window);
2171     mSlicerManagers[index]->SetFusionLevel(level);
2172     mSlicerManagers[index]->SetColorMap(0);
2173     mSlicerManagers[index]->Render();
2174   }
2175 }
2176 //------------------------------------------------------------------------------
2177
2178 //------------------------------------------------------------------------------
2179 void vvMainWindow::SaveAs()
2180 {
2181   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2182     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2183     return;
2184   }
2185
2186   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2187   int dimension = mSlicerManagers[index]->GetDimension();
2188   QStringList OutputListeFormat;
2189   OutputListeFormat.clear();
2190   if (dimension == 1) {
2191     OutputListeFormat.push_back(".mhd");
2192   }
2193   if (dimension == 2) {
2194     OutputListeFormat.push_back(".bmp");
2195     OutputListeFormat.push_back(".png");
2196     OutputListeFormat.push_back(".jpeg");
2197     OutputListeFormat.push_back(".tif");
2198     OutputListeFormat.push_back(".mhd");
2199     OutputListeFormat.push_back(".hdr");
2200     OutputListeFormat.push_back(".vox");
2201   } else if (dimension == 3) {
2202     OutputListeFormat.push_back(".mhd");
2203     OutputListeFormat.push_back(".hdr");
2204     OutputListeFormat.push_back(".vox");
2205   } else if (dimension == 4) {
2206     OutputListeFormat.push_back(".mhd");
2207   }
2208   QString Extensions = "AllFiles(*.*)";
2209   for (int i = 0; i < OutputListeFormat.count(); i++) {
2210     Extensions += ";;Images ( *";
2211     Extensions += OutputListeFormat[i];
2212     Extensions += ")";
2213   }
2214   QString fileName = QFileDialog::getSaveFileName(this,
2215                      tr("Save As"),
2216                      mSlicerManagers[index]->GetFileName().c_str(),
2217                      Extensions);
2218   if (!fileName.isEmpty()) {
2219     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2220     if (OutputListeFormat.contains(
2221           fileformat.c_str())) {
2222       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2223       std::string action = "Saving";
2224       vvProgressDialog progress("Saving "+fileName.toStdString());
2225       qApp->processEvents();
2226       vvImageWriter::Pointer writer = vvImageWriter::New();
2227       writer->SetOutputFileName(fileName.toStdString());
2228       writer->SetInput(mSlicerManagers[index]->GetImage());
2229       writer->Update();
2230       QApplication::restoreOverrideCursor();
2231       if (writer->GetLastError().size()) {
2232         QString error = "Saving did not succeed\n";
2233         error += writer->GetLastError().c_str();
2234         QMessageBox::information(this,tr("Saving Problem"),error);
2235         SaveAs();
2236       }
2237     } else {
2238       QString error = fileformat.c_str();
2239       if (error.isEmpty())
2240         error += "no file format specified !";
2241       else
2242         error += " format unknown !!!\n";
2243       QMessageBox::information(this,tr("Saving Problem"),error);
2244       SaveAs();
2245     }
2246   }
2247 }
2248 //------------------------------------------------------------------------------
2249
2250
2251 //------------------------------------------------------------------------------
2252 void vvMainWindow::AddLink(QString image1,QString image2)
2253 {
2254   unsigned int sm1 = 0;
2255   unsigned int sm2 = 0;
2256
2257   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2258     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2259       mSlicerManagers[i]->AddLink(image2.toStdString());
2260       sm1 = i;
2261     }
2262     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2263       mSlicerManagers[i]->AddLink(image1.toStdString());
2264       sm2 = i;
2265     }
2266   }
2267
2268   if (linkPanel->isLinkAll())   {
2269     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2270     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2271   }
2272   else {
2273     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2274   }
2275 }
2276
2277 //------------------------------------------------------------------------------
2278
2279
2280 //------------------------------------------------------------------------------
2281 void vvMainWindow::RemoveLink(QString image1,QString image2)
2282 {
2283   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2284     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2285       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2286     }
2287     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2288       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2289     }
2290   }
2291 }
2292 //------------------------------------------------------------------------------
2293
2294 //------------------------------------------------------------------------------
2295 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2296 {
2297   int index = 0;
2298   while(sm != mSlicerManagers[index])
2299     index++;
2300   index = (index+offset) % mSlicerManagers.size();
2301
2302   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2303   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2304   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2305   DisplayChanged(item,slicer+1);
2306 }
2307 //------------------------------------------------------------------------------
2308
2309 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2310 {
2311   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2312     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2313       for (int j = 0; j < 4; j++) {
2314         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2315         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2316         //UpdateTSlice(j,value);
2317       }
2318       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2319       break;
2320     }
2321   }
2322 }
2323 //------------------------------------------------------------------------------
2324
2325
2326 //------------------------------------------------------------------------------
2327 void vvMainWindow::NOHorizontalSliderMoved()
2328 {
2329   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2330   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2331 //  mCurrentTime = NOHorizontalSlider->value();
2332 }
2333 //------------------------------------------------------------------------------
2334
2335
2336 //------------------------------------------------------------------------------
2337 void vvMainWindow::NEHorizontalSliderMoved()
2338 {
2339   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2340   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2341 //  mCurrentTime = NEHorizontalSlider->value();
2342 }
2343 //------------------------------------------------------------------------------
2344
2345
2346 //------------------------------------------------------------------------------
2347 void vvMainWindow::SOHorizontalSliderMoved()
2348 {
2349   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2350   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2351   // mCurrentTime = SOHorizontalSlider->value();
2352 }
2353 //------------------------------------------------------------------------------
2354
2355
2356 //------------------------------------------------------------------------------
2357 void vvMainWindow::SEHorizontalSliderMoved()
2358 {
2359   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2360   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2361   // mCurrentTime = SEHorizontalSlider->value();
2362 }
2363 //------------------------------------------------------------------------------
2364
2365 //------------------------------------------------------------------------------
2366 void vvMainWindow::NOVerticalSliderChanged()
2367 {
2368   static int value=-1;
2369   if (value == NOVerticalSlider->value()) return;
2370   else value = NOVerticalSlider->value();
2371   //  int value = NOVerticalSlider->value();
2372   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2373     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2374       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2375         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2376         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2377
2378         // If nor Update/Render -> slider not work
2379         // only render = ok navigation, but for contour Update needed but slower ?
2380
2381         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2382         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2383       }
2384       break;
2385     }
2386   }
2387 }
2388 //------------------------------------------------------------------------------
2389
2390
2391 //------------------------------------------------------------------------------
2392 void vvMainWindow::NEVerticalSliderChanged()
2393 {
2394   static int value=-1;
2395   if (value == NEVerticalSlider->value()) return;
2396   else value = NEVerticalSlider->value();
2397   //  int value = NEVerticalSlider->value();
2398   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2399     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2400       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2401         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2402         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2403         mSlicerManagers[i]->UpdateSlice(1);
2404         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2405       }
2406       break;
2407     }
2408   }
2409 }
2410 //------------------------------------------------------------------------------
2411
2412
2413 //------------------------------------------------------------------------------
2414 void vvMainWindow::SOVerticalSliderChanged()
2415 {
2416   static int value=-1;
2417   if (value == SOVerticalSlider->value()) return;
2418   else value = SOVerticalSlider->value();
2419   //int value = SOVerticalSlider->value();
2420   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2421     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2422       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2423         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2424         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2425         mSlicerManagers[i]->UpdateSlice(2);
2426         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2427       }
2428       // else { DD("avoid SOVerticalSlider slicer update"); }
2429       break;
2430     }
2431   }
2432 }
2433 //------------------------------------------------------------------------------
2434
2435
2436 //------------------------------------------------------------------------------
2437 void vvMainWindow::SEVerticalSliderChanged()
2438 {
2439   static int value=-1;
2440   if (value == SEVerticalSlider->value()) return;
2441   else value = SEVerticalSlider->value();
2442   // int value = SEVerticalSlider->value();
2443   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2444     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2445       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2446         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2447         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2448         mSlicerManagers[i]->UpdateSlice(3);
2449         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2450       }
2451       break;
2452     }
2453   }
2454 }
2455 //------------------------------------------------------------------------------
2456
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::UpdateSlice(int slicer, int slice)
2460 {
2461   // DD("vvMainWindow::UpdateSlice");
2462 //   DD(slicer);
2463 //   DD(slice);
2464   if (slicer == 0) {
2465     //    if (slice != NOVerticalSlider->value())
2466     NOVerticalSlider->setValue(slice);
2467   } else {
2468     if (slicer == 1)
2469       NEVerticalSlider->setValue(slice);
2470     else {
2471       if (slicer == 2)
2472         SOVerticalSlider->setValue(slice);
2473       else {
2474         if (slicer == 3)
2475           SEVerticalSlider->setValue(slice);
2476       }
2477     }
2478   }
2479   // DD("vvMainWindow:UpdateSlice END");
2480 }
2481 //------------------------------------------------------------------------------
2482
2483
2484 //------------------------------------------------------------------------------
2485 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2486 {
2487   switch (slicer) {
2488   case 0:
2489     NOHorizontalSlider->setValue(slice);
2490     break;
2491   case 1:
2492     NEHorizontalSlider->setValue(slice);
2493     break;
2494   case 2:
2495     SOHorizontalSlider->setValue(slice);
2496     break;
2497   case 3:
2498     SEHorizontalSlider->setValue(slice);
2499     break;
2500   }
2501 }
2502 //------------------------------------------------------------------------------
2503
2504
2505 //------------------------------------------------------------------------------
2506 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2507 {
2508   int position = int((min+max)/2);
2509   int tPosition = int((tmin+tmax)/2);
2510   if (slicer == 0) {
2511     NOVerticalSlider->setValue(position);
2512     NOVerticalSlider->setRange(min,max);
2513     NOHorizontalSlider->setRange(tmin,tmax);
2514     NOHorizontalSlider->setValue(tPosition);
2515   } else if (slicer == 1) {
2516     NEVerticalSlider->setValue(position);
2517     NEVerticalSlider->setRange(min,max);
2518     NEHorizontalSlider->setRange(tmin,tmax);
2519     NEHorizontalSlider->setValue(tPosition);
2520   } else if (slicer == 2) {
2521     SOVerticalSlider->setValue(position);
2522     SOVerticalSlider->setRange(min,max);
2523     SOHorizontalSlider->setRange(tmin,tmax);
2524     SOHorizontalSlider->setValue(tPosition);
2525   } else if (slicer == 3) {
2526     SEVerticalSlider->setValue(position);
2527     SEVerticalSlider->setRange(min,max);
2528     SEHorizontalSlider->setRange(tmin,tmax);
2529     SEHorizontalSlider->setValue(tPosition);
2530   }
2531 }
2532 //------------------------------------------------------------------------------
2533
2534
2535 //------------------------------------------------------------------------------
2536 void vvMainWindow::SaveNOScreenshot()
2537 {
2538   SaveScreenshot(NOViewWidget);
2539 }
2540 //------------------------------------------------------------------------------
2541
2542
2543 //------------------------------------------------------------------------------
2544 void vvMainWindow::SaveNEScreenshot()
2545 {
2546   SaveScreenshot(NEViewWidget);
2547 }
2548 //------------------------------------------------------------------------------
2549
2550
2551 //------------------------------------------------------------------------------
2552 void vvMainWindow::SaveSOScreenshot()
2553 {
2554   SaveScreenshot(SOViewWidget);
2555 }
2556 //------------------------------------------------------------------------------
2557
2558
2559 //------------------------------------------------------------------------------
2560 void vvMainWindow::SaveSEScreenshot()
2561 {
2562   SaveScreenshot(SEViewWidget);
2563 }
2564 //------------------------------------------------------------------------------
2565
2566
2567 //------------------------------------------------------------------------------
2568 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2569 {
2570   QString Extensions = "Images( *.png);;";
2571   Extensions += "Images( *.jpg);;";
2572   Extensions += "Images( *.bmp);;";
2573   Extensions += "Images( *.tif);;";
2574   Extensions += "Images( *.ppm)";
2575 #ifdef VTK_USE_FFMPEG_ENCODER
2576   Extensions += "Images( *.avi)";
2577 #endif
2578 #ifdef VTK_USE_MPEG2_ENCODER
2579   Extensions += "Images( *.mpg)";
2580 #endif
2581
2582   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2583   QString fileName = QFileDialog::getSaveFileName(this,
2584                      tr("Save As"),
2585                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2586                      Extensions);
2587
2588   if (!fileName.isEmpty()) {
2589     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2590     w2i->SetInput(widget->GetRenderWindow());
2591     w2i->Update();
2592     vtkImageData *image = w2i->GetOutput();
2593
2594     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2595     if (!strcmp(ext, ".bmp")) {
2596       vtkBMPWriter *bmp = vtkBMPWriter::New();
2597       bmp->SetInput(image);
2598       bmp->SetFileName(fileName.toStdString().c_str());
2599       bmp->Write();
2600       bmp->Delete();
2601     } else if (!strcmp(ext, ".tif")) {
2602       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2603       tif->SetInput(image);
2604       tif->SetFileName(fileName.toStdString().c_str());
2605       tif->Write();
2606       tif->Delete();
2607     } else if (!strcmp(ext, ".ppm")) {
2608       vtkPNMWriter *pnm = vtkPNMWriter::New();
2609       pnm->SetInput(image);
2610       pnm->SetFileName(fileName.toStdString().c_str());
2611       pnm->Write();
2612       pnm->Delete();
2613     } else if (!strcmp(ext, ".png")) {
2614       vtkPNGWriter *png = vtkPNGWriter::New();
2615       png->SetInput(image);
2616       png->SetFileName(fileName.toStdString().c_str());
2617       png->Write();
2618       png->Delete();
2619     } else if (!strcmp(ext, ".jpg")) {
2620       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2621       jpg->SetInput(image);
2622       jpg->SetFileName(fileName.toStdString().c_str());
2623       jpg->Write();
2624       jpg->Delete();
2625 #ifdef VTK_USE_FFMPEG_ENCODER
2626     } else if (!strcmp(ext, ".avi")) {
2627       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2628       mpg->SetInput(image);
2629       mpg->SetFileName(fileName.toStdString().c_str());
2630       mpg->SetQuality(2);
2631       mpg->SetRate(5);
2632       mpg->Start();
2633
2634       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2635       int nSlice = vvImg->GetVTKImages().size();
2636       for(int i=0; i<nSlice; i++)
2637       {
2638         mSlicerManagers[smIndex]->SetNextTSlice(0);
2639         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2640         w2i->SetInput(widget->GetRenderWindow());
2641         w2i->Update();
2642         mpg->SetInput(w2i->GetOutput());
2643         mpg->Write();
2644       }
2645       mpg->End();
2646       mpg->Delete();
2647 #endif
2648 #ifdef VTK_USE_MPEG2_ENCODER
2649     } else if (!strcmp(ext, ".mpg")) {
2650       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2651       mpg->SetInput(image);
2652       mpg->SetFileName(fileName.toStdString().c_str());
2653       mpg->Start();
2654
2655       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2656       int nSlice = vvImg->GetVTKImages().size();
2657       for(int i=0; i<nSlice; i++)
2658       {
2659         mSlicerManagers[smIndex]->SetNextTSlice(0);
2660         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2661         w2i->SetInput(widget->GetRenderWindow());
2662         w2i->Update();
2663         mpg->SetInput(w2i->GetOutput());
2664         mpg->Write();
2665       }
2666       mpg->End();
2667       mpg->Delete();
2668 #endif
2669     } else {
2670       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2671     }
2672   }
2673 }
2674 //------------------------------------------------------------------------------
2675
2676
2677 //------------------------------------------------------------------------------
2678 void vvMainWindow::GoToCursor()
2679 {
2680   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2681   for (int column = 1; column < 5; column++) {
2682     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2683       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2684       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2685         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2686       mSlicerManagers[index]->UpdateViews(1,column-1);
2687       mSlicerManagers[index]->UpdateLinked(column-1);
2688       break;
2689     }
2690   }
2691 }
2692 //------------------------------------------------------------------------------
2693
2694 //------------------------------------------------------------------------------
2695 void vvMainWindow::PlayPause()
2696 {
2697   if (playMode) {
2698     playMode = 0;
2699     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2700     ImageInfoChanged();
2701     return;
2702   } else {
2703     int image_number=DataTree->topLevelItemCount();
2704     bool has_temporal;
2705     for (int i=0; i<image_number; i++)
2706       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2707         has_temporal=true;
2708         break;
2709       }
2710     if (has_temporal) {
2711       playMode = 1;
2712       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2713       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2714     }
2715   }
2716 }
2717 //------------------------------------------------------------------------------
2718
2719 //------------------------------------------------------------------------------
2720 void vvMainWindow::PlayNext()
2721 {
2722   if (playMode && !this->isHidden()) {
2723     int image_number=DataTree->topLevelItemCount();
2724     ///Only play one slicer per SM, and only if the SM is being displayed
2725     for (int i=0; i<image_number; i++)
2726       for (int j=0; j<4; j++)
2727         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2728             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2729           mSlicerManagers[i]->SetNextTSlice(j);
2730           break;
2731         }
2732     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2733   }
2734 }
2735 //------------------------------------------------------------------------------
2736
2737 void vvMainWindow::ShowLastImage()
2738 {
2739   if (mSlicerManagers.size() > 1) {
2740     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2741     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2742     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2743     DisplayChanged(item,1);
2744   }
2745 }
2746
2747 //------------------------------------------------------------------------------
2748 void vvMainWindow::UpdateRenderWindows()
2749 {
2750   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2751   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2752   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2753   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2754 }
2755 //------------------------------------------------------------------------------
2756
2757 //------------------------------------------------------------------------------
2758 void vvMainWindow::SegmentationOnCurrentImage()
2759 {
2760   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2761
2762   vvSegmentationDialog segmentation;
2763   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2764   segmentation.exec();
2765 }
2766 //------------------------------------------------------------------------------
2767
2768 void vvMainWindow::SurfaceViewerLaunch()
2769 {
2770   vvSurfaceViewerDialog surfaceViewer;
2771   surfaceViewer.exec();
2772 }
2773 //------------------------------------------------------------------------------
2774
2775
2776 //------------------------------------------------------------------------------
2777 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2778 {
2779   int number=0;
2780   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2781     vvSlicerManager * v = mSlicerManagers[l];
2782     if (v->GetBaseFileName() ==
2783         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2784       number = std::max(number, v->GetBaseFileNameNumber()+1);
2785     }
2786   }
2787   return number;
2788 }
2789 //------------------------------------------------------------------------------
2790
2791
2792 //------------------------------------------------------------------------------
2793 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2794 {
2795   // Change filename if another image exist with the same name
2796   int number = GetImageDuplicateFilenameNumber(filename);
2797
2798   // Create new SliceManager
2799   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2800   slicer_manager->SetImage(image);//, IMAGE, number);
2801   //  filename = filename+"_"+clitk::toString(number);
2802   slicer_manager->SetFilename(filename, number);
2803   mSlicerManagers.push_back(slicer_manager);
2804
2805   //create an item in the tree with good settings
2806   QTreeWidgetItem *item = new QTreeWidgetItem();
2807   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2808   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2809   qApp->processEvents();
2810
2811   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2812
2813   //Create the buttons for reload and close
2814   qApp->processEvents();
2815   QTreePushButton* cButton = new QTreePushButton;
2816   cButton->setItem(item);
2817   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2818   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2819   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2820           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2821
2822   QTreePushButton* rButton = new QTreePushButton;
2823   rButton->setItem(item);
2824   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2825   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2826   rButton->setEnabled(0);
2827   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2828           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2829
2830   DataTree->addTopLevelItem(item);
2831   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2832   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2833
2834   //set the id of the image
2835   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2836   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2837   mSlicerManagers.back()->SetId(id.toStdString());
2838
2839   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2840                       , id.toStdString());
2841
2842   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2843           this, SLOT(CurrentImageChanged(std::string)));
2844   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2845           this, SLOT(CurrentPickedImageChanged(std::string)));
2846   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2847           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2848   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2849           this, SLOT(VectorChanged(int,double,double,double, double)));
2850   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2851           this, SLOT(OverlayChanged(int,double,double)));
2852   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2853           this, SLOT(FusionChanged(int,double)));
2854   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2855           this,SLOT(WindowsChanged(int, int, int)));
2856   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2857           this,SLOT(WindowLevelChanged(double, double, int, int)));
2858   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2859           this,SLOT(UpdateSlice(int,int)));
2860   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2861           this,SLOT(UpdateTSlice(int, int)));
2862   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2863           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2864   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2865           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2866   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2867           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2868   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2869           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2870   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2871   UpdateTree();
2872   qApp->processEvents();
2873   InitSlicers();
2874   ShowLastImage();
2875   InitDisplay();
2876   qApp->processEvents();
2877
2878   // End
2879   ImageInfoChanged();
2880   return slicer_manager;
2881 }
2882 //------------------------------------------------------------------------------
2883
2884
2885 //------------------------------------------------------------------------------
2886 void vvMainWindow::UpdateCurrentSlicer()
2887 {
2888   int index = -1;
2889   if (DataTree->selectedItems().size() > 0) {
2890     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2891   }
2892   mSlicerManagerCurrentIndex = index;
2893 }
2894 //------------------------------------------------------------------------------
2895