vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #ifdef VTK_USE_FFMPEG_ENCODER
  72 #  include <vtkFFMPEGWriter.h>
  73 #endif
  74 #ifdef VTK_USE_MPEG2_ENCODER
  75 #  include <vtkMPEG2Writer.h>
  76 #endif
  77 #include <vtkMatrix4x4.h>
  78 #include <vtkTransform.h>
  79
  80 // Standard includes
  81 #include <iostream>
  82 #include <sstream>
  83 #include <iomanip>
  84
  85 #define COLUMN_TREE 0
  86 #define COLUMN_UL_VIEW 1
  87 #define COLUMN_UR_VIEW 2
  88 #define COLUMN_DL_VIEW 3
  89 #define COLUMN_DR_VIEW 4
  90 #define COLUMN_CLOSE_IMAGE 5
  91 #define COLUMN_RELOAD_IMAGE 6
  92 #define COLUMN_IMAGE_NAME 7
  93
  94 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  95
  96 /*Data Tree values
  97   0,Qt::UserRole full filename
  98   1,Qt::CheckStateRole checkbutton UL View
  99   1,Qt::UserRole overlay, fusion or vector
 100   2,Qt::CheckStateRole checkbutton UR View
 101   3,Qt::CheckStateRole checkbutton DL View
 102   4,Qt::CheckStateRole checkbutton DR View
 103   5,0  short filename
 104   5,Qt::UserRole mSlicerManager id*/
 105
 106 //------------------------------------------------------------------------------
 107 vvMainWindow::vvMainWindow():vvMainWindowBase()
 108 {
 109   setupUi(this); // this sets up the GUI
 110
 111   mInputPathName = "";
 112   mMenuTools = menuTools;
 113   //  mMenuSegmentation = menuSegmentation;
 114   mContextMenu = &contextMenu;
 115   mMenuExperimentalTools = menuExperimental;
 116   mMainWidget = this;
 117   mCurrentTime = -1;
 118   mCurrentSelectedImageId = "";
 119   mCurrentPickedImageId = "";
 120   mCurrentPickedImageIndex = 0;
 121
 122   //Init the contextMenu
 123   this->setContextMenuPolicy(Qt::CustomContextMenu);
 124   contextActions.resize(0);
 125   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 126                                   tr("O&pen new Image"));
 127   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 128   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 129   contextActions.push_back(actionOpen_new_image);
 130   contextMenu.addSeparator();
 131
 132   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 133                                tr("Close Current Image"));
 134   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 135   contextActions.push_back(actionClose_Image);
 136
 137   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 138                                 tr("Reload Current Image"));
 139   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 140   contextActions.push_back(actionReload_image);
 141
 142   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 143                               tr("Save Current Image"));
 144   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 145   contextActions.push_back(actionSave_image);
 146
 147   contextMenu.addSeparator();
 148
 149   contextMenu.addAction(actionAdd_VF_to_current_Image);
 150   contextActions.push_back(actionAdd_VF_to_current_Image);
 151
 152   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 153       tr("Add overlay image to current image"));
 154   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 155   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 156
 157   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 158
 159   contextMenu.addAction(actionAdd_fusion_image);
 160   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 161   contextActions.push_back(actionAdd_fusion_image);
 162
 163   // TRIAL DS
 164   /*
 165   QMenu * m = new QMenu(menubar);
 166   m->setTitle("TOTO");
 167   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 168   contextMenu.addMenu(m);
 169   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON"));
 171   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 172                      tr("BIDON2"));
 173   m->addAction(a);
 174   m->addAction(b);
 175   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 176   */
 177
 178   //init the DataTree
 179   mSlicerManagers.resize(0);
 180
 181   QStringList header;
 182   header.append("");
 183   header.append("TL");
 184   header.append("TR");
 185   header.append("BL");
 186   header.append("BR");
 187   header.append("");
 188   header.append("");
 189   header.append("Name");
 190
 191   DataTree->setHeaderLabels(header);
 192   DataTree->resizeColumnToContents(COLUMN_TREE);
 193   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 197   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 199   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 200
 201   viewMode = 1;
 202   documentation = new vvDocumentation();
 203   help_dialog = new vvHelpDialog();
 204   dicomSeriesSelector = new vvDicomSeriesSelector();
 205
 206   inverseButton->setEnabled(0);
 207   actionAdd_Overlay_to_current_Image->setEnabled(0);
 208   actionSave_As->setEnabled(0);
 209   actionAdd_VF_to_current_Image->setEnabled(0);
 210   actionAdd_fusion_image->setEnabled(0);
 211
 212   //init the sliders
 213   verticalSliders.push_back(NOVerticalSlider);
 214   verticalSliders.push_back(NEVerticalSlider);
 215   verticalSliders.push_back(SOVerticalSlider);
 216   verticalSliders.push_back(SEVerticalSlider);
 217
 218   for (int i =0; i < 4; i++)
 219     verticalSliders[i]->hide();
 220
 221   horizontalSliders.push_back(NOHorizontalSlider);
 222   horizontalSliders.push_back(NEHorizontalSlider);
 223   horizontalSliders.push_back(SOHorizontalSlider);
 224   horizontalSliders.push_back(SEHorizontalSlider);
 225
 226   for (int i =0; i < 4; i++)
 227     horizontalSliders[i]->hide();
 228
 229
 230   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 231   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 232   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 233   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 234
 235   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 236   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 237   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 238   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 239
 240   //connect everything
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 250   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 251   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 252   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 253   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 254   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 255   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 256   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 257   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 258
 259   ///////////////////////////////////////////////
 260   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 261   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 262   ///////////////////////////////////////////////
 263
 264   actionNorth_East_Window->setEnabled(0);
 265   actionNorth_West_Window->setEnabled(0);
 266   actionSouth_East_Window->setEnabled(0);
 267   actionSouth_West_Window->setEnabled(0);
 268
 269   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 270   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 271   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 272   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 273
 274   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 275   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 276           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 277
 278   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 279   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 281   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 282   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 283   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 284   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 285
 286
 287   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 288
 289   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 290   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 291   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 292   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 293   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 294           this,SLOT(SetFusionProperty(int,int,double,double)));
 295   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 296
 297   playMode = 0;//pause
 298   mFrameRate = 10;
 299   playButton->setEnabled(0);
 300   frameRateLabel->setEnabled(0);
 301   frameRateSpinBox->setEnabled(0);
 302   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 303   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 304
 305   goToCursorPushButton->setEnabled(0);
 306   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 307
 308   NOViewWidget->hide();
 309   NEViewWidget->hide();
 310   SOViewWidget->hide();
 311   SEViewWidget->hide();
 312
 313   //Recently opened files
 314   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 315   recentlyOpenedFilesMenu=NULL;
 316   if ( !recent_files.empty() ) {
 317     createRecentlyOpenedFilesMenu();
 318     updateRecentlyOpenedFilesMenu(recent_files);
 319   }
 320
 321   // Adding all new tools (insertion in the menu)
 322   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 323   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 324
 325   if (!CLITK_EXPERIMENTAL)
 326     menuExperimental->menuAction()->setVisible(false);
 327
 328
 329   QTimer * timerMemory = new QTimer(this);
 330   //timerMemory->setInterval(5);
 331   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 332   timerMemory->start(2000);
 333 }
 334 //------------------------------------------------------------------------------
 335 void vvMainWindow::show()
 336 {
 337   vvMainWindowBase::show();
 338   PopupRegisterForm(true);
 339 }
 340 //------------------------------------------------------------------------------
 341 void vvMainWindow::UpdateMemoryUsage()
 342 {
 343   //  clitk::PrintMemory(true);
 344   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 345   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 346 }
 347 //------------------------------------------------------------------------------
 348
 349
 350 //------------------------------------------------------------------------------
 351 void vvMainWindow::createRecentlyOpenedFilesMenu()
 352 {
 353   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 354   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 355   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 356   menuFile->insertSeparator(actionOpen_Image_With_Time);
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362
 363 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 364 {
 365   if(recentlyOpenedFilesMenu==NULL) {
 366     createRecentlyOpenedFilesMenu();
 367   } else {
 368     recentlyOpenedFilesMenu->clear();
 369   }
 370   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 371     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 372     recentlyOpenedFilesMenu->addAction(current);
 373     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 374   }
 375 }
 376 //------------------------------------------------------------------------------
 377
 378
 379 //------------------------------------------------------------------------------
 380 void vvMainWindow::ComputeMidPosition()
 381 {
 382   bool ok;
 383   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 384   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 385                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 386   if (ok) {
 387     vvMidPosition midp;
 388     midp.slicer_manager = mSlicerManagers[index];
 389     midp.reference_image_index = ref;
 390     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 391     midp.Update();
 392     if (midp.error)
 393       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 394     else {
 395       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 396       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 397     }
 398     QApplication::restoreOverrideCursor();
 399   }
 400 }
 401 //------------------------------------------------------------------------------
 402
 403
 404 //------------------------------------------------------------------------------
 405 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 406 {
 407   QTreeWidgetItem *item = new QTreeWidgetItem();
 408   item->setData(0,Qt::UserRole,"filename.vtk");
 409   item->setData(1,Qt::UserRole,tr("contour"));
 410   QBrush brush;
 411   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 412   brush.setStyle(Qt::SolidPattern);
 413   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 414   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 415
 416   for (int j = 1; j <= 4; j++)
 417     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 418
 419   QTreePushButton* cButton = new QTreePushButton;
 420   cButton->setItem(item);
 421   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 422   cButton->setToolTip(tr("close image"));
 423   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 424   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 425           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 426
 427   QTreePushButton* rButton = new QTreePushButton;
 428   rButton->setItem(item);
 429   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 430   rButton->setToolTip(tr("reload image"));
 431   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 432   rButton->setEnabled(false);
 433   //Not implemented
 434   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 435   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 436
 437   DataTree->topLevelItem(image_index)->setExpanded(1);
 438   DataTree->topLevelItem(image_index)->addChild(item);
 439   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 440   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 441   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 442   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 443
 444   UpdateTree();
 445   mSlicerManagers[image_index]->AddContour(contour,propagation);
 446   mSlicerManagers[image_index]->Render();
 447 }
 448 //------------------------------------------------------------------------------
 449
 450
 451 //------------------------------------------------------------------------------
 452 void vvMainWindow::OpenVTKContour()
 453 {
 454   if (mSlicerManagers.size() > 0) {
 455     QString Extensions = "Images ( *.vtk *.obj)";
 456     Extensions += ";;All Files (*)";
 457     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 458     if (file.isNull())
 459       return;
 460     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 461     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 462     vvMeshReader reader;
 463     reader.SetImage(mSlicerManagers[index]->GetImage());
 464     reader.SetModeToVTK();
 465     reader.SetFilename(file.toStdString());
 466     reader.Update();
 467     AddContour(index,reader.GetOutput()[0],false);
 468     QApplication::restoreOverrideCursor();
 469   }
 470 }
 471 //------------------------------------------------------------------------------
 472
 473
 474 //------------------------------------------------------------------------------
 475 void vvMainWindow::OpenDCStructContour()
 476 {
 477   if (mSlicerManagers.size() > 0) {
 478     QString Extensions = "Dicom Files ( *.dcm RS*)";
 479     Extensions += ";;All Files (*)";
 480     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 481     if (file.isNull())
 482       return;
 483     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 484     vvMeshReader reader;
 485     reader.SetFilename(file.toStdString());
 486     vvStructSelector selector;
 487     selector.SetStructures(reader.GetROINames());
 488     if (!mSlicerManagers[index]->GetVF().IsNull())
 489       selector.EnablePropagationCheckBox();
 490     if (selector.exec()) {
 491       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 492       reader.SetSelectedItems(selector.getSelectedItems());
 493       reader.SetImage(mSlicerManagers[index]->GetImage());
 494       if (selector.PropagationEnabled())
 495         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 496       reader.Update();
 497       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 498       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 499            i!=contours.end(); i++)
 500         AddContour(index,*i,selector.PropagationEnabled());
 501       QApplication::restoreOverrideCursor();
 502     }
 503   }
 504 }
 505 //------------------------------------------------------------------------------
 506
 507
 508 //------------------------------------------------------------------------------
 509 void vvMainWindow::ComputeDeformableRegistration()
 510 {
 511   if (mSlicerManagers.size() > 0) {
 512     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 513     vvDeformationDialog dialog(index,mSlicerManagers);
 514     if (dialog.exec()) {
 515       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 516       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 517       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 518     } else
 519       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 520   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::WarpImage()
 527 {
 528   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 529   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 530     bool ok;
 531     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 532                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 533     if (ok) {
 534       WarpImage(mSlicerManagers[index],ref);
 535     }
 536   } else
 537     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 538 }
 539 //------------------------------------------------------------------------------
 540
 541
 542 //------------------------------------------------------------------------------
 543 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 544 {
 545   if (!selected_slicer->GetVF().IsNull()) {
 546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 547     QFileInfo info(selected_slicer->GetFileName().c_str());
 548     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 549                      reference_phase,this);
 550     if (warp.ComputeWarpedImage()) {
 551       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 552       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 553       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 554       QApplication::restoreOverrideCursor();
 555     } else {
 556       QApplication::restoreOverrideCursor();
 557       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 558     }
 559   } else
 560     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 561 }
 562 //------------------------------------------------------------------------------
 563
 564
 565 //------------------------------------------------------------------------------
 566 vvMainWindow::~vvMainWindow()
 567 {
 568   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 569     if (mSlicerManagers[i] != NULL)
 570       delete mSlicerManagers[i];
 571   }
 572 }
 573 //------------------------------------------------------------------------------
 574
 575 //------------------------------------------------------------------------------
 576 QTabWidget * vvMainWindow::GetTab()
 577 {
 578   return tabWidget;
 579 }
 580 //------------------------------------------------------------------------------
 581
 582
 583 //------------------------------------------------------------------------------
 584 void vvMainWindow::MergeImages()
 585 {
 586   QString Extensions = EXTENSIONS;
 587   Extensions += ";;All Files (*)";
 588   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 589   if (files.isEmpty())
 590     return;
 591   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 592   std::vector<std::string> vector;
 593
 594   unsigned int currentDim = 0;
 595   std::vector<double> currentSpacing;
 596   std::vector<int> currentSize;
 597   std::vector<double> currentOrigin;
 598
 599   for (int i = 0; i < files.size(); i++) {
 600     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 601                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 602     reader->SetFileName(files[i].toStdString().c_str());
 603     reader->ReadImageInformation();
 604     if (reader)        {
 605       //NOViewWidget->hide();
 606       //NEViewWidget->hide();
 607       //SOViewWidget->hide();
 608       //SEViewWidget->hide();
 609       if (i == 0)
 610         currentDim = reader->GetNumberOfDimensions();
 611       bool IsOk = true;
 612       for (unsigned int j = 0; j < currentDim; j++) {
 613         if (i == 0) {
 614           if (j == 0) {
 615             currentSpacing.resize(currentDim);
 616             currentSize.resize(currentDim);
 617             currentOrigin.resize(currentDim);
 618           }
 619           currentOrigin[j] = reader->GetOrigin(j);
 620           currentSpacing[j] = reader->GetSpacing(j);
 621           currentSize[j] = reader->GetDimensions(j);
 622         } else if (currentDim != reader->GetNumberOfDimensions()
 623                    || currentSpacing[j] != reader->GetSpacing(j)
 624                    || currentSize[j] != (int)reader->GetDimensions(j)
 625                    || currentOrigin[j] != reader->GetOrigin(j)) {
 626           QString error = "Cannot read file (too different from others ";
 627           error += files[i].toStdString().c_str();
 628           QMessageBox::information(this,tr("Reading problem"),error);
 629           IsOk = false;
 630           break;
 631         }
 632       }
 633       if (IsOk)
 634         vector.push_back(files[i].toStdString());
 635     }
 636   }
 637   if (vector.size() > 0)
 638     LoadImages(vector, vvImageReader::MERGED);
 639 }
 640 //------------------------------------------------------------------------------
 641
 642 //------------------------------------------------------------------------------
 643 void vvMainWindow::SliceImages()
 644 {
 645   QString Extensions = EXTENSIONS;
 646   Extensions += ";;All Files (*)";
 647
 648   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 649   if (files.isEmpty())
 650     return;
 651   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 652   std::vector<std::string> vector;
 653   for (int i = 0; i < files.size(); i++)
 654     vector.push_back(files[i].toStdString());
 655   LoadImages(vector, vvImageReader::SLICED);
 656 }
 657 //------------------------------------------------------------------------------
 658
 659 //------------------------------------------------------------------------------
 660 void vvMainWindow::MergeImagesWithTime()
 661 {
 662   QString Extensions = EXTENSIONS;
 663   Extensions += ";;All Files (*)";
 664   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 665   if (files.isEmpty())
 666     return;
 667   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 668   std::vector<std::string> vector;
 669
 670   unsigned int currentDim = 0;
 671   std::vector<double> currentSpacing;
 672   std::vector<int> currentSize;
 673   std::vector<double> currentOrigin;
 674
 675   for (int i = 0; i < files.size(); i++) {
 676     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 677                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 678     if (reader) {
 679       reader->SetFileName(files[i].toStdString().c_str());
 680       reader->ReadImageInformation();
 681       if (i == 0)
 682         currentDim = reader->GetNumberOfDimensions();
 683       bool IsOk = true;
 684       for (unsigned int j = 0; j < currentDim; j++) {
 685         if (i == 0) {
 686           if (j == 0) {
 687             currentSpacing.resize(currentDim);
 688             currentSize.resize(currentDim);
 689             currentOrigin.resize(currentDim);
 690           }
 691           currentOrigin[j] = reader->GetOrigin(j);
 692           currentSpacing[j] = reader->GetSpacing(j);
 693           currentSize[j] = reader->GetDimensions(j);
 694         } else if (currentDim != reader->GetNumberOfDimensions()
 695                    || currentSpacing[j] != reader->GetSpacing(j)
 696                    || currentSize[j] != (int)reader->GetDimensions(j)
 697                    || currentOrigin[j] != reader->GetOrigin(j)) {
 698           QString error = "Cannot read file (too different from others ";
 699           error += files[i].toStdString().c_str();
 700           QMessageBox::information(this,tr("Reading problem"),error);
 701           IsOk = false;
 702           break;
 703         }
 704       }
 705       if (IsOk)
 706         vector.push_back(files[i].toStdString());
 707     } else {
 708       QString error = "Cannot read file info for ";
 709       error += files[i].toStdString().c_str();
 710       error += "\n";
 711       error += "Maybe you're trying to open an image in an unsupported format?\n";
 712       QMessageBox::information(this,tr("Reading problem"),error);
 713     }
 714   }
 715   sort(vector.begin(),vector.end());
 716   if (vector.size() > 1)
 717     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 718   else
 719     QMessageBox::warning(this,tr("Reading problem"),"You need to select at least two images to merge images with time.\nIf you only want to open one image, please use the \"Open Image\" function.");
 720 }
 721 //------------------------------------------------------------------------------
 722
 723
 724 //------------------------------------------------------------------------------
 725 void vvMainWindow::OpenDicom()
 726 {
 727   std::vector<std::string> files;
 728
 729   std::cout << "dicomSeriesSelector " << std::endl;
 730   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 731     files = *(dicomSeriesSelector->GetFilenames());
 732     LoadImages(files, vvImageReader::DICOM);
 733   }
 734 }
 735 //------------------------------------------------------------------------------
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenImages()
 739 {
 740   QString Extensions = EXTENSIONS;
 741   Extensions += ";;All Files (*)";
 742
 743   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 744   if (files.isEmpty())
 745     return;
 746   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 747   std::vector<std::string> vector;
 748   for (int i = 0; i < files.size(); i++)
 749     vector.push_back(files[i].toStdString());
 750   LoadImages(vector, vvImageReader::IMAGE);
 751 }
 752 //------------------------------------------------------------------------------
 753 void vvMainWindow::OpenRecentImage()
 754 {
 755   QAction * caller = qobject_cast<QAction*>(sender());
 756   std::vector<std::string> images;
 757   images.push_back(caller->text().toStdString());
 758   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 759   LoadImages(images, vvImageReader::IMAGE);
 760 }
 761 //------------------------------------------------------------------------------
 762
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::OpenImageWithTime()
 766 {
 767   QString Extensions = EXTENSIONS;
 768   Extensions += ";;All Files (*)";
 769
 770   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 771   if (files.isEmpty())
 772     return;
 773   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 774   std::vector<std::string> vector;
 775   for (int i = 0; i < files.size(); i++) {
 776     vector.push_back(files[i].toStdString());
 777   }
 778   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 779 }
 780 //------------------------------------------------------------------------------
 781
 782
 783 //------------------------------------------------------------------------------
 784 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 785 {
 786   //Separate the way to open images and dicoms
 787   int fileSize;
 788   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 789     fileSize = files.size();
 790   else
 791     fileSize = 1;
 792
 793   // For SLICED, we need the number of slices (ndim and #slices)
 794   std::vector<unsigned int> nSlices;
 795   nSlices.resize(files.size());
 796   std::fill(nSlices.begin(), nSlices.end(), 1);
 797   if (filetype == vvImageReader::SLICED) {
 798     for (int i = 0; i < fileSize; i++) {
 799       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 800       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 801       if (!header) {
 802         nSlices[i] = 0;
 803         QString error = "Cannot open file \n";
 804         error += files[i].c_str();
 805         QMessageBox::information(this,tr("Reading problem"),error);
 806         return;
 807       }
 808       if (header->GetNumberOfDimensions() < 3) {
 809         nSlices[i] = 0;
 810         QString error = "Dimension problem. Cannot slice \n";
 811         error += files[i].c_str();
 812         QMessageBox::information(this,tr("Reading problem"),error);
 813         return;
 814       }
 815       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 816     }
 817   }
 818
 819   //Only add to the list of recently opened files when a single file is opened,
 820   //to avoid polluting the list of recently opened files
 821   if (files.size() == 1) {
 822     QFileInfo finfo=tr(files[0].c_str());
 823     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 824     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 825   }
 826   //init the progress events
 827   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 828   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 829   qApp->processEvents();
 830
 831   int numberofsuccesulreads=0;
 832   //open images as 1 or multiples
 833   for (int i = 0; i < fileSize; i++) {
 834
 835     progress.SetText("Opening " + files[i]);
 836     progress.SetProgress(i,fileSize);
 837     qApp->processEvents();
 838
 839     for (unsigned int j = 0; j < nSlices[i]; j++) {
 840       //read the image and put it in mSlicerManagers
 841       vvSlicerManager* imageManager = new vvSlicerManager(4);
 842       qApp->processEvents();
 843
 844       bool SetImageSucceed=false;
 845
 846       // Change filename if an image with the same already exist
 847       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 848
 849       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 850         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 851       else {
 852         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 853       }
 854       if (!SetImageSucceed) {
 855         QApplication::restoreOverrideCursor();
 856         QString error = "Cannot open file \n";
 857         error += imageManager->GetLastError().c_str();
 858         QMessageBox::information(this,tr("Reading problem"),error);
 859         delete imageManager;
 860       } else {
 861         mSlicerManagers.push_back(imageManager);
 862
 863         //create an item in the tree with good settings
 864         QTreeWidgetItem *item = new QTreeWidgetItem();
 865         item->setData(0,Qt::UserRole,files[i].c_str());
 866         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 867         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 868         item->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   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1025   inverseButton->setEnabled(1);
1026
1027   goToCursorPushButton->setEnabled(1);
1028
1029   if (DataTree->selectedItems().size()) {
1030     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1031
1032     colorMapComboBox->setEnabled(1);
1033     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1034       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1035           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1036         colorMapComboBox->setEnabled(0);
1037         break;
1038       }
1039     }
1040
1041     std::vector<double> origin;
1042     std::vector<double> inputSpacing;
1043     std::vector<int> inputSize;
1044     std::vector<double> sizeMM;
1045     vtkSmartPointer<vtkMatrix4x4> transformation;
1046     int dimension=0;
1047     QString pixelType;
1048     QString inputSizeInBytes;
1049     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1050
1051     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1052       playButton->setEnabled(1);
1053       frameRateLabel->setEnabled(1);
1054       frameRateSpinBox->setEnabled(1);
1055     } else {
1056       playButton->setEnabled(0);
1057       frameRateLabel->setEnabled(0);
1058       frameRateSpinBox->setEnabled(0);
1059     }
1060
1061     //read image header
1062     int NPixel = 1;
1063
1064     vvImage::Pointer imageSelected;
1065     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1066       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1067       dimension = imageSelected->GetNumberOfDimensions();
1068       origin.resize(dimension);
1069       inputSpacing.resize(dimension);
1070       inputSize.resize(dimension);
1071       sizeMM.resize(dimension);
1072       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1073       for (int i = 0; i < dimension; i++) {
1074         origin[i] = imageSelected->GetOrigin()[i];
1075         inputSpacing[i] = imageSelected->GetSpacing()[i];
1076         inputSize[i] = imageSelected->GetSize()[i];
1077         sizeMM[i] = inputSize[i]*inputSpacing[i];
1078         NPixel *= inputSize[i];
1079       }
1080       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1081     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1082       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1083       dimension = imageSelected->GetNumberOfDimensions();
1084       origin.resize(dimension);
1085       inputSpacing.resize(dimension);
1086       inputSize.resize(dimension);
1087       sizeMM.resize(dimension);
1088       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1089       for (int i = 0; i < dimension; i++) {
1090         origin[i] = imageSelected->GetOrigin()[i];
1091         inputSpacing[i] = imageSelected->GetSpacing()[i];
1092         inputSize[i] = imageSelected->GetSize()[i];
1093         sizeMM[i] = inputSize[i]*inputSpacing[i];
1094         NPixel *= inputSize[i];
1095       }
1096       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1097     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1098       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1099       dimension = imageSelected->GetNumberOfDimensions();
1100       origin.resize(dimension);
1101       inputSpacing.resize(dimension);
1102       inputSize.resize(dimension);
1103       sizeMM.resize(dimension);
1104       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1105       for (int i = 0; i < dimension; i++) {
1106         origin[i] = imageSelected->GetOrigin()[i];
1107         inputSpacing[i] = imageSelected->GetSpacing()[i];
1108         inputSize[i] = imageSelected->GetSize()[i];
1109         sizeMM[i] = inputSize[i]*inputSpacing[i];
1110         NPixel *= inputSize[i];
1111       }
1112       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1113     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1114       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1115       dimension = imageSelected->GetNumberOfDimensions();
1116       origin.resize(dimension);
1117       inputSpacing.resize(dimension);
1118       inputSize.resize(dimension);
1119       sizeMM.resize(dimension);
1120       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1121       for (int i = 0; i < dimension; i++) {
1122         origin[i] = imageSelected->GetOrigin()[i];
1123         inputSpacing[i] = imageSelected->GetSpacing()[i];
1124         inputSize[i] = imageSelected->GetSize()[i];
1125         sizeMM[i] = inputSize[i]*inputSpacing[i];
1126         NPixel *= inputSize[i];
1127       }
1128       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1129     }
1130
1131     QString dim = QString::number(dimension) + " (";
1132     dim += pixelType + ")";
1133
1134     infoPanel->setFileName(image);
1135     infoPanel->setDimension(dim);
1136     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1137     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1138     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1139     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1140     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1141     transformation = imageSelected->GetTransform()->GetMatrix();
1142     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1143
1144     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1145                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1146     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1147     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1148
1149     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1150     for (int i = 0; i < 4; i++) {
1151       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1152         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1153         break;
1154       }
1155     }
1156     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1157     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1158     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1159     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1160
1161     infoPanel->setFileName(image);
1162     infoPanel->setDimension(dim);
1163     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1164     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1165     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1166     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1167     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1168
1169     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1170                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1171     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1172     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1173
1174     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1175     for (int i = 0; i < 4; i++) {
1176       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1177         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1178         break;
1179       }
1180     }
1181     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1182     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1183     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1184     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1185
1186     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1187       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1188       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1189                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1190                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1191     } else {
1192       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1193       overlayPanel->getVFProperty(-1,-1,-1);
1194     }
1195     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1196       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1197       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1198     } else {
1199       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1200       overlayPanel->getOverlayProperty(-1);
1201     }
1202     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1203       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1204       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1205                                       mSlicerManagers[index]->GetFusionColorMap(),
1206                                       mSlicerManagers[index]->GetFusionWindow(),
1207                                       mSlicerManagers[index]->GetFusionLevel());
1208     } else {
1209       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1210       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1211     }
1212   }
1213 }
1214 //------------------------------------------------------------------------------
1215
1216 //------------------------------------------------------------------------------
1217 void vvMainWindow::ShowDocumentation()
1218 {
1219   documentation->show();
1220 }
1221 //------------------------------------------------------------------------------
1222
1223 //------------------------------------------------------------------------------
1224 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1225 {
1226   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1227   if(!checkCanPush) {
1228     registerForm->show();
1229   } else {
1230     if(registerForm->canPush()) {
1231       registerForm->show();
1232       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1233     }
1234   }
1235 }
1236 //------------------------------------------------------------------------------
1237
1238 //------------------------------------------------------------------------------
1239 void vvMainWindow::ShowHelpDialog()
1240 {
1241   help_dialog->show();
1242 }
1243 //------------------------------------------------------------------------------
1244
1245 //------------------------------------------------------------------------------
1246 void vvMainWindow::ChangeViewMode()
1247 {
1248   QList<int> size;
1249   if (viewMode == 1) {
1250     viewMode = 0;
1251     size.push_back(1);
1252     size.push_back(0);
1253     splitter_3->setSizes(size);
1254     OSplitter->setSizes(size);
1255     DataTree->setColumnHidden(2,1);
1256     DataTree->setColumnHidden(3,1);
1257     DataTree->setColumnHidden(4,1);
1258   } else {
1259     viewMode = 1;
1260     size.push_back(1);
1261     size.push_back(1);
1262     splitter_3->setSizes(size);
1263     OSplitter->setSizes(size);
1264     DataTree->setColumnHidden(2,0);
1265     DataTree->setColumnHidden(3,0);
1266     DataTree->setColumnHidden(4,0);
1267   }
1268   UpdateRenderWindows();
1269   /*
1270   ** I don't know why but for both resized QVTKWidget we also need to render
1271   ** the associated Slicer to redraw crosses.
1272   */
1273   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1274     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1275       mSlicerManagers[i]->GetSlicer(0)->Render();
1276     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1277       mSlicerManagers[i]->GetSlicer(2)->Render();
1278   }
1279 }
1280 //------------------------------------------------------------------------------
1281
1282 //------------------------------------------------------------------------------
1283 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1284 {
1285   QString result = "";// QString::number(size);
1286   //result += " bytes (";
1287   if (size > 1000000000) {
1288     size /= 1000000000;
1289     result += QString::number(size);
1290     result += "Gb";//)";
1291   } else if (size > 1000000) {
1292     size /= 1000000;
1293     result += QString::number(size);
1294     result += "Mb";//)";
1295   } else if (size > 1000) {
1296     size /= 1000;
1297     result += QString::number(size);
1298     result += "kb";//)";
1299   }
1300   return result;
1301 }
1302 //------------------------------------------------------------------------------
1303
1304 //------------------------------------------------------------------------------
1305 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1306 {
1307   std::ostringstream strmatrix;
1308
1309   for (unsigned int i = 0; i < 4; i++) {
1310     for (unsigned int j = 0; j < 4; j++) {
1311       strmatrix.flags(ios::showpos);
1312       strmatrix.width(10);
1313       strmatrix.precision(3);
1314       strmatrix.setf(ios::fixed,ios::floatfield);
1315       strmatrix.fill(' ');
1316       strmatrix << std::left << matrix->GetElement(i, j);
1317       //strmatrix.width(10);
1318       strmatrix << " ";
1319     }
1320     strmatrix << std::endl;
1321   }
1322   QString result = strmatrix.str().c_str();
1323   return result;
1324 }
1325 //------------------------------------------------------------------------------
1326
1327 //------------------------------------------------------------------------------
1328 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1329 {
1330   QString result;
1331   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1332     if (i != 0)
1333       result += " ";
1334     result += QString::number(vectorDouble[i]);
1335   }
1336   return result;
1337 }
1338 //------------------------------------------------------------------------------
1339
1340 //------------------------------------------------------------------------------
1341 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1342 {
1343   QString result;
1344   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1345     if (i != 0)
1346       result += " ";
1347     result += QString::number(vectorInt[i]);
1348   }
1349   return result;
1350 }
1351 //------------------------------------------------------------------------------
1352
1353 //------------------------------------------------------------------------------
1354 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1355 {
1356   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1357   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1358     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1359       return i;
1360   }
1361   return -1;
1362 }
1363 //------------------------------------------------------------------------------
1364
1365 //------------------------------------------------------------------------------
1366 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1367 {
1368   QString id = sm->GetId().c_str();
1369   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1370     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1371       return DataTree->topLevelItem(i);
1372   }
1373   return NULL;
1374 }
1375 //------------------------------------------------------------------------------
1376
1377 //------------------------------------------------------------------------------
1378 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1379 {
1380   int index = GetSlicerIndexFromItem(clicked_item);
1381   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1382     return;
1383   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1384     //Trick to avoid redoing twice the job for a key (sr)
1385     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1386
1387     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1388     if (DataTree->topLevelItem(index) == current_row) {
1389       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1390       if (current_row == clicked_item) {
1391         //If we just activated a slicer
1392         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1393           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1394           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1395           DisplaySliders(i,column-1);
1396           std::map<std::string,int> overlay_counts;
1397           for (int child = 0; child < current_row->childCount(); child++) {
1398             std::string overlay_type =
1399               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1400             overlay_counts[overlay_type]++;
1401             current_row->child(child)->setData(column,Qt::CheckStateRole,
1402                                                current_row->data(column,Qt::CheckStateRole));
1403             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1404           }
1405         } else { //We don't allow simply desactivating a slicer
1406           clicked_item->setData(column,Qt::CheckStateRole,2);
1407           DisplayChanged(clicked_item, column);
1408           return;
1409         }
1410       }
1411       //if we clicked on the vector(or overlay) and not the image
1412       else {
1413         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1414           current_row->setData(column,Qt::CheckStateRole,2);
1415           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1416           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1417           DisplaySliders(i,column-1);
1418         }
1419         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1420         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1421         int overlay_index=0;
1422         for (int child = 0; child < current_row->childCount(); child++) {
1423           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1424             overlay_index++;
1425           if (current_row->child(child) == clicked_item) break;
1426         }
1427         clicked_slicer->SetActorVisibility(
1428           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1429       }
1430     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1431       current_row->setData(column,Qt::CheckStateRole,0);
1432       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1433       std::map<std::string,int> overlay_counts;
1434       for (int child = 0; child < current_row->childCount(); child++) {
1435         std::string overlay_type =
1436           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1437         overlay_counts[overlay_type]++;
1438         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1439         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1440         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1441       }
1442     }
1443     //mSlicerManagers[i]->SetColorMap(-1);
1444     mSlicerManagers[i]->SetColorMap();
1445   }
1446   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1447 }
1448 //------------------------------------------------------------------------------
1449
1450 void vvMainWindow::InitSlicers()
1451 {
1452   if (mSlicerManagers.size()) {
1453     mSlicerManagers.back()->GenerateDefaultLookupTable();
1454
1455     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1456     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1457     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1458     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1459   }
1460 }
1461
1462 //------------------------------------------------------------------------------
1463 void vvMainWindow::InitDisplay()
1464 {
1465   if (mSlicerManagers.size()) {
1466     //BE CAREFUL : this is absolutely necessary to set the interactor style
1467     //in order to have the same style instanciation for all SlicerManagers in
1468     // a same window
1469     for (int j = 0; j < 4; j++) {
1470       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1471       style->SetAutoAdjustCameraClippingRange(1);
1472       bool AlreadySelected = false;
1473       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1474         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1475
1476         //select the image only if previous are not selected
1477         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1478           mSlicerManagers[i]->UpdateSlicer(j,1);
1479           AlreadySelected = true;
1480         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1481           if (DataTree->selectedItems().size() == 0)
1482             DataTree->topLevelItem(i)->setSelected(1);
1483           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1484           mSlicerManagers[i]->UpdateSlicer(j,1);
1485           DisplaySliders(i,j);
1486         } else {
1487           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1488           mSlicerManagers[i]->UpdateSlicer(j,0);
1489         }
1490       }
1491       style->Delete();
1492     }
1493   }
1494 }
1495 //------------------------------------------------------------------------------
1496
1497 //------------------------------------------------------------------------------
1498 void vvMainWindow::DisplaySliders(int slicer, int window)
1499 {
1500   int range[2];
1501   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1502   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1503
1504   int tRange[2];
1505   tRange[0] = 0;
1506   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1507   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1508   bool showHorizontal = false;
1509   bool showVertical = false;
1510   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1511       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1512           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1513           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1514     showVertical = true;
1515   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1516       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1517       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1518     showHorizontal = true;
1519
1520   if (showVertical)
1521     verticalSliders[window]->show();
1522   else
1523     verticalSliders[window]->hide();
1524   verticalSliders[window]->setRange(range[0],range[1]);
1525   verticalSliders[window]->setValue(position);
1526
1527   if (showHorizontal)
1528     horizontalSliders[window]->show();
1529   else
1530     horizontalSliders[window]->hide();
1531   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1532   horizontalSliders[window]->setValue(tPosition);
1533 }
1534 //------------------------------------------------------------------------------
1535
1536 //------------------------------------------------------------------------------
1537 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1538 {
1539   int index = GetSlicerIndexFromItem(item);
1540
1541   if (DataTree->topLevelItem(index) != item) {
1542     QString warning = "Do you really want to close the overlay : ";
1543     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1544     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1545                        warning, 0, this);
1546     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1547     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1548     if (msgBox.exec() == QMessageBox::AcceptRole) {
1549       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1550       int overlay_index=0;
1551       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1552         if (DataTree->topLevelItem(index)->\
1553             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1554           overlay_index++;
1555         if (DataTree->topLevelItem(index)->child(child) == item) break;
1556       }
1557       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1558       mSlicerManagers[index]->SetColorMap(0);
1559       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1560       mSlicerManagers[index]->Render();
1561     }
1562   } else if (DataTree->topLevelItemCount() <= 1) {
1563     QString warning = "Do you really want to close the image : ";
1564     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1565     warning += "\nThis is the last image, you're about to close vv !!!";
1566     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1567                        warning, 0, this);
1568     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1569     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1570     if (msgBox.exec() == QMessageBox::AcceptRole) {
1571       this->close();
1572     }
1573   } else {
1574     QString warning = "Do you really want to close the image : ";
1575     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1576     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1577                        warning, 0, this);
1578     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1579     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1580     if (msgBox.exec() == QMessageBox::AcceptRole) {
1581
1582       // Tell tools that we close an image
1583       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1584
1585       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1586       DataTree->takeTopLevelItem(index);
1587       for (int i = 0; i < index; i++) {
1588         Manageriter++;
1589       }
1590       linkPanel->removeImage(index);
1591       mSlicerManagers[index]->RemoveActors();
1592       delete mSlicerManagers[index];
1593       mSlicerManagers.erase(Manageriter);
1594
1595       //
1596       InitDisplay();
1597     }
1598   }
1599   ImageInfoChanged();
1600 }
1601 //------------------------------------------------------------------------------
1602
1603 //------------------------------------------------------------------------------
1604 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1605 {
1606   // int index = GetSlicerIndexFromItem(item);
1607   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1608   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1609   //     mSlicerManagers[index]->ReloadVF();
1610   //   else
1611   //     mSlicerManagers[index]->Reload();
1612
1613   //   QApplication::restoreOverrideCursor();
1614   int index = GetSlicerIndexFromItem(item);
1615   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1616   QString role=item->data(1,Qt::UserRole).toString();
1617   if ( role == "vector"){
1618     mSlicerManagers[index]->ReloadVF();
1619   }
1620   else if (role == "overlay"){
1621     mSlicerManagers[index]->ReloadOverlay();
1622   }
1623   else if (role == "fusion"){
1624     mSlicerManagers[index]->ReloadFusion();
1625   }
1626   else{
1627     mSlicerManagers[index]->Reload();
1628   }
1629   // Update view and info
1630   ImageInfoChanged();
1631   mSlicerManagers[index]->Render();
1632   QApplication::restoreOverrideCursor();
1633 }
1634 //------------------------------------------------------------------------------
1635
1636 //------------------------------------------------------------------------------
1637 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1638 {
1639   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1640 }
1641 //------------------------------------------------------------------------------
1642
1643 //------------------------------------------------------------------------------
1644 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1645 {
1646   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1647 }
1648 //------------------------------------------------------------------------------
1649
1650 //------------------------------------------------------------------------------
1651 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1652 {
1653   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1654 }
1655 //------------------------------------------------------------------------------
1656
1657 //------------------------------------------------------------------------------
1658 void vvMainWindow::FusionChanged(int visibility, double value)
1659 {
1660   overlayPanel->getCurrentFusionInfo(visibility,value);
1661 }
1662 //------------------------------------------------------------------------------
1663
1664 //------------------------------------------------------------------------------
1665 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1666 {
1667   infoPanel->setViews(window, view, slice);
1668 }
1669 //------------------------------------------------------------------------------
1670
1671 //------------------------------------------------------------------------------
1672 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1673 {
1674   windowSpinBox->setValue(window);
1675   levelSpinBox->setValue(level);
1676   colorMapComboBox->setCurrentIndex(colormap);
1677   presetComboBox->setCurrentIndex(preset);
1678 }
1679 //------------------------------------------------------------------------------
1680
1681 //------------------------------------------------------------------------------
1682 void vvMainWindow::WindowLevelEdited()
1683 {
1684   presetComboBox->setCurrentIndex(6);
1685   UpdateWindowLevel();
1686 }
1687 //------------------------------------------------------------------------------
1688
1689 //------------------------------------------------------------------------------
1690 void vvMainWindow::UpdateWindowLevel()
1691 {
1692   if (DataTree->selectedItems().size()) {
1693     if (presetComboBox->currentIndex() == 7) //For ventilation
1694       colorMapComboBox->setCurrentIndex(5);
1695     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1696     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1697     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1698     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1699     mSlicerManagers[index]->Render();
1700     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1701     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1702   }
1703 }
1704 //------------------------------------------------------------------------------
1705
1706 //------------------------------------------------------------------------------
1707 void vvMainWindow::UpdateColorMap()
1708 {
1709   if (DataTree->selectedItems().size()) {
1710     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1711     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1712     mSlicerManagers[index]->Render();
1713   }
1714 }
1715 //------------------------------------------------------------------------------
1716 void vvMainWindow::SwitchWindowLevel()
1717 {
1718   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1719   int window = mSlicerManagers[index]->GetColorWindow();
1720   presetComboBox->setCurrentIndex(6);
1721   windowSpinBox->setValue(-window);
1722   UpdateWindowLevel();
1723 }
1724 //------------------------------------------------------------------------------
1725
1726 //------------------------------------------------------------------------------
1727 void vvMainWindow::ApplyWindowLevelToAllImages()
1728 {
1729   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1730     if (mSlicerManagers[i] == NULL)
1731       continue;
1732     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1733     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1734     mSlicerManagers[i]->SetPreset(6);
1735     mSlicerManagers[i]->Render();
1736   }
1737 }
1738 //------------------------------------------------------------------------------
1739
1740 //------------------------------------------------------------------------------
1741 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1742 {
1743   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1744     if (mSlicerManagers[i]->GetId() == id) {
1745       //mSlicerManagers[i]->SetTSlice(temps);
1746       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1747       mSlicerManagers[i]->UpdateViews(0,slicer);
1748       break;
1749     }
1750   }
1751 }
1752 //------------------------------------------------------------------------------
1753
1754 //------------------------------------------------------------------------------
1755 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1756 {
1757   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1758     if (id == mSlicerManagers[i]->GetId()) {
1759       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1760     }
1761   }
1762 }
1763 //------------------------------------------------------------------------------
1764
1765 //------------------------------------------------------------------------------
1766 void vvMainWindow::ShowContextMenu(QPoint point)
1767 {
1768   if (!DataTree->selectedItems().size()) {
1769     contextActions[1]->setEnabled(0);
1770     contextActions[2]->setEnabled(0);
1771     contextActions[3]->setEnabled(0);
1772     contextActions[4]->setEnabled(0);
1773     contextActions[5]->setEnabled(0);
1774     contextActions[6]->setEnabled(0);
1775   } else {
1776     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1777     contextActions[1]->setEnabled(1);
1778     contextActions[2]->setEnabled(
1779       DataTree->itemWidget(DataTree->selectedItems()[0],
1780                            COLUMN_RELOAD_IMAGE)->isEnabled());
1781     contextActions[3]->setEnabled(1);
1782     contextActions[5]->setEnabled(1);
1783     contextActions[6]->setEnabled(1);
1784
1785     if (mSlicerManagers[index]->GetDimension() < 3)
1786       contextActions[4]->setEnabled(0);
1787     else
1788       contextActions[4]->setEnabled(1);
1789   }
1790   contextMenu.exec(QCursor::pos());
1791 }
1792 //------------------------------------------------------------------------------
1793
1794 //------------------------------------------------------------------------------
1795 void vvMainWindow::CloseImage()
1796 {
1797   CloseImage(DataTree->selectedItems()[0],0);
1798 }
1799 //------------------------------------------------------------------------------
1800
1801 //------------------------------------------------------------------------------
1802 void vvMainWindow::ReloadImage()
1803 {
1804   ReloadImage(DataTree->selectedItems()[0],0);
1805 }
1806 //------------------------------------------------------------------------------
1807
1808 //------------------------------------------------------------------------------
1809 void vvMainWindow::SelectOverlayImage()
1810 {
1811   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1812
1813   //check if one overlay image is added
1814   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1815     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1816       QString error = "Cannot add more than one compared image\n";
1817       error += "Please remove first ";
1818       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1819       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1820       return;
1821     }
1822
1823   QString Extensions = EXTENSIONS;
1824   Extensions += ";;All Files (*)";
1825   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1826   if (!file.isEmpty())
1827     AddOverlayImage(index,file);
1828 }
1829 //------------------------------------------------------------------------------
1830
1831 //------------------------------------------------------------------------------
1832 void vvMainWindow::AddOverlayImage(int index, QString file)
1833 {
1834
1835   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1836   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1837                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1838   reader->SetFileName(file.toStdString().c_str());
1839   reader->ReadImageInformation();
1840   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1841   int dimension = reader->GetNumberOfDimensions();
1842   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1843   vvProgressDialog progress("Opening " + file.toStdString());
1844   qApp->processEvents();
1845
1846   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1847   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1848     //create an item in the tree with good settings
1849     QTreeWidgetItem *item = new QTreeWidgetItem();
1850     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1851     item->setData(1,Qt::UserRole,tr("overlay"));
1852     QFileInfo fileinfo(file); //Do not show the path
1853     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1854     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1855     qApp->processEvents();
1856
1857     for (int j = 1; j <= 4; j++) {
1858       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1859       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1860           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1861     }
1862
1863     //Create the buttons for reload and close
1864     qApp->processEvents();
1865     QTreePushButton* cButton = new QTreePushButton;
1866     cButton->setItem(item);
1867     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1868     cButton->setToolTip(tr("close image"));
1869     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1870     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1871             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1872
1873     QTreePushButton* rButton = new QTreePushButton;
1874     rButton->setItem(item);
1875     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1876     rButton->setToolTip(tr("reload image"));
1877     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1878     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1879             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1880
1881     DataTree->topLevelItem(index)->setExpanded(1);
1882     DataTree->topLevelItem(index)->addChild(item);
1883     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1884     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1885
1886     //set the id of the image
1887     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1888     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1889     UpdateTree();
1890     qApp->processEvents();
1891     ImageInfoChanged();
1892     QApplication::restoreOverrideCursor();
1893   } else {
1894     QApplication::restoreOverrideCursor();
1895     QString error = "Cannot import the new image.\n";
1896     error += mSlicerManagers[index]->GetLastError().c_str();
1897     QMessageBox::information(this,tr("Problem reading image !"),error);
1898   }
1899 }
1900 //------------------------------------------------------------------------------
1901
1902
1903 //------------------------------------------------------------------------------
1904 void vvMainWindow::AddROI(int index, QString file)
1905 {
1906   /*
1907   // Get slice manager
1908
1909   // Load image
1910
1911   vvImageReader * mReader = new vvImageReader;
1912   mReader->SetInputFilename(filename.toStdString());
1913   mReader->Update(IMAGE);
1914   if (mReader->GetLastError().size() != 0) {
1915     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1916     QString error = "Cannot open file \n";
1917     error += mReader->GetLastError().c_str();
1918     QMessageBox::information(this,tr("Reading problem"),error);
1919     delete mReader;
1920     return;
1921   }
1922   vvImage::Pointer roi = mReader->GetOutput();
1923
1924   // Create roi in new tool
1925   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1926   */
1927 }
1928 //------------------------------------------------------------------------------
1929
1930 //------------------------------------------------------------------------------
1931 void vvMainWindow::SelectFusionImage()
1932 {
1933   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1934
1935   //check if one fusion image is added
1936   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1937     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1938       QString error = "Cannot add more than one fusion image\n";
1939       error += "Please remove first ";
1940       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1941       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1942       return;
1943     }
1944
1945   QString Extensions = EXTENSIONS;
1946   Extensions += ";;All Files (*)";
1947   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1948   if (!file.isEmpty())
1949     AddFusionImage(index,file);
1950 }
1951 //------------------------------------------------------------------------------
1952
1953 //------------------------------------------------------------------------------
1954 void vvMainWindow::AddFusionImage(int index, QString file)
1955 {
1956   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1957   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1958                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1959   reader->SetFileName(file.toStdString().c_str());
1960   reader->ReadImageInformation();
1961   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1962   if (reader) {
1963     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1964     vvProgressDialog progress("Opening fusion");
1965     qApp->processEvents();
1966
1967     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1968     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1969                                           reader->GetNumberOfDimensions(), component)) {
1970       //create an item in the tree with good settings
1971       QTreeWidgetItem *item = new QTreeWidgetItem();
1972       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1973       item->setData(1,Qt::UserRole,tr("fusion"));
1974       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1975       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1976       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1977       qApp->processEvents();
1978
1979       for (int j = 1; j <= 4; j++) {
1980         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1981         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1982             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1983       }
1984
1985       //Create the buttons for reload and close
1986       qApp->processEvents();
1987       QTreePushButton* cButton = new QTreePushButton;
1988       cButton->setItem(item);
1989       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1990       cButton->setToolTip(tr("close image"));
1991       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1992       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1993               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1994
1995       QTreePushButton* rButton = new QTreePushButton;
1996       rButton->setItem(item);
1997       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1998       rButton->setToolTip(tr("reload image"));
1999       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2000       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2001               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2002
2003       DataTree->topLevelItem(index)->setExpanded(1);
2004       DataTree->topLevelItem(index)->addChild(item);
2005       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2006       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2007
2008       //set the id of the image
2009       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2010       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2011       UpdateTree();
2012       qApp->processEvents();
2013       ImageInfoChanged();
2014       QApplication::restoreOverrideCursor();
2015     } else {
2016       QApplication::restoreOverrideCursor();
2017       QString error = "Cannot import the new image.\n";
2018       error += mSlicerManagers[index]->GetLastError().c_str();
2019       QMessageBox::information(this,tr("Problem reading image !"),error);
2020     }
2021   } else {
2022     QString error = "Cannot import the new image.\n";
2023     QMessageBox::information(this,tr("Problem reading image !"),error);
2024   }
2025 }
2026 //------------------------------------------------------------------------------
2027
2028
2029 //------------------------------------------------------------------------------
2030 void vvMainWindow::OpenField()
2031 {
2032   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2033   //check if a vector field has already been added
2034   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2035     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2036       QString error = "Cannot add more than one vector field\n";
2037       error += "Please remove first ";
2038       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2039       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2040       return;
2041     }
2042
2043   QString Extensions = "Images ( *.mhd)";
2044   Extensions += ";;Images ( *.vf)";
2045   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2046   if (!file.isEmpty())
2047     AddField(file,index);
2048 }
2049 //------------------------------------------------------------------------------
2050
2051
2052 //------------------------------------------------------------------------------
2053 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2054 {
2055   //create an item in the tree with good settings
2056   QTreeWidgetItem *item = new QTreeWidgetItem();
2057   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2058   item->setData(1,Qt::UserRole,tr("vector"));
2059   QFileInfo fileinfo(filename); //Do not show the path
2060   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2061   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2062   qApp->processEvents();
2063
2064   for (int j = 1; j <= 4; j++) {
2065     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2066     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2067         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2068   }
2069
2070   //Create the buttons for reload and close
2071   qApp->processEvents();
2072   QTreePushButton* cButton = new QTreePushButton;
2073   cButton->setItem(item);
2074   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2075   cButton->setToolTip(tr("close vector field"));
2076   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2077   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2078           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2079
2080   QTreePushButton* rButton = new QTreePushButton;
2081   rButton->setItem(item);
2082   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2083   rButton->setToolTip(tr("reload vector field"));
2084   rButton->setEnabled(from_disk);
2085   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2086   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2087           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2088
2089   DataTree->topLevelItem(index)->setExpanded(1);
2090   DataTree->topLevelItem(index)->addChild(item);
2091   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2092   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2093
2094   //set the id of the image
2095   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2096   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2097   UpdateTree();
2098   qApp->processEvents();
2099   ImageInfoChanged();
2100   QApplication::restoreOverrideCursor();
2101 }
2102 //------------------------------------------------------------------------------
2103
2104
2105 //------------------------------------------------------------------------------
2106 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2107 {
2108   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2109   vvSlicerManager* imageManager = mSlicerManagers[index];
2110   if (imageManager->SetVF(vf,file.toStdString())) {
2111     AddFieldEntry(file,index,false);
2112   } else {
2113     QString error = "Cannot import the vector field for this image.\n";
2114     error += imageManager->GetLastError().c_str();
2115     QMessageBox::information(this,tr("Problem reading VF !"),error);
2116   }
2117   QApplication::restoreOverrideCursor();
2118 }
2119 //------------------------------------------------------------------------------
2120
2121
2122 //------------------------------------------------------------------------------
2123 void vvMainWindow::AddField(QString file,int index)
2124 {
2125   if (QFile::exists(file)) {
2126     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2127
2128     //init the progress events
2129     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2130     vvProgressDialog progress("Opening " + file.toStdString());
2131     qApp->processEvents();
2132
2133     //read the vector and put it in the current mSlicerManager
2134     vvSlicerManager* imageManager = mSlicerManagers[index];
2135     qApp->processEvents();
2136
2137     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2138     if (imageManager->SetVF(file.toStdString())) {
2139       imageManager->Render();
2140       AddFieldEntry(file,index,true);
2141     } else {
2142       QApplication::restoreOverrideCursor();
2143       QString error = "Cannot import the vector field for this image.\n";
2144       error += imageManager->GetLastError().c_str();
2145       QMessageBox::information(this,tr("Problem reading VF !"),error);
2146     }
2147   } else
2148     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2149
2150 }
2151 //------------------------------------------------------------------------------
2152
2153
2154 //------------------------------------------------------------------------------
2155 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2156 {
2157   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2158   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2159     for (int i = 0; i < 4; i++) {
2160       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2161       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2162       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2163       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2164       if (log > 0)
2165         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2166       else
2167         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2168     }
2169   }
2170 }
2171 //------------------------------------------------------------------------------
2172
2173
2174 //------------------------------------------------------------------------------
2175 void vvMainWindow::SetOverlayProperty(int color)
2176 {
2177   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2178   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2179     mSlicerManagers[index]->SetOverlayColor(color);
2180     mSlicerManagers[index]->SetColorMap(0);
2181     mSlicerManagers[index]->Render();
2182   }
2183 }
2184 //------------------------------------------------------------------------------
2185
2186 //------------------------------------------------------------------------------
2187 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2188 {
2189   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2190   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2191     mSlicerManagers[index]->SetFusionOpacity(opacity);
2192     mSlicerManagers[index]->SetFusionColorMap(colormap);
2193     mSlicerManagers[index]->SetFusionWindow(window);
2194     mSlicerManagers[index]->SetFusionLevel(level);
2195     mSlicerManagers[index]->SetColorMap(0);
2196     mSlicerManagers[index]->Render();
2197   }
2198 }
2199 //------------------------------------------------------------------------------
2200
2201 //------------------------------------------------------------------------------
2202 void vvMainWindow::SaveAs()
2203 {
2204   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2205     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2206     return;
2207   }
2208
2209   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2210   int dimension = mSlicerManagers[index]->GetDimension();
2211   QStringList OutputListeFormat;
2212   OutputListeFormat.clear();
2213   if (dimension == 1) {
2214     OutputListeFormat.push_back(".mhd");
2215   }
2216   if (dimension == 2) {
2217     OutputListeFormat.push_back(".bmp");
2218     OutputListeFormat.push_back(".png");
2219     OutputListeFormat.push_back(".jpeg");
2220     OutputListeFormat.push_back(".tif");
2221     OutputListeFormat.push_back(".mhd");
2222     OutputListeFormat.push_back(".hdr");
2223     OutputListeFormat.push_back(".vox");
2224   } else if (dimension == 3) {
2225     OutputListeFormat.push_back(".mhd");
2226     OutputListeFormat.push_back(".hdr");
2227     OutputListeFormat.push_back(".vox");
2228   } else if (dimension == 4) {
2229     OutputListeFormat.push_back(".mhd");
2230   }
2231   QString Extensions = "AllFiles(*.*)";
2232   for (int i = 0; i < OutputListeFormat.count(); i++) {
2233     Extensions += ";;Images ( *";
2234     Extensions += OutputListeFormat[i];
2235     Extensions += ")";
2236   }
2237   QString fileName = QFileDialog::getSaveFileName(this,
2238                      tr("Save As"),
2239                      mSlicerManagers[index]->GetFileName().c_str(),
2240                      Extensions);
2241   if (!fileName.isEmpty()) {
2242     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2243     if (OutputListeFormat.contains(
2244           fileformat.c_str())) {
2245       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2246       std::string action = "Saving";
2247       vvProgressDialog progress("Saving "+fileName.toStdString());
2248       qApp->processEvents();
2249       vvImageWriter::Pointer writer = vvImageWriter::New();
2250       writer->SetOutputFileName(fileName.toStdString());
2251       writer->SetInput(mSlicerManagers[index]->GetImage());
2252       writer->Update();
2253       QApplication::restoreOverrideCursor();
2254       if (writer->GetLastError().size()) {
2255         QString error = "Saving did not succeed\n";
2256         error += writer->GetLastError().c_str();
2257         QMessageBox::information(this,tr("Saving Problem"),error);
2258         SaveAs();
2259       }
2260     } else {
2261       QString error = fileformat.c_str();
2262       if (error.isEmpty())
2263         error += "no file format specified !";
2264       else
2265         error += " format unknown !!!\n";
2266       QMessageBox::information(this,tr("Saving Problem"),error);
2267       SaveAs();
2268     }
2269   }
2270 }
2271 //------------------------------------------------------------------------------
2272
2273
2274 //------------------------------------------------------------------------------
2275 void vvMainWindow::AddLink(QString image1,QString image2)
2276 {
2277   unsigned int sm1 = 0;
2278   unsigned int sm2 = 0;
2279
2280   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2281     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2282       mSlicerManagers[i]->AddLink(image2.toStdString());
2283       sm1 = i;
2284     }
2285     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2286       mSlicerManagers[i]->AddLink(image1.toStdString());
2287       sm2 = i;
2288     }
2289   }
2290
2291   if (linkPanel->isLinkAll())   {
2292     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2293     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2294   } else {
2295     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2296   }
2297 }
2298
2299 //------------------------------------------------------------------------------
2300
2301
2302 //------------------------------------------------------------------------------
2303 void vvMainWindow::RemoveLink(QString image1,QString image2)
2304 {
2305   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2306     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2307       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2308     }
2309     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2310       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2311     }
2312   }
2313 }
2314 //------------------------------------------------------------------------------
2315
2316 //------------------------------------------------------------------------------
2317 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2318 {
2319   int index = 0;
2320   while(sm != mSlicerManagers[index])
2321     index++;
2322   index = (index+offset) % mSlicerManagers.size();
2323
2324   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2325   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2326   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2327   DisplayChanged(item,slicer+1);
2328 }
2329 //------------------------------------------------------------------------------
2330
2331 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2332 {
2333   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2334     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2335       for (int j = 0; j < 4; j++) {
2336         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2337         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2338         //UpdateTSlice(j,value);
2339       }
2340       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2341       break;
2342     }
2343   }
2344 }
2345 //------------------------------------------------------------------------------
2346
2347
2348 //------------------------------------------------------------------------------
2349 void vvMainWindow::NOHorizontalSliderMoved()
2350 {
2351   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2352   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2353 //  mCurrentTime = NOHorizontalSlider->value();
2354 }
2355 //------------------------------------------------------------------------------
2356
2357
2358 //------------------------------------------------------------------------------
2359 void vvMainWindow::NEHorizontalSliderMoved()
2360 {
2361   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2362   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2363 //  mCurrentTime = NEHorizontalSlider->value();
2364 }
2365 //------------------------------------------------------------------------------
2366
2367
2368 //------------------------------------------------------------------------------
2369 void vvMainWindow::SOHorizontalSliderMoved()
2370 {
2371   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2372   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2373   // mCurrentTime = SOHorizontalSlider->value();
2374 }
2375 //------------------------------------------------------------------------------
2376
2377
2378 //------------------------------------------------------------------------------
2379 void vvMainWindow::SEHorizontalSliderMoved()
2380 {
2381   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2382   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2383   // mCurrentTime = SEHorizontalSlider->value();
2384 }
2385 //------------------------------------------------------------------------------
2386
2387 //------------------------------------------------------------------------------
2388 void vvMainWindow::NOVerticalSliderChanged()
2389 {
2390   static int value=-1;
2391   if (value == NOVerticalSlider->value()) return;
2392   else value = NOVerticalSlider->value();
2393   //  int value = NOVerticalSlider->value();
2394   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2395     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2396       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2397         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2398         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2399
2400         // If nor Update/Render -> slider not work
2401         // only render = ok navigation, but for contour Update needed but slower ?
2402
2403         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2404         //mSlicerManagers[i]->GetSlicer(0)->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::NEVerticalSliderChanged()
2415 {
2416   static int value=-1;
2417   if (value == NEVerticalSlider->value()) return;
2418   else value = NEVerticalSlider->value();
2419   //  int value = NEVerticalSlider->value();
2420   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2421     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2422       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2423         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2424         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2425         mSlicerManagers[i]->UpdateSlice(1);
2426         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2427       }
2428       break;
2429     }
2430   }
2431 }
2432 //------------------------------------------------------------------------------
2433
2434
2435 //------------------------------------------------------------------------------
2436 void vvMainWindow::SOVerticalSliderChanged()
2437 {
2438   static int value=-1;
2439   if (value == SOVerticalSlider->value()) return;
2440   else value = SOVerticalSlider->value();
2441   //int value = SOVerticalSlider->value();
2442   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2443     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2444       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2445         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2446         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2447         mSlicerManagers[i]->UpdateSlice(2);
2448         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2449       }
2450       // else { DD("avoid SOVerticalSlider slicer update"); }
2451       break;
2452     }
2453   }
2454 }
2455 //------------------------------------------------------------------------------
2456
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::SEVerticalSliderChanged()
2460 {
2461   static int value=-1;
2462   if (value == SEVerticalSlider->value()) return;
2463   else value = SEVerticalSlider->value();
2464   // int value = SEVerticalSlider->value();
2465   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2466     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2467       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2468         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2469         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2470         mSlicerManagers[i]->UpdateSlice(3);
2471         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2472       }
2473       break;
2474     }
2475   }
2476 }
2477 //------------------------------------------------------------------------------
2478
2479
2480 //------------------------------------------------------------------------------
2481 void vvMainWindow::UpdateSlice(int slicer, int slice)
2482 {
2483   // DD("vvMainWindow::UpdateSlice");
2484 //   DD(slicer);
2485 //   DD(slice);
2486   if (slicer == 0) {
2487     //    if (slice != NOVerticalSlider->value())
2488     NOVerticalSlider->setValue(slice);
2489   } else {
2490     if (slicer == 1)
2491       NEVerticalSlider->setValue(slice);
2492     else {
2493       if (slicer == 2)
2494         SOVerticalSlider->setValue(slice);
2495       else {
2496         if (slicer == 3)
2497           SEVerticalSlider->setValue(slice);
2498       }
2499     }
2500   }
2501   // DD("vvMainWindow:UpdateSlice END");
2502 }
2503 //------------------------------------------------------------------------------
2504
2505
2506 //------------------------------------------------------------------------------
2507 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2508 {
2509   switch (slicer) {
2510   case 0:
2511     NOHorizontalSlider->setValue(slice);
2512     break;
2513   case 1:
2514     NEHorizontalSlider->setValue(slice);
2515     break;
2516   case 2:
2517     SOHorizontalSlider->setValue(slice);
2518     break;
2519   case 3:
2520     SEHorizontalSlider->setValue(slice);
2521     break;
2522   }
2523 }
2524 //------------------------------------------------------------------------------
2525
2526
2527 //------------------------------------------------------------------------------
2528 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2529 {
2530   int position = int((min+max)/2);
2531   int tPosition = int((tmin+tmax)/2);
2532   if (slicer == 0) {
2533     NOVerticalSlider->setValue(position);
2534     NOVerticalSlider->setRange(min,max);
2535     NOHorizontalSlider->setRange(tmin,tmax);
2536     NOHorizontalSlider->setValue(tPosition);
2537   } else if (slicer == 1) {
2538     NEVerticalSlider->setValue(position);
2539     NEVerticalSlider->setRange(min,max);
2540     NEHorizontalSlider->setRange(tmin,tmax);
2541     NEHorizontalSlider->setValue(tPosition);
2542   } else if (slicer == 2) {
2543     SOVerticalSlider->setValue(position);
2544     SOVerticalSlider->setRange(min,max);
2545     SOHorizontalSlider->setRange(tmin,tmax);
2546     SOHorizontalSlider->setValue(tPosition);
2547   } else if (slicer == 3) {
2548     SEVerticalSlider->setValue(position);
2549     SEVerticalSlider->setRange(min,max);
2550     SEHorizontalSlider->setRange(tmin,tmax);
2551     SEHorizontalSlider->setValue(tPosition);
2552   }
2553 }
2554 //------------------------------------------------------------------------------
2555
2556
2557 //------------------------------------------------------------------------------
2558 void vvMainWindow::SaveNOScreenshot()
2559 {
2560   SaveScreenshot(NOViewWidget);
2561 }
2562 //------------------------------------------------------------------------------
2563
2564
2565 //------------------------------------------------------------------------------
2566 void vvMainWindow::SaveNEScreenshot()
2567 {
2568   SaveScreenshot(NEViewWidget);
2569 }
2570 //------------------------------------------------------------------------------
2571
2572
2573 //------------------------------------------------------------------------------
2574 void vvMainWindow::SaveSOScreenshot()
2575 {
2576   SaveScreenshot(SOViewWidget);
2577 }
2578 //------------------------------------------------------------------------------
2579
2580
2581 //------------------------------------------------------------------------------
2582 void vvMainWindow::SaveSEScreenshot()
2583 {
2584   SaveScreenshot(SEViewWidget);
2585 }
2586 //------------------------------------------------------------------------------
2587
2588
2589 //------------------------------------------------------------------------------
2590 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2591 {
2592   QString Extensions = "Images( *.png);;";
2593   Extensions += "Images( *.jpg);;";
2594   Extensions += "Images( *.bmp);;";
2595   Extensions += "Images( *.tif);;";
2596   Extensions += "Images( *.ppm)";
2597 #ifdef VTK_USE_FFMPEG_ENCODER
2598   Extensions += "Images( *.avi)";
2599 #endif
2600 #ifdef VTK_USE_MPEG2_ENCODER
2601   Extensions += "Images( *.mpg)";
2602 #endif
2603
2604   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2605   QString fileName = QFileDialog::getSaveFileName(this,
2606                      tr("Save As"),
2607                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2608                      Extensions);
2609
2610   if (!fileName.isEmpty()) {
2611     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2612     w2i->SetInput(widget->GetRenderWindow());
2613     w2i->Update();
2614     vtkImageData *image = w2i->GetOutput();
2615
2616     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2617     if (!strcmp(ext, ".bmp")) {
2618       vtkBMPWriter *bmp = vtkBMPWriter::New();
2619       bmp->SetInput(image);
2620       bmp->SetFileName(fileName.toStdString().c_str());
2621       bmp->Write();
2622       bmp->Delete();
2623     } else if (!strcmp(ext, ".tif")) {
2624       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2625       tif->SetInput(image);
2626       tif->SetFileName(fileName.toStdString().c_str());
2627       tif->Write();
2628       tif->Delete();
2629     } else if (!strcmp(ext, ".ppm")) {
2630       vtkPNMWriter *pnm = vtkPNMWriter::New();
2631       pnm->SetInput(image);
2632       pnm->SetFileName(fileName.toStdString().c_str());
2633       pnm->Write();
2634       pnm->Delete();
2635     } else if (!strcmp(ext, ".png")) {
2636       vtkPNGWriter *png = vtkPNGWriter::New();
2637       png->SetInput(image);
2638       png->SetFileName(fileName.toStdString().c_str());
2639       png->Write();
2640       png->Delete();
2641     } else if (!strcmp(ext, ".jpg")) {
2642       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2643       jpg->SetInput(image);
2644       jpg->SetFileName(fileName.toStdString().c_str());
2645       jpg->Write();
2646       jpg->Delete();
2647 #ifdef VTK_USE_FFMPEG_ENCODER
2648     } else if (!strcmp(ext, ".avi")) {
2649       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2650       mpg->SetInput(image);
2651       mpg->SetFileName(fileName.toStdString().c_str());
2652       mpg->SetQuality(2);
2653       mpg->SetRate(5);
2654       mpg->Start();
2655
2656       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2657       int nSlice = vvImg->GetVTKImages().size();
2658       for(int i=0; i<nSlice; i++) {
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 #ifdef VTK_USE_MPEG2_ENCODER
2670     } else if (!strcmp(ext, ".mpg")) {
2671       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2672       mpg->SetInput(image);
2673       mpg->SetFileName(fileName.toStdString().c_str());
2674       mpg->Start();
2675
2676       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2677       int nSlice = vvImg->GetVTKImages().size();
2678       for(int i=0; i<nSlice; i++) {
2679         mSlicerManagers[smIndex]->SetNextTSlice(0);
2680         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2681         w2i->SetInput(widget->GetRenderWindow());
2682         w2i->Update();
2683         mpg->SetInput(w2i->GetOutput());
2684         mpg->Write();
2685       }
2686       mpg->End();
2687       mpg->Delete();
2688 #endif
2689     } else {
2690       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2691     }
2692   }
2693 }
2694 //------------------------------------------------------------------------------
2695
2696
2697 //------------------------------------------------------------------------------
2698 void vvMainWindow::GoToCursor()
2699 {
2700   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2701   for (int column = 1; column < 5; column++) {
2702     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2703       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2704       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2705         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2706       mSlicerManagers[index]->UpdateViews(1,column-1);
2707       mSlicerManagers[index]->UpdateLinked(column-1);
2708       break;
2709     }
2710   }
2711 }
2712 //------------------------------------------------------------------------------
2713
2714 //------------------------------------------------------------------------------
2715 void vvMainWindow::PlayPause()
2716 {
2717   if (playMode) {
2718     playMode = 0;
2719     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2720     ImageInfoChanged();
2721     return;
2722   } else {
2723     int image_number=DataTree->topLevelItemCount();
2724     bool has_temporal;
2725     for (int i=0; i<image_number; i++)
2726       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2727         has_temporal=true;
2728         break;
2729       }
2730     if (has_temporal) {
2731       playMode = 1;
2732       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2733       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2734     }
2735   }
2736 }
2737 //------------------------------------------------------------------------------
2738
2739 //------------------------------------------------------------------------------
2740 void vvMainWindow::PlayNext()
2741 {
2742   if (playMode && !this->isHidden()) {
2743     int image_number=DataTree->topLevelItemCount();
2744     ///Only play one slicer per SM, and only if the SM is being displayed
2745     for (int i=0; i<image_number; i++)
2746       for (int j=0; j<4; j++)
2747         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2748             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2749           mSlicerManagers[i]->SetNextTSlice(j);
2750           break;
2751         }
2752     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2753   }
2754 }
2755 //------------------------------------------------------------------------------
2756
2757 void vvMainWindow::ShowLastImage()
2758 {
2759   if (mSlicerManagers.size() > 1) {
2760     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2761     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2762     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2763     DisplayChanged(item,1);
2764   }
2765 }
2766
2767 //------------------------------------------------------------------------------
2768 void vvMainWindow::UpdateRenderWindows()
2769 {
2770   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2771   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2772   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2773   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2774 }
2775 //------------------------------------------------------------------------------
2776
2777 //------------------------------------------------------------------------------
2778 void vvMainWindow::SegmentationOnCurrentImage()
2779 {
2780   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2781
2782   vvSegmentationDialog segmentation;
2783   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2784   segmentation.exec();
2785 }
2786 //------------------------------------------------------------------------------
2787
2788 void vvMainWindow::SurfaceViewerLaunch()
2789 {
2790   vvSurfaceViewerDialog surfaceViewer;
2791   surfaceViewer.exec();
2792 }
2793 //------------------------------------------------------------------------------
2794
2795
2796 //------------------------------------------------------------------------------
2797 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2798 {
2799   int number=0;
2800   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2801     vvSlicerManager * v = mSlicerManagers[l];
2802     if (v->GetBaseFileName() ==
2803         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2804       number = std::max(number, v->GetBaseFileNameNumber()+1);
2805     }
2806   }
2807   return number;
2808 }
2809 //------------------------------------------------------------------------------
2810
2811
2812 //------------------------------------------------------------------------------
2813 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2814 {
2815   // Change filename if another image exist with the same name
2816   int number = GetImageDuplicateFilenameNumber(filename);
2817
2818   // Create new SliceManager
2819   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2820   slicer_manager->SetImage(image);//, IMAGE, number);
2821   //  filename = filename+"_"+clitk::toString(number);
2822   slicer_manager->SetFilename(filename, number);
2823   mSlicerManagers.push_back(slicer_manager);
2824
2825   //create an item in the tree with good settings
2826   QTreeWidgetItem *item = new QTreeWidgetItem();
2827   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2828   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2829   qApp->processEvents();
2830
2831   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2832
2833   //Create the buttons for reload and close
2834   qApp->processEvents();
2835   QTreePushButton* cButton = new QTreePushButton;
2836   cButton->setItem(item);
2837   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2838   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2839   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2840           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2841
2842   QTreePushButton* rButton = new QTreePushButton;
2843   rButton->setItem(item);
2844   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2845   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2846   rButton->setEnabled(0);
2847   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2848           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2849
2850   DataTree->addTopLevelItem(item);
2851   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2852   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2853
2854   //set the id of the image
2855   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2856   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2857   mSlicerManagers.back()->SetId(id.toStdString());
2858
2859   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2860                       , id.toStdString());
2861
2862   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2863           this, SLOT(CurrentImageChanged(std::string)));
2864   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2865           this, SLOT(CurrentPickedImageChanged(std::string)));
2866   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2867           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2868   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2869           this, SLOT(VectorChanged(int,double,double,double, double)));
2870   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2871           this, SLOT(OverlayChanged(int,double,double)));
2872   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2873           this, SLOT(FusionChanged(int,double)));
2874   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2875           this,SLOT(WindowsChanged(int, int, int)));
2876   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2877           this,SLOT(WindowLevelChanged(double, double, int, int)));
2878   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2879           this,SLOT(UpdateSlice(int,int)));
2880   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2881           this,SLOT(UpdateTSlice(int, int)));
2882   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2883           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2884   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2885           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2886   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2887           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2888   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2889           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2890   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2891   UpdateTree();
2892   qApp->processEvents();
2893   InitSlicers();
2894   ShowLastImage();
2895   InitDisplay();
2896   qApp->processEvents();
2897
2898   // End
2899   ImageInfoChanged();
2900   return slicer_manager;
2901 }
2902 //------------------------------------------------------------------------------
2903
2904
2905 //------------------------------------------------------------------------------
2906 void vvMainWindow::UpdateCurrentSlicer()
2907 {
2908   int index = -1;
2909   if (DataTree->selectedItems().size() > 0) {
2910     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2911   }
2912   mSlicerManagerCurrentIndex = index;
2913 }
2914 //------------------------------------------------------------------------------
2915