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