vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #ifdef VTK_USE_FFMPEG_ENCODER
  72 #  include <vtkFFMPEGWriter.h>
  73 #endif
  74 #ifdef VTK_USE_MPEG2_ENCODER
  75 #  include <vtkMPEG2Writer.h>
  76 #endif
  77 #include <vtkMatrix4x4.h>
  78 #include <vtkTransform.h>
  79
  80 // Standard includes
  81 #include <iostream>
  82 #include <sstream>
  83 #include <iomanip>
  84
  85 #define COLUMN_TREE 0
  86 #define COLUMN_UL_VIEW 1
  87 #define COLUMN_UR_VIEW 2
  88 #define COLUMN_DL_VIEW 3
  89 #define COLUMN_DR_VIEW 4
  90 #define COLUMN_CLOSE_IMAGE 5
  91 #define COLUMN_RELOAD_IMAGE 6
  92 #define COLUMN_IMAGE_NAME 7
  93
  94 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  95
  96 /*Data Tree values
  97   0,Qt::UserRole full filename
  98   1,Qt::CheckStateRole checkbutton UL View
  99   1,Qt::UserRole overlay, fusion or vector
 100   2,Qt::CheckStateRole checkbutton UR View
 101   3,Qt::CheckStateRole checkbutton DL View
 102   4,Qt::CheckStateRole checkbutton DR View
 103   5,0  short filename
 104   5,Qt::UserRole mSlicerManager id*/
 105
 106 //------------------------------------------------------------------------------
 107 vvMainWindow::vvMainWindow():vvMainWindowBase()
 108 {
 109   setupUi(this); // this sets up the GUI
 110
 111   mInputPathName = "";
 112   mMenuTools = menuTools;
 113   //  mMenuSegmentation = menuSegmentation;
 114   mContextMenu = &contextMenu;
 115   mMenuExperimentalTools = menuExperimental;
 116   mMainWidget = this;
 117   mCurrentTime = -1;
 118   mCurrentSelectedImageId = "";
 119   mCurrentPickedImageId = "";
 120   mCurrentPickedImageIndex = 0;
 121
 122   //Init the contextMenu
 123   this->setContextMenuPolicy(Qt::CustomContextMenu);
 124   contextActions.resize(0);
 125   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 126                                   tr("O&pen new Image"));
 127   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 128   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 129   contextActions.push_back(actionOpen_new_image);
 130   contextMenu.addSeparator();
 131
 132   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 133                                tr("Close Current Image"));
 134   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 135   contextActions.push_back(actionClose_Image);
 136
 137   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 138                                 tr("Reload Current Image"));
 139   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 140   contextActions.push_back(actionReload_image);
 141
 142   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 143                               tr("Save Current Image"));
 144   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 145   contextActions.push_back(actionSave_image);
 146
 147   contextMenu.addSeparator();
 148
 149   contextMenu.addAction(actionAdd_VF_to_current_Image);
 150   contextActions.push_back(actionAdd_VF_to_current_Image);
 151
 152   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 153       tr("Add overlay image to current image"));
 154   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 155   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 156
 157   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 158
 159   contextMenu.addAction(actionAdd_fusion_image);
 160   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 161   contextActions.push_back(actionAdd_fusion_image);
 162
 163   // TRIAL DS
 164   /*
 165   QMenu * m = new QMenu(menubar);
 166   m->setTitle("TOTO");
 167   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 168   contextMenu.addMenu(m);
 169   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON"));
 171   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 172                      tr("BIDON2"));
 173   m->addAction(a);
 174   m->addAction(b);
 175   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 176   */
 177
 178   //init the DataTree
 179   mSlicerManagers.resize(0);
 180
 181   QStringList header;
 182   header.append("");
 183   header.append("TL");
 184   header.append("TR");
 185   header.append("BL");
 186   header.append("BR");
 187   header.append("");
 188   header.append("");
 189   header.append("Name");
 190
 191   DataTree->setHeaderLabels(header);
 192   DataTree->resizeColumnToContents(COLUMN_TREE);
 193   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 197   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 199   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 200
 201   viewMode = 1;
 202   documentation = new vvDocumentation();
 203   help_dialog = new vvHelpDialog();
 204   dicomSeriesSelector = new vvDicomSeriesSelector();
 205
 206   inverseButton->setEnabled(0);
 207   actionAdd_Overlay_to_current_Image->setEnabled(0);
 208   actionSave_As->setEnabled(0);
 209   actionAdd_VF_to_current_Image->setEnabled(0);
 210   actionAdd_fusion_image->setEnabled(0);
 211
 212   //init the sliders
 213   verticalSliders.push_back(NOVerticalSlider);
 214   verticalSliders.push_back(NEVerticalSlider);
 215   verticalSliders.push_back(SOVerticalSlider);
 216   verticalSliders.push_back(SEVerticalSlider);
 217
 218   for (int i =0; i < 4; i++)
 219     verticalSliders[i]->hide();
 220
 221   horizontalSliders.push_back(NOHorizontalSlider);
 222   horizontalSliders.push_back(NEHorizontalSlider);
 223   horizontalSliders.push_back(SOHorizontalSlider);
 224   horizontalSliders.push_back(SEHorizontalSlider);
 225
 226   for (int i =0; i < 4; i++)
 227     horizontalSliders[i]->hide();
 228
 229
 230   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 231   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 232   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 233   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 234
 235   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 236   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 237   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 238   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 239
 240   //connect everything
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 250   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 251   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 252   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 253   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 254   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 255   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 256   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 257   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 258
 259   ///////////////////////////////////////////////
 260   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 261   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 262   ///////////////////////////////////////////////
 263
 264   actionNorth_East_Window->setEnabled(0);
 265   actionNorth_West_Window->setEnabled(0);
 266   actionSouth_East_Window->setEnabled(0);
 267   actionSouth_West_Window->setEnabled(0);
 268
 269   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 270   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 271   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 272   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 273
 274   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 275   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 276           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 277
 278   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 279   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 281   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 282   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 283   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 284   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 285
 286
 287   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 288
 289   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 290   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 291   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 292   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 293   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 294           this,SLOT(SetFusionProperty(int,int,double,double)));
 295   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 296
 297   playMode = 0;//pause
 298   mFrameRate = 10;
 299   playButton->setEnabled(0);
 300   frameRateLabel->setEnabled(0);
 301   frameRateSpinBox->setEnabled(0);
 302   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 303   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 304
 305   goToCursorPushButton->setEnabled(0);
 306   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 307
 308   NOViewWidget->hide();
 309   NEViewWidget->hide();
 310   SOViewWidget->hide();
 311   SEViewWidget->hide();
 312
 313   //Recently opened files
 314   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 315   recentlyOpenedFilesMenu=NULL;
 316   if ( !recent_files.empty() ) {
 317     createRecentlyOpenedFilesMenu();
 318     updateRecentlyOpenedFilesMenu(recent_files);
 319   }
 320
 321   // Adding all new tools (insertion in the menu)
 322   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 323   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 324
 325   if (!CLITK_EXPERIMENTAL)
 326     menuExperimental->menuAction()->setVisible(false);
 327
 328
 329   QTimer * timerMemory = new QTimer(this);
 330   //timerMemory->setInterval(5);
 331   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 332   timerMemory->start(2000);
 333 }
 334 //------------------------------------------------------------------------------
 335 void vvMainWindow::show()
 336 {
 337   vvMainWindowBase::show();
 338   PopupRegisterForm(true);
 339 }
 340 //------------------------------------------------------------------------------
 341 void vvMainWindow::UpdateMemoryUsage()
 342 {
 343   //  clitk::PrintMemory(true);
 344   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 345   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 346 }
 347 //------------------------------------------------------------------------------
 348
 349
 350 //------------------------------------------------------------------------------
 351 void vvMainWindow::createRecentlyOpenedFilesMenu()
 352 {
 353   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 354   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 355   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 356   menuFile->insertSeparator(actionOpen_Image_With_Time);
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362
 363 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 364 {
 365   if(recentlyOpenedFilesMenu==NULL) {
 366     createRecentlyOpenedFilesMenu();
 367   } else {
 368     recentlyOpenedFilesMenu->clear();
 369   }
 370   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 371     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 372     recentlyOpenedFilesMenu->addAction(current);
 373     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 374   }
 375 }
 376 //------------------------------------------------------------------------------
 377
 378
 379 //------------------------------------------------------------------------------
 380 void vvMainWindow::ComputeMidPosition()
 381 {
 382   bool ok;
 383   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 384   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 385                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 386   if (ok) {
 387     vvMidPosition midp;
 388     midp.slicer_manager = mSlicerManagers[index];
 389     midp.reference_image_index = ref;
 390     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 391     midp.Update();
 392     if (midp.error)
 393       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 394     else {
 395       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 396       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 397     }
 398     QApplication::restoreOverrideCursor();
 399   }
 400 }
 401 //------------------------------------------------------------------------------
 402
 403
 404 //------------------------------------------------------------------------------
 405 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 406 {
 407   QTreeWidgetItem *item = new QTreeWidgetItem();
 408   item->setData(0,Qt::UserRole,"filename.vtk");
 409   item->setData(1,Qt::UserRole,tr("contour"));
 410   QBrush brush;
 411   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 412   brush.setStyle(Qt::SolidPattern);
 413   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 414   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 415
 416   for (int j = 1; j <= 4; j++)
 417     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 418
 419   QTreePushButton* cButton = new QTreePushButton;
 420   cButton->setItem(item);
 421   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 422   cButton->setToolTip(tr("close image"));
 423   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 424   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 425           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 426
 427   QTreePushButton* rButton = new QTreePushButton;
 428   rButton->setItem(item);
 429   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 430   rButton->setToolTip(tr("reload image"));
 431   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 432   rButton->setEnabled(false);
 433   //Not implemented
 434   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 435   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 436
 437   DataTree->topLevelItem(image_index)->setExpanded(1);
 438   DataTree->topLevelItem(image_index)->addChild(item);
 439   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 440   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 441   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 442   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 443
 444   UpdateTree();
 445   mSlicerManagers[image_index]->AddContour(contour,propagation);
 446   mSlicerManagers[image_index]->Render();
 447 }
 448 //------------------------------------------------------------------------------
 449
 450
 451 //------------------------------------------------------------------------------
 452 void vvMainWindow::OpenVTKContour()
 453 {
 454   if (mSlicerManagers.size() > 0) {
 455     QString Extensions = "Images ( *.vtk *.obj)";
 456     Extensions += ";;All Files (*)";
 457     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 458     if (file.isNull())
 459       return;
 460     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 461     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 462     vvMeshReader reader;
 463     reader.SetImage(mSlicerManagers[index]->GetImage());
 464     reader.SetModeToVTK();
 465     reader.SetFilename(file.toStdString());
 466     reader.Update();
 467     AddContour(index,reader.GetOutput()[0],false);
 468     QApplication::restoreOverrideCursor();
 469   }
 470 }
 471 //------------------------------------------------------------------------------
 472
 473
 474 //------------------------------------------------------------------------------
 475 void vvMainWindow::OpenDCStructContour()
 476 {
 477   if (mSlicerManagers.size() > 0) {
 478     QString Extensions = "Dicom Files ( *.dcm RS*)";
 479     Extensions += ";;All Files (*)";
 480     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 481     if (file.isNull())
 482       return;
 483     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 484     vvMeshReader reader;
 485     reader.SetFilename(file.toStdString());
 486     vvStructSelector selector;
 487     selector.SetStructures(reader.GetROINames());
 488     if (!mSlicerManagers[index]->GetVF().IsNull())
 489       selector.EnablePropagationCheckBox();
 490     if (selector.exec()) {
 491       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 492       reader.SetSelectedItems(selector.getSelectedItems());
 493       reader.SetImage(mSlicerManagers[index]->GetImage());
 494       if (selector.PropagationEnabled())
 495         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 496       reader.Update();
 497       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 498       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 499            i!=contours.end(); i++)
 500         AddContour(index,*i,selector.PropagationEnabled());
 501       QApplication::restoreOverrideCursor();
 502     }
 503   }
 504 }
 505 //------------------------------------------------------------------------------
 506
 507
 508 //------------------------------------------------------------------------------
 509 void vvMainWindow::ComputeDeformableRegistration()
 510 {
 511   if (mSlicerManagers.size() > 0) {
 512     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 513     vvDeformationDialog dialog(index,mSlicerManagers);
 514     if (dialog.exec()) {
 515       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 516       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 517       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 518     } else
 519       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 520   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::WarpImage()
 527 {
 528   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 529   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 530     bool ok;
 531     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 532                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 533     if (ok) {
 534       WarpImage(mSlicerManagers[index],ref);
 535     }
 536   } else
 537     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 538 }
 539 //------------------------------------------------------------------------------
 540
 541
 542 //------------------------------------------------------------------------------
 543 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 544 {
 545   if (!selected_slicer->GetVF().IsNull()) {
 546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 547     QFileInfo info(selected_slicer->GetFileName().c_str());
 548     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 549                      reference_phase,this);
 550     if (warp.ComputeWarpedImage()) {
 551       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 552       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 553       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 554       QApplication::restoreOverrideCursor();
 555     } else {
 556       QApplication::restoreOverrideCursor();
 557       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 558     }
 559   } else
 560     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 561 }
 562 //------------------------------------------------------------------------------
 563
 564
 565 //------------------------------------------------------------------------------
 566 vvMainWindow::~vvMainWindow()
 567 {
 568   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 569     if (mSlicerManagers[i] != NULL)
 570       delete mSlicerManagers[i];
 571   }
 572 }
 573 //------------------------------------------------------------------------------
 574
 575 //------------------------------------------------------------------------------
 576 QTabWidget * vvMainWindow::GetTab()
 577 {
 578   return tabWidget;
 579 }
 580 //------------------------------------------------------------------------------
 581
 582
 583 //------------------------------------------------------------------------------
 584 void vvMainWindow::MergeImages()
 585 {
 586   QString Extensions = EXTENSIONS;
 587   Extensions += ";;All Files (*)";
 588   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 589   if (files.isEmpty())
 590     return;
 591   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 592   std::vector<std::string> vector;
 593
 594   unsigned int currentDim = 0;
 595   std::vector<double> currentSpacing;
 596   std::vector<int> currentSize;
 597   std::vector<double> currentOrigin;
 598
 599   for (int i = 0; i < files.size(); i++) {
 600     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 601                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 602     reader->SetFileName(files[i].toStdString().c_str());
 603     reader->ReadImageInformation();
 604     if (reader)        {
 605       //NOViewWidget->hide();
 606       //NEViewWidget->hide();
 607       //SOViewWidget->hide();
 608       //SEViewWidget->hide();
 609       if (i == 0)
 610         currentDim = reader->GetNumberOfDimensions();
 611       bool IsOk = true;
 612       for (unsigned int j = 0; j < currentDim; j++) {
 613         if (i == 0) {
 614           if (j == 0) {
 615             currentSpacing.resize(currentDim);
 616             currentSize.resize(currentDim);
 617             currentOrigin.resize(currentDim);
 618           }
 619           currentOrigin[j] = reader->GetOrigin(j);
 620           currentSpacing[j] = reader->GetSpacing(j);
 621           currentSize[j] = reader->GetDimensions(j);
 622         } else if (currentDim != reader->GetNumberOfDimensions()
 623                    || currentSpacing[j] != reader->GetSpacing(j)
 624                    || currentSize[j] != (int)reader->GetDimensions(j)
 625                    || currentOrigin[j] != reader->GetOrigin(j)) {
 626           QString error = "Cannot read file (too different from others ";
 627           error += files[i].toStdString().c_str();
 628           QMessageBox::information(this,tr("Reading problem"),error);
 629           IsOk = false;
 630           break;
 631         }
 632       }
 633       if (IsOk)
 634         vector.push_back(files[i].toStdString());
 635     }
 636   }
 637   if (vector.size() > 0)
 638     LoadImages(vector, vvImageReader::MERGED);
 639 }
 640 //------------------------------------------------------------------------------
 641
 642 //------------------------------------------------------------------------------
 643 void vvMainWindow::SliceImages()
 644 {
 645   QString Extensions = EXTENSIONS;
 646   Extensions += ";;All Files (*)";
 647
 648   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 649   if (files.isEmpty())
 650     return;
 651   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 652   std::vector<std::string> vector;
 653   for (int i = 0; i < files.size(); i++)
 654     vector.push_back(files[i].toStdString());
 655   LoadImages(vector, vvImageReader::SLICED);
 656 }
 657 //------------------------------------------------------------------------------
 658
 659 //------------------------------------------------------------------------------
 660 void vvMainWindow::MergeImagesWithTime()
 661 {
 662   QString Extensions = EXTENSIONS;
 663   Extensions += ";;All Files (*)";
 664   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 665   if (files.isEmpty())
 666     return;
 667   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 668   std::vector<std::string> vector;
 669
 670   unsigned int currentDim = 0;
 671   std::vector<double> currentSpacing;
 672   std::vector<int> currentSize;
 673   std::vector<double> currentOrigin;
 674
 675   for (int i = 0; i < files.size(); i++) {
 676     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 677                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 678     if (reader) {
 679       reader->SetFileName(files[i].toStdString().c_str());
 680       reader->ReadImageInformation();
 681       if (i == 0)
 682         currentDim = reader->GetNumberOfDimensions();
 683       bool IsOk = true;
 684       for (unsigned int j = 0; j < currentDim; j++) {
 685         if (i == 0) {
 686           if (j == 0) {
 687             currentSpacing.resize(currentDim);
 688             currentSize.resize(currentDim);
 689             currentOrigin.resize(currentDim);
 690           }
 691           currentOrigin[j] = reader->GetOrigin(j);
 692           currentSpacing[j] = reader->GetSpacing(j);
 693           currentSize[j] = reader->GetDimensions(j);
 694         } else if (currentDim != reader->GetNumberOfDimensions()
 695                    || currentSpacing[j] != reader->GetSpacing(j)
 696                    || currentSize[j] != (int)reader->GetDimensions(j)
 697                    || currentOrigin[j] != reader->GetOrigin(j)) {
 698           QString error = "Cannot read file (too different from others ";
 699           error += files[i].toStdString().c_str();
 700           QMessageBox::information(this,tr("Reading problem"),error);
 701           IsOk = false;
 702           break;
 703         }
 704       }
 705       if (IsOk)
 706         vector.push_back(files[i].toStdString());
 707     } else {
 708       QString error = "Cannot read file info for ";
 709       error += files[i].toStdString().c_str();
 710       error += "\n";
 711       error += "Maybe you're trying to open an image in an unsupported format?\n";
 712       QMessageBox::information(this,tr("Reading problem"),error);
 713     }
 714   }
 715   sort(vector.begin(),vector.end());
 716   if (vector.size() > 1)
 717     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 718   else
 719     QMessageBox::warning(this,tr("Reading problem"),"You need to select at least two images to merge images with time.\nIf you only want to open one image, please use the \"Open Image\" function.");
 720 }
 721 //------------------------------------------------------------------------------
 722
 723
 724 //------------------------------------------------------------------------------
 725 void vvMainWindow::OpenDicom()
 726 {
 727   std::vector<std::string> files;
 728
 729   std::cout << "dicomSeriesSelector " << std::endl;
 730   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 731     files = *(dicomSeriesSelector->GetFilenames());
 732     LoadImages(files, vvImageReader::DICOM);
 733   }
 734 }
 735 //------------------------------------------------------------------------------
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenImages()
 739 {
 740   QString Extensions = EXTENSIONS;
 741   Extensions += ";;All Files (*)";
 742
 743   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 744   if (files.isEmpty())
 745     return;
 746   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 747   std::vector<std::string> vector;
 748   for (int i = 0; i < files.size(); i++)
 749     vector.push_back(files[i].toStdString());
 750   LoadImages(vector, vvImageReader::IMAGE);
 751 }
 752 //------------------------------------------------------------------------------
 753 void vvMainWindow::OpenRecentImage()
 754 {
 755   QAction * caller = qobject_cast<QAction*>(sender());
 756   std::vector<std::string> images;
 757   images.push_back(caller->text().toStdString());
 758   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 759   LoadImages(images, vvImageReader::IMAGE);
 760 }
 761 //------------------------------------------------------------------------------
 762
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::OpenImageWithTime()
 766 {
 767   QString Extensions = EXTENSIONS;
 768   Extensions += ";;All Files (*)";
 769
 770   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 771   if (files.isEmpty())
 772     return;
 773   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 774   std::vector<std::string> vector;
 775   for (int i = 0; i < files.size(); i++) {
 776     vector.push_back(files[i].toStdString());
 777   }
 778   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 779 }
 780 //------------------------------------------------------------------------------
 781
 782
 783 //------------------------------------------------------------------------------
 784 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 785 {
 786   //Separate the way to open images and dicoms
 787   int fileSize;
 788   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 789     fileSize = files.size();
 790   else
 791     fileSize = 1;
 792
 793   // For SLICED, we need the number of slices (ndim and #slices)
 794   std::vector<unsigned int> nSlices;
 795   nSlices.resize(files.size());
 796   std::fill(nSlices.begin(), nSlices.end(), 1);
 797   if (filetype == vvImageReader::SLICED) {
 798     for (int i = 0; i < fileSize; i++) {
 799       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 800       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 801       if (!header) {
 802         nSlices[i] = 0;
 803         QString error = "Cannot open file \n";
 804         error += files[i].c_str();
 805         QMessageBox::information(this,tr("Reading problem"),error);
 806         return;
 807       }
 808       if (header->GetNumberOfDimensions() < 3) {
 809         nSlices[i] = 0;
 810         QString error = "Dimension problem. Cannot slice \n";
 811         error += files[i].c_str();
 812         QMessageBox::information(this,tr("Reading problem"),error);
 813         return;
 814       }
 815       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 816     }
 817   }
 818
 819   //Only add to the list of recently opened files when a single file is opened,
 820   //to avoid polluting the list of recently opened files
 821   if (files.size() == 1) {
 822     QFileInfo finfo=tr(files[0].c_str());
 823     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 824     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 825   }
 826   //init the progress events
 827   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 828   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 829   qApp->processEvents();
 830
 831   int numberofsuccesulreads=0;
 832   //open images as 1 or multiples
 833   for (int i = 0; i < fileSize; i++) {
 834
 835     progress.SetText("Opening " + files[i]);
 836     progress.SetProgress(i,fileSize);
 837     qApp->processEvents();
 838
 839     for (unsigned int j = 0; j < nSlices[i]; j++) {
 840       //read the image and put it in mSlicerManagers
 841       vvSlicerManager* imageManager = new vvSlicerManager(4);
 842       qApp->processEvents();
 843
 844       bool SetImageSucceed=false;
 845
 846       // Change filename if an image with the same already exist
 847       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 848
 849       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 850         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 851       else {
 852         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 853       }
 854       if (!SetImageSucceed) {
 855         QApplication::restoreOverrideCursor();
 856         QString error = "Cannot open file \n";
 857         error += imageManager->GetLastError().c_str();
 858         QMessageBox::information(this,tr("Reading problem"),error);
 859         delete imageManager;
 860       } else {
 861         mSlicerManagers.push_back(imageManager);
 862
 863         //create an item in the tree with good settings
 864         QTreeWidgetItem *item = new QTreeWidgetItem();
 865         item->setData(0,Qt::UserRole,files[i].c_str());
 866         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 867         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 868         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 869         qApp->processEvents();
 870
 871         //Create the buttons for reload and close
 872         qApp->processEvents();
 873         QTreePushButton* cButton = new QTreePushButton;
 874         cButton->setItem(item);
 875         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 876         cButton->setToolTip(tr("close image"));
 877         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 878         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 879                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 880
 881         QTreePushButton* rButton = new QTreePushButton;
 882         rButton->setItem(item);
 883         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 884         rButton->setToolTip(tr("reload image"));
 885         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 886         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 887                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 888
 889         DataTree->addTopLevelItem(item);
 890         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 891         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 892
 893         //set the id of the image
 894         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 895         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 896         mSlicerManagers.back()->SetId(id.toStdString());
 897
 898         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 899
 900         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 901                 this,SLOT(CurrentImageChanged(std::string)));
 902         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 903                 this, SLOT(CurrentPickedImageChanged(std::string)));
 904         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 905                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 906         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 907                 this, SLOT(VectorChanged(int,double,double,double, double)));
 908         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 909                 this, SLOT(OverlayChanged(int,double,double)));
 910         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 911                 this, SLOT(FusionChanged(int,double)));
 912         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 913                 this,SLOT(WindowsChanged(int, int, int)));
 914         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 915                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 916         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 917                 this,SLOT(UpdateSlice(int,int)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 919                 this,SLOT(UpdateTSlice(int, int)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 921                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 923                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 925                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 926         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 927                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 928         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 929         InitSlicers();
 930         numberofsuccesulreads++;
 931       }
 932     }
 933   }
 934   if (numberofsuccesulreads) {
 935     NOViewWidget->show();
 936     NEViewWidget->show();
 937     SOViewWidget->show();
 938     SEViewWidget->show();
 939     UpdateTree();
 940     InitDisplay();
 941     ShowLastImage();
 942
 943     // Try to guess default WindowLevel
 944     double range[2];
 945     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 946     if ((range[0] == 0) && (range[1] == 1)) {
 947       presetComboBox->setCurrentIndex(5);// binary
 948     } else {
 949       // TODO
 950     }
 951   }
 952   QApplication::restoreOverrideCursor();
 953 }
 954 //------------------------------------------------------------------------------
 955
 956 //------------------------------------------------------------------------------
 957 void vvMainWindow::UpdateTree()
 958 {
 959   DataTree->resizeColumnToContents(COLUMN_TREE);
 960   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 963   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 964   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 965   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 966   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 967 }
 968 //------------------------------------------------------------------------------
 969
 970 //------------------------------------------------------------------------------
 971 void vvMainWindow::CurrentImageChanged(std::string id)
 972 {
 973   if (id == mCurrentSelectedImageId) return; // Do nothing
 974   int selected = 0;
 975   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 976     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 977       selected = i;
 978     } else {
 979       DataTree->topLevelItem(i)->setSelected(0);
 980     }
 981     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 982       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 983
 984   }
 985   DataTree->topLevelItem(selected)->setSelected(1);
 986   mCurrentSelectedImageId = id;
 987   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 988 }
 989 //------------------------------------------------------------------------------
 990
 991 //------------------------------------------------------------------------------
 992 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 993 {
 994   if (id == mCurrentPickedImageId) return; // Do nothing
 995   int selected = 0;
 996   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 997     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 998       selected = i;
 999     } else {
1000       DataTree->topLevelItem(i)->setSelected(0);
1001     }
1002     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1003       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1004
1005   }
1006   DataTree->topLevelItem(selected)->setSelected(1);
1007   mCurrentPickedImageId = id;
1008   mCurrentPickedImageIndex = selected;
1009 }
1010 //------------------------------------------------------------------------------
1011
1012 //------------------------------------------------------------------------------
1013 void vvMainWindow::ImageInfoChanged()
1014 {
1015   contextActions[6]->setEnabled(1);
1016   contextActions[5]->setEnabled(1);
1017   actionSave_As->setEnabled(1);
1018   actionAdd_VF_to_current_Image->setEnabled(1);
1019   actionAdd_fusion_image->setEnabled(1);
1020   actionNorth_East_Window->setEnabled(1);
1021   actionNorth_West_Window->setEnabled(1);
1022   actionSouth_East_Window->setEnabled(1);
1023   actionSouth_West_Window->setEnabled(1);
1024   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1025   inverseButton->setEnabled(1);
1026
1027   goToCursorPushButton->setEnabled(1);
1028
1029   if (DataTree->selectedItems().size()) {
1030     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1031
1032     colorMapComboBox->setEnabled(1);
1033     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1034       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1035           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1036         colorMapComboBox->setEnabled(0);
1037         break;
1038       }
1039     }
1040
1041     std::vector<double> origin;
1042     std::vector<double> inputSpacing;
1043     std::vector<int> inputSize;
1044     std::vector<double> sizeMM;
1045     vtkSmartPointer<vtkMatrix4x4> transformation;
1046     int dimension=0;
1047     QString pixelType;
1048     QString inputSizeInBytes;
1049     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1050
1051     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1052       playButton->setEnabled(1);
1053       frameRateLabel->setEnabled(1);
1054       frameRateSpinBox->setEnabled(1);
1055     } else {
1056       playButton->setEnabled(0);
1057       frameRateLabel->setEnabled(0);
1058       frameRateSpinBox->setEnabled(0);
1059     }
1060
1061     //read image header
1062     int NPixel = 1;
1063
1064     vvImage::Pointer imageSelected;
1065     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1066       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1067     } 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     std::cout << "Will get transform " << std::endl;
1107     transformation = imageSelected->GetTransform()->GetMatrix();
1108     std::cout << "Got transform " << std::endl;
1109     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1110
1111     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1112                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1113     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1114     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1115
1116     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1117     for (int i = 0; i < 4; i++) {
1118       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1119         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1120         break;
1121       }
1122     }
1123     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1124     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1125     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1126     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1127
1128     infoPanel->setFileName(image);
1129     infoPanel->setDimension(dim);
1130     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1131     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1132     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1133     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1134     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1135
1136     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1137                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1138     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1139     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1140
1141     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1142     for (int i = 0; i < 4; i++) {
1143       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1144         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1145         break;
1146       }
1147     }
1148     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1149     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1150     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1151     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1152
1153     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1154       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1155       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1156                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1157                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1158     } else {
1159       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1160       overlayPanel->getVFProperty(-1,-1,-1);
1161     }
1162     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1163       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1164       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1165     } else {
1166       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1167       overlayPanel->getOverlayProperty(-1);
1168     }
1169     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1170       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1171       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1172                                       mSlicerManagers[index]->GetFusionColorMap(),
1173                                       mSlicerManagers[index]->GetFusionWindow(),
1174                                       mSlicerManagers[index]->GetFusionLevel());
1175     } else {
1176       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1177       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1178     }
1179   }
1180 }
1181 //------------------------------------------------------------------------------
1182
1183 //------------------------------------------------------------------------------
1184 void vvMainWindow::ShowDocumentation()
1185 {
1186   documentation->show();
1187 }
1188 //------------------------------------------------------------------------------
1189
1190 //------------------------------------------------------------------------------
1191 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1192 {
1193   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1194   if(!checkCanPush) {
1195     registerForm->show();
1196   } else {
1197     if(registerForm->canPush()) {
1198       registerForm->show();
1199       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1200     }
1201   }
1202 }
1203 //------------------------------------------------------------------------------
1204
1205 //------------------------------------------------------------------------------
1206 void vvMainWindow::ShowHelpDialog()
1207 {
1208   help_dialog->show();
1209 }
1210 //------------------------------------------------------------------------------
1211
1212 //------------------------------------------------------------------------------
1213 void vvMainWindow::ChangeViewMode()
1214 {
1215   QList<int> size;
1216   if (viewMode == 1) {
1217     viewMode = 0;
1218     size.push_back(1);
1219     size.push_back(0);
1220     splitter_3->setSizes(size);
1221     OSplitter->setSizes(size);
1222     DataTree->setColumnHidden(2,1);
1223     DataTree->setColumnHidden(3,1);
1224     DataTree->setColumnHidden(4,1);
1225   } else {
1226     viewMode = 1;
1227     size.push_back(1);
1228     size.push_back(1);
1229     splitter_3->setSizes(size);
1230     OSplitter->setSizes(size);
1231     DataTree->setColumnHidden(2,0);
1232     DataTree->setColumnHidden(3,0);
1233     DataTree->setColumnHidden(4,0);
1234   }
1235   UpdateRenderWindows();
1236   /*
1237   ** I don't know why but for both resized QVTKWidget we also need to render
1238   ** the associated Slicer to redraw crosses.
1239   */
1240   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1241     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1242       mSlicerManagers[i]->GetSlicer(0)->Render();
1243     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1244       mSlicerManagers[i]->GetSlicer(2)->Render();
1245   }
1246 }
1247 //------------------------------------------------------------------------------
1248
1249 //------------------------------------------------------------------------------
1250 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1251 {
1252   QString result = "";// QString::number(size);
1253   //result += " bytes (";
1254   if (size > 1000000000) {
1255     size /= 1000000000;
1256     result += QString::number(size);
1257     result += "Gb";//)";
1258   } else if (size > 1000000) {
1259     size /= 1000000;
1260     result += QString::number(size);
1261     result += "Mb";//)";
1262   } else if (size > 1000) {
1263     size /= 1000;
1264     result += QString::number(size);
1265     result += "kb";//)";
1266   }
1267   return result;
1268 }
1269 //------------------------------------------------------------------------------
1270
1271 //------------------------------------------------------------------------------
1272 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1273 {
1274   std::ostringstream strmatrix;
1275
1276   for (unsigned int i = 0; i < 4; i++) {
1277     for (unsigned int j = 0; j < 4; j++) {
1278       strmatrix.flags(ios::showpos);
1279       strmatrix.width(10);
1280       strmatrix.precision(3);
1281       strmatrix.setf(ios::fixed,ios::floatfield);
1282       strmatrix.fill(' ');
1283       strmatrix << std::left << matrix->GetElement(i, j);
1284       //strmatrix.width(10);
1285       strmatrix << " ";
1286     }
1287     strmatrix << std::endl;
1288   }
1289   QString result = strmatrix.str().c_str();
1290   return result;
1291 }
1292 //------------------------------------------------------------------------------
1293
1294 //------------------------------------------------------------------------------
1295 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1296 {
1297   QString result;
1298   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1299     if (i != 0)
1300       result += " ";
1301     result += QString::number(vectorDouble[i]);
1302   }
1303   return result;
1304 }
1305 //------------------------------------------------------------------------------
1306
1307 //------------------------------------------------------------------------------
1308 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1309 {
1310   QString result;
1311   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1312     if (i != 0)
1313       result += " ";
1314     result += QString::number(vectorInt[i]);
1315   }
1316   return result;
1317 }
1318 //------------------------------------------------------------------------------
1319
1320 //------------------------------------------------------------------------------
1321 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1322 {
1323   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1324   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1325     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1326       return i;
1327   }
1328   return -1;
1329 }
1330 //------------------------------------------------------------------------------
1331
1332 //------------------------------------------------------------------------------
1333 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1334 {
1335   QString id = sm->GetId().c_str();
1336   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1337     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1338       return DataTree->topLevelItem(i);
1339   }
1340   return NULL;
1341 }
1342 //------------------------------------------------------------------------------
1343
1344 //------------------------------------------------------------------------------
1345 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1346 {
1347   int index = GetSlicerIndexFromItem(clicked_item);
1348   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1349     return;
1350   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1351     //Trick to avoid redoing twice the job for a key (sr)
1352     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1353
1354     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1355     if (DataTree->topLevelItem(index) == current_row) {
1356       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1357       if (current_row == clicked_item) {
1358         //If we just activated a slicer
1359         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1360           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1361           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1362           DisplaySliders(i,column-1);
1363           std::map<std::string,int> overlay_counts;
1364           for (int child = 0; child < current_row->childCount(); child++) {
1365             std::string overlay_type =
1366               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1367             overlay_counts[overlay_type]++;
1368             current_row->child(child)->setData(column,Qt::CheckStateRole,
1369                                                current_row->data(column,Qt::CheckStateRole));
1370             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1371           }
1372         } else { //We don't allow simply desactivating a slicer
1373           clicked_item->setData(column,Qt::CheckStateRole,2);
1374           DisplayChanged(clicked_item, column);
1375           return;
1376         }
1377       }
1378       //if we clicked on the vector(or overlay) and not the image
1379       else {
1380         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1381           current_row->setData(column,Qt::CheckStateRole,2);
1382           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1383           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1384           DisplaySliders(i,column-1);
1385         }
1386         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1387         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1388         int overlay_index=0;
1389         for (int child = 0; child < current_row->childCount(); child++) {
1390           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1391             overlay_index++;
1392           if (current_row->child(child) == clicked_item) break;
1393         }
1394         clicked_slicer->SetActorVisibility(
1395           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1396       }
1397     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1398       current_row->setData(column,Qt::CheckStateRole,0);
1399       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1400       std::map<std::string,int> overlay_counts;
1401       for (int child = 0; child < current_row->childCount(); child++) {
1402         std::string overlay_type =
1403           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1404         overlay_counts[overlay_type]++;
1405         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1406         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1407         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1408       }
1409     }
1410     //mSlicerManagers[i]->SetColorMap(-1);
1411     mSlicerManagers[i]->SetColorMap();
1412   }
1413   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1414 }
1415 //------------------------------------------------------------------------------
1416
1417 void vvMainWindow::InitSlicers()
1418 {
1419   if (mSlicerManagers.size()) {
1420     mSlicerManagers.back()->GenerateDefaultLookupTable();
1421
1422     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1423     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1424     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1425     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1426   }
1427 }
1428
1429 //------------------------------------------------------------------------------
1430 void vvMainWindow::InitDisplay()
1431 {
1432   if (mSlicerManagers.size()) {
1433     //BE CAREFUL : this is absolutely necessary to set the interactor style
1434     //in order to have the same style instanciation for all SlicerManagers in
1435     // a same window
1436     for (int j = 0; j < 4; j++) {
1437       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1438       style->SetAutoAdjustCameraClippingRange(1);
1439       bool AlreadySelected = false;
1440       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1441         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1442
1443         //select the image only if previous are not selected
1444         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1445           mSlicerManagers[i]->UpdateSlicer(j,1);
1446           AlreadySelected = true;
1447         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1448           if (DataTree->selectedItems().size() == 0)
1449             DataTree->topLevelItem(i)->setSelected(1);
1450           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1451           mSlicerManagers[i]->UpdateSlicer(j,1);
1452           DisplaySliders(i,j);
1453         } else {
1454           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1455           mSlicerManagers[i]->UpdateSlicer(j,0);
1456         }
1457       }
1458       style->Delete();
1459     }
1460   }
1461 }
1462 //------------------------------------------------------------------------------
1463
1464 //------------------------------------------------------------------------------
1465 void vvMainWindow::DisplaySliders(int slicer, int window)
1466 {
1467   int range[2];
1468   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1469   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1470
1471   int tRange[2];
1472   tRange[0] = 0;
1473   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1474   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1475   bool showHorizontal = false;
1476   bool showVertical = false;
1477   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1478       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1479           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1480           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1481     showVertical = true;
1482   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1483       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1484       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1485     showHorizontal = true;
1486
1487   if (showVertical)
1488     verticalSliders[window]->show();
1489   else
1490     verticalSliders[window]->hide();
1491   verticalSliders[window]->setRange(range[0],range[1]);
1492   verticalSliders[window]->setValue(position);
1493
1494   if (showHorizontal)
1495     horizontalSliders[window]->show();
1496   else
1497     horizontalSliders[window]->hide();
1498   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1499   horizontalSliders[window]->setValue(tPosition);
1500 }
1501 //------------------------------------------------------------------------------
1502
1503 //------------------------------------------------------------------------------
1504 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1505 {
1506   int index = GetSlicerIndexFromItem(item);
1507
1508   if (DataTree->topLevelItem(index) != item) {
1509     QString warning = "Do you really want to close the overlay : ";
1510     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1511     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1512                        warning, 0, this);
1513     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1514     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1515     if (msgBox.exec() == QMessageBox::AcceptRole) {
1516       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1517       int overlay_index=0;
1518       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1519         if (DataTree->topLevelItem(index)->\
1520             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1521           overlay_index++;
1522         if (DataTree->topLevelItem(index)->child(child) == item) break;
1523       }
1524       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1525       mSlicerManagers[index]->SetColorMap(0);
1526       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1527       mSlicerManagers[index]->Render();
1528     }
1529   } else if (DataTree->topLevelItemCount() <= 1) {
1530     QString warning = "Do you really want to close the image : ";
1531     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1532     warning += "\nThis is the last image, you're about to close vv !!!";
1533     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1534                        warning, 0, this);
1535     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1536     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1537     if (msgBox.exec() == QMessageBox::AcceptRole) {
1538       this->close();
1539     }
1540   } else {
1541     QString warning = "Do you really want to close the image : ";
1542     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1543     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1544                        warning, 0, this);
1545     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1546     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1547     if (msgBox.exec() == QMessageBox::AcceptRole) {
1548
1549       // Tell tools that we close an image
1550       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1551
1552       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1553       DataTree->takeTopLevelItem(index);
1554       for (int i = 0; i < index; i++) {
1555         Manageriter++;
1556       }
1557       linkPanel->removeImage(index);
1558       mSlicerManagers[index]->RemoveActors();
1559       delete mSlicerManagers[index];
1560       mSlicerManagers.erase(Manageriter);
1561
1562       //
1563       InitDisplay();
1564     }
1565   }
1566   ImageInfoChanged();
1567 }
1568 //------------------------------------------------------------------------------
1569
1570 //------------------------------------------------------------------------------
1571 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1572 {
1573   // int index = GetSlicerIndexFromItem(item);
1574   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1575   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1576   //     mSlicerManagers[index]->ReloadVF();
1577   //   else
1578   //     mSlicerManagers[index]->Reload();
1579
1580   //   QApplication::restoreOverrideCursor();
1581   int index = GetSlicerIndexFromItem(item);
1582   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1583   QString role=item->data(1,Qt::UserRole).toString();
1584   if ( role == "vector"){
1585     mSlicerManagers[index]->ReloadVF();
1586   }
1587   else if (role == "overlay"){
1588     mSlicerManagers[index]->ReloadOverlay();
1589   }
1590   else if (role == "fusion"){
1591     mSlicerManagers[index]->ReloadFusion();
1592   }
1593   else{
1594     mSlicerManagers[index]->Reload();
1595   }
1596   // Update view and info
1597   ImageInfoChanged();
1598   mSlicerManagers[index]->Render();
1599   QApplication::restoreOverrideCursor();
1600 }
1601 //------------------------------------------------------------------------------
1602
1603 //------------------------------------------------------------------------------
1604 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1605 {
1606   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1607 }
1608 //------------------------------------------------------------------------------
1609
1610 //------------------------------------------------------------------------------
1611 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1612 {
1613   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1614 }
1615 //------------------------------------------------------------------------------
1616
1617 //------------------------------------------------------------------------------
1618 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1619 {
1620   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1621 }
1622 //------------------------------------------------------------------------------
1623
1624 //------------------------------------------------------------------------------
1625 void vvMainWindow::FusionChanged(int visibility, double value)
1626 {
1627   overlayPanel->getCurrentFusionInfo(visibility,value);
1628 }
1629 //------------------------------------------------------------------------------
1630
1631 //------------------------------------------------------------------------------
1632 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1633 {
1634   infoPanel->setViews(window, view, slice);
1635 }
1636 //------------------------------------------------------------------------------
1637
1638 //------------------------------------------------------------------------------
1639 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1640 {
1641   windowSpinBox->setValue(window);
1642   levelSpinBox->setValue(level);
1643   colorMapComboBox->setCurrentIndex(colormap);
1644   presetComboBox->setCurrentIndex(preset);
1645 }
1646 //------------------------------------------------------------------------------
1647
1648 //------------------------------------------------------------------------------
1649 void vvMainWindow::WindowLevelEdited()
1650 {
1651   presetComboBox->setCurrentIndex(6);
1652   UpdateWindowLevel();
1653 }
1654 //------------------------------------------------------------------------------
1655
1656 //------------------------------------------------------------------------------
1657 void vvMainWindow::UpdateWindowLevel()
1658 {
1659   if (DataTree->selectedItems().size()) {
1660     if (presetComboBox->currentIndex() == 7) //For ventilation
1661       colorMapComboBox->setCurrentIndex(5);
1662     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1663     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1664     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1665     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1666     mSlicerManagers[index]->Render();
1667     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1668     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1669   }
1670 }
1671 //------------------------------------------------------------------------------
1672
1673 //------------------------------------------------------------------------------
1674 void vvMainWindow::UpdateColorMap()
1675 {
1676   if (DataTree->selectedItems().size()) {
1677     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1678     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1679     mSlicerManagers[index]->Render();
1680   }
1681 }
1682 //------------------------------------------------------------------------------
1683 void vvMainWindow::SwitchWindowLevel()
1684 {
1685   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1686   int window = mSlicerManagers[index]->GetColorWindow();
1687   presetComboBox->setCurrentIndex(6);
1688   windowSpinBox->setValue(-window);
1689   UpdateWindowLevel();
1690 }
1691 //------------------------------------------------------------------------------
1692
1693 //------------------------------------------------------------------------------
1694 void vvMainWindow::ApplyWindowLevelToAllImages()
1695 {
1696   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1697     if (mSlicerManagers[i] == NULL)
1698       continue;
1699     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1700     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1701     mSlicerManagers[i]->SetPreset(6);
1702     mSlicerManagers[i]->Render();
1703   }
1704 }
1705 //------------------------------------------------------------------------------
1706
1707 //------------------------------------------------------------------------------
1708 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1709 {
1710   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1711     if (mSlicerManagers[i]->GetId() == id) {
1712       //mSlicerManagers[i]->SetTSlice(temps);
1713       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1714       mSlicerManagers[i]->UpdateViews(0,slicer);
1715       break;
1716     }
1717   }
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1723 {
1724   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1725     if (id == mSlicerManagers[i]->GetId()) {
1726       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1727     }
1728   }
1729 }
1730 //------------------------------------------------------------------------------
1731
1732 //------------------------------------------------------------------------------
1733 void vvMainWindow::ShowContextMenu(QPoint point)
1734 {
1735   if (!DataTree->selectedItems().size()) {
1736     contextActions[1]->setEnabled(0);
1737     contextActions[2]->setEnabled(0);
1738     contextActions[3]->setEnabled(0);
1739     contextActions[4]->setEnabled(0);
1740     contextActions[5]->setEnabled(0);
1741     contextActions[6]->setEnabled(0);
1742   } else {
1743     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1744     contextActions[1]->setEnabled(1);
1745     contextActions[2]->setEnabled(
1746       DataTree->itemWidget(DataTree->selectedItems()[0],
1747                            COLUMN_RELOAD_IMAGE)->isEnabled());
1748     contextActions[3]->setEnabled(1);
1749     contextActions[5]->setEnabled(1);
1750     contextActions[6]->setEnabled(1);
1751
1752     if (mSlicerManagers[index]->GetDimension() < 3)
1753       contextActions[4]->setEnabled(0);
1754     else
1755       contextActions[4]->setEnabled(1);
1756   }
1757   contextMenu.exec(QCursor::pos());
1758 }
1759 //------------------------------------------------------------------------------
1760
1761 //------------------------------------------------------------------------------
1762 void vvMainWindow::CloseImage()
1763 {
1764   CloseImage(DataTree->selectedItems()[0],0);
1765 }
1766 //------------------------------------------------------------------------------
1767
1768 //------------------------------------------------------------------------------
1769 void vvMainWindow::ReloadImage()
1770 {
1771   ReloadImage(DataTree->selectedItems()[0],0);
1772 }
1773 //------------------------------------------------------------------------------
1774
1775 //------------------------------------------------------------------------------
1776 void vvMainWindow::SelectOverlayImage()
1777 {
1778   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1779
1780   //check if one overlay image is added
1781   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1782     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1783       QString error = "Cannot add more than one compared image\n";
1784       error += "Please remove first ";
1785       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1786       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1787       return;
1788     }
1789
1790   QString Extensions = EXTENSIONS;
1791   Extensions += ";;All Files (*)";
1792   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1793   if (!file.isEmpty())
1794     AddOverlayImage(index,file);
1795 }
1796 //------------------------------------------------------------------------------
1797
1798 //------------------------------------------------------------------------------
1799 void vvMainWindow::AddOverlayImage(int index, QString file)
1800 {
1801
1802   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1803   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1804                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1805   reader->SetFileName(file.toStdString().c_str());
1806   reader->ReadImageInformation();
1807   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1808   int dimension = reader->GetNumberOfDimensions();
1809   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1810   vvProgressDialog progress("Opening " + file.toStdString());
1811   qApp->processEvents();
1812
1813   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1814   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1815     //create an item in the tree with good settings
1816     QTreeWidgetItem *item = new QTreeWidgetItem();
1817     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1818     item->setData(1,Qt::UserRole,tr("overlay"));
1819     QFileInfo fileinfo(file); //Do not show the path
1820     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1821     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1822     qApp->processEvents();
1823
1824     for (int j = 1; j <= 4; j++) {
1825       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1826       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1827           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1828     }
1829
1830     //Create the buttons for reload and close
1831     qApp->processEvents();
1832     QTreePushButton* cButton = new QTreePushButton;
1833     cButton->setItem(item);
1834     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1835     cButton->setToolTip(tr("close image"));
1836     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1837     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1838             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1839
1840     QTreePushButton* rButton = new QTreePushButton;
1841     rButton->setItem(item);
1842     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1843     rButton->setToolTip(tr("reload image"));
1844     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1845     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1846             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1847
1848     DataTree->topLevelItem(index)->setExpanded(1);
1849     DataTree->topLevelItem(index)->addChild(item);
1850     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1851     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1852
1853     //set the id of the image
1854     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1855     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1856     UpdateTree();
1857     qApp->processEvents();
1858     ImageInfoChanged();
1859     QApplication::restoreOverrideCursor();
1860   } else {
1861     QApplication::restoreOverrideCursor();
1862     QString error = "Cannot import the new image.\n";
1863     error += mSlicerManagers[index]->GetLastError().c_str();
1864     QMessageBox::information(this,tr("Problem reading image !"),error);
1865   }
1866 }
1867 //------------------------------------------------------------------------------
1868
1869
1870 //------------------------------------------------------------------------------
1871 void vvMainWindow::AddROI(int index, QString file)
1872 {
1873   /*
1874   // Get slice manager
1875
1876   // Load image
1877
1878   vvImageReader * mReader = new vvImageReader;
1879   mReader->SetInputFilename(filename.toStdString());
1880   mReader->Update(IMAGE);
1881   if (mReader->GetLastError().size() != 0) {
1882     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1883     QString error = "Cannot open file \n";
1884     error += mReader->GetLastError().c_str();
1885     QMessageBox::information(this,tr("Reading problem"),error);
1886     delete mReader;
1887     return;
1888   }
1889   vvImage::Pointer roi = mReader->GetOutput();
1890
1891   // Create roi in new tool
1892   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1893   */
1894 }
1895 //------------------------------------------------------------------------------
1896
1897 //------------------------------------------------------------------------------
1898 void vvMainWindow::SelectFusionImage()
1899 {
1900   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1901
1902   //check if one fusion image is added
1903   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1904     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1905       QString error = "Cannot add more than one fusion image\n";
1906       error += "Please remove first ";
1907       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1908       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1909       return;
1910     }
1911
1912   QString Extensions = EXTENSIONS;
1913   Extensions += ";;All Files (*)";
1914   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1915   if (!file.isEmpty())
1916     AddFusionImage(index,file);
1917 }
1918 //------------------------------------------------------------------------------
1919
1920 //------------------------------------------------------------------------------
1921 void vvMainWindow::AddFusionImage(int index, QString file)
1922 {
1923   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1924   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1925                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1926   reader->SetFileName(file.toStdString().c_str());
1927   reader->ReadImageInformation();
1928   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1929   if (reader) {
1930     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1931     vvProgressDialog progress("Opening fusion");
1932     qApp->processEvents();
1933
1934     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1935     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1936                                           reader->GetNumberOfDimensions(), component)) {
1937       //create an item in the tree with good settings
1938       QTreeWidgetItem *item = new QTreeWidgetItem();
1939       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1940       item->setData(1,Qt::UserRole,tr("fusion"));
1941       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1942       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1943       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1944       qApp->processEvents();
1945
1946       for (int j = 1; j <= 4; j++) {
1947         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1948         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1949             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1950       }
1951
1952       //Create the buttons for reload and close
1953       qApp->processEvents();
1954       QTreePushButton* cButton = new QTreePushButton;
1955       cButton->setItem(item);
1956       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1957       cButton->setToolTip(tr("close image"));
1958       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1959       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1960               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1961
1962       QTreePushButton* rButton = new QTreePushButton;
1963       rButton->setItem(item);
1964       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1965       rButton->setToolTip(tr("reload image"));
1966       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1967       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1968               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1969
1970       DataTree->topLevelItem(index)->setExpanded(1);
1971       DataTree->topLevelItem(index)->addChild(item);
1972       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1973       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1974
1975       //set the id of the image
1976       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1977       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1978       UpdateTree();
1979       qApp->processEvents();
1980       ImageInfoChanged();
1981       QApplication::restoreOverrideCursor();
1982     } else {
1983       QApplication::restoreOverrideCursor();
1984       QString error = "Cannot import the new image.\n";
1985       error += mSlicerManagers[index]->GetLastError().c_str();
1986       QMessageBox::information(this,tr("Problem reading image !"),error);
1987     }
1988   } else {
1989     QString error = "Cannot import the new image.\n";
1990     QMessageBox::information(this,tr("Problem reading image !"),error);
1991   }
1992 }
1993 //------------------------------------------------------------------------------
1994
1995
1996 //------------------------------------------------------------------------------
1997 void vvMainWindow::OpenField()
1998 {
1999   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2000   //check if a vector field has already been added
2001   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2002     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2003       QString error = "Cannot add more than one vector field\n";
2004       error += "Please remove first ";
2005       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2006       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2007       return;
2008     }
2009
2010   QString Extensions = "Images ( *.mhd)";
2011   Extensions += ";;Images ( *.vf)";
2012   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2013   if (!file.isEmpty())
2014     AddField(file,index);
2015 }
2016 //------------------------------------------------------------------------------
2017
2018
2019 //------------------------------------------------------------------------------
2020 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2021 {
2022   //create an item in the tree with good settings
2023   QTreeWidgetItem *item = new QTreeWidgetItem();
2024   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2025   item->setData(1,Qt::UserRole,tr("vector"));
2026   QFileInfo fileinfo(filename); //Do not show the path
2027   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2028   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2029   qApp->processEvents();
2030
2031   for (int j = 1; j <= 4; j++) {
2032     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2033     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2034         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2035   }
2036
2037   //Create the buttons for reload and close
2038   qApp->processEvents();
2039   QTreePushButton* cButton = new QTreePushButton;
2040   cButton->setItem(item);
2041   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2042   cButton->setToolTip(tr("close vector field"));
2043   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2044   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2045           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2046
2047   QTreePushButton* rButton = new QTreePushButton;
2048   rButton->setItem(item);
2049   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2050   rButton->setToolTip(tr("reload vector field"));
2051   rButton->setEnabled(from_disk);
2052   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2053   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2054           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2055
2056   DataTree->topLevelItem(index)->setExpanded(1);
2057   DataTree->topLevelItem(index)->addChild(item);
2058   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2059   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2060
2061   //set the id of the image
2062   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2063   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2064   UpdateTree();
2065   qApp->processEvents();
2066   ImageInfoChanged();
2067   QApplication::restoreOverrideCursor();
2068 }
2069 //------------------------------------------------------------------------------
2070
2071
2072 //------------------------------------------------------------------------------
2073 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2074 {
2075   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2076   vvSlicerManager* imageManager = mSlicerManagers[index];
2077   if (imageManager->SetVF(vf,file.toStdString())) {
2078     AddFieldEntry(file,index,false);
2079   } else {
2080     QString error = "Cannot import the vector field for this image.\n";
2081     error += imageManager->GetLastError().c_str();
2082     QMessageBox::information(this,tr("Problem reading VF !"),error);
2083   }
2084   QApplication::restoreOverrideCursor();
2085 }
2086 //------------------------------------------------------------------------------
2087
2088
2089 //------------------------------------------------------------------------------
2090 void vvMainWindow::AddField(QString file,int index)
2091 {
2092   if (QFile::exists(file)) {
2093     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2094
2095     //init the progress events
2096     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2097     vvProgressDialog progress("Opening " + file.toStdString());
2098     qApp->processEvents();
2099
2100     //read the vector and put it in the current mSlicerManager
2101     vvSlicerManager* imageManager = mSlicerManagers[index];
2102     qApp->processEvents();
2103
2104     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2105     if (imageManager->SetVF(file.toStdString())) {
2106       imageManager->Render();
2107       AddFieldEntry(file,index,true);
2108     } else {
2109       QApplication::restoreOverrideCursor();
2110       QString error = "Cannot import the vector field for this image.\n";
2111       error += imageManager->GetLastError().c_str();
2112       QMessageBox::information(this,tr("Problem reading VF !"),error);
2113     }
2114   } else
2115     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2116
2117 }
2118 //------------------------------------------------------------------------------
2119
2120
2121 //------------------------------------------------------------------------------
2122 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2123 {
2124   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2125   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2126     for (int i = 0; i < 4; i++) {
2127       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2128       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2129       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2130       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2131       if (log > 0)
2132         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2133       else
2134         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2135     }
2136   }
2137 }
2138 //------------------------------------------------------------------------------
2139
2140
2141 //------------------------------------------------------------------------------
2142 void vvMainWindow::SetOverlayProperty(int color)
2143 {
2144   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2145   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2146     mSlicerManagers[index]->SetOverlayColor(color);
2147     mSlicerManagers[index]->SetColorMap(0);
2148     mSlicerManagers[index]->Render();
2149   }
2150 }
2151 //------------------------------------------------------------------------------
2152
2153 //------------------------------------------------------------------------------
2154 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2155 {
2156   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2157   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2158     mSlicerManagers[index]->SetFusionOpacity(opacity);
2159     mSlicerManagers[index]->SetFusionColorMap(colormap);
2160     mSlicerManagers[index]->SetFusionWindow(window);
2161     mSlicerManagers[index]->SetFusionLevel(level);
2162     mSlicerManagers[index]->SetColorMap(0);
2163     mSlicerManagers[index]->Render();
2164   }
2165 }
2166 //------------------------------------------------------------------------------
2167
2168 //------------------------------------------------------------------------------
2169 void vvMainWindow::SaveAs()
2170 {
2171   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2172     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2173     return;
2174   }
2175
2176   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2177   int dimension = mSlicerManagers[index]->GetDimension();
2178   QStringList OutputListeFormat;
2179   OutputListeFormat.clear();
2180   if (dimension == 1) {
2181     OutputListeFormat.push_back(".mhd");
2182   }
2183   if (dimension == 2) {
2184     OutputListeFormat.push_back(".bmp");
2185     OutputListeFormat.push_back(".png");
2186     OutputListeFormat.push_back(".jpeg");
2187     OutputListeFormat.push_back(".tif");
2188     OutputListeFormat.push_back(".mhd");
2189     OutputListeFormat.push_back(".hdr");
2190     OutputListeFormat.push_back(".vox");
2191   } else if (dimension == 3) {
2192     OutputListeFormat.push_back(".mhd");
2193     OutputListeFormat.push_back(".hdr");
2194     OutputListeFormat.push_back(".vox");
2195   } else if (dimension == 4) {
2196     OutputListeFormat.push_back(".mhd");
2197   }
2198   QString Extensions = "AllFiles(*.*)";
2199   for (int i = 0; i < OutputListeFormat.count(); i++) {
2200     Extensions += ";;Images ( *";
2201     Extensions += OutputListeFormat[i];
2202     Extensions += ")";
2203   }
2204   QString fileName = QFileDialog::getSaveFileName(this,
2205                      tr("Save As"),
2206                      mSlicerManagers[index]->GetFileName().c_str(),
2207                      Extensions);
2208   if (!fileName.isEmpty()) {
2209     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2210     if (OutputListeFormat.contains(
2211           fileformat.c_str())) {
2212       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2213       std::string action = "Saving";
2214       vvProgressDialog progress("Saving "+fileName.toStdString());
2215       qApp->processEvents();
2216       vvImageWriter::Pointer writer = vvImageWriter::New();
2217       writer->SetOutputFileName(fileName.toStdString());
2218       writer->SetInput(mSlicerManagers[index]->GetImage());
2219       writer->Update();
2220       QApplication::restoreOverrideCursor();
2221       if (writer->GetLastError().size()) {
2222         QString error = "Saving did not succeed\n";
2223         error += writer->GetLastError().c_str();
2224         QMessageBox::information(this,tr("Saving Problem"),error);
2225         SaveAs();
2226       }
2227     } else {
2228       QString error = fileformat.c_str();
2229       if (error.isEmpty())
2230         error += "no file format specified !";
2231       else
2232         error += " format unknown !!!\n";
2233       QMessageBox::information(this,tr("Saving Problem"),error);
2234       SaveAs();
2235     }
2236   }
2237 }
2238 //------------------------------------------------------------------------------
2239
2240
2241 //------------------------------------------------------------------------------
2242 void vvMainWindow::AddLink(QString image1,QString image2)
2243 {
2244   unsigned int sm1 = 0;
2245   unsigned int sm2 = 0;
2246
2247   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2248     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2249       mSlicerManagers[i]->AddLink(image2.toStdString());
2250       sm1 = i;
2251     }
2252     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2253       mSlicerManagers[i]->AddLink(image1.toStdString());
2254       sm2 = i;
2255     }
2256   }
2257
2258   if (linkPanel->isLinkAll())   {
2259     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2260     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2261   } else {
2262     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2263   }
2264 }
2265
2266 //------------------------------------------------------------------------------
2267
2268
2269 //------------------------------------------------------------------------------
2270 void vvMainWindow::RemoveLink(QString image1,QString image2)
2271 {
2272   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2273     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2274       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2275     }
2276     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2277       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2278     }
2279   }
2280 }
2281 //------------------------------------------------------------------------------
2282
2283 //------------------------------------------------------------------------------
2284 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2285 {
2286   int index = 0;
2287   while(sm != mSlicerManagers[index])
2288     index++;
2289   index = (index+offset) % mSlicerManagers.size();
2290
2291   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2292   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2293   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2294   DisplayChanged(item,slicer+1);
2295 }
2296 //------------------------------------------------------------------------------
2297
2298 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2299 {
2300   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2301     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2302       for (int j = 0; j < 4; j++) {
2303         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2304         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2305         //UpdateTSlice(j,value);
2306       }
2307       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2308       break;
2309     }
2310   }
2311 }
2312 //------------------------------------------------------------------------------
2313
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::NOHorizontalSliderMoved()
2317 {
2318   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2319   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2320 //  mCurrentTime = NOHorizontalSlider->value();
2321 }
2322 //------------------------------------------------------------------------------
2323
2324
2325 //------------------------------------------------------------------------------
2326 void vvMainWindow::NEHorizontalSliderMoved()
2327 {
2328   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2329   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2330 //  mCurrentTime = NEHorizontalSlider->value();
2331 }
2332 //------------------------------------------------------------------------------
2333
2334
2335 //------------------------------------------------------------------------------
2336 void vvMainWindow::SOHorizontalSliderMoved()
2337 {
2338   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2339   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2340   // mCurrentTime = SOHorizontalSlider->value();
2341 }
2342 //------------------------------------------------------------------------------
2343
2344
2345 //------------------------------------------------------------------------------
2346 void vvMainWindow::SEHorizontalSliderMoved()
2347 {
2348   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2349   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2350   // mCurrentTime = SEHorizontalSlider->value();
2351 }
2352 //------------------------------------------------------------------------------
2353
2354 //------------------------------------------------------------------------------
2355 void vvMainWindow::NOVerticalSliderChanged()
2356 {
2357   static int value=-1;
2358   if (value == NOVerticalSlider->value()) return;
2359   else value = NOVerticalSlider->value();
2360   //  int value = NOVerticalSlider->value();
2361   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2362     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2363       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2364         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2365         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2366
2367         // If nor Update/Render -> slider not work
2368         // only render = ok navigation, but for contour Update needed but slower ?
2369
2370         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2371         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2372       }
2373       break;
2374     }
2375   }
2376 }
2377 //------------------------------------------------------------------------------
2378
2379
2380 //------------------------------------------------------------------------------
2381 void vvMainWindow::NEVerticalSliderChanged()
2382 {
2383   static int value=-1;
2384   if (value == NEVerticalSlider->value()) return;
2385   else value = NEVerticalSlider->value();
2386   //  int value = NEVerticalSlider->value();
2387   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2388     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2389       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2390         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2391         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2392         mSlicerManagers[i]->UpdateSlice(1);
2393         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2394       }
2395       break;
2396     }
2397   }
2398 }
2399 //------------------------------------------------------------------------------
2400
2401
2402 //------------------------------------------------------------------------------
2403 void vvMainWindow::SOVerticalSliderChanged()
2404 {
2405   static int value=-1;
2406   if (value == SOVerticalSlider->value()) return;
2407   else value = SOVerticalSlider->value();
2408   //int value = SOVerticalSlider->value();
2409   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2410     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2411       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2412         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2413         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2414         mSlicerManagers[i]->UpdateSlice(2);
2415         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2416       }
2417       // else { DD("avoid SOVerticalSlider slicer update"); }
2418       break;
2419     }
2420   }
2421 }
2422 //------------------------------------------------------------------------------
2423
2424
2425 //------------------------------------------------------------------------------
2426 void vvMainWindow::SEVerticalSliderChanged()
2427 {
2428   static int value=-1;
2429   if (value == SEVerticalSlider->value()) return;
2430   else value = SEVerticalSlider->value();
2431   // int value = SEVerticalSlider->value();
2432   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2433     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2434       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2435         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2436         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2437         mSlicerManagers[i]->UpdateSlice(3);
2438         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2439       }
2440       break;
2441     }
2442   }
2443 }
2444 //------------------------------------------------------------------------------
2445
2446
2447 //------------------------------------------------------------------------------
2448 void vvMainWindow::UpdateSlice(int slicer, int slice)
2449 {
2450   // DD("vvMainWindow::UpdateSlice");
2451 //   DD(slicer);
2452 //   DD(slice);
2453   if (slicer == 0) {
2454     //    if (slice != NOVerticalSlider->value())
2455     NOVerticalSlider->setValue(slice);
2456   } else {
2457     if (slicer == 1)
2458       NEVerticalSlider->setValue(slice);
2459     else {
2460       if (slicer == 2)
2461         SOVerticalSlider->setValue(slice);
2462       else {
2463         if (slicer == 3)
2464           SEVerticalSlider->setValue(slice);
2465       }
2466     }
2467   }
2468   // DD("vvMainWindow:UpdateSlice END");
2469 }
2470 //------------------------------------------------------------------------------
2471
2472
2473 //------------------------------------------------------------------------------
2474 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2475 {
2476   switch (slicer) {
2477   case 0:
2478     NOHorizontalSlider->setValue(slice);
2479     break;
2480   case 1:
2481     NEHorizontalSlider->setValue(slice);
2482     break;
2483   case 2:
2484     SOHorizontalSlider->setValue(slice);
2485     break;
2486   case 3:
2487     SEHorizontalSlider->setValue(slice);
2488     break;
2489   }
2490 }
2491 //------------------------------------------------------------------------------
2492
2493
2494 //------------------------------------------------------------------------------
2495 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2496 {
2497   int position = int((min+max)/2);
2498   int tPosition = int((tmin+tmax)/2);
2499   if (slicer == 0) {
2500     NOVerticalSlider->setValue(position);
2501     NOVerticalSlider->setRange(min,max);
2502     NOHorizontalSlider->setRange(tmin,tmax);
2503     NOHorizontalSlider->setValue(tPosition);
2504   } else if (slicer == 1) {
2505     NEVerticalSlider->setValue(position);
2506     NEVerticalSlider->setRange(min,max);
2507     NEHorizontalSlider->setRange(tmin,tmax);
2508     NEHorizontalSlider->setValue(tPosition);
2509   } else if (slicer == 2) {
2510     SOVerticalSlider->setValue(position);
2511     SOVerticalSlider->setRange(min,max);
2512     SOHorizontalSlider->setRange(tmin,tmax);
2513     SOHorizontalSlider->setValue(tPosition);
2514   } else if (slicer == 3) {
2515     SEVerticalSlider->setValue(position);
2516     SEVerticalSlider->setRange(min,max);
2517     SEHorizontalSlider->setRange(tmin,tmax);
2518     SEHorizontalSlider->setValue(tPosition);
2519   }
2520 }
2521 //------------------------------------------------------------------------------
2522
2523
2524 //------------------------------------------------------------------------------
2525 void vvMainWindow::SaveNOScreenshot()
2526 {
2527   SaveScreenshot(NOViewWidget);
2528 }
2529 //------------------------------------------------------------------------------
2530
2531
2532 //------------------------------------------------------------------------------
2533 void vvMainWindow::SaveNEScreenshot()
2534 {
2535   SaveScreenshot(NEViewWidget);
2536 }
2537 //------------------------------------------------------------------------------
2538
2539
2540 //------------------------------------------------------------------------------
2541 void vvMainWindow::SaveSOScreenshot()
2542 {
2543   SaveScreenshot(SOViewWidget);
2544 }
2545 //------------------------------------------------------------------------------
2546
2547
2548 //------------------------------------------------------------------------------
2549 void vvMainWindow::SaveSEScreenshot()
2550 {
2551   SaveScreenshot(SEViewWidget);
2552 }
2553 //------------------------------------------------------------------------------
2554
2555
2556 //------------------------------------------------------------------------------
2557 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2558 {
2559   QString Extensions = "Images( *.png);;";
2560   Extensions += "Images( *.jpg);;";
2561   Extensions += "Images( *.bmp);;";
2562   Extensions += "Images( *.tif);;";
2563   Extensions += "Images( *.ppm)";
2564 #ifdef VTK_USE_FFMPEG_ENCODER
2565   Extensions += "Images( *.avi)";
2566 #endif
2567 #ifdef VTK_USE_MPEG2_ENCODER
2568   Extensions += "Images( *.mpg)";
2569 #endif
2570
2571   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2572   QString fileName = QFileDialog::getSaveFileName(this,
2573                      tr("Save As"),
2574                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2575                      Extensions);
2576
2577   if (!fileName.isEmpty()) {
2578     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2579     w2i->SetInput(widget->GetRenderWindow());
2580     w2i->Update();
2581     vtkImageData *image = w2i->GetOutput();
2582
2583     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2584     if (!strcmp(ext, ".bmp")) {
2585       vtkBMPWriter *bmp = vtkBMPWriter::New();
2586       bmp->SetInput(image);
2587       bmp->SetFileName(fileName.toStdString().c_str());
2588       bmp->Write();
2589       bmp->Delete();
2590     } else if (!strcmp(ext, ".tif")) {
2591       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2592       tif->SetInput(image);
2593       tif->SetFileName(fileName.toStdString().c_str());
2594       tif->Write();
2595       tif->Delete();
2596     } else if (!strcmp(ext, ".ppm")) {
2597       vtkPNMWriter *pnm = vtkPNMWriter::New();
2598       pnm->SetInput(image);
2599       pnm->SetFileName(fileName.toStdString().c_str());
2600       pnm->Write();
2601       pnm->Delete();
2602     } else if (!strcmp(ext, ".png")) {
2603       vtkPNGWriter *png = vtkPNGWriter::New();
2604       png->SetInput(image);
2605       png->SetFileName(fileName.toStdString().c_str());
2606       png->Write();
2607       png->Delete();
2608     } else if (!strcmp(ext, ".jpg")) {
2609       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2610       jpg->SetInput(image);
2611       jpg->SetFileName(fileName.toStdString().c_str());
2612       jpg->Write();
2613       jpg->Delete();
2614 #ifdef VTK_USE_FFMPEG_ENCODER
2615     } else if (!strcmp(ext, ".avi")) {
2616       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2617       mpg->SetInput(image);
2618       mpg->SetFileName(fileName.toStdString().c_str());
2619       mpg->SetQuality(2);
2620       mpg->SetRate(5);
2621       mpg->Start();
2622
2623       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2624       int nSlice = vvImg->GetVTKImages().size();
2625       for(int i=0; i<nSlice; i++) {
2626         mSlicerManagers[smIndex]->SetNextTSlice(0);
2627         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2628         w2i->SetInput(widget->GetRenderWindow());
2629         w2i->Update();
2630         mpg->SetInput(w2i->GetOutput());
2631         mpg->Write();
2632       }
2633       mpg->End();
2634       mpg->Delete();
2635 #endif
2636 #ifdef VTK_USE_MPEG2_ENCODER
2637     } else if (!strcmp(ext, ".mpg")) {
2638       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2639       mpg->SetInput(image);
2640       mpg->SetFileName(fileName.toStdString().c_str());
2641       mpg->Start();
2642
2643       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2644       int nSlice = vvImg->GetVTKImages().size();
2645       for(int i=0; i<nSlice; i++) {
2646         mSlicerManagers[smIndex]->SetNextTSlice(0);
2647         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2648         w2i->SetInput(widget->GetRenderWindow());
2649         w2i->Update();
2650         mpg->SetInput(w2i->GetOutput());
2651         mpg->Write();
2652       }
2653       mpg->End();
2654       mpg->Delete();
2655 #endif
2656     } else {
2657       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2658     }
2659   }
2660 }
2661 //------------------------------------------------------------------------------
2662
2663
2664 //------------------------------------------------------------------------------
2665 void vvMainWindow::GoToCursor()
2666 {
2667   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2668   for (int column = 1; column < 5; column++) {
2669     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2670       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2671       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2672         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2673       mSlicerManagers[index]->UpdateViews(1,column-1);
2674       mSlicerManagers[index]->UpdateLinked(column-1);
2675       break;
2676     }
2677   }
2678 }
2679 //------------------------------------------------------------------------------
2680
2681 //------------------------------------------------------------------------------
2682 void vvMainWindow::PlayPause()
2683 {
2684   if (playMode) {
2685     playMode = 0;
2686     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2687     ImageInfoChanged();
2688     return;
2689   } else {
2690     int image_number=DataTree->topLevelItemCount();
2691     bool has_temporal;
2692     for (int i=0; i<image_number; i++)
2693       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2694         has_temporal=true;
2695         break;
2696       }
2697     if (has_temporal) {
2698       playMode = 1;
2699       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2700       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2701     }
2702   }
2703 }
2704 //------------------------------------------------------------------------------
2705
2706 //------------------------------------------------------------------------------
2707 void vvMainWindow::PlayNext()
2708 {
2709   if (playMode && !this->isHidden()) {
2710     int image_number=DataTree->topLevelItemCount();
2711     ///Only play one slicer per SM, and only if the SM is being displayed
2712     for (int i=0; i<image_number; i++)
2713       for (int j=0; j<4; j++)
2714         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2715             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2716           mSlicerManagers[i]->SetNextTSlice(j);
2717           break;
2718         }
2719     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2720   }
2721 }
2722 //------------------------------------------------------------------------------
2723
2724 void vvMainWindow::ShowLastImage()
2725 {
2726   if (mSlicerManagers.size() > 1) {
2727     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2728     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2729     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2730     DisplayChanged(item,1);
2731   }
2732 }
2733
2734 //------------------------------------------------------------------------------
2735 void vvMainWindow::UpdateRenderWindows()
2736 {
2737   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2738   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2739   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2740   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2741 }
2742 //------------------------------------------------------------------------------
2743
2744 //------------------------------------------------------------------------------
2745 void vvMainWindow::SegmentationOnCurrentImage()
2746 {
2747   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2748
2749   vvSegmentationDialog segmentation;
2750   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2751   segmentation.exec();
2752 }
2753 //------------------------------------------------------------------------------
2754
2755 void vvMainWindow::SurfaceViewerLaunch()
2756 {
2757   vvSurfaceViewerDialog surfaceViewer;
2758   surfaceViewer.exec();
2759 }
2760 //------------------------------------------------------------------------------
2761
2762
2763 //------------------------------------------------------------------------------
2764 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2765 {
2766   int number=0;
2767   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2768     vvSlicerManager * v = mSlicerManagers[l];
2769     if (v->GetBaseFileName() ==
2770         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2771       number = std::max(number, v->GetBaseFileNameNumber()+1);
2772     }
2773   }
2774   return number;
2775 }
2776 //------------------------------------------------------------------------------
2777
2778
2779 //------------------------------------------------------------------------------
2780 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2781 {
2782   // Change filename if another image exist with the same name
2783   int number = GetImageDuplicateFilenameNumber(filename);
2784
2785   // Create new SliceManager
2786   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2787   slicer_manager->SetImage(image);//, IMAGE, number);
2788   //  filename = filename+"_"+clitk::toString(number);
2789   slicer_manager->SetFilename(filename, number);
2790   mSlicerManagers.push_back(slicer_manager);
2791
2792   //create an item in the tree with good settings
2793   QTreeWidgetItem *item = new QTreeWidgetItem();
2794   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2795   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2796   qApp->processEvents();
2797
2798   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2799
2800   //Create the buttons for reload and close
2801   qApp->processEvents();
2802   QTreePushButton* cButton = new QTreePushButton;
2803   cButton->setItem(item);
2804   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2805   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2806   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2807           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2808
2809   QTreePushButton* rButton = new QTreePushButton;
2810   rButton->setItem(item);
2811   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2812   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2813   rButton->setEnabled(0);
2814   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2815           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2816
2817   DataTree->addTopLevelItem(item);
2818   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2819   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2820
2821   //set the id of the image
2822   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2823   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2824   mSlicerManagers.back()->SetId(id.toStdString());
2825
2826   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2827                       , id.toStdString());
2828
2829   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2830           this, SLOT(CurrentImageChanged(std::string)));
2831   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2832           this, SLOT(CurrentPickedImageChanged(std::string)));
2833   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2834           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2835   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2836           this, SLOT(VectorChanged(int,double,double,double, double)));
2837   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2838           this, SLOT(OverlayChanged(int,double,double)));
2839   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2840           this, SLOT(FusionChanged(int,double)));
2841   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2842           this,SLOT(WindowsChanged(int, int, int)));
2843   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2844           this,SLOT(WindowLevelChanged(double, double, int, int)));
2845   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2846           this,SLOT(UpdateSlice(int,int)));
2847   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2848           this,SLOT(UpdateTSlice(int, int)));
2849   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2850           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2851   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2852           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2853   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2854           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2855   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2856           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2857   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2858   UpdateTree();
2859   qApp->processEvents();
2860   InitSlicers();
2861   ShowLastImage();
2862   InitDisplay();
2863   qApp->processEvents();
2864
2865   // End
2866   ImageInfoChanged();
2867   return slicer_manager;
2868 }
2869 //------------------------------------------------------------------------------
2870
2871
2872 //------------------------------------------------------------------------------
2873 void vvMainWindow::UpdateCurrentSlicer()
2874 {
2875   int index = -1;
2876   if (DataTree->selectedItems().size() > 0) {
2877     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2878   }
2879   mSlicerManagerCurrentIndex = index;
2880 }
2881 //------------------------------------------------------------------------------
2882