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->setData(1,Qt::UserRole,tr("image"));
 869         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 870         qApp->processEvents();
 871
 872         //Create the buttons for reload and close
 873         qApp->processEvents();
 874         QTreePushButton* cButton = new QTreePushButton;
 875         cButton->setItem(item);
 876         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 877         cButton->setToolTip(tr("close image"));
 878         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 879         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 880                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 881
 882         QTreePushButton* rButton = new QTreePushButton;
 883         rButton->setItem(item);
 884         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 885         rButton->setToolTip(tr("reload image"));
 886         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 887         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 888                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 889
 890         DataTree->addTopLevelItem(item);
 891         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 892         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 893
 894         //set the id of the image
 895         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 896         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 897         mSlicerManagers.back()->SetId(id.toStdString());
 898
 899         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 900
 901         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 902                 this,SLOT(CurrentImageChanged(std::string)));
 903         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 904                 this, SLOT(CurrentPickedImageChanged(std::string)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 906                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 907         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 908                 this, SLOT(VectorChanged(int,double,double,double, double)));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 910                 this, SLOT(OverlayChanged(int,double,double)));
 911         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 912                 this, SLOT(FusionChanged(int,double)));
 913         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 914                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 916                 this,SLOT(UpdateSlice(int,int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 918                 this,SLOT(UpdateTSlice(int, int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 920                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 922                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 923         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 924                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 925         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 926                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 927         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 928         InitSlicers();
 929         numberofsuccesulreads++;
 930       }
 931     }
 932   }
 933   if (numberofsuccesulreads) {
 934     NOViewWidget->show();
 935     NEViewWidget->show();
 936     SOViewWidget->show();
 937     SEViewWidget->show();
 938     UpdateTree();
 939     InitDisplay();
 940     ShowLastImage();
 941
 942     // Try to guess default WindowLevel
 943     double range[2];
 944     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 945     if ((range[0] == 0) && (range[1] == 1)) {
 946       presetComboBox->setCurrentIndex(5);// binary
 947     } else {
 948       // TODO
 949     }
 950   }
 951   QApplication::restoreOverrideCursor();
 952 }
 953 //------------------------------------------------------------------------------
 954
 955 //------------------------------------------------------------------------------
 956 void vvMainWindow::UpdateTree()
 957 {
 958   DataTree->resizeColumnToContents(COLUMN_TREE);
 959   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 963   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 964   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 965   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 966 }
 967 //------------------------------------------------------------------------------
 968
 969 //------------------------------------------------------------------------------
 970 void vvMainWindow::CurrentImageChanged(std::string id)
 971 {
 972   if (id == mCurrentSelectedImageId) return; // Do nothing
 973   int selected = 0;
 974   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 975     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 976       selected = i;
 977     } else {
 978       DataTree->topLevelItem(i)->setSelected(0);
 979     }
 980     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 981       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 982
 983   }
 984   DataTree->topLevelItem(selected)->setSelected(1);
 985   mCurrentSelectedImageId = id;
 986   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 987 }
 988 //------------------------------------------------------------------------------
 989
 990 //------------------------------------------------------------------------------
 991 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 992 {
 993   if (id == mCurrentPickedImageId) return; // Do nothing
 994   int selected = 0;
 995   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 996     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 997       selected = i;
 998     } else {
 999       DataTree->topLevelItem(i)->setSelected(0);
1000     }
1001     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1002       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1003
1004   }
1005   DataTree->topLevelItem(selected)->setSelected(1);
1006   mCurrentPickedImageId = id;
1007   mCurrentPickedImageIndex = selected;
1008 }
1009 //------------------------------------------------------------------------------
1010
1011 //------------------------------------------------------------------------------
1012 void vvMainWindow::ImageInfoChanged()
1013 {
1014   contextActions[6]->setEnabled(1);
1015   contextActions[5]->setEnabled(1);
1016   actionSave_As->setEnabled(1);
1017   actionAdd_VF_to_current_Image->setEnabled(1);
1018   actionAdd_fusion_image->setEnabled(1);
1019   actionNorth_East_Window->setEnabled(1);
1020   actionNorth_West_Window->setEnabled(1);
1021   actionSouth_East_Window->setEnabled(1);
1022   actionSouth_West_Window->setEnabled(1);
1023   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1024   inverseButton->setEnabled(1);
1025
1026   goToCursorPushButton->setEnabled(1);
1027
1028   if (DataTree->selectedItems().size()) {
1029     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1030
1031     colorMapComboBox->setEnabled(1);
1032     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1033       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1034           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1035         colorMapComboBox->setEnabled(0);
1036         break;
1037       }
1038     }
1039
1040     std::vector<double> origin;
1041     std::vector<double> inputSpacing;
1042     std::vector<int> inputSize;
1043     std::vector<double> sizeMM;
1044     vtkSmartPointer<vtkMatrix4x4> transformation;
1045     int dimension=0;
1046     QString pixelType;
1047     QString inputSizeInBytes;
1048     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1049
1050     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1051       playButton->setEnabled(1);
1052       frameRateLabel->setEnabled(1);
1053       frameRateSpinBox->setEnabled(1);
1054     } else {
1055       playButton->setEnabled(0);
1056       frameRateLabel->setEnabled(0);
1057       frameRateSpinBox->setEnabled(0);
1058     }
1059
1060     //read image header
1061     int NPixel = 1;
1062
1063     vvImage::Pointer imageSelected;
1064     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1065       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1066     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1067       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1068     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1069       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1070     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1071       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1072     }
1073     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1074       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1075     }
1076     else {
1077       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1078     }
1079
1080     dimension = imageSelected->GetNumberOfDimensions();
1081     origin.resize(dimension);
1082     inputSpacing.resize(dimension);
1083     inputSize.resize(dimension);
1084     sizeMM.resize(dimension);
1085     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1086     for (int i = 0; i < dimension; i++) {
1087       origin[i] = imageSelected->GetOrigin()[i];
1088       inputSpacing[i] = imageSelected->GetSpacing()[i];
1089       inputSize[i] = imageSelected->GetSize()[i];
1090       sizeMM[i] = inputSize[i]*inputSpacing[i];
1091       NPixel *= inputSize[i];
1092     }
1093     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1094
1095     QString dim = QString::number(dimension) + " (";
1096     dim += pixelType + ")";
1097
1098     infoPanel->setFileName(image);
1099     infoPanel->setDimension(dim);
1100     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1101     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1102     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1103     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1104     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1105     transformation = imageSelected->GetTransform()->GetMatrix();
1106     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1107
1108     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1109                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1110     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1111     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1112
1113     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1114     for (int i = 0; i < 4; i++) {
1115       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1116         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1117         break;
1118       }
1119     }
1120     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1121     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1122     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1123     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1124
1125     infoPanel->setFileName(image);
1126     infoPanel->setDimension(dim);
1127     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1128     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1129     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1130     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1131     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1132
1133     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1134                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1135     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1136     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1137
1138     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1139     for (int i = 0; i < 4; i++) {
1140       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1141         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1142         break;
1143       }
1144     }
1145     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1146     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1147     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1148     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1149
1150     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1151       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1152       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1153                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1154                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1155     } else {
1156       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1157       overlayPanel->getVFProperty(-1,-1,-1);
1158     }
1159     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1160       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1161       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1162     } else {
1163       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1164       overlayPanel->getOverlayProperty(-1);
1165     }
1166     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1167       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1168       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1169                                       mSlicerManagers[index]->GetFusionColorMap(),
1170                                       mSlicerManagers[index]->GetFusionWindow(),
1171                                       mSlicerManagers[index]->GetFusionLevel());
1172     } else {
1173       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1174       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1175     }
1176   }
1177 }
1178 //------------------------------------------------------------------------------
1179
1180 //------------------------------------------------------------------------------
1181 void vvMainWindow::ShowDocumentation()
1182 {
1183   documentation->show();
1184 }
1185 //------------------------------------------------------------------------------
1186
1187 //------------------------------------------------------------------------------
1188 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1189 {
1190   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1191   if(!checkCanPush) {
1192     registerForm->show();
1193   } else {
1194     if(registerForm->canPush()) {
1195       registerForm->show();
1196       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1197     }
1198   }
1199 }
1200 //------------------------------------------------------------------------------
1201
1202 //------------------------------------------------------------------------------
1203 void vvMainWindow::ShowHelpDialog()
1204 {
1205   help_dialog->show();
1206 }
1207 //------------------------------------------------------------------------------
1208
1209 //------------------------------------------------------------------------------
1210 void vvMainWindow::ChangeViewMode()
1211 {
1212   QList<int> size;
1213   if (viewMode == 1) {
1214     viewMode = 0;
1215     size.push_back(1);
1216     size.push_back(0);
1217     splitter_3->setSizes(size);
1218     OSplitter->setSizes(size);
1219     DataTree->setColumnHidden(2,1);
1220     DataTree->setColumnHidden(3,1);
1221     DataTree->setColumnHidden(4,1);
1222   } else {
1223     viewMode = 1;
1224     size.push_back(1);
1225     size.push_back(1);
1226     splitter_3->setSizes(size);
1227     OSplitter->setSizes(size);
1228     DataTree->setColumnHidden(2,0);
1229     DataTree->setColumnHidden(3,0);
1230     DataTree->setColumnHidden(4,0);
1231   }
1232   UpdateRenderWindows();
1233   /*
1234   ** I don't know why but for both resized QVTKWidget we also need to render
1235   ** the associated Slicer to redraw crosses.
1236   */
1237   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1238     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1239       mSlicerManagers[i]->GetSlicer(0)->Render();
1240     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1241       mSlicerManagers[i]->GetSlicer(2)->Render();
1242   }
1243 }
1244 //------------------------------------------------------------------------------
1245
1246 //------------------------------------------------------------------------------
1247 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1248 {
1249   QString result = "";// QString::number(size);
1250   //result += " bytes (";
1251   if (size > 1000000000) {
1252     size /= 1000000000;
1253     result += QString::number(size);
1254     result += "Gb";//)";
1255   } else if (size > 1000000) {
1256     size /= 1000000;
1257     result += QString::number(size);
1258     result += "Mb";//)";
1259   } else if (size > 1000) {
1260     size /= 1000;
1261     result += QString::number(size);
1262     result += "kb";//)";
1263   }
1264   return result;
1265 }
1266 //------------------------------------------------------------------------------
1267
1268 //------------------------------------------------------------------------------
1269 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1270 {
1271   std::ostringstream strmatrix;
1272
1273   for (unsigned int i = 0; i < 4; i++) {
1274     for (unsigned int j = 0; j < 4; j++) {
1275       strmatrix.flags(ios::showpos);
1276       strmatrix.width(10);
1277       strmatrix.precision(3);
1278       strmatrix.setf(ios::fixed,ios::floatfield);
1279       strmatrix.fill(' ');
1280       strmatrix << std::left << matrix->GetElement(i, j);
1281       //strmatrix.width(10);
1282       strmatrix << " ";
1283     }
1284     strmatrix << std::endl;
1285   }
1286   QString result = strmatrix.str().c_str();
1287   return result;
1288 }
1289 //------------------------------------------------------------------------------
1290
1291 //------------------------------------------------------------------------------
1292 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1293 {
1294   QString result;
1295   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1296     if (i != 0)
1297       result += " ";
1298     result += QString::number(vectorDouble[i]);
1299   }
1300   return result;
1301 }
1302 //------------------------------------------------------------------------------
1303
1304 //------------------------------------------------------------------------------
1305 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1306 {
1307   QString result;
1308   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1309     if (i != 0)
1310       result += " ";
1311     result += QString::number(vectorInt[i]);
1312   }
1313   return result;
1314 }
1315 //------------------------------------------------------------------------------
1316
1317 //------------------------------------------------------------------------------
1318 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1319 {
1320   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1321   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1322     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1323       return i;
1324   }
1325   return -1;
1326 }
1327 //------------------------------------------------------------------------------
1328
1329 //------------------------------------------------------------------------------
1330 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1331 {
1332   QString id = sm->GetId().c_str();
1333   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1334     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1335       return DataTree->topLevelItem(i);
1336   }
1337   return NULL;
1338 }
1339 //------------------------------------------------------------------------------
1340
1341 //------------------------------------------------------------------------------
1342 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1343 {
1344   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1345     return;
1346
1347   // Get parent information (might be the same item)
1348   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1349   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1350   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1351
1352   // Go over the complete item tree (only 2 levels, parents and children)
1353   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1354     // Trick to avoid redoing twice the job for a key (sr)
1355     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1356
1357     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1358     if(currentParentItem != clickedParentItem) {
1359       // Not the branch of the clicked item, uncheck all
1360
1361       // Parent
1362       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1363       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1364
1365       // Children
1366       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1367         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1368       }
1369     }
1370     else {
1371       // Branch of the clicked one: get check status from actor visibility in slicer
1372       // and toggle the clicked one
1373
1374       // Parent
1375       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1376       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1377
1378       // Update slicer (after getting visibility)
1379       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1380       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1381       DisplaySliders(slicerManagerIndex, column-1);
1382       if(clickedParentItem == clickedItem) {
1383         // Toggle
1384         vis = !draw || !vis;
1385       }
1386       clickedSlicer->SetActorVisibility("image", 0, vis);
1387       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1388
1389       // Children
1390       std::map<std::string, int> actorTypeCounts;
1391       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1392         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1393         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1394         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1395         if(currentChildItem == clickedItem) {
1396           // Toggle or force visibility if it was not on this branch so far
1397           vis = !draw || !vis;
1398           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1399         }
1400         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1401         actorTypeCounts[actorType]++;
1402       }
1403     }
1404   }
1405
1406   clickedSlicer->Render();
1407 }
1408 //------------------------------------------------------------------------------
1409
1410 void vvMainWindow::InitSlicers()
1411 {
1412   if (mSlicerManagers.size()) {
1413     mSlicerManagers.back()->GenerateDefaultLookupTable();
1414
1415     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1416     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1417     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1418     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1419   }
1420 }
1421
1422 //------------------------------------------------------------------------------
1423 void vvMainWindow::InitDisplay()
1424 {
1425   if (mSlicerManagers.size()) {
1426     //BE CAREFUL : this is absolutely necessary to set the interactor style
1427     //in order to have the same style instanciation for all SlicerManagers in
1428     // a same window
1429     for (int j = 0; j < 4; j++) {
1430       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1431       style->SetAutoAdjustCameraClippingRange(1);
1432       bool AlreadySelected = false;
1433       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1434         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1435
1436         //select the image only if previous are not selected
1437         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1438           mSlicerManagers[i]->UpdateSlicer(j,1);
1439           AlreadySelected = true;
1440         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1441           if (DataTree->selectedItems().size() == 0)
1442             DataTree->topLevelItem(i)->setSelected(1);
1443           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1444           mSlicerManagers[i]->UpdateSlicer(j,1);
1445           DisplaySliders(i,j);
1446         } else {
1447           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1448           mSlicerManagers[i]->UpdateSlicer(j,0);
1449         }
1450       }
1451       style->Delete();
1452     }
1453   }
1454 }
1455 //------------------------------------------------------------------------------
1456
1457 //------------------------------------------------------------------------------
1458 void vvMainWindow::DisplaySliders(int slicer, int window)
1459 {
1460   int range[2];
1461   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1462   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1463
1464   int tRange[2];
1465   tRange[0] = 0;
1466   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1467   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1468   bool showHorizontal = false;
1469   bool showVertical = false;
1470   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1471       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1472           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1473           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1474     showVertical = true;
1475   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1476       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1477       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1478     showHorizontal = true;
1479
1480   if (showVertical)
1481     verticalSliders[window]->show();
1482   else
1483     verticalSliders[window]->hide();
1484   verticalSliders[window]->setRange(range[0],range[1]);
1485   verticalSliders[window]->setValue(position);
1486
1487   if (showHorizontal)
1488     horizontalSliders[window]->show();
1489   else
1490     horizontalSliders[window]->hide();
1491   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1492   horizontalSliders[window]->setValue(tPosition);
1493 }
1494 //------------------------------------------------------------------------------
1495
1496 //------------------------------------------------------------------------------
1497 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1498 {
1499   int index = GetSlicerIndexFromItem(item);
1500
1501   if (DataTree->topLevelItem(index) != item) {
1502     QString warning = "Do you really want to close the overlay : ";
1503     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1504     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1505                        warning, 0, this);
1506     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1507     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1508     if (msgBox.exec() == QMessageBox::AcceptRole) {
1509       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1510       int overlay_index=0;
1511       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1512         if (DataTree->topLevelItem(index)->\
1513             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1514           overlay_index++;
1515         if (DataTree->topLevelItem(index)->child(child) == item) break;
1516       }
1517       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1518       mSlicerManagers[index]->SetColorMap(0);
1519       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1520       mSlicerManagers[index]->Render();
1521     }
1522   } else if (DataTree->topLevelItemCount() <= 1) {
1523     QString warning = "Do you really want to close the image : ";
1524     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1525     warning += "\nThis is the last image, you're about to close vv !!!";
1526     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1527                        warning, 0, this);
1528     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1529     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1530     if (msgBox.exec() == QMessageBox::AcceptRole) {
1531       this->close();
1532     }
1533   } else {
1534     QString warning = "Do you really want to close the image : ";
1535     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1536     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1537                        warning, 0, this);
1538     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1539     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1540     if (msgBox.exec() == QMessageBox::AcceptRole) {
1541
1542       // Tell tools that we close an image
1543       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1544
1545       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1546       DataTree->takeTopLevelItem(index);
1547       for (int i = 0; i < index; i++) {
1548         Manageriter++;
1549       }
1550       linkPanel->removeImage(index);
1551       mSlicerManagers[index]->RemoveActors();
1552       delete mSlicerManagers[index];
1553       mSlicerManagers.erase(Manageriter);
1554
1555       //
1556       InitDisplay();
1557     }
1558   }
1559   ImageInfoChanged();
1560 }
1561 //------------------------------------------------------------------------------
1562
1563 //------------------------------------------------------------------------------
1564 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1565 {
1566   // int index = GetSlicerIndexFromItem(item);
1567   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1568   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1569   //     mSlicerManagers[index]->ReloadVF();
1570   //   else
1571   //     mSlicerManagers[index]->Reload();
1572
1573   //   QApplication::restoreOverrideCursor();
1574   int index = GetSlicerIndexFromItem(item);
1575   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1576   QString role=item->data(1,Qt::UserRole).toString();
1577   if ( role == "vector"){
1578     mSlicerManagers[index]->ReloadVF();
1579   }
1580   else if (role == "overlay"){
1581     mSlicerManagers[index]->ReloadOverlay();
1582   }
1583   else if (role == "fusion"){
1584     mSlicerManagers[index]->ReloadFusion();
1585   }
1586   else{
1587     mSlicerManagers[index]->Reload();
1588   }
1589   // Update view and info
1590   ImageInfoChanged();
1591   mSlicerManagers[index]->Render();
1592   QApplication::restoreOverrideCursor();
1593 }
1594 //------------------------------------------------------------------------------
1595
1596 //------------------------------------------------------------------------------
1597 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1598 {
1599   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1600 }
1601 //------------------------------------------------------------------------------
1602
1603 //------------------------------------------------------------------------------
1604 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1605 {
1606   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1607 }
1608 //------------------------------------------------------------------------------
1609
1610 //------------------------------------------------------------------------------
1611 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1612 {
1613   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1614 }
1615 //------------------------------------------------------------------------------
1616
1617 //------------------------------------------------------------------------------
1618 void vvMainWindow::FusionChanged(int visibility, double value)
1619 {
1620   overlayPanel->getCurrentFusionInfo(visibility,value);
1621 }
1622 //------------------------------------------------------------------------------
1623
1624 //------------------------------------------------------------------------------
1625 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1626 {
1627   windowSpinBox->setValue(window);
1628   levelSpinBox->setValue(level);
1629   colorMapComboBox->setCurrentIndex(colormap);
1630   presetComboBox->setCurrentIndex(preset);
1631 }
1632 //------------------------------------------------------------------------------
1633
1634 //------------------------------------------------------------------------------
1635 void vvMainWindow::WindowLevelEdited()
1636 {
1637   presetComboBox->setCurrentIndex(6);
1638   UpdateWindowLevel();
1639 }
1640 //------------------------------------------------------------------------------
1641
1642 //------------------------------------------------------------------------------
1643 void vvMainWindow::UpdateWindowLevel()
1644 {
1645   if (DataTree->selectedItems().size()) {
1646     if (presetComboBox->currentIndex() == 7) //For ventilation
1647       colorMapComboBox->setCurrentIndex(5);
1648     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1649     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1650     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1651     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1652     mSlicerManagers[index]->Render();
1653     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1654     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1655   }
1656 }
1657 //------------------------------------------------------------------------------
1658
1659 //------------------------------------------------------------------------------
1660 void vvMainWindow::UpdateColorMap()
1661 {
1662   if (DataTree->selectedItems().size()) {
1663     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1664     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1665     mSlicerManagers[index]->Render();
1666   }
1667 }
1668 //------------------------------------------------------------------------------
1669 void vvMainWindow::SwitchWindowLevel()
1670 {
1671   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1672   int window = mSlicerManagers[index]->GetColorWindow();
1673   presetComboBox->setCurrentIndex(6);
1674   windowSpinBox->setValue(-window);
1675   UpdateWindowLevel();
1676 }
1677 //------------------------------------------------------------------------------
1678
1679 //------------------------------------------------------------------------------
1680 void vvMainWindow::ApplyWindowLevelToAllImages()
1681 {
1682   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1683     if (mSlicerManagers[i] == NULL)
1684       continue;
1685     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1686     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1687     mSlicerManagers[i]->SetPreset(6);
1688     mSlicerManagers[i]->Render();
1689   }
1690 }
1691 //------------------------------------------------------------------------------
1692
1693 //------------------------------------------------------------------------------
1694 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1695 {
1696   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1697     if (mSlicerManagers[i]->GetId() == id) {
1698       //mSlicerManagers[i]->SetTSlice(temps);
1699       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1700       mSlicerManagers[i]->UpdateViews(0,slicer);
1701       break;
1702     }
1703   }
1704 }
1705 //------------------------------------------------------------------------------
1706
1707 //------------------------------------------------------------------------------
1708 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1709 {
1710   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1711     if (id == mSlicerManagers[i]->GetId()) {
1712       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1713     }
1714   }
1715 }
1716 //------------------------------------------------------------------------------
1717
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::ShowContextMenu(QPoint point)
1720 {
1721   if (!DataTree->selectedItems().size()) {
1722     contextActions[1]->setEnabled(0);
1723     contextActions[2]->setEnabled(0);
1724     contextActions[3]->setEnabled(0);
1725     contextActions[4]->setEnabled(0);
1726     contextActions[5]->setEnabled(0);
1727     contextActions[6]->setEnabled(0);
1728   } else {
1729     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1730     contextActions[1]->setEnabled(1);
1731     contextActions[2]->setEnabled(
1732       DataTree->itemWidget(DataTree->selectedItems()[0],
1733                            COLUMN_RELOAD_IMAGE)->isEnabled());
1734     contextActions[3]->setEnabled(1);
1735     contextActions[5]->setEnabled(1);
1736     contextActions[6]->setEnabled(1);
1737
1738     if (mSlicerManagers[index]->GetDimension() < 3)
1739       contextActions[4]->setEnabled(0);
1740     else
1741       contextActions[4]->setEnabled(1);
1742   }
1743   contextMenu.exec(QCursor::pos());
1744 }
1745 //------------------------------------------------------------------------------
1746
1747 //------------------------------------------------------------------------------
1748 void vvMainWindow::CloseImage()
1749 {
1750   CloseImage(DataTree->selectedItems()[0],0);
1751 }
1752 //------------------------------------------------------------------------------
1753
1754 //------------------------------------------------------------------------------
1755 void vvMainWindow::ReloadImage()
1756 {
1757   ReloadImage(DataTree->selectedItems()[0],0);
1758 }
1759 //------------------------------------------------------------------------------
1760
1761 //------------------------------------------------------------------------------
1762 void vvMainWindow::SelectOverlayImage()
1763 {
1764   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1765
1766   //check if one overlay image is added
1767   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1768     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1769       QString error = "Cannot add more than one compared image\n";
1770       error += "Please remove first ";
1771       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1772       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1773       return;
1774     }
1775
1776   QString Extensions = EXTENSIONS;
1777   Extensions += ";;All Files (*)";
1778   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1779   if (!file.isEmpty())
1780     AddOverlayImage(index,file);
1781 }
1782 //------------------------------------------------------------------------------
1783
1784 //------------------------------------------------------------------------------
1785 void vvMainWindow::AddOverlayImage(int index, QString file)
1786 {
1787
1788   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1789   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1790                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1791   reader->SetFileName(file.toStdString().c_str());
1792   reader->ReadImageInformation();
1793   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1794   int dimension = reader->GetNumberOfDimensions();
1795   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1796   vvProgressDialog progress("Opening " + file.toStdString());
1797   qApp->processEvents();
1798
1799   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1800   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1801     //create an item in the tree with good settings
1802     QTreeWidgetItem *item = new QTreeWidgetItem();
1803     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1804     item->setData(1,Qt::UserRole,tr("overlay"));
1805     QFileInfo fileinfo(file); //Do not show the path
1806     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1807     item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1808     qApp->processEvents();
1809
1810     for (int j = 1; j <= 4; j++) {
1811       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1812     }
1813
1814     //Create the buttons for reload and close
1815     qApp->processEvents();
1816     QTreePushButton* cButton = new QTreePushButton;
1817     cButton->setItem(item);
1818     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1819     cButton->setToolTip(tr("close image"));
1820     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1821     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1822             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1823
1824     QTreePushButton* rButton = new QTreePushButton;
1825     rButton->setItem(item);
1826     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1827     rButton->setToolTip(tr("reload image"));
1828     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1829     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1830             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1831
1832     DataTree->topLevelItem(index)->setExpanded(1);
1833     DataTree->topLevelItem(index)->addChild(item);
1834     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1835     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1836
1837     //set the id of the image
1838     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1839     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1840     UpdateTree();
1841     qApp->processEvents();
1842     ImageInfoChanged();
1843     QApplication::restoreOverrideCursor();
1844   } else {
1845     QApplication::restoreOverrideCursor();
1846     QString error = "Cannot import the new image.\n";
1847     error += mSlicerManagers[index]->GetLastError().c_str();
1848     QMessageBox::information(this,tr("Problem reading image !"),error);
1849   }
1850 }
1851 //------------------------------------------------------------------------------
1852
1853
1854 //------------------------------------------------------------------------------
1855 void vvMainWindow::AddROI(int index, QString file)
1856 {
1857   /*
1858   // Get slice manager
1859
1860   // Load image
1861
1862   vvImageReader * mReader = new vvImageReader;
1863   mReader->SetInputFilename(filename.toStdString());
1864   mReader->Update(IMAGE);
1865   if (mReader->GetLastError().size() != 0) {
1866     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1867     QString error = "Cannot open file \n";
1868     error += mReader->GetLastError().c_str();
1869     QMessageBox::information(this,tr("Reading problem"),error);
1870     delete mReader;
1871     return;
1872   }
1873   vvImage::Pointer roi = mReader->GetOutput();
1874
1875   // Create roi in new tool
1876   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1877   */
1878 }
1879 //------------------------------------------------------------------------------
1880
1881 //------------------------------------------------------------------------------
1882 void vvMainWindow::SelectFusionImage()
1883 {
1884   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1885
1886   //check if one fusion image is added
1887   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1888     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1889       QString error = "Cannot add more than one fusion image\n";
1890       error += "Please remove first ";
1891       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1892       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1893       return;
1894     }
1895
1896   QString Extensions = EXTENSIONS;
1897   Extensions += ";;All Files (*)";
1898   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1899   if (!file.isEmpty())
1900     AddFusionImage(index,file);
1901 }
1902 //------------------------------------------------------------------------------
1903
1904 //------------------------------------------------------------------------------
1905 void vvMainWindow::AddFusionImage(int index, QString file)
1906 {
1907   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1908   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1909                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1910   reader->SetFileName(file.toStdString().c_str());
1911   reader->ReadImageInformation();
1912   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1913   if (reader) {
1914     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1915     vvProgressDialog progress("Opening fusion");
1916     qApp->processEvents();
1917
1918     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1919     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1920                                           reader->GetNumberOfDimensions(), component)) {
1921       //create an item in the tree with good settings
1922       QTreeWidgetItem *item = new QTreeWidgetItem();
1923       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1924       item->setData(1,Qt::UserRole,tr("fusion"));
1925       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1926       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1927       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
1928       qApp->processEvents();
1929
1930       for (int j = 1; j <= 4; j++) {
1931         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1932       }
1933
1934       //Create the buttons for reload and close
1935       qApp->processEvents();
1936       QTreePushButton* cButton = new QTreePushButton;
1937       cButton->setItem(item);
1938       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1939       cButton->setToolTip(tr("close image"));
1940       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1941       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1942               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1943
1944       QTreePushButton* rButton = new QTreePushButton;
1945       rButton->setItem(item);
1946       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1947       rButton->setToolTip(tr("reload image"));
1948       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1949       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1950               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1951
1952       DataTree->topLevelItem(index)->setExpanded(1);
1953       DataTree->topLevelItem(index)->addChild(item);
1954       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1955       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1956
1957       //set the id of the image
1958       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1959       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1960       UpdateTree();
1961       qApp->processEvents();
1962       ImageInfoChanged();
1963       QApplication::restoreOverrideCursor();
1964     } else {
1965       QApplication::restoreOverrideCursor();
1966       QString error = "Cannot import the new image.\n";
1967       error += mSlicerManagers[index]->GetLastError().c_str();
1968       QMessageBox::information(this,tr("Problem reading image !"),error);
1969     }
1970   } else {
1971     QString error = "Cannot import the new image.\n";
1972     QMessageBox::information(this,tr("Problem reading image !"),error);
1973   }
1974 }
1975 //------------------------------------------------------------------------------
1976
1977
1978 //------------------------------------------------------------------------------
1979 void vvMainWindow::OpenField()
1980 {
1981   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1982   //check if a vector field has already been added
1983   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1984     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1985       QString error = "Cannot add more than one vector field\n";
1986       error += "Please remove first ";
1987       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1988       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1989       return;
1990     }
1991
1992   QString Extensions = "Images ( *.mhd)";
1993   Extensions += ";;Images ( *.vf)";
1994   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1995   if (!file.isEmpty())
1996     AddField(file,index);
1997 }
1998 //------------------------------------------------------------------------------
1999
2000
2001 //------------------------------------------------------------------------------
2002 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2003 {
2004   //create an item in the tree with good settings
2005   QTreeWidgetItem *item = new QTreeWidgetItem();
2006   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2007   item->setData(1,Qt::UserRole,tr("vector"));
2008   QFileInfo fileinfo(filename); //Do not show the path
2009   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2010   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2011   qApp->processEvents();
2012
2013   for (int j = 1; j <= 4; j++) {
2014     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2015   }
2016
2017   //Create the buttons for reload and close
2018   qApp->processEvents();
2019   QTreePushButton* cButton = new QTreePushButton;
2020   cButton->setItem(item);
2021   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2022   cButton->setToolTip(tr("close vector field"));
2023   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2024   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2025           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2026
2027   QTreePushButton* rButton = new QTreePushButton;
2028   rButton->setItem(item);
2029   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2030   rButton->setToolTip(tr("reload vector field"));
2031   rButton->setEnabled(from_disk);
2032   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2033   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2034           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2035
2036   DataTree->topLevelItem(index)->setExpanded(1);
2037   DataTree->topLevelItem(index)->addChild(item);
2038   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2039   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2040
2041   //set the id of the image
2042   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2043   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2044   UpdateTree();
2045   qApp->processEvents();
2046   ImageInfoChanged();
2047   QApplication::restoreOverrideCursor();
2048 }
2049 //------------------------------------------------------------------------------
2050
2051
2052 //------------------------------------------------------------------------------
2053 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2054 {
2055   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2056   vvSlicerManager* imageManager = mSlicerManagers[index];
2057   if (imageManager->SetVF(vf,file.toStdString())) {
2058     AddFieldEntry(file,index,false);
2059   } else {
2060     QString error = "Cannot import the vector field for this image.\n";
2061     error += imageManager->GetLastError().c_str();
2062     QMessageBox::information(this,tr("Problem reading VF !"),error);
2063   }
2064   QApplication::restoreOverrideCursor();
2065 }
2066 //------------------------------------------------------------------------------
2067
2068
2069 //------------------------------------------------------------------------------
2070 void vvMainWindow::AddField(QString file,int index)
2071 {
2072   if (QFile::exists(file)) {
2073     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2074
2075     //init the progress events
2076     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2077     vvProgressDialog progress("Opening " + file.toStdString());
2078     qApp->processEvents();
2079
2080     //read the vector and put it in the current mSlicerManager
2081     vvSlicerManager* imageManager = mSlicerManagers[index];
2082     qApp->processEvents();
2083
2084     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2085     if (imageManager->SetVF(file.toStdString())) {
2086       imageManager->Render();
2087       AddFieldEntry(file,index,true);
2088     } else {
2089       QApplication::restoreOverrideCursor();
2090       QString error = "Cannot import the vector field for this image.\n";
2091       error += imageManager->GetLastError().c_str();
2092       QMessageBox::information(this,tr("Problem reading VF !"),error);
2093     }
2094   } else
2095     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2096
2097 }
2098 //------------------------------------------------------------------------------
2099
2100
2101 //------------------------------------------------------------------------------
2102 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2103 {
2104   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2105   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2106     for (int i = 0; i < 4; i++) {
2107       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2108       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2109       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2110       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2111       if (log > 0)
2112         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2113       else
2114         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2115     }
2116   }
2117 }
2118 //------------------------------------------------------------------------------
2119
2120
2121 //------------------------------------------------------------------------------
2122 void vvMainWindow::SetOverlayProperty(int color)
2123 {
2124   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2125   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2126     mSlicerManagers[index]->SetOverlayColor(color);
2127     mSlicerManagers[index]->SetColorMap(0);
2128     mSlicerManagers[index]->Render();
2129   }
2130 }
2131 //------------------------------------------------------------------------------
2132
2133 //------------------------------------------------------------------------------
2134 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2135 {
2136   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2137   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2138     mSlicerManagers[index]->SetFusionOpacity(opacity);
2139     mSlicerManagers[index]->SetFusionColorMap(colormap);
2140     mSlicerManagers[index]->SetFusionWindow(window);
2141     mSlicerManagers[index]->SetFusionLevel(level);
2142     mSlicerManagers[index]->SetColorMap(0);
2143     mSlicerManagers[index]->Render();
2144   }
2145 }
2146 //------------------------------------------------------------------------------
2147
2148 //------------------------------------------------------------------------------
2149 void vvMainWindow::SaveAs()
2150 {
2151   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2152     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2153     return;
2154   }
2155
2156   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2157   int dimension = mSlicerManagers[index]->GetDimension();
2158   QStringList OutputListeFormat;
2159   OutputListeFormat.clear();
2160   if (dimension == 1) {
2161     OutputListeFormat.push_back(".mhd");
2162   }
2163   if (dimension == 2) {
2164     OutputListeFormat.push_back(".bmp");
2165     OutputListeFormat.push_back(".png");
2166     OutputListeFormat.push_back(".jpeg");
2167     OutputListeFormat.push_back(".tif");
2168     OutputListeFormat.push_back(".mhd");
2169     OutputListeFormat.push_back(".hdr");
2170     OutputListeFormat.push_back(".vox");
2171   } else if (dimension == 3) {
2172     OutputListeFormat.push_back(".mhd");
2173     OutputListeFormat.push_back(".hdr");
2174     OutputListeFormat.push_back(".vox");
2175   } else if (dimension == 4) {
2176     OutputListeFormat.push_back(".mhd");
2177   }
2178   QString Extensions = "AllFiles(*.*)";
2179   for (int i = 0; i < OutputListeFormat.count(); i++) {
2180     Extensions += ";;Images ( *";
2181     Extensions += OutputListeFormat[i];
2182     Extensions += ")";
2183   }
2184   QString fileName = QFileDialog::getSaveFileName(this,
2185                      tr("Save As"),
2186                      mSlicerManagers[index]->GetFileName().c_str(),
2187                      Extensions);
2188   if (!fileName.isEmpty()) {
2189     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2190     if (OutputListeFormat.contains(
2191           fileformat.c_str())) {
2192       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2193       std::string action = "Saving";
2194       vvProgressDialog progress("Saving "+fileName.toStdString());
2195       qApp->processEvents();
2196       vvImageWriter::Pointer writer = vvImageWriter::New();
2197       writer->SetOutputFileName(fileName.toStdString());
2198       writer->SetInput(mSlicerManagers[index]->GetImage());
2199       writer->Update();
2200       QApplication::restoreOverrideCursor();
2201       if (writer->GetLastError().size()) {
2202         QString error = "Saving did not succeed\n";
2203         error += writer->GetLastError().c_str();
2204         QMessageBox::information(this,tr("Saving Problem"),error);
2205         SaveAs();
2206       }
2207     } else {
2208       QString error = fileformat.c_str();
2209       if (error.isEmpty())
2210         error += "no file format specified !";
2211       else
2212         error += " format unknown !!!\n";
2213       QMessageBox::information(this,tr("Saving Problem"),error);
2214       SaveAs();
2215     }
2216   }
2217 }
2218 //------------------------------------------------------------------------------
2219
2220
2221 //------------------------------------------------------------------------------
2222 void vvMainWindow::AddLink(QString image1,QString image2)
2223 {
2224   unsigned int sm1 = 0;
2225   unsigned int sm2 = 0;
2226
2227   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2228     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2229       mSlicerManagers[i]->AddLink(image2.toStdString());
2230       sm1 = i;
2231     }
2232     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2233       mSlicerManagers[i]->AddLink(image1.toStdString());
2234       sm2 = i;
2235     }
2236   }
2237
2238   if (linkPanel->isLinkAll())   {
2239     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2240     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2241   } else {
2242     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2243   }
2244 }
2245
2246 //------------------------------------------------------------------------------
2247
2248
2249 //------------------------------------------------------------------------------
2250 void vvMainWindow::RemoveLink(QString image1,QString image2)
2251 {
2252   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2253     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2254       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2255     }
2256     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2257       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2258     }
2259   }
2260 }
2261 //------------------------------------------------------------------------------
2262
2263 //------------------------------------------------------------------------------
2264 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2265 {
2266   int index = 0;
2267   while(sm != mSlicerManagers[index])
2268     index++;
2269   index = (index+offset) % mSlicerManagers.size();
2270
2271   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2272   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2273   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2274   DisplayChanged(item,slicer+1);
2275 }
2276 //------------------------------------------------------------------------------
2277
2278 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2279 {
2280   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2281     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2282       for (int j = 0; j < 4; j++) {
2283         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2284         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2285         //UpdateTSlice(j,value);
2286       }
2287       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2288       break;
2289     }
2290   }
2291 }
2292 //------------------------------------------------------------------------------
2293
2294
2295 //------------------------------------------------------------------------------
2296 void vvMainWindow::NOHorizontalSliderMoved()
2297 {
2298   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2299   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2300 //  mCurrentTime = NOHorizontalSlider->value();
2301 }
2302 //------------------------------------------------------------------------------
2303
2304
2305 //------------------------------------------------------------------------------
2306 void vvMainWindow::NEHorizontalSliderMoved()
2307 {
2308   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2309   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2310 //  mCurrentTime = NEHorizontalSlider->value();
2311 }
2312 //------------------------------------------------------------------------------
2313
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::SOHorizontalSliderMoved()
2317 {
2318   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2319   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2320   // mCurrentTime = SOHorizontalSlider->value();
2321 }
2322 //------------------------------------------------------------------------------
2323
2324
2325 //------------------------------------------------------------------------------
2326 void vvMainWindow::SEHorizontalSliderMoved()
2327 {
2328   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2329   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2330   // mCurrentTime = SEHorizontalSlider->value();
2331 }
2332 //------------------------------------------------------------------------------
2333
2334 //------------------------------------------------------------------------------
2335 void vvMainWindow::NOVerticalSliderChanged()
2336 {
2337   static int value=-1;
2338   if (value == NOVerticalSlider->value()) return;
2339   else value = NOVerticalSlider->value();
2340   //  int value = NOVerticalSlider->value();
2341   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2342     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2343       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2344         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2345         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2346
2347         // If nor Update/Render -> slider not work
2348         // only render = ok navigation, but for contour Update needed but slower ?
2349
2350         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2351         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2352       }
2353       break;
2354     }
2355   }
2356 }
2357 //------------------------------------------------------------------------------
2358
2359
2360 //------------------------------------------------------------------------------
2361 void vvMainWindow::NEVerticalSliderChanged()
2362 {
2363   static int value=-1;
2364   if (value == NEVerticalSlider->value()) return;
2365   else value = NEVerticalSlider->value();
2366   //  int value = NEVerticalSlider->value();
2367   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2368     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2369       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2370         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2371         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2372         mSlicerManagers[i]->UpdateSlice(1);
2373         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2374       }
2375       break;
2376     }
2377   }
2378 }
2379 //------------------------------------------------------------------------------
2380
2381
2382 //------------------------------------------------------------------------------
2383 void vvMainWindow::SOVerticalSliderChanged()
2384 {
2385   static int value=-1;
2386   if (value == SOVerticalSlider->value()) return;
2387   else value = SOVerticalSlider->value();
2388   //int value = SOVerticalSlider->value();
2389   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2390     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2391       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2392         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2393         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2394         mSlicerManagers[i]->UpdateSlice(2);
2395         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2396       }
2397       // else { DD("avoid SOVerticalSlider slicer update"); }
2398       break;
2399     }
2400   }
2401 }
2402 //------------------------------------------------------------------------------
2403
2404
2405 //------------------------------------------------------------------------------
2406 void vvMainWindow::SEVerticalSliderChanged()
2407 {
2408   static int value=-1;
2409   if (value == SEVerticalSlider->value()) return;
2410   else value = SEVerticalSlider->value();
2411   // int value = SEVerticalSlider->value();
2412   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2413     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2414       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2415         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2416         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2417         mSlicerManagers[i]->UpdateSlice(3);
2418         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2419       }
2420       break;
2421     }
2422   }
2423 }
2424 //------------------------------------------------------------------------------
2425
2426
2427 //------------------------------------------------------------------------------
2428 void vvMainWindow::UpdateSlice(int slicer, int slice)
2429 {
2430   // DD("vvMainWindow::UpdateSlice");
2431 //   DD(slicer);
2432 //   DD(slice);
2433   if (slicer == 0) {
2434     //    if (slice != NOVerticalSlider->value())
2435     NOVerticalSlider->setValue(slice);
2436   } else {
2437     if (slicer == 1)
2438       NEVerticalSlider->setValue(slice);
2439     else {
2440       if (slicer == 2)
2441         SOVerticalSlider->setValue(slice);
2442       else {
2443         if (slicer == 3)
2444           SEVerticalSlider->setValue(slice);
2445       }
2446     }
2447   }
2448   // DD("vvMainWindow:UpdateSlice END");
2449 }
2450 //------------------------------------------------------------------------------
2451
2452
2453 //------------------------------------------------------------------------------
2454 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2455 {
2456   switch (slicer) {
2457   case 0:
2458     NOHorizontalSlider->setValue(slice);
2459     break;
2460   case 1:
2461     NEHorizontalSlider->setValue(slice);
2462     break;
2463   case 2:
2464     SOHorizontalSlider->setValue(slice);
2465     break;
2466   case 3:
2467     SEHorizontalSlider->setValue(slice);
2468     break;
2469   }
2470 }
2471 //------------------------------------------------------------------------------
2472
2473
2474 //------------------------------------------------------------------------------
2475 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2476 {
2477   int position = int((min+max)/2);
2478   int tPosition = int((tmin+tmax)/2);
2479   if (slicer == 0) {
2480     NOVerticalSlider->setValue(position);
2481     NOVerticalSlider->setRange(min,max);
2482     NOHorizontalSlider->setRange(tmin,tmax);
2483     NOHorizontalSlider->setValue(tPosition);
2484   } else if (slicer == 1) {
2485     NEVerticalSlider->setValue(position);
2486     NEVerticalSlider->setRange(min,max);
2487     NEHorizontalSlider->setRange(tmin,tmax);
2488     NEHorizontalSlider->setValue(tPosition);
2489   } else if (slicer == 2) {
2490     SOVerticalSlider->setValue(position);
2491     SOVerticalSlider->setRange(min,max);
2492     SOHorizontalSlider->setRange(tmin,tmax);
2493     SOHorizontalSlider->setValue(tPosition);
2494   } else if (slicer == 3) {
2495     SEVerticalSlider->setValue(position);
2496     SEVerticalSlider->setRange(min,max);
2497     SEHorizontalSlider->setRange(tmin,tmax);
2498     SEHorizontalSlider->setValue(tPosition);
2499   }
2500 }
2501 //------------------------------------------------------------------------------
2502
2503
2504 //------------------------------------------------------------------------------
2505 void vvMainWindow::SaveNOScreenshot()
2506 {
2507   SaveScreenshot(NOViewWidget);
2508 }
2509 //------------------------------------------------------------------------------
2510
2511
2512 //------------------------------------------------------------------------------
2513 void vvMainWindow::SaveNEScreenshot()
2514 {
2515   SaveScreenshot(NEViewWidget);
2516 }
2517 //------------------------------------------------------------------------------
2518
2519
2520 //------------------------------------------------------------------------------
2521 void vvMainWindow::SaveSOScreenshot()
2522 {
2523   SaveScreenshot(SOViewWidget);
2524 }
2525 //------------------------------------------------------------------------------
2526
2527
2528 //------------------------------------------------------------------------------
2529 void vvMainWindow::SaveSEScreenshot()
2530 {
2531   SaveScreenshot(SEViewWidget);
2532 }
2533 //------------------------------------------------------------------------------
2534
2535
2536 //------------------------------------------------------------------------------
2537 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2538 {
2539   QString Extensions = "Images( *.png);;";
2540   Extensions += "Images( *.jpg);;";
2541   Extensions += "Images( *.bmp);;";
2542   Extensions += "Images( *.tif);;";
2543   Extensions += "Images( *.ppm)";
2544 #ifdef VTK_USE_FFMPEG_ENCODER
2545   Extensions += "Images( *.avi)";
2546 #endif
2547 #ifdef VTK_USE_MPEG2_ENCODER
2548   Extensions += "Images( *.mpg)";
2549 #endif
2550
2551   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2552   QString fileName = QFileDialog::getSaveFileName(this,
2553                      tr("Save As"),
2554                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2555                      Extensions);
2556
2557   if (!fileName.isEmpty()) {
2558     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2559     w2i->SetInput(widget->GetRenderWindow());
2560     w2i->Update();
2561     vtkImageData *image = w2i->GetOutput();
2562
2563     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2564     if (!strcmp(ext, ".bmp")) {
2565       vtkBMPWriter *bmp = vtkBMPWriter::New();
2566       bmp->SetInput(image);
2567       bmp->SetFileName(fileName.toStdString().c_str());
2568       bmp->Write();
2569       bmp->Delete();
2570     } else if (!strcmp(ext, ".tif")) {
2571       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2572       tif->SetInput(image);
2573       tif->SetFileName(fileName.toStdString().c_str());
2574       tif->Write();
2575       tif->Delete();
2576     } else if (!strcmp(ext, ".ppm")) {
2577       vtkPNMWriter *pnm = vtkPNMWriter::New();
2578       pnm->SetInput(image);
2579       pnm->SetFileName(fileName.toStdString().c_str());
2580       pnm->Write();
2581       pnm->Delete();
2582     } else if (!strcmp(ext, ".png")) {
2583       vtkPNGWriter *png = vtkPNGWriter::New();
2584       png->SetInput(image);
2585       png->SetFileName(fileName.toStdString().c_str());
2586       png->Write();
2587       png->Delete();
2588     } else if (!strcmp(ext, ".jpg")) {
2589       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2590       jpg->SetInput(image);
2591       jpg->SetFileName(fileName.toStdString().c_str());
2592       jpg->Write();
2593       jpg->Delete();
2594 #ifdef VTK_USE_FFMPEG_ENCODER
2595     } else if (!strcmp(ext, ".avi")) {
2596       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2597       mpg->SetInput(image);
2598       mpg->SetFileName(fileName.toStdString().c_str());
2599       mpg->SetQuality(2);
2600       mpg->SetRate(5);
2601       mpg->Start();
2602
2603       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2604       int nSlice = vvImg->GetVTKImages().size();
2605       for(int i=0; i<nSlice; i++) {
2606         mSlicerManagers[smIndex]->SetNextTSlice(0);
2607         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2608         w2i->SetInput(widget->GetRenderWindow());
2609         w2i->Update();
2610         mpg->SetInput(w2i->GetOutput());
2611         mpg->Write();
2612       }
2613       mpg->End();
2614       mpg->Delete();
2615 #endif
2616 #ifdef VTK_USE_MPEG2_ENCODER
2617     } else if (!strcmp(ext, ".mpg")) {
2618       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2619       mpg->SetInput(image);
2620       mpg->SetFileName(fileName.toStdString().c_str());
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     } else {
2637       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2638     }
2639   }
2640 }
2641 //------------------------------------------------------------------------------
2642
2643
2644 //------------------------------------------------------------------------------
2645 void vvMainWindow::GoToCursor()
2646 {
2647   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2648   for (int column = 1; column < 5; column++) {
2649     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2650       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2651       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2652         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2653       mSlicerManagers[index]->UpdateViews(1,column-1);
2654       mSlicerManagers[index]->UpdateLinked(column-1);
2655       break;
2656     }
2657   }
2658 }
2659 //------------------------------------------------------------------------------
2660
2661 //------------------------------------------------------------------------------
2662 void vvMainWindow::PlayPause()
2663 {
2664   if (playMode) {
2665     playMode = 0;
2666     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2667     ImageInfoChanged();
2668     return;
2669   } else {
2670     int image_number=DataTree->topLevelItemCount();
2671     bool has_temporal;
2672     for (int i=0; i<image_number; i++)
2673       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2674         has_temporal=true;
2675         break;
2676       }
2677     if (has_temporal) {
2678       playMode = 1;
2679       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2680       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2681     }
2682   }
2683 }
2684 //------------------------------------------------------------------------------
2685
2686 //------------------------------------------------------------------------------
2687 void vvMainWindow::PlayNext()
2688 {
2689   if (playMode && !this->isHidden()) {
2690     int image_number=DataTree->topLevelItemCount();
2691     ///Only play one slicer per SM, and only if the SM is being displayed
2692     for (int i=0; i<image_number; i++)
2693       for (int j=0; j<4; j++)
2694         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2695             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2696           mSlicerManagers[i]->SetNextTSlice(j);
2697           break;
2698         }
2699     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2700   }
2701 }
2702 //------------------------------------------------------------------------------
2703
2704 void vvMainWindow::ShowLastImage()
2705 {
2706   if (mSlicerManagers.size() > 1) {
2707     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2708     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2709     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2710     DisplayChanged(item,1);
2711   }
2712 }
2713
2714 //------------------------------------------------------------------------------
2715 void vvMainWindow::UpdateRenderWindows()
2716 {
2717   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2718   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2719   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2720   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2721 }
2722 //------------------------------------------------------------------------------
2723
2724 //------------------------------------------------------------------------------
2725 void vvMainWindow::SegmentationOnCurrentImage()
2726 {
2727   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2728
2729   vvSegmentationDialog segmentation;
2730   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2731   segmentation.exec();
2732 }
2733 //------------------------------------------------------------------------------
2734
2735 void vvMainWindow::SurfaceViewerLaunch()
2736 {
2737   vvSurfaceViewerDialog surfaceViewer;
2738   surfaceViewer.exec();
2739 }
2740 //------------------------------------------------------------------------------
2741
2742
2743 //------------------------------------------------------------------------------
2744 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2745 {
2746   int number=0;
2747   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2748     vvSlicerManager * v = mSlicerManagers[l];
2749     if (v->GetBaseFileName() ==
2750         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2751       number = std::max(number, v->GetBaseFileNameNumber()+1);
2752     }
2753   }
2754   return number;
2755 }
2756 //------------------------------------------------------------------------------
2757
2758
2759 //------------------------------------------------------------------------------
2760 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2761 {
2762   // Change filename if another image exist with the same name
2763   int number = GetImageDuplicateFilenameNumber(filename);
2764
2765   // Create new SliceManager
2766   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2767   slicer_manager->SetImage(image);//, IMAGE, number);
2768   //  filename = filename+"_"+clitk::toString(number);
2769   slicer_manager->SetFilename(filename, number);
2770   mSlicerManagers.push_back(slicer_manager);
2771
2772   //create an item in the tree with good settings
2773   QTreeWidgetItem *item = new QTreeWidgetItem();
2774   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2775   item->setData(1,Qt::UserRole,tr("image"));
2776   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2777   qApp->processEvents();
2778
2779   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2780
2781   //Create the buttons for reload and close
2782   qApp->processEvents();
2783   QTreePushButton* cButton = new QTreePushButton;
2784   cButton->setItem(item);
2785   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2786   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2787   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2788           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2789
2790   QTreePushButton* rButton = new QTreePushButton;
2791   rButton->setItem(item);
2792   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2793   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2794   rButton->setEnabled(0);
2795   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2796           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2797
2798   DataTree->addTopLevelItem(item);
2799   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2800   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2801
2802   //set the id of the image
2803   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2804   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2805   mSlicerManagers.back()->SetId(id.toStdString());
2806
2807   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2808                       , id.toStdString());
2809
2810   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2811           this, SLOT(CurrentImageChanged(std::string)));
2812   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2813           this, SLOT(CurrentPickedImageChanged(std::string)));
2814   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2815           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2816   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2817           this, SLOT(VectorChanged(int,double,double,double, double)));
2818   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2819           this, SLOT(OverlayChanged(int,double,double)));
2820   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2821           this, SLOT(FusionChanged(int,double)));
2822   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2823           this,SLOT(WindowLevelChanged(double, double, int, int)));
2824   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2825           this,SLOT(UpdateSlice(int,int)));
2826   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2827           this,SLOT(UpdateTSlice(int, int)));
2828   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2829           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2830   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2831           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2832   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2833           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2834   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2835           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2836   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2837   UpdateTree();
2838   qApp->processEvents();
2839   InitSlicers();
2840   ShowLastImage();
2841   InitDisplay();
2842   qApp->processEvents();
2843
2844   // End
2845   ImageInfoChanged();
2846   return slicer_manager;
2847 }
2848 //------------------------------------------------------------------------------
2849
2850
2851 //------------------------------------------------------------------------------
2852 void vvMainWindow::UpdateCurrentSlicer()
2853 {
2854   int index = -1;
2855   if (DataTree->selectedItems().size() > 0) {
2856     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2857   }
2858   mSlicerManagerCurrentIndex = index;
2859 }
2860 //------------------------------------------------------------------------------
2861