vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #include <vtkFFMPEGWriter.h>
  72 #ifdef VTK_USE_MPEG2_ENCODER
  73 #  include <vtkMPEG2Writer.h>
  74 #endif
  75 #include <vtkMatrix4x4.h>
  76 #include <vtkTransform.h>
  77
  78 // Standard includes
  79 #include <iostream>
  80 #include <sstream>
  81 #include <iomanip>
  82
  83 #define COLUMN_TREE 0
  84 #define COLUMN_UL_VIEW 1
  85 #define COLUMN_UR_VIEW 2
  86 #define COLUMN_DL_VIEW 3
  87 #define COLUMN_DR_VIEW 4
  88 #define COLUMN_CLOSE_IMAGE 5
  89 #define COLUMN_RELOAD_IMAGE 6
  90 #define COLUMN_IMAGE_NAME 7
  91
  92 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  93
  94 /*Data Tree values
  95   0,Qt::UserRole full filename
  96   1,Qt::CheckStateRole checkbutton UL View
  97   1,Qt::UserRole overlay, fusion or vector
  98   2,Qt::CheckStateRole checkbutton UR View
  99   3,Qt::CheckStateRole checkbutton DL View
 100   4,Qt::CheckStateRole checkbutton DR View
 101   5,0  short filename
 102   5,Qt::UserRole mSlicerManager id*/
 103
 104 //------------------------------------------------------------------------------
 105 vvMainWindow::vvMainWindow():vvMainWindowBase()
 106 {
 107   setupUi(this); // this sets up the GUI
 108
 109   mInputPathName = "";
 110   mMenuTools = menuTools;
 111   //  mMenuSegmentation = menuSegmentation;
 112   mContextMenu = &contextMenu;
 113   mMenuExperimentalTools = menuExperimental;
 114   mMainWidget = this;
 115   mCurrentTime = -1;
 116   mCurrentSelectedImageId = "";
 117   mCurrentPickedImageId = "";
 118   mCurrentPickedImageIndex = 0;
 119
 120   //Init the contextMenu
 121   this->setContextMenuPolicy(Qt::CustomContextMenu);
 122   contextActions.resize(0);
 123   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 124                                   tr("O&pen new Image"));
 125   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 126   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 127   contextActions.push_back(actionOpen_new_image);
 128   contextMenu.addSeparator();
 129
 130   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 131                                tr("Close Current Image"));
 132   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 133   contextActions.push_back(actionClose_Image);
 134
 135   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 136                                 tr("Reload Current Image"));
 137   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 138   contextActions.push_back(actionReload_image);
 139
 140   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 141                               tr("Save Current Image"));
 142   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 143   contextActions.push_back(actionSave_image);
 144
 145   contextMenu.addSeparator();
 146
 147   contextMenu.addAction(actionAdd_VF_to_current_Image);
 148   contextActions.push_back(actionAdd_VF_to_current_Image);
 149
 150   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 151       tr("Add overlay image to current image"));
 152   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 153   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 154
 155   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 156
 157   contextMenu.addAction(actionAdd_fusion_image);
 158   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 159   contextActions.push_back(actionAdd_fusion_image);
 160
 161   // TRIAL DS
 162   /*
 163   QMenu * m = new QMenu(menubar);
 164   m->setTitle("TOTO");
 165   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 166   contextMenu.addMenu(m);
 167   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 168                      tr("BIDON"));
 169   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON2"));
 171   m->addAction(a);
 172   m->addAction(b);
 173   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 174   */
 175
 176   //init the DataTree
 177   mSlicerManagers.resize(0);
 178
 179   QStringList header;
 180   header.append("");
 181   header.append("TL");
 182   header.append("TR");
 183   header.append("BL");
 184   header.append("BR");
 185   header.append("");
 186   header.append("");
 187   header.append("Name");
 188
 189   DataTree->setHeaderLabels(header);
 190   DataTree->resizeColumnToContents(COLUMN_TREE);
 191   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 198
 199   viewMode = 1;
 200   documentation = new vvDocumentation();
 201   help_dialog = new vvHelpDialog();
 202   dicomSeriesSelector = new vvDicomSeriesSelector();
 203
 204   inverseButton->setEnabled(0);
 205   actionAdd_Overlay_to_current_Image->setEnabled(0);
 206   actionSave_As->setEnabled(0);
 207   actionAdd_VF_to_current_Image->setEnabled(0);
 208   actionAdd_fusion_image->setEnabled(0);
 209
 210   //init the sliders
 211   verticalSliders.push_back(NOVerticalSlider);
 212   verticalSliders.push_back(NEVerticalSlider);
 213   verticalSliders.push_back(SOVerticalSlider);
 214   verticalSliders.push_back(SEVerticalSlider);
 215
 216   for (int i =0; i < 4; i++)
 217     verticalSliders[i]->hide();
 218
 219   horizontalSliders.push_back(NOHorizontalSlider);
 220   horizontalSliders.push_back(NEHorizontalSlider);
 221   horizontalSliders.push_back(SOHorizontalSlider);
 222   horizontalSliders.push_back(SEHorizontalSlider);
 223
 224   for (int i =0; i < 4; i++)
 225     horizontalSliders[i]->hide();
 226
 227
 228   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 229   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 230   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 231   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 232
 233   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 234   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 235   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 236   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 237
 238   //connect everything
 239   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 240   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 241   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 242   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 243   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 244   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 245   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 246   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 247   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 248   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 249   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 250   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 251   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 252   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 253   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 254   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 255   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 256
 257   ///////////////////////////////////////////////
 258   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 259   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 260   ///////////////////////////////////////////////
 261
 262   actionNorth_East_Window->setEnabled(0);
 263   actionNorth_West_Window->setEnabled(0);
 264   actionSouth_East_Window->setEnabled(0);
 265   actionSouth_West_Window->setEnabled(0);
 266
 267   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 268   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 269   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 270   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 271
 272   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 273   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 274           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 275
 276   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 277   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 278   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 279   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 280   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 281   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 282   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 283
 284
 285   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 286
 287   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 288   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 289   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 290   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 291   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 292           this,SLOT(SetFusionProperty(int,int,double,double)));
 293   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 294
 295   playMode = 0;//pause
 296   mFrameRate = 10;
 297   playButton->setEnabled(0);
 298   frameRateLabel->setEnabled(0);
 299   frameRateSpinBox->setEnabled(0);
 300   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 301   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 302
 303   goToCursorPushButton->setEnabled(0);
 304   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 305
 306   NOViewWidget->hide();
 307   NEViewWidget->hide();
 308   SOViewWidget->hide();
 309   SEViewWidget->hide();
 310
 311   //Recently opened files
 312   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 313   recentlyOpenedFilesMenu=NULL;
 314   if ( !recent_files.empty() ) {
 315     createRecentlyOpenedFilesMenu();
 316     updateRecentlyOpenedFilesMenu(recent_files);
 317   }
 318
 319   // Adding all new tools (insertion in the menu)
 320   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 321   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 322
 323   if (!CLITK_EXPERIMENTAL)
 324     menuExperimental->menuAction()->setVisible(false);
 325
 326
 327   QTimer * timerMemory = new QTimer(this);
 328   //timerMemory->setInterval(5);
 329   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 330   timerMemory->start(2000);
 331 }
 332 //------------------------------------------------------------------------------
 333 void vvMainWindow::show()
 334 {
 335   vvMainWindowBase::show();
 336   PopupRegisterForm(true);
 337 }
 338 //------------------------------------------------------------------------------
 339 void vvMainWindow::UpdateMemoryUsage()
 340 {
 341   //  clitk::PrintMemory(true);
 342   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 343   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 344 }
 345 //------------------------------------------------------------------------------
 346
 347
 348 //------------------------------------------------------------------------------
 349 void vvMainWindow::createRecentlyOpenedFilesMenu()
 350 {
 351   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 352   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 353   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 354   menuFile->insertSeparator(actionOpen_Image_With_Time);
 355 }
 356 //------------------------------------------------------------------------------
 357
 358
 359 //------------------------------------------------------------------------------
 360
 361 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 362 {
 363   if(recentlyOpenedFilesMenu==NULL) {
 364     createRecentlyOpenedFilesMenu();
 365   } else {
 366     recentlyOpenedFilesMenu->clear();
 367   }
 368   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 369     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 370     recentlyOpenedFilesMenu->addAction(current);
 371     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 372   }
 373 }
 374 //------------------------------------------------------------------------------
 375
 376
 377 //------------------------------------------------------------------------------
 378 void vvMainWindow::ComputeMidPosition()
 379 {
 380   bool ok;
 381   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 382   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 383                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 384   if (ok) {
 385     vvMidPosition midp;
 386     midp.slicer_manager = mSlicerManagers[index];
 387     midp.reference_image_index = ref;
 388     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 389     midp.Update();
 390     if (midp.error)
 391       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 392     else {
 393       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 394       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 395     }
 396     QApplication::restoreOverrideCursor();
 397   }
 398 }
 399 //------------------------------------------------------------------------------
 400
 401
 402 //------------------------------------------------------------------------------
 403 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 404 {
 405   QTreeWidgetItem *item = new QTreeWidgetItem();
 406   item->setData(0,Qt::UserRole,"filename.vtk");
 407   item->setData(1,Qt::UserRole,tr("contour"));
 408   QBrush brush;
 409   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 410   brush.setStyle(Qt::SolidPattern);
 411   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 412   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 413
 414   for (int j = 1; j <= 4; j++)
 415     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 416
 417   QTreePushButton* cButton = new QTreePushButton;
 418   cButton->setItem(item);
 419   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 420   cButton->setToolTip(tr("close image"));
 421   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 422   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 423           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 424
 425   QTreePushButton* rButton = new QTreePushButton;
 426   rButton->setItem(item);
 427   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 428   rButton->setToolTip(tr("reload image"));
 429   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 430   rButton->setEnabled(false);
 431   //Not implemented
 432   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 433   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 434
 435   DataTree->topLevelItem(image_index)->setExpanded(1);
 436   DataTree->topLevelItem(image_index)->addChild(item);
 437   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 438   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 439   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 440   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 441
 442   UpdateTree();
 443   mSlicerManagers[image_index]->AddContour(contour,propagation);
 444   mSlicerManagers[image_index]->Render();
 445 }
 446 //------------------------------------------------------------------------------
 447
 448
 449 //------------------------------------------------------------------------------
 450 void vvMainWindow::OpenVTKContour()
 451 {
 452   if (mSlicerManagers.size() > 0) {
 453     QString Extensions = "Images ( *.vtk *.obj)";
 454     Extensions += ";;All Files (*)";
 455     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 456     if (file.isNull())
 457       return;
 458     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 459     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 460     vvMeshReader reader;
 461     reader.SetImage(mSlicerManagers[index]->GetImage());
 462     reader.SetModeToVTK();
 463     reader.SetFilename(file.toStdString());
 464     reader.Update();
 465     AddContour(index,reader.GetOutput()[0],false);
 466     QApplication::restoreOverrideCursor();
 467   }
 468 }
 469 //------------------------------------------------------------------------------
 470
 471
 472 //------------------------------------------------------------------------------
 473 void vvMainWindow::OpenDCStructContour()
 474 {
 475   if (mSlicerManagers.size() > 0) {
 476     QString Extensions = "Dicom Files ( *.dcm RS*)";
 477     Extensions += ";;All Files (*)";
 478     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 479     if (file.isNull())
 480       return;
 481     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 482     vvMeshReader reader;
 483     reader.SetFilename(file.toStdString());
 484     vvStructSelector selector;
 485     selector.SetStructures(reader.GetROINames());
 486     if (!mSlicerManagers[index]->GetVF().IsNull())
 487       selector.EnablePropagationCheckBox();
 488     if (selector.exec()) {
 489       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 490       reader.SetSelectedItems(selector.getSelectedItems());
 491       reader.SetImage(mSlicerManagers[index]->GetImage());
 492       if (selector.PropagationEnabled())
 493         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 494       reader.Update();
 495       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 496       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 497            i!=contours.end(); i++)
 498         AddContour(index,*i,selector.PropagationEnabled());
 499       QApplication::restoreOverrideCursor();
 500     }
 501   }
 502 }
 503 //------------------------------------------------------------------------------
 504
 505
 506 //------------------------------------------------------------------------------
 507 void vvMainWindow::ComputeDeformableRegistration()
 508 {
 509   if (mSlicerManagers.size() > 0) {
 510     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 511     vvDeformationDialog dialog(index,mSlicerManagers);
 512     if (dialog.exec()) {
 513       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 514       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 515       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 516     } else
 517       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 518   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 519 }
 520 //------------------------------------------------------------------------------
 521
 522
 523 //------------------------------------------------------------------------------
 524 void vvMainWindow::WarpImage()
 525 {
 526   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 527   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 528     bool ok;
 529     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 530                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 531     if (ok) {
 532       WarpImage(mSlicerManagers[index],ref);
 533     }
 534   } else
 535     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 536 }
 537 //------------------------------------------------------------------------------
 538
 539
 540 //------------------------------------------------------------------------------
 541 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 542 {
 543   if (!selected_slicer->GetVF().IsNull()) {
 544     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 545     QFileInfo info(selected_slicer->GetFileName().c_str());
 546     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 547                      reference_phase,this);
 548     if (warp.ComputeWarpedImage()) {
 549       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 550       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 551       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 552       QApplication::restoreOverrideCursor();
 553     } else {
 554       QApplication::restoreOverrideCursor();
 555       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 556     }
 557   } else
 558     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 559 }
 560 //------------------------------------------------------------------------------
 561
 562
 563 //------------------------------------------------------------------------------
 564 vvMainWindow::~vvMainWindow()
 565 {
 566   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 567     if (mSlicerManagers[i] != NULL)
 568       delete mSlicerManagers[i];
 569   }
 570 }
 571 //------------------------------------------------------------------------------
 572
 573 //------------------------------------------------------------------------------
 574 QTabWidget * vvMainWindow::GetTab()
 575 {
 576   return tabWidget;
 577 }
 578 //------------------------------------------------------------------------------
 579
 580
 581 //------------------------------------------------------------------------------
 582 void vvMainWindow::MergeImages()
 583 {
 584   QString Extensions = EXTENSIONS;
 585   Extensions += ";;All Files (*)";
 586   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 587   if (files.isEmpty())
 588     return;
 589   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 590   std::vector<std::string> vector;
 591
 592   unsigned int currentDim = 0;
 593   std::vector<double> currentSpacing;
 594   std::vector<int> currentSize;
 595   std::vector<double> currentOrigin;
 596
 597   for (int i = 0; i < files.size(); i++) {
 598     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 599                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 600     reader->SetFileName(files[i].toStdString().c_str());
 601     reader->ReadImageInformation();
 602     if (reader)        {
 603       //NOViewWidget->hide();
 604       //NEViewWidget->hide();
 605       //SOViewWidget->hide();
 606       //SEViewWidget->hide();
 607       if (i == 0)
 608         currentDim = reader->GetNumberOfDimensions();
 609       bool IsOk = true;
 610       for (unsigned int j = 0; j < currentDim; j++) {
 611         if (i == 0) {
 612           if (j == 0) {
 613             currentSpacing.resize(currentDim);
 614             currentSize.resize(currentDim);
 615             currentOrigin.resize(currentDim);
 616           }
 617           currentOrigin[j] = reader->GetOrigin(j);
 618           currentSpacing[j] = reader->GetSpacing(j);
 619           currentSize[j] = reader->GetDimensions(j);
 620         } else if (currentDim != reader->GetNumberOfDimensions()
 621                    || currentSpacing[j] != reader->GetSpacing(j)
 622                    || currentSize[j] != (int)reader->GetDimensions(j)
 623                    || currentOrigin[j] != reader->GetOrigin(j)) {
 624           QString error = "Cannot read file (too different from others ";
 625           error += files[i].toStdString().c_str();
 626           QMessageBox::information(this,tr("Reading problem"),error);
 627           IsOk = false;
 628           break;
 629         }
 630       }
 631       if (IsOk)
 632         vector.push_back(files[i].toStdString());
 633     }
 634   }
 635   if (vector.size() > 0)
 636     LoadImages(vector, vvImageReader::MERGED);
 637 }
 638 //------------------------------------------------------------------------------
 639
 640 //------------------------------------------------------------------------------
 641 void vvMainWindow::SliceImages()
 642 {
 643   QString Extensions = EXTENSIONS;
 644   Extensions += ";;All Files (*)";
 645
 646   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 647   if (files.isEmpty())
 648     return;
 649   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 650   std::vector<std::string> vector;
 651   for (int i = 0; i < files.size(); i++)
 652     vector.push_back(files[i].toStdString());
 653   LoadImages(vector, vvImageReader::SLICED);
 654 }
 655 //------------------------------------------------------------------------------
 656
 657 //------------------------------------------------------------------------------
 658 void vvMainWindow::MergeImagesWithTime()
 659 {
 660   QString Extensions = EXTENSIONS;
 661   Extensions += ";;All Files (*)";
 662   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 663   if (files.isEmpty())
 664     return;
 665   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 666   std::vector<std::string> vector;
 667
 668   unsigned int currentDim = 0;
 669   std::vector<double> currentSpacing;
 670   std::vector<int> currentSize;
 671   std::vector<double> currentOrigin;
 672
 673   for (int i = 0; i < files.size(); i++) {
 674     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 675                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 676     if (reader) {
 677       reader->SetFileName(files[i].toStdString().c_str());
 678       reader->ReadImageInformation();
 679       if (i == 0)
 680         currentDim = reader->GetNumberOfDimensions();
 681       bool IsOk = true;
 682       for (unsigned int j = 0; j < currentDim; j++) {
 683         if (i == 0) {
 684           if (j == 0) {
 685             currentSpacing.resize(currentDim);
 686             currentSize.resize(currentDim);
 687             currentOrigin.resize(currentDim);
 688           }
 689           currentOrigin[j] = reader->GetOrigin(j);
 690           currentSpacing[j] = reader->GetSpacing(j);
 691           currentSize[j] = reader->GetDimensions(j);
 692         } else if (currentDim != reader->GetNumberOfDimensions()
 693                    || currentSpacing[j] != reader->GetSpacing(j)
 694                    || currentSize[j] != (int)reader->GetDimensions(j)
 695                    || currentOrigin[j] != reader->GetOrigin(j)) {
 696           QString error = "Cannot read file (too different from others ";
 697           error += files[i].toStdString().c_str();
 698           QMessageBox::information(this,tr("Reading problem"),error);
 699           IsOk = false;
 700           break;
 701         }
 702       }
 703       if (IsOk)
 704         vector.push_back(files[i].toStdString());
 705     } else {
 706       QString error = "Cannot read file info for ";
 707       error += files[i].toStdString().c_str();
 708       error += "\n";
 709       error += "Maybe you're trying to open an image in an unsupported format?\n";
 710       QMessageBox::information(this,tr("Reading problem"),error);
 711     }
 712   }
 713   sort(vector.begin(),vector.end());
 714   if (vector.size() > 1)
 715     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 716   else
 717     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.");
 718 }
 719 //------------------------------------------------------------------------------
 720
 721
 722 //------------------------------------------------------------------------------
 723 void vvMainWindow::OpenDicom()
 724 {
 725   std::vector<std::string> files;
 726
 727   std::cout << "dicomSeriesSelector " << std::endl;
 728   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 729     files = *(dicomSeriesSelector->GetFilenames());
 730     LoadImages(files, vvImageReader::DICOM);
 731   }
 732 }
 733 //------------------------------------------------------------------------------
 734
 735 //------------------------------------------------------------------------------
 736 void vvMainWindow::OpenImages()
 737 {
 738   QString Extensions = EXTENSIONS;
 739   Extensions += ";;All Files (*)";
 740
 741   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 742   if (files.isEmpty())
 743     return;
 744   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 745   std::vector<std::string> vector;
 746   for (int i = 0; i < files.size(); i++)
 747     vector.push_back(files[i].toStdString());
 748   LoadImages(vector, vvImageReader::IMAGE);
 749 }
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::OpenRecentImage()
 752 {
 753   QAction * caller = qobject_cast<QAction*>(sender());
 754   std::vector<std::string> images;
 755   images.push_back(caller->text().toStdString());
 756   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 757   LoadImages(images, vvImageReader::IMAGE);
 758 }
 759 //------------------------------------------------------------------------------
 760
 761
 762 //------------------------------------------------------------------------------
 763 void vvMainWindow::OpenImageWithTime()
 764 {
 765   QString Extensions = EXTENSIONS;
 766   Extensions += ";;All Files (*)";
 767
 768   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 769   if (files.isEmpty())
 770     return;
 771   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 772   std::vector<std::string> vector;
 773   for (int i = 0; i < files.size(); i++) {
 774     vector.push_back(files[i].toStdString());
 775   }
 776   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 777 }
 778 //------------------------------------------------------------------------------
 779
 780
 781 //------------------------------------------------------------------------------
 782 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 783 {
 784   //Separate the way to open images and dicoms
 785   int fileSize;
 786   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 787     fileSize = files.size();
 788   else
 789     fileSize = 1;
 790
 791   // For SLICED, we need the number of slices (ndim and #slices)
 792   std::vector<unsigned int> nSlices;
 793   nSlices.resize(files.size());
 794   std::fill(nSlices.begin(), nSlices.end(), 1);
 795   if (filetype == vvImageReader::SLICED) {
 796     for (int i = 0; i < fileSize; i++) {
 797       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 798       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 799       if (!header) {
 800         nSlices[i] = 0;
 801         QString error = "Cannot open file \n";
 802         error += files[i].c_str();
 803         QMessageBox::information(this,tr("Reading problem"),error);
 804         return;
 805       }
 806       if (header->GetNumberOfDimensions() < 3) {
 807         nSlices[i] = 0;
 808         QString error = "Dimension problem. Cannot slice \n";
 809         error += files[i].c_str();
 810         QMessageBox::information(this,tr("Reading problem"),error);
 811         return;
 812       }
 813       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 814     }
 815   }
 816
 817   //Only add to the list of recently opened files when a single file is opened,
 818   //to avoid polluting the list of recently opened files
 819   if (files.size() == 1) {
 820     QFileInfo finfo=tr(files[0].c_str());
 821     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 822     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 823   }
 824   //init the progress events
 825   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 826   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 827   qApp->processEvents();
 828
 829   int numberofsuccesulreads=0;
 830   //open images as 1 or multiples
 831   for (int i = 0; i < fileSize; i++) {
 832
 833     progress.SetText("Opening " + files[i]);
 834     progress.SetProgress(i,fileSize);
 835     qApp->processEvents();
 836
 837     for (unsigned int j = 0; j < nSlices[i]; j++) {
 838       //read the image and put it in mSlicerManagers
 839       vvSlicerManager* imageManager = new vvSlicerManager(4);
 840       qApp->processEvents();
 841
 842       bool SetImageSucceed=false;
 843
 844       // Change filename if an image with the same already exist
 845       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 846
 847       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 848         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 849       else {
 850         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 851       }
 852       if (!SetImageSucceed) {
 853         QApplication::restoreOverrideCursor();
 854         QString error = "Cannot open file \n";
 855         error += imageManager->GetLastError().c_str();
 856         QMessageBox::information(this,tr("Reading problem"),error);
 857         delete imageManager;
 858       } else {
 859         mSlicerManagers.push_back(imageManager);
 860
 861         //create an item in the tree with good settings
 862         QTreeWidgetItem *item = new QTreeWidgetItem();
 863         item->setData(0,Qt::UserRole,files[i].c_str());
 864         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 865         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 866         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 867         qApp->processEvents();
 868
 869         //Create the buttons for reload and close
 870         qApp->processEvents();
 871         QTreePushButton* cButton = new QTreePushButton;
 872         cButton->setItem(item);
 873         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 874         cButton->setToolTip(tr("close image"));
 875         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 876         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 877                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 878
 879         QTreePushButton* rButton = new QTreePushButton;
 880         rButton->setItem(item);
 881         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 882         rButton->setToolTip(tr("reload image"));
 883         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 884         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 885                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 886
 887         DataTree->addTopLevelItem(item);
 888         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 889         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 890
 891         //set the id of the image
 892         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 893         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 894         mSlicerManagers.back()->SetId(id.toStdString());
 895
 896         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 897
 898         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 899                 this,SLOT(CurrentImageChanged(std::string)));
 900         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 901                 this, SLOT(CurrentPickedImageChanged(std::string)));
 902         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 903                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 904         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 905                 this, SLOT(VectorChanged(int,double,double,double, double)));
 906         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 907                 this, SLOT(OverlayChanged(int,double,double)));
 908         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 909                 this, SLOT(FusionChanged(int,double)));
 910         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 911                 this,SLOT(WindowsChanged(int, int, int)));
 912         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 913                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 914         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 915                 this,SLOT(UpdateSlice(int,int)));
 916         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 917                 this,SLOT(UpdateTSlice(int, int)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 919                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 921                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 923                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 924         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 925                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 926         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 927         InitSlicers();
 928         numberofsuccesulreads++;
 929       }
 930     }
 931   }
 932   if (numberofsuccesulreads) {
 933     NOViewWidget->show();
 934     NEViewWidget->show();
 935     SOViewWidget->show();
 936     SEViewWidget->show();
 937     UpdateTree();
 938     InitDisplay();
 939     ShowLastImage();
 940
 941     // Try to guess default WindowLevel
 942     double range[2];
 943     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 944     if ((range[0] == 0) && (range[1] == 1)) {
 945       presetComboBox->setCurrentIndex(5);// binary
 946     } else {
 947       // TODO
 948     }
 949   }
 950   QApplication::restoreOverrideCursor();
 951 }
 952 //------------------------------------------------------------------------------
 953
 954 //------------------------------------------------------------------------------
 955 void vvMainWindow::UpdateTree()
 956 {
 957   DataTree->resizeColumnToContents(COLUMN_TREE);
 958   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 959   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 963   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 964   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 965 }
 966 //------------------------------------------------------------------------------
 967
 968 //------------------------------------------------------------------------------
 969 void vvMainWindow::CurrentImageChanged(std::string id)
 970 {
 971   if (id == mCurrentSelectedImageId) return; // Do nothing
 972   int selected = 0;
 973   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 974     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 975       selected = i;
 976     } else {
 977       DataTree->topLevelItem(i)->setSelected(0);
 978     }
 979     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 980       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 981
 982   }
 983   DataTree->topLevelItem(selected)->setSelected(1);
 984   mCurrentSelectedImageId = id;
 985   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 986 }
 987 //------------------------------------------------------------------------------
 988
 989 //------------------------------------------------------------------------------
 990 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 991 {
 992   if (id == mCurrentPickedImageId) return; // Do nothing
 993   int selected = 0;
 994   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 995     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 996       selected = i;
 997     } else {
 998       DataTree->topLevelItem(i)->setSelected(0);
 999     }
1000     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1001       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1002
1003   }
1004   DataTree->topLevelItem(selected)->setSelected(1);
1005   mCurrentPickedImageId = id;
1006   mCurrentPickedImageIndex = selected;
1007 }
1008 //------------------------------------------------------------------------------
1009
1010 //------------------------------------------------------------------------------
1011 void vvMainWindow::ImageInfoChanged()
1012 {
1013   contextActions[6]->setEnabled(1);
1014   contextActions[5]->setEnabled(1);
1015   actionSave_As->setEnabled(1);
1016   actionAdd_VF_to_current_Image->setEnabled(1);
1017   actionAdd_fusion_image->setEnabled(1);
1018   actionNorth_East_Window->setEnabled(1);
1019   actionNorth_West_Window->setEnabled(1);
1020   actionSouth_East_Window->setEnabled(1);
1021   actionSouth_West_Window->setEnabled(1);
1022   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1023   inverseButton->setEnabled(1);
1024
1025   goToCursorPushButton->setEnabled(1);
1026
1027   if (DataTree->selectedItems().size()) {
1028     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1029
1030     colorMapComboBox->setEnabled(1);
1031     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1032       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1033           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1034         colorMapComboBox->setEnabled(0);
1035         break;
1036       }
1037     }
1038
1039     std::vector<double> origin;
1040     std::vector<double> inputSpacing;
1041     std::vector<int> inputSize;
1042     std::vector<double> sizeMM;
1043     vtkSmartPointer<vtkMatrix4x4> transformation;
1044     int dimension=0;
1045     QString pixelType;
1046     QString inputSizeInBytes;
1047     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1048
1049     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1050       playButton->setEnabled(1);
1051       frameRateLabel->setEnabled(1);
1052       frameRateSpinBox->setEnabled(1);
1053     } else {
1054       playButton->setEnabled(0);
1055       frameRateLabel->setEnabled(0);
1056       frameRateSpinBox->setEnabled(0);
1057     }
1058
1059     //read image header
1060     int NPixel = 1;
1061
1062     vvImage::Pointer imageSelected;
1063     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1064       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1065       dimension = imageSelected->GetNumberOfDimensions();
1066       origin.resize(dimension);
1067       inputSpacing.resize(dimension);
1068       inputSize.resize(dimension);
1069       sizeMM.resize(dimension);
1070       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1071       for (int i = 0; i < dimension; i++) {
1072         origin[i] = imageSelected->GetOrigin()[i];
1073         inputSpacing[i] = imageSelected->GetSpacing()[i];
1074         inputSize[i] = imageSelected->GetSize()[i];
1075         sizeMM[i] = inputSize[i]*inputSpacing[i];
1076         NPixel *= inputSize[i];
1077       }
1078       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1079     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1080       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1081       dimension = imageSelected->GetNumberOfDimensions();
1082       origin.resize(dimension);
1083       inputSpacing.resize(dimension);
1084       inputSize.resize(dimension);
1085       sizeMM.resize(dimension);
1086       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1087       for (int i = 0; i < dimension; i++) {
1088         origin[i] = imageSelected->GetOrigin()[i];
1089         inputSpacing[i] = imageSelected->GetSpacing()[i];
1090         inputSize[i] = imageSelected->GetSize()[i];
1091         sizeMM[i] = inputSize[i]*inputSpacing[i];
1092         NPixel *= inputSize[i];
1093       }
1094       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1095     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1096       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1097       dimension = imageSelected->GetNumberOfDimensions();
1098       origin.resize(dimension);
1099       inputSpacing.resize(dimension);
1100       inputSize.resize(dimension);
1101       sizeMM.resize(dimension);
1102       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1103       for (int i = 0; i < dimension; i++) {
1104         origin[i] = imageSelected->GetOrigin()[i];
1105         inputSpacing[i] = imageSelected->GetSpacing()[i];
1106         inputSize[i] = imageSelected->GetSize()[i];
1107         sizeMM[i] = inputSize[i]*inputSpacing[i];
1108         NPixel *= inputSize[i];
1109       }
1110       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1113       dimension = imageSelected->GetNumberOfDimensions();
1114       origin.resize(dimension);
1115       inputSpacing.resize(dimension);
1116       inputSize.resize(dimension);
1117       sizeMM.resize(dimension);
1118       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1119       for (int i = 0; i < dimension; i++) {
1120         origin[i] = imageSelected->GetOrigin()[i];
1121         inputSpacing[i] = imageSelected->GetSpacing()[i];
1122         inputSize[i] = imageSelected->GetSize()[i];
1123         sizeMM[i] = inputSize[i]*inputSpacing[i];
1124         NPixel *= inputSize[i];
1125       }
1126       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1127     }
1128
1129     QString dim = QString::number(dimension) + " (";
1130     dim += pixelType + ")";
1131
1132     infoPanel->setFileName(image);
1133     infoPanel->setDimension(dim);
1134     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1135     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1136     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1137     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1138     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1139     transformation = imageSelected->GetTransform()->GetMatrix();
1140     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1141
1142     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1143                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1144     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1145     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1146
1147     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1148     for (int i = 0; i < 4; i++) {
1149       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1150         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1151         break;
1152       }
1153     }
1154     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1155     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1156     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1157     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1158
1159     infoPanel->setFileName(image);
1160     infoPanel->setDimension(dim);
1161     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1162     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1163     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1164     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1165     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1166
1167     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1168                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1169     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1170     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1171
1172     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1173     for (int i = 0; i < 4; i++) {
1174       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1175         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1176         break;
1177       }
1178     }
1179     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1180     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1181     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1182     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1183
1184     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1185       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1186       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1187                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1188                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1189     } else {
1190       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1191       overlayPanel->getVFProperty(-1,-1,-1);
1192     }
1193     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1194       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1195       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1196     } else {
1197       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1198       overlayPanel->getOverlayProperty(-1);
1199     }
1200     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1201       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1202       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1203                                       mSlicerManagers[index]->GetFusionColorMap(),
1204                                       mSlicerManagers[index]->GetFusionWindow(),
1205                                       mSlicerManagers[index]->GetFusionLevel());
1206     } else {
1207       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1208       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1209     }
1210   }
1211 }
1212 //------------------------------------------------------------------------------
1213
1214 //------------------------------------------------------------------------------
1215 void vvMainWindow::ShowDocumentation()
1216 {
1217   documentation->show();
1218 }
1219 //------------------------------------------------------------------------------
1220
1221 //------------------------------------------------------------------------------
1222 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1223 {
1224   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1225   if(!checkCanPush) {
1226     registerForm->show();
1227   } else {
1228     if(registerForm->canPush()) {
1229       registerForm->show();
1230       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1231     }
1232   }
1233 }
1234 //------------------------------------------------------------------------------
1235
1236 //------------------------------------------------------------------------------
1237 void vvMainWindow::ShowHelpDialog()
1238 {
1239   help_dialog->show();
1240 }
1241 //------------------------------------------------------------------------------
1242
1243 //------------------------------------------------------------------------------
1244 void vvMainWindow::ChangeViewMode()
1245 {
1246   QList<int> size;
1247   if (viewMode == 1) {
1248     viewMode = 0;
1249     size.push_back(1);
1250     size.push_back(0);
1251     splitter_3->setSizes(size);
1252     OSplitter->setSizes(size);
1253     DataTree->setColumnHidden(2,1);
1254     DataTree->setColumnHidden(3,1);
1255     DataTree->setColumnHidden(4,1);
1256   } else {
1257     viewMode = 1;
1258     size.push_back(1);
1259     size.push_back(1);
1260     splitter_3->setSizes(size);
1261     OSplitter->setSizes(size);
1262     DataTree->setColumnHidden(2,0);
1263     DataTree->setColumnHidden(3,0);
1264     DataTree->setColumnHidden(4,0);
1265   }
1266   UpdateRenderWindows();
1267   /*
1268   ** I don't know why but for both resized QVTKWidget we also need to render
1269   ** the associated Slicer to redraw crosses.
1270   */
1271   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1272     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1273       mSlicerManagers[i]->GetSlicer(0)->Render();
1274     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1275       mSlicerManagers[i]->GetSlicer(2)->Render();
1276   }
1277 }
1278 //------------------------------------------------------------------------------
1279
1280 //------------------------------------------------------------------------------
1281 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1282 {
1283   QString result = "";// QString::number(size);
1284   //result += " bytes (";
1285   if (size > 1000000000) {
1286     size /= 1000000000;
1287     result += QString::number(size);
1288     result += "Gb";//)";
1289   } else if (size > 1000000) {
1290     size /= 1000000;
1291     result += QString::number(size);
1292     result += "Mb";//)";
1293   } else if (size > 1000) {
1294     size /= 1000;
1295     result += QString::number(size);
1296     result += "kb";//)";
1297   }
1298   return result;
1299 }
1300 //------------------------------------------------------------------------------
1301
1302 //------------------------------------------------------------------------------
1303 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1304 {
1305   std::ostringstream strmatrix;
1306
1307   for (unsigned int i = 0; i < 4; i++) {
1308     for (unsigned int j = 0; j < 4; j++) {
1309       strmatrix.flags(ios::showpos);
1310       strmatrix.width(10);
1311       strmatrix.precision(3);
1312       strmatrix.setf(ios::fixed,ios::floatfield);
1313       strmatrix.fill(' ');
1314       strmatrix << std::left << matrix->GetElement(i, j);
1315       //strmatrix.width(10);
1316       strmatrix << " ";
1317     }
1318     strmatrix << std::endl;
1319   }
1320   QString result = strmatrix.str().c_str();
1321   return result;
1322 }
1323 //------------------------------------------------------------------------------
1324
1325 //------------------------------------------------------------------------------
1326 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1327 {
1328   QString result;
1329   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1330     if (i != 0)
1331       result += " ";
1332     result += QString::number(vectorDouble[i]);
1333   }
1334   return result;
1335 }
1336 //------------------------------------------------------------------------------
1337
1338 //------------------------------------------------------------------------------
1339 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1340 {
1341   QString result;
1342   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1343     if (i != 0)
1344       result += " ";
1345     result += QString::number(vectorInt[i]);
1346   }
1347   return result;
1348 }
1349 //------------------------------------------------------------------------------
1350
1351 //------------------------------------------------------------------------------
1352 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1353 {
1354   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1355   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1356     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1357       return i;
1358   }
1359   return -1;
1360 }
1361 //------------------------------------------------------------------------------
1362
1363 //------------------------------------------------------------------------------
1364 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1365 {
1366   QString id = sm->GetId().c_str();
1367   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1368     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1369       return DataTree->topLevelItem(i);
1370   }
1371   return NULL;
1372 }
1373 //------------------------------------------------------------------------------
1374
1375 //------------------------------------------------------------------------------
1376 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1377 {
1378   int index = GetSlicerIndexFromItem(clicked_item);
1379   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1380     return;
1381   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1382     //Trick to avoid redoing twice the job for a key (sr)
1383     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1384
1385     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1386     if (DataTree->topLevelItem(index) == current_row) {
1387       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1388       if (current_row == clicked_item) {
1389         //If we just activated a slicer
1390         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1391           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1392           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1393           DisplaySliders(i,column-1);
1394           std::map<std::string,int> overlay_counts;
1395           for (int child = 0; child < current_row->childCount(); child++) {
1396             std::string overlay_type =
1397               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1398             overlay_counts[overlay_type]++;
1399             current_row->child(child)->setData(column,Qt::CheckStateRole,
1400                                                current_row->data(column,Qt::CheckStateRole));
1401             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1402           }
1403         } else { //We don't allow simply desactivating a slicer
1404           clicked_item->setData(column,Qt::CheckStateRole,2);
1405           DisplayChanged(clicked_item, column);
1406           return;
1407         }
1408       }
1409       //if we clicked on the vector(or overlay) and not the image
1410       else {
1411         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1412           current_row->setData(column,Qt::CheckStateRole,2);
1413           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1414           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1415           DisplaySliders(i,column-1);
1416         }
1417         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1418         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1419         int overlay_index=0;
1420         for (int child = 0; child < current_row->childCount(); child++) {
1421           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1422             overlay_index++;
1423           if (current_row->child(child) == clicked_item) break;
1424         }
1425         clicked_slicer->SetActorVisibility(
1426           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1427       }
1428     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1429       current_row->setData(column,Qt::CheckStateRole,0);
1430       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1431       std::map<std::string,int> overlay_counts;
1432       for (int child = 0; child < current_row->childCount(); child++) {
1433         std::string overlay_type =
1434           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1435         overlay_counts[overlay_type]++;
1436         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1437         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1438         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1439       }
1440     }
1441     //mSlicerManagers[i]->SetColorMap(-1);
1442     mSlicerManagers[i]->SetColorMap();
1443   }
1444   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1445 }
1446 //------------------------------------------------------------------------------
1447
1448 void vvMainWindow::InitSlicers()
1449 {
1450   if (mSlicerManagers.size()) {
1451     mSlicerManagers.back()->GenerateDefaultLookupTable();
1452
1453     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1454     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1455     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1456     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1457   }
1458 }
1459
1460 //------------------------------------------------------------------------------
1461 void vvMainWindow::InitDisplay()
1462 {
1463   if (mSlicerManagers.size()) {
1464     //BE CAREFUL : this is absolutely necessary to set the interactor style
1465     //in order to have the same style instanciation for all SlicerManagers in
1466     // a same window
1467     for (int j = 0; j < 4; j++) {
1468       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1469       style->SetAutoAdjustCameraClippingRange(1);
1470       bool AlreadySelected = false;
1471       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1472         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1473
1474         //select the image only if previous are not selected
1475         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1476           mSlicerManagers[i]->UpdateSlicer(j,1);
1477           AlreadySelected = true;
1478         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1479           if (DataTree->selectedItems().size() == 0)
1480             DataTree->topLevelItem(i)->setSelected(1);
1481           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1482           mSlicerManagers[i]->UpdateSlicer(j,1);
1483           DisplaySliders(i,j);
1484         } else {
1485           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1486           mSlicerManagers[i]->UpdateSlicer(j,0);
1487         }
1488       }
1489       style->Delete();
1490     }
1491   }
1492 }
1493 //------------------------------------------------------------------------------
1494
1495 //------------------------------------------------------------------------------
1496 void vvMainWindow::DisplaySliders(int slicer, int window)
1497 {
1498   int range[2];
1499   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1500   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1501
1502   int tRange[2];
1503   tRange[0] = 0;
1504   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1505   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1506   bool showHorizontal = false;
1507   bool showVertical = false;
1508   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1509       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1510           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1511           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1512     showVertical = true;
1513   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1514       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1515       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1516     showHorizontal = true;
1517
1518   if (showVertical)
1519     verticalSliders[window]->show();
1520   else
1521     verticalSliders[window]->hide();
1522   verticalSliders[window]->setRange(range[0],range[1]);
1523   verticalSliders[window]->setValue(position);
1524
1525   if (showHorizontal)
1526     horizontalSliders[window]->show();
1527   else
1528     horizontalSliders[window]->hide();
1529   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1530   horizontalSliders[window]->setValue(tPosition);
1531 }
1532 //------------------------------------------------------------------------------
1533
1534 //------------------------------------------------------------------------------
1535 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1536 {
1537   int index = GetSlicerIndexFromItem(item);
1538
1539   if (DataTree->topLevelItem(index) != item) {
1540     QString warning = "Do you really want to close the overlay : ";
1541     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1542     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1543                        warning, 0, this);
1544     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1545     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1546     if (msgBox.exec() == QMessageBox::AcceptRole) {
1547       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1548       int overlay_index=0;
1549       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1550         if (DataTree->topLevelItem(index)->\
1551             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1552           overlay_index++;
1553         if (DataTree->topLevelItem(index)->child(child) == item) break;
1554       }
1555       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1556       mSlicerManagers[index]->SetColorMap(0);
1557       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1558       mSlicerManagers[index]->Render();
1559     }
1560   } else if (DataTree->topLevelItemCount() <= 1) {
1561     QString warning = "Do you really want to close the image : ";
1562     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1563     warning += "\nThis is the last image, you're about to close vv !!!";
1564     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1565                        warning, 0, this);
1566     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1567     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1568     if (msgBox.exec() == QMessageBox::AcceptRole) {
1569       this->close();
1570     }
1571   } else {
1572     QString warning = "Do you really want to close the image : ";
1573     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1574     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1575                        warning, 0, this);
1576     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1577     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1578     if (msgBox.exec() == QMessageBox::AcceptRole) {
1579
1580       // Tell tools that we close an image
1581       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1582
1583       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1584       DataTree->takeTopLevelItem(index);
1585       for (int i = 0; i < index; i++) {
1586         Manageriter++;
1587       }
1588       linkPanel->removeImage(index);
1589       mSlicerManagers[index]->RemoveActors();
1590       delete mSlicerManagers[index];
1591       mSlicerManagers.erase(Manageriter);
1592
1593       //
1594       InitDisplay();
1595     }
1596   }
1597   ImageInfoChanged();
1598 }
1599 //------------------------------------------------------------------------------
1600
1601 //------------------------------------------------------------------------------
1602 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1603 {
1604   // int index = GetSlicerIndexFromItem(item);
1605   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1606   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1607   //     mSlicerManagers[index]->ReloadVF();
1608   //   else
1609   //     mSlicerManagers[index]->Reload();
1610
1611   //   QApplication::restoreOverrideCursor();
1612   int index = GetSlicerIndexFromItem(item);
1613   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1614   QString role=item->data(1,Qt::UserRole).toString();
1615   if ( role == "vector")
1616     mSlicerManagers[index]->ReloadVF();
1617   else if (role == "overlay")
1618     mSlicerManagers[index]->ReloadOverlay();
1619   else if (role == "fusion")
1620     mSlicerManagers[index]->ReloadFusion();
1621   else
1622     mSlicerManagers[index]->Reload();
1623
1624   // Update view and info
1625   ImageInfoChanged();
1626   mSlicerManagers[index]->Render();
1627   QApplication::restoreOverrideCursor();
1628 }
1629 //------------------------------------------------------------------------------
1630
1631 //------------------------------------------------------------------------------
1632 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1633 {
1634   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1635 }
1636 //------------------------------------------------------------------------------
1637
1638 //------------------------------------------------------------------------------
1639 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1640 {
1641   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1642 }
1643 //------------------------------------------------------------------------------
1644
1645 //------------------------------------------------------------------------------
1646 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1647 {
1648   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1649 }
1650 //------------------------------------------------------------------------------
1651
1652 //------------------------------------------------------------------------------
1653 void vvMainWindow::FusionChanged(int visibility, double value)
1654 {
1655   overlayPanel->getCurrentFusionInfo(visibility,value);
1656 }
1657 //------------------------------------------------------------------------------
1658
1659 //------------------------------------------------------------------------------
1660 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1661 {
1662   infoPanel->setViews(window, view, slice);
1663 }
1664 //------------------------------------------------------------------------------
1665
1666 //------------------------------------------------------------------------------
1667 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1668 {
1669   windowSpinBox->setValue(window);
1670   levelSpinBox->setValue(level);
1671   colorMapComboBox->setCurrentIndex(colormap);
1672   presetComboBox->setCurrentIndex(preset);
1673 }
1674 //------------------------------------------------------------------------------
1675
1676 //------------------------------------------------------------------------------
1677 void vvMainWindow::WindowLevelEdited()
1678 {
1679   presetComboBox->setCurrentIndex(6);
1680   UpdateWindowLevel();
1681 }
1682 //------------------------------------------------------------------------------
1683
1684 //------------------------------------------------------------------------------
1685 void vvMainWindow::UpdateWindowLevel()
1686 {
1687   if (DataTree->selectedItems().size()) {
1688     if (presetComboBox->currentIndex() == 7) //For ventilation
1689       colorMapComboBox->setCurrentIndex(5);
1690     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1691     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1692     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1693     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1694     mSlicerManagers[index]->Render();
1695     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1696     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1697   }
1698 }
1699 //------------------------------------------------------------------------------
1700
1701 //------------------------------------------------------------------------------
1702 void vvMainWindow::UpdateColorMap()
1703 {
1704   if (DataTree->selectedItems().size()) {
1705     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1706     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1707     mSlicerManagers[index]->Render();
1708   }
1709 }
1710 //------------------------------------------------------------------------------
1711 void vvMainWindow::SwitchWindowLevel()
1712 {
1713   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1714   int window = mSlicerManagers[index]->GetColorWindow();
1715   presetComboBox->setCurrentIndex(6);
1716   windowSpinBox->setValue(-window);
1717   UpdateWindowLevel();
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::ApplyWindowLevelToAllImages()
1723 {
1724   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1725     if (mSlicerManagers[i] == NULL)
1726       continue;
1727     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1728     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1729     mSlicerManagers[i]->SetPreset(6);
1730     mSlicerManagers[i]->Render();
1731   }
1732 }
1733 //------------------------------------------------------------------------------
1734
1735 //------------------------------------------------------------------------------
1736 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1737 {
1738   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1739     if (mSlicerManagers[i]->GetId() == id) {
1740       //mSlicerManagers[i]->SetTSlice(temps);
1741       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1742       mSlicerManagers[i]->UpdateViews(0,slicer);
1743       break;
1744     }
1745   }
1746 }
1747 //------------------------------------------------------------------------------
1748
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1751 {
1752   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1753     if (id == mSlicerManagers[i]->GetId()) {
1754       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1755     }
1756   }
1757 }
1758 //------------------------------------------------------------------------------
1759
1760 //------------------------------------------------------------------------------
1761 void vvMainWindow::ShowContextMenu(QPoint point)
1762 {
1763   if (!DataTree->selectedItems().size()) {
1764     contextActions[1]->setEnabled(0);
1765     contextActions[2]->setEnabled(0);
1766     contextActions[3]->setEnabled(0);
1767     contextActions[4]->setEnabled(0);
1768     contextActions[5]->setEnabled(0);
1769     contextActions[6]->setEnabled(0);
1770   } else {
1771     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1772     contextActions[1]->setEnabled(1);
1773     contextActions[2]->setEnabled(
1774       DataTree->itemWidget(DataTree->selectedItems()[0],
1775                            COLUMN_RELOAD_IMAGE)->isEnabled());
1776     contextActions[3]->setEnabled(1);
1777     contextActions[5]->setEnabled(1);
1778     contextActions[6]->setEnabled(1);
1779
1780     if (mSlicerManagers[index]->GetDimension() < 3)
1781       contextActions[4]->setEnabled(0);
1782     else
1783       contextActions[4]->setEnabled(1);
1784   }
1785   contextMenu.exec(QCursor::pos());
1786 }
1787 //------------------------------------------------------------------------------
1788
1789 //------------------------------------------------------------------------------
1790 void vvMainWindow::CloseImage()
1791 {
1792   CloseImage(DataTree->selectedItems()[0],0);
1793 }
1794 //------------------------------------------------------------------------------
1795
1796 //------------------------------------------------------------------------------
1797 void vvMainWindow::ReloadImage()
1798 {
1799   ReloadImage(DataTree->selectedItems()[0],0);
1800 }
1801 //------------------------------------------------------------------------------
1802
1803 //------------------------------------------------------------------------------
1804 void vvMainWindow::SelectOverlayImage()
1805 {
1806   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1807
1808   //check if one overlay image is added
1809   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1810     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1811       QString error = "Cannot add more than one compared image\n";
1812       error += "Please remove first ";
1813       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1814       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1815       return;
1816     }
1817
1818   QString Extensions = EXTENSIONS;
1819   Extensions += ";;All Files (*)";
1820   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1821   if (!file.isEmpty())
1822     AddOverlayImage(index,file);
1823 }
1824 //------------------------------------------------------------------------------
1825
1826 //------------------------------------------------------------------------------
1827 void vvMainWindow::AddOverlayImage(int index, QString file)
1828 {
1829
1830   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1831   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1832                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1833   reader->SetFileName(file.toStdString().c_str());
1834   reader->ReadImageInformation();
1835   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1836   int dimension = reader->GetNumberOfDimensions();
1837   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1838   vvProgressDialog progress("Opening " + file.toStdString());
1839   qApp->processEvents();
1840
1841   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1842   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1843     //create an item in the tree with good settings
1844     QTreeWidgetItem *item = new QTreeWidgetItem();
1845     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1846     item->setData(1,Qt::UserRole,tr("overlay"));
1847     QFileInfo fileinfo(file); //Do not show the path
1848     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1849     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1850     qApp->processEvents();
1851
1852     for (int j = 1; j <= 4; j++) {
1853       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1854       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1855           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1856     }
1857
1858     //Create the buttons for reload and close
1859     qApp->processEvents();
1860     QTreePushButton* cButton = new QTreePushButton;
1861     cButton->setItem(item);
1862     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1863     cButton->setToolTip(tr("close image"));
1864     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1865     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1866             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1867
1868     QTreePushButton* rButton = new QTreePushButton;
1869     rButton->setItem(item);
1870     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1871     rButton->setToolTip(tr("reload image"));
1872     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1873     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1874             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1875
1876     DataTree->topLevelItem(index)->setExpanded(1);
1877     DataTree->topLevelItem(index)->addChild(item);
1878     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1879     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1880
1881     //set the id of the image
1882     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1883     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1884     UpdateTree();
1885     qApp->processEvents();
1886     ImageInfoChanged();
1887     QApplication::restoreOverrideCursor();
1888   } else {
1889     QApplication::restoreOverrideCursor();
1890     QString error = "Cannot import the new image.\n";
1891     error += mSlicerManagers[index]->GetLastError().c_str();
1892     QMessageBox::information(this,tr("Problem reading image !"),error);
1893   }
1894 }
1895 //------------------------------------------------------------------------------
1896
1897
1898 //------------------------------------------------------------------------------
1899 void vvMainWindow::AddROI(int index, QString file)
1900 {
1901   /*
1902   // Get slice manager
1903
1904   // Load image
1905
1906   vvImageReader * mReader = new vvImageReader;
1907   mReader->SetInputFilename(filename.toStdString());
1908   mReader->Update(IMAGE);
1909   if (mReader->GetLastError().size() != 0) {
1910     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1911     QString error = "Cannot open file \n";
1912     error += mReader->GetLastError().c_str();
1913     QMessageBox::information(this,tr("Reading problem"),error);
1914     delete mReader;
1915     return;
1916   }
1917   vvImage::Pointer roi = mReader->GetOutput();
1918
1919   // Create roi in new tool
1920   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1921   */
1922 }
1923 //------------------------------------------------------------------------------
1924
1925 //------------------------------------------------------------------------------
1926 void vvMainWindow::SelectFusionImage()
1927 {
1928   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1929
1930   //check if one fusion image is added
1931   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1932     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1933       QString error = "Cannot add more than one fusion image\n";
1934       error += "Please remove first ";
1935       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1936       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1937       return;
1938     }
1939
1940   QString Extensions = EXTENSIONS;
1941   Extensions += ";;All Files (*)";
1942   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1943   if (!file.isEmpty())
1944     AddFusionImage(index,file);
1945 }
1946 //------------------------------------------------------------------------------
1947
1948 //------------------------------------------------------------------------------
1949 void vvMainWindow::AddFusionImage(int index, QString file)
1950 {
1951   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1952   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1953                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1954   reader->SetFileName(file.toStdString().c_str());
1955   reader->ReadImageInformation();
1956   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1957   if (reader) {
1958     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1959     vvProgressDialog progress("Opening fusion");
1960     qApp->processEvents();
1961
1962     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1963     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1964                                           reader->GetNumberOfDimensions(), component)) {
1965       //create an item in the tree with good settings
1966       QTreeWidgetItem *item = new QTreeWidgetItem();
1967       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1968       item->setData(1,Qt::UserRole,tr("fusion"));
1969       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1970       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1971       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1972       qApp->processEvents();
1973
1974       for (int j = 1; j <= 4; j++) {
1975         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1976         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1977             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1978       }
1979
1980       //Create the buttons for reload and close
1981       qApp->processEvents();
1982       QTreePushButton* cButton = new QTreePushButton;
1983       cButton->setItem(item);
1984       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1985       cButton->setToolTip(tr("close image"));
1986       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1987       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1988               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1989
1990       QTreePushButton* rButton = new QTreePushButton;
1991       rButton->setItem(item);
1992       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1993       rButton->setToolTip(tr("reload image"));
1994       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1995       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1996               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1997
1998       DataTree->topLevelItem(index)->setExpanded(1);
1999       DataTree->topLevelItem(index)->addChild(item);
2000       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2001       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2002
2003       //set the id of the image
2004       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2005       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2006       UpdateTree();
2007       qApp->processEvents();
2008       ImageInfoChanged();
2009       QApplication::restoreOverrideCursor();
2010     } else {
2011       QApplication::restoreOverrideCursor();
2012       QString error = "Cannot import the new image.\n";
2013       error += mSlicerManagers[index]->GetLastError().c_str();
2014       QMessageBox::information(this,tr("Problem reading image !"),error);
2015     }
2016   } else {
2017     QString error = "Cannot import the new image.\n";
2018     QMessageBox::information(this,tr("Problem reading image !"),error);
2019   }
2020 }
2021 //------------------------------------------------------------------------------
2022
2023
2024 //------------------------------------------------------------------------------
2025 void vvMainWindow::OpenField()
2026 {
2027   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2028   //check if a vector field has already been added
2029   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2030     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2031       QString error = "Cannot add more than one vector field\n";
2032       error += "Please remove first ";
2033       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2034       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2035       return;
2036     }
2037
2038   QString Extensions = "Images ( *.mhd)";
2039   Extensions += ";;Images ( *.vf)";
2040   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2041   if (!file.isEmpty())
2042     AddField(file,index);
2043 }
2044 //------------------------------------------------------------------------------
2045
2046
2047 //------------------------------------------------------------------------------
2048 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2049 {
2050   //create an item in the tree with good settings
2051   QTreeWidgetItem *item = new QTreeWidgetItem();
2052   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2053   item->setData(1,Qt::UserRole,tr("vector"));
2054   QFileInfo fileinfo(filename); //Do not show the path
2055   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2056   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2057   qApp->processEvents();
2058
2059   for (int j = 1; j <= 4; j++) {
2060     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2061     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2062         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2063   }
2064
2065   //Create the buttons for reload and close
2066   qApp->processEvents();
2067   QTreePushButton* cButton = new QTreePushButton;
2068   cButton->setItem(item);
2069   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2070   cButton->setToolTip(tr("close vector field"));
2071   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2072   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2073           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2074
2075   QTreePushButton* rButton = new QTreePushButton;
2076   rButton->setItem(item);
2077   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2078   rButton->setToolTip(tr("reload vector field"));
2079   rButton->setEnabled(from_disk);
2080   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2081   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2082           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2083
2084   DataTree->topLevelItem(index)->setExpanded(1);
2085   DataTree->topLevelItem(index)->addChild(item);
2086   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2087   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2088
2089   //set the id of the image
2090   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2091   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2092   UpdateTree();
2093   qApp->processEvents();
2094   ImageInfoChanged();
2095   QApplication::restoreOverrideCursor();
2096 }
2097 //------------------------------------------------------------------------------
2098
2099
2100 //------------------------------------------------------------------------------
2101 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2102 {
2103   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2104   vvSlicerManager* imageManager = mSlicerManagers[index];
2105   if (imageManager->SetVF(vf,file.toStdString())) {
2106     AddFieldEntry(file,index,false);
2107   } else {
2108     QString error = "Cannot import the vector field for this image.\n";
2109     error += imageManager->GetLastError().c_str();
2110     QMessageBox::information(this,tr("Problem reading VF !"),error);
2111   }
2112   QApplication::restoreOverrideCursor();
2113 }
2114 //------------------------------------------------------------------------------
2115
2116
2117 //------------------------------------------------------------------------------
2118 void vvMainWindow::AddField(QString file,int index)
2119 {
2120   if (QFile::exists(file)) {
2121     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2122
2123     //init the progress events
2124     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2125     vvProgressDialog progress("Opening " + file.toStdString());
2126     qApp->processEvents();
2127
2128     //read the vector and put it in the current mSlicerManager
2129     vvSlicerManager* imageManager = mSlicerManagers[index];
2130     qApp->processEvents();
2131
2132     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2133     if (imageManager->SetVF(file.toStdString())) {
2134       imageManager->Render();
2135       AddFieldEntry(file,index,true);
2136     } else {
2137       QApplication::restoreOverrideCursor();
2138       QString error = "Cannot import the vector field for this image.\n";
2139       error += imageManager->GetLastError().c_str();
2140       QMessageBox::information(this,tr("Problem reading VF !"),error);
2141     }
2142   } else
2143     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2144
2145 }
2146 //------------------------------------------------------------------------------
2147
2148
2149 //------------------------------------------------------------------------------
2150 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2151 {
2152   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2153   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2154     for (int i = 0; i < 4; i++) {
2155       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2156       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2157       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2158       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2159       if (log > 0)
2160         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2161       else
2162         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2163     }
2164   }
2165 }
2166 //------------------------------------------------------------------------------
2167
2168
2169 //------------------------------------------------------------------------------
2170 void vvMainWindow::SetOverlayProperty(int color)
2171 {
2172   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2173   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2174     mSlicerManagers[index]->SetOverlayColor(color);
2175     mSlicerManagers[index]->SetColorMap(0);
2176     mSlicerManagers[index]->Render();
2177   }
2178 }
2179 //------------------------------------------------------------------------------
2180
2181 //------------------------------------------------------------------------------
2182 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2183 {
2184   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2185   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2186     mSlicerManagers[index]->SetFusionOpacity(opacity);
2187     mSlicerManagers[index]->SetFusionColorMap(colormap);
2188     mSlicerManagers[index]->SetFusionWindow(window);
2189     mSlicerManagers[index]->SetFusionLevel(level);
2190     mSlicerManagers[index]->SetColorMap(0);
2191     mSlicerManagers[index]->Render();
2192   }
2193 }
2194 //------------------------------------------------------------------------------
2195
2196 //------------------------------------------------------------------------------
2197 void vvMainWindow::SaveAs()
2198 {
2199   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2200     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2201     return;
2202   }
2203
2204   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2205   int dimension = mSlicerManagers[index]->GetDimension();
2206   QStringList OutputListeFormat;
2207   OutputListeFormat.clear();
2208   if (dimension == 1) {
2209     OutputListeFormat.push_back(".mhd");
2210   }
2211   if (dimension == 2) {
2212     OutputListeFormat.push_back(".bmp");
2213     OutputListeFormat.push_back(".png");
2214     OutputListeFormat.push_back(".jpeg");
2215     OutputListeFormat.push_back(".tif");
2216     OutputListeFormat.push_back(".mhd");
2217     OutputListeFormat.push_back(".hdr");
2218     OutputListeFormat.push_back(".vox");
2219   } else if (dimension == 3) {
2220     OutputListeFormat.push_back(".mhd");
2221     OutputListeFormat.push_back(".hdr");
2222     OutputListeFormat.push_back(".vox");
2223   } else if (dimension == 4) {
2224     OutputListeFormat.push_back(".mhd");
2225   }
2226   QString Extensions = "AllFiles(*.*)";
2227   for (int i = 0; i < OutputListeFormat.count(); i++) {
2228     Extensions += ";;Images ( *";
2229     Extensions += OutputListeFormat[i];
2230     Extensions += ")";
2231   }
2232   QString fileName = QFileDialog::getSaveFileName(this,
2233                      tr("Save As"),
2234                      mSlicerManagers[index]->GetFileName().c_str(),
2235                      Extensions);
2236   if (!fileName.isEmpty()) {
2237     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2238     if (OutputListeFormat.contains(
2239           fileformat.c_str())) {
2240       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2241       std::string action = "Saving";
2242       vvProgressDialog progress("Saving "+fileName.toStdString());
2243       qApp->processEvents();
2244       vvImageWriter::Pointer writer = vvImageWriter::New();
2245       writer->SetOutputFileName(fileName.toStdString());
2246       writer->SetInput(mSlicerManagers[index]->GetImage());
2247       writer->Update();
2248       QApplication::restoreOverrideCursor();
2249       if (writer->GetLastError().size()) {
2250         QString error = "Saving did not succeed\n";
2251         error += writer->GetLastError().c_str();
2252         QMessageBox::information(this,tr("Saving Problem"),error);
2253         SaveAs();
2254       }
2255     } else {
2256       QString error = fileformat.c_str();
2257       if (error.isEmpty())
2258         error += "no file format specified !";
2259       else
2260         error += " format unknown !!!\n";
2261       QMessageBox::information(this,tr("Saving Problem"),error);
2262       SaveAs();
2263     }
2264   }
2265 }
2266 //------------------------------------------------------------------------------
2267
2268
2269 //------------------------------------------------------------------------------
2270 void vvMainWindow::AddLink(QString image1,QString image2)
2271 {
2272   unsigned int sm1 = 0;
2273   unsigned int sm2 = 0;
2274
2275   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2276     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2277       mSlicerManagers[i]->AddLink(image2.toStdString());
2278       sm1 = i;
2279     }
2280     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2281       mSlicerManagers[i]->AddLink(image1.toStdString());
2282       sm2 = i;
2283     }
2284   }
2285
2286   if (linkPanel->isLinkAll())   {
2287     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2288     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2289   } else {
2290     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2291   }
2292 }
2293
2294 //------------------------------------------------------------------------------
2295
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::RemoveLink(QString image1,QString image2)
2299 {
2300   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2301     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2302       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2303     }
2304     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2305       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2306     }
2307   }
2308 }
2309 //------------------------------------------------------------------------------
2310
2311 //------------------------------------------------------------------------------
2312 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2313 {
2314   int index = 0;
2315   while(sm != mSlicerManagers[index])
2316     index++;
2317   index = (index+offset) % mSlicerManagers.size();
2318
2319   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2320   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2321   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2322   DisplayChanged(item,slicer+1);
2323 }
2324 //------------------------------------------------------------------------------
2325
2326 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2327 {
2328   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2329     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2330       for (int j = 0; j < 4; j++) {
2331         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2332         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2333         //UpdateTSlice(j,value);
2334       }
2335       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2336       break;
2337     }
2338   }
2339 }
2340 //------------------------------------------------------------------------------
2341
2342
2343 //------------------------------------------------------------------------------
2344 void vvMainWindow::NOHorizontalSliderMoved()
2345 {
2346   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2347   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2348 //  mCurrentTime = NOHorizontalSlider->value();
2349 }
2350 //------------------------------------------------------------------------------
2351
2352
2353 //------------------------------------------------------------------------------
2354 void vvMainWindow::NEHorizontalSliderMoved()
2355 {
2356   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2357   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2358 //  mCurrentTime = NEHorizontalSlider->value();
2359 }
2360 //------------------------------------------------------------------------------
2361
2362
2363 //------------------------------------------------------------------------------
2364 void vvMainWindow::SOHorizontalSliderMoved()
2365 {
2366   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2367   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2368   // mCurrentTime = SOHorizontalSlider->value();
2369 }
2370 //------------------------------------------------------------------------------
2371
2372
2373 //------------------------------------------------------------------------------
2374 void vvMainWindow::SEHorizontalSliderMoved()
2375 {
2376   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2377   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2378   // mCurrentTime = SEHorizontalSlider->value();
2379 }
2380 //------------------------------------------------------------------------------
2381
2382 //------------------------------------------------------------------------------
2383 void vvMainWindow::NOVerticalSliderChanged()
2384 {
2385   static int value=-1;
2386   if (value == NOVerticalSlider->value()) return;
2387   else value = NOVerticalSlider->value();
2388   //  int value = NOVerticalSlider->value();
2389   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2390     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2391       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2392         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2393         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2394
2395         // If nor Update/Render -> slider not work
2396         // only render = ok navigation, but for contour Update needed but slower ?
2397
2398         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2399         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2400       }
2401       break;
2402     }
2403   }
2404 }
2405 //------------------------------------------------------------------------------
2406
2407
2408 //------------------------------------------------------------------------------
2409 void vvMainWindow::NEVerticalSliderChanged()
2410 {
2411   static int value=-1;
2412   if (value == NEVerticalSlider->value()) return;
2413   else value = NEVerticalSlider->value();
2414   //  int value = NEVerticalSlider->value();
2415   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2416     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2417       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2418         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2419         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2420         mSlicerManagers[i]->UpdateSlice(1);
2421         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2422       }
2423       break;
2424     }
2425   }
2426 }
2427 //------------------------------------------------------------------------------
2428
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::SOVerticalSliderChanged()
2432 {
2433   static int value=-1;
2434   if (value == SOVerticalSlider->value()) return;
2435   else value = SOVerticalSlider->value();
2436   //int value = SOVerticalSlider->value();
2437   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2438     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2439       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2440         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2441         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2442         mSlicerManagers[i]->UpdateSlice(2);
2443         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2444       }
2445       // else { DD("avoid SOVerticalSlider slicer update"); }
2446       break;
2447     }
2448   }
2449 }
2450 //------------------------------------------------------------------------------
2451
2452
2453 //------------------------------------------------------------------------------
2454 void vvMainWindow::SEVerticalSliderChanged()
2455 {
2456   static int value=-1;
2457   if (value == SEVerticalSlider->value()) return;
2458   else value = SEVerticalSlider->value();
2459   // int value = SEVerticalSlider->value();
2460   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2461     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2462       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2463         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2464         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2465         mSlicerManagers[i]->UpdateSlice(3);
2466         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2467       }
2468       break;
2469     }
2470   }
2471 }
2472 //------------------------------------------------------------------------------
2473
2474
2475 //------------------------------------------------------------------------------
2476 void vvMainWindow::UpdateSlice(int slicer, int slice)
2477 {
2478   // DD("vvMainWindow::UpdateSlice");
2479 //   DD(slicer);
2480 //   DD(slice);
2481   if (slicer == 0) {
2482     //    if (slice != NOVerticalSlider->value())
2483     NOVerticalSlider->setValue(slice);
2484   } else {
2485     if (slicer == 1)
2486       NEVerticalSlider->setValue(slice);
2487     else {
2488       if (slicer == 2)
2489         SOVerticalSlider->setValue(slice);
2490       else {
2491         if (slicer == 3)
2492           SEVerticalSlider->setValue(slice);
2493       }
2494     }
2495   }
2496   // DD("vvMainWindow:UpdateSlice END");
2497 }
2498 //------------------------------------------------------------------------------
2499
2500
2501 //------------------------------------------------------------------------------
2502 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2503 {
2504   switch (slicer) {
2505   case 0:
2506     NOHorizontalSlider->setValue(slice);
2507     break;
2508   case 1:
2509     NEHorizontalSlider->setValue(slice);
2510     break;
2511   case 2:
2512     SOHorizontalSlider->setValue(slice);
2513     break;
2514   case 3:
2515     SEHorizontalSlider->setValue(slice);
2516     break;
2517   }
2518 }
2519 //------------------------------------------------------------------------------
2520
2521
2522 //------------------------------------------------------------------------------
2523 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2524 {
2525   int position = int((min+max)/2);
2526   int tPosition = int((tmin+tmax)/2);
2527   if (slicer == 0) {
2528     NOVerticalSlider->setValue(position);
2529     NOVerticalSlider->setRange(min,max);
2530     NOHorizontalSlider->setRange(tmin,tmax);
2531     NOHorizontalSlider->setValue(tPosition);
2532   } else if (slicer == 1) {
2533     NEVerticalSlider->setValue(position);
2534     NEVerticalSlider->setRange(min,max);
2535     NEHorizontalSlider->setRange(tmin,tmax);
2536     NEHorizontalSlider->setValue(tPosition);
2537   } else if (slicer == 2) {
2538     SOVerticalSlider->setValue(position);
2539     SOVerticalSlider->setRange(min,max);
2540     SOHorizontalSlider->setRange(tmin,tmax);
2541     SOHorizontalSlider->setValue(tPosition);
2542   } else if (slicer == 3) {
2543     SEVerticalSlider->setValue(position);
2544     SEVerticalSlider->setRange(min,max);
2545     SEHorizontalSlider->setRange(tmin,tmax);
2546     SEHorizontalSlider->setValue(tPosition);
2547   }
2548 }
2549 //------------------------------------------------------------------------------
2550
2551
2552 //------------------------------------------------------------------------------
2553 void vvMainWindow::SaveNOScreenshot()
2554 {
2555   SaveScreenshot(NOViewWidget);
2556 }
2557 //------------------------------------------------------------------------------
2558
2559
2560 //------------------------------------------------------------------------------
2561 void vvMainWindow::SaveNEScreenshot()
2562 {
2563   SaveScreenshot(NEViewWidget);
2564 }
2565 //------------------------------------------------------------------------------
2566
2567
2568 //------------------------------------------------------------------------------
2569 void vvMainWindow::SaveSOScreenshot()
2570 {
2571   SaveScreenshot(SOViewWidget);
2572 }
2573 //------------------------------------------------------------------------------
2574
2575
2576 //------------------------------------------------------------------------------
2577 void vvMainWindow::SaveSEScreenshot()
2578 {
2579   SaveScreenshot(SEViewWidget);
2580 }
2581 //------------------------------------------------------------------------------
2582
2583
2584 //------------------------------------------------------------------------------
2585 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2586 {
2587   QString Extensions = "Images( *.png);;";
2588   Extensions += "Images( *.jpg);;";
2589   Extensions += "Images( *.bmp);;";
2590   Extensions += "Images( *.tif);;";
2591   Extensions += "Images( *.ppm)";
2592 #ifdef VTK_USE_FFMPEG_ENCODER
2593   Extensions += "Images( *.avi)";
2594 #endif
2595 #ifdef VTK_USE_MPEG2_ENCODER
2596   Extensions += "Images( *.mpg)";
2597 #endif
2598
2599   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2600   QString fileName = QFileDialog::getSaveFileName(this,
2601                      tr("Save As"),
2602                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2603                      Extensions);
2604
2605   if (!fileName.isEmpty()) {
2606     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2607     w2i->SetInput(widget->GetRenderWindow());
2608     w2i->Update();
2609     vtkImageData *image = w2i->GetOutput();
2610
2611     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2612     if (!strcmp(ext, ".bmp")) {
2613       vtkBMPWriter *bmp = vtkBMPWriter::New();
2614       bmp->SetInput(image);
2615       bmp->SetFileName(fileName.toStdString().c_str());
2616       bmp->Write();
2617       bmp->Delete();
2618     } else if (!strcmp(ext, ".tif")) {
2619       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2620       tif->SetInput(image);
2621       tif->SetFileName(fileName.toStdString().c_str());
2622       tif->Write();
2623       tif->Delete();
2624     } else if (!strcmp(ext, ".ppm")) {
2625       vtkPNMWriter *pnm = vtkPNMWriter::New();
2626       pnm->SetInput(image);
2627       pnm->SetFileName(fileName.toStdString().c_str());
2628       pnm->Write();
2629       pnm->Delete();
2630     } else if (!strcmp(ext, ".png")) {
2631       vtkPNGWriter *png = vtkPNGWriter::New();
2632       png->SetInput(image);
2633       png->SetFileName(fileName.toStdString().c_str());
2634       png->Write();
2635       png->Delete();
2636     } else if (!strcmp(ext, ".jpg")) {
2637       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2638       jpg->SetInput(image);
2639       jpg->SetFileName(fileName.toStdString().c_str());
2640       jpg->Write();
2641       jpg->Delete();
2642 #ifdef VTK_USE_FFMPEG_ENCODER
2643     } else if (!strcmp(ext, ".avi")) {
2644       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2645       mpg->SetInput(image);
2646       mpg->SetFileName(fileName.toStdString().c_str());
2647       mpg->SetQuality(2);
2648       mpg->SetRate(5);
2649       mpg->Start();
2650
2651       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2652       int nSlice = vvImg->GetVTKImages().size();
2653       for(int i=0; i<nSlice; i++) {
2654         mSlicerManagers[smIndex]->SetNextTSlice(0);
2655         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2656         w2i->SetInput(widget->GetRenderWindow());
2657         w2i->Update();
2658         mpg->SetInput(w2i->GetOutput());
2659         mpg->Write();
2660       }
2661       mpg->End();
2662       mpg->Delete();
2663 #endif
2664 #ifdef VTK_USE_MPEG2_ENCODER
2665     } else if (!strcmp(ext, ".mpg")) {
2666       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2667       mpg->SetInput(image);
2668       mpg->SetFileName(fileName.toStdString().c_str());
2669       mpg->Start();
2670
2671       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2672       int nSlice = vvImg->GetVTKImages().size();
2673       for(int i=0; i<nSlice; i++) {
2674         mSlicerManagers[smIndex]->SetNextTSlice(0);
2675         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2676         w2i->SetInput(widget->GetRenderWindow());
2677         w2i->Update();
2678         mpg->SetInput(w2i->GetOutput());
2679         mpg->Write();
2680       }
2681       mpg->End();
2682       mpg->Delete();
2683 #endif
2684     } else {
2685       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2686     }
2687   }
2688 }
2689 //------------------------------------------------------------------------------
2690
2691
2692 //------------------------------------------------------------------------------
2693 void vvMainWindow::GoToCursor()
2694 {
2695   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2696   for (int column = 1; column < 5; column++) {
2697     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2698       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2699       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2700         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2701       mSlicerManagers[index]->UpdateViews(1,column-1);
2702       mSlicerManagers[index]->UpdateLinked(column-1);
2703       break;
2704     }
2705   }
2706 }
2707 //------------------------------------------------------------------------------
2708
2709 //------------------------------------------------------------------------------
2710 void vvMainWindow::PlayPause()
2711 {
2712   if (playMode) {
2713     playMode = 0;
2714     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2715     ImageInfoChanged();
2716     return;
2717   } else {
2718     int image_number=DataTree->topLevelItemCount();
2719     bool has_temporal;
2720     for (int i=0; i<image_number; i++)
2721       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2722         has_temporal=true;
2723         break;
2724       }
2725     if (has_temporal) {
2726       playMode = 1;
2727       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2728       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2729     }
2730   }
2731 }
2732 //------------------------------------------------------------------------------
2733
2734 //------------------------------------------------------------------------------
2735 void vvMainWindow::PlayNext()
2736 {
2737   if (playMode && !this->isHidden()) {
2738     int image_number=DataTree->topLevelItemCount();
2739     ///Only play one slicer per SM, and only if the SM is being displayed
2740     for (int i=0; i<image_number; i++)
2741       for (int j=0; j<4; j++)
2742         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2743             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2744           mSlicerManagers[i]->SetNextTSlice(j);
2745           break;
2746         }
2747     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2748   }
2749 }
2750 //------------------------------------------------------------------------------
2751
2752 void vvMainWindow::ShowLastImage()
2753 {
2754   if (mSlicerManagers.size() > 1) {
2755     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2756     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2757     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2758     DisplayChanged(item,1);
2759   }
2760 }
2761
2762 //------------------------------------------------------------------------------
2763 void vvMainWindow::UpdateRenderWindows()
2764 {
2765   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2766   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2767   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2768   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2769 }
2770 //------------------------------------------------------------------------------
2771
2772 //------------------------------------------------------------------------------
2773 void vvMainWindow::SegmentationOnCurrentImage()
2774 {
2775   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2776
2777   vvSegmentationDialog segmentation;
2778   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2779   segmentation.exec();
2780 }
2781 //------------------------------------------------------------------------------
2782
2783 void vvMainWindow::SurfaceViewerLaunch()
2784 {
2785   vvSurfaceViewerDialog surfaceViewer;
2786   surfaceViewer.exec();
2787 }
2788 //------------------------------------------------------------------------------
2789
2790
2791 //------------------------------------------------------------------------------
2792 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2793 {
2794   int number=0;
2795   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2796     vvSlicerManager * v = mSlicerManagers[l];
2797     if (v->GetBaseFileName() ==
2798         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2799       number = std::max(number, v->GetBaseFileNameNumber()+1);
2800     }
2801   }
2802   return number;
2803 }
2804 //------------------------------------------------------------------------------
2805
2806
2807 //------------------------------------------------------------------------------
2808 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2809 {
2810   // Change filename if another image exist with the same name
2811   int number = GetImageDuplicateFilenameNumber(filename);
2812
2813   // Create new SliceManager
2814   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2815   slicer_manager->SetImage(image);//, IMAGE, number);
2816   //  filename = filename+"_"+clitk::toString(number);
2817   slicer_manager->SetFilename(filename, number);
2818   mSlicerManagers.push_back(slicer_manager);
2819
2820   //create an item in the tree with good settings
2821   QTreeWidgetItem *item = new QTreeWidgetItem();
2822   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2823   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2824   qApp->processEvents();
2825
2826   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2827
2828   //Create the buttons for reload and close
2829   qApp->processEvents();
2830   QTreePushButton* cButton = new QTreePushButton;
2831   cButton->setItem(item);
2832   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2833   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2834   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2835           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2836
2837   QTreePushButton* rButton = new QTreePushButton;
2838   rButton->setItem(item);
2839   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2840   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2841   rButton->setEnabled(0);
2842   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2843           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2844
2845   DataTree->addTopLevelItem(item);
2846   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2847   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2848
2849   //set the id of the image
2850   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2851   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2852   mSlicerManagers.back()->SetId(id.toStdString());
2853
2854   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2855                       , id.toStdString());
2856
2857   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2858           this, SLOT(CurrentImageChanged(std::string)));
2859   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2860           this, SLOT(CurrentPickedImageChanged(std::string)));
2861   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2862           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2863   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2864           this, SLOT(VectorChanged(int,double,double,double, double)));
2865   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2866           this, SLOT(OverlayChanged(int,double,double)));
2867   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2868           this, SLOT(FusionChanged(int,double)));
2869   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2870           this,SLOT(WindowsChanged(int, int, int)));
2871   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2872           this,SLOT(WindowLevelChanged(double, double, int, int)));
2873   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2874           this,SLOT(UpdateSlice(int,int)));
2875   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2876           this,SLOT(UpdateTSlice(int, int)));
2877   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2878           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2879   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2880           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2881   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2882           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2883   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2884           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2885   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2886   UpdateTree();
2887   qApp->processEvents();
2888   InitSlicers();
2889   ShowLastImage();
2890   InitDisplay();
2891   qApp->processEvents();
2892
2893   // End
2894   ImageInfoChanged();
2895   return slicer_manager;
2896 }
2897 //------------------------------------------------------------------------------
2898
2899
2900 //------------------------------------------------------------------------------
2901 void vvMainWindow::UpdateCurrentSlicer()
2902 {
2903   int index = -1;
2904   if (DataTree->selectedItems().size() > 0) {
2905     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2906   }
2907   mSlicerManagerCurrentIndex = index;
2908 }
2909 //------------------------------------------------------------------------------
2910