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://oncora1.lyon.fnclcc.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
  25 // VV include
  26 #include "vvMainWindow.h"
  27 #include "vvHelpDialog.h"
  28 #include "vvDocumentation.h"
  29 #include "vvProgressDialog.h"
  30 #include "vvQDicomSeriesSelector.h"
  31 #include "vvSlicerManager.h"
  32 #include "clitkImageCommon.h"
  33 #include "vvSlicer.h"
  34 #include "vvInteractorStyleNavigator.h"
  35 #include "vvImageWriter.h"
  36 #include "vvSegmentationDialog.h"
  37 #include "vvSurfaceViewerDialog.h"
  38 #include "vvDeformationDialog.h"
  39 #include "vvImageWarp.h"
  40 #include "vvUtils.h"
  41 #include "vvMaximumIntensityProjection.h"
  42 #include "vvMidPosition.h"
  43 #include "vvMesh.h"
  44 #include "vvStructSelector.h"
  45 #include "vvMeshReader.h"
  46 #include "vvConstants.h"
  47 #include "clitkConfiguration.h"
  48
  49 // ITK include
  50 #include "itkImage.h"
  51 #include "itkImageFileReader.h"
  52 #include "itkByteSwapper.h"
  53 #include "itkCommand.h"
  54 #include "itkNumericSeriesFileNames.h"
  55
  56 // VTK include
  57 #include "vtkImageData.h"
  58 #include "vtkImageActor.h"
  59 #include "vtkCornerAnnotation.h"
  60 #include "vtkRenderWindow.h"
  61 #include "vtkRenderWindowInteractor.h"
  62 #include "vtkRenderer.h"
  63 #include "vtkRendererCollection.h"
  64 #include "vtkWindowToImageFilter.h"
  65 #include "vtkBMPWriter.h"
  66 #include "vtkTIFFWriter.h"
  67 #include "vtkPNMWriter.h"
  68 #include "vtkPNGWriter.h"
  69 #include "vtkJPEGWriter.h"
  70 #include "vtkMatrix4x4.h"
  71 #include "vtkTransform.h"
  72
  73 // Standard includes
  74 #include <iostream>
  75 #include <sstream>
  76 #include <iomanip>
  77
  78 #define COLUMN_TREE 0
  79 #define COLUMN_UL_VIEW 1
  80 #define COLUMN_UR_VIEW 2
  81 #define COLUMN_DL_VIEW 3
  82 #define COLUMN_DR_VIEW 4
  83 #define COLUMN_CLOSE_IMAGE 5
  84 #define COLUMN_RELOAD_IMAGE 6
  85 #define COLUMN_IMAGE_NAME 7
  86
  87 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr *.SCAN )"
  88
  89 /*Data Tree values
  90   0,Qt::UserRole full filename
  91   1,Qt::CheckStateRole checkbutton UL View
  92   1,Qt::UserRole overlay, fusion or vector
  93   2,Qt::CheckStateRole checkbutton UR View
  94   3,Qt::CheckStateRole checkbutton DL View
  95   4,Qt::CheckStateRole checkbutton DR View
  96   5,0  short filename
  97   5,Qt::UserRole mSlicerManager id*/
  98
  99 //------------------------------------------------------------------------------
 100 vvMainWindow::vvMainWindow():vvMainWindowBase()
 101 {
 102   setupUi(this); // this sets up the GUI
 103
 104   mInputPathName = "";
 105   mMenuTools = menuTools;
 106   //  mMenuSegmentation = menuSegmentation;
 107   mContextMenu = &contextMenu;
 108   mMenuExperimentalTools = menuExperimental;
 109   mMainWidget = this;
 110   mCurrentTime = -1;
 111   mCurrentSelectedImageId = "";
 112   mCurrentPickedImageId = "";
 113   mCurrentPickedImageIndex = 0;
 114
 115   //Init the contextMenu
 116   this->setContextMenuPolicy(Qt::CustomContextMenu);
 117   contextActions.resize(0);
 118   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 119                                   tr("O&pen new Image"));
 120   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 121   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 122   contextActions.push_back(actionOpen_new_image);
 123   contextMenu.addSeparator();
 124
 125   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 126                                tr("Close Current Image"));
 127   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 128   contextActions.push_back(actionClose_Image);
 129
 130   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 131                                 tr("Reload Current Image"));
 132   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 133   contextActions.push_back(actionReload_image);
 134
 135   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 136                               tr("Save Current Image"));
 137   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 138   contextActions.push_back(actionSave_image);
 139
 140   contextMenu.addSeparator();
 141
 142   contextMenu.addAction(actionAdd_VF_to_current_Image);
 143   contextActions.push_back(actionAdd_VF_to_current_Image);
 144
 145   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 146       tr("Add overlay image to current image"));
 147   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 148   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 149
 150   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 151
 152   contextMenu.addAction(actionAdd_fusion_image);
 153   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 154   contextActions.push_back(actionAdd_fusion_image);
 155
 156   // TRIAL DS
 157   /*
 158   QMenu * m = new QMenu(menubar);
 159   m->setTitle("TOTO");
 160   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 161   contextMenu.addMenu(m);
 162   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 163                      tr("BIDON"));
 164   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 165                      tr("BIDON2"));
 166   m->addAction(a);
 167   m->addAction(b);
 168   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 169   */
 170
 171   //init the DataTree
 172   mSlicerManagers.resize(0);
 173
 174   QStringList header;
 175   header.append("");
 176   header.append("TL");
 177   header.append("TR");
 178   header.append("BL");
 179   header.append("BR");
 180   header.append("");
 181   header.append("");
 182   header.append("Name");
 183
 184   DataTree->setHeaderLabels(header);
 185   DataTree->resizeColumnToContents(COLUMN_TREE);
 186   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 187   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 188   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 189   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 190   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 191   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 192   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 193
 194   viewMode = 1;
 195   documentation = new vvDocumentation();
 196   help_dialog = new vvHelpDialog();
 197   dicomSeriesSelector = new vvDicomSeriesSelector();
 198
 199   inverseButton->setEnabled(0);
 200   actionAdd_Overlay_to_current_Image->setEnabled(0);
 201   actionSave_As->setEnabled(0);
 202   actionAdd_VF_to_current_Image->setEnabled(0);
 203   actionAdd_fusion_image->setEnabled(0);
 204
 205   //init the sliders
 206   verticalSliders.push_back(NOVerticalSlider);
 207   verticalSliders.push_back(NEVerticalSlider);
 208   verticalSliders.push_back(SOVerticalSlider);
 209   verticalSliders.push_back(SEVerticalSlider);
 210
 211   for (int i =0; i < 4; i++)
 212     verticalSliders[i]->hide();
 213
 214   horizontalSliders.push_back(NOHorizontalSlider);
 215   horizontalSliders.push_back(NEHorizontalSlider);
 216   horizontalSliders.push_back(SOHorizontalSlider);
 217   horizontalSliders.push_back(SEHorizontalSlider);
 218
 219   for (int i =0; i < 4; i++)
 220     horizontalSliders[i]->hide();
 221
 222
 223   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 224   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 225   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 226   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 227
 228   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 229   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 230   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 231   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 232
 233   //connect everything
 234   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 235   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 236   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 237   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 238   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 239   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 240   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 241   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 242   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 243   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 244   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 245   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 246   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 247   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 248   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 249   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 250   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 251
 252   ///////////////////////////////////////////////
 253   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 254   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 255   ///////////////////////////////////////////////
 256
 257   actionNorth_East_Window->setEnabled(0);
 258   actionNorth_West_Window->setEnabled(0);
 259   actionSouth_East_Window->setEnabled(0);
 260   actionSouth_West_Window->setEnabled(0);
 261
 262   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 263   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 264   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 265   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 266
 267   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 268   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 269           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 270
 271   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 272   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 273   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 274   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 275   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 276   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 277   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 278
 279
 280   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 281
 282   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 283   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 284   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 285   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 286   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 287           this,SLOT(SetFusionProperty(int,int,double,double)));
 288   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 289
 290   playMode = 0;//pause
 291   mFrameRate = 10;
 292   playButton->setEnabled(0);
 293   frameRateLabel->setEnabled(0);
 294   frameRateSpinBox->setEnabled(0);
 295   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 296   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 297
 298   goToCursorPushButton->setEnabled(0);
 299   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 300
 301   NOViewWidget->hide();
 302   NEViewWidget->hide();
 303   SOViewWidget->hide();
 304   SEViewWidget->hide();
 305
 306   //Recently opened files
 307   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 308   if ( !recent_files.empty() ) {
 309     QMenu * rmenu = new QMenu("Recently opened files...");
 310     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 311     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 312     menuFile->insertSeparator(actionOpen_Image_With_Time);
 313     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 314       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 315                                    (*i).c_str(),this);
 316       rmenu->addAction(current);
 317       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 318     }
 319   }
 320
 321   // Adding all new tools (insertion in the menu)
 322   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 323
 324   if (!CLITK_EXPERIMENTAL)
 325     menuExperimental->menuAction()->setVisible(false);
 326
 327
 328   QTimer * timerMemory = new QTimer(this);
 329   //timerMemory->setInterval(5);
 330   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 331   timerMemory->start(2000);
 332
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::UpdateMemoryUsage()
 339 {
 340   //  clitk::PrintMemory(true);
 341   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 342   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 343 }
 344 //------------------------------------------------------------------------------
 345
 346
 347 //------------------------------------------------------------------------------
 348 void vvMainWindow::ComputeMIP()
 349 {
 350   vvMaximumIntensityProjection mip;
 351   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 352   QFileInfo info(selected_slicer->GetFileName().c_str());
 353   mip.Compute(selected_slicer);
 354   if (!mip.error)
 355     AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 356 }
 357 //------------------------------------------------------------------------------
 358
 359
 360 //------------------------------------------------------------------------------
 361 void vvMainWindow::ComputeMidPosition()
 362 {
 363   bool ok;
 364   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 365   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 366                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 367   if (ok) {
 368     vvMidPosition midp;
 369     midp.slicer_manager = mSlicerManagers[index];
 370     midp.reference_image_index = ref;
 371     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 372     midp.Update();
 373     if (midp.error)
 374       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 375     else {
 376       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 377       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 378     }
 379     QApplication::restoreOverrideCursor();
 380   }
 381 }
 382 //------------------------------------------------------------------------------
 383
 384
 385 //------------------------------------------------------------------------------
 386 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 387 {
 388   QTreeWidgetItem *item = new QTreeWidgetItem();
 389   item->setData(0,Qt::UserRole,"filename.vtk");
 390   item->setData(1,Qt::UserRole,tr("contour"));
 391   QBrush brush;
 392   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 393   brush.setStyle(Qt::SolidPattern);
 394   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 395   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 396
 397   for (int j = 1; j <= 4; j++)
 398     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 399
 400   QTreePushButton* cButton = new QTreePushButton;
 401   cButton->setItem(item);
 402   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 403   cButton->setToolTip(tr("close image"));
 404   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 405   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 406           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 407
 408   QTreePushButton* rButton = new QTreePushButton;
 409   rButton->setItem(item);
 410   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 411   rButton->setToolTip(tr("reload image"));
 412   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 413   rButton->setEnabled(false);
 414   //Not implemented
 415   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 416   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 417
 418   DataTree->topLevelItem(image_index)->setExpanded(1);
 419   DataTree->topLevelItem(image_index)->addChild(item);
 420   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 421   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 422   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 423   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 424
 425   UpdateTree();
 426   mSlicerManagers[image_index]->AddContour(contour,propagation);
 427   mSlicerManagers[image_index]->Render();
 428 }
 429 //------------------------------------------------------------------------------
 430
 431
 432 //------------------------------------------------------------------------------
 433 void vvMainWindow::OpenVTKContour()
 434 {
 435   if (mSlicerManagers.size() > 0) {
 436     QString Extensions = "Images ( *.vtk *.obj)";
 437     Extensions += ";;All Files (*)";
 438     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 439     if (file.isNull())
 440       return;
 441     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 442     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 443     vvMeshReader reader;
 444     reader.SetImage(mSlicerManagers[index]->GetImage());
 445     reader.SetModeToVTK();
 446     reader.SetFilename(file.toStdString());
 447     reader.Update();
 448     AddContour(index,reader.GetOutput()[0],false);
 449     QApplication::restoreOverrideCursor();
 450   }
 451 }
 452 //------------------------------------------------------------------------------
 453
 454
 455 //------------------------------------------------------------------------------
 456 void vvMainWindow::OpenDCStructContour()
 457 {
 458   if (mSlicerManagers.size() > 0) {
 459     QString Extensions = "Dicom Files ( *.dcm RS*)";
 460     Extensions += ";;All Files (*)";
 461     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 462     if (file.isNull())
 463       return;
 464     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 465     vvMeshReader reader;
 466     reader.SetFilename(file.toStdString());
 467     vvStructSelector selector;
 468     selector.SetStructures(reader.GetROINames());
 469     if (!mSlicerManagers[index]->GetVF().IsNull())
 470       selector.EnablePropagationCheckBox();
 471     if (selector.exec()) {
 472       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 473       reader.SetSelectedItems(selector.getSelectedItems());
 474       reader.SetImage(mSlicerManagers[index]->GetImage());
 475       if (selector.PropagationEnabled())
 476         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 477       reader.Update();
 478       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 479       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 480            i!=contours.end(); i++)
 481         AddContour(index,*i,selector.PropagationEnabled());
 482       QApplication::restoreOverrideCursor();
 483     }
 484   }
 485 }
 486 //------------------------------------------------------------------------------
 487
 488
 489 //------------------------------------------------------------------------------
 490 void vvMainWindow::ComputeDeformableRegistration()
 491 {
 492   if (mSlicerManagers.size() > 0) {
 493     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 494     vvDeformationDialog dialog(index,mSlicerManagers);
 495     if (dialog.exec()) {
 496       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 497       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 498       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 499     } else
 500       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 501   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 502 }
 503 //------------------------------------------------------------------------------
 504
 505
 506 //------------------------------------------------------------------------------
 507 void vvMainWindow::WarpImage()
 508 {
 509   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 510   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 511     bool ok;
 512     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 513                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 514     if (ok) {
 515       WarpImage(mSlicerManagers[index],ref);
 516     }
 517   } else
 518     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 519 }
 520 //------------------------------------------------------------------------------
 521
 522
 523 //------------------------------------------------------------------------------
 524 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 525 {
 526   if (!selected_slicer->GetVF().IsNull()) {
 527     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 528     QFileInfo info(selected_slicer->GetFileName().c_str());
 529     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 530                      reference_phase,this);
 531     if (warp.ComputeWarpedImage()) {
 532       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 533       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 534       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 535       QApplication::restoreOverrideCursor();
 536     } else {
 537       QApplication::restoreOverrideCursor();
 538       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 539     }
 540   } else
 541     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 542 }
 543 //------------------------------------------------------------------------------
 544
 545
 546 //------------------------------------------------------------------------------
 547 vvMainWindow::~vvMainWindow()
 548 {
 549   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 550     if (mSlicerManagers[i] != NULL)
 551       delete mSlicerManagers[i];
 552   }
 553 }
 554 //------------------------------------------------------------------------------
 555
 556 //------------------------------------------------------------------------------
 557 QTabWidget * vvMainWindow::GetTab()
 558 {
 559   return tabWidget;
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 void vvMainWindow::MergeImages()
 566 {
 567   QString Extensions = EXTENSIONS;
 568   Extensions += ";;All Files (*)";
 569   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 570   if (files.isEmpty())
 571     return;
 572   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 573   std::vector<std::string> vector;
 574
 575   unsigned int currentDim = 0;
 576   std::vector<double> currentSpacing;
 577   std::vector<int> currentSize;
 578   std::vector<double> currentOrigin;
 579
 580   for (int i = 0; i < files.size(); i++) {
 581     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 582                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 583     reader->SetFileName(files[i].toStdString().c_str());
 584     reader->ReadImageInformation();
 585     if (reader)        {
 586       //NOViewWidget->hide();
 587       //NEViewWidget->hide();
 588       //SOViewWidget->hide();
 589       //SEViewWidget->hide();
 590       if (i == 0)
 591         currentDim = reader->GetNumberOfDimensions();
 592       bool IsOk = true;
 593       for (unsigned int j = 0; j < currentDim; j++) {
 594         if (i == 0) {
 595           if (j == 0) {
 596             currentSpacing.resize(currentDim);
 597             currentSize.resize(currentDim);
 598             currentOrigin.resize(currentDim);
 599           }
 600           currentOrigin[j] = reader->GetOrigin(j);
 601           currentSpacing[j] = reader->GetSpacing(j);
 602           currentSize[j] = reader->GetDimensions(j);
 603         } else if (currentDim != reader->GetNumberOfDimensions()
 604                    || currentSpacing[j] != reader->GetSpacing(j)
 605                    || currentSize[j] != (int)reader->GetDimensions(j)
 606                    || currentOrigin[j] != reader->GetOrigin(j)) {
 607           QString error = "Cannot read file (too different from others ";
 608           error += files[i].toStdString().c_str();
 609           QMessageBox::information(this,tr("Reading problem"),error);
 610           IsOk = false;
 611           break;
 612         }
 613       }
 614       if (IsOk)
 615         vector.push_back(files[i].toStdString());
 616     }
 617   }
 618   if (vector.size() > 0)
 619     LoadImages(vector, MERGED);
 620 }
 621 //------------------------------------------------------------------------------
 622
 623 //------------------------------------------------------------------------------
 624 void vvMainWindow::SliceImages()
 625 {
 626   QString Extensions = EXTENSIONS;
 627   Extensions += ";;All Files (*)";
 628
 629   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 630   if (files.isEmpty())
 631     return;
 632   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 633   std::vector<std::string> vector;
 634   for (int i = 0; i < files.size(); i++)
 635     vector.push_back(files[i].toStdString());
 636   LoadImages(vector, SLICED);
 637 }
 638 //------------------------------------------------------------------------------
 639
 640 //------------------------------------------------------------------------------
 641 void vvMainWindow::MergeImagesWithTime()
 642 {
 643   QString Extensions = EXTENSIONS;
 644   Extensions += ";;All Files (*)";
 645   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 646   if (files.isEmpty())
 647     return;
 648   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 649   std::vector<std::string> vector;
 650
 651   unsigned int currentDim = 0;
 652   std::vector<double> currentSpacing;
 653   std::vector<int> currentSize;
 654   std::vector<double> currentOrigin;
 655
 656   for (int i = 0; i < files.size(); i++) {
 657     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 658                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 659     if (reader) {
 660       reader->SetFileName(files[i].toStdString().c_str());
 661       reader->ReadImageInformation();
 662       if (i == 0)
 663         currentDim = reader->GetNumberOfDimensions();
 664       bool IsOk = true;
 665       for (unsigned int j = 0; j < currentDim; j++) {
 666         if (i == 0) {
 667           if (j == 0) {
 668             currentSpacing.resize(currentDim);
 669             currentSize.resize(currentDim);
 670             currentOrigin.resize(currentDim);
 671           }
 672           currentOrigin[j] = reader->GetOrigin(j);
 673           currentSpacing[j] = reader->GetSpacing(j);
 674           currentSize[j] = reader->GetDimensions(j);
 675         } else if (currentDim != reader->GetNumberOfDimensions()
 676                    || currentSpacing[j] != reader->GetSpacing(j)
 677                    || currentSize[j] != (int)reader->GetDimensions(j)
 678                    || currentOrigin[j] != reader->GetOrigin(j)) {
 679           QString error = "Cannot read file (too different from others ";
 680           error += files[i].toStdString().c_str();
 681           QMessageBox::information(this,tr("Reading problem"),error);
 682           IsOk = false;
 683           break;
 684         }
 685       }
 686       if (IsOk)
 687         vector.push_back(files[i].toStdString());
 688     } else {
 689       QString error = "Cannot read file info for ";
 690       error += files[i].toStdString().c_str();
 691       error += "\n";
 692       error += "Maybe you're trying to open an image in an unsupported format?\n";
 693       QMessageBox::information(this,tr("Reading problem"),error);
 694     }
 695   }
 696   sort(vector.begin(),vector.end());
 697   if (vector.size() > 1)
 698     LoadImages(vector, MERGEDWITHTIME);
 699   else
 700     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.");
 701 }
 702 //------------------------------------------------------------------------------
 703
 704
 705 //------------------------------------------------------------------------------
 706 void vvMainWindow::OpenDicom()
 707 {
 708   std::vector<std::string> files;
 709
 710   std::cout << "dicomSeriesSelector " << std::endl;
 711   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 712     files = *(dicomSeriesSelector->GetFilenames());
 713     LoadImages(files,DICOM);
 714   }
 715 }
 716 //------------------------------------------------------------------------------
 717
 718 //------------------------------------------------------------------------------
 719 void vvMainWindow::OpenImages()
 720 {
 721   QString Extensions = EXTENSIONS;
 722   Extensions += ";;All Files (*)";
 723
 724   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 725   if (files.isEmpty())
 726     return;
 727   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 728   std::vector<std::string> vector;
 729   for (int i = 0; i < files.size(); i++)
 730     vector.push_back(files[i].toStdString());
 731   LoadImages(vector, IMAGE);
 732 }
 733 //------------------------------------------------------------------------------
 734 void vvMainWindow::OpenRecentImage()
 735 {
 736   QAction * caller = qobject_cast<QAction*>(sender());
 737   std::vector<std::string> images;
 738   images.push_back(caller->text().toStdString());
 739   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 740   LoadImages(images,IMAGE);
 741 }
 742 //------------------------------------------------------------------------------
 743
 744
 745 //------------------------------------------------------------------------------
 746 void vvMainWindow::OpenImageWithTime()
 747 {
 748   QString Extensions = EXTENSIONS;
 749   Extensions += ";;All Files (*)";
 750
 751   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 752   if (files.isEmpty())
 753     return;
 754   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 755   std::vector<std::string> vector;
 756   for (int i = 0; i < files.size(); i++) {
 757     vector.push_back(files[i].toStdString());
 758   }
 759   LoadImages(vector, IMAGEWITHTIME);
 760 }
 761 //------------------------------------------------------------------------------
 762
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 766 {
 767   //Separate the way to open images and dicoms
 768   int fileSize;
 769   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 770     fileSize = files.size();
 771   else
 772     fileSize = 1;
 773
 774   // For SLICED, we need the number of slices (ndim and #slices)
 775   std::vector<unsigned int> nSlices;
 776   nSlices.resize(files.size());
 777   std::fill(nSlices.begin(), nSlices.end(), 1);
 778   if (filetype == SLICED) {
 779     for (int i = 0; i < fileSize; i++) {
 780       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 781       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 782       if (!header) {
 783         nSlices[i] = 0;
 784         QString error = "Cannot open file \n";
 785         error += files[i].c_str();
 786         QMessageBox::information(this,tr("Reading problem"),error);
 787         return;
 788       }
 789       if (header->GetNumberOfDimensions() < 3) {
 790         nSlices[i] = 0;
 791         QString error = "Dimension problem. Cannot slice \n";
 792         error += files[i].c_str();
 793         QMessageBox::information(this,tr("Reading problem"),error);
 794         return;
 795       }
 796       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 797     }
 798   }
 799
 800   //Only add to the list of recently opened files when a single file is opened,
 801   //to avoid polluting the list of recently opened files
 802   if (files.size() == 1) {
 803     QFileInfo finfo=tr(files[0].c_str());
 804     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 805   }
 806   //init the progress events
 807   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 808   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 809   qApp->processEvents();
 810
 811   int numberofsuccesulreads=0;
 812   //open images as 1 or multiples
 813   for (int i = 0; i < fileSize; i++) {
 814
 815     progress.SetText("Opening " + files[i]);
 816     progress.SetProgress(i,fileSize);
 817     qApp->processEvents();
 818
 819     for (unsigned int j = 0; j < nSlices[i]; j++) {
 820       //read the image and put it in mSlicerManagers
 821       vvSlicerManager* imageManager = new vvSlicerManager(4);
 822       qApp->processEvents();
 823
 824       bool SetImageSucceed=false;
 825
 826       // Change filename if an image with the same already exist
 827       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 828
 829       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 830         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 831       else {
 832         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 833       }
 834       if (!SetImageSucceed) {
 835         QApplication::restoreOverrideCursor();
 836         QString error = "Cannot open file \n";
 837         error += imageManager->GetLastError().c_str();
 838         QMessageBox::information(this,tr("Reading problem"),error);
 839         delete imageManager;
 840       } else {
 841         mSlicerManagers.push_back(imageManager);
 842
 843         //create an item in the tree with good settings
 844         QTreeWidgetItem *item = new QTreeWidgetItem();
 845         item->setData(0,Qt::UserRole,files[i].c_str());
 846         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 847         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 848         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 849         qApp->processEvents();
 850
 851         //Create the buttons for reload and close
 852         qApp->processEvents();
 853         QTreePushButton* cButton = new QTreePushButton;
 854         cButton->setItem(item);
 855         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 856         cButton->setToolTip(tr("close image"));
 857         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 858         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 859                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 860
 861         QTreePushButton* rButton = new QTreePushButton;
 862         rButton->setItem(item);
 863         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 864         rButton->setToolTip(tr("reload image"));
 865         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 866         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 867                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 868
 869         DataTree->addTopLevelItem(item);
 870         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 871         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 872
 873         //set the id of the image
 874         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 875         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 876         mSlicerManagers.back()->SetId(id.toStdString());
 877
 878         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 879
 880         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 881                 this,SLOT(CurrentImageChanged(std::string)));
 882         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 883                 this, SLOT(CurrentPickedImageChanged(std::string)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 885                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 887                 this, SLOT(VectorChanged(int,double,double,double, double)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 889                 this, SLOT(OverlayChanged(int,double,double)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 891                 this, SLOT(FusionChanged(int,double)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 893                 this,SLOT(WindowsChanged(int, int, int)));
 894         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 895                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 896         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 897                 this,SLOT(UpdateSlice(int,int)));
 898         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 899                 this,SLOT(UpdateTSlice(int, int)));
 900         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 901                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 902         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 903                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 904         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 905                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 906         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 907                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 908         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 909         InitSlicers();
 910         numberofsuccesulreads++;
 911       }
 912     }
 913   }
 914   if (numberofsuccesulreads) {
 915     NOViewWidget->show();
 916     NEViewWidget->show();
 917     SOViewWidget->show();
 918     SEViewWidget->show();
 919     UpdateTree();
 920     InitDisplay();
 921     ShowLastImage();
 922
 923     // Try to guess default WindowLevel
 924     double range[2];
 925     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 926     if ((range[0] == 0) && (range[1] == 1)) {
 927       presetComboBox->setCurrentIndex(5);// binary
 928     } else {
 929       // TODO
 930     }
 931   }
 932   QApplication::restoreOverrideCursor();
 933 }
 934 //------------------------------------------------------------------------------
 935
 936 //------------------------------------------------------------------------------
 937 void vvMainWindow::UpdateTree()
 938 {
 939   DataTree->resizeColumnToContents(COLUMN_TREE);
 940   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 941   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 942   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 943   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 944   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 945   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 946   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 947 }
 948 //------------------------------------------------------------------------------
 949
 950 //------------------------------------------------------------------------------
 951 void vvMainWindow::CurrentImageChanged(std::string id)
 952 {
 953   if (id == mCurrentSelectedImageId) return; // Do nothing
 954   int selected = 0;
 955   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 956     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 957       selected = i;
 958     } else {
 959       DataTree->topLevelItem(i)->setSelected(0);
 960     }
 961     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 962       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 963
 964   }
 965   DataTree->topLevelItem(selected)->setSelected(1);
 966   mCurrentSelectedImageId = id;
 967   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 973 {
 974   if (id == mCurrentPickedImageId) return; // Do nothing
 975   int selected = 0;
 976   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 977     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 978       selected = i;
 979     } else {
 980       DataTree->topLevelItem(i)->setSelected(0);
 981     }
 982     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 983       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 984
 985   }
 986   DataTree->topLevelItem(selected)->setSelected(1);
 987   mCurrentPickedImageId = id;
 988   mCurrentPickedImageIndex = selected;
 989 }
 990 //------------------------------------------------------------------------------
 991
 992 //------------------------------------------------------------------------------
 993 void vvMainWindow::ImageInfoChanged()
 994 {
 995   contextActions[6]->setEnabled(1);
 996   contextActions[5]->setEnabled(1);
 997   actionSave_As->setEnabled(1);
 998   actionAdd_VF_to_current_Image->setEnabled(1);
 999   actionAdd_fusion_image->setEnabled(1);
1000   actionNorth_East_Window->setEnabled(1);
1001   actionNorth_West_Window->setEnabled(1);
1002   actionSouth_East_Window->setEnabled(1);
1003   actionSouth_West_Window->setEnabled(1);
1004   inverseButton->setEnabled(1);
1005
1006   goToCursorPushButton->setEnabled(1);
1007
1008   if (DataTree->selectedItems().size()) {
1009     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1010
1011     colorMapComboBox->setEnabled(1);
1012     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1013       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1014           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1015         colorMapComboBox->setEnabled(0);
1016         break;
1017       }
1018     }
1019
1020     std::vector<double> origin;
1021     std::vector<double> inputSpacing;
1022     std::vector<int> inputSize;
1023     std::vector<double> sizeMM;
1024     vtkSmartPointer<vtkMatrix4x4> transformation;
1025     int dimension=0;
1026     QString pixelType;
1027     QString inputSizeInBytes;
1028     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1029
1030     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1031       playButton->setEnabled(1);
1032       frameRateLabel->setEnabled(1);
1033       frameRateSpinBox->setEnabled(1);
1034     } else {
1035       playButton->setEnabled(0);
1036       frameRateLabel->setEnabled(0);
1037       frameRateSpinBox->setEnabled(0);
1038     }
1039
1040     //read image header
1041     int NPixel = 1;
1042
1043     vvImage::Pointer imageSelected;
1044     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1045       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1046       dimension = imageSelected->GetNumberOfDimensions();
1047       origin.resize(dimension);
1048       inputSpacing.resize(dimension);
1049       inputSize.resize(dimension);
1050       sizeMM.resize(dimension);
1051       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1052       for (int i = 0; i < dimension; i++) {
1053         origin[i] = imageSelected->GetOrigin()[i];
1054         inputSpacing[i] = imageSelected->GetSpacing()[i];
1055         inputSize[i] = imageSelected->GetSize()[i];
1056         sizeMM[i] = inputSize[i]*inputSpacing[i];
1057         NPixel *= inputSize[i];
1058       }
1059       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1060     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1061       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1062       dimension = imageSelected->GetNumberOfDimensions();
1063       origin.resize(dimension);
1064       inputSpacing.resize(dimension);
1065       inputSize.resize(dimension);
1066       sizeMM.resize(dimension);
1067       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1068       for (int i = 0; i < dimension; i++) {
1069         origin[i] = imageSelected->GetOrigin()[i];
1070         inputSpacing[i] = imageSelected->GetSpacing()[i];
1071         inputSize[i] = imageSelected->GetSize()[i];
1072         sizeMM[i] = inputSize[i]*inputSpacing[i];
1073         NPixel *= inputSize[i];
1074       }
1075       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1076     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1077       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1078       dimension = imageSelected->GetNumberOfDimensions();
1079       origin.resize(dimension);
1080       inputSpacing.resize(dimension);
1081       inputSize.resize(dimension);
1082       sizeMM.resize(dimension);
1083       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1084       for (int i = 0; i < dimension; i++) {
1085         origin[i] = imageSelected->GetOrigin()[i];
1086         inputSpacing[i] = imageSelected->GetSpacing()[i];
1087         inputSize[i] = imageSelected->GetSize()[i];
1088         sizeMM[i] = inputSize[i]*inputSpacing[i];
1089         NPixel *= inputSize[i];
1090       }
1091       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1092     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1093       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1094       dimension = imageSelected->GetNumberOfDimensions();
1095       origin.resize(dimension);
1096       inputSpacing.resize(dimension);
1097       inputSize.resize(dimension);
1098       sizeMM.resize(dimension);
1099       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1100       for (int i = 0; i < dimension; i++) {
1101         origin[i] = imageSelected->GetOrigin()[i];
1102         inputSpacing[i] = imageSelected->GetSpacing()[i];
1103         inputSize[i] = imageSelected->GetSize()[i];
1104         sizeMM[i] = inputSize[i]*inputSpacing[i];
1105         NPixel *= inputSize[i];
1106       }
1107       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1108     }
1109
1110     QString dim = QString::number(dimension) + " (";
1111     dim += pixelType + ")";
1112
1113     infoPanel->setFileName(image);
1114     infoPanel->setDimension(dim);
1115     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1116     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1117     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1118     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1119     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1120     transformation = imageSelected->GetTransform()->GetMatrix();
1121     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1122
1123     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1124                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1125     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1126     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1127
1128     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1129     for (int i = 0; i < 4; i++) {
1130       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1131         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1132         break;
1133       }
1134     }
1135     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1136     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1137     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1138     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1139
1140     infoPanel->setFileName(image);
1141     infoPanel->setDimension(dim);
1142     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1143     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1144     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1145     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1146     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1147
1148     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1149                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1150     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1151     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1152
1153     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1154     for (int i = 0; i < 4; i++) {
1155       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1156         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1157         break;
1158       }
1159     }
1160     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1161     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1162     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1163     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1164
1165     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1166       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1167       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1168                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1169                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1170     } else {
1171       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1172       overlayPanel->getVFProperty(-1,-1,-1);
1173     }
1174     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1175       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1176       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1177     } else {
1178       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1179       overlayPanel->getOverlayProperty(-1);
1180     }
1181     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1182       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1183       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1184                                       mSlicerManagers[index]->GetFusionColorMap(),
1185                                       mSlicerManagers[index]->GetFusionWindow(),
1186                                       mSlicerManagers[index]->GetFusionLevel());
1187     } else {
1188       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1189       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1190     }
1191   }
1192 }
1193 //------------------------------------------------------------------------------
1194
1195 //------------------------------------------------------------------------------
1196 void vvMainWindow::ShowDocumentation()
1197 {
1198   documentation->show();
1199 }
1200 //------------------------------------------------------------------------------
1201 void vvMainWindow::ShowHelpDialog()
1202 {
1203   help_dialog->show();
1204 }
1205 //------------------------------------------------------------------------------
1206
1207 //------------------------------------------------------------------------------
1208 void vvMainWindow::ChangeViewMode()
1209 {
1210   QListIterator<int> it0(splitter_3->sizes());
1211   QListIterator<int> it1(splitter_3->sizes());
1212   int max0 = 0;
1213   int max1 = 1;
1214   while (it0.hasNext()) {
1215     max0 += it0.next();
1216   }
1217   while (it1.hasNext()) {
1218     max1 += it1.next();
1219   }
1220   QList<int> size0;
1221   QList<int> size1;
1222   if (viewMode == 1) {
1223     viewMode = 0;
1224     size0.push_back(max0);
1225     size0.push_back(0);
1226     size1.push_back(max1);
1227     size1.push_back(0);
1228     splitter_3->setSizes(size0);
1229     OSplitter->setSizes(size1);
1230     DataTree->setColumnHidden(2,1);
1231     DataTree->setColumnHidden(3,1);
1232     DataTree->setColumnHidden(4,1);
1233   } else {
1234     viewMode = 1;
1235     size0.push_back(int(max0/2));
1236     size0.push_back(int(max0/2));
1237     size1.push_back(int(max1/2));
1238     size1.push_back(int(max1/2));
1239     splitter_3->setSizes(size0);
1240     OSplitter->setSizes(size1);
1241     DataTree->setColumnHidden(2,0);
1242     DataTree->setColumnHidden(3,0);
1243     DataTree->setColumnHidden(4,0);
1244   }
1245 }
1246 //------------------------------------------------------------------------------
1247
1248 //------------------------------------------------------------------------------
1249 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1250 {
1251   QString result = "";// QString::number(size);
1252   //result += " bytes (";
1253   if (size > 1000000000) {
1254     size /= 1000000000;
1255     result += QString::number(size);
1256     result += "Gb";//)";
1257   } else if (size > 1000000) {
1258     size /= 1000000;
1259     result += QString::number(size);
1260     result += "Mb";//)";
1261   } else if (size > 1000) {
1262     size /= 1000;
1263     result += QString::number(size);
1264     result += "kb";//)";
1265   }
1266   return result;
1267 }
1268 //------------------------------------------------------------------------------
1269
1270 //------------------------------------------------------------------------------
1271 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1272 {
1273   std::ostringstream strmatrix;
1274
1275   for (unsigned int i = 0; i < 4; i++) {
1276     for (unsigned int j = 0; j < 4; j++) {
1277       strmatrix.flags(ios::showpos);
1278       strmatrix.width(10);
1279       strmatrix.precision(3);
1280       strmatrix.setf(ios::fixed,ios::floatfield);
1281       strmatrix.fill(' ');
1282       strmatrix << std::left << matrix->GetElement(i, j);
1283       //strmatrix.width(10);
1284       strmatrix << " ";
1285     }
1286     strmatrix << std::endl;
1287   }
1288   QString result = strmatrix.str().c_str();
1289   return result;
1290 }
1291 //------------------------------------------------------------------------------
1292
1293 //------------------------------------------------------------------------------
1294 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1295 {
1296   QString result;
1297   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1298     if (i != 0)
1299       result += " ";
1300     result += QString::number(vectorDouble[i]);
1301   }
1302   return result;
1303 }
1304 //------------------------------------------------------------------------------
1305
1306 //------------------------------------------------------------------------------
1307 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1308 {
1309   QString result;
1310   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1311     if (i != 0)
1312       result += " ";
1313     result += QString::number(vectorInt[i]);
1314   }
1315   return result;
1316 }
1317 //------------------------------------------------------------------------------
1318
1319 //------------------------------------------------------------------------------
1320 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1321 {
1322   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1323   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1324     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1325       return i;
1326   }
1327   return -1;
1328 }
1329 //------------------------------------------------------------------------------
1330
1331 //------------------------------------------------------------------------------
1332 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1333 {
1334   QString id = sm->GetId().c_str();
1335   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1336     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1337       return DataTree->topLevelItem(i);
1338   }
1339   return NULL;
1340 }
1341 //------------------------------------------------------------------------------
1342
1343 //------------------------------------------------------------------------------
1344 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1345 {
1346   int index = GetSlicerIndexFromItem(clicked_item);
1347   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1348     return;
1349   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1350     //Trick to avoid redoing twice the job for a key (sr)
1351     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1352
1353     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1354     if (DataTree->topLevelItem(index) == current_row) {
1355       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1356       if (current_row == clicked_item) {
1357         //If we just activated a slicer
1358         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1359           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1360           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1361           DisplaySliders(i,column-1);
1362           std::map<std::string,int> overlay_counts;
1363           for (int child = 0; child < current_row->childCount(); child++) {
1364             std::string overlay_type =
1365               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1366             overlay_counts[overlay_type]++;
1367             current_row->child(child)->setData(column,Qt::CheckStateRole,
1368                                                current_row->data(column,Qt::CheckStateRole));
1369             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1370           }
1371         } else { //We don't allow simply desactivating a slicer
1372           clicked_item->setData(column,Qt::CheckStateRole,2);
1373           return;
1374         }
1375       }
1376       //if we clicked on the vector(or overlay) and not the image
1377       else {
1378         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1379           current_row->setData(column,Qt::CheckStateRole,2);
1380           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1381           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1382           DisplaySliders(i,column-1);
1383         }
1384         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1385         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1386         int overlay_index=0;
1387         for (int child = 0; child < current_row->childCount(); child++) {
1388           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1389             overlay_index++;
1390           if (current_row->child(child) == clicked_item) break;
1391         }
1392         clicked_slicer->SetActorVisibility(
1393           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1394       }
1395     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1396       current_row->setData(column,Qt::CheckStateRole,0);
1397       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1398       std::map<std::string,int> overlay_counts;
1399       for (int child = 0; child < current_row->childCount(); child++) {
1400         std::string overlay_type =
1401           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1402         overlay_counts[overlay_type]++;
1403         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1404         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1405         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1406       }
1407     }
1408     //mSlicerManagers[i]->SetColorMap(-1);
1409     mSlicerManagers[i]->SetColorMap();
1410   }
1411   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1412 }
1413 //------------------------------------------------------------------------------
1414
1415 void vvMainWindow::InitSlicers()
1416 {
1417   if (mSlicerManagers.size()) {
1418     mSlicerManagers.back()->GenerateDefaultLookupTable();
1419
1420     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1421     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1422     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1423     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1424   }
1425 }
1426
1427 //------------------------------------------------------------------------------
1428 void vvMainWindow::InitDisplay()
1429 {
1430   if (mSlicerManagers.size()) {
1431     //BE CAREFUL : this is absolutely necessary to set the interactor style
1432     //in order to have the same style instanciation for all SlicerManagers in
1433     // a same window
1434     for (int j = 0; j < 4; j++) {
1435       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1436       style->SetAutoAdjustCameraClippingRange(1);
1437       bool AlreadySelected = false;
1438       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1439         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1440
1441         //select the image only if previous are not selected
1442         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1443           mSlicerManagers[i]->UpdateSlicer(j,1);
1444           AlreadySelected = true;
1445         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1446           if (DataTree->selectedItems().size() == 0)
1447             DataTree->topLevelItem(i)->setSelected(1);
1448           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1449           mSlicerManagers[i]->UpdateSlicer(j,1);
1450           DisplaySliders(i,j);
1451         } else {
1452           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1453           mSlicerManagers[i]->UpdateSlicer(j,0);
1454         }
1455       }
1456       style->Delete();
1457     }
1458   }
1459 }
1460 //------------------------------------------------------------------------------
1461
1462 //------------------------------------------------------------------------------
1463 void vvMainWindow::DisplaySliders(int slicer, int window)
1464 {
1465   int range[2];
1466   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1467   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1468
1469   int tRange[2];
1470   tRange[0] = 0;
1471   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1472   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1473   bool showHorizontal = false;
1474   bool showVertical = false;
1475   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1476       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1477           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1478           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1479     showVertical = true;
1480   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1481       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1482       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1483     showHorizontal = true;
1484
1485   if (showVertical)
1486     verticalSliders[window]->show();
1487   else
1488     verticalSliders[window]->hide();
1489   verticalSliders[window]->setRange(range[0],range[1]);
1490   verticalSliders[window]->setValue(position);
1491
1492   if (showHorizontal)
1493     horizontalSliders[window]->show();
1494   else
1495     horizontalSliders[window]->hide();
1496   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1497   horizontalSliders[window]->setValue(tPosition);
1498 }
1499 //------------------------------------------------------------------------------
1500
1501 //------------------------------------------------------------------------------
1502 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1503 {
1504   int index = GetSlicerIndexFromItem(item);
1505
1506   if (DataTree->topLevelItem(index) != item) {
1507     QString warning = "Do you really want to close the overlay : ";
1508     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1509     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1510                        warning, 0, this);
1511     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1512     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1513     if (msgBox.exec() == QMessageBox::AcceptRole) {
1514       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1515       int overlay_index=0;
1516       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1517         if (DataTree->topLevelItem(index)->\
1518             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1519           overlay_index++;
1520         if (DataTree->topLevelItem(index)->child(child) == item) break;
1521       }
1522       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1523       mSlicerManagers[index]->SetColorMap(0);
1524       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1525       mSlicerManagers[index]->Render();
1526     }
1527   } else if (DataTree->topLevelItemCount() <= 1) {
1528     QString warning = "Do you really want to close the image : ";
1529     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1530     warning += "\nThis is the last image, you're about to close vv !!!";
1531     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1532                        warning, 0, this);
1533     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1534     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1535     if (msgBox.exec() == QMessageBox::AcceptRole) {
1536       this->close();
1537     }
1538   } else {
1539     QString warning = "Do you really want to close the image : ";
1540     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1541     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1542                        warning, 0, this);
1543     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1544     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1545     if (msgBox.exec() == QMessageBox::AcceptRole) {
1546
1547       // Tell tools that we close an image
1548       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1549
1550       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1551       DataTree->takeTopLevelItem(index);
1552       for (int i = 0; i < index; i++) {
1553         Manageriter++;
1554       }
1555       linkPanel->removeImage(index);
1556       mSlicerManagers[index]->RemoveActors();
1557       delete mSlicerManagers[index];
1558       mSlicerManagers.erase(Manageriter);
1559
1560       //
1561       InitDisplay();
1562     }
1563   }
1564   ImageInfoChanged();
1565 }
1566 //------------------------------------------------------------------------------
1567
1568 //------------------------------------------------------------------------------
1569 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1570 {
1571   // int index = GetSlicerIndexFromItem(item);
1572   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1573   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1574   //     mSlicerManagers[index]->ReloadVF();
1575   //   else
1576   //     mSlicerManagers[index]->Reload();
1577
1578   //   QApplication::restoreOverrideCursor();
1579   int index = GetSlicerIndexFromItem(item);
1580   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1581   QString role=item->data(1,Qt::UserRole).toString();
1582   if ( role == "vector")
1583     mSlicerManagers[index]->ReloadVF();
1584   else if (role == "overlay")
1585     mSlicerManagers[index]->ReloadOverlay();
1586   else if (role == "fusion")
1587     mSlicerManagers[index]->ReloadFusion();
1588   else
1589     mSlicerManagers[index]->Reload();
1590
1591   // Update view and info
1592   ImageInfoChanged();
1593   mSlicerManagers[index]->Render();
1594   QApplication::restoreOverrideCursor();
1595 }
1596 //------------------------------------------------------------------------------
1597
1598 //------------------------------------------------------------------------------
1599 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1600 {
1601   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1602 }
1603 //------------------------------------------------------------------------------
1604
1605 //------------------------------------------------------------------------------
1606 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1607 {
1608   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1609 }
1610 //------------------------------------------------------------------------------
1611
1612 //------------------------------------------------------------------------------
1613 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1614 {
1615   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1616 }
1617 //------------------------------------------------------------------------------
1618
1619 //------------------------------------------------------------------------------
1620 void vvMainWindow::FusionChanged(int visibility, double value)
1621 {
1622   overlayPanel->getCurrentFusionInfo(visibility,value);
1623 }
1624 //------------------------------------------------------------------------------
1625
1626 //------------------------------------------------------------------------------
1627 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1628 {
1629   infoPanel->setViews(window, view, slice);
1630 }
1631 //------------------------------------------------------------------------------
1632
1633 //------------------------------------------------------------------------------
1634 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1635 {
1636   windowSpinBox->setValue(window);
1637   levelSpinBox->setValue(level);
1638   colorMapComboBox->setCurrentIndex(colormap);
1639   presetComboBox->setCurrentIndex(preset);
1640 }
1641 //------------------------------------------------------------------------------
1642
1643 //------------------------------------------------------------------------------
1644 void vvMainWindow::WindowLevelEdited()
1645 {
1646   presetComboBox->setCurrentIndex(6);
1647   UpdateWindowLevel();
1648 }
1649 //------------------------------------------------------------------------------
1650
1651 //------------------------------------------------------------------------------
1652 void vvMainWindow::UpdateWindowLevel()
1653 {
1654   if (DataTree->selectedItems().size()) {
1655     if (presetComboBox->currentIndex() == 7) //For ventilation
1656       colorMapComboBox->setCurrentIndex(5);
1657     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1658     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1659     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1660     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1661     mSlicerManagers[index]->Render();
1662     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1663     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1664   }
1665 }
1666 //------------------------------------------------------------------------------
1667
1668 //------------------------------------------------------------------------------
1669 void vvMainWindow::UpdateColorMap()
1670 {
1671   if (DataTree->selectedItems().size()) {
1672     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1673     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1674     mSlicerManagers[index]->Render();
1675   }
1676 }
1677 //------------------------------------------------------------------------------
1678 void vvMainWindow::SwitchWindowLevel()
1679 {
1680   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1681   int window = mSlicerManagers[index]->GetColorWindow();
1682   presetComboBox->setCurrentIndex(6);
1683   windowSpinBox->setValue(-window);
1684   UpdateWindowLevel();
1685 }
1686 //------------------------------------------------------------------------------
1687
1688 //------------------------------------------------------------------------------
1689 void vvMainWindow::ApplyWindowLevelToAllImages()
1690 {
1691   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1692     if (mSlicerManagers[i] == NULL)
1693       continue;
1694     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1695     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1696     mSlicerManagers[i]->SetPreset(6);
1697     mSlicerManagers[i]->Render();
1698   }
1699 }
1700 //------------------------------------------------------------------------------
1701
1702 //------------------------------------------------------------------------------
1703 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1704 {
1705   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1706     if (mSlicerManagers[i]->GetId() == id) {
1707       //mSlicerManagers[i]->SetTSlice(temps);
1708       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1709       mSlicerManagers[i]->UpdateViews(0,slicer);
1710       break;
1711     }
1712   }
1713 }
1714 //------------------------------------------------------------------------------
1715
1716 //------------------------------------------------------------------------------
1717 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1718 {
1719   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1720     if (id == mSlicerManagers[i]->GetId()) {
1721       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1722     }
1723   }
1724 }
1725 //------------------------------------------------------------------------------
1726
1727 //------------------------------------------------------------------------------
1728 void vvMainWindow::ShowContextMenu(QPoint point)
1729 {
1730   if (!DataTree->selectedItems().size()) {
1731     contextActions[1]->setEnabled(0);
1732     contextActions[2]->setEnabled(0);
1733     contextActions[3]->setEnabled(0);
1734     contextActions[4]->setEnabled(0);
1735     contextActions[5]->setEnabled(0);
1736     contextActions[6]->setEnabled(0);
1737   } else {
1738     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1739     contextActions[1]->setEnabled(1);
1740     contextActions[2]->setEnabled(
1741       DataTree->itemWidget(DataTree->selectedItems()[0],
1742                            COLUMN_RELOAD_IMAGE)->isEnabled());
1743     contextActions[3]->setEnabled(1);
1744     contextActions[5]->setEnabled(1);
1745     contextActions[6]->setEnabled(1);
1746
1747     if (mSlicerManagers[index]->GetDimension() < 3)
1748       contextActions[4]->setEnabled(0);
1749     else
1750       contextActions[4]->setEnabled(1);
1751   }
1752   contextMenu.exec(QCursor::pos());
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::CloseImage()
1758 {
1759   CloseImage(DataTree->selectedItems()[0],0);
1760 }
1761 //------------------------------------------------------------------------------
1762
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::ReloadImage()
1765 {
1766   ReloadImage(DataTree->selectedItems()[0],0);
1767 }
1768 //------------------------------------------------------------------------------
1769
1770 //------------------------------------------------------------------------------
1771 void vvMainWindow::SelectOverlayImage()
1772 {
1773   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1774
1775   //check if one overlay image is added
1776   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1777     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1778       QString error = "Cannot add more than one compared image\n";
1779       error += "Please remove first ";
1780       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1781       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1782       return;
1783     }
1784
1785   QString Extensions = EXTENSIONS;
1786   Extensions += ";;All Files (*)";
1787   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1788   if (!file.isEmpty())
1789     AddOverlayImage(index,file);
1790 }
1791 //------------------------------------------------------------------------------
1792
1793 //------------------------------------------------------------------------------
1794 void vvMainWindow::AddOverlayImage(int index, QString file)
1795 {
1796
1797   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1798   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1799                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1800   reader->SetFileName(file.toStdString().c_str());
1801   reader->ReadImageInformation();
1802   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1803   int dimension = reader->GetNumberOfDimensions();
1804   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1805   vvProgressDialog progress("Opening " + file.toStdString());
1806   qApp->processEvents();
1807
1808   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1809   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1810     //create an item in the tree with good settings
1811     QTreeWidgetItem *item = new QTreeWidgetItem();
1812     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1813     item->setData(1,Qt::UserRole,tr("overlay"));
1814     QFileInfo fileinfo(file); //Do not show the path
1815     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1816     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1817     qApp->processEvents();
1818
1819     for (int j = 1; j <= 4; j++) {
1820       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1821       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1822           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1823     }
1824
1825     //Create the buttons for reload and close
1826     qApp->processEvents();
1827     QTreePushButton* cButton = new QTreePushButton;
1828     cButton->setItem(item);
1829     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1830     cButton->setToolTip(tr("close image"));
1831     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1832     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1833             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1834
1835     QTreePushButton* rButton = new QTreePushButton;
1836     rButton->setItem(item);
1837     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1838     rButton->setToolTip(tr("reload image"));
1839     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1840     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1841             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1842
1843     DataTree->topLevelItem(index)->setExpanded(1);
1844     DataTree->topLevelItem(index)->addChild(item);
1845     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1846     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1847
1848     //set the id of the image
1849     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1850     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1851     UpdateTree();
1852     qApp->processEvents();
1853     ImageInfoChanged();
1854     QApplication::restoreOverrideCursor();
1855   } else {
1856     QApplication::restoreOverrideCursor();
1857     QString error = "Cannot import the new image.\n";
1858     error += mSlicerManagers[index]->GetLastError().c_str();
1859     QMessageBox::information(this,tr("Problem reading image !"),error);
1860   }
1861 }
1862 //------------------------------------------------------------------------------
1863
1864
1865 //------------------------------------------------------------------------------
1866 void vvMainWindow::AddROI(int index, QString file)
1867 {
1868   /*
1869   // Get slice manager
1870
1871   // Load image
1872
1873   vvImageReader * mReader = new vvImageReader;
1874   mReader->SetInputFilename(filename.toStdString());
1875   mReader->Update(IMAGE);
1876   if (mReader->GetLastError().size() != 0) {
1877     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1878     QString error = "Cannot open file \n";
1879     error += mReader->GetLastError().c_str();
1880     QMessageBox::information(this,tr("Reading problem"),error);
1881     delete mReader;
1882     return;
1883   }
1884   vvImage::Pointer roi = mReader->GetOutput();
1885
1886   // Create roi in new tool
1887   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1888   */
1889 }
1890 //------------------------------------------------------------------------------
1891
1892 //------------------------------------------------------------------------------
1893 void vvMainWindow::SelectFusionImage()
1894 {
1895   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1896
1897   //check if one fusion image is added
1898   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1899     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1900       QString error = "Cannot add more than one fusion image\n";
1901       error += "Please remove first ";
1902       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1903       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1904       return;
1905     }
1906
1907   QString Extensions = EXTENSIONS;
1908   Extensions += ";;All Files (*)";
1909   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1910   if (!file.isEmpty())
1911     AddFusionImage(index,file);
1912 }
1913 //------------------------------------------------------------------------------
1914
1915 //------------------------------------------------------------------------------
1916 void vvMainWindow::AddFusionImage(int index, QString file)
1917 {
1918   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1919   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1920                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1921   reader->SetFileName(file.toStdString().c_str());
1922   reader->ReadImageInformation();
1923   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1924   if (reader) {
1925     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1926     vvProgressDialog progress("Opening fusion");
1927     qApp->processEvents();
1928
1929     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1930     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1931                                           reader->GetNumberOfDimensions(), component)) {
1932       //create an item in the tree with good settings
1933       QTreeWidgetItem *item = new QTreeWidgetItem();
1934       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1935       item->setData(1,Qt::UserRole,tr("fusion"));
1936       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1937       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1938       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1939       qApp->processEvents();
1940
1941       for (int j = 1; j <= 4; j++) {
1942         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1943         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1944             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1945       }
1946
1947       //Create the buttons for reload and close
1948       qApp->processEvents();
1949       QTreePushButton* cButton = new QTreePushButton;
1950       cButton->setItem(item);
1951       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1952       cButton->setToolTip(tr("close image"));
1953       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1954       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1955               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1956
1957       QTreePushButton* rButton = new QTreePushButton;
1958       rButton->setItem(item);
1959       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1960       rButton->setToolTip(tr("reload image"));
1961       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1962       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1963               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1964
1965       DataTree->topLevelItem(index)->setExpanded(1);
1966       DataTree->topLevelItem(index)->addChild(item);
1967       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1968       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1969
1970       //set the id of the image
1971       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1972       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1973       UpdateTree();
1974       qApp->processEvents();
1975       ImageInfoChanged();
1976       QApplication::restoreOverrideCursor();
1977     } else {
1978       QApplication::restoreOverrideCursor();
1979       QString error = "Cannot import the new image.\n";
1980       error += mSlicerManagers[index]->GetLastError().c_str();
1981       QMessageBox::information(this,tr("Problem reading image !"),error);
1982     }
1983   } else {
1984     QString error = "Cannot import the new image.\n";
1985     QMessageBox::information(this,tr("Problem reading image !"),error);
1986   }
1987 }
1988 //------------------------------------------------------------------------------
1989
1990
1991 //------------------------------------------------------------------------------
1992 void vvMainWindow::OpenField()
1993 {
1994   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1995   //check if a vector field has already been added
1996   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1997     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1998       QString error = "Cannot add more than one vector field\n";
1999       error += "Please remove first ";
2000       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2001       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2002       return;
2003     }
2004
2005   QString Extensions = "Images ( *.mhd)";
2006   Extensions += ";;Images ( *.vf)";
2007   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2008   if (!file.isEmpty())
2009     AddField(file,index);
2010 }
2011 //------------------------------------------------------------------------------
2012
2013
2014 //------------------------------------------------------------------------------
2015 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2016 {
2017   //create an item in the tree with good settings
2018   QTreeWidgetItem *item = new QTreeWidgetItem();
2019   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2020   item->setData(1,Qt::UserRole,tr("vector"));
2021   QFileInfo fileinfo(filename); //Do not show the path
2022   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2023   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2024   qApp->processEvents();
2025
2026   for (int j = 1; j <= 4; j++) {
2027     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2028     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2029         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2030   }
2031
2032   //Create the buttons for reload and close
2033   qApp->processEvents();
2034   QTreePushButton* cButton = new QTreePushButton;
2035   cButton->setItem(item);
2036   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2037   cButton->setToolTip(tr("close vector field"));
2038   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2039   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2040           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2041
2042   QTreePushButton* rButton = new QTreePushButton;
2043   rButton->setItem(item);
2044   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2045   rButton->setToolTip(tr("reload vector field"));
2046   rButton->setEnabled(from_disk);
2047   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2048   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2049           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2050
2051   DataTree->topLevelItem(index)->setExpanded(1);
2052   DataTree->topLevelItem(index)->addChild(item);
2053   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2054   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2055
2056   //set the id of the image
2057   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2058   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2059   UpdateTree();
2060   qApp->processEvents();
2061   ImageInfoChanged();
2062   QApplication::restoreOverrideCursor();
2063 }
2064 //------------------------------------------------------------------------------
2065
2066
2067 //------------------------------------------------------------------------------
2068 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2069 {
2070   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2071   vvSlicerManager* imageManager = mSlicerManagers[index];
2072   if (imageManager->SetVF(vf,file.toStdString())) {
2073     AddFieldEntry(file,index,false);
2074   } else {
2075     QString error = "Cannot import the vector field for this image.\n";
2076     error += imageManager->GetLastError().c_str();
2077     QMessageBox::information(this,tr("Problem reading VF !"),error);
2078   }
2079   QApplication::restoreOverrideCursor();
2080 }
2081 //------------------------------------------------------------------------------
2082
2083
2084 //------------------------------------------------------------------------------
2085 void vvMainWindow::AddField(QString file,int index)
2086 {
2087   if (QFile::exists(file)) {
2088     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2089
2090     //init the progress events
2091     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2092     vvProgressDialog progress("Opening " + file.toStdString());
2093     qApp->processEvents();
2094
2095     //read the vector and put it in the current mSlicerManager
2096     vvSlicerManager* imageManager = mSlicerManagers[index];
2097     qApp->processEvents();
2098
2099     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2100     if (imageManager->SetVF(file.toStdString())) {
2101       imageManager->Render();
2102       AddFieldEntry(file,index,true);
2103     } else {
2104       QApplication::restoreOverrideCursor();
2105       QString error = "Cannot import the vector field for this image.\n";
2106       error += imageManager->GetLastError().c_str();
2107       QMessageBox::information(this,tr("Problem reading VF !"),error);
2108     }
2109   } else
2110     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2111
2112 }
2113 //------------------------------------------------------------------------------
2114
2115
2116 //------------------------------------------------------------------------------
2117 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2118 {
2119   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2120   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2121     for (int i = 0; i < 4; i++) {
2122       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2123       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2124       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2125       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2126       if (log > 0)
2127         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2128       else
2129         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2130     }
2131   }
2132 }
2133 //------------------------------------------------------------------------------
2134
2135
2136 //------------------------------------------------------------------------------
2137 void vvMainWindow::SetOverlayProperty(int color)
2138 {
2139   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2140   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2141     mSlicerManagers[index]->SetOverlayColor(color);
2142     mSlicerManagers[index]->SetColorMap(0);
2143     mSlicerManagers[index]->Render();
2144   }
2145 }
2146 //------------------------------------------------------------------------------
2147
2148 //------------------------------------------------------------------------------
2149 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2150 {
2151   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2152   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2153     mSlicerManagers[index]->SetFusionOpacity(opacity);
2154     mSlicerManagers[index]->SetFusionColorMap(colormap);
2155     mSlicerManagers[index]->SetFusionWindow(window);
2156     mSlicerManagers[index]->SetFusionLevel(level);
2157     mSlicerManagers[index]->SetColorMap(0);
2158     mSlicerManagers[index]->Render();
2159   }
2160 }
2161 //------------------------------------------------------------------------------
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::SaveAs()
2165 {
2166   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2167     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2168     return;
2169   }
2170
2171   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2172   int dimension = mSlicerManagers[index]->GetDimension();
2173   QStringList OutputListeFormat;
2174   OutputListeFormat.clear();
2175   if (dimension == 1) {
2176     OutputListeFormat.push_back(".mhd");
2177   }
2178   if (dimension == 2) {
2179     OutputListeFormat.push_back(".bmp");
2180     OutputListeFormat.push_back(".png");
2181     OutputListeFormat.push_back(".jpeg");
2182     OutputListeFormat.push_back(".tif");
2183     OutputListeFormat.push_back(".mhd");
2184     OutputListeFormat.push_back(".hdr");
2185     OutputListeFormat.push_back(".vox");
2186   } else if (dimension == 3) {
2187     OutputListeFormat.push_back(".mhd");
2188     OutputListeFormat.push_back(".hdr");
2189     OutputListeFormat.push_back(".vox");
2190   } else if (dimension == 4) {
2191     OutputListeFormat.push_back(".mhd");
2192   }
2193   QString Extensions = "AllFiles(*.*)";
2194   for (int i = 0; i < OutputListeFormat.count(); i++) {
2195     Extensions += ";;Images ( *";
2196     Extensions += OutputListeFormat[i];
2197     Extensions += ")";
2198   }
2199   QString fileName = QFileDialog::getSaveFileName(this,
2200                      tr("Save As"),
2201                      mSlicerManagers[index]->GetFileName().c_str(),
2202                      Extensions);
2203   if (!fileName.isEmpty()) {
2204     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2205     if (OutputListeFormat.contains(
2206           fileformat.c_str())) {
2207       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2208       std::string action = "Saving";
2209       vvProgressDialog progress("Saving "+fileName.toStdString());
2210       qApp->processEvents();
2211       vvImageWriter *writer = new vvImageWriter;
2212       writer->SetOutputFileName(fileName.toStdString());
2213       writer->SetInput(mSlicerManagers[index]->GetImage());
2214       writer->Update();
2215       QApplication::restoreOverrideCursor();
2216       if (writer->GetLastError().size()) {
2217         QString error = "Saving did not succeed\n";
2218         error += writer->GetLastError().c_str();
2219         QMessageBox::information(this,tr("Saving Problem"),error);
2220         SaveAs();
2221       }
2222     } else {
2223       QString error = fileformat.c_str();
2224       if (error.isEmpty())
2225         error += "no file format specified !";
2226       else
2227         error += " format unknown !!!\n";
2228       QMessageBox::information(this,tr("Saving Problem"),error);
2229       SaveAs();
2230     }
2231   }
2232 }
2233 //------------------------------------------------------------------------------
2234
2235
2236 //------------------------------------------------------------------------------
2237 void vvMainWindow::AddLink(QString image1,QString image2)
2238 {
2239   unsigned int sm1 = 0;
2240   unsigned int sm2 = 0;
2241
2242   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2243     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2244       mSlicerManagers[i]->AddLink(image2.toStdString());
2245       sm1 = i;
2246     }
2247     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2248       mSlicerManagers[i]->AddLink(image1.toStdString());
2249       sm2 = i;
2250     }
2251   }
2252
2253   if (linkPanel->isLinkAll())   {
2254     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex]);
2255     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex]);
2256   }
2257   else {
2258     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1]);
2259   }
2260 }
2261
2262 //------------------------------------------------------------------------------
2263
2264
2265 //------------------------------------------------------------------------------
2266 void vvMainWindow::RemoveLink(QString image1,QString image2)
2267 {
2268   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2269     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2270       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2271     }
2272     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2273       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2274     }
2275   }
2276 }
2277 //------------------------------------------------------------------------------
2278
2279 //------------------------------------------------------------------------------
2280 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2281 {
2282   int index = 0;
2283   while(sm != mSlicerManagers[index])
2284     index++;
2285   index = (index+offset) % mSlicerManagers.size();
2286
2287   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2288   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2289   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2290   DisplayChanged(item,slicer+1);
2291 }
2292 //------------------------------------------------------------------------------
2293
2294 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2295 {
2296   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2297     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2298       for (int j = 0; j < 4; j++) {
2299         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2300         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2301         //UpdateTSlice(j,value);
2302       }
2303       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2304       break;
2305     }
2306   }
2307 }
2308 //------------------------------------------------------------------------------
2309
2310
2311 //------------------------------------------------------------------------------
2312 void vvMainWindow::NOHorizontalSliderMoved()
2313 {
2314   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2315   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2316 //  mCurrentTime = NOHorizontalSlider->value();
2317 }
2318 //------------------------------------------------------------------------------
2319
2320
2321 //------------------------------------------------------------------------------
2322 void vvMainWindow::NEHorizontalSliderMoved()
2323 {
2324   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2325   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2326 //  mCurrentTime = NEHorizontalSlider->value();
2327 }
2328 //------------------------------------------------------------------------------
2329
2330
2331 //------------------------------------------------------------------------------
2332 void vvMainWindow::SOHorizontalSliderMoved()
2333 {
2334   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2335   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2336   // mCurrentTime = SOHorizontalSlider->value();
2337 }
2338 //------------------------------------------------------------------------------
2339
2340
2341 //------------------------------------------------------------------------------
2342 void vvMainWindow::SEHorizontalSliderMoved()
2343 {
2344   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2345   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2346   // mCurrentTime = SEHorizontalSlider->value();
2347 }
2348 //------------------------------------------------------------------------------
2349
2350 //------------------------------------------------------------------------------
2351 void vvMainWindow::NOVerticalSliderChanged()
2352 {
2353   static int value=-1;
2354   if (value == NOVerticalSlider->value()) return;
2355   else value = NOVerticalSlider->value();
2356   //  int value = NOVerticalSlider->value();
2357   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2358     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2359       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2360         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2361         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2362
2363         // If nor Update/Render -> slider not work
2364         // only render = ok navigation, but for contour Update needed but slower ?
2365
2366         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2367         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2368       }
2369       break;
2370     }
2371   }
2372 }
2373 //------------------------------------------------------------------------------
2374
2375
2376 //------------------------------------------------------------------------------
2377 void vvMainWindow::NEVerticalSliderChanged()
2378 {
2379   static int value=-1;
2380   if (value == NEVerticalSlider->value()) return;
2381   else value = NEVerticalSlider->value();
2382   //  int value = NEVerticalSlider->value();
2383   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2384     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2385       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2386         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2387         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2388         mSlicerManagers[i]->UpdateSlice(1);
2389         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2390       }
2391       break;
2392     }
2393   }
2394 }
2395 //------------------------------------------------------------------------------
2396
2397
2398 //------------------------------------------------------------------------------
2399 void vvMainWindow::SOVerticalSliderChanged()
2400 {
2401   static int value=-1;
2402   if (value == SOVerticalSlider->value()) return;
2403   else value = SOVerticalSlider->value();
2404   //int value = SOVerticalSlider->value();
2405   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2406     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2407       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2408         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2409         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2410         mSlicerManagers[i]->UpdateSlice(2);
2411         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2412       }
2413       // else { DD("avoid SOVerticalSlider slicer update"); }
2414       break;
2415     }
2416   }
2417 }
2418 //------------------------------------------------------------------------------
2419
2420
2421 //------------------------------------------------------------------------------
2422 void vvMainWindow::SEVerticalSliderChanged()
2423 {
2424   static int value=-1;
2425   if (value == SEVerticalSlider->value()) return;
2426   else value = SEVerticalSlider->value();
2427   // int value = SEVerticalSlider->value();
2428   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2429     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2430       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2431         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2432         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2433         mSlicerManagers[i]->UpdateSlice(3);
2434         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2435       }
2436       break;
2437     }
2438   }
2439 }
2440 //------------------------------------------------------------------------------
2441
2442
2443 //------------------------------------------------------------------------------
2444 void vvMainWindow::UpdateSlice(int slicer, int slice)
2445 {
2446   // DD("vvMainWindow::UpdateSlice");
2447 //   DD(slicer);
2448 //   DD(slice);
2449   if (slicer == 0) {
2450     //    if (slice != NOVerticalSlider->value())
2451     NOVerticalSlider->setValue(slice);
2452   } else {
2453     if (slicer == 1)
2454       NEVerticalSlider->setValue(slice);
2455     else {
2456       if (slicer == 2)
2457         SOVerticalSlider->setValue(slice);
2458       else {
2459         if (slicer == 3)
2460           SEVerticalSlider->setValue(slice);
2461       }
2462     }
2463   }
2464   // DD("vvMainWindow:UpdateSlice END");
2465 }
2466 //------------------------------------------------------------------------------
2467
2468
2469 //------------------------------------------------------------------------------
2470 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2471 {
2472   switch (slicer) {
2473   case 0:
2474     NOHorizontalSlider->setValue(slice);
2475     break;
2476   case 1:
2477     NEHorizontalSlider->setValue(slice);
2478     break;
2479   case 2:
2480     SOHorizontalSlider->setValue(slice);
2481     break;
2482   case 3:
2483     SEHorizontalSlider->setValue(slice);
2484     break;
2485   }
2486 }
2487 //------------------------------------------------------------------------------
2488
2489
2490 //------------------------------------------------------------------------------
2491 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2492 {
2493   int position = int((min+max)/2);
2494   int tPosition = int((tmin+tmax)/2);
2495   if (slicer == 0) {
2496     NOVerticalSlider->setValue(position);
2497     NOVerticalSlider->setRange(min,max);
2498     NOHorizontalSlider->setRange(tmin,tmax);
2499     NOHorizontalSlider->setValue(tPosition);
2500   } else if (slicer == 1) {
2501     NEVerticalSlider->setValue(position);
2502     NEVerticalSlider->setRange(min,max);
2503     NEHorizontalSlider->setRange(tmin,tmax);
2504     NEHorizontalSlider->setValue(tPosition);
2505   } else if (slicer == 2) {
2506     SOVerticalSlider->setValue(position);
2507     SOVerticalSlider->setRange(min,max);
2508     SOHorizontalSlider->setRange(tmin,tmax);
2509     SOHorizontalSlider->setValue(tPosition);
2510   } else if (slicer == 3) {
2511     SEVerticalSlider->setValue(position);
2512     SEVerticalSlider->setRange(min,max);
2513     SEHorizontalSlider->setRange(tmin,tmax);
2514     SEHorizontalSlider->setValue(tPosition);
2515   }
2516 }
2517 //------------------------------------------------------------------------------
2518
2519
2520 //------------------------------------------------------------------------------
2521 void vvMainWindow::SaveNOScreenshot()
2522 {
2523   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2524   w2i->SetInput(NOViewWidget->GetRenderWindow());
2525   w2i->Update();
2526   SaveScreenshot(w2i->GetOutput());
2527   w2i->Delete();
2528 }
2529 //------------------------------------------------------------------------------
2530
2531
2532 //------------------------------------------------------------------------------
2533 void vvMainWindow::SaveNEScreenshot()
2534 {
2535   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2536   w2i->SetInput(NEViewWidget->GetRenderWindow());
2537   w2i->Update();
2538   SaveScreenshot(w2i->GetOutput());
2539   w2i->Delete();
2540 }
2541 //------------------------------------------------------------------------------
2542
2543
2544 //------------------------------------------------------------------------------
2545 void vvMainWindow::SaveSOScreenshot()
2546 {
2547   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2548   w2i->SetInput(SOViewWidget->GetRenderWindow());
2549   w2i->Update();
2550   SaveScreenshot(w2i->GetOutput());
2551   w2i->Delete();
2552 }
2553 //------------------------------------------------------------------------------
2554
2555
2556 //------------------------------------------------------------------------------
2557 void vvMainWindow::SaveSEScreenshot()
2558 {
2559   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2560   w2i->SetInput(SEViewWidget->GetRenderWindow());
2561   w2i->Update();
2562   SaveScreenshot(w2i->GetOutput());
2563   w2i->Delete();
2564 }
2565 //------------------------------------------------------------------------------
2566
2567
2568 //------------------------------------------------------------------------------
2569 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2570 {
2571   QString Extensions = "Images( *.png);;";
2572   Extensions += "Images( *.jpg);;";
2573   Extensions += "Images( *.bmp);;";
2574   Extensions += "Images( *.tif);;";
2575   Extensions += "Images( *.ppm)";
2576   QString fileName = QFileDialog::getSaveFileName(this,
2577                      tr("Save As"),
2578                      itksys::SystemTools::GetFilenamePath(
2579                        mSlicerManagers[0]->GetFileName()).c_str(),
2580                      Extensions);
2581   if (!fileName.isEmpty()) {
2582     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2583     if (!strcmp(ext, ".bmp")) {
2584       vtkBMPWriter *bmp = vtkBMPWriter::New();
2585       bmp->SetInput(image);
2586       bmp->SetFileName(fileName.toStdString().c_str());
2587       bmp->Write();
2588       bmp->Delete();
2589     } else if (!strcmp(ext, ".tif")) {
2590       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2591       tif->SetInput(image);
2592       tif->SetFileName(fileName.toStdString().c_str());
2593       tif->Write();
2594       tif->Delete();
2595     } else if (!strcmp(ext, ".ppm")) {
2596       vtkPNMWriter *pnm = vtkPNMWriter::New();
2597       pnm->SetInput(image);
2598       pnm->SetFileName(fileName.toStdString().c_str());
2599       pnm->Write();
2600       pnm->Delete();
2601     } else if (!strcmp(ext, ".png")) {
2602       vtkPNGWriter *png = vtkPNGWriter::New();
2603       png->SetInput(image);
2604       png->SetFileName(fileName.toStdString().c_str());
2605       png->Write();
2606       png->Delete();
2607     } else if (!strcmp(ext, ".jpg")) {
2608       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2609       jpg->SetInput(image);
2610       jpg->SetFileName(fileName.toStdString().c_str());
2611       jpg->Write();
2612       jpg->Delete();
2613     } else {
2614       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2615     }
2616   }
2617
2618 }
2619 //------------------------------------------------------------------------------
2620
2621
2622 //------------------------------------------------------------------------------
2623 void vvMainWindow::GoToCursor()
2624 {
2625   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2626   for (int column = 1; column < 5; column++) {
2627     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2628       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2629       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2630         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2631       mSlicerManagers[index]->UpdateViews(1,column-1);
2632       mSlicerManagers[index]->UpdateLinked(column-1);
2633       break;
2634     }
2635   }
2636 }
2637 //------------------------------------------------------------------------------
2638
2639 //------------------------------------------------------------------------------
2640 void vvMainWindow::PlayPause()
2641 {
2642   if (playMode) {
2643     playMode = 0;
2644     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2645     ImageInfoChanged();
2646     return;
2647   } else {
2648     int image_number=DataTree->topLevelItemCount();
2649     bool has_temporal;
2650     for (int i=0; i<image_number; i++)
2651       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2652         has_temporal=true;
2653         break;
2654       }
2655     if (has_temporal) {
2656       playMode = 1;
2657       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2658       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2659     }
2660   }
2661 }
2662 //------------------------------------------------------------------------------
2663
2664 //------------------------------------------------------------------------------
2665 void vvMainWindow::PlayNext()
2666 {
2667   if (playMode && !this->isHidden()) {
2668     int image_number=DataTree->topLevelItemCount();
2669     ///Only play one slicer per SM, and only if the SM is being displayed
2670     for (int i=0; i<image_number; i++)
2671       for (int j=0; j<4; j++)
2672         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2673             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2674           mSlicerManagers[i]->SetNextTSlice(j);
2675           break;
2676         }
2677     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2678   }
2679 }
2680 //------------------------------------------------------------------------------
2681
2682 void vvMainWindow::ShowLastImage()
2683 {
2684   if (mSlicerManagers.size() > 1) {
2685     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2686     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2687     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2688     DisplayChanged(item,1);
2689   }
2690 }
2691
2692 //------------------------------------------------------------------------------
2693 void vvMainWindow::UpdateRenderWindows()
2694 {
2695   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2696   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2697   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2698   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2699 }
2700 //------------------------------------------------------------------------------
2701
2702 //------------------------------------------------------------------------------
2703 void vvMainWindow::SegmentationOnCurrentImage()
2704 {
2705   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2706
2707   vvSegmentationDialog segmentation;
2708   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2709   segmentation.exec();
2710 }
2711 //------------------------------------------------------------------------------
2712
2713 void vvMainWindow::SurfaceViewerLaunch()
2714 {
2715   vvSurfaceViewerDialog surfaceViewer;
2716   surfaceViewer.exec();
2717 }
2718 //------------------------------------------------------------------------------
2719
2720
2721 //------------------------------------------------------------------------------
2722 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2723 {
2724   int number=0;
2725   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2726     vvSlicerManager * v = mSlicerManagers[l];
2727     if (v->GetBaseFileName() ==
2728         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2729       number = std::max(number, v->GetBaseFileNameNumber()+1);
2730     }
2731   }
2732   return number;
2733 }
2734 //------------------------------------------------------------------------------
2735
2736
2737 //------------------------------------------------------------------------------
2738 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2739 {
2740   // Change filename if another image exist with the same name
2741   int number = GetImageDuplicateFilenameNumber(filename);
2742
2743   // Create new SliceManager
2744   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2745   slicer_manager->SetImage(image);//, IMAGE, number);
2746   //  filename = filename+"_"+clitk::toString(number);
2747   slicer_manager->SetFilename(filename, number);
2748   mSlicerManagers.push_back(slicer_manager);
2749
2750   //create an item in the tree with good settings
2751   QTreeWidgetItem *item = new QTreeWidgetItem();
2752   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2753   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2754   qApp->processEvents();
2755
2756   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2757
2758   //Create the buttons for reload and close
2759   qApp->processEvents();
2760   QTreePushButton* cButton = new QTreePushButton;
2761   cButton->setItem(item);
2762   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2763   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2764   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2765           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2766
2767   QTreePushButton* rButton = new QTreePushButton;
2768   rButton->setItem(item);
2769   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2770   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2771   rButton->setEnabled(0);
2772   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2773           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2774
2775   DataTree->addTopLevelItem(item);
2776   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2777   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2778
2779   //set the id of the image
2780   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2781   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2782   mSlicerManagers.back()->SetId(id.toStdString());
2783
2784   linkPanel->addImage(filename, id.toStdString());
2785
2786   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2787           this, SLOT(CurrentImageChanged(std::string)));
2788   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2789           this, SLOT(CurrentPickedImageChanged(std::string)));
2790   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2791           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2792   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2793           this, SLOT(VectorChanged(int,double,double,double, double)));
2794   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2795           this, SLOT(OverlayChanged(int,double,double)));
2796   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2797           this, SLOT(FusionChanged(int,double)));
2798   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2799           this,SLOT(WindowsChanged(int, int, int)));
2800   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2801           this,SLOT(WindowLevelChanged(double, double, int, int)));
2802   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2803           this,SLOT(UpdateSlice(int,int)));
2804   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2805           this,SLOT(UpdateTSlice(int, int)));
2806   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2807           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2808   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2809           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2810   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2811           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2812   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2813           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2814   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2815   UpdateTree();
2816   qApp->processEvents();
2817   InitSlicers();
2818   ShowLastImage();
2819   InitDisplay();
2820   qApp->processEvents();
2821
2822   // End
2823   ImageInfoChanged();
2824   return slicer_manager;
2825 }
2826 //------------------------------------------------------------------------------
2827
2828
2829 //------------------------------------------------------------------------------
2830 void vvMainWindow::UpdateCurrentSlicer()
2831 {
2832   int index = -1;
2833   if (DataTree->selectedItems().size() > 0) {
2834     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2835   }
2836   mSlicerManagerCurrentIndex = index;
2837 }
2838 //------------------------------------------------------------------------------
2839