vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #ifdef VTK_USE_FFMPEG_ENCODER
  72 #  include <vtkFFMPEGWriter.h>
  73 #endif
  74 #ifdef VTK_USE_MPEG2_ENCODER
  75 #  include <vtkMPEG2Writer.h>
  76 #endif
  77 #include <vtkMatrix4x4.h>
  78 #include <vtkTransform.h>
  79
  80 // Standard includes
  81 #include <iostream>
  82 #include <sstream>
  83 #include <iomanip>
  84
  85 #define COLUMN_TREE 0
  86 #define COLUMN_UL_VIEW 1
  87 #define COLUMN_UR_VIEW 2
  88 #define COLUMN_DL_VIEW 3
  89 #define COLUMN_DR_VIEW 4
  90 #define COLUMN_CLOSE_IMAGE 5
  91 #define COLUMN_RELOAD_IMAGE 6
  92 #define COLUMN_IMAGE_NAME 7
  93
  94 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  95
  96 /*Data Tree values
  97   0,Qt::UserRole full filename
  98   1,Qt::CheckStateRole checkbutton UL View
  99   1,Qt::UserRole overlay, fusion or vector
 100   2,Qt::CheckStateRole checkbutton UR View
 101   3,Qt::CheckStateRole checkbutton DL View
 102   4,Qt::CheckStateRole checkbutton DR View
 103   5,0  short filename
 104   5,Qt::UserRole mSlicerManager id*/
 105
 106 //------------------------------------------------------------------------------
 107 vvMainWindow::vvMainWindow():vvMainWindowBase()
 108 {
 109   setupUi(this); // this sets up the GUI
 110
 111   mInputPathName = "";
 112   mMenuTools = menuTools;
 113   //  mMenuSegmentation = menuSegmentation;
 114   mContextMenu = &contextMenu;
 115   mMenuExperimentalTools = menuExperimental;
 116   mMainWidget = this;
 117   mCurrentTime = -1;
 118   mCurrentSelectedImageId = "";
 119   mCurrentPickedImageId = "";
 120   mCurrentPickedImageIndex = 0;
 121
 122   //Init the contextMenu
 123   this->setContextMenuPolicy(Qt::CustomContextMenu);
 124   contextActions.resize(0);
 125   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 126                                   tr("O&pen new Image"));
 127   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 128   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 129   contextActions.push_back(actionOpen_new_image);
 130   contextMenu.addSeparator();
 131
 132   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 133                                tr("Close Current Image"));
 134   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 135   contextActions.push_back(actionClose_Image);
 136
 137   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 138                                 tr("Reload Current Image"));
 139   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 140   contextActions.push_back(actionReload_image);
 141
 142   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 143                               tr("Save Current Image"));
 144   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 145   contextActions.push_back(actionSave_image);
 146
 147   contextMenu.addSeparator();
 148
 149   contextMenu.addAction(actionAdd_VF_to_current_Image);
 150   contextActions.push_back(actionAdd_VF_to_current_Image);
 151
 152   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 153       tr("Add overlay image to current image"));
 154   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 155   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 156
 157   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 158
 159   contextMenu.addAction(actionAdd_fusion_image);
 160   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 161   contextActions.push_back(actionAdd_fusion_image);
 162
 163   // TRIAL DS
 164   /*
 165   QMenu * m = new QMenu(menubar);
 166   m->setTitle("TOTO");
 167   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 168   contextMenu.addMenu(m);
 169   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON"));
 171   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 172                      tr("BIDON2"));
 173   m->addAction(a);
 174   m->addAction(b);
 175   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 176   */
 177
 178   //init the DataTree
 179   mSlicerManagers.resize(0);
 180
 181   QStringList header;
 182   header.append("");
 183   header.append("TL");
 184   header.append("TR");
 185   header.append("BL");
 186   header.append("BR");
 187   header.append("");
 188   header.append("");
 189   header.append("Name");
 190
 191   DataTree->setHeaderLabels(header);
 192   DataTree->resizeColumnToContents(COLUMN_TREE);
 193   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 197   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 199   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 200
 201   viewMode = 1;
 202   documentation = new vvDocumentation();
 203   help_dialog = new vvHelpDialog();
 204   dicomSeriesSelector = new vvDicomSeriesSelector();
 205
 206   inverseButton->setEnabled(0);
 207   actionAdd_Overlay_to_current_Image->setEnabled(0);
 208   actionSave_As->setEnabled(0);
 209   actionAdd_VF_to_current_Image->setEnabled(0);
 210   actionAdd_fusion_image->setEnabled(0);
 211
 212   //init the sliders
 213   verticalSliders.push_back(NOVerticalSlider);
 214   verticalSliders.push_back(NEVerticalSlider);
 215   verticalSliders.push_back(SOVerticalSlider);
 216   verticalSliders.push_back(SEVerticalSlider);
 217
 218   for (int i =0; i < 4; i++)
 219     verticalSliders[i]->hide();
 220
 221   horizontalSliders.push_back(NOHorizontalSlider);
 222   horizontalSliders.push_back(NEHorizontalSlider);
 223   horizontalSliders.push_back(SOHorizontalSlider);
 224   horizontalSliders.push_back(SEHorizontalSlider);
 225
 226   for (int i =0; i < 4; i++)
 227     horizontalSliders[i]->hide();
 228
 229
 230   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 231   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 232   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 233   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 234
 235   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 236   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 237   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 238   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 239
 240   //connect everything
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 250   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 251   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 252   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 253   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 254   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 255   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 256   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 257   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 258
 259   ///////////////////////////////////////////////
 260   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 261   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 262   ///////////////////////////////////////////////
 263
 264   actionNorth_East_Window->setEnabled(0);
 265   actionNorth_West_Window->setEnabled(0);
 266   actionSouth_East_Window->setEnabled(0);
 267   actionSouth_West_Window->setEnabled(0);
 268
 269   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 270   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 271   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 272   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 273
 274   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 275   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 276           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 277
 278   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 279   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 281   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 282   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 283   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 284   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 285
 286
 287   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 288
 289   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 290   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 291   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 292   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 293   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 294           this,SLOT(SetFusionProperty(int,int,double,double)));
 295   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 296
 297   playMode = 0;//pause
 298   mFrameRate = 10;
 299   playButton->setEnabled(0);
 300   frameRateLabel->setEnabled(0);
 301   frameRateSpinBox->setEnabled(0);
 302   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 303   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 304
 305   goToCursorPushButton->setEnabled(0);
 306   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 307
 308   NOViewWidget->hide();
 309   NEViewWidget->hide();
 310   SOViewWidget->hide();
 311   SEViewWidget->hide();
 312
 313   //Recently opened files
 314   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 315   recentlyOpenedFilesMenu=NULL;
 316   if ( !recent_files.empty() ) {
 317     createRecentlyOpenedFilesMenu();
 318     updateRecentlyOpenedFilesMenu(recent_files);
 319   }
 320
 321   // Adding all new tools (insertion in the menu)
 322   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 323   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 324
 325   if (!CLITK_EXPERIMENTAL)
 326     menuExperimental->menuAction()->setVisible(false);
 327
 328
 329   QTimer * timerMemory = new QTimer(this);
 330   //timerMemory->setInterval(5);
 331   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 332   timerMemory->start(2000);
 333 }
 334 //------------------------------------------------------------------------------
 335 void vvMainWindow::show()
 336 {
 337   vvMainWindowBase::show();
 338   PopupRegisterForm(true);
 339 }
 340 //------------------------------------------------------------------------------
 341 void vvMainWindow::UpdateMemoryUsage()
 342 {
 343   //  clitk::PrintMemory(true);
 344   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 345   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 346 }
 347 //------------------------------------------------------------------------------
 348
 349
 350 //------------------------------------------------------------------------------
 351 void vvMainWindow::createRecentlyOpenedFilesMenu()
 352 {
 353   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 354   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 355   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 356   menuFile->insertSeparator(actionOpen_Image_With_Time);
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362
 363 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 364 {
 365   if(recentlyOpenedFilesMenu==NULL) {
 366     createRecentlyOpenedFilesMenu();
 367   } else {
 368     recentlyOpenedFilesMenu->clear();
 369   }
 370   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 371     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 372     recentlyOpenedFilesMenu->addAction(current);
 373     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 374   }
 375 }
 376 //------------------------------------------------------------------------------
 377
 378
 379 //------------------------------------------------------------------------------
 380 void vvMainWindow::ComputeMidPosition()
 381 {
 382   bool ok;
 383   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 384   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 385                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 386   if (ok) {
 387     vvMidPosition midp;
 388     midp.slicer_manager = mSlicerManagers[index];
 389     midp.reference_image_index = ref;
 390     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 391     midp.Update();
 392     if (midp.error)
 393       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 394     else {
 395       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 396       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 397     }
 398     QApplication::restoreOverrideCursor();
 399   }
 400 }
 401 //------------------------------------------------------------------------------
 402
 403
 404 //------------------------------------------------------------------------------
 405 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 406 {
 407   QTreeWidgetItem *item = new QTreeWidgetItem();
 408   item->setData(0,Qt::UserRole,"filename.vtk");
 409   item->setData(1,Qt::UserRole,tr("contour"));
 410   QBrush brush;
 411   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 412   brush.setStyle(Qt::SolidPattern);
 413   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 414   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 415
 416   for (int j = 1; j <= 4; j++)
 417     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 418
 419   QTreePushButton* cButton = new QTreePushButton;
 420   cButton->setItem(item);
 421   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 422   cButton->setToolTip(tr("close image"));
 423   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 424   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 425           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 426
 427   QTreePushButton* rButton = new QTreePushButton;
 428   rButton->setItem(item);
 429   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 430   rButton->setToolTip(tr("reload image"));
 431   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 432   rButton->setEnabled(false);
 433   //Not implemented
 434   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 435   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 436
 437   DataTree->topLevelItem(image_index)->setExpanded(1);
 438   DataTree->topLevelItem(image_index)->addChild(item);
 439   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 440   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 441   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 442   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 443
 444   UpdateTree();
 445   mSlicerManagers[image_index]->AddContour(contour,propagation);
 446   mSlicerManagers[image_index]->Render();
 447 }
 448 //------------------------------------------------------------------------------
 449
 450
 451 //------------------------------------------------------------------------------
 452 void vvMainWindow::OpenVTKContour()
 453 {
 454   if (mSlicerManagers.size() > 0) {
 455     QString Extensions = "Images ( *.vtk *.obj)";
 456     Extensions += ";;All Files (*)";
 457     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 458     if (file.isNull())
 459       return;
 460     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 461     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 462     vvMeshReader reader;
 463     reader.SetImage(mSlicerManagers[index]->GetImage());
 464     reader.SetModeToVTK();
 465     reader.SetFilename(file.toStdString());
 466     reader.Update();
 467     AddContour(index,reader.GetOutput()[0],false);
 468     QApplication::restoreOverrideCursor();
 469   }
 470 }
 471 //------------------------------------------------------------------------------
 472
 473
 474 //------------------------------------------------------------------------------
 475 void vvMainWindow::OpenDCStructContour()
 476 {
 477   if (mSlicerManagers.size() > 0) {
 478     QString Extensions = "Dicom Files ( *.dcm RS*)";
 479     Extensions += ";;All Files (*)";
 480     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 481     if (file.isNull())
 482       return;
 483     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 484     vvMeshReader reader;
 485     reader.SetFilename(file.toStdString());
 486     vvStructSelector selector;
 487     selector.SetStructures(reader.GetROINames());
 488     if (!mSlicerManagers[index]->GetVF().IsNull())
 489       selector.EnablePropagationCheckBox();
 490     if (selector.exec()) {
 491       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 492       reader.SetSelectedItems(selector.getSelectedItems());
 493       reader.SetImage(mSlicerManagers[index]->GetImage());
 494       if (selector.PropagationEnabled())
 495         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 496       reader.Update();
 497       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 498       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 499            i!=contours.end(); i++)
 500         AddContour(index,*i,selector.PropagationEnabled());
 501       QApplication::restoreOverrideCursor();
 502     }
 503   }
 504 }
 505 //------------------------------------------------------------------------------
 506
 507
 508 //------------------------------------------------------------------------------
 509 void vvMainWindow::ComputeDeformableRegistration()
 510 {
 511   if (mSlicerManagers.size() > 0) {
 512     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 513     vvDeformationDialog dialog(index,mSlicerManagers);
 514     if (dialog.exec()) {
 515       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 516       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 517       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 518     } else
 519       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 520   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::WarpImage()
 527 {
 528   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 529   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 530     bool ok;
 531     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 532                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 533     if (ok) {
 534       WarpImage(mSlicerManagers[index],ref);
 535     }
 536   } else
 537     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 538 }
 539 //------------------------------------------------------------------------------
 540
 541
 542 //------------------------------------------------------------------------------
 543 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 544 {
 545   if (!selected_slicer->GetVF().IsNull()) {
 546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 547     QFileInfo info(selected_slicer->GetFileName().c_str());
 548     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 549                      reference_phase,this);
 550     if (warp.ComputeWarpedImage()) {
 551       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 552       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 553       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 554       QApplication::restoreOverrideCursor();
 555     } else {
 556       QApplication::restoreOverrideCursor();
 557       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 558     }
 559   } else
 560     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 561 }
 562 //------------------------------------------------------------------------------
 563
 564
 565 //------------------------------------------------------------------------------
 566 vvMainWindow::~vvMainWindow()
 567 {
 568   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 569     if (mSlicerManagers[i] != NULL)
 570       delete mSlicerManagers[i];
 571   }
 572 }
 573 //------------------------------------------------------------------------------
 574
 575 //------------------------------------------------------------------------------
 576 QTabWidget * vvMainWindow::GetTab()
 577 {
 578   return tabWidget;
 579 }
 580 //------------------------------------------------------------------------------
 581
 582
 583 //------------------------------------------------------------------------------
 584 void vvMainWindow::MergeImages()
 585 {
 586   QString Extensions = EXTENSIONS;
 587   Extensions += ";;All Files (*)";
 588   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 589   if (files.isEmpty())
 590     return;
 591   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 592   std::vector<std::string> vector;
 593
 594   unsigned int currentDim = 0;
 595   std::vector<double> currentSpacing;
 596   std::vector<int> currentSize;
 597   std::vector<double> currentOrigin;
 598
 599   for (int i = 0; i < files.size(); i++) {
 600     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 601                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 602     reader->SetFileName(files[i].toStdString().c_str());
 603     reader->ReadImageInformation();
 604     if (reader)        {
 605       //NOViewWidget->hide();
 606       //NEViewWidget->hide();
 607       //SOViewWidget->hide();
 608       //SEViewWidget->hide();
 609       if (i == 0)
 610         currentDim = reader->GetNumberOfDimensions();
 611       bool IsOk = true;
 612       for (unsigned int j = 0; j < currentDim; j++) {
 613         if (i == 0) {
 614           if (j == 0) {
 615             currentSpacing.resize(currentDim);
 616             currentSize.resize(currentDim);
 617             currentOrigin.resize(currentDim);
 618           }
 619           currentOrigin[j] = reader->GetOrigin(j);
 620           currentSpacing[j] = reader->GetSpacing(j);
 621           currentSize[j] = reader->GetDimensions(j);
 622         } else if (currentDim != reader->GetNumberOfDimensions()
 623                    || currentSpacing[j] != reader->GetSpacing(j)
 624                    || currentSize[j] != (int)reader->GetDimensions(j)
 625                    || currentOrigin[j] != reader->GetOrigin(j)) {
 626           QString error = "Cannot read file (too different from others ";
 627           error += files[i].toStdString().c_str();
 628           QMessageBox::information(this,tr("Reading problem"),error);
 629           IsOk = false;
 630           break;
 631         }
 632       }
 633       if (IsOk)
 634         vector.push_back(files[i].toStdString());
 635     }
 636   }
 637   if (vector.size() > 0)
 638     LoadImages(vector, vvImageReader::MERGED);
 639 }
 640 //------------------------------------------------------------------------------
 641
 642 //------------------------------------------------------------------------------
 643 void vvMainWindow::SliceImages()
 644 {
 645   QString Extensions = EXTENSIONS;
 646   Extensions += ";;All Files (*)";
 647
 648   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 649   if (files.isEmpty())
 650     return;
 651   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 652   std::vector<std::string> vector;
 653   for (int i = 0; i < files.size(); i++)
 654     vector.push_back(files[i].toStdString());
 655   LoadImages(vector, vvImageReader::SLICED);
 656 }
 657 //------------------------------------------------------------------------------
 658
 659 //------------------------------------------------------------------------------
 660 void vvMainWindow::MergeImagesWithTime()
 661 {
 662   QString Extensions = EXTENSIONS;
 663   Extensions += ";;All Files (*)";
 664   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 665   if (files.isEmpty())
 666     return;
 667   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 668   std::vector<std::string> vector;
 669
 670   unsigned int currentDim = 0;
 671   std::vector<double> currentSpacing;
 672   std::vector<int> currentSize;
 673   std::vector<double> currentOrigin;
 674
 675   for (int i = 0; i < files.size(); i++) {
 676     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 677                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 678     if (reader) {
 679       reader->SetFileName(files[i].toStdString().c_str());
 680       reader->ReadImageInformation();
 681       if (i == 0)
 682         currentDim = reader->GetNumberOfDimensions();
 683       bool IsOk = true;
 684       for (unsigned int j = 0; j < currentDim; j++) {
 685         if (i == 0) {
 686           if (j == 0) {
 687             currentSpacing.resize(currentDim);
 688             currentSize.resize(currentDim);
 689             currentOrigin.resize(currentDim);
 690           }
 691           currentOrigin[j] = reader->GetOrigin(j);
 692           currentSpacing[j] = reader->GetSpacing(j);
 693           currentSize[j] = reader->GetDimensions(j);
 694         } else if (currentDim != reader->GetNumberOfDimensions()
 695                    || currentSpacing[j] != reader->GetSpacing(j)
 696                    || currentSize[j] != (int)reader->GetDimensions(j)
 697                    || currentOrigin[j] != reader->GetOrigin(j)) {
 698           QString error = "Cannot read file (too different from others ";
 699           error += files[i].toStdString().c_str();
 700           QMessageBox::information(this,tr("Reading problem"),error);
 701           IsOk = false;
 702           break;
 703         }
 704       }
 705       if (IsOk)
 706         vector.push_back(files[i].toStdString());
 707     } else {
 708       QString error = "Cannot read file info for ";
 709       error += files[i].toStdString().c_str();
 710       error += "\n";
 711       error += "Maybe you're trying to open an image in an unsupported format?\n";
 712       QMessageBox::information(this,tr("Reading problem"),error);
 713     }
 714   }
 715   sort(vector.begin(),vector.end());
 716   if (vector.size() > 1)
 717     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 718   else
 719     QMessageBox::warning(this,tr("Reading problem"),"You need to select at least two images to merge images with time.\nIf you only want to open one image, please use the \"Open Image\" function.");
 720 }
 721 //------------------------------------------------------------------------------
 722
 723
 724 //------------------------------------------------------------------------------
 725 void vvMainWindow::OpenDicom()
 726 {
 727   std::vector<std::string> files;
 728
 729   std::cout << "dicomSeriesSelector " << std::endl;
 730   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 731     files = *(dicomSeriesSelector->GetFilenames());
 732     LoadImages(files, vvImageReader::DICOM);
 733   }
 734 }
 735 //------------------------------------------------------------------------------
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenImages()
 739 {
 740   QString Extensions = EXTENSIONS;
 741   Extensions += ";;All Files (*)";
 742
 743   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 744   if (files.isEmpty())
 745     return;
 746   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 747   std::vector<std::string> vector;
 748   for (int i = 0; i < files.size(); i++)
 749     vector.push_back(files[i].toStdString());
 750   LoadImages(vector, vvImageReader::IMAGE);
 751 }
 752 //------------------------------------------------------------------------------
 753 void vvMainWindow::OpenRecentImage()
 754 {
 755   QAction * caller = qobject_cast<QAction*>(sender());
 756   std::vector<std::string> images;
 757   images.push_back(caller->text().toStdString());
 758   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 759   LoadImages(images, vvImageReader::IMAGE);
 760 }
 761 //------------------------------------------------------------------------------
 762
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::OpenImageWithTime()
 766 {
 767   QString Extensions = EXTENSIONS;
 768   Extensions += ";;All Files (*)";
 769
 770   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 771   if (files.isEmpty())
 772     return;
 773   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 774   std::vector<std::string> vector;
 775   for (int i = 0; i < files.size(); i++) {
 776     vector.push_back(files[i].toStdString());
 777   }
 778   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 779 }
 780 //------------------------------------------------------------------------------
 781
 782
 783 //------------------------------------------------------------------------------
 784 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 785 {
 786   //Separate the way to open images and dicoms
 787   int fileSize;
 788   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 789     fileSize = files.size();
 790   else
 791     fileSize = 1;
 792
 793   // For SLICED, we need the number of slices (ndim and #slices)
 794   std::vector<unsigned int> nSlices;
 795   nSlices.resize(files.size());
 796   std::fill(nSlices.begin(), nSlices.end(), 1);
 797   if (filetype == vvImageReader::SLICED) {
 798     for (int i = 0; i < fileSize; i++) {
 799       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 800       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 801       if (!header) {
 802         nSlices[i] = 0;
 803         QString error = "Cannot open file \n";
 804         error += files[i].c_str();
 805         QMessageBox::information(this,tr("Reading problem"),error);
 806         return;
 807       }
 808       if (header->GetNumberOfDimensions() < 3) {
 809         nSlices[i] = 0;
 810         QString error = "Dimension problem. Cannot slice \n";
 811         error += files[i].c_str();
 812         QMessageBox::information(this,tr("Reading problem"),error);
 813         return;
 814       }
 815       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 816     }
 817   }
 818
 819   //Only add to the list of recently opened files when a single file is opened,
 820   //to avoid polluting the list of recently opened files
 821   if (files.size() == 1) {
 822     QFileInfo finfo=tr(files[0].c_str());
 823     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 824     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 825   }
 826   //init the progress events
 827   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 828   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 829   qApp->processEvents();
 830
 831   int numberofsuccesulreads=0;
 832   //open images as 1 or multiples
 833   for (int i = 0; i < fileSize; i++) {
 834
 835     progress.SetText("Opening " + files[i]);
 836     progress.SetProgress(i,fileSize);
 837     qApp->processEvents();
 838
 839     for (unsigned int j = 0; j < nSlices[i]; j++) {
 840       //read the image and put it in mSlicerManagers
 841       vvSlicerManager* imageManager = new vvSlicerManager(4);
 842       qApp->processEvents();
 843
 844       bool SetImageSucceed=false;
 845
 846       // Change filename if an image with the same already exist
 847       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 848
 849       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 850         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 851       else {
 852         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 853       }
 854       if (!SetImageSucceed) {
 855         QApplication::restoreOverrideCursor();
 856         QString error = "Cannot open file \n";
 857         error += imageManager->GetLastError().c_str();
 858         QMessageBox::information(this,tr("Reading problem"),error);
 859         delete imageManager;
 860       } else {
 861         mSlicerManagers.push_back(imageManager);
 862
 863         //create an item in the tree with good settings
 864         QTreeWidgetItem *item = new QTreeWidgetItem();
 865         item->setData(0,Qt::UserRole,files[i].c_str());
 866         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 867         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 868         item->setData(1,Qt::UserRole,tr("image"));
 869         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 870         qApp->processEvents();
 871
 872         //Create the buttons for reload and close
 873         qApp->processEvents();
 874         QTreePushButton* cButton = new QTreePushButton;
 875         cButton->setItem(item);
 876         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 877         cButton->setToolTip(tr("close image"));
 878         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 879         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 880                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 881
 882         QTreePushButton* rButton = new QTreePushButton;
 883         rButton->setItem(item);
 884         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 885         rButton->setToolTip(tr("reload image"));
 886         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 887         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 888                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 889
 890         DataTree->addTopLevelItem(item);
 891         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 892         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 893
 894         //set the id of the image
 895         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 896         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 897         mSlicerManagers.back()->SetId(id.toStdString());
 898
 899         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 900
 901         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 902                 this,SLOT(CurrentImageChanged(std::string)));
 903         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 904                 this, SLOT(CurrentPickedImageChanged(std::string)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 906                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 907         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 908                 this, SLOT(VectorChanged(int,double,double,double, double)));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 910                 this, SLOT(OverlayChanged(int,double,double)));
 911         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 912                 this, SLOT(FusionChanged(int,double)));
 913         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 914                 this,SLOT(WindowsChanged(int, int, int)));
 915         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 916                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 918                 this,SLOT(UpdateSlice(int,int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 920                 this,SLOT(UpdateTSlice(int, int)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 922                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 923         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 924                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 925         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 926                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 927         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 928                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 929         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 930         InitSlicers();
 931         numberofsuccesulreads++;
 932       }
 933     }
 934   }
 935   if (numberofsuccesulreads) {
 936     NOViewWidget->show();
 937     NEViewWidget->show();
 938     SOViewWidget->show();
 939     SEViewWidget->show();
 940     UpdateTree();
 941     InitDisplay();
 942     ShowLastImage();
 943
 944     // Try to guess default WindowLevel
 945     double range[2];
 946     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 947     if ((range[0] == 0) && (range[1] == 1)) {
 948       presetComboBox->setCurrentIndex(5);// binary
 949     } else {
 950       // TODO
 951     }
 952   }
 953   QApplication::restoreOverrideCursor();
 954 }
 955 //------------------------------------------------------------------------------
 956
 957 //------------------------------------------------------------------------------
 958 void vvMainWindow::UpdateTree()
 959 {
 960   DataTree->resizeColumnToContents(COLUMN_TREE);
 961   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 962   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 963   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 964   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 965   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 966   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 967   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::CurrentImageChanged(std::string id)
 973 {
 974   if (id == mCurrentSelectedImageId) 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   mCurrentSelectedImageId = id;
 988   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 989 }
 990 //------------------------------------------------------------------------------
 991
 992 //------------------------------------------------------------------------------
 993 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 994 {
 995   if (id == mCurrentPickedImageId) return; // Do nothing
 996   int selected = 0;
 997   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 998     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 999       selected = i;
1000     } else {
1001       DataTree->topLevelItem(i)->setSelected(0);
1002     }
1003     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1004       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1005
1006   }
1007   DataTree->topLevelItem(selected)->setSelected(1);
1008   mCurrentPickedImageId = id;
1009   mCurrentPickedImageIndex = selected;
1010 }
1011 //------------------------------------------------------------------------------
1012
1013 //------------------------------------------------------------------------------
1014 void vvMainWindow::ImageInfoChanged()
1015 {
1016   contextActions[6]->setEnabled(1);
1017   contextActions[5]->setEnabled(1);
1018   actionSave_As->setEnabled(1);
1019   actionAdd_VF_to_current_Image->setEnabled(1);
1020   actionAdd_fusion_image->setEnabled(1);
1021   actionNorth_East_Window->setEnabled(1);
1022   actionNorth_West_Window->setEnabled(1);
1023   actionSouth_East_Window->setEnabled(1);
1024   actionSouth_West_Window->setEnabled(1);
1025   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1026   inverseButton->setEnabled(1);
1027
1028   goToCursorPushButton->setEnabled(1);
1029
1030   if (DataTree->selectedItems().size()) {
1031     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1032
1033     colorMapComboBox->setEnabled(1);
1034     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1035       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1036           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1037         colorMapComboBox->setEnabled(0);
1038         break;
1039       }
1040     }
1041
1042     std::vector<double> origin;
1043     std::vector<double> inputSpacing;
1044     std::vector<int> inputSize;
1045     std::vector<double> sizeMM;
1046     vtkSmartPointer<vtkMatrix4x4> transformation;
1047     int dimension=0;
1048     QString pixelType;
1049     QString inputSizeInBytes;
1050     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1051
1052     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1053       playButton->setEnabled(1);
1054       frameRateLabel->setEnabled(1);
1055       frameRateSpinBox->setEnabled(1);
1056     } else {
1057       playButton->setEnabled(0);
1058       frameRateLabel->setEnabled(0);
1059       frameRateSpinBox->setEnabled(0);
1060     }
1061
1062     //read image header
1063     int NPixel = 1;
1064
1065     vvImage::Pointer imageSelected;
1066     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1067       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1068     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1069       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1070     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1071       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1072     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1073       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1074     }
1075     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1076       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1077     }
1078     else {
1079       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1080     }
1081
1082     dimension = imageSelected->GetNumberOfDimensions();
1083     origin.resize(dimension);
1084     inputSpacing.resize(dimension);
1085     inputSize.resize(dimension);
1086     sizeMM.resize(dimension);
1087     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1088     for (int i = 0; i < dimension; i++) {
1089       origin[i] = imageSelected->GetOrigin()[i];
1090       inputSpacing[i] = imageSelected->GetSpacing()[i];
1091       inputSize[i] = imageSelected->GetSize()[i];
1092       sizeMM[i] = inputSize[i]*inputSpacing[i];
1093       NPixel *= inputSize[i];
1094     }
1095     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1096
1097     QString dim = QString::number(dimension) + " (";
1098     dim += pixelType + ")";
1099
1100     infoPanel->setFileName(image);
1101     infoPanel->setDimension(dim);
1102     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1103     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1104     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1105     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1106     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1107     transformation = imageSelected->GetTransform()->GetMatrix();
1108     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1109
1110     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1111                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1112     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1113     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1114
1115     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1116     for (int i = 0; i < 4; i++) {
1117       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1118         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1119         break;
1120       }
1121     }
1122     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1123     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1124     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1125     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1126
1127     infoPanel->setFileName(image);
1128     infoPanel->setDimension(dim);
1129     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1130     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1131     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1132     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1133     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1134
1135     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1136                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1137     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1138     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1139
1140     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1141     for (int i = 0; i < 4; i++) {
1142       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1143         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1144         break;
1145       }
1146     }
1147     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1148     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1149     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1150     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1151
1152     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1153       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1154       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1155                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1156                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1157     } else {
1158       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1159       overlayPanel->getVFProperty(-1,-1,-1);
1160     }
1161     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1162       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1163       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1164     } else {
1165       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1166       overlayPanel->getOverlayProperty(-1);
1167     }
1168     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1169       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1170       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1171                                       mSlicerManagers[index]->GetFusionColorMap(),
1172                                       mSlicerManagers[index]->GetFusionWindow(),
1173                                       mSlicerManagers[index]->GetFusionLevel());
1174     } else {
1175       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1176       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1177     }
1178   }
1179 }
1180 //------------------------------------------------------------------------------
1181
1182 //------------------------------------------------------------------------------
1183 void vvMainWindow::ShowDocumentation()
1184 {
1185   documentation->show();
1186 }
1187 //------------------------------------------------------------------------------
1188
1189 //------------------------------------------------------------------------------
1190 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1191 {
1192   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1193   if(!checkCanPush) {
1194     registerForm->show();
1195   } else {
1196     if(registerForm->canPush()) {
1197       registerForm->show();
1198       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1199     }
1200   }
1201 }
1202 //------------------------------------------------------------------------------
1203
1204 //------------------------------------------------------------------------------
1205 void vvMainWindow::ShowHelpDialog()
1206 {
1207   help_dialog->show();
1208 }
1209 //------------------------------------------------------------------------------
1210
1211 //------------------------------------------------------------------------------
1212 void vvMainWindow::ChangeViewMode()
1213 {
1214   QList<int> size;
1215   if (viewMode == 1) {
1216     viewMode = 0;
1217     size.push_back(1);
1218     size.push_back(0);
1219     splitter_3->setSizes(size);
1220     OSplitter->setSizes(size);
1221     DataTree->setColumnHidden(2,1);
1222     DataTree->setColumnHidden(3,1);
1223     DataTree->setColumnHidden(4,1);
1224   } else {
1225     viewMode = 1;
1226     size.push_back(1);
1227     size.push_back(1);
1228     splitter_3->setSizes(size);
1229     OSplitter->setSizes(size);
1230     DataTree->setColumnHidden(2,0);
1231     DataTree->setColumnHidden(3,0);
1232     DataTree->setColumnHidden(4,0);
1233   }
1234   UpdateRenderWindows();
1235   /*
1236   ** I don't know why but for both resized QVTKWidget we also need to render
1237   ** the associated Slicer to redraw crosses.
1238   */
1239   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1240     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1241       mSlicerManagers[i]->GetSlicer(0)->Render();
1242     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1243       mSlicerManagers[i]->GetSlicer(2)->Render();
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 *clickedItem, int column)
1345 {
1346   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1347     return;
1348
1349   // Get parent information (might be the same item)
1350   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1351   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1352   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1353
1354   // Go over the complete item tree (only 2 levels, parents and children)
1355   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1356     // Trick to avoid redoing twice the job for a key (sr)
1357     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1358
1359     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1360     if(currentParentItem != clickedParentItem) {
1361       // Not the branch of the clicked item, uncheck all
1362
1363       // Parent
1364       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1365       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1366
1367       // Children
1368       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1369         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1370       }
1371     }
1372     else {
1373       // Branch of the clicked one: get check status from actor visibility in slicer
1374       // and toggle the clicked one
1375
1376       // Parent
1377       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1378       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1379
1380       // Update slicer (after getting visibility)
1381       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1382       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1383       DisplaySliders(slicerManagerIndex, column-1);
1384       if(clickedParentItem == clickedItem) {
1385         // Toggle or force visibility if it was not on this branch so far
1386         vis = !draw || !vis;
1387       }
1388       clickedSlicer->SetActorVisibility("image", 0, vis);
1389       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1390
1391       // Children
1392       std::map<std::string, int> actorTypeCounts;
1393       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1394         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1395         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1396         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1397         if(currentChildItem == clickedItem) {
1398           // Toggle or force visibility if it was not on this branch so far
1399           vis = !draw || !vis;
1400           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1401         }
1402         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1403         actorTypeCounts[actorType]++;
1404       }
1405     }
1406   }
1407
1408   clickedSlicer->Render();
1409 }
1410 //------------------------------------------------------------------------------
1411
1412 void vvMainWindow::InitSlicers()
1413 {
1414   if (mSlicerManagers.size()) {
1415     mSlicerManagers.back()->GenerateDefaultLookupTable();
1416
1417     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1418     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1419     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1420     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1421   }
1422 }
1423
1424 //------------------------------------------------------------------------------
1425 void vvMainWindow::InitDisplay()
1426 {
1427   if (mSlicerManagers.size()) {
1428     //BE CAREFUL : this is absolutely necessary to set the interactor style
1429     //in order to have the same style instanciation for all SlicerManagers in
1430     // a same window
1431     for (int j = 0; j < 4; j++) {
1432       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1433       style->SetAutoAdjustCameraClippingRange(1);
1434       bool AlreadySelected = false;
1435       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1436         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1437
1438         //select the image only if previous are not selected
1439         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1440           mSlicerManagers[i]->UpdateSlicer(j,1);
1441           AlreadySelected = true;
1442         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1443           if (DataTree->selectedItems().size() == 0)
1444             DataTree->topLevelItem(i)->setSelected(1);
1445           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1446           mSlicerManagers[i]->UpdateSlicer(j,1);
1447           DisplaySliders(i,j);
1448         } else {
1449           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1450           mSlicerManagers[i]->UpdateSlicer(j,0);
1451         }
1452       }
1453       style->Delete();
1454     }
1455   }
1456 }
1457 //------------------------------------------------------------------------------
1458
1459 //------------------------------------------------------------------------------
1460 void vvMainWindow::DisplaySliders(int slicer, int window)
1461 {
1462   int range[2];
1463   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1464   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1465
1466   int tRange[2];
1467   tRange[0] = 0;
1468   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1469   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1470   bool showHorizontal = false;
1471   bool showVertical = false;
1472   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1473       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1474           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1475           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1476     showVertical = true;
1477   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1478       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1479       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1480     showHorizontal = true;
1481
1482   if (showVertical)
1483     verticalSliders[window]->show();
1484   else
1485     verticalSliders[window]->hide();
1486   verticalSliders[window]->setRange(range[0],range[1]);
1487   verticalSliders[window]->setValue(position);
1488
1489   if (showHorizontal)
1490     horizontalSliders[window]->show();
1491   else
1492     horizontalSliders[window]->hide();
1493   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1494   horizontalSliders[window]->setValue(tPosition);
1495 }
1496 //------------------------------------------------------------------------------
1497
1498 //------------------------------------------------------------------------------
1499 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1500 {
1501   int index = GetSlicerIndexFromItem(item);
1502
1503   if (DataTree->topLevelItem(index) != item) {
1504     QString warning = "Do you really want to close the overlay : ";
1505     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1506     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1507                        warning, 0, this);
1508     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1509     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1510     if (msgBox.exec() == QMessageBox::AcceptRole) {
1511       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1512       int overlay_index=0;
1513       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1514         if (DataTree->topLevelItem(index)->\
1515             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1516           overlay_index++;
1517         if (DataTree->topLevelItem(index)->child(child) == item) break;
1518       }
1519       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1520       mSlicerManagers[index]->SetColorMap(0);
1521       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1522       mSlicerManagers[index]->Render();
1523     }
1524   } else if (DataTree->topLevelItemCount() <= 1) {
1525     QString warning = "Do you really want to close the image : ";
1526     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1527     warning += "\nThis is the last image, you're about to close vv !!!";
1528     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1529                        warning, 0, this);
1530     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1531     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1532     if (msgBox.exec() == QMessageBox::AcceptRole) {
1533       this->close();
1534     }
1535   } else {
1536     QString warning = "Do you really want to close the image : ";
1537     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1538     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1539                        warning, 0, this);
1540     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1541     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1542     if (msgBox.exec() == QMessageBox::AcceptRole) {
1543
1544       // Tell tools that we close an image
1545       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1546
1547       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1548       DataTree->takeTopLevelItem(index);
1549       for (int i = 0; i < index; i++) {
1550         Manageriter++;
1551       }
1552       linkPanel->removeImage(index);
1553       mSlicerManagers[index]->RemoveActors();
1554       delete mSlicerManagers[index];
1555       mSlicerManagers.erase(Manageriter);
1556
1557       //
1558       InitDisplay();
1559     }
1560   }
1561   ImageInfoChanged();
1562 }
1563 //------------------------------------------------------------------------------
1564
1565 //------------------------------------------------------------------------------
1566 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1567 {
1568   // int index = GetSlicerIndexFromItem(item);
1569   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1570   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1571   //     mSlicerManagers[index]->ReloadVF();
1572   //   else
1573   //     mSlicerManagers[index]->Reload();
1574
1575   //   QApplication::restoreOverrideCursor();
1576   int index = GetSlicerIndexFromItem(item);
1577   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1578   QString role=item->data(1,Qt::UserRole).toString();
1579   if ( role == "vector"){
1580     mSlicerManagers[index]->ReloadVF();
1581   }
1582   else if (role == "overlay"){
1583     mSlicerManagers[index]->ReloadOverlay();
1584   }
1585   else if (role == "fusion"){
1586     mSlicerManagers[index]->ReloadFusion();
1587   }
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, vvSlicer* refSlicer)
1718 {
1719   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1720     if (id == mSlicerManagers[i]->GetId()) {
1721       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
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, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
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, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
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, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
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::Pointer writer = vvImageWriter::New();
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], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2255     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2256   } else {
2257     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2258   }
2259 }
2260
2261 //------------------------------------------------------------------------------
2262
2263
2264 //------------------------------------------------------------------------------
2265 void vvMainWindow::RemoveLink(QString image1,QString image2)
2266 {
2267   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2268     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2269       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2270     }
2271     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2272       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2273     }
2274   }
2275 }
2276 //------------------------------------------------------------------------------
2277
2278 //------------------------------------------------------------------------------
2279 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2280 {
2281   int index = 0;
2282   while(sm != mSlicerManagers[index])
2283     index++;
2284   index = (index+offset) % mSlicerManagers.size();
2285
2286   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2287   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2288   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2289   DisplayChanged(item,slicer+1);
2290 }
2291 //------------------------------------------------------------------------------
2292
2293 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2294 {
2295   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2296     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2297       for (int j = 0; j < 4; j++) {
2298         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2299         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2300         //UpdateTSlice(j,value);
2301       }
2302       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2303       break;
2304     }
2305   }
2306 }
2307 //------------------------------------------------------------------------------
2308
2309
2310 //------------------------------------------------------------------------------
2311 void vvMainWindow::NOHorizontalSliderMoved()
2312 {
2313   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2314   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2315 //  mCurrentTime = NOHorizontalSlider->value();
2316 }
2317 //------------------------------------------------------------------------------
2318
2319
2320 //------------------------------------------------------------------------------
2321 void vvMainWindow::NEHorizontalSliderMoved()
2322 {
2323   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2324   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2325 //  mCurrentTime = NEHorizontalSlider->value();
2326 }
2327 //------------------------------------------------------------------------------
2328
2329
2330 //------------------------------------------------------------------------------
2331 void vvMainWindow::SOHorizontalSliderMoved()
2332 {
2333   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2334   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2335   // mCurrentTime = SOHorizontalSlider->value();
2336 }
2337 //------------------------------------------------------------------------------
2338
2339
2340 //------------------------------------------------------------------------------
2341 void vvMainWindow::SEHorizontalSliderMoved()
2342 {
2343   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2344   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2345   // mCurrentTime = SEHorizontalSlider->value();
2346 }
2347 //------------------------------------------------------------------------------
2348
2349 //------------------------------------------------------------------------------
2350 void vvMainWindow::NOVerticalSliderChanged()
2351 {
2352   static int value=-1;
2353   if (value == NOVerticalSlider->value()) return;
2354   else value = NOVerticalSlider->value();
2355   //  int value = NOVerticalSlider->value();
2356   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2357     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2358       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2359         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2360         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2361
2362         // If nor Update/Render -> slider not work
2363         // only render = ok navigation, but for contour Update needed but slower ?
2364
2365         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2366         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2367       }
2368       break;
2369     }
2370   }
2371 }
2372 //------------------------------------------------------------------------------
2373
2374
2375 //------------------------------------------------------------------------------
2376 void vvMainWindow::NEVerticalSliderChanged()
2377 {
2378   static int value=-1;
2379   if (value == NEVerticalSlider->value()) return;
2380   else value = NEVerticalSlider->value();
2381   //  int value = NEVerticalSlider->value();
2382   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2383     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2384       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2385         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2386         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2387         mSlicerManagers[i]->UpdateSlice(1);
2388         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2389       }
2390       break;
2391     }
2392   }
2393 }
2394 //------------------------------------------------------------------------------
2395
2396
2397 //------------------------------------------------------------------------------
2398 void vvMainWindow::SOVerticalSliderChanged()
2399 {
2400   static int value=-1;
2401   if (value == SOVerticalSlider->value()) return;
2402   else value = SOVerticalSlider->value();
2403   //int value = SOVerticalSlider->value();
2404   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2405     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2406       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2407         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2408         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2409         mSlicerManagers[i]->UpdateSlice(2);
2410         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2411       }
2412       // else { DD("avoid SOVerticalSlider slicer update"); }
2413       break;
2414     }
2415   }
2416 }
2417 //------------------------------------------------------------------------------
2418
2419
2420 //------------------------------------------------------------------------------
2421 void vvMainWindow::SEVerticalSliderChanged()
2422 {
2423   static int value=-1;
2424   if (value == SEVerticalSlider->value()) return;
2425   else value = SEVerticalSlider->value();
2426   // int value = SEVerticalSlider->value();
2427   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2428     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2429       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2430         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2431         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2432         mSlicerManagers[i]->UpdateSlice(3);
2433         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2434       }
2435       break;
2436     }
2437   }
2438 }
2439 //------------------------------------------------------------------------------
2440
2441
2442 //------------------------------------------------------------------------------
2443 void vvMainWindow::UpdateSlice(int slicer, int slice)
2444 {
2445   // DD("vvMainWindow::UpdateSlice");
2446 //   DD(slicer);
2447 //   DD(slice);
2448   if (slicer == 0) {
2449     //    if (slice != NOVerticalSlider->value())
2450     NOVerticalSlider->setValue(slice);
2451   } else {
2452     if (slicer == 1)
2453       NEVerticalSlider->setValue(slice);
2454     else {
2455       if (slicer == 2)
2456         SOVerticalSlider->setValue(slice);
2457       else {
2458         if (slicer == 3)
2459           SEVerticalSlider->setValue(slice);
2460       }
2461     }
2462   }
2463   // DD("vvMainWindow:UpdateSlice END");
2464 }
2465 //------------------------------------------------------------------------------
2466
2467
2468 //------------------------------------------------------------------------------
2469 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2470 {
2471   switch (slicer) {
2472   case 0:
2473     NOHorizontalSlider->setValue(slice);
2474     break;
2475   case 1:
2476     NEHorizontalSlider->setValue(slice);
2477     break;
2478   case 2:
2479     SOHorizontalSlider->setValue(slice);
2480     break;
2481   case 3:
2482     SEHorizontalSlider->setValue(slice);
2483     break;
2484   }
2485 }
2486 //------------------------------------------------------------------------------
2487
2488
2489 //------------------------------------------------------------------------------
2490 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2491 {
2492   int position = int((min+max)/2);
2493   int tPosition = int((tmin+tmax)/2);
2494   if (slicer == 0) {
2495     NOVerticalSlider->setValue(position);
2496     NOVerticalSlider->setRange(min,max);
2497     NOHorizontalSlider->setRange(tmin,tmax);
2498     NOHorizontalSlider->setValue(tPosition);
2499   } else if (slicer == 1) {
2500     NEVerticalSlider->setValue(position);
2501     NEVerticalSlider->setRange(min,max);
2502     NEHorizontalSlider->setRange(tmin,tmax);
2503     NEHorizontalSlider->setValue(tPosition);
2504   } else if (slicer == 2) {
2505     SOVerticalSlider->setValue(position);
2506     SOVerticalSlider->setRange(min,max);
2507     SOHorizontalSlider->setRange(tmin,tmax);
2508     SOHorizontalSlider->setValue(tPosition);
2509   } else if (slicer == 3) {
2510     SEVerticalSlider->setValue(position);
2511     SEVerticalSlider->setRange(min,max);
2512     SEHorizontalSlider->setRange(tmin,tmax);
2513     SEHorizontalSlider->setValue(tPosition);
2514   }
2515 }
2516 //------------------------------------------------------------------------------
2517
2518
2519 //------------------------------------------------------------------------------
2520 void vvMainWindow::SaveNOScreenshot()
2521 {
2522   SaveScreenshot(NOViewWidget);
2523 }
2524 //------------------------------------------------------------------------------
2525
2526
2527 //------------------------------------------------------------------------------
2528 void vvMainWindow::SaveNEScreenshot()
2529 {
2530   SaveScreenshot(NEViewWidget);
2531 }
2532 //------------------------------------------------------------------------------
2533
2534
2535 //------------------------------------------------------------------------------
2536 void vvMainWindow::SaveSOScreenshot()
2537 {
2538   SaveScreenshot(SOViewWidget);
2539 }
2540 //------------------------------------------------------------------------------
2541
2542
2543 //------------------------------------------------------------------------------
2544 void vvMainWindow::SaveSEScreenshot()
2545 {
2546   SaveScreenshot(SEViewWidget);
2547 }
2548 //------------------------------------------------------------------------------
2549
2550
2551 //------------------------------------------------------------------------------
2552 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2553 {
2554   QString Extensions = "Images( *.png);;";
2555   Extensions += "Images( *.jpg);;";
2556   Extensions += "Images( *.bmp);;";
2557   Extensions += "Images( *.tif);;";
2558   Extensions += "Images( *.ppm)";
2559 #ifdef VTK_USE_FFMPEG_ENCODER
2560   Extensions += "Images( *.avi)";
2561 #endif
2562 #ifdef VTK_USE_MPEG2_ENCODER
2563   Extensions += "Images( *.mpg)";
2564 #endif
2565
2566   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2567   QString fileName = QFileDialog::getSaveFileName(this,
2568                      tr("Save As"),
2569                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2570                      Extensions);
2571
2572   if (!fileName.isEmpty()) {
2573     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2574     w2i->SetInput(widget->GetRenderWindow());
2575     w2i->Update();
2576     vtkImageData *image = w2i->GetOutput();
2577
2578     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2579     if (!strcmp(ext, ".bmp")) {
2580       vtkBMPWriter *bmp = vtkBMPWriter::New();
2581       bmp->SetInput(image);
2582       bmp->SetFileName(fileName.toStdString().c_str());
2583       bmp->Write();
2584       bmp->Delete();
2585     } else if (!strcmp(ext, ".tif")) {
2586       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2587       tif->SetInput(image);
2588       tif->SetFileName(fileName.toStdString().c_str());
2589       tif->Write();
2590       tif->Delete();
2591     } else if (!strcmp(ext, ".ppm")) {
2592       vtkPNMWriter *pnm = vtkPNMWriter::New();
2593       pnm->SetInput(image);
2594       pnm->SetFileName(fileName.toStdString().c_str());
2595       pnm->Write();
2596       pnm->Delete();
2597     } else if (!strcmp(ext, ".png")) {
2598       vtkPNGWriter *png = vtkPNGWriter::New();
2599       png->SetInput(image);
2600       png->SetFileName(fileName.toStdString().c_str());
2601       png->Write();
2602       png->Delete();
2603     } else if (!strcmp(ext, ".jpg")) {
2604       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2605       jpg->SetInput(image);
2606       jpg->SetFileName(fileName.toStdString().c_str());
2607       jpg->Write();
2608       jpg->Delete();
2609 #ifdef VTK_USE_FFMPEG_ENCODER
2610     } else if (!strcmp(ext, ".avi")) {
2611       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2612       mpg->SetInput(image);
2613       mpg->SetFileName(fileName.toStdString().c_str());
2614       mpg->SetQuality(2);
2615       mpg->SetRate(5);
2616       mpg->Start();
2617
2618       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2619       int nSlice = vvImg->GetVTKImages().size();
2620       for(int i=0; i<nSlice; i++) {
2621         mSlicerManagers[smIndex]->SetNextTSlice(0);
2622         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2623         w2i->SetInput(widget->GetRenderWindow());
2624         w2i->Update();
2625         mpg->SetInput(w2i->GetOutput());
2626         mpg->Write();
2627       }
2628       mpg->End();
2629       mpg->Delete();
2630 #endif
2631 #ifdef VTK_USE_MPEG2_ENCODER
2632     } else if (!strcmp(ext, ".mpg")) {
2633       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2634       mpg->SetInput(image);
2635       mpg->SetFileName(fileName.toStdString().c_str());
2636       mpg->Start();
2637
2638       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2639       int nSlice = vvImg->GetVTKImages().size();
2640       for(int i=0; i<nSlice; i++) {
2641         mSlicerManagers[smIndex]->SetNextTSlice(0);
2642         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2643         w2i->SetInput(widget->GetRenderWindow());
2644         w2i->Update();
2645         mpg->SetInput(w2i->GetOutput());
2646         mpg->Write();
2647       }
2648       mpg->End();
2649       mpg->Delete();
2650 #endif
2651     } else {
2652       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2653     }
2654   }
2655 }
2656 //------------------------------------------------------------------------------
2657
2658
2659 //------------------------------------------------------------------------------
2660 void vvMainWindow::GoToCursor()
2661 {
2662   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2663   for (int column = 1; column < 5; column++) {
2664     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2665       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2666       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2667         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2668       mSlicerManagers[index]->UpdateViews(1,column-1);
2669       mSlicerManagers[index]->UpdateLinked(column-1);
2670       break;
2671     }
2672   }
2673 }
2674 //------------------------------------------------------------------------------
2675
2676 //------------------------------------------------------------------------------
2677 void vvMainWindow::PlayPause()
2678 {
2679   if (playMode) {
2680     playMode = 0;
2681     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2682     ImageInfoChanged();
2683     return;
2684   } else {
2685     int image_number=DataTree->topLevelItemCount();
2686     bool has_temporal;
2687     for (int i=0; i<image_number; i++)
2688       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2689         has_temporal=true;
2690         break;
2691       }
2692     if (has_temporal) {
2693       playMode = 1;
2694       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2695       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2696     }
2697   }
2698 }
2699 //------------------------------------------------------------------------------
2700
2701 //------------------------------------------------------------------------------
2702 void vvMainWindow::PlayNext()
2703 {
2704   if (playMode && !this->isHidden()) {
2705     int image_number=DataTree->topLevelItemCount();
2706     ///Only play one slicer per SM, and only if the SM is being displayed
2707     for (int i=0; i<image_number; i++)
2708       for (int j=0; j<4; j++)
2709         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2710             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2711           mSlicerManagers[i]->SetNextTSlice(j);
2712           break;
2713         }
2714     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2715   }
2716 }
2717 //------------------------------------------------------------------------------
2718
2719 void vvMainWindow::ShowLastImage()
2720 {
2721   if (mSlicerManagers.size() > 1) {
2722     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2723     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2724     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2725     DisplayChanged(item,1);
2726   }
2727 }
2728
2729 //------------------------------------------------------------------------------
2730 void vvMainWindow::UpdateRenderWindows()
2731 {
2732   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2733   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2734   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2735   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2736 }
2737 //------------------------------------------------------------------------------
2738
2739 //------------------------------------------------------------------------------
2740 void vvMainWindow::SegmentationOnCurrentImage()
2741 {
2742   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2743
2744   vvSegmentationDialog segmentation;
2745   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2746   segmentation.exec();
2747 }
2748 //------------------------------------------------------------------------------
2749
2750 void vvMainWindow::SurfaceViewerLaunch()
2751 {
2752   vvSurfaceViewerDialog surfaceViewer;
2753   surfaceViewer.exec();
2754 }
2755 //------------------------------------------------------------------------------
2756
2757
2758 //------------------------------------------------------------------------------
2759 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2760 {
2761   int number=0;
2762   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2763     vvSlicerManager * v = mSlicerManagers[l];
2764     if (v->GetBaseFileName() ==
2765         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2766       number = std::max(number, v->GetBaseFileNameNumber()+1);
2767     }
2768   }
2769   return number;
2770 }
2771 //------------------------------------------------------------------------------
2772
2773
2774 //------------------------------------------------------------------------------
2775 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2776 {
2777   // Change filename if another image exist with the same name
2778   int number = GetImageDuplicateFilenameNumber(filename);
2779
2780   // Create new SliceManager
2781   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2782   slicer_manager->SetImage(image);//, IMAGE, number);
2783   //  filename = filename+"_"+clitk::toString(number);
2784   slicer_manager->SetFilename(filename, number);
2785   mSlicerManagers.push_back(slicer_manager);
2786
2787   //create an item in the tree with good settings
2788   QTreeWidgetItem *item = new QTreeWidgetItem();
2789   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2790   item->setData(1,Qt::UserRole,tr("image"));
2791   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2792   qApp->processEvents();
2793
2794   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2795
2796   //Create the buttons for reload and close
2797   qApp->processEvents();
2798   QTreePushButton* cButton = new QTreePushButton;
2799   cButton->setItem(item);
2800   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2801   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2802   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2803           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2804
2805   QTreePushButton* rButton = new QTreePushButton;
2806   rButton->setItem(item);
2807   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2808   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2809   rButton->setEnabled(0);
2810   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2811           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2812
2813   DataTree->addTopLevelItem(item);
2814   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2815   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2816
2817   //set the id of the image
2818   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2819   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2820   mSlicerManagers.back()->SetId(id.toStdString());
2821
2822   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2823                       , id.toStdString());
2824
2825   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2826           this, SLOT(CurrentImageChanged(std::string)));
2827   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2828           this, SLOT(CurrentPickedImageChanged(std::string)));
2829   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2830           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2831   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2832           this, SLOT(VectorChanged(int,double,double,double, double)));
2833   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2834           this, SLOT(OverlayChanged(int,double,double)));
2835   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2836           this, SLOT(FusionChanged(int,double)));
2837   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2838           this,SLOT(WindowsChanged(int, int, int)));
2839   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2840           this,SLOT(WindowLevelChanged(double, double, int, int)));
2841   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2842           this,SLOT(UpdateSlice(int,int)));
2843   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2844           this,SLOT(UpdateTSlice(int, int)));
2845   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2846           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2847   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2848           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2849   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2850           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2851   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2852           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2853   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2854   UpdateTree();
2855   qApp->processEvents();
2856   InitSlicers();
2857   ShowLastImage();
2858   InitDisplay();
2859   qApp->processEvents();
2860
2861   // End
2862   ImageInfoChanged();
2863   return slicer_manager;
2864 }
2865 //------------------------------------------------------------------------------
2866
2867
2868 //------------------------------------------------------------------------------
2869 void vvMainWindow::UpdateCurrentSlicer()
2870 {
2871   int index = -1;
2872   if (DataTree->selectedItems().size() > 0) {
2873     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2874   }
2875   mSlicerManagerCurrentIndex = index;
2876 }
2877 //------------------------------------------------------------------------------
2878