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