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