vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ======================================================================-====*/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24
  25 // VV include
  26 #include "vvMainWindow.h"
  27 #include "vvHelpDialog.h"
  28 #include "vvDocumentation.h"
  29 #include "vvProgressDialog.h"
  30 #include "vvQDicomSeriesSelector.h"
  31 #include "vvSlicerManager.h"
  32 #include "clitkImageCommon.h"
  33 #include "vvSlicer.h"
  34 #include "vvInteractorStyleNavigator.h"
  35 #include "vvImageWriter.h"
  36 #include "vvSegmentationDialog.h"
  37 #include "vvSurfaceViewerDialog.h"
  38 #include "vvDeformationDialog.h"
  39 #include "vvImageWarp.h"
  40 #include "vvUtils.h"
  41 #include "vvMidPosition.h"
  42 #include "vvMesh.h"
  43 #include "vvStructSelector.h"
  44 #include "vvMeshReader.h"
  45 #include "vvConstants.h"
  46 #include "clitkConfiguration.h"
  47
  48 // ITK include
  49 #include <itkImage.h>
  50 #include <itkImageFileReader.h>
  51 #include <itkByteSwapper.h>
  52 #include <itkCommand.h>
  53 #include <itkNumericSeriesFileNames.h>
  54
  55 // VTK include
  56 #include <vtkImageData.h>
  57 #include <vtkImageActor.h>
  58 #include <vtkCornerAnnotation.h>
  59 #include <vtkRenderWindow.h>
  60 #include <vtkRenderWindowInteractor.h>
  61 #include <vtkRenderer.h>
  62 #include <vtkRendererCollection.h>
  63 #include <vtkWindowToImageFilter.h>
  64 #include <vtkBMPWriter.h>
  65 #include <vtkTIFFWriter.h>
  66 #include <vtkPNMWriter.h>
  67 #include <vtkPNGWriter.h>
  68 #include <vtkJPEGWriter.h>
  69 #include <vtkMPEG2Writer.h>
  70 #include <vtkMatrix4x4.h>
  71 #include <vtkTransform.h>
  72
  73 // Standard includes
  74 #include <iostream>
  75 #include <sstream>
  76 #include <iomanip>
  77
  78 #define COLUMN_TREE 0
  79 #define COLUMN_UL_VIEW 1
  80 #define COLUMN_UR_VIEW 2
  81 #define COLUMN_DL_VIEW 3
  82 #define COLUMN_DR_VIEW 4
  83 #define COLUMN_CLOSE_IMAGE 5
  84 #define COLUMN_RELOAD_IMAGE 6
  85 #define COLUMN_IMAGE_NAME 7
  86
  87 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr *.SCAN )"
  88
  89 /*Data Tree values
  90   0,Qt::UserRole full filename
  91   1,Qt::CheckStateRole checkbutton UL View
  92   1,Qt::UserRole overlay, fusion or vector
  93   2,Qt::CheckStateRole checkbutton UR View
  94   3,Qt::CheckStateRole checkbutton DL View
  95   4,Qt::CheckStateRole checkbutton DR View
  96   5,0  short filename
  97   5,Qt::UserRole mSlicerManager id*/
  98
  99 //------------------------------------------------------------------------------
 100 vvMainWindow::vvMainWindow():vvMainWindowBase()
 101 {
 102   setupUi(this); // this sets up the GUI
 103
 104   mInputPathName = "";
 105   mMenuTools = menuTools;
 106   //  mMenuSegmentation = menuSegmentation;
 107   mContextMenu = &contextMenu;
 108   mMenuExperimentalTools = menuExperimental;
 109   mMainWidget = this;
 110   mCurrentTime = -1;
 111   mCurrentSelectedImageId = "";
 112   mCurrentPickedImageId = "";
 113   mCurrentPickedImageIndex = 0;
 114
 115   //Init the contextMenu
 116   this->setContextMenuPolicy(Qt::CustomContextMenu);
 117   contextActions.resize(0);
 118   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 119                                   tr("O&pen new Image"));
 120   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 121   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 122   contextActions.push_back(actionOpen_new_image);
 123   contextMenu.addSeparator();
 124
 125   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 126                                tr("Close Current Image"));
 127   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 128   contextActions.push_back(actionClose_Image);
 129
 130   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 131                                 tr("Reload Current Image"));
 132   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 133   contextActions.push_back(actionReload_image);
 134
 135   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 136                               tr("Save Current Image"));
 137   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 138   contextActions.push_back(actionSave_image);
 139
 140   contextMenu.addSeparator();
 141
 142   contextMenu.addAction(actionAdd_VF_to_current_Image);
 143   contextActions.push_back(actionAdd_VF_to_current_Image);
 144
 145   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 146       tr("Add overlay image to current image"));
 147   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 148   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 149
 150   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 151
 152   contextMenu.addAction(actionAdd_fusion_image);
 153   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 154   contextActions.push_back(actionAdd_fusion_image);
 155
 156   // TRIAL DS
 157   /*
 158   QMenu * m = new QMenu(menubar);
 159   m->setTitle("TOTO");
 160   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 161   contextMenu.addMenu(m);
 162   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 163                      tr("BIDON"));
 164   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 165                      tr("BIDON2"));
 166   m->addAction(a);
 167   m->addAction(b);
 168   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 169   */
 170
 171   //init the DataTree
 172   mSlicerManagers.resize(0);
 173
 174   QStringList header;
 175   header.append("");
 176   header.append("TL");
 177   header.append("TR");
 178   header.append("BL");
 179   header.append("BR");
 180   header.append("");
 181   header.append("");
 182   header.append("Name");
 183
 184   DataTree->setHeaderLabels(header);
 185   DataTree->resizeColumnToContents(COLUMN_TREE);
 186   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 187   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 188   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 189   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 190   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 191   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 192   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 193
 194   viewMode = 1;
 195   documentation = new vvDocumentation();
 196   help_dialog = new vvHelpDialog();
 197   dicomSeriesSelector = new vvDicomSeriesSelector();
 198
 199   inverseButton->setEnabled(0);
 200   actionAdd_Overlay_to_current_Image->setEnabled(0);
 201   actionSave_As->setEnabled(0);
 202   actionAdd_VF_to_current_Image->setEnabled(0);
 203   actionAdd_fusion_image->setEnabled(0);
 204
 205   //init the sliders
 206   verticalSliders.push_back(NOVerticalSlider);
 207   verticalSliders.push_back(NEVerticalSlider);
 208   verticalSliders.push_back(SOVerticalSlider);
 209   verticalSliders.push_back(SEVerticalSlider);
 210
 211   for (int i =0; i < 4; i++)
 212     verticalSliders[i]->hide();
 213
 214   horizontalSliders.push_back(NOHorizontalSlider);
 215   horizontalSliders.push_back(NEHorizontalSlider);
 216   horizontalSliders.push_back(SOHorizontalSlider);
 217   horizontalSliders.push_back(SEHorizontalSlider);
 218
 219   for (int i =0; i < 4; i++)
 220     horizontalSliders[i]->hide();
 221
 222
 223   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 224   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 225   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 226   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 227
 228   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 229   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 230   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 231   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 232
 233   //connect everything
 234   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 235   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 236   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 237   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 238   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 239   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 240   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 241   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 242   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 243   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 244   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 245   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 246   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 247   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 248   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 249   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 250
 251   ///////////////////////////////////////////////
 252   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 253   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 254   ///////////////////////////////////////////////
 255
 256   actionNorth_East_Window->setEnabled(0);
 257   actionNorth_West_Window->setEnabled(0);
 258   actionSouth_East_Window->setEnabled(0);
 259   actionSouth_West_Window->setEnabled(0);
 260
 261   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 262   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 263   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 264   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 265
 266   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 267   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 268           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 269
 270   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 271   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 272   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 273   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 274   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 275   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 276   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 277
 278
 279   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 280
 281   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 282   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 283   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 284   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 285   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 286           this,SLOT(SetFusionProperty(int,int,double,double)));
 287   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 288
 289   playMode = 0;//pause
 290   mFrameRate = 10;
 291   playButton->setEnabled(0);
 292   frameRateLabel->setEnabled(0);
 293   frameRateSpinBox->setEnabled(0);
 294   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 295   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 296
 297   goToCursorPushButton->setEnabled(0);
 298   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 299
 300   NOViewWidget->hide();
 301   NEViewWidget->hide();
 302   SOViewWidget->hide();
 303   SEViewWidget->hide();
 304
 305   //Recently opened files
 306   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 307   if ( !recent_files.empty() ) {
 308     QMenu * rmenu = new QMenu("Recently opened files...");
 309     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 310     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 311     menuFile->insertSeparator(actionOpen_Image_With_Time);
 312     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 313       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 314                                    (*i).c_str(),this);
 315       rmenu->addAction(current);
 316       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 317     }
 318   }
 319
 320   // Adding all new tools (insertion in the menu)
 321   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 322
 323   if (!CLITK_EXPERIMENTAL)
 324     menuExperimental->menuAction()->setVisible(false);
 325
 326
 327   QTimer * timerMemory = new QTimer(this);
 328   //timerMemory->setInterval(5);
 329   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 330   timerMemory->start(2000);
 331
 332 }
 333 //------------------------------------------------------------------------------
 334
 335
 336 //------------------------------------------------------------------------------
 337 void vvMainWindow::UpdateMemoryUsage()
 338 {
 339   //  clitk::PrintMemory(true);
 340   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 341   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 342 }
 343 //------------------------------------------------------------------------------
 344
 345
 346 //------------------------------------------------------------------------------
 347 void vvMainWindow::ComputeMidPosition()
 348 {
 349   bool ok;
 350   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 351   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 352                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 353   if (ok) {
 354     vvMidPosition midp;
 355     midp.slicer_manager = mSlicerManagers[index];
 356     midp.reference_image_index = ref;
 357     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 358     midp.Update();
 359     if (midp.error)
 360       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 361     else {
 362       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 363       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 364     }
 365     QApplication::restoreOverrideCursor();
 366   }
 367 }
 368 //------------------------------------------------------------------------------
 369
 370
 371 //------------------------------------------------------------------------------
 372 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 373 {
 374   QTreeWidgetItem *item = new QTreeWidgetItem();
 375   item->setData(0,Qt::UserRole,"filename.vtk");
 376   item->setData(1,Qt::UserRole,tr("contour"));
 377   QBrush brush;
 378   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 379   brush.setStyle(Qt::SolidPattern);
 380   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 381   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 382
 383   for (int j = 1; j <= 4; j++)
 384     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 385
 386   QTreePushButton* cButton = new QTreePushButton;
 387   cButton->setItem(item);
 388   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 389   cButton->setToolTip(tr("close image"));
 390   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 391   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 392           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 393
 394   QTreePushButton* rButton = new QTreePushButton;
 395   rButton->setItem(item);
 396   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 397   rButton->setToolTip(tr("reload image"));
 398   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 399   rButton->setEnabled(false);
 400   //Not implemented
 401   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 402   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 403
 404   DataTree->topLevelItem(image_index)->setExpanded(1);
 405   DataTree->topLevelItem(image_index)->addChild(item);
 406   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 407   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 408   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 409   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 410
 411   UpdateTree();
 412   mSlicerManagers[image_index]->AddContour(contour,propagation);
 413   mSlicerManagers[image_index]->Render();
 414 }
 415 //------------------------------------------------------------------------------
 416
 417
 418 //------------------------------------------------------------------------------
 419 void vvMainWindow::OpenVTKContour()
 420 {
 421   if (mSlicerManagers.size() > 0) {
 422     QString Extensions = "Images ( *.vtk *.obj)";
 423     Extensions += ";;All Files (*)";
 424     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 425     if (file.isNull())
 426       return;
 427     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 428     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 429     vvMeshReader reader;
 430     reader.SetImage(mSlicerManagers[index]->GetImage());
 431     reader.SetModeToVTK();
 432     reader.SetFilename(file.toStdString());
 433     reader.Update();
 434     AddContour(index,reader.GetOutput()[0],false);
 435     QApplication::restoreOverrideCursor();
 436   }
 437 }
 438 //------------------------------------------------------------------------------
 439
 440
 441 //------------------------------------------------------------------------------
 442 void vvMainWindow::OpenDCStructContour()
 443 {
 444   if (mSlicerManagers.size() > 0) {
 445     QString Extensions = "Dicom Files ( *.dcm RS*)";
 446     Extensions += ";;All Files (*)";
 447     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 448     if (file.isNull())
 449       return;
 450     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 451     vvMeshReader reader;
 452     reader.SetFilename(file.toStdString());
 453     vvStructSelector selector;
 454     selector.SetStructures(reader.GetROINames());
 455     if (!mSlicerManagers[index]->GetVF().IsNull())
 456       selector.EnablePropagationCheckBox();
 457     if (selector.exec()) {
 458       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 459       reader.SetSelectedItems(selector.getSelectedItems());
 460       reader.SetImage(mSlicerManagers[index]->GetImage());
 461       if (selector.PropagationEnabled())
 462         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 463       reader.Update();
 464       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 465       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 466            i!=contours.end(); i++)
 467         AddContour(index,*i,selector.PropagationEnabled());
 468       QApplication::restoreOverrideCursor();
 469     }
 470   }
 471 }
 472 //------------------------------------------------------------------------------
 473
 474
 475 //------------------------------------------------------------------------------
 476 void vvMainWindow::ComputeDeformableRegistration()
 477 {
 478   if (mSlicerManagers.size() > 0) {
 479     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 480     vvDeformationDialog dialog(index,mSlicerManagers);
 481     if (dialog.exec()) {
 482       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 483       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 484       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 485     } else
 486       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 487   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 488 }
 489 //------------------------------------------------------------------------------
 490
 491
 492 //------------------------------------------------------------------------------
 493 void vvMainWindow::WarpImage()
 494 {
 495   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 496   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 497     bool ok;
 498     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 499                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 500     if (ok) {
 501       WarpImage(mSlicerManagers[index],ref);
 502     }
 503   } else
 504     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 505 }
 506 //------------------------------------------------------------------------------
 507
 508
 509 //------------------------------------------------------------------------------
 510 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 511 {
 512   if (!selected_slicer->GetVF().IsNull()) {
 513     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 514     QFileInfo info(selected_slicer->GetFileName().c_str());
 515     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 516                      reference_phase,this);
 517     if (warp.ComputeWarpedImage()) {
 518       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 519       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 520       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 521       QApplication::restoreOverrideCursor();
 522     } else {
 523       QApplication::restoreOverrideCursor();
 524       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 525     }
 526   } else
 527     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 528 }
 529 //------------------------------------------------------------------------------
 530
 531
 532 //------------------------------------------------------------------------------
 533 vvMainWindow::~vvMainWindow()
 534 {
 535   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 536     if (mSlicerManagers[i] != NULL)
 537       delete mSlicerManagers[i];
 538   }
 539 }
 540 //------------------------------------------------------------------------------
 541
 542 //------------------------------------------------------------------------------
 543 QTabWidget * vvMainWindow::GetTab()
 544 {
 545   return tabWidget;
 546 }
 547 //------------------------------------------------------------------------------
 548
 549
 550 //------------------------------------------------------------------------------
 551 void vvMainWindow::MergeImages()
 552 {
 553   QString Extensions = EXTENSIONS;
 554   Extensions += ";;All Files (*)";
 555   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 556   if (files.isEmpty())
 557     return;
 558   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 559   std::vector<std::string> vector;
 560
 561   unsigned int currentDim = 0;
 562   std::vector<double> currentSpacing;
 563   std::vector<int> currentSize;
 564   std::vector<double> currentOrigin;
 565
 566   for (int i = 0; i < files.size(); i++) {
 567     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 568                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 569     reader->SetFileName(files[i].toStdString().c_str());
 570     reader->ReadImageInformation();
 571     if (reader)        {
 572       //NOViewWidget->hide();
 573       //NEViewWidget->hide();
 574       //SOViewWidget->hide();
 575       //SEViewWidget->hide();
 576       if (i == 0)
 577         currentDim = reader->GetNumberOfDimensions();
 578       bool IsOk = true;
 579       for (unsigned int j = 0; j < currentDim; j++) {
 580         if (i == 0) {
 581           if (j == 0) {
 582             currentSpacing.resize(currentDim);
 583             currentSize.resize(currentDim);
 584             currentOrigin.resize(currentDim);
 585           }
 586           currentOrigin[j] = reader->GetOrigin(j);
 587           currentSpacing[j] = reader->GetSpacing(j);
 588           currentSize[j] = reader->GetDimensions(j);
 589         } else if (currentDim != reader->GetNumberOfDimensions()
 590                    || currentSpacing[j] != reader->GetSpacing(j)
 591                    || currentSize[j] != (int)reader->GetDimensions(j)
 592                    || currentOrigin[j] != reader->GetOrigin(j)) {
 593           QString error = "Cannot read file (too different from others ";
 594           error += files[i].toStdString().c_str();
 595           QMessageBox::information(this,tr("Reading problem"),error);
 596           IsOk = false;
 597           break;
 598         }
 599       }
 600       if (IsOk)
 601         vector.push_back(files[i].toStdString());
 602     }
 603   }
 604   if (vector.size() > 0)
 605     LoadImages(vector, MERGED);
 606 }
 607 //------------------------------------------------------------------------------
 608
 609 //------------------------------------------------------------------------------
 610 void vvMainWindow::SliceImages()
 611 {
 612   QString Extensions = EXTENSIONS;
 613   Extensions += ";;All Files (*)";
 614
 615   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 616   if (files.isEmpty())
 617     return;
 618   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 619   std::vector<std::string> vector;
 620   for (int i = 0; i < files.size(); i++)
 621     vector.push_back(files[i].toStdString());
 622   LoadImages(vector, SLICED);
 623 }
 624 //------------------------------------------------------------------------------
 625
 626 //------------------------------------------------------------------------------
 627 void vvMainWindow::MergeImagesWithTime()
 628 {
 629   QString Extensions = EXTENSIONS;
 630   Extensions += ";;All Files (*)";
 631   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 632   if (files.isEmpty())
 633     return;
 634   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 635   std::vector<std::string> vector;
 636
 637   unsigned int currentDim = 0;
 638   std::vector<double> currentSpacing;
 639   std::vector<int> currentSize;
 640   std::vector<double> currentOrigin;
 641
 642   for (int i = 0; i < files.size(); i++) {
 643     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 644                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 645     if (reader) {
 646       reader->SetFileName(files[i].toStdString().c_str());
 647       reader->ReadImageInformation();
 648       if (i == 0)
 649         currentDim = reader->GetNumberOfDimensions();
 650       bool IsOk = true;
 651       for (unsigned int j = 0; j < currentDim; j++) {
 652         if (i == 0) {
 653           if (j == 0) {
 654             currentSpacing.resize(currentDim);
 655             currentSize.resize(currentDim);
 656             currentOrigin.resize(currentDim);
 657           }
 658           currentOrigin[j] = reader->GetOrigin(j);
 659           currentSpacing[j] = reader->GetSpacing(j);
 660           currentSize[j] = reader->GetDimensions(j);
 661         } else if (currentDim != reader->GetNumberOfDimensions()
 662                    || currentSpacing[j] != reader->GetSpacing(j)
 663                    || currentSize[j] != (int)reader->GetDimensions(j)
 664                    || currentOrigin[j] != reader->GetOrigin(j)) {
 665           QString error = "Cannot read file (too different from others ";
 666           error += files[i].toStdString().c_str();
 667           QMessageBox::information(this,tr("Reading problem"),error);
 668           IsOk = false;
 669           break;
 670         }
 671       }
 672       if (IsOk)
 673         vector.push_back(files[i].toStdString());
 674     } else {
 675       QString error = "Cannot read file info for ";
 676       error += files[i].toStdString().c_str();
 677       error += "\n";
 678       error += "Maybe you're trying to open an image in an unsupported format?\n";
 679       QMessageBox::information(this,tr("Reading problem"),error);
 680     }
 681   }
 682   sort(vector.begin(),vector.end());
 683   if (vector.size() > 1)
 684     LoadImages(vector, MERGEDWITHTIME);
 685   else
 686     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.");
 687 }
 688 //------------------------------------------------------------------------------
 689
 690
 691 //------------------------------------------------------------------------------
 692 void vvMainWindow::OpenDicom()
 693 {
 694   std::vector<std::string> files;
 695
 696   std::cout << "dicomSeriesSelector " << std::endl;
 697   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 698     files = *(dicomSeriesSelector->GetFilenames());
 699     LoadImages(files,DICOM);
 700   }
 701 }
 702 //------------------------------------------------------------------------------
 703
 704 //------------------------------------------------------------------------------
 705 void vvMainWindow::OpenImages()
 706 {
 707   QString Extensions = EXTENSIONS;
 708   Extensions += ";;All Files (*)";
 709
 710   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 711   if (files.isEmpty())
 712     return;
 713   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 714   std::vector<std::string> vector;
 715   for (int i = 0; i < files.size(); i++)
 716     vector.push_back(files[i].toStdString());
 717   LoadImages(vector, IMAGE);
 718 }
 719 //------------------------------------------------------------------------------
 720 void vvMainWindow::OpenRecentImage()
 721 {
 722   QAction * caller = qobject_cast<QAction*>(sender());
 723   std::vector<std::string> images;
 724   images.push_back(caller->text().toStdString());
 725   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 726   LoadImages(images,IMAGE);
 727 }
 728 //------------------------------------------------------------------------------
 729
 730
 731 //------------------------------------------------------------------------------
 732 void vvMainWindow::OpenImageWithTime()
 733 {
 734   QString Extensions = EXTENSIONS;
 735   Extensions += ";;All Files (*)";
 736
 737   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 738   if (files.isEmpty())
 739     return;
 740   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 741   std::vector<std::string> vector;
 742   for (int i = 0; i < files.size(); i++) {
 743     vector.push_back(files[i].toStdString());
 744   }
 745   LoadImages(vector, IMAGEWITHTIME);
 746 }
 747 //------------------------------------------------------------------------------
 748
 749
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 752 {
 753   //Separate the way to open images and dicoms
 754   int fileSize;
 755   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 756     fileSize = files.size();
 757   else
 758     fileSize = 1;
 759
 760   // For SLICED, we need the number of slices (ndim and #slices)
 761   std::vector<unsigned int> nSlices;
 762   nSlices.resize(files.size());
 763   std::fill(nSlices.begin(), nSlices.end(), 1);
 764   if (filetype == SLICED) {
 765     for (int i = 0; i < fileSize; i++) {
 766       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 767       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 768       if (!header) {
 769         nSlices[i] = 0;
 770         QString error = "Cannot open file \n";
 771         error += files[i].c_str();
 772         QMessageBox::information(this,tr("Reading problem"),error);
 773         return;
 774       }
 775       if (header->GetNumberOfDimensions() < 3) {
 776         nSlices[i] = 0;
 777         QString error = "Dimension problem. Cannot slice \n";
 778         error += files[i].c_str();
 779         QMessageBox::information(this,tr("Reading problem"),error);
 780         return;
 781       }
 782       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 783     }
 784   }
 785
 786   //Only add to the list of recently opened files when a single file is opened,
 787   //to avoid polluting the list of recently opened files
 788   if (files.size() == 1) {
 789     QFileInfo finfo=tr(files[0].c_str());
 790     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 791   }
 792   //init the progress events
 793   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 794   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 795   qApp->processEvents();
 796
 797   int numberofsuccesulreads=0;
 798   //open images as 1 or multiples
 799   for (int i = 0; i < fileSize; i++) {
 800
 801     progress.SetText("Opening " + files[i]);
 802     progress.SetProgress(i,fileSize);
 803     qApp->processEvents();
 804
 805     for (unsigned int j = 0; j < nSlices[i]; j++) {
 806       //read the image and put it in mSlicerManagers
 807       vvSlicerManager* imageManager = new vvSlicerManager(4);
 808       qApp->processEvents();
 809
 810       bool SetImageSucceed=false;
 811
 812       // Change filename if an image with the same already exist
 813       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 814
 815       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 816         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 817       else {
 818         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 819       }
 820       if (!SetImageSucceed) {
 821         QApplication::restoreOverrideCursor();
 822         QString error = "Cannot open file \n";
 823         error += imageManager->GetLastError().c_str();
 824         QMessageBox::information(this,tr("Reading problem"),error);
 825         delete imageManager;
 826       } else {
 827         mSlicerManagers.push_back(imageManager);
 828
 829         //create an item in the tree with good settings
 830         QTreeWidgetItem *item = new QTreeWidgetItem();
 831         item->setData(0,Qt::UserRole,files[i].c_str());
 832         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 833         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 834         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 835         qApp->processEvents();
 836
 837         //Create the buttons for reload and close
 838         qApp->processEvents();
 839         QTreePushButton* cButton = new QTreePushButton;
 840         cButton->setItem(item);
 841         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 842         cButton->setToolTip(tr("close image"));
 843         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 844         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 845                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 846
 847         QTreePushButton* rButton = new QTreePushButton;
 848         rButton->setItem(item);
 849         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 850         rButton->setToolTip(tr("reload image"));
 851         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 852         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 853                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 854
 855         DataTree->addTopLevelItem(item);
 856         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 857         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 858
 859         //set the id of the image
 860         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 861         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 862         mSlicerManagers.back()->SetId(id.toStdString());
 863
 864         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 865
 866         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 867                 this,SLOT(CurrentImageChanged(std::string)));
 868         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 869                 this, SLOT(CurrentPickedImageChanged(std::string)));
 870         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 871                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 872         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 873                 this, SLOT(VectorChanged(int,double,double,double, double)));
 874         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 875                 this, SLOT(OverlayChanged(int,double,double)));
 876         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 877                 this, SLOT(FusionChanged(int,double)));
 878         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 879                 this,SLOT(WindowsChanged(int, int, int)));
 880         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 881                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 882         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 883                 this,SLOT(UpdateSlice(int,int)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 885                 this,SLOT(UpdateTSlice(int, int)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 887                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 889                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 891                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 892         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 893                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 894         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 895         InitSlicers();
 896         numberofsuccesulreads++;
 897       }
 898     }
 899   }
 900   if (numberofsuccesulreads) {
 901     NOViewWidget->show();
 902     NEViewWidget->show();
 903     SOViewWidget->show();
 904     SEViewWidget->show();
 905     UpdateTree();
 906     InitDisplay();
 907     ShowLastImage();
 908
 909     // Try to guess default WindowLevel
 910     double range[2];
 911     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 912     if ((range[0] == 0) && (range[1] == 1)) {
 913       presetComboBox->setCurrentIndex(5);// binary
 914     } else {
 915       // TODO
 916     }
 917   }
 918   QApplication::restoreOverrideCursor();
 919 }
 920 //------------------------------------------------------------------------------
 921
 922 //------------------------------------------------------------------------------
 923 void vvMainWindow::UpdateTree()
 924 {
 925   DataTree->resizeColumnToContents(COLUMN_TREE);
 926   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 927   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 928   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 929   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 930   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 931   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 932   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 933 }
 934 //------------------------------------------------------------------------------
 935
 936 //------------------------------------------------------------------------------
 937 void vvMainWindow::CurrentImageChanged(std::string id)
 938 {
 939   if (id == mCurrentSelectedImageId) return; // Do nothing
 940   int selected = 0;
 941   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 942     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 943       selected = i;
 944     } else {
 945       DataTree->topLevelItem(i)->setSelected(0);
 946     }
 947     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 948       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 949
 950   }
 951   DataTree->topLevelItem(selected)->setSelected(1);
 952   mCurrentSelectedImageId = id;
 953   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 954 }
 955 //------------------------------------------------------------------------------
 956
 957 //------------------------------------------------------------------------------
 958 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 959 {
 960   if (id == mCurrentPickedImageId) return; // Do nothing
 961   int selected = 0;
 962   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 963     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 964       selected = i;
 965     } else {
 966       DataTree->topLevelItem(i)->setSelected(0);
 967     }
 968     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 969       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 970
 971   }
 972   DataTree->topLevelItem(selected)->setSelected(1);
 973   mCurrentPickedImageId = id;
 974   mCurrentPickedImageIndex = selected;
 975 }
 976 //------------------------------------------------------------------------------
 977
 978 //------------------------------------------------------------------------------
 979 void vvMainWindow::ImageInfoChanged()
 980 {
 981   contextActions[6]->setEnabled(1);
 982   contextActions[5]->setEnabled(1);
 983   actionSave_As->setEnabled(1);
 984   actionAdd_VF_to_current_Image->setEnabled(1);
 985   actionAdd_fusion_image->setEnabled(1);
 986   actionNorth_East_Window->setEnabled(1);
 987   actionNorth_West_Window->setEnabled(1);
 988   actionSouth_East_Window->setEnabled(1);
 989   actionSouth_West_Window->setEnabled(1);
 990   inverseButton->setEnabled(1);
 991
 992   goToCursorPushButton->setEnabled(1);
 993
 994   if (DataTree->selectedItems().size()) {
 995     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 996
 997     colorMapComboBox->setEnabled(1);
 998     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 999       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1000           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1001         colorMapComboBox->setEnabled(0);
1002         break;
1003       }
1004     }
1005
1006     std::vector<double> origin;
1007     std::vector<double> inputSpacing;
1008     std::vector<int> inputSize;
1009     std::vector<double> sizeMM;
1010     vtkSmartPointer<vtkMatrix4x4> transformation;
1011     int dimension=0;
1012     QString pixelType;
1013     QString inputSizeInBytes;
1014     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1015
1016     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1017       playButton->setEnabled(1);
1018       frameRateLabel->setEnabled(1);
1019       frameRateSpinBox->setEnabled(1);
1020     } else {
1021       playButton->setEnabled(0);
1022       frameRateLabel->setEnabled(0);
1023       frameRateSpinBox->setEnabled(0);
1024     }
1025
1026     //read image header
1027     int NPixel = 1;
1028
1029     vvImage::Pointer imageSelected;
1030     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1031       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1032       dimension = imageSelected->GetNumberOfDimensions();
1033       origin.resize(dimension);
1034       inputSpacing.resize(dimension);
1035       inputSize.resize(dimension);
1036       sizeMM.resize(dimension);
1037       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1038       for (int i = 0; i < dimension; i++) {
1039         origin[i] = imageSelected->GetOrigin()[i];
1040         inputSpacing[i] = imageSelected->GetSpacing()[i];
1041         inputSize[i] = imageSelected->GetSize()[i];
1042         sizeMM[i] = inputSize[i]*inputSpacing[i];
1043         NPixel *= inputSize[i];
1044       }
1045       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1046     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1047       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1048       dimension = imageSelected->GetNumberOfDimensions();
1049       origin.resize(dimension);
1050       inputSpacing.resize(dimension);
1051       inputSize.resize(dimension);
1052       sizeMM.resize(dimension);
1053       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1054       for (int i = 0; i < dimension; i++) {
1055         origin[i] = imageSelected->GetOrigin()[i];
1056         inputSpacing[i] = imageSelected->GetSpacing()[i];
1057         inputSize[i] = imageSelected->GetSize()[i];
1058         sizeMM[i] = inputSize[i]*inputSpacing[i];
1059         NPixel *= inputSize[i];
1060       }
1061       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1062     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1063       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1064       dimension = imageSelected->GetNumberOfDimensions();
1065       origin.resize(dimension);
1066       inputSpacing.resize(dimension);
1067       inputSize.resize(dimension);
1068       sizeMM.resize(dimension);
1069       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1070       for (int i = 0; i < dimension; i++) {
1071         origin[i] = imageSelected->GetOrigin()[i];
1072         inputSpacing[i] = imageSelected->GetSpacing()[i];
1073         inputSize[i] = imageSelected->GetSize()[i];
1074         sizeMM[i] = inputSize[i]*inputSpacing[i];
1075         NPixel *= inputSize[i];
1076       }
1077       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1078     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1079       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1080       dimension = imageSelected->GetNumberOfDimensions();
1081       origin.resize(dimension);
1082       inputSpacing.resize(dimension);
1083       inputSize.resize(dimension);
1084       sizeMM.resize(dimension);
1085       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1086       for (int i = 0; i < dimension; i++) {
1087         origin[i] = imageSelected->GetOrigin()[i];
1088         inputSpacing[i] = imageSelected->GetSpacing()[i];
1089         inputSize[i] = imageSelected->GetSize()[i];
1090         sizeMM[i] = inputSize[i]*inputSpacing[i];
1091         NPixel *= inputSize[i];
1092       }
1093       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1094     }
1095
1096     QString dim = QString::number(dimension) + " (";
1097     dim += pixelType + ")";
1098
1099     infoPanel->setFileName(image);
1100     infoPanel->setDimension(dim);
1101     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1102     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1103     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1104     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1105     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1106     transformation = imageSelected->GetTransform()->GetMatrix();
1107     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1108
1109     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1110                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1111     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1112     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1113
1114     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1115     for (int i = 0; i < 4; i++) {
1116       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1117         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1118         break;
1119       }
1120     }
1121     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1122     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1123     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1124     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1125
1126     infoPanel->setFileName(image);
1127     infoPanel->setDimension(dim);
1128     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1129     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1130     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1131     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1132     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1133
1134     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1135                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1136     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1137     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1138
1139     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1140     for (int i = 0; i < 4; i++) {
1141       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1142         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1143         break;
1144       }
1145     }
1146     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1147     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1148     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1149     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1150
1151     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1152       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1153       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1154                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1155                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1156     } else {
1157       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1158       overlayPanel->getVFProperty(-1,-1,-1);
1159     }
1160     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1161       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1162       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1163     } else {
1164       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1165       overlayPanel->getOverlayProperty(-1);
1166     }
1167     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1168       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1169       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1170                                       mSlicerManagers[index]->GetFusionColorMap(),
1171                                       mSlicerManagers[index]->GetFusionWindow(),
1172                                       mSlicerManagers[index]->GetFusionLevel());
1173     } else {
1174       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1175       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1176     }
1177   }
1178 }
1179 //------------------------------------------------------------------------------
1180
1181 //------------------------------------------------------------------------------
1182 void vvMainWindow::ShowDocumentation()
1183 {
1184   documentation->show();
1185 }
1186 //------------------------------------------------------------------------------
1187 void vvMainWindow::ShowHelpDialog()
1188 {
1189   help_dialog->show();
1190 }
1191 //------------------------------------------------------------------------------
1192
1193 //------------------------------------------------------------------------------
1194 void vvMainWindow::ChangeViewMode()
1195 {
1196   QListIterator<int> it0(splitter_3->sizes());
1197   QListIterator<int> it1(splitter_3->sizes());
1198   int max0 = 0;
1199   int max1 = 1;
1200   while (it0.hasNext()) {
1201     max0 += it0.next();
1202   }
1203   while (it1.hasNext()) {
1204     max1 += it1.next();
1205   }
1206   QList<int> size0;
1207   QList<int> size1;
1208   if (viewMode == 1) {
1209     viewMode = 0;
1210     size0.push_back(max0);
1211     size0.push_back(0);
1212     size1.push_back(max1);
1213     size1.push_back(0);
1214     splitter_3->setSizes(size0);
1215     OSplitter->setSizes(size1);
1216     DataTree->setColumnHidden(2,1);
1217     DataTree->setColumnHidden(3,1);
1218     DataTree->setColumnHidden(4,1);
1219   } else {
1220     viewMode = 1;
1221     size0.push_back(int(max0/2));
1222     size0.push_back(int(max0/2));
1223     size1.push_back(int(max1/2));
1224     size1.push_back(int(max1/2));
1225     splitter_3->setSizes(size0);
1226     OSplitter->setSizes(size1);
1227     DataTree->setColumnHidden(2,0);
1228     DataTree->setColumnHidden(3,0);
1229     DataTree->setColumnHidden(4,0);
1230   }
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1236 {
1237   QString result = "";// QString::number(size);
1238   //result += " bytes (";
1239   if (size > 1000000000) {
1240     size /= 1000000000;
1241     result += QString::number(size);
1242     result += "Gb";//)";
1243   } else if (size > 1000000) {
1244     size /= 1000000;
1245     result += QString::number(size);
1246     result += "Mb";//)";
1247   } else if (size > 1000) {
1248     size /= 1000;
1249     result += QString::number(size);
1250     result += "kb";//)";
1251   }
1252   return result;
1253 }
1254 //------------------------------------------------------------------------------
1255
1256 //------------------------------------------------------------------------------
1257 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1258 {
1259   std::ostringstream strmatrix;
1260
1261   for (unsigned int i = 0; i < 4; i++) {
1262     for (unsigned int j = 0; j < 4; j++) {
1263       strmatrix.flags(ios::showpos);
1264       strmatrix.width(10);
1265       strmatrix.precision(3);
1266       strmatrix.setf(ios::fixed,ios::floatfield);
1267       strmatrix.fill(' ');
1268       strmatrix << std::left << matrix->GetElement(i, j);
1269       //strmatrix.width(10);
1270       strmatrix << " ";
1271     }
1272     strmatrix << std::endl;
1273   }
1274   QString result = strmatrix.str().c_str();
1275   return result;
1276 }
1277 //------------------------------------------------------------------------------
1278
1279 //------------------------------------------------------------------------------
1280 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1281 {
1282   QString result;
1283   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1284     if (i != 0)
1285       result += " ";
1286     result += QString::number(vectorDouble[i]);
1287   }
1288   return result;
1289 }
1290 //------------------------------------------------------------------------------
1291
1292 //------------------------------------------------------------------------------
1293 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1294 {
1295   QString result;
1296   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1297     if (i != 0)
1298       result += " ";
1299     result += QString::number(vectorInt[i]);
1300   }
1301   return result;
1302 }
1303 //------------------------------------------------------------------------------
1304
1305 //------------------------------------------------------------------------------
1306 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1307 {
1308   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1309   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1310     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1311       return i;
1312   }
1313   return -1;
1314 }
1315 //------------------------------------------------------------------------------
1316
1317 //------------------------------------------------------------------------------
1318 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1319 {
1320   QString id = sm->GetId().c_str();
1321   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1322     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1323       return DataTree->topLevelItem(i);
1324   }
1325   return NULL;
1326 }
1327 //------------------------------------------------------------------------------
1328
1329 //------------------------------------------------------------------------------
1330 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1331 {
1332   int index = GetSlicerIndexFromItem(clicked_item);
1333   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1334     return;
1335   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1336     //Trick to avoid redoing twice the job for a key (sr)
1337     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1338
1339     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1340     if (DataTree->topLevelItem(index) == current_row) {
1341       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1342       if (current_row == clicked_item) {
1343         //If we just activated a slicer
1344         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1345           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1346           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1347           DisplaySliders(i,column-1);
1348           std::map<std::string,int> overlay_counts;
1349           for (int child = 0; child < current_row->childCount(); child++) {
1350             std::string overlay_type =
1351               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1352             overlay_counts[overlay_type]++;
1353             current_row->child(child)->setData(column,Qt::CheckStateRole,
1354                                                current_row->data(column,Qt::CheckStateRole));
1355             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1356           }
1357         } else { //We don't allow simply desactivating a slicer
1358           clicked_item->setData(column,Qt::CheckStateRole,2);
1359           return;
1360         }
1361       }
1362       //if we clicked on the vector(or overlay) and not the image
1363       else {
1364         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1365           current_row->setData(column,Qt::CheckStateRole,2);
1366           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1367           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1368           DisplaySliders(i,column-1);
1369         }
1370         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1371         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1372         int overlay_index=0;
1373         for (int child = 0; child < current_row->childCount(); child++) {
1374           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1375             overlay_index++;
1376           if (current_row->child(child) == clicked_item) break;
1377         }
1378         clicked_slicer->SetActorVisibility(
1379           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1380       }
1381     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1382       current_row->setData(column,Qt::CheckStateRole,0);
1383       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1384       std::map<std::string,int> overlay_counts;
1385       for (int child = 0; child < current_row->childCount(); child++) {
1386         std::string overlay_type =
1387           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1388         overlay_counts[overlay_type]++;
1389         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1390         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1391         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1392       }
1393     }
1394     //mSlicerManagers[i]->SetColorMap(-1);
1395     mSlicerManagers[i]->SetColorMap();
1396   }
1397   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 void vvMainWindow::InitSlicers()
1402 {
1403   if (mSlicerManagers.size()) {
1404     mSlicerManagers.back()->GenerateDefaultLookupTable();
1405
1406     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1407     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1408     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1409     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1410   }
1411 }
1412
1413 //------------------------------------------------------------------------------
1414 void vvMainWindow::InitDisplay()
1415 {
1416   if (mSlicerManagers.size()) {
1417     //BE CAREFUL : this is absolutely necessary to set the interactor style
1418     //in order to have the same style instanciation for all SlicerManagers in
1419     // a same window
1420     for (int j = 0; j < 4; j++) {
1421       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1422       style->SetAutoAdjustCameraClippingRange(1);
1423       bool AlreadySelected = false;
1424       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1425         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1426
1427         //select the image only if previous are not selected
1428         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1429           mSlicerManagers[i]->UpdateSlicer(j,1);
1430           AlreadySelected = true;
1431         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1432           if (DataTree->selectedItems().size() == 0)
1433             DataTree->topLevelItem(i)->setSelected(1);
1434           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1435           mSlicerManagers[i]->UpdateSlicer(j,1);
1436           DisplaySliders(i,j);
1437         } else {
1438           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1439           mSlicerManagers[i]->UpdateSlicer(j,0);
1440         }
1441       }
1442       style->Delete();
1443     }
1444   }
1445 }
1446 //------------------------------------------------------------------------------
1447
1448 //------------------------------------------------------------------------------
1449 void vvMainWindow::DisplaySliders(int slicer, int window)
1450 {
1451   int range[2];
1452   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1453   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1454
1455   int tRange[2];
1456   tRange[0] = 0;
1457   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1458   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1459   bool showHorizontal = false;
1460   bool showVertical = false;
1461   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1462       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1463           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1464           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1465     showVertical = true;
1466   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1467       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1468       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1469     showHorizontal = true;
1470
1471   if (showVertical)
1472     verticalSliders[window]->show();
1473   else
1474     verticalSliders[window]->hide();
1475   verticalSliders[window]->setRange(range[0],range[1]);
1476   verticalSliders[window]->setValue(position);
1477
1478   if (showHorizontal)
1479     horizontalSliders[window]->show();
1480   else
1481     horizontalSliders[window]->hide();
1482   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1483   horizontalSliders[window]->setValue(tPosition);
1484 }
1485 //------------------------------------------------------------------------------
1486
1487 //------------------------------------------------------------------------------
1488 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1489 {
1490   int index = GetSlicerIndexFromItem(item);
1491
1492   if (DataTree->topLevelItem(index) != item) {
1493     QString warning = "Do you really want to close the overlay : ";
1494     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1495     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1496                        warning, 0, this);
1497     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1498     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1499     if (msgBox.exec() == QMessageBox::AcceptRole) {
1500       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1501       int overlay_index=0;
1502       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1503         if (DataTree->topLevelItem(index)->\
1504             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1505           overlay_index++;
1506         if (DataTree->topLevelItem(index)->child(child) == item) break;
1507       }
1508       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1509       mSlicerManagers[index]->SetColorMap(0);
1510       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1511       mSlicerManagers[index]->Render();
1512     }
1513   } else if (DataTree->topLevelItemCount() <= 1) {
1514     QString warning = "Do you really want to close the image : ";
1515     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1516     warning += "\nThis is the last image, you're about to close vv !!!";
1517     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1518                        warning, 0, this);
1519     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1520     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1521     if (msgBox.exec() == QMessageBox::AcceptRole) {
1522       this->close();
1523     }
1524   } else {
1525     QString warning = "Do you really want to close the image : ";
1526     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1527     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1528                        warning, 0, this);
1529     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1530     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1531     if (msgBox.exec() == QMessageBox::AcceptRole) {
1532
1533       // Tell tools that we close an image
1534       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1535
1536       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1537       DataTree->takeTopLevelItem(index);
1538       for (int i = 0; i < index; i++) {
1539         Manageriter++;
1540       }
1541       linkPanel->removeImage(index);
1542       mSlicerManagers[index]->RemoveActors();
1543       delete mSlicerManagers[index];
1544       mSlicerManagers.erase(Manageriter);
1545
1546       //
1547       InitDisplay();
1548     }
1549   }
1550   ImageInfoChanged();
1551 }
1552 //------------------------------------------------------------------------------
1553
1554 //------------------------------------------------------------------------------
1555 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1556 {
1557   // int index = GetSlicerIndexFromItem(item);
1558   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1559   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1560   //     mSlicerManagers[index]->ReloadVF();
1561   //   else
1562   //     mSlicerManagers[index]->Reload();
1563
1564   //   QApplication::restoreOverrideCursor();
1565   int index = GetSlicerIndexFromItem(item);
1566   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1567   QString role=item->data(1,Qt::UserRole).toString();
1568   if ( role == "vector")
1569     mSlicerManagers[index]->ReloadVF();
1570   else if (role == "overlay")
1571     mSlicerManagers[index]->ReloadOverlay();
1572   else if (role == "fusion")
1573     mSlicerManagers[index]->ReloadFusion();
1574   else
1575     mSlicerManagers[index]->Reload();
1576
1577   // Update view and info
1578   ImageInfoChanged();
1579   mSlicerManagers[index]->Render();
1580   QApplication::restoreOverrideCursor();
1581 }
1582 //------------------------------------------------------------------------------
1583
1584 //------------------------------------------------------------------------------
1585 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1586 {
1587   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1588 }
1589 //------------------------------------------------------------------------------
1590
1591 //------------------------------------------------------------------------------
1592 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1593 {
1594   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1595 }
1596 //------------------------------------------------------------------------------
1597
1598 //------------------------------------------------------------------------------
1599 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1600 {
1601   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1602 }
1603 //------------------------------------------------------------------------------
1604
1605 //------------------------------------------------------------------------------
1606 void vvMainWindow::FusionChanged(int visibility, double value)
1607 {
1608   overlayPanel->getCurrentFusionInfo(visibility,value);
1609 }
1610 //------------------------------------------------------------------------------
1611
1612 //------------------------------------------------------------------------------
1613 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1614 {
1615   infoPanel->setViews(window, view, slice);
1616 }
1617 //------------------------------------------------------------------------------
1618
1619 //------------------------------------------------------------------------------
1620 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1621 {
1622   windowSpinBox->setValue(window);
1623   levelSpinBox->setValue(level);
1624   colorMapComboBox->setCurrentIndex(colormap);
1625   presetComboBox->setCurrentIndex(preset);
1626 }
1627 //------------------------------------------------------------------------------
1628
1629 //------------------------------------------------------------------------------
1630 void vvMainWindow::WindowLevelEdited()
1631 {
1632   presetComboBox->setCurrentIndex(6);
1633   UpdateWindowLevel();
1634 }
1635 //------------------------------------------------------------------------------
1636
1637 //------------------------------------------------------------------------------
1638 void vvMainWindow::UpdateWindowLevel()
1639 {
1640   if (DataTree->selectedItems().size()) {
1641     if (presetComboBox->currentIndex() == 7) //For ventilation
1642       colorMapComboBox->setCurrentIndex(5);
1643     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1644     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1645     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1646     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1647     mSlicerManagers[index]->Render();
1648     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1649     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1650   }
1651 }
1652 //------------------------------------------------------------------------------
1653
1654 //------------------------------------------------------------------------------
1655 void vvMainWindow::UpdateColorMap()
1656 {
1657   if (DataTree->selectedItems().size()) {
1658     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1659     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1660     mSlicerManagers[index]->Render();
1661   }
1662 }
1663 //------------------------------------------------------------------------------
1664 void vvMainWindow::SwitchWindowLevel()
1665 {
1666   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1667   int window = mSlicerManagers[index]->GetColorWindow();
1668   presetComboBox->setCurrentIndex(6);
1669   windowSpinBox->setValue(-window);
1670   UpdateWindowLevel();
1671 }
1672 //------------------------------------------------------------------------------
1673
1674 //------------------------------------------------------------------------------
1675 void vvMainWindow::ApplyWindowLevelToAllImages()
1676 {
1677   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1678     if (mSlicerManagers[i] == NULL)
1679       continue;
1680     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1681     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1682     mSlicerManagers[i]->SetPreset(6);
1683     mSlicerManagers[i]->Render();
1684   }
1685 }
1686 //------------------------------------------------------------------------------
1687
1688 //------------------------------------------------------------------------------
1689 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1690 {
1691   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1692     if (mSlicerManagers[i]->GetId() == id) {
1693       //mSlicerManagers[i]->SetTSlice(temps);
1694       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1695       mSlicerManagers[i]->UpdateViews(0,slicer);
1696       break;
1697     }
1698   }
1699 }
1700 //------------------------------------------------------------------------------
1701
1702 //------------------------------------------------------------------------------
1703 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1704 {
1705   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1706     if (id == mSlicerManagers[i]->GetId()) {
1707       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1708     }
1709   }
1710 }
1711 //------------------------------------------------------------------------------
1712
1713 //------------------------------------------------------------------------------
1714 void vvMainWindow::ShowContextMenu(QPoint point)
1715 {
1716   if (!DataTree->selectedItems().size()) {
1717     contextActions[1]->setEnabled(0);
1718     contextActions[2]->setEnabled(0);
1719     contextActions[3]->setEnabled(0);
1720     contextActions[4]->setEnabled(0);
1721     contextActions[5]->setEnabled(0);
1722     contextActions[6]->setEnabled(0);
1723   } else {
1724     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1725     contextActions[1]->setEnabled(1);
1726     contextActions[2]->setEnabled(
1727       DataTree->itemWidget(DataTree->selectedItems()[0],
1728                            COLUMN_RELOAD_IMAGE)->isEnabled());
1729     contextActions[3]->setEnabled(1);
1730     contextActions[5]->setEnabled(1);
1731     contextActions[6]->setEnabled(1);
1732
1733     if (mSlicerManagers[index]->GetDimension() < 3)
1734       contextActions[4]->setEnabled(0);
1735     else
1736       contextActions[4]->setEnabled(1);
1737   }
1738   contextMenu.exec(QCursor::pos());
1739 }
1740 //------------------------------------------------------------------------------
1741
1742 //------------------------------------------------------------------------------
1743 void vvMainWindow::CloseImage()
1744 {
1745   CloseImage(DataTree->selectedItems()[0],0);
1746 }
1747 //------------------------------------------------------------------------------
1748
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::ReloadImage()
1751 {
1752   ReloadImage(DataTree->selectedItems()[0],0);
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::SelectOverlayImage()
1758 {
1759   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1760
1761   //check if one overlay image is added
1762   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1763     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1764       QString error = "Cannot add more than one compared image\n";
1765       error += "Please remove first ";
1766       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1767       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1768       return;
1769     }
1770
1771   QString Extensions = EXTENSIONS;
1772   Extensions += ";;All Files (*)";
1773   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1774   if (!file.isEmpty())
1775     AddOverlayImage(index,file);
1776 }
1777 //------------------------------------------------------------------------------
1778
1779 //------------------------------------------------------------------------------
1780 void vvMainWindow::AddOverlayImage(int index, QString file)
1781 {
1782
1783   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1784   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1785                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1786   reader->SetFileName(file.toStdString().c_str());
1787   reader->ReadImageInformation();
1788   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1789   int dimension = reader->GetNumberOfDimensions();
1790   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1791   vvProgressDialog progress("Opening " + file.toStdString());
1792   qApp->processEvents();
1793
1794   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1795   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1796     //create an item in the tree with good settings
1797     QTreeWidgetItem *item = new QTreeWidgetItem();
1798     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1799     item->setData(1,Qt::UserRole,tr("overlay"));
1800     QFileInfo fileinfo(file); //Do not show the path
1801     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1802     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1803     qApp->processEvents();
1804
1805     for (int j = 1; j <= 4; j++) {
1806       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1807       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1808           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1809     }
1810
1811     //Create the buttons for reload and close
1812     qApp->processEvents();
1813     QTreePushButton* cButton = new QTreePushButton;
1814     cButton->setItem(item);
1815     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1816     cButton->setToolTip(tr("close image"));
1817     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1818     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1819             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1820
1821     QTreePushButton* rButton = new QTreePushButton;
1822     rButton->setItem(item);
1823     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1824     rButton->setToolTip(tr("reload image"));
1825     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1826     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1827             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1828
1829     DataTree->topLevelItem(index)->setExpanded(1);
1830     DataTree->topLevelItem(index)->addChild(item);
1831     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1832     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1833
1834     //set the id of the image
1835     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1836     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1837     UpdateTree();
1838     qApp->processEvents();
1839     ImageInfoChanged();
1840     QApplication::restoreOverrideCursor();
1841   } else {
1842     QApplication::restoreOverrideCursor();
1843     QString error = "Cannot import the new image.\n";
1844     error += mSlicerManagers[index]->GetLastError().c_str();
1845     QMessageBox::information(this,tr("Problem reading image !"),error);
1846   }
1847 }
1848 //------------------------------------------------------------------------------
1849
1850
1851 //------------------------------------------------------------------------------
1852 void vvMainWindow::AddROI(int index, QString file)
1853 {
1854   /*
1855   // Get slice manager
1856
1857   // Load image
1858
1859   vvImageReader * mReader = new vvImageReader;
1860   mReader->SetInputFilename(filename.toStdString());
1861   mReader->Update(IMAGE);
1862   if (mReader->GetLastError().size() != 0) {
1863     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1864     QString error = "Cannot open file \n";
1865     error += mReader->GetLastError().c_str();
1866     QMessageBox::information(this,tr("Reading problem"),error);
1867     delete mReader;
1868     return;
1869   }
1870   vvImage::Pointer roi = mReader->GetOutput();
1871
1872   // Create roi in new tool
1873   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1874   */
1875 }
1876 //------------------------------------------------------------------------------
1877
1878 //------------------------------------------------------------------------------
1879 void vvMainWindow::SelectFusionImage()
1880 {
1881   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1882
1883   //check if one fusion image is added
1884   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1885     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1886       QString error = "Cannot add more than one fusion image\n";
1887       error += "Please remove first ";
1888       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1889       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1890       return;
1891     }
1892
1893   QString Extensions = EXTENSIONS;
1894   Extensions += ";;All Files (*)";
1895   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1896   if (!file.isEmpty())
1897     AddFusionImage(index,file);
1898 }
1899 //------------------------------------------------------------------------------
1900
1901 //------------------------------------------------------------------------------
1902 void vvMainWindow::AddFusionImage(int index, QString file)
1903 {
1904   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1905   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1906                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1907   reader->SetFileName(file.toStdString().c_str());
1908   reader->ReadImageInformation();
1909   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1910   if (reader) {
1911     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1912     vvProgressDialog progress("Opening fusion");
1913     qApp->processEvents();
1914
1915     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1916     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1917                                           reader->GetNumberOfDimensions(), component)) {
1918       //create an item in the tree with good settings
1919       QTreeWidgetItem *item = new QTreeWidgetItem();
1920       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1921       item->setData(1,Qt::UserRole,tr("fusion"));
1922       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1923       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1924       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1925       qApp->processEvents();
1926
1927       for (int j = 1; j <= 4; j++) {
1928         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1929         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1930             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1931       }
1932
1933       //Create the buttons for reload and close
1934       qApp->processEvents();
1935       QTreePushButton* cButton = new QTreePushButton;
1936       cButton->setItem(item);
1937       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1938       cButton->setToolTip(tr("close image"));
1939       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1940       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1941               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1942
1943       QTreePushButton* rButton = new QTreePushButton;
1944       rButton->setItem(item);
1945       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1946       rButton->setToolTip(tr("reload image"));
1947       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1948       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1949               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1950
1951       DataTree->topLevelItem(index)->setExpanded(1);
1952       DataTree->topLevelItem(index)->addChild(item);
1953       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1954       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1955
1956       //set the id of the image
1957       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1958       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1959       UpdateTree();
1960       qApp->processEvents();
1961       ImageInfoChanged();
1962       QApplication::restoreOverrideCursor();
1963     } else {
1964       QApplication::restoreOverrideCursor();
1965       QString error = "Cannot import the new image.\n";
1966       error += mSlicerManagers[index]->GetLastError().c_str();
1967       QMessageBox::information(this,tr("Problem reading image !"),error);
1968     }
1969   } else {
1970     QString error = "Cannot import the new image.\n";
1971     QMessageBox::information(this,tr("Problem reading image !"),error);
1972   }
1973 }
1974 //------------------------------------------------------------------------------
1975
1976
1977 //------------------------------------------------------------------------------
1978 void vvMainWindow::OpenField()
1979 {
1980   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1981   //check if a vector field has already been added
1982   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1983     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1984       QString error = "Cannot add more than one vector field\n";
1985       error += "Please remove first ";
1986       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1987       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1988       return;
1989     }
1990
1991   QString Extensions = "Images ( *.mhd)";
1992   Extensions += ";;Images ( *.vf)";
1993   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1994   if (!file.isEmpty())
1995     AddField(file,index);
1996 }
1997 //------------------------------------------------------------------------------
1998
1999
2000 //------------------------------------------------------------------------------
2001 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2002 {
2003   //create an item in the tree with good settings
2004   QTreeWidgetItem *item = new QTreeWidgetItem();
2005   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2006   item->setData(1,Qt::UserRole,tr("vector"));
2007   QFileInfo fileinfo(filename); //Do not show the path
2008   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2009   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2010   qApp->processEvents();
2011
2012   for (int j = 1; j <= 4; j++) {
2013     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2014     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2015         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2016   }
2017
2018   //Create the buttons for reload and close
2019   qApp->processEvents();
2020   QTreePushButton* cButton = new QTreePushButton;
2021   cButton->setItem(item);
2022   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2023   cButton->setToolTip(tr("close vector field"));
2024   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2025   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2026           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2027
2028   QTreePushButton* rButton = new QTreePushButton;
2029   rButton->setItem(item);
2030   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2031   rButton->setToolTip(tr("reload vector field"));
2032   rButton->setEnabled(from_disk);
2033   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2034   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2035           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2036
2037   DataTree->topLevelItem(index)->setExpanded(1);
2038   DataTree->topLevelItem(index)->addChild(item);
2039   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2040   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2041
2042   //set the id of the image
2043   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2044   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2045   UpdateTree();
2046   qApp->processEvents();
2047   ImageInfoChanged();
2048   QApplication::restoreOverrideCursor();
2049 }
2050 //------------------------------------------------------------------------------
2051
2052
2053 //------------------------------------------------------------------------------
2054 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2055 {
2056   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2057   vvSlicerManager* imageManager = mSlicerManagers[index];
2058   if (imageManager->SetVF(vf,file.toStdString())) {
2059     AddFieldEntry(file,index,false);
2060   } else {
2061     QString error = "Cannot import the vector field for this image.\n";
2062     error += imageManager->GetLastError().c_str();
2063     QMessageBox::information(this,tr("Problem reading VF !"),error);
2064   }
2065   QApplication::restoreOverrideCursor();
2066 }
2067 //------------------------------------------------------------------------------
2068
2069
2070 //------------------------------------------------------------------------------
2071 void vvMainWindow::AddField(QString file,int index)
2072 {
2073   if (QFile::exists(file)) {
2074     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2075
2076     //init the progress events
2077     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2078     vvProgressDialog progress("Opening " + file.toStdString());
2079     qApp->processEvents();
2080
2081     //read the vector and put it in the current mSlicerManager
2082     vvSlicerManager* imageManager = mSlicerManagers[index];
2083     qApp->processEvents();
2084
2085     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2086     if (imageManager->SetVF(file.toStdString())) {
2087       imageManager->Render();
2088       AddFieldEntry(file,index,true);
2089     } else {
2090       QApplication::restoreOverrideCursor();
2091       QString error = "Cannot import the vector field for this image.\n";
2092       error += imageManager->GetLastError().c_str();
2093       QMessageBox::information(this,tr("Problem reading VF !"),error);
2094     }
2095   } else
2096     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2097
2098 }
2099 //------------------------------------------------------------------------------
2100
2101
2102 //------------------------------------------------------------------------------
2103 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2104 {
2105   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2106   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2107     for (int i = 0; i < 4; i++) {
2108       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2109       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2110       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2111       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2112       if (log > 0)
2113         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2114       else
2115         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2116     }
2117   }
2118 }
2119 //------------------------------------------------------------------------------
2120
2121
2122 //------------------------------------------------------------------------------
2123 void vvMainWindow::SetOverlayProperty(int color)
2124 {
2125   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2126   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2127     mSlicerManagers[index]->SetOverlayColor(color);
2128     mSlicerManagers[index]->SetColorMap(0);
2129     mSlicerManagers[index]->Render();
2130   }
2131 }
2132 //------------------------------------------------------------------------------
2133
2134 //------------------------------------------------------------------------------
2135 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2136 {
2137   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2138   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2139     mSlicerManagers[index]->SetFusionOpacity(opacity);
2140     mSlicerManagers[index]->SetFusionColorMap(colormap);
2141     mSlicerManagers[index]->SetFusionWindow(window);
2142     mSlicerManagers[index]->SetFusionLevel(level);
2143     mSlicerManagers[index]->SetColorMap(0);
2144     mSlicerManagers[index]->Render();
2145   }
2146 }
2147 //------------------------------------------------------------------------------
2148
2149 //------------------------------------------------------------------------------
2150 void vvMainWindow::SaveAs()
2151 {
2152   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2153     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2154     return;
2155   }
2156
2157   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2158   int dimension = mSlicerManagers[index]->GetDimension();
2159   QStringList OutputListeFormat;
2160   OutputListeFormat.clear();
2161   if (dimension == 1) {
2162     OutputListeFormat.push_back(".mhd");
2163   }
2164   if (dimension == 2) {
2165     OutputListeFormat.push_back(".bmp");
2166     OutputListeFormat.push_back(".png");
2167     OutputListeFormat.push_back(".jpeg");
2168     OutputListeFormat.push_back(".tif");
2169     OutputListeFormat.push_back(".mhd");
2170     OutputListeFormat.push_back(".hdr");
2171     OutputListeFormat.push_back(".vox");
2172   } else if (dimension == 3) {
2173     OutputListeFormat.push_back(".mhd");
2174     OutputListeFormat.push_back(".hdr");
2175     OutputListeFormat.push_back(".vox");
2176   } else if (dimension == 4) {
2177     OutputListeFormat.push_back(".mhd");
2178   }
2179   QString Extensions = "AllFiles(*.*)";
2180   for (int i = 0; i < OutputListeFormat.count(); i++) {
2181     Extensions += ";;Images ( *";
2182     Extensions += OutputListeFormat[i];
2183     Extensions += ")";
2184   }
2185   QString fileName = QFileDialog::getSaveFileName(this,
2186                      tr("Save As"),
2187                      mSlicerManagers[index]->GetFileName().c_str(),
2188                      Extensions);
2189   if (!fileName.isEmpty()) {
2190     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2191     if (OutputListeFormat.contains(
2192           fileformat.c_str())) {
2193       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2194       std::string action = "Saving";
2195       vvProgressDialog progress("Saving "+fileName.toStdString());
2196       qApp->processEvents();
2197       vvImageWriter::Pointer writer = vvImageWriter::New();
2198       writer->SetOutputFileName(fileName.toStdString());
2199       writer->SetInput(mSlicerManagers[index]->GetImage());
2200       writer->Update();
2201       QApplication::restoreOverrideCursor();
2202       if (writer->GetLastError().size()) {
2203         QString error = "Saving did not succeed\n";
2204         error += writer->GetLastError().c_str();
2205         QMessageBox::information(this,tr("Saving Problem"),error);
2206         SaveAs();
2207       }
2208     } else {
2209       QString error = fileformat.c_str();
2210       if (error.isEmpty())
2211         error += "no file format specified !";
2212       else
2213         error += " format unknown !!!\n";
2214       QMessageBox::information(this,tr("Saving Problem"),error);
2215       SaveAs();
2216     }
2217   }
2218 }
2219 //------------------------------------------------------------------------------
2220
2221
2222 //------------------------------------------------------------------------------
2223 void vvMainWindow::AddLink(QString image1,QString image2)
2224 {
2225   unsigned int sm1 = 0;
2226   unsigned int sm2 = 0;
2227
2228   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2229     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2230       mSlicerManagers[i]->AddLink(image2.toStdString());
2231       sm1 = i;
2232     }
2233     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2234       mSlicerManagers[i]->AddLink(image1.toStdString());
2235       sm2 = i;
2236     }
2237   }
2238
2239   if (linkPanel->isLinkAll())   {
2240     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2241     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2242   }
2243   else {
2244     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2245   }
2246 }
2247
2248 //------------------------------------------------------------------------------
2249
2250
2251 //------------------------------------------------------------------------------
2252 void vvMainWindow::RemoveLink(QString image1,QString image2)
2253 {
2254   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2255     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2256       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2257     }
2258     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2259       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2260     }
2261   }
2262 }
2263 //------------------------------------------------------------------------------
2264
2265 //------------------------------------------------------------------------------
2266 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2267 {
2268   int index = 0;
2269   while(sm != mSlicerManagers[index])
2270     index++;
2271   index = (index+offset) % mSlicerManagers.size();
2272
2273   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2274   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2275   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2276   DisplayChanged(item,slicer+1);
2277 }
2278 //------------------------------------------------------------------------------
2279
2280 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2281 {
2282   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2283     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2284       for (int j = 0; j < 4; j++) {
2285         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2286         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2287         //UpdateTSlice(j,value);
2288       }
2289       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2290       break;
2291     }
2292   }
2293 }
2294 //------------------------------------------------------------------------------
2295
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::NOHorizontalSliderMoved()
2299 {
2300   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2301   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2302 //  mCurrentTime = NOHorizontalSlider->value();
2303 }
2304 //------------------------------------------------------------------------------
2305
2306
2307 //------------------------------------------------------------------------------
2308 void vvMainWindow::NEHorizontalSliderMoved()
2309 {
2310   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2311   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2312 //  mCurrentTime = NEHorizontalSlider->value();
2313 }
2314 //------------------------------------------------------------------------------
2315
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::SOHorizontalSliderMoved()
2319 {
2320   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2321   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2322   // mCurrentTime = SOHorizontalSlider->value();
2323 }
2324 //------------------------------------------------------------------------------
2325
2326
2327 //------------------------------------------------------------------------------
2328 void vvMainWindow::SEHorizontalSliderMoved()
2329 {
2330   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2331   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2332   // mCurrentTime = SEHorizontalSlider->value();
2333 }
2334 //------------------------------------------------------------------------------
2335
2336 //------------------------------------------------------------------------------
2337 void vvMainWindow::NOVerticalSliderChanged()
2338 {
2339   static int value=-1;
2340   if (value == NOVerticalSlider->value()) return;
2341   else value = NOVerticalSlider->value();
2342   //  int value = NOVerticalSlider->value();
2343   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2344     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2345       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2346         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2347         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2348
2349         // If nor Update/Render -> slider not work
2350         // only render = ok navigation, but for contour Update needed but slower ?
2351
2352         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2353         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2354       }
2355       break;
2356     }
2357   }
2358 }
2359 //------------------------------------------------------------------------------
2360
2361
2362 //------------------------------------------------------------------------------
2363 void vvMainWindow::NEVerticalSliderChanged()
2364 {
2365   static int value=-1;
2366   if (value == NEVerticalSlider->value()) return;
2367   else value = NEVerticalSlider->value();
2368   //  int value = NEVerticalSlider->value();
2369   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2370     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2371       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2372         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2373         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2374         mSlicerManagers[i]->UpdateSlice(1);
2375         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2376       }
2377       break;
2378     }
2379   }
2380 }
2381 //------------------------------------------------------------------------------
2382
2383
2384 //------------------------------------------------------------------------------
2385 void vvMainWindow::SOVerticalSliderChanged()
2386 {
2387   static int value=-1;
2388   if (value == SOVerticalSlider->value()) return;
2389   else value = SOVerticalSlider->value();
2390   //int value = SOVerticalSlider->value();
2391   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2392     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2393       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2394         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2395         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2396         mSlicerManagers[i]->UpdateSlice(2);
2397         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2398       }
2399       // else { DD("avoid SOVerticalSlider slicer update"); }
2400       break;
2401     }
2402   }
2403 }
2404 //------------------------------------------------------------------------------
2405
2406
2407 //------------------------------------------------------------------------------
2408 void vvMainWindow::SEVerticalSliderChanged()
2409 {
2410   static int value=-1;
2411   if (value == SEVerticalSlider->value()) return;
2412   else value = SEVerticalSlider->value();
2413   // int value = SEVerticalSlider->value();
2414   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2415     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2416       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2417         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2418         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2419         mSlicerManagers[i]->UpdateSlice(3);
2420         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2421       }
2422       break;
2423     }
2424   }
2425 }
2426 //------------------------------------------------------------------------------
2427
2428
2429 //------------------------------------------------------------------------------
2430 void vvMainWindow::UpdateSlice(int slicer, int slice)
2431 {
2432   // DD("vvMainWindow::UpdateSlice");
2433 //   DD(slicer);
2434 //   DD(slice);
2435   if (slicer == 0) {
2436     //    if (slice != NOVerticalSlider->value())
2437     NOVerticalSlider->setValue(slice);
2438   } else {
2439     if (slicer == 1)
2440       NEVerticalSlider->setValue(slice);
2441     else {
2442       if (slicer == 2)
2443         SOVerticalSlider->setValue(slice);
2444       else {
2445         if (slicer == 3)
2446           SEVerticalSlider->setValue(slice);
2447       }
2448     }
2449   }
2450   // DD("vvMainWindow:UpdateSlice END");
2451 }
2452 //------------------------------------------------------------------------------
2453
2454
2455 //------------------------------------------------------------------------------
2456 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2457 {
2458   switch (slicer) {
2459   case 0:
2460     NOHorizontalSlider->setValue(slice);
2461     break;
2462   case 1:
2463     NEHorizontalSlider->setValue(slice);
2464     break;
2465   case 2:
2466     SOHorizontalSlider->setValue(slice);
2467     break;
2468   case 3:
2469     SEHorizontalSlider->setValue(slice);
2470     break;
2471   }
2472 }
2473 //------------------------------------------------------------------------------
2474
2475
2476 //------------------------------------------------------------------------------
2477 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2478 {
2479   int position = int((min+max)/2);
2480   int tPosition = int((tmin+tmax)/2);
2481   if (slicer == 0) {
2482     NOVerticalSlider->setValue(position);
2483     NOVerticalSlider->setRange(min,max);
2484     NOHorizontalSlider->setRange(tmin,tmax);
2485     NOHorizontalSlider->setValue(tPosition);
2486   } else if (slicer == 1) {
2487     NEVerticalSlider->setValue(position);
2488     NEVerticalSlider->setRange(min,max);
2489     NEHorizontalSlider->setRange(tmin,tmax);
2490     NEHorizontalSlider->setValue(tPosition);
2491   } else if (slicer == 2) {
2492     SOVerticalSlider->setValue(position);
2493     SOVerticalSlider->setRange(min,max);
2494     SOHorizontalSlider->setRange(tmin,tmax);
2495     SOHorizontalSlider->setValue(tPosition);
2496   } else if (slicer == 3) {
2497     SEVerticalSlider->setValue(position);
2498     SEVerticalSlider->setRange(min,max);
2499     SEHorizontalSlider->setRange(tmin,tmax);
2500     SEHorizontalSlider->setValue(tPosition);
2501   }
2502 }
2503 //------------------------------------------------------------------------------
2504
2505
2506 //------------------------------------------------------------------------------
2507 void vvMainWindow::SaveNOScreenshot()
2508 {
2509   SaveScreenshot(NOViewWidget);
2510 }
2511 //------------------------------------------------------------------------------
2512
2513
2514 //------------------------------------------------------------------------------
2515 void vvMainWindow::SaveNEScreenshot()
2516 {
2517   SaveScreenshot(NEViewWidget);
2518 }
2519 //------------------------------------------------------------------------------
2520
2521
2522 //------------------------------------------------------------------------------
2523 void vvMainWindow::SaveSOScreenshot()
2524 {
2525   SaveScreenshot(SOViewWidget);
2526 }
2527 //------------------------------------------------------------------------------
2528
2529
2530 //------------------------------------------------------------------------------
2531 void vvMainWindow::SaveSEScreenshot()
2532 {
2533   SaveScreenshot(SEViewWidget);
2534 }
2535 //------------------------------------------------------------------------------
2536
2537
2538 //------------------------------------------------------------------------------
2539 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2540 {
2541   QString Extensions = "Images( *.png);;";
2542   Extensions += "Images( *.jpg);;";
2543   Extensions += "Images( *.bmp);;";
2544   Extensions += "Images( *.tif);;";
2545   Extensions += "Images( *.ppm)";
2546 #ifdef VTK_USE_MPEG2_ENCODER
2547   Extensions += "Images( *.mpg)";
2548 #endif
2549
2550   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2551   QString fileName = QFileDialog::getSaveFileName(this,
2552                      tr("Save As"),
2553                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2554                      Extensions);
2555
2556   if (!fileName.isEmpty()) {
2557     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2558     w2i->SetInput(widget->GetRenderWindow());
2559     w2i->Update();
2560     vtkImageData *image = w2i->GetOutput();
2561
2562     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2563     if (!strcmp(ext, ".bmp")) {
2564       vtkBMPWriter *bmp = vtkBMPWriter::New();
2565       bmp->SetInput(image);
2566       bmp->SetFileName(fileName.toStdString().c_str());
2567       bmp->Write();
2568       bmp->Delete();
2569     } else if (!strcmp(ext, ".tif")) {
2570       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2571       tif->SetInput(image);
2572       tif->SetFileName(fileName.toStdString().c_str());
2573       tif->Write();
2574       tif->Delete();
2575     } else if (!strcmp(ext, ".ppm")) {
2576       vtkPNMWriter *pnm = vtkPNMWriter::New();
2577       pnm->SetInput(image);
2578       pnm->SetFileName(fileName.toStdString().c_str());
2579       pnm->Write();
2580       pnm->Delete();
2581     } else if (!strcmp(ext, ".png")) {
2582       vtkPNGWriter *png = vtkPNGWriter::New();
2583       png->SetInput(image);
2584       png->SetFileName(fileName.toStdString().c_str());
2585       png->Write();
2586       png->Delete();
2587     } else if (!strcmp(ext, ".jpg")) {
2588       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2589       jpg->SetInput(image);
2590       jpg->SetFileName(fileName.toStdString().c_str());
2591       jpg->Write();
2592       jpg->Delete();
2593 #ifdef VTK_USE_MPEG2_ENCODER
2594     } else if (!strcmp(ext, ".mpg")) {
2595       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2596       mpg->SetInput(image);
2597       mpg->SetFileName(fileName.toStdString().c_str());
2598       mpg->Start();
2599
2600       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2601       int nSlice = vvImg->GetVTKImages().size();
2602       for(int i=0; i<nSlice; i++)
2603       {
2604         mSlicerManagers[smIndex]->SetNextTSlice(0);
2605         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2606         w2i->SetInput(widget->GetRenderWindow());
2607         w2i->Update();
2608         mpg->SetInput(w2i->GetOutput());
2609         mpg->Write();
2610       }
2611       mpg->End();
2612       mpg->Delete();
2613 #endif
2614     } else {
2615       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2616     }
2617   }
2618 }
2619 //------------------------------------------------------------------------------
2620
2621
2622 //------------------------------------------------------------------------------
2623 void vvMainWindow::GoToCursor()
2624 {
2625   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2626   for (int column = 1; column < 5; column++) {
2627     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2628       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2629       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2630         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2631       mSlicerManagers[index]->UpdateViews(1,column-1);
2632       mSlicerManagers[index]->UpdateLinked(column-1);
2633       break;
2634     }
2635   }
2636 }
2637 //------------------------------------------------------------------------------
2638
2639 //------------------------------------------------------------------------------
2640 void vvMainWindow::PlayPause()
2641 {
2642   if (playMode) {
2643     playMode = 0;
2644     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2645     ImageInfoChanged();
2646     return;
2647   } else {
2648     int image_number=DataTree->topLevelItemCount();
2649     bool has_temporal;
2650     for (int i=0; i<image_number; i++)
2651       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2652         has_temporal=true;
2653         break;
2654       }
2655     if (has_temporal) {
2656       playMode = 1;
2657       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2658       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2659     }
2660   }
2661 }
2662 //------------------------------------------------------------------------------
2663
2664 //------------------------------------------------------------------------------
2665 void vvMainWindow::PlayNext()
2666 {
2667   if (playMode && !this->isHidden()) {
2668     int image_number=DataTree->topLevelItemCount();
2669     ///Only play one slicer per SM, and only if the SM is being displayed
2670     for (int i=0; i<image_number; i++)
2671       for (int j=0; j<4; j++)
2672         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2673             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2674           mSlicerManagers[i]->SetNextTSlice(j);
2675           break;
2676         }
2677     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2678   }
2679 }
2680 //------------------------------------------------------------------------------
2681
2682 void vvMainWindow::ShowLastImage()
2683 {
2684   if (mSlicerManagers.size() > 1) {
2685     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2686     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2687     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2688     DisplayChanged(item,1);
2689   }
2690 }
2691
2692 //------------------------------------------------------------------------------
2693 void vvMainWindow::UpdateRenderWindows()
2694 {
2695   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2696   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2697   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2698   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2699 }
2700 //------------------------------------------------------------------------------
2701
2702 //------------------------------------------------------------------------------
2703 void vvMainWindow::SegmentationOnCurrentImage()
2704 {
2705   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2706
2707   vvSegmentationDialog segmentation;
2708   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2709   segmentation.exec();
2710 }
2711 //------------------------------------------------------------------------------
2712
2713 void vvMainWindow::SurfaceViewerLaunch()
2714 {
2715   vvSurfaceViewerDialog surfaceViewer;
2716   surfaceViewer.exec();
2717 }
2718 //------------------------------------------------------------------------------
2719
2720
2721 //------------------------------------------------------------------------------
2722 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2723 {
2724   int number=0;
2725   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2726     vvSlicerManager * v = mSlicerManagers[l];
2727     if (v->GetBaseFileName() ==
2728         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2729       number = std::max(number, v->GetBaseFileNameNumber()+1);
2730     }
2731   }
2732   return number;
2733 }
2734 //------------------------------------------------------------------------------
2735
2736
2737 //------------------------------------------------------------------------------
2738 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2739 {
2740   // Change filename if another image exist with the same name
2741   int number = GetImageDuplicateFilenameNumber(filename);
2742
2743   // Create new SliceManager
2744   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2745   slicer_manager->SetImage(image);//, IMAGE, number);
2746   //  filename = filename+"_"+clitk::toString(number);
2747   slicer_manager->SetFilename(filename, number);
2748   mSlicerManagers.push_back(slicer_manager);
2749
2750   //create an item in the tree with good settings
2751   QTreeWidgetItem *item = new QTreeWidgetItem();
2752   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2753   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2754   qApp->processEvents();
2755
2756   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2757
2758   //Create the buttons for reload and close
2759   qApp->processEvents();
2760   QTreePushButton* cButton = new QTreePushButton;
2761   cButton->setItem(item);
2762   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2763   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2764   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2765           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2766
2767   QTreePushButton* rButton = new QTreePushButton;
2768   rButton->setItem(item);
2769   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2770   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2771   rButton->setEnabled(0);
2772   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2773           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2774
2775   DataTree->addTopLevelItem(item);
2776   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2777   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2778
2779   //set the id of the image
2780   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2781   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2782   mSlicerManagers.back()->SetId(id.toStdString());
2783
2784   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2785                       , id.toStdString());
2786
2787   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2788           this, SLOT(CurrentImageChanged(std::string)));
2789   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2790           this, SLOT(CurrentPickedImageChanged(std::string)));
2791   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2792           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2793   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2794           this, SLOT(VectorChanged(int,double,double,double, double)));
2795   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2796           this, SLOT(OverlayChanged(int,double,double)));
2797   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2798           this, SLOT(FusionChanged(int,double)));
2799   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2800           this,SLOT(WindowsChanged(int, int, int)));
2801   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2802           this,SLOT(WindowLevelChanged(double, double, int, int)));
2803   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2804           this,SLOT(UpdateSlice(int,int)));
2805   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2806           this,SLOT(UpdateTSlice(int, int)));
2807   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2808           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2809   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2810           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2811   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2812           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2813   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2814           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2815   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2816   UpdateTree();
2817   qApp->processEvents();
2818   InitSlicers();
2819   ShowLastImage();
2820   InitDisplay();
2821   qApp->processEvents();
2822
2823   // End
2824   ImageInfoChanged();
2825   return slicer_manager;
2826 }
2827 //------------------------------------------------------------------------------
2828
2829
2830 //------------------------------------------------------------------------------
2831 void vvMainWindow::UpdateCurrentSlicer()
2832 {
2833   int index = -1;
2834   if (DataTree->selectedItems().size() > 0) {
2835     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2836   }
2837   mSlicerManagerCurrentIndex = index;
2838 }
2839 //------------------------------------------------------------------------------
2840