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 <vtkFFMPEGWriter.h>
  70 #include <vtkMPEG2Writer.h>
  71 #include <vtkMatrix4x4.h>
  72 #include <vtkTransform.h>
  73
  74 // Standard includes
  75 #include <iostream>
  76 #include <sstream>
  77 #include <iomanip>
  78
  79 #define COLUMN_TREE 0
  80 #define COLUMN_UL_VIEW 1
  81 #define COLUMN_UR_VIEW 2
  82 #define COLUMN_DL_VIEW 3
  83 #define COLUMN_DR_VIEW 4
  84 #define COLUMN_CLOSE_IMAGE 5
  85 #define COLUMN_RELOAD_IMAGE 6
  86 #define COLUMN_IMAGE_NAME 7
  87
  88 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr *.SCAN )"
  89
  90 /*Data Tree values
  91   0,Qt::UserRole full filename
  92   1,Qt::CheckStateRole checkbutton UL View
  93   1,Qt::UserRole overlay, fusion or vector
  94   2,Qt::CheckStateRole checkbutton UR View
  95   3,Qt::CheckStateRole checkbutton DL View
  96   4,Qt::CheckStateRole checkbutton DR View
  97   5,0  short filename
  98   5,Qt::UserRole mSlicerManager id*/
  99
 100 //------------------------------------------------------------------------------
 101 vvMainWindow::vvMainWindow():vvMainWindowBase()
 102 {
 103   setupUi(this); // this sets up the GUI
 104
 105   mInputPathName = "";
 106   mMenuTools = menuTools;
 107   //  mMenuSegmentation = menuSegmentation;
 108   mContextMenu = &contextMenu;
 109   mMenuExperimentalTools = menuExperimental;
 110   mMainWidget = this;
 111   mCurrentTime = -1;
 112   mCurrentSelectedImageId = "";
 113   mCurrentPickedImageId = "";
 114   mCurrentPickedImageIndex = 0;
 115
 116   //Init the contextMenu
 117   this->setContextMenuPolicy(Qt::CustomContextMenu);
 118   contextActions.resize(0);
 119   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 120                                   tr("O&pen new Image"));
 121   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 122   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 123   contextActions.push_back(actionOpen_new_image);
 124   contextMenu.addSeparator();
 125
 126   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 127                                tr("Close Current Image"));
 128   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 129   contextActions.push_back(actionClose_Image);
 130
 131   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 132                                 tr("Reload Current Image"));
 133   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 134   contextActions.push_back(actionReload_image);
 135
 136   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 137                               tr("Save Current Image"));
 138   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 139   contextActions.push_back(actionSave_image);
 140
 141   contextMenu.addSeparator();
 142
 143   contextMenu.addAction(actionAdd_VF_to_current_Image);
 144   contextActions.push_back(actionAdd_VF_to_current_Image);
 145
 146   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 147       tr("Add overlay image to current image"));
 148   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 149   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 150
 151   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 152
 153   contextMenu.addAction(actionAdd_fusion_image);
 154   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 155   contextActions.push_back(actionAdd_fusion_image);
 156
 157   // TRIAL DS
 158   /*
 159   QMenu * m = new QMenu(menubar);
 160   m->setTitle("TOTO");
 161   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 162   contextMenu.addMenu(m);
 163   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 164                      tr("BIDON"));
 165   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 166                      tr("BIDON2"));
 167   m->addAction(a);
 168   m->addAction(b);
 169   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 170   */
 171
 172   //init the DataTree
 173   mSlicerManagers.resize(0);
 174
 175   QStringList header;
 176   header.append("");
 177   header.append("TL");
 178   header.append("TR");
 179   header.append("BL");
 180   header.append("BR");
 181   header.append("");
 182   header.append("");
 183   header.append("Name");
 184
 185   DataTree->setHeaderLabels(header);
 186   DataTree->resizeColumnToContents(COLUMN_TREE);
 187   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 188   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 189   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 190   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 191   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 192   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 193   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 194
 195   viewMode = 1;
 196   documentation = new vvDocumentation();
 197   help_dialog = new vvHelpDialog();
 198   dicomSeriesSelector = new vvDicomSeriesSelector();
 199
 200   inverseButton->setEnabled(0);
 201   actionAdd_Overlay_to_current_Image->setEnabled(0);
 202   actionSave_As->setEnabled(0);
 203   actionAdd_VF_to_current_Image->setEnabled(0);
 204   actionAdd_fusion_image->setEnabled(0);
 205
 206   //init the sliders
 207   verticalSliders.push_back(NOVerticalSlider);
 208   verticalSliders.push_back(NEVerticalSlider);
 209   verticalSliders.push_back(SOVerticalSlider);
 210   verticalSliders.push_back(SEVerticalSlider);
 211
 212   for (int i =0; i < 4; i++)
 213     verticalSliders[i]->hide();
 214
 215   horizontalSliders.push_back(NOHorizontalSlider);
 216   horizontalSliders.push_back(NEHorizontalSlider);
 217   horizontalSliders.push_back(SOHorizontalSlider);
 218   horizontalSliders.push_back(SEHorizontalSlider);
 219
 220   for (int i =0; i < 4; i++)
 221     horizontalSliders[i]->hide();
 222
 223
 224   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 225   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 226   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 227   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 228
 229   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 230   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 231   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 232   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 233
 234   //connect everything
 235   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 236   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 237   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 238   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 239   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 240   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 241   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 242   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 243   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 244   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 245   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 246   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 247   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 248   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 249   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 250   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 251
 252   ///////////////////////////////////////////////
 253   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 254   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 255   ///////////////////////////////////////////////
 256
 257   actionNorth_East_Window->setEnabled(0);
 258   actionNorth_West_Window->setEnabled(0);
 259   actionSouth_East_Window->setEnabled(0);
 260   actionSouth_West_Window->setEnabled(0);
 261
 262   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 263   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 264   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 265   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 266
 267   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 268   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 269           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 270
 271   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 272   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 273   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 274   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 275   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 276   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 277   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 278
 279
 280   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 281
 282   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 283   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 284   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 285   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 286   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 287           this,SLOT(SetFusionProperty(int,int,double,double)));
 288   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 289
 290   playMode = 0;//pause
 291   mFrameRate = 10;
 292   playButton->setEnabled(0);
 293   frameRateLabel->setEnabled(0);
 294   frameRateSpinBox->setEnabled(0);
 295   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 296   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 297
 298   goToCursorPushButton->setEnabled(0);
 299   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 300
 301   NOViewWidget->hide();
 302   NEViewWidget->hide();
 303   SOViewWidget->hide();
 304   SEViewWidget->hide();
 305
 306   //Recently opened files
 307   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 308   if ( !recent_files.empty() ) {
 309     QMenu * rmenu = new QMenu("Recently opened files...");
 310     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 311     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 312     menuFile->insertSeparator(actionOpen_Image_With_Time);
 313     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 314       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 315                                    (*i).c_str(),this);
 316       rmenu->addAction(current);
 317       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 318     }
 319   }
 320
 321   // Adding all new tools (insertion in the menu)
 322   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 323
 324   if (!CLITK_EXPERIMENTAL)
 325     menuExperimental->menuAction()->setVisible(false);
 326
 327
 328   QTimer * timerMemory = new QTimer(this);
 329   //timerMemory->setInterval(5);
 330   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 331   timerMemory->start(2000);
 332
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::UpdateMemoryUsage()
 339 {
 340   //  clitk::PrintMemory(true);
 341   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 342   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 343 }
 344 //------------------------------------------------------------------------------
 345
 346
 347 //------------------------------------------------------------------------------
 348 void vvMainWindow::ComputeMidPosition()
 349 {
 350   bool ok;
 351   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 352   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 353                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 354   if (ok) {
 355     vvMidPosition midp;
 356     midp.slicer_manager = mSlicerManagers[index];
 357     midp.reference_image_index = ref;
 358     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 359     midp.Update();
 360     if (midp.error)
 361       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 362     else {
 363       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 364       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 365     }
 366     QApplication::restoreOverrideCursor();
 367   }
 368 }
 369 //------------------------------------------------------------------------------
 370
 371
 372 //------------------------------------------------------------------------------
 373 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 374 {
 375   QTreeWidgetItem *item = new QTreeWidgetItem();
 376   item->setData(0,Qt::UserRole,"filename.vtk");
 377   item->setData(1,Qt::UserRole,tr("contour"));
 378   QBrush brush;
 379   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 380   brush.setStyle(Qt::SolidPattern);
 381   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 382   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 383
 384   for (int j = 1; j <= 4; j++)
 385     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 386
 387   QTreePushButton* cButton = new QTreePushButton;
 388   cButton->setItem(item);
 389   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 390   cButton->setToolTip(tr("close image"));
 391   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 392   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 393           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 394
 395   QTreePushButton* rButton = new QTreePushButton;
 396   rButton->setItem(item);
 397   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 398   rButton->setToolTip(tr("reload image"));
 399   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 400   rButton->setEnabled(false);
 401   //Not implemented
 402   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 403   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 404
 405   DataTree->topLevelItem(image_index)->setExpanded(1);
 406   DataTree->topLevelItem(image_index)->addChild(item);
 407   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 408   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 409   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 410   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 411
 412   UpdateTree();
 413   mSlicerManagers[image_index]->AddContour(contour,propagation);
 414   mSlicerManagers[image_index]->Render();
 415 }
 416 //------------------------------------------------------------------------------
 417
 418
 419 //------------------------------------------------------------------------------
 420 void vvMainWindow::OpenVTKContour()
 421 {
 422   if (mSlicerManagers.size() > 0) {
 423     QString Extensions = "Images ( *.vtk *.obj)";
 424     Extensions += ";;All Files (*)";
 425     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 426     if (file.isNull())
 427       return;
 428     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 429     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 430     vvMeshReader reader;
 431     reader.SetImage(mSlicerManagers[index]->GetImage());
 432     reader.SetModeToVTK();
 433     reader.SetFilename(file.toStdString());
 434     reader.Update();
 435     AddContour(index,reader.GetOutput()[0],false);
 436     QApplication::restoreOverrideCursor();
 437   }
 438 }
 439 //------------------------------------------------------------------------------
 440
 441
 442 //------------------------------------------------------------------------------
 443 void vvMainWindow::OpenDCStructContour()
 444 {
 445   if (mSlicerManagers.size() > 0) {
 446     QString Extensions = "Dicom Files ( *.dcm RS*)";
 447     Extensions += ";;All Files (*)";
 448     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 449     if (file.isNull())
 450       return;
 451     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 452     vvMeshReader reader;
 453     reader.SetFilename(file.toStdString());
 454     vvStructSelector selector;
 455     selector.SetStructures(reader.GetROINames());
 456     if (!mSlicerManagers[index]->GetVF().IsNull())
 457       selector.EnablePropagationCheckBox();
 458     if (selector.exec()) {
 459       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 460       reader.SetSelectedItems(selector.getSelectedItems());
 461       reader.SetImage(mSlicerManagers[index]->GetImage());
 462       if (selector.PropagationEnabled())
 463         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 464       reader.Update();
 465       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 466       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 467            i!=contours.end(); i++)
 468         AddContour(index,*i,selector.PropagationEnabled());
 469       QApplication::restoreOverrideCursor();
 470     }
 471   }
 472 }
 473 //------------------------------------------------------------------------------
 474
 475
 476 //------------------------------------------------------------------------------
 477 void vvMainWindow::ComputeDeformableRegistration()
 478 {
 479   if (mSlicerManagers.size() > 0) {
 480     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 481     vvDeformationDialog dialog(index,mSlicerManagers);
 482     if (dialog.exec()) {
 483       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 484       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 485       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 486     } else
 487       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 488   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 489 }
 490 //------------------------------------------------------------------------------
 491
 492
 493 //------------------------------------------------------------------------------
 494 void vvMainWindow::WarpImage()
 495 {
 496   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 497   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 498     bool ok;
 499     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 500                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 501     if (ok) {
 502       WarpImage(mSlicerManagers[index],ref);
 503     }
 504   } else
 505     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 506 }
 507 //------------------------------------------------------------------------------
 508
 509
 510 //------------------------------------------------------------------------------
 511 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 512 {
 513   if (!selected_slicer->GetVF().IsNull()) {
 514     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 515     QFileInfo info(selected_slicer->GetFileName().c_str());
 516     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 517                      reference_phase,this);
 518     if (warp.ComputeWarpedImage()) {
 519       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 520       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 521       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 522       QApplication::restoreOverrideCursor();
 523     } else {
 524       QApplication::restoreOverrideCursor();
 525       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 526     }
 527   } else
 528     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 529 }
 530 //------------------------------------------------------------------------------
 531
 532
 533 //------------------------------------------------------------------------------
 534 vvMainWindow::~vvMainWindow()
 535 {
 536   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 537     if (mSlicerManagers[i] != NULL)
 538       delete mSlicerManagers[i];
 539   }
 540 }
 541 //------------------------------------------------------------------------------
 542
 543 //------------------------------------------------------------------------------
 544 QTabWidget * vvMainWindow::GetTab()
 545 {
 546   return tabWidget;
 547 }
 548 //------------------------------------------------------------------------------
 549
 550
 551 //------------------------------------------------------------------------------
 552 void vvMainWindow::MergeImages()
 553 {
 554   QString Extensions = EXTENSIONS;
 555   Extensions += ";;All Files (*)";
 556   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 557   if (files.isEmpty())
 558     return;
 559   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 560   std::vector<std::string> vector;
 561
 562   unsigned int currentDim = 0;
 563   std::vector<double> currentSpacing;
 564   std::vector<int> currentSize;
 565   std::vector<double> currentOrigin;
 566
 567   for (int i = 0; i < files.size(); i++) {
 568     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 569                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 570     reader->SetFileName(files[i].toStdString().c_str());
 571     reader->ReadImageInformation();
 572     if (reader)        {
 573       //NOViewWidget->hide();
 574       //NEViewWidget->hide();
 575       //SOViewWidget->hide();
 576       //SEViewWidget->hide();
 577       if (i == 0)
 578         currentDim = reader->GetNumberOfDimensions();
 579       bool IsOk = true;
 580       for (unsigned int j = 0; j < currentDim; j++) {
 581         if (i == 0) {
 582           if (j == 0) {
 583             currentSpacing.resize(currentDim);
 584             currentSize.resize(currentDim);
 585             currentOrigin.resize(currentDim);
 586           }
 587           currentOrigin[j] = reader->GetOrigin(j);
 588           currentSpacing[j] = reader->GetSpacing(j);
 589           currentSize[j] = reader->GetDimensions(j);
 590         } else if (currentDim != reader->GetNumberOfDimensions()
 591                    || currentSpacing[j] != reader->GetSpacing(j)
 592                    || currentSize[j] != (int)reader->GetDimensions(j)
 593                    || currentOrigin[j] != reader->GetOrigin(j)) {
 594           QString error = "Cannot read file (too different from others ";
 595           error += files[i].toStdString().c_str();
 596           QMessageBox::information(this,tr("Reading problem"),error);
 597           IsOk = false;
 598           break;
 599         }
 600       }
 601       if (IsOk)
 602         vector.push_back(files[i].toStdString());
 603     }
 604   }
 605   if (vector.size() > 0)
 606     LoadImages(vector, MERGED);
 607 }
 608 //------------------------------------------------------------------------------
 609
 610 //------------------------------------------------------------------------------
 611 void vvMainWindow::SliceImages()
 612 {
 613   QString Extensions = EXTENSIONS;
 614   Extensions += ";;All Files (*)";
 615
 616   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 617   if (files.isEmpty())
 618     return;
 619   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 620   std::vector<std::string> vector;
 621   for (int i = 0; i < files.size(); i++)
 622     vector.push_back(files[i].toStdString());
 623   LoadImages(vector, SLICED);
 624 }
 625 //------------------------------------------------------------------------------
 626
 627 //------------------------------------------------------------------------------
 628 void vvMainWindow::MergeImagesWithTime()
 629 {
 630   QString Extensions = EXTENSIONS;
 631   Extensions += ";;All Files (*)";
 632   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 633   if (files.isEmpty())
 634     return;
 635   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 636   std::vector<std::string> vector;
 637
 638   unsigned int currentDim = 0;
 639   std::vector<double> currentSpacing;
 640   std::vector<int> currentSize;
 641   std::vector<double> currentOrigin;
 642
 643   for (int i = 0; i < files.size(); i++) {
 644     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 645                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 646     if (reader) {
 647       reader->SetFileName(files[i].toStdString().c_str());
 648       reader->ReadImageInformation();
 649       if (i == 0)
 650         currentDim = reader->GetNumberOfDimensions();
 651       bool IsOk = true;
 652       for (unsigned int j = 0; j < currentDim; j++) {
 653         if (i == 0) {
 654           if (j == 0) {
 655             currentSpacing.resize(currentDim);
 656             currentSize.resize(currentDim);
 657             currentOrigin.resize(currentDim);
 658           }
 659           currentOrigin[j] = reader->GetOrigin(j);
 660           currentSpacing[j] = reader->GetSpacing(j);
 661           currentSize[j] = reader->GetDimensions(j);
 662         } else if (currentDim != reader->GetNumberOfDimensions()
 663                    || currentSpacing[j] != reader->GetSpacing(j)
 664                    || currentSize[j] != (int)reader->GetDimensions(j)
 665                    || currentOrigin[j] != reader->GetOrigin(j)) {
 666           QString error = "Cannot read file (too different from others ";
 667           error += files[i].toStdString().c_str();
 668           QMessageBox::information(this,tr("Reading problem"),error);
 669           IsOk = false;
 670           break;
 671         }
 672       }
 673       if (IsOk)
 674         vector.push_back(files[i].toStdString());
 675     } else {
 676       QString error = "Cannot read file info for ";
 677       error += files[i].toStdString().c_str();
 678       error += "\n";
 679       error += "Maybe you're trying to open an image in an unsupported format?\n";
 680       QMessageBox::information(this,tr("Reading problem"),error);
 681     }
 682   }
 683   sort(vector.begin(),vector.end());
 684   if (vector.size() > 1)
 685     LoadImages(vector, MERGEDWITHTIME);
 686   else
 687     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.");
 688 }
 689 //------------------------------------------------------------------------------
 690
 691
 692 //------------------------------------------------------------------------------
 693 void vvMainWindow::OpenDicom()
 694 {
 695   std::vector<std::string> files;
 696
 697   std::cout << "dicomSeriesSelector " << std::endl;
 698   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 699     files = *(dicomSeriesSelector->GetFilenames());
 700     LoadImages(files,DICOM);
 701   }
 702 }
 703 //------------------------------------------------------------------------------
 704
 705 //------------------------------------------------------------------------------
 706 void vvMainWindow::OpenImages()
 707 {
 708   QString Extensions = EXTENSIONS;
 709   Extensions += ";;All Files (*)";
 710
 711   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 712   if (files.isEmpty())
 713     return;
 714   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 715   std::vector<std::string> vector;
 716   for (int i = 0; i < files.size(); i++)
 717     vector.push_back(files[i].toStdString());
 718   LoadImages(vector, IMAGE);
 719 }
 720 //------------------------------------------------------------------------------
 721 void vvMainWindow::OpenRecentImage()
 722 {
 723   QAction * caller = qobject_cast<QAction*>(sender());
 724   std::vector<std::string> images;
 725   images.push_back(caller->text().toStdString());
 726   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 727   LoadImages(images,IMAGE);
 728 }
 729 //------------------------------------------------------------------------------
 730
 731
 732 //------------------------------------------------------------------------------
 733 void vvMainWindow::OpenImageWithTime()
 734 {
 735   QString Extensions = EXTENSIONS;
 736   Extensions += ";;All Files (*)";
 737
 738   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 739   if (files.isEmpty())
 740     return;
 741   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 742   std::vector<std::string> vector;
 743   for (int i = 0; i < files.size(); i++) {
 744     vector.push_back(files[i].toStdString());
 745   }
 746   LoadImages(vector, IMAGEWITHTIME);
 747 }
 748 //------------------------------------------------------------------------------
 749
 750
 751 //------------------------------------------------------------------------------
 752 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 753 {
 754   //Separate the way to open images and dicoms
 755   int fileSize;
 756   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 757     fileSize = files.size();
 758   else
 759     fileSize = 1;
 760
 761   // For SLICED, we need the number of slices (ndim and #slices)
 762   std::vector<unsigned int> nSlices;
 763   nSlices.resize(files.size());
 764   std::fill(nSlices.begin(), nSlices.end(), 1);
 765   if (filetype == SLICED) {
 766     for (int i = 0; i < fileSize; i++) {
 767       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 768       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 769       if (!header) {
 770         nSlices[i] = 0;
 771         QString error = "Cannot open file \n";
 772         error += files[i].c_str();
 773         QMessageBox::information(this,tr("Reading problem"),error);
 774         return;
 775       }
 776       if (header->GetNumberOfDimensions() < 3) {
 777         nSlices[i] = 0;
 778         QString error = "Dimension problem. Cannot slice \n";
 779         error += files[i].c_str();
 780         QMessageBox::information(this,tr("Reading problem"),error);
 781         return;
 782       }
 783       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 784     }
 785   }
 786
 787   //Only add to the list of recently opened files when a single file is opened,
 788   //to avoid polluting the list of recently opened files
 789   if (files.size() == 1) {
 790     QFileInfo finfo=tr(files[0].c_str());
 791     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 792   }
 793   //init the progress events
 794   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 795   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 796   qApp->processEvents();
 797
 798   int numberofsuccesulreads=0;
 799   //open images as 1 or multiples
 800   for (int i = 0; i < fileSize; i++) {
 801
 802     progress.SetText("Opening " + files[i]);
 803     progress.SetProgress(i,fileSize);
 804     qApp->processEvents();
 805
 806     for (unsigned int j = 0; j < nSlices[i]; j++) {
 807       //read the image and put it in mSlicerManagers
 808       vvSlicerManager* imageManager = new vvSlicerManager(4);
 809       qApp->processEvents();
 810
 811       bool SetImageSucceed=false;
 812
 813       // Change filename if an image with the same already exist
 814       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 815
 816       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 817         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 818       else {
 819         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 820       }
 821       if (!SetImageSucceed) {
 822         QApplication::restoreOverrideCursor();
 823         QString error = "Cannot open file \n";
 824         error += imageManager->GetLastError().c_str();
 825         QMessageBox::information(this,tr("Reading problem"),error);
 826         delete imageManager;
 827       } else {
 828         mSlicerManagers.push_back(imageManager);
 829
 830         //create an item in the tree with good settings
 831         QTreeWidgetItem *item = new QTreeWidgetItem();
 832         item->setData(0,Qt::UserRole,files[i].c_str());
 833         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 834         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 835         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 836         qApp->processEvents();
 837
 838         //Create the buttons for reload and close
 839         qApp->processEvents();
 840         QTreePushButton* cButton = new QTreePushButton;
 841         cButton->setItem(item);
 842         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 843         cButton->setToolTip(tr("close image"));
 844         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 845         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 846                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 847
 848         QTreePushButton* rButton = new QTreePushButton;
 849         rButton->setItem(item);
 850         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 851         rButton->setToolTip(tr("reload image"));
 852         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 853         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 854                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 855
 856         DataTree->addTopLevelItem(item);
 857         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 858         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 859
 860         //set the id of the image
 861         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 862         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 863         mSlicerManagers.back()->SetId(id.toStdString());
 864
 865         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 866
 867         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 868                 this,SLOT(CurrentImageChanged(std::string)));
 869         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 870                 this, SLOT(CurrentPickedImageChanged(std::string)));
 871         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 872                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 873         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 874                 this, SLOT(VectorChanged(int,double,double,double, double)));
 875         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 876                 this, SLOT(OverlayChanged(int,double,double)));
 877         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 878                 this, SLOT(FusionChanged(int,double)));
 879         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 880                 this,SLOT(WindowsChanged(int, int, int)));
 881         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 882                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 883         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 884                 this,SLOT(UpdateSlice(int,int)));
 885         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 886                 this,SLOT(UpdateTSlice(int, int)));
 887         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 888                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 889         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 890                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 891         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 892                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 893         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 894                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 895         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 896         InitSlicers();
 897         numberofsuccesulreads++;
 898       }
 899     }
 900   }
 901   if (numberofsuccesulreads) {
 902     NOViewWidget->show();
 903     NEViewWidget->show();
 904     SOViewWidget->show();
 905     SEViewWidget->show();
 906     UpdateTree();
 907     InitDisplay();
 908     ShowLastImage();
 909
 910     // Try to guess default WindowLevel
 911     double range[2];
 912     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 913     if ((range[0] == 0) && (range[1] == 1)) {
 914       presetComboBox->setCurrentIndex(5);// binary
 915     } else {
 916       // TODO
 917     }
 918   }
 919   QApplication::restoreOverrideCursor();
 920 }
 921 //------------------------------------------------------------------------------
 922
 923 //------------------------------------------------------------------------------
 924 void vvMainWindow::UpdateTree()
 925 {
 926   DataTree->resizeColumnToContents(COLUMN_TREE);
 927   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 928   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 929   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 930   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 931   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 932   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 933   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 934 }
 935 //------------------------------------------------------------------------------
 936
 937 //------------------------------------------------------------------------------
 938 void vvMainWindow::CurrentImageChanged(std::string id)
 939 {
 940   if (id == mCurrentSelectedImageId) return; // Do nothing
 941   int selected = 0;
 942   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 943     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 944       selected = i;
 945     } else {
 946       DataTree->topLevelItem(i)->setSelected(0);
 947     }
 948     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 949       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 950
 951   }
 952   DataTree->topLevelItem(selected)->setSelected(1);
 953   mCurrentSelectedImageId = id;
 954   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 955 }
 956 //------------------------------------------------------------------------------
 957
 958 //------------------------------------------------------------------------------
 959 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 960 {
 961   if (id == mCurrentPickedImageId) return; // Do nothing
 962   int selected = 0;
 963   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 964     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 965       selected = i;
 966     } else {
 967       DataTree->topLevelItem(i)->setSelected(0);
 968     }
 969     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 970       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 971
 972   }
 973   DataTree->topLevelItem(selected)->setSelected(1);
 974   mCurrentPickedImageId = id;
 975   mCurrentPickedImageIndex = selected;
 976 }
 977 //------------------------------------------------------------------------------
 978
 979 //------------------------------------------------------------------------------
 980 void vvMainWindow::ImageInfoChanged()
 981 {
 982   contextActions[6]->setEnabled(1);
 983   contextActions[5]->setEnabled(1);
 984   actionSave_As->setEnabled(1);
 985   actionAdd_VF_to_current_Image->setEnabled(1);
 986   actionAdd_fusion_image->setEnabled(1);
 987   actionNorth_East_Window->setEnabled(1);
 988   actionNorth_West_Window->setEnabled(1);
 989   actionSouth_East_Window->setEnabled(1);
 990   actionSouth_West_Window->setEnabled(1);
 991   inverseButton->setEnabled(1);
 992
 993   goToCursorPushButton->setEnabled(1);
 994
 995   if (DataTree->selectedItems().size()) {
 996     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 997
 998     colorMapComboBox->setEnabled(1);
 999     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1000       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1001           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1002         colorMapComboBox->setEnabled(0);
1003         break;
1004       }
1005     }
1006
1007     std::vector<double> origin;
1008     std::vector<double> inputSpacing;
1009     std::vector<int> inputSize;
1010     std::vector<double> sizeMM;
1011     vtkSmartPointer<vtkMatrix4x4> transformation;
1012     int dimension=0;
1013     QString pixelType;
1014     QString inputSizeInBytes;
1015     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1016
1017     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1018       playButton->setEnabled(1);
1019       frameRateLabel->setEnabled(1);
1020       frameRateSpinBox->setEnabled(1);
1021     } else {
1022       playButton->setEnabled(0);
1023       frameRateLabel->setEnabled(0);
1024       frameRateSpinBox->setEnabled(0);
1025     }
1026
1027     //read image header
1028     int NPixel = 1;
1029
1030     vvImage::Pointer imageSelected;
1031     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1032       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1033       dimension = imageSelected->GetNumberOfDimensions();
1034       origin.resize(dimension);
1035       inputSpacing.resize(dimension);
1036       inputSize.resize(dimension);
1037       sizeMM.resize(dimension);
1038       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1039       for (int i = 0; i < dimension; i++) {
1040         origin[i] = imageSelected->GetOrigin()[i];
1041         inputSpacing[i] = imageSelected->GetSpacing()[i];
1042         inputSize[i] = imageSelected->GetSize()[i];
1043         sizeMM[i] = inputSize[i]*inputSpacing[i];
1044         NPixel *= inputSize[i];
1045       }
1046       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1047     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1048       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1049       dimension = imageSelected->GetNumberOfDimensions();
1050       origin.resize(dimension);
1051       inputSpacing.resize(dimension);
1052       inputSize.resize(dimension);
1053       sizeMM.resize(dimension);
1054       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1055       for (int i = 0; i < dimension; i++) {
1056         origin[i] = imageSelected->GetOrigin()[i];
1057         inputSpacing[i] = imageSelected->GetSpacing()[i];
1058         inputSize[i] = imageSelected->GetSize()[i];
1059         sizeMM[i] = inputSize[i]*inputSpacing[i];
1060         NPixel *= inputSize[i];
1061       }
1062       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1063     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1064       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1065       dimension = imageSelected->GetNumberOfDimensions();
1066       origin.resize(dimension);
1067       inputSpacing.resize(dimension);
1068       inputSize.resize(dimension);
1069       sizeMM.resize(dimension);
1070       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1071       for (int i = 0; i < dimension; i++) {
1072         origin[i] = imageSelected->GetOrigin()[i];
1073         inputSpacing[i] = imageSelected->GetSpacing()[i];
1074         inputSize[i] = imageSelected->GetSize()[i];
1075         sizeMM[i] = inputSize[i]*inputSpacing[i];
1076         NPixel *= inputSize[i];
1077       }
1078       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1079     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1080       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1081       dimension = imageSelected->GetNumberOfDimensions();
1082       origin.resize(dimension);
1083       inputSpacing.resize(dimension);
1084       inputSize.resize(dimension);
1085       sizeMM.resize(dimension);
1086       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1087       for (int i = 0; i < dimension; i++) {
1088         origin[i] = imageSelected->GetOrigin()[i];
1089         inputSpacing[i] = imageSelected->GetSpacing()[i];
1090         inputSize[i] = imageSelected->GetSize()[i];
1091         sizeMM[i] = inputSize[i]*inputSpacing[i];
1092         NPixel *= inputSize[i];
1093       }
1094       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1095     }
1096
1097     QString dim = QString::number(dimension) + " (";
1098     dim += pixelType + ")";
1099
1100     infoPanel->setFileName(image);
1101     infoPanel->setDimension(dim);
1102     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1103     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1104     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1105     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1106     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1107     transformation = imageSelected->GetTransform()->GetMatrix();
1108     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1109
1110     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1111                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1112     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1113     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1114
1115     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1116     for (int i = 0; i < 4; i++) {
1117       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1118         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1119         break;
1120       }
1121     }
1122     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1123     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1124     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1125     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1126
1127     infoPanel->setFileName(image);
1128     infoPanel->setDimension(dim);
1129     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1130     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1131     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1132     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1133     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1134
1135     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1136                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1137     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1138     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1139
1140     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1141     for (int i = 0; i < 4; i++) {
1142       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1143         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1144         break;
1145       }
1146     }
1147     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1148     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1149     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1150     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1151
1152     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1153       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1154       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1155                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1156                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1157     } else {
1158       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1159       overlayPanel->getVFProperty(-1,-1,-1);
1160     }
1161     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1162       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1163       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1164     } else {
1165       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1166       overlayPanel->getOverlayProperty(-1);
1167     }
1168     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1169       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1170       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1171                                       mSlicerManagers[index]->GetFusionColorMap(),
1172                                       mSlicerManagers[index]->GetFusionWindow(),
1173                                       mSlicerManagers[index]->GetFusionLevel());
1174     } else {
1175       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1176       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1177     }
1178   }
1179 }
1180 //------------------------------------------------------------------------------
1181
1182 //------------------------------------------------------------------------------
1183 void vvMainWindow::ShowDocumentation()
1184 {
1185   documentation->show();
1186 }
1187 //------------------------------------------------------------------------------
1188 void vvMainWindow::ShowHelpDialog()
1189 {
1190   help_dialog->show();
1191 }
1192 //------------------------------------------------------------------------------
1193
1194 //------------------------------------------------------------------------------
1195 void vvMainWindow::ChangeViewMode()
1196 {
1197   QListIterator<int> it0(splitter_3->sizes());
1198   QListIterator<int> it1(splitter_3->sizes());
1199   int max0 = 0;
1200   int max1 = 1;
1201   while (it0.hasNext()) {
1202     max0 += it0.next();
1203   }
1204   while (it1.hasNext()) {
1205     max1 += it1.next();
1206   }
1207   QList<int> size0;
1208   QList<int> size1;
1209   if (viewMode == 1) {
1210     viewMode = 0;
1211     size0.push_back(max0);
1212     size0.push_back(0);
1213     size1.push_back(max1);
1214     size1.push_back(0);
1215     splitter_3->setSizes(size0);
1216     OSplitter->setSizes(size1);
1217     DataTree->setColumnHidden(2,1);
1218     DataTree->setColumnHidden(3,1);
1219     DataTree->setColumnHidden(4,1);
1220   } else {
1221     viewMode = 1;
1222     size0.push_back(int(max0/2));
1223     size0.push_back(int(max0/2));
1224     size1.push_back(int(max1/2));
1225     size1.push_back(int(max1/2));
1226     splitter_3->setSizes(size0);
1227     OSplitter->setSizes(size1);
1228     DataTree->setColumnHidden(2,0);
1229     DataTree->setColumnHidden(3,0);
1230     DataTree->setColumnHidden(4,0);
1231   }
1232 }
1233 //------------------------------------------------------------------------------
1234
1235 //------------------------------------------------------------------------------
1236 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1237 {
1238   QString result = "";// QString::number(size);
1239   //result += " bytes (";
1240   if (size > 1000000000) {
1241     size /= 1000000000;
1242     result += QString::number(size);
1243     result += "Gb";//)";
1244   } else if (size > 1000000) {
1245     size /= 1000000;
1246     result += QString::number(size);
1247     result += "Mb";//)";
1248   } else if (size > 1000) {
1249     size /= 1000;
1250     result += QString::number(size);
1251     result += "kb";//)";
1252   }
1253   return result;
1254 }
1255 //------------------------------------------------------------------------------
1256
1257 //------------------------------------------------------------------------------
1258 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1259 {
1260   std::ostringstream strmatrix;
1261
1262   for (unsigned int i = 0; i < 4; i++) {
1263     for (unsigned int j = 0; j < 4; j++) {
1264       strmatrix.flags(ios::showpos);
1265       strmatrix.width(10);
1266       strmatrix.precision(3);
1267       strmatrix.setf(ios::fixed,ios::floatfield);
1268       strmatrix.fill(' ');
1269       strmatrix << std::left << matrix->GetElement(i, j);
1270       //strmatrix.width(10);
1271       strmatrix << " ";
1272     }
1273     strmatrix << std::endl;
1274   }
1275   QString result = strmatrix.str().c_str();
1276   return result;
1277 }
1278 //------------------------------------------------------------------------------
1279
1280 //------------------------------------------------------------------------------
1281 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1282 {
1283   QString result;
1284   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1285     if (i != 0)
1286       result += " ";
1287     result += QString::number(vectorDouble[i]);
1288   }
1289   return result;
1290 }
1291 //------------------------------------------------------------------------------
1292
1293 //------------------------------------------------------------------------------
1294 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1295 {
1296   QString result;
1297   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1298     if (i != 0)
1299       result += " ";
1300     result += QString::number(vectorInt[i]);
1301   }
1302   return result;
1303 }
1304 //------------------------------------------------------------------------------
1305
1306 //------------------------------------------------------------------------------
1307 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1308 {
1309   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1310   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1311     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1312       return i;
1313   }
1314   return -1;
1315 }
1316 //------------------------------------------------------------------------------
1317
1318 //------------------------------------------------------------------------------
1319 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1320 {
1321   QString id = sm->GetId().c_str();
1322   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1323     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1324       return DataTree->topLevelItem(i);
1325   }
1326   return NULL;
1327 }
1328 //------------------------------------------------------------------------------
1329
1330 //------------------------------------------------------------------------------
1331 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1332 {
1333   int index = GetSlicerIndexFromItem(clicked_item);
1334   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1335     return;
1336   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1337     //Trick to avoid redoing twice the job for a key (sr)
1338     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1339
1340     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1341     if (DataTree->topLevelItem(index) == current_row) {
1342       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1343       if (current_row == clicked_item) {
1344         //If we just activated a slicer
1345         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1346           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1347           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1348           DisplaySliders(i,column-1);
1349           std::map<std::string,int> overlay_counts;
1350           for (int child = 0; child < current_row->childCount(); child++) {
1351             std::string overlay_type =
1352               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1353             overlay_counts[overlay_type]++;
1354             current_row->child(child)->setData(column,Qt::CheckStateRole,
1355                                                current_row->data(column,Qt::CheckStateRole));
1356             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1357           }
1358         } else { //We don't allow simply desactivating a slicer
1359           clicked_item->setData(column,Qt::CheckStateRole,2);
1360           return;
1361         }
1362       }
1363       //if we clicked on the vector(or overlay) and not the image
1364       else {
1365         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1366           current_row->setData(column,Qt::CheckStateRole,2);
1367           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1368           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1369           DisplaySliders(i,column-1);
1370         }
1371         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1372         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1373         int overlay_index=0;
1374         for (int child = 0; child < current_row->childCount(); child++) {
1375           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1376             overlay_index++;
1377           if (current_row->child(child) == clicked_item) break;
1378         }
1379         clicked_slicer->SetActorVisibility(
1380           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1381       }
1382     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1383       current_row->setData(column,Qt::CheckStateRole,0);
1384       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1385       std::map<std::string,int> overlay_counts;
1386       for (int child = 0; child < current_row->childCount(); child++) {
1387         std::string overlay_type =
1388           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1389         overlay_counts[overlay_type]++;
1390         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1391         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1392         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1393       }
1394     }
1395     //mSlicerManagers[i]->SetColorMap(-1);
1396     mSlicerManagers[i]->SetColorMap();
1397   }
1398   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1399 }
1400 //------------------------------------------------------------------------------
1401
1402 void vvMainWindow::InitSlicers()
1403 {
1404   if (mSlicerManagers.size()) {
1405     mSlicerManagers.back()->GenerateDefaultLookupTable();
1406
1407     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1408     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1409     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1410     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1411   }
1412 }
1413
1414 //------------------------------------------------------------------------------
1415 void vvMainWindow::InitDisplay()
1416 {
1417   if (mSlicerManagers.size()) {
1418     //BE CAREFUL : this is absolutely necessary to set the interactor style
1419     //in order to have the same style instanciation for all SlicerManagers in
1420     // a same window
1421     for (int j = 0; j < 4; j++) {
1422       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1423       style->SetAutoAdjustCameraClippingRange(1);
1424       bool AlreadySelected = false;
1425       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1426         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1427
1428         //select the image only if previous are not selected
1429         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1430           mSlicerManagers[i]->UpdateSlicer(j,1);
1431           AlreadySelected = true;
1432         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1433           if (DataTree->selectedItems().size() == 0)
1434             DataTree->topLevelItem(i)->setSelected(1);
1435           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1436           mSlicerManagers[i]->UpdateSlicer(j,1);
1437           DisplaySliders(i,j);
1438         } else {
1439           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1440           mSlicerManagers[i]->UpdateSlicer(j,0);
1441         }
1442       }
1443       style->Delete();
1444     }
1445   }
1446 }
1447 //------------------------------------------------------------------------------
1448
1449 //------------------------------------------------------------------------------
1450 void vvMainWindow::DisplaySliders(int slicer, int window)
1451 {
1452   int range[2];
1453   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1454   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1455
1456   int tRange[2];
1457   tRange[0] = 0;
1458   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1459   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1460   bool showHorizontal = false;
1461   bool showVertical = false;
1462   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1463       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1464           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1465           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1466     showVertical = true;
1467   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1468       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1469       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1470     showHorizontal = true;
1471
1472   if (showVertical)
1473     verticalSliders[window]->show();
1474   else
1475     verticalSliders[window]->hide();
1476   verticalSliders[window]->setRange(range[0],range[1]);
1477   verticalSliders[window]->setValue(position);
1478
1479   if (showHorizontal)
1480     horizontalSliders[window]->show();
1481   else
1482     horizontalSliders[window]->hide();
1483   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1484   horizontalSliders[window]->setValue(tPosition);
1485 }
1486 //------------------------------------------------------------------------------
1487
1488 //------------------------------------------------------------------------------
1489 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1490 {
1491   int index = GetSlicerIndexFromItem(item);
1492
1493   if (DataTree->topLevelItem(index) != item) {
1494     QString warning = "Do you really want to close the overlay : ";
1495     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1496     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1497                        warning, 0, this);
1498     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1499     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1500     if (msgBox.exec() == QMessageBox::AcceptRole) {
1501       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1502       int overlay_index=0;
1503       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1504         if (DataTree->topLevelItem(index)->\
1505             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1506           overlay_index++;
1507         if (DataTree->topLevelItem(index)->child(child) == item) break;
1508       }
1509       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1510       mSlicerManagers[index]->SetColorMap(0);
1511       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1512       mSlicerManagers[index]->Render();
1513     }
1514   } else if (DataTree->topLevelItemCount() <= 1) {
1515     QString warning = "Do you really want to close the image : ";
1516     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1517     warning += "\nThis is the last image, you're about to close vv !!!";
1518     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1519                        warning, 0, this);
1520     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1521     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1522     if (msgBox.exec() == QMessageBox::AcceptRole) {
1523       this->close();
1524     }
1525   } else {
1526     QString warning = "Do you really want to close the image : ";
1527     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1528     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1529                        warning, 0, this);
1530     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1531     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1532     if (msgBox.exec() == QMessageBox::AcceptRole) {
1533
1534       // Tell tools that we close an image
1535       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1536
1537       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1538       DataTree->takeTopLevelItem(index);
1539       for (int i = 0; i < index; i++) {
1540         Manageriter++;
1541       }
1542       linkPanel->removeImage(index);
1543       mSlicerManagers[index]->RemoveActors();
1544       delete mSlicerManagers[index];
1545       mSlicerManagers.erase(Manageriter);
1546
1547       //
1548       InitDisplay();
1549     }
1550   }
1551   ImageInfoChanged();
1552 }
1553 //------------------------------------------------------------------------------
1554
1555 //------------------------------------------------------------------------------
1556 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1557 {
1558   // int index = GetSlicerIndexFromItem(item);
1559   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1560   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1561   //     mSlicerManagers[index]->ReloadVF();
1562   //   else
1563   //     mSlicerManagers[index]->Reload();
1564
1565   //   QApplication::restoreOverrideCursor();
1566   int index = GetSlicerIndexFromItem(item);
1567   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1568   QString role=item->data(1,Qt::UserRole).toString();
1569   if ( role == "vector")
1570     mSlicerManagers[index]->ReloadVF();
1571   else if (role == "overlay")
1572     mSlicerManagers[index]->ReloadOverlay();
1573   else if (role == "fusion")
1574     mSlicerManagers[index]->ReloadFusion();
1575   else
1576     mSlicerManagers[index]->Reload();
1577
1578   // Update view and info
1579   ImageInfoChanged();
1580   mSlicerManagers[index]->Render();
1581   QApplication::restoreOverrideCursor();
1582 }
1583 //------------------------------------------------------------------------------
1584
1585 //------------------------------------------------------------------------------
1586 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1587 {
1588   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1589 }
1590 //------------------------------------------------------------------------------
1591
1592 //------------------------------------------------------------------------------
1593 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1594 {
1595   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1596 }
1597 //------------------------------------------------------------------------------
1598
1599 //------------------------------------------------------------------------------
1600 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1601 {
1602   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1603 }
1604 //------------------------------------------------------------------------------
1605
1606 //------------------------------------------------------------------------------
1607 void vvMainWindow::FusionChanged(int visibility, double value)
1608 {
1609   overlayPanel->getCurrentFusionInfo(visibility,value);
1610 }
1611 //------------------------------------------------------------------------------
1612
1613 //------------------------------------------------------------------------------
1614 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1615 {
1616   infoPanel->setViews(window, view, slice);
1617 }
1618 //------------------------------------------------------------------------------
1619
1620 //------------------------------------------------------------------------------
1621 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1622 {
1623   windowSpinBox->setValue(window);
1624   levelSpinBox->setValue(level);
1625   colorMapComboBox->setCurrentIndex(colormap);
1626   presetComboBox->setCurrentIndex(preset);
1627 }
1628 //------------------------------------------------------------------------------
1629
1630 //------------------------------------------------------------------------------
1631 void vvMainWindow::WindowLevelEdited()
1632 {
1633   presetComboBox->setCurrentIndex(6);
1634   UpdateWindowLevel();
1635 }
1636 //------------------------------------------------------------------------------
1637
1638 //------------------------------------------------------------------------------
1639 void vvMainWindow::UpdateWindowLevel()
1640 {
1641   if (DataTree->selectedItems().size()) {
1642     if (presetComboBox->currentIndex() == 7) //For ventilation
1643       colorMapComboBox->setCurrentIndex(5);
1644     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1645     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1646     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1647     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1648     mSlicerManagers[index]->Render();
1649     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1650     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1651   }
1652 }
1653 //------------------------------------------------------------------------------
1654
1655 //------------------------------------------------------------------------------
1656 void vvMainWindow::UpdateColorMap()
1657 {
1658   if (DataTree->selectedItems().size()) {
1659     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1660     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1661     mSlicerManagers[index]->Render();
1662   }
1663 }
1664 //------------------------------------------------------------------------------
1665 void vvMainWindow::SwitchWindowLevel()
1666 {
1667   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1668   int window = mSlicerManagers[index]->GetColorWindow();
1669   presetComboBox->setCurrentIndex(6);
1670   windowSpinBox->setValue(-window);
1671   UpdateWindowLevel();
1672 }
1673 //------------------------------------------------------------------------------
1674
1675 //------------------------------------------------------------------------------
1676 void vvMainWindow::ApplyWindowLevelToAllImages()
1677 {
1678   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1679     if (mSlicerManagers[i] == NULL)
1680       continue;
1681     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1682     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1683     mSlicerManagers[i]->SetPreset(6);
1684     mSlicerManagers[i]->Render();
1685   }
1686 }
1687 //------------------------------------------------------------------------------
1688
1689 //------------------------------------------------------------------------------
1690 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1691 {
1692   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1693     if (mSlicerManagers[i]->GetId() == id) {
1694       //mSlicerManagers[i]->SetTSlice(temps);
1695       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1696       mSlicerManagers[i]->UpdateViews(0,slicer);
1697       break;
1698     }
1699   }
1700 }
1701 //------------------------------------------------------------------------------
1702
1703 //------------------------------------------------------------------------------
1704 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1705 {
1706   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1707     if (id == mSlicerManagers[i]->GetId()) {
1708       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1709     }
1710   }
1711 }
1712 //------------------------------------------------------------------------------
1713
1714 //------------------------------------------------------------------------------
1715 void vvMainWindow::ShowContextMenu(QPoint point)
1716 {
1717   if (!DataTree->selectedItems().size()) {
1718     contextActions[1]->setEnabled(0);
1719     contextActions[2]->setEnabled(0);
1720     contextActions[3]->setEnabled(0);
1721     contextActions[4]->setEnabled(0);
1722     contextActions[5]->setEnabled(0);
1723     contextActions[6]->setEnabled(0);
1724   } else {
1725     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1726     contextActions[1]->setEnabled(1);
1727     contextActions[2]->setEnabled(
1728       DataTree->itemWidget(DataTree->selectedItems()[0],
1729                            COLUMN_RELOAD_IMAGE)->isEnabled());
1730     contextActions[3]->setEnabled(1);
1731     contextActions[5]->setEnabled(1);
1732     contextActions[6]->setEnabled(1);
1733
1734     if (mSlicerManagers[index]->GetDimension() < 3)
1735       contextActions[4]->setEnabled(0);
1736     else
1737       contextActions[4]->setEnabled(1);
1738   }
1739   contextMenu.exec(QCursor::pos());
1740 }
1741 //------------------------------------------------------------------------------
1742
1743 //------------------------------------------------------------------------------
1744 void vvMainWindow::CloseImage()
1745 {
1746   CloseImage(DataTree->selectedItems()[0],0);
1747 }
1748 //------------------------------------------------------------------------------
1749
1750 //------------------------------------------------------------------------------
1751 void vvMainWindow::ReloadImage()
1752 {
1753   ReloadImage(DataTree->selectedItems()[0],0);
1754 }
1755 //------------------------------------------------------------------------------
1756
1757 //------------------------------------------------------------------------------
1758 void vvMainWindow::SelectOverlayImage()
1759 {
1760   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1761
1762   //check if one overlay image is added
1763   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1764     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1765       QString error = "Cannot add more than one compared image\n";
1766       error += "Please remove first ";
1767       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1768       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1769       return;
1770     }
1771
1772   QString Extensions = EXTENSIONS;
1773   Extensions += ";;All Files (*)";
1774   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1775   if (!file.isEmpty())
1776     AddOverlayImage(index,file);
1777 }
1778 //------------------------------------------------------------------------------
1779
1780 //------------------------------------------------------------------------------
1781 void vvMainWindow::AddOverlayImage(int index, QString file)
1782 {
1783
1784   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1785   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1786                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1787   reader->SetFileName(file.toStdString().c_str());
1788   reader->ReadImageInformation();
1789   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1790   int dimension = reader->GetNumberOfDimensions();
1791   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1792   vvProgressDialog progress("Opening " + file.toStdString());
1793   qApp->processEvents();
1794
1795   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1796   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1797     //create an item in the tree with good settings
1798     QTreeWidgetItem *item = new QTreeWidgetItem();
1799     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1800     item->setData(1,Qt::UserRole,tr("overlay"));
1801     QFileInfo fileinfo(file); //Do not show the path
1802     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1803     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1804     qApp->processEvents();
1805
1806     for (int j = 1; j <= 4; j++) {
1807       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1808       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1809           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1810     }
1811
1812     //Create the buttons for reload and close
1813     qApp->processEvents();
1814     QTreePushButton* cButton = new QTreePushButton;
1815     cButton->setItem(item);
1816     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1817     cButton->setToolTip(tr("close image"));
1818     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1819     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1820             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1821
1822     QTreePushButton* rButton = new QTreePushButton;
1823     rButton->setItem(item);
1824     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1825     rButton->setToolTip(tr("reload image"));
1826     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1827     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1828             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1829
1830     DataTree->topLevelItem(index)->setExpanded(1);
1831     DataTree->topLevelItem(index)->addChild(item);
1832     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1833     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1834
1835     //set the id of the image
1836     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1837     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1838     UpdateTree();
1839     qApp->processEvents();
1840     ImageInfoChanged();
1841     QApplication::restoreOverrideCursor();
1842   } else {
1843     QApplication::restoreOverrideCursor();
1844     QString error = "Cannot import the new image.\n";
1845     error += mSlicerManagers[index]->GetLastError().c_str();
1846     QMessageBox::information(this,tr("Problem reading image !"),error);
1847   }
1848 }
1849 //------------------------------------------------------------------------------
1850
1851
1852 //------------------------------------------------------------------------------
1853 void vvMainWindow::AddROI(int index, QString file)
1854 {
1855   /*
1856   // Get slice manager
1857
1858   // Load image
1859
1860   vvImageReader * mReader = new vvImageReader;
1861   mReader->SetInputFilename(filename.toStdString());
1862   mReader->Update(IMAGE);
1863   if (mReader->GetLastError().size() != 0) {
1864     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1865     QString error = "Cannot open file \n";
1866     error += mReader->GetLastError().c_str();
1867     QMessageBox::information(this,tr("Reading problem"),error);
1868     delete mReader;
1869     return;
1870   }
1871   vvImage::Pointer roi = mReader->GetOutput();
1872
1873   // Create roi in new tool
1874   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1875   */
1876 }
1877 //------------------------------------------------------------------------------
1878
1879 //------------------------------------------------------------------------------
1880 void vvMainWindow::SelectFusionImage()
1881 {
1882   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1883
1884   //check if one fusion image is added
1885   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1886     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1887       QString error = "Cannot add more than one fusion image\n";
1888       error += "Please remove first ";
1889       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1890       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1891       return;
1892     }
1893
1894   QString Extensions = EXTENSIONS;
1895   Extensions += ";;All Files (*)";
1896   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1897   if (!file.isEmpty())
1898     AddFusionImage(index,file);
1899 }
1900 //------------------------------------------------------------------------------
1901
1902 //------------------------------------------------------------------------------
1903 void vvMainWindow::AddFusionImage(int index, QString file)
1904 {
1905   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1906   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1907                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1908   reader->SetFileName(file.toStdString().c_str());
1909   reader->ReadImageInformation();
1910   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1911   if (reader) {
1912     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1913     vvProgressDialog progress("Opening fusion");
1914     qApp->processEvents();
1915
1916     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1917     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1918                                           reader->GetNumberOfDimensions(), component)) {
1919       //create an item in the tree with good settings
1920       QTreeWidgetItem *item = new QTreeWidgetItem();
1921       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1922       item->setData(1,Qt::UserRole,tr("fusion"));
1923       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1924       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1925       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1926       qApp->processEvents();
1927
1928       for (int j = 1; j <= 4; j++) {
1929         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1930         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1931             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1932       }
1933
1934       //Create the buttons for reload and close
1935       qApp->processEvents();
1936       QTreePushButton* cButton = new QTreePushButton;
1937       cButton->setItem(item);
1938       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1939       cButton->setToolTip(tr("close image"));
1940       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1941       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1942               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1943
1944       QTreePushButton* rButton = new QTreePushButton;
1945       rButton->setItem(item);
1946       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1947       rButton->setToolTip(tr("reload image"));
1948       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1949       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1950               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1951
1952       DataTree->topLevelItem(index)->setExpanded(1);
1953       DataTree->topLevelItem(index)->addChild(item);
1954       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1955       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1956
1957       //set the id of the image
1958       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1959       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1960       UpdateTree();
1961       qApp->processEvents();
1962       ImageInfoChanged();
1963       QApplication::restoreOverrideCursor();
1964     } else {
1965       QApplication::restoreOverrideCursor();
1966       QString error = "Cannot import the new image.\n";
1967       error += mSlicerManagers[index]->GetLastError().c_str();
1968       QMessageBox::information(this,tr("Problem reading image !"),error);
1969     }
1970   } else {
1971     QString error = "Cannot import the new image.\n";
1972     QMessageBox::information(this,tr("Problem reading image !"),error);
1973   }
1974 }
1975 //------------------------------------------------------------------------------
1976
1977
1978 //------------------------------------------------------------------------------
1979 void vvMainWindow::OpenField()
1980 {
1981   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1982   //check if a vector field has already been added
1983   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1984     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1985       QString error = "Cannot add more than one vector field\n";
1986       error += "Please remove first ";
1987       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1988       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1989       return;
1990     }
1991
1992   QString Extensions = "Images ( *.mhd)";
1993   Extensions += ";;Images ( *.vf)";
1994   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1995   if (!file.isEmpty())
1996     AddField(file,index);
1997 }
1998 //------------------------------------------------------------------------------
1999
2000
2001 //------------------------------------------------------------------------------
2002 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2003 {
2004   //create an item in the tree with good settings
2005   QTreeWidgetItem *item = new QTreeWidgetItem();
2006   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2007   item->setData(1,Qt::UserRole,tr("vector"));
2008   QFileInfo fileinfo(filename); //Do not show the path
2009   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2010   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2011   qApp->processEvents();
2012
2013   for (int j = 1; j <= 4; j++) {
2014     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2015     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2016         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2017   }
2018
2019   //Create the buttons for reload and close
2020   qApp->processEvents();
2021   QTreePushButton* cButton = new QTreePushButton;
2022   cButton->setItem(item);
2023   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2024   cButton->setToolTip(tr("close vector field"));
2025   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2026   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2027           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2028
2029   QTreePushButton* rButton = new QTreePushButton;
2030   rButton->setItem(item);
2031   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2032   rButton->setToolTip(tr("reload vector field"));
2033   rButton->setEnabled(from_disk);
2034   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2035   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2036           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2037
2038   DataTree->topLevelItem(index)->setExpanded(1);
2039   DataTree->topLevelItem(index)->addChild(item);
2040   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2041   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2042
2043   //set the id of the image
2044   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2045   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2046   UpdateTree();
2047   qApp->processEvents();
2048   ImageInfoChanged();
2049   QApplication::restoreOverrideCursor();
2050 }
2051 //------------------------------------------------------------------------------
2052
2053
2054 //------------------------------------------------------------------------------
2055 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2056 {
2057   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2058   vvSlicerManager* imageManager = mSlicerManagers[index];
2059   if (imageManager->SetVF(vf,file.toStdString())) {
2060     AddFieldEntry(file,index,false);
2061   } else {
2062     QString error = "Cannot import the vector field for this image.\n";
2063     error += imageManager->GetLastError().c_str();
2064     QMessageBox::information(this,tr("Problem reading VF !"),error);
2065   }
2066   QApplication::restoreOverrideCursor();
2067 }
2068 //------------------------------------------------------------------------------
2069
2070
2071 //------------------------------------------------------------------------------
2072 void vvMainWindow::AddField(QString file,int index)
2073 {
2074   if (QFile::exists(file)) {
2075     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2076
2077     //init the progress events
2078     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2079     vvProgressDialog progress("Opening " + file.toStdString());
2080     qApp->processEvents();
2081
2082     //read the vector and put it in the current mSlicerManager
2083     vvSlicerManager* imageManager = mSlicerManagers[index];
2084     qApp->processEvents();
2085
2086     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2087     if (imageManager->SetVF(file.toStdString())) {
2088       imageManager->Render();
2089       AddFieldEntry(file,index,true);
2090     } else {
2091       QApplication::restoreOverrideCursor();
2092       QString error = "Cannot import the vector field for this image.\n";
2093       error += imageManager->GetLastError().c_str();
2094       QMessageBox::information(this,tr("Problem reading VF !"),error);
2095     }
2096   } else
2097     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2098
2099 }
2100 //------------------------------------------------------------------------------
2101
2102
2103 //------------------------------------------------------------------------------
2104 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2105 {
2106   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2107   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2108     for (int i = 0; i < 4; i++) {
2109       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2110       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2111       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2112       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2113       if (log > 0)
2114         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2115       else
2116         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2117     }
2118   }
2119 }
2120 //------------------------------------------------------------------------------
2121
2122
2123 //------------------------------------------------------------------------------
2124 void vvMainWindow::SetOverlayProperty(int color)
2125 {
2126   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2127   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2128     mSlicerManagers[index]->SetOverlayColor(color);
2129     mSlicerManagers[index]->SetColorMap(0);
2130     mSlicerManagers[index]->Render();
2131   }
2132 }
2133 //------------------------------------------------------------------------------
2134
2135 //------------------------------------------------------------------------------
2136 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2137 {
2138   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2139   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2140     mSlicerManagers[index]->SetFusionOpacity(opacity);
2141     mSlicerManagers[index]->SetFusionColorMap(colormap);
2142     mSlicerManagers[index]->SetFusionWindow(window);
2143     mSlicerManagers[index]->SetFusionLevel(level);
2144     mSlicerManagers[index]->SetColorMap(0);
2145     mSlicerManagers[index]->Render();
2146   }
2147 }
2148 //------------------------------------------------------------------------------
2149
2150 //------------------------------------------------------------------------------
2151 void vvMainWindow::SaveAs()
2152 {
2153   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2154     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2155     return;
2156   }
2157
2158   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2159   int dimension = mSlicerManagers[index]->GetDimension();
2160   QStringList OutputListeFormat;
2161   OutputListeFormat.clear();
2162   if (dimension == 1) {
2163     OutputListeFormat.push_back(".mhd");
2164   }
2165   if (dimension == 2) {
2166     OutputListeFormat.push_back(".bmp");
2167     OutputListeFormat.push_back(".png");
2168     OutputListeFormat.push_back(".jpeg");
2169     OutputListeFormat.push_back(".tif");
2170     OutputListeFormat.push_back(".mhd");
2171     OutputListeFormat.push_back(".hdr");
2172     OutputListeFormat.push_back(".vox");
2173   } else if (dimension == 3) {
2174     OutputListeFormat.push_back(".mhd");
2175     OutputListeFormat.push_back(".hdr");
2176     OutputListeFormat.push_back(".vox");
2177   } else if (dimension == 4) {
2178     OutputListeFormat.push_back(".mhd");
2179   }
2180   QString Extensions = "AllFiles(*.*)";
2181   for (int i = 0; i < OutputListeFormat.count(); i++) {
2182     Extensions += ";;Images ( *";
2183     Extensions += OutputListeFormat[i];
2184     Extensions += ")";
2185   }
2186   QString fileName = QFileDialog::getSaveFileName(this,
2187                      tr("Save As"),
2188                      mSlicerManagers[index]->GetFileName().c_str(),
2189                      Extensions);
2190   if (!fileName.isEmpty()) {
2191     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2192     if (OutputListeFormat.contains(
2193           fileformat.c_str())) {
2194       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2195       std::string action = "Saving";
2196       vvProgressDialog progress("Saving "+fileName.toStdString());
2197       qApp->processEvents();
2198       vvImageWriter::Pointer writer = vvImageWriter::New();
2199       writer->SetOutputFileName(fileName.toStdString());
2200       writer->SetInput(mSlicerManagers[index]->GetImage());
2201       writer->Update();
2202       QApplication::restoreOverrideCursor();
2203       if (writer->GetLastError().size()) {
2204         QString error = "Saving did not succeed\n";
2205         error += writer->GetLastError().c_str();
2206         QMessageBox::information(this,tr("Saving Problem"),error);
2207         SaveAs();
2208       }
2209     } else {
2210       QString error = fileformat.c_str();
2211       if (error.isEmpty())
2212         error += "no file format specified !";
2213       else
2214         error += " format unknown !!!\n";
2215       QMessageBox::information(this,tr("Saving Problem"),error);
2216       SaveAs();
2217     }
2218   }
2219 }
2220 //------------------------------------------------------------------------------
2221
2222
2223 //------------------------------------------------------------------------------
2224 void vvMainWindow::AddLink(QString image1,QString image2)
2225 {
2226   unsigned int sm1 = 0;
2227   unsigned int sm2 = 0;
2228
2229   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2230     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2231       mSlicerManagers[i]->AddLink(image2.toStdString());
2232       sm1 = i;
2233     }
2234     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2235       mSlicerManagers[i]->AddLink(image1.toStdString());
2236       sm2 = i;
2237     }
2238   }
2239
2240   if (linkPanel->isLinkAll())   {
2241     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2242     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2243   }
2244   else {
2245     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2246   }
2247 }
2248
2249 //------------------------------------------------------------------------------
2250
2251
2252 //------------------------------------------------------------------------------
2253 void vvMainWindow::RemoveLink(QString image1,QString image2)
2254 {
2255   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2256     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2257       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2258     }
2259     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2260       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2261     }
2262   }
2263 }
2264 //------------------------------------------------------------------------------
2265
2266 //------------------------------------------------------------------------------
2267 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2268 {
2269   int index = 0;
2270   while(sm != mSlicerManagers[index])
2271     index++;
2272   index = (index+offset) % mSlicerManagers.size();
2273
2274   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2275   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2276   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2277   DisplayChanged(item,slicer+1);
2278 }
2279 //------------------------------------------------------------------------------
2280
2281 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2282 {
2283   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2284     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2285       for (int j = 0; j < 4; j++) {
2286         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2287         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2288         //UpdateTSlice(j,value);
2289       }
2290       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2291       break;
2292     }
2293   }
2294 }
2295 //------------------------------------------------------------------------------
2296
2297
2298 //------------------------------------------------------------------------------
2299 void vvMainWindow::NOHorizontalSliderMoved()
2300 {
2301   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2302   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2303 //  mCurrentTime = NOHorizontalSlider->value();
2304 }
2305 //------------------------------------------------------------------------------
2306
2307
2308 //------------------------------------------------------------------------------
2309 void vvMainWindow::NEHorizontalSliderMoved()
2310 {
2311   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2312   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2313 //  mCurrentTime = NEHorizontalSlider->value();
2314 }
2315 //------------------------------------------------------------------------------
2316
2317
2318 //------------------------------------------------------------------------------
2319 void vvMainWindow::SOHorizontalSliderMoved()
2320 {
2321   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2322   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2323   // mCurrentTime = SOHorizontalSlider->value();
2324 }
2325 //------------------------------------------------------------------------------
2326
2327
2328 //------------------------------------------------------------------------------
2329 void vvMainWindow::SEHorizontalSliderMoved()
2330 {
2331   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2332   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2333   // mCurrentTime = SEHorizontalSlider->value();
2334 }
2335 //------------------------------------------------------------------------------
2336
2337 //------------------------------------------------------------------------------
2338 void vvMainWindow::NOVerticalSliderChanged()
2339 {
2340   static int value=-1;
2341   if (value == NOVerticalSlider->value()) return;
2342   else value = NOVerticalSlider->value();
2343   //  int value = NOVerticalSlider->value();
2344   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2345     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2346       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2347         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2348         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2349
2350         // If nor Update/Render -> slider not work
2351         // only render = ok navigation, but for contour Update needed but slower ?
2352
2353         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2354         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2355       }
2356       break;
2357     }
2358   }
2359 }
2360 //------------------------------------------------------------------------------
2361
2362
2363 //------------------------------------------------------------------------------
2364 void vvMainWindow::NEVerticalSliderChanged()
2365 {
2366   static int value=-1;
2367   if (value == NEVerticalSlider->value()) return;
2368   else value = NEVerticalSlider->value();
2369   //  int value = NEVerticalSlider->value();
2370   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2371     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2372       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2373         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2374         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2375         mSlicerManagers[i]->UpdateSlice(1);
2376         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2377       }
2378       break;
2379     }
2380   }
2381 }
2382 //------------------------------------------------------------------------------
2383
2384
2385 //------------------------------------------------------------------------------
2386 void vvMainWindow::SOVerticalSliderChanged()
2387 {
2388   static int value=-1;
2389   if (value == SOVerticalSlider->value()) return;
2390   else value = SOVerticalSlider->value();
2391   //int value = SOVerticalSlider->value();
2392   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2393     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2394       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2395         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2396         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2397         mSlicerManagers[i]->UpdateSlice(2);
2398         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2399       }
2400       // else { DD("avoid SOVerticalSlider slicer update"); }
2401       break;
2402     }
2403   }
2404 }
2405 //------------------------------------------------------------------------------
2406
2407
2408 //------------------------------------------------------------------------------
2409 void vvMainWindow::SEVerticalSliderChanged()
2410 {
2411   static int value=-1;
2412   if (value == SEVerticalSlider->value()) return;
2413   else value = SEVerticalSlider->value();
2414   // int value = SEVerticalSlider->value();
2415   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2416     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2417       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2418         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2419         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2420         mSlicerManagers[i]->UpdateSlice(3);
2421         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2422       }
2423       break;
2424     }
2425   }
2426 }
2427 //------------------------------------------------------------------------------
2428
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::UpdateSlice(int slicer, int slice)
2432 {
2433   // DD("vvMainWindow::UpdateSlice");
2434 //   DD(slicer);
2435 //   DD(slice);
2436   if (slicer == 0) {
2437     //    if (slice != NOVerticalSlider->value())
2438     NOVerticalSlider->setValue(slice);
2439   } else {
2440     if (slicer == 1)
2441       NEVerticalSlider->setValue(slice);
2442     else {
2443       if (slicer == 2)
2444         SOVerticalSlider->setValue(slice);
2445       else {
2446         if (slicer == 3)
2447           SEVerticalSlider->setValue(slice);
2448       }
2449     }
2450   }
2451   // DD("vvMainWindow:UpdateSlice END");
2452 }
2453 //------------------------------------------------------------------------------
2454
2455
2456 //------------------------------------------------------------------------------
2457 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2458 {
2459   switch (slicer) {
2460   case 0:
2461     NOHorizontalSlider->setValue(slice);
2462     break;
2463   case 1:
2464     NEHorizontalSlider->setValue(slice);
2465     break;
2466   case 2:
2467     SOHorizontalSlider->setValue(slice);
2468     break;
2469   case 3:
2470     SEHorizontalSlider->setValue(slice);
2471     break;
2472   }
2473 }
2474 //------------------------------------------------------------------------------
2475
2476
2477 //------------------------------------------------------------------------------
2478 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2479 {
2480   int position = int((min+max)/2);
2481   int tPosition = int((tmin+tmax)/2);
2482   if (slicer == 0) {
2483     NOVerticalSlider->setValue(position);
2484     NOVerticalSlider->setRange(min,max);
2485     NOHorizontalSlider->setRange(tmin,tmax);
2486     NOHorizontalSlider->setValue(tPosition);
2487   } else if (slicer == 1) {
2488     NEVerticalSlider->setValue(position);
2489     NEVerticalSlider->setRange(min,max);
2490     NEHorizontalSlider->setRange(tmin,tmax);
2491     NEHorizontalSlider->setValue(tPosition);
2492   } else if (slicer == 2) {
2493     SOVerticalSlider->setValue(position);
2494     SOVerticalSlider->setRange(min,max);
2495     SOHorizontalSlider->setRange(tmin,tmax);
2496     SOHorizontalSlider->setValue(tPosition);
2497   } else if (slicer == 3) {
2498     SEVerticalSlider->setValue(position);
2499     SEVerticalSlider->setRange(min,max);
2500     SEHorizontalSlider->setRange(tmin,tmax);
2501     SEHorizontalSlider->setValue(tPosition);
2502   }
2503 }
2504 //------------------------------------------------------------------------------
2505
2506
2507 //------------------------------------------------------------------------------
2508 void vvMainWindow::SaveNOScreenshot()
2509 {
2510   SaveScreenshot(NOViewWidget);
2511 }
2512 //------------------------------------------------------------------------------
2513
2514
2515 //------------------------------------------------------------------------------
2516 void vvMainWindow::SaveNEScreenshot()
2517 {
2518   SaveScreenshot(NEViewWidget);
2519 }
2520 //------------------------------------------------------------------------------
2521
2522
2523 //------------------------------------------------------------------------------
2524 void vvMainWindow::SaveSOScreenshot()
2525 {
2526   SaveScreenshot(SOViewWidget);
2527 }
2528 //------------------------------------------------------------------------------
2529
2530
2531 //------------------------------------------------------------------------------
2532 void vvMainWindow::SaveSEScreenshot()
2533 {
2534   SaveScreenshot(SEViewWidget);
2535 }
2536 //------------------------------------------------------------------------------
2537
2538
2539 //------------------------------------------------------------------------------
2540 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2541 {
2542   QString Extensions = "Images( *.png);;";
2543   Extensions += "Images( *.jpg);;";
2544   Extensions += "Images( *.bmp);;";
2545   Extensions += "Images( *.tif);;";
2546   Extensions += "Images( *.ppm)";
2547 #ifdef VTK_USE_FFMPEG_ENCODER
2548   Extensions += "Images( *.avi)";
2549 #endif
2550 #ifdef VTK_USE_MPEG2_ENCODER
2551   Extensions += "Images( *.mpg)";
2552 #endif
2553
2554   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2555   QString fileName = QFileDialog::getSaveFileName(this,
2556                      tr("Save As"),
2557                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2558                      Extensions);
2559
2560   if (!fileName.isEmpty()) {
2561     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2562     w2i->SetInput(widget->GetRenderWindow());
2563     w2i->Update();
2564     vtkImageData *image = w2i->GetOutput();
2565
2566     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2567     if (!strcmp(ext, ".bmp")) {
2568       vtkBMPWriter *bmp = vtkBMPWriter::New();
2569       bmp->SetInput(image);
2570       bmp->SetFileName(fileName.toStdString().c_str());
2571       bmp->Write();
2572       bmp->Delete();
2573     } else if (!strcmp(ext, ".tif")) {
2574       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2575       tif->SetInput(image);
2576       tif->SetFileName(fileName.toStdString().c_str());
2577       tif->Write();
2578       tif->Delete();
2579     } else if (!strcmp(ext, ".ppm")) {
2580       vtkPNMWriter *pnm = vtkPNMWriter::New();
2581       pnm->SetInput(image);
2582       pnm->SetFileName(fileName.toStdString().c_str());
2583       pnm->Write();
2584       pnm->Delete();
2585     } else if (!strcmp(ext, ".png")) {
2586       vtkPNGWriter *png = vtkPNGWriter::New();
2587       png->SetInput(image);
2588       png->SetFileName(fileName.toStdString().c_str());
2589       png->Write();
2590       png->Delete();
2591     } else if (!strcmp(ext, ".jpg")) {
2592       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2593       jpg->SetInput(image);
2594       jpg->SetFileName(fileName.toStdString().c_str());
2595       jpg->Write();
2596       jpg->Delete();
2597 #ifdef VTK_USE_FFMPEG_ENCODER
2598     } else if (!strcmp(ext, ".avi")) {
2599       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2600       mpg->SetInput(image);
2601       mpg->SetFileName(fileName.toStdString().c_str());
2602       mpg->SetQuality(2);
2603       mpg->SetRate(5);
2604       mpg->Start();
2605
2606       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2607       int nSlice = vvImg->GetVTKImages().size();
2608       for(int i=0; i<nSlice; i++)
2609       {
2610         mSlicerManagers[smIndex]->SetNextTSlice(0);
2611         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2612         w2i->SetInput(widget->GetRenderWindow());
2613         w2i->Update();
2614         mpg->SetInput(w2i->GetOutput());
2615         mpg->Write();
2616       }
2617       mpg->End();
2618       mpg->Delete();
2619 #endif
2620 #ifdef VTK_USE_MPEG2_ENCODER
2621     } else if (!strcmp(ext, ".mpg")) {
2622       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2623       mpg->SetInput(image);
2624       mpg->SetFileName(fileName.toStdString().c_str());
2625       mpg->Start();
2626
2627       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2628       int nSlice = vvImg->GetVTKImages().size();
2629       for(int i=0; i<nSlice; i++)
2630       {
2631         mSlicerManagers[smIndex]->SetNextTSlice(0);
2632         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2633         w2i->SetInput(widget->GetRenderWindow());
2634         w2i->Update();
2635         mpg->SetInput(w2i->GetOutput());
2636         mpg->Write();
2637       }
2638       mpg->End();
2639       mpg->Delete();
2640 #endif
2641     } else {
2642       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2643     }
2644   }
2645 }
2646 //------------------------------------------------------------------------------
2647
2648
2649 //------------------------------------------------------------------------------
2650 void vvMainWindow::GoToCursor()
2651 {
2652   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2653   for (int column = 1; column < 5; column++) {
2654     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2655       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2656       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2657         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2658       mSlicerManagers[index]->UpdateViews(1,column-1);
2659       mSlicerManagers[index]->UpdateLinked(column-1);
2660       break;
2661     }
2662   }
2663 }
2664 //------------------------------------------------------------------------------
2665
2666 //------------------------------------------------------------------------------
2667 void vvMainWindow::PlayPause()
2668 {
2669   if (playMode) {
2670     playMode = 0;
2671     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2672     ImageInfoChanged();
2673     return;
2674   } else {
2675     int image_number=DataTree->topLevelItemCount();
2676     bool has_temporal;
2677     for (int i=0; i<image_number; i++)
2678       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2679         has_temporal=true;
2680         break;
2681       }
2682     if (has_temporal) {
2683       playMode = 1;
2684       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2685       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2686     }
2687   }
2688 }
2689 //------------------------------------------------------------------------------
2690
2691 //------------------------------------------------------------------------------
2692 void vvMainWindow::PlayNext()
2693 {
2694   if (playMode && !this->isHidden()) {
2695     int image_number=DataTree->topLevelItemCount();
2696     ///Only play one slicer per SM, and only if the SM is being displayed
2697     for (int i=0; i<image_number; i++)
2698       for (int j=0; j<4; j++)
2699         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2700             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2701           mSlicerManagers[i]->SetNextTSlice(j);
2702           break;
2703         }
2704     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2705   }
2706 }
2707 //------------------------------------------------------------------------------
2708
2709 void vvMainWindow::ShowLastImage()
2710 {
2711   if (mSlicerManagers.size() > 1) {
2712     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2713     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2714     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2715     DisplayChanged(item,1);
2716   }
2717 }
2718
2719 //------------------------------------------------------------------------------
2720 void vvMainWindow::UpdateRenderWindows()
2721 {
2722   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2723   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2724   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2725   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2726 }
2727 //------------------------------------------------------------------------------
2728
2729 //------------------------------------------------------------------------------
2730 void vvMainWindow::SegmentationOnCurrentImage()
2731 {
2732   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2733
2734   vvSegmentationDialog segmentation;
2735   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2736   segmentation.exec();
2737 }
2738 //------------------------------------------------------------------------------
2739
2740 void vvMainWindow::SurfaceViewerLaunch()
2741 {
2742   vvSurfaceViewerDialog surfaceViewer;
2743   surfaceViewer.exec();
2744 }
2745 //------------------------------------------------------------------------------
2746
2747
2748 //------------------------------------------------------------------------------
2749 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2750 {
2751   int number=0;
2752   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2753     vvSlicerManager * v = mSlicerManagers[l];
2754     if (v->GetBaseFileName() ==
2755         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2756       number = std::max(number, v->GetBaseFileNameNumber()+1);
2757     }
2758   }
2759   return number;
2760 }
2761 //------------------------------------------------------------------------------
2762
2763
2764 //------------------------------------------------------------------------------
2765 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2766 {
2767   // Change filename if another image exist with the same name
2768   int number = GetImageDuplicateFilenameNumber(filename);
2769
2770   // Create new SliceManager
2771   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2772   slicer_manager->SetImage(image);//, IMAGE, number);
2773   //  filename = filename+"_"+clitk::toString(number);
2774   slicer_manager->SetFilename(filename, number);
2775   mSlicerManagers.push_back(slicer_manager);
2776
2777   //create an item in the tree with good settings
2778   QTreeWidgetItem *item = new QTreeWidgetItem();
2779   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2780   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2781   qApp->processEvents();
2782
2783   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2784
2785   //Create the buttons for reload and close
2786   qApp->processEvents();
2787   QTreePushButton* cButton = new QTreePushButton;
2788   cButton->setItem(item);
2789   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2790   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2791   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2792           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2793
2794   QTreePushButton* rButton = new QTreePushButton;
2795   rButton->setItem(item);
2796   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2797   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2798   rButton->setEnabled(0);
2799   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2800           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2801
2802   DataTree->addTopLevelItem(item);
2803   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2804   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2805
2806   //set the id of the image
2807   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2808   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2809   mSlicerManagers.back()->SetId(id.toStdString());
2810
2811   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2812                       , id.toStdString());
2813
2814   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2815           this, SLOT(CurrentImageChanged(std::string)));
2816   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2817           this, SLOT(CurrentPickedImageChanged(std::string)));
2818   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2819           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2820   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2821           this, SLOT(VectorChanged(int,double,double,double, double)));
2822   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2823           this, SLOT(OverlayChanged(int,double,double)));
2824   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2825           this, SLOT(FusionChanged(int,double)));
2826   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2827           this,SLOT(WindowsChanged(int, int, int)));
2828   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2829           this,SLOT(WindowLevelChanged(double, double, int, int)));
2830   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2831           this,SLOT(UpdateSlice(int,int)));
2832   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2833           this,SLOT(UpdateTSlice(int, int)));
2834   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2835           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2836   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2837           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2838   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2839           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2840   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2841           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2842   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2843   UpdateTree();
2844   qApp->processEvents();
2845   InitSlicers();
2846   ShowLastImage();
2847   InitDisplay();
2848   qApp->processEvents();
2849
2850   // End
2851   ImageInfoChanged();
2852   return slicer_manager;
2853 }
2854 //------------------------------------------------------------------------------
2855
2856
2857 //------------------------------------------------------------------------------
2858 void vvMainWindow::UpdateCurrentSlicer()
2859 {
2860   int index = -1;
2861   if (DataTree->selectedItems().size() > 0) {
2862     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2863   }
2864   mSlicerManagerCurrentIndex = index;
2865 }
2866 //------------------------------------------------------------------------------
2867