vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25
  26 // VV include
  27 #include "vvMainWindow.h"
  28 #include "vvHelpDialog.h"
  29 #include "vvRegisterForm.h"
  30 #include "vvDocumentation.h"
  31 #include "vvProgressDialog.h"
  32 #include "vvQDicomSeriesSelector.h"
  33 #include "vvSlicerManager.h"
  34 #include "clitkImageCommon.h"
  35 #include "vvSlicer.h"
  36 #include "vvInteractorStyleNavigator.h"
  37 #include "vvImageWriter.h"
  38 #include "vvSegmentationDialog.h"
  39 #include "vvSurfaceViewerDialog.h"
  40 #include "vvDeformationDialog.h"
  41 #include "vvImageWarp.h"
  42 #include "vvUtils.h"
  43 #include "vvMidPosition.h"
  44 #include "vvMesh.h"
  45 #include "vvStructSelector.h"
  46 #include "vvMeshReader.h"
  47 #include "clitkConfiguration.h"
  48
  49 // ITK include
  50 #include <itkImage.h>
  51 #include <itkImageFileReader.h>
  52 #include <itkByteSwapper.h>
  53 #include <itkCommand.h>
  54 #include <itkNumericSeriesFileNames.h>
  55
  56 // VTK include
  57 #include <vtkImageData.h>
  58 #include <vtkImageActor.h>
  59 #include <vtkCornerAnnotation.h>
  60 #include <vtkRenderWindow.h>
  61 #include <vtkRenderWindowInteractor.h>
  62 #include <vtkRenderer.h>
  63 #include <vtkRendererCollection.h>
  64 #include <vtkWindowToImageFilter.h>
  65 #include <vtkBMPWriter.h>
  66 #include <vtkTIFFWriter.h>
  67 #include <vtkPNMWriter.h>
  68 #include <vtkPNGWriter.h>
  69 #include <vtkJPEGWriter.h>
  70 #include <vtkFFMPEGWriter.h>
  71 #ifdef VTK_USE_MPEG2_ENCODER
  72   #include <vtkMPEG2Writer.h>
  73 #endif
  74 #include <vtkMatrix4x4.h>
  75 #include <vtkTransform.h>
  76
  77 // Standard includes
  78 #include <iostream>
  79 #include <sstream>
  80 #include <iomanip>
  81
  82 #define COLUMN_TREE 0
  83 #define COLUMN_UL_VIEW 1
  84 #define COLUMN_UR_VIEW 2
  85 #define COLUMN_DL_VIEW 3
  86 #define COLUMN_DR_VIEW 4
  87 #define COLUMN_CLOSE_IMAGE 5
  88 #define COLUMN_RELOAD_IMAGE 6
  89 #define COLUMN_IMAGE_NAME 7
  90
  91 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  92
  93 /*Data Tree values
  94   0,Qt::UserRole full filename
  95   1,Qt::CheckStateRole checkbutton UL View
  96   1,Qt::UserRole overlay, fusion or vector
  97   2,Qt::CheckStateRole checkbutton UR View
  98   3,Qt::CheckStateRole checkbutton DL View
  99   4,Qt::CheckStateRole checkbutton DR View
 100   5,0  short filename
 101   5,Qt::UserRole mSlicerManager id*/
 102
 103 //------------------------------------------------------------------------------
 104 vvMainWindow::vvMainWindow():vvMainWindowBase()
 105 {
 106   setupUi(this); // this sets up the GUI
 107
 108   mInputPathName = "";
 109   mMenuTools = menuTools;
 110   //  mMenuSegmentation = menuSegmentation;
 111   mContextMenu = &contextMenu;
 112   mMenuExperimentalTools = menuExperimental;
 113   mMainWidget = this;
 114   mCurrentTime = -1;
 115   mCurrentSelectedImageId = "";
 116   mCurrentPickedImageId = "";
 117   mCurrentPickedImageIndex = 0;
 118
 119   //Init the contextMenu
 120   this->setContextMenuPolicy(Qt::CustomContextMenu);
 121   contextActions.resize(0);
 122   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 123                                   tr("O&pen new Image"));
 124   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 125   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 126   contextActions.push_back(actionOpen_new_image);
 127   contextMenu.addSeparator();
 128
 129   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 130                                tr("Close Current Image"));
 131   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 132   contextActions.push_back(actionClose_Image);
 133
 134   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 135                                 tr("Reload Current Image"));
 136   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 137   contextActions.push_back(actionReload_image);
 138
 139   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 140                               tr("Save Current Image"));
 141   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 142   contextActions.push_back(actionSave_image);
 143
 144   contextMenu.addSeparator();
 145
 146   contextMenu.addAction(actionAdd_VF_to_current_Image);
 147   contextActions.push_back(actionAdd_VF_to_current_Image);
 148
 149   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 150       tr("Add overlay image to current image"));
 151   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 152   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 153
 154   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 155
 156   contextMenu.addAction(actionAdd_fusion_image);
 157   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 158   contextActions.push_back(actionAdd_fusion_image);
 159
 160   // TRIAL DS
 161   /*
 162   QMenu * m = new QMenu(menubar);
 163   m->setTitle("TOTO");
 164   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 165   contextMenu.addMenu(m);
 166   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 167                      tr("BIDON"));
 168   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON2"));
 170   m->addAction(a);
 171   m->addAction(b);
 172   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 173   */
 174
 175   //init the DataTree
 176   mSlicerManagers.resize(0);
 177
 178   QStringList header;
 179   header.append("");
 180   header.append("TL");
 181   header.append("TR");
 182   header.append("BL");
 183   header.append("BR");
 184   header.append("");
 185   header.append("");
 186   header.append("Name");
 187
 188   DataTree->setHeaderLabels(header);
 189   DataTree->resizeColumnToContents(COLUMN_TREE);
 190   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 191   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 195   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 197
 198   viewMode = 1;
 199   documentation = new vvDocumentation();
 200   help_dialog = new vvHelpDialog();
 201   dicomSeriesSelector = new vvDicomSeriesSelector();
 202
 203   inverseButton->setEnabled(0);
 204   actionAdd_Overlay_to_current_Image->setEnabled(0);
 205   actionSave_As->setEnabled(0);
 206   actionAdd_VF_to_current_Image->setEnabled(0);
 207   actionAdd_fusion_image->setEnabled(0);
 208
 209   //init the sliders
 210   verticalSliders.push_back(NOVerticalSlider);
 211   verticalSliders.push_back(NEVerticalSlider);
 212   verticalSliders.push_back(SOVerticalSlider);
 213   verticalSliders.push_back(SEVerticalSlider);
 214
 215   for (int i =0; i < 4; i++)
 216     verticalSliders[i]->hide();
 217
 218   horizontalSliders.push_back(NOHorizontalSlider);
 219   horizontalSliders.push_back(NEHorizontalSlider);
 220   horizontalSliders.push_back(SOHorizontalSlider);
 221   horizontalSliders.push_back(SEHorizontalSlider);
 222
 223   for (int i =0; i < 4; i++)
 224     horizontalSliders[i]->hide();
 225
 226
 227   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 228   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 229   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 230   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 231
 232   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 233   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 234   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 235   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 236
 237   //connect everything
 238   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 239   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 240   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 241   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 242   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 243   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 244   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 245   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 246   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 247   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 248   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 249   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 250   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 251   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 252   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 253   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 254
 255   ///////////////////////////////////////////////
 256   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 257   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 258   ///////////////////////////////////////////////
 259
 260   actionNorth_East_Window->setEnabled(0);
 261   actionNorth_West_Window->setEnabled(0);
 262   actionSouth_East_Window->setEnabled(0);
 263   actionSouth_West_Window->setEnabled(0);
 264
 265   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 266   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 267   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 268   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 269
 270   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 271   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 272           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 273
 274   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 275   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 276   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 277   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 278   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 279   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 280   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 281
 282
 283   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 284
 285   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 286   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 287   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 288   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 289   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 290           this,SLOT(SetFusionProperty(int,int,double,double)));
 291   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 292
 293   playMode = 0;//pause
 294   mFrameRate = 10;
 295   playButton->setEnabled(0);
 296   frameRateLabel->setEnabled(0);
 297   frameRateSpinBox->setEnabled(0);
 298   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 299   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 300
 301   goToCursorPushButton->setEnabled(0);
 302   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 303
 304   NOViewWidget->hide();
 305   NEViewWidget->hide();
 306   SOViewWidget->hide();
 307   SEViewWidget->hide();
 308
 309   //Recently opened files
 310   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 311   if ( !recent_files.empty() ) {
 312     QMenu * rmenu = new QMenu("Recently opened files...");
 313     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 314     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 315     menuFile->insertSeparator(actionOpen_Image_With_Time);
 316     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 317       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 318                                    (*i).c_str(),this);
 319       rmenu->addAction(current);
 320       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 321     }
 322   }
 323
 324   // Adding all new tools (insertion in the menu)
 325   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 326
 327   if (!CLITK_EXPERIMENTAL)
 328     menuExperimental->menuAction()->setVisible(false);
 329
 330
 331   QTimer * timerMemory = new QTimer(this);
 332   //timerMemory->setInterval(5);
 333   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 334   timerMemory->start(2000);
 335
 336
 337   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://localhost/vvregister/write.php"));
 338   registerForm->show();
 339
 340 }
 341 //------------------------------------------------------------------------------
 342
 343
 344 //------------------------------------------------------------------------------
 345 void vvMainWindow::UpdateMemoryUsage()
 346 {
 347   //  clitk::PrintMemory(true);
 348   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 349   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 350 }
 351 //------------------------------------------------------------------------------
 352
 353
 354 //------------------------------------------------------------------------------
 355 void vvMainWindow::ComputeMidPosition()
 356 {
 357   bool ok;
 358   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 359   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 360                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 361   if (ok) {
 362     vvMidPosition midp;
 363     midp.slicer_manager = mSlicerManagers[index];
 364     midp.reference_image_index = ref;
 365     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 366     midp.Update();
 367     if (midp.error)
 368       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 369     else {
 370       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 371       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 372     }
 373     QApplication::restoreOverrideCursor();
 374   }
 375 }
 376 //------------------------------------------------------------------------------
 377
 378
 379 //------------------------------------------------------------------------------
 380 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 381 {
 382   QTreeWidgetItem *item = new QTreeWidgetItem();
 383   item->setData(0,Qt::UserRole,"filename.vtk");
 384   item->setData(1,Qt::UserRole,tr("contour"));
 385   QBrush brush;
 386   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 387   brush.setStyle(Qt::SolidPattern);
 388   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 389   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 390
 391   for (int j = 1; j <= 4; j++)
 392     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 393
 394   QTreePushButton* cButton = new QTreePushButton;
 395   cButton->setItem(item);
 396   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 397   cButton->setToolTip(tr("close image"));
 398   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 399   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 400           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 401
 402   QTreePushButton* rButton = new QTreePushButton;
 403   rButton->setItem(item);
 404   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 405   rButton->setToolTip(tr("reload image"));
 406   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 407   rButton->setEnabled(false);
 408   //Not implemented
 409   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 410   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 411
 412   DataTree->topLevelItem(image_index)->setExpanded(1);
 413   DataTree->topLevelItem(image_index)->addChild(item);
 414   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 415   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 416   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 417   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 418
 419   UpdateTree();
 420   mSlicerManagers[image_index]->AddContour(contour,propagation);
 421   mSlicerManagers[image_index]->Render();
 422 }
 423 //------------------------------------------------------------------------------
 424
 425
 426 //------------------------------------------------------------------------------
 427 void vvMainWindow::OpenVTKContour()
 428 {
 429   if (mSlicerManagers.size() > 0) {
 430     QString Extensions = "Images ( *.vtk *.obj)";
 431     Extensions += ";;All Files (*)";
 432     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 433     if (file.isNull())
 434       return;
 435     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 436     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 437     vvMeshReader reader;
 438     reader.SetImage(mSlicerManagers[index]->GetImage());
 439     reader.SetModeToVTK();
 440     reader.SetFilename(file.toStdString());
 441     reader.Update();
 442     AddContour(index,reader.GetOutput()[0],false);
 443     QApplication::restoreOverrideCursor();
 444   }
 445 }
 446 //------------------------------------------------------------------------------
 447
 448
 449 //------------------------------------------------------------------------------
 450 void vvMainWindow::OpenDCStructContour()
 451 {
 452   if (mSlicerManagers.size() > 0) {
 453     QString Extensions = "Dicom Files ( *.dcm RS*)";
 454     Extensions += ";;All Files (*)";
 455     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 456     if (file.isNull())
 457       return;
 458     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 459     vvMeshReader reader;
 460     reader.SetFilename(file.toStdString());
 461     vvStructSelector selector;
 462     selector.SetStructures(reader.GetROINames());
 463     if (!mSlicerManagers[index]->GetVF().IsNull())
 464       selector.EnablePropagationCheckBox();
 465     if (selector.exec()) {
 466       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 467       reader.SetSelectedItems(selector.getSelectedItems());
 468       reader.SetImage(mSlicerManagers[index]->GetImage());
 469       if (selector.PropagationEnabled())
 470         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 471       reader.Update();
 472       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 473       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 474            i!=contours.end(); i++)
 475         AddContour(index,*i,selector.PropagationEnabled());
 476       QApplication::restoreOverrideCursor();
 477     }
 478   }
 479 }
 480 //------------------------------------------------------------------------------
 481
 482
 483 //------------------------------------------------------------------------------
 484 void vvMainWindow::ComputeDeformableRegistration()
 485 {
 486   if (mSlicerManagers.size() > 0) {
 487     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 488     vvDeformationDialog dialog(index,mSlicerManagers);
 489     if (dialog.exec()) {
 490       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 491       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 492       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 493     } else
 494       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 495   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 496 }
 497 //------------------------------------------------------------------------------
 498
 499
 500 //------------------------------------------------------------------------------
 501 void vvMainWindow::WarpImage()
 502 {
 503   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 504   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 505     bool ok;
 506     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 507                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 508     if (ok) {
 509       WarpImage(mSlicerManagers[index],ref);
 510     }
 511   } else
 512     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 513 }
 514 //------------------------------------------------------------------------------
 515
 516
 517 //------------------------------------------------------------------------------
 518 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 519 {
 520   if (!selected_slicer->GetVF().IsNull()) {
 521     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 522     QFileInfo info(selected_slicer->GetFileName().c_str());
 523     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 524                      reference_phase,this);
 525     if (warp.ComputeWarpedImage()) {
 526       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 527       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 528       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 529       QApplication::restoreOverrideCursor();
 530     } else {
 531       QApplication::restoreOverrideCursor();
 532       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 533     }
 534   } else
 535     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 536 }
 537 //------------------------------------------------------------------------------
 538
 539
 540 //------------------------------------------------------------------------------
 541 vvMainWindow::~vvMainWindow()
 542 {
 543   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 544     if (mSlicerManagers[i] != NULL)
 545       delete mSlicerManagers[i];
 546   }
 547 }
 548 //------------------------------------------------------------------------------
 549
 550 //------------------------------------------------------------------------------
 551 QTabWidget * vvMainWindow::GetTab()
 552 {
 553   return tabWidget;
 554 }
 555 //------------------------------------------------------------------------------
 556
 557
 558 //------------------------------------------------------------------------------
 559 void vvMainWindow::MergeImages()
 560 {
 561   QString Extensions = EXTENSIONS;
 562   Extensions += ";;All Files (*)";
 563   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 564   if (files.isEmpty())
 565     return;
 566   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 567   std::vector<std::string> vector;
 568
 569   unsigned int currentDim = 0;
 570   std::vector<double> currentSpacing;
 571   std::vector<int> currentSize;
 572   std::vector<double> currentOrigin;
 573
 574   for (int i = 0; i < files.size(); i++) {
 575     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 576                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 577     reader->SetFileName(files[i].toStdString().c_str());
 578     reader->ReadImageInformation();
 579     if (reader)        {
 580       //NOViewWidget->hide();
 581       //NEViewWidget->hide();
 582       //SOViewWidget->hide();
 583       //SEViewWidget->hide();
 584       if (i == 0)
 585         currentDim = reader->GetNumberOfDimensions();
 586       bool IsOk = true;
 587       for (unsigned int j = 0; j < currentDim; j++) {
 588         if (i == 0) {
 589           if (j == 0) {
 590             currentSpacing.resize(currentDim);
 591             currentSize.resize(currentDim);
 592             currentOrigin.resize(currentDim);
 593           }
 594           currentOrigin[j] = reader->GetOrigin(j);
 595           currentSpacing[j] = reader->GetSpacing(j);
 596           currentSize[j] = reader->GetDimensions(j);
 597         } else if (currentDim != reader->GetNumberOfDimensions()
 598                    || currentSpacing[j] != reader->GetSpacing(j)
 599                    || currentSize[j] != (int)reader->GetDimensions(j)
 600                    || currentOrigin[j] != reader->GetOrigin(j)) {
 601           QString error = "Cannot read file (too different from others ";
 602           error += files[i].toStdString().c_str();
 603           QMessageBox::information(this,tr("Reading problem"),error);
 604           IsOk = false;
 605           break;
 606         }
 607       }
 608       if (IsOk)
 609         vector.push_back(files[i].toStdString());
 610     }
 611   }
 612   if (vector.size() > 0)
 613     LoadImages(vector, vvImageReader::MERGED);
 614 }
 615 //------------------------------------------------------------------------------
 616
 617 //------------------------------------------------------------------------------
 618 void vvMainWindow::SliceImages()
 619 {
 620   QString Extensions = EXTENSIONS;
 621   Extensions += ";;All Files (*)";
 622
 623   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 624   if (files.isEmpty())
 625     return;
 626   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 627   std::vector<std::string> vector;
 628   for (int i = 0; i < files.size(); i++)
 629     vector.push_back(files[i].toStdString());
 630   LoadImages(vector, vvImageReader::SLICED);
 631 }
 632 //------------------------------------------------------------------------------
 633
 634 //------------------------------------------------------------------------------
 635 void vvMainWindow::MergeImagesWithTime()
 636 {
 637   QString Extensions = EXTENSIONS;
 638   Extensions += ";;All Files (*)";
 639   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 640   if (files.isEmpty())
 641     return;
 642   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 643   std::vector<std::string> vector;
 644
 645   unsigned int currentDim = 0;
 646   std::vector<double> currentSpacing;
 647   std::vector<int> currentSize;
 648   std::vector<double> currentOrigin;
 649
 650   for (int i = 0; i < files.size(); i++) {
 651     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 652                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 653     if (reader) {
 654       reader->SetFileName(files[i].toStdString().c_str());
 655       reader->ReadImageInformation();
 656       if (i == 0)
 657         currentDim = reader->GetNumberOfDimensions();
 658       bool IsOk = true;
 659       for (unsigned int j = 0; j < currentDim; j++) {
 660         if (i == 0) {
 661           if (j == 0) {
 662             currentSpacing.resize(currentDim);
 663             currentSize.resize(currentDim);
 664             currentOrigin.resize(currentDim);
 665           }
 666           currentOrigin[j] = reader->GetOrigin(j);
 667           currentSpacing[j] = reader->GetSpacing(j);
 668           currentSize[j] = reader->GetDimensions(j);
 669         } else if (currentDim != reader->GetNumberOfDimensions()
 670                    || currentSpacing[j] != reader->GetSpacing(j)
 671                    || currentSize[j] != (int)reader->GetDimensions(j)
 672                    || currentOrigin[j] != reader->GetOrigin(j)) {
 673           QString error = "Cannot read file (too different from others ";
 674           error += files[i].toStdString().c_str();
 675           QMessageBox::information(this,tr("Reading problem"),error);
 676           IsOk = false;
 677           break;
 678         }
 679       }
 680       if (IsOk)
 681         vector.push_back(files[i].toStdString());
 682     } else {
 683       QString error = "Cannot read file info for ";
 684       error += files[i].toStdString().c_str();
 685       error += "\n";
 686       error += "Maybe you're trying to open an image in an unsupported format?\n";
 687       QMessageBox::information(this,tr("Reading problem"),error);
 688     }
 689   }
 690   sort(vector.begin(),vector.end());
 691   if (vector.size() > 1)
 692     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 693   else
 694     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.");
 695 }
 696 //------------------------------------------------------------------------------
 697
 698
 699 //------------------------------------------------------------------------------
 700 void vvMainWindow::OpenDicom()
 701 {
 702   std::vector<std::string> files;
 703
 704   std::cout << "dicomSeriesSelector " << std::endl;
 705   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 706     files = *(dicomSeriesSelector->GetFilenames());
 707     LoadImages(files, vvImageReader::DICOM);
 708   }
 709 }
 710 //------------------------------------------------------------------------------
 711
 712 //------------------------------------------------------------------------------
 713 void vvMainWindow::OpenImages()
 714 {
 715   QString Extensions = EXTENSIONS;
 716   Extensions += ";;All Files (*)";
 717
 718   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 719   if (files.isEmpty())
 720     return;
 721   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 722   std::vector<std::string> vector;
 723   for (int i = 0; i < files.size(); i++)
 724     vector.push_back(files[i].toStdString());
 725   LoadImages(vector, vvImageReader::IMAGE);
 726 }
 727 //------------------------------------------------------------------------------
 728 void vvMainWindow::OpenRecentImage()
 729 {
 730   QAction * caller = qobject_cast<QAction*>(sender());
 731   std::vector<std::string> images;
 732   images.push_back(caller->text().toStdString());
 733   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 734   LoadImages(images, vvImageReader::IMAGE);
 735 }
 736 //------------------------------------------------------------------------------
 737
 738
 739 //------------------------------------------------------------------------------
 740 void vvMainWindow::OpenImageWithTime()
 741 {
 742   QString Extensions = EXTENSIONS;
 743   Extensions += ";;All Files (*)";
 744
 745   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 746   if (files.isEmpty())
 747     return;
 748   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 749   std::vector<std::string> vector;
 750   for (int i = 0; i < files.size(); i++) {
 751     vector.push_back(files[i].toStdString());
 752   }
 753   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 754 }
 755 //------------------------------------------------------------------------------
 756
 757
 758 //------------------------------------------------------------------------------
 759 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 760 {
 761   //Separate the way to open images and dicoms
 762   int fileSize;
 763   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 764     fileSize = files.size();
 765   else
 766     fileSize = 1;
 767
 768   // For SLICED, we need the number of slices (ndim and #slices)
 769   std::vector<unsigned int> nSlices;
 770   nSlices.resize(files.size());
 771   std::fill(nSlices.begin(), nSlices.end(), 1);
 772   if (filetype == vvImageReader::SLICED) {
 773     for (int i = 0; i < fileSize; i++) {
 774       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 775       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 776       if (!header) {
 777         nSlices[i] = 0;
 778         QString error = "Cannot open file \n";
 779         error += files[i].c_str();
 780         QMessageBox::information(this,tr("Reading problem"),error);
 781         return;
 782       }
 783       if (header->GetNumberOfDimensions() < 3) {
 784         nSlices[i] = 0;
 785         QString error = "Dimension problem. Cannot slice \n";
 786         error += files[i].c_str();
 787         QMessageBox::information(this,tr("Reading problem"),error);
 788         return;
 789       }
 790       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 791     }
 792   }
 793
 794   //Only add to the list of recently opened files when a single file is opened,
 795   //to avoid polluting the list of recently opened files
 796   if (files.size() == 1) {
 797     QFileInfo finfo=tr(files[0].c_str());
 798     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 799   }
 800   //init the progress events
 801   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 802   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 803   qApp->processEvents();
 804
 805   int numberofsuccesulreads=0;
 806   //open images as 1 or multiples
 807   for (int i = 0; i < fileSize; i++) {
 808
 809     progress.SetText("Opening " + files[i]);
 810     progress.SetProgress(i,fileSize);
 811     qApp->processEvents();
 812
 813     for (unsigned int j = 0; j < nSlices[i]; j++) {
 814       //read the image and put it in mSlicerManagers
 815       vvSlicerManager* imageManager = new vvSlicerManager(4);
 816       qApp->processEvents();
 817
 818       bool SetImageSucceed=false;
 819
 820       // Change filename if an image with the same already exist
 821       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 822
 823       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 824         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 825       else {
 826         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 827       }
 828       if (!SetImageSucceed) {
 829         QApplication::restoreOverrideCursor();
 830         QString error = "Cannot open file \n";
 831         error += imageManager->GetLastError().c_str();
 832         QMessageBox::information(this,tr("Reading problem"),error);
 833         delete imageManager;
 834       } else {
 835         mSlicerManagers.push_back(imageManager);
 836
 837         //create an item in the tree with good settings
 838         QTreeWidgetItem *item = new QTreeWidgetItem();
 839         item->setData(0,Qt::UserRole,files[i].c_str());
 840         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 841         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 842         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 843         qApp->processEvents();
 844
 845         //Create the buttons for reload and close
 846         qApp->processEvents();
 847         QTreePushButton* cButton = new QTreePushButton;
 848         cButton->setItem(item);
 849         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 850         cButton->setToolTip(tr("close image"));
 851         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 852         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 853                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 854
 855         QTreePushButton* rButton = new QTreePushButton;
 856         rButton->setItem(item);
 857         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 858         rButton->setToolTip(tr("reload image"));
 859         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 860         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 861                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 862
 863         DataTree->addTopLevelItem(item);
 864         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 865         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 866
 867         //set the id of the image
 868         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 869         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 870         mSlicerManagers.back()->SetId(id.toStdString());
 871
 872         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 873
 874         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 875                 this,SLOT(CurrentImageChanged(std::string)));
 876         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 877                 this, SLOT(CurrentPickedImageChanged(std::string)));
 878         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 879                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 880         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 881                 this, SLOT(VectorChanged(int,double,double,double, double)));
 882         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 883                 this, SLOT(OverlayChanged(int,double,double)));
 884         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 885                 this, SLOT(FusionChanged(int,double)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 887                 this,SLOT(WindowsChanged(int, int, int)));
 888         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 889                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 891                 this,SLOT(UpdateSlice(int,int)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 893                 this,SLOT(UpdateTSlice(int, int)));
 894         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 895                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 896         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 897                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 898         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 899                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 900         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 901                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 902         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 903         InitSlicers();
 904         numberofsuccesulreads++;
 905       }
 906     }
 907   }
 908   if (numberofsuccesulreads) {
 909     NOViewWidget->show();
 910     NEViewWidget->show();
 911     SOViewWidget->show();
 912     SEViewWidget->show();
 913     UpdateTree();
 914     InitDisplay();
 915     ShowLastImage();
 916
 917     // Try to guess default WindowLevel
 918     double range[2];
 919     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 920     if ((range[0] == 0) && (range[1] == 1)) {
 921       presetComboBox->setCurrentIndex(5);// binary
 922     } else {
 923       // TODO
 924     }
 925   }
 926   QApplication::restoreOverrideCursor();
 927 }
 928 //------------------------------------------------------------------------------
 929
 930 //------------------------------------------------------------------------------
 931 void vvMainWindow::UpdateTree()
 932 {
 933   DataTree->resizeColumnToContents(COLUMN_TREE);
 934   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 935   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 936   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 937   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 938   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 939   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 940   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 941 }
 942 //------------------------------------------------------------------------------
 943
 944 //------------------------------------------------------------------------------
 945 void vvMainWindow::CurrentImageChanged(std::string id)
 946 {
 947   if (id == mCurrentSelectedImageId) return; // Do nothing
 948   int selected = 0;
 949   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 950     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 951       selected = i;
 952     } else {
 953       DataTree->topLevelItem(i)->setSelected(0);
 954     }
 955     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 956       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 957
 958   }
 959   DataTree->topLevelItem(selected)->setSelected(1);
 960   mCurrentSelectedImageId = id;
 961   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 962 }
 963 //------------------------------------------------------------------------------
 964
 965 //------------------------------------------------------------------------------
 966 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 967 {
 968   if (id == mCurrentPickedImageId) return; // Do nothing
 969   int selected = 0;
 970   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 971     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 972       selected = i;
 973     } else {
 974       DataTree->topLevelItem(i)->setSelected(0);
 975     }
 976     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 977       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 978
 979   }
 980   DataTree->topLevelItem(selected)->setSelected(1);
 981   mCurrentPickedImageId = id;
 982   mCurrentPickedImageIndex = selected;
 983 }
 984 //------------------------------------------------------------------------------
 985
 986 //------------------------------------------------------------------------------
 987 void vvMainWindow::ImageInfoChanged()
 988 {
 989   contextActions[6]->setEnabled(1);
 990   contextActions[5]->setEnabled(1);
 991   actionSave_As->setEnabled(1);
 992   actionAdd_VF_to_current_Image->setEnabled(1);
 993   actionAdd_fusion_image->setEnabled(1);
 994   actionNorth_East_Window->setEnabled(1);
 995   actionNorth_West_Window->setEnabled(1);
 996   actionSouth_East_Window->setEnabled(1);
 997   actionSouth_West_Window->setEnabled(1);
 998   inverseButton->setEnabled(1);
 999
1000   goToCursorPushButton->setEnabled(1);
1001
1002   if (DataTree->selectedItems().size()) {
1003     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1004
1005     colorMapComboBox->setEnabled(1);
1006     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1007       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1008           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1009         colorMapComboBox->setEnabled(0);
1010         break;
1011       }
1012     }
1013
1014     std::vector<double> origin;
1015     std::vector<double> inputSpacing;
1016     std::vector<int> inputSize;
1017     std::vector<double> sizeMM;
1018     vtkSmartPointer<vtkMatrix4x4> transformation;
1019     int dimension=0;
1020     QString pixelType;
1021     QString inputSizeInBytes;
1022     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1023
1024     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1025       playButton->setEnabled(1);
1026       frameRateLabel->setEnabled(1);
1027       frameRateSpinBox->setEnabled(1);
1028     } else {
1029       playButton->setEnabled(0);
1030       frameRateLabel->setEnabled(0);
1031       frameRateSpinBox->setEnabled(0);
1032     }
1033
1034     //read image header
1035     int NPixel = 1;
1036
1037     vvImage::Pointer imageSelected;
1038     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1039       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1040       dimension = imageSelected->GetNumberOfDimensions();
1041       origin.resize(dimension);
1042       inputSpacing.resize(dimension);
1043       inputSize.resize(dimension);
1044       sizeMM.resize(dimension);
1045       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1046       for (int i = 0; i < dimension; i++) {
1047         origin[i] = imageSelected->GetOrigin()[i];
1048         inputSpacing[i] = imageSelected->GetSpacing()[i];
1049         inputSize[i] = imageSelected->GetSize()[i];
1050         sizeMM[i] = inputSize[i]*inputSpacing[i];
1051         NPixel *= inputSize[i];
1052       }
1053       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1054     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1055       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1056       dimension = imageSelected->GetNumberOfDimensions();
1057       origin.resize(dimension);
1058       inputSpacing.resize(dimension);
1059       inputSize.resize(dimension);
1060       sizeMM.resize(dimension);
1061       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1062       for (int i = 0; i < dimension; i++) {
1063         origin[i] = imageSelected->GetOrigin()[i];
1064         inputSpacing[i] = imageSelected->GetSpacing()[i];
1065         inputSize[i] = imageSelected->GetSize()[i];
1066         sizeMM[i] = inputSize[i]*inputSpacing[i];
1067         NPixel *= inputSize[i];
1068       }
1069       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1070     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1071       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1072       dimension = imageSelected->GetNumberOfDimensions();
1073       origin.resize(dimension);
1074       inputSpacing.resize(dimension);
1075       inputSize.resize(dimension);
1076       sizeMM.resize(dimension);
1077       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1078       for (int i = 0; i < dimension; i++) {
1079         origin[i] = imageSelected->GetOrigin()[i];
1080         inputSpacing[i] = imageSelected->GetSpacing()[i];
1081         inputSize[i] = imageSelected->GetSize()[i];
1082         sizeMM[i] = inputSize[i]*inputSpacing[i];
1083         NPixel *= inputSize[i];
1084       }
1085       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1086     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1087       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1088       dimension = imageSelected->GetNumberOfDimensions();
1089       origin.resize(dimension);
1090       inputSpacing.resize(dimension);
1091       inputSize.resize(dimension);
1092       sizeMM.resize(dimension);
1093       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1094       for (int i = 0; i < dimension; i++) {
1095         origin[i] = imageSelected->GetOrigin()[i];
1096         inputSpacing[i] = imageSelected->GetSpacing()[i];
1097         inputSize[i] = imageSelected->GetSize()[i];
1098         sizeMM[i] = inputSize[i]*inputSpacing[i];
1099         NPixel *= inputSize[i];
1100       }
1101       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1102     }
1103
1104     QString dim = QString::number(dimension) + " (";
1105     dim += pixelType + ")";
1106
1107     infoPanel->setFileName(image);
1108     infoPanel->setDimension(dim);
1109     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1110     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1111     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1112     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1113     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1114     transformation = imageSelected->GetTransform()->GetMatrix();
1115     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1116
1117     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1118                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1119     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1120     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1121
1122     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1123     for (int i = 0; i < 4; i++) {
1124       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1125         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1126         break;
1127       }
1128     }
1129     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1130     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1131     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1132     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1133
1134     infoPanel->setFileName(image);
1135     infoPanel->setDimension(dim);
1136     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1137     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1138     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1139     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1140     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1141
1142     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1143                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1144     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1145     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1146
1147     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1148     for (int i = 0; i < 4; i++) {
1149       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1150         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1151         break;
1152       }
1153     }
1154     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1155     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1156     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1157     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1158
1159     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1160       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1161       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1162                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1163                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1164     } else {
1165       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1166       overlayPanel->getVFProperty(-1,-1,-1);
1167     }
1168     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1169       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1170       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1171     } else {
1172       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1173       overlayPanel->getOverlayProperty(-1);
1174     }
1175     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1176       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1177       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1178                                       mSlicerManagers[index]->GetFusionColorMap(),
1179                                       mSlicerManagers[index]->GetFusionWindow(),
1180                                       mSlicerManagers[index]->GetFusionLevel());
1181     } else {
1182       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1183       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1184     }
1185   }
1186 }
1187 //------------------------------------------------------------------------------
1188
1189 //------------------------------------------------------------------------------
1190 void vvMainWindow::ShowDocumentation()
1191 {
1192   documentation->show();
1193 }
1194 //------------------------------------------------------------------------------
1195 void vvMainWindow::ShowHelpDialog()
1196 {
1197   help_dialog->show();
1198 }
1199 //------------------------------------------------------------------------------
1200
1201 //------------------------------------------------------------------------------
1202 void vvMainWindow::ChangeViewMode()
1203 {
1204   QListIterator<int> it0(splitter_3->sizes());
1205   QListIterator<int> it1(splitter_3->sizes());
1206   int max0 = 0;
1207   int max1 = 1;
1208   while (it0.hasNext()) {
1209     max0 += it0.next();
1210   }
1211   while (it1.hasNext()) {
1212     max1 += it1.next();
1213   }
1214   QList<int> size0;
1215   QList<int> size1;
1216   if (viewMode == 1) {
1217     viewMode = 0;
1218     size0.push_back(max0);
1219     size0.push_back(0);
1220     size1.push_back(max1);
1221     size1.push_back(0);
1222     splitter_3->setSizes(size0);
1223     OSplitter->setSizes(size1);
1224     DataTree->setColumnHidden(2,1);
1225     DataTree->setColumnHidden(3,1);
1226     DataTree->setColumnHidden(4,1);
1227   } else {
1228     viewMode = 1;
1229     size0.push_back(int(max0/2));
1230     size0.push_back(int(max0/2));
1231     size1.push_back(int(max1/2));
1232     size1.push_back(int(max1/2));
1233     splitter_3->setSizes(size0);
1234     OSplitter->setSizes(size1);
1235     DataTree->setColumnHidden(2,0);
1236     DataTree->setColumnHidden(3,0);
1237     DataTree->setColumnHidden(4,0);
1238   }
1239 }
1240 //------------------------------------------------------------------------------
1241
1242 //------------------------------------------------------------------------------
1243 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1244 {
1245   QString result = "";// QString::number(size);
1246   //result += " bytes (";
1247   if (size > 1000000000) {
1248     size /= 1000000000;
1249     result += QString::number(size);
1250     result += "Gb";//)";
1251   } else if (size > 1000000) {
1252     size /= 1000000;
1253     result += QString::number(size);
1254     result += "Mb";//)";
1255   } else if (size > 1000) {
1256     size /= 1000;
1257     result += QString::number(size);
1258     result += "kb";//)";
1259   }
1260   return result;
1261 }
1262 //------------------------------------------------------------------------------
1263
1264 //------------------------------------------------------------------------------
1265 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1266 {
1267   std::ostringstream strmatrix;
1268
1269   for (unsigned int i = 0; i < 4; i++) {
1270     for (unsigned int j = 0; j < 4; j++) {
1271       strmatrix.flags(ios::showpos);
1272       strmatrix.width(10);
1273       strmatrix.precision(3);
1274       strmatrix.setf(ios::fixed,ios::floatfield);
1275       strmatrix.fill(' ');
1276       strmatrix << std::left << matrix->GetElement(i, j);
1277       //strmatrix.width(10);
1278       strmatrix << " ";
1279     }
1280     strmatrix << std::endl;
1281   }
1282   QString result = strmatrix.str().c_str();
1283   return result;
1284 }
1285 //------------------------------------------------------------------------------
1286
1287 //------------------------------------------------------------------------------
1288 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1289 {
1290   QString result;
1291   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1292     if (i != 0)
1293       result += " ";
1294     result += QString::number(vectorDouble[i]);
1295   }
1296   return result;
1297 }
1298 //------------------------------------------------------------------------------
1299
1300 //------------------------------------------------------------------------------
1301 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1302 {
1303   QString result;
1304   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1305     if (i != 0)
1306       result += " ";
1307     result += QString::number(vectorInt[i]);
1308   }
1309   return result;
1310 }
1311 //------------------------------------------------------------------------------
1312
1313 //------------------------------------------------------------------------------
1314 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1315 {
1316   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1317   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1318     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1319       return i;
1320   }
1321   return -1;
1322 }
1323 //------------------------------------------------------------------------------
1324
1325 //------------------------------------------------------------------------------
1326 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1327 {
1328   QString id = sm->GetId().c_str();
1329   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1330     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1331       return DataTree->topLevelItem(i);
1332   }
1333   return NULL;
1334 }
1335 //------------------------------------------------------------------------------
1336
1337 //------------------------------------------------------------------------------
1338 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1339 {
1340   int index = GetSlicerIndexFromItem(clicked_item);
1341   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1342     return;
1343   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1344     //Trick to avoid redoing twice the job for a key (sr)
1345     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1346
1347     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1348     if (DataTree->topLevelItem(index) == current_row) {
1349       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1350       if (current_row == clicked_item) {
1351         //If we just activated a slicer
1352         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1353           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1354           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1355           DisplaySliders(i,column-1);
1356           std::map<std::string,int> overlay_counts;
1357           for (int child = 0; child < current_row->childCount(); child++) {
1358             std::string overlay_type =
1359               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1360             overlay_counts[overlay_type]++;
1361             current_row->child(child)->setData(column,Qt::CheckStateRole,
1362                                                current_row->data(column,Qt::CheckStateRole));
1363             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1364           }
1365         } else { //We don't allow simply desactivating a slicer
1366           clicked_item->setData(column,Qt::CheckStateRole,2);
1367           return;
1368         }
1369       }
1370       //if we clicked on the vector(or overlay) and not the image
1371       else {
1372         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1373           current_row->setData(column,Qt::CheckStateRole,2);
1374           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1375           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1376           DisplaySliders(i,column-1);
1377         }
1378         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1379         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1380         int overlay_index=0;
1381         for (int child = 0; child < current_row->childCount(); child++) {
1382           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1383             overlay_index++;
1384           if (current_row->child(child) == clicked_item) break;
1385         }
1386         clicked_slicer->SetActorVisibility(
1387           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1388       }
1389     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1390       current_row->setData(column,Qt::CheckStateRole,0);
1391       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1392       std::map<std::string,int> overlay_counts;
1393       for (int child = 0; child < current_row->childCount(); child++) {
1394         std::string overlay_type =
1395           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1396         overlay_counts[overlay_type]++;
1397         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1398         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1399         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1400       }
1401     }
1402     //mSlicerManagers[i]->SetColorMap(-1);
1403     mSlicerManagers[i]->SetColorMap();
1404   }
1405   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1406 }
1407 //------------------------------------------------------------------------------
1408
1409 void vvMainWindow::InitSlicers()
1410 {
1411   if (mSlicerManagers.size()) {
1412     mSlicerManagers.back()->GenerateDefaultLookupTable();
1413
1414     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1415     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1416     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1417     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1418   }
1419 }
1420
1421 //------------------------------------------------------------------------------
1422 void vvMainWindow::InitDisplay()
1423 {
1424   if (mSlicerManagers.size()) {
1425     //BE CAREFUL : this is absolutely necessary to set the interactor style
1426     //in order to have the same style instanciation for all SlicerManagers in
1427     // a same window
1428     for (int j = 0; j < 4; j++) {
1429       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1430       style->SetAutoAdjustCameraClippingRange(1);
1431       bool AlreadySelected = false;
1432       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1433         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1434
1435         //select the image only if previous are not selected
1436         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1437           mSlicerManagers[i]->UpdateSlicer(j,1);
1438           AlreadySelected = true;
1439         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1440           if (DataTree->selectedItems().size() == 0)
1441             DataTree->topLevelItem(i)->setSelected(1);
1442           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1443           mSlicerManagers[i]->UpdateSlicer(j,1);
1444           DisplaySliders(i,j);
1445         } else {
1446           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1447           mSlicerManagers[i]->UpdateSlicer(j,0);
1448         }
1449       }
1450       style->Delete();
1451     }
1452   }
1453 }
1454 //------------------------------------------------------------------------------
1455
1456 //------------------------------------------------------------------------------
1457 void vvMainWindow::DisplaySliders(int slicer, int window)
1458 {
1459   int range[2];
1460   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1461   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1462
1463   int tRange[2];
1464   tRange[0] = 0;
1465   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1466   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1467   bool showHorizontal = false;
1468   bool showVertical = false;
1469   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1470       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1471           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1472           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1473     showVertical = true;
1474   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1475       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1476       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1477     showHorizontal = true;
1478
1479   if (showVertical)
1480     verticalSliders[window]->show();
1481   else
1482     verticalSliders[window]->hide();
1483   verticalSliders[window]->setRange(range[0],range[1]);
1484   verticalSliders[window]->setValue(position);
1485
1486   if (showHorizontal)
1487     horizontalSliders[window]->show();
1488   else
1489     horizontalSliders[window]->hide();
1490   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1491   horizontalSliders[window]->setValue(tPosition);
1492 }
1493 //------------------------------------------------------------------------------
1494
1495 //------------------------------------------------------------------------------
1496 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1497 {
1498   int index = GetSlicerIndexFromItem(item);
1499
1500   if (DataTree->topLevelItem(index) != item) {
1501     QString warning = "Do you really want to close the overlay : ";
1502     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1503     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1504                        warning, 0, this);
1505     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1506     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1507     if (msgBox.exec() == QMessageBox::AcceptRole) {
1508       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1509       int overlay_index=0;
1510       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1511         if (DataTree->topLevelItem(index)->\
1512             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1513           overlay_index++;
1514         if (DataTree->topLevelItem(index)->child(child) == item) break;
1515       }
1516       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1517       mSlicerManagers[index]->SetColorMap(0);
1518       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1519       mSlicerManagers[index]->Render();
1520     }
1521   } else if (DataTree->topLevelItemCount() <= 1) {
1522     QString warning = "Do you really want to close the image : ";
1523     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1524     warning += "\nThis is the last image, you're about to close vv !!!";
1525     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1526                        warning, 0, this);
1527     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1528     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1529     if (msgBox.exec() == QMessageBox::AcceptRole) {
1530       this->close();
1531     }
1532   } else {
1533     QString warning = "Do you really want to close the image : ";
1534     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1535     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1536                        warning, 0, this);
1537     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1538     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1539     if (msgBox.exec() == QMessageBox::AcceptRole) {
1540
1541       // Tell tools that we close an image
1542       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1543
1544       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1545       DataTree->takeTopLevelItem(index);
1546       for (int i = 0; i < index; i++) {
1547         Manageriter++;
1548       }
1549       linkPanel->removeImage(index);
1550       mSlicerManagers[index]->RemoveActors();
1551       delete mSlicerManagers[index];
1552       mSlicerManagers.erase(Manageriter);
1553
1554       //
1555       InitDisplay();
1556     }
1557   }
1558   ImageInfoChanged();
1559 }
1560 //------------------------------------------------------------------------------
1561
1562 //------------------------------------------------------------------------------
1563 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1564 {
1565   // int index = GetSlicerIndexFromItem(item);
1566   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1567   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1568   //     mSlicerManagers[index]->ReloadVF();
1569   //   else
1570   //     mSlicerManagers[index]->Reload();
1571
1572   //   QApplication::restoreOverrideCursor();
1573   int index = GetSlicerIndexFromItem(item);
1574   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1575   QString role=item->data(1,Qt::UserRole).toString();
1576   if ( role == "vector")
1577     mSlicerManagers[index]->ReloadVF();
1578   else if (role == "overlay")
1579     mSlicerManagers[index]->ReloadOverlay();
1580   else if (role == "fusion")
1581     mSlicerManagers[index]->ReloadFusion();
1582   else
1583     mSlicerManagers[index]->Reload();
1584
1585   // Update view and info
1586   ImageInfoChanged();
1587   mSlicerManagers[index]->Render();
1588   QApplication::restoreOverrideCursor();
1589 }
1590 //------------------------------------------------------------------------------
1591
1592 //------------------------------------------------------------------------------
1593 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1594 {
1595   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1596 }
1597 //------------------------------------------------------------------------------
1598
1599 //------------------------------------------------------------------------------
1600 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1601 {
1602   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1603 }
1604 //------------------------------------------------------------------------------
1605
1606 //------------------------------------------------------------------------------
1607 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1608 {
1609   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1610 }
1611 //------------------------------------------------------------------------------
1612
1613 //------------------------------------------------------------------------------
1614 void vvMainWindow::FusionChanged(int visibility, double value)
1615 {
1616   overlayPanel->getCurrentFusionInfo(visibility,value);
1617 }
1618 //------------------------------------------------------------------------------
1619
1620 //------------------------------------------------------------------------------
1621 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1622 {
1623   infoPanel->setViews(window, view, slice);
1624 }
1625 //------------------------------------------------------------------------------
1626
1627 //------------------------------------------------------------------------------
1628 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1629 {
1630   windowSpinBox->setValue(window);
1631   levelSpinBox->setValue(level);
1632   colorMapComboBox->setCurrentIndex(colormap);
1633   presetComboBox->setCurrentIndex(preset);
1634 }
1635 //------------------------------------------------------------------------------
1636
1637 //------------------------------------------------------------------------------
1638 void vvMainWindow::WindowLevelEdited()
1639 {
1640   presetComboBox->setCurrentIndex(6);
1641   UpdateWindowLevel();
1642 }
1643 //------------------------------------------------------------------------------
1644
1645 //------------------------------------------------------------------------------
1646 void vvMainWindow::UpdateWindowLevel()
1647 {
1648   if (DataTree->selectedItems().size()) {
1649     if (presetComboBox->currentIndex() == 7) //For ventilation
1650       colorMapComboBox->setCurrentIndex(5);
1651     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1652     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1653     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1654     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1655     mSlicerManagers[index]->Render();
1656     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1657     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1658   }
1659 }
1660 //------------------------------------------------------------------------------
1661
1662 //------------------------------------------------------------------------------
1663 void vvMainWindow::UpdateColorMap()
1664 {
1665   if (DataTree->selectedItems().size()) {
1666     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1667     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1668     mSlicerManagers[index]->Render();
1669   }
1670 }
1671 //------------------------------------------------------------------------------
1672 void vvMainWindow::SwitchWindowLevel()
1673 {
1674   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1675   int window = mSlicerManagers[index]->GetColorWindow();
1676   presetComboBox->setCurrentIndex(6);
1677   windowSpinBox->setValue(-window);
1678   UpdateWindowLevel();
1679 }
1680 //------------------------------------------------------------------------------
1681
1682 //------------------------------------------------------------------------------
1683 void vvMainWindow::ApplyWindowLevelToAllImages()
1684 {
1685   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1686     if (mSlicerManagers[i] == NULL)
1687       continue;
1688     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1689     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1690     mSlicerManagers[i]->SetPreset(6);
1691     mSlicerManagers[i]->Render();
1692   }
1693 }
1694 //------------------------------------------------------------------------------
1695
1696 //------------------------------------------------------------------------------
1697 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1698 {
1699   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1700     if (mSlicerManagers[i]->GetId() == id) {
1701       //mSlicerManagers[i]->SetTSlice(temps);
1702       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1703       mSlicerManagers[i]->UpdateViews(0,slicer);
1704       break;
1705     }
1706   }
1707 }
1708 //------------------------------------------------------------------------------
1709
1710 //------------------------------------------------------------------------------
1711 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1712 {
1713   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1714     if (id == mSlicerManagers[i]->GetId()) {
1715       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1716     }
1717   }
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::ShowContextMenu(QPoint point)
1723 {
1724   if (!DataTree->selectedItems().size()) {
1725     contextActions[1]->setEnabled(0);
1726     contextActions[2]->setEnabled(0);
1727     contextActions[3]->setEnabled(0);
1728     contextActions[4]->setEnabled(0);
1729     contextActions[5]->setEnabled(0);
1730     contextActions[6]->setEnabled(0);
1731   } else {
1732     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1733     contextActions[1]->setEnabled(1);
1734     contextActions[2]->setEnabled(
1735       DataTree->itemWidget(DataTree->selectedItems()[0],
1736                            COLUMN_RELOAD_IMAGE)->isEnabled());
1737     contextActions[3]->setEnabled(1);
1738     contextActions[5]->setEnabled(1);
1739     contextActions[6]->setEnabled(1);
1740
1741     if (mSlicerManagers[index]->GetDimension() < 3)
1742       contextActions[4]->setEnabled(0);
1743     else
1744       contextActions[4]->setEnabled(1);
1745   }
1746   contextMenu.exec(QCursor::pos());
1747 }
1748 //------------------------------------------------------------------------------
1749
1750 //------------------------------------------------------------------------------
1751 void vvMainWindow::CloseImage()
1752 {
1753   CloseImage(DataTree->selectedItems()[0],0);
1754 }
1755 //------------------------------------------------------------------------------
1756
1757 //------------------------------------------------------------------------------
1758 void vvMainWindow::ReloadImage()
1759 {
1760   ReloadImage(DataTree->selectedItems()[0],0);
1761 }
1762 //------------------------------------------------------------------------------
1763
1764 //------------------------------------------------------------------------------
1765 void vvMainWindow::SelectOverlayImage()
1766 {
1767   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1768
1769   //check if one overlay image is added
1770   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1771     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1772       QString error = "Cannot add more than one compared image\n";
1773       error += "Please remove first ";
1774       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1775       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1776       return;
1777     }
1778
1779   QString Extensions = EXTENSIONS;
1780   Extensions += ";;All Files (*)";
1781   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1782   if (!file.isEmpty())
1783     AddOverlayImage(index,file);
1784 }
1785 //------------------------------------------------------------------------------
1786
1787 //------------------------------------------------------------------------------
1788 void vvMainWindow::AddOverlayImage(int index, QString file)
1789 {
1790
1791   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1792   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1793                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1794   reader->SetFileName(file.toStdString().c_str());
1795   reader->ReadImageInformation();
1796   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1797   int dimension = reader->GetNumberOfDimensions();
1798   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1799   vvProgressDialog progress("Opening " + file.toStdString());
1800   qApp->processEvents();
1801
1802   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1803   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1804     //create an item in the tree with good settings
1805     QTreeWidgetItem *item = new QTreeWidgetItem();
1806     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1807     item->setData(1,Qt::UserRole,tr("overlay"));
1808     QFileInfo fileinfo(file); //Do not show the path
1809     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1810     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1811     qApp->processEvents();
1812
1813     for (int j = 1; j <= 4; j++) {
1814       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1815       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1816           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1817     }
1818
1819     //Create the buttons for reload and close
1820     qApp->processEvents();
1821     QTreePushButton* cButton = new QTreePushButton;
1822     cButton->setItem(item);
1823     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1824     cButton->setToolTip(tr("close image"));
1825     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1826     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1827             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1828
1829     QTreePushButton* rButton = new QTreePushButton;
1830     rButton->setItem(item);
1831     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1832     rButton->setToolTip(tr("reload image"));
1833     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1834     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1835             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1836
1837     DataTree->topLevelItem(index)->setExpanded(1);
1838     DataTree->topLevelItem(index)->addChild(item);
1839     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1840     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1841
1842     //set the id of the image
1843     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1844     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1845     UpdateTree();
1846     qApp->processEvents();
1847     ImageInfoChanged();
1848     QApplication::restoreOverrideCursor();
1849   } else {
1850     QApplication::restoreOverrideCursor();
1851     QString error = "Cannot import the new image.\n";
1852     error += mSlicerManagers[index]->GetLastError().c_str();
1853     QMessageBox::information(this,tr("Problem reading image !"),error);
1854   }
1855 }
1856 //------------------------------------------------------------------------------
1857
1858
1859 //------------------------------------------------------------------------------
1860 void vvMainWindow::AddROI(int index, QString file)
1861 {
1862   /*
1863   // Get slice manager
1864
1865   // Load image
1866
1867   vvImageReader * mReader = new vvImageReader;
1868   mReader->SetInputFilename(filename.toStdString());
1869   mReader->Update(IMAGE);
1870   if (mReader->GetLastError().size() != 0) {
1871     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1872     QString error = "Cannot open file \n";
1873     error += mReader->GetLastError().c_str();
1874     QMessageBox::information(this,tr("Reading problem"),error);
1875     delete mReader;
1876     return;
1877   }
1878   vvImage::Pointer roi = mReader->GetOutput();
1879
1880   // Create roi in new tool
1881   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1882   */
1883 }
1884 //------------------------------------------------------------------------------
1885
1886 //------------------------------------------------------------------------------
1887 void vvMainWindow::SelectFusionImage()
1888 {
1889   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1890
1891   //check if one fusion image is added
1892   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1893     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1894       QString error = "Cannot add more than one fusion image\n";
1895       error += "Please remove first ";
1896       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1897       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1898       return;
1899     }
1900
1901   QString Extensions = EXTENSIONS;
1902   Extensions += ";;All Files (*)";
1903   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1904   if (!file.isEmpty())
1905     AddFusionImage(index,file);
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::AddFusionImage(int index, QString file)
1911 {
1912   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1913   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1914                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1915   reader->SetFileName(file.toStdString().c_str());
1916   reader->ReadImageInformation();
1917   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1918   if (reader) {
1919     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1920     vvProgressDialog progress("Opening fusion");
1921     qApp->processEvents();
1922
1923     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1924     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1925                                           reader->GetNumberOfDimensions(), component)) {
1926       //create an item in the tree with good settings
1927       QTreeWidgetItem *item = new QTreeWidgetItem();
1928       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1929       item->setData(1,Qt::UserRole,tr("fusion"));
1930       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1931       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1932       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1933       qApp->processEvents();
1934
1935       for (int j = 1; j <= 4; j++) {
1936         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1937         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1938             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1939       }
1940
1941       //Create the buttons for reload and close
1942       qApp->processEvents();
1943       QTreePushButton* cButton = new QTreePushButton;
1944       cButton->setItem(item);
1945       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1946       cButton->setToolTip(tr("close image"));
1947       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1948       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1949               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1950
1951       QTreePushButton* rButton = new QTreePushButton;
1952       rButton->setItem(item);
1953       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1954       rButton->setToolTip(tr("reload image"));
1955       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1956       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1957               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1958
1959       DataTree->topLevelItem(index)->setExpanded(1);
1960       DataTree->topLevelItem(index)->addChild(item);
1961       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1962       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1963
1964       //set the id of the image
1965       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1966       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1967       UpdateTree();
1968       qApp->processEvents();
1969       ImageInfoChanged();
1970       QApplication::restoreOverrideCursor();
1971     } else {
1972       QApplication::restoreOverrideCursor();
1973       QString error = "Cannot import the new image.\n";
1974       error += mSlicerManagers[index]->GetLastError().c_str();
1975       QMessageBox::information(this,tr("Problem reading image !"),error);
1976     }
1977   } else {
1978     QString error = "Cannot import the new image.\n";
1979     QMessageBox::information(this,tr("Problem reading image !"),error);
1980   }
1981 }
1982 //------------------------------------------------------------------------------
1983
1984
1985 //------------------------------------------------------------------------------
1986 void vvMainWindow::OpenField()
1987 {
1988   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1989   //check if a vector field has already been added
1990   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1991     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1992       QString error = "Cannot add more than one vector field\n";
1993       error += "Please remove first ";
1994       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1995       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1996       return;
1997     }
1998
1999   QString Extensions = "Images ( *.mhd)";
2000   Extensions += ";;Images ( *.vf)";
2001   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2002   if (!file.isEmpty())
2003     AddField(file,index);
2004 }
2005 //------------------------------------------------------------------------------
2006
2007
2008 //------------------------------------------------------------------------------
2009 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2010 {
2011   //create an item in the tree with good settings
2012   QTreeWidgetItem *item = new QTreeWidgetItem();
2013   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2014   item->setData(1,Qt::UserRole,tr("vector"));
2015   QFileInfo fileinfo(filename); //Do not show the path
2016   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2017   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2018   qApp->processEvents();
2019
2020   for (int j = 1; j <= 4; j++) {
2021     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2022     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2023         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2024   }
2025
2026   //Create the buttons for reload and close
2027   qApp->processEvents();
2028   QTreePushButton* cButton = new QTreePushButton;
2029   cButton->setItem(item);
2030   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2031   cButton->setToolTip(tr("close vector field"));
2032   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2033   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2034           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2035
2036   QTreePushButton* rButton = new QTreePushButton;
2037   rButton->setItem(item);
2038   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2039   rButton->setToolTip(tr("reload vector field"));
2040   rButton->setEnabled(from_disk);
2041   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2042   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2043           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2044
2045   DataTree->topLevelItem(index)->setExpanded(1);
2046   DataTree->topLevelItem(index)->addChild(item);
2047   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2048   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2049
2050   //set the id of the image
2051   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2052   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2053   UpdateTree();
2054   qApp->processEvents();
2055   ImageInfoChanged();
2056   QApplication::restoreOverrideCursor();
2057 }
2058 //------------------------------------------------------------------------------
2059
2060
2061 //------------------------------------------------------------------------------
2062 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2063 {
2064   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2065   vvSlicerManager* imageManager = mSlicerManagers[index];
2066   if (imageManager->SetVF(vf,file.toStdString())) {
2067     AddFieldEntry(file,index,false);
2068   } else {
2069     QString error = "Cannot import the vector field for this image.\n";
2070     error += imageManager->GetLastError().c_str();
2071     QMessageBox::information(this,tr("Problem reading VF !"),error);
2072   }
2073   QApplication::restoreOverrideCursor();
2074 }
2075 //------------------------------------------------------------------------------
2076
2077
2078 //------------------------------------------------------------------------------
2079 void vvMainWindow::AddField(QString file,int index)
2080 {
2081   if (QFile::exists(file)) {
2082     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2083
2084     //init the progress events
2085     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2086     vvProgressDialog progress("Opening " + file.toStdString());
2087     qApp->processEvents();
2088
2089     //read the vector and put it in the current mSlicerManager
2090     vvSlicerManager* imageManager = mSlicerManagers[index];
2091     qApp->processEvents();
2092
2093     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2094     if (imageManager->SetVF(file.toStdString())) {
2095       imageManager->Render();
2096       AddFieldEntry(file,index,true);
2097     } else {
2098       QApplication::restoreOverrideCursor();
2099       QString error = "Cannot import the vector field for this image.\n";
2100       error += imageManager->GetLastError().c_str();
2101       QMessageBox::information(this,tr("Problem reading VF !"),error);
2102     }
2103   } else
2104     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2105
2106 }
2107 //------------------------------------------------------------------------------
2108
2109
2110 //------------------------------------------------------------------------------
2111 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2112 {
2113   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2114   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2115     for (int i = 0; i < 4; i++) {
2116       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2117       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2118       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2119       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2120       if (log > 0)
2121         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2122       else
2123         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2124     }
2125   }
2126 }
2127 //------------------------------------------------------------------------------
2128
2129
2130 //------------------------------------------------------------------------------
2131 void vvMainWindow::SetOverlayProperty(int color)
2132 {
2133   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2134   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2135     mSlicerManagers[index]->SetOverlayColor(color);
2136     mSlicerManagers[index]->SetColorMap(0);
2137     mSlicerManagers[index]->Render();
2138   }
2139 }
2140 //------------------------------------------------------------------------------
2141
2142 //------------------------------------------------------------------------------
2143 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2144 {
2145   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2146   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2147     mSlicerManagers[index]->SetFusionOpacity(opacity);
2148     mSlicerManagers[index]->SetFusionColorMap(colormap);
2149     mSlicerManagers[index]->SetFusionWindow(window);
2150     mSlicerManagers[index]->SetFusionLevel(level);
2151     mSlicerManagers[index]->SetColorMap(0);
2152     mSlicerManagers[index]->Render();
2153   }
2154 }
2155 //------------------------------------------------------------------------------
2156
2157 //------------------------------------------------------------------------------
2158 void vvMainWindow::SaveAs()
2159 {
2160   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2161     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2162     return;
2163   }
2164
2165   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2166   int dimension = mSlicerManagers[index]->GetDimension();
2167   QStringList OutputListeFormat;
2168   OutputListeFormat.clear();
2169   if (dimension == 1) {
2170     OutputListeFormat.push_back(".mhd");
2171   }
2172   if (dimension == 2) {
2173     OutputListeFormat.push_back(".bmp");
2174     OutputListeFormat.push_back(".png");
2175     OutputListeFormat.push_back(".jpeg");
2176     OutputListeFormat.push_back(".tif");
2177     OutputListeFormat.push_back(".mhd");
2178     OutputListeFormat.push_back(".hdr");
2179     OutputListeFormat.push_back(".vox");
2180   } else if (dimension == 3) {
2181     OutputListeFormat.push_back(".mhd");
2182     OutputListeFormat.push_back(".hdr");
2183     OutputListeFormat.push_back(".vox");
2184   } else if (dimension == 4) {
2185     OutputListeFormat.push_back(".mhd");
2186   }
2187   QString Extensions = "AllFiles(*.*)";
2188   for (int i = 0; i < OutputListeFormat.count(); i++) {
2189     Extensions += ";;Images ( *";
2190     Extensions += OutputListeFormat[i];
2191     Extensions += ")";
2192   }
2193   QString fileName = QFileDialog::getSaveFileName(this,
2194                      tr("Save As"),
2195                      mSlicerManagers[index]->GetFileName().c_str(),
2196                      Extensions);
2197   if (!fileName.isEmpty()) {
2198     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2199     if (OutputListeFormat.contains(
2200           fileformat.c_str())) {
2201       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2202       std::string action = "Saving";
2203       vvProgressDialog progress("Saving "+fileName.toStdString());
2204       qApp->processEvents();
2205       vvImageWriter::Pointer writer = vvImageWriter::New();
2206       writer->SetOutputFileName(fileName.toStdString());
2207       writer->SetInput(mSlicerManagers[index]->GetImage());
2208       writer->Update();
2209       QApplication::restoreOverrideCursor();
2210       if (writer->GetLastError().size()) {
2211         QString error = "Saving did not succeed\n";
2212         error += writer->GetLastError().c_str();
2213         QMessageBox::information(this,tr("Saving Problem"),error);
2214         SaveAs();
2215       }
2216     } else {
2217       QString error = fileformat.c_str();
2218       if (error.isEmpty())
2219         error += "no file format specified !";
2220       else
2221         error += " format unknown !!!\n";
2222       QMessageBox::information(this,tr("Saving Problem"),error);
2223       SaveAs();
2224     }
2225   }
2226 }
2227 //------------------------------------------------------------------------------
2228
2229
2230 //------------------------------------------------------------------------------
2231 void vvMainWindow::AddLink(QString image1,QString image2)
2232 {
2233   unsigned int sm1 = 0;
2234   unsigned int sm2 = 0;
2235
2236   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2237     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2238       mSlicerManagers[i]->AddLink(image2.toStdString());
2239       sm1 = i;
2240     }
2241     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2242       mSlicerManagers[i]->AddLink(image1.toStdString());
2243       sm2 = i;
2244     }
2245   }
2246
2247   if (linkPanel->isLinkAll())   {
2248     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2249     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2250   }
2251   else {
2252     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2253   }
2254 }
2255
2256 //------------------------------------------------------------------------------
2257
2258
2259 //------------------------------------------------------------------------------
2260 void vvMainWindow::RemoveLink(QString image1,QString image2)
2261 {
2262   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2263     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2264       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2265     }
2266     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2267       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2268     }
2269   }
2270 }
2271 //------------------------------------------------------------------------------
2272
2273 //------------------------------------------------------------------------------
2274 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2275 {
2276   int index = 0;
2277   while(sm != mSlicerManagers[index])
2278     index++;
2279   index = (index+offset) % mSlicerManagers.size();
2280
2281   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2282   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2283   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2284   DisplayChanged(item,slicer+1);
2285 }
2286 //------------------------------------------------------------------------------
2287
2288 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2289 {
2290   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2291     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2292       for (int j = 0; j < 4; j++) {
2293         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2294         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2295         //UpdateTSlice(j,value);
2296       }
2297       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2298       break;
2299     }
2300   }
2301 }
2302 //------------------------------------------------------------------------------
2303
2304
2305 //------------------------------------------------------------------------------
2306 void vvMainWindow::NOHorizontalSliderMoved()
2307 {
2308   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2309   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2310 //  mCurrentTime = NOHorizontalSlider->value();
2311 }
2312 //------------------------------------------------------------------------------
2313
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::NEHorizontalSliderMoved()
2317 {
2318   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2319   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2320 //  mCurrentTime = NEHorizontalSlider->value();
2321 }
2322 //------------------------------------------------------------------------------
2323
2324
2325 //------------------------------------------------------------------------------
2326 void vvMainWindow::SOHorizontalSliderMoved()
2327 {
2328   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2329   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2330   // mCurrentTime = SOHorizontalSlider->value();
2331 }
2332 //------------------------------------------------------------------------------
2333
2334
2335 //------------------------------------------------------------------------------
2336 void vvMainWindow::SEHorizontalSliderMoved()
2337 {
2338   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2339   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2340   // mCurrentTime = SEHorizontalSlider->value();
2341 }
2342 //------------------------------------------------------------------------------
2343
2344 //------------------------------------------------------------------------------
2345 void vvMainWindow::NOVerticalSliderChanged()
2346 {
2347   static int value=-1;
2348   if (value == NOVerticalSlider->value()) return;
2349   else value = NOVerticalSlider->value();
2350   //  int value = NOVerticalSlider->value();
2351   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2352     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2353       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2354         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2355         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2356
2357         // If nor Update/Render -> slider not work
2358         // only render = ok navigation, but for contour Update needed but slower ?
2359
2360         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2361         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2362       }
2363       break;
2364     }
2365   }
2366 }
2367 //------------------------------------------------------------------------------
2368
2369
2370 //------------------------------------------------------------------------------
2371 void vvMainWindow::NEVerticalSliderChanged()
2372 {
2373   static int value=-1;
2374   if (value == NEVerticalSlider->value()) return;
2375   else value = NEVerticalSlider->value();
2376   //  int value = NEVerticalSlider->value();
2377   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2378     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2379       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2380         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2381         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2382         mSlicerManagers[i]->UpdateSlice(1);
2383         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2384       }
2385       break;
2386     }
2387   }
2388 }
2389 //------------------------------------------------------------------------------
2390
2391
2392 //------------------------------------------------------------------------------
2393 void vvMainWindow::SOVerticalSliderChanged()
2394 {
2395   static int value=-1;
2396   if (value == SOVerticalSlider->value()) return;
2397   else value = SOVerticalSlider->value();
2398   //int value = SOVerticalSlider->value();
2399   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2400     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2401       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2402         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2403         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2404         mSlicerManagers[i]->UpdateSlice(2);
2405         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2406       }
2407       // else { DD("avoid SOVerticalSlider slicer update"); }
2408       break;
2409     }
2410   }
2411 }
2412 //------------------------------------------------------------------------------
2413
2414
2415 //------------------------------------------------------------------------------
2416 void vvMainWindow::SEVerticalSliderChanged()
2417 {
2418   static int value=-1;
2419   if (value == SEVerticalSlider->value()) return;
2420   else value = SEVerticalSlider->value();
2421   // int value = SEVerticalSlider->value();
2422   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2423     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2424       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2425         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2426         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2427         mSlicerManagers[i]->UpdateSlice(3);
2428         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2429       }
2430       break;
2431     }
2432   }
2433 }
2434 //------------------------------------------------------------------------------
2435
2436
2437 //------------------------------------------------------------------------------
2438 void vvMainWindow::UpdateSlice(int slicer, int slice)
2439 {
2440   // DD("vvMainWindow::UpdateSlice");
2441 //   DD(slicer);
2442 //   DD(slice);
2443   if (slicer == 0) {
2444     //    if (slice != NOVerticalSlider->value())
2445     NOVerticalSlider->setValue(slice);
2446   } else {
2447     if (slicer == 1)
2448       NEVerticalSlider->setValue(slice);
2449     else {
2450       if (slicer == 2)
2451         SOVerticalSlider->setValue(slice);
2452       else {
2453         if (slicer == 3)
2454           SEVerticalSlider->setValue(slice);
2455       }
2456     }
2457   }
2458   // DD("vvMainWindow:UpdateSlice END");
2459 }
2460 //------------------------------------------------------------------------------
2461
2462
2463 //------------------------------------------------------------------------------
2464 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2465 {
2466   switch (slicer) {
2467   case 0:
2468     NOHorizontalSlider->setValue(slice);
2469     break;
2470   case 1:
2471     NEHorizontalSlider->setValue(slice);
2472     break;
2473   case 2:
2474     SOHorizontalSlider->setValue(slice);
2475     break;
2476   case 3:
2477     SEHorizontalSlider->setValue(slice);
2478     break;
2479   }
2480 }
2481 //------------------------------------------------------------------------------
2482
2483
2484 //------------------------------------------------------------------------------
2485 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2486 {
2487   int position = int((min+max)/2);
2488   int tPosition = int((tmin+tmax)/2);
2489   if (slicer == 0) {
2490     NOVerticalSlider->setValue(position);
2491     NOVerticalSlider->setRange(min,max);
2492     NOHorizontalSlider->setRange(tmin,tmax);
2493     NOHorizontalSlider->setValue(tPosition);
2494   } else if (slicer == 1) {
2495     NEVerticalSlider->setValue(position);
2496     NEVerticalSlider->setRange(min,max);
2497     NEHorizontalSlider->setRange(tmin,tmax);
2498     NEHorizontalSlider->setValue(tPosition);
2499   } else if (slicer == 2) {
2500     SOVerticalSlider->setValue(position);
2501     SOVerticalSlider->setRange(min,max);
2502     SOHorizontalSlider->setRange(tmin,tmax);
2503     SOHorizontalSlider->setValue(tPosition);
2504   } else if (slicer == 3) {
2505     SEVerticalSlider->setValue(position);
2506     SEVerticalSlider->setRange(min,max);
2507     SEHorizontalSlider->setRange(tmin,tmax);
2508     SEHorizontalSlider->setValue(tPosition);
2509   }
2510 }
2511 //------------------------------------------------------------------------------
2512
2513
2514 //------------------------------------------------------------------------------
2515 void vvMainWindow::SaveNOScreenshot()
2516 {
2517   SaveScreenshot(NOViewWidget);
2518 }
2519 //------------------------------------------------------------------------------
2520
2521
2522 //------------------------------------------------------------------------------
2523 void vvMainWindow::SaveNEScreenshot()
2524 {
2525   SaveScreenshot(NEViewWidget);
2526 }
2527 //------------------------------------------------------------------------------
2528
2529
2530 //------------------------------------------------------------------------------
2531 void vvMainWindow::SaveSOScreenshot()
2532 {
2533   SaveScreenshot(SOViewWidget);
2534 }
2535 //------------------------------------------------------------------------------
2536
2537
2538 //------------------------------------------------------------------------------
2539 void vvMainWindow::SaveSEScreenshot()
2540 {
2541   SaveScreenshot(SEViewWidget);
2542 }
2543 //------------------------------------------------------------------------------
2544
2545
2546 //------------------------------------------------------------------------------
2547 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2548 {
2549   QString Extensions = "Images( *.png);;";
2550   Extensions += "Images( *.jpg);;";
2551   Extensions += "Images( *.bmp);;";
2552   Extensions += "Images( *.tif);;";
2553   Extensions += "Images( *.ppm)";
2554 #ifdef VTK_USE_FFMPEG_ENCODER
2555   Extensions += "Images( *.avi)";
2556 #endif
2557 #ifdef VTK_USE_MPEG2_ENCODER
2558   Extensions += "Images( *.mpg)";
2559 #endif
2560
2561   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2562   QString fileName = QFileDialog::getSaveFileName(this,
2563                      tr("Save As"),
2564                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2565                      Extensions);
2566
2567   if (!fileName.isEmpty()) {
2568     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2569     w2i->SetInput(widget->GetRenderWindow());
2570     w2i->Update();
2571     vtkImageData *image = w2i->GetOutput();
2572
2573     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2574     if (!strcmp(ext, ".bmp")) {
2575       vtkBMPWriter *bmp = vtkBMPWriter::New();
2576       bmp->SetInput(image);
2577       bmp->SetFileName(fileName.toStdString().c_str());
2578       bmp->Write();
2579       bmp->Delete();
2580     } else if (!strcmp(ext, ".tif")) {
2581       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2582       tif->SetInput(image);
2583       tif->SetFileName(fileName.toStdString().c_str());
2584       tif->Write();
2585       tif->Delete();
2586     } else if (!strcmp(ext, ".ppm")) {
2587       vtkPNMWriter *pnm = vtkPNMWriter::New();
2588       pnm->SetInput(image);
2589       pnm->SetFileName(fileName.toStdString().c_str());
2590       pnm->Write();
2591       pnm->Delete();
2592     } else if (!strcmp(ext, ".png")) {
2593       vtkPNGWriter *png = vtkPNGWriter::New();
2594       png->SetInput(image);
2595       png->SetFileName(fileName.toStdString().c_str());
2596       png->Write();
2597       png->Delete();
2598     } else if (!strcmp(ext, ".jpg")) {
2599       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2600       jpg->SetInput(image);
2601       jpg->SetFileName(fileName.toStdString().c_str());
2602       jpg->Write();
2603       jpg->Delete();
2604 #ifdef VTK_USE_FFMPEG_ENCODER
2605     } else if (!strcmp(ext, ".avi")) {
2606       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2607       mpg->SetInput(image);
2608       mpg->SetFileName(fileName.toStdString().c_str());
2609       mpg->SetQuality(2);
2610       mpg->SetRate(5);
2611       mpg->Start();
2612
2613       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2614       int nSlice = vvImg->GetVTKImages().size();
2615       for(int i=0; i<nSlice; i++)
2616       {
2617         mSlicerManagers[smIndex]->SetNextTSlice(0);
2618         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2619         w2i->SetInput(widget->GetRenderWindow());
2620         w2i->Update();
2621         mpg->SetInput(w2i->GetOutput());
2622         mpg->Write();
2623       }
2624       mpg->End();
2625       mpg->Delete();
2626 #endif
2627 #ifdef VTK_USE_MPEG2_ENCODER
2628     } else if (!strcmp(ext, ".mpg")) {
2629       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2630       mpg->SetInput(image);
2631       mpg->SetFileName(fileName.toStdString().c_str());
2632       mpg->Start();
2633
2634       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2635       int nSlice = vvImg->GetVTKImages().size();
2636       for(int i=0; i<nSlice; i++)
2637       {
2638         mSlicerManagers[smIndex]->SetNextTSlice(0);
2639         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2640         w2i->SetInput(widget->GetRenderWindow());
2641         w2i->Update();
2642         mpg->SetInput(w2i->GetOutput());
2643         mpg->Write();
2644       }
2645       mpg->End();
2646       mpg->Delete();
2647 #endif
2648     } else {
2649       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2650     }
2651   }
2652 }
2653 //------------------------------------------------------------------------------
2654
2655
2656 //------------------------------------------------------------------------------
2657 void vvMainWindow::GoToCursor()
2658 {
2659   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2660   for (int column = 1; column < 5; column++) {
2661     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2662       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2663       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2664         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2665       mSlicerManagers[index]->UpdateViews(1,column-1);
2666       mSlicerManagers[index]->UpdateLinked(column-1);
2667       break;
2668     }
2669   }
2670 }
2671 //------------------------------------------------------------------------------
2672
2673 //------------------------------------------------------------------------------
2674 void vvMainWindow::PlayPause()
2675 {
2676   if (playMode) {
2677     playMode = 0;
2678     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2679     ImageInfoChanged();
2680     return;
2681   } else {
2682     int image_number=DataTree->topLevelItemCount();
2683     bool has_temporal;
2684     for (int i=0; i<image_number; i++)
2685       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2686         has_temporal=true;
2687         break;
2688       }
2689     if (has_temporal) {
2690       playMode = 1;
2691       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2692       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2693     }
2694   }
2695 }
2696 //------------------------------------------------------------------------------
2697
2698 //------------------------------------------------------------------------------
2699 void vvMainWindow::PlayNext()
2700 {
2701   if (playMode && !this->isHidden()) {
2702     int image_number=DataTree->topLevelItemCount();
2703     ///Only play one slicer per SM, and only if the SM is being displayed
2704     for (int i=0; i<image_number; i++)
2705       for (int j=0; j<4; j++)
2706         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2707             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2708           mSlicerManagers[i]->SetNextTSlice(j);
2709           break;
2710         }
2711     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2712   }
2713 }
2714 //------------------------------------------------------------------------------
2715
2716 void vvMainWindow::ShowLastImage()
2717 {
2718   if (mSlicerManagers.size() > 1) {
2719     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2720     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2721     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2722     DisplayChanged(item,1);
2723   }
2724 }
2725
2726 //------------------------------------------------------------------------------
2727 void vvMainWindow::UpdateRenderWindows()
2728 {
2729   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2730   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2731   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2732   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2733 }
2734 //------------------------------------------------------------------------------
2735
2736 //------------------------------------------------------------------------------
2737 void vvMainWindow::SegmentationOnCurrentImage()
2738 {
2739   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2740
2741   vvSegmentationDialog segmentation;
2742   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2743   segmentation.exec();
2744 }
2745 //------------------------------------------------------------------------------
2746
2747 void vvMainWindow::SurfaceViewerLaunch()
2748 {
2749   vvSurfaceViewerDialog surfaceViewer;
2750   surfaceViewer.exec();
2751 }
2752 //------------------------------------------------------------------------------
2753
2754
2755 //------------------------------------------------------------------------------
2756 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2757 {
2758   int number=0;
2759   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2760     vvSlicerManager * v = mSlicerManagers[l];
2761     if (v->GetBaseFileName() ==
2762         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2763       number = std::max(number, v->GetBaseFileNameNumber()+1);
2764     }
2765   }
2766   return number;
2767 }
2768 //------------------------------------------------------------------------------
2769
2770
2771 //------------------------------------------------------------------------------
2772 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2773 {
2774   // Change filename if another image exist with the same name
2775   int number = GetImageDuplicateFilenameNumber(filename);
2776
2777   // Create new SliceManager
2778   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2779   slicer_manager->SetImage(image);//, IMAGE, number);
2780   //  filename = filename+"_"+clitk::toString(number);
2781   slicer_manager->SetFilename(filename, number);
2782   mSlicerManagers.push_back(slicer_manager);
2783
2784   //create an item in the tree with good settings
2785   QTreeWidgetItem *item = new QTreeWidgetItem();
2786   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2787   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2788   qApp->processEvents();
2789
2790   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2791
2792   //Create the buttons for reload and close
2793   qApp->processEvents();
2794   QTreePushButton* cButton = new QTreePushButton;
2795   cButton->setItem(item);
2796   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2797   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2798   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2799           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2800
2801   QTreePushButton* rButton = new QTreePushButton;
2802   rButton->setItem(item);
2803   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2804   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2805   rButton->setEnabled(0);
2806   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2807           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2808
2809   DataTree->addTopLevelItem(item);
2810   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2811   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2812
2813   //set the id of the image
2814   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2815   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2816   mSlicerManagers.back()->SetId(id.toStdString());
2817
2818   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2819                       , id.toStdString());
2820
2821   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2822           this, SLOT(CurrentImageChanged(std::string)));
2823   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2824           this, SLOT(CurrentPickedImageChanged(std::string)));
2825   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2826           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2827   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2828           this, SLOT(VectorChanged(int,double,double,double, double)));
2829   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2830           this, SLOT(OverlayChanged(int,double,double)));
2831   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2832           this, SLOT(FusionChanged(int,double)));
2833   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2834           this,SLOT(WindowsChanged(int, int, int)));
2835   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2836           this,SLOT(WindowLevelChanged(double, double, int, int)));
2837   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2838           this,SLOT(UpdateSlice(int,int)));
2839   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2840           this,SLOT(UpdateTSlice(int, int)));
2841   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2842           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2843   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2844           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2845   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2846           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2847   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2848           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2849   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2850   UpdateTree();
2851   qApp->processEvents();
2852   InitSlicers();
2853   ShowLastImage();
2854   InitDisplay();
2855   qApp->processEvents();
2856
2857   // End
2858   ImageInfoChanged();
2859   return slicer_manager;
2860 }
2861 //------------------------------------------------------------------------------
2862
2863
2864 //------------------------------------------------------------------------------
2865 void vvMainWindow::UpdateCurrentSlicer()
2866 {
2867   int index = -1;
2868   if (DataTree->selectedItems().size() > 0) {
2869     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2870   }
2871   mSlicerManagerCurrentIndex = index;
2872 }
2873 //------------------------------------------------------------------------------
2874