vv/vvSlicer.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 <QMessageBox>
  20 #include <QString>
  21
  22 #include "vvSlicer.h"
  23 #include "vvImage.h"
  24 #include "vvSlicerManagerCommand.h"
  25 #include "vvGlyphSource.h"
  26 #include "vvGlyph2D.h"
  27
  28 #include <vtkVersion.h>
  29 #include <vtkExtentTranslator.h>
  30 #include <vtkAlgorithm.h>
  31 #include <vtkExecutive.h>
  32 #include <vtkStreamingDemandDrivenPipeline.h>
  33 #include <vtkInformation.h>
  34 #include <vtkTextProperty.h>
  35 #include <vtkTextActor.h>
  36 #include <vtkTextSource.h>
  37 #include <vtkActor2D.h>
  38 #include <vtkCursor2D.h>
  39 #include <vtkPolyDataMapper2D.h>
  40 #include <vtkProperty2D.h>
  41 #include <vtkCornerAnnotation.h>
  42 #include <vtkImageMapToWindowLevelColors.h>
  43 #include <vtkImageData.h>
  44 #include <vtkImageActor.h>
  45 #include <vvBlendImageActor.h>
  46 #include <vtkToolkits.h>
  47 #include <vtkObjectFactory.h>
  48 #include <vtkPointData.h>
  49 #include <vtkDataArray.h>
  50 #include <vtkFloatArray.h>
  51 #include <vtkClipPolyData.h>
  52 #include <vtkActor2DCollection.h>
  53 #include <vtkGlyph3D.h>
  54 #include <vtkMath.h>
  55 #include <vtkCursor3D.h>
  56 #include <vtkProperty.h>
  57 #include <vtkLight.h>
  58 #include <vtkLightCollection.h>
  59 #include <vtkScalarBarActor.h>
  60 #include <vtkLookupTable.h>
  61
  62 #include <vtkRenderer.h>
  63 #include <vtkRendererCollection.h>
  64 #include <vtkRenderWindow.h>
  65 #include <vtkRenderWindowInteractor.h>
  66 #include <vtkCamera.h>
  67 #include <vtkCallbackCommand.h>
  68 #include <vtkCommand.h>
  69 #include <vtkPolyDataMapper.h>
  70 #include <vtkBox.h>
  71
  72 #include <vtkExtractVOI.h>
  73 #include <vtkSphereSource.h>
  74 #include <vtkCutter.h>
  75 #include <vtkAssignAttribute.h>
  76 #include <vtkImageAccumulate.h>
  77 #include <vtkImageReslice.h>
  78 #include <vtkOpenGLImageSliceMapper.h>
  79 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  80 #  include <vtkImageMapper3D.h>
  81 #  include <vtkImageSliceMapper.h>
  82 #endif
  83
  84 vtkStandardNewMacro(vvSlicer);
  85 static void copyExtent(int* in, int* to){
  86  for(int i=0; i<6; ++i)
  87  {
  88         to[i]=in[i];
  89  }
  90 }
  91 //------------------------------------------------------------------------------
  92 vvSlicer::vvSlicer()
  93 { //out << __func__ << endl;
  94         mFusionSequenceCode = -1;
  95   this->UnInstallPipeline();
  96   mImage = NULL;
  97   mReducedExtent = new int[6];
  98   mRegisterExtent = new int[6];
  99   mCurrentTSlice = 0;
 100   mCurrentFusionTSlice = 0;
 101   mCurrentOverlayTSlice = 0;
 102   mUseReducedExtent = false;
 103
 104   mCurrent[0] = -VTK_DOUBLE_MAX;
 105   mCurrent[1] = -VTK_DOUBLE_MAX;
 106   mCurrent[2] = -VTK_DOUBLE_MAX;
 107
 108   mCursor[0] = 0;//-VTK_DOUBLE_MAX;
 109   mCursor[1] = 0;//-VTK_DOUBLE_MAX;
 110   mCursor[2] = 0;//-VTK_DOUBLE_MAX;
 111   mCursor[3] = 0;//-VTK_DOUBLE_MAX;
 112
 113   mSubSampling = 5;
 114   mScale = 1;
 115   mVFLog = 0;
 116   mVFWidth = 1;
 117   mVFColor[0] = 0;
 118   mVFColor[1] = 1;
 119   mVFColor[2] = 0;
 120
 121   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 122   crossCursor->AllOff();
 123   crossCursor->AxesOn();
 124   crossCursor->SetTranslationMode(1);
 125   crossCursor->SetRadius(2);
 126
 127   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 128 #if VTK_MAJOR_VERSION <= 5
 129   pdm->SetInput(crossCursor->GetOutput());
 130 #else
 131   pdm->SetInputData(crossCursor->GetOutput());
 132 #endif
 133
 134   pdmA = vtkSmartPointer<vtkActor2D>::New();
 135   pdmA->SetMapper(pdm);
 136   pdmA->GetProperty()->SetColor(255,10,212);
 137   pdmA->SetVisibility(0);
 138   pdmA->SetPickable(0);
 139
 140   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 141   ca->GetTextProperty()->SetColor(255,10,212);
 142   ca->SetVisibility(1);
 143   mFileName = "";
 144
 145   mVF = NULL;
 146   mOverlay = NULL;
 147   mFusion = NULL;
 148   mLandmarks = NULL;
 149
 150   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 151   //legend->SetTitle("test!");
 152   legend->SetPosition(0.82,0.18);
 153   legend->SetWidth(0.1);
 154   legend->SetVisibility(0);
 155   legend->SetLabelFormat("%.1f");
 156   this->GetRenderer()->AddActor(legend);
 157   showFusionLegend = false;
 158
 159   this->InstallPipeline();
 160
 161   mLinkOverlayWindowLevel = true;
 162   mImageVisibility = true;
 163
 164 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 165   this->GetImageActor()->GetMapper()->BorderOn();
 166 #endif
 167
 168   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 169   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 170   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 171   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 172   mFirstSetSliceOrientation = true;
 173 }
 174 //------------------------------------------------------------------------------
 175
 176
 177 //------------------------------------------------------------------------------
 178 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 179 { //out << __func__ << endl;
 180   return mOverlayMapper.GetPointer();
 181 }
 182 //------------------------------------------------------------------------------
 183
 184
 185 //------------------------------------------------------------------------------
 186 vvBlendImageActor* vvSlicer::GetOverlayActor()
 187 { //out << __func__ << endl;
 188   return mOverlayActor.GetPointer();
 189 }
 190 //------------------------------------------------------------------------------
 191
 192
 193 //------------------------------------------------------------------------------
 194 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 195 { //out << __func__ << endl;
 196   return mFusionMapper.GetPointer();
 197 }
 198 //------------------------------------------------------------------------------
 199
 200
 201 //------------------------------------------------------------------------------
 202 vtkImageActor* vvSlicer::GetFusionActor()
 203 { //out << __func__ << endl;
 204   return mFusionActor.GetPointer();
 205 }
 206 //------------------------------------------------------------------------------
 207
 208
 209 //------------------------------------------------------------------------------
 210 vtkActor* vvSlicer::GetVFActor()
 211 { //out << __func__ << endl;
 212   return mVFActor.GetPointer();
 213 }
 214 //------------------------------------------------------------------------------
 215
 216
 217 //------------------------------------------------------------------------------
 218 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 219 { //out << __func__ << endl;
 220   return ca.GetPointer();
 221 }
 222 //------------------------------------------------------------------------------
 223
 224
 225 //------------------------------------------------------------------------------
 226 void vvSlicer::EnableReducedExtent(bool b)
 227 { //out << __func__ << endl;
 228   mUseReducedExtent = b;
 229 }
 230 //------------------------------------------------------------------------------
 231
 232
 233 //------------------------------------------------------------------------------
 234 void vvSlicer::SetReducedExtent(int * ext)
 235 { //out << __func__ << endl;
 236   copyExtent(ext, mReducedExtent);
 237 }
 238 //------------------------------------------------------------------------------
 239
 240
 241 //------------------------------------------------------------------------------
 242 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 243 { //out << __func__ << endl;
 244
 245   mSurfaceCutActors.push_back(new vvMeshActor());
 246   if (propagate)
 247     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 248   else
 249     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 250   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 251   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 252
 253   SetContourSlice();
 254 }
 255 //------------------------------------------------------------------------------
 256
 257
 258 //------------------------------------------------------------------------------
 259 void vvSlicer::ToggleContourSuperposition()
 260 { //out << __func__ << endl;
 261   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 262        i!=mSurfaceCutActors.end(); i++)
 263     (*i)->ToggleSuperposition();
 264 }
 265 //------------------------------------------------------------------------------
 266
 267
 268 //------------------------------------------------------------------------------
 269 void vvSlicer::SetCursorColor(int r,int g, int b)
 270 { //out << __func__ << endl;
 271   pdmA->GetProperty()->SetColor(r,g,b);
 272 }
 273 //------------------------------------------------------------------------------
 274
 275
 276 //------------------------------------------------------------------------------
 277 void vvSlicer::SetCursorVisibility(bool s)
 278 { //out << __func__ << endl;
 279   pdmA->SetVisibility(s);
 280 }
 281 //------------------------------------------------------------------------------
 282
 283
 284 //------------------------------------------------------------------------------
 285 bool vvSlicer::GetCursorVisibility()
 286 { //out << __func__ << endl;
 287   return pdmA->GetVisibility();
 288 }
 289 //------------------------------------------------------------------------------
 290
 291
 292 //------------------------------------------------------------------------------
 293 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 294 { //out << __func__ << endl;
 295   ca->SetVisibility(s);
 296 }
 297 //------------------------------------------------------------------------------
 298
 299
 300 //------------------------------------------------------------------------------
 301 bool vvSlicer::GetCornerAnnotationVisibility()
 302 { //out << __func__ << endl;
 303   return ca->GetVisibility();
 304 }
 305 //------------------------------------------------------------------------------
 306
 307
 308 //------------------------------------------------------------------------------
 309 vvSlicer::~vvSlicer()
 310 { //out << __func__ << endl;
 311   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 312        i!=mSurfaceCutActors.end(); i++)
 313     delete (*i);
 314   delete [] mReducedExtent;
 315   delete [] mRegisterExtent;
 316 }
 317 //------------------------------------------------------------------------------
 318
 319 //------------------------------------------------------------------------------
 320 double* vvSlicer::GetCurrentPosition()
 321 { //out << __func__ << endl;
 322   return mCurrentBeforeSlicingTransform;
 323 }
 324 //------------------------------------------------------------------------------
 325
 326 //------------------------------------------------------------------------------
 327 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 328 { //out << __func__ << endl;
 329   mCurrentBeforeSlicingTransform[0]=x;
 330   mCurrentBeforeSlicingTransform[1]=y;
 331   mCurrentBeforeSlicingTransform[2]=z;
 332   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 333   if (t>=0) SetTSlice(t);
 334 }
 335 //------------------------------------------------------------------------------
 336
 337
 338 //------------------------------------------------------------------------------
 339 void vvSlicer::SetImage(vvImage::Pointer image)
 340 { //out << __func__ << endl;
 341   if (image->GetVTKImages().size()) {
 342     mImage = image;
 343
 344     if (!mImageReslice) {
 345       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 346       mImageReslice->SetInterpolationModeToLinear();
 347       mImageReslice->AutoCropOutputOn();
 348       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 349     }
 350
 351     mConcatenatedTransform->Identity();
 352     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 353     mConcatenatedTransform->Concatenate(mSlicingTransform);
 354     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 355 #if VTK_MAJOR_VERSION <= 5
 356     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 357 #else
 358     mImageReslice->SetInputData(0, mImage->GetFirstVTKImageData());
 359 #endif
 360     mImageReslice->UpdateInformation();
 361
 362 #if VTK_MAJOR_VERSION <= 5
 363     this->Superclass::SetInput(mImageReslice->GetOutput());
 364 #else
 365     this->Superclass::SetInputConnection(mImageReslice->GetOutputPort());
 366 #endif
 367
 368     int extent[6];
 369 #if VTK_MAJOR_VERSION <= 5
 370     this->GetInput()->GetWholeExtent(extent);
 371 #else
 372     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 373     copyExtent(ext, extent);
 374 #endif
 375
 376     // Prevent crash when reload -> change slice if outside extent
 377     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 378       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 379     }
 380
 381     // Make sure that the required part image has been computed
 382     extent[SliceOrientation*2] = Slice;
 383     extent[SliceOrientation*2+1] = Slice;
 384
 385 #if VTK_MAJOR_VERSION <= 5
 386     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 387     mImageReslice->GetOutput()->Update();
 388 #else
 389     mImageReslice->SetUpdateExtent(extent);
 390     mImageReslice->Update();
 391 #endif
 392
 393     this->UpdateDisplayExtent();
 394
 395     mCurrentTSlice = 0;
 396     ca->SetText(0,mFileName.c_str());
 397   }
 398 }
 399 //------------------------------------------------------------------------------
 400
 401
 402 //------------------------------------------------------------------------------
 403 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 404 { //out << __func__ << endl;
 405   if (overlay->GetVTKImages().size()) {
 406     mOverlay = overlay;
 407     mOverlayVisibility = true;
 408
 409     if (!mOverlayReslice) {
 410       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 411       mOverlayReslice->SetInterpolationModeToLinear();
 412       mOverlayReslice->AutoCropOutputOn();
 413       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 414     }
 415
 416     mConcatenatedOverlayTransform->Identity();
 417     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 418     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 419     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 420 #if VTK_MAJOR_VERSION <= 5
 421     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 422 #else
 423     mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
 424 #endif
 425     mImageReslice->UpdateInformation();
 426     mOverlayReslice->Update();
 427
 428     if (!mOverlayMapper)
 429       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 430 #if VTK_MAJOR_VERSION <= 5
 431     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 432 #else
 433     mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
 434 #endif
 435
 436     if (!mOverlayActor) {
 437       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 438 #if VTK_MAJOR_VERSION <= 5
 439       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 440 #else
 441       mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
 442 #endif
 443       mOverlayActor->SetPickable(0);
 444       mOverlayActor->SetVisibility(true);
 445       mOverlayActor->SetOpacity(0.5);
 446 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 447       mOverlayActor->GetMapper()->BorderOn();
 448 #endif
 449       }
 450
 451     //stupid but necessary : the Overlay need to be rendered before fusion
 452     if (mFusionActor) {
 453       this->GetRenderer()->RemoveActor(mFusionActor);
 454       this->GetRenderer()->AddActor(mOverlayActor);
 455       this->GetRenderer()->AddActor(mFusionActor);
 456     } else
 457       this->GetRenderer()->AddActor(mOverlayActor);
 458
 459     //Synchronize orientation and slice
 460     AdjustResliceToSliceOrientation(mOverlayReslice);
 461     this->UpdateDisplayExtent();
 462     this->SetTSlice(mCurrentTSlice);
 463   }
 464 }
 465 //------------------------------------------------------------------------------
 466
 467
 468 //------------------------------------------------------------------------------
 469 void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
 470 { //out << __func__ << endl;
 471         mFusionSequenceCode = fusionSequenceCode;
 472   if (fusion->GetVTKImages().size()) {
 473     mFusion = fusion;
 474     mFusionVisibility = true;
 475
 476     if (!mFusionReslice) {
 477       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 478       mFusionReslice->SetInterpolationModeToLinear();
 479       mFusionReslice->AutoCropOutputOn();
 480       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 481     }
 482
 483     mConcatenatedFusionTransform->Identity();
 484     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 485     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 486     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 487 #if VTK_MAJOR_VERSION <= 5
 488     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 489 #else
 490     mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
 491 #endif
 492     mFusionReslice->Update();
 493
 494     if (!mFusionMapper)
 495       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 496
 497     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 498     lut->SetRange(0, 1);
 499     lut->SetValueRange(0, 1);
 500     lut->SetSaturationRange(0, 0);
 501     lut->Build();
 502     mFusionMapper->SetLookupTable(lut);
 503 #if VTK_MAJOR_VERSION <= 5
 504     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 505 #else
 506     mFusionMapper->SetInputData(mFusionReslice->GetOutput());
 507 #endif
 508
 509     if (!mFusionActor) {
 510       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 511 #if VTK_MAJOR_VERSION <= 5
 512       mFusionActor->SetInput(mFusionMapper->GetOutput());
 513 #else
 514       mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
 515 #endif
 516       mFusionActor->SetPickable(0);
 517       mFusionActor->SetVisibility(true);
 518       mFusionActor->SetOpacity(0.7);
 519 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 520       mFusionActor->GetMapper()->BorderOn();
 521 #endif
 522
 523       this->GetRenderer()->AddActor(mFusionActor);
 524     }
 525
 526     //Synchronize orientation and slice
 527     AdjustResliceToSliceOrientation(mFusionReslice);
 528     this->UpdateDisplayExtent();
 529     this->SetTSlice(mCurrentTSlice);
 530   }
 531 }
 532 //------------------------------------------------------------------------------
 533
 534
 535 //------------------------------------------------------------------------------
 536 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 537 { //out << __func__ << endl;
 538   bool vis = false;
 539   if (actor_type == "image")
 540     vis = mImageVisibility;
 541   else if (actor_type == "vector")
 542     vis = mVFVisibility;
 543   else if (actor_type == "overlay")
 544     vis = mOverlayVisibility;
 545   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 546     vis = mFusionVisibility;
 547   else if (actor_type == "contour")
 548     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 549   return vis;
 550 }
 551 //------------------------------------------------------------------------------
 552
 553 //------------------------------------------------------------------------------
 554 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 555 { //out << __func__ << endl;
 556   if (actor_type == "image")
 557     mImageVisibility = vis;
 558   else if (actor_type == "vector")
 559     mVFVisibility = vis;
 560   else if (actor_type == "overlay")
 561     mOverlayVisibility = vis;
 562   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 563     mFusionVisibility = vis;
 564   else if (actor_type == "contour")
 565     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 566   UpdateDisplayExtent();
 567 }
 568 //------------------------------------------------------------------------------
 569
 570 //------------------------------------------------------------------------------
 571 void vvSlicer::SetVF(vvImage::Pointer vf)
 572 { //out << __func__ << endl;
 573   if (vf->GetVTKImages().size()) {
 574     mVF = vf;
 575     mVFVisibility = true;
 576
 577     if (!mAAFilter) {
 578       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 579       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 580       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 581     }
 582 #if VTK_MAJOR_VERSION <= 5
 583     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 584     mAAFilter->SetInput(mVOIFilter->GetOutput());
 585 #else
 586     mVOIFilter->SetInputData(vf->GetFirstVTKImageData());
 587     mAAFilter->SetInputData(mVOIFilter->GetOutput());
 588 #endif
 589     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 590     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 591
 592     if (!mArrow)
 593       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 594     mArrow->SetGlyphTypeToSpecificArrow();
 595     mArrow->SetScale(mScale);
 596     mArrow->FilledOff();
 597
 598     // Glyph the gradient vector (with arrows)
 599     if (!mGlyphFilter)
 600       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 601 #if VTK_MAJOR_VERSION <= 5
 602     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 603     mGlyphFilter->SetSource(mArrow->GetOutput());
 604 #else
 605     mGlyphFilter->SetInputData(mAAFilter->GetOutput());
 606     mGlyphFilter->SetSourceData(mArrow->GetOutput());
 607 #endif
 608     mGlyphFilter->ScalingOn();
 609     mGlyphFilter->SetScaleModeToScaleByVector();
 610     mGlyphFilter->OrientOn();
 611     mGlyphFilter->SetVectorModeToUseVector();
 612     mGlyphFilter->SetColorModeToColorByVector();
 613
 614     if (!mVFColorLUT)
 615       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 616
 617     double mVFColorHSV[3];
 618     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 619     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 620     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 621     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 622
 623     if (!mVFMapper)
 624       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 625 #if VTK_MAJOR_VERSION <= 5
 626     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 627 #else
 628     mVFMapper->SetInputData(mGlyphFilter->GetOutput());
 629 #endif
 630     mVFMapper->ImmediateModeRenderingOn();
 631     mVFMapper->SetLookupTable(mVFColorLUT);
 632
 633     if (!mVFActor)
 634       mVFActor = vtkSmartPointer<vtkActor>::New();
 635     mVFActor->SetMapper(mVFMapper);
 636     mVFActor->SetPickable(0);
 637     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 638     this->UpdateDisplayExtent();
 639     this->GetRenderer()->AddActor(mVFActor);
 640
 641     //Synchronize slice
 642     SetTSlice(mCurrentTSlice);
 643   }
 644 }
 645 //------------------------------------------------------------------------------
 646
 647
 648 //------------------------------------------------------------------------------
 649 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 650 { //out << __func__ << endl;
 651   mLandmarks = landmarks;
 652   if (landmarks) {
 653
 654     if (!mCross)
 655       mCross = vtkSmartPointer<vtkCursor3D>::New();
 656         if (!mClipBox)
 657       mClipBox = vtkSmartPointer<vtkBox>::New();
 658     if (!mLandClipper)
 659       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 660     if (!mLandGlyph)
 661       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 662     if (!mLandMapper)
 663       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 664     if (!mLandActor)
 665       mLandActor = vtkSmartPointer<vtkActor>::New();
 666
 667     mCross->SetFocalPoint(0.0,0.0,0.0);
 668     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 669     mCross->AllOff();
 670     mCross->AxesOn();
 671
 672     mLandClipper->SetClipFunction(mClipBox);
 673     mLandClipper->InsideOutOn();
 674 #if VTK_MAJOR_VERSION <= 5
 675     mLandClipper->SetInput(mLandmarks->GetOutput());
 676
 677     mLandGlyph->SetSource(mCross->GetOutput());
 678     mLandGlyph->SetInput(mLandClipper->GetOutput());
 679 #else
 680     mLandClipper->SetInputData(mLandmarks->GetOutput());
 681
 682     mLandGlyph->SetSourceData(mCross->GetOutput());
 683     mLandGlyph->SetInputData(mLandClipper->GetOutput());
 684 #endif
 685     //mLandGlyph->SetIndexModeToScalar();
 686     //mLandGlyph->SetRange(0,1);
 687     //mLandGlyph->ScalingOff();
 688
 689     //mLandGlyph->SetColorModeToColorByScalar();
 690
 691     mLandGlyph->SetScaleModeToDataScalingOff();
 692     mLandGlyph->SetIndexModeToOff();
 693
 694     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 695     //mLandMapper->ScalarVisibilityOff();
 696
 697     mLandActor->SetMapper(mLandMapper);
 698     mLandActor->GetProperty()->SetColor(255,10,212);
 699     mLandActor->SetPickable(0);
 700     mLandActor->SetVisibility(true);
 701     this->UpdateDisplayExtent();
 702     this->GetRenderer()->AddActor(mLandActor);
 703   }
 704 }
 705 //------------------------------------------------------------------------------
 706
 707 //------------------------------------------------------------------------------
 708 //FIXME: this function leaks memory, we should fix it someday :)
 709 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 710 { //out << __func__ << endl;
 711   if (actor_type == "vector") {
 712     Renderer->RemoveActor(mVFActor);
 713     mGlyphFilter=NULL;
 714     mVF = NULL;
 715     mArrow = NULL;
 716     mAAFilter=NULL;
 717     mVOIFilter = NULL;
 718     mVFMapper = NULL;
 719     mVFActor = NULL;
 720   }
 721   if (actor_type == "overlay") {
 722     Renderer->RemoveActor(mOverlayActor);
 723     mOverlay = NULL;
 724     mOverlayActor = NULL;
 725     mOverlayMapper = NULL;
 726   }
 727   if ( (actor_type == "fusion") || (actor_type == "fusionSequence") ) {
 728     Renderer->RemoveActor(mFusionActor);
 729     mFusion = NULL;
 730     mFusionActor = NULL;
 731     mFusionMapper = NULL;
 732   }
 733   if (actor_type == "contour") {
 734     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 735     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 736   }
 737 }
 738 //------------------------------------------------------------------------------
 739
 740
 741 //------------------------------------------------------------------------------
 742 void vvSlicer::SetVFSubSampling(int sub)
 743 { //out << __func__ << endl;
 744   if (mVOIFilter) {
 745     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 746     mSubSampling = sub;
 747   }
 748   UpdateDisplayExtent();
 749   Render();
 750 }
 751 //------------------------------------------------------------------------------
 752
 753
 754 //------------------------------------------------------------------------------
 755 void vvSlicer::SetVFScale(int scale)
 756 { //out << __func__ << endl;
 757   mScale = scale;
 758   if (mArrow)
 759     mArrow->SetScale(mScale);
 760   UpdateDisplayExtent();
 761   Render();
 762 }
 763 //------------------------------------------------------------------------------
 764
 765 //------------------------------------------------------------------------------
 766 void vvSlicer::SetVFWidth(int width)
 767 { //out << __func__ << endl;
 768   mVFWidth = width;
 769   if (mVFActor)
 770     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 771   UpdateDisplayExtent();
 772   Render();
 773 }
 774 //------------------------------------------------------------------------------
 775
 776
 777 //------------------------------------------------------------------------------
 778 void vvSlicer::SetVFLog(int log)
 779 { //out << __func__ << endl;
 780   mVFLog = log;
 781   if (mGlyphFilter) {
 782     mGlyphFilter->SetUseLog(mVFLog);
 783     mGlyphFilter->Modified();
 784   }
 785   UpdateDisplayExtent();
 786   Render();
 787 }
 788 //------------------------------------------------------------------------------
 789
 790
 791 //------------------------------------------------------------------------------
 792 void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
 793 { //out << __func__ << endl;
 794         if (!updateLinkedImages) {
 795                 mCurrentTSlice = t;
 796 #if VTK_MAJOR_VERSION <= 5
 797                 mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 798 #else
 799                 mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 800 #endif
 801                 // Update transform
 802                 mConcatenatedTransform->Identity();
 803                 mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 804                 mConcatenatedTransform->Concatenate(mSlicingTransform);
 805                 UpdateDisplayExtent();
 806                 return;
 807         }
 808   if (t < 0)
 809     mCurrentTSlice = 0;
 810   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 811     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 812   else
 813     mCurrentTSlice = t;
 814
 815   // Update transform
 816   mConcatenatedTransform->Identity();
 817   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 818   mConcatenatedTransform->Concatenate(mSlicingTransform);
 819
 820   // Update image data
 821 #if VTK_MAJOR_VERSION <= 5
 822    mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 823 #else
 824   mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 825 #endif
 826   if (mVF && mVFActor->GetVisibility()) {
 827     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 828 #if VTK_MAJOR_VERSION <= 5
 829       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 830 #else
 831       mVOIFilter->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
 832 #endif
 833   }
 834   //update the overlay
 835   if (mOverlay && mOverlayActor->GetVisibility()) {
 836     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 837       mCurrentOverlayTSlice = t;
 838 #if VTK_MAJOR_VERSION <= 5
 839       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 840 #else
 841       mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 842 #endif
 843       // Update overlay transform
 844       mConcatenatedOverlayTransform->Identity();
 845       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 846       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 847     }
 848   }
 849   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 850   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 851     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 852       mCurrentFusionTSlice = t;
 853 #if VTK_MAJOR_VERSION <= 5
 854       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 855 #else
 856       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 857 #endif
 858
 859       // Update fusion transform
 860       mConcatenatedFusionTransform->Identity();
 861       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 862       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 863     }
 864   }
 865   if (mSurfaceCutActors.size() > 0)
 866     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 867          i!=mSurfaceCutActors.end(); i++)
 868       (*i)->SetTimeSlice(mCurrentTSlice);
 869   UpdateDisplayExtent();
 870 }
 871 //------------------------------------------------------------------------------
 872
 873
 874 //------------------------------------------------------------------------------
 875 void vvSlicer::SetFusionSequenceTSlice(int t)
 876 { //out << __func__ << endl;
 877   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 878     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 879       mCurrentFusionTSlice = t;
 880 #if VTK_MAJOR_VERSION <= 5
 881       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 882 #else
 883       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 884 #endif
 885       // Update fusion transform
 886       mConcatenatedFusionTransform->Identity();
 887       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 888       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 889     }
 890   }
 891
 892   UpdateDisplayExtent();
 893 }
 894 //------------------------------------------------------------------------------
 895
 896
 897 //------------------------------------------------------------------------------
 898 int vvSlicer::GetTSlice()
 899 { //out << __func__ << endl;
 900   return mCurrentTSlice;
 901 }
 902 //------------------------------------------------------------------------------
 903
 904 //------------------------------------------------------------------------------
 905 int vvSlicer::GetMaxCurrentTSlice()
 906 { //out << __func__ << endl;
 907   int t = mCurrentTSlice;
 908   if(mOverlay)
 909     t = std::max(t, mCurrentOverlayTSlice);
 910   if(mFusion&& (mFusionSequenceCode<0)) //ignore fusionSequence data: for these, the times are not to be related (this way)
 911     t = std::max(t, mCurrentFusionTSlice);
 912   return t;
 913 }
 914 //------------------------------------------------------------------------------
 915
 916 //------------------------------------------------------------------------------
 917 int vvSlicer::GetFusionTSlice()
 918 { //out << __func__ << endl;
 919   return mCurrentFusionTSlice;
 920 }
 921 //------------------------------------------------------------------------------
 922
 923 //------------------------------------------------------------------------------
 924 int vvSlicer::GetOverlayTSlice()
 925 { //out << __func__ << endl;
 926   return mCurrentOverlayTSlice;
 927 }
 928 //------------------------------------------------------------------------------
 929
 930 //------------------------------------------------------------------------------
 931 void vvSlicer::SetSliceOrientation(int orientation)
 932 { //out << __func__ << endl;
 933   //if 2D image, force to watch in Axial View
 934   int extent[6];
 935 #if VTK_MAJOR_VERSION <= 5
 936     this->GetInput()->GetWholeExtent(extent);
 937 #else
 938     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 939     copyExtent(ext, extent);
 940 #endif
 941
 942   if (extent[5]-extent[4] <= 2)
 943     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 944
 945   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 946       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 947     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 948     return;
 949   }
 950
 951   this->SliceOrientation = orientation;
 952
 953   if(mFusion)
 954     AdjustResliceToSliceOrientation(mFusionReslice);
 955
 956   if(mOverlay)
 957     AdjustResliceToSliceOrientation(mOverlayReslice);
 958
 959   // Update the viewer
 960
 961   // Go to current cursor position
 962   // double* cursorPos = GetCursorPosition();
 963   // DDV(cursorPos, 3);
 964   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 965
 966   if (mFirstSetSliceOrientation) {
 967     int *range = this->GetSliceRange();
 968     if (range)
 969       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 970 #if VTK_MAJOR_VERSION <= 5
 971       mFirstSetSliceOrientation = false;
 972 #endif
 973   }
 974   else if (this->Renderer && this->GetInput()) {
 975     double s = mCursor[orientation];
 976     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 977     this->Slice = static_cast<int>(sCursor);
 978   }
 979
 980   this->UpdateOrientation();
 981
 982   this->UpdateDisplayExtent();
 983
 984   if (mFirstSetSliceOrientation) {
 985     mFirstSetSliceOrientation = false;
 986   }
 987
 988   if (this->Renderer && this->GetInput()) {
 989     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 990     this->Renderer->ResetCamera();
 991     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 992   }
 993
 994   SetContourSlice();
 995 }
 996 //----------------------------------------------------------------------------
 997
 998 //------------------------------------------------------------------------------
 999 // This function ensures that we sample the slices of a vtkImageReslice filter
1000 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
1001 // In other words, we change the grid of the reslice in the same way as the grid
1002 // of the displayed image in the slicing direction.
1003 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1004 { //out << __func__ << endl;
1005   // Reset autocrop and update output information
1006   reslice->SetOutputOriginToDefault();
1007   reslice->SetOutputSpacingToDefault();
1008 #if VTK_MAJOR_VERSION <= 5
1009   reslice->GetOutput()->UpdateInformation();
1010 #else
1011   reslice->UpdateInformation();
1012 #endif
1013
1014   // Ge new origin / spacing
1015   double origin[3];
1016   double spacing[3];
1017   reslice->GetOutput()->GetOrigin(origin);
1018   reslice->GetOutput()->GetSpacing(spacing);
1019
1020   // Use similar spacing as the image in the direction SliceOrientation
1021   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1022
1023   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1024   // Step 1: from world coordinates to image coordinates
1025   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1026   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1027
1028   // Step 2: round to nearest grid positionInc. This has been validated as the only
1029   // way to have something consistent with the thickness of a 2D slice visible on the
1030   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1031   // between two slices, one will never be able to see this 2D slice (bug #1883).
1032   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1033
1034   // Step 3: back to world coordinates
1035   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1036   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1037
1038   // Set new spacing and origin
1039   reslice->SetOutputOrigin(origin);
1040   reslice->SetOutputSpacing(spacing);
1041   reslice->UpdateInformation();
1042 }
1043 //------------------------------------------------------------------------------
1044
1045 //----------------------------------------------------------------------------
1046 int * vvSlicer::GetExtent()
1047 { //out << __func__ << endl;
1048   int *w_ext;
1049   if (mUseReducedExtent) {
1050     w_ext = mReducedExtent;
1051   }
1052   else {
1053 #if VTK_MAJOR_VERSION <= 5
1054     w_ext = GetInput()->GetWholeExtent();
1055 #else
1056     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1057 #endif
1058   }
1059   return w_ext;
1060 }
1061 //----------------------------------------------------------------------------
1062
1063
1064 //----------------------------------------------------------------------------
1065 int vvSlicer::GetOrientation()
1066 { //out << __func__ << endl;
1067   return this->SliceOrientation;
1068 }
1069 //----------------------------------------------------------------------------
1070
1071
1072 //----------------------------------------------------------------------------
1073 void vvSlicer::UpdateDisplayExtent()
1074 { //out << __func__ << endl;
1075   vtkImageData *input = this->GetInput();
1076
1077   if (!input || !this->ImageActor) {
1078     return;
1079   }
1080
1081 #if VTK_MAJOR_VERSION <= 5
1082   input->UpdateInformation();
1083 #endif
1084   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1085
1086   // Local copy of extent
1087   int w_ext[6];
1088   int* ext = GetExtent();
1089   copyExtent(ext, w_ext);
1090
1091   // Set slice value
1092
1093   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1094   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1095
1096   // Image actor
1097   this->ImageActor->SetVisibility(mImageVisibility);
1098 #if VTK_MAJOR_VERSION <= 5
1099   this->ImageActor->SetDisplayExtent(w_ext);
1100 #else
1101   vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1102   try {
1103         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1104   } catch (const std::bad_cast& e) {
1105                 std::cerr << e.what() << std::endl;
1106                 std::cerr << "Conversion error" << std::endl;
1107                 return;
1108   }
1109   if (mFirstSetSliceOrientation) {
1110     copyExtent(ext, mRegisterExtent);
1111     this->ImageActor->SetDisplayExtent(w_ext); //initialisation
1112   } else {
1113     int w_croppingRegion[6];
1114     copyExtent(mRegisterExtent, w_croppingRegion);
1115     this->ImageActor->SetDisplayExtent(w_ext);
1116     w_croppingRegion[ this->SliceOrientation*2   ] = this->Slice;
1117     w_croppingRegion[ this->SliceOrientation*2+1 ] = this->Slice;
1118     mapperOpenGL->SetCroppingRegion(w_croppingRegion);
1119   }
1120 #endif
1121
1122 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1123   // Fix for bug #1882
1124   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1125 #endif
1126
1127   // Overlay image actor
1128   if (mOverlay && mOverlayVisibility) {
1129     AdjustResliceToSliceOrientation(mOverlayReslice);
1130     int overExtent[6];
1131     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1132 #if VTK_MAJOR_VERSION <= 5
1133     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1134 #else
1135     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1136 #endif
1137     mOverlayActor->SetVisibility(!out);
1138     mOverlayActor->SetDisplayExtent( overExtent );
1139 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1140     // Fix for bug #1882
1141     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1142 #endif
1143   }
1144   else if(mOverlay)
1145     mOverlayActor->SetVisibility(false);
1146
1147   // Fusion image actor
1148   if (mFusion && mFusionVisibility) {
1149     AdjustResliceToSliceOrientation(mFusionReslice);
1150     int fusExtent[6];
1151     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1152 #if VTK_MAJOR_VERSION <= 5
1153     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1154 #else
1155     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1156 #endif
1157     mFusionActor->SetVisibility(!out);
1158     mFusionActor->SetDisplayExtent( fusExtent );
1159 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1160     // Fix for bug #1882
1161     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1162 #endif
1163   }
1164   else if(mFusion)
1165     mFusionActor->SetVisibility(false);
1166   // Vector field actor
1167   double* camera = Renderer->GetActiveCamera()->GetPosition();
1168   double* image_bounds = ImageActor->GetBounds();
1169   double position[3] = {0, 0, 0};
1170   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1171
1172   //print_vector<double, 6>("camera", camera);
1173   //print_vector<double, 6>("image_bounds", image_bounds);
1174   //print_vector<double, 3>("position", position);
1175
1176   // find where to place the VF actor. to deal with
1177   // z-buffer issues, the VF is placed right in front of the image,
1178   // subject to a small offset. the position actually depends on the
1179   // the location of the camera relative to the image.
1180   double offset = 1;
1181   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1182     offset = -1;
1183
1184   if (mVF && mVFVisibility) {
1185     int vfExtent[6];
1186 #if VTK_MAJOR_VERSION <= 5
1187     mVF->GetVTKImages()[0]->UpdateInformation();
1188 #else
1189     //this->UpdateInformation();
1190 #endif
1191     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
1192 #if VTK_MAJOR_VERSION <= 5
1193     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1194 #else
1195     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1196 #endif
1197     mVFActor->SetVisibility(!out);
1198     mVOIFilter->SetVOI(vfExtent);
1199     int orientation[3] = {1,1,1};
1200     orientation[this->SliceOrientation] = 0;
1201     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1202     mVFMapper->Update();
1203
1204     position[this->SliceOrientation] += offset;
1205     mVFActor->SetPosition(position);
1206   }
1207   else if(mVF)
1208     mVFActor->SetVisibility(false);
1209
1210   // Landmarks actor
1211   if (mLandActor) {
1212     if (mClipBox) {
1213       double bounds [6];
1214       for(unsigned int i=0; i<6; i++)
1215         bounds[i] = ImageActor->GetBounds()[i];
1216       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1217       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1218       mClipBox->SetBounds(bounds);
1219       UpdateLandmarks();
1220     }
1221
1222     position[this->SliceOrientation] = offset;
1223     mLandActor->SetPosition(position);
1224   }
1225
1226   // Figure out the correct clipping range
1227   if (this->Renderer) {
1228     if (this->InteractorStyle &&
1229         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1230       this->Renderer->ResetCameraClippingRange();
1231     } else {
1232       vtkCamera *cam = this->Renderer->GetActiveCamera();
1233       if (cam) {
1234         double bounds[6];
1235         this->ImageActor->GetBounds(bounds);
1236         double spos = (double)bounds[this->SliceOrientation * 2];
1237         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1238         double range = fabs(spos - cpos);
1239         double *spacing = input->GetSpacing();
1240         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1241         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1242       }
1243     }
1244   }
1245 }
1246 //----------------------------------------------------------------------------
1247
1248 //----------------------------------------------------------------------------
1249 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1250                                                 vtkImageData *targetImage, int targetExtent[6])
1251 { //out << __func__ << endl;
1252   double dExtents[6];
1253   for(unsigned int i=0; i<6; i++) {
1254     // From source voxel coordinates to world coordinates
1255     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1256
1257     // From world coordinates to floating point target voxel coordinates
1258     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1259
1260     // Round to current slice or larger extent
1261     if(i/2==this->GetOrientation())
1262       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1263     else if(i%2==1)
1264       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1265     else
1266       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1267   }
1268 }
1269 //----------------------------------------------------------------------------
1270
1271 //----------------------------------------------------------------------------
1272 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1273 { //out << __func__ << endl;
1274   bool out = false;
1275   int maxBound = 6;
1276
1277   for (int i = 0; i < maxBound; i = i+2) {
1278     //if we are totally outside the image
1279     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1280       out = true;
1281       break;
1282     }
1283     //crop to the limit of the image
1284     extent[i] = std::max(extent[i], refExtent[i]);
1285     extent[i] = std::min(extent[i], refExtent[i+1]);;
1286     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1287     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1288   }
1289   if (out)
1290     for (int i = 0; i < maxBound; i = i+2) {
1291       extent[i] = refExtent[i];
1292       extent[i+1] = refExtent[i];
1293     }
1294   return out;
1295 }
1296 //----------------------------------------------------------------------------
1297
1298
1299 //----------------------------------------------------------------------------
1300 void vvSlicer::UpdateOrientation()
1301 { //out << __func__ << endl;
1302   // Set the camera position
1303   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1304   if (cam) {
1305     switch (this->SliceOrientation) {
1306     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1307       cam->SetFocalPoint(0,0,0);
1308       cam->SetPosition(0,0,-1); // -1 if medical ?
1309       cam->SetViewUp(0,-1,0);
1310       break;
1311
1312     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1313       cam->SetFocalPoint(0,0,0);
1314       cam->SetPosition(0,-1,0); // 1 if medical ?
1315       cam->SetViewUp(0,0,1);
1316       break;
1317
1318     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1319       cam->SetFocalPoint(0,0,0);
1320       cam->SetPosition(-1,0,0); // -1 if medical ?
1321       cam->SetViewUp(0,0,1);
1322       break;
1323     }
1324   }
1325 }
1326 //----------------------------------------------------------------------------
1327
1328
1329 //----------------------------------------------------------------------------
1330 void vvSlicer::SetOpacity(double s)
1331 { //out << __func__ << endl;
1332   this->GetImageActor()->SetOpacity(s);
1333 }
1334 //----------------------------------------------------------------------------
1335
1336
1337 //----------------------------------------------------------------------------
1338 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1339 { //out << __func__ << endl;
1340   this->Superclass::SetRenderWindow(rw);
1341   this->SetupInteractor(rw->GetInteractor());
1342   ca->SetImageActor(this->GetImageActor());
1343   ca->SetWindowLevel(this->GetWindowLevel());
1344   ca->SetText(3, "<window>\n<level>");
1345
1346   double bounds[6];
1347   double max = 65000;
1348
1349   bounds[0] = -max;
1350   bounds[1] = max;
1351   bounds[2] = -max;
1352   bounds[3] = max;
1353   bounds[4] = -max;
1354   bounds[5] = max;
1355   crossCursor->SetModelBounds(bounds);
1356
1357   this->GetRenderer()->AddActor(pdmA);
1358   this->GetRenderer()->AddActor(ca);
1359   this->GetRenderer()->ResetCamera();
1360
1361   //this is just a mapping between the labeling of the orientations presented to the user and
1362   //the one used by vtk
1363   SetSliceOrientation(2-(orientation%3));
1364   ResetCamera();
1365 }
1366 //----------------------------------------------------------------------------
1367
1368
1369 //----------------------------------------------------------------------------
1370 void vvSlicer::ResetCamera()
1371 { //out << __func__ << endl;
1372   this->GetRenderer()->ResetCamera();
1373 }
1374 //----------------------------------------------------------------------------
1375
1376
1377 //----------------------------------------------------------------------------
1378 void vvSlicer::SetDisplayMode(bool i)
1379 { //out << __func__ << endl;
1380         this->GetRenderer()->SetDraw(i);
1381         if (i) UpdateDisplayExtent();
1382 }
1383 //----------------------------------------------------------------------------
1384
1385
1386 //----------------------------------------------------------------------------
1387 void vvSlicer::FlipHorizontalView()
1388 { //out << __func__ << endl;
1389   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1390   if (cam) {
1391     double *position = cam->GetPosition();
1392     double factor[3] = {1, 1, 1};
1393     factor[this->SliceOrientation] = -1;
1394     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1395
1396 /*    switch (this->SliceOrientation) {
1397     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1398       cam->SetPosition(position[0],position[1],-position[2]);
1399       break;
1400
1401     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1402       cam->SetPosition(position[0],-position[1],position[2]);
1403       break;
1404
1405     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1406       cam->SetPosition(-position[0],position[1],position[2]);
1407       break;
1408     }*/
1409
1410     this->Renderer->ResetCameraClippingRange();
1411     this->UpdateDisplayExtent();
1412   }
1413 }
1414 //----------------------------------------------------------------------------
1415
1416
1417 //----------------------------------------------------------------------------
1418 void vvSlicer::FlipVerticalView()
1419 { //out << __func__ << endl;
1420   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1421   if (cam) {
1422     FlipHorizontalView();
1423     double *viewup = cam->GetViewUp();
1424     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1425     this->UpdateDisplayExtent();
1426   }
1427 }
1428 //----------------------------------------------------------------------------
1429
1430
1431 //----------------------------------------------------------------------------
1432 void vvSlicer::SetColorWindow(double window)
1433 { //out << __func__ << endl;
1434   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1435   if ( LUT ) {
1436     double level = this->GetWindowLevel()->GetLevel();
1437     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1438     LUT->Build();
1439   }
1440   this->vtkImageViewer2::SetColorWindow(window);
1441 }
1442 //----------------------------------------------------------------------------
1443
1444 //----------------------------------------------------------------------------
1445 void vvSlicer::SetColorLevel(double level)
1446 { //out << __func__ << endl;
1447   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1448   if ( LUT ) {
1449     double window = this->GetWindowLevel()->GetWindow();
1450     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1451     LUT->Build();
1452   }
1453   this->vtkImageViewer2::SetColorLevel(level);
1454 }
1455 //----------------------------------------------------------------------------
1456
1457 //----------------------------------------------------------------------------
1458 double vvSlicer::GetOverlayColorWindow()
1459 { //out << __func__ << endl;
1460   if(mOverlayMapper)
1461     return mOverlayMapper->GetWindow();
1462   else
1463     return 0.;
1464 }
1465 //----------------------------------------------------------------------------
1466
1467 //----------------------------------------------------------------------------
1468 double vvSlicer::GetOverlayColorLevel()
1469 { //out << __func__ << endl;
1470   if(mOverlayMapper)
1471     return mOverlayMapper->GetLevel();
1472   else
1473     return 0.;
1474 }
1475 //----------------------------------------------------------------------------
1476
1477 //----------------------------------------------------------------------------
1478 void vvSlicer::SetOverlayColorWindow(double window)
1479 { //out << __func__ << endl;
1480   if(mOverlayMapper)
1481     mOverlayMapper->SetWindow(window);
1482 }
1483 //----------------------------------------------------------------------------
1484
1485 //----------------------------------------------------------------------------
1486 void vvSlicer::SetOverlayColorLevel(double level)
1487 { //out << __func__ << endl;
1488   if(mOverlayMapper)
1489     mOverlayMapper->SetLevel(level);
1490 }
1491 //----------------------------------------------------------------------------
1492
1493 //----------------------------------------------------------------------------
1494 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1495 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1496 { //out << __func__ << endl;
1497   //Get mouse pointer position in view coordinates
1498   double corner1[3];
1499   double corner2[3];
1500   for(int i=0; i<3; i++) {
1501     corner1[i] = mCurrent[i];
1502     corner2[i] = mCurrent[i];
1503   }
1504
1505   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1506   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1507
1508   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1509   int w, h;
1510   this->Renderer->GetTiledSize(&w, &h);
1511   corner1[0] -= 0.2*h/(double)w;
1512   corner2[0] += 0.2*h/(double)w;
1513   corner1[1] -= 0.2;
1514   corner2[1] += 0.2;
1515   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1516   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1517
1518   //Convert to image pixel coordinates (rounded)
1519   transform->TransformPoint(corner1, corner1);
1520   transform->TransformPoint(corner2, corner2);
1521   int iLocalExtents[6];
1522   for(int i=0; i<3; i++) {
1523     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1524     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1525
1526     iLocalExtents[i*2  ] = lrint(corner1[i]);
1527     iLocalExtents[i*2+1] = lrint(corner2[i]);
1528
1529     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1530       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1531   }
1532
1533   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1534 #if VTK_MAJOR_VERSION <= 5
1535   voiFilter->SetInput(image);
1536 #else
1537   voiFilter->SetInputData(image);
1538 #endif
1539   voiFilter->SetVOI(iLocalExtents);
1540   voiFilter->Update();
1541   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1542     min = 0;
1543     max = 0;
1544     return;
1545   }
1546
1547   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1548 #if VTK_MAJOR_VERSION <= 5
1549   accFilter->SetInput(voiFilter->GetOutput());
1550 #else
1551   accFilter->SetInputData(voiFilter->GetOutput());
1552 #endif
1553   accFilter->Update();
1554
1555   min = *(accFilter->GetMin());
1556   max = *(accFilter->GetMax());
1557 }
1558 //----------------------------------------------------------------------------
1559
1560 //----------------------------------------------------------------------------
1561 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1562 { //out << __func__ << endl;
1563   ix = lrint(X);
1564   iy = lrint(Y);
1565   iz = lrint(Z);
1566 #if VTK_MAJOR_VERSION <= 5
1567   if (ix < image->GetWholeExtent()[0] ||
1568       ix > image->GetWholeExtent()[1] ||
1569       iy < image->GetWholeExtent()[2] ||
1570       iy > image->GetWholeExtent()[3] ||
1571       iz < image->GetWholeExtent()[4] ||
1572       iz > image->GetWholeExtent()[5] )
1573     return std::numeric_limits<double>::quiet_NaN();
1574   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1575   image->Update();
1576 #else
1577   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1578       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1579       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1580       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1581       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1582       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1583     return std::numeric_limits<double>::quiet_NaN();
1584   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1585   //image->Update();
1586 #endif
1587
1588   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1589 }
1590 //----------------------------------------------------------------------------
1591
1592 //----------------------------------------------------------------------------
1593 void vvSlicer::Render()
1594 { //out << __func__ << endl;
1595   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1596     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1597     legend->UseOpacityOn();
1598     legend->SetVisibility(1);
1599   }
1600   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1601     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1602     legend->UseOpacityOff();
1603     legend->SetVisibility(1);
1604   } else legend->SetVisibility(0);
1605
1606   if (ca->GetVisibility()) {
1607     std::stringstream worldPos(" ");
1608     double pt[3];
1609     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1610     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1611     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1612     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1613 #if VTK_MAJOR_VERSION <= 5
1614     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1615         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1616         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1617         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1618         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1619         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1620
1621
1622       int ix, iy, iz;
1623       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1624
1625       if(ImageActor->GetVisibility())
1626         worldPos << "data value : " << value << std::endl;
1627
1628       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1629                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1630                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1631                           << mCurrentTSlice
1632                           << std::endl;
1633       worldPos << "pixel : " << ix << ' '
1634                              << iy << ' '
1635                              << iz << ' '
1636                              << mCurrentTSlice
1637                              << std::endl;
1638     }
1639 #else
1640     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1641         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1642         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1643         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1644         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1645         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1646
1647       int ix, iy, iz;
1648       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1649
1650       if(ImageActor->GetVisibility())
1651         worldPos << "data value : " << value << std::endl;
1652
1653       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1654                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1655                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1656                           << mCurrentTSlice
1657                           << std::endl;
1658       worldPos << "pixel : " << ix << ' '
1659                              << iy << ' '
1660                              << iz << ' '
1661                              << mCurrentTSlice
1662                              << std::endl;
1663
1664     }
1665 #endif
1666     ca->SetText(1,worldPos.str().c_str());
1667
1668     std::stringstream slicePos;
1669     slicePos << "Slice: " << this->GetSlice();
1670     ca->SetText(2, slicePos.str().c_str());
1671   }
1672
1673   if (pdmA->GetVisibility()) {
1674     double x = mCursor[0];
1675     double y = mCursor[1];
1676     double z = mCursor[2];
1677     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1678     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1679     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1680 #if VTK_MAJOR_VERSION <= 5
1681     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1682         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1683         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1684         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1685         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1686         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1687       vtkRenderer * renderer = this->Renderer;
1688
1689       renderer->WorldToView(x,y,z);
1690       renderer->ViewToNormalizedViewport(x,y,z);
1691       renderer->NormalizedViewportToViewport(x,y);
1692       renderer->ViewportToNormalizedDisplay(x,y);
1693       renderer->NormalizedDisplayToDisplay(x,y);
1694       crossCursor->SetFocalPoint(x,y,z);
1695     } else
1696       crossCursor->SetFocalPoint(-1,-1,z);
1697     crossCursor->Update();
1698   }
1699 #else
1700     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1701     try {
1702         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1703     } catch (const std::bad_cast& e) {
1704                 std::cerr << e.what() << std::endl;
1705                 std::cerr << "Conversion error" << std::endl;
1706                 return;
1707         }
1708     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1709         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1710         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1711         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1712         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1713         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1714       vtkRenderer * renderer = this->Renderer;
1715
1716       renderer->WorldToView(x,y,z);
1717       renderer->ViewToNormalizedViewport(x,y,z);
1718       renderer->NormalizedViewportToViewport(x,y);
1719       renderer->ViewportToNormalizedDisplay(x,y);
1720       renderer->NormalizedDisplayToDisplay(x,y);
1721       crossCursor->SetFocalPoint(x,y,z);
1722     } else
1723       crossCursor->SetFocalPoint(-1,-1,z);
1724     crossCursor->Update();
1725   }
1726 #endif
1727
1728   if (mOverlay && mOverlayActor->GetVisibility()) {
1729     if(mLinkOverlayWindowLevel) {
1730       mOverlayMapper->SetWindow(this->GetColorWindow());
1731       mOverlayMapper->SetLevel(this->GetColorLevel());
1732     }
1733 #if VTK_MAJOR_VERSION <= 5
1734     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1735 #else
1736     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1737 #endif
1738     mOverlayMapper->Update();
1739   }
1740   if (mFusion && mFusionActor->GetVisibility()) {
1741 #if VTK_MAJOR_VERSION <= 5
1742     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1743 #else
1744     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1745 #endif
1746     mFusionMapper->Update();
1747   }
1748   if (mLandMapper)
1749     UpdateLandmarks();
1750
1751   this->GetRenderWindow()->Render();
1752 }
1753 //----------------------------------------------------------------------------
1754
1755
1756 //----------------------------------------------------------------------------
1757 void vvSlicer::UpdateCursorPosition()
1758 { //out << __func__ << endl;
1759   pdmA->SetVisibility(true);
1760   mCursor[0] = mCurrent[0];
1761   mCursor[1] = mCurrent[1];
1762   mCursor[2] = mCurrent[2];
1763   mCursor[3] = mCurrentTSlice;
1764 }
1765 //----------------------------------------------------------------------------
1766
1767
1768 //----------------------------------------------------------------------------
1769 void vvSlicer::UpdateLandmarks()
1770 { //out << __func__ << endl;
1771   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1772   if (pd->GetPoints()) {
1773     //mLandGlyph->SetRange(0,1);
1774     //mLandGlyph->Modified();
1775     //mLandGlyph->Update();
1776
1777     mClipBox->Modified();
1778     mLandClipper->Update();
1779     mLandMapper->Update();
1780     //Let's add the captions
1781     //First remove all captions:
1782     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1783         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1784         //allActors2D->Remove (mLandLabelActors[i]);
1785     }
1786     mLandLabelActors.clear();
1787     //Next add the captions to the displayed points
1788     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1789           double *position = mLandClipper->GetOutput()->GetPoint(id);
1790       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1791       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1792       label_actor->SetCaption(label);
1793       label_actor->SetAttachmentPoint(position);
1794       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1795       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1796       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1797       label_actor->GetCaptionTextProperty()->SetBold(0);
1798       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1799       label_actor->BorderOff();
1800       label_actor->LeaderOff();
1801       label_actor->ThreeDimensionalLeaderOff();
1802       mLandLabelActors.push_back(label_actor);
1803       this->Renderer->AddActor2D(mLandLabelActors[id]);
1804      }
1805   }
1806
1807 }
1808 //----------------------------------------------------------------------------
1809
1810
1811 //----------------------------------------------------------------------------
1812 void vvSlicer::SetSlice(int slice)
1813 { //out << __func__ << endl;
1814   int *range = this->GetSliceRange();
1815   if (range) {
1816     if (slice < range[0]) {
1817       slice = range[0];
1818     } else if (slice > range[1]) {
1819       slice = range[1];
1820     }
1821   }
1822
1823   if (this->Slice == slice) {
1824     return;
1825   }
1826
1827   this->Slice = slice;
1828   SetContourSlice();
1829   this->Modified();
1830   this->UpdateDisplayExtent();
1831
1832   // Seems to work without this line
1833   //this->Render();
1834 }
1835 //----------------------------------------------------------------------------
1836
1837 //----------------------------------------------------------------------------
1838 int vvSlicer::GetTMax()
1839 { //out << __func__ << endl;
1840   int tmax = (int)mImage->GetVTKImages().size() - 1;
1841   if(mOverlay)
1842     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1843   return tmax;
1844 }
1845 //----------------------------------------------------------------------------
1846
1847 //----------------------------------------------------------------------------
1848 void vvSlicer::SetContourSlice()
1849 { //out << __func__ << endl;
1850   if (mSurfaceCutActors.size() > 0)
1851     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1852          i!=mSurfaceCutActors.end(); i++) {
1853
1854       (*i)->SetSlicingOrientation(this->SliceOrientation);
1855       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1856                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1857     }
1858 }
1859 //----------------------------------------------------------------------------
1860
1861
1862 //----------------------------------------------------------------------------
1863 void vvSlicer::ForceUpdateDisplayExtent()
1864 { //out << __func__ << endl;
1865   this->UpdateDisplayExtent();
1866 }
1867 //----------------------------------------------------------------------------
1868
1869
1870 //----------------------------------------------------------------------------
1871 int* vvSlicer::GetDisplayExtent()
1872 { //out << __func__ << endl;
1873   return this->GetImageActor()->GetDisplayExtent();
1874 }
1875 //----------------------------------------------------------------------------
1876
1877
1878 //----------------------------------------------------------------------------
1879 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1880 { //out << __func__ << endl;
1881   this->Superclass::PrintSelf(os, indent);
1882 }
1883 //----------------------------------------------------------------------------
1884
1885
1886 //----------------------------------------------------------------------------
1887 void vvSlicer::SetVFColor(double r, double g, double b)
1888 { //out << __func__ << endl;
1889   double mVFColorHSV[3];
1890   mVFColor[0] = r;
1891   mVFColor[1] = g;
1892   mVFColor[2] = b;
1893
1894   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1895   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1896   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1897   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1898
1899   this->Render();
1900 }
1901 //----------------------------------------------------------------------------
1902
1903
1904 //----------------------------------------------------------------------------
1905 void vvSlicer::SetRegisterExtent(int ext[6])
1906 { //out << __func__ << endl;
1907     copyExtent(ext, mRegisterExtent);
1908 }
1909 //----------------------------------------------------------------------------
1910
1911
1912 //----------------------------------------------------------------------------
1913 void vvSlicer::GetRegisterExtent(int ext[6])
1914 { //out << __func__ << endl;
1915     copyExtent(mRegisterExtent, ext);
1916 }
1917 //----------------------------------------------------------------------------
1918