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->SetInputData(mOverlayReslice->GetOutput());
 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
 844       // Update overlay transform
 845       mConcatenatedOverlayTransform->Identity();
 846       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 847       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 848     }
 849   }
 850   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 851   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 852     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 853       mCurrentFusionTSlice = t;
 854 #if VTK_MAJOR_VERSION <= 5
 855       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 856 #else
 857       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 858 #endif
 859
 860       // Update fusion transform
 861       mConcatenatedFusionTransform->Identity();
 862       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 863       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 864     }
 865   }
 866   if (mSurfaceCutActors.size() > 0)
 867     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 868          i!=mSurfaceCutActors.end(); i++)
 869       (*i)->SetTimeSlice(mCurrentTSlice);
 870   UpdateDisplayExtent();
 871 }
 872 //------------------------------------------------------------------------------
 873
 874
 875 //------------------------------------------------------------------------------
 876 void vvSlicer::SetFusionSequenceTSlice(int t)
 877 { //out << __func__ << endl;
 878   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 879     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 880       mCurrentFusionTSlice = t;
 881 #if VTK_MAJOR_VERSION <= 5
 882       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 883 #else
 884       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 885 #endif
 886       // Update fusion transform
 887       mConcatenatedFusionTransform->Identity();
 888       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 889       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 890     }
 891   }
 892
 893   UpdateDisplayExtent();
 894 }
 895 //------------------------------------------------------------------------------
 896
 897
 898 //------------------------------------------------------------------------------
 899 int vvSlicer::GetTSlice()
 900 { //out << __func__ << endl;
 901   return mCurrentTSlice;
 902 }
 903 //------------------------------------------------------------------------------
 904
 905 //------------------------------------------------------------------------------
 906 int vvSlicer::GetMaxCurrentTSlice()
 907 { //out << __func__ << endl;
 908   int t = mCurrentTSlice;
 909   if(mOverlay)
 910     t = std::max(t, mCurrentOverlayTSlice);
 911   if(mFusion&& (mFusionSequenceCode<0)) //ignore fusionSequence data: for these, the times are not to be related (this way)
 912     t = std::max(t, mCurrentFusionTSlice);
 913   return t;
 914 }
 915 //------------------------------------------------------------------------------
 916
 917 //------------------------------------------------------------------------------
 918 int vvSlicer::GetFusionTSlice()
 919 { //out << __func__ << endl;
 920   return mCurrentFusionTSlice;
 921 }
 922 //------------------------------------------------------------------------------
 923
 924 //------------------------------------------------------------------------------
 925 int vvSlicer::GetOverlayTSlice()
 926 { //out << __func__ << endl;
 927   return mCurrentOverlayTSlice;
 928 }
 929 //------------------------------------------------------------------------------
 930
 931 //------------------------------------------------------------------------------
 932 void vvSlicer::SetSliceOrientation(int orientation)
 933 { //out << __func__ << endl;
 934   //if 2D image, force to watch in Axial View
 935   int extent[6];
 936 #if VTK_MAJOR_VERSION <= 5
 937     this->GetInput()->GetWholeExtent(extent);
 938 #else
 939     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 940     copyExtent(ext, extent);
 941 #endif
 942
 943   if (extent[5]-extent[4] <= 2)
 944     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 945
 946   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 947       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 948     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 949     return;
 950   }
 951
 952   this->SliceOrientation = orientation;
 953
 954   if(mFusion)
 955     AdjustResliceToSliceOrientation(mFusionReslice);
 956
 957   if(mOverlay)
 958     AdjustResliceToSliceOrientation(mOverlayReslice);
 959
 960   // Update the viewer
 961
 962   // Go to current cursor position
 963   // double* cursorPos = GetCursorPosition();
 964   // DDV(cursorPos, 3);
 965   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 966
 967   if (mFirstSetSliceOrientation) {
 968     int *range = this->GetSliceRange();
 969     if (range)
 970       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 971 #if VTK_MAJOR_VERSION <= 5
 972       mFirstSetSliceOrientation = false;
 973 #endif
 974   }
 975   else if (this->Renderer && this->GetInput()) {
 976     double s = mCursor[orientation];
 977     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 978     this->Slice = static_cast<int>(sCursor);
 979   }
 980
 981   this->UpdateOrientation();
 982
 983   this->UpdateDisplayExtent();
 984
 985   if (mFirstSetSliceOrientation) {
 986     mFirstSetSliceOrientation = false;
 987   }
 988
 989   if (this->Renderer && this->GetInput()) {
 990     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 991     this->Renderer->ResetCamera();
 992     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 993   }
 994
 995   SetContourSlice();
 996 }
 997 //----------------------------------------------------------------------------
 998
 999 //------------------------------------------------------------------------------
1000 // This function ensures that we sample the slices of a vtkImageReslice filter
1001 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
1002 // In other words, we change the grid of the reslice in the same way as the grid
1003 // of the displayed image in the slicing direction.
1004 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1005 { //out << __func__ << endl;
1006   // Reset autocrop and update output information
1007   reslice->SetOutputOriginToDefault();
1008   reslice->SetOutputSpacingToDefault();
1009 #if VTK_MAJOR_VERSION <= 5
1010   reslice->GetOutput()->UpdateInformation();
1011 #else
1012   reslice->UpdateInformation();
1013 #endif
1014
1015   // Ge new origin / spacing
1016   double origin[3];
1017   double spacing[3];
1018   reslice->GetOutput()->GetOrigin(origin);
1019   reslice->GetOutput()->GetSpacing(spacing);
1020
1021   // Use similar spacing as the image in the direction SliceOrientation
1022   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1023
1024   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1025   // Step 1: from world coordinates to image coordinates
1026   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1027   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1028
1029   // Step 2: round to nearest grid positionInc. This has been validated as the only
1030   // way to have something consistent with the thickness of a 2D slice visible on the
1031   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1032   // between two slices, one will never be able to see this 2D slice (bug #1883).
1033   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1034
1035   // Step 3: back to world coordinates
1036   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1037   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1038
1039   // Set new spacing and origin
1040   reslice->SetOutputOrigin(origin);
1041   reslice->SetOutputSpacing(spacing);
1042   reslice->UpdateInformation();
1043 }
1044 //------------------------------------------------------------------------------
1045
1046 //----------------------------------------------------------------------------
1047 int * vvSlicer::GetExtent()
1048 { //out << __func__ << endl;
1049   int *w_ext;
1050   if (mUseReducedExtent) {
1051     w_ext = mReducedExtent;
1052   }
1053   else {
1054 #if VTK_MAJOR_VERSION <= 5
1055     w_ext = GetInput()->GetWholeExtent();
1056 #else
1057     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1058 #endif
1059   }
1060   return w_ext;
1061 }
1062 //----------------------------------------------------------------------------
1063
1064
1065 //----------------------------------------------------------------------------
1066 int vvSlicer::GetOrientation()
1067 { //out << __func__ << endl;
1068   return this->SliceOrientation;
1069 }
1070 //----------------------------------------------------------------------------
1071
1072
1073 //----------------------------------------------------------------------------
1074 void vvSlicer::UpdateDisplayExtent()
1075 { //out << __func__ << endl;
1076   vtkImageData *input = this->GetInput();
1077
1078   if (!input || !this->ImageActor) {
1079     return;
1080   }
1081
1082 #if VTK_MAJOR_VERSION <= 5
1083   input->UpdateInformation();
1084 #endif
1085   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1086
1087   // Local copy of extent
1088   int w_ext[6];
1089   int* ext = GetExtent();
1090   copyExtent(ext, w_ext);
1091
1092   // Set slice value
1093
1094   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1095   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1096
1097   // Image actor
1098   this->ImageActor->SetVisibility(mImageVisibility);
1099 #if VTK_MAJOR_VERSION <= 5
1100   this->ImageActor->SetDisplayExtent(w_ext);
1101 #else
1102   vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1103   try {
1104         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1105   } catch (const std::bad_cast& e) {
1106                 std::cerr << e.what() << std::endl;
1107                 std::cerr << "Conversion error" << std::endl;
1108                 return;
1109   }
1110   if (mFirstSetSliceOrientation) {
1111     copyExtent(ext, mRegisterExtent);
1112     this->ImageActor->SetDisplayExtent(w_ext); //initialisation
1113   } else {
1114     int w_croppingRegion[6];
1115     copyExtent(mRegisterExtent, w_croppingRegion);
1116     this->ImageActor->SetDisplayExtent(w_ext);
1117     w_croppingRegion[ this->SliceOrientation*2   ] = this->Slice;
1118     w_croppingRegion[ this->SliceOrientation*2+1 ] = this->Slice;
1119     mapperOpenGL->SetCroppingRegion(w_croppingRegion);
1120   }
1121 #endif
1122
1123 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1124   // Fix for bug #1882
1125   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1126 #endif
1127
1128   // Overlay image actor
1129   if (mOverlay && mOverlayVisibility) {
1130     AdjustResliceToSliceOrientation(mOverlayReslice);
1131     int overExtent[6];
1132     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1133 #if VTK_MAJOR_VERSION <= 5
1134     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1135 #else
1136     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1137 #endif
1138     mOverlayActor->SetVisibility(!out);
1139     mOverlayActor->SetDisplayExtent( overExtent );
1140 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1141     // Fix for bug #1882
1142     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1143 #endif
1144   }
1145   else if(mOverlay)
1146     mOverlayActor->SetVisibility(false);
1147
1148   // Fusion image actor
1149   if (mFusion && mFusionVisibility) {
1150     AdjustResliceToSliceOrientation(mFusionReslice);
1151     int fusExtent[6];
1152     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1153 #if VTK_MAJOR_VERSION <= 5
1154     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1155 #else
1156     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1157 #endif
1158     mFusionActor->SetVisibility(!out);
1159     mFusionActor->SetDisplayExtent( fusExtent );
1160 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1161     // Fix for bug #1882
1162     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1163 #endif
1164   }
1165   else if(mFusion)
1166     mFusionActor->SetVisibility(false);
1167   // Vector field actor
1168   double* camera = Renderer->GetActiveCamera()->GetPosition();
1169   double* image_bounds = ImageActor->GetBounds();
1170   double position[3] = {0, 0, 0};
1171   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1172
1173   //print_vector<double, 6>("camera", camera);
1174   //print_vector<double, 6>("image_bounds", image_bounds);
1175   //print_vector<double, 3>("position", position);
1176
1177   // find where to place the VF actor. to deal with
1178   // z-buffer issues, the VF is placed right in front of the image,
1179   // subject to a small offset. the position actually depends on the
1180   // the location of the camera relative to the image.
1181   double offset = 1;
1182   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1183     offset = -1;
1184
1185   if (mVF && mVFVisibility) {
1186     int vfExtent[6];
1187 #if VTK_MAJOR_VERSION <= 5
1188     mVF->GetVTKImages()[0]->UpdateInformation();
1189 #else
1190     //this->UpdateInformation();
1191 #endif
1192     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
1193 #if VTK_MAJOR_VERSION <= 5
1194     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1195 #else
1196     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetInformation()->Get(vtkDataObject::DATA_EXTENT()));
1197 #endif
1198     mVFActor->SetVisibility(!out);
1199     mVOIFilter->SetVOI(vfExtent);
1200     int orientation[3] = {1,1,1};
1201     orientation[this->SliceOrientation] = 0;
1202     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1203     mVFMapper->Update();
1204
1205     position[this->SliceOrientation] += offset;
1206     mVFActor->SetPosition(position);
1207   }
1208   else if(mVF)
1209     mVFActor->SetVisibility(false);
1210
1211   // Landmarks actor
1212   if (mLandActor) {
1213     if (mClipBox) {
1214       double bounds [6];
1215       for(unsigned int i=0; i<6; i++)
1216         bounds[i] = ImageActor->GetBounds()[i];
1217       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1218       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1219       mClipBox->SetBounds(bounds);
1220       UpdateLandmarks();
1221     }
1222
1223     position[this->SliceOrientation] = offset;
1224     mLandActor->SetPosition(position);
1225   }
1226
1227   // Figure out the correct clipping range
1228   if (this->Renderer) {
1229     if (this->InteractorStyle &&
1230         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1231       this->Renderer->ResetCameraClippingRange();
1232     } else {
1233       vtkCamera *cam = this->Renderer->GetActiveCamera();
1234       if (cam) {
1235         double bounds[6];
1236         this->ImageActor->GetBounds(bounds);
1237         double spos = (double)bounds[this->SliceOrientation * 2];
1238         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1239         double range = fabs(spos - cpos);
1240         double *spacing = input->GetSpacing();
1241         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1242         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1243       }
1244     }
1245   }
1246 }
1247 //----------------------------------------------------------------------------
1248
1249 //----------------------------------------------------------------------------
1250 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1251                                                 vtkImageData *targetImage, int targetExtent[6])
1252 { //out << __func__ << endl;
1253   double dExtents[6];
1254   for(unsigned int i=0; i<6; i++) {
1255     // From source voxel coordinates to world coordinates
1256     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1257
1258     // From world coordinates to floating point target voxel coordinates
1259     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1260
1261     // Round to current slice or larger extent
1262     if(i/2==this->GetOrientation())
1263       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1264     else if(i%2==1)
1265       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1266     else
1267       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1268   }
1269 }
1270 //----------------------------------------------------------------------------
1271
1272 //----------------------------------------------------------------------------
1273 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1274 { //out << __func__ << endl;
1275   bool out = false;
1276   int maxBound = 6;
1277
1278   for (int i = 0; i < maxBound; i = i+2) {
1279     //if we are totally outside the image
1280     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1281       out = true;
1282       break;
1283     }
1284     //crop to the limit of the image
1285     extent[i] = std::max(extent[i], refExtent[i]);
1286     extent[i] = std::min(extent[i], refExtent[i+1]);;
1287     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1288     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1289   }
1290   if (out)
1291     for (int i = 0; i < maxBound; i = i+2) {
1292       extent[i] = refExtent[i];
1293       extent[i+1] = refExtent[i];
1294     }
1295   return out;
1296 }
1297 //----------------------------------------------------------------------------
1298
1299
1300 //----------------------------------------------------------------------------
1301 void vvSlicer::UpdateOrientation()
1302 { //out << __func__ << endl;
1303   // Set the camera position
1304   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1305   if (cam) {
1306     switch (this->SliceOrientation) {
1307     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1308       cam->SetFocalPoint(0,0,0);
1309       cam->SetPosition(0,0,-1); // -1 if medical ?
1310       cam->SetViewUp(0,-1,0);
1311       break;
1312
1313     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1314       cam->SetFocalPoint(0,0,0);
1315       cam->SetPosition(0,-1,0); // 1 if medical ?
1316       cam->SetViewUp(0,0,1);
1317       break;
1318
1319     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1320       cam->SetFocalPoint(0,0,0);
1321       cam->SetPosition(-1,0,0); // -1 if medical ?
1322       cam->SetViewUp(0,0,1);
1323       break;
1324     }
1325   }
1326 }
1327 //----------------------------------------------------------------------------
1328
1329
1330 //----------------------------------------------------------------------------
1331 void vvSlicer::SetOpacity(double s)
1332 { //out << __func__ << endl;
1333   this->GetImageActor()->SetOpacity(s);
1334 }
1335 //----------------------------------------------------------------------------
1336
1337
1338 //----------------------------------------------------------------------------
1339 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1340 { //out << __func__ << endl;
1341   this->Superclass::SetRenderWindow(rw);
1342   this->SetupInteractor(rw->GetInteractor());
1343   ca->SetImageActor(this->GetImageActor());
1344   ca->SetWindowLevel(this->GetWindowLevel());
1345   ca->SetText(3, "<window>\n<level>");
1346
1347   double bounds[6];
1348   double max = 65000;
1349
1350   bounds[0] = -max;
1351   bounds[1] = max;
1352   bounds[2] = -max;
1353   bounds[3] = max;
1354   bounds[4] = -max;
1355   bounds[5] = max;
1356   crossCursor->SetModelBounds(bounds);
1357
1358   this->GetRenderer()->AddActor(pdmA);
1359   this->GetRenderer()->AddActor(ca);
1360   this->GetRenderer()->ResetCamera();
1361
1362   //this is just a mapping between the labeling of the orientations presented to the user and
1363   //the one used by vtk
1364   SetSliceOrientation(2-(orientation%3));
1365   ResetCamera();
1366 }
1367 //----------------------------------------------------------------------------
1368
1369
1370 //----------------------------------------------------------------------------
1371 void vvSlicer::ResetCamera()
1372 { //out << __func__ << endl;
1373   this->GetRenderer()->ResetCamera();
1374 }
1375 //----------------------------------------------------------------------------
1376
1377
1378 //----------------------------------------------------------------------------
1379 void vvSlicer::SetDisplayMode(bool i)
1380 { //out << __func__ << endl;
1381         this->GetRenderer()->SetDraw(i);
1382         if (i) UpdateDisplayExtent();
1383 }
1384 //----------------------------------------------------------------------------
1385
1386
1387 //----------------------------------------------------------------------------
1388 void vvSlicer::FlipHorizontalView()
1389 { //out << __func__ << endl;
1390   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1391   if (cam) {
1392     double *position = cam->GetPosition();
1393     double factor[3] = {1, 1, 1};
1394     factor[this->SliceOrientation] = -1;
1395     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1396
1397 /*    switch (this->SliceOrientation) {
1398     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1399       cam->SetPosition(position[0],position[1],-position[2]);
1400       break;
1401
1402     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1403       cam->SetPosition(position[0],-position[1],position[2]);
1404       break;
1405
1406     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1407       cam->SetPosition(-position[0],position[1],position[2]);
1408       break;
1409     }*/
1410
1411     this->Renderer->ResetCameraClippingRange();
1412     this->UpdateDisplayExtent();
1413   }
1414 }
1415 //----------------------------------------------------------------------------
1416
1417
1418 //----------------------------------------------------------------------------
1419 void vvSlicer::FlipVerticalView()
1420 { //out << __func__ << endl;
1421   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1422   if (cam) {
1423     FlipHorizontalView();
1424     double *viewup = cam->GetViewUp();
1425     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1426     this->UpdateDisplayExtent();
1427   }
1428 }
1429 //----------------------------------------------------------------------------
1430
1431
1432 //----------------------------------------------------------------------------
1433 void vvSlicer::SetColorWindow(double window)
1434 { //out << __func__ << endl;
1435   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1436   if ( LUT ) {
1437     double level = this->GetWindowLevel()->GetLevel();
1438     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1439     LUT->Build();
1440   }
1441   this->vtkImageViewer2::SetColorWindow(window);
1442 }
1443 //----------------------------------------------------------------------------
1444
1445 //----------------------------------------------------------------------------
1446 void vvSlicer::SetColorLevel(double level)
1447 { //out << __func__ << endl;
1448   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1449   if ( LUT ) {
1450     double window = this->GetWindowLevel()->GetWindow();
1451     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1452     LUT->Build();
1453   }
1454   this->vtkImageViewer2::SetColorLevel(level);
1455 }
1456 //----------------------------------------------------------------------------
1457
1458 //----------------------------------------------------------------------------
1459 double vvSlicer::GetOverlayColorWindow()
1460 { //out << __func__ << endl;
1461   if(mOverlayMapper)
1462     return mOverlayMapper->GetWindow();
1463   else
1464     return 0.;
1465 }
1466 //----------------------------------------------------------------------------
1467
1468 //----------------------------------------------------------------------------
1469 double vvSlicer::GetOverlayColorLevel()
1470 { //out << __func__ << endl;
1471   if(mOverlayMapper)
1472     return mOverlayMapper->GetLevel();
1473   else
1474     return 0.;
1475 }
1476 //----------------------------------------------------------------------------
1477
1478 //----------------------------------------------------------------------------
1479 void vvSlicer::SetOverlayColorWindow(double window)
1480 { //out << __func__ << endl;
1481   if(mOverlayMapper)
1482     mOverlayMapper->SetWindow(window);
1483 }
1484 //----------------------------------------------------------------------------
1485
1486 //----------------------------------------------------------------------------
1487 void vvSlicer::SetOverlayColorLevel(double level)
1488 { //out << __func__ << endl;
1489   if(mOverlayMapper)
1490     mOverlayMapper->SetLevel(level);
1491 }
1492 //----------------------------------------------------------------------------
1493
1494 //----------------------------------------------------------------------------
1495 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1496 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1497 { //out << __func__ << endl;
1498   //Get mouse pointer position in view coordinates
1499   double corner1[3];
1500   double corner2[3];
1501   for(int i=0; i<3; i++) {
1502     corner1[i] = mCurrent[i];
1503     corner2[i] = mCurrent[i];
1504   }
1505
1506   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1507   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1508
1509   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1510   int w, h;
1511   this->Renderer->GetTiledSize(&w, &h);
1512   corner1[0] -= 0.2*h/(double)w;
1513   corner2[0] += 0.2*h/(double)w;
1514   corner1[1] -= 0.2;
1515   corner2[1] += 0.2;
1516   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1517   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1518
1519   //Convert to image pixel coordinates (rounded)
1520   transform->TransformPoint(corner1, corner1);
1521   transform->TransformPoint(corner2, corner2);
1522   int iLocalExtents[6];
1523   for(int i=0; i<3; i++) {
1524     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1525     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1526
1527     iLocalExtents[i*2  ] = lrint(corner1[i]);
1528     iLocalExtents[i*2+1] = lrint(corner2[i]);
1529
1530     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1531       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1532   }
1533
1534   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1535 #if VTK_MAJOR_VERSION <= 5
1536   voiFilter->SetInput(image);
1537 #else
1538   voiFilter->SetInputData(image);
1539 #endif
1540   voiFilter->SetVOI(iLocalExtents);
1541   voiFilter->Update();
1542   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1543     min = 0;
1544     max = 0;
1545     return;
1546   }
1547
1548   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1549 #if VTK_MAJOR_VERSION <= 5
1550   accFilter->SetInput(voiFilter->GetOutput());
1551 #else
1552   accFilter->SetInputData(voiFilter->GetOutput());
1553 #endif
1554   accFilter->Update();
1555
1556   min = *(accFilter->GetMin());
1557   max = *(accFilter->GetMax());
1558 }
1559 //----------------------------------------------------------------------------
1560
1561 //----------------------------------------------------------------------------
1562 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1563 { //out << __func__ << endl;
1564   ix = lrint(X);
1565   iy = lrint(Y);
1566   iz = lrint(Z);
1567 #if VTK_MAJOR_VERSION <= 5
1568   if (ix < image->GetWholeExtent()[0] ||
1569       ix > image->GetWholeExtent()[1] ||
1570       iy < image->GetWholeExtent()[2] ||
1571       iy > image->GetWholeExtent()[3] ||
1572       iz < image->GetWholeExtent()[4] ||
1573       iz > image->GetWholeExtent()[5] )
1574     return std::numeric_limits<double>::quiet_NaN();
1575   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1576   image->Update();
1577 #else
1578   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1579       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1580       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1581       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1582       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1583       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1584     return std::numeric_limits<double>::quiet_NaN();
1585   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1586   //image->Update();
1587 #endif
1588
1589   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1590 }
1591 //----------------------------------------------------------------------------
1592
1593 //----------------------------------------------------------------------------
1594 void vvSlicer::Render()
1595 { //out << __func__ << endl;
1596
1597   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1598     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1599     legend->UseOpacityOn();
1600     legend->SetVisibility(1);
1601   }
1602   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1603     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1604     legend->UseOpacityOff();
1605     legend->SetVisibility(1);
1606   } else legend->SetVisibility(0);
1607
1608   if (ca->GetVisibility()) {
1609     std::stringstream worldPos(" ");
1610     double pt[3];
1611     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1612     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1613     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1614     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1615 #if VTK_MAJOR_VERSION <= 5
1616     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1617         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1618         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1619         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1620         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1621         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1622
1623
1624       int ix, iy, iz;
1625       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1626
1627       if(ImageActor->GetVisibility())
1628         worldPos << "data value : " << value << std::endl;
1629
1630       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1631                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1632                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1633                           << mCurrentTSlice
1634                           << std::endl;
1635       worldPos << "pixel : " << ix << ' '
1636                              << iy << ' '
1637                              << iz << ' '
1638                              << mCurrentTSlice
1639                              << std::endl;
1640     }
1641 #else
1642     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1643         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1644         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1645         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1646         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1647         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1648
1649       int ix, iy, iz;
1650       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1651
1652       if(ImageActor->GetVisibility())
1653         worldPos << "data value : " << value << std::endl;
1654
1655       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1656                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1657                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1658                           << mCurrentTSlice
1659                           << std::endl;
1660       worldPos << "pixel : " << ix << ' '
1661                              << iy << ' '
1662                              << iz << ' '
1663                              << mCurrentTSlice
1664                              << std::endl;
1665
1666     }
1667 #endif
1668     ca->SetText(1,worldPos.str().c_str());
1669
1670     std::stringstream slicePos;
1671     slicePos << "Slice: " << this->GetSlice();
1672     ca->SetText(2, slicePos.str().c_str());
1673   }
1674
1675   if (pdmA->GetVisibility()) {
1676     double x = mCursor[0];
1677     double y = mCursor[1];
1678     double z = mCursor[2];
1679     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1680     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1681     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1682 #if VTK_MAJOR_VERSION <= 5
1683     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1684         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1685         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1686         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1687         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1688         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1689       vtkRenderer * renderer = this->Renderer;
1690
1691       renderer->WorldToView(x,y,z);
1692       renderer->ViewToNormalizedViewport(x,y,z);
1693       renderer->NormalizedViewportToViewport(x,y);
1694       renderer->ViewportToNormalizedDisplay(x,y);
1695       renderer->NormalizedDisplayToDisplay(x,y);
1696       crossCursor->SetFocalPoint(x,y,z);
1697     } else
1698       crossCursor->SetFocalPoint(-1,-1,z);
1699     crossCursor->Update();
1700   }
1701 #else
1702     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1703     try {
1704         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1705     } catch (const std::bad_cast& e) {
1706                 std::cerr << e.what() << std::endl;
1707                 std::cerr << "Conversion error" << std::endl;
1708                 return;
1709         }
1710     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1711         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1712         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1713         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1714         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1715         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1716       vtkRenderer * renderer = this->Renderer;
1717
1718       renderer->WorldToView(x,y,z);
1719       renderer->ViewToNormalizedViewport(x,y,z);
1720       renderer->NormalizedViewportToViewport(x,y);
1721       renderer->ViewportToNormalizedDisplay(x,y);
1722       renderer->NormalizedDisplayToDisplay(x,y);
1723       crossCursor->SetFocalPoint(x,y,z);
1724     } else
1725       crossCursor->SetFocalPoint(-1,-1,z);
1726     crossCursor->Update();
1727   }
1728 #endif
1729
1730   if (mOverlay && mOverlayActor->GetVisibility()) {
1731     if(mLinkOverlayWindowLevel) {
1732       mOverlayMapper->SetWindow(this->GetColorWindow());
1733       mOverlayMapper->SetLevel(this->GetColorLevel());
1734     }
1735 #if VTK_MAJOR_VERSION <= 5
1736     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1737 #else
1738     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1739 #endif
1740     mOverlayMapper->Update();
1741   }
1742   if (mFusion && mFusionActor->GetVisibility()) {
1743 #if VTK_MAJOR_VERSION <= 5
1744     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1745 #else
1746     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1747 #endif
1748     mFusionMapper->Update();
1749   }
1750   if (mLandMapper)
1751     UpdateLandmarks();
1752
1753     this->GetRenderWindow()->Render();
1754 }
1755 //----------------------------------------------------------------------------
1756
1757
1758 //----------------------------------------------------------------------------
1759 void vvSlicer::UpdateCursorPosition()
1760 { //out << __func__ << endl;
1761   pdmA->SetVisibility(true);
1762   mCursor[0] = mCurrent[0];
1763   mCursor[1] = mCurrent[1];
1764   mCursor[2] = mCurrent[2];
1765   mCursor[3] = mCurrentTSlice;
1766 }
1767 //----------------------------------------------------------------------------
1768
1769
1770 //----------------------------------------------------------------------------
1771 void vvSlicer::UpdateLandmarks()
1772 { //out << __func__ << endl;
1773   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1774   if (pd->GetPoints()) {
1775     //mLandGlyph->SetRange(0,1);
1776     //mLandGlyph->Modified();
1777     //mLandGlyph->Update();
1778
1779     mClipBox->Modified();
1780     mLandClipper->Update();
1781     mLandMapper->Update();
1782     //Let's add the captions
1783     //First remove all captions:
1784     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1785         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1786         //allActors2D->Remove (mLandLabelActors[i]);
1787     }
1788     mLandLabelActors.clear();
1789     //Next add the captions to the displayed points
1790     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1791           double *position = mLandClipper->GetOutput()->GetPoint(id);
1792       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1793       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1794       label_actor->SetCaption(label);
1795       label_actor->SetAttachmentPoint(position);
1796       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1797       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1798       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1799       label_actor->GetCaptionTextProperty()->SetBold(0);
1800       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1801       label_actor->BorderOff();
1802       label_actor->LeaderOff();
1803       label_actor->ThreeDimensionalLeaderOff();
1804       mLandLabelActors.push_back(label_actor);
1805       this->Renderer->AddActor2D(mLandLabelActors[id]);
1806      }
1807   }
1808
1809 }
1810 //----------------------------------------------------------------------------
1811
1812
1813 //----------------------------------------------------------------------------
1814 void vvSlicer::SetSlice(int slice)
1815 { //out << __func__ << endl;
1816   int *range = this->GetSliceRange();
1817   if (range) {
1818     if (slice < range[0]) {
1819       slice = range[0];
1820     } else if (slice > range[1]) {
1821       slice = range[1];
1822     }
1823   }
1824
1825   if (this->Slice == slice) {
1826     return;
1827   }
1828
1829   this->Slice = slice;
1830   SetContourSlice();
1831   this->Modified();
1832   this->UpdateDisplayExtent();
1833
1834   // Seems to work without this line
1835   //this->Render();
1836 }
1837 //----------------------------------------------------------------------------
1838
1839 //----------------------------------------------------------------------------
1840 int vvSlicer::GetTMax()
1841 { //out << __func__ << endl;
1842   int tmax = (int)mImage->GetVTKImages().size() - 1;
1843   if(mOverlay)
1844     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1845   return tmax;
1846 }
1847 //----------------------------------------------------------------------------
1848
1849 //----------------------------------------------------------------------------
1850 void vvSlicer::SetContourSlice()
1851 { //out << __func__ << endl;
1852   if (mSurfaceCutActors.size() > 0)
1853     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1854          i!=mSurfaceCutActors.end(); i++) {
1855
1856       (*i)->SetSlicingOrientation(this->SliceOrientation);
1857       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1858                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1859     }
1860 }
1861 //----------------------------------------------------------------------------
1862
1863
1864 //----------------------------------------------------------------------------
1865 void vvSlicer::ForceUpdateDisplayExtent()
1866 { //out << __func__ << endl;
1867   this->UpdateDisplayExtent();
1868 }
1869 //----------------------------------------------------------------------------
1870
1871
1872 //----------------------------------------------------------------------------
1873 int* vvSlicer::GetDisplayExtent()
1874 { //out << __func__ << endl;
1875   return this->GetImageActor()->GetDisplayExtent();
1876 }
1877 //----------------------------------------------------------------------------
1878
1879
1880 //----------------------------------------------------------------------------
1881 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1882 { //out << __func__ << endl;
1883   this->Superclass::PrintSelf(os, indent);
1884 }
1885 //----------------------------------------------------------------------------
1886
1887
1888 //----------------------------------------------------------------------------
1889 void vvSlicer::SetVFColor(double r, double g, double b)
1890 { //out << __func__ << endl;
1891   double mVFColorHSV[3];
1892   mVFColor[0] = r;
1893   mVFColor[1] = g;
1894   mVFColor[2] = b;
1895
1896   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1897   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1898   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1899   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1900
1901   this->Render();
1902 }
1903 //----------------------------------------------------------------------------
1904
1905
1906 //----------------------------------------------------------------------------
1907 void vvSlicer::SetRegisterExtent(int ext[6])
1908 { //out << __func__ << endl;
1909     copyExtent(ext, mRegisterExtent);
1910 }
1911 //----------------------------------------------------------------------------
1912
1913
1914 //----------------------------------------------------------------------------
1915 void vvSlicer::GetRegisterExtent(int ext[6])
1916 { //out << __func__ << endl;
1917     copyExtent(mRegisterExtent, ext);
1918 }
1919 //----------------------------------------------------------------------------
1920