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 {
  94         mFusionSequenceCode = -1;
  95   this->UnInstallPipeline();
  96   mImage = NULL;
  97   mReducedExtent = new int[6];
  98   mRegisterExtent = NULL;
  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->SetInputConnection(crossCursor->GetOutputPort(0));
 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 {
 180   return mOverlayMapper.GetPointer();
 181 }
 182 //------------------------------------------------------------------------------
 183
 184
 185 //------------------------------------------------------------------------------
 186 vvBlendImageActor* vvSlicer::GetOverlayActor()
 187 {
 188   return mOverlayActor.GetPointer();
 189 }
 190 //------------------------------------------------------------------------------
 191
 192
 193 //------------------------------------------------------------------------------
 194 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 195 {
 196   return mFusionMapper.GetPointer();
 197 }
 198 //------------------------------------------------------------------------------
 199
 200
 201 //------------------------------------------------------------------------------
 202 vtkImageActor* vvSlicer::GetFusionActor()
 203 {
 204   return mFusionActor.GetPointer();
 205 }
 206 //------------------------------------------------------------------------------
 207
 208
 209 //------------------------------------------------------------------------------
 210 vtkActor* vvSlicer::GetVFActor()
 211 {
 212   return mVFActor.GetPointer();
 213 }
 214 //------------------------------------------------------------------------------
 215
 216
 217 //------------------------------------------------------------------------------
 218 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 219 {
 220   return ca.GetPointer();
 221 }
 222 //------------------------------------------------------------------------------
 223
 224
 225 //------------------------------------------------------------------------------
 226 void vvSlicer::EnableReducedExtent(bool b)
 227 {
 228   mUseReducedExtent = b;
 229 }
 230 //------------------------------------------------------------------------------
 231
 232
 233 //------------------------------------------------------------------------------
 234 void vvSlicer::SetReducedExtent(int * ext)
 235 {
 236   copyExtent(ext, mReducedExtent);
 237 }
 238 //------------------------------------------------------------------------------
 239
 240
 241 //------------------------------------------------------------------------------
 242 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 243 {
 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 {
 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 {
 271   pdmA->GetProperty()->SetColor(r,g,b);
 272 }
 273 //------------------------------------------------------------------------------
 274
 275
 276 //------------------------------------------------------------------------------
 277 void vvSlicer::SetCursorVisibility(bool s)
 278 {
 279   pdmA->SetVisibility(s);
 280 }
 281 //------------------------------------------------------------------------------
 282
 283
 284 //------------------------------------------------------------------------------
 285 bool vvSlicer::GetCursorVisibility()
 286 {
 287   return pdmA->GetVisibility();
 288 }
 289 //------------------------------------------------------------------------------
 290
 291
 292 //------------------------------------------------------------------------------
 293 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 294 {
 295   ca->SetVisibility(s);
 296 }
 297 //------------------------------------------------------------------------------
 298
 299
 300 //------------------------------------------------------------------------------
 301 bool vvSlicer::GetCornerAnnotationVisibility()
 302 {
 303   return ca->GetVisibility();
 304 }
 305 //------------------------------------------------------------------------------
 306
 307
 308 //------------------------------------------------------------------------------
 309 vvSlicer::~vvSlicer()
 310 {
 311   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 312        i!=mSurfaceCutActors.end(); i++)
 313     delete (*i);
 314   delete [] mReducedExtent;
 315 }
 316 //------------------------------------------------------------------------------
 317
 318 //------------------------------------------------------------------------------
 319 double* vvSlicer::GetCurrentPosition()
 320 {
 321   return mCurrentBeforeSlicingTransform;
 322 }
 323 //------------------------------------------------------------------------------
 324
 325 //------------------------------------------------------------------------------
 326 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 327 {
 328   mCurrentBeforeSlicingTransform[0]=x;
 329   mCurrentBeforeSlicingTransform[1]=y;
 330   mCurrentBeforeSlicingTransform[2]=z;
 331   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 332   if (t>=0) SetTSlice(t);
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvSlicer::SetImage(vvImage::Pointer image)
 339 {
 340   if (image->GetVTKImages().size()) {
 341     mImage = image;
 342
 343     if (!mImageReslice) {
 344       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 345       mImageReslice->SetInterpolationModeToLinear();
 346       mImageReslice->AutoCropOutputOn();
 347       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 348     }
 349
 350     mConcatenatedTransform->Identity();
 351     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 352     mConcatenatedTransform->Concatenate(mSlicingTransform);
 353     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 354 #if VTK_MAJOR_VERSION <= 5
 355     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 356 #else
 357     mImageReslice->SetInputData(0, mImage->GetFirstVTKImageData());
 358 #endif
 359     mImageReslice->UpdateInformation();
 360
 361 #if VTK_MAJOR_VERSION <= 5
 362     this->Superclass::SetInput(mImageReslice->GetOutput());
 363 #else
 364     this->Superclass::SetInputConnection(mImageReslice->GetOutputPort());
 365 #endif
 366
 367     int extent[6];
 368 #if VTK_MAJOR_VERSION <= 5
 369     this->GetInput()->GetWholeExtent(extent);
 370 #else
 371     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 372     copyExtent(ext, extent);
 373 #endif
 374
 375     // Prevent crash when reload -> change slice if outside extent
 376     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 377       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 378     }
 379
 380     // Make sure that the required part image has been computed
 381     extent[SliceOrientation*2] = Slice;
 382     extent[SliceOrientation*2+1] = Slice;
 383 #if VTK_MAJOR_VERSION <= 5
 384     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 385     mImageReslice->GetOutput()->Update();
 386 #else
 387     mImageReslice->SetUpdateExtent(extent);
 388     mImageReslice->Update();
 389 #endif
 390
 391     this->UpdateDisplayExtent();
 392
 393     mCurrentTSlice = 0;
 394     ca->SetText(0,mFileName.c_str());
 395   }
 396 }
 397 //------------------------------------------------------------------------------
 398
 399
 400 //------------------------------------------------------------------------------
 401 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 402 {
 403   if (overlay->GetVTKImages().size()) {
 404     mOverlay = overlay;
 405     mOverlayVisibility = true;
 406
 407     if (!mOverlayReslice) {
 408       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 409       mOverlayReslice->SetInterpolationModeToLinear();
 410       mOverlayReslice->AutoCropOutputOn();
 411       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 412     }
 413
 414     mConcatenatedOverlayTransform->Identity();
 415     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 416     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 417     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 418 #if VTK_MAJOR_VERSION <= 5
 419     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 420 #else
 421     mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
 422 #endif
 423     mOverlayReslice->Update();
 424
 425     if (!mOverlayMapper)
 426       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 427 #if VTK_MAJOR_VERSION <= 5
 428     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 429 #else
 430     mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
 431 #endif
 432
 433     if (!mOverlayActor) {
 434       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 435 #if VTK_MAJOR_VERSION <= 5
 436       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 437 #else
 438       mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
 439 #endif
 440       mOverlayActor->SetPickable(0);
 441       mOverlayActor->SetVisibility(true);
 442       mOverlayActor->SetOpacity(0.5);
 443 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 444       mOverlayActor->GetMapper()->BorderOn();
 445 #endif
 446       }
 447
 448     //stupid but necessary : the Overlay need to be rendered before fusion
 449     if (mFusionActor) {
 450       this->GetRenderer()->RemoveActor(mFusionActor);
 451       this->GetRenderer()->AddActor(mOverlayActor);
 452       this->GetRenderer()->AddActor(mFusionActor);
 453     } else
 454       this->GetRenderer()->AddActor(mOverlayActor);
 455
 456     //Synchronize orientation and slice
 457     AdjustResliceToSliceOrientation(mOverlayReslice);
 458     this->UpdateDisplayExtent();
 459     this->SetTSlice(mCurrentTSlice);
 460   }
 461 }
 462 //------------------------------------------------------------------------------
 463
 464
 465 //------------------------------------------------------------------------------
 466 void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
 467 {
 468         mFusionSequenceCode = fusionSequenceCode;
 469   if (fusion->GetVTKImages().size()) {
 470     mFusion = fusion;
 471     mFusionVisibility = true;
 472
 473     if (!mFusionReslice) {
 474       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 475       mFusionReslice->SetInterpolationModeToLinear();
 476       mFusionReslice->AutoCropOutputOn();
 477       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 478     }
 479
 480     mConcatenatedFusionTransform->Identity();
 481     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 482     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 483     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 484 #if VTK_MAJOR_VERSION <= 5
 485     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 486 #else
 487     mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
 488 #endif
 489     mFusionReslice->Update();
 490
 491     if (!mFusionMapper)
 492       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 493
 494     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 495     lut->SetRange(0, 1);
 496     lut->SetValueRange(0, 1);
 497     lut->SetSaturationRange(0, 0);
 498     lut->Build();
 499     mFusionMapper->SetLookupTable(lut);
 500 #if VTK_MAJOR_VERSION <= 5
 501     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 502 #else
 503     mFusionMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
 504 #endif
 505
 506     if (!mFusionActor) {
 507       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 508 #if VTK_MAJOR_VERSION <= 5
 509       mFusionActor->SetInput(mFusionMapper->GetOutput());
 510 #else
 511       mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
 512 #endif
 513       mFusionActor->SetPickable(0);
 514       mFusionActor->SetVisibility(true);
 515       mFusionActor->SetOpacity(0.7);
 516 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 517       mFusionActor->GetMapper()->BorderOn();
 518 #endif
 519
 520       this->GetRenderer()->AddActor(mFusionActor);
 521     }
 522
 523     //Synchronize orientation and slice
 524     AdjustResliceToSliceOrientation(mFusionReslice);
 525     this->UpdateDisplayExtent();
 526     this->SetTSlice(mCurrentTSlice);
 527   }
 528 }
 529 //------------------------------------------------------------------------------
 530
 531
 532 //------------------------------------------------------------------------------
 533 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 534 {
 535   bool vis = false;
 536   if (actor_type == "image")
 537     vis = mImageVisibility;
 538   else if (actor_type == "vector")
 539     vis = mVFVisibility;
 540   else if (actor_type == "overlay")
 541     vis = mOverlayVisibility;
 542   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 543     vis = mFusionVisibility;
 544   else if (actor_type == "contour")
 545     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 546   return vis;
 547 }
 548 //------------------------------------------------------------------------------
 549
 550 //------------------------------------------------------------------------------
 551 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 552 {
 553   if (actor_type == "image")
 554     mImageVisibility = vis;
 555   else if (actor_type == "vector")
 556     mVFVisibility = vis;
 557   else if (actor_type == "overlay")
 558     mOverlayVisibility = vis;
 559   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 560     mFusionVisibility = vis;
 561   else if (actor_type == "contour")
 562     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 563   UpdateDisplayExtent();
 564 }
 565 //------------------------------------------------------------------------------
 566
 567 //------------------------------------------------------------------------------
 568 void vvSlicer::SetVF(vvImage::Pointer vf)
 569 {
 570   if (vf->GetVTKImages().size()) {
 571     mVF = vf;
 572     mVFVisibility = true;
 573
 574     if (!mAAFilter) {
 575       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 576       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 577       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 578     }
 579 #if VTK_MAJOR_VERSION <= 5
 580     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 581     mAAFilter->SetInput(mVOIFilter->GetOutput());
 582 #else
 583     mVOIFilter->SetInputData(vf->GetFirstVTKImageData());
 584     mAAFilter->SetInputConnection(mVOIFilter->GetOutputPort());
 585 #endif
 586     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 587     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 588
 589     if (!mArrow)
 590       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 591     mArrow->SetGlyphTypeToSpecificArrow();
 592     mArrow->SetScale(mScale);
 593     mArrow->FilledOff();
 594
 595     // Glyph the gradient vector (with arrows)
 596     if (!mGlyphFilter)
 597       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 598 #if VTK_MAJOR_VERSION <= 5
 599     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 600     mGlyphFilter->SetSource(mArrow->GetOutput());
 601 #else
 602     mGlyphFilter->SetInputConnection(mAAFilter->GetOutputPort());
 603     mGlyphFilter->SetSourceConnection(mArrow->GetOutputPort());
 604 #endif
 605     mGlyphFilter->ScalingOn();
 606     mGlyphFilter->SetScaleModeToScaleByVector();
 607     mGlyphFilter->OrientOn();
 608     mGlyphFilter->SetVectorModeToUseVector();
 609     mGlyphFilter->SetColorModeToColorByVector();
 610
 611     if (!mVFColorLUT)
 612       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 613
 614     double mVFColorHSV[3];
 615     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 616     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 617     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 618     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 619
 620     if (!mVFMapper)
 621       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 622 #if VTK_MAJOR_VERSION <= 5
 623     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 624 #else
 625     mVFMapper->SetInputConnection(mGlyphFilter->GetOutputPort());
 626 #endif
 627     mVFMapper->ImmediateModeRenderingOn();
 628     mVFMapper->SetLookupTable(mVFColorLUT);
 629
 630     if (!mVFActor)
 631       mVFActor = vtkSmartPointer<vtkActor>::New();
 632     mVFActor->SetMapper(mVFMapper);
 633     mVFActor->SetPickable(0);
 634     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 635     this->UpdateDisplayExtent();
 636     this->GetRenderer()->AddActor(mVFActor);
 637
 638     //Synchronize slice
 639     SetTSlice(mCurrentTSlice);
 640   }
 641 }
 642 //------------------------------------------------------------------------------
 643
 644
 645 //------------------------------------------------------------------------------
 646 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 647 {
 648   mLandmarks = landmarks;
 649   if (landmarks) {
 650
 651     if (!mCross)
 652       mCross = vtkSmartPointer<vtkCursor3D>::New();
 653         if (!mClipBox)
 654       mClipBox = vtkSmartPointer<vtkBox>::New();
 655     if (!mLandClipper)
 656       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 657     if (!mLandGlyph)
 658       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 659     if (!mLandMapper)
 660       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 661     if (!mLandActor)
 662       mLandActor = vtkSmartPointer<vtkActor>::New();
 663
 664     mCross->SetFocalPoint(0.0,0.0,0.0);
 665     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 666     mCross->AllOff();
 667     mCross->AxesOn();
 668
 669     mLandClipper->SetClipFunction(mClipBox);
 670     mLandClipper->InsideOutOn();
 671 #if VTK_MAJOR_VERSION <= 5
 672     mLandClipper->SetInput(mLandmarks->GetOutput());
 673
 674     mLandGlyph->SetSource(mCross->GetOutput());
 675     mLandGlyph->SetInput(mLandClipper->GetOutput());
 676 #else
 677     mLandClipper->SetInputData(mLandmarks->GetOutput());
 678
 679     mLandGlyph->SetSourceConnection(mCross->GetOutputPort());
 680     mLandGlyph->SetInputConnection(mLandClipper->GetOutputPort());
 681 #endif
 682     //mLandGlyph->SetIndexModeToScalar();
 683     //mLandGlyph->SetRange(0,1);
 684     //mLandGlyph->ScalingOff();
 685
 686     //mLandGlyph->SetColorModeToColorByScalar();
 687
 688     mLandGlyph->SetScaleModeToDataScalingOff();
 689     mLandGlyph->SetIndexModeToOff();
 690
 691     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 692     //mLandMapper->ScalarVisibilityOff();
 693
 694     mLandActor->SetMapper(mLandMapper);
 695     mLandActor->GetProperty()->SetOpacity(0.995);  //in order to get VTK to turn on the alpha-blending in OpenGL
 696     mLandActor->GetProperty()->SetColor(255,10,212);
 697     mLandActor->SetPickable(0);
 698     mLandActor->SetVisibility(true);
 699     this->UpdateDisplayExtent();
 700     this->GetRenderer()->AddActor(mLandActor);
 701   }
 702 }
 703 //------------------------------------------------------------------------------
 704
 705 //------------------------------------------------------------------------------
 706 //FIXME: this function leaks memory, we should fix it someday :)
 707 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 708 {
 709   if (actor_type == "vector") {
 710     Renderer->RemoveActor(mVFActor);
 711     mGlyphFilter=NULL;
 712     mVF = NULL;
 713     mArrow = NULL;
 714     mAAFilter=NULL;
 715     mVOIFilter = NULL;
 716     mVFMapper = NULL;
 717     mVFActor = NULL;
 718   }
 719   if (actor_type == "overlay") {
 720     Renderer->RemoveActor(mOverlayActor);
 721     mOverlay = NULL;
 722     mOverlayActor = NULL;
 723     mOverlayMapper = NULL;
 724   }
 725   if ( (actor_type == "fusion") || (actor_type == "fusionSequence") ) {
 726     Renderer->RemoveActor(mFusionActor);
 727     mFusion = NULL;
 728     mFusionActor = NULL;
 729     mFusionMapper = NULL;
 730   }
 731   if (actor_type == "contour") {
 732     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 733     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 734   }
 735 }
 736 //------------------------------------------------------------------------------
 737
 738
 739 //------------------------------------------------------------------------------
 740 void vvSlicer::SetVFSubSampling(int sub)
 741 {
 742   if (mVOIFilter) {
 743     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 744     mSubSampling = sub;
 745   }
 746   UpdateDisplayExtent();
 747   Render();
 748 }
 749 //------------------------------------------------------------------------------
 750
 751
 752 //------------------------------------------------------------------------------
 753 void vvSlicer::SetVFScale(int scale)
 754 {
 755   mScale = scale;
 756   if (mArrow)
 757     mArrow->SetScale(mScale);
 758   UpdateDisplayExtent();
 759   Render();
 760 }
 761 //------------------------------------------------------------------------------
 762
 763 //------------------------------------------------------------------------------
 764 void vvSlicer::SetVFWidth(int width)
 765 {
 766   mVFWidth = width;
 767   if (mVFActor)
 768     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 769   UpdateDisplayExtent();
 770   Render();
 771 }
 772 //------------------------------------------------------------------------------
 773
 774
 775 //------------------------------------------------------------------------------
 776 void vvSlicer::SetVFLog(int log)
 777 {
 778   mVFLog = log;
 779   if (mGlyphFilter) {
 780     mGlyphFilter->SetUseLog(mVFLog);
 781     mGlyphFilter->Modified();
 782   }
 783   UpdateDisplayExtent();
 784   Render();
 785 }
 786 //------------------------------------------------------------------------------
 787
 788
 789 //------------------------------------------------------------------------------
 790 void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
 791 {
 792         if (!updateLinkedImages) {
 793                 mCurrentTSlice = t;
 794 #if VTK_MAJOR_VERSION <= 5
 795                 mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 796 #else
 797                 mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 798 #endif
 799                 // Update transform
 800                 mConcatenatedTransform->Identity();
 801                 mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 802                 mConcatenatedTransform->Concatenate(mSlicingTransform);
 803                 UpdateDisplayExtent();
 804                 return;
 805         }
 806   if (t < 0)
 807     mCurrentTSlice = 0;
 808   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 809     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 810   else
 811     mCurrentTSlice = t;
 812
 813   // Update transform
 814   mConcatenatedTransform->Identity();
 815   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 816   mConcatenatedTransform->Concatenate(mSlicingTransform);
 817
 818   // Update image data
 819 #if VTK_MAJOR_VERSION <= 5
 820    mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 821 #else
 822   mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 823 #endif
 824   if (mVF && mVFActor->GetVisibility()) {
 825     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 826 #if VTK_MAJOR_VERSION <= 5
 827       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 828 #else
 829       mVOIFilter->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
 830 #endif
 831   }
 832   //update the overlay
 833   if (mOverlay && mOverlayActor->GetVisibility()) {
 834     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 835       mCurrentOverlayTSlice = t;
 836 #if VTK_MAJOR_VERSION <= 5
 837       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 838 #else
 839       mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 840 #endif
 841       // Update overlay transform
 842       mConcatenatedOverlayTransform->Identity();
 843       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 844       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 845     }
 846   }
 847   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 848   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 849     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 850       mCurrentFusionTSlice = t;
 851 #if VTK_MAJOR_VERSION <= 5
 852       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 853 #else
 854       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 855 #endif
 856
 857       // Update fusion transform
 858       mConcatenatedFusionTransform->Identity();
 859       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 860       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 861     }
 862   }
 863   if (mSurfaceCutActors.size() > 0)
 864     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 865          i!=mSurfaceCutActors.end(); i++)
 866       (*i)->SetTimeSlice(mCurrentTSlice);
 867   UpdateDisplayExtent();
 868 }
 869 //------------------------------------------------------------------------------
 870
 871
 872 //------------------------------------------------------------------------------
 873 void vvSlicer::SetFusionSequenceTSlice(int t)
 874 {
 875   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 876     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 877       mCurrentFusionTSlice = t;
 878 #if VTK_MAJOR_VERSION <= 5
 879       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 880 #else
 881       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 882 #endif
 883       // Update fusion transform
 884       mConcatenatedFusionTransform->Identity();
 885       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 886       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 887     }
 888   }
 889
 890   UpdateDisplayExtent();
 891 }
 892 //------------------------------------------------------------------------------
 893
 894
 895 //------------------------------------------------------------------------------
 896 int vvSlicer::GetTSlice()
 897 {
 898   return mCurrentTSlice;
 899 }
 900 //------------------------------------------------------------------------------
 901
 902 //------------------------------------------------------------------------------
 903 int vvSlicer::GetMaxCurrentTSlice()
 904 {
 905   int t = mCurrentTSlice;
 906   if(mOverlay)
 907     t = std::max(t, mCurrentOverlayTSlice);
 908   if(mFusion&& (mFusionSequenceCode<0)) //ignore fusionSequence data: for these, the times are not to be related (this way)
 909     t = std::max(t, mCurrentFusionTSlice);
 910   return t;
 911 }
 912 //------------------------------------------------------------------------------
 913
 914 //------------------------------------------------------------------------------
 915 int vvSlicer::GetFusionTSlice()
 916 {
 917   return mCurrentFusionTSlice;
 918 }
 919 //------------------------------------------------------------------------------
 920
 921 //------------------------------------------------------------------------------
 922 int vvSlicer::GetOverlayTSlice()
 923 {
 924   return mCurrentOverlayTSlice;
 925 }
 926 //------------------------------------------------------------------------------
 927
 928 //------------------------------------------------------------------------------
 929 void vvSlicer::SetSliceOrientation(int orientation)
 930 {
 931   //if 2D image, force to watch in Axial View
 932   int extent[6];
 933 #if VTK_MAJOR_VERSION <= 5
 934     this->GetInput()->GetWholeExtent(extent);
 935 #else
 936     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 937     copyExtent(ext, extent);
 938 #endif
 939
 940   if (extent[5]-extent[4] <= 2)
 941     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 942
 943   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 944       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 945     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 946     return;
 947   }
 948
 949   this->SliceOrientation = orientation;
 950
 951   if(mFusion)
 952     AdjustResliceToSliceOrientation(mFusionReslice);
 953
 954   if(mOverlay)
 955     AdjustResliceToSliceOrientation(mOverlayReslice);
 956
 957   // Update the viewer
 958
 959   // Go to current cursor position
 960   // double* cursorPos = GetCursorPosition();
 961   // DDV(cursorPos, 3);
 962   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 963
 964   if (mFirstSetSliceOrientation) {
 965     int *range = this->GetSliceRange();
 966     if (range)
 967       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 968 #if VTK_MAJOR_VERSION <= 5
 969       mFirstSetSliceOrientation = false;
 970 #endif
 971   }
 972   else if (this->Renderer && this->GetInput()) {
 973     double s = mCursor[orientation];
 974     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
 975     this->Slice = static_cast<int>(sCursor);
 976   }
 977
 978   this->UpdateOrientation();
 979
 980   this->UpdateDisplayExtent();
 981
 982   if (mFirstSetSliceOrientation) {
 983     mFirstSetSliceOrientation = false;
 984   }
 985
 986   if (this->Renderer && this->GetInput()) {
 987     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 988     this->Renderer->ResetCamera();
 989     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 990   }
 991
 992   SetContourSlice();
 993 }
 994 //----------------------------------------------------------------------------
 995
 996 //------------------------------------------------------------------------------
 997 // This function ensures that we sample the slices of a vtkImageReslice filter
 998 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 999 // In other words, we change the grid of the reslice in the same way as the grid
1000 // of the displayed image in the slicing direction.
1001 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1002 {
1003   // Reset autocrop and update output information
1004   reslice->SetOutputOriginToDefault();
1005   reslice->SetOutputSpacingToDefault();
1006 #if VTK_MAJOR_VERSION <= 5
1007   reslice->GetOutput()->UpdateInformation();
1008 #else
1009   reslice->UpdateInformation();
1010 #endif
1011
1012   // Ge new origin / spacing
1013   double origin[3];
1014   double spacing[3];
1015   reslice->GetOutput()->GetOrigin(origin);
1016   reslice->GetOutput()->GetSpacing(spacing);
1017
1018   // Use similar spacing as the image in the direction SliceOrientation
1019   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1020
1021   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1022   // Step 1: from world coordinates to image coordinates
1023   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1024   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1025
1026   // Step 2: round to nearest grid positionInc. This has been validated as the only
1027   // way to have something consistent with the thickness of a 2D slice visible on the
1028   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1029   // between two slices, one will never be able to see this 2D slice (bug #1883).
1030   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1031
1032   // Step 3: back to world coordinates
1033   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1034   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1035
1036   // Set new spacing and origin
1037   reslice->SetOutputOrigin(origin);
1038   reslice->SetOutputSpacing(spacing);
1039   reslice->UpdateInformation();
1040 }
1041 //------------------------------------------------------------------------------
1042
1043 //----------------------------------------------------------------------------
1044 int * vvSlicer::GetExtent()
1045 {
1046   int *w_ext;
1047   if (mUseReducedExtent) {
1048     w_ext = mReducedExtent;
1049   }
1050   else {
1051 #if VTK_MAJOR_VERSION <= 5
1052     w_ext = GetInput()->GetWholeExtent();
1053 #else
1054     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1055 #endif
1056   }
1057   return w_ext;
1058 }
1059 //----------------------------------------------------------------------------
1060
1061
1062 //----------------------------------------------------------------------------
1063 int vvSlicer::GetOrientation()
1064 {
1065   return this->SliceOrientation;
1066 }
1067 //----------------------------------------------------------------------------
1068
1069
1070 //----------------------------------------------------------------------------
1071 void vvSlicer::UpdateDisplayExtent()
1072 {
1073   vtkImageData *input = this->GetInput();
1074   if (!input || !this->ImageActor) {
1075     return;
1076   }
1077
1078 #if VTK_MAJOR_VERSION <= 5
1079   input->UpdateInformation();
1080 #else
1081   mRegisterExtent = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1082 #endif
1083   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1084
1085   // Local copy of extent
1086   int w_ext[6];
1087 #if VTK_MAJOR_VERSION <= 5
1088   int* ext = GetExtent();
1089 #else
1090   int* ext = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1091 #endif
1092   copyExtent(ext, w_ext);
1093   if (mUseReducedExtent) {
1094         copyExtent(mReducedExtent, w_ext);
1095     }
1096   // Set slice value
1097
1098   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1099   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1100
1101   // Image actor
1102   this->ImageActor->SetVisibility(mImageVisibility);
1103   this->ImageActor->SetDisplayExtent(w_ext);
1104
1105 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1106   // Fix for bug #1882
1107   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1108 #endif
1109
1110   // Overlay image actor
1111   if (mOverlay && mOverlayVisibility) {
1112     AdjustResliceToSliceOrientation(mOverlayReslice);
1113     int overExtent[6];
1114 #if VTK_MAJOR_VERSION <= 5
1115     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1116     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1117 #else
1118     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mOverlayReslice->GetOutput(), overExtent);
1119     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1120 #endif
1121     mOverlayActor->SetVisibility(!out);
1122     mOverlayActor->SetDisplayExtent( overExtent );
1123 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1124     // Fix for bug #1882
1125     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1126 #endif
1127   }
1128   else if(mOverlay)
1129     mOverlayActor->SetVisibility(false);
1130
1131   // Fusion image actor
1132   if (mFusion && mFusionVisibility) {
1133     AdjustResliceToSliceOrientation(mFusionReslice);
1134     int fusExtent[6];
1135 #if VTK_MAJOR_VERSION <= 5
1136     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1137     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1138 #else
1139     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mFusionReslice->GetOutput(), fusExtent);
1140     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1141 #endif
1142     mFusionActor->SetVisibility(!out);
1143     mFusionActor->SetDisplayExtent( fusExtent );
1144 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1145     // Fix for bug #1882
1146     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1147 #endif
1148   }
1149   else if(mFusion)
1150     mFusionActor->SetVisibility(false);
1151   // Vector field actor
1152   double* camera = Renderer->GetActiveCamera()->GetPosition();
1153   double* image_bounds = ImageActor->GetBounds();
1154   double position[3] = {0, 0, 0};
1155   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1156
1157   //print_vector<double, 6>("camera", camera);
1158   //print_vector<double, 6>("image_bounds", image_bounds);
1159   //print_vector<double, 3>("position", position);
1160
1161   // find where to place the VF actor. to deal with
1162   // z-buffer issues, the VF is placed right in front of the image,
1163   // subject to a small offset. the position actually depends on the
1164   // the location of the camera relative to the image.
1165   double offset = 1;
1166   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1167     offset = -1;
1168
1169   if (mVF && mVFVisibility) {
1170     int vfExtent[6];
1171 #if VTK_MAJOR_VERSION <= 5
1172     mVF->GetVTKImages()[0]->UpdateInformation();
1173     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
1174     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1175 #else
1176     //this->UpdateInformation();
1177     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mVF->GetVTKImages()[0], vfExtent);
1178     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1179 #endif
1180     mVFActor->SetVisibility(!out);
1181     mVOIFilter->SetVOI(vfExtent);
1182     int orientation[3] = {1,1,1};
1183     orientation[this->SliceOrientation] = 0;
1184     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1185     position[this->SliceOrientation] += offset;
1186     mVFActor->SetPosition(position);
1187     mVFActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
1188     mVFMapper->Update();
1189
1190   }
1191   else if(mVF)
1192     mVFActor->SetVisibility(false);
1193
1194   // Landmarks actor
1195   if (mLandActor) {
1196     if (mClipBox) {
1197       double bounds [6];
1198       for(unsigned int i=0; i<6; i++)
1199         bounds[i] = ImageActor->GetBounds()[i];
1200       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1201       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1202       mClipBox->SetBounds(bounds);
1203       UpdateLandmarks();
1204     }
1205
1206     position[this->SliceOrientation] = offset;
1207     mLandActor->SetPosition(position);
1208   }
1209
1210   // Figure out the correct clipping range
1211   if (this->Renderer) {
1212     if (this->InteractorStyle &&
1213         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1214       this->Renderer->ResetCameraClippingRange();
1215     } else {
1216       vtkCamera *cam = this->Renderer->GetActiveCamera();
1217       if (cam) {
1218         double bounds[6];
1219         this->ImageActor->GetBounds(bounds);
1220         double spos = (double)bounds[this->SliceOrientation * 2];
1221         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1222         double range = fabs(spos - cpos);
1223         double *spacing = input->GetSpacing();
1224         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1225         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1226       }
1227     }
1228   }
1229 }
1230 //----------------------------------------------------------------------------
1231
1232 //----------------------------------------------------------------------------
1233 void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
1234                                                 vtkImageData *targetImage, int targetExtent[6])
1235 {
1236   double dExtents[6];
1237   double *origin, *spacing;
1238   origin = sourceImage->Get(vtkDataObject::ORIGIN());
1239   spacing = sourceImage->Get(vtkDataObject::SPACING());
1240   for(unsigned int i=0; i<6; i++) {
1241     // From source voxel coordinates to world coordinates
1242     dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
1243
1244     // From world coordinates to floating point target voxel coordinates
1245     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1246
1247     // Round to current slice or larger extent
1248     if(i/2==this->GetOrientation())
1249       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1250     else if(i%2==1)
1251       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1252     else
1253       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1254   }
1255 }
1256 //----------------------------------------------------------------------------
1257
1258 //----------------------------------------------------------------------------
1259 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1260                                                 vtkImageData *targetImage, int targetExtent[6])
1261 {
1262   double dExtents[6];
1263   for(unsigned int i=0; i<6; i++) {
1264     // From source voxel coordinates to world coordinates
1265     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1266
1267     // From world coordinates to floating point target voxel coordinates
1268     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1269
1270     // Round to current slice or larger extent
1271     if(i/2==this->GetOrientation())
1272       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1273     else if(i%2==1)
1274       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1275     else
1276       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1277   }
1278 }
1279 //----------------------------------------------------------------------------
1280
1281 //----------------------------------------------------------------------------
1282 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1283 {
1284   bool out = false;
1285   int maxBound = 6;
1286
1287   for (int i = 0; i < maxBound; i = i+2) {
1288     //if we are totally outside the image
1289     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1290       out = true;
1291       break;
1292     }
1293     //crop to the limit of the image
1294     extent[i] = std::max(extent[i], refExtent[i]);
1295     extent[i] = std::min(extent[i], refExtent[i+1]);;
1296     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1297     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1298   }
1299   if (out)
1300     for (int i = 0; i < maxBound; i = i+2) {
1301       extent[i] = refExtent[i];
1302       extent[i+1] = refExtent[i];
1303     }
1304   return out;
1305 }
1306 //----------------------------------------------------------------------------
1307
1308
1309 //----------------------------------------------------------------------------
1310 void vvSlicer::UpdateOrientation()
1311 {
1312   // Set the camera position
1313   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1314   if (cam) {
1315     switch (this->SliceOrientation) {
1316     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1317       cam->SetFocalPoint(0,0,0);
1318       cam->SetPosition(0,0,-1); // -1 if medical ?
1319       cam->SetViewUp(0,-1,0);
1320       break;
1321
1322     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1323       cam->SetFocalPoint(0,0,0);
1324       cam->SetPosition(0,-1,0); // 1 if medical ?
1325       cam->SetViewUp(0,0,1);
1326       break;
1327
1328     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1329       cam->SetFocalPoint(0,0,0);
1330       cam->SetPosition(-1,0,0); // -1 if medical ?
1331       cam->SetViewUp(0,0,1);
1332       break;
1333     }
1334   }
1335 }
1336 //----------------------------------------------------------------------------
1337
1338
1339 //----------------------------------------------------------------------------
1340 void vvSlicer::SetOpacity(double s)
1341 {
1342   this->GetImageActor()->SetOpacity(s);
1343 }
1344 //----------------------------------------------------------------------------
1345
1346
1347 //----------------------------------------------------------------------------
1348 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1349 {
1350   this->Superclass::SetRenderWindow(rw);
1351   this->SetupInteractor(rw->GetInteractor());
1352   ca->SetImageActor(this->GetImageActor());
1353   ca->SetWindowLevel(this->GetWindowLevel());
1354   ca->SetText(3, "<window>\n<level>");
1355
1356   double bounds[6];
1357   double max = 65000;
1358
1359   bounds[0] = -max;
1360   bounds[1] = max;
1361   bounds[2] = -max;
1362   bounds[3] = max;
1363   bounds[4] = -max;
1364   bounds[5] = max;
1365   crossCursor->SetModelBounds(bounds);
1366
1367   this->GetRenderer()->AddActor(pdmA);
1368   this->GetRenderer()->AddActor(ca);
1369   this->GetRenderer()->ResetCamera();
1370
1371   //this is just a mapping between the labeling of the orientations presented to the user and
1372   //the one used by vtk
1373   SetSliceOrientation(2-(orientation%3));
1374   ResetCamera();
1375 }
1376 //----------------------------------------------------------------------------
1377
1378
1379 //----------------------------------------------------------------------------
1380 void vvSlicer::ResetCamera()
1381 {
1382   this->GetRenderer()->ResetCamera();
1383 }
1384 //----------------------------------------------------------------------------
1385
1386
1387 //----------------------------------------------------------------------------
1388 void vvSlicer::SetDisplayMode(bool i)
1389 {
1390         this->GetRenderer()->SetDraw(i);
1391         if (i) UpdateDisplayExtent();
1392 }
1393 //----------------------------------------------------------------------------
1394
1395
1396 //----------------------------------------------------------------------------
1397 void vvSlicer::FlipHorizontalView()
1398 {
1399   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1400   if (cam) {
1401     double *position = cam->GetPosition();
1402     double factor[3] = {1, 1, 1};
1403     factor[this->SliceOrientation] = -1;
1404     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1405
1406 /*    switch (this->SliceOrientation) {
1407     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1408       cam->SetPosition(position[0],position[1],-position[2]);
1409       break;
1410
1411     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1412       cam->SetPosition(position[0],-position[1],position[2]);
1413       break;
1414
1415     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1416       cam->SetPosition(-position[0],position[1],position[2]);
1417       break;
1418     }*/
1419
1420     this->Renderer->ResetCameraClippingRange();
1421     this->UpdateDisplayExtent();
1422   }
1423 }
1424 //----------------------------------------------------------------------------
1425
1426
1427 //----------------------------------------------------------------------------
1428 void vvSlicer::FlipVerticalView()
1429 {
1430   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1431   if (cam) {
1432     FlipHorizontalView();
1433     double *viewup = cam->GetViewUp();
1434     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1435     this->UpdateDisplayExtent();
1436   }
1437 }
1438 //----------------------------------------------------------------------------
1439
1440
1441 //----------------------------------------------------------------------------
1442 void vvSlicer::SetColorWindow(double window)
1443 {
1444   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1445   if ( LUT ) {
1446     double level = this->GetWindowLevel()->GetLevel();
1447     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1448     LUT->Build();
1449   }
1450   this->vtkImageViewer2::SetColorWindow(window);
1451 }
1452 //----------------------------------------------------------------------------
1453
1454 //----------------------------------------------------------------------------
1455 void vvSlicer::SetColorLevel(double level)
1456 {
1457   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1458   if ( LUT ) {
1459     double window = this->GetWindowLevel()->GetWindow();
1460     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1461     LUT->Build();
1462   }
1463   this->vtkImageViewer2::SetColorLevel(level);
1464 }
1465 //----------------------------------------------------------------------------
1466
1467 //----------------------------------------------------------------------------
1468 double vvSlicer::GetOverlayColorWindow()
1469 {
1470   if(mOverlayMapper)
1471     return mOverlayMapper->GetWindow();
1472   else
1473     return 0.;
1474 }
1475 //----------------------------------------------------------------------------
1476
1477 //----------------------------------------------------------------------------
1478 double vvSlicer::GetOverlayColorLevel()
1479 {
1480   if(mOverlayMapper)
1481     return mOverlayMapper->GetLevel();
1482   else
1483     return 0.;
1484 }
1485 //----------------------------------------------------------------------------
1486
1487 //----------------------------------------------------------------------------
1488 void vvSlicer::SetOverlayColorWindow(double window)
1489 {
1490   if(mOverlayMapper)
1491     mOverlayMapper->SetWindow(window);
1492 }
1493 //----------------------------------------------------------------------------
1494
1495 //----------------------------------------------------------------------------
1496 void vvSlicer::SetOverlayColorLevel(double level)
1497 {
1498   if(mOverlayMapper)
1499     mOverlayMapper->SetLevel(level);
1500 }
1501 //----------------------------------------------------------------------------
1502
1503 //----------------------------------------------------------------------------
1504 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1505 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1506 {
1507   //Get mouse pointer position in view coordinates
1508   double corner1[3];
1509   double corner2[3];
1510   for(int i=0; i<3; i++) {
1511     corner1[i] = mCurrent[i];
1512     corner2[i] = mCurrent[i];
1513   }
1514
1515   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1516   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1517
1518   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1519   int w, h;
1520   this->Renderer->GetTiledSize(&w, &h);
1521   corner1[0] -= 0.2*h/(double)w;
1522   corner2[0] += 0.2*h/(double)w;
1523   corner1[1] -= 0.2;
1524   corner2[1] += 0.2;
1525   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1526   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1527
1528   //Convert to image pixel coordinates (rounded)
1529   transform->TransformPoint(corner1, corner1);
1530   transform->TransformPoint(corner2, corner2);
1531   int iLocalExtents[6];
1532   for(int i=0; i<3; i++) {
1533     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1534     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1535
1536     iLocalExtents[i*2  ] = lrint(corner1[i]);
1537     iLocalExtents[i*2+1] = lrint(corner2[i]);
1538
1539     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1540       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1541   }
1542
1543   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1544 #if VTK_MAJOR_VERSION <= 5
1545   voiFilter->SetInput(image);
1546 #else
1547   voiFilter->SetInputData(image);
1548 #endif
1549   voiFilter->SetVOI(iLocalExtents);
1550   voiFilter->Update();
1551   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1552     min = 0;
1553     max = 0;
1554     return;
1555   }
1556
1557   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1558 #if VTK_MAJOR_VERSION <= 5
1559   accFilter->SetInput(voiFilter->GetOutput());
1560 #else
1561   accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
1562 #endif
1563   accFilter->Update();
1564
1565   min = *(accFilter->GetMin());
1566   max = *(accFilter->GetMax());
1567 }
1568 //----------------------------------------------------------------------------
1569
1570 //----------------------------------------------------------------------------
1571 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1572 {
1573   ix = lrint(X);
1574   iy = lrint(Y);
1575   iz = lrint(Z);
1576 #if VTK_MAJOR_VERSION <= 5
1577   if (ix < image->GetWholeExtent()[0] ||
1578       ix > image->GetWholeExtent()[1] ||
1579       iy < image->GetWholeExtent()[2] ||
1580       iy > image->GetWholeExtent()[3] ||
1581       iz < image->GetWholeExtent()[4] ||
1582       iz > image->GetWholeExtent()[5] )
1583     return std::numeric_limits<double>::quiet_NaN();
1584   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1585   image->Update();
1586 #else
1587   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1588       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1589       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1590       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1591       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1592       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1593     return std::numeric_limits<double>::quiet_NaN();
1594   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1595   //image->Update();
1596 #endif
1597
1598   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1599 }
1600 //----------------------------------------------------------------------------
1601
1602 //----------------------------------------------------------------------------
1603 void vvSlicer::Render()
1604 {
1605   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1606     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1607     legend->UseOpacityOn();
1608     legend->SetVisibility(1);
1609   }
1610   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1611     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1612     legend->UseOpacityOff();
1613     legend->SetVisibility(1);
1614   } else legend->SetVisibility(0);
1615
1616   if (ca->GetVisibility()) {
1617
1618     std::stringstream worldPos(" ");
1619     double pt[3];
1620     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1621     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1622     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1623     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1624 #if VTK_MAJOR_VERSION <= 5
1625     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1626         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1627         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1628         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1629         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1630         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1631
1632
1633       int ix, iy, iz;
1634       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1635
1636       if(ImageActor->GetVisibility())
1637         worldPos << "data value : " << value << std::endl;
1638
1639       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1640                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1641                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1642                           << mCurrentTSlice
1643                           << std::endl;
1644       worldPos << "pixel : " << ix << ' '
1645                              << iy << ' '
1646                              << iz << ' '
1647                              << mCurrentTSlice
1648                              << std::endl;
1649     }
1650 #else
1651     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1652         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1653         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1654         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1655         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1656         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1657
1658       int ix, iy, iz;
1659       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1660
1661       if(ImageActor->GetVisibility())
1662         worldPos << "data value : " << value << std::endl;
1663
1664       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1665                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1666                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1667                           << mCurrentTSlice
1668                           << std::endl;
1669       worldPos << "pixel : " << ix << ' '
1670                              << iy << ' '
1671                              << iz << ' '
1672                              << mCurrentTSlice
1673                              << std::endl;
1674
1675     }
1676 #endif
1677     ca->SetText(1,worldPos.str().c_str());
1678
1679     std::stringstream slicePos;
1680     slicePos << "Slice: " << this->GetSlice();
1681     ca->SetText(2, slicePos.str().c_str());
1682   }
1683
1684   if (pdmA->GetVisibility()) {
1685     double x = mCursor[0];
1686     double y = mCursor[1];
1687     double z = mCursor[2];
1688     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1689     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1690     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1691 #if VTK_MAJOR_VERSION <= 5
1692     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1693         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1694         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1695         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1696         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1697         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1698       vtkRenderer * renderer = this->Renderer;
1699
1700       renderer->WorldToView(x,y,z);
1701       renderer->ViewToNormalizedViewport(x,y,z);
1702       renderer->NormalizedViewportToViewport(x,y);
1703       renderer->ViewportToNormalizedDisplay(x,y);
1704       renderer->NormalizedDisplayToDisplay(x,y);
1705       crossCursor->SetFocalPoint(x,y,z);
1706     } else
1707       crossCursor->SetFocalPoint(-1,-1,z);
1708     crossCursor->Update();
1709   }
1710 #else
1711     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1712     try {
1713         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1714     } catch (const std::bad_cast& e) {
1715                 std::cerr << e.what() << std::endl;
1716                 std::cerr << "Conversion error" << std::endl;
1717                 return;
1718         }
1719
1720     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1721         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1722         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1723         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1724         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1725         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1726       vtkRenderer * renderer = this->Renderer;
1727
1728       renderer->WorldToView(x,y,z);
1729       renderer->ViewToNormalizedViewport(x,y,z);
1730       renderer->NormalizedViewportToViewport(x,y);
1731       renderer->ViewportToNormalizedDisplay(x,y);
1732       renderer->NormalizedDisplayToDisplay(x,y);
1733       crossCursor->SetFocalPoint(x,y,z);
1734     } else
1735       crossCursor->SetFocalPoint(-1,-1,z);
1736     crossCursor->Update();
1737   }
1738 #endif
1739
1740   if (mOverlay && mOverlayActor->GetVisibility()) {
1741     if(mLinkOverlayWindowLevel) {
1742       mOverlayMapper->SetWindow(this->GetColorWindow());
1743       mOverlayMapper->SetLevel(this->GetColorLevel());
1744     }
1745 #if VTK_MAJOR_VERSION <= 5
1746     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1747 #else
1748     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1749 #endif
1750     mOverlayMapper->Update();
1751   }
1752   if (mFusion && mFusionActor->GetVisibility()) {
1753 #if VTK_MAJOR_VERSION <= 5
1754     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1755 #else
1756     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1757 #endif
1758     mFusionMapper->Update();
1759   }
1760   if (mLandMapper)
1761     UpdateLandmarks();
1762
1763     this->GetRenderWindow()->Render();
1764 }
1765 //----------------------------------------------------------------------------
1766
1767
1768 //----------------------------------------------------------------------------
1769 void vvSlicer::UpdateCursorPosition()
1770 {
1771   pdmA->SetVisibility(true);
1772   mCursor[0] = mCurrent[0];
1773   mCursor[1] = mCurrent[1];
1774   mCursor[2] = mCurrent[2];
1775   mCursor[3] = mCurrentTSlice;
1776 }
1777 //----------------------------------------------------------------------------
1778
1779
1780 //----------------------------------------------------------------------------
1781 void vvSlicer::UpdateLandmarks()
1782 {
1783   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1784   if (pd->GetPoints()) {
1785     //mLandGlyph->SetRange(0,1);
1786     //mLandGlyph->Modified();
1787     //mLandGlyph->Update();
1788
1789     mClipBox->Modified();
1790     mLandClipper->Update();
1791     mLandMapper->Update();
1792     //Let's add the captions
1793     //First remove all captions:
1794     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1795         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1796         //allActors2D->Remove (mLandLabelActors[i]);
1797     }
1798     mLandLabelActors.clear();
1799     //Next add the captions to the displayed points
1800     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1801           double *position = mLandClipper->GetOutput()->GetPoint(id);
1802       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1803       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1804       label_actor->SetCaption(label);
1805       label_actor->SetAttachmentPoint(position);
1806       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1807       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1808       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1809       label_actor->GetCaptionTextProperty()->SetBold(0);
1810       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1811       label_actor->BorderOff();
1812       label_actor->LeaderOff();
1813       label_actor->ThreeDimensionalLeaderOff();
1814       mLandLabelActors.push_back(label_actor);
1815       this->Renderer->AddActor2D(mLandLabelActors[id]);
1816      }
1817   }
1818
1819 }
1820 //----------------------------------------------------------------------------
1821
1822
1823 //----------------------------------------------------------------------------
1824 void vvSlicer::SetSlice(int slice)
1825 {
1826   int *range = this->GetSliceRange();
1827   if (range) {
1828     if (slice < range[0]) {
1829       slice = range[0];
1830     } else if (slice > range[1]) {
1831       slice = range[1];
1832     }
1833   }
1834
1835   if (this->Slice == slice) {
1836     return;
1837   }
1838
1839   this->Slice = slice;
1840   SetContourSlice();
1841   this->Modified();
1842   this->UpdateDisplayExtent();
1843
1844   // Seems to work without this line
1845   //this->Render();
1846 }
1847 //----------------------------------------------------------------------------
1848
1849 //----------------------------------------------------------------------------
1850 int vvSlicer::GetTMax()
1851 {
1852   int tmax = (int)mImage->GetVTKImages().size() - 1;
1853   if(mOverlay)
1854     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1855   return tmax;
1856 }
1857 //----------------------------------------------------------------------------
1858
1859 //----------------------------------------------------------------------------
1860 void vvSlicer::SetContourSlice()
1861 {
1862   if (mSurfaceCutActors.size() > 0)
1863     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1864          i!=mSurfaceCutActors.end(); i++) {
1865
1866       (*i)->SetSlicingOrientation(this->SliceOrientation);
1867       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1868                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1869     }
1870 }
1871 //----------------------------------------------------------------------------
1872
1873
1874 //----------------------------------------------------------------------------
1875 void vvSlicer::ForceUpdateDisplayExtent()
1876 {
1877   this->UpdateDisplayExtent();
1878 }
1879 //----------------------------------------------------------------------------
1880
1881
1882 //----------------------------------------------------------------------------
1883 int* vvSlicer::GetDisplayExtent()
1884 {
1885   return this->GetImageActor()->GetDisplayExtent();
1886 }
1887 //----------------------------------------------------------------------------
1888
1889
1890 //----------------------------------------------------------------------------
1891 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1892 {
1893   this->Superclass::PrintSelf(os, indent);
1894 }
1895 //----------------------------------------------------------------------------
1896
1897
1898 //----------------------------------------------------------------------------
1899 void vvSlicer::SetVFColor(double r, double g, double b)
1900 {
1901   double mVFColorHSV[3];
1902   mVFColor[0] = r;
1903   mVFColor[1] = g;
1904   mVFColor[2] = b;
1905
1906   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1907   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1908   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1909   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1910
1911   this->Render();
1912 }
1913 //----------------------------------------------------------------------------
1914
1915
1916 //----------------------------------------------------------------------------
1917 void vvSlicer::SetRegisterExtent(int ext[6])
1918 {
1919     copyExtent(ext, mRegisterExtent);
1920 }
1921 //----------------------------------------------------------------------------
1922
1923
1924 //----------------------------------------------------------------------------
1925 void vvSlicer::GetRegisterExtent(int ext[6])
1926 {
1927     copyExtent(mRegisterExtent, ext);
1928 }
1929 //----------------------------------------------------------------------------
1930