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 #include "vvUtils.h"
  28
  29 #include <vtkVersion.h>
  30 #include <vtkExtentTranslator.h>
  31 #include <vtkAlgorithm.h>
  32 #include <vtkExecutive.h>
  33 #include <vtkStreamingDemandDrivenPipeline.h>
  34 #include <vtkInformation.h>
  35 #include <vtkTextProperty.h>
  36 #include <vtkTextActor.h>
  37 #include <vtkTextSource.h>
  38 #include <vtkActor2D.h>
  39 #include <vtkCursor2D.h>
  40 #include <vtkPolyDataMapper2D.h>
  41 #include <vtkProperty2D.h>
  42 #include <vtkCornerAnnotation.h>
  43 #include <vtkImageMapToWindowLevelColors.h>
  44 #include <vtkImageData.h>
  45 #include <vtkImageActor.h>
  46 #include <vvBlendImageActor.h>
  47 #include <vtkToolkits.h>
  48 #include <vtkObjectFactory.h>
  49 #include <vtkPointData.h>
  50 #include <vtkDataArray.h>
  51 #include <vtkFloatArray.h>
  52 #include <vtkClipPolyData.h>
  53 #include <vtkActor2DCollection.h>
  54 #include <vtkGlyph3D.h>
  55 #include <vtkMath.h>
  56 #include <vtkCursor3D.h>
  57 #include <vtkProperty.h>
  58 #include <vtkLight.h>
  59 #include <vtkLightCollection.h>
  60 #include <vtkScalarBarActor.h>
  61 #include <vtkImageProperty.h>
  62 #include <vtkLookupTable.h>
  63
  64 #include <vtkRenderer.h>
  65 #include <vtkRendererCollection.h>
  66 #include <vtkRenderWindow.h>
  67 #include <vtkRenderWindowInteractor.h>
  68 #include <vtkCamera.h>
  69 #include <vtkCallbackCommand.h>
  70 #include <vtkCommand.h>
  71 #include <vtkPolyDataMapper.h>
  72 #include <vtkBox.h>
  73
  74 #include <vtkExtractVOI.h>
  75 #include <vtkSphereSource.h>
  76 #include <vtkCutter.h>
  77 #include <vtkAssignAttribute.h>
  78 #include <vtkImageAccumulate.h>
  79 #include <vtkImageReslice.h>
  80 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  81 #  include <vtkOpenGLImageSliceMapper.h>
  82 #  include <vtkImageMapper3D.h>
  83 #  include <vtkImageSliceMapper.h>
  84 #endif
  85
  86 vtkStandardNewMacro(vvSlicer);
  87 static void copyExtent(int* in, int* to){
  88  for(int i=0; i<6; ++i)
  89  {
  90         to[i]=in[i];
  91  }
  92 }
  93 //------------------------------------------------------------------------------
  94 vvSlicer::vvSlicer()
  95 {
  96         mFusionSequenceCode = -1;
  97   this->UnInstallPipeline();
  98   mImage = NULL;
  99   mReducedExtent = new int[6];
 100   mRegisterExtent = NULL;
 101   mCurrentTSlice = 0;
 102   mCurrentFusionTSlice = 0;
 103   mCurrentOverlayTSlice = 0;
 104   mUseReducedExtent = false;
 105
 106   mCurrent[0] = -VTK_DOUBLE_MAX;
 107   mCurrent[1] = -VTK_DOUBLE_MAX;
 108   mCurrent[2] = -VTK_DOUBLE_MAX;
 109
 110   mCursor[0] = 0;//-VTK_DOUBLE_MAX;
 111   mCursor[1] = 0;//-VTK_DOUBLE_MAX;
 112   mCursor[2] = 0;//-VTK_DOUBLE_MAX;
 113   mCursor[3] = 0;//-VTK_DOUBLE_MAX;
 114
 115   mSubSampling = 5;
 116   mScale = 1;
 117   mVFLog = 0;
 118   mVFWidth = 1;
 119   mVFColor[0] = 0;
 120   mVFColor[1] = 1;
 121   mVFColor[2] = 0;
 122
 123   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 124   crossCursor->AllOff();
 125   crossCursor->AxesOn();
 126   crossCursor->SetTranslationMode(1);
 127   crossCursor->SetRadius(2);
 128
 129   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 130 #if VTK_MAJOR_VERSION <= 5
 131   pdm->SetInput(crossCursor->GetOutput());
 132 #else
 133   pdm->SetInputConnection(crossCursor->GetOutputPort(0));
 134 #endif
 135
 136   pdmA = vtkSmartPointer<vtkActor2D>::New();
 137   pdmA->SetMapper(pdm);
 138   pdmA->GetProperty()->SetColor(255,10,212);
 139   pdmA->SetVisibility(0);
 140   pdmA->SetPickable(0);
 141
 142   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 143   ca->GetTextProperty()->SetColor(255,10,212);
 144   ca->SetVisibility(1);
 145   mFileName = "";
 146
 147   mVF = NULL;
 148   mOverlay = NULL;
 149   mFusion = NULL;
 150   mLandmarks = NULL;
 151
 152   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 153   //legend->SetTitle("test!");
 154   legend->SetPosition(0.82,0.08);
 155   //legend->SetWidth(0.1);
 156   legend->SetVisibility(0);
 157   legend->SetLabelFormat("%.1e");
 158   this->GetRenderer()->AddActor(legend);
 159   showFusionLegend = false;
 160
 161   this->InstallPipeline();
 162
 163   mLinkOverlayWindowLevel = true;
 164   mImageVisibility = true;
 165
 166 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 167   this->GetImageActor()->GetMapper()->BorderOn();
 168 #endif
 169
 170   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 171   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 172   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 173   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 174   mConcatenatedVFTransform = vtkSmartPointer<vtkTransform>::New();
 175   mFirstSetSliceOrientation = true;
 176 }
 177 //------------------------------------------------------------------------------
 178
 179
 180 //------------------------------------------------------------------------------
 181 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 182 {
 183   return mOverlayMapper.GetPointer();
 184 }
 185 //------------------------------------------------------------------------------
 186
 187
 188 //------------------------------------------------------------------------------
 189 vvBlendImageActor* vvSlicer::GetOverlayActor()
 190 {
 191   return mOverlayActor.GetPointer();
 192 }
 193 //------------------------------------------------------------------------------
 194
 195
 196 //------------------------------------------------------------------------------
 197 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 198 {
 199   return mFusionMapper.GetPointer();
 200 }
 201 //------------------------------------------------------------------------------
 202
 203
 204 //------------------------------------------------------------------------------
 205 vtkImageActor* vvSlicer::GetFusionActor()
 206 {
 207   return mFusionActor.GetPointer();
 208 }
 209 //------------------------------------------------------------------------------
 210
 211
 212 //------------------------------------------------------------------------------
 213 vtkActor* vvSlicer::GetVFActor()
 214 {
 215   return mVFActor.GetPointer();
 216 }
 217 //------------------------------------------------------------------------------
 218
 219
 220 //------------------------------------------------------------------------------
 221 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 222 {
 223   return ca.GetPointer();
 224 }
 225 //------------------------------------------------------------------------------
 226
 227
 228 //------------------------------------------------------------------------------
 229 void vvSlicer::EnableReducedExtent(bool b)
 230 {
 231   mUseReducedExtent = b;
 232 }
 233 //------------------------------------------------------------------------------
 234
 235
 236 //------------------------------------------------------------------------------
 237 void vvSlicer::SetReducedExtent(int * ext)
 238 {
 239   copyExtent(ext, mReducedExtent);
 240 }
 241 //------------------------------------------------------------------------------
 242
 243
 244 //------------------------------------------------------------------------------
 245 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 246 {
 247
 248   mSurfaceCutActors.push_back(new vvMeshActor());
 249   if (propagate)
 250     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 251   else
 252     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 253   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 254   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 255
 256   SetContourSlice();
 257 }
 258 //------------------------------------------------------------------------------
 259
 260
 261 //------------------------------------------------------------------------------
 262 void vvSlicer::ToggleContourSuperposition()
 263 {
 264   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 265        i!=mSurfaceCutActors.end(); i++)
 266     (*i)->ToggleSuperposition();
 267 }
 268 //------------------------------------------------------------------------------
 269
 270
 271 //------------------------------------------------------------------------------
 272 void vvSlicer::SetCursorColor(int r,int g, int b)
 273 {
 274   pdmA->GetProperty()->SetColor(r,g,b);
 275 }
 276 //------------------------------------------------------------------------------
 277
 278
 279 //------------------------------------------------------------------------------
 280 void vvSlicer::SetCursorVisibility(bool s)
 281 {
 282   pdmA->SetVisibility(s);
 283 }
 284 //------------------------------------------------------------------------------
 285
 286
 287 //------------------------------------------------------------------------------
 288 bool vvSlicer::GetCursorVisibility()
 289 {
 290   return pdmA->GetVisibility();
 291 }
 292 //------------------------------------------------------------------------------
 293
 294
 295 //------------------------------------------------------------------------------
 296 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 297 {
 298   ca->SetVisibility(s);
 299 }
 300 //------------------------------------------------------------------------------
 301
 302
 303 //------------------------------------------------------------------------------
 304 bool vvSlicer::GetCornerAnnotationVisibility()
 305 {
 306   return ca->GetVisibility();
 307 }
 308 //------------------------------------------------------------------------------
 309
 310
 311 //------------------------------------------------------------------------------
 312 vvSlicer::~vvSlicer()
 313 {
 314   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 315        i!=mSurfaceCutActors.end(); i++)
 316     delete (*i);
 317   delete [] mReducedExtent;
 318 }
 319 //------------------------------------------------------------------------------
 320
 321 //------------------------------------------------------------------------------
 322 double* vvSlicer::GetCurrentPosition()
 323 {
 324   return mCurrentBeforeSlicingTransform;
 325 }
 326 //------------------------------------------------------------------------------
 327
 328 //------------------------------------------------------------------------------
 329 void vvSlicer::SetInterpolationImageReslice(int interpolation)
 330 {
 331   mImageReslice->SetInterpolationMode(interpolation);
 332 }
 333 //------------------------------------------------------------------------------
 334
 335 //------------------------------------------------------------------------------
 336 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 337 {
 338   mCurrentBeforeSlicingTransform[0]=x;
 339   mCurrentBeforeSlicingTransform[1]=y;
 340   mCurrentBeforeSlicingTransform[2]=z;
 341   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 342   if (t>=0) SetTSlice(t);
 343 }
 344 //------------------------------------------------------------------------------
 345
 346
 347 //------------------------------------------------------------------------------
 348 void vvSlicer::SetImage(vvImage::Pointer image)
 349 {
 350   if (image->GetVTKImages().size()) {
 351     mImage = image;
 352
 353     if (!mImageReslice) {
 354       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 355       mImageReslice->SetInterpolationModeToLinear();
 356       SetInterpolationImageReslice(getInterpolationFavoriteStatus());
 357       GetImageActor()->SetInterpolate(getInterpolationFavoriteStatus());
 358       mImageReslice->AutoCropOutputOn();
 359       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 360     }
 361
 362     mConcatenatedTransform->Identity();
 363     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 364     mConcatenatedTransform->Concatenate(mSlicingTransform);
 365     mImageReslice->SetResliceAxes(mConcatenatedTransform->GetMatrix());
 366 #if VTK_MAJOR_VERSION <= 5
 367     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 368 #else
 369     mImageReslice->SetInputData(0, mImage->GetFirstVTKImageData());
 370 #endif
 371     mImageReslice->UpdateInformation();
 372
 373 #if VTK_MAJOR_VERSION <= 5
 374     this->Superclass::SetInput(mImageReslice->GetOutput());
 375 #else
 376     this->Superclass::SetInputConnection(mImageReslice->GetOutputPort());
 377 #endif
 378
 379     int extent[6];
 380 #if VTK_MAJOR_VERSION <= 5
 381     this->GetInput()->GetWholeExtent(extent);
 382 #else
 383     mImageReslice->GetOutput()->GetExtent(extent);
 384 #endif
 385
 386     // Prevent crash when reload -> change slice if outside extent
 387     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 388       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 389     }
 390
 391     // Make sure that the required part image has been computed
 392     extent[SliceOrientation*2] = Slice;
 393     extent[SliceOrientation*2+1] = Slice;
 394 #if VTK_MAJOR_VERSION <= 5
 395     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 396     mImageReslice->GetOutput()->Update();
 397 #elif VTK_MAJOR_VERSION >= 8 || (VTK_MAJOR_VERSION == 7 && VTK_MINOR_VERSION >= 1)
 398     mImageReslice->UpdateExtent(extent);
 399     mImageReslice->Update();
 400 #else
 401     mImageReslice->SetUpdateExtent(extent);
 402     mImageReslice->Update();
 403 #endif
 404
 405     this->UpdateDisplayExtent();
 406
 407     mCurrentTSlice = 0;
 408     ca->SetText(0,mFileName.c_str());
 409   }
 410 }
 411 //------------------------------------------------------------------------------
 412
 413
 414 //------------------------------------------------------------------------------
 415 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 416 {
 417   if (overlay->GetVTKImages().size()) {
 418     mOverlay = overlay;
 419     mOverlayVisibility = true;
 420
 421     if (!mOverlayReslice) {
 422       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 423       mOverlayReslice->SetInterpolationModeToLinear();
 424       mOverlayReslice->AutoCropOutputOn();
 425       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 426     }
 427
 428     mConcatenatedOverlayTransform->Identity();
 429     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 430     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 431     mOverlayReslice->SetResliceAxes(mConcatenatedOverlayTransform->GetMatrix());
 432 #if VTK_MAJOR_VERSION <= 5
 433     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 434     mImageReslice->UpdateInformation();
 435 #else
 436     mOverlayReslice->SetInputData(0, mOverlay->GetFirstVTKImageData());
 437 #endif
 438     mOverlayReslice->Update();
 439
 440     if (!mOverlayMapper)
 441       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 442 #if VTK_MAJOR_VERSION <= 5
 443     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 444 #else
 445     mOverlayMapper->SetInputConnection(mOverlayReslice->GetOutputPort(0));
 446 #endif
 447
 448     if (!mOverlayActor) {
 449       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 450 #if VTK_MAJOR_VERSION <= 5
 451       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 452 #else
 453       mOverlayActor->GetMapper()->SetInputConnection(mOverlayMapper->GetOutputPort());
 454 #endif
 455       mOverlayActor->SetPickable(0);
 456       mOverlayActor->SetVisibility(true);
 457       mOverlayActor->SetOpacity(0.5);
 458 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 459       mOverlayActor->GetMapper()->BorderOn();
 460 #endif
 461       mOverlayActor->SetInterpolate(getInterpolationFavoriteStatus());
 462       }
 463
 464     //stupid but necessary : the Overlay need to be rendered before fusion
 465     if (mFusionActor) {
 466       this->GetRenderer()->RemoveActor(mFusionActor);
 467       this->GetRenderer()->AddActor(mOverlayActor);
 468       this->GetRenderer()->AddActor(mFusionActor);
 469     } else
 470       this->GetRenderer()->AddActor(mOverlayActor);
 471
 472     //Synchronize orientation and slice
 473     AdjustResliceToSliceOrientation(mOverlayReslice);
 474     this->UpdateDisplayExtent();
 475     this->SetTSlice(mCurrentTSlice);
 476   }
 477 }
 478 //------------------------------------------------------------------------------
 479
 480
 481 //------------------------------------------------------------------------------
 482 void vvSlicer::SetFusion(vvImage::Pointer fusion, int fusionSequenceCode)
 483 {
 484         mFusionSequenceCode = fusionSequenceCode;
 485   if (fusion->GetVTKImages().size()) {
 486     mFusion = fusion;
 487     mFusionVisibility = true;
 488
 489     if (!mFusionReslice) {
 490       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 491       mFusionReslice->SetInterpolationModeToLinear();
 492       mFusionReslice->AutoCropOutputOn();
 493       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 494     }
 495
 496     mConcatenatedFusionTransform->Identity();
 497     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 498     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 499     mFusionReslice->SetResliceAxes(mConcatenatedFusionTransform->GetMatrix());
 500 #if VTK_MAJOR_VERSION <= 5
 501     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 502     mFusionReslice->UpdateInformation();
 503 #else
 504     mFusionReslice->SetInputData(0, mFusion->GetFirstVTKImageData());
 505 #endif
 506     mFusionReslice->Update();
 507
 508     if (!mFusionMapper)
 509       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 510
 511     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 512     lut->SetRange(0, 1);
 513     lut->SetValueRange(0, 1);
 514     lut->SetSaturationRange(0, 0);
 515     lut->Build();
 516     mFusionMapper->SetLookupTable(lut);
 517 #if VTK_MAJOR_VERSION <= 5
 518     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 519 #else
 520     mFusionMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
 521 #endif
 522
 523     if (!mFusionActor) {
 524       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 525 #if VTK_MAJOR_VERSION <= 5
 526       mFusionActor->SetInput(mFusionMapper->GetOutput());
 527 #else
 528       mFusionActor->GetMapper()->SetInputConnection(mFusionMapper->GetOutputPort());
 529 #endif
 530       mFusionActor->SetPickable(0);
 531       mFusionActor->SetVisibility(true);
 532       mFusionActor->SetOpacity(0.7);
 533 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 534       mFusionActor->GetMapper()->BorderOn();
 535 #endif
 536
 537       mFusionActor->SetInterpolate(getInterpolationFavoriteStatus());
 538       this->GetRenderer()->AddActor(mFusionActor);
 539     }
 540
 541     //Synchronize orientation and slice
 542     AdjustResliceToSliceOrientation(mFusionReslice);
 543     this->UpdateDisplayExtent();
 544     this->SetTSlice(mCurrentTSlice);
 545   }
 546 }
 547 //------------------------------------------------------------------------------
 548
 549
 550 //------------------------------------------------------------------------------
 551 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 552 {
 553   bool vis = false;
 554   if (actor_type == "image")
 555     vis = mImageVisibility;
 556   else if (actor_type == "vector")
 557     vis = mVFVisibility;
 558   else if (actor_type == "overlay")
 559     vis = mOverlayVisibility;
 560   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 561     vis = mFusionVisibility;
 562   else if (actor_type == "contour")
 563     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 564   return vis;
 565 }
 566 //------------------------------------------------------------------------------
 567
 568 //------------------------------------------------------------------------------
 569 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 570 {
 571   if (actor_type == "image")
 572     mImageVisibility = vis;
 573   else if (actor_type == "vector")
 574     mVFVisibility = vis;
 575   else if (actor_type == "overlay")
 576     mOverlayVisibility = vis;
 577   else if ( (actor_type == "fusion") || (actor_type == "fusionSequence") )
 578     mFusionVisibility = vis;
 579   else if (actor_type == "contour")
 580     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 581   UpdateDisplayExtent();
 582 }
 583 //------------------------------------------------------------------------------
 584
 585 //------------------------------------------------------------------------------
 586 void vvSlicer::SetVF(vvImage::Pointer vf)
 587 {
 588   if (vf->GetVTKImages().size()) {
 589     mVF = vf;
 590     mVFVisibility = true;
 591
 592     if (!mAAFilter) {
 593       mVFReslice = vtkSmartPointer<vtkImageReslice>::New();
 594       mVFReslice->SetInterpolationModeToLinear();
 595       mVFReslice->AutoCropOutputOn();
 596       mVFReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 597       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 598       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 599       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 600     }
 601
 602     mConcatenatedVFTransform->Identity();
 603     mConcatenatedVFTransform->Concatenate(mVF->GetTransform()[0]);
 604     mConcatenatedVFTransform->Concatenate(mSlicingTransform);
 605     mVFReslice->SetResliceAxes(mConcatenatedVFTransform->GetMatrix());
 606 #if VTK_MAJOR_VERSION <= 5
 607     mVFReslice->SetInput(0, mVF->GetFirstVTKImageData());
 608 #else
 609     mVFReslice->SetInputData(0, mVF->GetFirstVTKImageData());
 610 #endif
 611     mVFReslice->Update();
 612
 613 #if VTK_MAJOR_VERSION <= 5
 614     mVOIFilter->SetInput(mVFReslice->GetOutput());
 615     mAAFilter->SetInput(mVOIFilter->GetOutput());
 616 #else
 617     mVOIFilter->SetInputConnection(mVFReslice->GetOutputPort());
 618     mAAFilter->SetInputConnection(mVOIFilter->GetOutputPort());
 619 #endif
 620     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 621     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 622
 623     if (!mArrow)
 624       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 625     mArrow->SetGlyphTypeToSpecificArrow();
 626     mArrow->SetScale(mScale);
 627     mArrow->FilledOff();
 628
 629     // Glyph the gradient vector (with arrows)
 630     if (!mGlyphFilter)
 631       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 632 #if VTK_MAJOR_VERSION <= 5
 633     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 634     mGlyphFilter->SetSource(mArrow->GetOutput());
 635 #else
 636     mGlyphFilter->SetInputConnection(mAAFilter->GetOutputPort());
 637     mGlyphFilter->SetSourceConnection(mArrow->GetOutputPort());
 638 #endif
 639     mGlyphFilter->ScalingOn();
 640     mGlyphFilter->SetScaleModeToScaleByVector();
 641     mGlyphFilter->OrientOn();
 642     mGlyphFilter->SetVectorModeToUseVector();
 643     mGlyphFilter->SetColorModeToColorByVector();
 644
 645     if (!mVFColorLUT)
 646       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 647
 648     double mVFColorHSV[3];
 649     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 650     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 651     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 652     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 653
 654     if (!mVFMapper)
 655       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 656 #if VTK_MAJOR_VERSION <= 5
 657     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 658 #else
 659     mVFMapper->SetInputConnection(mGlyphFilter->GetOutputPort());
 660 #endif
 661 #ifndef VTK_OPENGL2
 662     mVFMapper->ImmediateModeRenderingOn();
 663 #endif
 664     mVFMapper->SetLookupTable(mVFColorLUT);
 665
 666     if (!mVFActor)
 667       mVFActor = vtkSmartPointer<vtkActor>::New();
 668     mVFActor->SetMapper(mVFMapper);
 669     mVFActor->SetPickable(0);
 670     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 671     this->UpdateDisplayExtent();
 672     this->GetRenderer()->AddActor(mVFActor);
 673
 674     //Synchronize slice
 675     SetTSlice(mCurrentTSlice);
 676   }
 677 }
 678 //------------------------------------------------------------------------------
 679
 680
 681 //------------------------------------------------------------------------------
 682 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 683 {
 684   mLandmarks = landmarks;
 685   if (landmarks) {
 686
 687     if (!mCross)
 688       mCross = vtkSmartPointer<vtkCursor3D>::New();
 689         if (!mClipBox)
 690       mClipBox = vtkSmartPointer<vtkBox>::New();
 691     if (!mLandClipper)
 692       mLandClipper = vtkSmartPointer<vvClipPolyData>::New();
 693     if (!mLandGlyph)
 694       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 695     if (!mLandMapper)
 696       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 697     if (!mLandActor)
 698       mLandActor = vtkSmartPointer<vtkActor>::New();
 699
 700     mCross->SetFocalPoint(0.0,0.0,0.0);
 701     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 702     mCross->AllOff();
 703     mCross->AxesOn();
 704
 705     mLandClipper->SetClipFunction(mClipBox);
 706     mLandClipper->InsideOutOn();
 707 #if VTK_MAJOR_VERSION <= 5
 708     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 709     mLandmarkTransform->SetInput(mLandmarks->GetOutput());
 710     mConcatenatedTransform->Identity();
 711     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 712     mConcatenatedTransform->Concatenate(mSlicingTransform);
 713     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 714     mLandClipper->SetInput(mLandmarkTransform->GetOutput());
 715
 716     mLandGlyph->SetSource(mCross->GetOutput());
 717     mLandGlyph->SetInput(mLandClipper->GetOutput());
 718 #else
 719     mLandmarkTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 720     mLandmarkTransform->SetInputData(mLandmarks->GetOutput());
 721     mConcatenatedTransform->Identity();
 722     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 723     mConcatenatedTransform->Concatenate(mSlicingTransform);
 724     mLandmarkTransform->SetTransform(mConcatenatedTransform->GetInverse());
 725     mLandClipper->SetInputConnection(mLandmarkTransform->GetOutputPort());
 726
 727     mLandGlyph->SetSourceConnection(mCross->GetOutputPort());
 728     mLandGlyph->SetInputConnection(mLandClipper->GetOutputPort());
 729 #endif
 730     //mLandGlyph->SetIndexModeToScalar();
 731     //mLandGlyph->SetRange(0,1);
 732     //mLandGlyph->ScalingOff();
 733
 734     //mLandGlyph->SetColorModeToColorByScalar();
 735
 736     mLandGlyph->SetScaleModeToDataScalingOff();
 737     mLandGlyph->SetIndexModeToOff();
 738
 739     mLandMapper->SetInputConnection(mLandGlyph->GetOutputPort());
 740     //mLandMapper->ScalarVisibilityOff();
 741
 742     mLandActor->SetMapper(mLandMapper);
 743     mLandActor->GetProperty()->SetOpacity(0.995);  //in order to get VTK to turn on the alpha-blending in OpenGL
 744     mLandActor->GetProperty()->SetColor(255,10,212);
 745     mLandActor->SetPickable(0);
 746     mLandActor->SetVisibility(true);
 747     this->UpdateDisplayExtent();
 748   }
 749 }
 750 //------------------------------------------------------------------------------
 751
 752 //------------------------------------------------------------------------------
 753 //FIXME: this function leaks memory, we should fix it someday :)
 754 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 755 {
 756   if (actor_type == "vector") {
 757     Renderer->RemoveActor(mVFActor);
 758     mGlyphFilter=NULL;
 759     mVF = NULL;
 760     mArrow = NULL;
 761     mAAFilter=NULL;
 762     mVOIFilter = NULL;
 763     mVFMapper = NULL;
 764     mVFActor = NULL;
 765   }
 766   if (actor_type == "overlay") {
 767     Renderer->RemoveActor(mOverlayActor);
 768     mOverlay = NULL;
 769     mOverlayActor = NULL;
 770     mOverlayMapper = NULL;
 771   }
 772   if ( (actor_type == "fusion") || (actor_type == "fusionSequence") ) {
 773     Renderer->RemoveActor(mFusionActor);
 774     mFusion = NULL;
 775     mFusionActor = NULL;
 776     mFusionMapper = NULL;
 777   }
 778   if (actor_type == "contour") {
 779     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 780     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 781   }
 782 }
 783 //------------------------------------------------------------------------------
 784
 785
 786 //------------------------------------------------------------------------------
 787 void vvSlicer::SetVFSubSampling(int sub)
 788 {
 789   if (mVOIFilter) {
 790     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 791     mSubSampling = sub;
 792   }
 793   UpdateDisplayExtent();
 794   Render();
 795 }
 796 //------------------------------------------------------------------------------
 797
 798
 799 //------------------------------------------------------------------------------
 800 void vvSlicer::SetVFScale(int scale)
 801 {
 802   mScale = scale;
 803   if (mArrow)
 804     mArrow->SetScale(mScale);
 805   UpdateDisplayExtent();
 806   Render();
 807 }
 808 //------------------------------------------------------------------------------
 809
 810 //------------------------------------------------------------------------------
 811 void vvSlicer::SetVFWidth(int width)
 812 {
 813   mVFWidth = width;
 814   if (mVFActor)
 815     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 816   UpdateDisplayExtent();
 817   Render();
 818 }
 819 //------------------------------------------------------------------------------
 820
 821
 822 //------------------------------------------------------------------------------
 823 void vvSlicer::SetVFLog(int log)
 824 {
 825   mVFLog = log;
 826   if (mGlyphFilter) {
 827     mGlyphFilter->SetUseLog(mVFLog);
 828     mGlyphFilter->Modified();
 829   }
 830   UpdateDisplayExtent();
 831   Render();
 832 }
 833 //------------------------------------------------------------------------------
 834
 835
 836 //------------------------------------------------------------------------------
 837 void vvSlicer::SetTSlice(int t, bool updateLinkedImages)
 838 {
 839         if (!updateLinkedImages) {
 840                 mCurrentTSlice = t;
 841 #if VTK_MAJOR_VERSION <= 5
 842                 mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 843 #else
 844                 mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 845 #endif
 846                 // Update transform
 847                 mConcatenatedTransform->Identity();
 848                 mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 849                 mConcatenatedTransform->Concatenate(mSlicingTransform);
 850                 UpdateDisplayExtent();
 851                 return;
 852         }
 853   if (t < 0)
 854     mCurrentTSlice = 0;
 855   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 856     mCurrentTSlice = mImage->GetVTKImages().size() -1;
 857   else
 858     mCurrentTSlice = t;
 859
 860   // Update transform
 861   mConcatenatedTransform->Identity();
 862   mConcatenatedTransform->Concatenate(mImage->GetTransform()[mCurrentTSlice]);
 863   mConcatenatedTransform->Concatenate(mSlicingTransform);
 864
 865   // Update image data
 866 #if VTK_MAJOR_VERSION <= 5
 867    mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 868 #else
 869   mImageReslice->SetInputData( mImage->GetVTKImages()[mCurrentTSlice] );
 870 #endif
 871   if (mVF && mVFActor->GetVisibility()) {
 872     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 873 #if VTK_MAJOR_VERSION <= 5
 874       mVFReslice->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 875 #else
 876       mVFReslice->SetInputData(mVF->GetVTKImages()[mCurrentTSlice]);
 877 #endif
 878       // Update overlay transform
 879       mConcatenatedVFTransform->Identity();
 880       mConcatenatedVFTransform->Concatenate(mVF->GetTransform()[mCurrentTSlice]);
 881       mConcatenatedVFTransform->Concatenate(mSlicingTransform);
 882   }
 883   //update the overlay
 884   if (mOverlay && mOverlayActor->GetVisibility()) {
 885     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 886       mCurrentOverlayTSlice = t;
 887 #if VTK_MAJOR_VERSION <= 5
 888       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 889 #else
 890       mOverlayReslice->SetInputData( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 891 #endif
 892       // Update overlay transform
 893       mConcatenatedOverlayTransform->Identity();
 894       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 895       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 896     }
 897   }
 898   //update the fusion ; except in case this is a fusionSequence, in which case both 'times' should be independent.
 899   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode<0)) {
 900     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 901       mCurrentFusionTSlice = t;
 902 #if VTK_MAJOR_VERSION <= 5
 903       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 904 #else
 905       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 906 #endif
 907
 908       // Update fusion transform
 909       mConcatenatedFusionTransform->Identity();
 910       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 911       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 912     }
 913   }
 914   if (mSurfaceCutActors.size() > 0)
 915     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 916          i!=mSurfaceCutActors.end(); i++)
 917       (*i)->SetTimeSlice(mCurrentTSlice);
 918   UpdateDisplayExtent();
 919 }
 920 //------------------------------------------------------------------------------
 921
 922
 923 //------------------------------------------------------------------------------
 924 void vvSlicer::SetFusionSequenceTSlice(int t)
 925 {
 926   if (mFusion && mFusionActor->GetVisibility() && (mFusionSequenceCode>=0)) {
 927     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 928       mCurrentFusionTSlice = t;
 929 #if VTK_MAJOR_VERSION <= 5
 930       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 931 #else
 932       mFusionReslice->SetInputData( mFusion->GetVTKImages()[mCurrentFusionTSlice] );
 933 #endif
 934       // Update fusion transform
 935       mConcatenatedFusionTransform->Identity();
 936       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]); //not really useful...
 937       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 938     }
 939   }
 940
 941   UpdateDisplayExtent();
 942 }
 943 //------------------------------------------------------------------------------
 944
 945
 946 //------------------------------------------------------------------------------
 947 int vvSlicer::GetTSlice()
 948 {
 949   return mCurrentTSlice;
 950 }
 951 //------------------------------------------------------------------------------
 952
 953 //------------------------------------------------------------------------------
 954 int vvSlicer::GetMaxCurrentTSlice()
 955 {
 956   int t = mCurrentTSlice;
 957   if(mOverlay && mOverlayActor->GetVisibility())
 958     t = std::max(t, mCurrentOverlayTSlice);
 959   if(mFusion&& (mFusionSequenceCode<0) && mFusionActor->GetVisibility()) //ignore fusionSequence data: for these, the times are not to be related (this way)
 960     t = std::max(t, mCurrentFusionTSlice);
 961   return t;
 962 }
 963 //------------------------------------------------------------------------------
 964
 965 //------------------------------------------------------------------------------
 966 int vvSlicer::GetFusionTSlice()
 967 {
 968   return mCurrentFusionTSlice;
 969 }
 970 //------------------------------------------------------------------------------
 971
 972 //------------------------------------------------------------------------------
 973 int vvSlicer::GetOverlayTSlice()
 974 {
 975   return mCurrentOverlayTSlice;
 976 }
 977 //------------------------------------------------------------------------------
 978
 979 //------------------------------------------------------------------------------
 980 void vvSlicer::SetSliceOrientation(int orientation)
 981 {
 982   //if 2D image, force to watch in Axial View
 983   int extent[6];
 984 #if VTK_MAJOR_VERSION <= 5
 985     this->GetInput()->GetWholeExtent(extent);
 986 #else
 987     int* ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
 988     copyExtent(ext, extent);
 989 #endif
 990
 991   if (extent[5]-extent[4] <= 2)
 992     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 993
 994   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 995       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 996     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 997     return;
 998   }
 999
1000   this->SliceOrientation = orientation;
1001
1002   if(mFusion)
1003     AdjustResliceToSliceOrientation(mFusionReslice);
1004
1005   if(mOverlay)
1006     AdjustResliceToSliceOrientation(mOverlayReslice);
1007
1008   if(mVF)
1009     AdjustResliceToSliceOrientation(mVFReslice);
1010
1011   // Update the viewer
1012
1013   // Go to current cursor position
1014   // double* cursorPos = GetCursorPosition();
1015   // DDV(cursorPos, 3);
1016   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
1017
1018   if (mFirstSetSliceOrientation) {
1019     int *range = this->GetSliceRange();
1020     if (range)
1021       this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
1022 #if VTK_MAJOR_VERSION <= 5
1023       mFirstSetSliceOrientation = false;
1024 #endif
1025   }
1026   else if (this->Renderer && this->GetInput()) {
1027     double s = mCursor[orientation];
1028     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
1029     this->Slice = static_cast<int>(sCursor);
1030   }
1031
1032   this->UpdateOrientation();
1033
1034   this->UpdateDisplayExtent();
1035
1036   if (mFirstSetSliceOrientation) {
1037     mFirstSetSliceOrientation = false;
1038   }
1039
1040   if (this->Renderer && this->GetInput()) {
1041     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
1042     this->Renderer->ResetCamera();
1043     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
1044   }
1045
1046   SetContourSlice();
1047 }
1048 //----------------------------------------------------------------------------
1049
1050 //------------------------------------------------------------------------------
1051 // This function ensures that we sample the slices of a vtkImageReslice filter
1052 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
1053 // In other words, we change the grid of the reslice in the same way as the grid
1054 // of the displayed image in the slicing direction.
1055 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
1056 {
1057   // Reset autocrop and update output information
1058   reslice->SetOutputOriginToDefault();
1059   reslice->SetOutputSpacingToDefault();
1060 #if VTK_MAJOR_VERSION <= 5
1061   reslice->GetOutput()->UpdateInformation();
1062 #else
1063   reslice->UpdateInformation();
1064 #endif
1065
1066   // Ge new origin / spacing
1067   double origin[3];
1068   double spacing[3];
1069   reslice->GetOutput()->GetOrigin(origin);
1070   reslice->GetOutput()->GetSpacing(spacing);
1071
1072   // Use similar spacing as the image in the direction SliceOrientation
1073   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1074
1075   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
1076   // Step 1: from world coordinates to image coordinates
1077   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1078   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1079
1080   // Step 2: round to nearest grid positionInc. This has been validated as the only
1081   // way to have something consistent with the thickness of a 2D slice visible on the
1082   // other slices. The thickness is accounted for so if the 2D slice is to thin and
1083   // between two slices, one will never be able to see this 2D slice (bug #1883).
1084   origin[this->SliceOrientation] = itk::Math::Round<double>(origin[this->SliceOrientation]);
1085
1086   // Step 3: back to world coordinates
1087   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
1088   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
1089
1090   // Set new spacing and origin
1091   reslice->SetOutputOrigin(origin);
1092   reslice->SetOutputSpacing(spacing);
1093   reslice->UpdateInformation();
1094 #if VTK_MAJOR_VERSION <= 5
1095   reslice->GetOutput()->UpdateInformation();
1096 #endif
1097 }
1098 //------------------------------------------------------------------------------
1099
1100 //----------------------------------------------------------------------------
1101 int * vvSlicer::GetExtent()
1102 {
1103   int *w_ext;
1104   if (mUseReducedExtent) {
1105     w_ext = mReducedExtent;
1106   }
1107   else {
1108 #if VTK_MAJOR_VERSION <= 5
1109     w_ext = GetInput()->GetWholeExtent();
1110 #else
1111     w_ext = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1112 #endif
1113   }
1114   return w_ext;
1115 }
1116 //----------------------------------------------------------------------------
1117
1118
1119 //----------------------------------------------------------------------------
1120 int vvSlicer::GetOrientation()
1121 {
1122   return this->SliceOrientation;
1123 }
1124 //----------------------------------------------------------------------------
1125
1126
1127 //----------------------------------------------------------------------------
1128 void vvSlicer::UpdateDisplayExtent()
1129 {
1130   emit UpdateDisplayExtentBegin(mSlicerNumber);
1131   vtkImageData *input = this->GetInput();
1132   if (!input || !this->ImageActor) {
1133     return;
1134   }
1135
1136 #if VTK_MAJOR_VERSION <= 5
1137   input->UpdateInformation();
1138 #else
1139   mRegisterExtent = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1140 #endif
1141   this->SetSlice( this->GetSlice() ); //SR: make sure the update let the slice in extents
1142
1143   // Local copy of extent
1144   int w_ext[6];
1145 #if VTK_MAJOR_VERSION <= 5
1146   int* ext = GetExtent();
1147 #else
1148   int* ext = mImageReslice->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT());
1149 #endif
1150   copyExtent(ext, w_ext);
1151   if (mUseReducedExtent) {
1152         copyExtent(mReducedExtent, w_ext);
1153     }
1154   // Set slice value
1155
1156   w_ext[ this->SliceOrientation*2   ] = this->Slice;
1157   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
1158
1159   // Image actor
1160   this->ImageActor->SetVisibility(mImageVisibility);
1161   this->ImageActor->SetDisplayExtent(w_ext);
1162
1163 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1164   // Fix for bug #1882
1165   dynamic_cast<vtkImageSliceMapper *>(this->ImageActor->GetMapper())->SetOrientation(this->GetOrientation());
1166 #endif
1167
1168   // Overlay image actor
1169   if (mOverlay && mOverlayVisibility) {
1170     AdjustResliceToSliceOrientation(mOverlayReslice);
1171     int overExtent[6];
1172 #if VTK_MAJOR_VERSION <= 5
1173     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
1174     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
1175 #else
1176     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mOverlayReslice->GetOutput(), overExtent);
1177     bool out = ClipDisplayedExtent(overExtent, mOverlayMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1178 #endif
1179     mOverlayActor->SetVisibility(!out);
1180     mOverlayActor->SetDisplayExtent( overExtent );
1181 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1182     // Fix for bug #1882
1183     dynamic_cast<vtkImageSliceMapper *>(mOverlayActor->GetMapper())->SetOrientation(this->GetOrientation());
1184 #endif
1185   }
1186   else if(mOverlay)
1187     mOverlayActor->SetVisibility(false);
1188
1189   // Fusion image actor
1190   if (mFusion && mFusionVisibility) {
1191     AdjustResliceToSliceOrientation(mFusionReslice);
1192     int fusExtent[6];
1193 #if VTK_MAJOR_VERSION <= 5
1194     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
1195     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
1196 #else
1197     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mFusionReslice->GetOutput(), fusExtent);
1198     bool out = ClipDisplayedExtent(fusExtent, mFusionMapper->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1199 #endif
1200     mFusionActor->SetVisibility(!out);
1201     mFusionActor->SetDisplayExtent( fusExtent );
1202 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
1203     // Fix for bug #1882
1204     dynamic_cast<vtkImageSliceMapper *>(mFusionActor->GetMapper())->SetOrientation(this->GetOrientation());
1205 #endif
1206   }
1207   else if(mFusion)
1208     mFusionActor->SetVisibility(false);
1209   // Vector field actor
1210   double* camera = Renderer->GetActiveCamera()->GetPosition();
1211   double* image_bounds = ImageActor->GetBounds();
1212   double position[3] = {0, 0, 0};
1213   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
1214
1215   //print_vector<double, 6>("camera", camera);
1216   //print_vector<double, 6>("image_bounds", image_bounds);
1217   //print_vector<double, 3>("position", position);
1218
1219   // find where to place the VF actor. to deal with
1220   // z-buffer issues, the VF is placed right in front of the image,
1221   // subject to a small offset. the position actually depends on the
1222   // the location of the camera relative to the image.
1223   double offset = 1;
1224   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
1225     offset = -1;
1226
1227   if (mVF && mVFVisibility) {
1228     AdjustResliceToSliceOrientation(mVFReslice);
1229     int vfExtent[6];
1230 #if VTK_MAJOR_VERSION <= 5
1231     mVF->GetVTKImages()[0]->UpdateInformation();
1232     this->ConvertImageToImageDisplayExtent(input, w_ext, mVFReslice->GetOutput(), vfExtent);
1233     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
1234 #else
1235     mVOIFilter->Update();
1236     this->ConvertImageToImageDisplayExtent(mImageReslice->GetOutputInformation(0), w_ext, mVFReslice->GetOutput(), vfExtent);
1237     bool out = ClipDisplayedExtent(vfExtent, mVOIFilter->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT()));
1238 #endif
1239     mVFActor->SetVisibility(!out);
1240     mVOIFilter->SetVOI(vfExtent);
1241     int orientation[3] = {1,1,1};
1242     orientation[this->SliceOrientation] = 0;
1243     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
1244     position[this->SliceOrientation] += offset;
1245     mVFActor->SetPosition(position);
1246     mVFActor->GetProperty()->SetOpacity(0.995); //in order to get VTK to turn on the alpha-blending in OpenGL
1247     mVFMapper->Update();
1248
1249   }
1250   else if(mVF)
1251     mVFActor->SetVisibility(false);
1252
1253
1254     double boundsT [6];
1255       for(unsigned int i=0; i<6; i++)
1256         boundsT[i] = ImageActor->GetBounds()[i];
1257       boundsT[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1258       boundsT[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1259
1260
1261   // Landmarks actor
1262   if (mLandActor) {
1263     if (mClipBox) {
1264       RemoveLandmarks();
1265     }
1266
1267     position[this->SliceOrientation] = offset;
1268     mLandActor->SetPosition(position);
1269   }
1270
1271   // Figure out the correct clipping range
1272   if (this->Renderer) {
1273     if (this->InteractorStyle &&
1274         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
1275       this->Renderer->ResetCameraClippingRange();
1276     } else {
1277       vtkCamera *cam = this->Renderer->GetActiveCamera();
1278       if (cam) {
1279         double bounds[6];
1280         this->ImageActor->GetBounds(bounds);
1281         double spos = (double)bounds[this->SliceOrientation * 2];
1282         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
1283         double range = fabs(spos - cpos);
1284         double *spacing = input->GetSpacing();
1285         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
1286         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
1287       }
1288     }
1289
1290     if (mLandActor) {
1291         if (mClipBox) {
1292             DisplayLandmarks();
1293         }
1294     }
1295   }
1296   emit UpdateDisplayExtentEnd(mSlicerNumber);
1297 }
1298 //----------------------------------------------------------------------------
1299
1300 //----------------------------------------------------------------------------
1301 void vvSlicer::ConvertImageToImageDisplayExtent(vtkInformation *sourceImage, const int sourceExtent[6],
1302                                                 vtkImageData *targetImage, int targetExtent[6])
1303 {
1304   double dExtents[6];
1305   double *origin, *spacing;
1306   origin = sourceImage->Get(vtkDataObject::ORIGIN());
1307   spacing = sourceImage->Get(vtkDataObject::SPACING());
1308   for(unsigned int i=0; i<6; i++) {
1309     // From source voxel coordinates to world coordinates
1310     dExtents[i] = origin[i/2] + spacing[i/2] * sourceExtent[i];
1311
1312     // From world coordinates to floating point target voxel coordinates
1313     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1314
1315     // Round to current slice or larger extent
1316     if(i/2==this->GetOrientation())
1317       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1318     else if(i%2==1)
1319       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1320     else
1321       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1322   }
1323 }
1324 //----------------------------------------------------------------------------
1325
1326 //----------------------------------------------------------------------------
1327 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
1328                                                 vtkImageData *targetImage, int targetExtent[6])
1329 {
1330   double dExtents[6];
1331   for(unsigned int i=0; i<6; i++) {
1332     // From source voxel coordinates to world coordinates
1333     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1334
1335     // From world coordinates to floating point target voxel coordinates
1336     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1337
1338     // Round to current slice or larger extent
1339     if(i/2==this->GetOrientation())
1340       targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1341     else if(i%2==1)
1342       targetExtent[i] = itk::Math::Ceil<double>(dExtents[i]);
1343     else
1344       targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1345   }
1346 }
1347 //----------------------------------------------------------------------------
1348
1349 //----------------------------------------------------------------------------
1350 bool vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1351 {
1352   bool out = false;
1353   int maxBound = 6;
1354
1355   for (int i = 0; i < maxBound; i = i+2) {
1356     //if we are totally outside the image
1357     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1358       out = true;
1359       break;
1360     }
1361     //crop to the limit of the image
1362     extent[i] = std::max(extent[i], refExtent[i]);
1363     extent[i] = std::min(extent[i], refExtent[i+1]);;
1364     extent[i+1] = std::max(extent[i+1], refExtent[i]);
1365     extent[i+1] = std::min(extent[i+1], refExtent[i+1]);;
1366   }
1367   if (out)
1368     for (int i = 0; i < maxBound; i = i+2) {
1369       extent[i] = refExtent[i];
1370       extent[i+1] = refExtent[i];
1371     }
1372   return out;
1373 }
1374 //----------------------------------------------------------------------------
1375
1376
1377 //----------------------------------------------------------------------------
1378 void vvSlicer::UpdateOrientation()
1379 {
1380   // Set the camera position
1381   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1382   if (cam) {
1383     switch (this->SliceOrientation) {
1384     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1385       cam->SetFocalPoint(0,0,0);
1386       cam->SetPosition(0,0,-1); // -1 if medical ?
1387       cam->SetViewUp(0,-1,0);
1388       break;
1389
1390     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1391       cam->SetFocalPoint(0,0,0);
1392       cam->SetPosition(0,-1,0); // 1 if medical ?
1393       cam->SetViewUp(0,0,1);
1394       break;
1395
1396     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1397       cam->SetFocalPoint(0,0,0);
1398       cam->SetPosition(-1,0,0); // -1 if medical ?
1399       cam->SetViewUp(0,0,1);
1400       break;
1401     }
1402   }
1403 }
1404 //----------------------------------------------------------------------------
1405
1406
1407 //----------------------------------------------------------------------------
1408 void vvSlicer::SetOpacity(double s)
1409 {
1410   this->GetImageActor()->SetOpacity(s);
1411 }
1412 //----------------------------------------------------------------------------
1413
1414
1415 //----------------------------------------------------------------------------
1416 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1417 {
1418   this->Superclass::SetRenderWindow(rw);
1419   this->SetupInteractor(rw->GetInteractor());
1420   ca->SetImageActor(this->GetImageActor());
1421   ca->SetWindowLevel(this->GetWindowLevel());
1422   ca->SetText(3, "<window>\n<level>");
1423
1424   double bounds[6];
1425   double max = 65000;
1426
1427   bounds[0] = -max;
1428   bounds[1] = max;
1429   bounds[2] = -max;
1430   bounds[3] = max;
1431   bounds[4] = -max;
1432   bounds[5] = max;
1433   crossCursor->SetModelBounds(bounds);
1434
1435   this->GetRenderer()->AddActor(pdmA);
1436   this->GetRenderer()->AddActor(ca);
1437   this->GetRenderer()->ResetCamera();
1438
1439   //this is just a mapping between the labeling of the orientations presented to the user and
1440   //the one used by vtk
1441   SetSliceOrientation(2-(orientation%3));
1442   ResetCamera();
1443 }
1444 //----------------------------------------------------------------------------
1445
1446
1447 //----------------------------------------------------------------------------
1448 void vvSlicer::ResetCamera()
1449 {
1450   this->GetRenderer()->ResetCamera();
1451 }
1452 //----------------------------------------------------------------------------
1453
1454
1455 //----------------------------------------------------------------------------
1456 void vvSlicer::SetDisplayMode(bool i)
1457 {
1458         this->GetRenderer()->SetDraw(i);
1459         if (i) UpdateDisplayExtent();
1460 }
1461 //----------------------------------------------------------------------------
1462
1463
1464 //----------------------------------------------------------------------------
1465 void vvSlicer::FlipHorizontalView()
1466 {
1467   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1468   if (cam) {
1469     double *position = cam->GetPosition();
1470     double factor[3] = {1, 1, 1};
1471     factor[this->SliceOrientation] = -1;
1472     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1473
1474 /*    switch (this->SliceOrientation) {
1475     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1476       cam->SetPosition(position[0],position[1],-position[2]);
1477       break;
1478
1479     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1480       cam->SetPosition(position[0],-position[1],position[2]);
1481       break;
1482
1483     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1484       cam->SetPosition(-position[0],position[1],position[2]);
1485       break;
1486     }*/
1487
1488     this->Renderer->ResetCameraClippingRange();
1489     this->UpdateDisplayExtent();
1490   }
1491 }
1492 //----------------------------------------------------------------------------
1493
1494
1495 //----------------------------------------------------------------------------
1496 void vvSlicer::FlipVerticalView()
1497 {
1498   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1499   if (cam) {
1500     FlipHorizontalView();
1501     double *viewup = cam->GetViewUp();
1502     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1503     this->UpdateDisplayExtent();
1504   }
1505 }
1506 //----------------------------------------------------------------------------
1507
1508
1509 //----------------------------------------------------------------------------
1510 void vvSlicer::SetColorWindow(double window)
1511 {
1512   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1513   if ( LUT ) {
1514     double level = this->GetWindowLevel()->GetLevel();
1515     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1516     LUT->Build();
1517   }
1518   this->vtkImageViewer2::SetColorWindow(window);
1519 }
1520 //----------------------------------------------------------------------------
1521
1522 //----------------------------------------------------------------------------
1523 void vvSlicer::SetColorLevel(double level)
1524 {
1525   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1526   if ( LUT ) {
1527     double window = this->GetWindowLevel()->GetWindow();
1528     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1529     LUT->Build();
1530   }
1531   this->vtkImageViewer2::SetColorLevel(level);
1532 }
1533 //----------------------------------------------------------------------------
1534
1535 //----------------------------------------------------------------------------
1536 double vvSlicer::GetOverlayColorWindow()
1537 {
1538   if(mOverlayMapper)
1539     return mOverlayMapper->GetWindow();
1540   else
1541     return 0.;
1542 }
1543 //----------------------------------------------------------------------------
1544
1545 //----------------------------------------------------------------------------
1546 double vvSlicer::GetOverlayColorLevel()
1547 {
1548   if(mOverlayMapper)
1549     return mOverlayMapper->GetLevel();
1550   else
1551     return 0.;
1552 }
1553 //----------------------------------------------------------------------------
1554
1555 //----------------------------------------------------------------------------
1556 void vvSlicer::SetOverlayColorWindow(double window)
1557 {
1558   if(mOverlayMapper)
1559     mOverlayMapper->SetWindow(window);
1560 }
1561 //----------------------------------------------------------------------------
1562
1563 //----------------------------------------------------------------------------
1564 void vvSlicer::SetOverlayColorLevel(double level)
1565 {
1566   if(mOverlayMapper)
1567     mOverlayMapper->SetLevel(level);
1568 }
1569 //----------------------------------------------------------------------------
1570
1571 //----------------------------------------------------------------------------
1572 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1573 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1574 {
1575   //Get mouse pointer position in view coordinates
1576   double corner1[3];
1577   double corner2[3];
1578   for(int i=0; i<3; i++) {
1579     corner1[i] = mCurrent[i];
1580     corner2[i] = mCurrent[i];
1581   }
1582
1583   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1584   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1585
1586   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1587   int w, h;
1588   this->Renderer->GetTiledSize(&w, &h);
1589   corner1[0] -= 0.2*h/(double)w;
1590   corner2[0] += 0.2*h/(double)w;
1591   corner1[1] -= 0.2;
1592   corner2[1] += 0.2;
1593   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1594   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1595
1596   //Convert to image pixel coordinates (rounded)
1597   transform->TransformPoint(corner1, corner1);
1598   transform->TransformPoint(corner2, corner2);
1599   int iLocalExtents[6];
1600   for(int i=0; i<3; i++) {
1601     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1602     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1603
1604     iLocalExtents[i*2  ] = lrint(corner1[i]);
1605     iLocalExtents[i*2+1] = lrint(corner2[i]);
1606
1607     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1608       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1609
1610 #if VTK_MAJOR_VERSION > 5
1611     for(int j=0;j<2; j++) {
1612       if(iLocalExtents[i*2+j]< mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i])
1613         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i];
1614
1615       if(iLocalExtents[i*2+j]> mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1])
1616         iLocalExtents[i*2+j] = mImageReslice->GetInputInformation()->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT())[2*i+1];
1617     }
1618 #endif
1619   }
1620
1621   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1622 #if VTK_MAJOR_VERSION <= 5
1623   voiFilter->SetInput(image);
1624 #else
1625   voiFilter->SetInputData(image);
1626 #endif
1627   voiFilter->SetVOI(iLocalExtents);
1628   voiFilter->Update();
1629   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1630     min = 0;
1631     max = 0;
1632     return;
1633   }
1634
1635   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1636 #if VTK_MAJOR_VERSION <= 5
1637   accFilter->SetInput(voiFilter->GetOutput());
1638 #else
1639   accFilter->SetInputConnection(voiFilter->GetOutputPort(0));
1640 #endif
1641   accFilter->Update();
1642
1643   min = *(accFilter->GetMin());
1644   max = *(accFilter->GetMax());
1645 }
1646 //----------------------------------------------------------------------------
1647
1648 //----------------------------------------------------------------------------
1649 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1650 {
1651   ix = lrint(X);
1652   iy = lrint(Y);
1653   iz = lrint(Z);
1654 #if VTK_MAJOR_VERSION <= 5
1655   if (ix < image->GetWholeExtent()[0] ||
1656       ix > image->GetWholeExtent()[1] ||
1657       iy < image->GetWholeExtent()[2] ||
1658       iy > image->GetWholeExtent()[3] ||
1659       iz < image->GetWholeExtent()[4] ||
1660       iz > image->GetWholeExtent()[5] )
1661     return std::numeric_limits<double>::quiet_NaN();
1662   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1663   image->Update();
1664 #else
1665   if (ix < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0] ||
1666       ix > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1] ||
1667       iy < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2] ||
1668       iy > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3] ||
1669       iz < image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4] ||
1670       iz > image->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5] )
1671     return std::numeric_limits<double>::quiet_NaN();
1672   //image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1673   //image->Update();
1674 #endif
1675   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1676 }
1677 //----------------------------------------------------------------------------
1678
1679 //----------------------------------------------------------------------------
1680 void vvSlicer::Render()
1681 {
1682   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1683     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1684     legend->UseOpacityOn();
1685     legend->SetVisibility(1);
1686   }
1687   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1688     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1689     legend->UseOpacityOff();
1690     legend->SetVisibility(1);
1691   } else legend->SetVisibility(0);
1692
1693   if (ca->GetVisibility()) {
1694     std::stringstream worldPos(" ");
1695     double pt[3];
1696     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1697     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1698     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1699     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1700 #if VTK_MAJOR_VERSION <= 5
1701     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1702         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1703         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1704         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1705         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1706         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1707 #else
1708     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[0]-0.5 &&
1709         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[1]+0.5 &&
1710         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[2]-0.5 &&
1711         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[3]+0.5 &&
1712         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[4]-0.5 &&
1713         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetInformation()->Get(vtkDataObject::DATA_EXTENT())[5]+0.5) {
1714 #endif
1715       int ix, iy, iz;
1716       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1717       if(ImageActor->GetVisibility())
1718         worldPos << "data value : " << value << std::endl;
1719       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1720                           << lrint(mCurrent[1]) << ' '
1721                           << lrint(mCurrent[2]) << ' '
1722                           << mCurrentTSlice
1723                           << std::endl;
1724       worldPos << "pixel : " << ix << ' '
1725                              << iy << ' '
1726                              << iz << ' '
1727                              << mCurrentTSlice
1728                              << std::endl;
1729
1730     }
1731     ca->SetText(1,worldPos.str().c_str());
1732
1733     std::stringstream slicePos;
1734     slicePos << "Slice: " << this->GetSlice();
1735     ca->SetText(2, slicePos.str().c_str());
1736   }
1737
1738   if (pdmA->GetVisibility()) {
1739     double x = mCursor[0];
1740     double y = mCursor[1];
1741     double z = mCursor[2];
1742     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1743     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1744     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1745 #if VTK_MAJOR_VERSION <= 5
1746     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0]-0.5 &&
1747         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+0.5 &&
1748         yCursor >= this->GetImageActor()->GetDisplayExtent()[2]-0.5 &&
1749         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+0.5 &&
1750         zCursor >= this->GetImageActor()->GetDisplayExtent()[4]-0.5 &&
1751         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+0.5 ) {
1752       vtkRenderer * renderer = this->Renderer;
1753
1754       renderer->WorldToView(x,y,z);
1755       renderer->ViewToNormalizedViewport(x,y,z);
1756       renderer->NormalizedViewportToViewport(x,y);
1757       renderer->ViewportToNormalizedDisplay(x,y);
1758       renderer->NormalizedDisplayToDisplay(x,y);
1759       crossCursor->SetFocalPoint(x,y,z);
1760     } else
1761       crossCursor->SetFocalPoint(-1,-1,z);
1762     crossCursor->Update();
1763   }
1764 #else
1765     vtkSmartPointer<vtkOpenGLImageSliceMapper> mapperOpenGL= vtkSmartPointer<vtkOpenGLImageSliceMapper>::New();
1766     try {
1767         mapperOpenGL = dynamic_cast<vtkOpenGLImageSliceMapper*>(GetImageActor()->GetMapper());
1768     } catch (const std::bad_cast& e) {
1769                 std::cerr << e.what() << std::endl;
1770                 std::cerr << "Conversion error" << std::endl;
1771                 return;
1772         }
1773
1774     if (xCursor >= mapperOpenGL->GetCroppingRegion()[0]-0.5 &&
1775         xCursor < mapperOpenGL->GetCroppingRegion()[1]+0.5 &&
1776         yCursor >= mapperOpenGL->GetCroppingRegion()[2]-0.5 &&
1777         yCursor < mapperOpenGL->GetCroppingRegion()[3]+0.5 &&
1778         zCursor >= mapperOpenGL->GetCroppingRegion()[4]-0.5 &&
1779         zCursor < mapperOpenGL->GetCroppingRegion()[5]+0.5 ) {
1780       vtkRenderer * renderer = this->Renderer;
1781
1782       renderer->WorldToView(x,y,z);
1783       renderer->ViewToNormalizedViewport(x,y,z);
1784       renderer->NormalizedViewportToViewport(x,y);
1785       renderer->ViewportToNormalizedDisplay(x,y);
1786       renderer->NormalizedDisplayToDisplay(x,y);
1787       crossCursor->SetFocalPoint(x,y,z);
1788     } else
1789       crossCursor->SetFocalPoint(-1,-1,z);
1790     crossCursor->Update();
1791   }
1792 #endif
1793
1794   if (mOverlay && mOverlayActor->GetVisibility()) {
1795     if(mLinkOverlayWindowLevel) {
1796       mOverlayMapper->SetWindow(this->GetColorWindow());
1797       mOverlayMapper->SetLevel(this->GetColorLevel());
1798     }
1799 #if VTK_MAJOR_VERSION <= 5
1800     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1801 #elif VTK_MAJOR_VERSION >= 8 || (VTK_MAJOR_VERSION == 7 && VTK_MINOR_VERSION >= 1)
1802     mOverlayMapper->UpdateExtent(mOverlayActor->GetDisplayExtent());
1803 #else
1804     mOverlayMapper->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1805 #endif
1806     mOverlayMapper->Update();
1807   }
1808   if (mFusion && mFusionActor->GetVisibility()) {
1809 #if VTK_MAJOR_VERSION <= 5
1810     mFusionMapper->GetOutput()->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1811 #elif VTK_MAJOR_VERSION >= 8 || (VTK_MAJOR_VERSION == 7 && VTK_MINOR_VERSION >= 1)
1812     mFusionMapper->UpdateExtent(mFusionActor->GetDisplayExtent());
1813 #else
1814     mFusionMapper->SetUpdateExtent(mFusionActor->GetDisplayExtent());
1815 #endif
1816     mFusionMapper->Update();
1817   }
1818   if (mLandMapper) {
1819     RemoveLandmarks();
1820     DisplayLandmarks();
1821   }
1822
1823     this->GetRenderWindow()->Render();
1824 }
1825 //----------------------------------------------------------------------------
1826
1827
1828 //----------------------------------------------------------------------------
1829 void vvSlicer::UpdateCursorPosition()
1830 {
1831   pdmA->SetVisibility(true);
1832   mCursor[0] = mCurrent[0];
1833   mCursor[1] = mCurrent[1];
1834   mCursor[2] = mCurrent[2];
1835   mCursor[3] = mCurrentTSlice;
1836 }
1837 //----------------------------------------------------------------------------
1838
1839
1840 //----------------------------------------------------------------------------
1841 void vvSlicer::RemoveLandmarks()
1842 {
1843   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1844   if (pd->GetPoints()) {
1845
1846     //First remove all captions:
1847     for(unsigned int i=0;i<mLandLabelActors.size();i++) {
1848         this->Renderer->RemoveActor2D(mLandLabelActors[i]);
1849         //allActors2D->Remove (mLandLabelActors[i]);
1850     }
1851     mLandLabelActors.clear();
1852   }
1853 }
1854 //----------------------------------------------------------------------------
1855
1856
1857 //----------------------------------------------------------------------------
1858 void vvSlicer::DisplayLandmarks()
1859 {
1860
1861   double bounds [6];
1862   for(unsigned int i=0; i<6; i++)
1863     bounds[i] = ImageActor->GetBounds()[i];
1864   bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1865   bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
1866   mClipBox->SetBounds(bounds);
1867
1868
1869   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandmarks->GetOutput());
1870   if (pd->GetPoints()) {
1871     this->GetRenderer()->AddActor(mLandActor);
1872     //mLandGlyph->SetRange(0,1);
1873     //mLandGlyph->Modified();
1874     //mLandGlyph->Update();
1875     mClipBox->Modified();
1876     mLandClipper->Update();
1877     mLandMapper->Update();
1878     //Next add the captions to the displayed points
1879     for (vtkIdType id=0; id<mLandClipper->GetOutput()->GetNumberOfPoints(); id++) {
1880           double *position = mLandClipper->GetOutput()->GetPoint(id);
1881       vtkStdString label = static_cast<vtkStringArray*>(mLandClipper->GetOutput()->GetPointData()->GetAbstractArray("labels"))->GetValue(id);
1882       vtkSmartPointer<vtkCaptionActor2D> label_actor = vtkSmartPointer<vtkCaptionActor2D>::New();
1883       label_actor->SetCaption(label);
1884       label_actor->SetAttachmentPoint(position);
1885       label_actor->GetCaptionTextProperty()->SetColor(1,0,0);
1886       label_actor->GetCaptionTextProperty()->SetOrientation(33.333333);
1887       label_actor->GetCaptionTextProperty()->SetFontFamilyToTimes();
1888       label_actor->GetCaptionTextProperty()->SetBold(0);
1889       label_actor->GetCaptionTextProperty()->SetFontSize(6);
1890       label_actor->BorderOff();
1891       label_actor->LeaderOff();
1892       label_actor->ThreeDimensionalLeaderOff();
1893       mLandLabelActors.push_back(label_actor);
1894       this->Renderer->AddActor2D(mLandLabelActors[id]);
1895      }
1896   }
1897
1898 }
1899 //----------------------------------------------------------------------------
1900
1901
1902 //----------------------------------------------------------------------------
1903 void vvSlicer::SetSlice(int slice)
1904 {
1905   int *range = this->GetSliceRange();
1906   if (range) {
1907     if (slice < range[0]) {
1908       slice = range[0];
1909     } else if (slice > range[1]) {
1910       slice = range[1];
1911     }
1912   }
1913
1914   if (this->Slice == slice) {
1915     return;
1916   }
1917
1918   this->Slice = slice;
1919   SetContourSlice();
1920   this->Modified();
1921   this->UpdateDisplayExtent();
1922
1923   // Seems to work without this line
1924   //this->Render();
1925 }
1926 //----------------------------------------------------------------------------
1927
1928 //----------------------------------------------------------------------------
1929 int vvSlicer::GetTMax()
1930 {
1931   int tmax = (int)mImage->GetVTKImages().size() - 1;
1932   if(mOverlay)
1933     tmax = std::max(tmax, (int)mOverlay->GetVTKImages().size()-1);
1934   return tmax;
1935 }
1936 //----------------------------------------------------------------------------
1937
1938 //----------------------------------------------------------------------------
1939 void vvSlicer::SetContourSlice()
1940 {
1941   if (mSurfaceCutActors.size() > 0)
1942     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1943          i!=mSurfaceCutActors.end(); i++) {
1944
1945       (*i)->SetSlicingOrientation(this->SliceOrientation);
1946       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1947                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1948     }
1949 }
1950 //----------------------------------------------------------------------------
1951
1952
1953 //----------------------------------------------------------------------------
1954 void vvSlicer::ForceUpdateDisplayExtent()
1955 {
1956   this->UpdateDisplayExtent();
1957 }
1958 //----------------------------------------------------------------------------
1959
1960
1961 //----------------------------------------------------------------------------
1962 int* vvSlicer::GetDisplayExtent()
1963 {
1964   return this->GetImageActor()->GetDisplayExtent();
1965 }
1966 //----------------------------------------------------------------------------
1967
1968
1969 //----------------------------------------------------------------------------
1970 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1971 {
1972   this->Superclass::PrintSelf(os, indent);
1973 }
1974 //----------------------------------------------------------------------------
1975
1976
1977 //----------------------------------------------------------------------------
1978 void vvSlicer::SetVFColor(double r, double g, double b)
1979 {
1980   double mVFColorHSV[3];
1981   mVFColor[0] = r;
1982   mVFColor[1] = g;
1983   mVFColor[2] = b;
1984
1985   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1986   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1987   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1988   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1989
1990   this->Render();
1991 }
1992 //----------------------------------------------------------------------------
1993
1994
1995 //----------------------------------------------------------------------------
1996 void vvSlicer::SetRegisterExtent(int ext[6])
1997 {
1998     copyExtent(ext, mRegisterExtent);
1999 }
2000 //----------------------------------------------------------------------------
2001
2002
2003 //----------------------------------------------------------------------------
2004 void vvSlicer::GetRegisterExtent(int ext[6])
2005 {
2006     copyExtent(mRegisterExtent, ext);
2007 }
2008 //----------------------------------------------------------------------------
2009