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 "vvSlicer.h"
  20 #include "vvImage.h"
  21 #include "vvSlicerManagerCommand.h"
  22 #include "vvGlyphSource.h"
  23 #include "vvGlyph2D.h"
  24 #include "vvImageMapToWLColors.h"
  25
  26 #include <vtkTextProperty.h>
  27 #include <vtkTextActor.h>
  28 #include <vtkTextSource.h>
  29 #include <vtkActor2D.h>
  30 #include <vtkCursor2D.h>
  31 #include <vtkPolyDataMapper2D.h>
  32 #include <vtkProperty2D.h>
  33 #include <vtkCornerAnnotation.h>
  34 #include <vtkImageMapToWindowLevelColors.h>
  35 #include <vtkImageData.h>
  36 #include <vtkImageActor.h>
  37 #include <vvBlendImageActor.h>
  38 #include <vtkToolkits.h>
  39 #include <vtkObjectFactory.h>
  40 #include <vtkPointData.h>
  41 #include <vtkDataArray.h>
  42 #include <vtkFloatArray.h>
  43 #include <vtkClipPolyData.h>
  44 #include <vtkGlyph3D.h>
  45 #include <vtkMath.h>
  46 #include <vtkCursor3D.h>
  47 #include <vtkProperty.h>
  48 #include <vtkLight.h>
  49 #include <vtkLightCollection.h>
  50 #include <vtkScalarBarActor.h>
  51 #include <vtkLookupTable.h>
  52
  53 #include <vtkRenderer.h>
  54 #include <vtkRendererCollection.h>
  55 #include <vtkRenderWindow.h>
  56 #include <vtkRenderWindowInteractor.h>
  57 #include <vtkCamera.h>
  58 #include <vtkCallbackCommand.h>
  59 #include <vtkCommand.h>
  60 #include <vtkPolyDataMapper.h>
  61 #include <vtkBox.h>
  62
  63 #include <vtkExtractVOI.h>
  64 #include <vtkSphereSource.h>
  65 #include <vtkCutter.h>
  66 #include <vtkAssignAttribute.h>
  67 #include <vtkImageAccumulate.h>
  68 #include <vtkImageReslice.h>
  69 #include <vtkImageMapper3D.h>
  70
  71 vtkCxxRevisionMacro(vvSlicer, "DummyRevision");
  72 vtkStandardNewMacro(vvSlicer);
  73 static void copyExtent(int* in, int* to){
  74  for(int i=0; i<6; ++i) to[i]=in[i];
  75 }
  76 //------------------------------------------------------------------------------
  77 vvSlicer::vvSlicer()
  78 {
  79   this->UnInstallPipeline();
  80   mImage = NULL;
  81   mReducedExtent = new int[6];
  82   mCurrentTSlice = 0;
  83   mUseReducedExtent = false;
  84
  85   mCurrent[0] = -VTK_DOUBLE_MAX;
  86   mCurrent[1] = -VTK_DOUBLE_MAX;
  87   mCurrent[2] = -VTK_DOUBLE_MAX;
  88
  89   mCursor[0] = -VTK_DOUBLE_MAX;
  90   mCursor[1] = -VTK_DOUBLE_MAX;
  91   mCursor[2] = -VTK_DOUBLE_MAX;
  92   mCursor[3] = -VTK_DOUBLE_MAX;
  93
  94   mSubSampling = 5;
  95   mScale = 1;
  96   mVFLog = 0;
  97   mVFWidth = 1;
  98   mVFColor[0] = 0;
  99   mVFColor[1] = 1;
 100   mVFColor[2] = 0;
 101
 102   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 103   crossCursor->AllOff();
 104   crossCursor->AxesOn();
 105   crossCursor->SetTranslationMode(1);
 106   crossCursor->SetRadius(2);
 107
 108   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 109   pdm->SetInput(crossCursor->GetOutput());
 110
 111   pdmA = vtkSmartPointer<vtkActor2D>::New();
 112   pdmA->SetMapper(pdm);
 113   pdmA->GetProperty()->SetColor(255,10,212);
 114   pdmA->SetVisibility(0);
 115   pdmA->SetPickable(0);
 116
 117   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 118   ca->GetTextProperty()->SetColor(255,10,212);
 119   ca->SetVisibility(1);
 120   mFileName = "";
 121
 122   mVF = NULL;
 123   mOverlay = NULL;
 124   mFusion = NULL;
 125   mLandmarks = NULL;
 126
 127   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 128   //legend->SetTitle("test!");
 129   legend->SetPosition(0.82,0.18);
 130   legend->SetWidth(0.1);
 131   legend->SetVisibility(0);
 132   legend->SetLabelFormat("%.1f");
 133   this->GetRenderer()->AddActor(legend);
 134   showFusionLegend = false;
 135
 136   this->WindowLevel->Delete();
 137   this->WindowLevel = vvImageMapToWLColors::New();
 138
 139   this->InstallPipeline();
 140
 141   mLinkOverlayWindowLevel = true;
 142
 143 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 144   this->GetImageActor()->GetMapper()->BorderOn();
 145 #endif
 146 }
 147 //------------------------------------------------------------------------------
 148
 149
 150 //------------------------------------------------------------------------------
 151 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 152 {
 153   return mOverlayMapper.GetPointer();
 154 }
 155 //------------------------------------------------------------------------------
 156
 157
 158 //------------------------------------------------------------------------------
 159 vvBlendImageActor* vvSlicer::GetOverlayActor()
 160 {
 161   return mOverlayActor.GetPointer();
 162 }
 163 //------------------------------------------------------------------------------
 164
 165
 166 //------------------------------------------------------------------------------
 167 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 168 {
 169   return mFusionMapper.GetPointer();
 170 }
 171 //------------------------------------------------------------------------------
 172
 173
 174 //------------------------------------------------------------------------------
 175 vtkImageActor* vvSlicer::GetFusionActor()
 176 {
 177   return mFusionActor.GetPointer();
 178 }
 179 //------------------------------------------------------------------------------
 180
 181
 182 //------------------------------------------------------------------------------
 183 vtkActor* vvSlicer::GetVFActor()
 184 {
 185   return mVFActor.GetPointer();
 186 }
 187 //------------------------------------------------------------------------------
 188
 189
 190 //------------------------------------------------------------------------------
 191 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 192 {
 193   return ca.GetPointer();
 194 }
 195 //------------------------------------------------------------------------------
 196
 197
 198 //------------------------------------------------------------------------------
 199 void vvSlicer::EnableReducedExtent(bool b)
 200 {
 201   mUseReducedExtent = b;
 202 }
 203 //------------------------------------------------------------------------------
 204
 205
 206 //------------------------------------------------------------------------------
 207 void vvSlicer::SetReducedExtent(int * ext)
 208 {
 209   copyExtent(ext, mReducedExtent);
 210 }
 211 //------------------------------------------------------------------------------
 212
 213
 214 //------------------------------------------------------------------------------
 215 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 216 {
 217
 218   mSurfaceCutActors.push_back(new vvMeshActor());
 219   if (propagate)
 220     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 221   else
 222     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 223   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 224   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 225
 226   SetContourSlice();
 227 }
 228 //------------------------------------------------------------------------------
 229
 230
 231 //------------------------------------------------------------------------------
 232 void vvSlicer::ToggleContourSuperposition()
 233 {
 234   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 235        i!=mSurfaceCutActors.end(); i++)
 236     (*i)->ToggleSuperposition();
 237 }
 238 //------------------------------------------------------------------------------
 239
 240
 241 //------------------------------------------------------------------------------
 242 void vvSlicer::SetCursorColor(int r,int g, int b)
 243 {
 244   pdmA->GetProperty()->SetColor(r,g,b);
 245 }
 246 //------------------------------------------------------------------------------
 247
 248
 249 //------------------------------------------------------------------------------
 250 void vvSlicer::SetCursorVisibility(bool s)
 251 {
 252   pdmA->SetVisibility(s);
 253 }
 254 //------------------------------------------------------------------------------
 255
 256
 257 //------------------------------------------------------------------------------
 258 bool vvSlicer::GetCursorVisibility()
 259 {
 260   return pdmA->GetVisibility();
 261 }
 262 //------------------------------------------------------------------------------
 263
 264
 265 //------------------------------------------------------------------------------
 266 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 267 {
 268   ca->SetVisibility(s);
 269 }
 270 //------------------------------------------------------------------------------
 271
 272
 273 //------------------------------------------------------------------------------
 274 bool vvSlicer::GetCornerAnnotationVisibility()
 275 {
 276   return ca->GetVisibility();
 277 }
 278 //------------------------------------------------------------------------------
 279
 280
 281 //------------------------------------------------------------------------------
 282 vvSlicer::~vvSlicer()
 283 {
 284   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 285        i!=mSurfaceCutActors.end(); i++)
 286     delete (*i);
 287   delete [] mReducedExtent;
 288 }
 289 //------------------------------------------------------------------------------
 290
 291
 292 //------------------------------------------------------------------------------
 293 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 294 {
 295   mCurrent[0] = x;
 296   mCurrent[1] = y;
 297   mCurrent[2] = z;
 298   mCurrentTSlice = t;
 299 }
 300 //------------------------------------------------------------------------------
 301
 302
 303 //------------------------------------------------------------------------------
 304 void vvSlicer::SetImage(vvImage::Pointer image)
 305 {
 306   if (image->GetVTKImages().size()) {
 307     mImage = image;
 308
 309     if (!mImageReslice) {
 310       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 311       mImageReslice->SetInterpolationModeToLinear();
 312       mImageReslice->AutoCropOutputOn();
 313       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 314     }
 315     mImageReslice->SetResliceTransform(mImage->GetTransform());
 316     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 317     mImageReslice->UpdateInformation();
 318
 319     this->Superclass::SetInput(mImageReslice->GetOutput());
 320
 321     int extent[6];
 322     this->GetInput()->GetWholeExtent(extent);
 323
 324     // Prevent crash when reload -> change slice if outside extent
 325     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 326       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 327     }
 328
 329     // Make sure that the required part image has been computed
 330     extent[SliceOrientation*2] = Slice;
 331     extent[SliceOrientation*2+1] = Slice;
 332     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 333     mImageReslice->GetOutput()->Update();
 334
 335     this->UpdateDisplayExtent();
 336
 337     mCurrentTSlice = 0;
 338     ca->SetText(0,mFileName.c_str());
 339   }
 340 }
 341 //------------------------------------------------------------------------------
 342
 343
 344 //------------------------------------------------------------------------------
 345 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 346 {
 347   if (overlay->GetVTKImages().size()) {
 348     mOverlay = overlay;
 349
 350     if (!mOverlayReslice) {
 351       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 352       mOverlayReslice->SetInterpolationModeToLinear();
 353       mOverlayReslice->AutoCropOutputOn();
 354       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 355     }
 356     mOverlayReslice->SetResliceTransform(mOverlay->GetTransform());
 357     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 358
 359     if (!mOverlayMapper)
 360       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 361     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 362
 363     if (!mOverlayActor) {
 364       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 365       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 366       mOverlayActor->SetPickable(0);
 367       mOverlayActor->SetVisibility(true);
 368       mOverlayActor->SetOpacity(0.5);
 369 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 370       mOverlayActor->GetMapper()->BorderOn();
 371 #endif
 372       }
 373
 374     //stupid but necessary : the Overlay need to be rendered before fusion
 375     if (mFusionActor) {
 376       this->GetRenderer()->RemoveActor(mFusionActor);
 377       this->GetRenderer()->AddActor(mOverlayActor);
 378       this->GetRenderer()->AddActor(mFusionActor);
 379     } else
 380       this->GetRenderer()->AddActor(mOverlayActor);
 381
 382     //Synchronize orientation and slice
 383     AdjustResliceToSliceOrientation(mOverlayReslice);
 384     this->UpdateDisplayExtent();
 385     this->SetTSlice(mCurrentTSlice);
 386   }
 387 }
 388 //------------------------------------------------------------------------------
 389
 390
 391 //------------------------------------------------------------------------------
 392 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 393 {
 394   if (fusion->GetVTKImages().size()) {
 395     mFusion = fusion;
 396
 397     if (!mFusionReslice) {
 398       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 399       mFusionReslice->SetInterpolationModeToLinear();
 400       mFusionReslice->AutoCropOutputOn();
 401       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 402     }
 403     mFusionReslice->SetResliceTransform(mFusion->GetTransform());
 404     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 405
 406     if (!mFusionMapper)
 407       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 408
 409     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 410     lut->SetRange(0, 1);
 411     lut->SetValueRange(0, 1);
 412     lut->SetSaturationRange(0, 0);
 413     lut->Build();
 414     mFusionMapper->SetLookupTable(lut);
 415     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 416
 417     if (!mFusionActor) {
 418       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 419       mFusionActor->SetInput(mFusionMapper->GetOutput());
 420       mFusionActor->SetPickable(0);
 421       mFusionActor->SetVisibility(true);
 422       mFusionActor->SetOpacity(0.7);
 423 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 424       mFusionActor->GetMapper()->BorderOn();
 425 #endif
 426       this->GetRenderer()->AddActor(mFusionActor);
 427     }
 428
 429     //Synchronize orientation and slice
 430     AdjustResliceToSliceOrientation(mFusionReslice);
 431     this->UpdateDisplayExtent();
 432     this->SetTSlice(mCurrentTSlice);
 433   }
 434 }
 435 //------------------------------------------------------------------------------
 436
 437
 438 //------------------------------------------------------------------------------
 439 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 440 {
 441   bool vis = false;
 442   if (actor_type == "image") {
 443     vis = this->ImageActor->GetVisibility();
 444   }
 445   else if (actor_type == "vector") {
 446     vis = this->mVFActor->GetVisibility();
 447   }
 448   else if (actor_type == "overlay") {
 449     vis = this->mOverlayActor->GetVisibility();
 450   }
 451   else if (actor_type == "fusion") {
 452     vis = this->mFusionActor->GetVisibility();
 453   }
 454   else if (actor_type == "contour")
 455     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 456
 457   return vis;
 458 }
 459 //------------------------------------------------------------------------------
 460
 461 //------------------------------------------------------------------------------
 462 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 463 {
 464   if (actor_type == "image") {
 465     this->ImageActor->SetVisibility(vis);
 466   }
 467   else if (actor_type == "vector") {
 468     this->mVFActor->SetVisibility(vis);
 469   }
 470   else if (actor_type == "overlay") {
 471     this->mOverlayActor->SetVisibility(vis);
 472   }
 473   else if (actor_type == "fusion") {
 474     this->mFusionActor->SetVisibility(vis);
 475   }
 476   else if (actor_type == "contour")
 477     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 478   UpdateDisplayExtent();
 479 }
 480 //------------------------------------------------------------------------------
 481
 482 //------------------------------------------------------------------------------
 483 void vvSlicer::SetVF(vvImage::Pointer vf)
 484 {
 485   if (vf->GetVTKImages().size()) {
 486     mVF = vf;
 487
 488     if (!mAAFilter) {
 489       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 490       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 491       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 492     }
 493     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 494     mAAFilter->SetInput(mVOIFilter->GetOutput());
 495     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 496     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 497
 498     if (!mArrow)
 499       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 500     mArrow->SetGlyphTypeToSpecificArrow();
 501     mArrow->SetScale(mScale);
 502     mArrow->FilledOff();
 503
 504     // Glyph the gradient vector (with arrows)
 505     if (!mGlyphFilter)
 506       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 507     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 508     mGlyphFilter->SetSource(mArrow->GetOutput());
 509     mGlyphFilter->ScalingOn();
 510     mGlyphFilter->SetScaleModeToScaleByVector();
 511     mGlyphFilter->OrientOn();
 512     mGlyphFilter->SetVectorModeToUseVector();
 513     mGlyphFilter->SetColorModeToColorByVector();
 514
 515     if (!mVFColorLUT)
 516       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 517
 518     double mVFColorHSV[3];
 519     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 520     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 521     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 522     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 523
 524     if (!mVFMapper)
 525       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 526     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 527     mVFMapper->ImmediateModeRenderingOn();
 528     mVFMapper->SetLookupTable(mVFColorLUT);
 529
 530     if (!mVFActor)
 531       mVFActor = vtkSmartPointer<vtkActor>::New();
 532     mVFActor->SetMapper(mVFMapper);
 533     mVFActor->SetPickable(0);
 534     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 535     this->UpdateDisplayExtent();
 536     this->GetRenderer()->AddActor(mVFActor);
 537
 538     //Synchronize slice
 539     SetTSlice(mCurrentTSlice);
 540   }
 541 }
 542 //------------------------------------------------------------------------------
 543
 544
 545 //------------------------------------------------------------------------------
 546 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 547 {
 548   mLandmarks = landmarks;
 549   if (landmarks) {
 550
 551     if (!mCross)
 552       mCross = vtkSmartPointer<vtkCursor3D>::New();
 553     mCross->SetFocalPoint(0.0,0.0,0.0);
 554     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 555     mCross->AllOff();
 556     mCross->AxesOn();
 557
 558     if (!mLandGlyph)
 559       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 560     mLandGlyph->SetSource(mCross->GetOutput());
 561     mLandGlyph->SetInput(landmarks->GetOutput());
 562     //mLandGlyph->SetIndexModeToScalar();
 563     mLandGlyph->SetRange(0,1);
 564     mLandGlyph->ScalingOff();
 565
 566     mLandGlyph->SetColorModeToColorByScalar();
 567
 568     if (!mClipBox)
 569       mClipBox = vtkSmartPointer<vtkBox>::New();
 570     if (!mLandClipper)
 571       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 572     mLandClipper->InsideOutOn();
 573     mLandClipper->SetInput(mLandGlyph->GetOutput());
 574     mLandClipper->SetClipFunction(mClipBox);
 575
 576     if (!mLandMapper)
 577       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 578     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 579     //mLandMapper->ScalarVisibilityOff();
 580
 581     if (!mLandActor)
 582       mLandActor = vtkSmartPointer<vtkActor>::New();
 583     mLandActor->SetMapper(mLandMapper);
 584     mLandActor->GetProperty()->SetColor(255,10,212);
 585     mLandActor->SetPickable(0);
 586     mLandActor->SetVisibility(true);
 587     this->UpdateDisplayExtent();
 588     this->GetRenderer()->AddActor(mLandActor);
 589   }
 590 }
 591 //------------------------------------------------------------------------------
 592
 593 //------------------------------------------------------------------------------
 594 //FIXME: this function leaks memory, we should fix it someday :)
 595 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 596 {
 597   if (actor_type == "vector") {
 598     Renderer->RemoveActor(mVFActor);
 599     mGlyphFilter=NULL;
 600     mVF = NULL;
 601     mArrow = NULL;
 602     mAAFilter=NULL;
 603     mVOIFilter = NULL;
 604     mVFMapper = NULL;
 605     mVFActor = NULL;
 606   }
 607   if (actor_type == "overlay") {
 608     Renderer->RemoveActor(mOverlayActor);
 609     mOverlay = NULL;
 610     mOverlayActor = NULL;
 611     mOverlayMapper = NULL;
 612   }
 613   if (actor_type == "fusion") {
 614     Renderer->RemoveActor(mFusionActor);
 615     mFusion = NULL;
 616     mFusionActor = NULL;
 617     mFusionMapper = NULL;
 618   }
 619   if (actor_type == "contour") {
 620     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 621     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 622   }
 623 }
 624 //------------------------------------------------------------------------------
 625
 626
 627 //------------------------------------------------------------------------------
 628 void vvSlicer::SetVFSubSampling(int sub)
 629 {
 630   if (mVOIFilter) {
 631     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 632     mSubSampling = sub;
 633   }
 634   UpdateDisplayExtent();
 635   Render();
 636 }
 637 //------------------------------------------------------------------------------
 638
 639
 640 //------------------------------------------------------------------------------
 641 void vvSlicer::SetVFScale(int scale)
 642 {
 643   mScale = scale;
 644   if (mArrow)
 645     mArrow->SetScale(mScale);
 646   UpdateDisplayExtent();
 647   Render();
 648 }
 649 //------------------------------------------------------------------------------
 650
 651 //------------------------------------------------------------------------------
 652 void vvSlicer::SetVFWidth(int width)
 653 {
 654   mVFWidth = width;
 655   if (mVFActor)
 656     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 657   UpdateDisplayExtent();
 658   Render();
 659 }
 660 //------------------------------------------------------------------------------
 661
 662
 663 //------------------------------------------------------------------------------
 664 void vvSlicer::SetVFLog(int log)
 665 {
 666   mVFLog = log;
 667   if (mGlyphFilter) {
 668     mGlyphFilter->SetUseLog(mVFLog);
 669     mGlyphFilter->Modified();
 670   }
 671   UpdateDisplayExtent();
 672   Render();
 673 }
 674 //------------------------------------------------------------------------------
 675
 676
 677 //------------------------------------------------------------------------------
 678 void vvSlicer::SetTSlice(int t)
 679 {
 680   if (t < 0)
 681     t = 0;
 682   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 683     t = mImage->GetVTKImages().size() -1;
 684
 685   mCurrentTSlice = t;
 686   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 687   if (mVF && mVFActor->GetVisibility()) {
 688     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 689       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 690   }
 691   if (mOverlay && mOverlayActor->GetVisibility()) {
 692     if (mOverlay->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 693       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentTSlice] );
 694   }
 695   if (mFusion && mFusionActor->GetVisibility()) {
 696     if (mFusion->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 697       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentTSlice]);
 698   }
 699   if (mSurfaceCutActors.size() > 0)
 700     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 701          i!=mSurfaceCutActors.end(); i++)
 702       (*i)->SetTimeSlice(mCurrentTSlice);
 703   UpdateDisplayExtent();
 704 }
 705 //------------------------------------------------------------------------------
 706
 707
 708 //------------------------------------------------------------------------------
 709 int vvSlicer::GetTSlice()
 710 {
 711   return mCurrentTSlice;
 712 }
 713 //------------------------------------------------------------------------------
 714
 715 //------------------------------------------------------------------------------
 716 void vvSlicer::SetSliceOrientation(int orientation)
 717 {
 718   //if 2D image, force to watch in Axial View
 719   int extent[6];
 720   this->GetInput()->GetWholeExtent(extent);
 721   if (extent[5]-extent[4] <= 2)
 722     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 723
 724   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 725       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 726     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 727     return;
 728   }
 729
 730   this->SliceOrientation = orientation;
 731
 732   if(mFusion)
 733     AdjustResliceToSliceOrientation(mFusionReslice);
 734
 735   if(mOverlay)
 736     AdjustResliceToSliceOrientation(mOverlayReslice);
 737
 738   // Update the viewer
 739   int *range = this->GetSliceRange();
 740   if (range)
 741     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 742
 743   // Go to current cursor position
 744   // double* cursorPos = GetCursorPosition();
 745   // DDV(cursorPos, 3);
 746   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 747
 748   this->UpdateOrientation();
 749   this->UpdateDisplayExtent();
 750
 751   if (this->Renderer && this->GetInput()) {
 752     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 753     this->Renderer->ResetCamera();
 754     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 755   }
 756
 757   SetContourSlice();
 758 }
 759 //----------------------------------------------------------------------------
 760
 761 //------------------------------------------------------------------------------
 762 // This function ensures that we sample the slices of a vtkImageReslice filter
 763 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 764 // In other words, we change the grid of the reslice in the same way as the grid
 765 // of the displayed image in the slicing direction.
 766 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 767 {
 768   // Reset autocrop and update output information
 769   reslice->SetOutputOriginToDefault();
 770   reslice->SetOutputSpacingToDefault();
 771   reslice->GetOutput()->UpdateInformation();
 772
 773   // Ge new origin / spacing
 774   double origin[3];
 775   double spacing[3];
 776   reslice->GetOutput()->GetOrigin(origin);
 777   reslice->GetOutput()->GetSpacing(spacing);
 778
 779   // Use similar spacing as the image in the direction SliceOrientation
 780   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 781
 782   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 783   // Step 1: from world coordinates to image coordinates
 784   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 785   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 786   // Step 2: round to superior grid positionInc
 787   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 788   // Step 3: back to world coordinates
 789   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 790   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 791
 792   // Set new spacing and origin
 793   reslice->SetOutputOrigin(origin);
 794   reslice->SetOutputSpacing(spacing);
 795   reslice->UpdateInformation();
 796   reslice->GetOutput()->UpdateInformation();
 797 }
 798 //------------------------------------------------------------------------------
 799
 800 //----------------------------------------------------------------------------
 801 int * vvSlicer::GetExtent(){
 802   int *w_ext;
 803   if (mUseReducedExtent) {
 804     w_ext = mReducedExtent;
 805   } else w_ext = GetInput()->GetWholeExtent();
 806   return w_ext;
 807 }
 808 //----------------------------------------------------------------------------
 809
 810
 811 //----------------------------------------------------------------------------
 812 int vvSlicer::GetOrientation()
 813 {
 814   return this->SliceOrientation;
 815 }
 816 //----------------------------------------------------------------------------
 817
 818
 819 //----------------------------------------------------------------------------
 820 void vvSlicer::UpdateDisplayExtent()
 821 {
 822   vtkImageData *input = this->GetInput();
 823   if (!input || !this->ImageActor) {
 824     return;
 825   }
 826   input->UpdateInformation();
 827
 828   // Local copy of extent
 829   int w_ext[6];
 830   int* ext = GetExtent();
 831   copyExtent(ext, w_ext);
 832   // Set slice value
 833   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 834   w_ext[ this->SliceOrientation*2   ] = s;
 835   w_ext[ this->SliceOrientation*2+1 ] = s;
 836
 837   // Image actor
 838   this->ImageActor->SetDisplayExtent(w_ext);
 839
 840   // Overlay image actor
 841   if (mOverlay && mOverlayActor->GetVisibility()) {
 842     AdjustResliceToSliceOrientation(mOverlayReslice);
 843     int overExtent[6];
 844     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 845     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 846     mOverlayActor->SetDisplayExtent( overExtent );
 847   }
 848
 849   // Fusion image actor
 850   if (mFusion && mFusionActor->GetVisibility()) {
 851     AdjustResliceToSliceOrientation(mFusionReslice);
 852     int fusExtent[6];
 853     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 854     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 855     mFusionActor->SetDisplayExtent(fusExtent);
 856   }
 857
 858   // Vector field actor
 859   double* camera = Renderer->GetActiveCamera()->GetPosition();
 860   double* image_bounds = ImageActor->GetBounds();
 861   double position[3] = {0, 0, 0};
 862   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 863
 864   //print_vector<double, 6>("camera", camera);
 865   //print_vector<double, 6>("image_bounds", image_bounds);
 866   //print_vector<double, 3>("position", position);
 867
 868   // find where to place the VF actor. to deal with
 869   // z-buffer issues, the VF is placed right in front of the image,
 870   // subject to a small offset. the position actually depends on the
 871   // the location of the camera relative to the image.
 872   double offset = 1;
 873   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 874     offset = -1;
 875
 876   if (mVF && mVFActor->GetVisibility()) {
 877     int vfExtent[6];
 878     mVF->GetVTKImages()[0]->UpdateInformation();
 879     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 880     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 881     mVOIFilter->SetVOI(vfExtent);
 882     int orientation[3] = {1,1,1};
 883     orientation[this->SliceOrientation] = 0;
 884     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 885     mVFMapper->Update();
 886
 887     position[this->SliceOrientation] += offset;
 888     mVFActor->SetPosition(position);
 889   }
 890
 891   // Landmarks actor
 892   if (mLandActor) {
 893     if (mClipBox) {
 894       double bounds [6];
 895       for(unsigned int i=0; i<6; i++)
 896         bounds[i] = ImageActor->GetBounds()[i];
 897       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 898       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 899       mClipBox->SetBounds(bounds);
 900       UpdateLandmarks();
 901     }
 902
 903     position[this->SliceOrientation] = offset;
 904     mLandActor->SetPosition(position);
 905   }
 906
 907   // Figure out the correct clipping range
 908   if (this->Renderer) {
 909     if (this->InteractorStyle &&
 910         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 911       this->Renderer->ResetCameraClippingRange();
 912     } else {
 913       vtkCamera *cam = this->Renderer->GetActiveCamera();
 914       if (cam) {
 915         double bounds[6];
 916         this->ImageActor->GetBounds(bounds);
 917         double spos = (double)bounds[this->SliceOrientation * 2];
 918         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 919         double range = fabs(spos - cpos);
 920         double *spacing = input->GetSpacing();
 921         double avg_spacing =
 922           ((double)spacing[0] + (double)spacing[1] + (double)spacing[2]) / 3.0;
 923         cam->SetClippingRange(range - avg_spacing * 3.0, range + avg_spacing * 3.0);
 924       }
 925     }
 926   }
 927
 928 }
 929 //----------------------------------------------------------------------------
 930
 931 //----------------------------------------------------------------------------
 932 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 933                                                 vtkImageData *targetImage, int targetExtent[6])
 934 {
 935   double dExtents[6];
 936   for(unsigned int i=0; i<6; i++) {
 937     // From source voxel coordinates to world coordinates
 938     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 939
 940     // From world coordinates to floating point target voxel coordinates
 941     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 942
 943     // Round to nearest
 944     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 945     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
 946   }
 947 }
 948 //----------------------------------------------------------------------------
 949
 950 //----------------------------------------------------------------------------
 951 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 952 {
 953   bool out = false;
 954   int maxBound = 6;
 955
 956   //2D overlay on 3D image specific case
 957   if (refExtent[4] == refExtent[5]) {
 958     maxBound = 4;
 959     extent[4] = refExtent[4];
 960     extent[5] = refExtent[5];
 961   }
 962
 963   for (int i = 0; i < maxBound; i = i+2) {
 964     //if we are totally outside the image
 965     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 966       out = true;
 967       break;
 968     }
 969     //crop to the limit of the image
 970     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 971     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 972     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 973     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 974   }
 975   if (out)
 976     for (int i = 0; i < maxBound; i = i+2) {
 977       extent[i] = refExtent[i];
 978       extent[i+1] = refExtent[i];
 979     }
 980 }
 981 //----------------------------------------------------------------------------
 982
 983
 984 //----------------------------------------------------------------------------
 985 void vvSlicer::UpdateOrientation()
 986 {
 987   // Set the camera position
 988   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
 989   if (cam) {
 990     switch (this->SliceOrientation) {
 991     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 992       cam->SetFocalPoint(0,0,0);
 993       cam->SetPosition(0,0,-1); // -1 if medical ?
 994       cam->SetViewUp(0,-1,0);
 995       break;
 996
 997     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 998       cam->SetFocalPoint(0,0,0);
 999       cam->SetPosition(0,-1,0); // 1 if medical ?
1000       cam->SetViewUp(0,0,1);
1001       break;
1002
1003     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1004       cam->SetFocalPoint(0,0,0);
1005       cam->SetPosition(-1,0,0); // -1 if medical ?
1006       cam->SetViewUp(0,0,1);
1007       break;
1008     }
1009   }
1010 }
1011 //----------------------------------------------------------------------------
1012
1013
1014 //----------------------------------------------------------------------------
1015 void vvSlicer::SetOpacity(double s)
1016 {
1017   this->GetImageActor()->SetOpacity(s);
1018 }
1019 //----------------------------------------------------------------------------
1020
1021
1022 //----------------------------------------------------------------------------
1023 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1024 {
1025   this->Superclass::SetRenderWindow(rw);
1026   this->SetupInteractor(rw->GetInteractor());
1027   ca->SetImageActor(this->GetImageActor());
1028   ca->SetWindowLevel(this->GetWindowLevel());
1029   ca->SetText(2, "<slice>");
1030   ca->SetText(3, "<window>\n<level>");
1031
1032   double bounds[6];
1033   double max = 65000;
1034
1035   bounds[0] = -max;
1036   bounds[1] = max;
1037   bounds[2] = -max;
1038   bounds[3] = max;
1039   bounds[4] = -max;
1040   bounds[5] = max;
1041
1042   crossCursor->SetModelBounds(bounds);
1043   this->GetRenderer()->AddActor(pdmA);
1044   this->GetRenderer()->AddActor(ca);
1045   this->GetRenderer()->ResetCamera();
1046
1047   //this is just a mapping between the labeling of the orientations presented to the user and
1048   //the one used by vtk
1049   SetSliceOrientation(2-(orientation%3));
1050   ResetCamera();
1051 }
1052 //----------------------------------------------------------------------------
1053
1054
1055 //----------------------------------------------------------------------------
1056 void vvSlicer::ResetCamera()
1057 {
1058   this->GetRenderer()->ResetCamera();
1059 }
1060 //----------------------------------------------------------------------------
1061
1062
1063 //----------------------------------------------------------------------------
1064 void vvSlicer::SetDisplayMode(bool i)
1065 {
1066   this->GetRenderer()->SetDraw(i);
1067   if (i)
1068     UpdateDisplayExtent();
1069 }
1070 //----------------------------------------------------------------------------
1071
1072
1073 //----------------------------------------------------------------------------
1074 void vvSlicer::FlipHorizontalView()
1075 {
1076   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1077   if (cam) {
1078     double *position = cam->GetPosition();
1079     double factor[3] = {1, 1, 1};
1080     factor[this->SliceOrientation] = -1;
1081     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1082
1083 /*    switch (this->SliceOrientation) {
1084     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1085       cam->SetPosition(position[0],position[1],-position[2]);
1086       break;
1087
1088     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1089       cam->SetPosition(position[0],-position[1],position[2]);
1090       break;
1091
1092     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1093       cam->SetPosition(-position[0],position[1],position[2]);
1094       break;
1095     }*/
1096
1097     this->Renderer->ResetCameraClippingRange();
1098     this->UpdateDisplayExtent();
1099   }
1100 }
1101 //----------------------------------------------------------------------------
1102
1103
1104 //----------------------------------------------------------------------------
1105 void vvSlicer::FlipVerticalView()
1106 {
1107   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1108   if (cam) {
1109     FlipHorizontalView();
1110     double *viewup = cam->GetViewUp();
1111     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1112     this->UpdateDisplayExtent();
1113   }
1114 }
1115 //----------------------------------------------------------------------------
1116
1117
1118 //----------------------------------------------------------------------------
1119 void vvSlicer::SetColorWindow(double window)
1120 {
1121   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1122   if ( LUT ) {
1123     double level = this->GetWindowLevel()->GetLevel();
1124     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1125     LUT->Build();
1126   }
1127   this->vtkImageViewer2::SetColorWindow(window);
1128 }
1129 //----------------------------------------------------------------------------
1130
1131 //----------------------------------------------------------------------------
1132 void vvSlicer::SetColorLevel(double level)
1133 {
1134   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1135   if ( LUT ) {
1136     double window = this->GetWindowLevel()->GetWindow();
1137     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1138     LUT->Build();
1139   }
1140   this->vtkImageViewer2::SetColorLevel(level);
1141 }
1142 //----------------------------------------------------------------------------
1143
1144 //----------------------------------------------------------------------------
1145 double vvSlicer::GetOverlayColorWindow()
1146 {
1147   if(mOverlayMapper)
1148     return mOverlayMapper->GetWindow();
1149   else
1150     return 0.;
1151 }
1152 //----------------------------------------------------------------------------
1153
1154 //----------------------------------------------------------------------------
1155 double vvSlicer::GetOverlayColorLevel()
1156 {
1157   if(mOverlayMapper)
1158     return mOverlayMapper->GetLevel();
1159   else
1160     return 0.;
1161 }
1162 //----------------------------------------------------------------------------
1163
1164 //----------------------------------------------------------------------------
1165 void vvSlicer::SetOverlayColorWindow(double window)
1166 {
1167   mOverlayMapper->SetWindow(window);
1168 }
1169 //----------------------------------------------------------------------------
1170
1171 //----------------------------------------------------------------------------
1172 void vvSlicer::SetOverlayColorLevel(double level)
1173 {
1174   mOverlayMapper->SetLevel(level);
1175 }
1176 //----------------------------------------------------------------------------
1177
1178 //----------------------------------------------------------------------------
1179 // Returns the min an the max value in a 41x41 region around the mouse pointer
1180 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1181 {
1182   //Get mouse pointer position in view coordinates
1183   double corner1[3];
1184   double corner2[3];
1185   for(int i=0; i<3; i++) {
1186     corner1[i] = mCurrent[i];
1187     corner2[i] = mCurrent[i];
1188   }
1189
1190   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1191   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1192
1193   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1194   int w, h;
1195   this->Renderer->GetTiledSize(&w, &h);
1196   corner1[0] -= 0.2*h/(double)w;
1197   corner2[0] += 0.2*h/(double)w;
1198   corner1[1] -= 0.2;
1199   corner2[1] += 0.2;
1200   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1201   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1202
1203   //Convert to image pixel coordinates (rounded)
1204   transform->TransformPoint(corner1, corner1);
1205   transform->TransformPoint(corner2, corner2);
1206   int iLocalExtents[6];
1207   for(int i=0; i<3; i++) {
1208     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1209     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1210
1211     iLocalExtents[i*2  ] = lrint(corner1[i]);
1212     iLocalExtents[i*2+1] = lrint(corner2[i]);
1213
1214     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1215       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1216   }
1217
1218   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1219   voiFilter->SetInput(image);
1220   voiFilter->SetVOI(iLocalExtents);
1221   voiFilter->Update();
1222   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1223     min = 0;
1224     max = 0;
1225     return;
1226   }
1227
1228   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1229   accFilter->SetInput(voiFilter->GetOutput());
1230   accFilter->Update();
1231
1232   min = *(accFilter->GetMin());
1233   max = *(accFilter->GetMax());
1234 }
1235 //----------------------------------------------------------------------------
1236
1237 //----------------------------------------------------------------------------
1238 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1239 {
1240   ix = lrint(X);
1241   iy = lrint(Y);
1242   iz = lrint(Z);
1243   if (ix < image->GetWholeExtent()[0] ||
1244       ix > image->GetWholeExtent()[1] ||
1245       iy < image->GetWholeExtent()[2] ||
1246       iy > image->GetWholeExtent()[3] ||
1247       iz < image->GetWholeExtent()[4] ||
1248       iz > image->GetWholeExtent()[5] )
1249     return std::numeric_limits<double>::quiet_NaN();
1250
1251   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1252   image->Update();
1253   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1254 }
1255 //----------------------------------------------------------------------------
1256
1257 //----------------------------------------------------------------------------
1258 void vvSlicer::Render()
1259 {
1260   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1261     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1262     legend->UseOpacityOn();
1263     legend->SetVisibility(1);
1264   }
1265   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1266     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1267     legend->UseOpacityOff();
1268     legend->SetVisibility(1);
1269   } else legend->SetVisibility(0);
1270
1271   if (ca->GetVisibility()) {
1272     std::stringstream worldPos;
1273     double X = (mCurrent[0] - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1274     double Y = (mCurrent[1] - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1275     double Z = (mCurrent[2] - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1276
1277 //     if (X < this->GetInput()->GetWholeExtent()[0]) X = this->GetInput()->GetWholeExtent()[0];
1278 //     else if (X > this->GetInput()->GetWholeExtent()[1]) X = this->GetInput()->GetWholeExtent()[1];
1279 //     if (Y < this->GetInput()->GetWholeExtent()[2]) Y = this->GetInput()->GetWholeExtent()[2];
1280 //     else if (Y > this->GetInput()->GetWholeExtent()[3]) Y = this->GetInput()->GetWholeExtent()[3];
1281 //     if (Z < this->GetInput()->GetWholeExtent()[4]) Z = this->GetInput()->GetWholeExtent()[4];
1282 //     else if (Z > this->GetInput()->GetWholeExtent()[5]) Z = this->GetInput()->GetWholeExtent()[5];
1283
1284     if (X >= this->GetInput()->GetWholeExtent()[0] &&
1285         X <= this->GetInput()->GetWholeExtent()[1] &&
1286         Y >= this->GetInput()->GetWholeExtent()[2] &&
1287         Y <= this->GetInput()->GetWholeExtent()[3] &&
1288         Z >= this->GetInput()->GetWholeExtent()[4] &&
1289         Z <= this->GetInput()->GetWholeExtent()[5]) {
1290
1291
1292       int ix, iy, iz;
1293       double value = this->GetScalarComponentAsDouble(this->GetInput(), X, Y, Z, ix, iy, iz);
1294
1295       if(ImageActor->GetVisibility())
1296         worldPos << "data value : " << value << std::endl;
1297
1298       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1299                           << lrint(mCurrent[1]) << ' '
1300                           << lrint(mCurrent[2]) << ' '
1301                           << mCurrentTSlice
1302                           << std::endl;
1303       worldPos << "pixel : " << ix << ' '
1304                              << iy << ' '
1305                              << iz << ' '
1306                              << mCurrentTSlice
1307                              << std::endl;
1308     }
1309     ca->SetText(1,worldPos.str().c_str());
1310   }
1311
1312   if (pdmA->GetVisibility()) {
1313     double x = mCursor[0];
1314     double y = mCursor[1];
1315     double z = mCursor[2];
1316     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1317     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1318     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1319
1320     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1321         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1322         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1323         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1324         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1325         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1326       vtkRenderer * renderer = this->Renderer;
1327
1328       renderer->WorldToView(x,y,z);
1329       renderer->ViewToNormalizedViewport(x,y,z);
1330       renderer->NormalizedViewportToViewport(x,y);
1331       renderer->ViewportToNormalizedDisplay(x,y);
1332       renderer->NormalizedDisplayToDisplay(x,y);
1333       crossCursor->SetFocalPoint(x,y,z);
1334     } else
1335       crossCursor->SetFocalPoint(-1,-1,z);
1336   }
1337
1338
1339   if (mOverlay && mOverlayActor->GetVisibility()) {
1340     if(mLinkOverlayWindowLevel) {
1341       mOverlayMapper->SetWindow(this->GetColorWindow());
1342       mOverlayMapper->SetLevel(this->GetColorLevel());
1343     }
1344     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1345     mOverlayMapper->GetOutput()->Update();
1346     mOverlayMapper->Update();
1347   }
1348   if (mLandMapper)
1349     UpdateLandmarks();
1350
1351   this->GetRenderWindow()->Render();
1352 }
1353 //----------------------------------------------------------------------------
1354
1355
1356 //----------------------------------------------------------------------------
1357 void vvSlicer::UpdateCursorPosition()
1358 {
1359   pdmA->SetVisibility(true);
1360   mCursor[0] = mCurrent[0];
1361   mCursor[1] = mCurrent[1];
1362   mCursor[2] = mCurrent[2];
1363   mCursor[3] = mCurrentTSlice;
1364 }
1365 //----------------------------------------------------------------------------
1366
1367
1368 //----------------------------------------------------------------------------
1369 void vvSlicer::UpdateLandmarks()
1370 {
1371   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1372   if (pd->GetPoints()) {
1373     mLandGlyph->SetRange(0,1);
1374     mLandGlyph->Modified();
1375     mLandGlyph->Update();
1376
1377     mClipBox->Modified();
1378     mLandClipper->Update();
1379     mLandMapper->Update();
1380   }
1381
1382 }
1383 //----------------------------------------------------------------------------
1384
1385
1386 //----------------------------------------------------------------------------
1387 void vvSlicer::SetSlice(int slice)
1388 {
1389   int *range = this->GetSliceRange();
1390   if (range) {
1391     if (slice < range[0]) {
1392       slice = range[0];
1393     } else if (slice > range[1]) {
1394       slice = range[1];
1395     }
1396   }
1397
1398   if (this->Slice == slice) {
1399     return;
1400   }
1401
1402   this->Slice = slice;
1403   SetContourSlice();
1404   this->Modified();
1405   this->UpdateDisplayExtent();
1406
1407   // Seems to work without this line
1408   //this->Render();
1409 }
1410 //----------------------------------------------------------------------------
1411
1412
1413 //----------------------------------------------------------------------------
1414 void vvSlicer::SetContourSlice()
1415 {
1416   if (mSurfaceCutActors.size() > 0)
1417     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1418          i!=mSurfaceCutActors.end(); i++) {
1419
1420       (*i)->SetSlicingOrientation(this->SliceOrientation);
1421       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1422                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1423     }
1424 }
1425 //----------------------------------------------------------------------------
1426
1427
1428 //----------------------------------------------------------------------------
1429 void vvSlicer::ForceUpdateDisplayExtent()
1430 {
1431   this->UpdateDisplayExtent();
1432 }
1433 //----------------------------------------------------------------------------
1434
1435
1436 //----------------------------------------------------------------------------
1437 int* vvSlicer::GetDisplayExtent()
1438 {
1439   return this->GetImageActor()->GetDisplayExtent();
1440 }
1441 //----------------------------------------------------------------------------
1442
1443
1444 //----------------------------------------------------------------------------
1445 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1446 {
1447   this->Superclass::PrintSelf(os, indent);
1448 }
1449 //----------------------------------------------------------------------------
1450
1451 //----------------------------------------------------------------------------
1452 void vvSlicer::SetVFColor(double r, double g, double b)
1453 {
1454   double mVFColorHSV[3];
1455   mVFColor[0] = r;
1456   mVFColor[1] = g;
1457   mVFColor[2] = b;
1458
1459   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1460   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1461   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1462   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1463
1464   this->Render();
1465 }
1466