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