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   std::string text = "F1 = sagital; F2 = coronal; F3 = axial\n";
 102   text += "F5 = horizontal flip; F6 = vertical flip\n\n";
 103   text += "0,1,2,3,4,5 : preset windowing\n";
 104   text += "6,7,8,9 : preset colormap\n";
 105   text += "z : local windowing\n";
 106   text += "r : reset view\n";
 107   text += "l : reload image\n";
 108   text += "f : fly to mouse position\n";
 109   text += "g : go to cross hair position\n\n";
 110   text += "Up,down : change slice\n";
 111   text += "Left,right : change tenporal slice\n\n";
 112   text += "Scrollbar (or w/x) : zoom in/out\n";
 113   text += "left button : synchronize all views\n";
 114   text += "middle button : grab image\n";
 115   text += "right button : change windowing\n";
 116
 117   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 118   crossCursor->AllOff();
 119   crossCursor->AxesOn();
 120   crossCursor->SetTranslationMode(1);
 121   crossCursor->SetRadius(2);
 122
 123   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 124   pdm->SetInput(crossCursor->GetOutput());
 125
 126   pdmA = vtkSmartPointer<vtkActor2D>::New();
 127   pdmA->SetMapper(pdm);
 128   pdmA->GetProperty()->SetColor(255,10,212);
 129   pdmA->SetVisibility(0);
 130   pdmA->SetPickable(0);
 131
 132   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 133   ca->GetTextProperty()->SetColor(255,10,212);
 134   ca->SetVisibility(1);
 135   mFileName = "";
 136
 137   mVF = NULL;
 138   mOverlay = NULL;
 139   mFusion = NULL;
 140   mLandmarks = NULL;
 141
 142   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 143   //legend->SetTitle("test!");
 144   legend->SetPosition(0.82,0.18);
 145   legend->SetWidth(0.1);
 146   legend->SetVisibility(0);
 147   legend->SetLabelFormat("%.1f");
 148   this->GetRenderer()->AddActor(legend);
 149
 150   this->WindowLevel->Delete();
 151   this->WindowLevel = vvImageMapToWLColors::New();
 152
 153   this->InstallPipeline();
 154 }
 155 //------------------------------------------------------------------------------
 156
 157
 158 //------------------------------------------------------------------------------
 159 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 160 {
 161   return mOverlayMapper.GetPointer();
 162 }
 163 //------------------------------------------------------------------------------
 164
 165
 166 //------------------------------------------------------------------------------
 167 vvBlendImageActor* vvSlicer::GetOverlayActor()
 168 {
 169   return mOverlayActor.GetPointer();
 170 }
 171 //------------------------------------------------------------------------------
 172
 173
 174 //------------------------------------------------------------------------------
 175 vtkImageMapToWindowLevelColors* vvSlicer::GetFusionMapper()
 176 {
 177   return mFusionMapper.GetPointer();
 178 }
 179 //------------------------------------------------------------------------------
 180
 181
 182 //------------------------------------------------------------------------------
 183 vtkImageActor* vvSlicer::GetFusionActor()
 184 {
 185   return mFusionActor.GetPointer();
 186 }
 187 //------------------------------------------------------------------------------
 188
 189
 190 //------------------------------------------------------------------------------
 191 vtkActor* vvSlicer::GetVFActor()
 192 {
 193   return mVFActor.GetPointer();
 194 }
 195 //------------------------------------------------------------------------------
 196
 197
 198 //------------------------------------------------------------------------------
 199 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 200 {
 201   return ca.GetPointer();
 202 }
 203 //------------------------------------------------------------------------------
 204
 205
 206 //------------------------------------------------------------------------------
 207 void vvSlicer::EnableReducedExtent(bool b)
 208 {
 209   mUseReducedExtent = b;
 210 }
 211 //------------------------------------------------------------------------------
 212
 213
 214 //------------------------------------------------------------------------------
 215 void vvSlicer::SetReducedExtent(int * ext)
 216 {
 217   copyExtent(ext, mReducedExtent);
 218 }
 219 //------------------------------------------------------------------------------
 220
 221
 222 //------------------------------------------------------------------------------
 223 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 224 {
 225
 226   mSurfaceCutActors.push_back(new vvMeshActor());
 227   if (propagate)
 228     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 229   else
 230     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 231   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 232   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 233
 234   SetContourSlice();
 235 }
 236 //------------------------------------------------------------------------------
 237
 238
 239 //------------------------------------------------------------------------------
 240 void vvSlicer::ToggleContourSuperposition()
 241 {
 242   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 243        i!=mSurfaceCutActors.end(); i++)
 244     (*i)->ToggleSuperposition();
 245 }
 246 //------------------------------------------------------------------------------
 247
 248
 249 //------------------------------------------------------------------------------
 250 void vvSlicer::SetCursorColor(int r,int g, int b)
 251 {
 252   pdmA->GetProperty()->SetColor(r,g,b);
 253 }
 254 //------------------------------------------------------------------------------
 255
 256
 257 //------------------------------------------------------------------------------
 258 void vvSlicer::SetCursorVisibility(bool s)
 259 {
 260   pdmA->SetVisibility(s);
 261 }
 262 //------------------------------------------------------------------------------
 263
 264
 265 //------------------------------------------------------------------------------
 266 bool vvSlicer::GetCursorVisibility()
 267 {
 268   return pdmA->GetVisibility();
 269 }
 270 //------------------------------------------------------------------------------
 271
 272
 273 //------------------------------------------------------------------------------
 274 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 275 {
 276   ca->SetVisibility(s);
 277 }
 278 //------------------------------------------------------------------------------
 279
 280
 281 //------------------------------------------------------------------------------
 282 bool vvSlicer::GetCornerAnnotationVisibility()
 283 {
 284   return ca->GetVisibility();
 285 }
 286 //------------------------------------------------------------------------------
 287
 288
 289 //------------------------------------------------------------------------------
 290 vvSlicer::~vvSlicer()
 291 {
 292   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 293        i!=mSurfaceCutActors.end(); i++)
 294     delete (*i);
 295   delete [] mReducedExtent;
 296 }
 297 //------------------------------------------------------------------------------
 298
 299
 300 //------------------------------------------------------------------------------
 301 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 302 {
 303   mCurrent[0] = x;
 304   mCurrent[1] = y;
 305   mCurrent[2] = z;
 306   mCurrentTSlice = t;
 307 }
 308 //------------------------------------------------------------------------------
 309
 310
 311 //------------------------------------------------------------------------------
 312 void vvSlicer::SetImage(vvImage::Pointer image)
 313 {
 314   if (image->GetVTKImages().size()) {
 315     mImage = image;
 316
 317     if (!mImageReslice) {
 318       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 319       mImageReslice->SetInterpolationModeToLinear();
 320       mImageReslice->AutoCropOutputOn();
 321       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 322     }
 323     mImageReslice->SetResliceTransform(mImage->GetTransform());
 324     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 325     mImageReslice->UpdateInformation();
 326
 327     this->Superclass::SetInput(mImageReslice->GetOutput());
 328
 329     int extent[6];
 330     this->GetInput()->GetWholeExtent(extent);
 331
 332     // Prevent crash when reload -> change slice if outside extent
 333     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 334       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 335     }
 336
 337     // Make sure that the required part image has been computed
 338     extent[SliceOrientation*2] = Slice;
 339     extent[SliceOrientation*2+1] = Slice;
 340     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 341     mImageReslice->GetOutput()->Update();
 342
 343     this->UpdateDisplayExtent();
 344
 345     mCurrentTSlice = 0;
 346     ca->SetText(0,mFileName.c_str());
 347   }
 348 }
 349 //------------------------------------------------------------------------------
 350
 351
 352 //------------------------------------------------------------------------------
 353 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 354 {
 355   if (overlay->GetVTKImages().size()) {
 356     mOverlay = overlay;
 357
 358     if (!mOverlayReslice) {
 359       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 360       mOverlayReslice->SetInterpolationModeToLinear();
 361       mOverlayReslice->AutoCropOutputOn();
 362       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 363     }
 364     mOverlayReslice->SetResliceTransform(mOverlay->GetTransform());
 365     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 366
 367     if (!mOverlayMapper)
 368       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 369     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 370
 371     if (!mOverlayActor) {
 372       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 373       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 374       mOverlayActor->SetPickable(0);
 375       mOverlayActor->SetVisibility(false);
 376       mOverlayActor->SetOpacity(0.5);
 377     }
 378
 379     //stupid but necessary : the Overlay need to be rendered before fusion
 380     if (mFusionActor) {
 381       this->GetRenderer()->RemoveActor(mFusionActor);
 382       this->GetRenderer()->AddActor(mOverlayActor);
 383       this->GetRenderer()->AddActor(mFusionActor);
 384     } else
 385       this->GetRenderer()->AddActor(mOverlayActor);
 386
 387     //Synchronize orientation and slice
 388     this->SetSliceOrientation(this->SliceOrientation);
 389     this->SetTSlice(mCurrentTSlice);
 390   }
 391 }
 392 //------------------------------------------------------------------------------
 393
 394
 395 //------------------------------------------------------------------------------
 396 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 397 {
 398   if (fusion->GetVTKImages().size()) {
 399     mFusion = fusion;
 400
 401     if (!mFusionReslice) {
 402       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 403       mFusionReslice->SetInterpolationModeToLinear();
 404       mFusionReslice->AutoCropOutputOn();
 405       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 406     }
 407     mFusionReslice->SetResliceTransform(mFusion->GetTransform());
 408     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 409
 410     if (!mFusionMapper)
 411       mFusionMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 412     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 413
 414     if (!mFusionActor) {
 415       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 416       mFusionActor->SetInput(mFusionMapper->GetOutput());
 417       mFusionActor->SetPickable(0);
 418       mFusionActor->SetVisibility(false);
 419       mFusionActor->SetOpacity(0.7);
 420       this->GetRenderer()->AddActor(mFusionActor);
 421     }
 422
 423     //Synchronize orientation and slice
 424     this->SetSliceOrientation(this->SliceOrientation);
 425     this->SetTSlice(mCurrentTSlice);
 426   }
 427 }
 428 //------------------------------------------------------------------------------
 429
 430
 431 //------------------------------------------------------------------------------
 432 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 433 {
 434   if (actor_type == "vector") {
 435     this->mVFActor->SetVisibility(vis);
 436   }
 437   if (actor_type == "overlay") {
 438     this->mOverlayActor->SetVisibility(vis);
 439   }
 440   if (actor_type == "fusion") {
 441     this->mFusionActor->SetVisibility(vis);
 442   }
 443   if (actor_type == "contour")
 444     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 445   UpdateDisplayExtent();
 446 }
 447 //------------------------------------------------------------------------------
 448
 449
 450 //------------------------------------------------------------------------------
 451 void vvSlicer::SetVF(vvImage::Pointer vf)
 452 {
 453   if (vf->GetVTKImages().size()) {
 454     mVF = vf;
 455
 456     if (!mAAFilter) {
 457       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 458       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 459       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 460     }
 461     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 462     mAAFilter->SetInput(mVOIFilter->GetOutput());
 463     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 464     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 465
 466     if (!mArrow)
 467       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 468     mArrow->SetGlyphTypeToSpecificArrow();
 469     mArrow->SetScale(mScale);
 470     mArrow->FilledOff();
 471
 472     // Glyph the gradient vector (with arrows)
 473     if (!mGlyphFilter)
 474       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 475     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 476     mGlyphFilter->SetSource(mArrow->GetOutput());
 477     mGlyphFilter->ScalingOn();
 478     mGlyphFilter->SetScaleModeToScaleByVector();
 479     mGlyphFilter->OrientOn();
 480     mGlyphFilter->SetVectorModeToUseVector();
 481     mGlyphFilter->SetColorModeToColorByVector();
 482
 483     if (!mVFColorLUT)
 484       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 485
 486     double mVFColorHSV[3];
 487     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 488     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 489     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 490     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 491
 492     if (!mVFMapper)
 493       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 494     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 495     mVFMapper->ImmediateModeRenderingOn();
 496     mVFMapper->SetLookupTable(mVFColorLUT);
 497
 498     if (!mVFActor)
 499       mVFActor = vtkSmartPointer<vtkActor>::New();
 500     mVFActor->SetMapper(mVFMapper);
 501     mVFActor->SetPickable(0);
 502     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 503     this->UpdateDisplayExtent();
 504     this->GetRenderer()->AddActor(mVFActor);
 505
 506     //Synchronize slice
 507     SetTSlice(mCurrentTSlice);
 508   }
 509 }
 510 //------------------------------------------------------------------------------
 511
 512
 513 //------------------------------------------------------------------------------
 514 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 515 {
 516   mLandmarks = landmarks;
 517   if (landmarks) {
 518
 519     if (!mCross)
 520       mCross = vtkSmartPointer<vtkCursor3D>::New();
 521     mCross->SetFocalPoint(0.0,0.0,0.0);
 522     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 523     mCross->AllOff();
 524     mCross->AxesOn();
 525
 526     if (!mLandGlyph)
 527       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 528     mLandGlyph->SetSource(mCross->GetOutput());
 529     mLandGlyph->SetInput(landmarks->GetOutput());
 530     //mLandGlyph->SetIndexModeToScalar();
 531     mLandGlyph->SetRange(0,1);
 532     mLandGlyph->ScalingOff();
 533
 534     mLandGlyph->SetColorModeToColorByScalar();
 535
 536     if (!mClipBox)
 537       mClipBox = vtkSmartPointer<vtkBox>::New();
 538     if (!mLandClipper)
 539       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 540     mLandClipper->InsideOutOn();
 541     mLandClipper->SetInput(mLandGlyph->GetOutput());
 542     mLandClipper->SetClipFunction(mClipBox);
 543
 544     if (!mLandMapper)
 545       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 546     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 547     //mLandMapper->ScalarVisibilityOff();
 548
 549     if (!mLandActor)
 550       mLandActor = vtkSmartPointer<vtkActor>::New();
 551     mLandActor->SetMapper(mLandMapper);
 552     mLandActor->GetProperty()->SetColor(255,10,212);
 553     mLandActor->SetPickable(0);
 554     mLandActor->SetVisibility(true);
 555     this->UpdateDisplayExtent();
 556     this->GetRenderer()->AddActor(mLandActor);
 557   }
 558 }
 559 //------------------------------------------------------------------------------
 560
 561 //------------------------------------------------------------------------------
 562 //FIXME: this function leaks memory, we should fix it someday :)
 563 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 564 {
 565   if (actor_type == "vector") {
 566     Renderer->RemoveActor(mVFActor);
 567     mGlyphFilter=NULL;
 568     mVF = NULL;
 569     mArrow = NULL;
 570     mAAFilter=NULL;
 571     mVOIFilter = NULL;
 572     mVFMapper = NULL;
 573     mVFActor = NULL;
 574   }
 575   if (actor_type == "overlay") {
 576     Renderer->RemoveActor(mOverlayActor);
 577     mOverlay = NULL;
 578     mOverlayActor = NULL;
 579     mOverlayMapper = NULL;
 580   }
 581   if (actor_type == "fusion") {
 582     Renderer->RemoveActor(mFusionActor);
 583     mFusion = NULL;
 584     mFusionActor = NULL;
 585     mFusionMapper = NULL;
 586   }
 587   if (actor_type == "contour") {
 588     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 589     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 590   }
 591 }
 592 //------------------------------------------------------------------------------
 593
 594
 595 //------------------------------------------------------------------------------
 596 void vvSlicer::SetVFSubSampling(int sub)
 597 {
 598   if (mVOIFilter) {
 599     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 600     mSubSampling = sub;
 601   }
 602   UpdateDisplayExtent();
 603   Render();
 604 }
 605 //------------------------------------------------------------------------------
 606
 607
 608 //------------------------------------------------------------------------------
 609 void vvSlicer::SetVFScale(int scale)
 610 {
 611   mScale = scale;
 612   if (mArrow)
 613     mArrow->SetScale(mScale);
 614   UpdateDisplayExtent();
 615   Render();
 616 }
 617 //------------------------------------------------------------------------------
 618
 619 //------------------------------------------------------------------------------
 620 void vvSlicer::SetVFWidth(int width)
 621 {
 622   mVFWidth = width;
 623   if (mVFActor)
 624     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 625   UpdateDisplayExtent();
 626   Render();
 627 }
 628 //------------------------------------------------------------------------------
 629
 630
 631 //------------------------------------------------------------------------------
 632 void vvSlicer::SetVFLog(int log)
 633 {
 634   mVFLog = log;
 635   if (mGlyphFilter) {
 636     mGlyphFilter->SetUseLog(mVFLog);
 637     mGlyphFilter->Modified();
 638   }
 639   UpdateDisplayExtent();
 640   Render();
 641 }
 642 //------------------------------------------------------------------------------
 643
 644
 645 //------------------------------------------------------------------------------
 646 void vvSlicer::SetTSlice(int t)
 647 {
 648   if (t < 0)
 649     t = 0;
 650   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 651     t = mImage->GetVTKImages().size() -1;
 652
 653   if (mCurrentTSlice == t) return;
 654
 655   mCurrentTSlice = t;
 656   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 657   if (mVF && mVFActor->GetVisibility()) {
 658     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 659       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 660   }
 661   if (mOverlay && mOverlayActor->GetVisibility()) {
 662     if (mOverlay->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 663       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentTSlice] );
 664   }
 665   if (mFusion && mFusionActor->GetVisibility()) {
 666     if (mFusion->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 667       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentTSlice]);
 668   }
 669   if (mSurfaceCutActors.size() > 0)
 670     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 671          i!=mSurfaceCutActors.end(); i++)
 672       (*i)->SetTimeSlice(mCurrentTSlice);
 673   UpdateDisplayExtent();
 674 }
 675 //------------------------------------------------------------------------------
 676
 677
 678 //------------------------------------------------------------------------------
 679 int vvSlicer::GetTSlice()
 680 {
 681   return mCurrentTSlice;
 682 }
 683 //------------------------------------------------------------------------------
 684
 685 //------------------------------------------------------------------------------
 686 void vvSlicer::SetSliceOrientation(int orientation)
 687 {
 688   //if 2D image, force to watch in Axial View
 689   int extent[6];
 690   this->GetInput()->GetWholeExtent(extent);
 691   if (extent[5]-extent[4] <= 2)
 692     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 693
 694   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 695       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 696     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 697     return;
 698   }
 699
 700   this->SliceOrientation = orientation;
 701
 702   if(mFusion)
 703     AdjustResliceToSliceOrientation(mFusionReslice);
 704
 705   if(mOverlay)
 706     AdjustResliceToSliceOrientation(mOverlayReslice);
 707
 708   // Update the viewer
 709   int *range = this->GetSliceRange();
 710   if (range)
 711     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 712
 713   // Go to current cursor position
 714   // double* cursorPos = GetCursorPosition();
 715   // DDV(cursorPos, 3);
 716   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 717
 718   this->UpdateOrientation();
 719   this->UpdateDisplayExtent();
 720
 721   if (this->Renderer && this->GetInput()) {
 722     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 723     this->Renderer->ResetCamera();
 724     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 725   }
 726
 727   SetContourSlice();
 728 }
 729 //----------------------------------------------------------------------------
 730
 731 //------------------------------------------------------------------------------
 732 // This function ensures that we sample the slices of a vtkImageReslice filter
 733 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 734 // In other words, we change the grid of the reslice in the same way as the grid
 735 // of the displayed image in the slicing direction.
 736 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 737 {
 738   // Reset autocrop
 739   double origin[3] = {VTK_DOUBLE_MAX, VTK_DOUBLE_MAX, VTK_DOUBLE_MAX};
 740   double spacing[3] = {VTK_DOUBLE_MAX, VTK_DOUBLE_MAX, VTK_DOUBLE_MAX};
 741   reslice->SetOutputOrigin(origin);
 742   reslice->SetOutputSpacing(spacing);
 743   reslice->GetOutput()->UpdateInformation();
 744   reslice->GetOutput()->GetOrigin(origin);
 745   reslice->GetOutput()->GetSpacing(spacing);
 746
 747   // Use similar spacing as the image in the direction SliceOrientation
 748   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 749
 750   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 751   // Step 1: from world coordinates to image coordinates
 752   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 753   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 754   // Step 2: round to superior grid positionInc
 755   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 756   // Step 3: back to world coordinates
 757   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 758   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 759
 760   // Set new spacing and origin
 761   reslice->SetOutputOrigin(origin);
 762   reslice->SetOutputSpacing(spacing);
 763   reslice->UpdateInformation();
 764 }
 765 //------------------------------------------------------------------------------
 766
 767 //----------------------------------------------------------------------------
 768 int * vvSlicer::GetExtent(){
 769   int *w_ext;
 770   if (mUseReducedExtent) {
 771     w_ext = mReducedExtent;
 772   } else w_ext = GetInput()->GetWholeExtent();
 773   return w_ext;
 774 }
 775 //----------------------------------------------------------------------------
 776
 777
 778 //----------------------------------------------------------------------------
 779 int vvSlicer::GetOrientation()
 780 {
 781   return this->SliceOrientation;
 782 }
 783 //----------------------------------------------------------------------------
 784
 785
 786 //----------------------------------------------------------------------------
 787 void vvSlicer::UpdateDisplayExtent()
 788 {
 789   vtkImageData *input = this->GetInput();
 790   if (!input || !this->ImageActor) {
 791     return;
 792   }
 793   input->UpdateInformation();
 794
 795   // Local copy of extent
 796   int w_ext[6];
 797   copyExtent(GetExtent(), w_ext);
 798   // Set slice value
 799   w_ext[ this->SliceOrientation*2   ] = this->Slice;
 800   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
 801
 802   // Image actor
 803   this->ImageActor->SetDisplayExtent(w_ext);
 804
 805   // Overlay image actor
 806   if (mOverlay && mOverlayActor->GetVisibility()) {
 807     int overExtent[6];
 808     mOverlayReslice->GetOutput()->UpdateInformation();
 809     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 810     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 811     mOverlayActor->SetDisplayExtent( overExtent );
 812   }
 813
 814   // Fusion image actor
 815   if (mFusion && mFusionActor->GetVisibility()) {
 816     int fusExtent[6];
 817     mFusionReslice->GetOutput()->UpdateInformation();
 818     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 819     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 820     mFusionActor->SetDisplayExtent(fusExtent);
 821   }
 822
 823   // Vector field actor
 824   double* camera = Renderer->GetActiveCamera()->GetPosition();
 825   double* image_bounds = ImageActor->GetBounds();
 826   double position[3] = {0, 0, 0};
 827   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 828
 829   //print_vector<double, 6>("camera", camera);
 830   //print_vector<double, 6>("image_bounds", image_bounds);
 831   //print_vector<double, 3>("position", position);
 832
 833   // find where to place the VF actor. to deal with
 834   // z-buffer issues, the VF is placed right in front of the image,
 835   // subject to a small offset. the position actually depends on the
 836   // the location of the camera relative to the image.
 837   double offset = 1;
 838   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 839     offset = -1;
 840
 841   if (mVF && mVFActor->GetVisibility()) {
 842     int vfExtent[6];
 843     mVF->GetVTKImages()[0]->UpdateInformation();
 844     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 845     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 846     mVOIFilter->SetVOI(vfExtent);
 847     int orientation[3] = {1,1,1};
 848     orientation[this->SliceOrientation] = 0;
 849     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 850     mVFMapper->Update();
 851
 852     position[this->SliceOrientation] += offset;
 853     mVFActor->SetPosition(position);
 854   }
 855
 856   // Landmarks actor
 857   if (mLandActor) {
 858     if (mClipBox) {
 859       double bounds [6];
 860       for(unsigned int i=0; i<6; i++)
 861         bounds[i] = ImageActor->GetBounds()[i];
 862       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 863       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 864       mClipBox->SetBounds(bounds);
 865       UpdateLandmarks();
 866     }
 867
 868     position[this->SliceOrientation] = offset;
 869     mLandActor->SetPosition(position);
 870   }
 871
 872   // Figure out the correct clipping range
 873   if (this->Renderer) {
 874     if (this->InteractorStyle &&
 875         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 876       this->Renderer->ResetCameraClippingRange();
 877     } else {
 878       vtkCamera *cam = this->Renderer->GetActiveCamera();
 879       if (cam) {
 880         double bounds[6];
 881         this->ImageActor->GetBounds(bounds);
 882         double spos = (double)bounds[this->SliceOrientation * 2];
 883         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 884         double range = fabs(spos - cpos);
 885         double *spacing = input->GetSpacing();
 886         double avg_spacing =
 887           ((double)spacing[0] + (double)spacing[1] + (double)spacing[2]) / 3.0;
 888         cam->SetClippingRange(range - avg_spacing * 3.0, range + avg_spacing * 3.0);
 889       }
 890     }
 891   }
 892
 893 }
 894 //----------------------------------------------------------------------------
 895
 896 //----------------------------------------------------------------------------
 897 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 898                                                 vtkImageData *targetImage, int targetExtent[6])
 899 {
 900   double dExtents[6];
 901   for(unsigned int i=0; i<6; i++) {
 902     // From source voxel coordinates to world coordinates
 903     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 904
 905     // From world coordinates to floating point target voxel coordinates
 906     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 907
 908     // Round to nearest
 909     targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 910   }
 911 }
 912 //----------------------------------------------------------------------------
 913
 914 //----------------------------------------------------------------------------
 915 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 916 {
 917   bool out = false;
 918   int maxBound = 6;
 919
 920   //2D overlay on 3D image specific case
 921   if (refExtent[4] == refExtent[5]) {
 922     maxBound = 4;
 923     extent[4] = refExtent[4];
 924     extent[5] = refExtent[5];
 925   }
 926
 927   for (int i = 0; i < maxBound; i = i+2) {
 928     //if we are totally outside the image
 929     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 930       out = true;
 931       break;
 932     }
 933     //crop to the limit of the image
 934     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 935     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 936     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 937     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 938   }
 939   if (out)
 940     for (int i = 0; i < maxBound; i = i+2) {
 941       extent[i] = refExtent[i];
 942       extent[i+1] = refExtent[i];
 943     }
 944 }
 945 //----------------------------------------------------------------------------
 946
 947
 948 //----------------------------------------------------------------------------
 949 void vvSlicer::UpdateOrientation()
 950 {
 951   // Set the camera position
 952   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
 953   if (cam) {
 954     switch (this->SliceOrientation) {
 955     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 956       cam->SetFocalPoint(0,0,0);
 957       cam->SetPosition(0,0,-1); // -1 if medical ?
 958       cam->SetViewUp(0,-1,0);
 959       break;
 960
 961     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 962       cam->SetFocalPoint(0,0,0);
 963       cam->SetPosition(0,-1,0); // 1 if medical ?
 964       cam->SetViewUp(0,0,1);
 965       break;
 966
 967     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 968       cam->SetFocalPoint(0,0,0);
 969       cam->SetPosition(-1,0,0); // -1 if medical ?
 970       cam->SetViewUp(0,0,1);
 971       break;
 972     }
 973   }
 974 }
 975 //----------------------------------------------------------------------------
 976
 977
 978 //----------------------------------------------------------------------------
 979 void vvSlicer::SetOpacity(double s)
 980 {
 981   this->GetImageActor()->SetOpacity(s);
 982 }
 983 //----------------------------------------------------------------------------
 984
 985
 986 //----------------------------------------------------------------------------
 987 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
 988 {
 989   this->Superclass::SetRenderWindow(rw);
 990   this->SetupInteractor(rw->GetInteractor());
 991   ca->SetImageActor(this->GetImageActor());
 992   ca->SetWindowLevel(this->GetWindowLevel());
 993   ca->SetText(2, "<slice>");
 994   ca->SetText(3, "<window>\n<level>");
 995
 996   double bounds[6];
 997   double max = 65000;
 998
 999   bounds[0] = -max;
1000   bounds[1] = max;
1001   bounds[2] = -max;
1002   bounds[3] = max;
1003   bounds[4] = -max;
1004   bounds[5] = max;
1005
1006   crossCursor->SetModelBounds(bounds);
1007   this->GetRenderer()->AddActor(pdmA);
1008   this->GetRenderer()->AddActor(ca);
1009   this->GetRenderer()->ResetCamera();
1010
1011   //this is just a mapping between the labeling of the orientations presented to the user and
1012   //the one used by vtk
1013   SetSliceOrientation(2-(orientation%3));
1014   ResetCamera();
1015 }
1016 //----------------------------------------------------------------------------
1017
1018
1019 //----------------------------------------------------------------------------
1020 void vvSlicer::ResetCamera()
1021 {
1022   this->GetRenderer()->ResetCamera();
1023 }
1024 //----------------------------------------------------------------------------
1025
1026
1027 //----------------------------------------------------------------------------
1028 void vvSlicer::SetDisplayMode(bool i)
1029 {
1030   this->GetImageActor()->SetVisibility(i);
1031   this->GetAnnotation()->SetVisibility(i);
1032   this->GetRenderer()->SetDraw(i);
1033   if (mLandActor)
1034     mLandActor->SetVisibility(i);
1035   pdmA->SetVisibility(i);
1036   if (i)
1037     UpdateDisplayExtent();
1038 }
1039 //----------------------------------------------------------------------------
1040
1041
1042 //----------------------------------------------------------------------------
1043 void vvSlicer::FlipHorizontalView()
1044 {
1045   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1046   if (cam) {
1047     double *position = cam->GetPosition();
1048     switch (this->SliceOrientation) {
1049     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1050       cam->SetPosition(position[0],position[1],-position[2]);
1051       break;
1052
1053     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1054       cam->SetPosition(position[0],-position[1],position[2]);
1055       break;
1056
1057     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1058       cam->SetPosition(-position[0],position[1],position[2]);
1059       break;
1060     }
1061     this->Renderer->ResetCameraClippingRange();
1062     this->UpdateDisplayExtent();
1063   }
1064 }
1065 //----------------------------------------------------------------------------
1066
1067
1068 //----------------------------------------------------------------------------
1069 void vvSlicer::FlipVerticalView()
1070 {
1071   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1072   if (cam) {
1073     FlipHorizontalView();
1074     double *viewup = cam->GetViewUp();
1075     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1076     this->UpdateDisplayExtent();
1077   }
1078 }
1079 //----------------------------------------------------------------------------
1080
1081
1082 //----------------------------------------------------------------------------
1083 void vvSlicer::SetColorWindow(double window)
1084 {
1085   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1086   if ( LUT ) {
1087     double level = this->GetWindowLevel()->GetLevel();
1088     LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
1089     LUT->Build();
1090   }
1091   this->vtkImageViewer2::SetColorWindow(window);
1092 }
1093 //----------------------------------------------------------------------------
1094
1095
1096 //----------------------------------------------------------------------------
1097 void vvSlicer::SetColorLevel(double level)
1098 {
1099   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1100   if ( LUT ) {
1101     double window = this->GetWindowLevel()->GetWindow();
1102     LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
1103     LUT->Build();
1104   }
1105   this->vtkImageViewer2::SetColorLevel(level);
1106 }
1107 //----------------------------------------------------------------------------
1108
1109 //----------------------------------------------------------------------------
1110 // Returns the min an the max value in a 41x41 region around the mouse pointer
1111 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max)
1112 {
1113   //Get mouse pointer position in view coordinates
1114   double fLocalExtents[6];
1115   for(int i=0; i<3; i++) {
1116     fLocalExtents[i*2  ] = mCurrent[i];
1117     fLocalExtents[i*2+1] = mCurrent[i];
1118   }
1119   this->Renderer->WorldToView(fLocalExtents[0], fLocalExtents[2], fLocalExtents[4]);
1120   this->Renderer->WorldToView(fLocalExtents[1], fLocalExtents[3], fLocalExtents[5]);
1121   for(int i=0; i<3; i++) {
1122     if (i!=SliceOrientation) { //SR: assumes that SliceOrientation is valid in ViewCoordinates (???)
1123       fLocalExtents[i*2  ] -= 0.2;
1124       fLocalExtents[i*2+1] += 0.2;
1125     }
1126   }
1127   this->Renderer->ViewToWorld(fLocalExtents[0], fLocalExtents[2], fLocalExtents[4]);
1128   this->Renderer->ViewToWorld(fLocalExtents[1], fLocalExtents[3], fLocalExtents[5]);
1129
1130   //Convert to image pixel coordinates (rounded)
1131   int iLocalExtents[6];
1132   for(int i=0; i<3; i++) {
1133     fLocalExtents[i*2  ] = (fLocalExtents[i*2  ] - this->GetInput()->GetOrigin()[i])/this->GetInput()->GetSpacing()[i];
1134     fLocalExtents[i*2+1] = (fLocalExtents[i*2+1] - this->GetInput()->GetOrigin()[i])/this->GetInput()->GetSpacing()[i];
1135
1136     iLocalExtents[i*2  ] = lrint(fLocalExtents[i*2  ]);
1137     iLocalExtents[i*2+1] = lrint(fLocalExtents[i*2+1]);
1138
1139     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1140       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1141   }
1142
1143   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1144   voiFilter->SetInput(this->GetInput());
1145   voiFilter->SetVOI(iLocalExtents);
1146   voiFilter->Update();
1147   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1148     min = 0;
1149     max = 0;
1150     return;
1151   }
1152
1153   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1154   accFilter->SetInput(voiFilter->GetOutput());
1155   accFilter->Update();
1156
1157   min = *(accFilter->GetMin());
1158   max = *(accFilter->GetMax());
1159 }
1160 //----------------------------------------------------------------------------
1161
1162 //----------------------------------------------------------------------------
1163 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1164 {
1165   ix = lrint(X);
1166   iy = lrint(Y);
1167   iz = lrint(Z);
1168   if (ix < image->GetWholeExtent()[0] ||
1169       ix > image->GetWholeExtent()[1] ||
1170       iy < image->GetWholeExtent()[2] ||
1171       iy > image->GetWholeExtent()[3] ||
1172       iz < image->GetWholeExtent()[4] ||
1173       iz > image->GetWholeExtent()[5] )
1174     return std::numeric_limits<double>::quiet_NaN();
1175
1176   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1177   image->Update();
1178   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1179 }
1180 //----------------------------------------------------------------------------
1181
1182 //----------------------------------------------------------------------------
1183 void vvSlicer::Render()
1184 {
1185   if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay && !this->mFusion) {
1186     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1187     legend->SetVisibility(1);
1188   } else legend->SetVisibility(0);
1189
1190   if (ca->GetVisibility()) {
1191     std::stringstream worldPos;
1192     double X = (mCurrent[0] - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1193     double Y = (mCurrent[1] - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1194     double Z = (mCurrent[2] - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1195
1196 //     if (X < this->GetInput()->GetWholeExtent()[0]) X = this->GetInput()->GetWholeExtent()[0];
1197 //     else if (X > this->GetInput()->GetWholeExtent()[1]) X = this->GetInput()->GetWholeExtent()[1];
1198 //     if (Y < this->GetInput()->GetWholeExtent()[2]) Y = this->GetInput()->GetWholeExtent()[2];
1199 //     else if (Y > this->GetInput()->GetWholeExtent()[3]) Y = this->GetInput()->GetWholeExtent()[3];
1200 //     if (Z < this->GetInput()->GetWholeExtent()[4]) Z = this->GetInput()->GetWholeExtent()[4];
1201 //     else if (Z > this->GetInput()->GetWholeExtent()[5]) Z = this->GetInput()->GetWholeExtent()[5];
1202
1203     if (X >= this->GetInput()->GetWholeExtent()[0] &&
1204         X <= this->GetInput()->GetWholeExtent()[1] &&
1205         Y >= this->GetInput()->GetWholeExtent()[2] &&
1206         Y <= this->GetInput()->GetWholeExtent()[3] &&
1207         Z >= this->GetInput()->GetWholeExtent()[4] &&
1208         Z <= this->GetInput()->GetWholeExtent()[5]) {
1209
1210
1211       int ix, iy, iz;
1212       double value = this->GetScalarComponentAsDouble(this->GetInput(), X, Y, Z, ix, iy, iz);
1213
1214       worldPos << "data value : " << value << std::endl;
1215       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1216                           << lrint(mCurrent[1]) << ' '
1217                           << lrint(mCurrent[2]) << ' '
1218                           << mCurrentTSlice
1219                           << std::endl;
1220       worldPos << "pixel : " << ix << ' '
1221                              << iy << ' '
1222                              << iz << ' '
1223                              << mCurrentTSlice
1224                              << std::endl;
1225     }
1226     ca->SetText(1,worldPos.str().c_str());
1227   }
1228
1229   if (pdmA->GetVisibility()) {
1230     double x = mCursor[0];
1231     double y = mCursor[1];
1232     double z = mCursor[2];
1233     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1234     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1235     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1236
1237     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1238         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1239         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1240         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1241         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1242         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1243       vtkRenderer * renderer = this->Renderer;
1244
1245       renderer->WorldToView(x,y,z);
1246       renderer->ViewToNormalizedViewport(x,y,z);
1247       renderer->NormalizedViewportToViewport(x,y);
1248       renderer->ViewportToNormalizedDisplay(x,y);
1249       renderer->NormalizedDisplayToDisplay(x,y);
1250       crossCursor->SetFocalPoint(x,y,z);
1251     } else
1252       crossCursor->SetFocalPoint(-1,-1,z);
1253   }
1254
1255
1256   if (mOverlay && mOverlayActor->GetVisibility()) {
1257     mOverlayMapper->SetWindow(this->GetColorWindow());
1258     mOverlayMapper->SetLevel(this->GetColorLevel());
1259     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1260     mOverlayMapper->GetOutput()->Update();
1261     mOverlayMapper->Update();
1262   }
1263   if (mLandMapper)
1264     UpdateLandmarks();
1265
1266   this->GetRenderWindow()->Render();
1267 }
1268 //----------------------------------------------------------------------------
1269
1270
1271 //----------------------------------------------------------------------------
1272 void vvSlicer::UpdateCursorPosition()
1273 {
1274   if (this->GetImageActor()->GetVisibility()) {
1275     pdmA->SetVisibility(true);
1276     mCursor[0] = mCurrent[0];
1277     mCursor[1] = mCurrent[1];
1278     mCursor[2] = mCurrent[2];
1279     mCursor[3] = mCurrentTSlice;
1280   }
1281 }
1282 //----------------------------------------------------------------------------
1283
1284
1285 //----------------------------------------------------------------------------
1286 void vvSlicer::UpdateLandmarks()
1287 {
1288   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1289   if (pd->GetPoints()) {
1290     mLandGlyph->SetRange(0,1);
1291     mLandGlyph->Modified();
1292     mLandGlyph->Update();
1293
1294     mClipBox->Modified();
1295     mLandClipper->Update();
1296     mLandMapper->Update();
1297   }
1298
1299 }
1300 //----------------------------------------------------------------------------
1301
1302
1303 //----------------------------------------------------------------------------
1304 void vvSlicer::SetSlice(int slice)
1305 {
1306   int *range = this->GetSliceRange();
1307   if (range) {
1308     if (slice < range[0]) {
1309       slice = range[0];
1310     } else if (slice > range[1]) {
1311       slice = range[1];
1312     }
1313   }
1314
1315   if (this->Slice == slice) {
1316     return;
1317   }
1318
1319   this->Slice = slice;
1320   SetContourSlice();
1321   this->Modified();
1322   this->UpdateDisplayExtent();
1323
1324   // Seems to work without this line
1325   //this->Render();
1326 }
1327 //----------------------------------------------------------------------------
1328
1329
1330 //----------------------------------------------------------------------------
1331 void vvSlicer::SetContourSlice()
1332 {
1333   if (mSurfaceCutActors.size() > 0)
1334     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1335          i!=mSurfaceCutActors.end(); i++) {
1336
1337       (*i)->SetSlicingOrientation(this->SliceOrientation);
1338       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1339                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1340     }
1341 }
1342 //----------------------------------------------------------------------------
1343
1344
1345 //----------------------------------------------------------------------------
1346 void vvSlicer::ForceUpdateDisplayExtent()
1347 {
1348   this->UpdateDisplayExtent();
1349 }
1350 //----------------------------------------------------------------------------
1351
1352
1353 //----------------------------------------------------------------------------
1354 int* vvSlicer::GetDisplayExtent()
1355 {
1356   return this->GetImageActor()->GetDisplayExtent();
1357 }
1358 //----------------------------------------------------------------------------
1359
1360
1361 //----------------------------------------------------------------------------
1362 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1363 {
1364   this->Superclass::PrintSelf(os, indent);
1365 }
1366 //----------------------------------------------------------------------------
1367
1368 //----------------------------------------------------------------------------
1369 void vvSlicer::SetVFColor(double r, double g, double b)
1370 {
1371   double mVFColorHSV[3];
1372   mVFColor[0] = r;
1373   mVFColor[1] = g;
1374   mVFColor[2] = b;
1375
1376   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1377   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1378   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1379   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1380
1381   this->Render();
1382 }
1383