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
 759   double origin[3] = {VTK_DOUBLE_MAX, VTK_DOUBLE_MAX, VTK_DOUBLE_MAX};
 760   double spacing[3] = {VTK_DOUBLE_MAX, VTK_DOUBLE_MAX, VTK_DOUBLE_MAX};
 761   reslice->SetOutputOrigin(origin);
 762   reslice->SetOutputSpacing(spacing);
 763   reslice->GetOutput()->UpdateInformation();
 764   reslice->GetOutput()->GetOrigin(origin);
 765   reslice->GetOutput()->GetSpacing(spacing);
 766
 767   // Use similar spacing as the image in the direction SliceOrientation
 768   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 769
 770   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 771   // Step 1: from world coordinates to image coordinates
 772   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 773   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 774   // Step 2: round to superior grid positionInc
 775   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 776   // Step 3: back to world coordinates
 777   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 778   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 779
 780   // Set new spacing and origin
 781   reslice->SetOutputOrigin(origin);
 782   reslice->SetOutputSpacing(spacing);
 783   reslice->UpdateInformation();
 784   reslice->GetOutput()->UpdateInformation();
 785 }
 786 //------------------------------------------------------------------------------
 787
 788 //----------------------------------------------------------------------------
 789 int * vvSlicer::GetExtent(){
 790   int *w_ext;
 791   if (mUseReducedExtent) {
 792     w_ext = mReducedExtent;
 793   } else w_ext = GetInput()->GetWholeExtent();
 794   return w_ext;
 795 }
 796 //----------------------------------------------------------------------------
 797
 798
 799 //----------------------------------------------------------------------------
 800 int vvSlicer::GetOrientation()
 801 {
 802   return this->SliceOrientation;
 803 }
 804 //----------------------------------------------------------------------------
 805
 806
 807 //----------------------------------------------------------------------------
 808 void vvSlicer::UpdateDisplayExtent()
 809 {
 810   vtkImageData *input = this->GetInput();
 811   if (!input || !this->ImageActor) {
 812     return;
 813   }
 814   input->UpdateInformation();
 815
 816   // Local copy of extent
 817   int w_ext[6];
 818   copyExtent(GetExtent(), w_ext);
 819   // Set slice value
 820   w_ext[ this->SliceOrientation*2   ] = this->Slice;
 821   w_ext[ this->SliceOrientation*2+1 ] = this->Slice;
 822
 823   // Image actor
 824   this->ImageActor->SetDisplayExtent(w_ext);
 825
 826   // Overlay image actor
 827   if (mOverlay && mOverlayActor->GetVisibility()) {
 828     AdjustResliceToSliceOrientation(mOverlayReslice);
 829     int overExtent[6];
 830     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 831     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 832     mOverlayActor->SetDisplayExtent( overExtent );
 833   }
 834
 835   // Fusion image actor
 836   if (mFusion && mFusionActor->GetVisibility()) {
 837     AdjustResliceToSliceOrientation(mFusionReslice);
 838     int fusExtent[6];
 839     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 840     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 841     mFusionActor->SetDisplayExtent(fusExtent);
 842   }
 843
 844   // Vector field actor
 845   double* camera = Renderer->GetActiveCamera()->GetPosition();
 846   double* image_bounds = ImageActor->GetBounds();
 847   double position[3] = {0, 0, 0};
 848   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 849
 850   //print_vector<double, 6>("camera", camera);
 851   //print_vector<double, 6>("image_bounds", image_bounds);
 852   //print_vector<double, 3>("position", position);
 853
 854   // find where to place the VF actor. to deal with
 855   // z-buffer issues, the VF is placed right in front of the image,
 856   // subject to a small offset. the position actually depends on the
 857   // the location of the camera relative to the image.
 858   double offset = 1;
 859   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 860     offset = -1;
 861
 862   if (mVF && mVFActor->GetVisibility()) {
 863     int vfExtent[6];
 864     mVF->GetVTKImages()[0]->UpdateInformation();
 865     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 866     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 867     mVOIFilter->SetVOI(vfExtent);
 868     int orientation[3] = {1,1,1};
 869     orientation[this->SliceOrientation] = 0;
 870     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 871     mVFMapper->Update();
 872
 873     position[this->SliceOrientation] += offset;
 874     mVFActor->SetPosition(position);
 875   }
 876
 877   // Landmarks actor
 878   if (mLandActor) {
 879     if (mClipBox) {
 880       double bounds [6];
 881       for(unsigned int i=0; i<6; i++)
 882         bounds[i] = ImageActor->GetBounds()[i];
 883       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 884       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 885       mClipBox->SetBounds(bounds);
 886       UpdateLandmarks();
 887     }
 888
 889     position[this->SliceOrientation] = offset;
 890     mLandActor->SetPosition(position);
 891   }
 892
 893   // Figure out the correct clipping range
 894   if (this->Renderer) {
 895     if (this->InteractorStyle &&
 896         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 897       this->Renderer->ResetCameraClippingRange();
 898     } else {
 899       vtkCamera *cam = this->Renderer->GetActiveCamera();
 900       if (cam) {
 901         double bounds[6];
 902         this->ImageActor->GetBounds(bounds);
 903         double spos = (double)bounds[this->SliceOrientation * 2];
 904         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 905         double range = fabs(spos - cpos);
 906         double *spacing = input->GetSpacing();
 907         double avg_spacing =
 908           ((double)spacing[0] + (double)spacing[1] + (double)spacing[2]) / 3.0;
 909         cam->SetClippingRange(range - avg_spacing * 3.0, range + avg_spacing * 3.0);
 910       }
 911     }
 912   }
 913
 914 }
 915 //----------------------------------------------------------------------------
 916
 917 //----------------------------------------------------------------------------
 918 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 919                                                 vtkImageData *targetImage, int targetExtent[6])
 920 {
 921   double dExtents[6];
 922   for(unsigned int i=0; i<6; i++) {
 923     // From source voxel coordinates to world coordinates
 924     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 925
 926     // From world coordinates to floating point target voxel coordinates
 927     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 928
 929     // Round to nearest
 930     targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 931   }
 932 }
 933 //----------------------------------------------------------------------------
 934
 935 //----------------------------------------------------------------------------
 936 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 937 {
 938   bool out = false;
 939   int maxBound = 6;
 940
 941   //2D overlay on 3D image specific case
 942   if (refExtent[4] == refExtent[5]) {
 943     maxBound = 4;
 944     extent[4] = refExtent[4];
 945     extent[5] = refExtent[5];
 946   }
 947
 948   for (int i = 0; i < maxBound; i = i+2) {
 949     //if we are totally outside the image
 950     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 951       out = true;
 952       break;
 953     }
 954     //crop to the limit of the image
 955     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 956     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 957     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 958     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 959   }
 960   if (out)
 961     for (int i = 0; i < maxBound; i = i+2) {
 962       extent[i] = refExtent[i];
 963       extent[i+1] = refExtent[i];
 964     }
 965 }
 966 //----------------------------------------------------------------------------
 967
 968
 969 //----------------------------------------------------------------------------
 970 void vvSlicer::UpdateOrientation()
 971 {
 972   // Set the camera position
 973   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
 974   if (cam) {
 975     switch (this->SliceOrientation) {
 976     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 977       cam->SetFocalPoint(0,0,0);
 978       cam->SetPosition(0,0,-1); // -1 if medical ?
 979       cam->SetViewUp(0,-1,0);
 980       break;
 981
 982     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 983       cam->SetFocalPoint(0,0,0);
 984       cam->SetPosition(0,-1,0); // 1 if medical ?
 985       cam->SetViewUp(0,0,1);
 986       break;
 987
 988     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 989       cam->SetFocalPoint(0,0,0);
 990       cam->SetPosition(-1,0,0); // -1 if medical ?
 991       cam->SetViewUp(0,0,1);
 992       break;
 993     }
 994   }
 995 }
 996 //----------------------------------------------------------------------------
 997
 998
 999 //----------------------------------------------------------------------------
1000 void vvSlicer::SetOpacity(double s)
1001 {
1002   this->GetImageActor()->SetOpacity(s);
1003 }
1004 //----------------------------------------------------------------------------
1005
1006
1007 //----------------------------------------------------------------------------
1008 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1009 {
1010   this->Superclass::SetRenderWindow(rw);
1011   this->SetupInteractor(rw->GetInteractor());
1012   ca->SetImageActor(this->GetImageActor());
1013   ca->SetWindowLevel(this->GetWindowLevel());
1014   ca->SetText(2, "<slice>");
1015   ca->SetText(3, "<window>\n<level>");
1016
1017   double bounds[6];
1018   double max = 65000;
1019
1020   bounds[0] = -max;
1021   bounds[1] = max;
1022   bounds[2] = -max;
1023   bounds[3] = max;
1024   bounds[4] = -max;
1025   bounds[5] = max;
1026
1027   crossCursor->SetModelBounds(bounds);
1028   this->GetRenderer()->AddActor(pdmA);
1029   this->GetRenderer()->AddActor(ca);
1030   this->GetRenderer()->ResetCamera();
1031
1032   //this is just a mapping between the labeling of the orientations presented to the user and
1033   //the one used by vtk
1034   SetSliceOrientation(2-(orientation%3));
1035   ResetCamera();
1036 }
1037 //----------------------------------------------------------------------------
1038
1039
1040 //----------------------------------------------------------------------------
1041 void vvSlicer::ResetCamera()
1042 {
1043   this->GetRenderer()->ResetCamera();
1044 }
1045 //----------------------------------------------------------------------------
1046
1047
1048 //----------------------------------------------------------------------------
1049 void vvSlicer::SetDisplayMode(bool i)
1050 {
1051   this->GetRenderer()->SetDraw(i);
1052   if (i)
1053     UpdateDisplayExtent();
1054 }
1055 //----------------------------------------------------------------------------
1056
1057
1058 //----------------------------------------------------------------------------
1059 void vvSlicer::FlipHorizontalView()
1060 {
1061   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1062   if (cam) {
1063     double *position = cam->GetPosition();
1064     double factor[3] = {1, 1, 1};
1065     factor[this->SliceOrientation] = -1;
1066     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1067
1068 /*    switch (this->SliceOrientation) {
1069     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1070       cam->SetPosition(position[0],position[1],-position[2]);
1071       break;
1072
1073     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1074       cam->SetPosition(position[0],-position[1],position[2]);
1075       break;
1076
1077     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1078       cam->SetPosition(-position[0],position[1],position[2]);
1079       break;
1080     }*/
1081
1082     this->Renderer->ResetCameraClippingRange();
1083     this->UpdateDisplayExtent();
1084   }
1085 }
1086 //----------------------------------------------------------------------------
1087
1088
1089 //----------------------------------------------------------------------------
1090 void vvSlicer::FlipVerticalView()
1091 {
1092   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1093   if (cam) {
1094     FlipHorizontalView();
1095     double *viewup = cam->GetViewUp();
1096     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1097     this->UpdateDisplayExtent();
1098   }
1099 }
1100 //----------------------------------------------------------------------------
1101
1102
1103 //----------------------------------------------------------------------------
1104 void vvSlicer::SetColorWindow(double window)
1105 {
1106   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1107   if ( LUT ) {
1108     double level = this->GetWindowLevel()->GetLevel();
1109     LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
1110     LUT->Build();
1111   }
1112   this->vtkImageViewer2::SetColorWindow(window);
1113 }
1114 //----------------------------------------------------------------------------
1115
1116 //----------------------------------------------------------------------------
1117 void vvSlicer::SetColorLevel(double level)
1118 {
1119   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1120   if ( LUT ) {
1121     double window = this->GetWindowLevel()->GetWindow();
1122     LUT->SetTableRange(level-fabs(window)/4,level+fabs(window)/4);
1123     LUT->Build();
1124   }
1125   this->vtkImageViewer2::SetColorLevel(level);
1126 }
1127 //----------------------------------------------------------------------------
1128
1129 //----------------------------------------------------------------------------
1130 double vvSlicer::GetOverlayColorWindow()
1131 {
1132   if(mOverlayMapper)
1133     return mOverlayMapper->GetWindow();
1134   else
1135     return 0.;
1136 }
1137 //----------------------------------------------------------------------------
1138
1139 //----------------------------------------------------------------------------
1140 double vvSlicer::GetOverlayColorLevel()
1141 {
1142   if(mOverlayMapper)
1143     return mOverlayMapper->GetLevel();
1144   else
1145     return 0.;
1146 }
1147 //----------------------------------------------------------------------------
1148
1149 //----------------------------------------------------------------------------
1150 void vvSlicer::SetOverlayColorWindow(double window)
1151 {
1152   mOverlayMapper->SetWindow(window);
1153 }
1154 //----------------------------------------------------------------------------
1155
1156 //----------------------------------------------------------------------------
1157 void vvSlicer::SetOverlayColorLevel(double level)
1158 {
1159   mOverlayMapper->SetLevel(level);
1160 }
1161 //----------------------------------------------------------------------------
1162
1163 //----------------------------------------------------------------------------
1164 // Returns the min an the max value in a 41x41 region around the mouse pointer
1165 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image)
1166 {
1167   //Get mouse pointer position in view coordinates
1168   double fLocalExtents[6];
1169   for(int i=0; i<3; i++) {
1170     fLocalExtents[i*2  ] = mCurrent[i];
1171     fLocalExtents[i*2+1] = mCurrent[i];
1172   }
1173   this->Renderer->WorldToView(fLocalExtents[0], fLocalExtents[2], fLocalExtents[4]);
1174   this->Renderer->WorldToView(fLocalExtents[1], fLocalExtents[3], fLocalExtents[5]);
1175   for(int i=0; i<3; i++) {
1176     if (i!=SliceOrientation) { //SR: assumes that SliceOrientation is valid in ViewCoordinates (???)
1177       fLocalExtents[i*2  ] -= 0.2;
1178       fLocalExtents[i*2+1] += 0.2;
1179     }
1180   }
1181   this->Renderer->ViewToWorld(fLocalExtents[0], fLocalExtents[2], fLocalExtents[4]);
1182   this->Renderer->ViewToWorld(fLocalExtents[1], fLocalExtents[3], fLocalExtents[5]);
1183
1184   //Convert to image pixel coordinates (rounded)
1185   int iLocalExtents[6];
1186   for(int i=0; i<3; i++) {
1187     fLocalExtents[i*2  ] = (fLocalExtents[i*2  ] - image->GetOrigin()[i])/image->GetSpacing()[i];
1188     fLocalExtents[i*2+1] = (fLocalExtents[i*2+1] - image->GetOrigin()[i])/image->GetSpacing()[i];
1189
1190     iLocalExtents[i*2  ] = lrint(fLocalExtents[i*2  ]);
1191     iLocalExtents[i*2+1] = lrint(fLocalExtents[i*2+1]);
1192
1193     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1194       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1195   }
1196
1197   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1198   voiFilter->SetInput(image);
1199   voiFilter->SetVOI(iLocalExtents);
1200   voiFilter->Update();
1201   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1202     min = 0;
1203     max = 0;
1204     return;
1205   }
1206
1207   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1208   accFilter->SetInput(voiFilter->GetOutput());
1209   accFilter->Update();
1210
1211   min = *(accFilter->GetMin());
1212   max = *(accFilter->GetMax());
1213 }
1214 //----------------------------------------------------------------------------
1215
1216 //----------------------------------------------------------------------------
1217 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1218 {
1219   ix = lrint(X);
1220   iy = lrint(Y);
1221   iz = lrint(Z);
1222   if (ix < image->GetWholeExtent()[0] ||
1223       ix > image->GetWholeExtent()[1] ||
1224       iy < image->GetWholeExtent()[2] ||
1225       iy > image->GetWholeExtent()[3] ||
1226       iz < image->GetWholeExtent()[4] ||
1227       iz > image->GetWholeExtent()[5] )
1228     return std::numeric_limits<double>::quiet_NaN();
1229
1230   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1231   image->Update();
1232   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1233 }
1234 //----------------------------------------------------------------------------
1235
1236 //----------------------------------------------------------------------------
1237 void vvSlicer::Render()
1238 {
1239   if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay && !this->mFusion) {
1240     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1241     legend->SetVisibility(1);
1242   } else legend->SetVisibility(0);
1243
1244   if (ca->GetVisibility()) {
1245     std::stringstream worldPos;
1246     double X = (mCurrent[0] - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1247     double Y = (mCurrent[1] - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1248     double Z = (mCurrent[2] - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1249
1250 //     if (X < this->GetInput()->GetWholeExtent()[0]) X = this->GetInput()->GetWholeExtent()[0];
1251 //     else if (X > this->GetInput()->GetWholeExtent()[1]) X = this->GetInput()->GetWholeExtent()[1];
1252 //     if (Y < this->GetInput()->GetWholeExtent()[2]) Y = this->GetInput()->GetWholeExtent()[2];
1253 //     else if (Y > this->GetInput()->GetWholeExtent()[3]) Y = this->GetInput()->GetWholeExtent()[3];
1254 //     if (Z < this->GetInput()->GetWholeExtent()[4]) Z = this->GetInput()->GetWholeExtent()[4];
1255 //     else if (Z > this->GetInput()->GetWholeExtent()[5]) Z = this->GetInput()->GetWholeExtent()[5];
1256
1257     if (X >= this->GetInput()->GetWholeExtent()[0] &&
1258         X <= this->GetInput()->GetWholeExtent()[1] &&
1259         Y >= this->GetInput()->GetWholeExtent()[2] &&
1260         Y <= this->GetInput()->GetWholeExtent()[3] &&
1261         Z >= this->GetInput()->GetWholeExtent()[4] &&
1262         Z <= this->GetInput()->GetWholeExtent()[5]) {
1263
1264
1265       int ix, iy, iz;
1266       double value = this->GetScalarComponentAsDouble(this->GetInput(), X, Y, Z, ix, iy, iz);
1267
1268       if(ImageActor->GetVisibility())
1269         worldPos << "data value : " << value << std::endl;
1270
1271       worldPos << "mm : " << lrint(mCurrent[0]) << ' '
1272                           << lrint(mCurrent[1]) << ' '
1273                           << lrint(mCurrent[2]) << ' '
1274                           << mCurrentTSlice
1275                           << std::endl;
1276       worldPos << "pixel : " << ix << ' '
1277                              << iy << ' '
1278                              << iz << ' '
1279                              << mCurrentTSlice
1280                              << std::endl;
1281     }
1282     ca->SetText(1,worldPos.str().c_str());
1283   }
1284
1285   if (pdmA->GetVisibility()) {
1286     double x = mCursor[0];
1287     double y = mCursor[1];
1288     double z = mCursor[2];
1289     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1290     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1291     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1292
1293     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1294         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1295         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1296         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1297         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1298         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1299       vtkRenderer * renderer = this->Renderer;
1300
1301       renderer->WorldToView(x,y,z);
1302       renderer->ViewToNormalizedViewport(x,y,z);
1303       renderer->NormalizedViewportToViewport(x,y);
1304       renderer->ViewportToNormalizedDisplay(x,y);
1305       renderer->NormalizedDisplayToDisplay(x,y);
1306       crossCursor->SetFocalPoint(x,y,z);
1307     } else
1308       crossCursor->SetFocalPoint(-1,-1,z);
1309   }
1310
1311
1312   if (mOverlay && mOverlayActor->GetVisibility()) {
1313     if(mLinkOverlayWindowLevel) {
1314       mOverlayMapper->SetWindow(this->GetColorWindow());
1315       mOverlayMapper->SetLevel(this->GetColorLevel());
1316     }
1317     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1318     mOverlayMapper->GetOutput()->Update();
1319     mOverlayMapper->Update();
1320   }
1321   if (mLandMapper)
1322     UpdateLandmarks();
1323
1324   this->GetRenderWindow()->Render();
1325 }
1326 //----------------------------------------------------------------------------
1327
1328
1329 //----------------------------------------------------------------------------
1330 void vvSlicer::UpdateCursorPosition()
1331 {
1332   pdmA->SetVisibility(true);
1333   mCursor[0] = mCurrent[0];
1334   mCursor[1] = mCurrent[1];
1335   mCursor[2] = mCurrent[2];
1336   mCursor[3] = mCurrentTSlice;
1337 }
1338 //----------------------------------------------------------------------------
1339
1340
1341 //----------------------------------------------------------------------------
1342 void vvSlicer::UpdateLandmarks()
1343 {
1344   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1345   if (pd->GetPoints()) {
1346     mLandGlyph->SetRange(0,1);
1347     mLandGlyph->Modified();
1348     mLandGlyph->Update();
1349
1350     mClipBox->Modified();
1351     mLandClipper->Update();
1352     mLandMapper->Update();
1353   }
1354
1355 }
1356 //----------------------------------------------------------------------------
1357
1358
1359 //----------------------------------------------------------------------------
1360 void vvSlicer::SetSlice(int slice)
1361 {
1362   int *range = this->GetSliceRange();
1363   if (range) {
1364     if (slice < range[0]) {
1365       slice = range[0];
1366     } else if (slice > range[1]) {
1367       slice = range[1];
1368     }
1369   }
1370
1371   if (this->Slice == slice) {
1372     return;
1373   }
1374
1375   this->Slice = slice;
1376   SetContourSlice();
1377   this->Modified();
1378   this->UpdateDisplayExtent();
1379
1380   // Seems to work without this line
1381   //this->Render();
1382 }
1383 //----------------------------------------------------------------------------
1384
1385
1386 //----------------------------------------------------------------------------
1387 void vvSlicer::SetContourSlice()
1388 {
1389   if (mSurfaceCutActors.size() > 0)
1390     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1391          i!=mSurfaceCutActors.end(); i++) {
1392
1393       (*i)->SetSlicingOrientation(this->SliceOrientation);
1394       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1395                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1396     }
1397 }
1398 //----------------------------------------------------------------------------
1399
1400
1401 //----------------------------------------------------------------------------
1402 void vvSlicer::ForceUpdateDisplayExtent()
1403 {
1404   this->UpdateDisplayExtent();
1405 }
1406 //----------------------------------------------------------------------------
1407
1408
1409 //----------------------------------------------------------------------------
1410 int* vvSlicer::GetDisplayExtent()
1411 {
1412   return this->GetImageActor()->GetDisplayExtent();
1413 }
1414 //----------------------------------------------------------------------------
1415
1416
1417 //----------------------------------------------------------------------------
1418 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1419 {
1420   this->Superclass::PrintSelf(os, indent);
1421 }
1422 //----------------------------------------------------------------------------
1423
1424 //----------------------------------------------------------------------------
1425 void vvSlicer::SetVFColor(double r, double g, double b)
1426 {
1427   double mVFColorHSV[3];
1428   mVFColor[0] = r;
1429   mVFColor[1] = g;
1430   mVFColor[2] = b;
1431
1432   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1433   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1434   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1435   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1436
1437   this->Render();
1438 }
1439