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 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
  70 #  include <vtkImageMapper3D.h>
  71 #endif
  72
  73 vtkCxxRevisionMacro(vvSlicer, "DummyRevision");
  74 vtkStandardNewMacro(vvSlicer);
  75 static void copyExtent(int* in, int* to){
  76  for(int i=0; i<6; ++i) to[i]=in[i];
  77 }
  78 //------------------------------------------------------------------------------
  79 vvSlicer::vvSlicer()
  80 {
  81   this->UnInstallPipeline();
  82   mImage = NULL;
  83   mReducedExtent = new int[6];
  84   mCurrentTSlice = 0;
  85   mUseReducedExtent = false;
  86
  87   mCurrent[0] = -VTK_DOUBLE_MAX;
  88   mCurrent[1] = -VTK_DOUBLE_MAX;
  89   mCurrent[2] = -VTK_DOUBLE_MAX;
  90
  91   mCursor[0] = -VTK_DOUBLE_MAX;
  92   mCursor[1] = -VTK_DOUBLE_MAX;
  93   mCursor[2] = -VTK_DOUBLE_MAX;
  94   mCursor[3] = -VTK_DOUBLE_MAX;
  95
  96   mSubSampling = 5;
  97   mScale = 1;
  98   mVFLog = 0;
  99   mVFWidth = 1;
 100   mVFColor[0] = 0;
 101   mVFColor[1] = 1;
 102   mVFColor[2] = 0;
 103
 104   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 105   crossCursor->AllOff();
 106   crossCursor->AxesOn();
 107   crossCursor->SetTranslationMode(1);
 108   crossCursor->SetRadius(2);
 109
 110   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 111   pdm->SetInput(crossCursor->GetOutput());
 112
 113   pdmA = vtkSmartPointer<vtkActor2D>::New();
 114   pdmA->SetMapper(pdm);
 115   pdmA->GetProperty()->SetColor(255,10,212);
 116   pdmA->SetVisibility(0);
 117   pdmA->SetPickable(0);
 118
 119   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 120   ca->GetTextProperty()->SetColor(255,10,212);
 121   ca->SetVisibility(1);
 122   mFileName = "";
 123
 124   mVF = NULL;
 125   mOverlay = NULL;
 126   mFusion = NULL;
 127   mLandmarks = NULL;
 128
 129   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 130   //legend->SetTitle("test!");
 131   legend->SetPosition(0.82,0.18);
 132   legend->SetWidth(0.1);
 133   legend->SetVisibility(0);
 134   legend->SetLabelFormat("%.1f");
 135   this->GetRenderer()->AddActor(legend);
 136   showFusionLegend = false;
 137
 138   this->WindowLevel->Delete();
 139   this->WindowLevel = vvImageMapToWLColors::New();
 140
 141   this->InstallPipeline();
 142
 143   mLinkOverlayWindowLevel = true;
 144
 145 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 146   this->GetImageActor()->GetMapper()->BorderOn();
 147 #endif
 148
 149   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 150   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 151 }
 152 //------------------------------------------------------------------------------
 153
 154
 155 //------------------------------------------------------------------------------
 156 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 157 {
 158   return mOverlayMapper.GetPointer();
 159 }
 160 //------------------------------------------------------------------------------
 161
 162
 163 //------------------------------------------------------------------------------
 164 vvBlendImageActor* vvSlicer::GetOverlayActor()
 165 {
 166   return mOverlayActor.GetPointer();
 167 }
 168 //------------------------------------------------------------------------------
 169
 170
 171 //------------------------------------------------------------------------------
 172 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 173 {
 174   return mFusionMapper.GetPointer();
 175 }
 176 //------------------------------------------------------------------------------
 177
 178
 179 //------------------------------------------------------------------------------
 180 vtkImageActor* vvSlicer::GetFusionActor()
 181 {
 182   return mFusionActor.GetPointer();
 183 }
 184 //------------------------------------------------------------------------------
 185
 186
 187 //------------------------------------------------------------------------------
 188 vtkActor* vvSlicer::GetVFActor()
 189 {
 190   return mVFActor.GetPointer();
 191 }
 192 //------------------------------------------------------------------------------
 193
 194
 195 //------------------------------------------------------------------------------
 196 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 197 {
 198   return ca.GetPointer();
 199 }
 200 //------------------------------------------------------------------------------
 201
 202
 203 //------------------------------------------------------------------------------
 204 void vvSlicer::EnableReducedExtent(bool b)
 205 {
 206   mUseReducedExtent = b;
 207 }
 208 //------------------------------------------------------------------------------
 209
 210
 211 //------------------------------------------------------------------------------
 212 void vvSlicer::SetReducedExtent(int * ext)
 213 {
 214   copyExtent(ext, mReducedExtent);
 215 }
 216 //------------------------------------------------------------------------------
 217
 218
 219 //------------------------------------------------------------------------------
 220 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 221 {
 222
 223   mSurfaceCutActors.push_back(new vvMeshActor());
 224   if (propagate)
 225     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 226   else
 227     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 228   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 229   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 230
 231   SetContourSlice();
 232 }
 233 //------------------------------------------------------------------------------
 234
 235
 236 //------------------------------------------------------------------------------
 237 void vvSlicer::ToggleContourSuperposition()
 238 {
 239   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 240        i!=mSurfaceCutActors.end(); i++)
 241     (*i)->ToggleSuperposition();
 242 }
 243 //------------------------------------------------------------------------------
 244
 245
 246 //------------------------------------------------------------------------------
 247 void vvSlicer::SetCursorColor(int r,int g, int b)
 248 {
 249   pdmA->GetProperty()->SetColor(r,g,b);
 250 }
 251 //------------------------------------------------------------------------------
 252
 253
 254 //------------------------------------------------------------------------------
 255 void vvSlicer::SetCursorVisibility(bool s)
 256 {
 257   pdmA->SetVisibility(s);
 258 }
 259 //------------------------------------------------------------------------------
 260
 261
 262 //------------------------------------------------------------------------------
 263 bool vvSlicer::GetCursorVisibility()
 264 {
 265   return pdmA->GetVisibility();
 266 }
 267 //------------------------------------------------------------------------------
 268
 269
 270 //------------------------------------------------------------------------------
 271 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 272 {
 273   ca->SetVisibility(s);
 274 }
 275 //------------------------------------------------------------------------------
 276
 277
 278 //------------------------------------------------------------------------------
 279 bool vvSlicer::GetCornerAnnotationVisibility()
 280 {
 281   return ca->GetVisibility();
 282 }
 283 //------------------------------------------------------------------------------
 284
 285
 286 //------------------------------------------------------------------------------
 287 vvSlicer::~vvSlicer()
 288 {
 289   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 290        i!=mSurfaceCutActors.end(); i++)
 291     delete (*i);
 292   delete [] mReducedExtent;
 293 }
 294 //------------------------------------------------------------------------------
 295
 296 //------------------------------------------------------------------------------
 297 double* vvSlicer::GetCurrentPosition()
 298 {
 299   return mCurrentBeforeSlicingTransform;
 300 }
 301 //------------------------------------------------------------------------------
 302
 303 //------------------------------------------------------------------------------
 304 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 305 {
 306   mCurrentBeforeSlicingTransform[0]=x;
 307   mCurrentBeforeSlicingTransform[1]=y;
 308   mCurrentBeforeSlicingTransform[2]=z;
 309   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 310   mCurrentTSlice = t;
 311 }
 312 //------------------------------------------------------------------------------
 313
 314
 315 //------------------------------------------------------------------------------
 316 void vvSlicer::SetImage(vvImage::Pointer image)
 317 {
 318   if (image->GetVTKImages().size()) {
 319     mImage = image;
 320
 321     if (!mImageReslice) {
 322       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 323       mImageReslice->SetInterpolationModeToLinear();
 324       mImageReslice->AutoCropOutputOn();
 325       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 326     }
 327
 328     mConcatenatedTransform->Identity();
 329     mConcatenatedTransform->Concatenate(mImage->GetTransform());
 330     mConcatenatedTransform->Concatenate(mSlicingTransform);
 331     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 332     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 333     mImageReslice->UpdateInformation();
 334
 335     this->Superclass::SetInput(mImageReslice->GetOutput());
 336
 337     int extent[6];
 338     this->GetInput()->GetWholeExtent(extent);
 339
 340     // Prevent crash when reload -> change slice if outside extent
 341     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 342       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 343     }
 344
 345     // Make sure that the required part image has been computed
 346     extent[SliceOrientation*2] = Slice;
 347     extent[SliceOrientation*2+1] = Slice;
 348     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 349     mImageReslice->GetOutput()->Update();
 350
 351     this->UpdateDisplayExtent();
 352
 353     mCurrentTSlice = 0;
 354     ca->SetText(0,mFileName.c_str());
 355   }
 356 }
 357 //------------------------------------------------------------------------------
 358
 359
 360 //------------------------------------------------------------------------------
 361 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 362 {
 363   if (overlay->GetVTKImages().size()) {
 364     mOverlay = overlay;
 365
 366     if (!mOverlayReslice) {
 367       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 368       mOverlayReslice->SetInterpolationModeToLinear();
 369       mOverlayReslice->AutoCropOutputOn();
 370       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 371     }
 372     mOverlayReslice->SetResliceTransform(mOverlay->GetTransform());
 373     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 374
 375     if (!mOverlayMapper)
 376       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 377     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 378
 379     if (!mOverlayActor) {
 380       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 381       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 382       mOverlayActor->SetPickable(0);
 383       mOverlayActor->SetVisibility(true);
 384       mOverlayActor->SetOpacity(0.5);
 385 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 386       mOverlayActor->GetMapper()->BorderOn();
 387 #endif
 388       }
 389
 390     //stupid but necessary : the Overlay need to be rendered before fusion
 391     if (mFusionActor) {
 392       this->GetRenderer()->RemoveActor(mFusionActor);
 393       this->GetRenderer()->AddActor(mOverlayActor);
 394       this->GetRenderer()->AddActor(mFusionActor);
 395     } else
 396       this->GetRenderer()->AddActor(mOverlayActor);
 397
 398     //Synchronize orientation and slice
 399     AdjustResliceToSliceOrientation(mOverlayReslice);
 400     this->UpdateDisplayExtent();
 401     this->SetTSlice(mCurrentTSlice);
 402   }
 403 }
 404 //------------------------------------------------------------------------------
 405
 406
 407 //------------------------------------------------------------------------------
 408 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 409 {
 410   if (fusion->GetVTKImages().size()) {
 411     mFusion = fusion;
 412
 413     if (!mFusionReslice) {
 414       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 415       mFusionReslice->SetInterpolationModeToLinear();
 416       mFusionReslice->AutoCropOutputOn();
 417       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 418     }
 419     mFusionReslice->SetResliceTransform(mFusion->GetTransform());
 420     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 421
 422     if (!mFusionMapper)
 423       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 424
 425     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 426     lut->SetRange(0, 1);
 427     lut->SetValueRange(0, 1);
 428     lut->SetSaturationRange(0, 0);
 429     lut->Build();
 430     mFusionMapper->SetLookupTable(lut);
 431     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 432
 433     if (!mFusionActor) {
 434       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 435       mFusionActor->SetInput(mFusionMapper->GetOutput());
 436       mFusionActor->SetPickable(0);
 437       mFusionActor->SetVisibility(true);
 438       mFusionActor->SetOpacity(0.7);
 439 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 440       mFusionActor->GetMapper()->BorderOn();
 441 #endif
 442       this->GetRenderer()->AddActor(mFusionActor);
 443     }
 444
 445     //Synchronize orientation and slice
 446     AdjustResliceToSliceOrientation(mFusionReslice);
 447     this->UpdateDisplayExtent();
 448     this->SetTSlice(mCurrentTSlice);
 449   }
 450 }
 451 //------------------------------------------------------------------------------
 452
 453
 454 //------------------------------------------------------------------------------
 455 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 456 {
 457   bool vis = false;
 458   if (actor_type == "image") {
 459     vis = this->ImageActor->GetVisibility();
 460   }
 461   else if (actor_type == "vector") {
 462     vis = this->mVFActor->GetVisibility();
 463   }
 464   else if (actor_type == "overlay") {
 465     vis = this->mOverlayActor->GetVisibility();
 466   }
 467   else if (actor_type == "fusion") {
 468     vis = this->mFusionActor->GetVisibility();
 469   }
 470   else if (actor_type == "contour")
 471     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 472
 473   return vis;
 474 }
 475 //------------------------------------------------------------------------------
 476
 477 //------------------------------------------------------------------------------
 478 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 479 {
 480   if (actor_type == "image") {
 481     this->ImageActor->SetVisibility(vis);
 482   }
 483   else if (actor_type == "vector") {
 484     this->mVFActor->SetVisibility(vis);
 485   }
 486   else if (actor_type == "overlay") {
 487     this->mOverlayActor->SetVisibility(vis);
 488   }
 489   else if (actor_type == "fusion") {
 490     this->mFusionActor->SetVisibility(vis);
 491   }
 492   else if (actor_type == "contour")
 493     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 494   UpdateDisplayExtent();
 495 }
 496 //------------------------------------------------------------------------------
 497
 498 //------------------------------------------------------------------------------
 499 void vvSlicer::SetVF(vvImage::Pointer vf)
 500 {
 501   if (vf->GetVTKImages().size()) {
 502     mVF = vf;
 503
 504     if (!mAAFilter) {
 505       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 506       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 507       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 508     }
 509     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 510     mAAFilter->SetInput(mVOIFilter->GetOutput());
 511     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 512     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 513
 514     if (!mArrow)
 515       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 516     mArrow->SetGlyphTypeToSpecificArrow();
 517     mArrow->SetScale(mScale);
 518     mArrow->FilledOff();
 519
 520     // Glyph the gradient vector (with arrows)
 521     if (!mGlyphFilter)
 522       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 523     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 524     mGlyphFilter->SetSource(mArrow->GetOutput());
 525     mGlyphFilter->ScalingOn();
 526     mGlyphFilter->SetScaleModeToScaleByVector();
 527     mGlyphFilter->OrientOn();
 528     mGlyphFilter->SetVectorModeToUseVector();
 529     mGlyphFilter->SetColorModeToColorByVector();
 530
 531     if (!mVFColorLUT)
 532       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 533
 534     double mVFColorHSV[3];
 535     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 536     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 537     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 538     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 539
 540     if (!mVFMapper)
 541       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 542     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 543     mVFMapper->ImmediateModeRenderingOn();
 544     mVFMapper->SetLookupTable(mVFColorLUT);
 545
 546     if (!mVFActor)
 547       mVFActor = vtkSmartPointer<vtkActor>::New();
 548     mVFActor->SetMapper(mVFMapper);
 549     mVFActor->SetPickable(0);
 550     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 551     this->UpdateDisplayExtent();
 552     this->GetRenderer()->AddActor(mVFActor);
 553
 554     //Synchronize slice
 555     SetTSlice(mCurrentTSlice);
 556   }
 557 }
 558 //------------------------------------------------------------------------------
 559
 560
 561 //------------------------------------------------------------------------------
 562 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 563 {
 564   mLandmarks = landmarks;
 565   if (landmarks) {
 566
 567     if (!mCross)
 568       mCross = vtkSmartPointer<vtkCursor3D>::New();
 569     mCross->SetFocalPoint(0.0,0.0,0.0);
 570     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 571     mCross->AllOff();
 572     mCross->AxesOn();
 573
 574     if (!mLandGlyph)
 575       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 576     mLandGlyph->SetSource(mCross->GetOutput());
 577     mLandGlyph->SetInput(landmarks->GetOutput());
 578     //mLandGlyph->SetIndexModeToScalar();
 579     mLandGlyph->SetRange(0,1);
 580     mLandGlyph->ScalingOff();
 581
 582     mLandGlyph->SetColorModeToColorByScalar();
 583
 584     if (!mClipBox)
 585       mClipBox = vtkSmartPointer<vtkBox>::New();
 586     if (!mLandClipper)
 587       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 588     mLandClipper->InsideOutOn();
 589     mLandClipper->SetInput(mLandGlyph->GetOutput());
 590     mLandClipper->SetClipFunction(mClipBox);
 591
 592     if (!mLandMapper)
 593       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 594     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 595     //mLandMapper->ScalarVisibilityOff();
 596
 597     if (!mLandActor)
 598       mLandActor = vtkSmartPointer<vtkActor>::New();
 599     mLandActor->SetMapper(mLandMapper);
 600     mLandActor->GetProperty()->SetColor(255,10,212);
 601     mLandActor->SetPickable(0);
 602     mLandActor->SetVisibility(true);
 603     this->UpdateDisplayExtent();
 604     this->GetRenderer()->AddActor(mLandActor);
 605   }
 606 }
 607 //------------------------------------------------------------------------------
 608
 609 //------------------------------------------------------------------------------
 610 //FIXME: this function leaks memory, we should fix it someday :)
 611 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 612 {
 613   if (actor_type == "vector") {
 614     Renderer->RemoveActor(mVFActor);
 615     mGlyphFilter=NULL;
 616     mVF = NULL;
 617     mArrow = NULL;
 618     mAAFilter=NULL;
 619     mVOIFilter = NULL;
 620     mVFMapper = NULL;
 621     mVFActor = NULL;
 622   }
 623   if (actor_type == "overlay") {
 624     Renderer->RemoveActor(mOverlayActor);
 625     mOverlay = NULL;
 626     mOverlayActor = NULL;
 627     mOverlayMapper = NULL;
 628   }
 629   if (actor_type == "fusion") {
 630     Renderer->RemoveActor(mFusionActor);
 631     mFusion = NULL;
 632     mFusionActor = NULL;
 633     mFusionMapper = NULL;
 634   }
 635   if (actor_type == "contour") {
 636     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 637     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 638   }
 639 }
 640 //------------------------------------------------------------------------------
 641
 642
 643 //------------------------------------------------------------------------------
 644 void vvSlicer::SetVFSubSampling(int sub)
 645 {
 646   if (mVOIFilter) {
 647     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 648     mSubSampling = sub;
 649   }
 650   UpdateDisplayExtent();
 651   Render();
 652 }
 653 //------------------------------------------------------------------------------
 654
 655
 656 //------------------------------------------------------------------------------
 657 void vvSlicer::SetVFScale(int scale)
 658 {
 659   mScale = scale;
 660   if (mArrow)
 661     mArrow->SetScale(mScale);
 662   UpdateDisplayExtent();
 663   Render();
 664 }
 665 //------------------------------------------------------------------------------
 666
 667 //------------------------------------------------------------------------------
 668 void vvSlicer::SetVFWidth(int width)
 669 {
 670   mVFWidth = width;
 671   if (mVFActor)
 672     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 673   UpdateDisplayExtent();
 674   Render();
 675 }
 676 //------------------------------------------------------------------------------
 677
 678
 679 //------------------------------------------------------------------------------
 680 void vvSlicer::SetVFLog(int log)
 681 {
 682   mVFLog = log;
 683   if (mGlyphFilter) {
 684     mGlyphFilter->SetUseLog(mVFLog);
 685     mGlyphFilter->Modified();
 686   }
 687   UpdateDisplayExtent();
 688   Render();
 689 }
 690 //------------------------------------------------------------------------------
 691
 692
 693 //------------------------------------------------------------------------------
 694 void vvSlicer::SetTSlice(int t)
 695 {
 696   if (t < 0)
 697     t = 0;
 698   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 699     t = mImage->GetVTKImages().size() -1;
 700
 701   mCurrentTSlice = t;
 702   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 703   if (mVF && mVFActor->GetVisibility()) {
 704     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 705       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 706   }
 707   if (mOverlay && mOverlayActor->GetVisibility()) {
 708     if (mOverlay->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 709       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentTSlice] );
 710   }
 711   if (mFusion && mFusionActor->GetVisibility()) {
 712     if (mFusion->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 713       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentTSlice]);
 714   }
 715   if (mSurfaceCutActors.size() > 0)
 716     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 717          i!=mSurfaceCutActors.end(); i++)
 718       (*i)->SetTimeSlice(mCurrentTSlice);
 719   UpdateDisplayExtent();
 720 }
 721 //------------------------------------------------------------------------------
 722
 723
 724 //------------------------------------------------------------------------------
 725 int vvSlicer::GetTSlice()
 726 {
 727   return mCurrentTSlice;
 728 }
 729 //------------------------------------------------------------------------------
 730
 731 //------------------------------------------------------------------------------
 732 void vvSlicer::SetSliceOrientation(int orientation)
 733 {
 734   //if 2D image, force to watch in Axial View
 735   int extent[6];
 736   this->GetInput()->GetWholeExtent(extent);
 737   if (extent[5]-extent[4] <= 2)
 738     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 739
 740   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 741       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 742     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 743     return;
 744   }
 745
 746   this->SliceOrientation = orientation;
 747
 748   if(mFusion)
 749     AdjustResliceToSliceOrientation(mFusionReslice);
 750
 751   if(mOverlay)
 752     AdjustResliceToSliceOrientation(mOverlayReslice);
 753
 754   // Update the viewer
 755   int *range = this->GetSliceRange();
 756   if (range)
 757     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 758
 759   // Go to current cursor position
 760   // double* cursorPos = GetCursorPosition();
 761   // DDV(cursorPos, 3);
 762   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 763
 764   this->UpdateOrientation();
 765   this->UpdateDisplayExtent();
 766
 767   if (this->Renderer && this->GetInput()) {
 768     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 769     this->Renderer->ResetCamera();
 770     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 771   }
 772
 773   SetContourSlice();
 774 }
 775 //----------------------------------------------------------------------------
 776
 777 //------------------------------------------------------------------------------
 778 // This function ensures that we sample the slices of a vtkImageReslice filter
 779 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 780 // In other words, we change the grid of the reslice in the same way as the grid
 781 // of the displayed image in the slicing direction.
 782 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 783 {
 784   // Reset autocrop and update output information
 785   reslice->SetOutputOriginToDefault();
 786   reslice->SetOutputSpacingToDefault();
 787   reslice->GetOutput()->UpdateInformation();
 788
 789   // Ge new origin / spacing
 790   double origin[3];
 791   double spacing[3];
 792   reslice->GetOutput()->GetOrigin(origin);
 793   reslice->GetOutput()->GetSpacing(spacing);
 794
 795   // Use similar spacing as the image in the direction SliceOrientation
 796   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 797
 798   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 799   // Step 1: from world coordinates to image coordinates
 800   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 801   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 802   // Step 2: round to superior grid positionInc
 803   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 804   // Step 3: back to world coordinates
 805   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 806   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 807
 808   // Set new spacing and origin
 809   reslice->SetOutputOrigin(origin);
 810   reslice->SetOutputSpacing(spacing);
 811   reslice->UpdateInformation();
 812   reslice->GetOutput()->UpdateInformation();
 813 }
 814 //------------------------------------------------------------------------------
 815
 816 //----------------------------------------------------------------------------
 817 int * vvSlicer::GetExtent(){
 818   int *w_ext;
 819   if (mUseReducedExtent) {
 820     w_ext = mReducedExtent;
 821   } else w_ext = GetInput()->GetWholeExtent();
 822   return w_ext;
 823 }
 824 //----------------------------------------------------------------------------
 825
 826
 827 //----------------------------------------------------------------------------
 828 int vvSlicer::GetOrientation()
 829 {
 830   return this->SliceOrientation;
 831 }
 832 //----------------------------------------------------------------------------
 833
 834
 835 //----------------------------------------------------------------------------
 836 void vvSlicer::UpdateDisplayExtent()
 837 {
 838   vtkImageData *input = this->GetInput();
 839   if (!input || !this->ImageActor) {
 840     return;
 841   }
 842   input->UpdateInformation();
 843
 844   // Local copy of extent
 845   int w_ext[6];
 846   int* ext = GetExtent();
 847   copyExtent(ext, w_ext);
 848   // Set slice value
 849   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 850   w_ext[ this->SliceOrientation*2   ] = s;
 851   w_ext[ this->SliceOrientation*2+1 ] = s;
 852
 853   // Image actor
 854   this->ImageActor->SetDisplayExtent(w_ext);
 855
 856   // Overlay image actor
 857   if (mOverlay && mOverlayActor->GetVisibility()) {
 858     AdjustResliceToSliceOrientation(mOverlayReslice);
 859     int overExtent[6];
 860     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 861     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 862     mOverlayActor->SetDisplayExtent( overExtent );
 863   }
 864
 865   // Fusion image actor
 866   if (mFusion && mFusionActor->GetVisibility()) {
 867     AdjustResliceToSliceOrientation(mFusionReslice);
 868     int fusExtent[6];
 869     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 870     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 871     mFusionActor->SetDisplayExtent(fusExtent);
 872   }
 873
 874   // Vector field actor
 875   double* camera = Renderer->GetActiveCamera()->GetPosition();
 876   double* image_bounds = ImageActor->GetBounds();
 877   double position[3] = {0, 0, 0};
 878   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 879
 880   //print_vector<double, 6>("camera", camera);
 881   //print_vector<double, 6>("image_bounds", image_bounds);
 882   //print_vector<double, 3>("position", position);
 883
 884   // find where to place the VF actor. to deal with
 885   // z-buffer issues, the VF is placed right in front of the image,
 886   // subject to a small offset. the position actually depends on the
 887   // the location of the camera relative to the image.
 888   double offset = 1;
 889   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 890     offset = -1;
 891
 892   if (mVF && mVFActor->GetVisibility()) {
 893     int vfExtent[6];
 894     mVF->GetVTKImages()[0]->UpdateInformation();
 895     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 896     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 897     mVOIFilter->SetVOI(vfExtent);
 898     int orientation[3] = {1,1,1};
 899     orientation[this->SliceOrientation] = 0;
 900     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 901     mVFMapper->Update();
 902
 903     position[this->SliceOrientation] += offset;
 904     mVFActor->SetPosition(position);
 905   }
 906
 907   // Landmarks actor
 908   if (mLandActor) {
 909     if (mClipBox) {
 910       double bounds [6];
 911       for(unsigned int i=0; i<6; i++)
 912         bounds[i] = ImageActor->GetBounds()[i];
 913       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 914       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 915       mClipBox->SetBounds(bounds);
 916       UpdateLandmarks();
 917     }
 918
 919     position[this->SliceOrientation] = offset;
 920     mLandActor->SetPosition(position);
 921   }
 922
 923   // Figure out the correct clipping range
 924   if (this->Renderer) {
 925     if (this->InteractorStyle &&
 926         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 927       this->Renderer->ResetCameraClippingRange();
 928     } else {
 929       vtkCamera *cam = this->Renderer->GetActiveCamera();
 930       if (cam) {
 931         double bounds[6];
 932         this->ImageActor->GetBounds(bounds);
 933         double spos = (double)bounds[this->SliceOrientation * 2];
 934         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 935         double range = fabs(spos - cpos);
 936         double *spacing = input->GetSpacing();
 937         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
 938         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
 939       }
 940     }
 941   }
 942
 943 }
 944 //----------------------------------------------------------------------------
 945
 946 //----------------------------------------------------------------------------
 947 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 948                                                 vtkImageData *targetImage, int targetExtent[6])
 949 {
 950   double dExtents[6];
 951   for(unsigned int i=0; i<6; i++) {
 952     // From source voxel coordinates to world coordinates
 953     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
 954
 955     // From world coordinates to floating point target voxel coordinates
 956     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
 957
 958     // Round to nearest
 959     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
 960     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
 961   }
 962 }
 963 //----------------------------------------------------------------------------
 964
 965 //----------------------------------------------------------------------------
 966 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
 967 {
 968   bool out = false;
 969   int maxBound = 6;
 970
 971   //2D overlay on 3D image specific case
 972   if (refExtent[4] == refExtent[5]) {
 973     maxBound = 4;
 974     extent[4] = refExtent[4];
 975     extent[5] = refExtent[5];
 976   }
 977
 978   for (int i = 0; i < maxBound; i = i+2) {
 979     //if we are totally outside the image
 980     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
 981       out = true;
 982       break;
 983     }
 984     //crop to the limit of the image
 985     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
 986     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
 987     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
 988     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
 989   }
 990   if (out)
 991     for (int i = 0; i < maxBound; i = i+2) {
 992       extent[i] = refExtent[i];
 993       extent[i+1] = refExtent[i];
 994     }
 995 }
 996 //----------------------------------------------------------------------------
 997
 998
 999 //----------------------------------------------------------------------------
1000 void vvSlicer::UpdateOrientation()
1001 {
1002   // Set the camera position
1003   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1004   if (cam) {
1005     switch (this->SliceOrientation) {
1006     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1007       cam->SetFocalPoint(0,0,0);
1008       cam->SetPosition(0,0,-1); // -1 if medical ?
1009       cam->SetViewUp(0,-1,0);
1010       break;
1011
1012     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1013       cam->SetFocalPoint(0,0,0);
1014       cam->SetPosition(0,-1,0); // 1 if medical ?
1015       cam->SetViewUp(0,0,1);
1016       break;
1017
1018     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1019       cam->SetFocalPoint(0,0,0);
1020       cam->SetPosition(-1,0,0); // -1 if medical ?
1021       cam->SetViewUp(0,0,1);
1022       break;
1023     }
1024   }
1025 }
1026 //----------------------------------------------------------------------------
1027
1028
1029 //----------------------------------------------------------------------------
1030 void vvSlicer::SetOpacity(double s)
1031 {
1032   this->GetImageActor()->SetOpacity(s);
1033 }
1034 //----------------------------------------------------------------------------
1035
1036
1037 //----------------------------------------------------------------------------
1038 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1039 {
1040   this->Superclass::SetRenderWindow(rw);
1041   this->SetupInteractor(rw->GetInteractor());
1042   ca->SetImageActor(this->GetImageActor());
1043   ca->SetWindowLevel(this->GetWindowLevel());
1044   ca->SetText(2, "<slice>");
1045   ca->SetText(3, "<window>\n<level>");
1046
1047   double bounds[6];
1048   double max = 65000;
1049
1050   bounds[0] = -max;
1051   bounds[1] = max;
1052   bounds[2] = -max;
1053   bounds[3] = max;
1054   bounds[4] = -max;
1055   bounds[5] = max;
1056
1057   crossCursor->SetModelBounds(bounds);
1058   this->GetRenderer()->AddActor(pdmA);
1059   this->GetRenderer()->AddActor(ca);
1060   this->GetRenderer()->ResetCamera();
1061
1062   //this is just a mapping between the labeling of the orientations presented to the user and
1063   //the one used by vtk
1064   SetSliceOrientation(2-(orientation%3));
1065   ResetCamera();
1066 }
1067 //----------------------------------------------------------------------------
1068
1069
1070 //----------------------------------------------------------------------------
1071 void vvSlicer::ResetCamera()
1072 {
1073   this->GetRenderer()->ResetCamera();
1074 }
1075 //----------------------------------------------------------------------------
1076
1077
1078 //----------------------------------------------------------------------------
1079 void vvSlicer::SetDisplayMode(bool i)
1080 {
1081   this->GetRenderer()->SetDraw(i);
1082   if (i)
1083     UpdateDisplayExtent();
1084 }
1085 //----------------------------------------------------------------------------
1086
1087
1088 //----------------------------------------------------------------------------
1089 void vvSlicer::FlipHorizontalView()
1090 {
1091   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1092   if (cam) {
1093     double *position = cam->GetPosition();
1094     double factor[3] = {1, 1, 1};
1095     factor[this->SliceOrientation] = -1;
1096     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1097
1098 /*    switch (this->SliceOrientation) {
1099     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1100       cam->SetPosition(position[0],position[1],-position[2]);
1101       break;
1102
1103     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1104       cam->SetPosition(position[0],-position[1],position[2]);
1105       break;
1106
1107     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1108       cam->SetPosition(-position[0],position[1],position[2]);
1109       break;
1110     }*/
1111
1112     this->Renderer->ResetCameraClippingRange();
1113     this->UpdateDisplayExtent();
1114   }
1115 }
1116 //----------------------------------------------------------------------------
1117
1118
1119 //----------------------------------------------------------------------------
1120 void vvSlicer::FlipVerticalView()
1121 {
1122   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1123   if (cam) {
1124     FlipHorizontalView();
1125     double *viewup = cam->GetViewUp();
1126     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1127     this->UpdateDisplayExtent();
1128   }
1129 }
1130 //----------------------------------------------------------------------------
1131
1132
1133 //----------------------------------------------------------------------------
1134 void vvSlicer::SetColorWindow(double window)
1135 {
1136   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1137   if ( LUT ) {
1138     double level = this->GetWindowLevel()->GetLevel();
1139     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1140     LUT->Build();
1141   }
1142   this->vtkImageViewer2::SetColorWindow(window);
1143 }
1144 //----------------------------------------------------------------------------
1145
1146 //----------------------------------------------------------------------------
1147 void vvSlicer::SetColorLevel(double level)
1148 {
1149   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1150   if ( LUT ) {
1151     double window = this->GetWindowLevel()->GetWindow();
1152     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1153     LUT->Build();
1154   }
1155   this->vtkImageViewer2::SetColorLevel(level);
1156 }
1157 //----------------------------------------------------------------------------
1158
1159 //----------------------------------------------------------------------------
1160 double vvSlicer::GetOverlayColorWindow()
1161 {
1162   if(mOverlayMapper)
1163     return mOverlayMapper->GetWindow();
1164   else
1165     return 0.;
1166 }
1167 //----------------------------------------------------------------------------
1168
1169 //----------------------------------------------------------------------------
1170 double vvSlicer::GetOverlayColorLevel()
1171 {
1172   if(mOverlayMapper)
1173     return mOverlayMapper->GetLevel();
1174   else
1175     return 0.;
1176 }
1177 //----------------------------------------------------------------------------
1178
1179 //----------------------------------------------------------------------------
1180 void vvSlicer::SetOverlayColorWindow(double window)
1181 {
1182   mOverlayMapper->SetWindow(window);
1183 }
1184 //----------------------------------------------------------------------------
1185
1186 //----------------------------------------------------------------------------
1187 void vvSlicer::SetOverlayColorLevel(double level)
1188 {
1189   mOverlayMapper->SetLevel(level);
1190 }
1191 //----------------------------------------------------------------------------
1192
1193 //----------------------------------------------------------------------------
1194 // Returns the min an the max value in a 41x41 region around the mouse pointer
1195 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1196 {
1197   //Get mouse pointer position in view coordinates
1198   double corner1[3];
1199   double corner2[3];
1200   for(int i=0; i<3; i++) {
1201     corner1[i] = mCurrent[i];
1202     corner2[i] = mCurrent[i];
1203   }
1204
1205   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1206   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1207
1208   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1209   int w, h;
1210   this->Renderer->GetTiledSize(&w, &h);
1211   corner1[0] -= 0.2*h/(double)w;
1212   corner2[0] += 0.2*h/(double)w;
1213   corner1[1] -= 0.2;
1214   corner2[1] += 0.2;
1215   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1216   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1217
1218   //Convert to image pixel coordinates (rounded)
1219   transform->TransformPoint(corner1, corner1);
1220   transform->TransformPoint(corner2, corner2);
1221   int iLocalExtents[6];
1222   for(int i=0; i<3; i++) {
1223     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1224     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1225
1226     iLocalExtents[i*2  ] = lrint(corner1[i]);
1227     iLocalExtents[i*2+1] = lrint(corner2[i]);
1228
1229     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1230       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1231   }
1232
1233   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1234   voiFilter->SetInput(image);
1235   voiFilter->SetVOI(iLocalExtents);
1236   voiFilter->Update();
1237   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1238     min = 0;
1239     max = 0;
1240     return;
1241   }
1242
1243   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1244   accFilter->SetInput(voiFilter->GetOutput());
1245   accFilter->Update();
1246
1247   min = *(accFilter->GetMin());
1248   max = *(accFilter->GetMax());
1249 }
1250 //----------------------------------------------------------------------------
1251
1252 //----------------------------------------------------------------------------
1253 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1254 {
1255   ix = lrint(X);
1256   iy = lrint(Y);
1257   iz = lrint(Z);
1258   if (ix < image->GetWholeExtent()[0] ||
1259       ix > image->GetWholeExtent()[1] ||
1260       iy < image->GetWholeExtent()[2] ||
1261       iy > image->GetWholeExtent()[3] ||
1262       iz < image->GetWholeExtent()[4] ||
1263       iz > image->GetWholeExtent()[5] )
1264     return std::numeric_limits<double>::quiet_NaN();
1265
1266   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1267   image->Update();
1268   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1269 }
1270 //----------------------------------------------------------------------------
1271
1272 //----------------------------------------------------------------------------
1273 void vvSlicer::Render()
1274 {
1275   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1276     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1277     legend->UseOpacityOn();
1278     legend->SetVisibility(1);
1279   }
1280   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1281     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1282     legend->UseOpacityOff();
1283     legend->SetVisibility(1);
1284   } else legend->SetVisibility(0);
1285
1286   if (ca->GetVisibility()) {
1287     std::stringstream worldPos;
1288     double pt[3];
1289     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1290     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1291     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1292     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1293
1294     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1295         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1296         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1297         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1298         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1299         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1300
1301
1302       int ix, iy, iz;
1303       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1304
1305       if(ImageActor->GetVisibility())
1306         worldPos << "data value : " << value << std::endl;
1307
1308       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1309                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1310                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1311                           << mCurrentTSlice
1312                           << std::endl;
1313       worldPos << "pixel : " << ix << ' '
1314                              << iy << ' '
1315                              << iz << ' '
1316                              << mCurrentTSlice
1317                              << std::endl;
1318     }
1319     ca->SetText(1,worldPos.str().c_str());
1320   }
1321
1322   if (pdmA->GetVisibility()) {
1323     double x = mCursor[0];
1324     double y = mCursor[1];
1325     double z = mCursor[2];
1326     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1327     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1328     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1329
1330     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1331         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1332         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1333         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1334         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1335         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1336       vtkRenderer * renderer = this->Renderer;
1337
1338       renderer->WorldToView(x,y,z);
1339       renderer->ViewToNormalizedViewport(x,y,z);
1340       renderer->NormalizedViewportToViewport(x,y);
1341       renderer->ViewportToNormalizedDisplay(x,y);
1342       renderer->NormalizedDisplayToDisplay(x,y);
1343       crossCursor->SetFocalPoint(x,y,z);
1344     } else
1345       crossCursor->SetFocalPoint(-1,-1,z);
1346   }
1347
1348
1349   if (mOverlay && mOverlayActor->GetVisibility()) {
1350     if(mLinkOverlayWindowLevel) {
1351       mOverlayMapper->SetWindow(this->GetColorWindow());
1352       mOverlayMapper->SetLevel(this->GetColorLevel());
1353     }
1354     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1355     mOverlayMapper->GetOutput()->Update();
1356     mOverlayMapper->Update();
1357   }
1358   if (mLandMapper)
1359     UpdateLandmarks();
1360
1361   this->GetRenderWindow()->Render();
1362 }
1363 //----------------------------------------------------------------------------
1364
1365
1366 //----------------------------------------------------------------------------
1367 void vvSlicer::UpdateCursorPosition()
1368 {
1369   pdmA->SetVisibility(true);
1370   mCursor[0] = mCurrent[0];
1371   mCursor[1] = mCurrent[1];
1372   mCursor[2] = mCurrent[2];
1373   mCursor[3] = mCurrentTSlice;
1374 }
1375 //----------------------------------------------------------------------------
1376
1377
1378 //----------------------------------------------------------------------------
1379 void vvSlicer::UpdateLandmarks()
1380 {
1381   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1382   if (pd->GetPoints()) {
1383     mLandGlyph->SetRange(0,1);
1384     mLandGlyph->Modified();
1385     mLandGlyph->Update();
1386
1387     mClipBox->Modified();
1388     mLandClipper->Update();
1389     mLandMapper->Update();
1390   }
1391
1392 }
1393 //----------------------------------------------------------------------------
1394
1395
1396 //----------------------------------------------------------------------------
1397 void vvSlicer::SetSlice(int slice)
1398 {
1399   int *range = this->GetSliceRange();
1400   if (range) {
1401     if (slice < range[0]) {
1402       slice = range[0];
1403     } else if (slice > range[1]) {
1404       slice = range[1];
1405     }
1406   }
1407
1408   if (this->Slice == slice) {
1409     return;
1410   }
1411
1412   this->Slice = slice;
1413   SetContourSlice();
1414   this->Modified();
1415   this->UpdateDisplayExtent();
1416
1417   // Seems to work without this line
1418   //this->Render();
1419 }
1420 //----------------------------------------------------------------------------
1421
1422
1423 //----------------------------------------------------------------------------
1424 void vvSlicer::SetContourSlice()
1425 {
1426   if (mSurfaceCutActors.size() > 0)
1427     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1428          i!=mSurfaceCutActors.end(); i++) {
1429
1430       (*i)->SetSlicingOrientation(this->SliceOrientation);
1431       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1432                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1433     }
1434 }
1435 //----------------------------------------------------------------------------
1436
1437
1438 //----------------------------------------------------------------------------
1439 void vvSlicer::ForceUpdateDisplayExtent()
1440 {
1441   this->UpdateDisplayExtent();
1442 }
1443 //----------------------------------------------------------------------------
1444
1445
1446 //----------------------------------------------------------------------------
1447 int* vvSlicer::GetDisplayExtent()
1448 {
1449   return this->GetImageActor()->GetDisplayExtent();
1450 }
1451 //----------------------------------------------------------------------------
1452
1453
1454 //----------------------------------------------------------------------------
1455 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1456 {
1457   this->Superclass::PrintSelf(os, indent);
1458 }
1459 //----------------------------------------------------------------------------
1460
1461 //----------------------------------------------------------------------------
1462 void vvSlicer::SetVFColor(double r, double g, double b)
1463 {
1464   double mVFColorHSV[3];
1465   mVFColor[0] = r;
1466   mVFColor[1] = g;
1467   mVFColor[2] = b;
1468
1469   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1470   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1471   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1472   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1473
1474   this->Render();
1475 }
1476