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   mCurrentFusionTSlice = 0;
  86   mCurrentOverlayTSlice = 0;
  87   mUseReducedExtent = false;
  88
  89   mCurrent[0] = -VTK_DOUBLE_MAX;
  90   mCurrent[1] = -VTK_DOUBLE_MAX;
  91   mCurrent[2] = -VTK_DOUBLE_MAX;
  92
  93   mCursor[0] = -VTK_DOUBLE_MAX;
  94   mCursor[1] = -VTK_DOUBLE_MAX;
  95   mCursor[2] = -VTK_DOUBLE_MAX;
  96   mCursor[3] = -VTK_DOUBLE_MAX;
  97
  98   mSubSampling = 5;
  99   mScale = 1;
 100   mVFLog = 0;
 101   mVFWidth = 1;
 102   mVFColor[0] = 0;
 103   mVFColor[1] = 1;
 104   mVFColor[2] = 0;
 105
 106   crossCursor = vtkSmartPointer<vtkCursor2D>::New();
 107   crossCursor->AllOff();
 108   crossCursor->AxesOn();
 109   crossCursor->SetTranslationMode(1);
 110   crossCursor->SetRadius(2);
 111
 112   pdm = vtkSmartPointer<vtkPolyDataMapper2D>::New();
 113   pdm->SetInput(crossCursor->GetOutput());
 114
 115   pdmA = vtkSmartPointer<vtkActor2D>::New();
 116   pdmA->SetMapper(pdm);
 117   pdmA->GetProperty()->SetColor(255,10,212);
 118   pdmA->SetVisibility(0);
 119   pdmA->SetPickable(0);
 120
 121   ca = vtkSmartPointer<vtkCornerAnnotation>::New();
 122   ca->GetTextProperty()->SetColor(255,10,212);
 123   ca->SetVisibility(1);
 124   mFileName = "";
 125
 126   mVF = NULL;
 127   mOverlay = NULL;
 128   mFusion = NULL;
 129   mLandmarks = NULL;
 130
 131   legend = vtkSmartPointer<vtkScalarBarActor>::New();
 132   //legend->SetTitle("test!");
 133   legend->SetPosition(0.82,0.18);
 134   legend->SetWidth(0.1);
 135   legend->SetVisibility(0);
 136   legend->SetLabelFormat("%.1f");
 137   this->GetRenderer()->AddActor(legend);
 138   showFusionLegend = false;
 139
 140   this->WindowLevel->Delete();
 141   this->WindowLevel = vvImageMapToWLColors::New();
 142
 143   this->InstallPipeline();
 144
 145   mLinkOverlayWindowLevel = true;
 146
 147 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 148   this->GetImageActor()->GetMapper()->BorderOn();
 149 #endif
 150
 151   mSlicingTransform = vtkSmartPointer<vtkTransform>::New();
 152   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
 153   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
 154   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
 155 }
 156 //------------------------------------------------------------------------------
 157
 158
 159 //------------------------------------------------------------------------------
 160 vtkImageMapToWindowLevelColors* vvSlicer::GetOverlayMapper()
 161 {
 162   return mOverlayMapper.GetPointer();
 163 }
 164 //------------------------------------------------------------------------------
 165
 166
 167 //------------------------------------------------------------------------------
 168 vvBlendImageActor* vvSlicer::GetOverlayActor()
 169 {
 170   return mOverlayActor.GetPointer();
 171 }
 172 //------------------------------------------------------------------------------
 173
 174
 175 //------------------------------------------------------------------------------
 176 vtkImageMapToColors* vvSlicer::GetFusionMapper()
 177 {
 178   return mFusionMapper.GetPointer();
 179 }
 180 //------------------------------------------------------------------------------
 181
 182
 183 //------------------------------------------------------------------------------
 184 vtkImageActor* vvSlicer::GetFusionActor()
 185 {
 186   return mFusionActor.GetPointer();
 187 }
 188 //------------------------------------------------------------------------------
 189
 190
 191 //------------------------------------------------------------------------------
 192 vtkActor* vvSlicer::GetVFActor()
 193 {
 194   return mVFActor.GetPointer();
 195 }
 196 //------------------------------------------------------------------------------
 197
 198
 199 //------------------------------------------------------------------------------
 200 vtkCornerAnnotation* vvSlicer::GetAnnotation()
 201 {
 202   return ca.GetPointer();
 203 }
 204 //------------------------------------------------------------------------------
 205
 206
 207 //------------------------------------------------------------------------------
 208 void vvSlicer::EnableReducedExtent(bool b)
 209 {
 210   mUseReducedExtent = b;
 211 }
 212 //------------------------------------------------------------------------------
 213
 214
 215 //------------------------------------------------------------------------------
 216 void vvSlicer::SetReducedExtent(int * ext)
 217 {
 218   copyExtent(ext, mReducedExtent);
 219 }
 220 //------------------------------------------------------------------------------
 221
 222
 223 //------------------------------------------------------------------------------
 224 void vvSlicer::AddContour(vvMesh::Pointer contour,bool propagate)
 225 {
 226
 227   mSurfaceCutActors.push_back(new vvMeshActor());
 228   if (propagate)
 229     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice,mVF);
 230   else
 231     mSurfaceCutActors.back()->Init(contour,mCurrentTSlice);
 232   mSurfaceCutActors.back()->SetSlicingOrientation(SliceOrientation);
 233   this->GetRenderer()->AddActor(mSurfaceCutActors.back()->GetActor());
 234
 235   SetContourSlice();
 236 }
 237 //------------------------------------------------------------------------------
 238
 239
 240 //------------------------------------------------------------------------------
 241 void vvSlicer::ToggleContourSuperposition()
 242 {
 243   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 244        i!=mSurfaceCutActors.end(); i++)
 245     (*i)->ToggleSuperposition();
 246 }
 247 //------------------------------------------------------------------------------
 248
 249
 250 //------------------------------------------------------------------------------
 251 void vvSlicer::SetCursorColor(int r,int g, int b)
 252 {
 253   pdmA->GetProperty()->SetColor(r,g,b);
 254 }
 255 //------------------------------------------------------------------------------
 256
 257
 258 //------------------------------------------------------------------------------
 259 void vvSlicer::SetCursorVisibility(bool s)
 260 {
 261   pdmA->SetVisibility(s);
 262 }
 263 //------------------------------------------------------------------------------
 264
 265
 266 //------------------------------------------------------------------------------
 267 bool vvSlicer::GetCursorVisibility()
 268 {
 269   return pdmA->GetVisibility();
 270 }
 271 //------------------------------------------------------------------------------
 272
 273
 274 //------------------------------------------------------------------------------
 275 void vvSlicer::SetCornerAnnotationVisibility(bool s)
 276 {
 277   ca->SetVisibility(s);
 278 }
 279 //------------------------------------------------------------------------------
 280
 281
 282 //------------------------------------------------------------------------------
 283 bool vvSlicer::GetCornerAnnotationVisibility()
 284 {
 285   return ca->GetVisibility();
 286 }
 287 //------------------------------------------------------------------------------
 288
 289
 290 //------------------------------------------------------------------------------
 291 vvSlicer::~vvSlicer()
 292 {
 293   for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 294        i!=mSurfaceCutActors.end(); i++)
 295     delete (*i);
 296   delete [] mReducedExtent;
 297 }
 298 //------------------------------------------------------------------------------
 299
 300 //------------------------------------------------------------------------------
 301 double* vvSlicer::GetCurrentPosition()
 302 {
 303   return mCurrentBeforeSlicingTransform;
 304 }
 305 //------------------------------------------------------------------------------
 306
 307 //------------------------------------------------------------------------------
 308 void vvSlicer::SetCurrentPosition(double x, double y, double z, int t)
 309 {
 310   mCurrentBeforeSlicingTransform[0]=x;
 311   mCurrentBeforeSlicingTransform[1]=y;
 312   mCurrentBeforeSlicingTransform[2]=z;
 313   mSlicingTransform->GetInverse()->TransformPoint(mCurrentBeforeSlicingTransform,mCurrent);
 314   SetTSlice(t);
 315 }
 316 //------------------------------------------------------------------------------
 317
 318
 319 //------------------------------------------------------------------------------
 320 void vvSlicer::SetImage(vvImage::Pointer image)
 321 {
 322   if (image->GetVTKImages().size()) {
 323     mImage = image;
 324
 325     if (!mImageReslice) {
 326       mImageReslice = vtkSmartPointer<vtkImageReslice>::New();
 327       mImageReslice->SetInterpolationModeToLinear();
 328       mImageReslice->AutoCropOutputOn();
 329       mImageReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 330     }
 331
 332     mConcatenatedTransform->Identity();
 333     mConcatenatedTransform->Concatenate(mImage->GetTransform()[0]);
 334     mConcatenatedTransform->Concatenate(mSlicingTransform);
 335     mImageReslice->SetResliceTransform(mConcatenatedTransform);
 336     mImageReslice->SetInput(0, mImage->GetFirstVTKImageData());
 337     mImageReslice->UpdateInformation();
 338
 339     this->Superclass::SetInput(mImageReslice->GetOutput());
 340
 341     int extent[6];
 342     this->GetInput()->GetWholeExtent(extent);
 343
 344     // Prevent crash when reload -> change slice if outside extent
 345     if (Slice < extent[SliceOrientation*2] || Slice>=extent[SliceOrientation*2+1]) {
 346       Slice = (extent[SliceOrientation*2+1]+extent[SliceOrientation*2])/2.0;
 347     }
 348
 349     // Make sure that the required part image has been computed
 350     extent[SliceOrientation*2] = Slice;
 351     extent[SliceOrientation*2+1] = Slice;
 352     mImageReslice->GetOutput()->SetUpdateExtent(extent);
 353     mImageReslice->GetOutput()->Update();
 354
 355     this->UpdateDisplayExtent();
 356
 357     mCurrentTSlice = 0;
 358     ca->SetText(0,mFileName.c_str());
 359   }
 360 }
 361 //------------------------------------------------------------------------------
 362
 363
 364 //------------------------------------------------------------------------------
 365 void vvSlicer::SetOverlay(vvImage::Pointer overlay)
 366 {
 367   if (overlay->GetVTKImages().size()) {
 368     mOverlay = overlay;
 369
 370     if (!mOverlayReslice) {
 371       mOverlayReslice = vtkSmartPointer<vtkImageReslice>::New();
 372       mOverlayReslice->SetInterpolationModeToLinear();
 373       mOverlayReslice->AutoCropOutputOn();
 374       mOverlayReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 375     }
 376
 377     mConcatenatedOverlayTransform->Identity();
 378     mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[0]);
 379     mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 380     mOverlayReslice->SetResliceTransform(mConcatenatedOverlayTransform);
 381     mOverlayReslice->SetInput(0, mOverlay->GetFirstVTKImageData());
 382     mImageReslice->UpdateInformation();
 383
 384     if (!mOverlayMapper)
 385       mOverlayMapper = vtkSmartPointer<vtkImageMapToWindowLevelColors>::New();
 386     mOverlayMapper->SetInput(mOverlayReslice->GetOutput());
 387
 388     if (!mOverlayActor) {
 389       mOverlayActor = vtkSmartPointer<vvBlendImageActor>::New();
 390       mOverlayActor->SetInput(mOverlayMapper->GetOutput());
 391       mOverlayActor->SetPickable(0);
 392       mOverlayActor->SetVisibility(true);
 393       mOverlayActor->SetOpacity(0.5);
 394 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 395       mOverlayActor->GetMapper()->BorderOn();
 396 #endif
 397       }
 398
 399     //stupid but necessary : the Overlay need to be rendered before fusion
 400     if (mFusionActor) {
 401       this->GetRenderer()->RemoveActor(mFusionActor);
 402       this->GetRenderer()->AddActor(mOverlayActor);
 403       this->GetRenderer()->AddActor(mFusionActor);
 404     } else
 405       this->GetRenderer()->AddActor(mOverlayActor);
 406
 407     //Synchronize orientation and slice
 408     AdjustResliceToSliceOrientation(mOverlayReslice);
 409     this->UpdateDisplayExtent();
 410     this->SetTSlice(mCurrentTSlice);
 411   }
 412 }
 413 //------------------------------------------------------------------------------
 414
 415
 416 //------------------------------------------------------------------------------
 417 void vvSlicer::SetFusion(vvImage::Pointer fusion)
 418 {
 419   if (fusion->GetVTKImages().size()) {
 420     mFusion = fusion;
 421
 422     if (!mFusionReslice) {
 423       mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
 424       mFusionReslice->SetInterpolationModeToLinear();
 425       mFusionReslice->AutoCropOutputOn();
 426       mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
 427     }
 428
 429     mConcatenatedFusionTransform->Identity();
 430     mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[0]);
 431     mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 432     mFusionReslice->SetResliceTransform(mConcatenatedFusionTransform);
 433     mFusionReslice->SetInput(0, mFusion->GetFirstVTKImageData());
 434     mFusionReslice->UpdateInformation();
 435
 436     if (!mFusionMapper)
 437       mFusionMapper = vtkSmartPointer<vtkImageMapToColors>::New();
 438
 439     vtkSmartPointer<vtkLookupTable> lut = vtkLookupTable::New();
 440     lut->SetRange(0, 1);
 441     lut->SetValueRange(0, 1);
 442     lut->SetSaturationRange(0, 0);
 443     lut->Build();
 444     mFusionMapper->SetLookupTable(lut);
 445     mFusionMapper->SetInput(mFusionReslice->GetOutput());
 446
 447     if (!mFusionActor) {
 448       mFusionActor = vtkSmartPointer<vtkImageActor>::New();
 449       mFusionActor->SetInput(mFusionMapper->GetOutput());
 450       mFusionActor->SetPickable(0);
 451       mFusionActor->SetVisibility(true);
 452       mFusionActor->SetOpacity(0.7);
 453 #if VTK_MAJOR_VERSION >= 6 || (VTK_MAJOR_VERSION >= 5 && VTK_MINOR_VERSION >= 10)
 454       mFusionActor->GetMapper()->BorderOn();
 455 #endif
 456       this->GetRenderer()->AddActor(mFusionActor);
 457     }
 458
 459     //Synchronize orientation and slice
 460     AdjustResliceToSliceOrientation(mFusionReslice);
 461     this->UpdateDisplayExtent();
 462     this->SetTSlice(mCurrentTSlice);
 463   }
 464 }
 465 //------------------------------------------------------------------------------
 466
 467
 468 //------------------------------------------------------------------------------
 469 bool vvSlicer::GetActorVisibility(const std::string& actor_type, int overlay_index)
 470 {
 471   bool vis = false;
 472   if (actor_type == "image") {
 473     vis = this->ImageActor->GetVisibility();
 474   }
 475   else if (actor_type == "vector") {
 476     vis = this->mVFActor->GetVisibility();
 477   }
 478   else if (actor_type == "overlay") {
 479     vis = this->mOverlayActor->GetVisibility();
 480   }
 481   else if (actor_type == "fusion") {
 482     vis = this->mFusionActor->GetVisibility();
 483   }
 484   else if (actor_type == "contour")
 485     vis = this->mSurfaceCutActors[overlay_index]->GetActor()->GetVisibility();
 486
 487   return vis;
 488 }
 489 //------------------------------------------------------------------------------
 490
 491 //------------------------------------------------------------------------------
 492 void vvSlicer::SetActorVisibility(const std::string& actor_type, int overlay_index ,bool vis)
 493 {
 494   if (actor_type == "image") {
 495     this->ImageActor->SetVisibility(vis);
 496   }
 497   else if (actor_type == "vector") {
 498     this->mVFActor->SetVisibility(vis);
 499   }
 500   else if (actor_type == "overlay") {
 501     this->mOverlayActor->SetVisibility(vis);
 502   }
 503   else if (actor_type == "fusion") {
 504     this->mFusionActor->SetVisibility(vis);
 505   }
 506   else if (actor_type == "contour")
 507     this->mSurfaceCutActors[overlay_index]->GetActor()->SetVisibility(vis);
 508   UpdateDisplayExtent();
 509 }
 510 //------------------------------------------------------------------------------
 511
 512 //------------------------------------------------------------------------------
 513 void vvSlicer::SetVF(vvImage::Pointer vf)
 514 {
 515   if (vf->GetVTKImages().size()) {
 516     mVF = vf;
 517
 518     if (!mAAFilter) {
 519       mAAFilter= vtkSmartPointer<vtkAssignAttribute>::New();
 520       mVOIFilter = vtkSmartPointer<vtkExtractVOI>::New();
 521       mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 522     }
 523     mVOIFilter->SetInput(vf->GetFirstVTKImageData());
 524     mAAFilter->SetInput(mVOIFilter->GetOutput());
 525     ///This tells VTK to use the scalar (pixel) data of the image to draw the little arrows
 526     mAAFilter->Assign(vtkDataSetAttributes::SCALARS, vtkDataSetAttributes::VECTORS, vtkAssignAttribute::POINT_DATA);
 527
 528     if (!mArrow)
 529       mArrow = vtkSmartPointer<vvGlyphSource>::New();
 530     mArrow->SetGlyphTypeToSpecificArrow();
 531     mArrow->SetScale(mScale);
 532     mArrow->FilledOff();
 533
 534     // Glyph the gradient vector (with arrows)
 535     if (!mGlyphFilter)
 536       mGlyphFilter = vtkSmartPointer<vvGlyph2D>::New();
 537     mGlyphFilter->SetInput(mAAFilter->GetOutput());
 538     mGlyphFilter->SetSource(mArrow->GetOutput());
 539     mGlyphFilter->ScalingOn();
 540     mGlyphFilter->SetScaleModeToScaleByVector();
 541     mGlyphFilter->OrientOn();
 542     mGlyphFilter->SetVectorModeToUseVector();
 543     mGlyphFilter->SetColorModeToColorByVector();
 544
 545     if (!mVFColorLUT)
 546       mVFColorLUT = vtkSmartPointer<vtkLookupTable>::New();
 547
 548     double mVFColorHSV[3];
 549     vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
 550     mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
 551     mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
 552     mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
 553
 554     if (!mVFMapper)
 555       mVFMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 556     mVFMapper->SetInput(mGlyphFilter->GetOutput());
 557     mVFMapper->ImmediateModeRenderingOn();
 558     mVFMapper->SetLookupTable(mVFColorLUT);
 559
 560     if (!mVFActor)
 561       mVFActor = vtkSmartPointer<vtkActor>::New();
 562     mVFActor->SetMapper(mVFMapper);
 563     mVFActor->SetPickable(0);
 564     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 565     this->UpdateDisplayExtent();
 566     this->GetRenderer()->AddActor(mVFActor);
 567
 568     //Synchronize slice
 569     SetTSlice(mCurrentTSlice);
 570   }
 571 }
 572 //------------------------------------------------------------------------------
 573
 574
 575 //------------------------------------------------------------------------------
 576 void vvSlicer::SetLandmarks(vvLandmarks* landmarks)
 577 {
 578   mLandmarks = landmarks;
 579   if (landmarks) {
 580
 581     if (!mCross)
 582       mCross = vtkSmartPointer<vtkCursor3D>::New();
 583     mCross->SetFocalPoint(0.0,0.0,0.0);
 584     mCross->SetModelBounds(-10,10,-10,10,-10,10);
 585     mCross->AllOff();
 586     mCross->AxesOn();
 587
 588     if (!mLandGlyph)
 589       mLandGlyph = vtkSmartPointer<vtkGlyph3D>::New();
 590     mLandGlyph->SetSource(mCross->GetOutput());
 591     mLandGlyph->SetInput(landmarks->GetOutput());
 592     //mLandGlyph->SetIndexModeToScalar();
 593     mLandGlyph->SetRange(0,1);
 594     mLandGlyph->ScalingOff();
 595
 596     mLandGlyph->SetColorModeToColorByScalar();
 597
 598     if (!mClipBox)
 599       mClipBox = vtkSmartPointer<vtkBox>::New();
 600     if (!mLandClipper)
 601       mLandClipper = vtkSmartPointer<vtkClipPolyData>::New();
 602     mLandClipper->InsideOutOn();
 603     mLandClipper->SetInput(mLandGlyph->GetOutput());
 604     mLandClipper->SetClipFunction(mClipBox);
 605
 606     if (!mLandMapper)
 607       mLandMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 608     mLandMapper->SetInputConnection(mLandClipper->GetOutputPort());
 609     //mLandMapper->ScalarVisibilityOff();
 610
 611     if (!mLandActor)
 612       mLandActor = vtkSmartPointer<vtkActor>::New();
 613     mLandActor->SetMapper(mLandMapper);
 614     mLandActor->GetProperty()->SetColor(255,10,212);
 615     mLandActor->SetPickable(0);
 616     mLandActor->SetVisibility(true);
 617     this->UpdateDisplayExtent();
 618     this->GetRenderer()->AddActor(mLandActor);
 619   }
 620 }
 621 //------------------------------------------------------------------------------
 622
 623 //------------------------------------------------------------------------------
 624 //FIXME: this function leaks memory, we should fix it someday :)
 625 void vvSlicer::RemoveActor(const std::string& actor_type, int overlay_index)
 626 {
 627   if (actor_type == "vector") {
 628     Renderer->RemoveActor(mVFActor);
 629     mGlyphFilter=NULL;
 630     mVF = NULL;
 631     mArrow = NULL;
 632     mAAFilter=NULL;
 633     mVOIFilter = NULL;
 634     mVFMapper = NULL;
 635     mVFActor = NULL;
 636   }
 637   if (actor_type == "overlay") {
 638     Renderer->RemoveActor(mOverlayActor);
 639     mOverlay = NULL;
 640     mOverlayActor = NULL;
 641     mOverlayMapper = NULL;
 642   }
 643   if (actor_type == "fusion") {
 644     Renderer->RemoveActor(mFusionActor);
 645     mFusion = NULL;
 646     mFusionActor = NULL;
 647     mFusionMapper = NULL;
 648   }
 649   if (actor_type == "contour") {
 650     Renderer->RemoveActor(this->mSurfaceCutActors[overlay_index]->GetActor());
 651     mSurfaceCutActors.erase(mSurfaceCutActors.begin()+overlay_index);
 652   }
 653 }
 654 //------------------------------------------------------------------------------
 655
 656
 657 //------------------------------------------------------------------------------
 658 void vvSlicer::SetVFSubSampling(int sub)
 659 {
 660   if (mVOIFilter) {
 661     mVOIFilter->SetSampleRate(mSubSampling,mSubSampling,mSubSampling);
 662     mSubSampling = sub;
 663   }
 664   UpdateDisplayExtent();
 665   Render();
 666 }
 667 //------------------------------------------------------------------------------
 668
 669
 670 //------------------------------------------------------------------------------
 671 void vvSlicer::SetVFScale(int scale)
 672 {
 673   mScale = scale;
 674   if (mArrow)
 675     mArrow->SetScale(mScale);
 676   UpdateDisplayExtent();
 677   Render();
 678 }
 679 //------------------------------------------------------------------------------
 680
 681 //------------------------------------------------------------------------------
 682 void vvSlicer::SetVFWidth(int width)
 683 {
 684   mVFWidth = width;
 685   if (mVFActor)
 686     mVFActor->GetProperty()->SetLineWidth(mVFWidth);
 687   UpdateDisplayExtent();
 688   Render();
 689 }
 690 //------------------------------------------------------------------------------
 691
 692
 693 //------------------------------------------------------------------------------
 694 void vvSlicer::SetVFLog(int log)
 695 {
 696   mVFLog = log;
 697   if (mGlyphFilter) {
 698     mGlyphFilter->SetUseLog(mVFLog);
 699     mGlyphFilter->Modified();
 700   }
 701   UpdateDisplayExtent();
 702   Render();
 703 }
 704 //------------------------------------------------------------------------------
 705
 706
 707 //------------------------------------------------------------------------------
 708 void vvSlicer::SetTSlice(int t)
 709 {
 710   if (t < 0)
 711     t = 0;
 712   else if ((unsigned int)t >= mImage->GetVTKImages().size())
 713     t = mImage->GetVTKImages().size() -1;
 714
 715   // Update transform
 716   mConcatenatedTransform->Identity();
 717   mConcatenatedTransform->Concatenate(mImage->GetTransform()[t]);
 718   mConcatenatedTransform->Concatenate(mSlicingTransform);
 719
 720   // Update image data
 721   mCurrentTSlice = t;
 722   mImageReslice->SetInput( mImage->GetVTKImages()[mCurrentTSlice] );
 723   if (mVF && mVFActor->GetVisibility()) {
 724     if (mVF->GetVTKImages().size() > (unsigned int)mCurrentTSlice)
 725       mVOIFilter->SetInput(mVF->GetVTKImages()[mCurrentTSlice]);
 726   }
 727   if (mOverlay && mOverlayActor->GetVisibility()) {
 728     if (mOverlay->GetVTKImages().size() > (unsigned int)t) {
 729       mCurrentOverlayTSlice = t;
 730       mOverlayReslice->SetInput( mOverlay->GetVTKImages()[mCurrentOverlayTSlice] );
 731
 732       // Update overlay transform
 733       mConcatenatedOverlayTransform->Identity();
 734       mConcatenatedOverlayTransform->Concatenate(mOverlay->GetTransform()[mCurrentOverlayTSlice]);
 735       mConcatenatedOverlayTransform->Concatenate(mSlicingTransform);
 736     }
 737   }
 738   if (mFusion && mFusionActor->GetVisibility()) {
 739     if (mFusion->GetVTKImages().size() > (unsigned int)t) {
 740       mCurrentFusionTSlice = t;
 741       mFusionReslice->SetInput( mFusion->GetVTKImages()[mCurrentFusionTSlice]);
 742
 743       // Update fusion transform
 744       mConcatenatedFusionTransform->Identity();
 745       mConcatenatedFusionTransform->Concatenate(mFusion->GetTransform()[mCurrentFusionTSlice]);
 746       mConcatenatedFusionTransform->Concatenate(mSlicingTransform);
 747     }
 748   }
 749   if (mSurfaceCutActors.size() > 0)
 750     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
 751          i!=mSurfaceCutActors.end(); i++)
 752       (*i)->SetTimeSlice(mCurrentTSlice);
 753   UpdateDisplayExtent();
 754 }
 755 //------------------------------------------------------------------------------
 756
 757
 758 //------------------------------------------------------------------------------
 759 int vvSlicer::GetTSlice()
 760 {
 761   return mCurrentTSlice;
 762 }
 763 //------------------------------------------------------------------------------
 764
 765 //------------------------------------------------------------------------------
 766 int vvSlicer::GetFusionTSlice()
 767 {
 768   return mCurrentFusionTSlice;
 769 }
 770 //------------------------------------------------------------------------------
 771
 772 //------------------------------------------------------------------------------
 773 int vvSlicer::GetOverlayTSlice()
 774 {
 775   return mCurrentOverlayTSlice;
 776 }
 777 //------------------------------------------------------------------------------
 778
 779 //------------------------------------------------------------------------------
 780 void vvSlicer::SetSliceOrientation(int orientation)
 781 {
 782   //if 2D image, force to watch in Axial View
 783   int extent[6];
 784   this->GetInput()->GetWholeExtent(extent);
 785   if (extent[5]-extent[4] <= 2)
 786     orientation = vtkImageViewer2::SLICE_ORIENTATION_XY;
 787
 788   if (orientation < vtkImageViewer2::SLICE_ORIENTATION_YZ ||
 789       orientation > vtkImageViewer2::SLICE_ORIENTATION_XY) {
 790     vtkErrorMacro("Error - invalid slice orientation " << orientation);
 791     return;
 792   }
 793
 794   this->SliceOrientation = orientation;
 795
 796   if(mFusion)
 797     AdjustResliceToSliceOrientation(mFusionReslice);
 798
 799   if(mOverlay)
 800     AdjustResliceToSliceOrientation(mOverlayReslice);
 801
 802   // Update the viewer
 803   int *range = this->GetSliceRange();
 804   if (range)
 805     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 806
 807   // Go to current cursor position
 808   // double* cursorPos = GetCursorPosition();
 809   // DDV(cursorPos, 3);
 810   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 811
 812   this->UpdateOrientation();
 813   this->UpdateDisplayExtent();
 814
 815   if (this->Renderer && this->GetInput()) {
 816     double scale = this->Renderer->GetActiveCamera()->GetParallelScale();
 817     this->Renderer->ResetCamera();
 818     this->Renderer->GetActiveCamera()->SetParallelScale(scale);
 819   }
 820
 821   SetContourSlice();
 822 }
 823 //----------------------------------------------------------------------------
 824
 825 //------------------------------------------------------------------------------
 826 // This function ensures that we sample the slices of a vtkImageReslice filter
 827 // in the direction of the slicer (SliceOrientation) similarly as mImageReslice.
 828 // In other words, we change the grid of the reslice in the same way as the grid
 829 // of the displayed image in the slicing direction.
 830 void vvSlicer::AdjustResliceToSliceOrientation(vtkImageReslice *reslice)
 831 {
 832   // Reset autocrop and update output information
 833   reslice->SetOutputOriginToDefault();
 834   reslice->SetOutputSpacingToDefault();
 835   reslice->GetOutput()->UpdateInformation();
 836
 837   // Ge new origin / spacing
 838   double origin[3];
 839   double spacing[3];
 840   reslice->GetOutput()->GetOrigin(origin);
 841   reslice->GetOutput()->GetSpacing(spacing);
 842
 843   // Use similar spacing as the image in the direction SliceOrientation
 844   spacing[this->SliceOrientation] = mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 845
 846   // Modify origin to be on the image grid in the direction SliceOrientation in 3 steps
 847   // Step 1: from world coordinates to image coordinates
 848   origin[this->SliceOrientation] -= mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 849   origin[this->SliceOrientation] /= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 850   // Step 2: round to superior grid positionInc
 851   origin[this->SliceOrientation] = itk::Math::Ceil<double>(origin[this->SliceOrientation]);
 852   // Step 3: back to world coordinates
 853   origin[this->SliceOrientation] *= mImageReslice->GetOutput()->GetSpacing()[this->SliceOrientation];
 854   origin[this->SliceOrientation] += mImageReslice->GetOutput()->GetOrigin()[this->SliceOrientation];
 855
 856   // Set new spacing and origin
 857   reslice->SetOutputOrigin(origin);
 858   reslice->SetOutputSpacing(spacing);
 859   reslice->UpdateInformation();
 860   reslice->GetOutput()->UpdateInformation();
 861 }
 862 //------------------------------------------------------------------------------
 863
 864 //----------------------------------------------------------------------------
 865 int * vvSlicer::GetExtent(){
 866   int *w_ext;
 867   if (mUseReducedExtent) {
 868     w_ext = mReducedExtent;
 869   } else w_ext = GetInput()->GetWholeExtent();
 870   return w_ext;
 871 }
 872 //----------------------------------------------------------------------------
 873
 874
 875 //----------------------------------------------------------------------------
 876 int vvSlicer::GetOrientation()
 877 {
 878   return this->SliceOrientation;
 879 }
 880 //----------------------------------------------------------------------------
 881
 882
 883 //----------------------------------------------------------------------------
 884 void vvSlicer::UpdateDisplayExtent()
 885 {
 886   vtkImageData *input = this->GetInput();
 887   if (!input || !this->ImageActor) {
 888     return;
 889   }
 890   input->UpdateInformation();
 891
 892   // Local copy of extent
 893   int w_ext[6];
 894   int* ext = GetExtent();
 895   copyExtent(ext, w_ext);
 896   // Set slice value
 897   int s = this->Slice > ext[this->SliceOrientation*2+1] ? ext[this->SliceOrientation*2 + 1] : this->Slice;
 898   w_ext[ this->SliceOrientation*2   ] = s;
 899   w_ext[ this->SliceOrientation*2+1 ] = s;
 900
 901   // Image actor
 902   this->ImageActor->SetDisplayExtent(w_ext);
 903
 904   // Overlay image actor
 905   if (mOverlay && mOverlayActor->GetVisibility()) {
 906     AdjustResliceToSliceOrientation(mOverlayReslice);
 907     int overExtent[6];
 908     this->ConvertImageToImageDisplayExtent(input, w_ext, mOverlayReslice->GetOutput(), overExtent);
 909     ClipDisplayedExtent(overExtent, mOverlayMapper->GetInput()->GetWholeExtent());
 910     mOverlayActor->SetDisplayExtent( overExtent );
 911   }
 912
 913   // Fusion image actor
 914   if (mFusion && mFusionActor->GetVisibility()) {
 915     AdjustResliceToSliceOrientation(mFusionReslice);
 916     int fusExtent[6];
 917     this->ConvertImageToImageDisplayExtent(input, w_ext, mFusionReslice->GetOutput(), fusExtent);
 918     ClipDisplayedExtent(fusExtent, mFusionMapper->GetInput()->GetWholeExtent());
 919     mFusionActor->SetDisplayExtent(fusExtent);
 920   }
 921
 922   // Vector field actor
 923   double* camera = Renderer->GetActiveCamera()->GetPosition();
 924   double* image_bounds = ImageActor->GetBounds();
 925   double position[3] = {0, 0, 0};
 926   position[this->SliceOrientation] = image_bounds[this->SliceOrientation*2];
 927
 928   //print_vector<double, 6>("camera", camera);
 929   //print_vector<double, 6>("image_bounds", image_bounds);
 930   //print_vector<double, 3>("position", position);
 931
 932   // find where to place the VF actor. to deal with
 933   // z-buffer issues, the VF is placed right in front of the image,
 934   // subject to a small offset. the position actually depends on the
 935   // the location of the camera relative to the image.
 936   double offset = 1;
 937   if (camera[this->SliceOrientation] < image_bounds[this->SliceOrientation*2])
 938     offset = -1;
 939
 940   if (mVF && mVFActor->GetVisibility()) {
 941     int vfExtent[6];
 942     mVF->GetVTKImages()[0]->UpdateInformation();
 943     this->ConvertImageToImageDisplayExtent(input, w_ext, mVF->GetVTKImages()[0], vfExtent);
 944     ClipDisplayedExtent(vfExtent, mVOIFilter->GetInput()->GetWholeExtent());
 945     mVOIFilter->SetVOI(vfExtent);
 946     int orientation[3] = {1,1,1};
 947     orientation[this->SliceOrientation] = 0;
 948     mGlyphFilter->SetOrientation(orientation[0], orientation[1], orientation[2]);
 949     mVFMapper->Update();
 950
 951     position[this->SliceOrientation] += offset;
 952     mVFActor->SetPosition(position);
 953   }
 954
 955   // Landmarks actor
 956   if (mLandActor) {
 957     if (mClipBox) {
 958       double bounds [6];
 959       for(unsigned int i=0; i<6; i++)
 960         bounds[i] = ImageActor->GetBounds()[i];
 961       bounds[ this->SliceOrientation*2   ] = ImageActor->GetBounds()[ this->SliceOrientation*2  ]-fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 962       bounds[ this->SliceOrientation*2+1 ] = ImageActor->GetBounds()[ this->SliceOrientation*2+1 ]+fabs(this->GetInput()->GetSpacing()[this->SliceOrientation]);
 963       mClipBox->SetBounds(bounds);
 964       UpdateLandmarks();
 965     }
 966
 967     position[this->SliceOrientation] = offset;
 968     mLandActor->SetPosition(position);
 969   }
 970
 971   // Figure out the correct clipping range
 972   if (this->Renderer) {
 973     if (this->InteractorStyle &&
 974         this->InteractorStyle->GetAutoAdjustCameraClippingRange()) {
 975       this->Renderer->ResetCameraClippingRange();
 976     } else {
 977       vtkCamera *cam = this->Renderer->GetActiveCamera();
 978       if (cam) {
 979         double bounds[6];
 980         this->ImageActor->GetBounds(bounds);
 981         double spos = (double)bounds[this->SliceOrientation * 2];
 982         double cpos = (double)cam->GetPosition()[this->SliceOrientation];
 983         double range = fabs(spos - cpos);
 984         double *spacing = input->GetSpacing();
 985         double sumSpacing = spacing[0] + spacing[1] + spacing[2];
 986         cam->SetClippingRange(range - sumSpacing, range + sumSpacing);
 987       }
 988     }
 989   }
 990
 991 }
 992 //----------------------------------------------------------------------------
 993
 994 //----------------------------------------------------------------------------
 995 void vvSlicer::ConvertImageToImageDisplayExtent(vtkImageData *sourceImage, const int sourceExtent[6],
 996                                                 vtkImageData *targetImage, int targetExtent[6])
 997 {
 998   double dExtents[6];
 999   for(unsigned int i=0; i<6; i++) {
1000     // From source voxel coordinates to world coordinates
1001     dExtents[i] = sourceImage->GetOrigin()[i/2] + sourceImage->GetSpacing()[i/2] * sourceExtent[i];
1002
1003     // From world coordinates to floating point target voxel coordinates
1004     dExtents[i] = (dExtents[i]- targetImage->GetOrigin()[i/2]) / targetImage->GetSpacing()[i/2];
1005
1006     // Round to nearest
1007     //targetExtent[i] = itk::Math::Round<double>(dExtents[i]);
1008     targetExtent[i] = itk::Math::Floor<double>(dExtents[i]);
1009   }
1010 }
1011 //----------------------------------------------------------------------------
1012
1013 //----------------------------------------------------------------------------
1014 void vvSlicer::ClipDisplayedExtent(int extent[6], int refExtent[6])
1015 {
1016   bool out = false;
1017   int maxBound = 6;
1018
1019   //2D overlay on 3D image specific case
1020   if (refExtent[4] == refExtent[5]) {
1021     maxBound = 4;
1022     extent[4] = refExtent[4];
1023     extent[5] = refExtent[5];
1024   }
1025
1026   for (int i = 0; i < maxBound; i = i+2) {
1027     //if we are totally outside the image
1028     if ( extent[i] > refExtent[i+1] || extent[i+1] < refExtent[i] ) {
1029       out = true;
1030       break;
1031     }
1032     //crop to the limit of the image
1033     extent[i] = (extent[i] > refExtent[i]) ? extent[i] : refExtent[i];
1034     extent[i] = (extent[i] < refExtent[i+1]) ? extent[i] : refExtent[i+1];
1035     extent[i+1] = (extent[i+1] > refExtent[i]) ? extent[i+1] : refExtent[i];
1036     extent[i+1] = (extent[i+1] < refExtent[i+1]) ? extent[i+1] : refExtent[i+1];
1037   }
1038   if (out)
1039     for (int i = 0; i < maxBound; i = i+2) {
1040       extent[i] = refExtent[i];
1041       extent[i+1] = refExtent[i];
1042     }
1043 }
1044 //----------------------------------------------------------------------------
1045
1046
1047 //----------------------------------------------------------------------------
1048 void vvSlicer::UpdateOrientation()
1049 {
1050   // Set the camera position
1051   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1052   if (cam) {
1053     switch (this->SliceOrientation) {
1054     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1055       cam->SetFocalPoint(0,0,0);
1056       cam->SetPosition(0,0,-1); // -1 if medical ?
1057       cam->SetViewUp(0,-1,0);
1058       break;
1059
1060     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1061       cam->SetFocalPoint(0,0,0);
1062       cam->SetPosition(0,-1,0); // 1 if medical ?
1063       cam->SetViewUp(0,0,1);
1064       break;
1065
1066     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1067       cam->SetFocalPoint(0,0,0);
1068       cam->SetPosition(-1,0,0); // -1 if medical ?
1069       cam->SetViewUp(0,0,1);
1070       break;
1071     }
1072   }
1073 }
1074 //----------------------------------------------------------------------------
1075
1076
1077 //----------------------------------------------------------------------------
1078 void vvSlicer::SetOpacity(double s)
1079 {
1080   this->GetImageActor()->SetOpacity(s);
1081 }
1082 //----------------------------------------------------------------------------
1083
1084
1085 //----------------------------------------------------------------------------
1086 void vvSlicer::SetRenderWindow(int orientation, vtkRenderWindow * rw)
1087 {
1088   this->Superclass::SetRenderWindow(rw);
1089   this->SetupInteractor(rw->GetInteractor());
1090   ca->SetImageActor(this->GetImageActor());
1091   ca->SetWindowLevel(this->GetWindowLevel());
1092   ca->SetText(2, "<slice>");
1093   ca->SetText(3, "<window>\n<level>");
1094
1095   double bounds[6];
1096   double max = 65000;
1097
1098   bounds[0] = -max;
1099   bounds[1] = max;
1100   bounds[2] = -max;
1101   bounds[3] = max;
1102   bounds[4] = -max;
1103   bounds[5] = max;
1104
1105   crossCursor->SetModelBounds(bounds);
1106   this->GetRenderer()->AddActor(pdmA);
1107   this->GetRenderer()->AddActor(ca);
1108   this->GetRenderer()->ResetCamera();
1109
1110   //this is just a mapping between the labeling of the orientations presented to the user and
1111   //the one used by vtk
1112   SetSliceOrientation(2-(orientation%3));
1113   ResetCamera();
1114 }
1115 //----------------------------------------------------------------------------
1116
1117
1118 //----------------------------------------------------------------------------
1119 void vvSlicer::ResetCamera()
1120 {
1121   this->GetRenderer()->ResetCamera();
1122 }
1123 //----------------------------------------------------------------------------
1124
1125
1126 //----------------------------------------------------------------------------
1127 void vvSlicer::SetDisplayMode(bool i)
1128 {
1129   this->GetRenderer()->SetDraw(i);
1130   if (i)
1131     UpdateDisplayExtent();
1132 }
1133 //----------------------------------------------------------------------------
1134
1135
1136 //----------------------------------------------------------------------------
1137 void vvSlicer::FlipHorizontalView()
1138 {
1139   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1140   if (cam) {
1141     double *position = cam->GetPosition();
1142     double factor[3] = {1, 1, 1};
1143     factor[this->SliceOrientation] = -1;
1144     cam->SetPosition(factor[0]*position[0],factor[1]*position[1],factor[2]*position[2]);
1145
1146 /*    switch (this->SliceOrientation) {
1147     case vtkImageViewer2::SLICE_ORIENTATION_XY:
1148       cam->SetPosition(position[0],position[1],-position[2]);
1149       break;
1150
1151     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
1152       cam->SetPosition(position[0],-position[1],position[2]);
1153       break;
1154
1155     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
1156       cam->SetPosition(-position[0],position[1],position[2]);
1157       break;
1158     }*/
1159
1160     this->Renderer->ResetCameraClippingRange();
1161     this->UpdateDisplayExtent();
1162   }
1163 }
1164 //----------------------------------------------------------------------------
1165
1166
1167 //----------------------------------------------------------------------------
1168 void vvSlicer::FlipVerticalView()
1169 {
1170   vtkCamera *cam = this->Renderer ? this->Renderer->GetActiveCamera() : NULL;
1171   if (cam) {
1172     FlipHorizontalView();
1173     double *viewup = cam->GetViewUp();
1174     cam->SetViewUp(-viewup[0],-viewup[1],-viewup[2]);
1175     this->UpdateDisplayExtent();
1176   }
1177 }
1178 //----------------------------------------------------------------------------
1179
1180
1181 //----------------------------------------------------------------------------
1182 void vvSlicer::SetColorWindow(double window)
1183 {
1184   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1185   if ( LUT ) {
1186     double level = this->GetWindowLevel()->GetLevel();
1187     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1188     LUT->Build();
1189   }
1190   this->vtkImageViewer2::SetColorWindow(window);
1191 }
1192 //----------------------------------------------------------------------------
1193
1194 //----------------------------------------------------------------------------
1195 void vvSlicer::SetColorLevel(double level)
1196 {
1197   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(this->GetWindowLevel()->GetLookupTable());
1198   if ( LUT ) {
1199     double window = this->GetWindowLevel()->GetWindow();
1200     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1201     LUT->Build();
1202   }
1203   this->vtkImageViewer2::SetColorLevel(level);
1204 }
1205 //----------------------------------------------------------------------------
1206
1207 //----------------------------------------------------------------------------
1208 double vvSlicer::GetOverlayColorWindow()
1209 {
1210   if(mOverlayMapper)
1211     return mOverlayMapper->GetWindow();
1212   else
1213     return 0.;
1214 }
1215 //----------------------------------------------------------------------------
1216
1217 //----------------------------------------------------------------------------
1218 double vvSlicer::GetOverlayColorLevel()
1219 {
1220   if(mOverlayMapper)
1221     return mOverlayMapper->GetLevel();
1222   else
1223     return 0.;
1224 }
1225 //----------------------------------------------------------------------------
1226
1227 //----------------------------------------------------------------------------
1228 void vvSlicer::SetOverlayColorWindow(double window)
1229 {
1230   mOverlayMapper->SetWindow(window);
1231 }
1232 //----------------------------------------------------------------------------
1233
1234 //----------------------------------------------------------------------------
1235 void vvSlicer::SetOverlayColorLevel(double level)
1236 {
1237   mOverlayMapper->SetLevel(level);
1238 }
1239 //----------------------------------------------------------------------------
1240
1241 //----------------------------------------------------------------------------
1242 // Returns the min an the max value in a 20%x20% region around the mouse pointer
1243 void vvSlicer::GetExtremasAroundMousePointer(double & min, double & max, vtkImageData *image, vtkTransform *transform)
1244 {
1245   //Get mouse pointer position in view coordinates
1246   double corner1[3];
1247   double corner2[3];
1248   for(int i=0; i<3; i++) {
1249     corner1[i] = mCurrent[i];
1250     corner2[i] = mCurrent[i];
1251   }
1252
1253   this->Renderer->WorldToView(corner1[0], corner1[1], corner1[2]);
1254   this->Renderer->WorldToView(corner2[0], corner2[1], corner2[2]);
1255
1256   // In view coordinates, x is the slicer width and y is the slicer height are the in-plane axis
1257   int w, h;
1258   this->Renderer->GetTiledSize(&w, &h);
1259   corner1[0] -= 0.2*h/(double)w;
1260   corner2[0] += 0.2*h/(double)w;
1261   corner1[1] -= 0.2;
1262   corner2[1] += 0.2;
1263   this->Renderer->ViewToWorld(corner1[0], corner1[1], corner1[2]);
1264   this->Renderer->ViewToWorld(corner2[0], corner2[1], corner2[2]);
1265
1266   //Convert to image pixel coordinates (rounded)
1267   transform->TransformPoint(corner1, corner1);
1268   transform->TransformPoint(corner2, corner2);
1269   int iLocalExtents[6];
1270   for(int i=0; i<3; i++) {
1271     corner1[i] = (corner1[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1272     corner2[i] = (corner2[i] - image->GetOrigin()[i])/image->GetSpacing()[i];
1273
1274     iLocalExtents[i*2  ] = lrint(corner1[i]);
1275     iLocalExtents[i*2+1] = lrint(corner2[i]);
1276
1277     if(iLocalExtents[i*2  ]>iLocalExtents[i*2+1])
1278       std::swap(iLocalExtents[i*2], iLocalExtents[i*2+1]);
1279   }
1280
1281   vtkSmartPointer<vtkExtractVOI> voiFilter = vtkSmartPointer<vtkExtractVOI>::New();
1282   voiFilter->SetInput(image);
1283   voiFilter->SetVOI(iLocalExtents);
1284   voiFilter->Update();
1285   if (!voiFilter->GetOutput()->GetNumberOfPoints()) {
1286     min = 0;
1287     max = 0;
1288     return;
1289   }
1290
1291   vtkSmartPointer<vtkImageAccumulate> accFilter = vtkSmartPointer<vtkImageAccumulate>::New();
1292   accFilter->SetInput(voiFilter->GetOutput());
1293   accFilter->Update();
1294
1295   min = *(accFilter->GetMin());
1296   max = *(accFilter->GetMax());
1297 }
1298 //----------------------------------------------------------------------------
1299
1300 //----------------------------------------------------------------------------
1301 double vvSlicer::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int &ix, int &iy, int &iz, int component)
1302 {
1303   ix = lrint(X);
1304   iy = lrint(Y);
1305   iz = lrint(Z);
1306   if (ix < image->GetWholeExtent()[0] ||
1307       ix > image->GetWholeExtent()[1] ||
1308       iy < image->GetWholeExtent()[2] ||
1309       iy > image->GetWholeExtent()[3] ||
1310       iz < image->GetWholeExtent()[4] ||
1311       iz > image->GetWholeExtent()[5] )
1312     return std::numeric_limits<double>::quiet_NaN();
1313
1314   image->SetUpdateExtent(ix, ix, iy, iy, iz, iz);
1315   image->Update();
1316   return image->GetScalarComponentAsDouble(ix, iy, iz, component);
1317 }
1318 //----------------------------------------------------------------------------
1319
1320 //----------------------------------------------------------------------------
1321 void vvSlicer::Render()
1322 {
1323   if (this->mFusion && mFusionActor->GetVisibility() && showFusionLegend) {
1324     legend->SetLookupTable(this->GetFusionMapper()->GetLookupTable());
1325     legend->UseOpacityOn();
1326     legend->SetVisibility(1);
1327   }
1328   else if (this->GetWindowLevel()->GetLookupTable() && !this->mOverlay)  {
1329     legend->SetLookupTable(this->GetWindowLevel()->GetLookupTable());
1330     legend->UseOpacityOff();
1331     legend->SetVisibility(1);
1332   } else legend->SetVisibility(0);
1333
1334   if (ca->GetVisibility()) {
1335     std::stringstream worldPos;
1336     double pt[3];
1337     mConcatenatedTransform->TransformPoint(mCurrent, pt);
1338     double X = (pt[0] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[0])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[0];
1339     double Y = (pt[1] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[1])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[1];
1340     double Z = (pt[2] - mImage->GetVTKImages()[mCurrentTSlice]->GetOrigin()[2])/mImage->GetVTKImages()[mCurrentTSlice]->GetSpacing()[2];
1341
1342     if (X >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[0]-0.5 &&
1343         X <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[1]+0.5 &&
1344         Y >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[2]-0.5 &&
1345         Y <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[3]+0.5 &&
1346         Z >= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[4]-0.5 &&
1347         Z <= mImage->GetVTKImages()[mCurrentTSlice]->GetWholeExtent()[5]+0.5) {
1348
1349
1350       int ix, iy, iz;
1351       double value = this->GetScalarComponentAsDouble(mImage->GetVTKImages()[mCurrentTSlice], X, Y, Z, ix, iy, iz);
1352
1353       if(ImageActor->GetVisibility())
1354         worldPos << "data value : " << value << std::endl;
1355
1356       worldPos << "mm : " << lrint(mCurrentBeforeSlicingTransform[0]) << ' '
1357                           << lrint(mCurrentBeforeSlicingTransform[1]) << ' '
1358                           << lrint(mCurrentBeforeSlicingTransform[2]) << ' '
1359                           << mCurrentTSlice
1360                           << std::endl;
1361       worldPos << "pixel : " << ix << ' '
1362                              << iy << ' '
1363                              << iz << ' '
1364                              << mCurrentTSlice
1365                              << std::endl;
1366     }
1367     ca->SetText(1,worldPos.str().c_str());
1368   }
1369
1370   if (pdmA->GetVisibility()) {
1371     double x = mCursor[0];
1372     double y = mCursor[1];
1373     double z = mCursor[2];
1374     double xCursor = (x - this->GetInput()->GetOrigin()[0])/this->GetInput()->GetSpacing()[0];
1375     double yCursor = (y - this->GetInput()->GetOrigin()[1])/this->GetInput()->GetSpacing()[1];
1376     double zCursor = (z - this->GetInput()->GetOrigin()[2])/this->GetInput()->GetSpacing()[2];
1377
1378     if (xCursor >= this->GetImageActor()->GetDisplayExtent()[0] &&
1379         xCursor < this->GetImageActor()->GetDisplayExtent()[1]+1 &&
1380         yCursor >= this->GetImageActor()->GetDisplayExtent()[2] &&
1381         yCursor < this->GetImageActor()->GetDisplayExtent()[3]+1 &&
1382         zCursor >= this->GetImageActor()->GetDisplayExtent()[4] &&
1383         zCursor < this->GetImageActor()->GetDisplayExtent()[5]+1 ) {
1384       vtkRenderer * renderer = this->Renderer;
1385
1386       renderer->WorldToView(x,y,z);
1387       renderer->ViewToNormalizedViewport(x,y,z);
1388       renderer->NormalizedViewportToViewport(x,y);
1389       renderer->ViewportToNormalizedDisplay(x,y);
1390       renderer->NormalizedDisplayToDisplay(x,y);
1391       crossCursor->SetFocalPoint(x,y,z);
1392     } else
1393       crossCursor->SetFocalPoint(-1,-1,z);
1394   }
1395
1396
1397   if (mOverlay && mOverlayActor->GetVisibility()) {
1398     if(mLinkOverlayWindowLevel) {
1399       mOverlayMapper->SetWindow(this->GetColorWindow());
1400       mOverlayMapper->SetLevel(this->GetColorLevel());
1401     }
1402     mOverlayMapper->GetOutput()->SetUpdateExtent(mOverlayActor->GetDisplayExtent());
1403     mOverlayMapper->GetOutput()->Update();
1404     mOverlayMapper->Update();
1405   }
1406   if (mLandMapper)
1407     UpdateLandmarks();
1408
1409   this->GetRenderWindow()->Render();
1410 }
1411 //----------------------------------------------------------------------------
1412
1413
1414 //----------------------------------------------------------------------------
1415 void vvSlicer::UpdateCursorPosition()
1416 {
1417   pdmA->SetVisibility(true);
1418   mCursor[0] = mCurrent[0];
1419   mCursor[1] = mCurrent[1];
1420   mCursor[2] = mCurrent[2];
1421   mCursor[3] = mCurrentTSlice;
1422 }
1423 //----------------------------------------------------------------------------
1424
1425
1426 //----------------------------------------------------------------------------
1427 void vvSlicer::UpdateLandmarks()
1428 {
1429   vtkPolyData *pd = static_cast<vtkPolyData*>(mLandClipper->GetInput());
1430   if (pd->GetPoints()) {
1431     mLandGlyph->SetRange(0,1);
1432     mLandGlyph->Modified();
1433     mLandGlyph->Update();
1434
1435     mClipBox->Modified();
1436     mLandClipper->Update();
1437     mLandMapper->Update();
1438   }
1439
1440 }
1441 //----------------------------------------------------------------------------
1442
1443
1444 //----------------------------------------------------------------------------
1445 void vvSlicer::SetSlice(int slice)
1446 {
1447   int *range = this->GetSliceRange();
1448   if (range) {
1449     if (slice < range[0]) {
1450       slice = range[0];
1451     } else if (slice > range[1]) {
1452       slice = range[1];
1453     }
1454   }
1455
1456   if (this->Slice == slice) {
1457     return;
1458   }
1459
1460   this->Slice = slice;
1461   SetContourSlice();
1462   this->Modified();
1463   this->UpdateDisplayExtent();
1464
1465   // Seems to work without this line
1466   //this->Render();
1467 }
1468 //----------------------------------------------------------------------------
1469
1470
1471 //----------------------------------------------------------------------------
1472 void vvSlicer::SetContourSlice()
1473 {
1474   if (mSurfaceCutActors.size() > 0)
1475     for (std::vector<vvMeshActor*>::iterator i=mSurfaceCutActors.begin();
1476          i!=mSurfaceCutActors.end(); i++) {
1477
1478       (*i)->SetSlicingOrientation(this->SliceOrientation);
1479       (*i)->SetCutSlice((this->Slice)*this->GetImage()->GetSpacing()[this->SliceOrientation]+
1480                         this->GetImage()->GetOrigin()[this->SliceOrientation]);
1481     }
1482 }
1483 //----------------------------------------------------------------------------
1484
1485
1486 //----------------------------------------------------------------------------
1487 void vvSlicer::ForceUpdateDisplayExtent()
1488 {
1489   this->UpdateDisplayExtent();
1490 }
1491 //----------------------------------------------------------------------------
1492
1493
1494 //----------------------------------------------------------------------------
1495 int* vvSlicer::GetDisplayExtent()
1496 {
1497   return this->GetImageActor()->GetDisplayExtent();
1498 }
1499 //----------------------------------------------------------------------------
1500
1501
1502 //----------------------------------------------------------------------------
1503 void vvSlicer::PrintSelf(ostream& os, vtkIndent indent)
1504 {
1505   this->Superclass::PrintSelf(os, indent);
1506 }
1507 //----------------------------------------------------------------------------
1508
1509 //----------------------------------------------------------------------------
1510 void vvSlicer::SetVFColor(double r, double g, double b)
1511 {
1512   double mVFColorHSV[3];
1513   mVFColor[0] = r;
1514   mVFColor[1] = g;
1515   mVFColor[2] = b;
1516
1517   vtkMath::RGBToHSV(mVFColor, mVFColorHSV);
1518   mVFColorLUT->SetHueRange(mVFColorHSV[0], mVFColorHSV[0]);
1519   mVFColorLUT->SetSaturationRange(mVFColorHSV[1],mVFColorHSV[1]);
1520   mVFColorLUT->SetValueRange(mVFColorHSV[2], mVFColorHSV[2]);
1521
1522   this->Render();
1523 }
1524