vv/vvSlicerManager.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://oncora1.lyon.fnclcc.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 "vvSlicerManager.h"
  20 #include "vvSlicer.h"
  21 #include "vvImage.h"
  22 #include "vvSlicerManagerCommand.h"
  23 #include "vvInteractorStyleNavigator.h"
  24 #include "vvLandmarks.h"
  25 #include "vvMesh.h"
  26 #include "vvImageMapToWLColors.h"
  27 #include "vvBlendImageActor.h"
  28
  29 #include <vtkImageActor.h>
  30 #include <vtkImageData.h>
  31 #include <vtkRenderWindow.h>
  32 #include <vtkRendererCollection.h>
  33 #include <vtkRenderWindowInteractor.h>
  34 #include <vtkImageMapToWindowLevelColors.h>
  35 #include <vtkWindowLevelLookupTable.h>
  36 #include <vtkColorTransferFunction.h>
  37 #include <vtkImageClip.h>
  38 #include <vtkLODActor.h>
  39 #include <vtkPointData.h>
  40 #include <vtksys/SystemTools.hxx>
  41 #include <vtkCamera.h>
  42
  43 #include <qfileinfo.h>
  44
  45 //----------------------------------------------------------------------------
  46 vvSlicerManager::vvSlicerManager(int numberOfSlicers)
  47 {
  48   mFileName = "";
  49   mId = "";
  50   mVFName = "";
  51   mOverlayName = "";
  52   mFusionName = "";
  53   mVFId = "";
  54   mLastError = "";
  55   mType = vvImageReader::UNDEFINEDIMAGETYPE;
  56   mColorMap = 0;
  57   mPreset = 0;
  58   mOverlayColor = 130;
  59
  60   mFusionOpacity = 30;
  61   mFusionThresOpacity = 1;
  62   mFusionColorMap = 3;
  63   mFusionWindow = 1000;
  64   mFusionLevel = 1000;
  65   mFusionShowLegend = true;
  66
  67   mLandmarks = NULL;
  68   mLinkedId.resize(0);
  69
  70   for ( int i = 0; i < numberOfSlicers; i++)
  71     mSlicers.push_back(vtkSmartPointer<vvSlicer>::New());
  72   mSelectedSlicer = -1;
  73
  74   mPreviousSlice.resize(numberOfSlicers);
  75   mPreviousTSlice.resize(numberOfSlicers);
  76   mSlicingPreset = WORLD_SLICING;
  77 }
  78 //----------------------------------------------------------------------------
  79
  80
  81 //----------------------------------------------------------------------------
  82 vvSlicerManager::~vvSlicerManager()
  83 {
  84   if (mLandmarks)
  85     delete mLandmarks;
  86 }
  87 //----------------------------------------------------------------------------
  88
  89
  90 //------------------------------------------------------------------------------
  91 void vvSlicerManager::SetFilename(std::string filename, int number)
  92 {
  93   mFileName = filename;
  94   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
  95   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
  96   mBaseFileNameNumber = number;
  97
  98   mFileName = mBaseFileName;
  99   if (number != 0) {
 100     mFileName.append("_"+clitk::toString(number));
 101   }
 102   mFileName.append(vtksys::SystemTools::GetFilenameLastExtension(filename));
 103
 104   for(unsigned int i=0; i<mSlicers.size(); i++) {
 105     mSlicers[i]->SetFileName(mFileName);//vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 106   }
 107
 108 }
 109 //------------------------------------------------------------------------------
 110
 111
 112 //----------------------------------------------------------------------------
 113 void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)
 114 {
 115   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 116     mSlicers[i]->AddContour(contour,propagate);
 117   }
 118 }
 119 //----------------------------------------------------------------------------
 120
 121
 122 //----------------------------------------------------------------------------
 123 void vvSlicerManager::ToggleContourSuperposition()
 124 {
 125   for ( unsigned int i = 0; i < mSlicers.size(); i++)
 126     mSlicers[i]->ToggleContourSuperposition();
 127 }
 128 //----------------------------------------------------------------------------
 129
 130 //----------------------------------------------------------------------------
 131 std::string vvSlicerManager::GetListOfAbsoluteFilePathInOneString(const std::string &actorType)
 132 {
 133   vvImageReader *reader = NULL;
 134
 135   if(actorType=="image")
 136     reader = mReader;
 137   else if(actorType=="overlay")
 138     reader = mOverlayReader;
 139   else if(actorType=="fusion")
 140     reader = mFusionReader;
 141   else if(actorType=="vector")
 142     reader = mVectorReader;
 143
 144   if(!reader)
 145     return "";
 146
 147   std::string list;
 148   for(unsigned int i=0; i<reader->GetInputFilenames().size(); i++){
 149     QFileInfo fileinfo(reader->GetInputFilenames()[i].c_str()); //Do not show the path
 150     if(i)
 151       list += '\n';
 152     list += fileinfo.absoluteFilePath().toStdString();
 153   }
 154   return list;
 155 }
 156 //----------------------------------------------------------------------------
 157
 158
 159 //----------------------------------------------------------------------------
 160 bool vvSlicerManager::SetImage(std::string filename, vvImageReader::LoadedImageType type, int n, unsigned int slice)
 161 {
 162   mType = type;
 163   if (mReader.IsNull())
 164     mReader = vvImageReader::New();
 165   std::vector<std::string> filenames;
 166   filenames.push_back(filename);
 167   mReader->SetInputFilenames(filenames);
 168   mReader->SetSlice(slice); // Only used for SLICED type
 169   mReader->Update(type);
 170
 171   SetFilename(filename, n);
 172   //  mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
 173   //mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
 174   //mBaseFileNameNumber = n;
 175
 176   if (mReader->GetLastError().size() == 0) {
 177     mImage=mReader->GetOutput();
 178     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 179       mSlicers[i]->SetFileName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 180       mSlicers[i]->SetImage(mReader->GetOutput());
 181     }
 182   } else {
 183     mLastError = mReader->GetLastError();
 184     return false;
 185   }
 186   // if (n!=0) {
 187   //   mFileName.append("_"+clitk::toString(n));
 188   // }
 189   return true;
 190 }
 191 //----------------------------------------------------------------------------
 192
 193
 194 //----------------------------------------------------------------------------
 195 void vvSlicerManager::SetImage(vvImage::Pointer image)
 196 {
 197   mImage=image;
 198   for (unsigned int i = 0; i < mSlicers.size(); i++) {
 199     mSlicers[i]->SetImage(image);
 200   }
 201 }
 202 //----------------------------------------------------------------------------
 203
 204
 205 //----------------------------------------------------------------------------
 206 bool vvSlicerManager::SetImages(std::vector<std::string> filenames, vvImageReader::LoadedImageType type, int n)
 207 {
 208   mType = type;
 209   std::string fileWithoutExtension = vtksys::SystemTools::GetFilenameWithoutExtension(filenames[0]);
 210   if (type == vvImageReader::DICOM)
 211     fileWithoutExtension += "_dicom";
 212   else if (type == vvImageReader::MERGED)
 213     fileWithoutExtension += "_merged";
 214   else if (type == vvImageReader::MERGEDWITHTIME)
 215     fileWithoutExtension += "_merged_wt";
 216
 217   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
 218   mFileName = fileWithoutExtension + vtksys::SystemTools::GetFilenameExtension(filenames[0]);
 219   if (mReader.IsNull())
 220     mReader = vvImageReader::New();
 221   mReader->SetInputFilenames(filenames);
 222   mReader->Update(type);
 223
 224   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
 225   mBaseFileNameNumber = n;
 226
 227   if (mReader->GetLastError().size() == 0) {
 228     mImage=mReader->GetOutput();
 229     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 230       mSlicers[i]->SetFileName(fileWithoutExtension);
 231       mSlicers[i]->SetImage(mReader->GetOutput());
 232     }
 233   } else {
 234     mLastError = mReader->GetLastError();
 235     return false;
 236   }
 237   if (n!=0) {
 238     mFileName.append("_"+clitk::toString(n));
 239   }
 240   return true;
 241 }
 242 //----------------------------------------------------------------------------
 243
 244
 245 //----------------------------------------------------------------------------
 246 bool vvSlicerManager::SetOverlay(std::vector<std::string> filenames,int dim, std::string component, vvImageReader::LoadedImageType type)
 247 {
 248   mOverlayName = filenames[0];
 249   mOverlayComponent = component;
 250   if (dim > mImage->GetNumberOfDimensions()) {
 251     mLastError = " Overlay dimension cannot be greater than reference image!";
 252     return false;
 253   }
 254   if (mOverlayReader.IsNull())
 255     mOverlayReader = vvImageReader::New();
 256   mOverlayReader->SetInputFilenames(filenames);
 257   mOverlayReader->Update(type);
 258   if (mOverlayReader->GetLastError().size() == 0) {
 259     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 260       mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 261     }
 262   } else {
 263     mLastError = mOverlayReader->GetLastError();
 264     return false;
 265   }
 266   return true;
 267 }
 268 //----------------------------------------------------------------------------
 269
 270
 271 //----------------------------------------------------------------------------
 272 bool vvSlicerManager::SetFusion(std::string filename,int dim, std::string component)
 273 {
 274   mFusionName = filename;
 275   mFusionComponent = component;
 276   if (dim > mImage->GetNumberOfDimensions()) {
 277     mLastError = " Overlay dimension cannot be greater then reference image!";
 278     return false;
 279   }
 280   if (mFusionReader.IsNull())
 281     mFusionReader = vvImageReader::New();
 282   std::vector<std::string> filenames;
 283   filenames.push_back(filename);
 284   mFusionReader->SetInputFilenames(filenames);
 285   mFusionReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 286   if (mFusionReader->GetLastError().size() == 0) {
 287     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 288       mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 289     }
 290   } else {
 291     mLastError = mFusionReader->GetLastError();
 292     return false;
 293   }
 294   double *fusRange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
 295   mFusionLevel = (fusRange[0]+fusRange[1])/2;
 296   mFusionWindow = fusRange[1]-fusRange[0];
 297
 298   return true;
 299 }
 300 //----------------------------------------------------------------------------
 301
 302
 303 //----------------------------------------------------------------------------
 304 bool vvSlicerManager::SetVF(std::string filename)
 305 {
 306   if (mVectorReader.IsNull())
 307     mVectorReader = vvImageReader::New();
 308   mVectorReader->SetInputFilename(filename);
 309
 310   if (mType == vvImageReader::IMAGEWITHTIME)
 311     mVectorReader->Update(vvImageReader::VECTORFIELDWITHTIME);
 312   else
 313     mVectorReader->Update(vvImageReader::VECTORFIELD);
 314   if (mVectorReader->GetLastError().size() != 0) {
 315     mLastError = mVectorReader->GetLastError();
 316     return false;
 317   } else
 318     return SetVF(mVectorReader->GetOutput(),filename);
 319 }
 320 //----------------------------------------------------------------------------
 321
 322
 323 //----------------------------------------------------------------------------
 324 bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)
 325 {
 326   if (vf->GetNumberOfDimensions() > mImage->GetNumberOfDimensions()) {
 327     mLastError = "Sorry, vector field dimension cannot be greater then reference image.";
 328     return false;
 329   }
 330   if (vf->GetNumberOfDimensions() == 4) {
 331     if (vf->GetSpacing()[3] != mImage->GetSpacing()[3]) {
 332       mLastError = "Sorry, vector field time spacing cannot be different from time spacing of the reference image.";
 333       return false;
 334     }
 335     if (vf->GetOrigin()[3] != mImage->GetOrigin()[3]) {
 336       mLastError = "Sorry, vector field time origin cannot be different from time origin of the reference image.";
 337       return false;
 338     }
 339   }
 340   mVF=vf;
 341   mVFName = filename;
 342   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 343     mSlicers[i]->SetVF(vf);
 344   }
 345   return true;
 346 }
 347 //----------------------------------------------------------------------------
 348
 349
 350 //----------------------------------------------------------------------------
 351 vvSlicer* vvSlicerManager::GetSlicer(int i)
 352 {
 353   return mSlicers[i];
 354 }
 355 //----------------------------------------------------------------------------
 356
 357
 358 //----------------------------------------------------------------------------
 359 void vvSlicerManager::UpdateSlicer(int num, bool state)
 360 {
 361   if (mSlicers[num]->GetImage())
 362     mSlicers[num]->SetDisplayMode(state);
 363 }
 364 //----------------------------------------------------------------------------
 365
 366
 367 //----------------------------------------------------------------------------
 368 void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)
 369 {
 370   mSlicers[i]->SetRenderWindow(i,RW);
 371 }
 372 //----------------------------------------------------------------------------
 373
 374
 375 //----------------------------------------------------------------------------
 376 void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* style)
 377 {
 378   vvSlicerManagerCommand *smc = vvSlicerManagerCommand::New();
 379   smc->SM = this;
 380   smc->SetSlicerNumber(i);
 381   mSlicers[i]->GetRenderWindow()->GetInteractor()->SetInteractorStyle(style);
 382
 383   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 384     GetInteractorStyle()->AddObserver(vtkCommand::KeyPressEvent, smc);
 385   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 386     GetInteractorStyle()->AddObserver(vtkCommand::WindowLevelEvent, smc);
 387   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 388     GetInteractorStyle()->AddObserver(vtkCommand::EndWindowLevelEvent, smc);
 389   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 390     GetInteractorStyle()->AddObserver(vtkCommand::StartWindowLevelEvent, smc);
 391   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 392     GetInteractorStyle()->AddObserver(vtkCommand::PickEvent, smc);
 393   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 394     GetInteractorStyle()->AddObserver(vtkCommand::StartPickEvent, smc);
 395   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 396     GetInteractorStyle()->AddObserver(vtkCommand::LeaveEvent, smc);
 397   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 398     GetInteractorStyle()->AddObserver(vtkCommand::UserEvent, smc);
 399   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 400     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelForwardEvent, smc);
 401   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 402     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelBackwardEvent, smc);
 403   // mSlicers[i]->GetRenderWindow()->GetInteractor()->
 404   //   GetInteractorStyle()->AddObserver(vtkCommand::LeftButtonReleaseEvent, smc);
 405   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 406     GetInteractorStyle()->AddObserver(vtkCommand::EndPickEvent, smc);
 407   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 408     GetInteractorStyle()->AddObserver(vtkCommand::EndInteractionEvent, smc);
 409   smc->Delete();
 410 }
 411 //----------------------------------------------------------------------------
 412
 413
 414 //----------------------------------------------------------------------------
 415 void vvSlicerManager::LeftButtonReleaseEvent(int slicer)
 416 {
 417   emit LeftButtonReleaseSignal(slicer);
 418 }
 419 //----------------------------------------------------------------------------
 420
 421 //----------------------------------------------------------------------------
 422 void vvSlicerManager::SetSliceOrientation(int slicer, int orientation)
 423 {
 424   mSlicers[slicer]->SetSliceOrientation(orientation);
 425   emit UpdateOrientation(slicer, orientation);
 426 }
 427 //----------------------------------------------------------------------------
 428
 429 //----------------------------------------------------------------------------
 430 int vvSlicerManager::GetTSlice()
 431 {
 432   return mSlicers[0]->GetTSlice();
 433 }
 434 //----------------------------------------------------------------------------
 435
 436 //----------------------------------------------------------------------------
 437 void vvSlicerManager::SetTSlice(int slice)
 438 {
 439   if (slice < 0)
 440     slice = 0;
 441   else if (slice > mSlicers[0]->GetTMax())
 442     slice = mSlicers[0]->GetTMax();
 443   if (mLandmarks)
 444     mLandmarks->SetTime(slice);
 445   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 446     if (slice != mSlicers[i]->GetMaxCurrentTSlice()) {
 447       mSlicers[i]->SetTSlice(slice);
 448       UpdateTSlice(i);
 449     }
 450   }
 451 }
 452 //----------------------------------------------------------------------------
 453
 454
 455 //----------------------------------------------------------------------------
 456 void vvSlicerManager::SetNextTSlice(int originating_slicer)
 457 {
 458   int t = mSlicers[0]->GetMaxCurrentTSlice();
 459   t++;
 460   if (t > mSlicers[0]->GetTMax())
 461     t = 0;
 462   //std::cout << "vvSlicerManager::SetNextTSlice" << std::endl;
 463   emit UpdateTSlice(originating_slicer,t);
 464 }
 465 //----------------------------------------------------------------------------
 466
 467
 468 //----------------------------------------------------------------------------
 469 void vvSlicerManager::SetPreviousTSlice(int originating_slicer)
 470 {
 471   int t = mSlicers[0]->GetMaxCurrentTSlice();
 472   t--;
 473   if (t < 0)
 474     t = mSlicers[0]->GetTMax();
 475   //std::cout << "vvSlicerManager::SetPreviousTSlice" << std::endl;
 476   emit UpdateTSlice(originating_slicer,t);
 477 }
 478 //----------------------------------------------------------------------------
 479
 480
 481 //----------------------------------------------------------------------------
 482 void vvSlicerManager::ToggleInterpolation()
 483 {
 484   bool interpolate=!(mSlicers[0]->GetImageActor()->GetInterpolate());
 485   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 486     mSlicers[i]->GetImageActor()->SetInterpolate(interpolate);
 487     if (mSlicers[i]->GetOverlayActor())
 488       mSlicers[i]->GetOverlayActor()->SetInterpolate(interpolate);
 489     if (mSlicers[i]->GetFusionActor())
 490       mSlicers[i]->GetFusionActor()->SetInterpolate(interpolate);
 491   }
 492 }
 493 //----------------------------------------------------------------------------
 494
 495
 496 //----------------------------------------------------------------------------
 497 void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)
 498 {
 499   if (tslice < 0)
 500     tslice = 0;
 501   else if (tslice > mSlicers[slicer]->GetTMax())
 502     tslice = mSlicers[slicer]->GetTMax();
 503   if (mLandmarks)
 504     mLandmarks->SetTime(tslice);
 505
 506   if (mSlicers[slicer]->GetMaxCurrentTSlice() == tslice) return;
 507
 508   mSlicers[slicer]->SetTSlice(tslice);
 509
 510   if(mSlicingPreset==VOXELS_SLICING) {
 511     vtkMatrix4x4 *imageTransformInverse = vtkMatrix4x4::New();
 512     mImage->GetTransform()[mSlicers[slicer]->GetTSlice()]->GetInverse(imageTransformInverse);
 513     this->GetSlicer(slicer)->GetSlicingTransform()->SetMatrix(imageTransformInverse);
 514     imageTransformInverse->Delete();
 515   }
 516
 517   UpdateTSlice(slicer);
 518 }
 519 //----------------------------------------------------------------------------
 520
 521
 522 //----------------------------------------------------------------------------
 523 void vvSlicerManager::SetColorWindow(double s)
 524 {
 525   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 526     mSlicers[i]->SetColorWindow(s);
 527   }
 528 }
 529 //----------------------------------------------------------------------------
 530
 531 //----------------------------------------------------------------------------
 532 void vvSlicerManager::SetColorLevel(double s)
 533 {
 534   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 535     mSlicers[i]->SetColorLevel(s);
 536   }
 537 }
 538 //----------------------------------------------------------------------------
 539
 540 //----------------------------------------------------------------------------
 541 void vvSlicerManager::SetOverlayColorWindow(double s)
 542 {
 543   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 544     mSlicers[i]->SetOverlayColorWindow(s);
 545   }
 546 }
 547 //----------------------------------------------------------------------------
 548
 549 //----------------------------------------------------------------------------
 550 void vvSlicerManager::SetOverlayColorLevel(double s)
 551 {
 552   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 553     mSlicers[i]->SetOverlayColorLevel(s);
 554   }
 555 }
 556 //----------------------------------------------------------------------------
 557
 558 //----------------------------------------------------------------------------
 559 void vvSlicerManager::SetLinkOverlayWindowLevel(bool b)
 560 {
 561   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 562     mSlicers[i]->SetLinkOverlayWindowLevel(b);
 563   }
 564 }
 565 //----------------------------------------------------------------------------
 566
 567 //----------------------------------------------------------------------------
 568 void vvSlicerManager::SetCursorAndCornerAnnotationVisibility(int s)
 569 {
 570   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 571     mSlicers[i]->SetCursorVisibility(s);
 572     mSlicers[i]->SetCornerAnnotationVisibility(s);
 573   }
 574 }
 575 //----------------------------------------------------------------------------
 576
 577 //----------------------------------------------------------------------------
 578 void vvSlicerManager::SetOpacity(int i, double factor)
 579 {
 580   mSlicers[i]->SetOpacity(1/factor);
 581 }
 582 //----------------------------------------------------------------------------
 583
 584
 585 //----------------------------------------------------------------------------
 586 void vvSlicerManager::UpdateViews(int current,int slicer)
 587 {
 588   double p[3], pt[3];
 589   p[0] = mSlicers[slicer]->GetCurrentPosition()[0];
 590   p[1] = mSlicers[slicer]->GetCurrentPosition()[1];
 591   p[2] = mSlicers[slicer]->GetCurrentPosition()[2];
 592   mSlicers[slicer]->GetSlicingTransform()->GetInverse()->TransformPoint(p, pt);
 593
 594   double x = (pt[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0])
 595     /mSlicers[slicer]->GetInput()->GetSpacing()[0];
 596   double y = (pt[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1])
 597     /mSlicers[slicer]->GetInput()->GetSpacing()[1];
 598   double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])
 599     /mSlicers[slicer]->GetInput()->GetSpacing()[2];
 600
 601   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&
 602       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&
 603       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&
 604       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3]+0.5 &&
 605       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4]-0.5 &&
 606       z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5) {
 607     mSlicers[slicer]->UpdateCursorPosition();
 608     mSlicers[slicer]->SetCursorColor(10,212,255);
 609     mSelectedSlicer = slicer;
 610
 611     switch (mSlicers[slicer]->GetSliceOrientation()) {
 612     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 613       if (mSlicers[slicer]->GetSlice() != (int)lrint(z))
 614         mSlicers[slicer]->SetSlice((int)lrint(z));
 615       break;
 616
 617     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 618       if (mSlicers[slicer]->GetSlice() != (int)lrint(y))
 619         mSlicers[slicer]->SetSlice((int)lrint(y));
 620       break;
 621
 622     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 623       if (mSlicers[slicer]->GetSlice() != (int)lrint(x))
 624         mSlicers[slicer]->SetSlice((int)lrint(x));
 625       break;
 626     }
 627     mSlicers[slicer]->Render();
 628
 629     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 630       if (i != (unsigned int)slicer
 631           && mSlicers[i]->GetRenderer()->GetDraw()
 632           && mSlicers[i]->GetRenderWindow()->GetSize()[0] > 2
 633           && mSlicers[i]->GetRenderWindow()->GetSize()[1] > 2) {
 634         mSlicers[i]->SetCurrentPosition(p[0], p[1], p[2], mSlicers[slicer]->GetMaxCurrentTSlice());
 635         mSlicers[i]->UpdateCursorPosition();
 636         if (current) { //do not display corner annotation if image is the one picked
 637           mSlicers[i]->SetCurrentPosition(-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,
 638                                           -VTK_DOUBLE_MAX, mSlicers[slicer]->GetMaxCurrentTSlice());
 639           mSlicers[i]->SetCursorColor(255,10,212);
 640         } else {
 641           mSlicers[i]->SetCursorColor(150,10,282);
 642         }
 643         switch (mSlicers[i]->GetSliceOrientation()) {
 644         case vtkImageViewer2::SLICE_ORIENTATION_XY:
 645           if (mSlicers[i]->GetSlice() != (int)floor(z))
 646             mSlicers[i]->SetSlice((int)floor(z));
 647           break;
 648
 649         case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 650           if (mSlicers[i]->GetSlice() != (int)floor(y))
 651             mSlicers[i]->SetSlice((int)floor(y));
 652           break;
 653
 654         case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 655           if (mSlicers[i]->GetSlice() != (int)floor(x))
 656             mSlicers[i]->SetSlice((int)floor(x));
 657           break;
 658         }
 659
 660         mSlicers[i]->Render();
 661
 662         UpdateSlice(i);
 663         UpdateTSlice(i);
 664       }
 665     }
 666   }
 667 }
 668 //----------------------------------------------------------------------------
 669
 670
 671 //----------------------------------------------------------------------------
 672 void vvSlicerManager::UpdateLinked(int slicer)
 673 {
 674   double p[3], pt[3];
 675   p[0] = mSlicers[slicer]->GetCurrentPosition()[0];
 676   p[1] = mSlicers[slicer]->GetCurrentPosition()[1];
 677   p[2] = mSlicers[slicer]->GetCurrentPosition()[2];
 678   mSlicers[slicer]->GetSlicingTransform()->GetInverse()->TransformPoint(p, pt);
 679   double x = (pt[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0]) / mSlicers[slicer]->GetInput()->GetSpacing()[0];
 680   double y = (pt[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1]) / mSlicers[slicer]->GetInput()->GetSpacing()[1];
 681   double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2]) / mSlicers[slicer]->GetInput()->GetSpacing()[2];
 682
 683   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&
 684       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&
 685       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&
 686       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3]+0.5 &&
 687       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4]-0.5 &&
 688       z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5) {
 689     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++) {
 690       emit UpdateLinkManager(*i, slicer, p[0], p[1], p[2], mSlicers[slicer]->GetMaxCurrentTSlice());
 691     }
 692   }
 693 }
 694 //----------------------------------------------------------------------------
 695
 696 //----------------------------------------------------------------------------
 697 void vvSlicerManager::UpdateLinkedNavigation(vvSlicer *refSlicer, bool bPropagate)
 698 {
 699   vtkCamera *refCam = refSlicer->GetRenderer()->GetActiveCamera();
 700
 701   double refPosition[3];
 702   refCam->GetPosition(refPosition);
 703   refPosition[refSlicer->GetSliceOrientation()] = refSlicer->GetSlice() *
 704       refSlicer->GetInput()->GetSpacing()[refSlicer->GetSliceOrientation()] +
 705       refSlicer->GetInput()->GetOrigin()[refSlicer->GetSliceOrientation()];
 706
 707   refSlicer->GetSlicingTransform()->TransformPoint(refPosition, refPosition);
 708   mSlicers[0]->GetSlicingTransform()->GetInverse()->TransformPoint(refPosition, refPosition);
 709
 710   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 711     vtkCamera *camera = mSlicers[i]->GetRenderer()->GetActiveCamera();
 712     camera->SetParallelScale(refCam->GetParallelScale());
 713
 714     double position[3], focal[3];
 715     camera->GetPosition(position);
 716     camera->GetFocalPoint(focal);
 717
 718     for(int j=0; j<3; j++) {
 719       if(j!=mSlicers[i]->GetSliceOrientation()) {
 720         position[j] = refPosition[j];
 721         focal[j]    = refPosition[j];
 722       }
 723     }
 724
 725     camera->SetFocalPoint(focal);
 726     camera->SetPosition(position);
 727
 728     //Fix for bug #243
 729     mSlicers[i]->ForceUpdateDisplayExtent();
 730   }
 731
 732   Render();
 733   if(bPropagate)
 734     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++)
 735       emit UpdateLinkedNavigation(*i, this, refSlicer);
 736 }
 737 //----------------------------------------------------------------------------
 738
 739 //----------------------------------------------------------------------------
 740 double vvSlicerManager::GetColorWindow() const
 741 {
 742   if (mSlicers.size())
 743     return mSlicers[0]->GetColorWindow();
 744   return -1;
 745 }
 746 //----------------------------------------------------------------------------
 747
 748
 749 //----------------------------------------------------------------------------
 750 double vvSlicerManager::GetColorLevel() const
 751 {
 752   if (mSlicers.size())
 753     return mSlicers[0]->GetColorLevel();
 754   return -1;
 755 }
 756 //----------------------------------------------------------------------------
 757
 758 //----------------------------------------------------------------------------
 759 double vvSlicerManager::GetOverlayColorWindow() const
 760 {
 761   if (mSlicers.size())
 762     return mSlicers[0]->GetOverlayColorWindow();
 763   return -1;
 764 }
 765 //----------------------------------------------------------------------------
 766
 767 //----------------------------------------------------------------------------
 768 double vvSlicerManager::GetOverlayColorLevel() const
 769 {
 770   if (mSlicers.size())
 771     return mSlicers[0]->GetOverlayColorLevel();
 772   return -1;
 773 }
 774 //----------------------------------------------------------------------------
 775
 776 //----------------------------------------------------------------------------
 777 bool vvSlicerManager::GetLinkOverlayWindowLevel() const
 778 {
 779   if (mSlicers.size())
 780     return mSlicers[0]->GetLinkOverlayWindowLevel();
 781   return -1;
 782 }
 783 //----------------------------------------------------------------------------
 784
 785 //------------------------------------------------------------------------------
 786 void vvSlicerManager::ResetTransformationToIdentity(const std::string actorType)
 787 {
 788   if(actorType == "image")
 789     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 790       this->GetImage()->GetTransform()[i]->Identity();
 791   else if(actorType == "overlay")
 792     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 793       this->GetSlicer(0)->GetOverlay()->GetTransform()[i]->Identity();
 794   else if(actorType == "fusion")
 795     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 796       this->GetSlicer(0)->GetFusion()->GetTransform()[i]->Identity();
 797   else if(actorType == "vf")
 798     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 799       this->GetVF()->GetTransform()[i]->Identity();
 800   else
 801     return;
 802
 803   for(int i=0; i< this->GetNumberOfSlicers(); i++){
 804     this->GetSlicer(i)->ForceUpdateDisplayExtent();
 805     this->GetSlicer(i)->ResetCamera();
 806     this->GetSlicer(i)->Render();
 807   }
 808 }
 809 //------------------------------------------------------------------------------
 810
 811 //----------------------------------------------------------------------------
 812 void vvSlicerManager::Render()
 813 {
 814   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 815     mSlicers[i]->Render();
 816   }
 817 }
 818 //----------------------------------------------------------------------------
 819
 820
 821 //----------------------------------------------------------------------------
 822 void vvSlicerManager::GenerateDefaultLookupTable()
 823 {
 824   SetPreset(mPreset);
 825   SetColorMap(mColorMap);
 826 }
 827 //----------------------------------------------------------------------------
 828
 829
 830 //----------------------------------------------------------------------------
 831 void vvSlicerManager::Reload()
 832 {
 833   mReader->Update(mType);
 834   mImage=mReader->GetOutput();
 835   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 836     mSlicers[i]->SetImage(mImage);
 837   }
 838 }
 839 //----------------------------------------------------------------------------
 840
 841
 842 //----------------------------------------------------------------------------
 843 void vvSlicerManager::ReloadFusion()
 844 {
 845   mFusionReader->Update(mImage->GetNumberOfDimensions(),mFusionComponent.c_str(),mType);
 846
 847   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 848     mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 849     mSlicers[i]->Render();
 850   }
 851 }
 852 //----------------------------------------------------------------------------
 853
 854
 855 //----------------------------------------------------------------------------
 856 void vvSlicerManager::ReloadOverlay()
 857 {
 858   mOverlayReader->Update(mImage->GetNumberOfDimensions(),mOverlayComponent.c_str(),mType);
 859   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 860     mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 861     mSlicers[i]->Render();
 862   }
 863 }
 864 //----------------------------------------------------------------------------
 865
 866
 867 //----------------------------------------------------------------------------
 868 void vvSlicerManager::ReloadVF()
 869 {
 870   mVectorReader->Update(vvImageReader::VECTORFIELD); //deletes the old images through the VF::Init() function
 871   mVF=mVectorReader->GetOutput();
 872   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 873     mSlicers[i]->SetVF(mVF);
 874     mSlicers[i]->Render();
 875   }
 876 }
 877 //----------------------------------------------------------------------------
 878
 879
 880 //----------------------------------------------------------------------------
 881 void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_index)
 882 {
 883   if (actor_type =="overlay")
 884     mOverlayReader = NULL;
 885
 886   if (actor_type =="fusion")
 887     mFusionReader = NULL;
 888
 889   for (unsigned int i = 0; i < mSlicers.size(); i++)
 890     mSlicers[i]->RemoveActor(actor_type,overlay_index);
 891
 892   if (actor_type=="vector") {
 893     mVF=NULL;
 894     mVectorReader=NULL;
 895   }
 896 }
 897 //----------------------------------------------------------------------------
 898
 899
 900 //----------------------------------------------------------------------------
 901 void vvSlicerManager::RemoveActors()
 902 {
 903   ///This method leaks a few objects. See RemoveActor for what a
 904   ///correct implementation would look like
 905   //DS -> probably due to the reader (now released in the
 906   //RemoveActor() function. (I hope)
 907   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 908     mSlicers[i]->SetDisplayMode(0);
 909     mSlicers[i]->GetRenderer()->RemoveActor(mSlicers[i]->GetImageActor());
 910   }
 911 }
 912 //----------------------------------------------------------------------------
 913
 914
 915 //----------------------------------------------------------------------------
 916 void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
 917 {
 918   //  int view = mSlicers[slicer]->GetSliceOrientation();
 919   //  int slice = mSlicers[slicer]->GetSlice();
 920   double x = mSlicers[slicer]->GetCursorPosition()[0];
 921   double y = mSlicers[slicer]->GetCursorPosition()[1];
 922   double z = mSlicers[slicer]->GetCursorPosition()[2];
 923   double X = (x - mSlicers[slicer]->GetInput()->GetOrigin()[0])/
 924     mSlicers[slicer]->GetInput()->GetSpacing()[0];
 925   double Y = (y - mSlicers[slicer]->GetInput()->GetOrigin()[1])/
 926     mSlicers[slicer]->GetInput()->GetSpacing()[1];
 927   double Z = (z - mSlicers[slicer]->GetInput()->GetOrigin()[2])/
 928     mSlicers[slicer]->GetInput()->GetSpacing()[2];
 929   double value = -VTK_DOUBLE_MAX;
 930   int displayVec = 0;
 931   double xVec=0, yVec=0, zVec=0, valueVec=0;
 932   int displayOver = 0;
 933   int displayFus = 0;
 934   double valueOver=0, valueFus=0;
 935   if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 936       X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 937       Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 938       Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 939       Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 940       Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {
 941     value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);
 942
 943     if (mSlicers[slicer]->GetVFActor() ) {
 944       displayVec = 1;
 945       unsigned int currentTime = mSlicers[slicer]->GetMaxCurrentTSlice();
 946       vtkImageData *vf = NULL;
 947
 948       if (mSlicers[slicer]->GetVF()->GetVTKImages().size() > currentTime)
 949         vf = mSlicers[slicer]->GetVF()->GetVTKImages()[currentTime];
 950       else
 951         vf = mSlicers[slicer]->GetVF()->GetVTKImages()[0];
 952
 953       if (vf) {
 954         double Xvf = (x - vf->GetOrigin()[0])/ vf->GetSpacing()[0];
 955         double Yvf = (y - vf->GetOrigin()[1])/ vf->GetSpacing()[1];
 956         double Zvf = (z - vf->GetOrigin()[2])/ vf->GetSpacing()[2];
 957         xVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 0);
 958         yVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 1);
 959         zVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 2);
 960         valueVec = sqrt(xVec*xVec + yVec*yVec + zVec*zVec);
 961       }
 962     }
 963     if (mSlicers[slicer]->GetOverlayActor() ) {
 964       displayOver = 1;
 965       vtkImageData *overlay = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetOverlayMapper()->GetInput());
 966       double Xover = (x - overlay->GetOrigin()[0]) / overlay->GetSpacing()[0];
 967       double Yover = (y - overlay->GetOrigin()[1]) / overlay->GetSpacing()[1];
 968       double Zover = (z - overlay->GetOrigin()[2]) / overlay->GetSpacing()[2];
 969       valueOver = this->GetScalarComponentAsDouble(overlay, Xover, Yover, Zover);
 970     }
 971     if (mSlicers[slicer]->GetFusionActor() ) {
 972       displayFus = 1;
 973       vtkImageData *fusion = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetFusionMapper()->GetInput());
 974       double Xover = (x - fusion->GetOrigin()[0]) / fusion->GetSpacing()[0];
 975       double Yover = (y - fusion->GetOrigin()[1]) / fusion->GetSpacing()[1];
 976       double Zover = (z - fusion->GetOrigin()[2]) / fusion->GetSpacing()[2];
 977       valueFus = this->GetScalarComponentAsDouble(fusion, Xover, Yover, Zover);
 978     }
 979     emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),
 980                         x,y,z,X,Y,Z,value);
 981     emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);
 982     emit UpdateOverlay(displayOver,valueOver,value);
 983     emit UpdateFusion(displayFus,valueFus);
 984   }
 985 }
 986 //----------------------------------------------------------------------------
 987
 988
 989 //----------------------------------------------------------------------------
 990 void vvSlicerManager::Activated()
 991 {
 992   emit currentImageChanged(mId);
 993 }
 994 //----------------------------------------------------------------------------
 995
 996
 997 //----------------------------------------------------------------------------
 998 void vvSlicerManager::Picked()
 999 {
1000   emit currentPickedImageChanged(mId);
1001 }
1002 //----------------------------------------------------------------------------
1003
1004
1005 //----------------------------------------------------------------------------
1006 void vvSlicerManager::UpdateWindowLevel()
1007 {
1008   emit WindowLevelChanged();
1009 }
1010 //----------------------------------------------------------------------------
1011
1012
1013 //----------------------------------------------------------------------------
1014 void vvSlicerManager::UpdateSlice(int slicer)
1015 {
1016   if (mPreviousSlice[slicer] == mSlicers[slicer]->GetSlice()) {
1017     //DD("============= NOTHING");
1018     return;
1019   }
1020   //std::cout << "vvSlicerManager::UpdateSlice " << slicer << " " << mSlicers[slicer]->GetSlice() << std::endl;
1021   emit UpdateSlice(slicer, mSlicers[slicer]->GetSlice());
1022   mSlicers[slicer]->Render(); // DS <-- I add this, this could/must be the only Render ...
1023   mPreviousSlice[slicer] = mSlicers[slicer]->GetSlice();
1024 }
1025 //----------------------------------------------------------------------------
1026
1027
1028 //----------------------------------------------------------------------------
1029 void vvSlicerManager::UpdateTSlice(int slicer)
1030 {
1031   int slice = mSlicers[slicer]->GetSlice();
1032   int tslice = mSlicers[slicer]->GetMaxCurrentTSlice();
1033   if (mPreviousSlice[slicer] == slice) {
1034     if (mPreviousTSlice[slicer] == tslice) {
1035       //      DD("************** NOTHING ***********");
1036       return;
1037     }
1038   }
1039   mPreviousSlice[slicer] = slice;
1040   mPreviousTSlice[slicer] = tslice;
1041   //std::cout << "vvSlicerManager::UpdateTSlice " << slicer << " " << tslice << std::endl;
1042   emit UpdateTSlice(slicer, tslice);
1043 }
1044 //----------------------------------------------------------------------------
1045
1046
1047 //----------------------------------------------------------------------------
1048 void vvSlicerManager::UpdateSliceRange(int slicer)
1049 {
1050   emit UpdateSliceRange(slicer,
1051                         mSlicers[slicer]->GetSliceRange()[0], mSlicers[slicer]->GetSliceRange()[1],
1052                         0,mSlicers[slicer]->GetTMax());
1053 }
1054 //----------------------------------------------------------------------------
1055
1056 //----------------------------------------------------------------------------
1057 void vvSlicerManager::SetSlicingPreset(SlicingPresetType preset)
1058 {
1059   if(mSlicingPreset==preset)
1060     return;
1061
1062   vtkMatrix4x4 *imageTransformInverse = vtkMatrix4x4::New();
1063   mImage->GetTransform()[this->GetTSlice()]->GetInverse(imageTransformInverse);
1064
1065   for(int i=0; i< this->GetNumberOfSlicers(); i++){
1066     vvSlicer *s = this->GetSlicer(i);
1067     switch(preset)
1068     {
1069     case WORLD_SLICING:
1070       s->GetSlicingTransform()->Identity();
1071       break;
1072     case VOXELS_SLICING:
1073       s->GetSlicingTransform()->SetMatrix(imageTransformInverse);
1074       break;
1075     default:
1076       imageTransformInverse->Delete();
1077       return;
1078     }
1079     s->ForceUpdateDisplayExtent();
1080     s->SetSlice((s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2+1]
1081                 +s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2])/2.0);
1082     s->ResetCamera();
1083     s->Render();
1084   }
1085
1086   imageTransformInverse->Delete();
1087   mSlicingPreset = preset;
1088 }
1089
1090 //----------------------------------------------------------------------------
1091
1092 //----------------------------------------------------------------------------
1093 void vvSlicerManager::SetPreset(int preset)
1094 {
1095   //vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
1096   double window = mSlicers[0]->GetColorWindow();
1097   double level = mSlicers[0]->GetColorLevel();
1098
1099   std::string component_type=mImage->GetScalarTypeAsITKString();
1100   switch (preset) {
1101   case 0:
1102     double range[2];
1103     mImage->GetScalarRange(range);
1104     window = range[1] - range[0];
1105     level = (range[1] + range[0])* 0.5;
1106     break;
1107   case 1:
1108     window = 2000;
1109     level = 0;
1110     break;
1111   case 2:
1112     window = 400;
1113     level = 20;
1114     break;
1115   case 3: // lungs (same as FOCAL)
1116     window = 1700;
1117     level = -300;
1118     break;
1119   case 4:
1120     window = 1000;
1121     level = 500;
1122     break;
1123   case 5:
1124     window = 1;
1125     level = 0.5;
1126     break;
1127   case 6:
1128     break;
1129   case 7:
1130     window=1.;
1131     level=0.;
1132     break;
1133   }
1134   mPreset = preset;
1135   this->SetColorWindow(window);
1136   this->SetColorLevel(level);
1137
1138   //if (LUT)
1139   //{
1140   //    SetColorMap(-1);
1141   //}
1142 }
1143 //----------------------------------------------------------------------------
1144
1145
1146 //----------------------------------------------------------------------------
1147 void vvSlicerManager::SetLocalColorWindowing(const int slicer, const bool bCtrlKey)
1148 {
1149   double min, max;
1150   if(bCtrlKey && this->mSlicers[slicer]->GetFusion()) {
1151     int t = mSlicers[slicer]->GetFusionTSlice();
1152     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1153                                                           this->mSlicers[slicer]->GetFusion()->GetVTKImages()[t],
1154                                                           this->mSlicers[slicer]->GetConcatenatedFusionTransform());
1155     this->SetFusionWindow(max-min);
1156     this->SetFusionLevel(0.5*(min+max));
1157     this->SetColorMap(mColorMap);
1158   }
1159   else if(bCtrlKey && this->mSlicers[slicer]->GetOverlay()) {
1160     int t = mSlicers[slicer]->GetOverlayTSlice();
1161     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1162                                                           this->mSlicers[slicer]->GetOverlay()->GetVTKImages()[t],
1163                                                           this->mSlicers[slicer]->GetConcatenatedOverlayTransform());
1164     if(this->mSlicers[slicer]->GetLinkOverlayWindowLevel()){
1165       this->SetColorWindow(max-min);
1166       this->SetColorLevel(0.5*(min+max));
1167     } else {
1168       this->SetOverlayColorWindow(max-min);
1169       this->SetOverlayColorLevel(0.5*(min+max));
1170     }
1171   }
1172   else {
1173     int t = this->GetTSlice();
1174     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1175                                                           this->mSlicers[slicer]->GetImage()->GetVTKImages()[t],
1176                                                           this->mSlicers[slicer]->GetConcatenatedTransform());
1177     this->SetColorWindow(max-min);
1178     this->SetColorLevel(0.5*(min+max));
1179     this->SetPreset(6);
1180   }
1181   this->Render();
1182   this->UpdateWindowLevel();
1183 }
1184 //----------------------------------------------------------------------------
1185
1186
1187 //----------------------------------------------------------------------------
1188 void vvSlicerManager::SetColorMap(int colormap)
1189 {
1190   double range[2];
1191   range[0] = mSlicers[0]->GetInput()->GetScalarRange()[0];
1192   range[1] = mSlicers[0]->GetInput()->GetScalarRange()[1];
1193
1194   double window = mSlicers[0]->GetWindowLevel()->GetWindow();
1195   double level = mSlicers[0]->GetWindowLevel()->GetLevel();
1196
1197   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
1198   switch (colormap) {
1199   case -1:
1200     break;
1201   case 0:
1202     LUT = NULL;
1203     break;
1204   case 1:
1205     if (LUT == NULL)
1206       LUT = vtkLookupTable::New();
1207     LUT->SetValueRange(0,1);
1208     LUT->SetSaturationRange(1,1);
1209     LUT->SetHueRange(0,0.18);
1210     break;
1211   case 2:
1212     if (LUT == NULL)
1213       LUT = vtkLookupTable::New();
1214     LUT->SetValueRange(0,1);
1215     LUT->SetSaturationRange(1,1);
1216     LUT->SetHueRange(0.4,0.80);
1217     break;
1218   case 3:
1219     if (LUT == NULL)
1220       LUT = vtkLookupTable::New();
1221     LUT->SetValueRange(0.5,1);
1222     LUT->SetSaturationRange(1,1);
1223     LUT->SetHueRange(0.666,0);
1224     break;
1225   case 4:
1226     if (LUT == NULL)
1227       LUT = vtkLookupTable::New();
1228     LUT->SetValueRange(1,1);
1229     LUT->SetSaturationRange(1,1);
1230     LUT->SetHueRange(0,1);
1231     LUT->SetAlphaRange(1, 1);
1232     break;
1233   case 5:
1234     if (LUT == NULL)
1235       LUT = vtkLookupTable::New();
1236     LUT->SetValueRange(1,1);
1237     LUT->SetSaturationRange(1,1);
1238     LUT->SetHueRange(1,0.1);
1239     //LUT->SetRampToLinear();
1240     break;
1241   }
1242   if (LUT) {
1243     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1244     LUT->Build();
1245   }
1246   vtkWindowLevelLookupTable* fusLUT = NULL;
1247   if (mSlicers[0]->GetFusion()) { // && mFusionColorMap >= 0) {
1248     fusLUT = vtkWindowLevelLookupTable::New();
1249     double fusRange [2];
1250     fusRange[0] = mFusionLevel - mFusionWindow/2;
1251     fusRange[1] = mFusionLevel + mFusionWindow/2;
1252     double* frange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
1253     fusLUT->SetTableRange(frange);
1254     fusLUT->SetValueRange(1,1);
1255     fusLUT->SetSaturationRange(1,1);
1256     fusLUT->SetAlphaRange(1, 1);
1257     fusLUT->SetWindow(mFusionWindow);
1258     fusLUT->SetLevel(mFusionLevel);
1259     if (mFusionColorMap == 1)
1260       fusLUT->SetHueRange(0,0.18);
1261     else if (mFusionColorMap == 2)
1262       fusLUT->SetHueRange(0.4,0.80);
1263     else if (mFusionColorMap == 3)
1264     {
1265       fusLUT->SetHueRange(0.666, 0);
1266       fusLUT->SetValueRange(0.5, 1);
1267     }
1268     else if (mFusionColorMap == 4)
1269       fusLUT->SetHueRange(0,1);
1270     else if (mFusionColorMap <= 0)
1271     {
1272       fusLUT->SetValueRange(0,1);
1273       fusLUT->SetSaturationRange(0,0);
1274     }
1275
1276     fusLUT->ForceBuild();
1277     double v[4];
1278
1279     // set color table transparency
1280     //double alpha_range=(double)mFusionThresOpacity/10;
1281     double range_end = fusRange[0] + (double)mFusionThresOpacity*(fusRange[1] - fusRange[0])/100;
1282     double curr_value = fusRange[0];
1283     int nvalues = fusLUT->GetNumberOfTableValues();
1284     for (double i = 0; curr_value < range_end; i++) {
1285       fusLUT->GetTableValue(i, v);
1286       v[3] = 0;
1287       //if (curr_value >= -alpha_range && curr_value <= alpha_range) v[3] = pow(fabs(curr_value/alpha_range),2);
1288       //else v[3] = 1;
1289       fusLUT->SetTableValue(i, v);
1290       curr_value += (fusRange[1] - fusRange[0])/nvalues;
1291     }
1292   }
1293   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
1294
1295     if (mSlicers[i]->GetOverlay()) {
1296       vtkLookupTable* supLUT = vtkLookupTable::New();
1297       supLUT->SetTableRange(range[0],range[1]);
1298       supLUT->SetValueRange(1,1);
1299       supLUT->SetSaturationRange(1,1);
1300       supLUT->SetHueRange(double(mOverlayColor)/360,double(mOverlayColor)/360);
1301       supLUT->Build();
1302       vtkLookupTable* invLUT = vtkLookupTable::New();
1303       invLUT->SetTableRange(range[0],range[1]);
1304       invLUT->SetValueRange(1,1);
1305       invLUT->SetSaturationRange(1,1);
1306       invLUT->SetHueRange(double((mOverlayColor+180)%360)/360,double((mOverlayColor+180)%360)/360);
1307       invLUT->Build();
1308       dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
1309         ->SetWindowLevelMode(true);
1310       mSlicers[i]->GetWindowLevel()->SetLookupTable(supLUT);
1311       mSlicers[i]->GetOverlayMapper()->SetLookupTable(invLUT);
1312       invLUT->Delete();
1313       supLUT->Delete();
1314     } else if (mSlicers[i]->GetOverlay()) {
1315       //dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
1316       //->SetWindowLevelMode(false);
1317       mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
1318     } else {
1319       mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
1320     }
1321
1322     if (mSlicers[i]->GetFusion()) {
1323       mSlicers[i]->ShowFusionLegend(mFusionShowLegend);
1324       mSlicers[i]->GetFusionMapper()->SetLookupTable(fusLUT);
1325       mSlicers[i]->GetFusionActor()->SetOpacity(double(mFusionOpacity)/100);
1326     }
1327   }
1328   if (fusLUT)
1329     fusLUT->Delete();
1330   if (colormap >= 0)
1331     mColorMap = colormap;
1332 }
1333 //----------------------------------------------------------------------------
1334
1335
1336 //----------------------------------------------------------------------------
1337 vvLandmarks* vvSlicerManager::GetLandmarks()
1338 {
1339   if (mLandmarks == NULL) {
1340     mLandmarks = new vvLandmarks(mSlicers[0]->GetTMax()+1);
1341     for (unsigned int i = 0; i < mSlicers.size(); i++)
1342       mSlicers[i]->SetLandmarks(mLandmarks);
1343   }
1344   return mLandmarks;
1345 }
1346 //----------------------------------------------------------------------------
1347
1348
1349 //----------------------------------------------------------------------------
1350 void vvSlicerManager::AddLandmark(float x,float y,float z,float t)
1351 {
1352   double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];
1353   double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];
1354   double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];
1355   if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0]-0.5 &&
1356       x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1]+0.5 &&
1357       y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2]-0.5 &&
1358       y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3]+0.5 &&
1359       z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4]-0.5 &&
1360       z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5) {
1361     double value = this->GetScalarComponentAsDouble(mSlicers[0]->GetInput(), x_index, y_index, z_index);
1362     this->GetLandmarks()->AddLandmark(x,y,z,t,value);
1363     emit LandmarkAdded();
1364   }
1365 }
1366 //----------------------------------------------------------------------------
1367
1368 //----------------------------------------------------------------------------
1369 void vvSlicerManager::PrevImage(int slicer)
1370 {
1371   emit ChangeImageWithIndexOffset(this, slicer, -1);
1372 }
1373 //----------------------------------------------------------------------------
1374
1375 //----------------------------------------------------------------------------
1376 void vvSlicerManager::NextImage(int slicer)
1377 {
1378   emit ChangeImageWithIndexOffset(this, slicer,  1);
1379 }
1380 //----------------------------------------------------------------------------
1381
1382 //----------------------------------------------------------------------------
1383 void vvSlicerManager::VerticalSliderHasChanged(int slicer, int slice)
1384 {
1385   emit AVerticalSliderHasChanged(slicer, slice);
1386 }
1387
1388 //----------------------------------------------------------------------------
1389
1390 //----------------------------------------------------------------------------
1391 double vvSlicerManager::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int component)
1392 {
1393   int ix, iy, iz;
1394   return mSlicers[0]->GetScalarComponentAsDouble(image, X, Y, Z, ix, iy, iz, component);
1395 }
1396 //----------------------------------------------------------------------------