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
  73   mPreviousSlice.resize(numberOfSlicers);
  74   mPreviousTSlice.resize(numberOfSlicers);
  75   mSlicingPreset = WORLD_SLICING;
  76 }
  77 //----------------------------------------------------------------------------
  78
  79
  80 //----------------------------------------------------------------------------
  81 vvSlicerManager::~vvSlicerManager()
  82 {
  83   if (mLandmarks)
  84     delete mLandmarks;
  85 }
  86 //----------------------------------------------------------------------------
  87
  88
  89 //------------------------------------------------------------------------------
  90 void vvSlicerManager::SetFilename(std::string filename, int number)
  91 {
  92   mFileName = filename;
  93   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
  94   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
  95   mBaseFileNameNumber = number;
  96
  97   mFileName = mBaseFileName;
  98   if (number != 0) {
  99     mFileName.append("_"+clitk::toString(number));
 100   }
 101   mFileName.append(vtksys::SystemTools::GetFilenameLastExtension(filename));
 102
 103   for(unsigned int i=0; i<mSlicers.size(); i++) {
 104     mSlicers[i]->SetFileName(mFileName);//vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 105   }
 106
 107 }
 108 //------------------------------------------------------------------------------
 109
 110
 111 //----------------------------------------------------------------------------
 112 void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)
 113 {
 114   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 115     mSlicers[i]->AddContour(contour,propagate);
 116   }
 117 }
 118 //----------------------------------------------------------------------------
 119
 120
 121 //----------------------------------------------------------------------------
 122 void vvSlicerManager::ToggleContourSuperposition()
 123 {
 124   for ( unsigned int i = 0; i < mSlicers.size(); i++)
 125     mSlicers[i]->ToggleContourSuperposition();
 126 }
 127 //----------------------------------------------------------------------------
 128
 129 //----------------------------------------------------------------------------
 130 std::string vvSlicerManager::GetListOfAbsoluteFilePathInOneString(const std::string &actorType)
 131 {
 132   vvImageReader *reader = NULL;
 133
 134   if(actorType=="image")
 135     reader = mReader;
 136   else if(actorType=="overlay")
 137     reader = mOverlayReader;
 138   else if(actorType=="fusion")
 139     reader = mFusionReader;
 140   else if(actorType=="vector")
 141     reader = mVectorReader;
 142
 143   if(!reader)
 144     return "";
 145
 146   std::string list;
 147   for(unsigned int i=0; i<reader->GetInputFilenames().size(); i++){
 148     QFileInfo fileinfo(reader->GetInputFilenames()[i].c_str()); //Do not show the path
 149     if(i)
 150       list += '\n';
 151     list += fileinfo.absoluteFilePath().toStdString();
 152   }
 153   return list;
 154 }
 155 //----------------------------------------------------------------------------
 156
 157
 158 //----------------------------------------------------------------------------
 159 bool vvSlicerManager::SetImage(std::string filename, vvImageReader::LoadedImageType type, int n, unsigned int slice)
 160 {
 161   mType = type;
 162   if (mReader.IsNull())
 163     mReader = vvImageReader::New();
 164   std::vector<std::string> filenames;
 165   filenames.push_back(filename);
 166   mReader->SetInputFilenames(filenames);
 167   mReader->SetSlice(slice); // Only used for SLICED type
 168   mReader->Update(type);
 169
 170   SetFilename(filename, n);
 171   //  mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
 172   //mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
 173   //mBaseFileNameNumber = n;
 174
 175   if (mReader->GetLastError().size() == 0) {
 176     mImage=mReader->GetOutput();
 177     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 178       mSlicers[i]->SetFileName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename));
 179       mSlicers[i]->SetImage(mReader->GetOutput());
 180     }
 181   } else {
 182     mLastError = mReader->GetLastError();
 183     return false;
 184   }
 185   // if (n!=0) {
 186   //   mFileName.append("_"+clitk::toString(n));
 187   // }
 188   return true;
 189 }
 190 //----------------------------------------------------------------------------
 191
 192
 193 //----------------------------------------------------------------------------
 194 void vvSlicerManager::SetImage(vvImage::Pointer image)
 195 {
 196   mImage=image;
 197   for (unsigned int i = 0; i < mSlicers.size(); i++) {
 198     mSlicers[i]->SetImage(image);
 199   }
 200 }
 201 //----------------------------------------------------------------------------
 202
 203
 204 //----------------------------------------------------------------------------
 205 bool vvSlicerManager::SetImages(std::vector<std::string> filenames, vvImageReader::LoadedImageType type, int n)
 206 {
 207   mType = type;
 208   std::string fileWithoutExtension = vtksys::SystemTools::GetFilenameWithoutExtension(filenames[0]);
 209   if (type == vvImageReader::DICOM)
 210     fileWithoutExtension += "_dicom";
 211   else if (type == vvImageReader::MERGED)
 212     fileWithoutExtension += "_merged";
 213   else if (type == vvImageReader::MERGEDWITHTIME)
 214     fileWithoutExtension += "_merged_wt";
 215
 216   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
 217   mFileName = fileWithoutExtension + vtksys::SystemTools::GetFilenameExtension(filenames[0]);
 218   if (mReader.IsNull())
 219     mReader = vvImageReader::New();
 220   mReader->SetInputFilenames(filenames);
 221   mReader->Update(type);
 222
 223   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
 224   mBaseFileNameNumber = n;
 225
 226   if (mReader->GetLastError().size() == 0) {
 227     mImage=mReader->GetOutput();
 228     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 229       mSlicers[i]->SetFileName(fileWithoutExtension);
 230       mSlicers[i]->SetImage(mReader->GetOutput());
 231     }
 232   } else {
 233     mLastError = mReader->GetLastError();
 234     return false;
 235   }
 236   if (n!=0) {
 237     mFileName.append("_"+clitk::toString(n));
 238   }
 239   return true;
 240 }
 241 //----------------------------------------------------------------------------
 242
 243
 244 //----------------------------------------------------------------------------
 245 bool vvSlicerManager::SetOverlay(std::string filename,int dim, std::string component)
 246 {
 247   mOverlayName = filename;
 248   mOverlayComponent = component;
 249   if (dim > mImage->GetNumberOfDimensions()) {
 250     mLastError = " Overlay dimension cannot be greater then reference image!";
 251     return false;
 252   }
 253   if (mOverlayReader.IsNull())
 254     mOverlayReader = vvImageReader::New();
 255   std::vector<std::string> filenames;
 256   filenames.push_back(filename);
 257   mOverlayReader->SetInputFilenames(filenames);
 258   mOverlayReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 259   if (mOverlayReader->GetLastError().size() == 0) {
 260     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 261       mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 262     }
 263   } else {
 264     mLastError = mOverlayReader->GetLastError();
 265     return false;
 266   }
 267   return true;
 268 }
 269 //----------------------------------------------------------------------------
 270
 271
 272 //----------------------------------------------------------------------------
 273 bool vvSlicerManager::SetFusion(std::string filename,int dim, std::string component)
 274 {
 275   mFusionName = filename;
 276   mFusionComponent = component;
 277   if (dim > mImage->GetNumberOfDimensions()) {
 278     mLastError = " Overlay dimension cannot be greater then reference image!";
 279     return false;
 280   }
 281   if (mFusionReader.IsNull())
 282     mFusionReader = vvImageReader::New();
 283   std::vector<std::string> filenames;
 284   filenames.push_back(filename);
 285   mFusionReader->SetInputFilenames(filenames);
 286   mFusionReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
 287   if (mFusionReader->GetLastError().size() == 0) {
 288     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 289       mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 290     }
 291   } else {
 292     mLastError = mFusionReader->GetLastError();
 293     return false;
 294   }
 295   double *fusRange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
 296   mFusionLevel = (fusRange[0]+fusRange[1])/2;
 297   mFusionWindow = fusRange[1]-fusRange[0];
 298
 299   return true;
 300 }
 301 //----------------------------------------------------------------------------
 302
 303
 304 //----------------------------------------------------------------------------
 305 bool vvSlicerManager::SetVF(std::string filename)
 306 {
 307   if (mVectorReader.IsNull())
 308     mVectorReader = vvImageReader::New();
 309   mVectorReader->SetInputFilename(filename);
 310
 311   if (mType == vvImageReader::IMAGEWITHTIME)
 312     mVectorReader->Update(vvImageReader::VECTORFIELDWITHTIME);
 313   else
 314     mVectorReader->Update(vvImageReader::VECTORFIELD);
 315   if (mVectorReader->GetLastError().size() != 0) {
 316     mLastError = mVectorReader->GetLastError();
 317     return false;
 318   } else
 319     return SetVF(mVectorReader->GetOutput(),filename);
 320 }
 321 //----------------------------------------------------------------------------
 322
 323
 324 //----------------------------------------------------------------------------
 325 bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)
 326 {
 327   if (vf->GetNumberOfDimensions() > mImage->GetNumberOfDimensions()) {
 328     mLastError = "Sorry, vector field dimension cannot be greater then reference image.";
 329     return false;
 330   }
 331   if (vf->GetNumberOfDimensions() == 4) {
 332     if (vf->GetSpacing()[3] != mImage->GetSpacing()[3]) {
 333       mLastError = "Sorry, vector field time spacing cannot be different from time spacing of the reference image.";
 334       return false;
 335     }
 336     if (vf->GetOrigin()[3] != mImage->GetOrigin()[3]) {
 337       mLastError = "Sorry, vector field time origin cannot be different from time origin of the reference image.";
 338       return false;
 339     }
 340   }
 341   mVF=vf;
 342   mVFName = filename;
 343   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 344     mSlicers[i]->SetVF(vf);
 345   }
 346   return true;
 347 }
 348 //----------------------------------------------------------------------------
 349
 350
 351 //----------------------------------------------------------------------------
 352 vvSlicer* vvSlicerManager::GetSlicer(int i)
 353 {
 354   return mSlicers[i];
 355 }
 356 //----------------------------------------------------------------------------
 357
 358
 359 //----------------------------------------------------------------------------
 360 void vvSlicerManager::UpdateSlicer(int num, bool state)
 361 {
 362   if (mSlicers[num]->GetImage())
 363     mSlicers[num]->SetDisplayMode(state);
 364 }
 365 //----------------------------------------------------------------------------
 366
 367
 368 //----------------------------------------------------------------------------
 369 void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)
 370 {
 371   mSlicers[i]->SetRenderWindow(i,RW);
 372 }
 373 //----------------------------------------------------------------------------
 374
 375
 376 //----------------------------------------------------------------------------
 377 void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* style)
 378 {
 379   vvSlicerManagerCommand *smc = vvSlicerManagerCommand::New();
 380   smc->SM = this;
 381   smc->SetSlicerNumber(i);
 382   mSlicers[i]->GetRenderWindow()->GetInteractor()->SetInteractorStyle(style);
 383
 384   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 385     GetInteractorStyle()->AddObserver(vtkCommand::KeyPressEvent, smc);
 386   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 387     GetInteractorStyle()->AddObserver(vtkCommand::WindowLevelEvent, smc);
 388   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 389     GetInteractorStyle()->AddObserver(vtkCommand::EndWindowLevelEvent, smc);
 390   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 391     GetInteractorStyle()->AddObserver(vtkCommand::StartWindowLevelEvent, smc);
 392   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 393     GetInteractorStyle()->AddObserver(vtkCommand::PickEvent, smc);
 394   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 395     GetInteractorStyle()->AddObserver(vtkCommand::StartPickEvent, smc);
 396   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 397     GetInteractorStyle()->AddObserver(vtkCommand::LeaveEvent, smc);
 398   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 399     GetInteractorStyle()->AddObserver(vtkCommand::UserEvent, smc);
 400   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 401     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelForwardEvent, smc);
 402   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 403     GetInteractorStyle()->AddObserver(vtkCommand::MouseWheelBackwardEvent, smc);
 404   // mSlicers[i]->GetRenderWindow()->GetInteractor()->
 405   //   GetInteractorStyle()->AddObserver(vtkCommand::LeftButtonReleaseEvent, smc);
 406   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 407     GetInteractorStyle()->AddObserver(vtkCommand::EndPickEvent, smc);
 408   mSlicers[i]->GetRenderWindow()->GetInteractor()->
 409     GetInteractorStyle()->AddObserver(vtkCommand::EndInteractionEvent, smc);
 410   smc->Delete();
 411 }
 412 //----------------------------------------------------------------------------
 413
 414
 415 //----------------------------------------------------------------------------
 416 void vvSlicerManager::LeftButtonReleaseEvent(int slicer)
 417 {
 418   emit LeftButtonReleaseSignal(slicer);
 419 }
 420 //----------------------------------------------------------------------------
 421
 422 //----------------------------------------------------------------------------
 423 void vvSlicerManager::SetSliceOrientation(int slicer, int orientation)
 424 {
 425   mSlicers[slicer]->SetSliceOrientation(orientation);
 426   emit UpdateOrientation(slicer, orientation);
 427 }
 428 //----------------------------------------------------------------------------
 429
 430 //----------------------------------------------------------------------------
 431 int vvSlicerManager::GetTSlice()
 432 {
 433   return mSlicers[0]->GetTSlice();
 434 }
 435 //----------------------------------------------------------------------------
 436
 437 //----------------------------------------------------------------------------
 438 void vvSlicerManager::SetTSlice(int slice)
 439 {
 440   if (slice < 0)
 441     slice = 0;
 442   else if (slice > mSlicers[0]->GetTMax())
 443     slice = mSlicers[0]->GetTMax();
 444   if (mLandmarks)
 445     mLandmarks->SetTime(slice);
 446   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 447     if (slice != mSlicers[i]->GetTSlice()) {
 448       mSlicers[i]->SetTSlice(slice);
 449       UpdateTSlice(i);
 450     }
 451   }
 452 }
 453 //----------------------------------------------------------------------------
 454
 455
 456 //----------------------------------------------------------------------------
 457 void vvSlicerManager::SetNextTSlice(int originating_slicer)
 458 {
 459   int t = mSlicers[0]->GetTSlice();
 460   t++;
 461   if (t > mSlicers[0]->GetTMax())
 462     t = 0;
 463   //std::cout << "vvSlicerManager::SetNextTSlice" << std::endl;
 464   emit UpdateTSlice(originating_slicer,t);
 465 }
 466 //----------------------------------------------------------------------------
 467
 468
 469 //----------------------------------------------------------------------------
 470 void vvSlicerManager::SetPreviousTSlice(int originating_slicer)
 471 {
 472   int t = mSlicers[0]->GetTSlice();
 473   t--;
 474   if (t < 0)
 475     t = mSlicers[0]->GetTMax();
 476   //std::cout << "vvSlicerManager::SetPreviousTSlice" << std::endl;
 477   emit UpdateTSlice(originating_slicer,t);
 478 }
 479 //----------------------------------------------------------------------------
 480
 481
 482 //----------------------------------------------------------------------------
 483 void vvSlicerManager::ToggleInterpolation()
 484 {
 485   bool interpolate=!(mSlicers[0]->GetImageActor()->GetInterpolate());
 486   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 487     mSlicers[i]->GetImageActor()->SetInterpolate(interpolate);
 488     if (mSlicers[i]->GetOverlayActor())
 489       mSlicers[i]->GetOverlayActor()->SetInterpolate(interpolate);
 490     if (mSlicers[i]->GetFusionActor())
 491       mSlicers[i]->GetFusionActor()->SetInterpolate(interpolate);
 492   }
 493 }
 494 //----------------------------------------------------------------------------
 495
 496
 497 //----------------------------------------------------------------------------
 498 void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)
 499 {
 500   if (tslice < 0)
 501     tslice = 0;
 502   else if (tslice > mSlicers[slicer]->GetTMax())
 503     tslice = mSlicers[slicer]->GetTMax();
 504   if (mLandmarks)
 505     mLandmarks->SetTime(tslice);
 506
 507   if (mSlicers[slicer]->GetTSlice() == tslice) return;
 508
 509   if(mSlicingPreset==VOXELS_SLICING) {
 510     vtkMatrix4x4 *imageTransformInverse = vtkMatrix4x4::New();
 511     mImage->GetTransform()[tslice]->GetInverse(imageTransformInverse);
 512     this->GetSlicer(slicer)->GetSlicingTransform()->SetMatrix(imageTransformInverse);
 513     imageTransformInverse->Delete();
 514   }
 515
 516   mSlicers[slicer]->SetTSlice(tslice);
 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
 610     switch (mSlicers[slicer]->GetSliceOrientation()) {
 611     case vtkImageViewer2::SLICE_ORIENTATION_XY:
 612       if (mSlicers[slicer]->GetSlice() != (int)lrint(z))
 613         mSlicers[slicer]->SetSlice((int)lrint(z));
 614       break;
 615
 616     case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 617       if (mSlicers[slicer]->GetSlice() != (int)lrint(y))
 618         mSlicers[slicer]->SetSlice((int)lrint(y));
 619       break;
 620
 621     case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 622       if (mSlicers[slicer]->GetSlice() != (int)lrint(x))
 623         mSlicers[slicer]->SetSlice((int)lrint(x));
 624       break;
 625     }
 626     mSlicers[slicer]->Render();
 627
 628     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 629       if (i != (unsigned int)slicer
 630           && mSlicers[i]->GetRenderer()->GetDraw()
 631           && mSlicers[i]->GetRenderWindow()->GetSize()[0] > 2
 632           && mSlicers[i]->GetRenderWindow()->GetSize()[1] > 2) {
 633         mSlicers[i]->SetCurrentPosition(p[0], p[1], p[2], mSlicers[slicer]->GetTSlice());
 634         mSlicers[i]->UpdateCursorPosition();
 635         if (current) { //do not display corner annotation if image is the one picked
 636           mSlicers[i]->SetCurrentPosition(-VTK_DOUBLE_MAX,-VTK_DOUBLE_MAX,
 637                                           -VTK_DOUBLE_MAX, mSlicers[slicer]->GetTSlice());
 638           mSlicers[i]->SetCursorColor(255,10,212);
 639         } else {
 640           mSlicers[i]->SetCursorColor(150,10,282);
 641         }
 642         switch (mSlicers[i]->GetSliceOrientation()) {
 643         case vtkImageViewer2::SLICE_ORIENTATION_XY:
 644           if (mSlicers[i]->GetSlice() != (int)floor(z))
 645             mSlicers[i]->SetSlice((int)floor(z));
 646           break;
 647
 648         case vtkImageViewer2::SLICE_ORIENTATION_XZ:
 649           if (mSlicers[i]->GetSlice() != (int)floor(y))
 650             mSlicers[i]->SetSlice((int)floor(y));
 651           break;
 652
 653         case vtkImageViewer2::SLICE_ORIENTATION_YZ:
 654           if (mSlicers[i]->GetSlice() != (int)floor(x))
 655             mSlicers[i]->SetSlice((int)floor(x));
 656           break;
 657         }
 658
 659         mSlicers[i]->Render();
 660
 661         UpdateSlice(i);
 662         UpdateTSlice(i);
 663       }
 664     }
 665   }
 666 }
 667 //----------------------------------------------------------------------------
 668
 669
 670 //----------------------------------------------------------------------------
 671 void vvSlicerManager::UpdateLinked(int slicer)
 672 {
 673   double p[3], pt[3];
 674   p[0] = mSlicers[slicer]->GetCurrentPosition()[0];
 675   p[1] = mSlicers[slicer]->GetCurrentPosition()[1];
 676   p[2] = mSlicers[slicer]->GetCurrentPosition()[2];
 677   mSlicers[slicer]->GetSlicingTransform()->GetInverse()->TransformPoint(p, pt);
 678   double x = (pt[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0]) / mSlicers[slicer]->GetInput()->GetSpacing()[0];
 679   double y = (pt[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1]) / mSlicers[slicer]->GetInput()->GetSpacing()[1];
 680   double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2]) / mSlicers[slicer]->GetInput()->GetSpacing()[2];
 681
 682   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&
 683       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&
 684       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&
 685       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3]+0.5 &&
 686       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4]-0.5 &&
 687       z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5) {
 688     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++) {
 689       emit UpdateLinkManager(*i, slicer,mSlicers[slicer]->GetCurrentPosition()[0],
 690                              mSlicers[slicer]->GetCurrentPosition()[1],
 691                              mSlicers[slicer]->GetCurrentPosition()[2],mSlicers[slicer]->GetTSlice());
 692     }
 693   }
 694 }
 695 //----------------------------------------------------------------------------
 696
 697 //----------------------------------------------------------------------------
 698 void vvSlicerManager::UpdateLinkedNavigation(vvSlicer *refSlicer, bool bPropagate)
 699 {
 700   vtkCamera *refCam = refSlicer->GetRenderer()->GetActiveCamera();
 701   double refPosition[3], refFocal[3];
 702   refCam->GetPosition(refPosition);
 703   refCam->GetFocalPoint(refFocal);
 704
 705   refSlicer->GetSlicingTransform()->TransformPoint(refPosition);
 706   refSlicer->GetSlicingTransform()->TransformPoint(refFocal);
 707   mSlicers[0]->GetSlicingTransform()->GetInverse()->TransformPoint(refPosition);
 708   mSlicers[0]->GetSlicingTransform()->GetInverse()->TransformPoint(refFocal);
 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     if(refSlicer->GetSliceOrientation()==mSlicers[i]->GetSliceOrientation()) {
 719       for(int i=0; i<3; i++) {
 720         position[i] = refPosition[i];
 721         focal[i]    = refFocal[i];
 722       }
 723     }
 724
 725     if(refSlicer->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XY) {
 726       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XZ) {
 727         position[0] = refPosition[0];
 728         focal[0]    = refFocal[0];
 729       }
 730       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_YZ) {
 731         position[1] = refPosition[1];
 732         focal[1]    = refFocal[1];
 733       }
 734     }
 735
 736     if(refSlicer->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XZ) {
 737       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_YZ) {
 738         position[2] = refPosition[2];
 739         focal[2]    = refFocal[2];
 740       }
 741       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XY) {
 742         position[0] = refPosition[0];
 743         focal[0]    = refFocal[0];
 744       }
 745     }
 746
 747     if(refSlicer->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_YZ) {
 748       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XY) {
 749         position[1] = refPosition[1];
 750         focal[1]    = refFocal[1];
 751       }
 752       if(mSlicers[i]->GetSliceOrientation()==vtkImageViewer2::SLICE_ORIENTATION_XZ) {
 753         position[2] = refPosition[2];
 754         focal[2]    = refFocal[2];
 755       }
 756     }
 757 DD(camera->GetFocalPoint()[0] << ' ' << camera->GetFocalPoint()[1] << ' ' << camera->GetFocalPoint()[2])
 758     camera->SetFocalPoint(focal);
 759 DD(camera->GetFocalPoint()[0] << ' ' << camera->GetFocalPoint()[1] << ' ' << camera->GetFocalPoint()[2])
 760 DD(camera->GetPosition()[0] << ' ' << camera->GetPosition()[1] << ' ' << camera->GetPosition()[2])
 761     camera->SetPosition(position);
 762 DD(camera->GetPosition()[0] << ' ' << camera->GetPosition()[1] << ' ' << camera->GetPosition()[2])
 763
 764     //Fix for bug #243
 765     mSlicers[i]->ForceUpdateDisplayExtent();
 766   }
 767
 768   Render();
 769   if(bPropagate)
 770     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++)
 771       emit UpdateLinkedNavigation(*i, this, refSlicer);
 772 }
 773 //----------------------------------------------------------------------------
 774
 775 //----------------------------------------------------------------------------
 776 double vvSlicerManager::GetColorWindow()
 777 {
 778   if (mSlicers.size())
 779     return mSlicers[0]->GetColorWindow();
 780   return -1;
 781 }
 782 //----------------------------------------------------------------------------
 783
 784
 785 //----------------------------------------------------------------------------
 786 double vvSlicerManager::GetColorLevel()
 787 {
 788   if (mSlicers.size())
 789     return mSlicers[0]->GetColorLevel();
 790   return -1;
 791 }
 792 //----------------------------------------------------------------------------
 793
 794 //----------------------------------------------------------------------------
 795 double vvSlicerManager::GetOverlayColorWindow() const
 796 {
 797   if (mSlicers.size())
 798     return mSlicers[0]->GetOverlayColorWindow();
 799   return -1;
 800 }
 801 //----------------------------------------------------------------------------
 802
 803 //----------------------------------------------------------------------------
 804 double vvSlicerManager::GetOverlayColorLevel() const
 805 {
 806   if (mSlicers.size())
 807     return mSlicers[0]->GetOverlayColorLevel();
 808   return -1;
 809 }
 810 //----------------------------------------------------------------------------
 811
 812 //----------------------------------------------------------------------------
 813 bool vvSlicerManager::GetLinkOverlayWindowLevel() const
 814 {
 815   if (mSlicers.size())
 816     return mSlicers[0]->GetLinkOverlayWindowLevel();
 817   return -1;
 818 }
 819 //----------------------------------------------------------------------------
 820
 821 //------------------------------------------------------------------------------
 822 void vvSlicerManager::ResetTransformationToIdentity(const std::string actorType)
 823 {
 824   if(actorType == "image")
 825     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 826       this->GetImage()->GetTransform()[i]->Identity();
 827   else if(actorType == "overlay")
 828     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 829       this->GetSlicer(0)->GetOverlay()->GetTransform()[i]->Identity();
 830   else if(actorType == "fusion")
 831     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 832       this->GetSlicer(0)->GetFusion()->GetTransform()[i]->Identity();
 833   else if(actorType == "vf")
 834     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
 835       this->GetVF()->GetTransform()[i]->Identity();
 836   else
 837     return;
 838
 839   for(int i=0; i< this->GetNumberOfSlicers(); i++){
 840     this->GetSlicer(i)->ForceUpdateDisplayExtent();
 841     this->GetSlicer(i)->ResetCamera();
 842     this->GetSlicer(i)->Render();
 843   }
 844 }
 845 //------------------------------------------------------------------------------
 846
 847 //----------------------------------------------------------------------------
 848 void vvSlicerManager::Render()
 849 {
 850   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 851     mSlicers[i]->Render();
 852   }
 853 }
 854 //----------------------------------------------------------------------------
 855
 856
 857 //----------------------------------------------------------------------------
 858 void vvSlicerManager::GenerateDefaultLookupTable()
 859 {
 860   SetPreset(mPreset);
 861   SetColorMap(mColorMap);
 862 }
 863 //----------------------------------------------------------------------------
 864
 865
 866 //----------------------------------------------------------------------------
 867 void vvSlicerManager::Reload()
 868 {
 869   mReader->Update(mType);
 870   mImage=mReader->GetOutput();
 871   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 872     mSlicers[i]->SetImage(mImage);
 873   }
 874 }
 875 //----------------------------------------------------------------------------
 876
 877
 878 //----------------------------------------------------------------------------
 879 void vvSlicerManager::ReloadFusion()
 880 {
 881   mFusionReader->Update(mImage->GetNumberOfDimensions(),mFusionComponent.c_str(),mType);
 882
 883   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 884     mSlicers[i]->SetFusion(mFusionReader->GetOutput());
 885     mSlicers[i]->Render();
 886   }
 887 }
 888 //----------------------------------------------------------------------------
 889
 890
 891 //----------------------------------------------------------------------------
 892 void vvSlicerManager::ReloadOverlay()
 893 {
 894   mOverlayReader->Update(mImage->GetNumberOfDimensions(),mOverlayComponent.c_str(),mType);
 895   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 896     mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
 897     mSlicers[i]->Render();
 898   }
 899 }
 900 //----------------------------------------------------------------------------
 901
 902
 903 //----------------------------------------------------------------------------
 904 void vvSlicerManager::ReloadVF()
 905 {
 906   mVectorReader->Update(vvImageReader::VECTORFIELD); //deletes the old images through the VF::Init() function
 907   mVF=mVectorReader->GetOutput();
 908   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 909     mSlicers[i]->SetVF(mVF);
 910     mSlicers[i]->Render();
 911   }
 912 }
 913 //----------------------------------------------------------------------------
 914
 915
 916 //----------------------------------------------------------------------------
 917 void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_index)
 918 {
 919   if (actor_type =="overlay")
 920     mOverlayReader = NULL;
 921
 922   if (actor_type =="fusion")
 923     mFusionReader = NULL;
 924
 925   for (unsigned int i = 0; i < mSlicers.size(); i++)
 926     mSlicers[i]->RemoveActor(actor_type,overlay_index);
 927
 928   if (actor_type=="vector") {
 929     mVF=NULL;
 930     mVectorReader=NULL;
 931   }
 932 }
 933 //----------------------------------------------------------------------------
 934
 935
 936 //----------------------------------------------------------------------------
 937 void vvSlicerManager::RemoveActors()
 938 {
 939   ///This method leaks a few objects. See RemoveActor for what a
 940   ///correct implementation would look like
 941   //DS -> probably due to the reader (now released in the
 942   //RemoveActor() function. (I hope)
 943   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 944     mSlicers[i]->SetDisplayMode(0);
 945     mSlicers[i]->GetRenderer()->RemoveActor(mSlicers[i]->GetImageActor());
 946   }
 947 }
 948 //----------------------------------------------------------------------------
 949
 950
 951 //----------------------------------------------------------------------------
 952 void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
 953 {
 954   //  int view = mSlicers[slicer]->GetSliceOrientation();
 955   //  int slice = mSlicers[slicer]->GetSlice();
 956   double x = mSlicers[slicer]->GetCursorPosition()[0];
 957   double y = mSlicers[slicer]->GetCursorPosition()[1];
 958   double z = mSlicers[slicer]->GetCursorPosition()[2];
 959   double X = (x - mSlicers[slicer]->GetInput()->GetOrigin()[0])/
 960     mSlicers[slicer]->GetInput()->GetSpacing()[0];
 961   double Y = (y - mSlicers[slicer]->GetInput()->GetOrigin()[1])/
 962     mSlicers[slicer]->GetInput()->GetSpacing()[1];
 963   double Z = (z - mSlicers[slicer]->GetInput()->GetOrigin()[2])/
 964     mSlicers[slicer]->GetInput()->GetSpacing()[2];
 965   double value = -VTK_DOUBLE_MAX;
 966   int displayVec = 0;
 967   double xVec=0, yVec=0, zVec=0, valueVec=0;
 968   int displayOver = 0;
 969   int displayFus = 0;
 970   double valueOver=0, valueFus=0;
 971   if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
 972       X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
 973       Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
 974       Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
 975       Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
 976       Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {
 977     value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);
 978
 979     if (mSlicers[slicer]->GetVFActor() ) {
 980       displayVec = 1;
 981       unsigned int currentTime = mSlicers[slicer]->GetTSlice();
 982       vtkImageData *vf = NULL;
 983
 984       if (mSlicers[slicer]->GetVF()->GetVTKImages().size() > currentTime)
 985         vf = mSlicers[slicer]->GetVF()->GetVTKImages()[currentTime];
 986       else
 987         vf = mSlicers[slicer]->GetVF()->GetVTKImages()[0];
 988
 989       if (vf) {
 990         double Xvf = (x - vf->GetOrigin()[0])/ vf->GetSpacing()[0];
 991         double Yvf = (y - vf->GetOrigin()[1])/ vf->GetSpacing()[1];
 992         double Zvf = (z - vf->GetOrigin()[2])/ vf->GetSpacing()[2];
 993         xVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 0);
 994         yVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 1);
 995         zVec = this->GetScalarComponentAsDouble( vf, Xvf, Yvf, Zvf, 2);
 996         valueVec = sqrt(xVec*xVec + yVec*yVec + zVec*zVec);
 997       }
 998     }
 999     if (mSlicers[slicer]->GetOverlayActor() ) {
1000       displayOver = 1;
1001       vtkImageData *overlay = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetOverlayMapper()->GetInput());
1002       double Xover = (x - overlay->GetOrigin()[0]) / overlay->GetSpacing()[0];
1003       double Yover = (y - overlay->GetOrigin()[1]) / overlay->GetSpacing()[1];
1004       double Zover = (z - overlay->GetOrigin()[2]) / overlay->GetSpacing()[2];
1005       valueOver = this->GetScalarComponentAsDouble(overlay, Xover, Yover, Zover);
1006     }
1007     if (mSlicers[slicer]->GetFusionActor() ) {
1008       displayFus = 1;
1009       vtkImageData *fusion = dynamic_cast<vtkImageData*>(mSlicers[slicer]->GetFusionMapper()->GetInput());
1010       double Xover = (x - fusion->GetOrigin()[0]) / fusion->GetSpacing()[0];
1011       double Yover = (y - fusion->GetOrigin()[1]) / fusion->GetSpacing()[1];
1012       double Zover = (z - fusion->GetOrigin()[2]) / fusion->GetSpacing()[2];
1013       valueFus = this->GetScalarComponentAsDouble(fusion, Xover, Yover, Zover);
1014     }
1015     emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),
1016                         x,y,z,X,Y,Z,value);
1017     emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);
1018     emit UpdateOverlay(displayOver,valueOver,value);
1019     emit UpdateFusion(displayFus,valueFus);
1020   }
1021 }
1022 //----------------------------------------------------------------------------
1023
1024
1025 //----------------------------------------------------------------------------
1026 void vvSlicerManager::Activated()
1027 {
1028   emit currentImageChanged(mId);
1029 }
1030 //----------------------------------------------------------------------------
1031
1032
1033 //----------------------------------------------------------------------------
1034 void vvSlicerManager::Picked()
1035 {
1036   emit currentPickedImageChanged(mId);
1037 }
1038 //----------------------------------------------------------------------------
1039
1040
1041 //----------------------------------------------------------------------------
1042 void vvSlicerManager::UpdateWindowLevel()
1043 {
1044   emit WindowLevelChanged();
1045 }
1046 //----------------------------------------------------------------------------
1047
1048
1049 //----------------------------------------------------------------------------
1050 void vvSlicerManager::UpdateSlice(int slicer)
1051 {
1052   if (mPreviousSlice[slicer] == mSlicers[slicer]->GetSlice()) {
1053     //DD("============= NOTHING");
1054     return;
1055   }
1056   //std::cout << "vvSlicerManager::UpdateSlice " << slicer << " " << mSlicers[slicer]->GetSlice() << std::endl;
1057   emit UpdateSlice(slicer, mSlicers[slicer]->GetSlice());
1058   mSlicers[slicer]->Render(); // DS <-- I add this, this could/must be the only Render ...
1059   mPreviousSlice[slicer] = mSlicers[slicer]->GetSlice();
1060 }
1061 //----------------------------------------------------------------------------
1062
1063
1064 //----------------------------------------------------------------------------
1065 void vvSlicerManager::UpdateTSlice(int slicer)
1066 {
1067   int slice = mSlicers[slicer]->GetSlice();
1068   int tslice = mSlicers[slicer]->GetTSlice();
1069   if (mPreviousSlice[slicer] == slice) {
1070     if (mPreviousTSlice[slicer] == tslice) {
1071       //      DD("************** NOTHING ***********");
1072       return;
1073     }
1074   }
1075   mPreviousSlice[slicer] = slice;
1076   mPreviousTSlice[slicer] = tslice;
1077   //std::cout << "vvSlicerManager::UpdateTSlice " << slicer << " " << tslice << std::endl;
1078   emit UpdateTSlice(slicer, tslice);
1079 }
1080 //----------------------------------------------------------------------------
1081
1082
1083 //----------------------------------------------------------------------------
1084 void vvSlicerManager::UpdateSliceRange(int slicer)
1085 {
1086   emit UpdateSliceRange(slicer,
1087                         mSlicers[slicer]->GetSliceRange()[0], mSlicers[slicer]->GetSliceRange()[1],
1088                         0,mSlicers[slicer]->GetTMax());
1089 }
1090 //----------------------------------------------------------------------------
1091
1092 //----------------------------------------------------------------------------
1093 void vvSlicerManager::SetSlicingPreset(SlicingPresetType preset)
1094 {
1095   if(mSlicingPreset==preset)
1096     return;
1097
1098   vtkMatrix4x4 *imageTransformInverse = vtkMatrix4x4::New();
1099   mImage->GetTransform()[this->GetTSlice()]->GetInverse(imageTransformInverse);
1100
1101   for(int i=0; i< this->GetNumberOfSlicers(); i++){
1102     vvSlicer *s = this->GetSlicer(i);
1103     switch(preset)
1104     {
1105     case WORLD_SLICING:
1106       s->GetSlicingTransform()->Identity();
1107       break;
1108     case VOXELS_SLICING:
1109       s->GetSlicingTransform()->SetMatrix(imageTransformInverse);
1110       break;
1111     default:
1112       imageTransformInverse->Delete();
1113       return;
1114     }
1115     s->ForceUpdateDisplayExtent();
1116     s->SetSlice((s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2+1]
1117                 +s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2])/2.0);
1118     s->ResetCamera();
1119     s->Render();
1120   }
1121
1122   imageTransformInverse->Delete();
1123   mSlicingPreset = preset;
1124 }
1125
1126 //----------------------------------------------------------------------------
1127
1128 //----------------------------------------------------------------------------
1129 void vvSlicerManager::SetPreset(int preset)
1130 {
1131   //vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
1132   double window = mSlicers[0]->GetColorWindow();
1133   double level = mSlicers[0]->GetColorLevel();
1134
1135   std::string component_type=mImage->GetScalarTypeAsITKString();
1136   switch (preset) {
1137   case 0:
1138     double range[2];
1139     mImage->GetScalarRange(range);
1140     window = range[1] - range[0];
1141     level = (range[1] + range[0])* 0.5;
1142     break;
1143   case 1:
1144     window = 2000;
1145     level = 0;
1146     break;
1147   case 2:
1148     window = 400;
1149     level = 20;
1150     break;
1151   case 3:
1152     window = 1500;
1153     level = -500;
1154     break;
1155   case 4:
1156     window = 1000;
1157     level = 500;
1158     break;
1159   case 5:
1160     window = 1;
1161     level = 0.5;
1162     break;
1163   case 6:
1164     break;
1165   case 7:
1166     window=1.;
1167     level=0.;
1168     break;
1169   }
1170   mPreset = preset;
1171   this->SetColorWindow(window);
1172   this->SetColorLevel(level);
1173
1174   //if (LUT)
1175   //{
1176   //    SetColorMap(-1);
1177   //}
1178 }
1179 //----------------------------------------------------------------------------
1180
1181
1182 //----------------------------------------------------------------------------
1183 void vvSlicerManager::SetLocalColorWindowing(const int slicer, const bool bCtrlKey)
1184 {
1185   double min, max;
1186   int t = this->GetTSlice();
1187   if(bCtrlKey && this->mSlicers[slicer]->GetFusion()) {
1188     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1189                                                           this->mSlicers[slicer]->GetFusion()->GetVTKImages()[t],
1190                                                           this->mSlicers[slicer]->GetFusion()->GetTransform()[t]);
1191     this->SetFusionWindow(max-min);
1192     this->SetFusionLevel(0.5*(min+max));
1193     this->SetColorMap(mColorMap);
1194   }
1195   else if(bCtrlKey && this->mSlicers[slicer]->GetOverlay()) {
1196     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1197                                                           this->mSlicers[slicer]->GetOverlay()->GetVTKImages()[t],
1198                                                           this->mSlicers[slicer]->GetOverlay()->GetTransform()[t]);
1199     if(this->mSlicers[slicer]->GetLinkOverlayWindowLevel()){
1200       this->SetColorWindow(max-min);
1201       this->SetColorLevel(0.5*(min+max));
1202     } else {
1203       this->SetOverlayColorWindow(max-min);
1204       this->SetOverlayColorLevel(0.5*(min+max));
1205     }
1206   }
1207   else {
1208     this->mSlicers[slicer]->GetExtremasAroundMousePointer(min, max,
1209                                                           this->mSlicers[slicer]->GetImage()->GetVTKImages()[t],
1210                                                           this->mSlicers[slicer]->GetConcatenatedTransform());
1211     this->SetColorWindow(max-min);
1212     this->SetColorLevel(0.5*(min+max));
1213     this->SetPreset(6);
1214   }
1215   this->Render();
1216   this->UpdateWindowLevel();
1217 }
1218 //----------------------------------------------------------------------------
1219
1220
1221 //----------------------------------------------------------------------------
1222 void vvSlicerManager::SetColorMap(int colormap)
1223 {
1224   double range[2];
1225   range[0] = mSlicers[0]->GetInput()->GetScalarRange()[0];
1226   range[1] = mSlicers[0]->GetInput()->GetScalarRange()[1];
1227
1228   double window = mSlicers[0]->GetWindowLevel()->GetWindow();
1229   double level = mSlicers[0]->GetWindowLevel()->GetLevel();
1230
1231   vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
1232   switch (colormap) {
1233   case -1:
1234     break;
1235   case 0:
1236     LUT = NULL;
1237     break;
1238   case 1:
1239     if (LUT == NULL)
1240       LUT = vtkLookupTable::New();
1241     LUT->SetValueRange(0,1);
1242     LUT->SetSaturationRange(1,1);
1243     LUT->SetHueRange(0,0.18);
1244     break;
1245   case 2:
1246     if (LUT == NULL)
1247       LUT = vtkLookupTable::New();
1248     LUT->SetValueRange(0,1);
1249     LUT->SetSaturationRange(1,1);
1250     LUT->SetHueRange(0.4,0.80);
1251     break;
1252   case 3:
1253     if (LUT == NULL)
1254       LUT = vtkLookupTable::New();
1255     LUT->SetValueRange(0.5,1);
1256     LUT->SetSaturationRange(1,1);
1257     LUT->SetHueRange(0.666,0);
1258     break;
1259   case 4:
1260     if (LUT == NULL)
1261       LUT = vtkLookupTable::New();
1262     LUT->SetValueRange(1,1);
1263     LUT->SetSaturationRange(1,1);
1264     LUT->SetHueRange(0,1);
1265     LUT->SetAlphaRange(1, 1);
1266     break;
1267   case 5:
1268     if (LUT == NULL)
1269       LUT = vtkLookupTable::New();
1270     LUT->SetValueRange(1,1);
1271     LUT->SetSaturationRange(1,1);
1272     LUT->SetHueRange(1,0.1);
1273     //LUT->SetRampToLinear();
1274     break;
1275   }
1276   if (LUT) {
1277     LUT->SetTableRange(level-fabs(window)/2,level+fabs(window)/2);
1278     LUT->Build();
1279   }
1280   vtkWindowLevelLookupTable* fusLUT = NULL;
1281   if (mSlicers[0]->GetFusion()) { // && mFusionColorMap >= 0) {
1282     fusLUT = vtkWindowLevelLookupTable::New();
1283     double fusRange [2];
1284     fusRange[0] = mFusionLevel - mFusionWindow/2;
1285     fusRange[1] = mFusionLevel + mFusionWindow/2;
1286     double* frange = mFusionReader->GetOutput()->GetVTKImages()[0]->GetScalarRange();
1287     fusLUT->SetTableRange(frange);
1288     fusLUT->SetValueRange(1,1);
1289     fusLUT->SetSaturationRange(1,1);
1290     fusLUT->SetAlphaRange(1, 1);
1291     fusLUT->SetWindow(mFusionWindow);
1292     fusLUT->SetLevel(mFusionLevel);
1293     if (mFusionColorMap == 1)
1294       fusLUT->SetHueRange(0,0.18);
1295     else if (mFusionColorMap == 2)
1296       fusLUT->SetHueRange(0.4,0.80);
1297     else if (mFusionColorMap == 3)
1298     {
1299       fusLUT->SetHueRange(0.666, 0);
1300       fusLUT->SetValueRange(0.5, 1);
1301     }
1302     else if (mFusionColorMap == 4)
1303       fusLUT->SetHueRange(0,1);
1304     else if (mFusionColorMap <= 0)
1305     {
1306       fusLUT->SetValueRange(0,1);
1307       fusLUT->SetSaturationRange(0,0);
1308     }
1309
1310     fusLUT->ForceBuild();
1311     double v[4];
1312
1313     // set color table transparency
1314     //double alpha_range=(double)mFusionThresOpacity/10;
1315     double range_end = fusRange[0] + (double)mFusionThresOpacity*(fusRange[1] - fusRange[0])/100;
1316     double curr_value = fusRange[0];
1317     int nvalues = fusLUT->GetNumberOfTableValues();
1318     for (double i = 0; curr_value < range_end; i++) {
1319       fusLUT->GetTableValue(i, v);
1320       v[3] = 0;
1321       //if (curr_value >= -alpha_range && curr_value <= alpha_range) v[3] = pow(fabs(curr_value/alpha_range),2);
1322       //else v[3] = 1;
1323       fusLUT->SetTableValue(i, v);
1324       curr_value += (fusRange[1] - fusRange[0])/nvalues;
1325     }
1326   }
1327   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
1328
1329     if (mSlicers[i]->GetOverlay()) {
1330       vtkLookupTable* supLUT = vtkLookupTable::New();
1331       supLUT->SetTableRange(range[0],range[1]);
1332       supLUT->SetValueRange(1,1);
1333       supLUT->SetSaturationRange(1,1);
1334       supLUT->SetHueRange(double(mOverlayColor)/360,double(mOverlayColor)/360);
1335       supLUT->Build();
1336       vtkLookupTable* invLUT = vtkLookupTable::New();
1337       invLUT->SetTableRange(range[0],range[1]);
1338       invLUT->SetValueRange(1,1);
1339       invLUT->SetSaturationRange(1,1);
1340       invLUT->SetHueRange(double((mOverlayColor+180)%360)/360,double((mOverlayColor+180)%360)/360);
1341       invLUT->Build();
1342       dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
1343         ->SetWindowLevelMode(true);
1344       mSlicers[i]->GetWindowLevel()->SetLookupTable(supLUT);
1345       mSlicers[i]->GetOverlayMapper()->SetLookupTable(invLUT);
1346       invLUT->Delete();
1347       supLUT->Delete();
1348     } else if (mSlicers[i]->GetOverlay()) {
1349       //dynamic_cast<vvImageMapToWLColors*>(mSlicers[i]->GetWindowLevel())
1350       //->SetWindowLevelMode(false);
1351       mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
1352     } else {
1353       mSlicers[i]->GetWindowLevel()->SetLookupTable(LUT);
1354     }
1355
1356     if (mSlicers[i]->GetFusion()) {
1357       mSlicers[i]->ShowFusionLegend(mFusionShowLegend);
1358       mSlicers[i]->GetFusionMapper()->SetLookupTable(fusLUT);
1359       mSlicers[i]->GetFusionActor()->SetOpacity(double(mFusionOpacity)/100);
1360     }
1361   }
1362   if (fusLUT)
1363     fusLUT->Delete();
1364   if (colormap >= 0)
1365     mColorMap = colormap;
1366 }
1367 //----------------------------------------------------------------------------
1368
1369
1370 //----------------------------------------------------------------------------
1371 vvLandmarks* vvSlicerManager::GetLandmarks()
1372 {
1373   if (mLandmarks == NULL) {
1374     mLandmarks = new vvLandmarks(mSlicers[0]->GetTMax()+1);
1375     for (unsigned int i = 0; i < mSlicers.size(); i++)
1376       mSlicers[i]->SetLandmarks(mLandmarks);
1377   }
1378   return mLandmarks;
1379 }
1380 //----------------------------------------------------------------------------
1381
1382
1383 //----------------------------------------------------------------------------
1384 void vvSlicerManager::AddLandmark(float x,float y,float z,float t)
1385 {
1386   double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];
1387   double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];
1388   double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];
1389   if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0]-0.5 &&
1390       x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1]+0.5 &&
1391       y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2]-0.5 &&
1392       y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3]+0.5 &&
1393       z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4]-0.5 &&
1394       z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5) {
1395     double value = this->GetScalarComponentAsDouble(mSlicers[0]->GetInput(), x_index, y_index, z_index);
1396     this->GetLandmarks()->AddLandmark(x,y,z,t,value);
1397     emit LandmarkAdded();
1398   }
1399 }
1400 //----------------------------------------------------------------------------
1401
1402 //----------------------------------------------------------------------------
1403 void vvSlicerManager::PrevImage(int slicer)
1404 {
1405   emit ChangeImageWithIndexOffset(this, slicer, -1);
1406 }
1407 //----------------------------------------------------------------------------
1408
1409 //----------------------------------------------------------------------------
1410 void vvSlicerManager::NextImage(int slicer)
1411 {
1412   emit ChangeImageWithIndexOffset(this, slicer,  1);
1413 }
1414 //----------------------------------------------------------------------------
1415
1416 //----------------------------------------------------------------------------
1417 void vvSlicerManager::VerticalSliderHasChanged(int slicer, int slice)
1418 {
1419   emit AVerticalSliderHasChanged(slicer, slice);
1420 }
1421
1422 //----------------------------------------------------------------------------
1423
1424 //----------------------------------------------------------------------------
1425 double vvSlicerManager::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int component)
1426 {
1427   int ix, iy, iz;
1428   return mSlicers[0]->GetScalarComponentAsDouble(image, X, Y, Z, ix, iy, iz, component);
1429 }
1430 //----------------------------------------------------------------------------