vv/vvToolProfile.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 #include <QFileDialog>
  20 #include <QShortcut>
  21
  22 #include <algorithm>
  23
  24 // vv
  25 #include "vvToolProfile.h"
  26 #include "vvProgressDialog.h"
  27 #include "vvSlicerManager.h"
  28 #include "vvSlicer.h"
  29 #include "vvToolInputSelectorWidget.h"
  30
  31 // vtk
  32 #include <vtkAxis.h>
  33 #include <vtkImageActor.h>
  34 #include <vtkCamera.h>
  35 #include <vtkImageClip.h>
  36 #include <vtkRenderWindow.h>
  37 #include <vtkChartXY.h>
  38 #include <vtkPlot.h>
  39 #include <vtkRendererCollection.h>
  40 #include <vtkRenderer.h>
  41
  42 #include <vtkLine.h>
  43 #include <vtkCellArray.h>
  44 #include <vtkCellData.h>
  45 #include <vtkPolyDataMapper.h>
  46 #include <vtkProperty.h>
  47 #include <vtkBox.h>
  48 #include <vtkInformation.h>
  49
  50 #ifdef Q_OS_OSX
  51 # include "vvOSXHelper.h"
  52 #endif
  53
  54 //------------------------------------------------------------------------------
  55 // Create the tool and automagically (I like this word) insert it in
  56 // the main window menu.
  57 ADD_TOOL(vvToolProfile);
  58 //------------------------------------------------------------------------------
  59
  60
  61 //------------------------------------------------------------------------------
  62 void vvToolProfile::Initialize()
  63 {
  64   SetToolName("Profile");
  65   SetToolMenuName("Intensity Profile");
  66   SetToolIconFilename(":/common/icons/profile.png");
  67   SetToolTip("Display the intensity profile between 2 points of the image.");
  68   SetToolExperimental(false);
  69 }
  70 //------------------------------------------------------------------------------
  71
  72
  73 //------------------------------------------------------------------------------
  74 vvToolProfile::vvToolProfile(vvMainWindowBase * parent, Qt::WindowFlags f)
  75   :vvToolWidgetBase(parent,f),
  76    vvToolBase<vvToolProfile>(parent),
  77    Ui::vvToolProfile()
  78 {
  79   // GUI Initialization
  80   Ui_vvToolProfile::setupUi(mToolWidget);
  81
  82   QShortcut *shortcutPoint1 = new QShortcut(QKeySequence("Ctrl+1"), parent);
  83   shortcutPoint1->setContext(Qt::ApplicationShortcut);
  84   QObject::connect(shortcutPoint1, SIGNAL(activated()), this, SLOT(selectPoint1()));
  85   QShortcut *shortcutPoint2 = new QShortcut(QKeySequence("Ctrl+2"), parent);
  86   shortcutPoint2->setContext(Qt::ApplicationShortcut);
  87   QObject::connect(shortcutPoint2, SIGNAL(activated()), this, SLOT(selectPoint2()));
  88
  89   // Connect signals & slots
  90   connect(mSelectPoint1Button, SIGNAL(clicked()), this, SLOT(selectPoint1()));
  91   connect(mSelectPoint2Button, SIGNAL(clicked()), this, SLOT(selectPoint2()));
  92   connect(mCancelPointsButton, SIGNAL(clicked()), this, SLOT(cancelPoints()));
  93   connect(mSaveProfileButton, SIGNAL(clicked()), this, SLOT(SaveAs()));
  94
  95   // Initialize some widget
  96   ProfileWidget->hide();
  97   mPoint1 = NULL;
  98   mPoint2 = NULL;
  99
 100   mPoint1Selected = false;
 101   mPoint2Selected = false;
 102
 103   mView = vtkSmartPointer<vtkContextView>::New();
 104   vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
 105   chart->SetAutoSize(false);
 106   chart->SetRenderEmpty(true);
 107   mView->GetScene()->AddItem(chart);
 108   this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
 109   this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
 110   ProfileWidget->show();
 111
 112 #ifdef Q_OS_OSX
 113   disableGLHiDPI(ProfileWidget->winId());
 114 #endif
 115
 116   // Main filter
 117   mFilter = clitk::ProfileImageGenericFilter::New();
 118
 119   // Set how many inputs are needed for this tool
 120   AddInputSelector("Select one image", mFilter);
 121 }
 122 //------------------------------------------------------------------------------
 123
 124
 125 //------------------------------------------------------------------------------
 126 vvToolProfile::~vvToolProfile()
 127 {
 128   delete [] mPoint1;
 129   delete [] mPoint2;
 130 }
 131 //------------------------------------------------------------------------------
 132
 133
 134 //------------------------------------------------------------------------------
 135 void vvToolProfile::selectPoint1()
 136 {
 137   QString position = "";
 138
 139   if(mCurrentSlicerManager) {
 140     if (mPoint1Selected) {
 141       ProfileWidget->hide();
 142       vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
 143       chart->SetAutoSize(false);
 144       chart->SetRenderEmpty(true);
 145       mView->GetScene()->ClearItems();
 146       mView->GetScene()->AddItem(chart);
 147       this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
 148       this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
 149       ProfileWidget->show();
 150       mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P1", mPoint1[3]);
 151     }
 152
 153     mPoint1Selected = false;
 154
 155     if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
 156       double *pos;
 157       pos = new double [4];
 158       pos[0] = pos[1] = pos[2] = pos[3] = 0;
 159
 160       int i(0);
 161       while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
 162         pos[i] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetCursorPosition()[i];
 163         ++i;
 164       }
 165       double posTransformed[3];
 166       mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetConcatenatedTransform()->TransformPoint(pos, posTransformed);
 167       i = 0;
 168       while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
 169         pos[i] = posTransformed[i];
 170         mPoint1[i] = round((pos[i] - mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i])/mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i]);
 171         pos[i] = mPoint1[i]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i]; //Ensure to be at the center of the voxel
 172         position += QString::number(mPoint1[i],'f',0) + " ";
 173         ++i;
 174       }
 175       if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
 176         pos[3] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetTSlice();
 177         mPoint1[3] = pos[3];
 178         position += QString::number(mPoint1[3],'f',0) + " ";
 179       }
 180       mPoint1Selected = true;
 181       mCurrentSlicerManager->AddLandmarkProfile(pos[0], pos[1], pos[2], pos[3]);
 182       mCurrentSlicerManager->GetLandmarks()->GetLabels()->SetNumberOfValues(mCurrentSlicerManager->GetLandmarks()->GetLabels()->GetNumberOfValues()-1);
 183       mCurrentSlicerManager->GetLandmarks()->GetLabels()->Modified();
 184       mCurrentSlicerManager->GetLandmarks()->GetLabels()->InsertNextValue("P1");
 185     }
 186   }
 187   mPosPoint1Label->setText(position);
 188   isPointsSelected();
 189   mCurrentSlicerManager->Render();
 190 }
 191 //------------------------------------------------------------------------------
 192
 193
 194 //------------------------------------------------------------------------------
 195 void vvToolProfile::selectPoint2()
 196 {
 197   QString position = "";
 198
 199   if(mCurrentSlicerManager) {
 200     if (mPoint2Selected) {
 201       ProfileWidget->hide();
 202       vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
 203       chart->SetAutoSize(false);
 204       chart->SetRenderEmpty(true);
 205       mView->GetScene()->ClearItems();
 206       mView->GetScene()->AddItem(chart);
 207       this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
 208       this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
 209       ProfileWidget->show();
 210       mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P2", mPoint2[3]);
 211     }
 212
 213     mPoint2Selected = false;
 214
 215     if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
 216       double *pos;
 217       pos = new double [4];
 218       pos[0] = pos[1] = pos[2] = pos[3] = 0;;
 219
 220       int i(0);
 221       while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
 222         pos[i] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetCursorPosition()[i];
 223         ++i;
 224       }
 225       double posTransformed[3];
 226       mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetConcatenatedTransform()->TransformPoint(pos, posTransformed);
 227       i = 0;
 228       while (i<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && i<3) {
 229         pos[i] = posTransformed[i];
 230         mPoint2[i] = round((pos[i] - mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i])/mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i]);
 231         pos[i] = mPoint2[i]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[i] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[i]; //Ensure to be at the center of the voxel
 232         position += QString::number(mPoint2[i],'f',0) + " ";
 233         ++i;
 234       }
 235       if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
 236         pos[3] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetTSlice();
 237         mPoint2[3] = pos[3];
 238         position += QString::number(mPoint2[3],'f',0) + " ";
 239       }
 240       mPoint2Selected = true;
 241       mCurrentSlicerManager->AddLandmarkProfile(pos[0], pos[1], pos[2], pos[3]);
 242       mCurrentSlicerManager->GetLandmarks()->GetLabels()->SetNumberOfValues(mCurrentSlicerManager->GetLandmarks()->GetLabels()->GetNumberOfValues()-1);
 243       mCurrentSlicerManager->GetLandmarks()->GetLabels()->Modified();
 244       mCurrentSlicerManager->GetLandmarks()->GetLabels()->InsertNextValue("P2");
 245     }
 246   }
 247   mPosPoint2Label->setText(position);
 248   isPointsSelected();
 249   mCurrentSlicerManager->Render();
 250 }
 251 //------------------------------------------------------------------------------
 252
 253 //------------------------------------------------------------------------------
 254 bool vvToolProfile::isPointsSelected()
 255 {
 256   if (mPoint1Selected && mPoint2Selected) {
 257       mSaveProfileButton->setEnabled(true);
 258       computeProfile();
 259       SetPoints();
 260       for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
 261         DisplayLine(i);
 262         connect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentBegin(int)), this, SLOT(DeleteLine(int)));
 263         connect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentEnd(int)), this, SLOT(DisplayLine(int)));
 264       }
 265       mCurrentSlicerManager->Render();
 266   }
 267   else {
 268       mSaveProfileButton->setEnabled(false);
 269       for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
 270         disconnect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentBegin(int)), this, SLOT(DeleteLine(int)));
 271         disconnect(mCurrentSlicerManager->GetSlicer(i), SIGNAL(UpdateDisplayExtentEnd(int)), this, SLOT(DisplayLine(int)));
 272         mCurrentSlicerManager->GetSlicer(i)->GetRenderer()->RemoveActor(mLineActors[i]);
 273       }
 274
 275   }
 276   return (mPoint1Selected && mPoint2Selected);
 277 }
 278 //------------------------------------------------------------------------------
 279
 280
 281 //------------------------------------------------------------------------------
 282 void vvToolProfile::computeProfile()
 283 {
 284     if (!mCurrentSlicerManager) close();
 285     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 286     GetArgsInfoFromGUI();
 287     ProfileWidget->hide();
 288
 289     // Main filter
 290     mFilter->SetInputVVImage(mCurrentImage);
 291     mFilter->SetArgsInfo(mArgsInfo);
 292     mFilter->Update();
 293
 294     //Creation of the XY chart
 295     vtkSmartPointer<vtkTable> table = vtkSmartPointer<vtkTable>::New();
 296     vtkSmartPointer<vtkFloatArray> arrX = vtkSmartPointer<vtkFloatArray>::New();
 297     vtkSmartPointer<vtkFloatArray> arrY = vtkSmartPointer<vtkFloatArray>::New();
 298     arrX = mFilter->GetArrayX();
 299     arrY = mFilter->GetArrayY();
 300     arrX->SetName("Distance (mm)");
 301     arrY->SetName("Intensity");
 302
 303     table->AddColumn(arrX);
 304     table->AddColumn(arrY);
 305
 306     mView->GetRenderer()->SetBackground(1.0, 1.0, 1.0);
 307
 308     vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
 309     chart->SetAutoSize(true);
 310     mView->GetScene()->ClearItems();
 311     mView->GetScene()->AddItem(chart);
 312     vtkPlot *line = chart->AddPlot(vtkChart::LINE);
 313 #if VTK_MAJOR_VERSION <= 5
 314     line->SetInput(table, 0, 1);
 315 #else
 316     line->SetInputData(table, 0, 1);
 317 #endif
 318     line->SetColor(0, 255, 0, 255);
 319     line->SetWidth(1.0);
 320     chart->GetAxis(vtkAxis::LEFT)->SetTitle("Intensity");
 321     chart->GetAxis(vtkAxis::BOTTOM)->SetTitle("Distance (mm)");
 322
 323     this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
 324     this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
 325     ProfileWidget->show();
 326
 327     QApplication::restoreOverrideCursor();
 328 }
 329 //------------------------------------------------------------------------------
 330
 331
 332 //------------------------------------------------------------------------------
 333 void vvToolProfile::cancelPoints()
 334 {
 335   if (mPoint1Selected)
 336     mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P1", mPoint1[3]);
 337   if (mPoint2Selected)
 338     mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P2", mPoint2[3]);
 339   ProfileWidget->hide();
 340   vtkSmartPointer<vtkChartXY> chart = vtkSmartPointer<vtkChartXY>::New();
 341   chart->SetAutoSize(false);
 342   chart->SetRenderEmpty(true);
 343   mView->GetScene()->ClearItems();
 344   mView->GetScene()->AddItem(chart);
 345   this->ProfileWidget->GetRenderWindow()->GetRenderers()->RemoveAllItems();
 346   this->ProfileWidget->GetRenderWindow()->AddRenderer(mView->GetRenderer());
 347   ProfileWidget->show();
 348
 349   QString position = "";
 350   mPosPoint1Label->setText(position);
 351   mPosPoint2Label->setText(position);
 352   mPoint1Selected = false;
 353   mPoint2Selected = false;
 354   mSaveProfileButton->setEnabled(false);
 355   isPointsSelected();
 356   mCurrentSlicerManager->Render();
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362 void vvToolProfile::RemoveVTKObjects()
 363 {
 364   if (mCurrentSlicerManager)
 365   {
 366     connect(mCurrentSlicerManager, SIGNAL(callAddLandmark(float,float,float,float)), mCurrentSlicerManager, SLOT(AddLandmark(float,float,float,float)));
 367
 368     for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
 369       mCurrentSlicerManager->GetSlicer(i)->GetRenderer()->RemoveActor(mLineActors[i]);
 370     }
 371
 372     if (mPoint1Selected)
 373       mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P1", mPoint1[3]);
 374     if (mPoint2Selected)
 375       mCurrentSlicerManager->GetLandmarks()->RemoveLandmarkWithLabel("P2", mPoint2[3]);
 376
 377     mCurrentSlicerManager->Render();
 378   }
 379 }
 380 //------------------------------------------------------------------------------
 381
 382
 383 //------------------------------------------------------------------------------
 384 bool vvToolProfile::close()
 385 {
 386   //RemoveVTKObjects();
 387
 388   return vvToolWidgetBase::close();
 389 }
 390 //------------------------------------------------------------------------------
 391
 392
 393 //------------------------------------------------------------------------------
 394 void vvToolProfile::closeEvent(QCloseEvent *event)
 395 {
 396   RemoveVTKObjects();
 397   event->accept();
 398 }
 399 //------------------------------------------------------------------------------
 400
 401
 402 //------------------------------------------------------------------------------
 403 void vvToolProfile::reject()
 404 {
 405   // DD("vvToolProfile::reject");
 406   RemoveVTKObjects();
 407   return vvToolWidgetBase::reject();
 408 }
 409 //------------------------------------------------------------------------------
 410
 411
 412 //------------------------------------------------------------------------------
 413 void vvToolProfile::InputIsSelected(vvSlicerManager * m)
 414 {
 415   mCurrentSlicerManager = m;
 416
 417   mPoint1 = new double[4];
 418   mPoint1[0] = mPoint1[1] = mPoint1[2] = mPoint1[3] = 0;
 419   mPoint2 = new double[4];
 420   mPoint2[0] = mPoint2[1] = mPoint2[2] = mPoint2[3] = 0;
 421
 422   mSaveProfileButton->setEnabled(false);
 423   mTextFileName = "Profile.txt";
 424   InitializeLine();
 425
 426   disconnect(mCurrentSlicerManager, SIGNAL(callAddLandmark(float,float,float,float)), mCurrentSlicerManager, SLOT(AddLandmark(float,float,float,float)));
 427 }
 428 //------------------------------------------------------------------------------
 429
 430
 431 //------------------------------------------------------------------------------
 432 void vvToolProfile::GetArgsInfoFromGUI()
 433 {
 434
 435   /* //KEEP THIS FOR READING GGO FROM FILE
 436      int argc=1;
 437      std::string a = "toto";
 438      char * const* argv = new char*;
 439      //a.c_str();
 440      struct cmdline_parser_params p;
 441      p.check_required = 0;
 442      int good = cmdline_parser_ext(argc, argv, &args_info, &p);
 443      DD(good);
 444   */
 445   cmdline_parser_clitkProfileImage_init(&mArgsInfo); // Initialisation to default
 446
 447   mArgsInfo.verbose_flag = false;
 448
 449   mArgsInfo.point1_arg = mPoint1;
 450   mArgsInfo.point2_arg = mPoint2;
 451   mArgsInfo.point1_given = mCurrentSlicerManager->GetImage()->GetNumberOfDimensions();
 452   mArgsInfo.point2_given = mCurrentSlicerManager->GetImage()->GetNumberOfDimensions();
 453
 454   // Required (even if not used)
 455   mArgsInfo.input_given = 0;
 456   mArgsInfo.output_given = 0;
 457
 458   mArgsInfo.input_arg = new char;
 459   mArgsInfo.output_arg = new char;
 460
 461
 462 }
 463 //------------------------------------------------------------------------------
 464
 465
 466 //------------------------------------------------------------------------------
 467 void vvToolProfile::apply()
 468 {
 469   close();
 470 }
 471 //------------------------------------------------------------------------------
 472
 473
 474 //------------------------------------------------------------------------------
 475 void vvToolProfile::SaveAs()
 476 {
 477   QStringList OutputListeFormat;
 478   OutputListeFormat.clear();
 479   OutputListeFormat.push_back(".txt");
 480
 481   QString Extensions = "AllFiles(*.*)";
 482   for (int i = 0; i < OutputListeFormat.count(); i++) {
 483     Extensions += ";;Text File ( *";
 484     Extensions += OutputListeFormat[i];
 485     Extensions += ")";
 486   }
 487   QString fileName = QFileDialog::getSaveFileName(this, tr("Save As"), mTextFileName.c_str(), Extensions);
 488   if (!fileName.isEmpty()) {
 489     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
 490     QString fileQFormat = fileformat.c_str();
 491     if (OutputListeFormat.contains(fileformat.c_str()) || fileQFormat.isEmpty()) {
 492         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 493         std::string action = "Saving";
 494         vvProgressDialog progress("Saving "+fileName.toStdString());
 495         qApp->processEvents();
 496
 497         if (!mCurrentSlicerManager || !isPointsSelected()) {
 498             close();
 499             return;
 500         }
 501
 502         // Output
 503         mTextFileName = fileName.toStdString();
 504         if (fileQFormat.isEmpty())
 505             mTextFileName += ".txt";
 506         ofstream fileOpen(mTextFileName.c_str(), std::ofstream::trunc);
 507
 508         if(!fileOpen) {
 509             cerr << "Error during saving" << endl;
 510             QApplication::restoreOverrideCursor();
 511             close();
 512             return;
 513         }
 514
 515         vtkSmartPointer<vtkFloatArray> arrX = vtkSmartPointer<vtkFloatArray>::New();
 516         vtkSmartPointer<vtkFloatArray> arrY = vtkSmartPointer<vtkFloatArray>::New();
 517         vtkSmartPointer<vtkFloatArray> coords = vtkSmartPointer<vtkFloatArray>::New();
 518         arrX = mFilter->GetArrayX();
 519         arrY = mFilter->GetArrayY();
 520         coords = mFilter->GetCoord();
 521         double *tuple;
 522         tuple = new double[mCurrentSlicerManager->GetImage()->GetNumberOfDimensions()];
 523         int i(0);
 524         fileOpen << "The Bresenham algorithm is used to travel along the line. Values represent the center of each crossed voxel (in voxel and mm)" << endl;
 525         fileOpen << "Id" << "\t" << "Value" << "\t" ;
 526         fileOpen << "x(vox)" << "\t" << "y(vox)" << "\t";
 527         if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=3)
 528             fileOpen << "z(vox)" << "\t";
 529         if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=4)
 530             fileOpen << "t" << "\t";
 531         fileOpen << "x(mm)" << "\t" << "y(mm)" << "\t";
 532         if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=3)
 533             fileOpen << "z(mm)" << "\t";
 534         if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() >=4)
 535             fileOpen << "t" << "\t";
 536         fileOpen << endl;
 537
 538         while (i<arrX->GetNumberOfTuples()) {
 539             fileOpen << i << "\t" << arrY->GetTuple(i)[0] << "\t" ;
 540
 541             coords->GetTuple(i, tuple);
 542             for (int j=0; j<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() ; ++j) {
 543                 fileOpen << tuple[j] << "\t" ;
 544             }
 545             int j(0);
 546             while (j<mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() && j<3) {
 547                 fileOpen << tuple[j]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[j]+mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[j] << "\t" ;
 548                 ++j;
 549             }
 550             if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
 551                 fileOpen << tuple[3] << "\t" ;
 552             }
 553             fileOpen << endl;
 554             ++i;
 555         }
 556
 557         delete [] tuple;
 558
 559         fileOpen.close();
 560         QApplication::restoreOverrideCursor();
 561     } else {
 562       QString error = fileformat.c_str();
 563       error += " format unknown !!!\n";
 564       QMessageBox::information(this,tr("Saving Problem"),error);
 565       SaveAs();
 566     }
 567   }
 568 }
 569 //------------------------------------------------------------------------------
 570
 571
 572 //------------------------------------------------------------------------------
 573 void vvToolProfile::DeleteLine(int slicer)
 574 {
 575   if (!mPoint1Selected && !mPoint2Selected)
 576     return;
 577
 578   if(mCurrentSlicerManager) {
 579       if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
 580           mCurrentSlicerManager->GetSlicer(slicer)->GetRenderer()->RemoveActor(mLineActors[slicer]);
 581       }
 582    }
 583 }
 584 //------------------------------------------------------------------------------
 585
 586
 587 //------------------------------------------------------------------------------
 588 void vvToolProfile::DisplayLine(int slicer)
 589 {
 590   if (!mPoint1Selected && !mPoint2Selected)
 591     return;
 592
 593   if(mCurrentSlicerManager) {
 594       if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
 595           double currentSlice = (mCurrentSlicerManager->GetSlicer(slicer)->GetSlice()*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetInput()->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetInput()->GetOrigin()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] - mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] )/ mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()];
 596           if (std::min(mPoint1[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()],mPoint2[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]) <= currentSlice && std::max(mPoint1[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()],mPoint2[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]) >= currentSlice) {
 597             vtkSmartPointer<vtkBox> clippingBox = vtkSmartPointer<vtkBox>::New();
 598             double extent[6];
 599             for (int j=0; j<6; ++j) {
 600                 extent[j] = mCurrentSlicerManager->GetSlicer(slicer)->GetExtent()[j];
 601             }
 602             extent[2*mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()] = mCurrentSlicerManager->GetSlicer(slicer)->GetImageActor()->GetBounds()[ mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()*2 ]-fabs(mCurrentSlicerManager->GetSlicer(slicer)->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]);
 603             extent[2*mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()+1] = mCurrentSlicerManager->GetSlicer(slicer)->GetImageActor()->GetBounds()[ mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()*2+1 ]+fabs(mCurrentSlicerManager->GetSlicer(slicer)->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[mCurrentSlicerManager->GetSlicer(slicer)->GetOrientation()]);
 604             clippingBox->SetBounds(extent);
 605
 606             vtkSmartPointer<vtkClipPolyData> clipper = vtkSmartPointer<vtkClipPolyData>::New();
 607             clipper->SetClipFunction(clippingBox);
 608 #if VTK_MAJOR_VERSION <= 5
 609             clipper->SetInput(mLinesPolyData);
 610 #else
 611             mLineTransform = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
 612             mLineTransform->SetInputData(mLinesPolyData);
 613             mLineTransform->SetTransform(mCurrentSlicerManager->GetSlicer(slicer)->GetConcatenatedTransform()->GetInverse());
 614             clipper->SetInputConnection(mLineTransform->GetOutputPort());
 615 #endif
 616             clipper->InsideOutOff();
 617             clipper->Update();
 618             vtkSmartPointer<vtkPolyDataMapper> lineMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
 619 #if VTK_MAJOR_VERSION <= 5
 620             lineMapper->SetInput(clipper->GetOutput());
 621 #else
 622             lineMapper->SetInputData(clipper->GetOutput());
 623 #endif
 624
 625             mLineActors[slicer]->SetMapper(lineMapper);
 626             mLineActors[slicer]->GetProperty()->SetOpacity(0.995);
 627
 628             mCurrentSlicerManager->GetSlicer(slicer)->GetRenderer()->AddActor(mLineActors[slicer]);
 629          }
 630       }
 631   }
 632 }
 633 //------------------------------------------------------------------------------
 634
 635
 636 //------------------------------------------------------------------------------
 637 void vvToolProfile::InitializeLine()
 638 {
 639   if(mCurrentSlicerManager) {
 640
 641       mLinesPolyData = vtkSmartPointer<vtkPolyData>::New();
 642
 643       vtkSmartPointer<vtkPoints> pts = vtkSmartPointer<vtkPoints>::New();
 644       double pos[4];
 645       pos[0] = pos[1] = pos[2] = pos[3] = 0;
 646       pts->InsertNextPoint(pos);
 647       pts->InsertNextPoint(pos);
 648       mLinesPolyData->SetPoints(pts);
 649
 650       vtkSmartPointer<vtkCellArray> lines = vtkSmartPointer<vtkCellArray>::New();
 651       vtkSmartPointer<vtkLine> line = vtkSmartPointer<vtkLine>::New();
 652       line->GetPointIds()->SetId(0, 0); // the second 0 is the index of the 1st point in mLinesPolyData's points (pts)
 653       line->GetPointIds()->SetId(1, 1); // the second 1 is the index of the 2nd point in mLinesPolyData's points (pts)
 654       lines->InsertNextCell(line);
 655       mLinesPolyData->SetLines(lines);
 656
 657       unsigned char red[3] = { 255, 0, 0 };
 658       vtkSmartPointer<vtkUnsignedCharArray> colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
 659       colors->SetNumberOfComponents(3);
 660       colors->InsertNextTupleValue(red);
 661       mLinesPolyData->GetCellData()->SetScalars(colors);
 662
 663       for(int i=0;i<mCurrentSlicerManager->GetNumberOfSlicers(); i++) {
 664         mLineActors.push_back(vtkSmartPointer<vtkActor>::New());
 665       }
 666    }
 667 }
 668 //------------------------------------------------------------------------------
 669
 670
 671 //------------------------------------------------------------------------------
 672 void vvToolProfile::SetPoints()
 673 {
 674   if (!mPoint1Selected && !mPoint2Selected)
 675     return;
 676
 677   if(mCurrentSlicerManager) {
 678       if(mCurrentSlicerManager->GetSelectedSlicer() != -1) {
 679           /*double *pos;
 680           pos = new double [4];
 681           pos[0] = pos[1] = pos[2] = pos[3] = 0;
 682
 683           int i(0);
 684           while (i<3) {
 685             pos[i] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetCursorPosition()[i];
 686             ++i;
 687           }
 688           if (mCurrentSlicerManager->GetImage()->GetNumberOfDimensions() == 4) {
 689             pos[3] = mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetTSlice();
 690           } */
 691
 692           double p0[4], p1[4];
 693           p0[0] = mPoint1[0]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[0] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[0];
 694           p0[1] = mPoint1[1]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[1] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[1];
 695           p0[2] = mPoint1[2]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[2] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[2];
 696           p0[3] = mPoint1[3];
 697
 698           p1[0] = mPoint2[0]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[0] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[0];
 699           p1[1] = mPoint2[1]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[1] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[1];
 700           p1[2] = mPoint2[2]*mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetSpacing()[2] + mCurrentSlicerManager->GetSlicer(mCurrentSlicerManager->GetSelectedSlicer())->GetImage()->GetVTKImages()[mCurrentSlicerManager->GetTSlice()]->GetOrigin()[2];
 701           p1[3] = mPoint2[3];
 702
 703           vtkSmartPointer<vtkPoints> pts = mLinesPolyData->GetPoints();
 704           pts->SetPoint(0,p0);
 705           pts->SetPoint(1,p1);
 706     }
 707   }
 708 }
 709 //------------------------------------------------------------------------------
 710
 711