src/creaImageIOGimmickView.cpp

   1 /*
   2 # ---------------------------------------------------------------------
   3 #
   4 # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
   5 #                        pour la Santé)
   6 # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
   7 # Previous Authors : Laurent Guigues, Jean-Pierre Roux
   8 # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
   9 #
  10 #  This software is governed by the CeCILL-B license under French law and
  11 #  abiding by the rules of distribution of free software. You can  use,
  12 #  modify and/ or redistribute the software under the terms of the CeCILL-B
  13 #  license as circulated by CEA, CNRS and INRIA at the following URL
  14 #  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  15 #  or in the file LICENSE.txt.
  16 #
  17 #  As a counterpart to the access to the source code and  rights to copy,
  18 #  modify and redistribute granted by the license, users are provided only
  19 #  with a limited warranty  and the software's author,  the holder of the
  20 #  economic rights,  and the successive licensors  have only  limited
  21 #  liability.
  22 #
  23 #  The fact that you are presently reading this means that you have had
  24 #  knowledge of the CeCILL-B license and that you accept its terms.
  25 # ------------------------------------------------------------------------
  26 */
  27
  28
  29 #include <creaImageIOGimmickView.h>
  30
  31 #include "boost/filesystem.hpp"
  32
  33 #if defined(USE_GDCM)
  34 #include <gdcmGlobal.h>
  35 #include <gdcmSerieHelper.h>
  36 #include <gdcmFileHelper.h>
  37 #include <gdcmUtil.h>
  38 #include <vtkGdcmReader.h>
  39
  40 #endif
  41
  42 #include <vtkMetaImageWriter.h>
  43
  44 /*#if defined(USE_GDCM2)
  45 #include <vtkGDCMImageReader.h>
  46 #include "gdcmSystem.h"
  47 #include "gdcmCryptographicMessageSyntax.h"
  48 #include "gdcmUIDGenerator.h"
  49 #include "gdcmAnonymizer.h"
  50 #include "gdcmGlobal.h"
  51 #endif*/
  52 #if defined(_WIN32)
  53 #pragma warning(disable: 4996)
  54 #endif
  55
  56 namespace fs = boost::filesystem;
  57 namespace creaImageIO
  58 {
  59
  60         ///Class used to represent the actual state of the image selected and to perform comparisons on its values
  61   class ImageExtent
  62   {
  63   public:
  64     ImageExtent(const std::string& x, const std::string& y, const std::string& z, const std::string& t)
  65         {
  66                 sscanf(x.c_str(),"%d",&mExtent[0]);
  67                 sscanf(y.c_str(),"%d",&mExtent[1]);
  68                 sscanf(z.c_str(),"%d",&mExtent[2]);
  69                 sscanf(t.c_str(),"%d",&mExtent[3]);
  70                 if(x==""){mExtent[0]=1;}
  71                 if(y==""){mExtent[1]=1;}
  72                 if(z==""){mExtent[2]=1;}
  73                 if(t==""){mExtent[3]=1;}
  74
  75                 if (mExtent[3]>1) mDim=4;
  76                 else if (mExtent[2]>1) mDim=3;
  77                 else if (mExtent[1]>1) mDim=2;
  78                 else if (mExtent[0]>1) mDim=1;
  79                 else mDim=0;
  80         }
  81
  82
  83         ///Clears the extent
  84     void Clear() { mExtent[0] = mExtent[1] = mExtent[2] = mExtent[3] = 1; }
  85
  86         ///Returns true if the two extents are compatible
  87     bool IsCompatible( const ImageExtent& );
  88
  89         ///Adds the extent passed as a parameter to the current extent
  90     void Add ( const ImageExtent& );
  91
  92         ///Returns the ieth position of the extent
  93     int Get(int i) { return mExtent[i]; }
  94
  95         ///Returns the dimension of the current image
  96     void SetDimension(int dim) { mDim=dim; }
  97
  98         ///Returns the dimension of the current image
  99     int GetDimension() { return mDim; }
 100
 101   private:
 102     int mExtent[4];
 103     int mDim;
 104   };
 105
 106   //======================================================================
 107
 108   //======================================================================
 109   // CTor
 110   GimmickView::GimmickView(boost::shared_ptr<Gimmick> gimmick, int threads)
 111     : mGimmick(gimmick),
 112           mReader(threads)
 113   {
 114     GimmickDebugMessage(1,"GimmickView::GimmickView"
 115                         <<std::endl);
 116         // Anciently started the threads ...
 117     // Threads now automatically start at first image request
 118     //mReader.Start();
 119
 120   }
 121   //======================================================================
 122
 123   //======================================================================
 124   /// Destructor
 125   GimmickView::~GimmickView()
 126   {
 127           printf("EED GimmickView::~GimmickView  DESTROCTEUR \n");
 128     GimmickDebugMessage(1,"GimmickView::~GimmickView"
 129                         <<std::endl);
 130   }
 131    //======================================================================
 132
 133   //======================================================================
 134   /// Initializes the view :
 135   /// Creates the TreeViews for all the TreeHandler of the Controller
 136   ///
 137   void GimmickView::Initialize()
 138   {
 139         mReaderStarted=false;
 140   }
 141   //======================================================================
 142
 143   //======================================================================
 144   /// Finalize
 145   void GimmickView::Finalize()
 146   {
 147           printf("EED GimmickView::Finalize  \n");
 148   }
 149
 150   //======================================================================
 151
 152   //======================================================================
 153   /// Create the tree views
 154   void GimmickView::CreateTreeViews()
 155   {
 156     GimmickMessage(2,"Creating the tree views"<<std::endl);
 157     Gimmick::TreeHandlerMapType::const_iterator i;
 158     for (i = mGimmick->GetTreeHandlerMap().begin();
 159          i!= mGimmick->GetTreeHandlerMap().end();
 160          ++i)
 161       {
 162         this->CreateTreeView(i->second);
 163       }
 164   }
 165
 166   /// Create a tree view with a given name
 167   void GimmickView::CreateSingleTreeView(std::string &i_name)
 168   {
 169         this->CreateTreeView(mGimmick->GetTreeHandlerMap()[i_name]);
 170
 171   }
 172
 173
 174   //======================================================================
 175
 176   //======================================================================
 177   /// Updates the TreeView of given name from level l to bottom
 178   /// (calls the virtual method TreeView::Update())
 179   void GimmickView::UpdateTreeViewLevel(const std::string& t, int l)
 180   {
 181     TreeViewMapType::iterator i;
 182     i = GetTreeViewMap().find(t);
 183     if ( i == GetTreeViewMap().end() )
 184       {
 185         GimmickError("INTERNAL ERROR : GimmickView::UpdateTreeView : '"
 186                      <<t<<"' is not in TreeViewMap");
 187       }
 188     i->second->UpdateLevel(l);
 189   }
 190
 191   //======================================================================
 192   /// Clears the status and begins a new selection process
 193   void GimmickView::ResetExtent()
 194   {
 195           if(mImageExtent!=0)
 196           {
 197                   mImageExtent.reset();
 198           }
 199           valid=true;
 200   }
 201
 202   //======================================================================
 203
 204   //======================================================================
 205   bool ImageExtent::IsCompatible(const ImageExtent& ie)
 206   {
 207           bool compatible=true;
 208           ImageExtent * extent= (ImageExtent*)&ie;
 209           if((*extent).Get(0)!=Get(0)
 210                  || (*extent).Get(1)!=Get(1))
 211           {
 212                   compatible=false;
 213           }
 214           return compatible;
 215   }
 216
 217   //======================================================================
 218
 219   //======================================================================
 220   void ImageExtent::Add(const ImageExtent& ie)
 221   {
 222           ImageExtent * extent= (ImageExtent*)&ie;
 223           mExtent[2]+=(*extent).Get(2);
 224           if(mExtent[2]>1)
 225           {
 226           SetDimension(3);
 227           }
 228   }
 229
 230   //======================================================================
 231   /// No selected image
 232   bool GimmickView::NoValidateSelected ()
 233   {
 234         GimmickDebugMessage(2,"Validating selected"<<std::endl);
 235         std::string mMessage;
 236         mMessage="Cannot have 0 images selected!";
 237         valid=false;
 238         modifyValidationSignal(valid);
 239         SetMessage(mMessage);
 240         return valid;
 241   }
 242
 243   //======================================================================
 244   ///Validates the dimension compliance of the images with the maximum and
 245   ///minimum given, and between their sizes
 246   bool GimmickView::ValidateSelected (tree::Node* sel, int min_dim, int max_dim)
 247   {
 248         GimmickDebugMessage(2,"Validating selected"<<std::endl);
 249         std::string mMessage;
 250
 251         if(sel==0)
 252         {
 253                 mMessage="Cannot have 0 images selected!";
 254                 valid=false;
 255         }
 256         else
 257         {
 258                         boost::shared_ptr<ImageExtent> ie=boost::shared_ptr<ImageExtent>(new ImageExtent((*sel).GetAttribute("D0028_0010"),
 259                                                                         (*sel).GetAttribute("D0028_0011"),
 260                                                                         (*sel).GetAttribute("D0028_0012"),
 261                                                                         ""));
 262
 263         if(mImageExtent==0)
 264         {
 265                 mImageExtent=ie;
 266                 if((mImageExtent->Get(min_dim-1)<2)||(mImageExtent->Get(max_dim)>1))
 267                 {
 268                         valid=false;
 269                 }
 270                 else
 271                 {
 272                         std::stringstream out;
 273                         out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
 274                         mMessage = out.str();
 275                         mImageExtent->SetDimension(2);
 276                         valid=true;
 277                 }
 278         }
 279         else
 280         {
 281                 if(mImageExtent->IsCompatible(*ie))
 282                 {
 283                         if(mImageExtent->GetDimension()==max_dim && mImageExtent->Get(max_dim)>2)
 284                         {
 285                                 std::stringstream out;
 286                                 out<<"Cannot add this image to selection : would result in a "<<mImageExtent->GetDimension()+1<<"D image!";
 287                                 mMessage=out.str();
 288                                 valid=false;
 289                         }
 290                         else if(max_dim<3)
 291                         {
 292                                 std::stringstream out;
 293                                 out<<"Selecting "<<mImageExtent->GetDimension()<<"D images is not allowed !";
 294                                 mMessage=out.str();
 295                                 valid=false;
 296                         }
 297                         else if(min_dim==3 && (ie->Get(2)+mImageExtent->Get(2))<2)
 298                         {
 299                                 std::stringstream out;
 300                                 out << "Cannot build the selection as it would result in a ";
 301                                 out << mImageExtent->GetDimension();
 302                                 out << "D image, and the minimum is ";
 303                                 out << min_dim;
 304                                 out << "D!";
 305                                 mMessage=out.str();
 306                                 valid=false;
 307                         }
 308                         else
 309                         {
 310                                 mImageExtent->Add(*ie);
 311                                 std::stringstream out;
 312                                 out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
 313                                 mMessage = out.str();
 314                         }
 315                 }
 316                 else
 317                 {
 318                         mMessage="The selected images are not compatible.";
 319                         valid=false;
 320                 }
 321           }
 322         }
 323
 324         modifyValidationSignal(valid);
 325         SetMessage(mMessage);
 326         return valid;
 327   }
 328
 329   //======================================================================
 330   void GimmickView::modifyValidationSignal(bool ivalid)
 331   {
 332
 333           mValidationSignal(ivalid);
 334   }
 335
 336   void GimmickView::stopReader()
 337   {
 338           mReader.Stop();
 339   }
 340
 341    //======================================================================
 342   ///Reads Images (Non Threaded)
 343 void GimmickView::ReadImagesNotThreaded(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
 344 {
 345         stopReader();
 346 /* remember!
 347
 348 #define GIMMICK_NO_IMAGE_SELECTION 0
 349 #define GIMMICK_2D_IMAGE_SELECTION 2
 350 #define GIMMICK_3D_IMAGE_SELECTION 3
 351 #define GIMMICK_4D_IMAGE_SELECTION 4
 352
 353 #define NATIVE 0
 354 #define _2D    2
 355 #define _3D    3
 356
 357 */
 358         // Create the output data
 359         if (im.size()==1)
 360         {
 361                 vtkImageData * out=vtkImageData::New();
 362                 out->ShallowCopy(mReader.GetImage(im.front()));
 363                 s.push_back(out);
 364         }
 365     else if (im.size()>1) // Test inutile ? JPR
 366         {
 367                 vtkImageData* first = mReader.GetImage( im.front());
 368                 if (dimension == 2)
 369                 {
 370                  // n3D
 371                     std::vector<std::string>::iterator it;
 372                         for (it=im.begin(); it!=im.end(); ++it)
 373                         {
 374                                 vtkImageData* out = vtkImageData::New();
 375                                 out->ShallowCopy(mReader.GetImage(*it));
 376                                 s.push_back(out);
 377                         }
 378                 }
 379                 else
 380                 {
 381                         // n*2D to 3D
 382                         vtkImageData* out = vtkImageData::New();
 383 //                      out->CopyStructure(first);
 384                         int ext[6];
 385                         //first->GetExtent(ext);  // JPR
 386 //EED 2017-01-01 Migration VTK7
 387 #if VTK_MAJOR_VERSION <= 5
 388                         first->GetWholeExtent(ext);  // renvoie egalement 0,0 en Z // JPR
 389 #else
 390                         first->GetExtent(ext);  // renvoie egalement 0,0 en Z // JPR
 391 #endif
 392
 393                         if(ext[5] == 0)
 394                         {
 395                                 ext[5] = (int)im.size()-1;
 396                         }
 397                         else
 398                         {
 399                                 ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes - JPR
 400                         }
 401                         out->SetExtent(ext);
 402
 403                         // LG : TODO : Z Spacing  ?
 404
 405                         int dim[3];
 406                         first->GetDimensions(dim);
 407                         out->SetDimensions(dim[0], dim[1], (int)im.size() );
 408
 409 //EED 2017-01-01 Migration VTK7
 410 #if VTK_MAJOR_VERSION <= 5
 411                         out->SetScalarType(first->GetScalarType());
 412                         out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 413                         out->AllocateScalars();
 414                         out->Update();
 415 #else
 416                         out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
 417 #endif
 418
 419                         unsigned long imsize = dim[0] * dim[1];
 420                         imsize = imsize * dim[2] ;  // deal with multiframes // JPR
 421
 422
 423 //EED 03-11-2009
 424                         // differents formats char , short, etc...
 425                         // differents components 1..3  ex. jpg ->RGB 3
 426                         imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 427
 428
 429                         // Order the file name vector
 430
 431                         double spc[3];
 432                         first->GetSpacing(spc);
 433
 434                         // OrderTheFileNameVector is not here anymore.
 435                         // Try orderFilesWithZSpacing from OutputModel FCY
 436                         // spc[2]=OrderTheFileNameVector(im);
 437                         spc[2] =1;
 438
 439                         out->SetSpacing(spc);
 440
 441                         int slice = 0;
 442                         std::vector<std::string>::iterator it;
 443
 444                         for (it=im.begin(); it!=im.end(); ++it)
 445                         {
 446                                 vtkImageData* cur = mReader.GetImage( (*it) );
 447                                 memcpy(out->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
 448                                 slice++;
 449                         }
 450                         s.push_back(out);
 451
 452                 }  // dimension == 3
 453
 454         }  // size >1
 455
 456 }
 457   //======================================================================
 458
 459
 460
 461         //////////////////////////////////////////////////////////
 462         // Test if the image is a multiple or single frame.
 463         // For the moment only with the creation of vtkImageDta.
 464         // TO DO with image size and dim!!!
 465         //////////////////////////////////////////////////////////
 466         bool GimmickView::isSingle(const std::string i_file)
 467         {
 468                 bool bres = true;
 469                 vtkImageData* first = mReader.GetImage( i_file);
 470                 int dim[3];
 471                 first->GetDimensions(dim);
 472                 if (dim[2] > 1)
 473                 {
 474                         bres = false;
 475                 }
 476                 else
 477                 {
 478                 }
 479                 return bres;
 480         }
 481
 482         //////////////////////////////////////////////////////////
 483         // get Attributes values for a file
 484         //////////////////////////////////////////////////////////
 485
 486         void GimmickView::getAttributes(const std::string i_file, std::map<std::string, std::string> &o_infos, OutputAttr i_attr)
 487         {
 488                 if(i_attr.inside.size() >0)
 489                 {
 490                         mGimmick->GetAttributes(i_file,o_infos,i_attr);
 491                 }
 492                 if(i_attr.outside.size()>0)
 493                 {
 494                         mReader.getAttributes(i_file,o_infos, i_attr.outside);
 495                 }
 496         }
 497
 498         //////////////////////////////////////////////////////////
 499         // create an output structure with n entries = n output
 500         //////////////////////////////////////////////////////////
 501         void GimmickView::readImages1(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 502                          OutputAttr i_attr)
 503         {
 504                 i_attr.outside.push_back("D0019_100a");  // simens Number Of Images In Mosaic
 505                 std::vector<std::string>::iterator it;
 506                 for (it=im.begin(); it!=im.end(); ++it)
 507                 {
 508                         OutStrGimmick out;
 509                         out.img = vtkImageData::New();
 510                         out.img->ShallowCopy(mReader.GetImage(*it));
 511                         if(i_attr.mult)
 512                         {
 513                                 getAttributes((*it),out.infos,i_attr);
 514                         }
 515                         o_output.push_back(out);
 516                 }
 517                 // If we want only one output information structure, we set it outside the loop
 518                 if(!i_attr.mult)
 519                 {
 520                         getAttributes(im.front(), o_output.front().infos, i_attr);
 521                 }
 522
 523         }
 524
 525         //////////////////////////////////////////////////////////
 526         // create an output structure with n entries = 1 output
 527         //////////////////////////////////////////////////////////
 528         void GimmickView::readImages3(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 529                          OutputAttr i_attr, double i_zspc)
 530         {
 531                 OutStrGimmick out;
 532                 vtkImageData* first = mReader.GetImage( im.front());
 533                 out.img  = vtkImageData::New();
 534                 int ext[6];
 535 //EED 2017-01-01 Migration VTK7
 536 #if VTK_MAJOR_VERSION <= 5
 537                 first->GetWholeExtent(ext);  // send also 0,0 in Z
 538 #else
 539                 first->GetExtent(ext);  // send also 0,0 in Z
 540 #endif
 541                 if(ext[5] == 0)
 542                 {
 543                         ext[5] = (int)im.size()-1;
 544                 } else {
 545                         ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes
 546                 }
 547                 out.img->SetExtent(ext);
 548                 int dim[3];
 549                 double spac[3];
 550                 first->GetDimensions(dim);
 551                 first->GetSpacing(spac);
 552                 out.img->SetSpacing(spac);
 553                 out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
 554
 555
 556
 557 //EED 2017-01-01 Migration VTK7
 558 #if VTK_MAJOR_VERSION <= 5
 559                 out.img->SetScalarType(first->GetScalarType());
 560                 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 561                 out.img->AllocateScalars();
 562                 out.img->Update();
 563 #else
 564                 out.img->AllocateScalars(first->GetScalarType(), first->GetNumberOfScalarComponents());
 565 #endif
 566
 567
 568                 unsigned long imsize = dim[0] * dim[1];
 569                 imsize = imsize * dim[2] ;  // deal with multiframes here
 570                 // differents formats char , short, etc...
 571                 // differents components 1..3  ex. jpg ->RGB 3
 572                 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 573                 // Order the file name vector already did with the OutputModel!!!
 574                 //!!!!out.img->SetSpacing(i_zspc);
 575                 int slice = 0;
 576                 std::vector<std::string>::iterator it;
 577                 for (it=im.begin(); it!=im.end(); ++it)
 578                 {
 579                         vtkImageData* cur = mReader.GetImage( (*it) );
 580                         memcpy(out.img->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
 581                         slice++;
 582                 }
 583
 584                 getAttributes(im.front(),out.infos, i_attr);
 585                 o_output.push_back(out);
 586         }
 587
 588
 589         // TO DO  NO VERY SURE : NEED TO BE TESTED
 590         //////////////////////////////////////////////////////////
 591         // create an output structure with n entries (T size) = T output (n size)
 592         //////////////////////////////////////////////////////////
 593         void GimmickView::readImages2(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 594                          OutputAttr i_attr, double i_zspc)
 595         {
 596                 vtkImageData* first = mReader.GetImage( im.front());
 597                 int dim[3];
 598                 double spac[3];
 599                 first->GetDimensions(dim);
 600                 first->GetSpacing(spac);
 601                 // differents formats char , short, etc...
 602                 // differents components 1..3  ex. jpg ->RGB 3
 603                 unsigned long imsize = dim[0] * dim[1];
 604                 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 605
 606                 // Order the file name vector already did with the OutputModel!!!
 607                 std::vector<std::string>::iterator it;
 608                 std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
 609
 610                 for (it=im.begin(); it!=im.end(); ++it)//, it_out ++)
 611                 {
 612                         vtkImageData* cur = mReader.GetImage( (*it) );
 613                         for (int slice= 0 ; slice <dim[2]; slice++)
 614                         {
 615                                 OutStrGimmick out;
 616                                 out.img = vtkImageData::New();
 617                                 out.img->SetSpacing(spac);
 618                                 int ext[6];
 619 //EED 2017-01-01 Migration VTK7
 620 #if VTK_MAJOR_VERSION <= 5
 621                                 first->GetWholeExtent(ext);  // send also 0,0 in Z
 622 #else
 623                                 first->GetExtent(ext);  // send also 0,0 in Z
 624 #endif
 625                                 ext[5] = 0;
 626                                 out.img->SetExtent(ext);
 627                                 out.img->SetDimensions(dim[0], dim[1], 1 );
 628
 629 //EED 2017-01-01 Migration VTK7
 630 #if VTK_MAJOR_VERSION <= 5
 631                                 out.img->SetScalarType(first->GetScalarType());
 632                                 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 633                                 out.img->AllocateScalars();
 634                                 out.img->Update();
 635 #else
 636                                 out.img->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
 637 #endif
 638
 639
 640                                 memcpy(out.img->GetScalarPointer(0,0,0), cur->GetScalarPointer(0,0,slice), imsize);
 641                                 o_output.push_back(out);
 642                         }
 643         //              if(i_attr.mult)
 644                 //              getAttributes((*it),(*it_out).infos,i_attr);
 645                 }
 646                 if(!i_attr.mult)
 647                 {
 648                         getAttributes(im.front(), o_output.front().infos,i_attr);
 649                 }
 650
 651         }
 652
 653         //////////////////////////////////////////////////////////
 654         // create an output structure with n entries (T size) = T + n output
 655         //////////////////////////////////////////////////////////
 656         void GimmickView::readImages4(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 657                          OutputAttr i_attr)
 658         {
 659                 std::vector<std::string>::iterator it;
 660                 std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
 661                 vtkImageData* first = mReader.GetImage( im.front());
 662                 int dim[3];
 663                 first->GetDimensions(dim);
 664
 665                 for (int slice= 0 ; slice <dim[2]; slice++)
 666                 {
 667                         OutStrGimmick out;
 668                         out.img = vtkImageData::New();
 669
 670                         int ext[6];
 671
 672 //EED 2017-01-01 Migration VTK7
 673 #if VTK_MAJOR_VERSION <= 5
 674                         first->GetWholeExtent(ext);  // send also 0,0 in Z
 675 #else
 676                         first->GetExtent(ext);  // send also 0,0 in Z
 677 #endif
 678
 679                         double spac[6];
 680                         ext[5] = 0;
 681                         out.img->SetExtent(ext);
 682                         first->GetSpacing(spac);
 683                         out.img->SetSpacing(spac);
 684                         out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
 685
 686 //EED 2017-01-01 Migration VTK7
 687 #if VTK_MAJOR_VERSION <= 5
 688                         out.img->SetScalarType(first->GetScalarType());
 689                         out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 690                         out.img->AllocateScalars();
 691                         out.img->Update();
 692 #else
 693                         out.img->AllocateScalars(first->GetScalarType(), first->GetNumberOfScalarComponents());
 694 #endif
 695
 696                         unsigned long imsize = dim[0] * dim[1];
 697                         imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 698                         int index = 0;
 699
 700                         for (it=im.begin(); it!=im.end(); ++it, index ++)
 701                         {
 702                                 vtkImageData* cur = mReader.GetImage( (*it) );
 703                                 memcpy(out.img->GetScalarPointer(0,0,index), cur->GetScalarPointer(0,0,slice), imsize);
 704                                 o_output.push_back(out);
 705                         }
 706                 }
 707                 if(!i_attr.mult) // No sense to take informations in all images
 708                 {
 709                         getAttributes(im.front(), o_output.front().infos,i_attr);
 710                 }
 711
 712         }
 713
 714
 715 //////////////////////////////////////////////////////////////////////////////////////////////////////////////
 716 // Global function to read Images and create wished output (informations, multiple, type and size of output...)
 717 // In function of type (file, vector) and size, the correct readImages function is selected
 718 //////////////////////////////////////////////////////////////////////////////////////////////////////////////
 719         void GimmickView::readImages(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 720                          OutputAttr i_attr, int i_dim, double i_zspc)
 721         {
 722                 int size = (int)im.size();
 723                 if ( size == 0)
 724                 {
 725                         return;
 726                 } else if (size == 1) {
 727                         // Simplest case
 728                         // Only one image : give it
 729                         // But take in count multiframe possibility
 730                         if ( isSingle(im.front()) || i_dim != 1)
 731                         {
 732                                  readImages1(o_output,im, i_attr);
 733                         } else {
 734                                  readImages2(o_output,im, i_attr,i_zspc);
 735                         }
 736                 } else {
 737                         // multiple or single frame
 738                         if ( isSingle(im.front()) )
 739                         {
 740                                 //we deal with 2D images
 741                                 if(i_dim == 1)
 742                                 {
 743                                         // 2D to 3D
 744                                         readImages3(o_output,im, i_attr,i_zspc);
 745                                 } else {
 746                                         readImages1(o_output,im, i_attr);
 747                                 }
 748                         } else {
 749                                 // we deal with multiple frames n x (2D x T)
 750                                 // Differents outputs are avaialable
 751                                 if(i_dim == 1)
 752                                 {
 753                                         // put all in one output
 754                                         readImages3(o_output,im, i_attr,i_zspc);
 755                                 } else if( i_dim == 2) {
 756                                         // put in a vector of n x T (2D)
 757                                         readImages2(o_output,im, i_attr,i_zspc);
 758                                 } else if( i_dim == 3) {
 759                                         // put in a vector of n (2D x T)
 760                                         // No transformations.
 761                                         readImages1(o_output,im, i_attr);
 762                                 } else {
 763                                         // put in a vector of T (2D x n)
 764                                         readImages4(o_output,im, i_attr);
 765                                 } // i_dim
 766                         } //isSingle(im.front())
 767                 } // if size
 768
 769 //EED UnMosaic step...
 770 //How to verifie if is a mosaic file , with how many images inside??
 771
 772         }
 773
 774
 775
 776 void GimmickView::ReadImagesNotThreadedInVector(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
 777 {
 778         // Create the output data
 779         if (im.size()==1)
 780         {
 781                 // Only one image : give it
 782                 vtkImageData* out = vtkImageData::New();
 783                 GimmickDebugMessage(3, "State Check: Full Filename: "
 784                                                 <<im.front()
 785                                                 <<std::endl);
 786                 out->ShallowCopy(mReader.GetImage(im.front()));
 787                 s.push_back( out );
 788         }
 789         else if (im.size()>1) // Test inutile ? JPR
 790         {
 791                 /// \TODO fix unused variable 'first'
 792 //              vtkImageData* first = mReader.GetImage( im.front());
 793                 if (dimension == 2)
 794                 {
 795                  // n3D
 796                   std::vector<std::string>::iterator it;
 797                         for (it=im.begin(); it!=im.end(); ++it)
 798                         {
 799                                 vtkImageData* out = vtkImageData::New();
 800                                 out->ShallowCopy(mReader.GetImage(*it));
 801                                 s.push_back(out);
 802                         } // for
 803                 } else {
 804                         // n2D to 3D // NO!
 805                         // n *2D + T in a vector :
 806
 807                         std::vector<std::string>::iterator it;
 808                         for (it=im.begin(); it!=im.end(); ++it)
 809                         {
 810                                 vtkImageData* out = mReader.GetImage( (*it));
 811                                 s.push_back(out);
 812                         } // for
 813                 } // if dimension
 814         } // if im.size
 815 }
 816   //======================================================================
 817
 818   //======================================================================
 819   ///Requests the reading of an image
 820   void GimmickView::RequestReading(tree::Node* n,
 821           int prio, int selection_index, boost::shared_ptr<ImagePointerHolder> p)
 822   {
 823           if(!mReaderStarted)
 824           {
 825                 mReader.Start();
 826                 mReaderStarted=true;
 827           }
 828     ImageEventType t(n,selection_index);
 829         t.pointerHolder = p;
 830     mImageEventMap[n->GetAttribute("FullFileName")] = t;
 831     mReader.Request(this,n->GetAttribute("FullFileName"),prio);
 832   }
 833   //======================================================================
 834
 835   //======================================================================
 836   void GimmickView::
 837   OnMultiThreadImageReaderEvent(const std::string& filename,
 838                                 MultiThreadImageReaderUser::EventType e,
 839                                 vtkImageData* image)
 840   {
 841     GimmickDebugMessage(7,
 842                         "MultiThreadImageReader event : "<<e<<std::endl);
 843         if (e==ImageLoaded)
 844         {
 845                 if (filename.size()==0)
 846                 {
 847                   //What to do in this case?
 848                   /*
 849                         GimmickDebugMessage(5,
 850                                         "Pushing unknown image in queue"
 851                                         <<std::endl);
 852                         mImageEventQueue.push_back(ImageEventType(image));*/
 853                         return;
 854                 }
 855                 ImageEventTypeMap::iterator i;
 856 //JCP 22-06-2009, test mImageEventMap.size() > 0
 857                 if(mImageEventMap.size()>0){
 858                         i = mImageEventMap.find(filename);
 859                         if (i!=mImageEventMap.end())
 860                         {
 861                                 GimmickDebugMessage(5,
 862                                                 "Putting image of file '"<<filename<<"' on pointer"
 863                                                 <<std::endl);
 864                                 ImageEventType ie(i->second);
 865                                 ie.image = image;
 866                                 ie.pointerHolder->Set(ie.image);
 867                                 //mImageEventMap.erase(i);
 868                         }
 869                 }
 870         }
 871         else if (e==Error)
 872         {
 873                 std::string mess="ERROR: MultiThreadImageReader: Cannot read image in file ";
 874                 mess+=filename;
 875                 mess+="\n";
 876                 GimmickMessage(1,mess);
 877                 ImageEventTypeMap::iterator i;
 878                 i = mImageEventMap.find(filename);
 879                 if (i!=mImageEventMap.end())
 880                 {
 881                 ImageEventType ie(i->second);
 882                 ie.image = image;
 883                 ie.pointerHolder->Set(GetDefaultImage());
 884                 //mImageEventMap.erase(i);
 885                 }
 886         }
 887
 888         else if (e==ImageUnloaded)
 889         {
 890                 std::string mess="Unloaded image in file ";
 891                 mess+=filename;
 892                 mess+="\n";
 893                 GimmickMessage(1,mess);
 894                                 ImageEventTypeMap::iterator i;
 895                 i = mImageEventMap.find(filename);
 896                 if (i!=mImageEventMap.end())
 897                 {
 898                 ImageEventType ie(i->second);
 899                 ie.image = image;
 900                 ie.pointerHolder->Set(GetDefaultImage());
 901                 //mImageEventMap.erase(i);
 902                 }
 903         }
 904   }
 905
 906   //====================================================================
 907
 908   //====================================================================
 909   void GimmickView::ConnectValidationObserver(ValidationCallbackType callback)
 910   {
 911     mValidationSignal.connect(callback);
 912   }
 913
 914
 915 #if defined(USE_GDCM)
 916 ////////////////////////////////////////////////////////////////////////
 917 void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
 918 {
 919         bool res = true;
 920    std::vector<GDCM_NAME_SPACE::FileHelper *> filesH;
 921    std::vector<std::string> suid;
 922    std::map<std::string, std::string> msuid;
 923    std::string tempuid = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 924    int i = 1;
 925    std::vector<std::string>::iterator it = i_filenames.begin();
 926    for(; it != i_filenames.end(); it++)
 927    {
 928
 929            GDCM_NAME_SPACE::File *file;
 930            file = GDCM_NAME_SPACE::File::New(  );
 931            file->SetLoadMode( GDCM_NAME_SPACE::LD_ALL );
 932            file->SetFileName( (*it).c_str() );
 933            res = file->Load();
 934            if ( !res )
 935            {
 936                         std::cerr << "Sorry, " <<  (*it).c_str()  <<"  not a gdcm-readable "
 937                  << "DICOM / ACR File" <<std::endl;
 938                         file ->Delete();
 939        //return 0;
 940                 }
 941                 std::cout << " ... is readable " << std::endl;
 942
 943                 // We need a gdcm::FileHelper, since we want to load the pixels
 944                 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(file);
 945
 946 //Borrame
 947 //EED   uint8_t *imageData = fh->GetImageData();
 948
 949            // Institution name
 950            file->AddAnonymizeElement(0x0008, 0x0080, "*");
 951            // Patient's name
 952            file->AddAnonymizeElement(0x0010, 0x0010, "*");
 953            // Patient's ID
 954            file->AddAnonymizeElement( 0x0010, 0x0020,"1515" );
 955            // Study Instance UID
 956            file->AddAnonymizeElement(0x0020, 0x000d, tempuid );
 957            // Telephone
 958            file->AddAnonymizeElement(0x0010, 0x2154, "3615" );
 959
 960            // Aware user will add here more fields to anonymize here
 961
 962            // The gdcm::File is modified in memory
 963
 964            file->AnonymizeFile();
 965
 966
 967            i++;
 968            fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
 969
 970            fh->WriteDcmExplVR(file->GetFileName() +".ano1" );
 971            std::cout << i <<"  End Anonymize" << std::endl;
 972            file->ClearAnonymizeList();
 973            file->Delete();
 974            fh->Delete();
 975    }
 976 }
 977 #endif
 978 #if defined(USE_GDCM2)
 979 void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
 980 {
 981 }
 982 #endif
 983 ////////////////////////////////////////////////////////////////////////
 984 //void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
 985 //{
 986 //
 987 //      gdcm::FileMetaInformation::SetSourceApplicationEntityTitle( "gdcmanon" );
 988 //    gdcm::Global& g = gdcm::Global::GetInstance();
 989 //      //if( !resourcespath )
 990 // //   {
 991 //      //      const char *xmlpathenv = getenv("GDCM_RESOURCES_PATH");
 992 //      //      if( xmlpathenv )
 993 //      //        {
 994 //      //        // Make sure to look for XML dict in user explicitly specified dir first:
 995 //      //        xmlpath = xmlpathenv;
 996 //      //        resourcespath = 1;
 997 //      //        }
 998 // //   }
 999 // // if( resourcespath )
1000 // //   {
1001 // //   // xmlpath is set either by the cmd line option or the env var
1002 // //   if( !g.Prepend( xmlpath.c_str() ) )
1003 // //     {
1004 // //     std::cerr << "Specified Resources Path is not valid: " << xmlpath << std::endl;
1005 // //     return 1;
1006 // //     }
1007 // //   }
1008 //  // All set, then load the XML files:
1009 //  if( !g.LoadResourcesFiles() )
1010 //  {
1011 //    return ;
1012 //  }
1013 //  const gdcm::Defs &defs = g.GetDefs(); (void)defs;
1014 //  if( !rootuid )
1015 //    {
1016 //    // only read the env var if no explicit cmd line option
1017 //    // maybe there is an env var defined... let's check
1018 //    const char *rootuid_env = getenv("GDCM_ROOT_UID");
1019 //    if( rootuid_env )
1020 //      {
1021 //      rootuid = 1;
1022 //      root = rootuid_env;
1023 //      }
1024 //    }
1025 //  if( rootuid )
1026 //    {
1027 //    // root is set either by the cmd line option or the env var
1028 //    if( !gdcm::UIDGenerator::IsValid( root.c_str() ) )
1029 //      {
1030 //      std::cerr << "specified Root UID is not valid: " << root << std::endl;
1031 //      return 1;
1032 //      }
1033 //    gdcm::UIDGenerator::SetRoot( root.c_str() );
1034 //    }
1035 //
1036 //      if(type == 0)
1037 //      {
1038 //                 // Get private key/certificate
1039 //           gdcm::CryptographicMessageSyntax cms;
1040 //              if( !dumb_mode )
1041 //              {
1042 //                      if( !GetRSAKeys(cms, rsa_path.c_str(), cert_path.c_str() ) )
1043 //                      {
1044 //                              return 1;
1045 //                      }
1046 //                      cms.SetCipherType( ciphertype );
1047 //              }
1048 //
1049 //      // Setup gdcm::Anonymizer
1050 //      gdcm::Anonymizer anon;
1051 //              if( !dumb_mode )
1052 //              anon.SetCryptographicMessageSyntax( &cms );
1053 //
1054 //              if( dumb_mode )
1055 //              {
1056 //                      for(unsigned int i = 0; i < nfiles; ++i)
1057 //              {
1058 //              const char *in  = filenames[i].c_str();
1059 //              const char *out = outfilenames[i].c_str();
1060 //              if( !AnonymizeOneFileDumb(anon, in, out, empty_tags, remove_tags, replace_tags_value) )
1061 //        {
1062 //                      //std::cerr << "Could not anonymize: " << in << std::endl;
1063 //                      return 1;
1064 //              }
1065 //      }
1066 //    }
1067 //  //else
1068 //  //  {
1069 //  //  for(unsigned int i = 0; i < nfiles; ++i)
1070 //  //    {
1071 //  //    const char *in  = filenames[i].c_str();
1072 //  //    const char *out = outfilenames[i].c_str();
1073 //  //    if( !AnonymizeOneFile(anon, in, out) )
1074 //  //      {
1075 //  //      //std::cerr << "Could not anonymize: " << in << std::endl;
1076 //  //      return 1;
1077 //  //      }
1078 //  //    }
1079 //  //  }
1080 //      }
1081 //}
1082 //
1083 } // EO namespace creaImageIO