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