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