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                         int ext[6];
 380                         //first->GetExtent(ext);  // JPR
 381 //EED 2017-01-01 Migration VTK7
 382 #if VTK_MAJOR_VERSION <= 5
 383                         first->GetWholeExtent(ext);  // renvoie egalement 0,0 en Z // JPR
 384 #else
 385                         first->GetExtent(ext);  // renvoie egalement 0,0 en Z // JPR
 386 #endif
 387
 388                         if(ext[5] == 0)
 389                         {
 390                                 ext[5] = (int)im.size()-1;
 391                         }
 392                         else
 393                         {
 394                                 ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes - JPR
 395                         }
 396                         out->SetExtent(ext);
 397
 398                         // LG : TODO : Z Spacing  ?
 399
 400                         int dim[3];
 401                         first->GetDimensions(dim);
 402                         out->SetDimensions(dim[0], dim[1], (int)im.size() );
 403
 404 //EED 2017-01-01 Migration VTK7
 405 #if VTK_MAJOR_VERSION <= 5
 406                         out->SetScalarType(first->GetScalarType());
 407                         out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 408                         out->AllocateScalars();
 409                         out->Update();
 410 #else
 411                         out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
 412 #endif
 413
 414                         unsigned long imsize = dim[0] * dim[1];
 415                         imsize = imsize * dim[2] ;  // deal with multiframes // JPR
 416
 417
 418 //EED 03-11-2009
 419                         // differents formats char , short, etc...
 420                         // differents components 1..3  ex. jpg ->RGB 3
 421                         imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 422
 423
 424                         // Order the file name vector
 425
 426                         double spc[3];
 427                         first->GetSpacing(spc);
 428
 429                         // OrderTheFileNameVector is not here anymore.
 430                         // Try orderFilesWithZSpacing from OutputModel FCY
 431                         // spc[2]=OrderTheFileNameVector(im);
 432                         spc[2] =1;
 433
 434                         out->SetSpacing(spc);
 435
 436                         int slice = 0;
 437                         std::vector<std::string>::iterator it;
 438
 439                         for (it=im.begin(); it!=im.end(); ++it)
 440                         {
 441                                 vtkImageData* cur = mReader.GetImage( (*it) );
 442                                 memcpy(out->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
 443                                 slice++;
 444                         }
 445                         s.push_back(out);
 446
 447                 }  // dimension == 3
 448
 449         }  // size >1
 450
 451 }
 452   //======================================================================
 453
 454
 455
 456         //////////////////////////////////////////////////////////
 457         // Test if the image is a multiple or single frame.
 458         // For the moment only with the creation of vtkImageDta.
 459         // TO DO with image size and dim!!!
 460         //////////////////////////////////////////////////////////
 461         bool GimmickView::isSingle(const std::string i_file)
 462         {
 463                 bool bres = true;
 464                 vtkImageData* first = mReader.GetImage( i_file);
 465                 int dim[3];
 466                 first->GetDimensions(dim);
 467                 if (dim[2] > 1)
 468                 {
 469                         bres = false;
 470                 }
 471                 else
 472                 {
 473                 }
 474                 return bres;
 475         }
 476
 477         //////////////////////////////////////////////////////////
 478         // get Attributes values for a file
 479         //////////////////////////////////////////////////////////
 480
 481         void GimmickView::getAttributes(const std::string i_file, std::map<std::string, std::string> &o_infos, OutputAttr i_attr)
 482         {
 483                 if(i_attr.inside.size() >0)
 484                 {
 485                         mGimmick->GetAttributes(i_file,o_infos,i_attr);
 486                 }
 487                 if(i_attr.outside.size()>0)
 488                 {
 489                         mReader.getAttributes(i_file,o_infos, i_attr.outside);
 490                 }
 491         }
 492
 493         //////////////////////////////////////////////////////////
 494         // create an output structure with n entries = n output
 495         //////////////////////////////////////////////////////////
 496         void GimmickView::readImages1(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 497                          OutputAttr i_attr)
 498         {
 499
 500                 i_attr.outside.push_back("D0019_100a");  // simens Number Of Images In Mosaic
 501
 502 //EED Borrame
 503                 int i,isize=i_attr.outside.size();
 504                 for (i=0;i<isize;i++)
 505                 {
 506                 printf("EED GimmickView::readImages1 A  i_attr out %s \n", i_attr.outside[i].c_str());
 507                 }
 508
 509
 510
 511                 std::vector<std::string>::iterator it;
 512                 for (it=im.begin(); it!=im.end(); ++it)
 513                 {
 514                         OutStrGimmick out;
 515                         out.img = vtkImageData::New();
 516                         out.img->ShallowCopy(mReader.GetImage(*it));
 517 printf("EED GimmickView::readImages1 A\n ");
 518                         if(i_attr.mult)
 519                         {
 520                                 getAttributes((*it),out.infos,i_attr);
 521 printf("EED GimmickView::readImages1 B   %s \n ", out.infos.find("D0019_100a")->second.c_str() );
 522                         }
 523                         o_output.push_back(out);
 524                 }
 525                 // If we want only one output information structure, we set it outside the loop
 526                 if(!i_attr.mult)
 527                 {
 528                         getAttributes(im.front(), o_output.front().infos, i_attr);
 529 printf("EED GimmickView::readImages1 C   %s \n ", o_output.front().infos.find("D0019_100a")->second.c_str() );
 530                 }
 531
 532         }
 533
 534         //////////////////////////////////////////////////////////
 535         // create an output structure with n entries = 1 output
 536         //////////////////////////////////////////////////////////
 537         void GimmickView::readImages3(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 538                          OutputAttr i_attr, double i_zspc)
 539         {
 540                 OutStrGimmick out;
 541                 vtkImageData* first = mReader.GetImage( im.front());
 542                 out.img  = vtkImageData::New();
 543                 int ext[6];
 544 //EED 2017-01-01 Migration VTK7
 545 #if VTK_MAJOR_VERSION <= 5
 546                 first->GetWholeExtent(ext);  // send also 0,0 in Z
 547 #else
 548                 first->GetExtent(ext);  // send also 0,0 in Z
 549 #endif
 550                 if(ext[5] == 0)
 551                 {
 552                         ext[5] = (int)im.size()-1;
 553                 } else {
 554                         ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes
 555                 }
 556                 out.img->SetExtent(ext);
 557                 int dim[3];
 558                 double spac[3];
 559                 first->GetDimensions(dim);
 560                 first->GetSpacing(spac);
 561                 out.img->SetSpacing(spac);
 562                 out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
 563
 564
 565
 566 //EED 2017-01-01 Migration VTK7
 567 #if VTK_MAJOR_VERSION <= 5
 568                 out.img->SetScalarType(first->GetScalarType());
 569                 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 570                 out.img->AllocateScalars();
 571                 out.img->Update();
 572 #else
 573                 out.img->AllocateScalars(first->GetScalarType(), first->GetNumberOfScalarComponents());
 574 #endif
 575
 576
 577                 unsigned long imsize = dim[0] * dim[1];
 578                 imsize = imsize * dim[2] ;  // deal with multiframes here
 579                 // differents formats char , short, etc...
 580                 // differents components 1..3  ex. jpg ->RGB 3
 581                 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 582                 // Order the file name vector already did with the OutputModel!!!
 583                 //!!!!out.img->SetSpacing(i_zspc);
 584                 int slice = 0;
 585                 std::vector<std::string>::iterator it;
 586                 for (it=im.begin(); it!=im.end(); ++it)
 587                 {
 588                         vtkImageData* cur = mReader.GetImage( (*it) );
 589                         memcpy(out.img->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
 590                         slice++;
 591                 }
 592                 getAttributes(im.front(),out.infos, i_attr);
 593                 o_output.push_back(out);
 594         }
 595
 596
 597         // TO DO  NO VERY SURE : NEED TO BE TESTED
 598         //////////////////////////////////////////////////////////
 599         // create an output structure with n entries (T size) = T output (n size)
 600         //////////////////////////////////////////////////////////
 601         void GimmickView::readImages2(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 602                          OutputAttr i_attr, double i_zspc)
 603         {
 604                 vtkImageData* first = mReader.GetImage( im.front());
 605                 int dim[3];
 606                 double spac[3];
 607                 first->GetDimensions(dim);
 608                 first->GetSpacing(spac);
 609                 // differents formats char , short, etc...
 610                 // differents components 1..3  ex. jpg ->RGB 3
 611                 unsigned long imsize = dim[0] * dim[1];
 612                 imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 613
 614                 // Order the file name vector already did with the OutputModel!!!
 615                 std::vector<std::string>::iterator it;
 616                 std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
 617
 618                 for (it=im.begin(); it!=im.end(); ++it)//, it_out ++)
 619                 {
 620                         vtkImageData* cur = mReader.GetImage( (*it) );
 621                         for (int slice= 0 ; slice <dim[2]; slice++)
 622                         {
 623                                 OutStrGimmick out;
 624                                 out.img = vtkImageData::New();
 625                                 out.img->SetSpacing(spac);
 626                                 int ext[6];
 627 //EED 2017-01-01 Migration VTK7
 628 #if VTK_MAJOR_VERSION <= 5
 629                                 first->GetWholeExtent(ext);  // send also 0,0 in Z
 630 #else
 631                                 first->GetExtent(ext);  // send also 0,0 in Z
 632 #endif
 633                                 ext[5] = 0;
 634                                 out.img->SetExtent(ext);
 635                                 out.img->SetDimensions(dim[0], dim[1], 1 );
 636
 637 //EED 2017-01-01 Migration VTK7
 638 #if VTK_MAJOR_VERSION <= 5
 639                                 out.img->SetScalarType(first->GetScalarType());
 640                                 out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 641                                 out.img->AllocateScalars();
 642                                 out.img->Update();
 643 #else
 644                                 out.img->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
 645 #endif
 646
 647
 648                                 memcpy(out.img->GetScalarPointer(0,0,0), cur->GetScalarPointer(0,0,slice), imsize);
 649                                 o_output.push_back(out);
 650                         }
 651         //              if(i_attr.mult)
 652                 //              getAttributes((*it),(*it_out).infos,i_attr);
 653                 }
 654                 if(!i_attr.mult)
 655                 {
 656                         getAttributes(im.front(), o_output.front().infos,i_attr);
 657                 }
 658
 659         }
 660
 661         //////////////////////////////////////////////////////////
 662         // create an output structure with n entries (T size) = T + n output
 663         //////////////////////////////////////////////////////////
 664         void GimmickView::readImages4(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 665                          OutputAttr i_attr)
 666         {
 667                 std::vector<std::string>::iterator it;
 668                 std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
 669                 vtkImageData* first = mReader.GetImage( im.front());
 670                 int dim[3];
 671                 first->GetDimensions(dim);
 672
 673                 for (int slice= 0 ; slice <dim[2]; slice++)
 674                 {
 675                         OutStrGimmick out;
 676                         out.img = vtkImageData::New();
 677
 678                         int ext[6];
 679
 680 //EED 2017-01-01 Migration VTK7
 681 #if VTK_MAJOR_VERSION <= 5
 682                         first->GetWholeExtent(ext);  // send also 0,0 in Z
 683 #else
 684                         first->GetExtent(ext);  // send also 0,0 in Z
 685 #endif
 686
 687                         double spac[6];
 688                         ext[5] = 0;
 689                         out.img->SetExtent(ext);
 690                         first->GetSpacing(spac);
 691                         out.img->SetSpacing(spac);
 692                         out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
 693
 694 //EED 2017-01-01 Migration VTK7
 695 #if VTK_MAJOR_VERSION <= 5
 696                         out.img->SetScalarType(first->GetScalarType());
 697                         out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
 698                         out.img->AllocateScalars();
 699                         out.img->Update();
 700 #else
 701                         out.img->AllocateScalars(first->GetScalarType(), first->GetNumberOfScalarComponents());
 702 #endif
 703
 704                         unsigned long imsize = dim[0] * dim[1];
 705                         imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
 706                         int index = 0;
 707
 708                         for (it=im.begin(); it!=im.end(); ++it, index ++)
 709                         {
 710                                 vtkImageData* cur = mReader.GetImage( (*it) );
 711                                 memcpy(out.img->GetScalarPointer(0,0,index), cur->GetScalarPointer(0,0,slice), imsize);
 712                                 o_output.push_back(out);
 713                         }
 714                 }
 715                 if(!i_attr.mult) // No sense to take informations in all images
 716                 {
 717                         getAttributes(im.front(), o_output.front().infos,i_attr);
 718                 }
 719
 720         }
 721
 722
 723 //////////////////////////////////////////////////////////////////////////////////////////////////////////////
 724 // Global function to read Images and create wished output (informations, multiple, type and size of output...)
 725 // In function of type (file, vector) and size, the correct readImages function is selected
 726 //////////////////////////////////////////////////////////////////////////////////////////////////////////////
 727         void GimmickView::readImages(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
 728                          OutputAttr i_attr, int i_dim, double i_zspc)
 729         {
 730                 int size = (int)im.size();
 731                 if ( size == 0)
 732                 {
 733                         return;
 734                 } else if (size == 1) {
 735                         // Simplest case
 736                         // Only one image : give it
 737                         // But take in count multiframe possibility
 738                         if ( isSingle(im.front()) || i_dim != 1)
 739                         {
 740                                  readImages1(o_output,im, i_attr);
 741                         } else {
 742                                  readImages2(o_output,im, i_attr,i_zspc);
 743                         }
 744                 } else {
 745                         // multiple or single frame
 746                         if ( isSingle(im.front()) )
 747                         {
 748                                 //we deal with 2D images
 749                                 if(i_dim == 1)
 750                                 {
 751                                         // 2D to 3D
 752                                         readImages3(o_output,im, i_attr,i_zspc);
 753                                 } else {
 754                                         readImages1(o_output,im, i_attr);
 755                                 }
 756                         } else {
 757                                 // we deal with multiple frames n x (2D x T)
 758                                 // Differents outputs are avaialable
 759                                 if(i_dim == 1)
 760                                 {
 761                                         // put all in one output
 762                                         readImages3(o_output,im, i_attr,i_zspc);
 763                                 } else if( i_dim == 2) {
 764                                         // put in a vector of n x T (2D)
 765                                         readImages2(o_output,im, i_attr,i_zspc);
 766                                 } else if( i_dim == 3) {
 767                                         // put in a vector of n (2D x T)
 768                                         // No transformations.
 769                                         readImages1(o_output,im, i_attr);
 770                                 } else {
 771                                         // put in a vector of T (2D x n)
 772                                         readImages4(o_output,im, i_attr);
 773                                 } // i_dim
 774                         } //isSingle(im.front())
 775                 } // if size
 776
 777 //EED UnMosaic step...
 778 //How to verifie if is a mosaic file , with how many images inside??
 779
 780         }
 781
 782
 783
 784 void GimmickView::ReadImagesNotThreadedInVector(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
 785 {
 786         // Create the output data
 787         if (im.size()==1)
 788         {
 789                 // Only one image : give it
 790                 vtkImageData* out = vtkImageData::New();
 791                 GimmickDebugMessage(3, "State Check: Full Filename: "
 792                                                 <<im.front()
 793                                                 <<std::endl);
 794                 out->ShallowCopy(mReader.GetImage(im.front()));
 795                 s.push_back( out );
 796         }
 797         else if (im.size()>1) // Test inutile ? JPR
 798         {
 799                 /// \TODO fix unused variable 'first'
 800 //              vtkImageData* first = mReader.GetImage( im.front());
 801                 if (dimension == 2)
 802                 {
 803                  // n3D
 804                   std::vector<std::string>::iterator it;
 805                         for (it=im.begin(); it!=im.end(); ++it)
 806                         {
 807                                 vtkImageData* out = vtkImageData::New();
 808                                 out->ShallowCopy(mReader.GetImage(*it));
 809                                 s.push_back(out);
 810                         } // for
 811                 } else {
 812                         // n2D to 3D // NO!
 813                         // n *2D + T in a vector :
 814
 815                         std::vector<std::string>::iterator it;
 816                         for (it=im.begin(); it!=im.end(); ++it)
 817                         {
 818                                 vtkImageData* out = mReader.GetImage( (*it));
 819                                 s.push_back(out);
 820                         } // for
 821                 } // if dimension
 822         } // if im.size
 823 }
 824   //======================================================================
 825
 826   //======================================================================
 827   ///Requests the reading of an image
 828   void GimmickView::RequestReading(tree::Node* n,
 829           int prio, int selection_index, boost::shared_ptr<ImagePointerHolder> p)
 830   {
 831           if(!mReaderStarted)
 832           {
 833                 mReader.Start();
 834                 mReaderStarted=true;
 835           }
 836     ImageEventType t(n,selection_index);
 837         t.pointerHolder = p;
 838     mImageEventMap[n->GetAttribute("FullFileName")] = t;
 839     mReader.Request(this,n->GetAttribute("FullFileName"),prio);
 840   }
 841   //======================================================================
 842
 843   //======================================================================
 844   void GimmickView::
 845   OnMultiThreadImageReaderEvent(const std::string& filename,
 846                                 MultiThreadImageReaderUser::EventType e,
 847                                 vtkImageData* image)
 848   {
 849     GimmickDebugMessage(7,
 850                         "MultiThreadImageReader event : "<<e<<std::endl);
 851         if (e==ImageLoaded)
 852         {
 853                 if (filename.size()==0)
 854                 {
 855                   //What to do in this case?
 856                   /*
 857                         GimmickDebugMessage(5,
 858                                         "Pushing unknown image in queue"
 859                                         <<std::endl);
 860                         mImageEventQueue.push_back(ImageEventType(image));*/
 861                         return;
 862                 }
 863                 ImageEventTypeMap::iterator i;
 864 //JCP 22-06-2009, test mImageEventMap.size() > 0
 865                 if(mImageEventMap.size()>0){
 866                         i = mImageEventMap.find(filename);
 867                         if (i!=mImageEventMap.end())
 868                         {
 869                                 GimmickDebugMessage(5,
 870                                                 "Putting image of file '"<<filename<<"' on pointer"
 871                                                 <<std::endl);
 872                                 ImageEventType ie(i->second);
 873                                 ie.image = image;
 874                                 ie.pointerHolder->Set(ie.image);
 875                                 //mImageEventMap.erase(i);
 876                         }
 877                 }
 878         }
 879         else if (e==Error)
 880         {
 881                 std::string mess="ERROR: MultiThreadImageReader: Cannot read image in file ";
 882                 mess+=filename;
 883                 mess+="\n";
 884                 GimmickMessage(1,mess);
 885                 ImageEventTypeMap::iterator i;
 886                 i = mImageEventMap.find(filename);
 887                 if (i!=mImageEventMap.end())
 888                 {
 889                 ImageEventType ie(i->second);
 890                 ie.image = image;
 891                 ie.pointerHolder->Set(GetDefaultImage());
 892                 //mImageEventMap.erase(i);
 893                 }
 894         }
 895
 896         else if (e==ImageUnloaded)
 897         {
 898                 std::string mess="Unloaded image in file ";
 899                 mess+=filename;
 900                 mess+="\n";
 901                 GimmickMessage(1,mess);
 902                                 ImageEventTypeMap::iterator i;
 903                 i = mImageEventMap.find(filename);
 904                 if (i!=mImageEventMap.end())
 905                 {
 906                 ImageEventType ie(i->second);
 907                 ie.image = image;
 908                 ie.pointerHolder->Set(GetDefaultImage());
 909                 //mImageEventMap.erase(i);
 910                 }
 911         }
 912   }
 913
 914   //====================================================================
 915
 916   //====================================================================
 917   void GimmickView::ConnectValidationObserver(ValidationCallbackType callback)
 918   {
 919     mValidationSignal.connect(callback);
 920   }
 921
 922
 923 #if defined(USE_GDCM)
 924 ////////////////////////////////////////////////////////////////////////
 925 void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
 926 {
 927         bool res = true;
 928    std::vector<GDCM_NAME_SPACE::FileHelper *> filesH;
 929    std::vector<std::string> suid;
 930    std::map<std::string, std::string> msuid;
 931    std::string tempuid = GDCM_NAME_SPACE::Util::CreateUniqueUID();
 932    int i = 1;
 933    std::vector<std::string>::iterator it = i_filenames.begin();
 934    for(; it != i_filenames.end(); it++)
 935    {
 936
 937            GDCM_NAME_SPACE::File *file;
 938            file = GDCM_NAME_SPACE::File::New(  );
 939            file->SetLoadMode( GDCM_NAME_SPACE::LD_ALL );
 940            file->SetFileName( (*it).c_str() );
 941            res = file->Load();
 942            if ( !res )
 943            {
 944                         std::cerr << "Sorry, " <<  (*it).c_str()  <<"  not a gdcm-readable "
 945                  << "DICOM / ACR File" <<std::endl;
 946                         file ->Delete();
 947        //return 0;
 948                 }
 949                 std::cout << " ... is readable " << std::endl;
 950
 951                 // We need a gdcm::FileHelper, since we want to load the pixels
 952                 GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(file);
 953
 954 //Borrame
 955 //EED   uint8_t *imageData = fh->GetImageData();
 956
 957            // Institution name
 958            file->AddAnonymizeElement(0x0008, 0x0080, "*");
 959            // Patient's name
 960            file->AddAnonymizeElement(0x0010, 0x0010, "*");
 961            // Patient's ID
 962            file->AddAnonymizeElement( 0x0010, 0x0020,"1515" );
 963            // Study Instance UID
 964            file->AddAnonymizeElement(0x0020, 0x000d, tempuid );
 965            // Telephone
 966            file->AddAnonymizeElement(0x0010, 0x2154, "3615" );
 967
 968            // Aware user will add here more fields to anonymize here
 969
 970            // The gdcm::File is modified in memory
 971
 972            file->AnonymizeFile();
 973
 974
 975            i++;
 976            fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
 977
 978            fh->WriteDcmExplVR(file->GetFileName() +".ano1" );
 979            std::cout << i <<"  End Anonymize" << std::endl;
 980            file->ClearAnonymizeList();
 981            file->Delete();
 982            fh->Delete();
 983    }
 984 }
 985 #endif
 986 #if defined(USE_GDCM2)
 987 void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
 988 {
 989 }
 990 #endif
 991 ////////////////////////////////////////////////////////////////////////
 992 //void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
 993 //{
 994 //
 995 //      gdcm::FileMetaInformation::SetSourceApplicationEntityTitle( "gdcmanon" );
 996 //    gdcm::Global& g = gdcm::Global::GetInstance();
 997 //      //if( !resourcespath )
 998 // //   {
 999 //      //      const char *xmlpathenv = getenv("GDCM_RESOURCES_PATH");
1000 //      //      if( xmlpathenv )
1001 //      //        {
1002 //      //        // Make sure to look for XML dict in user explicitly specified dir first:
1003 //      //        xmlpath = xmlpathenv;
1004 //      //        resourcespath = 1;
1005 //      //        }
1006 // //   }
1007 // // if( resourcespath )
1008 // //   {
1009 // //   // xmlpath is set either by the cmd line option or the env var
1010 // //   if( !g.Prepend( xmlpath.c_str() ) )
1011 // //     {
1012 // //     std::cerr << "Specified Resources Path is not valid: " << xmlpath << std::endl;
1013 // //     return 1;
1014 // //     }
1015 // //   }
1016 //  // All set, then load the XML files:
1017 //  if( !g.LoadResourcesFiles() )
1018 //  {
1019 //    return ;
1020 //  }
1021 //  const gdcm::Defs &defs = g.GetDefs(); (void)defs;
1022 //  if( !rootuid )
1023 //    {
1024 //    // only read the env var if no explicit cmd line option
1025 //    // maybe there is an env var defined... let's check
1026 //    const char *rootuid_env = getenv("GDCM_ROOT_UID");
1027 //    if( rootuid_env )
1028 //      {
1029 //      rootuid = 1;
1030 //      root = rootuid_env;
1031 //      }
1032 //    }
1033 //  if( rootuid )
1034 //    {
1035 //    // root is set either by the cmd line option or the env var
1036 //    if( !gdcm::UIDGenerator::IsValid( root.c_str() ) )
1037 //      {
1038 //      std::cerr << "specified Root UID is not valid: " << root << std::endl;
1039 //      return 1;
1040 //      }
1041 //    gdcm::UIDGenerator::SetRoot( root.c_str() );
1042 //    }
1043 //
1044 //      if(type == 0)
1045 //      {
1046 //                 // Get private key/certificate
1047 //           gdcm::CryptographicMessageSyntax cms;
1048 //              if( !dumb_mode )
1049 //              {
1050 //                      if( !GetRSAKeys(cms, rsa_path.c_str(), cert_path.c_str() ) )
1051 //                      {
1052 //                              return 1;
1053 //                      }
1054 //                      cms.SetCipherType( ciphertype );
1055 //              }
1056 //
1057 //      // Setup gdcm::Anonymizer
1058 //      gdcm::Anonymizer anon;
1059 //              if( !dumb_mode )
1060 //              anon.SetCryptographicMessageSyntax( &cms );
1061 //
1062 //              if( dumb_mode )
1063 //              {
1064 //                      for(unsigned int i = 0; i < nfiles; ++i)
1065 //              {
1066 //              const char *in  = filenames[i].c_str();
1067 //              const char *out = outfilenames[i].c_str();
1068 //              if( !AnonymizeOneFileDumb(anon, in, out, empty_tags, remove_tags, replace_tags_value) )
1069 //        {
1070 //                      //std::cerr << "Could not anonymize: " << in << std::endl;
1071 //                      return 1;
1072 //              }
1073 //      }
1074 //    }
1075 //  //else
1076 //  //  {
1077 //  //  for(unsigned int i = 0; i < nfiles; ++i)
1078 //  //    {
1079 //  //    const char *in  = filenames[i].c_str();
1080 //  //    const char *out = outfilenames[i].c_str();
1081 //  //    if( !AnonymizeOneFile(anon, in, out) )
1082 //  //      {
1083 //  //      //std::cerr << "Could not anonymize: " << in << std::endl;
1084 //  //      return 1;
1085 //  //      }
1086 //  //    }
1087 //  //  }
1088 //      }
1089 //}
1090 //
1091 } // EO namespace creaImageIO