src/creaImageIOGimmickView.cpp

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