src/creaImageIOGimmickView.cpp

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