src/creaImageIOGimmickView.cpp

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