bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx

   1 //=====
   2 // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
   3 //=====
   4 #include "bbcreaVtkReadMHDPlane.h"
   5 #include "bbcreaVtkPackage.h"
   6
   7 #include "stdio.h"
   8
   9
  10 #define _LARGEFILE64_SOURCE
  11
  12 #include <stdio.h>
  13 #include <sys/types.h>
  14
  15 #if defined(_WIN32)
  16 #else
  17 #include <unistd.h>
  18 #endif // defined(_WIN32)
  19
  20 #include <stdlib.h>
  21 #include <errno.h>
  22 #include <string.h>
  23 #include <sys/stat.h>
  24 #include <fcntl.h>
  25
  26 namespace bbcreaVtk
  27 {
  28
  29 BBTK_ADD_BLACK_BOX_TO_PACKAGE(creaVtk,ReadMHDPlane)
  30 BBTK_BLACK_BOX_IMPLEMENTATION(ReadMHDPlane,bbtk::AtomicBlackBox);
  31 //=====
  32 // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
  33 //=====
  34
  35
  36 vtkImageData* ReadMHDPlane::CreateDefaultImage()
  37 {
  38         int i;
  39         int sizeX, sizeY, sizeZ;
  40         sizeX = 200;
  41         sizeY = sizeX;
  42         sizeZ = 1;
  43         vtkImageData *newImage = vtkImageData::New();
  44         newImage->Initialize();
  45         newImage->SetScalarTypeToUnsignedChar();
  46         newImage->SetSpacing( 1,1,1 );
  47         newImage->SetDimensions(  sizeX,sizeY,sizeZ );
  48         newImage->SetWholeExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
  49         newImage->SetExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
  50         newImage->SetNumberOfScalarComponents(1);
  51         newImage->AllocateScalars();
  52         newImage->Update();
  53         memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
  54         for (i=0; i<sizeX; i++)
  55         {
  56                 newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
  57                 newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
  58         } // for i
  59         return newImage;
  60 }
  61
  62 vtkImageData* ReadMHDPlane::ChangeOrientation(vtkImageData* imgOrg)
  63 {
  64         int     width = bbGetInputWidth();
  65         int     ext[6];
  66         int     sizeXOrg, sizeYOrg,sizeZOrg;
  67         int     sizeXDst, sizeYDst,sizeZDst;
  68         imgOrg->GetWholeExtent(ext);
  69         int     sizeLine;
  70
  71         sizeXOrg        = ext[1]-ext[0]+1;
  72         sizeYOrg        = ext[3]-ext[2]+1;
  73         sizeZOrg        = ext[5]-ext[4]+1;
  74
  75         if (bbGetInputDirectionPlane()=="XY")
  76         {
  77                 sizeXDst        = ext[1]-ext[0]+1;
  78                 sizeYDst        = ext[3]-ext[2]+1;
  79                 sizeZDst        = width;
  80         } // XY
  81         if (bbGetInputDirectionPlane()=="YZ")
  82         {
  83                 sizeXDst        = width;
  84                 sizeYDst        = ext[1]-ext[0]+1;
  85                 sizeZDst        = ext[3]-ext[2]+1;
  86                 sizeLine        = sizeYDst;
  87         } // YZ
  88         if (bbGetInputDirectionPlane()=="ZX")
  89         {
  90                 sizeXDst        = ext[1]-ext[0]+1;
  91                 sizeYDst        = width;
  92                 sizeZDst        = ext[3]-ext[2]+1;
  93                 sizeLine        = sizeXDst;
  94         } // ZX
  95         vtkImageData *imgDst  = vtkImageData::New();
  96         imgDst->Initialize();
  97         imgDst->SetScalarType( imgOrg->GetScalarType() );
  98         imgDst->SetSpacing( imgOrg->GetSpacing() );
  99         imgDst->SetDimensions( sizeXDst,sizeYDst,sizeZDst );
 100         imgDst->SetWholeExtent(0,sizeXDst-1,0,sizeYDst-1,0,sizeZDst-1 );
 101         imgDst->SetExtent(0,sizeXDst-1,0,sizeYDst-1,0,sizeZDst-1 );
 102         imgDst->SetNumberOfScalarComponents(1);
 103         imgDst->AllocateScalars();
 104         imgDst->Update();
 105
 106         char *ptrDst,*ptrOrg;
 107         int sizeBytes = imgOrg->GetScalarSize();
 108         int sizeLineBytes = sizeLine*imgOrg->GetScalarSize();
 109         int xx,yy,zz;
 110
 111         long int sizeXDstBytes          = sizeXDst*sizeBytes;
 112         long int sizeXYDstBytes         = sizeXDst*sizeYDst*sizeBytes;
 113         long int sizeXYDstBytes2        = sizeXDst*sizeYDst*sizeBytes*2;
 114         long int sizeXYZDstBytes        = sizeXDst*sizeYDst*sizeZDst*sizeBytes;
 115         long int sizeXYZDstBytes1       = sizeXDst*sizeYDst*(sizeZDst-1)*sizeBytes;
 116
 117         ptrOrg = (char*)( imgOrg->GetScalarPointer() );
 118
 119         if (bbGetInputDirectionPlane()=="XY")
 120         {
 121                 memcpy ( imgDst->GetScalarPointer(), ptrOrg , sizeXDst*sizeYDst*sizeZDst*(imgOrg->GetScalarSize()) );
 122         } // if XY
 123
 124         if (bbGetInputDirectionPlane()=="ZX")
 125         {
 126                 ptrDst = (char*)( imgDst->GetScalarPointer(0,0,sizeYOrg-00-1) );
 127                 for( zz=0 ; zz<sizeZOrg ; zz++)
 128                 {
 129 //                      ptrDst=(char*)( imgDst->GetScalarPointer(0,zz,sizeYOrg-00-1) );
 130                         for( yy=0 ; yy<sizeYOrg ; yy++)
 131                         {
 132 //                              ptrOrg=(char*)( imgOrg->GetScalarPointer(0,yy,zz) );
 133 //                              ptrDst=(char*)( imgDst->GetScalarPointer(0,zz,sizeYOrg-yy-1) );
 134                                 memcpy ( ptrDst, ptrOrg , sizeLineBytes );
 135                                 ptrOrg = ptrOrg + sizeLineBytes;
 136                                 ptrDst = ptrDst - sizeXYDstBytes;
 137                         } // for yy
 138                         ptrDst = ptrDst + sizeXDstBytes;
 139                         ptrDst = ptrDst + sizeXYZDstBytes;
 140                 } // for zz
 141         } // ZX
 142
 143         if (bbGetInputDirectionPlane()=="YZ")
 144         {
 145                 ptrDst = (char*)( imgDst->GetScalarPointer(0,0,sizeYOrg-0-1) );
 146                 for( zz=0 ; zz<sizeZOrg ; zz++)
 147                 {
 148                         ptrDst=(char*)( imgDst->GetScalarPointer(zz,0,sizeYOrg-0-1) );
 149                         for( yy=0 ; yy<sizeYOrg ; yy++)
 150                         {
 151 //                              ptrDst=(char*)( imgDst->GetScalarPointer(zz,0,sizeYOrg-yy-1) );
 152                                 for( xx=0 ; xx<sizeXOrg ; xx++)
 153                                 {
 154 //                                      ptrOrg=(char*)( imgOrg->GetScalarPointer(xx,yy,zz) );
 155 //                                      ptrDst=(char*)( imgDst->GetScalarPointer(zz,xx,sizeYOrg-yy-1) );
 156                                         memcpy ( ptrDst, ptrOrg , sizeBytes );
 157                                         ptrOrg+= sizeBytes;
 158                                         ptrDst+= sizeXDstBytes;
 159                                 } /// for xx
 160                                 ptrDst = ptrDst - sizeXYDstBytes2;
 161                         } // for yy
 162                         ptrDst = ptrDst + sizeXYZDstBytes;
 163 //                      ptrDst++;
 164                 } // for zz
 165         } // ZX
 166
 167         return imgDst;
 168 }
 169
 170 void ReadMHDPlane::Read64lseek(std::string fileNameIn, std::string plane)
 171 {
 172         int             slice;
 173         int             width;
 174         width = bbGetInputWidth();
 175         if (width<=0 ) { width=1; }
 176         slice = bbGetInputSlice();
 177         if (slice<0 ) { slice=0; }
 178         int             dimX=-1,dimY=-1,dimZ=-1;
 179         int             dim=-1;
 180         std::string formattype("VOID");
 181         std::string elementdatafile("VOID");
 182         float           spcX=-1,spcY=-1,spcZ=-1;
 183         float           ox=-1,oy=-1,oz=-1;
 184         long int        headersize=0;
 185         vtkImageData *newImage=NULL;
 186         char mystring[250];
 187         char strTmp[30];
 188         char strTmp2[30];
 189         FILE *ffIn      = fopen( fileNameIn.c_str() , "r");
 190         long long dataSize;
 191         if (ffIn!=NULL)
 192         {
 193                 newImage = vtkImageData::New();
 194                 while(!feof(ffIn))
 195                 {
 196             strcpy(mystring,"\n");
 197                         fgets(mystring,250,ffIn);
 198                 if (strncmp("NDims",mystring,5)==0)                     { sscanf(mystring,"%s %s %d"            ,strTmp, strTmp, &dim);                                                                 }
 199                 if (strncmp("DimSize",mystring,6)==0)                   { sscanf(mystring,"%s %s %d %d %d"      ,strTmp, strTmp, &dimX, &dimY,&dimZ);                                   }
 200                         if (strncmp("ElementType",mystring,11)==0)              { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); formattype=strTmp2;                  }
 201                         if (strncmp("ElementSpacing",mystring,14)==0)   { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &spcX,&spcY,&spcZ);                                    }
 202                         if (strncmp("ElementSize",mystring,11)==0)              { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &spcX,&spcY,&spcZ);                                    }
 203                 if (strncmp("Offset",mystring,6)==0)                    { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &ox, &oy, &oz);                                                }
 204                 if (strncmp("HeaderSize",mystring,10)==0)               { sscanf(mystring,"%s %s %ld"           ,strTmp, strTmp, &headersize);                                                  }
 205                         if (strncmp("ElementDataFile",mystring,15)==0)  { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2;             }
 206                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)                   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 207                 if (strncmp("ElementType = VTK_CHAR",mystring,22)==0)                   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 208                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)                  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 209                 if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0)  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 210                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0)                 { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 211                 if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 212                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)                  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 213                 if (strncmp("ElementType = VTK_SHORT",mystring,23)==0)                  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 214                 if (strncmp("ElementType = MET_UINT",mystring,22)==0)                   { newImage->SetScalarTypeToUnsignedInt();       dataSize=sizeof(unsigned int);  }
 215                 if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,30)==0)   { newImage->SetScalarTypeToUnsignedInt();       dataSize=sizeof(unsigned int);  }
 216                 if (strncmp("ElementType = MET_INT",mystring,21)==0)                    { newImage->SetScalarTypeToInt();                       dataSize=sizeof(int);                   }
 217                 if (strncmp("ElementType = VTK_INT",mystring,21)==0)                    { newImage->SetScalarTypeToInt();                       dataSize=sizeof(int);                   }
 218                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)                  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 219                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)                  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 220                 if (strncmp("ElementType = MET_LONG",mystring,22)==0)                   { newImage->SetScalarTypeToLong();                      dataSize=sizeof(long);                  }
 221                 if (strncmp("ElementType = VTK_LONG",mystring,22)==0)                   { newImage->SetScalarTypeToLong();                      dataSize=sizeof(long);                  }
 222                 if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0)                 { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 223                 if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0)                 { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 224         } // while
 225                 fclose(ffIn);
 226                 newImage->Initialize();
 227                 int             fd;
 228                 long long       ret;
 229                 std::size_t found;
 230                 std::string filename;
 231                 found                                   = fileNameIn.find_last_of("/\\");
 232                 filename                                = fileNameIn.substr(0,found+1) + elementdatafile ;
 233                 long long       pos;
 234                 long long lsize                 = dimX*dimY*width *dataSize;
 235 #if defined(_WIN32)
 236                    _sopen_s( &fd, filename.c_str(), _O_RDONLY, _SH_DENYNO, 0 );
 237 #else
 238                 fd = open ( filename.c_str() ,  O_RDONLY|O_LARGEFILE );
 239 #endif // defined(_WIN32)
 240                 if (fd < 0)
 241                 {
 242                         printf("EED ReadMHDPlane::Read64lseek   WARNNING! raw file not exist\n");
 243                         fprintf(stderr, "%s\n", strerror(errno));
 244                         newImage=CreateDefaultImage();
 245 //                      exit(1);
 246                 }
 247                 if ((plane=="XY") && (fd>=0))
 248                 {
 249                         newImage->SetSpacing( spcX,spcY,spcZ );
 250                         newImage->SetDimensions(  dimX,dimY,width );
 251                         newImage->SetWholeExtent(0,  dimX-1,0,dimY-1,0,width-1 );
 252                         newImage->SetExtent(0,  dimX-1,0,dimY-1,0,width-1 );
 253                         newImage->SetNumberOfScalarComponents(1);
 254                         newImage->AllocateScalars();
 255                         newImage->Update();
 256                         pos = dimX*dimY*(long long)slice*dataSize;
 257 #if defined(_WIN32)
 258                         if (_lseeki64( fd, pos, SEEK_SET ) < 0)
 259 #else
 260                         if (lseek64(fd, pos, SEEK_SET) < 0)
 261 #endif // defined(_WIN32)
 262                         {
 263                                 printf("EED ReadMHDPlane::Read64lseek \n");
 264                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 265                                 exit(1);
 266                         }
 267                         if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0)
 268                         {
 269                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 270                                 exit(1);
 271                         }
 272                 }  // if PLANE XY
 273                 if ((plane=="ZX") && (fd>=0))
 274                 {
 275                         newImage->SetSpacing( spcX,spcZ,spcY );
 276                         newImage->SetDimensions(  dimX,dimZ,width );
 277                         newImage->SetWholeExtent(0,  dimX-1,0,dimZ-1,0,width-1 );
 278                         newImage->SetExtent(0,  dimX-1,0,dimZ-1,0,width-1 );
 279                         newImage->SetNumberOfScalarComponents(1);
 280                         newImage->AllocateScalars();
 281                         newImage->Update();
 282                         int iWidth;
 283                         for (iWidth=0;iWidth<width;iWidth++)
 284                         {
 285                                 copy_ZX_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize);
 286                         }
 287                 }  // if PLANE XZ
 288                 if ((plane=="YZ") && (fd>=0))
 289                 {
 290                         newImage->SetSpacing( spcY,spcZ,spcX );
 291                         newImage->SetDimensions(  dimY,dimZ,width );
 292                         newImage->SetWholeExtent(0,  dimY-1,0,dimZ-1,0,width-1 );
 293                         newImage->SetExtent(0,  dimY-1,0,dimZ-1,0,width-1 );
 294                         newImage->SetNumberOfScalarComponents(1);
 295                         newImage->AllocateScalars();
 296                         newImage->Update();
 297                         int iWidth;
 298                         for (iWidth=0;iWidth<width;iWidth++)
 299                         {
 300                                 copy_YZ_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize);
 301                         }
 302                 }  // if PLANE YZ
 303 #if defined(_WIN32)
 304                 _close (fd);
 305 #else
 306                 close (fd);
 307 #endif // defined(_WIN32)
 308         } else {
 309                 newImage=CreateDefaultImage();
 310         } // if  ffIn
 311         bbSetOutputOut( newImage );
 312         bbSetOutputOut2( ChangeOrientation(newImage) );
 313 }
 314
 315
 316 void ReadMHDPlane::copy_YZ_plane(int fd,vtkImageData *newImage,int slice,int iWidth,int dimX,int dimY,int dimZ,int dataSize)
 317 {
 318         long long int j;
 319         long long int i;
 320         long long       ret;
 321         long long       pos;
 322         long long sizeBytesPlane = dimX*dimY*dataSize;
 323         char *pImage;
 324         for (j=0;j<dimZ;j++)
 325         {
 326                 for (i=0;i<dimY;i++)
 327                 {
 328                         pos = ((long long int)slice+iWidth + i*dimX + j*dimX*dimY)*dataSize ;
 329 #if defined(_WIN32)
 330                         if (_lseeki64( fd, pos , SEEK_SET ) < 0)
 331 #else
 332                         if (lseek64(fd, pos , SEEK_SET) < 0)
 333 #endif // defined(_WIN32)
 334                         {
 335                                 printf("EED ReadMHDPlane::Read64lseek \n");
 336                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 337                                 exit(1);
 338                         }
 339
 340                         pImage=(char*)(newImage->GetScalarPointer(i, dimZ-1-j,iWidth ));
 341                         if ((ret = read(fd, pImage , dataSize)) < 0)
 342                         {
 343                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 344                                 exit(1);
 345                         }
 346                         } // for i
 347                 } // for j
 348 }
 349
 350
 351 void ReadMHDPlane::copy_ZX_plane(int fd,vtkImageData *newImage,int slice,int iWidth,int dimX,int dimY,int dimZ,int dataSize)
 352 {
 353         long long int j;
 354         long long       ret;
 355         long long       pos;
 356         pos = dimX*(long long int)slice*dataSize;
 357         long long sizeBytesPlane = dimX*dimY*dataSize;
 358         char *pImage = (char*)( newImage->GetScalarPointer(0,0,iWidth) );
 359         for (j=dimZ-1;j>=0;j--)
 360         {
 361 #if defined(_WIN32)
 362                 if (_lseeki64( fd, pos + j*sizeBytesPlane , SEEK_SET ) < 0)
 363 #else
 364                 if (lseek64(fd, pos + j*sizeBytesPlane , SEEK_SET) < 0)
 365 #endif // defined(_WIN32)
 366                 {
 367                         printf("EED ReadMHDPlane::Read64lseek \n");
 368                         fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 369                         exit(1);
 370                 }
 371                 if ((ret = read(fd, pImage , dimX*dataSize)) < 0)
 372                 {
 373                         fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 374                         exit(1);
 375                 }
 376                 pImage = pImage+dimX*dataSize;
 377         } // for j
 378 }
 379
 380 void ReadMHDPlane::Process()
 381 {
 382         if (bbGetInputActive()==true)
 383         {
 384 printf("EED ReadMHDPlane::Process %d \n", bbGetInputSlice() );
 385                 if (bbGetInputType()==0)
 386                 {
 387                         //-- Split FileName
 388                         std::string inputfilename;
 389                         std::size_t found               =       bbGetInputFileName().find_last_of("/\\");
 390                         std::string path                =       bbGetInputFileName().substr(0,found+1);
 391                         std::string filename    =       bbGetInputFileName().substr(found+1);
 392         #ifdef _WIN32
 393                         path=path+"YZ_ZX\\";
 394         #else
 395                         path=path+"YZ_ZX/";
 396         #endif
 397                         if (bbGetInputDirectionPlane()=="XY") { inputfilename = bbGetInputFileName();           } // if XY
 398                         if (bbGetInputDirectionPlane()=="YZ") { inputfilename = path+filename+"_YZ.mhd";        } // if YZ
 399                         if (bbGetInputDirectionPlane()=="ZX") { inputfilename = path+filename+"_ZX.mhd";        } // if XZ
 400                         Read64lseek( inputfilename ,"XY");
 401                 }
 402                 if (bbGetInputType()==1)
 403                 {
 404                         Read64lseek( bbGetInputFileName(), bbGetInputDirectionPlane() );
 405                 }
 406         } // if active
 407 }
 408
 409 //=====
 410 // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
 411 //=====
 412 void ReadMHDPlane::bbUserSetDefaultValues()
 413 {
 414 //  SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX
 415 //    Here we initialize the input 'In' to 0
 416    bbSetInputActive(true);
 417    bbSetInputFileName("");
 418    bbSetInputSlice(0);
 419    bbSetInputType(1);
 420    bbSetInputWidth(1);
 421    bbSetInputDirectionPlane("XY");
 422 }
 423
 424 //=====
 425 // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
 426 //=====
 427 void ReadMHDPlane::bbUserInitializeProcessing()
 428 {
 429 //  THE INITIALIZATION METHOD BODY :
 430 //    Here does nothing
 431 //    but this is where you should allocate the internal/output pointers
 432 //    if any
 433 }
 434
 435 //=====
 436 // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
 437 //=====
 438 void ReadMHDPlane::bbUserFinalizeProcessing()
 439 {
 440 //  THE FINALIZATION METHOD BODY :
 441 //    Here does nothing
 442 //    but this is where you should desallocate the internal/output pointers
 443 //    if any
 444 }
 445
 446 } // EO namespace bbcreaVtk
 447
 448