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
  63 void ReadMHDPlane::ReadNormalMHD()
  64 {
  65 // THE MAIN PROCESSING METHOD BODY
  66 //   Here we simply set the input 'In' value to the output 'Out'
  67 //   And print out the output value
  68 // INPUT/OUTPUT ACCESSORS ARE OF THE FORM :
  69 //    void bbSet{Input|Output}NAME(const TYPE&)
  70 //    const TYPE& bbGet{Input|Output}NAME() const
  71 //    Where :
  72 //    * NAME is the name of the input/output
  73 //      (the one provided in the attribute 'name' of the tag 'input')
  74 //    * TYPE is the C++ type of the input/output
  75 //      (the one provided in the attribute 'type' of the tag 'input')
  76
  77 //    bbSetOutputOut( bbGetInputIn() );
  78 //    std::cout << "Output value = " <<bbGetOutputOut() << std::endl;
  79
  80         std::string inputfilename;
  81
  82         if (bbGetInputDirectionPlane()=="XY")
  83         {
  84                 inputfilename=bbGetInputFileName();
  85         } // if XY
  86
  87
  88         if ((bbGetInputDirectionPlane()=="YZ") || (bbGetInputDirectionPlane()=="ZX"))
  89         {
  90
  91                 //-- Split FileName
  92                 std::size_t found               =       bbGetInputFileName().find_last_of("/\\");
  93                 std::string path                =       bbGetInputFileName().substr(0,found+1);
  94                 std::string filename    =       bbGetInputFileName().substr(found+1);
  95 #ifdef _WIN32
  96                 path=path+"YZ_ZX\\";
  97 #else
  98                 path=path+"YZ_ZX/";
  99 #endif
 100
 101
 102                 if (bbGetInputDirectionPlane()=="YZ")
 103                 {
 104                         inputfilename = path+filename+"_YZ.mhd";
 105                 } // if YZ
 106
 107                 if (bbGetInputDirectionPlane()=="ZX")
 108                 {
 109                         inputfilename = path+filename+"_ZX.mhd";
 110                 } // XZ
 111         } // if YZ || XZ
 112
 113         vtkImageData *newImage;
 114         long long int newHeaderSize;
 115     std::string newFileName=inputfilename+"-OneSlice";
 116
 117     int sx,sy,sz;
 118     char mystring[250];
 119     char strTmp[20];
 120         bool ok=true;
 121     FILE *ffIn  = fopen(inputfilename.c_str(),"r");
 122         if (ffIn!=NULL)
 123         {
 124             FILE *ffOut = fopen(newFileName.c_str(),"w");
 125
 126         while(!feof(ffIn))
 127         {
 128             strcpy(mystring,"\n");
 129                         fgets(mystring,250,ffIn);
 130                 if (strncmp("NDims",mystring,5)==0) {strcpy(mystring,"NDims = 2\n");}
 131                 if (strncmp("DimSize",mystring,6)==0)
 132                         {
 133                                 sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz);
 134                                 sprintf(mystring,"DimSize = %d %d\n",sx,sy);
 135                         newHeaderSize = (long long int)sx*(long long int)sy*(long long int)bbGetInputSlice();
 136                                 if (bbGetInputSlice()>=sz) {ok=false;}
 137                         } // if
 138                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)   { newHeaderSize=newHeaderSize*1; }
 139                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)  { newHeaderSize=newHeaderSize*1; }
 140                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
 141                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)  { newHeaderSize=newHeaderSize*2; }
 142                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)  { newHeaderSize=newHeaderSize*4; }
 143                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)  { newHeaderSize=newHeaderSize*4; }
 144                 if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
 145                 if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
 146                 if (strncmp("ElementDataFile",mystring,15)==0)
 147                         {
 148                                 fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize );
 149                         } // if
 150                 fprintf(ffOut,mystring);
 151         } // while
 152                 fclose(ffIn);
 153                 fclose(ffOut);
 154
 155                 if (ok==true)
 156                 {
 157                         vtkMetaImageReader * reader = vtkMetaImageReader::New();
 158                         reader->SetFileName( newFileName.c_str() );
 159                         reader->Update();
 160                         newImage = reader->GetOutput();
 161                 } // if ok
 162         } else {
 163                 ok=false;
 164                 printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() );
 165         }
 166
 167         if (ok==false)
 168         {
 169                 newImage=CreateDefaultImage();
 170         } // if ok
 171
 172         bbSetOutputOut( newImage );
 173
 174 }
 175
 176 void ReadMHDPlane::Read64lseek()
 177 {
 178
 179         int             dimX=-1,dimY=-1,dimZ=-1;
 180         int             dim=-1;
 181         std::string formattype("VOID");
 182         std::string elementdatafile("VOID");
 183         float           spcX=-1,spcY=-1,spcZ=-1;
 184         float           ox=-1,oy=-1,oz=-1;
 185         long int        headersize=0;
 186
 187         vtkImageData *newImage=NULL;
 188
 189         char mystring[250];
 190         char strTmp[30];
 191         char strTmp2[30];
 192         FILE *ffIn      = fopen(bbGetInputFileName().c_str(),"r");
 193         long long dataSize;
 194
 195         if (ffIn!=NULL)
 196         {
 197                 newImage = vtkImageData::New();
 198
 199                 while(!feof(ffIn))
 200                 {
 201             strcpy(mystring,"\n");
 202                         fgets(mystring,250,ffIn);
 203                 if (strncmp("NDims",mystring,5)==0)                     { sscanf(mystring,"%s %s %d"            ,strTmp, strTmp, &dim);                                 }
 204                 if (strncmp("DimSize",mystring,6)==0)                   { sscanf(mystring,"%s %s %d %d %d"      ,strTmp, strTmp, &dimX, &dimY,&dimZ);   }
 205                         if (strncmp("ElementType",mystring,11)==0)              { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); formattype=strTmp2;                  }
 206                         if (strncmp("ElementSpacing",mystring,11)==0)   { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &spcX,&spcY,&spcZ);    }
 207                 if (strncmp("Offset",mystring,6)==0)                    { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &ox, &oy, &oz);                }
 208                 if (strncmp("HeaderSize",mystring,10)==0)               { sscanf(mystring,"%s %s %ld"           ,strTmp, strTmp, &headersize);                  }
 209                         if (strncmp("ElementDataFile",mystring,15)==0)  { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2;             }
 210
 211                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 212                 if (strncmp("ElementType = VTK_CHAR",mystring,22)==0)   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 213                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 214                 if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0)  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 215                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 216                 if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 217                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 218                 if (strncmp("ElementType = VTK_SHORT",mystring,23)==0)  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 219                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 220                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 221                 if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 222                 if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 223
 224         } // while
 225                 fclose(ffIn);
 226
 227                 newImage->Initialize();
 228
 229
 230                 int fd;
 231                 long long ret;
 232                 std::size_t found;
 233                 std::string filename;
 234                 found                                   =       bbGetInputFileName().find_last_of("/\\");
 235                 filename                                = bbGetInputFileName().substr(0,found+1) + elementdatafile ;
 236                 long long pos;
 237
 238                 long long lsize                 = dimX*dimY*1 *dataSize;
 239
 240
 241 #if defined(_WIN32)
 242                    _sopen_s( &fd, filename.c_str(), _O_RDONLY, _SH_DENYNO, 0 );
 243 #else
 244                 fd = open ( filename.c_str() ,  O_RDONLY|O_LARGEFILE );
 245 #endif // defined(_WIN32)
 246
 247
 248
 249                 if (fd < 0)
 250                 {
 251                         printf("EED ReadMHDPlane::Read64lseek \n");
 252                         fprintf(stderr, "%s\n", strerror(errno));
 253                         exit(1);
 254                 }
 255
 256                 if (bbGetInputDirectionPlane()=="XY")
 257                 {
 258                         newImage->SetSpacing( spcX,spcY,spcZ );
 259                         newImage->SetDimensions(  dimX,dimY,1 );
 260                         newImage->SetWholeExtent(0,  dimX-1,0,dimY-1,0,0 );
 261                         newImage->SetExtent(0,  dimX-1,0,dimY-1,0,0 );
 262                         newImage->SetNumberOfScalarComponents(1);
 263                         newImage->AllocateScalars();
 264                         newImage->Update();
 265                         pos = dimX*dimY*(long long)bbGetInputSlice()*dataSize;
 266 #if defined(_WIN32)
 267                         if (_lseeki64( fd, pos, SEEK_SET ) < 0)
 268 #else
 269                         if (lseek64(fd, pos, SEEK_SET) < 0)
 270 #endif // defined(_WIN32)
 271                         {
 272                                 printf("EED ReadMHDPlane::Read64lseek \n");
 273                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 274                                 exit(1);
 275                         }
 276
 277                         if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0)
 278                         {
 279                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 280                                 exit(1);
 281                         }
 282                 }  // if PLANE XY
 283
 284                 if (bbGetInputDirectionPlane()=="XZ")
 285                 {
 286                         long long int j;
 287                         newImage->SetSpacing( spcX,spcZ,spcY );
 288                         newImage->SetDimensions(  dimX,dimZ,1 );
 289                         newImage->SetWholeExtent(0,  dimX-1,0,dimZ-1,0,0 );
 290                         newImage->SetExtent(0,  dimX-1,0,dimZ-1,0,0 );
 291                         newImage->SetNumberOfScalarComponents(1);
 292                         newImage->AllocateScalars();
 293                         newImage->Update();
 294                         long long sizeBytesPlane = dimX*dimY*dataSize;
 295                         pos = dimX*(long long int)bbGetInputSlice()*dataSize;
 296                         char *pImage = (char*)(newImage->GetScalarPointer());
 297                         for (j=0;j<dimZ;j++)
 298                         {
 299 #if defined(_WIN32)
 300                                 if (_lseeki64( fd, pos + j*sizeBytesPlane , SEEK_SET ) < 0)
 301 #else
 302                                 if (lseek64(fd, pos + j*sizeBytesPlane , SEEK_SET) < 0)
 303 #endif // defined(_WIN32)
 304                                 {
 305                                         printf("EED ReadMHDPlane::Read64lseek \n");
 306                                         fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 307                                         exit(1);
 308                                 }
 309
 310                                 if ((ret = read(fd, pImage , dimX*dataSize)) < 0)
 311                                 {
 312                                         fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 313                                         exit(1);
 314                                 }
 315                                 pImage = pImage+dimX*dataSize;
 316                         } // for j
 317                 }  // if PLANE XZ
 318
 319
 320                 if (bbGetInputDirectionPlane()=="YZ")
 321                 {
 322                         long long int j;
 323                         long long int i;
 324                         newImage->SetSpacing( spcY,spcZ,spcX );
 325                         newImage->SetDimensions(  dimY,dimZ,1 );
 326                         newImage->SetWholeExtent(0,  dimY-1,0,dimZ-1,0,0 );
 327                         newImage->SetExtent(0,  dimY-1,0,dimZ-1,0,0 );
 328                         newImage->SetNumberOfScalarComponents(1);
 329                         newImage->AllocateScalars();
 330                         newImage->Update();
 331                         long long sizeBytesPlane = dimX*dimY*dataSize;
 332                         char *pImage;
 333                         for (j=0;j<dimZ;j++)
 334                         {
 335                                 for (i=0;i<dimY;i++)
 336                                 {
 337                                         pos = ((long long int)bbGetInputSlice() + i*dimX + j*dimX*dimY)*dataSize ;
 338 #if defined(_WIN32)
 339                                         if (_lseeki64( fd, pos , SEEK_SET ) < 0)
 340 #else
 341                                         if (lseek64(fd, pos , SEEK_SET) < 0)
 342 #endif // defined(_WIN32)
 343                                         {
 344                                                 printf("EED ReadMHDPlane::Read64lseek \n");
 345                                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 346                                                 exit(1);
 347                                         }
 348
 349                                         pImage=(char*)(newImage->GetScalarPointer(i, j,0 ));
 350                                         if ((ret = read(fd, pImage , dataSize)) < 0)
 351                                         {
 352                                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 353                                                 exit(1);
 354                                         }
 355                                 }
 356                         } // for j
 357                 }  // if PLANE YZ
 358 #if defined(_WIN32)
 359                 _close (fd);
 360 #else
 361                 close (fd);
 362 #endif // defined(_WIN32)
 363         } else {
 364                 newImage=CreateDefaultImage();
 365         } // if  ffIn
 366
 367         bbSetOutputOut( newImage );
 368
 369 }
 370
 371
 372 void ReadMHDPlane::Process()
 373 {
 374         if (bbGetInputType()==0)
 375         {
 376                 ReadNormalMHD();
 377         }
 378
 379         if (bbGetInputType()==1)
 380         {
 381                 Read64lseek();
 382         }
 383
 384 }
 385 //=====
 386 // 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)
 387 //=====
 388 void ReadMHDPlane::bbUserSetDefaultValues()
 389 {
 390
 391 //  SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX
 392 //    Here we initialize the input 'In' to 0
 393    bbSetInputFileName("");
 394    bbSetInputSlice(0);
 395    bbSetInputType(1);
 396    bbSetInputDirectionPlane("XY");
 397
 398 }
 399 //=====
 400 // 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)
 401 //=====
 402 void ReadMHDPlane::bbUserInitializeProcessing()
 403 {
 404
 405 //  THE INITIALIZATION METHOD BODY :
 406 //    Here does nothing
 407 //    but this is where you should allocate the internal/output pointers
 408 //    if any
 409
 410
 411 }
 412 //=====
 413 // 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)
 414 //=====
 415 void ReadMHDPlane::bbUserFinalizeProcessing()
 416 {
 417
 418 //  THE FINALIZATION METHOD BODY :
 419 //    Here does nothing
 420 //    but this is where you should desallocate the internal/output pointers
 421 //    if any
 422
 423 }
 424 }
 425 // EO namespace bbcreaVtk
 426
 427