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         int slice;
  82         int width;
  83
  84         if (bbGetInputDirectionPlane()=="XY")
  85         {
  86                 inputfilename=bbGetInputFileName();
  87         } // if XY
  88
  89
  90         if ((bbGetInputDirectionPlane()=="YZ") || (bbGetInputDirectionPlane()=="ZX"))
  91         {
  92
  93                 //-- Split FileName
  94                 std::size_t found               =       bbGetInputFileName().find_last_of("/\\");
  95                 std::string path                =       bbGetInputFileName().substr(0,found+1);
  96                 std::string filename    =       bbGetInputFileName().substr(found+1);
  97 #ifdef _WIN32
  98                 path=path+"YZ_ZX\\";
  99 #else
 100                 path=path+"YZ_ZX/";
 101 #endif
 102
 103
 104                 if (bbGetInputDirectionPlane()=="YZ")
 105                 {
 106                         inputfilename = path+filename+"_YZ.mhd";
 107                 } // if YZ
 108
 109                 if (bbGetInputDirectionPlane()=="ZX")
 110                 {
 111                         inputfilename = path+filename+"_ZX.mhd";
 112                 } // XZ
 113         } // if YZ || XZ
 114
 115         width = bbGetInputWidth();
 116         if (width<=0 ) { width=1; }
 117
 118         slice = bbGetInputSlice();
 119         if (slice<0 ) { slice=0; }
 120
 121
 122         vtkImageData *newImage;
 123         long long int newHeaderSize;
 124     std::string newFileName=inputfilename+"-OneSlice";
 125
 126     int sx,sy,sz;
 127     char mystring[250];
 128     char strTmp[20];
 129         bool ok=true;
 130     FILE *ffIn  = fopen(inputfilename.c_str(),"r");
 131         if (ffIn!=NULL)
 132         {
 133             FILE *ffOut = fopen(newFileName.c_str(),"w");
 134
 135         while(!feof(ffIn))
 136         {
 137             strcpy(mystring,"\n");
 138                         fgets(mystring,250,ffIn);
 139                 if (strncmp("NDims",mystring,5)==0)
 140                         {
 141                                 if (width==1)
 142                                 {
 143                                         strcpy(mystring,"NDims = 2\n");
 144                                 } else {
 145                                         strcpy(mystring,"NDims = 3\n");
 146                                 }
 147                         }
 148                 if (strncmp("DimSize",mystring,6)==0)
 149                         {
 150                                 sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz);
 151
 152                                 if (width==1)
 153                                 {
 154                                         sprintf(mystring,"DimSize = %d %d\n",sx,sy);
 155                                 } else {
 156                                         sprintf(mystring,"DimSize = %d %d %d\n",sx,sy,width);
 157                                 }
 158
 159                         newHeaderSize = (long long int)sx*(long long int)sy*(long long int)slice;
 160                                 if (bbGetInputSlice()>=sz) {ok=false;}
 161                         } // if
 162                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)   { newHeaderSize=newHeaderSize*1; }
 163                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)  { newHeaderSize=newHeaderSize*1; }
 164                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
 165                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)  { newHeaderSize=newHeaderSize*2; }
 166                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)  { newHeaderSize=newHeaderSize*4; }
 167                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)  { newHeaderSize=newHeaderSize*4; }
 168                 if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
 169                 if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
 170                 if (strncmp("ElementDataFile",mystring,15)==0)
 171                         {
 172                                 fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize );
 173                         } // if
 174                 fprintf(ffOut,mystring);
 175         } // while
 176                 fclose(ffIn);
 177                 fclose(ffOut);
 178
 179                 if (ok==true)
 180                 {
 181                         vtkMetaImageReader * reader = vtkMetaImageReader::New();
 182                         reader->SetFileName( newFileName.c_str() );
 183                         reader->Update();
 184                         newImage = reader->GetOutput();
 185                 } // if ok
 186         } else {
 187                 ok=false;
 188                 printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() );
 189         }
 190
 191         if (ok==false)
 192         {
 193                 newImage=CreateDefaultImage();
 194         } // if ok
 195
 196         bbSetOutputOut( newImage );
 197 }
 198
 199
 200
 201
 202
 203 void ReadMHDPlane::Read64lseek()
 204 {
 205         int             slice;
 206         int             width;
 207
 208         width = bbGetInputWidth();
 209         if (width<=0 ) { width=1; }
 210
 211         slice = bbGetInputSlice();
 212         if (slice<0 ) { slice=0; }
 213
 214         int             dimX=-1,dimY=-1,dimZ=-1;
 215         int             dim=-1;
 216         std::string formattype("VOID");
 217         std::string elementdatafile("VOID");
 218         float           spcX=-1,spcY=-1,spcZ=-1;
 219         float           ox=-1,oy=-1,oz=-1;
 220         long int        headersize=0;
 221
 222         vtkImageData *newImage=NULL;
 223
 224         char mystring[250];
 225         char strTmp[30];
 226         char strTmp2[30];
 227         FILE *ffIn      = fopen(bbGetInputFileName().c_str(),"r");
 228 printf("EED ReadMHDPlane::Read64lseek filename %s %p\n", bbGetInputFileName().c_str(), ffIn );
 229         long long dataSize;
 230
 231         if (ffIn!=NULL)
 232         {
 233                 newImage = vtkImageData::New();
 234
 235                 while(!feof(ffIn))
 236                 {
 237             strcpy(mystring,"\n");
 238                         fgets(mystring,250,ffIn);
 239                 if (strncmp("NDims",mystring,5)==0)                     { sscanf(mystring,"%s %s %d"            ,strTmp, strTmp, &dim);                                 }
 240                 if (strncmp("DimSize",mystring,6)==0)                   { sscanf(mystring,"%s %s %d %d %d"      ,strTmp, strTmp, &dimX, &dimY,&dimZ);   }
 241                         if (strncmp("ElementType",mystring,11)==0)              { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); formattype=strTmp2;                  }
 242                         if (strncmp("ElementSpacing",mystring,14)==0)   { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &spcX,&spcY,&spcZ);    }
 243                         if (strncmp("ElementSize",mystring,11)==0)              { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &spcX,&spcY,&spcZ);    }
 244                 if (strncmp("Offset",mystring,6)==0)                    { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &ox, &oy, &oz);                }
 245                 if (strncmp("HeaderSize",mystring,10)==0)               { sscanf(mystring,"%s %s %ld"           ,strTmp, strTmp, &headersize);                  }
 246                         if (strncmp("ElementDataFile",mystring,15)==0)  { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2;             }
 247
 248                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)                   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 249                 if (strncmp("ElementType = VTK_CHAR",mystring,22)==0)                   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 250                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)                  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 251                 if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0)  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 252                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0)                 { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 253                 if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 254                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)                  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 255                 if (strncmp("ElementType = VTK_SHORT",mystring,23)==0)                  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 256                 if (strncmp("ElementType = MET_UINT",mystring,24)==0)                   { newImage->SetScalarTypeToUnsignedInt();       dataSize=sizeof(unsigned int);  }
 257                 if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,32)==0)   { newImage->SetScalarTypeToUnsignedInt();       dataSize=sizeof(unsigned int);  }
 258                 if (strncmp("ElementType = MET_INT",mystring,24)==0)                    { newImage->SetScalarTypeToInt();                       dataSize=sizeof(int);                   }
 259                 if (strncmp("ElementType = VTK_INT",mystring,32)==0)                    { newImage->SetScalarTypeToInt();                       dataSize=sizeof(int);                   }
 260                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)                  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 261                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)                  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 262                 if (strncmp("ElementType = MET_LONG",mystring,23)==0)                   { newImage->SetScalarTypeToLong();                      dataSize=sizeof(long);                  }
 263                 if (strncmp("ElementType = VTK_LONG",mystring,23)==0)                   { newImage->SetScalarTypeToLong();                      dataSize=sizeof(long);                  }
 264                 if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0)                 { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 265                 if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0)                 { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 266
 267         } // while
 268                 fclose(ffIn);
 269
 270                 newImage->Initialize();
 271
 272
 273                 int             fd;
 274                 long long       ret;
 275                 std::size_t found;
 276                 std::string filename;
 277                 found                                   = bbGetInputFileName().find_last_of("/\\");
 278                 filename                                = bbGetInputFileName().substr(0,found+1) + elementdatafile ;
 279                 long long       pos;
 280
 281                 long long lsize                 = dimX*dimY*width *dataSize;
 282
 283
 284 #if defined(_WIN32)
 285                    _sopen_s( &fd, filename.c_str(), _O_RDONLY, _SH_DENYNO, 0 );
 286 #else
 287                 fd = open ( filename.c_str() ,  O_RDONLY|O_LARGEFILE );
 288 #endif // defined(_WIN32)
 289
 290
 291                 if (fd < 0)
 292                 {
 293                         printf("EED ReadMHDPlane::Read64lseek   WARNNING! raw file not exist\n");
 294                         fprintf(stderr, "%s\n", strerror(errno));
 295                         newImage=CreateDefaultImage();
 296 //                      exit(1);
 297                 }
 298
 299
 300                 if ((bbGetInputDirectionPlane()=="XY") && (fd>=0))
 301                 {
 302                         newImage->SetSpacing( spcX,spcY,spcZ );
 303                         newImage->SetDimensions(  dimX,dimY,width );
 304                         newImage->SetWholeExtent(0,  dimX-1,0,dimY-1,0,width-1 );
 305                         newImage->SetExtent(0,  dimX-1,0,dimY-1,0,width-1 );
 306                         newImage->SetNumberOfScalarComponents(1);
 307                         newImage->AllocateScalars();
 308                         newImage->Update();
 309                         pos = dimX*dimY*(long long)slice*dataSize;
 310 #if defined(_WIN32)
 311                         if (_lseeki64( fd, pos, SEEK_SET ) < 0)
 312 #else
 313                         if (lseek64(fd, pos, SEEK_SET) < 0)
 314 #endif // defined(_WIN32)
 315                         {
 316                                 printf("EED ReadMHDPlane::Read64lseek \n");
 317                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 318                                 exit(1);
 319                         }
 320
 321                         if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0)
 322                         {
 323                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 324                                 exit(1);
 325                         }
 326                 }  // if PLANE XY
 327
 328                 if ((bbGetInputDirectionPlane()=="XZ") && (fd>=0))
 329                 {
 330                         newImage->SetSpacing( spcX,spcZ,spcY );
 331                         newImage->SetDimensions(  dimX,dimZ,width );
 332                         newImage->SetWholeExtent(0,  dimX-1,0,dimZ-1,0,width-1 );
 333                         newImage->SetExtent(0,  dimX-1,0,dimZ-1,0,width-1 );
 334                         newImage->SetNumberOfScalarComponents(1);
 335                         newImage->AllocateScalars();
 336                         newImage->Update();
 337                         int iWidth;
 338                         for (iWidth=0;iWidth<width;iWidth++)
 339                         {
 340                                 copy_XZ_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize);
 341                         }
 342                 }  // if PLANE XZ
 343
 344                 if ((bbGetInputDirectionPlane()=="YZ") && (fd>=0))
 345                 {
 346                         newImage->SetSpacing( spcY,spcZ,spcX );
 347                         newImage->SetDimensions(  dimY,dimZ,width );
 348                         newImage->SetWholeExtent(0,  dimY-1,0,dimZ-1,0,width-1 );
 349                         newImage->SetExtent(0,  dimY-1,0,dimZ-1,0,width-1 );
 350                         newImage->SetNumberOfScalarComponents(1);
 351                         newImage->AllocateScalars();
 352                         newImage->Update();
 353                         int iWidth;
 354                         for (iWidth=0;iWidth<width;iWidth++)
 355                         {
 356                                 copy_YZ_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize);
 357                         }
 358
 359                 }  // if PLANE YZ
 360 #if defined(_WIN32)
 361                 _close (fd);
 362 #else
 363                 close (fd);
 364 #endif // defined(_WIN32)
 365         } else {
 366                 newImage=CreateDefaultImage();
 367         } // if  ffIn
 368
 369         bbSetOutputOut( newImage );
 370 }
 371
 372
 373 void ReadMHDPlane::copy_YZ_plane(int fd,vtkImageData *newImage,int slice,int iWidth,int dimX,int dimY,int dimZ,int dataSize)
 374 {
 375         long long int j;
 376         long long int i;
 377         long long       ret;
 378         long long       pos;
 379         long long sizeBytesPlane = dimX*dimY*dataSize;
 380         char *pImage;
 381         for (j=0;j<dimZ;j++)
 382         {
 383                 for (i=0;i<dimY;i++)
 384                 {
 385                         pos = ((long long int)slice+iWidth + i*dimX + j*dimX*dimY)*dataSize ;
 386 #if defined(_WIN32)
 387                         if (_lseeki64( fd, pos , SEEK_SET ) < 0)
 388 #else
 389                         if (lseek64(fd, pos , SEEK_SET) < 0)
 390 #endif // defined(_WIN32)
 391                         {
 392                                 printf("EED ReadMHDPlane::Read64lseek \n");
 393                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 394                                 exit(1);
 395                         }
 396
 397                         pImage=(char*)(newImage->GetScalarPointer(i, dimZ-1-j,iWidth ));
 398                         if ((ret = read(fd, pImage , dataSize)) < 0)
 399                         {
 400                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 401                                 exit(1);
 402                         }
 403                         } // for i
 404                 } // for j
 405 }
 406
 407
 408 void ReadMHDPlane::copy_XZ_plane(int fd,vtkImageData *newImage,int slice,int iWidth,int dimX,int dimY,int dimZ,int dataSize)
 409 {
 410         long long int j;
 411         long long       ret;
 412         long long       pos;
 413         pos = dimX*(long long int)slice*dataSize;
 414         long long sizeBytesPlane = dimX*dimY*dataSize;
 415         char *pImage = (char*)( newImage->GetScalarPointer(0,0,iWidth) );
 416         for (j=dimZ-1;j>=0;j--)
 417         {
 418 #if defined(_WIN32)
 419                 if (_lseeki64( fd, pos + j*sizeBytesPlane , SEEK_SET ) < 0)
 420 #else
 421                 if (lseek64(fd, pos + j*sizeBytesPlane , SEEK_SET) < 0)
 422 #endif // defined(_WIN32)
 423                 {
 424                         printf("EED ReadMHDPlane::Read64lseek \n");
 425                         fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 426                         exit(1);
 427                 }
 428
 429                 if ((ret = read(fd, pImage , dimX*dataSize)) < 0)
 430                 {
 431                         fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 432                         exit(1);
 433                 }
 434                 pImage = pImage+dimX*dataSize;
 435         } // for j
 436 }
 437
 438
 439
 440 void ReadMHDPlane::Process()
 441 {
 442         if (bbGetInputType()==0)
 443         {
 444                 ReadNormalMHD();
 445         }
 446
 447         if (bbGetInputType()==1)
 448         {
 449                 Read64lseek();
 450         }
 451
 452 }
 453 //=====
 454 // 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)
 455 //=====
 456 void ReadMHDPlane::bbUserSetDefaultValues()
 457 {
 458
 459 //  SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX
 460 //    Here we initialize the input 'In' to 0
 461    bbSetInputFileName("");
 462    bbSetInputSlice(0);
 463    bbSetInputType(1);
 464    bbSetInputWidth(1);
 465    bbSetInputDirectionPlane("XY");
 466
 467 }
 468 //=====
 469 // 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)
 470 //=====
 471 void ReadMHDPlane::bbUserInitializeProcessing()
 472 {
 473
 474 //  THE INITIALIZATION METHOD BODY :
 475 //    Here does nothing
 476 //    but this is where you should allocate the internal/output pointers
 477 //    if any
 478
 479
 480 }
 481 //=====
 482 // 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)
 483 //=====
 484 void ReadMHDPlane::bbUserFinalizeProcessing()
 485 {
 486
 487 //  THE FINALIZATION METHOD BODY :
 488 //    Here does nothing
 489 //    but this is where you should desallocate the internal/output pointers
 490 //    if any
 491
 492 }
 493 }
 494 // EO namespace bbcreaVtk
 495
 496