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