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 #include <sys/types.h>
  10 #include <unistd.h>
  11
  12
  13
  14
  15 #define _LARGEFILE64_SOURCE
  16
  17 #include <stdio.h>
  18 #include <sys/types.h>
  19 #include <unistd.h>
  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 void ReadMHDPlane::ReadNormalMHD()
  36 {
  37 // THE MAIN PROCESSING METHOD BODY
  38 //   Here we simply set the input 'In' value to the output 'Out'
  39 //   And print out the output value
  40 // INPUT/OUTPUT ACCESSORS ARE OF THE FORM :
  41 //    void bbSet{Input|Output}NAME(const TYPE&)
  42 //    const TYPE& bbGet{Input|Output}NAME() const
  43 //    Where :
  44 //    * NAME is the name of the input/output
  45 //      (the one provided in the attribute 'name' of the tag 'input')
  46 //    * TYPE is the C++ type of the input/output
  47 //      (the one provided in the attribute 'type' of the tag 'input')
  48
  49 //    bbSetOutputOut( bbGetInputIn() );
  50 //    std::cout << "Output value = " <<bbGetOutputOut() << std::endl;
  51
  52         std::string inputfilename;
  53
  54         if (bbGetInputDirectionPlane()=="XY")
  55         {
  56                 inputfilename=bbGetInputFileName();
  57         } // if XY
  58
  59
  60         if ((bbGetInputDirectionPlane()=="YZ") || (bbGetInputDirectionPlane()=="ZX"))
  61         {
  62
  63                 //-- Split FileName
  64                 std::size_t found               =       bbGetInputFileName().find_last_of("/\\");
  65                 std::string path                =       bbGetInputFileName().substr(0,found+1);
  66                 std::string filename    =       bbGetInputFileName().substr(found+1);
  67 #ifdef _WIN32
  68                 path=path+"YZ_ZX\\";
  69 #else
  70                 path=path+"YZ_ZX/";
  71 #endif
  72
  73
  74                 if (bbGetInputDirectionPlane()=="YZ")
  75                 {
  76                         inputfilename = path+filename+"_YZ.mhd";
  77                 } // if YZ
  78
  79                 if (bbGetInputDirectionPlane()=="ZX")
  80                 {
  81                         inputfilename = path+filename+"_ZX.mhd";
  82                 } // XZ
  83         } // if YZ || XZ
  84
  85         vtkImageData *newImage;
  86         long long int newHeaderSize;
  87     std::string newFileName=inputfilename+"-OneSlice";
  88
  89     int sx,sy,sz;
  90     char mystring[250];
  91     char strTmp[20];
  92         bool ok=true;
  93     FILE *ffIn  = fopen(inputfilename.c_str(),"r");
  94         if (ffIn!=NULL)
  95         {
  96             FILE *ffOut = fopen(newFileName.c_str(),"w");
  97
  98         while(!feof(ffIn))
  99         {
 100             strcpy(mystring,"\n");
 101                         fgets(mystring,250,ffIn);
 102                 if (strncmp("NDims",mystring,5)==0) {strcpy(mystring,"NDims = 2\n");}
 103                 if (strncmp("DimSize",mystring,6)==0)
 104                         {
 105                                 sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz);
 106                                 sprintf(mystring,"DimSize = %d %d\n",sx,sy);
 107                         newHeaderSize = (long long int)sx*(long long int)sy*(long long int)bbGetInputSlice();
 108                                 if (bbGetInputSlice()>=sz) {ok=false;}
 109                         } // if
 110                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)   { newHeaderSize=newHeaderSize*1; }
 111                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)  { newHeaderSize=newHeaderSize*1; }
 112                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
 113                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)  { newHeaderSize=newHeaderSize*2; }
 114                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)  { newHeaderSize=newHeaderSize*4; }
 115                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)  { newHeaderSize=newHeaderSize*4; }
 116                 if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
 117                 if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
 118                 if (strncmp("ElementDataFile",mystring,15)==0)
 119                         {
 120                                 fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize );
 121                         } // if
 122                 fprintf(ffOut,mystring);
 123         } // while
 124                 fclose(ffIn);
 125                 fclose(ffOut);
 126
 127                 if (ok==true)
 128                 {
 129                         vtkMetaImageReader * reader = vtkMetaImageReader::New();
 130                         reader->SetFileName( newFileName.c_str() );
 131                         reader->Update();
 132                         newImage = reader->GetOutput();
 133                 } // if ok
 134         } else {
 135                 ok=false;
 136                 printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() );
 137         }
 138
 139         if (ok==false)
 140         {
 141                 int i;
 142                 int sizeX, sizeY, sizeZ;
 143                 sizeX = 200;
 144                 sizeY = sizeX;
 145                 sizeZ = 1;
 146                 newImage = vtkImageData::New();
 147                 newImage->Initialize();
 148                 newImage->SetScalarTypeToUnsignedChar();
 149                 newImage->SetSpacing( 1,1,1 );
 150                 newImage->SetDimensions(  sizeX,sizeY,sizeZ );
 151                 newImage->SetWholeExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
 152                 newImage->SetExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
 153                 newImage->SetNumberOfScalarComponents(1);
 154                 newImage->AllocateScalars();
 155                 newImage->Update();
 156                 memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
 157                 for (i=0; i<sizeX; i++)
 158                 {
 159                         newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
 160                         newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
 161                 } // for i
 162         } // if ok
 163
 164         bbSetOutputOut( newImage );
 165
 166 }
 167
 168 void ReadMHDPlane::Read64lseek()
 169 {
 170
 171         int             dimX=-1,dimY=-1,dimZ=-1;
 172         int             dim=-1;
 173         std::string formattype("VOID");
 174         std::string elementdatafile("VOID");
 175         float           spcX=-1,spcY=-1,spcZ=-1;
 176         float           ox=-1,oy=-1,oz=-1;
 177         long int        headersize=0;
 178
 179         vtkImageData *newImage;
 180
 181         char mystring[250];
 182         char strTmp[30];
 183         char strTmp2[30];
 184         FILE *ffIn      = fopen(bbGetInputFileName().c_str(),"r");
 185         long long dataSize;
 186
 187
 188
 189         if (ffIn!=NULL)
 190         {
 191                 newImage = vtkImageData::New();
 192
 193                 while(!feof(ffIn))
 194                 {
 195             strcpy(mystring,"\n");
 196                         fgets(mystring,250,ffIn);
 197                 if (strncmp("NDims",mystring,5)==0)                     { sscanf(mystring,"%s %s %d"            ,strTmp, strTmp, &dim);                                 }
 198                 if (strncmp("DimSize",mystring,6)==0)                   { sscanf(mystring,"%s %s %d %d %d"      ,strTmp, strTmp, &dimX, &dimY,&dimZ);   }
 199                         if (strncmp("ElementType",mystring,11)==0)              { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); formattype=strTmp2;                  }
 200                         if (strncmp("ElementSpacing",mystring,11)==0)   { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &spcX,&spcY,&spcZ);    }
 201                 if (strncmp("Offset",mystring,6)==0)                    { sscanf(mystring,"%s %s %f %f %f"      ,strTmp, strTmp, &ox, &oy, &oz);                }
 202                 if (strncmp("HeaderSize",mystring,10)==0)               { sscanf(mystring,"%s %s %ld"           ,strTmp, strTmp, &headersize);                  }
 203                         if (strncmp("ElementDataFile",mystring,15)==0)  { sscanf(mystring,"%s %s %s"            ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2;             }
 204
 205                 if (strncmp("ElementType = MET_CHAR",mystring,22)==0)   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 206                 if (strncmp("ElementType = VTK_CHAR",mystring,22)==0)   { newImage->SetScalarTypeToChar();                      dataSize=sizeof(char);                  }
 207                 if (strncmp("ElementType = MET_UCHAR",mystring,23)==0)  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 208                 if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0)  { newImage->SetScalarTypeToUnsignedChar();      dataSize=sizeof(unsigned char); }
 209                 if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 210                 if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort();     dataSize=sizeof(unsigned short);}
 211                 if (strncmp("ElementType = MET_SHORT",mystring,23)==0)  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 212                 if (strncmp("ElementType = VTK_SHORT",mystring,23)==0)  { newImage->SetScalarTypeToShort();                     dataSize=sizeof(short);                 }
 213                 if (strncmp("ElementType = MET_FLOAT",mystring,23)==0)  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 214                 if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0)  { newImage->SetScalarTypeToFloat();                     dataSize=sizeof(float);                 }
 215                 if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 216                 if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble();            dataSize=sizeof(double);                }
 217
 218         } // while
 219                 fclose(ffIn);
 220
 221                 newImage->Initialize();
 222
 223
 224                 int fd;
 225                 long long ret;
 226                 std::size_t found;
 227                 std::string filename;
 228                 found                                   =       bbGetInputFileName().find_last_of("/\\");
 229                 filename                                = bbGetInputFileName().substr(0,found+1) + elementdatafile ;
 230                 long long pos;
 231
 232                 long long lsize                 = dimX*dimY*1 *dataSize;
 233                 fd = open ( filename.c_str() ,  O_RDONLY|O_LARGEFILE );
 234                 if (fd < 0)
 235                 {
 236                         printf("EED ReadMHDPlane::Read64lseek \n");
 237                         fprintf(stderr, "%s\n", strerror(errno));
 238                         exit(1);
 239                 }
 240
 241                 if (bbGetInputDirectionPlane()=="XY")
 242                 {
 243                         newImage->SetSpacing( spcX,spcY,spcZ );
 244                         newImage->SetDimensions(  dimX,dimY,1 );
 245                         newImage->SetWholeExtent(0,  dimX-1,0,dimY-1,0,0 );
 246                         newImage->SetExtent(0,  dimX-1,0,dimY-1,0,0 );
 247                         newImage->SetNumberOfScalarComponents(1);
 248                         newImage->AllocateScalars();
 249                         newImage->Update();
 250                         pos = dimX*dimY*(long long)bbGetInputSlice()*dataSize;
 251                         if (lseek64(fd, pos, SEEK_SET) < 0)
 252                         {
 253                                 printf("EED ReadMHDPlane::Read64lseek \n");
 254                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 255                                 exit(1);
 256                         }
 257
 258                         if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0)
 259                         {
 260                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 261                                 exit(1);
 262                         }
 263                 }  // if PLANE XY
 264
 265
 266                 if (bbGetInputDirectionPlane()=="XZ")
 267                 {
 268                         long long int j;
 269                         newImage->SetSpacing( spcX,spcZ,spcY );
 270                         newImage->SetDimensions(  dimX,dimZ,1 );
 271                         newImage->SetWholeExtent(0,  dimX-1,0,dimZ-1,0,0 );
 272                         newImage->SetExtent(0,  dimX-1,0,dimZ-1,0,0 );
 273                         newImage->SetNumberOfScalarComponents(1);
 274                         newImage->AllocateScalars();
 275                         newImage->Update();
 276                         long long sizeBytesPlane = dimX*dimY*dataSize;
 277                         pos = dimX*(long long int)bbGetInputSlice()*dataSize;
 278                         void *pImage = newImage->GetScalarPointer();
 279                         for (j=0;j<dimZ;j++)
 280                         {
 281 printf("EED EED ReadMHDPlane::Read64lseek XZ j=%d \n", j);
 282                                 if (lseek64(fd, pos + j*sizeBytesPlane , SEEK_SET) < 0)
 283                                 {
 284                                         printf("EED ReadMHDPlane::Read64lseek \n");
 285                                         fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 286                                         exit(1);
 287                                 }
 288
 289                                 if ((ret = read(fd, pImage , dimX*dataSize)) < 0)
 290                                 {
 291                                         fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 292                                         exit(1);
 293                                 }
 294                                 pImage=pImage+dimX*dataSize;
 295                         } // for j
 296                 }  // if PLANE XY
 297
 298
 299                 if (bbGetInputDirectionPlane()=="YZ")
 300                 {
 301                         long long int j;
 302                         long long int i;
 303                         newImage->SetSpacing( spcY,spcZ,spcX );
 304                         newImage->SetDimensions(  dimY,dimZ,1 );
 305                         newImage->SetWholeExtent(0,  dimY-1,0,dimZ-1,0,0 );
 306                         newImage->SetExtent(0,  dimY-1,0,dimZ-1,0,0 );
 307                         newImage->SetNumberOfScalarComponents(1);
 308                         newImage->AllocateScalars();
 309                         newImage->Update();
 310                         long long sizeBytesPlane = dimX*dimY*dataSize;
 311 //                      pos = dimX*(long long int)bbGetInputSlice()*dataSize;
 312                         void *pImage;
 313                         for (j=0;j<dimZ;j++)
 314                         {
 315 printf("EED EED ReadMHDPlane::Read64lseek YZ i=%d j=%d \n", i,j);
 316                                 for (i=0;i<dimY;i++)
 317                                 {
 318                                         pos = ((long long int)bbGetInputSlice() + i*dimX + j*dimX*dimY)*dataSize ;
 319                                         if (lseek64(fd, pos  , SEEK_SET) < 0)
 320                                         {
 321                                                 printf("EED ReadMHDPlane::Read64lseek \n");
 322                                                 fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
 323                                                 exit(1);
 324                                         }
 325
 326                                         pImage=newImage->GetScalarPointer(i, j,0 );
 327                                         if ((ret = read(fd, pImage , dataSize)) < 0)
 328                                         {
 329                                                 fprintf(stderr, "Failed reading: %s\n", strerror(errno));
 330                                                 exit(1);
 331                                         }
 332                                 }
 333                         } // for j
 334                 }  // if PLANE XY
 335
 336
 337                 close (fd);
 338
 339                 bbSetOutputOut( newImage );
 340         } // if
 341
 342
 343 }
 344
 345
 346 void ReadMHDPlane::Process()
 347 {
 348         if (bbGetInputType()==0)
 349         {
 350                 ReadNormalMHD();
 351         }
 352
 353         if (bbGetInputType()==1)
 354         {
 355                 Read64lseek();
 356         }
 357
 358 }
 359 //=====
 360 // 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)
 361 //=====
 362 void ReadMHDPlane::bbUserSetDefaultValues()
 363 {
 364
 365 //  SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX
 366 //    Here we initialize the input 'In' to 0
 367    bbSetInputFileName("");
 368    bbSetInputSlice(0);
 369    bbSetInputType(0);
 370    bbSetInputDirectionPlane("XY");
 371
 372 }
 373 //=====
 374 // 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)
 375 //=====
 376 void ReadMHDPlane::bbUserInitializeProcessing()
 377 {
 378
 379 //  THE INITIALIZATION METHOD BODY :
 380 //    Here does nothing
 381 //    but this is where you should allocate the internal/output pointers
 382 //    if any
 383
 384
 385 }
 386 //=====
 387 // 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)
 388 //=====
 389 void ReadMHDPlane::bbUserFinalizeProcessing()
 390 {
 391
 392 //  THE FINALIZATION METHOD BODY :
 393 //    Here does nothing
 394 //    but this is where you should desallocate the internal/output pointers
 395 //    if any
 396
 397 }
 398 }
 399 // EO namespace bbcreaVtk
 400
 401