From: Eduardo DAVILA Date: Fri, 22 Apr 2016 07:56:54 +0000 (+0200) Subject: #2711 creaVtk Feature New Normal - new Box ReadMHDPlane X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=b677e4fad72323711d5cc783d274628aea81bebe;p=creaVtk.git #2711 creaVtk Feature New Normal - new Box ReadMHDPlane --- diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx index ae2b8cc..56e8590 100644 --- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx +++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx @@ -6,6 +6,23 @@ #include "stdio.h" +#include +#include + + + + +#define _LARGEFILE64_SOURCE + +#include +#include +#include +#include +#include +#include +#include +#include + namespace bbcreaVtk { @@ -14,9 +31,9 @@ BBTK_BLACK_BOX_IMPLEMENTATION(ReadMHDPlane,bbtk::AtomicBlackBox); //===== // 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) //===== -void ReadMHDPlane::Process() -{ +void ReadMHDPlane::ReadNormalMHD() +{ // THE MAIN PROCESSING METHOD BODY // Here we simply set the input 'In' value to the output 'Out' // And print out the output value @@ -66,7 +83,7 @@ void ReadMHDPlane::Process() } // if YZ || XZ vtkImageData *newImage; - long int newHeaderSize; + long long int newHeaderSize; std::string newFileName=inputfilename+"-OneSlice"; int sx,sy,sz; @@ -87,7 +104,7 @@ void ReadMHDPlane::Process() { sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz); sprintf(mystring,"DimSize = %d %d\n",sx,sy); - newHeaderSize = sx*sy*bbGetInputSlice(); + newHeaderSize = (long long int)sx*(long long int)sy*(long long int)bbGetInputSlice(); if (bbGetInputSlice()>=sz) {ok=false;} } // if if (strncmp("ElementType = MET_CHAR",mystring,22)==0) { newHeaderSize=newHeaderSize*1; } @@ -100,7 +117,7 @@ void ReadMHDPlane::Process() if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");} if (strncmp("ElementDataFile",mystring,15)==0) { - fprintf(ffOut,"HeaderSize = %ld\n\n", newHeaderSize ); + fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize ); } // if fprintf(ffOut,mystring); } // while @@ -146,6 +163,198 @@ void ReadMHDPlane::Process() bbSetOutputOut( newImage ); +} + +void ReadMHDPlane::Read64lseek() +{ + + int dimX=-1,dimY=-1,dimZ=-1; + int dim=-1; + std::string formattype("VOID"); + std::string elementdatafile("VOID"); + float spcX=-1,spcY=-1,spcZ=-1; + float ox=-1,oy=-1,oz=-1; + long int headersize=0; + + vtkImageData *newImage; + + char mystring[250]; + char strTmp[30]; + char strTmp2[30]; + FILE *ffIn = fopen(bbGetInputFileName().c_str(),"r"); + long long dataSize; + + + + if (ffIn!=NULL) + { + newImage = vtkImageData::New(); + + while(!feof(ffIn)) + { + strcpy(mystring,"\n"); + fgets(mystring,250,ffIn); + if (strncmp("NDims",mystring,5)==0) { sscanf(mystring,"%s %s %d" ,strTmp, strTmp, &dim); } + if (strncmp("DimSize",mystring,6)==0) { sscanf(mystring,"%s %s %d %d %d" ,strTmp, strTmp, &dimX, &dimY,&dimZ); } + if (strncmp("ElementType",mystring,11)==0) { sscanf(mystring,"%s %s %s" ,strTmp, strTmp, strTmp2); formattype=strTmp2; } + if (strncmp("ElementSpacing",mystring,11)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &spcX,&spcY,&spcZ); } + if (strncmp("Offset",mystring,6)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &ox, &oy, &oz); } + if (strncmp("HeaderSize",mystring,10)==0) { sscanf(mystring,"%s %s %ld" ,strTmp, strTmp, &headersize); } + if (strncmp("ElementDataFile",mystring,15)==0) { sscanf(mystring,"%s %s %s" ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2; } + + if (strncmp("ElementType = MET_CHAR",mystring,22)==0) { newImage->SetScalarTypeToChar(); dataSize=sizeof(char); } + if (strncmp("ElementType = VTK_CHAR",mystring,22)==0) { newImage->SetScalarTypeToChar(); dataSize=sizeof(char); } + if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) { newImage->SetScalarTypeToUnsignedChar(); dataSize=sizeof(unsigned char); } + if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0) { newImage->SetScalarTypeToUnsignedChar(); dataSize=sizeof(unsigned char); } + if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newImage->SetScalarTypeToUnsignedShort(); dataSize=sizeof(unsigned short);} + if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort(); dataSize=sizeof(unsigned short);} + if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { newImage->SetScalarTypeToShort(); dataSize=sizeof(short); } + if (strncmp("ElementType = VTK_SHORT",mystring,23)==0) { newImage->SetScalarTypeToShort(); dataSize=sizeof(short); } + if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { newImage->SetScalarTypeToFloat(); dataSize=sizeof(float); } + if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) { newImage->SetScalarTypeToFloat(); dataSize=sizeof(float); } + if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble(); dataSize=sizeof(double); } + if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble(); dataSize=sizeof(double); } + + } // while + fclose(ffIn); + + newImage->Initialize(); + + + int fd; + long long ret; + std::size_t found; + std::string filename; + found = bbGetInputFileName().find_last_of("/\\"); + filename = bbGetInputFileName().substr(0,found+1) + elementdatafile ; + long long pos; + + long long lsize = dimX*dimY*1 *dataSize; + fd = open ( filename.c_str() , O_RDONLY|O_LARGEFILE ); + if (fd < 0) + { + printf("EED ReadMHDPlane::Read64lseek \n"); + fprintf(stderr, "%s\n", strerror(errno)); + exit(1); + } + + if (bbGetInputDirectionPlane()=="XY") + { + newImage->SetSpacing( spcX,spcY,spcZ ); + newImage->SetDimensions( dimX,dimY,1 ); + newImage->SetWholeExtent(0, dimX-1,0,dimY-1,0,0 ); + newImage->SetExtent(0, dimX-1,0,dimY-1,0,0 ); + newImage->SetNumberOfScalarComponents(1); + newImage->AllocateScalars(); + newImage->Update(); + pos = dimX*dimY*(long long)bbGetInputSlice()*dataSize; + if (lseek64(fd, pos, SEEK_SET) < 0) + { + printf("EED ReadMHDPlane::Read64lseek \n"); + fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno)); + exit(1); + } + + if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0) + { + fprintf(stderr, "Failed reading: %s\n", strerror(errno)); + exit(1); + } + } // if PLANE XY + + + if (bbGetInputDirectionPlane()=="XZ") + { + long long int j; + newImage->SetSpacing( spcX,spcZ,spcY ); + newImage->SetDimensions( dimX,dimZ,1 ); + newImage->SetWholeExtent(0, dimX-1,0,dimZ-1,0,0 ); + newImage->SetExtent(0, dimX-1,0,dimZ-1,0,0 ); + newImage->SetNumberOfScalarComponents(1); + newImage->AllocateScalars(); + newImage->Update(); + long long sizeBytesPlane = dimX*dimY*dataSize; + pos = dimX*(long long int)bbGetInputSlice()*dataSize; + void *pImage = newImage->GetScalarPointer(); + for (j=0;jSetSpacing( spcY,spcZ,spcX ); + newImage->SetDimensions( dimY,dimZ,1 ); + newImage->SetWholeExtent(0, dimY-1,0,dimZ-1,0,0 ); + newImage->SetExtent(0, dimY-1,0,dimZ-1,0,0 ); + newImage->SetNumberOfScalarComponents(1); + newImage->AllocateScalars(); + newImage->Update(); + long long sizeBytesPlane = dimX*dimY*dataSize; +// pos = dimX*(long long int)bbGetInputSlice()*dataSize; + void *pImage; + for (j=0;jGetScalarPointer(i, j,0 ); + if ((ret = read(fd, pImage , dataSize)) < 0) + { + fprintf(stderr, "Failed reading: %s\n", strerror(errno)); + exit(1); + } + } + } // for j + } // if PLANE XY + + + close (fd); + + bbSetOutputOut( newImage ); + } // if + + +} + + +void ReadMHDPlane::Process() +{ + if (bbGetInputType()==0) + { + ReadNormalMHD(); + } + + if (bbGetInputType()==1) + { + Read64lseek(); + } + } //===== // 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) @@ -157,6 +366,7 @@ void ReadMHDPlane::bbUserSetDefaultValues() // Here we initialize the input 'In' to 0 bbSetInputFileName(""); bbSetInputSlice(0); + bbSetInputType(0); bbSetInputDirectionPlane("XY"); } diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h index 53cc07c..8dfd228 100644 --- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h +++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h @@ -3,6 +3,12 @@ //===== #ifndef __bbcreaVtkReadMHDPlane_h_INCLUDED__ #define __bbcreaVtkReadMHDPlane_h_INCLUDED__ + + + + + + #include "bbcreaVtk_EXPORT.h" #include "bbtkAtomicBlackBox.h" #include "iostream" @@ -24,8 +30,13 @@ class bbcreaVtk_EXPORT ReadMHDPlane BBTK_DECLARE_INPUT(FileName,std::string); BBTK_DECLARE_INPUT(Slice,int); BBTK_DECLARE_INPUT(DirectionPlane,std::string); + BBTK_DECLARE_INPUT(Type,int); BBTK_DECLARE_OUTPUT(Out,vtkImageData*); BBTK_PROCESS(Process); + + void ReadNormalMHD(); + void Read64lseek(); + void Process(); //===== // 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) @@ -40,6 +51,7 @@ BBTK_BEGIN_DESCRIBE_BLACK_BOX(ReadMHDPlane,bbtk::AtomicBlackBox); BBTK_INPUT(ReadMHDPlane,FileName,"Image file name",std::string,""); BBTK_INPUT(ReadMHDPlane,Slice,"Slice number",int,""); BBTK_INPUT(ReadMHDPlane,DirectionPlane,"Direction plane: XY (default), YZ , XZ",std::string,""); + BBTK_INPUT(ReadMHDPlane,Type,"(0 default) 0 = Normal mhd, 1 = lseek64",int,""); BBTK_OUTPUT(ReadMHDPlane,Out,"Image 2D",vtkImageData*,""); BBTK_END_DESCRIBE_BLACK_BOX(ReadMHDPlane); //=====