#include "stdio.h"
+
+#define _LARGEFILE64_SOURCE
+
+#include <stdio.h>
+#include <sys/types.h>
+
+#if defined(_WIN32)
+#else
+#include <unistd.h>
+#endif // defined(_WIN32)
+
+#include <stdlib.h>
+#include <errno.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+
namespace bbcreaVtk
{
//=====
// 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
// bbSetOutputOut( bbGetInputIn() );
// std::cout << "Output value = " <<bbGetOutputOut() << std::endl;
+ std::string inputfilename;
+ if (bbGetInputDirectionPlane()=="XY")
+ {
+ inputfilename=bbGetInputFileName();
+ } // if XY
+
+
+ if ((bbGetInputDirectionPlane()=="YZ") || (bbGetInputDirectionPlane()=="ZX"))
+ {
+ //-- Split FileName
+ std::size_t found = bbGetInputFileName().find_last_of("/\\");
+ std::string path = bbGetInputFileName().substr(0,found+1);
+ std::string filename = bbGetInputFileName().substr(found+1);
+#ifdef _WIN32
+ path=path+"YZ_ZX\\";
+#else
+ path=path+"YZ_ZX/";
+#endif
+
+
+ if (bbGetInputDirectionPlane()=="YZ")
+ {
+ inputfilename = path+filename+"_YZ.mhd";
+ } // if YZ
- long int newHeaderSize;
- std::string newFileName=bbGetInputFileName()+"-OneSlice";
+ if (bbGetInputDirectionPlane()=="ZX")
+ {
+ inputfilename = path+filename+"_ZX.mhd";
+ } // XZ
+ } // if YZ || XZ
+
+ vtkImageData *newImage;
+ long long int newHeaderSize;
+ std::string newFileName=inputfilename+"-OneSlice";
int sx,sy,sz;
char mystring[250];
char strTmp[20];
- FILE *ffOut = fopen(newFileName.c_str(),"w+");
- FILE *ffIn = fopen(bbGetInputFileName().c_str(),"r+");
-
- while(!feof(ffIn))
- {
- strcpy(mystring,"\n");
- fgets(mystring,250,ffIn);
- if (strncmp("NDims",mystring,5)==0) {strcpy(mystring,"NDims = 2\n");}
- if (strncmp("DimSize",mystring,6)==0)
+ bool ok=true;
+ FILE *ffIn = fopen(inputfilename.c_str(),"r");
+ if (ffIn!=NULL)
{
- sscanf(mystring,"%s %s %d %d",strTmp, strTmp, &sx, &sy);
- sprintf(mystring,"DimSize = %d %d\n",sx,sy);
- newHeaderSize = sx*sy*bbGetInputSlice();
- }
- if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
- if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { newHeaderSize=newHeaderSize*2; }
- if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { newHeaderSize=newHeaderSize*2; }
- if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
- if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
- if (strncmp("ElementDataFile",mystring,15)==0)
+ FILE *ffOut = fopen(newFileName.c_str(),"w");
+
+ while(!feof(ffIn))
+ {
+ strcpy(mystring,"\n");
+ fgets(mystring,250,ffIn);
+ if (strncmp("NDims",mystring,5)==0) {strcpy(mystring,"NDims = 2\n");}
+ if (strncmp("DimSize",mystring,6)==0)
+ {
+ sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz);
+ sprintf(mystring,"DimSize = %d %d\n",sx,sy);
+ 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; }
+ if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) { newHeaderSize=newHeaderSize*1; }
+ if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
+ if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { newHeaderSize=newHeaderSize*2; }
+ if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { newHeaderSize=newHeaderSize*4; }
+ if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) { newHeaderSize=newHeaderSize*4; }
+ if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
+ if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
+ if (strncmp("ElementDataFile",mystring,15)==0)
+ {
+ fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize );
+ } // if
+ fprintf(ffOut,mystring);
+ } // while
+ fclose(ffIn);
+ fclose(ffOut);
+
+ if (ok==true)
+ {
+ vtkMetaImageReader * reader = vtkMetaImageReader::New();
+ reader->SetFileName( newFileName.c_str() );
+ reader->Update();
+ newImage = reader->GetOutput();
+ } // if ok
+ } else {
+ ok=false;
+ printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() );
+ }
+
+ if (ok==false)
{
- fprintf(ffOut,"HeaderSize = %ld\n\n", newHeaderSize );
- }
- fprintf(ffOut,mystring);
- }
-
-/*
- fprintf(ff,"ObjectType = Image\n");
- fprintf(ff,"NDims = 2\n");
- fprintf(ff,"BinaryData = True\n");
- fprintf(ff,"BinaryDataByteOrderMSB = False\n");
- fprintf(ff,"CompressedData = False\n");
- fprintf(ff,"TransformMatrix = 1 0 0 0 1 0 0 0 1\n");
- fprintf(ff,"CenterOfRotation = 0 0 0\n");
- fprintf(ff,"ElementSpacing = 0.7 0.7 0.7\n");
- fprintf(ff,"DimSize = 512 512\n");
- fprintf(ff,"AnatomicalOrientation = ???\n");
- fprintf(ff,"ElementType = MET_SHORT\n");
- fprintf(ff,"ElementNumberOfChannels = 1\n");
- fprintf(ff,"Offset = 0 0 0\n");
- fprintf(ff,"HeaderSize = %ld\n", newHeaderSize );
- fprintf(ff,"ElementDataFile = inspi1_ana.raw\n");
-*/
-
- fclose(ffIn);
- fclose(ffOut);
-
-
- vtkMetaImageReader * reader = vtkMetaImageReader::New();
- reader->SetFileName( newFileName.c_str() );
- reader->Update();
-
- bbSetOutputOut( reader->GetOutput() );
+ int i;
+ int sizeX, sizeY, sizeZ;
+ sizeX = 200;
+ sizeY = sizeX;
+ sizeZ = 1;
+ newImage = vtkImageData::New();
+ newImage->Initialize();
+ newImage->SetScalarTypeToUnsignedChar();
+ newImage->SetSpacing( 1,1,1 );
+ newImage->SetDimensions( sizeX,sizeY,sizeZ );
+ newImage->SetWholeExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
+ newImage->SetExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 );
+ newImage->SetNumberOfScalarComponents(1);
+ newImage->AllocateScalars();
+ newImage->Update();
+ memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
+ for (i=0; i<sizeX; i++)
+ {
+ newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
+ newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
+ } // for i
+ } // if ok
+
+ 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;
+
+
+#if defined(_WIN32)
+ _sopen_s( &fd, filename.c_str(), _O_RDONLY, _SH_DENYNO, 0 );
+#else
+ fd = open ( filename.c_str() , O_RDONLY|O_LARGEFILE );
+#endif // defined(_WIN32)
+
+
+
+ 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 defined(_WIN32)
+ if (_lseeki64( fd, pos, SEEK_SET ) < 0)
+#else
+ if (lseek64(fd, pos, SEEK_SET) < 0)
+#endif // defined(_WIN32)
+
+ {
+ 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;j<dimZ;j++)
+ {
+printf("EED EED ReadMHDPlane::Read64lseek XZ j=%d \n", j);
+ if (lseek64(fd, pos + j*sizeBytesPlane , 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, pImage , dimX*dataSize)) < 0)
+ {
+ fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+ exit(1);
+ }
+ pImage=pImage+dimX*dataSize;
+ } // for j
+ } // if PLANE XZ
+
+
+ if (bbGetInputDirectionPlane()=="YZ")
+ {
+ long long int j;
+ long long int i;
+ newImage->SetSpacing( 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;j<dimZ;j++)
+ {
+printf("EED EED ReadMHDPlane::Read64lseek YZ i=%d j=%d \n", i,j);
+ for (i=0;i<dimY;i++)
+ {
+ pos = ((long long int)bbGetInputSlice() + i*dimX + j*dimX*dimY)*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);
+ }
+
+ pImage=newImage->GetScalarPointer(i, j,0 );
+ if ((ret = read(fd, pImage , dataSize)) < 0)
+ {
+ fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+ exit(1);
+ }
+ }
+ } // for j
+ } // if PLANE YZ
+ */
+
+#if defined(_WIN32)
+ _close (fd);
+#else
+ close (fd);
+#endif // defined(_WIN32)
+
+ bbSetOutputOut( newImage );
+ } // if
+
+
+}
+
+
+void ReadMHDPlane::Process()
+{
+ if (bbGetInputType()==0)
+ {
+ ReadNormalMHD();
+ }
+
+ if (bbGetInputType()==1)
+ {
+ Read64lseek();
+ }
}
//=====
// Here we initialize the input 'In' to 0
bbSetInputFileName("");
bbSetInputSlice(0);
+ bbSetInputType(1);
+ bbSetInputDirectionPlane("XY");
}
//=====
git://git.creatis.insa-lyon.fr / creaVtk.git / blobdiff