tpcecat.h File Reference

Header file for libtpcecat. More...

#include "tpcclibConfig.h"
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdint.h>
#include <stdlib.h>
#include <strings.h>
#include <ctype.h>
#include <float.h>
#include <unistd.h>
#include <locale.h>
#include <time.h>
#include "tpcextensions.h"
#include "tpcift.h"

Go to the source code of this file.

Data Structures
struct	ECAT_MATDIR
struct	ECAT_MATRIXLIST
struct	ECAT_MATVAL

Macros
#define	BACKUP_EXTENSION   ".bak"
#define	ECATBLKSIZE   512

Functions
int	ecatReadBlock (const char *filename, FILE *fp, const unsigned int blocknumber, unsigned char *data)
int	ecatVerifyMagic (const char *filename, FILE *fp)
int	ecatWriteMainheader (IFT *ift, unsigned char *buf, TPCSTATUS *status)
int	ecatReadMainheader (const unsigned char *buf, IFT *ift, TPCSTATUS *status)
void	ecatMListInit (ECAT_MATRIXLIST *ml)
void	ecatMListFree (ECAT_MATRIXLIST *ml)
void	ecatMListReadId (int format, unsigned int id, ECAT_MATVAL *mv)
unsigned int	ecatMListMakeId (int format, unsigned int frame, unsigned int plane, unsigned int gate, unsigned int data, unsigned int bed)
unsigned int	ecatMValToId (int format, ECAT_MATVAL *mv)
int	ecatMListRead (int format, FILE *fp, ECAT_MATRIXLIST *ml, TPCSTATUS *status)
void	ecatMListPrint (int format, ECAT_MATRIXLIST *ml, FILE *fp)

Detailed Description

Header file for libtpcecat.

Author

Vesa Oikonen

Definition in file tpcecat.h.

Macro Definition Documentation

BACKUP_EXTENSION

#define BACKUP_EXTENSION   ".bak"

Backup file extension

Definition at line 31 of file tpcecat.h.

ECATBLKSIZE

#define ECATBLKSIZE   512

ECAT matrix block size

Definition at line 37 of file tpcecat.h.

Referenced by ecatMListRead(), ecatReadBlock(), ecatVerifyMagic(), and imgWrite().

Function Documentation

ecatMListFree()

void ecatMListFree

(

ECAT_MATRIXLIST *

ml

)

Free memory allocated for ECAT matrix list. All contents are destroyed.

Precondition

Before first use initialize the struct with ecatMListInit().

See also

ecatMListInit

Parameters

ml	Pointer to matrix list.

Definition at line 38 of file ecatmatrixlist.c.

  {
  if(ml==NULL) return;
  if(ml->matrixSpace>0) free((char*)(ml->matdir));
  ml->matrixSpace=ml->matrixNr=0;
}

Referenced by ecatMListRead().

ecatMListInit()

void ecatMListInit

(

ECAT_MATRIXLIST *

ml

)

Initiate the ECAT matrix list struct before any use.

See also

ecatMListFree, ecatMListRead, ecatMListPrint

Parameters

ml	Pointer to matrix list.

Definition at line 23 of file ecatmatrixlist.c.

  {
  if(ml==NULL) return;
  ml->matdir=NULL;
  ml->matrixSpace=ml->matrixNr=0;
}

ecatMListMakeId()

unsigned int ecatMListMakeId	(	int	format,
		unsigned int	frame,
		unsigned int	plane,
		unsigned int	gate,
		unsigned int	data,
		unsigned int	bed )

Make matrix identifier (matnum) code for specific matrix.

See also

ecatMListReadId, ecatMValToId

Returns

The matrix identifier.

Parameters

format	ECAT format: 6 or 7.
frame	Frame [0..511] for ECAT7, [0..4095] for ECAT6.
plane	Plane [0..1023] for ECAT7, [0..255] for ECAT6.
gate	Gate [0..63].
data	Data [0..7] for ECAT7, [0..3] for ECAT6.
bed	Bed position [0..15].

Definition at line 84 of file ecatmatrixlist.c.

  {
  if(format==7) {
    return(
      (frame & 0x1FF) |        /* frame */
      ((plane & 0x300) << 1) | /* plane high */
      ((data & 0x4) << 9) |    /* data high */
      ((bed & 0xF) << 12) |    /* bed */
      ((plane & 0xFF) << 16) | /* plane low */
      ((gate & 0x3F) << 24) |  /* gate */
      ((data & 0x3) << 30)     /* data low */
    );
  } else if(format==6) {
    return(
      (frame&0xFFF) |
      ((bed&0xF)<<12) |
      ((plane&0xFF)<<16) |
      ((gate&0x3F)<<24) |
      ((data&0x3)<<30)
    );
  }
  return(0);
}

Referenced by ecatMValToId().

ecatMListPrint()

void ecatMListPrint	(	int	format,
		ECAT_MATRIXLIST *	ml,
		FILE *	fp )

Print ECAT matrix list.

See also

ecatMListInit, ecatMListRead, ecatMListFree

Parameters

format	ECAT format: 6 or 7.
ml	Pointer to matrix list to print.
fp	File pointer to print to; usually stdout.

Definition at line 250 of file ecatmatrixlist.c.

  {
  if(ml==NULL || fp==NULL) return;
  ECAT_MATVAL mv;
 
  fprintf(fp, "nr\tmatrix\tpl\tfr\tgate\tbed\tstartblk\tblknr\n");
  for(unsigned int i=0; i<ml->matrixNr; i++) {
    ecatMListReadId(format, ml->matdir[i].id, &mv);
    fprintf(fp, "%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\n", i+1, ml->matdir[i].id,
      mv.plane, mv.frame, mv.gate, mv.bed,
      ml->matdir[i].strtblk, 1+ml->matdir[i].endblk-ml->matdir[i].strtblk);
  }
  return;
}

ecatMListRead()

int ecatMListRead	(	int	format,
		FILE *	fp,
		ECAT_MATRIXLIST *	ml,
		TPCSTATUS *	status )

Read ECAT matrix list from ECAT file.

See also

ecatMListInit, ecatMListPrint, ecatMListFree

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

format	ECAT format: 6 or 7.
fp	File pointer of file, opened with fp=fopen(filename, "rb"), to read the matrix list from.
ml	Pointer to initiated matrix list; any previous content is deleted.

Precondition

Matrix list must be initiated (once) before calling this.

Parameters

status

Pointer to status data; enter NULL if not needed.

Definition at line 140 of file ecatmatrixlist.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(verbose>0) {printf("%s(%d, ...)\n", __func__, format); fflush(stdout);}
 
  if(fp==NULL || ml==NULL)  {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_FAIL);
    return(TPCERROR_FAIL);
  }
 
  /* Is current platform little endian (1) or not (0) ? */
  int little=endianLittle();
  if(verbose>2) {
    if(little) printf("little endian platform\n"); else printf("big endian platform\n");
  }
 
  /* Make sure that matrix list is empty */
  ecatMListFree(ml);
 
  /* Read the blocks belonging to the matrix list */
  unsigned int blk=2; // Matrix list starts at block 2
  unsigned int blkNext=0, blkPrev=0, nrFree=0, nrUsed=0;
  unsigned int dirbuf[ECATBLKSIZE/4];
  do {
    /* Read the data block */
    if(verbose>1) printf("  reading block %u\n", blk);
    int ret=ecatReadBlock(NULL, fp, blk, (unsigned char*)dirbuf);
    if(ret!=TPCERROR_OK) {
      if(verbose>0) fprintf(stderr, "Error: cannot read block %u\n", blk);
      ecatMListFree(ml);
      statusSet(status, __func__, __FILE__, __LINE__, ret);
      return(ret);
    }
    /* Byte order conversion for integers in little/big endian platforms */
    if(little && format==7) swawbip(dirbuf, ECATBLKSIZE);
    if(!little && format==6) swawbip(dirbuf, ECATBLKSIZE);
    /* Read the "header" integers from the block */
    nrFree  = dirbuf[0];
    blkNext = dirbuf[1];
    blkPrev = dirbuf[2];
    nrUsed  = dirbuf[3];
    if(verbose>2)
      printf("nrFree=%u blkNext=%u blkPrev=%u nrUsed=%u\n", nrFree, blkNext, blkPrev, nrUsed);
    /* Allocate (more) memory for the matrix list */
    if(ml->matrixSpace==0) {
      ml->matrixSpace=ECATBLKSIZE/4;
      ml->matdir=(ECAT_MATDIR*)malloc(ml->matrixSpace*sizeof(ECAT_MATDIR));
    } else if(ml->matrixSpace<(ml->matrixNr+ECATBLKSIZE/4)) {
      ml->matrixSpace+=ECATBLKSIZE/4;
      ml->matdir=(ECAT_MATDIR*)realloc(ml->matdir, sizeof(ECAT_MATDIR)*ml->matrixSpace);
    }
    if(ml->matdir==NULL) {
      ecatMListFree(ml);
      statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OUT_OF_MEMORY);
      return(TPCERROR_OUT_OF_MEMORY);
    }
    /* Add the content of this block to the matrix list */
    for(unsigned int i=4; i<ECATBLKSIZE/4; i+=4) if(dirbuf[i]>0) {
      ml->matdir[ml->matrixNr].id=dirbuf[i];
      ml->matdir[ml->matrixNr].strtblk=dirbuf[i+1];
      ml->matdir[ml->matrixNr].endblk=dirbuf[i+2];
      ml->matdir[ml->matrixNr].status=dirbuf[i+3];
      if(verbose>3) {
        printf("matnum=%u strtblk=%u endblk=%u matstat=%u matrixNr=%u\n",
          ml->matdir[ml->matrixNr].id, ml->matdir[ml->matrixNr].strtblk,
          ml->matdir[ml->matrixNr].endblk, ml->matdir[ml->matrixNr].status,
          ml->matrixNr);
      }
      /* verify that referred data block can be found in the file */
      fpos_t current_fp; fgetpos(fp, &current_fp); // save current file position
      int ret=fseeko(fp, (off_t)(ml->matdir[ml->matrixNr].endblk-1)*ECATBLKSIZE, SEEK_SET);
      fsetpos(fp, &current_fp);  // back to saved file position
      if(ret==0) { // end block can be found
        ml->matrixNr++; // save this matrix into the list
      } else { // not found, file probably broken
        if(verbose>0) {
          printf("matnum %d points to data outside of file.\n", ml->matdir[ml->matrixNr].id);
          fflush(stdout);
        }
        // matrixNr not incremented, thus this matrix is left out of the list
      }
    }
    blk=blkNext;
  } while(feof(fp)==0 && blk>2);
 
  if(ml->matrixNr==0) {
    ecatMListFree(ml);
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_DATA);
    return(TPCERROR_NO_DATA);
  }
  if(verbose>1) printf("  matrixNr := %u\n", ml->matrixNr);
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(TPCERROR_OK);
}

ecatMListReadId()

void ecatMListReadId	(	int	format,
		unsigned int	id,
		ECAT_MATVAL *	mv )

Read matrix identifier code (matnum) into matrix value structure.

See also

ecatMListMakeId, ecatMValToId, ecatMListPrint

Parameters

format	ECAT format: 6 or 7.
id	Matrix identifier code (matnum) to decode.
mv	Pointer to data structure in where frame, plane etc numbers are written.

Definition at line 52 of file ecatmatrixlist.c.

  {
  if(mv==NULL) return;
  mv->frame=mv->plane=mv->gate=mv->data=mv->bed=0;
  if(format==7) {
    mv->frame = id & 0x1FF;
    mv->plane = ((id >> 16) & 0xFF) + ((id >> 1) & 0x300);
    mv->gate  = (id >> 24) & 0x3F;
    mv->data  = ((id >> 30) & 0x3) + ((id >> 9) & 0x4);
    mv->bed   = (id >> 12) & 0xF;
  } else if(format==6) {
    mv->frame = id&0xFFF;
    mv->plane = (id>>16)&0xFF;
    mv->gate  = (id>>24)&0x3F;
    mv->data  = (id>>30)&0x3;
    mv->bed   = (id>>12)&0xF;
  }
  return;
}

Referenced by ecatMListPrint().

ecatMValToId()

unsigned int ecatMValToId	(	int	format,
		ECAT_MATVAL *	mv )

Make matrix identifier (matnum) code for specific matrix.

See also

ecatMListReadId, ecatMListMakeId

Returns

The matrix identifier.

Parameters

format	ECAT format: 6 or 7.
mv	Pointer to data structure from where frame, plane etc numbers are read.

Definition at line 124 of file ecatmatrixlist.c.

  {
  if(mv==NULL) return(0);
  return(ecatMListMakeId(format, mv->frame, mv->plane, mv->gate, mv->data, mv->bed));
}

ecatReadBlock()

int ecatReadBlock	(	const char *	filename,
		FILE *	fp,
		const unsigned int	blocknumber,
		unsigned char *	data )

Read specified data block from an ECAT file.

See also

ecatVerifyMagic

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

filename	Name of file to open and read specified data block; file is closed after reading; enter NULL to use the file pointer (next argument) instead.
fp	File pointer of file, opened with fp=fopen(filename, "rb"), to read the specified data block from; enter NULL to open file (previous argument) locally. This function leaves the file pointer to the end of data block.
blocknumber	Block number to read; enter 0 to read the block from current file pointer position, if file pointer was given.
data	Pointer to write block data in; must be allocated for at least ECATBLKSIZE bytes.

Definition at line 23 of file ecatio.c.

  {
  if(filename==NULL && fp==NULL) return(TPCERROR_FAIL);
  if(data==NULL) return(TPCERROR_FAIL);
 
  if(fp!=NULL) { // read from given file pointer
 
    /* If block number was given, then seek the block */
    if(blocknumber>0) {
      if(fseeko(fp, (off_t)(blocknumber-1)*ECATBLKSIZE, SEEK_SET) != 0) 
        return(TPCERROR_NO_DATA);
    }
    /* Read the block */
    if(fread(data, ECATBLKSIZE, 1, fp)<1) return(TPCERROR_CANNOT_READ);
 
  } else { // read from given file name
 
    /* Open file for read */
    FILE *localfp=fopen(filename, "rb");
    if(localfp==NULL) return(TPCERROR_CANNOT_OPEN);
 
    /* If block number was given, then seek the block */
    if(blocknumber>0) {
      if(fseeko(localfp, (off_t)(blocknumber-1)*ECATBLKSIZE, SEEK_SET) != 0)
        {fclose(localfp); return(TPCERROR_NO_DATA);}
    }
    /* Read the block */
    if(fread(data, ECATBLKSIZE, 1, localfp)<1) {fclose(localfp); return(TPCERROR_CANNOT_READ);}
    fclose(localfp);
 
  }
 
  /* That's it then */
  return(TPCERROR_OK);
}

Referenced by ecatMListRead(), and ecatVerifyMagic().

ecatReadMainheader()

int ecatReadMainheader	(	const unsigned char *	buf,
		IFT *	ift,
		TPCSTATUS *	status )

Read ECAT main header from data block into IFT struct.

Remarks

Stub function.

See also

ecatWriteMainheader, ecatVerifyMagic

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

buf	Pointer to data block containing main header.
ift	Pointer to initiated IFT struct; any previous contents are NOT deleted.
status	Pointer to status data; enter NULL if not needed.

Definition at line 100 of file ecatheader.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(verbose>0) {printf("%s()\n", __func__); fflush(stdout);}
 
  if(buf==NULL || ift==NULL)  {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_FAIL);
    return(TPCERROR_FAIL);
  }
 
  /* Is current platform little endian (1) or not (0) ? */
  int little=endianLittle();
  if(verbose>1) {
    if(little) printf("little endian platform\n");
    else printf("big endian platform\n");
  }
 
  /* Check if the start matches the ECAT 7 magic numbers */
  int format=6;
  if(strncmp((char*)buf, "MATRIX72v", 9)==0 || strncmp((char*)buf, "MATRIX7011", 10)==0) format=7;
  if(verbose>1) {printf("format := %d\n", format); fflush(stdout);}
 
  /* Copy the header fields to IFT; byte swapping when necessary */
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FORMAT);
  char tmp[512];
 
  if(format==7) {
 
    strlcpy(tmp, (char*)buf+0, 15);
    if(iftPut(ift, "magic_number", tmp, 0, NULL)!=0) return(TPCERROR_INVALID_FORMAT);
    strlcpy(tmp, (char*)buf+14, 33);
    if(iftPut(ift, "original_file_name", tmp, 0, NULL)!=0) return(TPCERROR_INVALID_FORMAT);
 
  } else { // ECAT 6
 
    strlcpy(tmp, (char*)buf+0, 15);
    if(iftPut(ift, "magic_number", tmp, 0, NULL)!=0) return(TPCERROR_INVALID_FORMAT);
    strlcpy(tmp, (char*)buf+28, 21);
    if(iftPut(ift, "original_file_name", tmp, 0, NULL)!=0) return(TPCERROR_INVALID_FORMAT);
 
  }
 
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(TPCERROR_OK);
}

ecatVerifyMagic()

int ecatVerifyMagic	(	const char *	filename,
		FILE *	fp )

Verify that given file (either file name or file pointer) appears to be ECAT file, based on the magic number.

ECAT 7 has defined magic numbers, which are checked. ECAT 6 format does not a defined magic number, therefore here the file is only checked to not indicate anything else than ECAT 6.

Returns

Returns 0 if magic number is definitely not ECAT; 7 if ECAT 7 magic number is found, and 6 if magic number does not indicate anything other than ECAT 6.

Author

Vesa Oikonen

Parameters

filename	Name of file to open and to verify for the magic number; file is closed after reading; enter NULL to use the file pointer (next argument) instead.
fp	File pointer of file to check, opened with fp=fopen(filename, "rb"); enter NULL to open file (previous argument) locally. This function rewinds the file pointer to start before and after reading the data.

Definition at line 84 of file ecatio.c.

  {
 
  /* Read the first data block (512 bytes) */
  unsigned char buf[ECATBLKSIZE];
  int ret=ecatReadBlock(filename, fp, 0, buf);
  if(fp!=NULL) rewind(fp);
  if(ret!=TPCERROR_OK) return(0);
 
  /* Check if the start matches the ECAT 7 magic numbers */
  if(strncmp((char*)buf, "MATRIX72v", 9)==0 || strncmp((char*)buf, "MATRIX7011", 10)==0) return(7);
 
  /* ECAT 6 does not have defined magic numbers, but check anyway */
  if(strncmp((char*)buf, "MATRIX6", 7)==0 || strncmp((char*)buf, "ECAT6", 5)==0) return(6);
 
  /* Check that we do NOT have DICOM magic number */
  if(strncmp((char*)buf+128, "DICM", 4)==0) return(0);
 
  /* Check that we do NOT have NIfTI magic number */
  if(strncmp((char*)buf+344, "ni1", 3)==0 || strncmp((char*)buf, "n+1", 3)==0) return(0);
 
  /* Check that we do NOT have Interfile magic number */
  if(strncmp((char*)buf, "!INTERFILE", 10)==0) return(0);
 
  /* There is no indication that this IS NOT an ECAT 6 file */
  return(6);
}

ecatWriteMainheader()

int ecatWriteMainheader	(	IFT *	ift,
		unsigned char *	buf,
		TPCSTATUS *	status )

Write ECAT main header from IFT struct into data block.

Remarks

Stub function.

See also

ecatReadMainheader, ecatVerifyMagic

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

ift	Pointer to IFT struct containing main header fields; contents are not modified.
buf	Pointer to data block of size ECATBLKSIZE bytes.
status	Pointer to status data; enter NULL if not needed.

Definition at line 25 of file ecatheader.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(verbose>0) {printf("%s()\n", __func__); fflush(stdout);}
 
  if(ift==NULL || buf==NULL)  {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_FAIL);
    return(TPCERROR_FAIL);
  }
  if(ift->keyNr<1)  {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_MISSING_DATA);
    return(TPCERROR_MISSING_DATA);
  }
 
  /* Is current platform little endian (1) or not (0) ? */
  int little=endianLittle();
  if(verbose>1) {
    if(little) printf("little endian platform\n");
    else printf("big endian platform\n");
  }
 
  /* Determine ECAT format version */
  int format=6;
  /* If ECAT 7 magic_number not found, then assume ECAT 6 */
  int ii=iftFindKey(ift, "magic_number", 0);
  if(ii>=0) {
    if(strncmp(ift->item[ii].value, "MATRIX72v", 9)==0 || 
       strncmp(ift->item[ii].value, "MATRIX7011", 10)==0) format=7;
  }
  if(verbose>1) {printf("format := %d\n", format); fflush(stdout);}
 
  /* Copy the header fields; byte swapping when necessary */
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_MISSING_DATA);
  char tmp[512];
 
  if(format==7) {
 
    ii=iftFindKey(ift, "magic_number", 0);
    if(ii>=0) strlcpy(tmp, ift->item[ii].value, 15); else strcpy(tmp, "MATRIX72v");
    memcpy((char*)buf+0, tmp, 14);
 
    ii=iftFindKey(ift, "original_file_name", 0);
    if(ii>=0) strlcpy(tmp, ift->item[ii].value, 33); else strcpy(tmp, "");
    memcpy((char*)buf+14, tmp, 32);
 
  } else { // ECAT 6
 
    ii=iftFindKey(ift, "magic_number", 0);
    if(ii>=0) strlcpy(tmp, ift->item[ii].value, 15); else strcpy(tmp, "MATRIX6");
    memcpy((char*)buf+0, tmp, 14);
 
    ii=iftFindKey(ift, "original_file_name", 0);
    if(ii>=0) strlcpy(tmp, ift->item[ii].value, 21); else strcpy(tmp, "");
    memcpy((char*)buf+28, tmp, 20);
 
  }
 
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(TPCERROR_OK);
}

Referenced by imgWrite().