analyzeio.c File Reference

Procedures for Analyze images. More...

#include "tpcclibConfig.h"
#include "tpcnifti.h"

Go to the source code of this file.

Functions
int	anaExists (const char *filename, char *hdrfile, char *imgfile, char *siffile, ANALYZE_DSR *header, TPCSTATUS *status)
int	anaReadHeader (const char *filename, ANALYZE_DSR *dsr, int verbose)

Detailed Description

Procedures for Analyze images.

Definition in file analyzeio.c.

Function Documentation

anaExists()

int anaExists	(	const char *	filename,
		char *	hdrfile,
		char *	imgfile,
		char *	siffile,
		ANALYZE_DSR *	header,
		TPCSTATUS *	status )

Verify if specified file name is an Analyze 7.5 file.

Todo

Add tests.

See also

anaReadHeader, niftiExists, micropetExists

Returns

Returns 1 if it is Analyze, 0 if not.

Parameters

filename	File name, either header file, image file, or base name without extensions.
hdrfile	If file name refers to an Analyze file, then header file name will be written in this char pointer (space needs to allocated by caller); If header and image are combined, then this will be the name of combined file; enter NULL if not needed.
imgfile	If file name refers to an Analyze file, then image file name will be written in this char pointer (space needs to allocated by caller); If header and image are combined, then this will be the name of combined file; enter NULL if not needed.
siffile	If file name refers to an Analyze file, and if SIF exists, then SIF file name will be written in this char pointer (space needs to allocated by caller); enter NULL if not needed.
header	Pointer to Analyze header, which is filled in this function; enter NULL, if not needed.
status	Pointer to status data; enter NULL if not needed.

Definition at line 16 of file analyzeio.c.

  {
  int verbose=0; if(status!=NULL) verbose=status->verbose;
  if(verbose>0) {printf("%s(%s, ...)\n", __func__, filename); fflush(stdout);}
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
 
  /* Initiate output */
  if(hdrfile!=NULL) hdrfile[0]=(char)0;
  if(imgfile!=NULL) imgfile[0]=(char)0;
  if(siffile!=NULL) siffile[0]=(char)0;
 
  /* Empty file name means not Analyze file */
  if(strnlen(filename, 2)<1) {
    statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_INVALID_FILENAME);
    return(0);
  }
 
  /* Construct the base file name wo extensions */
  char basefile[FILENAME_MAX]; strlcpy(basefile, filename, FILENAME_MAX); 
  // If file exists it has extensions (similar than NIfTI-1)
  if(fileExist(basefile)) niftiBasename(basefile);
  if(verbose>1) printf("  basefile := %s\n", basefile);
 
  /* Combined header and image file exists? */
  int combined=0;
  char temp[FILENAME_MAX+10], localhdrfile[FILENAME_MAX];
  localhdrfile[0]=(char)0;
  strcpy(temp, basefile); strcat(temp, ".nii");
  if(fileExist(temp)) {
    if(verbose>1) printf("  %s exists.\n", temp);
    /* Preserve header and image file names */
    strcpy(localhdrfile, temp);
    if(hdrfile!=NULL) strlcpy(hdrfile, temp, FILENAME_MAX);
    if(imgfile!=NULL) strlcpy(imgfile, temp, FILENAME_MAX);
    combined=1;
  } else {
    if(verbose>1) printf("  %s does not exist.\n", temp);
    /* Not combined file, therefore check that header file exists */
    strcpy(temp, basefile); strcat(temp, ".hdr");
    if(!fileExist(temp)) {
      strcpy(temp, basefile); strcat(temp, ".img.hdr");
      if(!fileExist(temp)) {
        if(verbose>1) printf("  hdr file not found.\n");
        statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_MISSING_HEADER);
        return(0);
      }
    }
    /* Preserve file name of the header */
    strlcpy(localhdrfile, temp, FILENAME_MAX);
    if(hdrfile!=NULL) strlcpy(hdrfile, temp, FILENAME_MAX);
    if(verbose>1) printf("  %s is found.\n", localhdrfile);
    /* Not combined file, therefore check that image file exists */
    strcpy(temp, basefile); strcat(temp, ".img");
    if(!fileExist(temp)) {
      if(verbose>1) printf("  %s not found.\n", temp);
      statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_NO_FILE);
      return(0);
    }
    /* Preserve image filename */
    if(imgfile!=NULL) strlcpy(imgfile, temp, FILENAME_MAX);
    if(verbose>1) printf("  %s is found.\n", temp);
  }
  if(verbose>1) {printf("  combined := %d\n", combined); fflush(stdout);}
 
  /* Read header to check that this indeed is Analyze */
  {
    ANALYZE_DSR *dsr, local_dsr; if(header==NULL) dsr=&local_dsr; else dsr=header;
    int ret=anaReadHeader(localhdrfile, dsr, verbose-2);
    if(ret!=TPCERROR_OK) {
      if(verbose>1) {
        printf("  %s was not identified as Analyze header file.\n", localhdrfile); fflush(stdout);}
      statusSet(status, __func__, __FILE__, __LINE__, ret);
      return(0);
    }
    if(verbose>1) {printf("  %s is identified as Analyze.\n", localhdrfile); fflush(stdout);}
  }
 
  /* SIF exists? */
  strcpy(temp, basefile); strcat(temp, ".sif");
  if(verbose>3) printf("  checking if %s exists\n", temp);
  if(!fileExist(temp)) {
    strcpy(temp, basefile); strcat(temp, ".img.sif");
    if(verbose>3) printf("  checking if %s exists\n", temp);
    if(!fileExist(temp)) {
      strcpy(temp, basefile); strcat(temp, ".nii.sif");
      if(verbose>3) printf("  checking if %s exists\n", temp);
      if(!fileExist(temp)) {
        if(verbose>0) printf("  SIF not found or accessible.\n");
        statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
        return(1); // but otherwise ok NIfTI
      }
    }
  }
  /* Preserve SIF filename */
  if(siffile!=NULL) strcpy(siffile, temp);
  if(verbose>1) {printf("  %s is found.\n", temp); fflush(stdout);}
 
  statusSet(status, __func__, __FILE__, __LINE__, TPCERROR_OK);
  return(1);
}

Referenced by imgRead().

anaReadHeader()

int anaReadHeader	(	const char *	filename,
		ANALYZE_DSR *	dsr,
		int	verbose )

Read Analyze header contents.

Todo

Add tests.

See also

anaExists, micropetHeaderRead

Returns

enum tpcerror (TPCERROR_OK when successful).

Parameters

filename	Name of file to read (including path and extension).
dsr	Pointer to previously allocated header structure.
verbose	Verbose level; if zero, then nothing is printed to stderr or stdout

Definition at line 144 of file analyzeio.c.

  {
  if(verbose>0) {printf("%s(%s, ...)\n", __func__, filename); fflush(stdout);}
 
  /* Check arguments */
  if(strnlen(filename, 2)<1) return(TPCERROR_INVALID_FILENAME);
  if(dsr==NULL) 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");
  }
 
  /* Open file */
  FILE *fp=fopen(filename, "rb"); if(fp==NULL) return(TPCERROR_CANNOT_OPEN);
 
  /* Try to read the size of header, which should be stored in the beginning as
     4-byte integer in both NIfTI and Analyze header files. */
  int same_order=1;
  int hdrSize=0;
  {
    char buf[4];
    if(fread(buf, 4, 1, fp)<1) {fclose(fp); return(TPCERROR_CANNOT_READ);}
    memcpy(&hdrSize, buf, 4); 
    if(hdrSize!=ANALYZE_HEADER_SIZE && hdrSize!=NIFTI2_HEADER_SIZE) {
      swawbip(&hdrSize, 4); same_order=0;
    }
    if(verbose>1) {printf("  sizeof_hdr := %d\n", hdrSize); fflush(stdout);}
    if(hdrSize==NIFTI2_HEADER_SIZE) {
      if(verbose>1) {printf("  NIfTI-2 header size.\n"); fflush(stdout);}
      fclose(fp); return(TPCERROR_INVALID_FORMAT);
    } else if(hdrSize==ANALYZE_HEADER_SIZE) {
      if(verbose>1) {printf("  Analyze or NIfTI-1 header size.\n"); fflush(stdout);}
    } else {
      if(verbose>1) {printf("  invalid Analyze sizeof_hdr\n"); fflush(stdout);}
      return(TPCERROR_INVALID_FORMAT);
    }
  }
 
 
  /* Read file into Analyze header structure */
  if(verbose>1) {printf("  reading header as binary data\n"); fflush(stdout);}
  unsigned char buf[ANALYZE_HEADER_SIZE];
  if(fread(buf, ANALYZE_HEADER_SIZE, 1, fp)<1) {fclose(fp); return(TPCERROR_CANNOT_READ);}
  /* Close file */
  fclose(fp);
 
  /* Check that header does not have the Nifti Magic number */
  char magic[4]; 
  memcpy(magic, buf+344, 4); magic[3]=(char)0;
  if(strcasecmp(magic, "ni1")==0 || strcasecmp(magic, "n+1")==0) {
    if(verbose>1) {printf("  Nifti magic number was found"); fflush(stdout);}
    return(TPCERROR_INVALID_FORMAT);
  }
 
  /* Set the original byte order */
  if(same_order) dsr->byte_order=little;
  else {if(little==1) dsr->byte_order=0; else dsr->byte_order=1;}
 
  /* Set key header structure contents */
  dsr->h.sizeof_hdr=hdrSize;
  memcpy(dsr->h.data_type, buf+4, 10);
  memcpy(dsr->h.db_name, buf+14, 18);
  if(!same_order) swawbip(buf+32, 4);
  memcpy(&dsr->h.extents, buf+32, 4);
  if(!same_order) swabip(buf+36, 2);
  memcpy(&dsr->h.session_error, buf+36, 2);
  memcpy(&dsr->h.regular, buf+38, 1);
  memcpy(&dsr->h.hkey_un0, buf+39, 1);
 
  /* Set image dimension header structure contents */
  if(!same_order) swabip(buf+40, 16);
  memcpy(dsr->h.dim, buf+40, 16);
  if(!same_order) swabip(buf+56, 2);
  memcpy(&dsr->h.unused8, buf+56, 2);
  if(!same_order) swabip(buf+58, 2);
  memcpy(&dsr->h.unused9, buf+58, 2);
  if(!same_order) swabip(buf+60, 2);
  memcpy(&dsr->h.unused10, buf+60, 2);
  if(!same_order) swabip(buf+62, 2);
  memcpy(&dsr->h.unused11, buf+62, 2);
  if(!same_order) swabip(buf+64, 2);
  memcpy(&dsr->h.unused12, buf+64, 2);
  if(!same_order) swabip(buf+66, 2);
  memcpy(&dsr->h.unused13, buf+66, 2);
  if(!same_order) swabip(buf+68, 2);
  memcpy(&dsr->h.unused14, buf+68, 2);
  if(!same_order) swabip(buf+70, 2);
  memcpy(&dsr->h.datatype, buf+70, 2);
  if(!same_order) swabip(buf+72, 2);
  memcpy(&dsr->h.bitpix, buf+72, 2);
  if(!same_order) swabip(buf+74, 2);
  memcpy(&dsr->h.dim_un0, buf+74, 2);
  if(!same_order) swawbip(buf+76, 32);
  memcpy(dsr->h.pixdim, buf+76, 32);
  if(!same_order) swawbip(buf+108, 4);
  memcpy(&dsr->h.vox_offset, buf+108, 4);
  if(!same_order) swawbip(buf+112, 4);
  memcpy(&dsr->h.funused1, buf+112, 4);
  if(!same_order) swawbip(buf+116, 4);
  memcpy(&dsr->h.funused2, buf+116, 4);
  if(!same_order) swawbip(buf+120, 4);
  memcpy(&dsr->h.funused3, buf+120, 4);
  if(!same_order) swawbip(buf+124, 4);
  memcpy(&dsr->h.cal_max, buf+124, 4);
  if(!same_order) swawbip(buf+128, 4);
  memcpy(&dsr->h.cal_min, buf+128, 4);
  if(!same_order) swawbip(buf+132, 4);
  memcpy(&dsr->h.compressed, buf+132, 4);
  if(!same_order) swawbip(buf+136, 4);
  memcpy(&dsr->h.verified, buf+136, 4);
  if(!same_order) swawbip(buf+140, 4);
  memcpy(&dsr->h.glmax, buf+140, 4);
  if(!same_order) swawbip(buf+144, 4);
  memcpy(&dsr->h.glmin, buf+144, 4);
 
  /* Set data history header structure contents */
  memcpy(dsr->h.descrip, buf+148, 80);
  memcpy(dsr->h.aux_file, buf+228, 24);
  memcpy(&dsr->h.orient, buf+252, 1);
  memcpy(dsr->h.originator, buf+253, 10);
  memcpy(dsr->h.generated, buf+263, 10);
  memcpy(dsr->h.scannum, buf+273, 10);
  memcpy(dsr->h.patient_id, buf+283, 10);
  memcpy(dsr->h.exp_date, buf+293, 10);
  memcpy(dsr->h.exp_time, buf+303, 10);
  memcpy(dsr->h.hist_un0, buf+313, 3);
  if(!same_order) swawbip(buf+316, 4);
  memcpy(&dsr->h.views, buf+316, 4);
  if(!same_order) swawbip(buf+320, 4);
  memcpy(&dsr->h.vols_added, buf+320, 4);
  if(!same_order) swawbip(buf+324, 4);
  memcpy(&dsr->h.start_field, buf+324,4);
  if(!same_order) swawbip(buf+328, 4);
  memcpy(&dsr->h.field_skip, buf+328, 4);
  if(!same_order) swawbip(buf+332, 4);
  memcpy(&dsr->h.omax, buf+332, 4);
  if(!same_order) swawbip(buf+336, 4);
  memcpy(&dsr->h.omin, buf+336, 4);
  if(!same_order) swawbip(buf+340, 4);
  memcpy(&dsr->h.smax, buf+340, 4);
  if(!same_order) swawbip(buf+344, 4);
  memcpy(&dsr->h.smin, buf+344, 4);
 
  /* Check header contents */
  if(dsr->h.extents!=16384 && dsr->h.extents!=0) {
    if(verbose>0) printf("h.extents := %d\n", dsr->h.extents);
    return(TPCERROR_UNSUPPORTED);
  }
  if(dsr->h.regular!='r') {
    if(verbose>1) printf("h.regular := %c\n", dsr->h.regular);
    return(TPCERROR_UNSUPPORTED);
  }
 
  if(verbose>1) {printf("  complete Analyze header was read.\n"); fflush(stdout);}
 
  return(TPCERROR_OK);
}

Referenced by anaExists().