io.c

/*!
\file  io.c
\brief Various file I/O functions.

This file contains various functions that perform I/O.

\date Started 4/10/95
\author George
\version\verbatim $Id: io.c 18951 2015-08-08 20:10:46Z karypis $ \endverbatim
*/

#ifdef HAVE_GETLINE
/* Get getline to be defined. */
#define _GNU_SOURCE
#include <stdio.h>
#undef _GNU_SOURCE
#endif

#include <GKlib.h>

/*************************************************************************
* This function opens a file
**************************************************************************/
FILE *gk_fopen(char *fname, char *mode, const char *msg)
{
  FILE *fp;
  char errmsg[8192];

  fp = fopen(fname, mode);
  if (fp != NULL)
    return fp;

  sprintf(errmsg,"file: %s, mode: %s, [%s]", fname, mode, msg);
  perror(errmsg);
  errexit("Failed on gk_fopen()\n");

  return NULL;
}


/*************************************************************************
* This function closes a file
**************************************************************************/
void gk_fclose(FILE *fp)
{
  fclose(fp);
}


/*************************************************************************/
/*! This function is a wrapper around the read() function that ensures 
    that all data is been read, by issuing multiple read requests.
    The only time when not 'count' items are read is when the EOF has been
    reached.
*/
/*************************************************************************/
ssize_t gk_read(int fd, void *vbuf, size_t count)
{
  char *buf = (char *)vbuf;
  ssize_t rsize, tsize=count;

  do {
    if ((rsize = read(fd, buf, tsize)) == -1)
      return -1;
    buf   += rsize;
    tsize -= rsize;
  } while (tsize > 0 && rsize > 0);

  return count-tsize;
}


/*************************************************************************/
/*! This function is a wrapper around the write() function that ensures 
    that all data is been written, by issueing multiple write requests.
*/
/*************************************************************************/
ssize_t gk_write(int fd, void *vbuf, size_t count)
{
  char *buf = (char *)vbuf;
  ssize_t size, tsize=count;

  do {
    if ((size = write(fd, buf, tsize)) == -1)
      return -1;
    buf   += size;
    tsize -= size;
  } while (tsize > 0);

  return count;
}


/*************************************************************************/
/*! This function is the GKlib implementation of glibc's getline()
    function.
    \returns -1 if the EOF has been reached, otherwise it returns the 
             number of bytes read.
*/
/*************************************************************************/
ssize_t gk_getline(char **lineptr, size_t *n, FILE *stream)
{
#ifdef HAVE_GETLINE
  return getline(lineptr, n, stream);
#else
  size_t i;
  int ch;

  if (feof(stream))
    return -1;  

  /* Initial memory allocation if *lineptr is NULL */
  if (*lineptr == NULL || *n == 0) {
    *n = 1024;
    *lineptr = gk_malloc((*n)*sizeof(char), "gk_getline: lineptr");
  }

  /* get into the main loop */
  i = 0;
  while ((ch = getc(stream)) != EOF) {
    (*lineptr)[i++] = (char)ch;

    /* reallocate memory if reached at the end of the buffer. The +1 is for '\0' */
    if (i+1 == *n) { 
      *n = 2*(*n);
      *lineptr = gk_realloc(*lineptr, (*n)*sizeof(char), "gk_getline: lineptr");
    }
      
    if (ch == '\n')
      break;
  }
  (*lineptr)[i] = '\0';

  return (i == 0 ? -1 : i);
#endif
}


/*************************************************************************/
/*! This function reads the contents of a text file and returns it in the
    form of an array of strings.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
char **gk_readfile(char *fname, size_t *r_nlines)
{
  size_t lnlen, nlines=0;
  char *line=NULL, **lines=NULL;
  FILE *fpin;

  gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
  if (nlines > 0) {
    lines = (char **)gk_malloc(nlines*sizeof(char *), "gk_readfile: lines");

    fpin = gk_fopen(fname, "r", "gk_readfile");
    nlines = 0;
    while (gk_getline(&line, &lnlen, fpin) != -1) {
      gk_strtprune(line, "\n\r");
      lines[nlines++] = gk_strdup(line);
    }
    gk_fclose(fpin);
  }

  gk_free((void **)&line, LTERM);

  if (r_nlines != NULL)
    *r_nlines  = nlines;

  return lines;
}


/*************************************************************************/
/*! This function reads the contents of a file and returns it in the
    form of an array of int32_t.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
int32_t *gk_i32readfile(char *fname, size_t *r_nlines)
{
  size_t lnlen, nlines=0;
  char *line=NULL;
  int32_t *array=NULL;
  FILE *fpin;

  gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
  if (nlines > 0) {
    array = gk_i32malloc(nlines, "gk_i32readfile: array");

    fpin = gk_fopen(fname, "r", "gk_readfile");
    nlines = 0;

    while (gk_getline(&line, &lnlen, fpin) != -1) {
      sscanf(line, "%"SCNd32, &array[nlines++]);
    }

    gk_fclose(fpin);
  }

  gk_free((void **)&line, LTERM);

  if (r_nlines != NULL)
    *r_nlines  = nlines;

  return array;
}

/*************************************************************************/
/*! This function reads the contents of a file and returns it in the
    form of an array of int64_t.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
int64_t *gk_i64readfile(char *fname, size_t *r_nlines)
{
  size_t lnlen, nlines=0;
  char *line=NULL;
  int64_t *array=NULL;
  FILE *fpin;

  gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
  if (nlines > 0) {
    array = gk_i64malloc(nlines, "gk_i64readfile: array");

    fpin = gk_fopen(fname, "r", "gk_readfile");
    nlines = 0;

    while (gk_getline(&line, &lnlen, fpin) != -1) {
      sscanf(line, "%"SCNd64, &array[nlines++]);
    }

    gk_fclose(fpin);
  }

  gk_free((void **)&line, LTERM);

  if (r_nlines != NULL)
    *r_nlines  = nlines;

  return array;
}

/*************************************************************************/
/*! This function reads the contents of a file and returns it in the
    form of an array of ssize_t.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
ssize_t *gk_zreadfile(char *fname, size_t *r_nlines)
{
  size_t lnlen, nlines=0;
  char *line=NULL;
  ssize_t *array=NULL;
  FILE *fpin;

  gk_getfilestats(fname, &nlines, NULL, NULL, NULL);
  if (nlines > 0) {
    array = gk_zmalloc(nlines, "gk_zreadfile: array");

    fpin = gk_fopen(fname, "r", "gk_readfile");
    nlines = 0;

    while (gk_getline(&line, &lnlen, fpin) != -1) {
      sscanf(line, "%zd", &array[nlines++]);
    }

    gk_fclose(fpin);
  }

  gk_free((void **)&line, LTERM);

  if (r_nlines != NULL)
    *r_nlines  = nlines;

  return array;
}

/*************************************************************************/
/*! This function reads the contents of a binary file and returns it in the
    form of an array of char.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
char *gk_creadfilebin(char *fname, size_t *r_nelmnts)
{
  size_t nelmnts;
  ssize_t fsize;
  char *array=NULL;
  FILE *fpin;

  *r_nelmnts = 0;

  fsize = gk_getfsize(fname);

  if (fsize == -1) {
    gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname);
    return NULL;
  }

  nelmnts = fsize;
  array = gk_cmalloc(nelmnts, "gk_creadfilebin: array");

  fpin = gk_fopen(fname, "rb", "gk_creadfilebin");
  if (fread(array, sizeof(char), nelmnts, fpin) != nelmnts) {
    gk_errexit(SIGERR, "Failed to read the number of words requested. %zu\n", nelmnts);
    gk_free((void **)&array, LTERM);
    return NULL;
  }
  gk_fclose(fpin);

  *r_nelmnts = nelmnts;

  return array;
}

/*************************************************************************/
/*! This function writes the contents of an array into a binary file.
    \param fname is the name of the file
    \param n the number of elements in the array.
    \param a the array to be written out.
*/
/*************************************************************************/
size_t gk_cwritefilebin(char *fname, size_t n, char *a)
{
  size_t fsize;
  FILE *fp;

  fp = gk_fopen(fname, "wb", "gk_writefilebin");

  fsize = fwrite(a, sizeof(char), n, fp);

  gk_fclose(fp);

  return fsize;
}

/*************************************************************************/
/*! This function reads the contents of a binary file and returns it in the
    form of an array of int32_t.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
int32_t *gk_i32readfilebin(char *fname, size_t *r_nelmnts)
{
  size_t nelmnts;
  ssize_t fsize;
  int32_t *array=NULL;
  FILE *fpin;

  *r_nelmnts = 0;

  fsize = gk_getfsize(fname);

  if (fsize == -1) {
    gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname);
    return NULL;
  }

  if (fsize%sizeof(int32_t) != 0) {
    gk_errexit(SIGERR, "The size [%zd] of the file [%s] is not in multiples of sizeof(int32_t).\n", fsize, fname);
    return NULL;
  }

  nelmnts = fsize/sizeof(int32_t);
  array = gk_i32malloc(nelmnts, "gk_i32readfilebin: array");

  fpin = gk_fopen(fname, "rb", "gk_i32readfilebin");
  
  if (fread(array, sizeof(int32_t), nelmnts, fpin) != nelmnts) {
    gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
    gk_free((void **)&array, LTERM);
    return NULL;
  }
  gk_fclose(fpin);

  *r_nelmnts = nelmnts;

  return array;
}

/*************************************************************************/
/*! This function writes the contents of an array into a binary file.
    \param fname is the name of the file
    \param n the number of elements in the array.
    \param a the array to be written out.
*/
/*************************************************************************/
size_t gk_i32writefilebin(char *fname, size_t n, int32_t *a)
{
  size_t fsize;
  FILE *fp;

  fp = gk_fopen(fname, "wb", "gk_writefilebin");

  fsize = fwrite(a, sizeof(int32_t), n, fp);

  gk_fclose(fp);

  return fsize;
}

/*************************************************************************/
/*! This function reads the contents of a binary file and returns it in the
    form of an array of int64_t.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
int64_t *gk_i64readfilebin(char *fname, size_t *r_nelmnts)
{
  size_t nelmnts;
  ssize_t fsize;
  int64_t *array=NULL;
  FILE *fpin;

  *r_nelmnts = 0;

  fsize = gk_getfsize(fname);

  if (fsize == -1) {
    gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname);
    return NULL;
  }

  if (fsize%sizeof(int64_t) != 0) {
    gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(int64_t).\n");
    return NULL;
  }

  nelmnts = fsize/sizeof(int64_t);
  array = gk_i64malloc(nelmnts, "gk_i64readfilebin: array");

  fpin = gk_fopen(fname, "rb", "gk_i64readfilebin");
  
  if (fread(array, sizeof(int64_t), nelmnts, fpin) != nelmnts) {
    gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
    gk_free((void **)&array, LTERM);
    return NULL;
  }
  gk_fclose(fpin);

  *r_nelmnts = nelmnts;

  return array;
}

/*************************************************************************/
/*! This function writes the contents of an array into a binary file.
    \param fname is the name of the file
    \param n the number of elements in the array.
    \param a the array to be written out.
*/
/*************************************************************************/
size_t gk_i64writefilebin(char *fname, size_t n, int64_t *a)
{
  size_t fsize;
  FILE *fp;

  fp = gk_fopen(fname, "wb", "gk_writefilebin");

  fsize = fwrite(a, sizeof(int64_t), n, fp);

  gk_fclose(fp);

  return fsize;
}

/*************************************************************************/
/*! This function reads the contents of a binary file and returns it in the
    form of an array of ssize_t.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
ssize_t *gk_zreadfilebin(char *fname, size_t *r_nelmnts)
{
  size_t nelmnts;
  ssize_t fsize;
  ssize_t *array=NULL;
  FILE *fpin;

  *r_nelmnts = 0;

  fsize = gk_getfsize(fname);

  if (fsize == -1) {
    gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname);
    return NULL;
  }

  if (fsize%sizeof(ssize_t) != 0) {
    gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(ssize_t).\n");
    return NULL;
  }

  nelmnts = fsize/sizeof(ssize_t);
  array = gk_zmalloc(nelmnts, "gk_zreadfilebin: array");

  fpin = gk_fopen(fname, "rb", "gk_zreadfilebin");
  
  if (fread(array, sizeof(ssize_t), nelmnts, fpin) != nelmnts) {
    gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
    gk_free((void **)&array, LTERM);
    return NULL;
  }
  gk_fclose(fpin);

  *r_nelmnts = nelmnts;

  return array;
}

/*************************************************************************/
/*! This function writes the contents of an array into a binary file.
    \param fname is the name of the file
    \param n the number of elements in the array.
    \param a the array to be written out.
*/
/*************************************************************************/
size_t gk_zwritefilebin(char *fname, size_t n, ssize_t *a)
{
  size_t fsize;
  FILE *fp;

  fp = gk_fopen(fname, "wb", "gk_writefilebin");

  fsize = fwrite(a, sizeof(ssize_t), n, fp);

  gk_fclose(fp);

  return fsize;
}

/*************************************************************************/
/*! This function reads the contents of a binary file and returns it in the
    form of an array of float.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
float *gk_freadfilebin(char *fname, size_t *r_nelmnts)
{
  size_t nelmnts;
  ssize_t fsize;
  float *array=NULL;
  FILE *fpin;

  *r_nelmnts = 0;

  fsize = gk_getfsize(fname);

  if (fsize == -1) {
    gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname);
    return NULL;
  }

  if (fsize%sizeof(float) != 0) {
    gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(float).\n");
    return NULL;
  }

  nelmnts = fsize/sizeof(float);
  array = gk_fmalloc(nelmnts, "gk_freadfilebin: array");

  fpin = gk_fopen(fname, "rb", "gk_freadfilebin");
  
  if (fread(array, sizeof(float), nelmnts, fpin) != nelmnts) {
    gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
    gk_free((void **)&array, LTERM);
    return NULL;
  }
  gk_fclose(fpin);

  *r_nelmnts = nelmnts;

  return array;
}

/*************************************************************************/
/*! This function writes the contents of an array into a binary file.
    \param fname is the name of the file
    \param n the number of elements in the array.
    \param a the array to be written out.
*/
/*************************************************************************/
size_t gk_fwritefilebin(char *fname, size_t n, float *a)
{
  size_t fsize;
  FILE *fp;

  fp = gk_fopen(fname, "wb", "gk_fwritefilebin");

  fsize = fwrite(a, sizeof(float), n, fp);

  gk_fclose(fp);

  return fsize;
}

/*************************************************************************/
/*! This function reads the contents of a binary file and returns it in the
    form of an array of double.
    \param fname is the name of the file
    \param r_nlines is the number of lines in the file. If it is NULL,
           this information is not returned.
*/
/*************************************************************************/
double *gk_dreadfilebin(char *fname, size_t *r_nelmnts)
{
  size_t nelmnts;
  ssize_t fsize;
  double *array=NULL;
  FILE *fpin;

  *r_nelmnts = 0;

  fsize = gk_getfsize(fname);

  if (fsize == -1) {
    gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname);
    return NULL;
  }

  if (fsize%sizeof(double) != 0) {
    gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(double).\n");
    return NULL;
  }

  nelmnts = fsize/sizeof(double);
  array = gk_dmalloc(nelmnts, "gk_dreadfilebin: array");

  fpin = gk_fopen(fname, "rb", "gk_dreadfilebin");
  
  if (fread(array, sizeof(double), nelmnts, fpin) != nelmnts) {
    gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts);
    gk_free((void **)&array, LTERM);
    return NULL;
  }
  gk_fclose(fpin);

  *r_nelmnts = nelmnts;

  return array;
}

/*************************************************************************/
/*! This function writes the contents of an array into a binary file.
    \param fname is the name of the file
    \param n the number of elements in the array.
    \param a the array to be written out.
*/
/*************************************************************************/
size_t gk_dwritefilebin(char *fname, size_t n, double *a)
{
  size_t fsize;
  FILE *fp;

  fp = gk_fopen(fname, "wb", "gk_writefilebin");

  fsize = fwrite(a, sizeof(double), n, fp);

  gk_fclose(fp);

  return fsize;
}