src/input.h

input_pgm(): Importing Portable Gray Map (PGM) images
input_gfs(): Gerris simulation format
input_grd(): Raster format (Esri grid)
- Usage
  - Examples

input_pgm(): Importing Portable Gray Map (PGM) images

This function reads in the PGM file in file fp and imports the corresponding values into field s. The grayscale is normalised and inverted so that the maximum value in field s is one (black) and the minimum value is zero (white).

By default the origin of the image (lower-left corner) is assumed to be at (0,0) and the width of the image is set to L0. This can be changed using the optional ox, oy and width parameters.

#include "utils.h"

void input_pgm (scalar s, FILE * fp,
		double ox = 0., double oy = 0., double width = L0)
{
  char line[81];
  if (!fgets (line, 81, fp)) {
    fprintf (stderr, "input_pgm: could not read magic number\n");
    exit (1);
  }
  if (strcmp (line, "P2\n") && strcmp (line, "P5\n")) {
    fprintf (stderr, "input_pgm: magic number '%s' does not match PGM\n", 
	     line);
    exit (1);
  }
  int binary = !strcmp (line, "P5\n");
  if (!fgets (line, 81, fp)) {
    fprintf (stderr, "input_pgm: could not read width and height\n");
    exit (1);
  }
  int W, H;
  while (line[0] == '#' && fgets (line, 81, fp));
  if (line[0] == '#' || sscanf (line, "%d %d", &W, &H) != 2) {
    fprintf (stderr, "input_pgm: could not read width and height\n");
    exit (1);
  }
  if (!fgets (line, 81, fp)) {
    fprintf (stderr, "input_pgm: could not read maxval\n");
    exit (1);
  }
  int maxval;
  if (sscanf (line, "%d", &maxval) != 1) {
    fprintf (stderr, "input_pgm: could not read maxval\n");
    exit (1);
  }
  if (maxval < 256) {
    unsigned char * a = qmalloc (W*H, unsigned char);
    size_t n = 0;
    if (binary)
      n = fread (a, 1, W*H, fp);
    else {
      int v;
      while (n < W*H && fscanf (fp, "%d ", &v) == 1)
	a[n++] = v;
    }
    if (n != W*H) {
      fprintf (stderr, "input_pgm: read only %ld values\n", n);
      exit (1);
    }
    foreach() {
      int i = (x - ox)*W/width, j = (y - oy)*W/width;
      if (i >= 0 && i < W && j >= 0 && j < H)
	s[] = 1. - a[(H - 1 - j)*W + i]/(double)maxval;
      else
	s[] = 0.;
    }
    free (a);
  }
  else {
    unsigned short * a = qmalloc (W*H, unsigned short);
    size_t n = 0;
    if (binary)
      n = fread (a, 2, W*H, fp);
    else {
      int v;
      while (n < W*H && fscanf (fp, "%d ", &v) == 1)
	a[n++] = v;
    }
    if (n != W*H) {
      fprintf (stderr, "input_pgm: read only %ld values\n", n);
      exit (1);
    }
    foreach() {
      int i = (x - ox)*W/width, j = (y - oy)*W/width;
      if (i >= 0 && i < W && j >= 0 && j < H)
	s[] = 1. - a[(H - 1 - j)*W + i]/(double)maxval;
      else
	s[] = 0.;
    }
    free (a);
  }
}

static void next_char (FILE * fp, int target)
{
  int c = fgetc(fp), para = 0;
  while (c != EOF && (c != target || para > 0)) {
    if (c == '{') para++;
    if (c == '}') para--;
    c = fgetc(fp);
  }
  if (c != target) {
    fprintf (stderr, "input_gfs(): error: expecting '%c'\n", target);
    exit (1);
  }
}

static int next_string (FILE * fp, const char * target)
{
  int slen = strlen (target), para = 0;
  char s[slen + 1];
  s[slen] = '\0';
  int len = 0, c = fgetc (fp);
  while (c != EOF && len < slen) {
    if (c == '{') para++;
    if (c == '}') para--;
    s[len++] = c;
    c = fgetc (fp);
  }
  while (c != EOF && para >= 0) {
    if (!strcmp (s, target) && para == 0)
      break;
    if (c == '{') para++;
    if (c == '}') para--;
    for (int i = 0; i < slen - 1; i++)
      s[i] = s[i+1];
    s[slen - 1] = c;
    c = fgetc (fp);
  }
  if (strcmp (s, target))
    c = -1;
  return c;
}

input_gfs(): Gerris simulation format

The function reads simulation data in the format used in Gerris simulation files. This is the reciprocal function of output_gfs().

The arguments and their default values are:

fp: a file pointer. Default is file or stdin.
list: a list of scalar fields to read. Default is all.
file: the name of the file to read from (mutually exclusive with fp).

trace
void input_gfs (FILE * fp = stdin,
		scalar * list = NULL,
		char * file = NULL)
{
  not_mpi_compatible();
  
  if (file && !(fp = fopen (file, "r"))) {
    perror (file);
    exit (1);
  }

  bool input_all = (list == all);
  if (!list) list = all;

  #if TREE
  init_grid (1);
  #endif

  next_char (fp, '{');
  
  char * s = qmalloc (1, char);
  int len = 0;
  int c = fgetc(fp);
  while (c != EOF && c != '}') {
    s[len++] = c;
    qrealloc (s, len + 1, char);
    s[len] = '\0';
    c = fgetc(fp);
  }
  if (c != '}') {
    fprintf (stderr, "input_gfs(): error: expecting '}'\n");
    exit (1);
  }
  
  char * s1 = strstr (s, "variables");
  if (!s1) {
    fprintf (stderr, "input_gfs(): error: expecting 'variables'\n");
    exit (1);
  }

  s1 = strstr (s1, "=");
  if (!s1) {
    fprintf (stderr, "input_gfs(): error: expecting '='\n");
    exit (1);
  }
  s1++;

  while (strchr (" \t", *s1))
    s1++;

  scalar * input = NULL;
  s1 = strtok (s1, ", \t");
  while (s1) {
    char * name = replace (s1, '_', '.', false);
    bool found = false;
    for (scalar s in list)
      if (!is_constant(s) && s.name && !strcmp (s.name, name)) {
	input = list_append (input, s);
	found = true; break;
      }
    if (!found) {
      if (input_all) {
	scalar s = new scalar;
	free (s.name);
	s.name = strdup (name);
	input = list_append (input, s);
      }
      else
	input = list_append (input, (scalar){INT_MAX});
    }
    free (name);
    s1 = strtok (NULL, ", \t");
  }
  free (s);

  next_char (fp, '{');
  double t1 = 0.;
  if (next_string (fp, "Time") >= 0) {
    next_char (fp, '{');
    next_char (fp, 't');
    next_char (fp, '=');
    if (fscanf (fp, "%lf", &t1) != 1) {
      fprintf (stderr, "input_gfs(): error: expecting 't'\n");
      exit (1);
    }
    next_char (fp, '}');
    next_char (fp, '}');
  }

  if (next_string (fp, "Box") < 0) {
    fprintf (stderr, "input_gfs(): error: expecting 'GfsBox'\n");
    exit (1);
  }

  next_char (fp, '{');
  next_char (fp, '{');
  next_char (fp, '\n');

  scalar * listm = {cm,fm};
  scalar * listr = !is_constant(cm) ? listm : NULL;
  NOT_UNUSED (listr);

  foreach_cell() {
    unsigned flags;
    if (fread (&flags, sizeof (unsigned), 1, fp) != 1) {
      fprintf (stderr, "input_gfs(): error: expecting 'flags'\n");
      exit (1);
    }
    if (!(flags & (1 << 4)) && is_leaf(cell))
      refine_cell (point, listr, 0, NULL);
    double a;
    if (fread (&a, sizeof (double), 1, fp) != 1 || a != -1) {
      fprintf (stderr, "input_gfs(): error: expecting '-1'\n");
      exit (1);
    }
    for (scalar s in input) {
      if (fread (&a, sizeof (double), 1, fp) != 1) {
	fprintf (stderr, "input_gfs(): error: expecting a scalar\n");
	exit (1);
      }
      if (s.i != INT_MAX) {
	if (s.v.x.i >= 0) {
	  // this is a vector component, we need to rotate from
	  // Z-ordering (Gerris) to N-ordering (Basilisk)
#if dimension >= 2
	  if (s.v.x.i == s.i) {
	    s = s.v.y;
	    s[] = a;
	  }
	  else if (s.v.y.i == s.i) {
	    s = s.v.x;
	    s[] = - a;
	  }
#endif
#if dimension >= 3
	  else
	    s[] = a;
#endif
	}
	else	
	  s[] = a;
      }
    }
    if (is_leaf(cell))
      continue;
  }
  for (scalar s in listm)
    if (!is_constant(s))
      s.dirty = true;
  for (scalar s in input)
    if (!is_constant(s))
      s.dirty = true;

  free (input);
  if (file)
    fclose (fp);

  // the events are advanced to catch up with the time
  while (t < t1 && events (false))
    t = tnext;
  events (false);
}

input_grd(): Raster format (Esri grid)

This function reads a scalar field from a Raster file. This is the reciprocal function of output_grd().

The arguments and their default values are:

s: the scalar where the data will be stored. No default value. You must specify this parameter
fp: a file pointer. Default is file or stdin.
file: the name of the file to read from (mutually exclusive with fp).
nodatavalue: the value of the NoDataValue. Default is the same as that defined in the raster file.
linear: if true, the raster data is bilinearly interpolated. Default is false.
periodic: if true, the x-axis is treated as periodic. Default is false.
zero: if true NoDataValue are replaced by zero. Default is false.
smooth: the number of Laplacian smoothing passes applied to the data before interpolation. Default is zero.

void input_grd (scalar s,
		FILE * fp = stdin, const char * file = NULL,
		double nodatavalue = 0.,
		bool linear = false, bool periodic = false, bool zero = false,
		int smooth = 0)
{
  scalar input = s;

  if (file && !(fp = fopen (file, "r"))) {
    perror (file);
    exit (1);
  }
  
  // Variables for the Raster data
  double DeltaGRD;
  int nx, ny;
  double XG0, YG0, ndv;

  // header
  char waste[100];
  if (fscanf (fp, "%s %d", waste, &nx) != 2) {
    fprintf (stderr, "input_grd(): error reading 'nx'\n");
    if (file) fclose (fp);
    return;
  }
  if (fscanf (fp, "%s %d", waste, &ny) != 2) {
    fprintf (stderr, "input_grd(): error reading 'ny'\n");
    if (file) fclose (fp);
    return;
  }
  if (fscanf (fp, "%s %lf", waste, &XG0) != 2) {
    fprintf (stderr, "input_grd(): error reading 'XG0'\n");
    if (file) fclose (fp);
    return;    
  }
  if (fscanf (fp, "%s %lf", waste, &YG0) != 2) {
    fprintf (stderr, "input_grd(): error reading 'YG0'\n");
    if (file) fclose (fp);
    return;    
  }
  if (fscanf (fp, "%s %lf", waste, &DeltaGRD) != 2) {
    fprintf (stderr, "input_grd(): error reading 'DeltaGRD'\n");
    if (file) fclose (fp);
    return;    
  }
  if (fscanf (fp, "%s %lf", waste, &ndv) != 2) {
    fprintf (stderr, "input_grd(): error reading 'ndv'\n");
    if (file) fclose (fp);
    return;    
  }

  //default value of NoData value
  if (!nodatavalue)
    nodatavalue = ndv;

  // read the data
  double * value = qmalloc (nx*ny, double);
  for (int i = ny - 1; i >= 0; i--)
    for (int j = 0 ; j < nx; j++) {
      if (fscanf (fp, "%lf ", &value[j + i*nx]) != 1) {
	fprintf (stderr, "input_grd(): error reading value %d,%d\n", i, j);
	if (file) fclose (fp);
	free (value);
	return;
      }
      if (zero && value[j + i*nx] == ndv)
	value[j + i*nx] = 0.;
    }

  // Laplacian smoothing
  if (smooth > 0) {
    double * smoothed = qmalloc (nx*ny, double);
    for (int s = 0; s < smooth; s++) {
      for (int i = 0; i < ny; i++)
	for (int j = 0 ; j < nx; j++) {
	  int n = 0;
	  smoothed[j + i*nx] = 0.;
	  for (int k = -1; k <= 1; k++)
	    for (int l = -1; l <= 1; l++)
	      if ((l != 0 || k != 0) &&
		  i + k >= 0 && i + k < ny &&
		  j + l >= 0 && j + l < nx &&
		  value[j + l + (i + k)*nx] != ndv)
		smoothed[j + i*nx] += value[j + l + (i + k)*nx], n++;
	  if (n == 0)
	    smoothed[j + i*nx] = zero ? 0. : ndv;
	  else
	    smoothed[j + i*nx] /= n;
	}
      swap (double *, value, smoothed);
    }
    free (smoothed);
  }
  
  bool warning = false;  
  foreach (serial) {
    if (periodic || input.boundary[right] == periodic_bc) {
      if (x > XG0 + nx*DeltaGRD)
	x -= nx*DeltaGRD;
      else if (x < XG0)
	x += nx*DeltaGRD;
    }
    // Test if the point in the Basilisk area is included in the raster area
    int j = (x - XG0 + DeltaGRD/2.)/DeltaGRD;
    int i = (y - YG0 + DeltaGRD/2.)/DeltaGRD;    
    if (i >= 0 && i < ny && j >= 0 && j < nx) {
      double val;
      // Test if we are on the ring of data around the raster grid
      int j1 = (x - XG0)/DeltaGRD;
      int i1 = (y - YG0)/DeltaGRD;
      if (linear && i1 >= 0 && j1 >= 0 && i1 < ny - 1 && j1 < nx - 1 &&
	  value[j1 + i1*nx] != ndv && value[j1 + 1 + i1*nx] != ndv &&
	  value[j1 + (i1 + 1)*nx] != ndv && value[j1 + 1 + (i1 + 1)*nx] != ndv) {
	// bi-linear interpolation
	double dx = x - (j1*DeltaGRD + XG0);
	double dy = y - (i1*DeltaGRD + YG0);
	val = (value[j1 + i1*nx] +
	       dx*(value[j1 + 1 + i1*nx] - value[j1 + i1*nx])/DeltaGRD +
	       dy*(value[j1 + (i1 + 1)*nx] - value[j1 + i1*nx])/DeltaGRD +
	       dx*dy*(value[j1 + i1*nx] + value[j1 + 1 + (i1 + 1)*nx] -
		      value[j1 + (i1 + 1)*nx] - value[j1 + 1 + i1*nx])
	       /sq(DeltaGRD));
      }
      else
	val = value[j + i*nx];
      if (val == ndv)
	input[] = nodata;
      else
	input[] = val;
    }
    else {
      input[] = nodata;
      warning = true;
    }
  }
  free (value);
  
  if (warning)
    fprintf (stderr,
	     "input_grd(): Warning: Raster data is not covering all"
	     " the simulation area\n");

  if (file)
    fclose (fp);
}

Usage

Examples

The Gulf Stream