Get the missing metadata information from command line parameters.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5/trunk@207 4825ed28-b72c-4eae-9704-e50c059e567d

1 files changed, 53 insertions, 22 deletions

diff --git a/src/util/hdf5_convert_from_sdf.c b/src/util/hdf5_convert_from_sdf.c
index ef0ca79..dcd5da5 100644
--- a/src/util/hdf5_convert_from_sdf.c
+++ b/src/util/hdf5_convert_from_sdf.c
@@ -84,37 +84,47 @@ CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_util_hdf5_convert_from_sdf_c)
 int main (int argc, char **argv)
 {
   int i, j;
-  int version, rank, dsize, csize, grouptype;
+  int version, rank, dsize, csize;
+  const int grouptype = CCTK_GF;
   int *dims;
   double timestep;
-  char *varname, *groupname, *coordname, *tag;
+  char *varname, *coordname, *tag;
+  const char *groupname;
   gft_sdf_file_data *infile;
-  double *coords, *data, *bbox;
+  double *coords, *data, *bbox, *origin, *delta;
   hid_t outfile, dataset, dataspace, attr, attrDataspace;
   hid_t group, hdf5String;
   hsize_t hdf5Dims[MAXDIM];
   int iteration, timelevel, ntimelevels;
   char hdf5DatasetName[2 * MAXNAMESIZE];
+  const char *cactus_version = "Cactus Beta14";
 
 
-  if (argc <= 2)
+  if (argc != 7)
   {
-    fprintf (stderr, "Usage: %s <inputfile> <outputfile>\n", argv[0]);
-    fprintf (stderr, "   eg. %s foo.sdf bar.h5\n", argv[0]);
+    fprintf (stderr, "Usage: %s <groupname> <iteration> <timelevel> "
+             "<ntimelevels> <inputfile> <outputfile>\n", argv[0]);
+    fprintf (stderr, "   eg. %s ADMBase::metric 0 0 3 foobar.sdf gxx.h5\n",
+             argv[0]);
     return (0);
   }
 
-  infile = gft_open_sdf_file (argv[1]);
+  groupname = argv[1];
+  iteration = atoi (argv[2]);
+  timelevel = atoi (argv[3]);
+  ntimelevels = atoi (argv[4]);
+
+  infile = gft_open_sdf_file (argv[5]);
   if (! infile)
   {
-    printf ("Could not open SDF input file '%s'\n", argv[1]);
+    printf ("Could not open SDF input file '%s'\n", argv[5]);
     return (-1);
   }
 
-  outfile = H5Fcreate (argv[2], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+  outfile = H5Fcreate (argv[6], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
   if (outfile < 0)
   {
-    fprintf (stderr, "Could not create HDF5 output file '%s'\n", argv[2]);
+    fprintf (stderr, "Could not create HDF5 output file '%s'\n", argv[6]);
     return (-1);
   }
 
@@ -122,6 +132,8 @@ int main (int argc, char **argv)
             "  Cactus SDF-to-HDF5 Converter\n"
             "  ----------------------------\n");
 
+  CHECK_ERROR (hdf5String = H5Tcopy (H5T_C_S1));
+
   /* add a dummy GLOBAL_ATTRIBUTES_GROUP so that the HDF5 file is recognized as
      unchunked Cactus data */
   CHECK_ERROR (group = H5Gcreate (outfile, GLOBAL_ATTRIBUTES_GROUP, 0));
@@ -145,23 +157,18 @@ int main (int argc, char **argv)
   CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &i));
   CHECK_ERROR (H5Aclose (attr));
 
-  CHECK_ERROR (H5Gclose (group));
-
-  CHECK_ERROR (hdf5String = H5Tcopy (H5T_C_S1));
+  CHECK_ERROR (H5Tset_size (hdf5String, strlen (cactus_version)));
+  CHECK_ERROR (attr = H5Acreate (group, "Cactus version", hdf5String,
+                                 attrDataspace, H5P_DEFAULT));
+  CHECK_ERROR (H5Awrite (attr, hdf5String, cactus_version));
+  CHECK_ERROR (H5Aclose (attr));
 
-  /*** FIXME: get iteration number and timelevel information from user ***/
-  iteration = timelevel = 0;
-  ntimelevels = 1;
-  grouptype = CCTK_GF;
-  groupname = "grid::coordinates";
+  CHECK_ERROR (H5Gclose (group));
 
   while (low_read_sdf_stream (1, infile->fp, &timestep, &version, &rank, &dsize,
                               &csize, &varname, &coordname, &tag, &dims, &bbox,
                               &coords, &data))
   {
-    /*** FIXME: give the dataset a valid variable name ***/
-    varname = strdup ("grid::x");
-
     printf ("Processing dataset '%s' (timestep %f)\n", varname, timestep);
 
     /* convert from int to hsize_t */
@@ -177,6 +184,7 @@ int main (int argc, char **argv)
                                       H5T_NATIVE_DOUBLE,dataspace,H5P_DEFAULT));
     CHECK_ERROR (H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
                            H5P_DEFAULT, data));
+    CHECK_ERROR (H5Sclose (dataspace));
 
     /* attach necessary attributes */
     CHECK_ERROR (H5Tset_size (hdf5String, strlen (groupname)));
@@ -195,9 +203,31 @@ int main (int argc, char **argv)
     CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &ntimelevels));
     CHECK_ERROR (H5Aclose (attr));
 
-    CHECK_ERROR (H5Dclose (dataset));
+    CHECK_ERROR (attr = H5Acreate (dataset, "time", H5T_NATIVE_DOUBLE,
+                                   attrDataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_DOUBLE, &timestep));
+    CHECK_ERROR (H5Aclose (attr));
 
+    /* set origin/delta from bbox information */
+    origin = malloc (2*rank * sizeof (double));
+    delta  = origin + rank;
+    for (j = 0; j < rank; j++)
+    {
+      origin[j] = bbox[2*j+0];
+      delta[j]  = (bbox[2*j+1] - bbox[2*j+0]) / (dims[j] - 1);
+    }
+    hdf5Dims[0] = rank;
+    CHECK_ERROR (dataspace = H5Screate_simple (1, hdf5Dims, NULL));
+    CHECK_ERROR (attr = H5Acreate (dataset, "origin", H5T_NATIVE_DOUBLE,
+                                   dataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_DOUBLE, origin));
+    CHECK_ERROR (H5Aclose (attr));
+    CHECK_ERROR (attr = H5Acreate (dataset, "delta", H5T_NATIVE_DOUBLE,
+                                   dataspace, H5P_DEFAULT));
+    CHECK_ERROR (H5Awrite (attr, H5T_NATIVE_DOUBLE, delta));
+    CHECK_ERROR (H5Aclose (attr));
     CHECK_ERROR (H5Sclose (dataspace));
+    CHECK_ERROR (H5Dclose (dataset));
 
     free (varname);
     free (coordname);
@@ -206,6 +236,7 @@ int main (int argc, char **argv)
     free (bbox);
     free (coords);
     free (data);
+    free (origin);
 
     /*** FIXME: increment iteration number to distinguish datasets ***/
     iteration++;