int _PD_cksum_var_read(PDBfile *file, char *name, char *type,
syment *ep, void *vr)
{int rv, ok;
inti ni, len;
intb bpi;
unsigned char rdig[PD_CKSUM_LEN], cdig[PD_CKSUM_LEN];
char *path;
rv = TRUE;
/* if requested, check MD5 checksum for this var */
if ((file->cksum.use & PD_MD5_RW) && (strstr(name, PD_MD5_DIR) == NULL))
{len = strlen(PD_MD5_DIR) + strlen(name) + strlen(PD_MD5_SUFFIX) + 2;
path = CMAKE_N(char, len);
/* read checksum as /&md5/<varname> */
snprintf(path, len, "%s%s", PD_MD5_DIR, name);
if (PD_query_entry(file, path, NULL) == NULL)
/* if preferred form is not there check archaic form - /&md5/<varname>-md5 */
{snprintf(path, len, "%s%s%s", PD_MD5_DIR, name, PD_MD5_SUFFIX);
/* make sure &md5 var has been created */
if (PD_query_entry(file, path, NULL) == NULL)
PD_error("NO MD5 CHECKSUM AVAILABLE FOR THIS VARIABLE - _PD_CKSUM_VAR_READ",
PD_READ);}
else
{ni = _PD_comp_num(ep->dimensions);
bpi = _PD_lookup_size(type, file->host_chart);
/* do checksum in local memory on vr just read */
memset(cdig, 0, PD_CKSUM_LEN);
PM_md5_checksum_array(vr, ni, bpi, cdig);
/* read previous checksum */
PD_read(file, path, rdig);
CFREE(path);
/* return -1 and set PD_error if MD5 mismatch */
ok = _PD_cksum_compare(cdig, rdig);
if (ok == FALSE)
{rv = -1;
/* NOTE: this must be treated as generic because of the PD_read above */
PD_error("MD5 CHECKSUM OF VARIABLE FAILED - _PD_CKSUM_VAR_READ",
PD_GENERIC);};};};
int main(int argc, char** argv)
{
if(argc < 4) {
fprintf(stderr, "Useage: %s <input file> <output file> <t stride>\n", argv[0]);
return 1;
}
int tstride;
if(sscanf(argv[3], "%d", &tstride) != 1) {
fprintf(stderr, "\tERROR: t stride must be an integer\n");
return 1;
}
// Open input file
PDBfile *in;
if((in = PD_open(argv[1], "r")) == NULL) {
fprintf(stderr, "\tERROR: Could not open input file '%s'\n", argv[1]);
return 1;
}
// Open output file
PDBfile *out;
if((out = PD_open(argv[2], "w")) == NULL) {
fprintf(stderr, "\tERROR: Could not open output file '%s'\n", argv[2]);
return 1;
}
// Get list of variables
int nvars;
char **var_names = PD_ls(in, NULL, NULL, &nvars);
if((var_names == (char**) NULL) || (nvars < 1)) {
fprintf(stderr, "\tERROR: No variables\n");
return 1;
}
// Go through the variables
char *varname;
for(int var=0;var<nvars;var++) {
varname = var_names[var];
syment *ep; // PDB query types
dimdes* dims;
// Query size of the variable
if((ep = PD_query_entry(in, varname, NULL)) == (syment*) NULL) {
fprintf(stderr, "\tError querying variable %s\n", varname);
return 1;
}
dims = PD_entry_dimensions(ep);
int nd = 0; // Count number of dimensions
int varsize = 1; // Number of elements
long inds[12];
while(dims != (dimdes*) NULL) {
long min, max;
min = dims->index_min;
max = dims->index_max;
if(nd > 3) {
fprintf(stderr, "\tERROR: Can't handle variable '%s': more than 4D\n", varname);
return 2;
}
inds[3*nd] = min; inds[3*nd + 1] = max; inds[3*nd + 2] = 1L;
varsize *= max - min + 1;
nd++;
dims = dims->next;
}
// Get variable type
char *typ;
typ = PD_entry_type(ep);
if((strcmp(varname, "t_array") == 0) && (nd == 1)) {
float *fdata = new float[varsize];
// Read the data from the PDB file
inds[2] = tstride;
int nread;
if( (nread = PD_read_as_alt(in, varname, "float", fdata, inds)) == 0) {
fprintf(stderr, "\tWARNING: Could not read t_array. Ignoring\n");
delete[] fdata;
continue;
}
inds[0] = 0L;
inds[1] = nread-1;
inds[2] = 1L;
if(PD_write_alt(out, varname, "float", fdata, 1, inds) == FALSE) {
fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname);
}
delete[] fdata;
}else if(nd == 4) {
// Reducing time resolution
if(strcasecmp(typ, "integer") == 0) {
int *idata = new int[varsize];
// Read the data from the PDB file
inds[2] = tstride;
int nread;
if( (nread = PD_read_as_alt(in, varname, "integer", idata, inds)) == 0) {
fprintf(stderr, "\tWARNING: Could not read '%s'. Ignoring\n", varname);
delete[] idata;
continue;
}
if( nread % (varsize / (inds[1] - inds[0] + 1)) != 0 ) {
fprintf(stderr, "ERROR: Accounting error: (%ld, %ld), %d, %d\n", inds[0], inds[1], varsize, nread);
delete[] idata;
continue;
}
nread = nread / (varsize / (inds[1] - inds[0] + 1));
inds[0] = 0L;
inds[1] = nread - 1;
inds[2] = 1L;
if(PD_write_alt(out, varname, "integer", idata, 4, inds) == FALSE) {
fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname);
}
delete[] idata;
}else if( (strcasecmp(typ, "float") == 0) ||
(strcasecmp(typ, "double") == 0) ) {
// Convert doubles to floats
float *fdata = new float[varsize];
// Read the data from the PDB file
inds[2] = tstride;
int nread;
if( (nread = PD_read_as_alt(in, varname, "float", fdata, inds)) == 0) {
fprintf(stderr, "\tWARNING: Could not read '%s'. Ignoring\n", varname);
delete[] fdata;
continue;
}
if( nread % (varsize / (inds[1] - inds[0] + 1)) != 0 ) {
fprintf(stderr, "ERROR: Accounting error: (%ld, %ld), %d, %d\n", inds[0], inds[1], varsize, nread);
delete[] fdata;
continue;
}
nread = nread / (varsize / (inds[1] - inds[0] + 1));
inds[0] = 0L;
inds[1] = nread - 1;
inds[2] = 1L;
if(PD_write_alt(out, varname, "float", fdata, 4, inds) == FALSE) {
fprintf(stderr, "\tWARNING: Could not write '%s'. Ignoring\n", varname);
}
delete[] fdata;
}else {
fprintf(stderr, "\tWARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, typ);
}
}else {
// Just copy the data across
if(strcasecmp(typ, "integer") == 0) {
int *idata = new int[varsize];
// Read the data from the PDB file
if (PD_read_as(in, varname, "integer", idata) == 0) {
fprintf(stderr, "\t\tWARNING: Could not read variable. Ignoring\n");
delete[] idata;
continue;
}
if(PD_write_alt(out, varname, "integer", idata, nd, inds) == FALSE) {
fprintf(stderr, "\tWARNING: Could not write variable '%s'\n", varname);
}
delete[] idata;
}else if( (strcasecmp(typ, "float") == 0) ||
(strcasecmp(typ, "double") == 0) ) {
// Convert doubles to floats
float *fdata = new float[varsize];
// Read the data from the PDB file
if (PD_read_as(in, varname, "float", fdata) == 0) {
fprintf(stderr, "\tWARNING: Could not read variable '%s'. Ignoring\n", varname);
delete[] fdata;
continue;
}
if(PD_write_alt(out, varname, "float", fdata, nd, inds) == FALSE) {
fprintf(stderr, "\tWARNING: Could not write variable '%s'\n", varname);
}
delete[] fdata;
}else {
fprintf(stderr, "WARNING: '%s' has unrecognised type '%s'. Ignoring\n", varname, typ);
}
}
}
PD_close(in);
PD_close(out);
return 0;
}
