bool
Streaker::FindMaterial(PDBFileObject *pdb, int *zDimensions, int zDims)
{
// Let's see if there's an ireg variable.
bool hasMaterial = false;
PDBfile *pdbPtr = pdb->filePointer();
int numVars = 0;
char *m = 0;
char **varList = PD_ls(pdbPtr, NULL /*path*/, NULL /*pattern*/, &numVars);
if(varList != NULL)
{
for(int j = 0; j < numVars; ++j)
{
if(strncmp(varList[j], "ireg@", 5) == 0)
{
// Get more information about ireg.
TypeEnum t;
std::string typeString;
int nTotalElements;
int *dimensions;
int nDims;
pdb->SymbolExists(varList[j], &t, typeString,
&nTotalElements, &dimensions, &nDims);
// Check whether ireg is the same size as zvar.
bool sameSize = nDims == zDims;
if(sameSize)
{
for(int k = 0; k < nDims; ++k)
sameSize &= (zDimensions[k] == dimensions[k]);
}
// If ireg is the same size then we can add a material var.
if(sameSize && t == INTEGERARRAY_TYPE)
{
m = varList[j];
hasMaterial = true;
break;
}
}
}
}
// If we have not yet read the matnos then do that now.
if(hasMaterial && matvar.size() == 0)
{
// Read the matvar array and determine a list of material numbers. This can
// conceivably be a lot of data since we're reading the whole array for
// this PDB file, which could contain several time steps.
int *ireg = 0, nvals = 0;
if(pdb->GetIntegerArray(m, &ireg, &nvals))
{
// Get a unique set of material numbers.
std::set<int> mats;
int *ptr = ireg;
for(int i = 0; i < nvals; ++i)
{
int mat = *ptr++;
if(mat > 0)
mats.insert(mat);
}
delete [] ireg;
if(mats.size() > 0)
{
this->matvar = std::string(m);
for(std::set<int>::const_iterator it = mats.begin();
it != mats.end(); ++it)
{
this->matnos.push_back(*it);
}
// Set up the material names. Try and be consistent with the
// PPZ reader.
stringVector names;
if(PP_ZFileReader::ReadMaterialNames(pdb, matnos.size(), names))
{
for(size_t i = 0; i < names.size(); ++i)
this->matNames.push_back(names[i]);
}
else
{
for(size_t i = 0; i < matnos.size(); ++i)
{
char tmp[10];
SNPRINTF(tmp, 10, "%d", matnos[i]);
this->matNames.push_back(tmp);
}
}
}
else
hasMaterial = false;
}
}
SFREE(varList);
return hasMaterial;
}
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;
}