void bi::InputNetCDFBuffer::readMask0(const VarType type,
Mask<ON_HOST>& mask) {
typedef temp_host_matrix<real>::type temp_matrix_type;
mask.resize(m.getNumVars(type), false);
Var* var;
int r;
long start, len;
/* sparse masks */
for (r = 0; r < int(recDims.size()); ++r) {
if (timeVars[r] < 0) {
BOOST_AUTO(range, modelVars.equal_range(r));
BOOST_AUTO(iter, range.first);
BOOST_AUTO(end, range.second);
start = 0;
len = nc_inq_dimlen(ncid, recDims[r]);
temp_matrix_type C(iter->second->getNumDims(), len);
readCoords(coordVars[r], start, len, C);
for (; iter != end; ++iter) {
var = iter->second;
if (var->getType() == type) {
mask.addSparseMask(var->getId(), C.size2());
serialiseCoords(var, C, mask.getIndices(var->getId()));
}
}
}
}
/* dense masks */
r = -1; // for those vars not associated with a record dimension
BOOST_AUTO(range, modelVars.equal_range(r));
BOOST_AUTO(iter, range.first);
BOOST_AUTO(end, range.second);
for (; iter != end; ++iter) {
var = iter->second;
if (var->getType() == type) {
mask.addDenseMask(var->getId(), var->getSize());
}
}
}
void bi::InputNetCDFBuffer::readMask(const size_t k, const VarType type,
Mask<ON_HOST>& mask) {
typedef temp_host_matrix<real>::type temp_matrix_type;
mask.resize(m.getNumVars(type), false);
Var* var;
int r;
long start, len;
for (r = 0; r < int(recDims.size()); ++r) {
if (timeVars[r] >= 0) {
start = recStarts[k][r];
len = recLens[k][r];
if (len > 0) {
BOOST_AUTO(range, modelVars.equal_range(r));
BOOST_AUTO(iter, range.first);
BOOST_AUTO(end, range.second);
if (coordVars[r] >= 0) {
/* sparse mask */
temp_matrix_type C(iter->second->getNumDims(), len);
readCoords(coordVars[r], start, len, C);
for (; iter != end; ++iter) {
var = iter->second;
if (var->getType() == type) {
mask.addSparseMask(var->getId(), len);
serialiseCoords(var, C, mask.getIndices(var->getId()));
}
}
} else {
/* dense mask */
for (; iter != end; ++iter) {
var = iter->second;
if (var->getType() == type) {
mask.addDenseMask(var->getId(), var->getSize());
}
}
}
}
}
}
}
/* A private function for parsing log header files.
* This is responsible for initialize the Log classes as well
*/
int LogGroup::parseLogHeaders()
{
int nVars;
int lineNum;
char *line;
char *str1;
char *str2;
char *str3;
char *str4;
char *headerName;
int i;
int headerSize;
int len;
LogData *currLogData;
Var *currVar;
// Foreach log header
for (i = 0; i < nHeaders_; i++) {
// Allocate headerName
len = strlen(pathToBinaryData_) + strlen(headers_[i]) + 2;
headerName = new char[len];
// Full path of log header
sprintf(headerName, "%s/%s", pathToBinaryData_, headers_[i]);
// Open log header
if ((fp_ = fopen(headerName, "r")) == NULL) {
fprintf(stderr,
"\nERROR:\nCouldn't open file \"%s\" \n",
headerName);
return (-1);
}
// Allocate strings, we know that buffers can't be
// longer than file!
// Since headers are typically small, allocate them at ]
// the header size
fseek(fp_, 0, SEEK_END);
headerSize = ftell(fp_);
::rewind(fp_);
line = new char[headerSize + 1]; // Not sure about +1 :)
str1 = new char[headerSize + 1];
str2 = new char[headerSize + 1];
str3 = new char[headerSize + 1];
str4 = new char[headerSize + 1];
// Parse rest of file
lineNum = 0;
while (fgets(line, headerSize, fp_) != NULL) {
lineNum++;
/* <log_file_name> <data_type> <units> <param_name>
or
<log_file_name> byte_order is [lit|big]_endian
*/
if ( sscanf(line, "%s %s %s %s", str1, str2, str3, str4) == 4 ) {
// Byte order statement and top of a log group?
if (!strcmp(str2, "byte_order")) {
LogData *ld = new LogData;
log.push_back(ld);
currLogData = log[nGroups_];
nGroups_++;
// New binary file
currLogData->setBinaryFileName(str1);
// Set byte order
if (!strcmp(str4, "big_endian")) {
currLogData->dataByteOrder = 1;
} else {
currLogData->dataByteOrder = 0;
}
continue;
}
// Check for binary file name mismatches
if (strcmp(str1, currLogData->getBinaryFileName())) {
printf("ERROR: Parsing log header \"%s\".\n"
" Line %d. Binary file name "
"mismatch with \"%s\".\n"
" May need little/big endian "
"specification.\n\n",
headerName, lineNum,
currLogData->getBinaryFileName());
return (-1);
}
// New variable
Var *v = new Var;
currLogData->vars.push_back(v);
nVars = currLogData->getNumVars();
currVar = currLogData->vars[nVars];
nVars++;
currLogData->setNumVars(nVars);
// Set Type
if (currVar->setType(str2) < 0) {
printf("ERROR: In log header \"%s\".\n"
" Line %d. Type \"%s\" is "
"not supported.\n",
headerName, lineNum, str2);
return (-1);
}
// For Release-07 we need to convert the old unit specs by
// adding explicit asterisk for multiplication. )
{
char new_units_spec[100];
new_units_spec[0] = 0;
if ( convert_units_spec (str3, new_units_spec) != 0 ) {
printf (" ERROR: Attempt to convert old units-spec, \"%s\" failed.\n\n",str3);
return (-1);
}
delete [] str3;
len = strlen(new_units_spec);
str3 = new char[len + 1] ;
strcpy(str3, new_units_spec);
}
// Initialize Unit class
if ( ! strcmp(str3,"--")) {
currVar->setUnit(str3);
} else {
currVar->setUnit(map_trick_units_to_udunits(str3));
}
// Set Var Name
currVar->setVarName(str4) ;
if (currVar->getSize() < 0) {
printf("ERROR: In log header \"%s\".\n"
" Line %d. Problem with var "
"name \"%s\" . \n",
headerName, lineNum, str4);
return (-1);
}
}
}
fclose(fp_);
delete[]line;
delete[]str1;
delete[]str2;
delete[]str3;
delete[]str4;
delete[]headerName;
}
return 1;
}
