void LoadDNSSCD::updateProperties(API::Run &run,
std::map<std::string, T> &metadata,
std::string time) {
typename std::map<std::string, T>::iterator it = metadata.begin();
while (it != metadata.end()) {
TimeSeriesProperty<T> *timeSeries(nullptr);
std::string name(it->first);
std::string units;
// std::regex does not work for rhel7, thus boost
boost::regex reg("([-_a-zA-Z]+)\\[(.*)]");
boost::smatch match;
if (boost::regex_search(name, match, reg) && match.size() > 2) {
std::string new_name(match.str(1));
units.assign(match.str(2));
name = new_name;
}
if (run.hasProperty(name)) {
timeSeries = dynamic_cast<TimeSeriesProperty<T> *>(run.getLogData(name));
if (!timeSeries)
throw std::invalid_argument(
"Log '" + name +
"' already exists but the values are a different type.");
} else {
timeSeries = new TimeSeriesProperty<T>(name);
if (!units.empty())
timeSeries->setUnits(units);
run.addProperty(timeSeries);
}
timeSeries->addValue(time, it->second);
++it;
}
}
/**
* Recursively add properties from a nexus file to
* the workspace run.
*
* @param nxfileID :: Nexus file handle to be parsed, just after an NXopengroup
* @param runDetails :: where to add properties
* @param parent_name :: nexus caller name
* @param parent_class :: nexus caller class
* @param level :: current level in nexus tree
*
*/
void LoadHelper::recurseAndAddNexusFieldsToWsRun(NXhandle nxfileID, API::Run& runDetails,
std::string& parent_name, std::string& parent_class, int level)
{
std::string indent_str(level * 2, ' '); // Two space by indent level
// Link ?
// Attributes ?
// Classes
NXstatus getnextentry_status; ///< return status
int datatype; ///< NX data type if a dataset, e.g. NX_CHAR, NX_FLOAT32, see napi.h
char nxname[NX_MAXNAMELEN], nxclass[NX_MAXNAMELEN];
nxname[0] = '0';
nxclass[0] = '0';
bool has_entry = true; // follows getnextentry_status
while (has_entry)
{
getnextentry_status = NXgetnextentry(nxfileID, nxname, nxclass, &datatype);
if (getnextentry_status == NX_OK)
{
g_log.debug() << indent_str << parent_name << "." << nxname << " ; " << nxclass << std::endl;
NXstatus opengroup_status;
NXstatus opendata_status;
if ((opengroup_status = NXopengroup(nxfileID, nxname, nxclass)) == NX_OK)
{
// Go down to one level
std::string p_nxname(nxname); //current names can be useful for next level
std::string p_nxclass(nxclass);
recurseAndAddNexusFieldsToWsRun(nxfileID, runDetails, p_nxname, p_nxclass, level + 1);
NXclosegroup(nxfileID);
} // if(NXopengroup
else if ((opendata_status = NXopendata(nxfileID, nxname)) == NX_OK)
{
//dump_attributes(nxfileID, indent_str);
g_log.debug() << indent_str << nxname << " opened." << std::endl;
if (parent_class == "NXData" || parent_class == "NXMonitor" || std::string(nxname) == "data")
{
g_log.debug() << indent_str << "skipping " << parent_class << " (" << nxname << ")"
<< std::endl;
/* nothing */
}
else
{ // create a property
int rank;
int dims[4];
int type;
dims[0] = dims[1] = dims[2] = dims[3] = 0;
std::string property_name = (parent_name.empty() ? nxname : parent_name + "." + nxname);
g_log.debug() << indent_str << "considering property " << property_name << std::endl;
// Get the value
NXgetinfo(nxfileID, &rank, dims, &type);
// Note, we choose to only build properties on small float arrays
// filter logic is below
bool build_small_float_array = false; // default
if ((type == NX_FLOAT32) || (type == NX_FLOAT64))
{
if ((rank == 1) && (dims[0] <= 9))
{
build_small_float_array = true;
}
else
{
g_log.debug() << indent_str << "ignored multi dimension float data on "
<< property_name << std::endl;
}
}
else if (type != NX_CHAR)
{
if ((rank != 1) || (dims[0] != 1) || (dims[1] != 1) || (dims[2] != 1) || (dims[3] != 1))
{
g_log.debug() << indent_str << "ignored multi dimension data on " << property_name
<< std::endl;
}
}
void *dataBuffer;
NXmalloc(&dataBuffer, rank, dims, type);
if (NXgetdata(nxfileID, dataBuffer) != NX_OK)
{
NXfree(&dataBuffer);
throw std::runtime_error("Cannot read data from NeXus file");
}
if (type == NX_CHAR)
{
std::string property_value((const char *) dataBuffer);
if (boost::algorithm::ends_with(property_name, "_time"))
{
// That's a time value! Convert to Mantid standard
property_value = dateTimeInIsoFormat(property_value);
}
runDetails.addProperty(property_name, property_value);
}
else if ((type == NX_FLOAT32) || (type == NX_FLOAT64) || (type == NX_INT16)
|| (type == NX_INT32) || (type == NX_UINT16))
{
// Look for "units"
NXstatus units_status;
char units_sbuf[NX_MAXNAMELEN];
int units_len = NX_MAXNAMELEN;
int units_type = NX_CHAR;
units_status = NXgetattr(nxfileID, const_cast<char*>("units"), (void *) units_sbuf,
&units_len, &units_type);
if (units_status != NX_ERROR)
{
g_log.debug() << indent_str << "[ " << property_name << " has unit " << units_sbuf
<< " ]" << std::endl;
}
if ((type == NX_FLOAT32) || (type == NX_FLOAT64))
{
// Mantid numerical properties are double only.
double property_double_value = 0.0;
// Simple case, one value
if (dims[0] == 1)
{
if (type == NX_FLOAT32)
{
property_double_value = *((float*) dataBuffer);
}
else if (type == NX_FLOAT64)
{
property_double_value = *((double*) dataBuffer);
}
if (units_status != NX_ERROR)
runDetails.addProperty(property_name, property_double_value,
std::string(units_sbuf));
else
runDetails.addProperty(property_name, property_double_value);
}
else if (build_small_float_array)
{
// An array, converted to "name_index", with index < 10 (see test above)
for (int dim_index = 0; dim_index < dims[0]; dim_index++)
{
if (type == NX_FLOAT32)
{
property_double_value = ((float*) dataBuffer)[dim_index];
}
else if (type == NX_FLOAT64)
{
property_double_value = ((double*) dataBuffer)[dim_index];
}
std::string indexed_property_name = property_name + std::string("_")
+ boost::lexical_cast<std::string>(dim_index);
if (units_status != NX_ERROR)
runDetails.addProperty(indexed_property_name, property_double_value,
std::string(units_sbuf));
else
runDetails.addProperty(indexed_property_name, property_double_value);
}
}
}
else
{
// int case
int property_int_value = 0;
if (type == NX_INT16)
{
property_int_value = *((short int*) dataBuffer);
}
else if (type == NX_INT32)
{
property_int_value = *((int*) dataBuffer);
}
else if (type == NX_UINT16)
{
property_int_value = *((short unsigned int*) dataBuffer);
}
if (units_status != NX_ERROR)
runDetails.addProperty(property_name, property_int_value, std::string(units_sbuf));
else
runDetails.addProperty(property_name, property_int_value);
} // if (type==...
}
else
{
g_log.debug() << indent_str << "unexpected data on " << property_name << std::endl;
} // test on nxdata type
NXfree(&dataBuffer);
dataBuffer = NULL;
} // if (parent_class == "NXData" || parent_class == "NXMonitor") else
NXclosedata(nxfileID);
}
else
{
g_log.debug() << indent_str << "unexpected status (" << opendata_status << ") on " << nxname
<< std::endl;
}
}
else if (getnextentry_status == NX_EOD)
{
g_log.debug() << indent_str << "End of Dir" << std::endl;
has_entry = false; // end of loop
}
else
{
g_log.debug() << indent_str << "unexpected status (" << getnextentry_status << ")"
<< std::endl;
has_entry = false; // end of loop
}
} // while
} // recurseAndAddNexusFieldsToWsRun