//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/LoadNexusLogs.h"
#include "MantidNexusCPP/NeXusException.hpp"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidAPI/FileProperty.h"
#include <cctype>
#include <Poco/Path.h>
#include <Poco/DateTimeFormatter.h>
#include <Poco/DateTimeParser.h>
#include <Poco/DateTimeFormat.h>
#include <boost/scoped_array.hpp>
#include "MantidDataHandling/LoadTOFRawNexus.h"
namespace Mantid
{
namespace DataHandling
{
// Register the algorithm into the algorithm factory
DECLARE_ALGORITHM(LoadNexusLogs)
/// Sets documentation strings for this algorithm
void LoadNexusLogs::initDocs()
{
this->setWikiSummary("Loads run logs (temperature, pulse charges, etc.) from a NeXus file and adds it to the run information in a [[workspace]].");
this->setOptionalMessage("Loads run logs (temperature, pulse charges, etc.) from a NeXus file and adds it to the run information in a workspace.");
}
using namespace Kernel;
using API::WorkspaceProperty;
using API::MatrixWorkspace;
using API::MatrixWorkspace_sptr;
using API::FileProperty;
using std::size_t;
/// Empty default constructor
LoadNexusLogs::LoadNexusLogs()
{}
/// Initialisation method.
void LoadNexusLogs::init()
{
declareProperty(new WorkspaceProperty<MatrixWorkspace>("Workspace","Anonymous",Direction::InOut));
std::vector<std::string> exts;
exts.push_back(".nxs");
exts.push_back(".n*");
declareProperty(new FileProperty("Filename", "", FileProperty::Load, exts),
"The name of the Nexus file to load" );
declareProperty(new PropertyWithValue<bool>("OverwriteLogs", true, Direction::Input));
}
/** Executes the algorithm. Reading in the file and creating and populating
* the output workspace
*
* @throw Exception::FileError If the Nexus file cannot be found/opened
* @throw std::invalid_argument If the optional properties are set to invalid values
*/
void LoadNexusLogs::exec()
{
std::string filename = getPropertyValue("Filename");
MatrixWorkspace_sptr workspace = getProperty("Workspace");
// Find the entry name to use (normally "entry" for SNS, "raw_data_1" for ISIS)
std::string entry_name = LoadTOFRawNexus::getEntryName(filename);
::NeXus::File file(filename);
// Find the root entry
try
{
file.openGroup(entry_name, "NXentry");
}
catch(::NeXus::Exception&)
{
throw std::invalid_argument("Unknown NeXus file format found in file '" + filename + "'");
}
// print out the entry level fields
std::map<std::string,std::string> entries = file.getEntries();
std::map<std::string,std::string>::const_iterator iend = entries.end();
for(std::map<std::string,std::string>::const_iterator it = entries.begin();
it != iend; it++)
{
std::string group_name(it->first);
std::string group_class(it->second);
if( group_name == "DASlogs" || group_class == "IXrunlog" ||
group_class == "IXselog" )
{
loadLogs(file, group_name, group_class, workspace);
}
}
file.close();
if( !workspace->run().hasProperty("gd_prtn_chrg") )
{
try
{
//Use the DAS logs to integrate the proton charge (if any).
workspace->mutableRun().integrateProtonCharge();
}
catch (Exception::NotFoundError &)
{
//Ignore not found property error.
}
}
}
/**
* Load log entries from the given group
* @param file :: A reference to the NeXus file handle opened such that the
* next call can be to open the named group
* @param entry_name :: The name of the log entry
* @param_entry_class :: The class type of the log entry
* @param workspace :: A pointer to the workspace to store the logs
*/
void LoadNexusLogs::loadLogs(::NeXus::File & file, const std::string & entry_name,
const std::string & entry_class,
MatrixWorkspace_sptr workspace) const
{
file.openGroup(entry_name, entry_class);
std::map<std::string,std::string> entries = file.getEntries();
std::map<std::string,std::string>::const_iterator iend = entries.end();
for(std::map<std::string,std::string>::const_iterator itr = entries.begin();
itr != iend; itr++)
{
std::string log_class = itr->second;
if( log_class == "NXlog" || log_class == "NXpositioner" )
{
loadNXLog(file, itr->first, log_class, workspace);
}
else if( log_class == "IXseblock" )
{
loadSELog(file, itr->first, workspace);
}
}
file.closeGroup();
}
/**
* Load an NX log entry a group type that has value and time entries.
* @param file :: A reference to the NeXus file handle opened at the parent group
* @param entry_name :: The name of the log entry
* @param entry_class :: The type of the entry
* @param workspace :: A pointer to the workspace to store the logs
*/
void LoadNexusLogs::loadNXLog(::NeXus::File & file, const std::string & entry_name,
const std::string & entry_class,
MatrixWorkspace_sptr workspace) const
{
file.openGroup(entry_name, entry_class);
// Validate the NX log class.
std::map<std::string, std::string> entries = file.getEntries();
if ((entries.find("value") == entries.end()) ||
(entries.find("time") == entries.end()) )
{
g_log.warning() << "Invalid NXlog entry " << entry_name
<< " found. Did not contain 'value' and 'time'.\n";
file.closeGroup();
return;
}
// whether or not to overwrite logs on workspace
bool overwritelogs = this->getProperty("OverwriteLogs");
try
{
Kernel::Property *logValue = createTimeSeries(file, entry_name);
workspace->mutableRun().addProperty(logValue, overwritelogs);
}
catch(::NeXus::Exception &e)
{
g_log.warning() << "NXlog entry " << entry_name
<< " gave an error when loading:'" << e.what() << "'.\n";
}
file.closeGroup();
}
/**
* Load an SE log entry
* @param file :: A reference to the NeXus file handle opened at the parent group
* @param entry_name :: The name of the log entry
* @param workspace :: A pointer to the workspace to store the logs
*/
void LoadNexusLogs::loadSELog(::NeXus::File & file, const std::string & entry_name,
MatrixWorkspace_sptr workspace) const
{
// Open the entry
file.openGroup(entry_name, "IXseblock");
std::string propName = entry_name;
if (workspace->run().hasProperty(propName))
{
propName = "selog_" + propName;
}
// There are two possible entries:
// value_log - A time series entry. This can contain a corrupt value entry so if it does use the value one
// value - A single value float entry
Kernel::Property *logValue(NULL);
std::map<std::string, std::string> entries = file.getEntries();
if( entries.find("value_log") != entries.end() )
{
try
{
try
{
file.openGroup("value_log", "NXlog");
}
catch(::NeXus::Exception&)
{
file.closeGroup();
throw;
}
logValue = createTimeSeries(file, propName);
file.closeGroup();
}
catch(::NeXus::Exception& e)
{
g_log.warning() << "IXseblock entry '" << entry_name << "' gave an error when loading "
<< "a time series:'" << e.what() << "'. Skipping entry\n";
file.closeGroup(); //value_log
file.closeGroup();//entry_name
return;
}
}
else if( entries.find("value") != entries.end() )
{
try
{
// This may have a larger dimension than 1 bit it has no time field so take the first entry
file.openData("value");
::NeXus::Info info = file.getInfo();
if( info.type == ::NeXus::FLOAT32 )
{
boost::scoped_array<float> value(new float[info.dims[0]]);
file.getData(value.get());
file.closeData();
logValue = new Kernel::PropertyWithValue<double>(propName, static_cast<double>(value[0]), true);
}
else
{
file.closeGroup();
return;
}
}
catch(::NeXus::Exception& e)
{
g_log.warning() << "IXseblock entry " << entry_name << " gave an error when loading "
<< "a single value:'" << e.what() << "'.\n";
file.closeData();
file.closeGroup();
return;
}
}
else
{
g_log.warning() << "IXseblock entry " << entry_name
<< " cannot be read, skipping entry.\n";
file.closeGroup();
return;
}
workspace->mutableRun().addProperty(logValue);
file.closeGroup();
}
/**
* Creates a time series property from the currently opened log entry. It is assumed to
* have been checked to have a time field and the value entry's name is given as an argument
* @param file :: A reference to the file handle
* @param prop_name :: The name of the property
* @returns A pointer to a new property containing the time series
*/
Kernel::Property * LoadNexusLogs::createTimeSeries(::NeXus::File & file,
const std::string & prop_name) const
{
file.openData("time");
//----- Start time is an ISO8601 string date and time. ------
std::string start;
try
{
file.getAttr("start", start);
}
catch (::NeXus::Exception &)
{
//Some logs have "offset" instead of start
try
{
file.getAttr("offset", start);
}
catch (::NeXus::Exception &)
{
g_log.warning() << "Log entry has no start time indicated.\n";
file.closeData();
throw;
}
}
//Convert to date and time
Kernel::DateAndTime start_time = Kernel::DateAndTime(start);
std::string time_units;
file.getAttr("units", time_units);
if( time_units.find("second") != 0 && time_units != "minutes" )
{
file.closeData();
throw ::NeXus::Exception("Unsupported time unit '" + time_units + "'");
}
//--- Load the seconds into a double array ---
std::vector<double> time_double;
try
{
file.getDataCoerce(time_double);
}
catch (::NeXus::Exception &e)
{
g_log.warning() << "Log entry 's time field could not be loaded: '" << e.what() << "'.\n";
file.closeData();
throw;
}
file.closeData(); // Close time data
// Convert to seconds if needed
if( time_units == "minutes" )
{
std::transform(time_double.begin(),time_double.end(), time_double.begin(),
std::bind2nd(std::multiplies<double>(),60.0));
}
// Now the values: Could be a string, int or double
file.openData("value");
// Get the units of the property
std::string value_units("");
try
{
file.getAttr("units", value_units);
}
catch (::NeXus::Exception &)
{
//Ignore missing units field.
value_units = "";
}
// Now the actual data
::NeXus::Info info = file.getInfo();
// Check the size
if( size_t(info.dims[0]) != time_double.size() )
{
file.closeData();
throw ::NeXus::Exception("Invalid value entry for time series");
}
if( file.isDataInt() ) // Int type
{
std::vector<int> values;
try
{
file.getDataCoerce(values);
file.closeData();
}
catch(::NeXus::Exception&)
{
file.closeData();
throw;
}
//Make an int TSP
TimeSeriesProperty<int> * tsp = new TimeSeriesProperty<int>(prop_name);
tsp->create(start_time, time_double, values);
tsp->setUnits(value_units);
return tsp;
}
else if( info.type == ::NeXus::CHAR )
{
std::string values;
const int item_length = info.dims[1];
try
{
const int nitems = info.dims[0];
const int total_length = nitems*item_length;
boost::scoped_array<char> val_array(new char[total_length]);
file.getData(val_array.get());
file.closeData();
values = std::string(val_array.get(), total_length);
}
catch(::NeXus::Exception&)
{
file.closeData();
throw;
}
// The string may contain non-printable (i.e. control) characters, replace these
std::replace_if(values.begin(), values.end(), iscntrl, ' ');
TimeSeriesProperty<std::string> * tsp = new TimeSeriesProperty<std::string>(prop_name);
std::vector<DateAndTime> times;
DateAndTime::createVector(start_time, time_double, times);
const size_t ntimes = times.size();
for(size_t i = 0; i < ntimes; ++i)
{
std::string value_i = std::string(values.data() + i*item_length, item_length);
tsp->addValue(times[i], value_i);
}
tsp->setUnits(value_units);
return tsp;
}
else if( info.type == ::NeXus::FLOAT32 || info.type == ::NeXus::FLOAT64 )
{
std::vector<double> values;
try
{
file.getDataCoerce(values);
file.closeData();
}
catch(::NeXus::Exception&)
{
file.closeData();
throw;
}
TimeSeriesProperty<double> * tsp = new TimeSeriesProperty<double>(prop_name);
tsp->create(start_time, time_double, values);
tsp->setUnits(value_units);
return tsp;
}
else
{
throw ::NeXus::Exception("Invalid value type for time series. Only int, double or strings are "
"supported");
}
}
} // namespace DataHandling
} // namespace Mantid