/*
* Write a certain number of log entries (from beginning) to file
*/
void ProcessDasNexusLog::writeLogtoFile(API::MatrixWorkspace_sptr ws,
std::string logname,
size_t numentriesoutput,
std::string outputfilename) {
// 1. Get log
Kernel::Property *log = ws->run().getProperty(logname);
Kernel::TimeSeriesProperty<double> *tslog =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(log);
if (!tslog)
throw std::runtime_error("Invalid time series log: it could not be cast "
"(interpreted) as a time series property");
std::vector<Kernel::DateAndTime> times = tslog->timesAsVector();
std::vector<double> values = tslog->valuesAsVector();
// 2. Write out
std::ofstream ofs;
ofs.open(outputfilename.c_str(), std::ios::out);
ofs << "# Absolute Time (nanosecond)\tPulse Time (nanosecond)\tTOF (ms)\n";
Kernel::DateAndTime prevtime(0);
std::vector<double> tofs;
for (size_t i = 0; i < numentriesoutput; i++) {
Kernel::DateAndTime tnow = times[i];
if (tnow > prevtime) {
// (a) Process previous logs
std::sort(tofs.begin(), tofs.end());
for (double tof : tofs) {
Kernel::DateAndTime temptime =
prevtime + static_cast<int64_t>(tof * 100);
ofs << temptime.totalNanoseconds() << "\t" << tnow.totalNanoseconds()
<< "\t" << tof * 0.1 << '\n';
}
// (b) Clear
tofs.clear();
// (c) Update time
prevtime = tnow;
}
// (d) Push the current value
tofs.push_back(values[i]);
} // ENDFOR
// Clear the last
if (!tofs.empty()) {
// (a) Process previous logs: note value is in unit of 100 nano-second
std::sort(tofs.begin(), tofs.end());
for (double tof : tofs) {
Kernel::DateAndTime temptime = prevtime + static_cast<int64_t>(tof * 100);
ofs << temptime.totalNanoseconds() << "\t" << prevtime.totalNanoseconds()
<< "\t" << tof * 0.1 << '\n';
}
} else {
throw std::runtime_error("Impossible for this to happen!");
}
ofs.close();
} // END Function
/*
* Convert DAS log to a vector of absolute time
* @param orderedtofs: tofs with abstimevec
*/
void ProcessDasNexusLog::convertToAbsoluteTime(
API::MatrixWorkspace_sptr ws, std::string logname,
std::vector<Kernel::DateAndTime> &abstimevec,
std::vector<double> &orderedtofs) {
// 1. Get log
Kernel::Property *log = ws->run().getProperty(logname);
Kernel::TimeSeriesProperty<double> *tslog =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(log);
if (!tslog)
throw std::runtime_error("Invalid time series log: it could not be cast "
"(interpreted) as a time series property");
std::vector<Kernel::DateAndTime> times = tslog->timesAsVector();
std::vector<double> values = tslog->valuesAsVector();
// 2. Get converted
size_t numsamepulses = 0;
std::vector<double> tofs;
Kernel::DateAndTime prevtime(0);
for (size_t i = 0; i < times.size(); i++) {
Kernel::DateAndTime tnow = times[i];
if (tnow > prevtime) {
// (a) Process previous logs
std::sort(tofs.begin(), tofs.end());
for (size_t j = 0; j < tofs.size(); j++) {
Kernel::DateAndTime temptime =
prevtime + static_cast<int64_t>(tofs[j] * 100);
abstimevec.push_back(temptime);
orderedtofs.push_back(tofs[j]);
}
// (b) Clear
tofs.clear();
// (c) Update time
prevtime = tnow;
} else {
numsamepulses++;
}
// (d) Push the current value
tofs.push_back(values[i]);
} // ENDFOR
// Clear the last
if (!tofs.empty()) {
// (a) Process previous logs: note value is in unit of 100 nano-second
std::sort(tofs.begin(), tofs.end());
for (size_t j = 0; j < tofs.size(); j++) {
Kernel::DateAndTime temptime =
prevtime + static_cast<int64_t>(tofs[j] * 100);
abstimevec.push_back(temptime);
orderedtofs.push_back(tofs[j]);
}
} else {
throw std::runtime_error("Impossible for this to happen!");
}
return;
} // END Function
/*
* Check log in workspace
*/
void ProcessDasNexusLog::checkLog(API::MatrixWorkspace_sptr ws,
std::string logname) {
// 1. Get log
Kernel::Property *log = ws->run().getProperty(logname);
if (!log) {
g_log.error() << "Log " << logname << " does not exist!" << std::endl;
throw std::invalid_argument("Non-exising log name");
}
Kernel::TimeSeriesProperty<double> *tslog =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(log);
if (!tslog) {
g_log.error() << "Log " << logname << " is not time series log"
<< std::endl;
throw std::invalid_argument("Log type error!");
}
// 2. Survey
std::vector<Kernel::DateAndTime> times = tslog->timesAsVector();
g_log.information() << "Entries of times = " << times.size() << std::endl;
size_t countsame = 0;
size_t countinverse = 0;
for (size_t i = 1; i < times.size(); i++) {
Kernel::DateAndTime tprev = times[i - 1];
Kernel::DateAndTime tpres = times[i];
if (tprev == tpres)
countsame++;
else if (tprev > tpres)
countinverse++;
}
// 3. Output
Kernel::DateAndTime t0(ws->run().getProperty("run_start")->value());
Kernel::time_duration dts = times[0] - t0;
Kernel::time_duration dtf = times[times.size() - 1] - t0;
size_t f = times.size() - 1;
g_log.information() << "Number of Equal Time Stamps = " << countsame
<< std::endl;
g_log.information() << "Number of Inverted Time Stamps = " << countinverse
<< std::endl;
g_log.information() << "Run Start = " << t0.totalNanoseconds() << std::endl;
g_log.information() << "First Log (Absolute Time, Relative Time): "
<< times[0].totalNanoseconds() << ", "
<< Kernel::DateAndTime::nanosecondsFromDuration(dts)
<< std::endl;
g_log.information() << "Last Log (Absolute Time, Relative Time): "
<< times[f].totalNanoseconds() << ", "
<< Kernel::DateAndTime::nanosecondsFromDuration(dtf)
<< std::endl;
return;
}
/** Export part of designated log to an file in column format and a output file
* @param logname :: name of log to export
* @param numentries :: number of log entries to export
* @param outputeventws :: boolean. output workspace is event workspace if
* true.
*/
void ExportTimeSeriesLog::exportLog(string logname, int numentries,
bool outputeventws) {
// 1. Get log, time, and etc.
std::vector<Kernel::DateAndTime> times;
std::vector<double> values;
if (logname.size() > 0) {
// Log
Kernel::TimeSeriesProperty<double> *tlog =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
m_dataWS->run().getProperty(logname));
if (!tlog) {
std::stringstream errmsg;
errmsg << "TimeSeriesProperty Log " << logname
<< " does not exist in workspace " << m_dataWS->getName();
g_log.error(errmsg.str());
throw std::invalid_argument(errmsg.str());
}
times = tlog->timesAsVector();
values = tlog->valuesAsVector();
} else {
throw std::runtime_error("Log name cannot be left empty.");
}
// 2. Determine number of export log
if (numentries == EMPTY_INT()) {
numentries = static_cast<int>(times.size());
} else if (numentries <= 0) {
stringstream errmsg;
errmsg << "For Export Log, NumberEntriesExport must be greater than 0. "
"Input = " << numentries;
g_log.error(errmsg.str());
throw std::runtime_error(errmsg.str());
} else if (static_cast<size_t>(numentries) > times.size()) {
numentries = static_cast<int>(times.size());
}
// 3. Create otuput workspace
if (outputeventws) {
setupEventWorkspace(numentries, times, values);
} else {
setupWorkspace2D(numentries, times, values);
}
return;
}
/** Export part of designated log to an file in column format and a output file
* @brief ExportTimeSeriesLog::exportLog
* @param logname :: name of log to export
* @param timeunit :: unit of time for input start/stop time and output
* @param starttime :: relative start time of the output time series log
* @param stoptime :: relative stop time of the output time series log
* @param exportepoch :: flag to output time as epoch time/absolute time
* @param outputeventws :: boolean. output workspace is event workspace if
* @param numentries :: number of log entries to export
*/
void ExportTimeSeriesLog::exportLog(const std::string &logname,
const std::string timeunit,
const double &starttime,
const double &stoptime,
const bool exportepoch, bool outputeventws,
int numentries) {
// Get log, time, and etc.
std::vector<Kernel::DateAndTime> times;
std::vector<double> values;
if (logname.size() > 0) {
// Log
Kernel::TimeSeriesProperty<double> *tlog =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
m_inputWS->run().getProperty(logname));
if (!tlog) {
std::stringstream errmsg;
errmsg << "TimeSeriesProperty Log " << logname
<< " does not exist in workspace " << m_inputWS->getName();
g_log.error(errmsg.str());
throw std::invalid_argument(errmsg.str());
}
times = tlog->timesAsVector();
values = tlog->valuesAsVector();
} else {
throw std::runtime_error("Log name cannot be left empty.");
}
// Get start time, stop time and unit factor
double timeunitfactor = 1.;
if (timeunit.compare("Seconds") == 0)
timeunitfactor = 1.E-9;
// Get index for start time
size_t i_start = 0;
size_t i_stop = times.size() - 1;
// Rule out the case that start time is behind last log entry
bool i_start_cal = false;
if (starttime != EMPTY_DBL()) {
int64_t timerangens =
times.back().totalNanoseconds() - times.front().totalNanoseconds();
double timerange = static_cast<double>(timerangens) * timeunitfactor;
g_log.debug() << "Time range is " << timerange << ", Start time is "
<< starttime << "\n";
if (timerange < starttime) {
i_start = times.size() - 1;
i_start_cal = true;
}
}
if ((!i_start_cal) && (starttime != EMPTY_DBL() || stoptime != EMPTY_DBL())) {
bool export_partial = calculateTimeSeriesRangeByTime(
times, starttime, i_start, stoptime, i_stop, timeunitfactor);
if (!export_partial)
throw std::runtime_error(
"Unable to find proton_charge for run start time. "
"Failed to get partial time series.");
}
// Determine number of export log
if (numentries == EMPTY_INT()) {
numentries = static_cast<int>(times.size());
} else if (numentries <= 0) {
stringstream errmsg;
errmsg << "For Export Log, NumberEntriesExport must be greater than 0. "
"Input = " << numentries;
g_log.error(errmsg.str());
throw std::runtime_error(errmsg.str());
} else if (static_cast<size_t>(numentries) > times.size()) {
numentries = static_cast<int>(times.size());
}
// Create otuput workspace
if (outputeventws) {
setupEventWorkspace(i_start, i_stop, numentries, times, values,
exportepoch);
} else {
setupWorkspace2D(i_start, i_stop, numentries, times, values, exportepoch,
timeunitfactor);
}
return;
}
/** 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 + "'");
}
/// Use frequency start for Monitor19 and Special1_19 logs with "No Time" for
/// SNAP
try {
file.openPath("DASlogs");
try {
file.openGroup("frequency", "NXlog");
try {
file.openData("time");
//----- Start time is an ISO8601 string date and time. ------
try {
file.getAttr("start", freqStart);
} catch (::NeXus::Exception &) {
// Some logs have "offset" instead of start
try {
file.getAttr("offset", freqStart);
} catch (::NeXus::Exception &) {
g_log.warning() << "Log entry has no start time indicated.\n";
file.closeData();
throw;
}
}
file.closeData();
} catch (::NeXus::Exception &) {
// No time. This is not an SNS SNAP file
}
file.closeGroup();
} catch (::NeXus::Exception &) {
// No time. This is not an SNS frequency group
}
file.closeGroup();
} catch (::NeXus::Exception &) {
// No time. This is not an SNS group
}
// 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" || group_name == "framelog") {
loadLogs(file, group_name, group_class, workspace);
}
if (group_class == "IXperiods") {
loadNPeriods(file, workspace);
}
}
// If there's measurement information, load that info as logs.
loadAndApplyMeasurementInfo(&file, *workspace);
// Freddie Akeroyd 12/10/2011
// current ISIS implementation contains an additional indirection between
// collected frames via an
// "event_frame_number" array in NXevent_data (which eliminates frames with no
// events).
// the proton_log is for all frames and so is longer than the event_index
// array, so we need to
// filter the proton_charge log based on event_frame_number
// This difference will be removed in future for compatibility with SNS, but
// the code below will allow current SANS2D files to load
if (workspace->mutableRun().hasProperty("proton_log")) {
std::vector<int> event_frame_number;
this->getLogger().notice()
<< "Using old ISIS proton_log and event_frame_number indirection..."
<< std::endl;
try {
// Find the bank/name corresponding to the first event data entry, i.e.
// one with type NXevent_data.
file.openPath("/" + entry_name);
std::map<std::string, std::string> entries = file.getEntries();
std::map<std::string, std::string>::const_iterator it = entries.begin();
std::string eventEntry;
for (; it != entries.end(); ++it) {
if (it->second == "NXevent_data") {
eventEntry = it->first;
break;
}
}
this->getLogger().debug()
<< "Opening"
<< " /" + entry_name + "/" + eventEntry + "/event_frame_number"
<< " to find the event_frame_number\n";
file.openPath("/" + entry_name + "/" + eventEntry +
"/event_frame_number");
file.getData(event_frame_number);
} catch (const ::NeXus::Exception &) {
this->getLogger().warning() << "Unable to load event_frame_number - "
"filtering events by time will not work "
<< std::endl;
}
file.openPath("/" + entry_name);
if (!event_frame_number.empty()) // ISIS indirection - see above comments
{
Kernel::TimeSeriesProperty<double> *plog =
dynamic_cast<Kernel::TimeSeriesProperty<double> *>(
workspace->mutableRun().getProperty("proton_log"));
if (!plog)
throw std::runtime_error(
"Could not cast (interpret) proton_log as a time "
"series property. Cannot continue.");
Kernel::TimeSeriesProperty<double> *pcharge =
new Kernel::TimeSeriesProperty<double>("proton_charge");
std::vector<double> pval;
std::vector<Mantid::Kernel::DateAndTime> ptime;
pval.reserve(event_frame_number.size());
ptime.reserve(event_frame_number.size());
std::vector<Mantid::Kernel::DateAndTime> plogt = plog->timesAsVector();
std::vector<double> plogv = plog->valuesAsVector();
for (auto number : event_frame_number) {
ptime.push_back(plogt[number]);
pval.push_back(plogv[number]);
}
pcharge->create(ptime, pval);
pcharge->setUnits("uAh");
workspace->mutableRun().addProperty(pcharge, true);
}
}
try {
// Read the start and end time strings
file.openData("start_time");
Kernel::DateAndTime start(file.getStrData());
file.closeData();
file.openData("end_time");
Kernel::DateAndTime end(file.getStrData());
file.closeData();
workspace->mutableRun().setStartAndEndTime(start, end);
} catch (::NeXus::Exception &) {
}
if (!workspace->run().hasProperty("gd_prtn_chrg")) {
// Try pulling it from the main proton_charge entry first
try {
file.openData("proton_charge");
std::vector<double> values;
file.getDataCoerce(values);
std::string units;
file.getAttr("units", units);
double charge = values.front();
if (units.find("picoCoulomb") != std::string::npos) {
charge *= 1.e-06 / 3600.;
}
workspace->mutableRun().setProtonCharge(charge);
} catch (::NeXus::Exception &) {
// Try and integrate the proton logs
try {
// Use the DAS logs to integrate the proton charge (if any).
workspace->mutableRun().getProtonCharge();
} catch (Exception::NotFoundError &) {
// Ignore not found property error.
}
}
}
// Close the file
file.close();
}