void LoadLLB::loadTimeDetails(NeXus::NXEntry &entry) {
m_wavelength = entry.getFloat("nxbeam/incident_wavelength");
// Apparently this is in the wrong units
// http://iramis.cea.fr/Phocea/file.php?class=page&reload=1227895533&file=21/How_to_install_and_use_the_Fitmib_suite_v28112008.pdf
m_channelWidth = entry.getInt("nxmonitor/channel_width") * 0.1;
g_log.debug("Nexus Data:");
g_log.debug() << " ChannelWidth: " << m_channelWidth << '\n';
g_log.debug() << " Wavelength: " << m_wavelength << '\n';
}
/**
* Load data found in nexus file
*
* @param entry :: The Nexus entry
* @param monitorsData :: Monitors data already loaded
*
*/
void LoadILLReflectometry::loadDataIntoTheWorkSpace(
NeXus::NXEntry &entry, std::vector<std::vector<int>> monitorsData) {
m_wavelength = entry.getFloat("wavelength");
double ei = m_loader.calculateEnergy(m_wavelength);
m_localWorkspace->mutableRun().addProperty<double>("Ei", ei,
true); // overwrite
// read in the data
NXData dataGroup = entry.openNXData("data");
NXInt data = dataGroup.openIntData();
// load the counts from the file into memory
data.load();
// Assign calculated bins to first X axis
//// m_localWorkspace->dataX(0).assign(detectorTofBins.begin(),
/// detectorTofBins.end());
size_t spec = 0;
size_t nb_monitors = monitorsData.size();
Progress progress(this, 0, 1,
m_numberOfTubes * m_numberOfPixelsPerTube + nb_monitors);
// Assign tof values to first X axis
// 1) Get some parameters from nexus file and properties
// Note : This should be changed following future D17/ILL nexus file
// improvement.
const std::string propTOF0 = "monitor1.time_of_flight_0";
auto tof_channel_width_prop = dynamic_cast<PropertyWithValue<double> *>(
m_localWorkspace->run().getProperty(propTOF0));
if (!tof_channel_width_prop)
throw std::runtime_error("Could not cast (interpret) the property " +
propTOF0 + " (channel width) as a floating point "
"value.");
m_channelWidth = *tof_channel_width_prop; /* PAR1[95] */
const std::string propTOF2 = "monitor1.time_of_flight_2";
auto tof_delay_prop = dynamic_cast<PropertyWithValue<double> *>(
m_localWorkspace->run().getProperty(propTOF2));
if (!tof_delay_prop)
throw std::runtime_error("Could not cast (interpret) the property " +
propTOF2 +
" (ToF delay) as a floating point value.");
double tof_delay = *tof_delay_prop; /* PAR1[96] */
double POFF = entry.getFloat("instrument/VirtualChopper/poff"); /* par1[54] */
double open_offset =
entry.getFloat("instrument/VirtualChopper/open_offset"); /* par1[56] */
double mean_chop_1_phase = 0.0;
double mean_chop_2_phase = 0.0;
// [30/09/14] Test on availability of VirtualChopper data
double chop1_speed = entry.getFloat(
"instrument/VirtualChopper/chopper1_speed_average"); /* PAR2[109] */
if (chop1_speed != 0.0) {
// Virtual Chopper entries are valid
// double mean_chop_1_phase =
// entry.getFloat("instrument/VirtualChopper/chopper1_phase_average"); /*
// PAR2[110] */
// this entry seems to be wrong for now, we use the old one instead [YR
// 5/06/2014]
mean_chop_1_phase = entry.getFloat("instrument/Chopper1/phase");
mean_chop_2_phase = entry.getFloat(
"instrument/VirtualChopper/chopper2_phase_average"); /* PAR2[114] */
} else {
// Use Chopper values instead
chop1_speed =
entry.getFloat("instrument/Chopper1/rotation_speed"); /* PAR2[109] */
mean_chop_1_phase = entry.getFloat("instrument/Chopper1/phase");
mean_chop_2_phase = entry.getFloat("instrument/Chopper2/phase");
}
g_log.debug() << "m_numberOfChannels: " << m_numberOfChannels << std::endl;
g_log.debug() << "m_channelWidth: " << m_channelWidth << std::endl;
g_log.debug() << "tof_delay: " << tof_delay << std::endl;
g_log.debug() << "POFF: " << POFF << std::endl;
g_log.debug() << "open_offset: " << open_offset << std::endl;
g_log.debug() << "mean_chop_2_phase: " << mean_chop_2_phase << std::endl;
g_log.debug() << "mean_chop_1_phase: " << mean_chop_1_phase << std::endl;
g_log.debug() << "chop1_speed: " << chop1_speed << std::endl;
double t_TOF2 = 0.0;
if (chop1_speed == 0.0) {
g_log.debug() << "Warning: chop1_speed is null." << std::endl;
// stay with t_TOF2 to O.0
} else {
// Thanks to Miguel Gonzales/ILL for this TOF formula
t_TOF2 = -1.e6 * 60.0 * (POFF - 45.0 + mean_chop_2_phase -
mean_chop_1_phase + open_offset) /
(2.0 * 360 * chop1_speed);
}
g_log.debug() << "t_TOF2: " << t_TOF2 << std::endl;
// 2) Compute tof values
for (size_t timechannelnumber = 0; timechannelnumber <= m_numberOfChannels;
++timechannelnumber) {
double t_TOF1 =
(static_cast<int>(timechannelnumber) + 0.5) * m_channelWidth +
tof_delay;
m_localWorkspace->dataX(0)[timechannelnumber] = t_TOF1 + t_TOF2;
}
// Load monitors
for (size_t im = 0; im < nb_monitors; im++) {
if (im > 0) {
m_localWorkspace->dataX(im) = m_localWorkspace->readX(0);
}
// Assign Y
int *monitor_p = monitorsData[im].data();
m_localWorkspace->dataY(im)
.assign(monitor_p, monitor_p + m_numberOfChannels);
progress.report();
}
// Then Tubes
for (size_t i = 0; i < m_numberOfTubes; ++i) {
for (size_t j = 0; j < m_numberOfPixelsPerTube; ++j) {
// just copy the time binning axis to every spectra
m_localWorkspace->dataX(spec + nb_monitors) = m_localWorkspace->readX(0);
//// Assign Y
int *data_p = &data(static_cast<int>(i), static_cast<int>(j), 0);
m_localWorkspace->dataY(spec + nb_monitors)
.assign(data_p, data_p + m_numberOfChannels);
// Assign Error
MantidVec &E = m_localWorkspace->dataE(spec + nb_monitors);
std::transform(data_p, data_p + m_numberOfChannels, E.begin(),
LoadHelper::calculateStandardError);
++spec;
progress.report();
}
} // for m_numberOfTubes
} // LoadILLIndirect::loadDataIntoTheWorkSpace
/*
* Loads metadata present in the nexus file
*/
void LoadILLSANS::loadMetaData(const NeXus::NXEntry &entry,
const std::string &instrumentNamePath) {
g_log.debug("Loading metadata...");
API::Run &runDetails = m_localWorkspace->mutableRun();
int runNum = entry.getInt("run_number");
std::string run_num = std::to_string(runNum);
runDetails.addProperty("run_number", run_num);
if (entry.getFloat("mode") == 0.0) { // Not TOF
runDetails.addProperty<std::string>("tof_mode", "Non TOF");
} else {
runDetails.addProperty<std::string>("tof_mode", "TOF");
}
std::string desc =
m_loader.getStringFromNexusPath(entry, "sample_description");
runDetails.addProperty("sample_description", desc);
std::string start_time = entry.getString("start_time");
start_time = m_loader.dateTimeInIsoFormat(start_time);
runDetails.addProperty("run_start", start_time);
std::string end_time = entry.getString("end_time");
end_time = m_loader.dateTimeInIsoFormat(end_time);
runDetails.addProperty("run_end", end_time);
double duration = entry.getFloat("duration");
runDetails.addProperty("timer", duration);
double wavelength =
entry.getFloat(instrumentNamePath + "/selector/wavelength");
g_log.debug() << "Wavelength found in the nexus file: " << wavelength << '\n';
if (wavelength <= 0) {
g_log.debug() << "Mode = " << entry.getFloat("mode") << '\n';
g_log.information("The wavelength present in the NeXus file <= 0.");
if (entry.getFloat("mode") == 0.0) { // Not TOF
throw std::runtime_error("Working in Non TOF mode and the wavelength in "
"the file is <=0 !!! Check with the instrument "
"scientist!");
}
} else {
double wavelengthRes =
entry.getFloat(instrumentNamePath + "/selector/wavelength_res");
runDetails.addProperty<double>("wavelength", wavelength);
double ei = m_loader.calculateEnergy(wavelength);
runDetails.addProperty<double>("Ei", ei, true);
// wavelength
m_defaultBinning[0] = wavelength - wavelengthRes * wavelength * 0.01 / 2;
m_defaultBinning[1] = wavelength + wavelengthRes * wavelength * 0.01 / 2;
}
// Put the detector distances:
// std::string detectorPath(instrumentNamePath + "/detector");
// // Just for Sample - RearDetector
// double sampleDetectorDistance =
// m_loader.getDoubleFromNexusPath(entry,detectorPath + "/det2_calc");
// runDetails.addProperty("sample_detector_distance",
// sampleDetectorDistance);
}
void LoadILLSANS::initWorkSpace(NeXus::NXEntry &firstEntry,
const std::string &instrumentPath) {
g_log.debug("Fetching data...");
NXData dataGroup1 = firstEntry.openNXData("data1");
NXInt dataRear = dataGroup1.openIntData();
dataRear.load();
NXData dataGroup2 = firstEntry.openNXData("data2");
NXInt dataRight = dataGroup2.openIntData();
dataRight.load();
NXData dataGroup3 = firstEntry.openNXData("data3");
NXInt dataLeft = dataGroup3.openIntData();
dataLeft.load();
NXData dataGroup4 = firstEntry.openNXData("data4");
NXInt dataDown = dataGroup4.openIntData();
dataDown.load();
NXData dataGroup5 = firstEntry.openNXData("data5");
NXInt dataUp = dataGroup5.openIntData();
dataUp.load();
g_log.debug("Checking channel numbers...");
// check number of channels
if (dataRear.dim2() != dataRight.dim2() &&
dataRight.dim2() != dataLeft.dim2() &&
dataLeft.dim2() != dataDown.dim2() && dataDown.dim2() != dataUp.dim2()) {
throw std::runtime_error(
"The time bins have not the same dimension for all the 5 detectors!");
}
int numberOfHistograms =
dataRear.dim0() * dataRear.dim1() + dataRight.dim0() * dataRight.dim1() +
dataLeft.dim0() * dataLeft.dim1() + dataDown.dim0() * dataDown.dim1() +
dataUp.dim0() * dataUp.dim1();
g_log.debug("Creating empty workspace...");
// TODO : Must put this 2 somewhere else: number of monitors!
createEmptyWorkspace(numberOfHistograms + 2, dataRear.dim2());
loadMetaData(firstEntry, instrumentPath);
std::vector<double> binningRear, binningRight, binningLeft, binningDown,
binningUp;
if (firstEntry.getFloat("mode") == 0.0) { // Not TOF
g_log.debug("Getting default wavelength bins...");
binningRear = m_defaultBinning;
binningRight = m_defaultBinning;
binningLeft = m_defaultBinning;
binningDown = m_defaultBinning;
binningUp = m_defaultBinning;
} else {
g_log.debug("Getting wavelength bins from the nexus file...");
std::string binPathPrefix(instrumentPath + "/tof/tof_wavelength_detector");
binningRear =
m_loader.getTimeBinningFromNexusPath(firstEntry, binPathPrefix + "1");
binningRight =
m_loader.getTimeBinningFromNexusPath(firstEntry, binPathPrefix + "2");
binningLeft =
m_loader.getTimeBinningFromNexusPath(firstEntry, binPathPrefix + "3");
binningDown =
m_loader.getTimeBinningFromNexusPath(firstEntry, binPathPrefix + "4");
binningUp =
m_loader.getTimeBinningFromNexusPath(firstEntry, binPathPrefix + "5");
}
g_log.debug("Loading the data into the workspace...");
size_t nextIndex = loadDataIntoWorkspaceFromMonitors(firstEntry, 0);
nextIndex = loadDataIntoWorkspaceFromHorizontalTubes(dataRear, binningRear,
nextIndex);
nextIndex = loadDataIntoWorkspaceFromVerticalTubes(dataRight, binningRight,
nextIndex);
nextIndex =
loadDataIntoWorkspaceFromVerticalTubes(dataLeft, binningLeft, nextIndex);
nextIndex = loadDataIntoWorkspaceFromHorizontalTubes(dataDown, binningDown,
nextIndex);
nextIndex =
loadDataIntoWorkspaceFromHorizontalTubes(dataUp, binningUp, nextIndex);
}