void LoadSINQFocus::initWorkSpace(NeXus::NXEntry& entry) {
// read in the data
NXData dataGroup = entry.openNXData("merged");
NXInt data = dataGroup.openIntData();
m_numberOfTubes = static_cast<size_t>(data.dim0());
m_numberOfPixelsPerTube = 1;
m_numberOfChannels = static_cast<size_t>(data.dim1());
// dim0 * m_numberOfPixelsPerTube is the total number of detectors
m_numberOfHistograms = m_numberOfTubes * m_numberOfPixelsPerTube;
g_log.debug() << "NumberOfTubes: " << m_numberOfTubes << std::endl;
g_log.debug() << "NumberOfPixelsPerTube: " << m_numberOfPixelsPerTube
<< std::endl;
g_log.debug() << "NumberOfChannels: " << m_numberOfChannels << std::endl;
// Now create the output workspace
// Might need to get this value from the number of monitors in the Nexus file
// params:
// workspace type,
// total number of spectra + (number of monitors = 0),
// bin boundaries = m_numberOfChannels + 1
// Z/time dimension
m_localWorkspace = WorkspaceFactory::Instance().create("Workspace2D",
m_numberOfHistograms, m_numberOfChannels + 1, m_numberOfChannels);
m_localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create(
"TOF");
m_localWorkspace->setYUnitLabel("Counts");
}
/**
* Load Data details (number of tubes, channels, etc)
*
* @param entry First entry of nexus file
*/
void LoadILLReflectometry::loadDataDetails(NeXus::NXEntry &entry) {
// PSD data D17 256 x 1 x 1000
// PSD data Figaro 1 x 256 x 1000
if (m_acqMode) {
NXFloat timeOfFlight = entry.openNXFloat("instrument/PSD/time_of_flight");
timeOfFlight.load();
m_channelWidth = static_cast<double>(timeOfFlight[0]);
m_numberOfChannels = size_t(timeOfFlight[1]);
m_tofDelay = timeOfFlight[2];
if (m_instrument == Supported::Figaro) {
NXFloat eDelay = entry.openNXFloat("instrument/Theta/edelay_delay");
eDelay.load();
m_tofDelay += static_cast<double>(eDelay[0]);
}
} else { // monochromatic mode
m_numberOfChannels = 1;
}
NXInt nChannels = entry.openNXInt("instrument/PSD/detsize");
nChannels.load();
m_numberOfHistograms = nChannels[0];
g_log.debug()
<< "Please note that ILL reflectometry instruments have "
"several tubes, after integration one "
"tube remains in the Nexus file.\n Number of tubes (banks): 1\n";
g_log.debug() << "Number of pixels per tube (number of detectors and number "
"of histograms): " << m_numberOfHistograms << '\n';
g_log.debug() << "Number of time channels: " << m_numberOfChannels << '\n';
g_log.debug() << "Channel width: " << m_channelWidth << " 1e-6 sec\n";
g_log.debug() << "TOF delay: " << m_tofDelay << '\n';
}
/**
* Load monitors data found in nexus file
*
* @param entry :: The Nexus entry
*
*/
std::vector<std::vector<int>>
LoadILLReflectometry::loadMonitors(NeXus::NXEntry &entry) {
// read in the data
g_log.debug("Fetching monitor data...");
NXData dataGroup = entry.openNXData("monitor1/data");
NXInt data = dataGroup.openIntData();
// load the counts from the file into memory
data.load();
std::vector<std::vector<int>> monitors(
1); // vector of monitors with one entry
std::vector<int> monitor1(data(), data() + data.size());
monitors[0].swap(monitor1);
// There is two monitors in data file, but the second one seems to be always 0
dataGroup = entry.openNXData("monitor2/data");
data = dataGroup.openIntData();
data.load();
std::vector<int> monitor2(data(), data() + data.size());
monitors.push_back(monitor2);
return monitors;
}
/**
* Load data from nexus file
*
* @param entry :: The Nexus file entry
* @param monitorsData :: Monitors data already loaded
* @param xVals :: X values
*/
void LoadILLReflectometry::loadData(
NeXus::NXEntry &entry, const std::vector<std::vector<int>> &monitorsData,
const std::vector<double> &xVals) {
g_log.debug("Loading data...");
NXData dataGroup = entry.openNXData("data");
NXInt data = dataGroup.openIntData();
// load the counts from the file into memory
data.load();
const size_t nb_monitors = monitorsData.size();
Progress progress(this, 0, 1, m_numberOfHistograms + nb_monitors);
// write monitors
if (!xVals.empty()) {
HistogramData::BinEdges binEdges(xVals);
// write data
for (size_t j = 0; j < m_numberOfHistograms; ++j) {
const int *data_p = &data(0, static_cast<int>(j), 0);
const HistogramData::Counts counts(data_p, data_p + m_numberOfChannels);
m_localWorkspace->setHistogram(j, binEdges, std::move(counts));
progress.report();
for (size_t im = 0; im < nb_monitors; ++im) {
const int *monitor_p = monitorsData[im].data();
const HistogramData::Counts counts(monitor_p,
monitor_p + m_numberOfChannels);
m_localWorkspace->setHistogram(im + m_numberOfHistograms, binEdges,
std::move(counts));
progress.report();
}
}
} else
g_log.debug("Vector of x values is empty");
}
void LoadSINQFocus::loadDataIntoTheWorkSpace(NeXus::NXEntry& entry) {
// read in the data
NXData dataGroup = entry.openNXData("merged");
NXInt data = dataGroup.openIntData();
data.load();
std::vector<double> timeBinning = m_loader.getTimeBinningFromNexusPath(entry, "merged/time_binning");
m_localWorkspace->dataX(0).assign(timeBinning.begin(),timeBinning.end());
Progress progress(this, 0, 1, m_numberOfTubes * m_numberOfPixelsPerTube);
size_t spec = 0;
for (size_t i = 0; i < m_numberOfTubes; ++i) {
for (size_t j = 0; j < m_numberOfPixelsPerTube; ++j) {
if (spec > 0) {
// just copy the time binning axis to every spectra
m_localWorkspace->dataX(spec) = m_localWorkspace->readX(0);
}
// Assign Y
int* data_p = &data(static_cast<int>(i), static_cast<int>(j));
m_localWorkspace->dataY(spec).assign(data_p,
data_p + m_numberOfChannels);
// Assign Error
MantidVec& E = m_localWorkspace->dataE(spec);
std::transform(data_p, data_p + m_numberOfChannels, E.begin(),
LoadSINQFocus::calculateError);
++spec;
progress.report();
}
}
g_log.debug() << "Data loading into WS done...." << std::endl;
}
/**
* Load single monitor
*
* @param entry :: The Nexus entry
* @param monitor_data :: A std::string containing the Nexus path to the monitor
*data
* @return monitor :: A std::vector containing monitor values
*/
std::vector<int>
LoadILLReflectometry::loadSingleMonitor(NeXus::NXEntry &entry,
const std::string &monitor_data) {
NXData dataGroup = entry.openNXData(monitor_data);
NXInt data = dataGroup.openIntData();
// load counts
data.load();
return std::vector<int>(data(), data() + data.size());
}
/**
* Load Data details (number of tubes, channels, etc)
* @param entry First entry of nexus file
*/
void LoadILLReflectometry::loadDataDetails(NeXus::NXEntry &entry) {
// read in the data
NXData dataGroup = entry.openNXData("data");
NXInt data = dataGroup.openIntData();
m_numberOfTubes = static_cast<size_t>(data.dim0());
m_numberOfPixelsPerTube = static_cast<size_t>(data.dim1());
m_numberOfChannels = static_cast<size_t>(data.dim2());
}
/**
* Init names of sample logs based on instrument specific NeXus file
* entries
*
* @param entry :: the NeXus file entry
*/
void LoadILLReflectometry::initNames(NeXus::NXEntry &entry) {
std::string instrumentNamePath = m_loader.findInstrumentNexusPath(entry);
std::string instrumentName =
entry.getString(instrumentNamePath.append("/name"));
if (instrumentName.empty())
throw std::runtime_error(
"Cannot set the instrument name from the Nexus file!");
boost::to_lower(instrumentName);
if (instrumentName == "d17") {
m_instrument = Supported::D17;
} else if (instrumentName == "figaro") {
m_instrument = Supported::Figaro;
} else {
std::ostringstream str;
str << "Unsupported instrument: " << instrumentName << '.';
throw std::runtime_error(str.str());
}
g_log.debug() << "Instrument name: " << instrumentName << '\n';
if (m_instrument == Supported::D17) {
m_detectorDistanceName = "det";
m_detectorAngleName = "dan.value";
m_sampleAngleName = "san.value";
m_offsetFrom = "VirtualChopper";
m_offsetName = "open_offset";
m_chopper1Name = "Chopper1";
m_chopper2Name = "Chopper2";
} else if (m_instrument == Supported::Figaro) {
// For Figaro, the DTR field contains the sample-to-detector distance
// when the detector is at the horizontal position (angle = 0).
m_detectorDistanceName = "DTR";
m_detectorAngleName = "VirtualAxis.DAN_actual_angle";
m_sampleAngleName = "CollAngle.actual_coll_angle";
m_offsetFrom = "CollAngle";
m_offsetName = "openOffset";
// Figaro: find out which of the four choppers are used
NXFloat firstChopper =
entry.openNXFloat("instrument/ChopperSetting/firstChopper");
firstChopper.load();
NXFloat secondChopper =
entry.openNXFloat("instrument/ChopperSetting/secondChopper");
secondChopper.load();
m_chopper1Name = "CH" + std::to_string(int(firstChopper[0]));
m_chopper2Name = "CH" + std::to_string(int(secondChopper[0]));
}
// get acquisition mode
NXInt acqMode = entry.openNXInt("acquisition_mode");
acqMode.load();
m_acqMode = acqMode[0];
m_acqMode ? g_log.debug("TOF mode") : g_log.debug("Monochromatic Mode");
}
size_t
LoadILLSANS::loadDataIntoWorkspaceFromMonitors(NeXus::NXEntry &firstEntry,
size_t firstIndex) {
// let's find the monitors
// For D33 should be monitor1 and monitor2
for (std::vector<NXClassInfo>::const_iterator it =
firstEntry.groups().begin();
it != firstEntry.groups().end(); ++it) {
if (it->nxclass == "NXmonitor") {
NXData dataGroup = firstEntry.openNXData(it->nxname);
NXInt data = dataGroup.openIntData();
data.load();
g_log.debug() << "Monitor: " << it->nxname << " dims = " << data.dim0()
<< "x" << data.dim1() << "x" << data.dim2() << '\n';
const size_t vectorSize = data.dim2() + 1;
std::vector<double> positionsBinning;
positionsBinning.reserve(vectorSize);
for (size_t i = 0; i < vectorSize; i++)
positionsBinning.push_back(static_cast<double>(i));
// Assign X
m_localWorkspace->dataX(firstIndex)
.assign(positionsBinning.begin(), positionsBinning.end());
// Assign Y
m_localWorkspace->dataY(firstIndex).assign(data(), data() + data.dim2());
// Assign Error
MantidVec &E = m_localWorkspace->dataE(firstIndex);
std::transform(data(), data() + data.dim2(), E.begin(),
LoadHelper::calculateStandardError);
// Add average monitor counts to a property:
double averageMonitorCounts =
std::accumulate(data(), data() + data.dim2(), 0) /
static_cast<double>(data.dim2());
// make sure the monitor has values!
if (averageMonitorCounts > 0) {
API::Run &runDetails = m_localWorkspace->mutableRun();
runDetails.addProperty("monitor", averageMonitorCounts, true);
}
firstIndex++;
}
}
return firstIndex;
}
/**
* Load monitors data found in nexus file
*
* @param entry :: The Nexus entry
*
*/
std::vector<std::vector<int>>
LoadILLIndirect::loadMonitors(NeXus::NXEntry &entry) {
// read in the data
g_log.debug("Fetching monitor data...");
NXData dataGroup = entry.openNXData("monitor/data");
NXInt data = dataGroup.openIntData();
// load the counts from the file into memory
data.load();
// For the moment, we are aware of only one monitor entry, but we keep the
// generalized case of n monitors
std::vector<std::vector<int>> monitors(1);
std::vector<int> monitor(data(), data() + data.size());
monitors[0].swap(monitor);
return monitors;
}
/**
* Load data about the sample
* @param local_workspace :: The workspace to load the logs to.
* @param entry :: The Nexus entry
*/
void LoadISISNexus2::loadSampleData(DataObjects::Workspace2D_sptr local_workspace, NXEntry & entry)
{
/// Sample geometry
NXInt spb = entry.openNXInt("isis_vms_compat/SPB");
// Just load the index we need, not the whole block. The flag is the third value in
spb.load(1, 2);
int geom_id = spb[0];
local_workspace->mutableSample().setGeometryFlag(spb[0]);
NXFloat rspb = entry.openNXFloat("isis_vms_compat/RSPB");
// Just load the indices we need, not the whole block. The values start from the 4th onward
rspb.load(3, 3);
double thick(rspb[0]), height(rspb[1]), width(rspb[2]);
local_workspace->mutableSample().setThickness(thick);
local_workspace->mutableSample().setHeight(height);
local_workspace->mutableSample().setWidth(width);
g_log.debug() << "Sample geometry - ID: " << geom_id << ", thickness: " << thick << ", height: " << height << ", width: " << width << "\n";
}
/**
* Read the bin masking information from the mantid_workspace_i/workspace group.
* @param wksp_cls :: The data group
* @param local_workspace :: The workspace to read into
*/
void LoadNexusProcessed::readBinMasking(NXData & wksp_cls, API::MatrixWorkspace_sptr local_workspace)
{
if (wksp_cls.getDataSetInfo("masked_spectra").stat == NX_ERROR)
{
return;
}
NXInt spec = wksp_cls.openNXInt("masked_spectra");
spec.load();
NXInt bins = wksp_cls.openNXInt("masked_bins");
bins.load();
NXDouble weights = wksp_cls.openNXDouble("mask_weights");
weights.load();
const int n = spec.dim0();
const int n1 = n - 1;
for(int i = 0; i < n; ++i)
{
int si = spec(i,0);
int j0 = spec(i,1);
int j1 = i < n1 ? spec(i+1,1) : bins.dim0();
for(int j = j0; j < j1; ++j)
{
local_workspace->flagMasked(si,bins[j],weights[j]);
}
}
}
/**
* Load a given period into the workspace
* @param period :: The period number to load (starting from 1)
* @param entry :: The opened root entry node for accessing the monitor and data nodes
* @param local_workspace :: The workspace to place the data in
*/
void LoadISISNexus2::loadPeriodData(int64_t period, NXEntry & entry, DataObjects::Workspace2D_sptr local_workspace)
{
int64_t hist_index = 0;
int64_t period_index(period - 1);
int64_t first_monitor_spectrum = 0;
if( !m_monitors.empty() )
{
first_monitor_spectrum = m_monitors.begin()->first;
hist_index = first_monitor_spectrum - 1;
for(std::map<int64_t,std::string>::const_iterator it = m_monitors.begin();
it != m_monitors.end(); ++it)
{
NXData monitor = entry.openNXData(it->second);
NXInt mondata = monitor.openIntData();
m_progress->report("Loading monitor");
mondata.load(1,static_cast<int>(period-1)); // TODO this is just wrong
MantidVec& Y = local_workspace->dataY(hist_index);
Y.assign(mondata(),mondata() + m_numberOfChannels);
MantidVec& E = local_workspace->dataE(hist_index);
std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt);
local_workspace->getAxis(1)->spectraNo(hist_index) = static_cast<specid_t>(it->first);
NXFloat timeBins = monitor.openNXFloat("time_of_flight");
timeBins.load();
local_workspace->dataX(hist_index).assign(timeBins(),timeBins() + timeBins.dim0());
hist_index++;
}
if (first_monitor_spectrum > 1)
{
hist_index = 0;
}
}
if( m_have_detector )
{
NXData nxdata = entry.openNXData("detector_1");
NXDataSetTyped<int> data = nxdata.openIntData();
data.open();
//Start with thelist members that are lower than the required spectrum
const int * const spec_begin = m_spec.get();
std::vector<int64_t>::iterator min_end = m_spec_list.end();
if( !m_spec_list.empty() )
{
// If we have a list, by now it is ordered so first pull in the range below the starting block range
// Note the reverse iteration as we want the last one
if( m_range_supplied )
{
min_end = std::find_if(m_spec_list.begin(), m_spec_list.end(), std::bind2nd(std::greater<int>(), m_spec_min));
}
for( std::vector<int64_t>::iterator itr = m_spec_list.begin(); itr < min_end; ++itr )
{
// Load each
int64_t spectra_no = (*itr);
// For this to work correctly, we assume that the spectrum list increases monotonically
int64_t filestart = std::lower_bound(spec_begin,m_spec_end,spectra_no) - spec_begin;
m_progress->report("Loading data");
loadBlock(data, static_cast<int64_t>(1), period_index, filestart, hist_index, spectra_no, local_workspace);
}
}
if( m_range_supplied )
{
// When reading in blocks we need to be careful that the range is exactly divisible by the blocksize
// and if not have an extra read of the left overs
const int64_t blocksize = 8;
const int64_t rangesize = (m_spec_max - m_spec_min + 1) - m_monitors.size();
const int64_t fullblocks = rangesize / blocksize;
int64_t read_stop = 0;
int64_t spectra_no = m_spec_min;
if (first_monitor_spectrum == 1)
{// this if crudely checks whether the monitors are at the begining or end of the spectra
spectra_no += static_cast<int>(m_monitors.size());
}
// For this to work correctly, we assume that the spectrum list increases monotonically
int64_t filestart = std::lower_bound(spec_begin,m_spec_end,spectra_no) - spec_begin;
if( fullblocks > 0 )
{
read_stop = (fullblocks * blocksize);// + m_monitors.size(); //RNT: I think monitors are excluded from the data
//for( ; hist_index < read_stop; )
for(int64_t i = 0; i < fullblocks; ++i)
{
loadBlock(data, blocksize, period_index, filestart, hist_index, spectra_no, local_workspace);
filestart += blocksize;
}
}
int64_t finalblock = rangesize - (fullblocks * blocksize);
if( finalblock > 0 )
{
loadBlock(data, finalblock, period_index, filestart, hist_index, spectra_no, local_workspace);
}
}
//Load in the last of the list indices
for( std::vector<int64_t>::iterator itr = min_end; itr < m_spec_list.end(); ++itr )
{
// Load each
int64_t spectra_no = (*itr);
// For this to work correctly, we assume that the spectrum list increases monotonically
int64_t filestart = std::lower_bound(spec_begin,m_spec_end,spectra_no) - spec_begin;
loadBlock(data, 1, period_index, filestart, hist_index, spectra_no, local_workspace);
}
}
try
{
const std::string title = entry.getString("title");
local_workspace->setTitle(title);
// write the title into the log file (run object)
local_workspace->mutableRun().addProperty("run_title", title, true);
}
catch (std::runtime_error &)
{
g_log.debug() << "No title was found in the input file, " << getPropertyValue("Filename") << std::endl;
}
}
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);
}
/**
* 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
/**
* Load data found in nexus file
*
* @param entry :: The Nexus entry
* @param monitorsData :: Monitors data already loaded
*
*/
void LoadILLIndirect::loadDataIntoTheWorkSpace(
NeXus::NXEntry &entry, std::vector<std::vector<int>> monitorsData) {
// read in the data
NXData dataGroup = entry.openNXData("data");
NXInt data = dataGroup.openIntData();
// load the counts from the file into memory
data.load();
// Same for Simple Detectors
NXData dataSDGroup = entry.openNXData("dataSD");
NXInt dataSD = dataSDGroup.openIntData();
// load the counts from the file into memory
dataSD.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();
size_t nb_SD_detectors = dataSD.dim0();
Progress progress(this, 0, 1, m_numberOfTubes * m_numberOfPixelsPerTube +
nb_monitors + nb_SD_detectors);
// Assign fake values to first X axis <<to be completed>>
for (size_t i = 0; i <= m_numberOfChannels; ++i) {
m_localWorkspace->dataX(0)[i] = double(i);
}
// First, Monitor
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(),
LoadILLIndirect::calculateError);
++spec;
progress.report();
}
} // for m_numberOfTubes
// Then add Simple Detector (SD)
for (int i = 0; i < dataSD.dim0(); ++i) {
// just copy again the time binning axis to every spectra
m_localWorkspace->dataX(spec + nb_monitors + i) =
m_localWorkspace->readX(0);
// Assign Y
int *dataSD_p = &dataSD(i, 0, 0);
m_localWorkspace->dataY(spec + nb_monitors + i)
.assign(dataSD_p, dataSD_p + m_numberOfChannels);
progress.report();
}
} // LoadILLIndirect::loadDataIntoTheWorkSpace
/**
* Load a given period into the workspace
* @param period :: The period number to load (starting from 1)
* @param entry :: The opened root entry node for accessing the monitor and data
* nodes
* @param local_workspace :: The workspace to place the data in
* @param update_spectra2det_mapping :: reset spectra-detector map to the one
* calculated earlier. (Warning! -- this map has to be calculated correctly!)
*/
void
LoadISISNexus2::loadPeriodData(int64_t period, NXEntry &entry,
DataObjects::Workspace2D_sptr &local_workspace,
bool update_spectra2det_mapping) {
int64_t hist_index = 0;
int64_t period_index(period - 1);
// int64_t first_monitor_spectrum = 0;
for (auto block = m_spectraBlocks.begin(); block != m_spectraBlocks.end();
++block) {
if (block->isMonitor) {
NXData monitor = entry.openNXData(block->monName);
NXInt mondata = monitor.openIntData();
m_progress->report("Loading monitor");
mondata.load(1, static_cast<int>(period - 1)); // TODO this is just wrong
MantidVec &Y = local_workspace->dataY(hist_index);
Y.assign(mondata(), mondata() + m_monBlockInfo.numberOfChannels);
MantidVec &E = local_workspace->dataE(hist_index);
std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt);
if (update_spectra2det_mapping) {
// local_workspace->getAxis(1)->setValue(hist_index,
// static_cast<specid_t>(it->first));
auto spec = local_workspace->getSpectrum(hist_index);
specid_t specID = m_specInd2specNum_map.at(hist_index);
spec->setDetectorIDs(
m_spec2det_map.getDetectorIDsForSpectrumNo(specID));
spec->setSpectrumNo(specID);
}
NXFloat timeBins = monitor.openNXFloat("time_of_flight");
timeBins.load();
local_workspace->dataX(hist_index)
.assign(timeBins(), timeBins() + timeBins.dim0());
hist_index++;
} else if (m_have_detector) {
NXData nxdata = entry.openNXData("detector_1");
NXDataSetTyped<int> data = nxdata.openIntData();
data.open();
// Start with the list members that are lower than the required spectrum
const int *const spec_begin = m_spec.get();
// When reading in blocks we need to be careful that the range is exactly
// divisible by the block-size
// and if not have an extra read of the left overs
const int64_t blocksize = 8;
const int64_t rangesize = block->last - block->first + 1;
const int64_t fullblocks = rangesize / blocksize;
int64_t spectra_no = block->first;
// For this to work correctly, we assume that the spectrum list increases
// monotonically
int64_t filestart =
std::lower_bound(spec_begin, m_spec_end, spectra_no) - spec_begin;
if (fullblocks > 0) {
for (int64_t i = 0; i < fullblocks; ++i) {
loadBlock(data, blocksize, period_index, filestart, hist_index,
spectra_no, local_workspace);
filestart += blocksize;
}
}
int64_t finalblock = rangesize - (fullblocks * blocksize);
if (finalblock > 0) {
loadBlock(data, finalblock, period_index, filestart, hist_index,
spectra_no, local_workspace);
}
}
}
try {
const std::string title = entry.getString("title");
local_workspace->setTitle(title);
// write the title into the log file (run object)
local_workspace->mutableRun().addProperty("run_title", title, true);
} catch (std::runtime_error &) {
g_log.debug() << "No title was found in the input file, "
<< getPropertyValue("Filename") << std::endl;
}
}
