/**
* 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;
}
}
/** Load the event_workspace field
*
* @param wksp_cls
* @param progressStart
* @param progressRange
* @return
*/
API::MatrixWorkspace_sptr LoadNexusProcessed::loadEventEntry(NXData & wksp_cls, NXDouble & xbins,
const double& progressStart, const double& progressRange)
{
NXDataSetTyped<int64_t> indices_data = wksp_cls.openNXDataSet<int64_t>("indices");
indices_data.load();
boost::shared_array<int64_t> indices = indices_data.sharedBuffer();
int numspec = indices_data.dim0()-1;
int num_xbins = xbins.dim0();
if (num_xbins < 2) num_xbins = 2;
EventWorkspace_sptr ws = boost::dynamic_pointer_cast<EventWorkspace>
(WorkspaceFactory::Instance().create("EventWorkspace", numspec, num_xbins, num_xbins-1));
// Set the YUnit label
ws->setYUnit(indices_data.attributes("units"));
std::string unitLabel = indices_data.attributes("unit_label");
if (unitLabel.empty()) unitLabel = indices_data.attributes("units");
ws->setYUnitLabel(unitLabel);
//Handle optional fields.
// TODO: Handle inconsistent sizes
boost::shared_array<int64_t> pulsetimes;
if (wksp_cls.isValid("pulsetime"))
{
NXDataSetTyped<int64_t> pulsetime = wksp_cls.openNXDataSet<int64_t>("pulsetime");
pulsetime.load();
pulsetimes = pulsetime.sharedBuffer();
}
boost::shared_array<double> tofs;
if (wksp_cls.isValid("tof"))
{
NXDouble tof = wksp_cls.openNXDouble("tof");
tof.load();
tofs = tof.sharedBuffer();
}
boost::shared_array<float> error_squareds;
if (wksp_cls.isValid("error_squared"))
{
NXFloat error_squared = wksp_cls.openNXFloat("error_squared");
error_squared.load();
error_squareds = error_squared.sharedBuffer();
}
boost::shared_array<float> weights;
if (wksp_cls.isValid("weight"))
{
NXFloat weight = wksp_cls.openNXFloat("weight");
weight.load();
weights = weight.sharedBuffer();
}
// What type of event lists?
EventType type = TOF;
if (tofs && pulsetimes && weights && error_squareds)
type = WEIGHTED;
else if ((tofs && weights && error_squareds))
type = WEIGHTED_NOTIME;
else if (pulsetimes && tofs)
type = TOF;
else
throw std::runtime_error("Could not figure out the type of event list!");
// Create all the event lists
PARALLEL_FOR_NO_WSP_CHECK()
for (int wi=0; wi < numspec; wi++)
{
PARALLEL_START_INTERUPT_REGION
int64_t index_start = indices[wi];
int64_t index_end = indices[wi+1];
if (index_end >= index_start)
{
EventList & el = ws->getEventList(wi);
el.switchTo(type);
// Allocate all the required memory
el.reserve(index_end - index_start);
el.clearDetectorIDs();
for (long i=index_start; i<index_end; i++)
switch (type)
{
case TOF:
el.addEventQuickly( TofEvent( tofs[i], DateAndTime(pulsetimes[i])) );
break;
case WEIGHTED:
el.addEventQuickly( WeightedEvent( tofs[i], DateAndTime(pulsetimes[i]), weights[i], error_squareds[i]) );
break;
case WEIGHTED_NOTIME:
el.addEventQuickly( WeightedEventNoTime( tofs[i], weights[i], error_squareds[i]) );
break;
}
// Set the X axis
if (this->m_shared_bins)
el.setX(this->m_xbins);
else
{
MantidVec x;
x.resize(xbins.dim0());
for (int i=0; i < xbins.dim0(); i++)
x[i] = xbins(wi, i);
el.setX(x);
}
}
progress(progressStart + progressRange*(1.0/numspec));
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Clean up some stuff
ws->doneAddingEventLists();
return ws;
}
/**
* 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;
}
}
