/**
* Loads the mapping between index -> set of detector IDs
*
* If "detector_index", "detector_count" and "detector_list" are all present,
* use these to get the mapping, otherwise spectrum number = detector ID
* (one-to-one)
*
* The spectrum spectrum_index[i] maps to detector_count[i] detectors, whose
* detector IDs are in detector_list starting at the index detector_index[i]
*
* @returns :: map of index -> detector IDs
* @throws std::runtime_error if fails to read data from file
*/
std::map<int, std::set<int>>
LoadMuonNexus2::loadDetectorMapping(const Mantid::NeXus::NXInt &spectrumIndex) {
std::map<int, std::set<int>> mapping;
const int nSpectra = spectrumIndex.dim0();
// Find and open the data group
NXRoot root(getPropertyValue("Filename"));
NXEntry entry = root.openEntry(m_entry_name);
const std::string detectorName = [&entry]() {
// Only the first NXdata found
for (auto &group : entry.groups()) {
std::string className = group.nxclass;
if (className == "NXdata") {
return group.nxname;
}
}
throw std::runtime_error("No NXdata found in file");
}();
NXData dataGroup = entry.openNXData(detectorName);
// Usually for muon data, detector id = spectrum number
// If not, the optional groups "detector_index", "detector_list" and
// "detector_count" will be present to map one to the other
const bool hasDetectorMapping = dataGroup.containsDataSet("detector_index") &&
dataGroup.containsDataSet("detector_list") &&
dataGroup.containsDataSet("detector_count");
if (hasDetectorMapping) {
// Read detector IDs
try {
const auto detIndex = dataGroup.openNXInt("detector_index");
const auto detCount = dataGroup.openNXInt("detector_count");
const auto detList = dataGroup.openNXInt("detector_list");
const int nSpectra = detIndex.dim0();
for (int i = 0; i < nSpectra; ++i) {
const int start = detIndex[i];
const int nDetectors = detCount[i];
std::set<int> detIDs;
for (int jDet = 0; jDet < nDetectors; ++jDet) {
detIDs.insert(detList[start + jDet]);
}
mapping[i] = detIDs;
}
} catch (const ::NeXus::Exception &err) {
// Throw a more user-friendly message
std::ostringstream message;
message << "Failed to read detector mapping: " << err.what();
throw std::runtime_error(message.str());
}
} else {
for (int i = 0; i < nSpectra; ++i) {
mapping[i] = std::set<int>{spectrumIndex[i]};
}
}
return mapping;
}
/**
* Load a table
*/
API::Workspace_sptr LoadNexusProcessed::loadTableEntry(NXEntry & entry)
{
API::ITableWorkspace_sptr workspace;
workspace = Mantid::API::WorkspaceFactory::Instance().createTable("TableWorkspace");
NXData nx_tw = entry.openNXData("table_workspace");
std::vector<double> values;
bool hasNumberOfRowBeenSet = false;
//int numberOfRows = 0;
int columnNumber = 1;
do
{
std::string str = "column_" + boost::lexical_cast<std::string>(columnNumber);
NXInfo info = nx_tw.getDataSetInfo(str.c_str());
if (info.stat == NX_ERROR)
{
break;
}
if ( info.type == NX_FLOAT64 )
{
NXDouble nxDouble = nx_tw.openNXDouble(str.c_str());
std::string columnTitle = nxDouble.attributes("name");
if (!columnTitle.empty())
{
workspace->addColumn("double", columnTitle);
nxDouble.load();
int length = nxDouble.dim0();
if ( !hasNumberOfRowBeenSet )
{
workspace->setRowCount(length);
hasNumberOfRowBeenSet = true;
}
for (int i = 0; i < length; i++)
workspace->cell<double>(i,columnNumber-1) = *(nxDouble() + i);
}
}
else if ( info.type == NX_CHAR )
{
NXChar data = nx_tw.openNXChar(str.c_str());
std::string columnTitle = data.attributes("name");
if (!columnTitle.empty())
{
workspace->addColumn("str", columnTitle);
int nRows = info.dims[0];
if ( !hasNumberOfRowBeenSet )
{
workspace->setRowCount(nRows);
hasNumberOfRowBeenSet = true;
}
int maxStr = info.dims[1];
std::string fromCrap(maxStr,' ');
data.load();
for (int iR = 0; iR < nRows; iR++)
{
for (int i = 0; i < maxStr; i++)
fromCrap[i] = *(data()+i+maxStr*iR);
workspace->cell<std::string>(iR,columnNumber-1) = fromCrap;
}
}
}
columnNumber++;
} while ( 1 );
return boost::static_pointer_cast<API::Workspace>(workspace);
}
/**
* 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 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;
}
}
/**Method takes input parameters which describe monitor loading and analyze
*them against spectra/monitor block information in the file.
* The result is the option if monitors can be loaded together with spectra or
*mast be treated separately
* and additional information on how to treat monitor spectra.
*
*@param entry :: entry to the NeXus file, opened at root folder
*@param spectrum_index :: array of spectra indexes of the data present in
*the file
*@param ndets :: size of the spectrum index array
*@param n_vms_compat_spectra :: number of data entries containing common time
*bins (e.g. all spectra, or all spectra and monitors or some spectra (this is
*not fully supported)
*@param monitors :: map connecting monitor spectra ID against
*monitor group name in the file.
*@param excludeMonitors :: input property indicating if it is requested to
*exclude monitors from the target workspace
*@param separateMonitors :: input property indicating if it is requested to
*load monitors separately (and exclude them from target data workspace this way)
*
*@param OvelapMonitors :: output property containing the list of monitors
*ID for monitors, which are also included with spectra.
*@return excludeMonitors :: indicator if monitors should or mast be excluded
*from the main data workspace if they can not be loaded with the data
* (contain different number of time channels)
*
*/
bool LoadISISNexus2::findSpectraDetRangeInFile(
NXEntry &entry, boost::shared_array<int> &spectrum_index, int64_t ndets,
int64_t n_vms_compat_spectra, std::map<int64_t, std::string> &monitors,
bool excludeMonitors, bool separateMonitors,
std::map<int64_t, std::string> &OvelapMonitors) {
OvelapMonitors.clear();
size_t nmons = monitors.size();
if (nmons > 0) {
NXInt chans = entry.openNXInt(m_monitors.begin()->second + "/data");
m_monBlockInfo = DataBlock(chans);
m_monBlockInfo.numberOfSpectra = nmons; // each monitor is in separate group
// so number of spectra is equal to
// number of groups.
// identify monitor ID range.
for (auto it = monitors.begin(); it != monitors.end(); it++) {
int64_t mon_id = static_cast<int64_t>(it->first);
if (m_monBlockInfo.spectraID_min > mon_id)
m_monBlockInfo.spectraID_min = mon_id;
if (m_monBlockInfo.spectraID_max < mon_id)
m_monBlockInfo.spectraID_max = mon_id;
}
if (m_monBlockInfo.spectraID_max - m_monBlockInfo.spectraID_min + 1 !=
static_cast<int64_t>(nmons)) {
g_log.warning() << "When trying to find the range of monitor spectra: "
"non-consequent monitor ID-s in the monitor block. "
"Unexpected situation for the loader\n";
}
// at this stage we assume that the only going to load monitors
m_loadBlockInfo = m_monBlockInfo;
}
if (ndets == 0) {
separateMonitors = false; // only monitors in the main workspace. No
// detectors. Will be loaded in the main workspace
// Possible function exit point
return separateMonitors;
}
// detectors are present in the file
NXData nxData = entry.openNXData("detector_1");
NXInt data = nxData.openIntData();
m_detBlockInfo = DataBlock(data);
// We assume again that this spectrum list ID increase monotonically
m_detBlockInfo.spectraID_min = spectrum_index[0];
m_detBlockInfo.spectraID_max = spectrum_index[ndets - 1];
if (m_detBlockInfo.spectraID_max - m_detBlockInfo.spectraID_min + 1 !=
static_cast<int64_t>(m_detBlockInfo.numberOfSpectra)) {
g_log.warning() << "When trying to find the range of monitor spectra: "
"non-consequent spectra ID-s in the detectors block. "
"Unexpected situation for the loader\n";
}
m_loadBlockInfo = m_detBlockInfo;
// now we are analyzing what is actually going or can be loaded
bool removeMonitors = excludeMonitors || separateMonitors;
if (((m_detBlockInfo.numberOfPeriods != m_monBlockInfo.numberOfPeriods) ||
(m_detBlockInfo.numberOfChannels != m_monBlockInfo.numberOfChannels)) &&
nmons > 0) {
// detectors and monitors have different characteristics. Can be loaded only
// to separate workspaces.
if (!removeMonitors) {
g_log.warning() << " Performing separate loading as can not load spectra "
"and monitors in the single workspace:\n";
g_log.warning() << " Monitors data contain :"
<< m_monBlockInfo.numberOfChannels
<< " time channels and: "
<< m_monBlockInfo.numberOfPeriods << " period(s)\n";
g_log.warning() << " Spectra data contain :"
<< m_detBlockInfo.numberOfChannels
<< " time channels and: "
<< m_detBlockInfo.numberOfPeriods << " period(s)\n";
}
separateMonitors = true;
removeMonitors = true;
}
int64_t spectraID_min =
std::min(m_monBlockInfo.spectraID_min, m_detBlockInfo.spectraID_min);
int64_t spectraID_max =
std::max(m_monBlockInfo.spectraID_max, m_detBlockInfo.spectraID_max);
size_t totNumOfSpectra =
m_monBlockInfo.numberOfSpectra + m_detBlockInfo.numberOfSpectra;
if (!removeMonitors) {
m_loadBlockInfo.numberOfSpectra = totNumOfSpectra;
m_loadBlockInfo.spectraID_min = spectraID_min;
m_loadBlockInfo.spectraID_max = spectraID_max;
}
if (separateMonitors)
m_loadBlockInfo = m_detBlockInfo;
// verify integrity of the monitor and detector information
if ((totNumOfSpectra == static_cast<size_t>(n_vms_compat_spectra)) &&
(spectraID_max - spectraID_min + 1 ==
static_cast<int64_t>(n_vms_compat_spectra))) {
// all information written in the file is correct, there are no spurious
// spectra and detectors & monitors form continuous block on HDD
return separateMonitors;
}
// something is wrong and we need to analyze spectra map. Currently we can
// identify and manage the case when all monitor's spectra are written
// together with detectors
// make settings for this situation
m_detBlockInfo.numberOfSpectra -= m_monBlockInfo.numberOfSpectra;
m_loadBlockInfo.numberOfSpectra -= m_monBlockInfo.numberOfSpectra;
std::map<int64_t, std::string> remaining_monitors;
if (removeMonitors) {
for (auto it = monitors.begin(); it != monitors.end(); it++) {
if (it->first >= m_detBlockInfo.spectraID_min &&
it->first <= m_detBlockInfo.spectraID_max) { // monitors ID-s are
// included with spectra
// ID-s -- let's try not
// to load it twice.
OvelapMonitors.insert(*it);
} else {
remaining_monitors.insert(*it);
}
}
}
monitors.swap(remaining_monitors);
return separateMonitors;
}