/**
* 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";
}
/**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;
}