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LoadEventNexus.h
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LoadEventNexus.h
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#ifndef MANTID_DATAHANDLING_LOADEVENTNEXUS_H_
#define MANTID_DATAHANDLING_LOADEVENTNEXUS_H_
#include "MantidAPI/IFileLoader.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidDataHandling/BankPulseTimes.h"
#include "MantidDataHandling/EventWorkspaceCollection.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/Events.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
#include "MantidKernel/OptionalBool.h"
#include "MantidKernel/TimeSeriesProperty.h"
#ifdef _WIN32 // fixing windows issue causing conflict between
// winnt char and nexus char
#undef CHAR
#endif
// clang-format off
#include <nexus/NeXusFile.hpp>
#include <nexus/NeXusException.hpp>
// clang-format on
#include <boost/lexical_cast.hpp>
#include <boost/scoped_array.hpp>
#include <functional>
#include <random>
#include <memory>
#include <mutex>
#include <numeric>
namespace Mantid {
namespace DataHandling {
/** @class LoadEventNexus LoadEventNexus.h Nexus/LoadEventNexus.h
Load Event Nexus files.
Required Properties:
<UL>
<LI> Filename - The name of and path to the input NeXus file </LI>
<LI> Workspace - The name of the workspace to output</LI>
</UL>
@date Sep 27, 2010
Copyright © 2010 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
National Laboratory & European Spallation Source
This file is part of Mantid.
Mantid is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
Mantid is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
File change history is stored at: <https://github.com/mantidproject/mantid>
*/
class DLLExport LoadEventNexus
: public API::IFileLoader<Kernel::NexusDescriptor> {
public:
LoadEventNexus();
const std::string name() const override { return "LoadEventNexus"; };
/// Summary of algorithms purpose
const std::string summary() const override {
return "Loads an Event NeXus file and stores as an "
"EventWorkspace. Optionally, you can filter out events falling "
"outside a range of times-of-flight and/or a time interval.";
}
/// Version
int version() const override { return 1; };
const std::vector<std::string> seeAlso() const override {
return {"LoadISISNexus", "LoadEventAndCompress"};
}
/// Category
const std::string category() const override { return "DataHandling\\Nexus"; }
/// Returns a confidence value that this algorithm can load a file
int confidence(Kernel::NexusDescriptor &descriptor) const override;
template <typename T>
static boost::shared_ptr<BankPulseTimes> runLoadNexusLogs(
const std::string &nexusfilename, T localWorkspace, Algorithm &alg,
bool returnpulsetimes, int &nPeriods,
std::unique_ptr<const Kernel::TimeSeriesProperty<int>> &periodLog);
template <typename T>
static void loadEntryMetadata(const std::string &nexusfilename, T WS,
const std::string &entry_name);
/// Load instrument from Nexus file if possible, else from IDF spacified by
/// Nexus file
template <typename T>
static bool loadInstrument(const std::string &nexusfilename, T localWorkspace,
const std::string &top_entry_name, Algorithm *alg);
/// Load instrument for Nexus file
template <typename T>
static bool
runLoadIDFFromNexus(const std::string &nexusfilename, T localWorkspace,
const std::string &top_entry_name, Algorithm *alg);
/// Load instrument from IDF file specified by Nexus file
template <typename T>
static bool
runLoadInstrument(const std::string &nexusfilename, T localWorkspace,
const std::string &top_entry_name, Algorithm *alg);
static void loadSampleDataISIScompatibility(::NeXus::File &file,
EventWorkspaceCollection &WS);
/// method used to return instrument name for some old ISIS files where it is
/// not written properly within the instrument
static std::string readInstrumentFromISIS_VMSCompat(::NeXus::File &hFile);
public:
/// The name and path of the input file
std::string m_filename;
/// The workspace being filled out
boost::shared_ptr<EventWorkspaceCollection> m_ws;
/// Filter by a minimum time-of-flight
double filter_tof_min;
/// Filter by a maximum time-of-flight
double filter_tof_max;
/// Minimum spectrum to load
int32_t m_specMin;
/// Maximum spectrum to load
int32_t m_specMax;
/// Filter by start time
Mantid::Types::Core::DateAndTime filter_time_start;
/// Filter by stop time
Mantid::Types::Core::DateAndTime filter_time_stop;
/// Mutex protecting tof limits
std::mutex m_tofMutex;
/// Limits found to tof
double longest_tof;
/// Limits found to tof
double shortest_tof;
/// Count of all the "bad" tofs found. These are events with TOF > 2e8
/// microsec
size_t bad_tofs;
/// A count of events discarded because they came from a pixel that's not in
/// the IDF
size_t discarded_events;
/// Tolerance for CompressEvents; use -1 to mean don't compress.
double compressTolerance;
/// Pulse times for ALL banks, taken from proton_charge log.
boost::shared_ptr<BankPulseTimes> m_allBanksPulseTimes;
/// name of top level NXentry to use
std::string m_top_entry_name;
std::unique_ptr<::NeXus::File> m_file;
protected:
Parallel::ExecutionMode getParallelExecutionMode(
const std::map<std::string, Parallel::StorageMode> &storageModes)
const override;
private:
/// Intialisation code
void init() override;
/// Execution code
void exec() override;
bool canUseParallelLoader(const bool haveWeights,
const bool oldNeXusFileNames,
const std::string &classType) const;
DataObjects::EventWorkspace_sptr createEmptyEventWorkspace();
void loadEvents(API::Progress *const prog, const bool monitors);
void createSpectraMapping(
const std::string &nxsfile, const bool monitorsOnly,
const std::vector<std::string> &bankNames = std::vector<std::string>());
void deleteBanks(EventWorkspaceCollection_sptr workspace,
std::vector<std::string> bankNames);
bool hasEventMonitors();
void runLoadMonitors();
/// Set the filters on TOF.
void setTimeFilters(const bool monitors);
/// Load a spectra mapping from the given file
std::unique_ptr<std::pair<std::vector<int32_t>, std::vector<int32_t>>>
loadISISVMSSpectraMapping(const std::string &entry_name);
template <typename T> void filterDuringPause(T workspace);
/// Set the top entry field name
void setTopEntryName();
/// to open the nexus file with specific exception handling/message
void safeOpenFile(const std::string fname);
/// Was the instrument loaded?
bool m_instrument_loaded_correctly;
/// Do we load the sample logs?
bool loadlogs;
/// have the logs been loaded?
bool m_logs_loaded_correctly;
/// True if the event_id is spectrum no not pixel ID
bool event_id_is_spec;
};
//-----------------------------------------------------------------------------
// ISIS event corrections
//-----------------------------------------------------------------------------
/**
* Load the time of flight data. file must have open the group containing
* "time_of_flight" data set. This will add a offset to all of the
* time-of-flight values or a random number to each time-of-flight. It
* should only ever be called on event files that have a "detector_1_events"
* group inside the "NXentry". It is an old ISIS requirement that is rarely
* used now.
*
* Due to hardware issues with retro-fitting event mode to old electronics,
* ISIS event mode is really a very fine histogram with between 1 and 2
* microseconds bins.
*
* If we just took "middle of bin" as the true event time here then WISH
* observed strange ripples when they added spectra. The solution was to
* randomise the probability of an event within the bin.
*
* This randomisation is now performed in the control program which also writes
* the "event_time_offset_shift" dataset (with a single value of "random") when
* it has been performed. If this dataset is present in an event file then no
* randomisation is performed in LoadEventNexus.
*
* This code should remain for loading older ISIS event datasets.
*
* @param file :: The nexus file to read from.
* @param localWorkspace :: The event workspace collection to write to.
* @param binsName :: bins name
* @param start_wi :: First workspace index to process
* @param end_wi :: Last workspace index to process
*/
template <typename T>
void makeTimeOfFlightDataFuzzy(::NeXus::File &file, T localWorkspace,
const std::string &binsName, size_t start_wi = 0,
size_t end_wi = 0) {
const std::string EVENT_TIME_SHIFT_TAG("event_time_offset_shift");
// first check if the data is already randomized
const auto entries = file.getEntries();
if (entries.find(EVENT_TIME_SHIFT_TAG) != entries.end()) {
std::string event_shift_type;
file.readData(EVENT_TIME_SHIFT_TAG, event_shift_type);
if (event_shift_type == "random") {
return;
}
}
// if the data is not randomized randomize it uniformly within each bin
file.openData(binsName);
// time of flights of events
std::vector<float> tofsFile;
file.getData(tofsFile);
file.closeData();
// todo: try to find if tof can be reduced to just 3 numbers: start, end and
// dt
if (end_wi <= start_wi) {
end_wi = localWorkspace->getNumberHistograms();
}
// random number generator
std::mt19937 rng;
// loop over spectra
for (size_t wi = start_wi; wi < end_wi; ++wi) {
DataObjects::EventList &event_list = localWorkspace->getSpectrum(wi);
if (event_list.empty())
continue;
// sort the events
event_list.sortTof();
auto tofsEventList = event_list.getTofs();
size_t n = tofsFile.size();
// iterate over the events and time bins
auto ev = tofsEventList.begin();
auto ev_end = tofsEventList.end();
for (size_t i = 1; i < n; ++i) {
double right = double(tofsFile[i]);
// find the right boundary for the current event
if ((ev != ev_end) && (right < *ev)) {
continue;
}
// count events which have the same right boundary
size_t m = 0;
while ((ev != ev_end) && (*ev < right)) {
++ev;
++m; // count events in the i-th bin
}
if (m > 0) { // m events in this bin
double left = double(tofsFile[i - 1]);
// spread the events uniformly inside the bin
std::uniform_real_distribution<double> flat(left, right);
std::vector<double> random_numbers(m);
for (double &random_number : random_numbers) {
random_number = flat(rng);
}
std::sort(random_numbers.begin(), random_numbers.end());
auto it = random_numbers.begin();
for (auto ev1 = ev - m; ev1 != ev; ++ev1, ++it) {
*ev1 = *it;
}
}
} // for i
event_list.setTofs(tofsEventList);
event_list.sortTof();
} // for wi
}
/**
* ISIS specific method for dealing with wide events. Check if time_of_flight
* can be found in the file and load it.
*
* THIS ONLY APPLIES TO ISIS FILES WITH "detector_1_events" IN THE "NXentry."
*
* @param file :: The nexus file to read from.
* @param localWorkspace :: The event workspace collection which events will be
*modified.
* @param entry_name :: An NXentry tag in the file
* @param classType :: The type of the events: either detector or monitor
*/
template <typename T>
void adjustTimeOfFlightISISLegacy(::NeXus::File &file, T localWorkspace,
const std::string &entry_name,
const std::string &classType) {
bool done = false;
// Go to the root, and then top entry
file.openPath("/");
file.openGroup(entry_name, "NXentry");
using string_map_t = std::map<std::string, std::string>;
string_map_t entries = file.getEntries();
if (entries.find("detector_1_events") == entries.end()) { // not an ISIS file
return;
}
// try if monitors have their own bins
if (classType == "NXmonitor") {
std::vector<std::string> bankNames;
for (string_map_t::const_iterator it = entries.begin(); it != entries.end();
++it) {
std::string entry_name(it->first);
std::string entry_class(it->second);
if (entry_class == classType) {
bankNames.push_back(entry_name);
}
}
for (size_t i = 0; i < bankNames.size(); ++i) {
const std::string &mon = bankNames[i];
file.openGroup(mon, classType);
entries = file.getEntries();
if (entries.find("event_time_bins") == entries.end()) {
// bins = entries.find("time_of_flight"); // I think time_of_flight
// doesn't work here
// if (bins == entries.end())
//{
done = false;
file.closeGroup();
break; // done == false => use bins from the detectors
//}
}
done = true;
makeTimeOfFlightDataFuzzy(file, localWorkspace, "event_time_bins", i,
i + 1);
file.closeGroup();
}
}
if (!done) {
// first check detector_1_events
file.openGroup("detector_1_events", "NXevent_data");
entries = file.getEntries();
for (string_map_t::const_iterator it = entries.begin(); it != entries.end();
++it) {
if (it->first == "time_of_flight" || it->first == "event_time_bins") {
makeTimeOfFlightDataFuzzy(file, localWorkspace, it->first);
done = true;
}
}
file.closeGroup(); // detector_1_events
if (!done) { // if time_of_flight was not found try
// instrument/dae/time_channels_#
file.openGroup("instrument", "NXinstrument");
file.openGroup("dae", "IXdae");
entries = file.getEntries();
size_t time_channels_number = 0;
for (string_map_t::const_iterator it = entries.begin();
it != entries.end(); ++it) {
// check if there are groups with names "time_channels_#" and select the
// one with the highest number
if (it->first.size() > 14 &&
it->first.substr(0, 14) == "time_channels_") {
size_t n = boost::lexical_cast<size_t>(it->first.substr(14));
if (n > time_channels_number) {
time_channels_number = n;
}
}
}
if (time_channels_number > 0) // the numbers start with 1
{
file.openGroup("time_channels_" + std::to_string(time_channels_number),
"IXtime_channels");
entries = file.getEntries();
for (string_map_t::const_iterator it = entries.begin();
it != entries.end(); ++it) {
if (it->first == "time_of_flight" || it->first == "event_time_bins") {
makeTimeOfFlightDataFuzzy(file, localWorkspace, it->first);
}
}
file.closeGroup();
}
file.closeGroup(); // dae
file.closeGroup(); // instrument
}
}
// close top entry (or entry given in entry_name)
file.closeGroup();
}
//-----------------------------------------------------------------------------
/** Load the instrument definition file specified by info in the NXS file.
*
* @param nexusfilename :: Used to pick the instrument.
* @param localWorkspace :: Templated workspace in which to put the instrument
*geometry
* @param top_entry_name :: entry name at the top of the NXS file
* @param alg :: Handle of the algorithm
* @return true if successful
*/
template <typename T>
bool LoadEventNexus::runLoadInstrument(const std::string &nexusfilename,
T localWorkspace,
const std::string &top_entry_name,
Algorithm *alg) {
std::string instrument;
// Get the instrument name
::NeXus::File nxfile(nexusfilename);
// Start with the base entry
nxfile.openGroup(top_entry_name, "NXentry");
// Open the instrument
nxfile.openGroup("instrument", "NXinstrument");
try {
nxfile.openData("name");
instrument = nxfile.getStrData();
alg->getLogger().debug() << "Instrument name read from NeXus file is "
<< instrument << '\n';
} catch (::NeXus::Exception &) {
// Try to fall back to isis compatibility options
nxfile.closeGroup();
instrument = readInstrumentFromISIS_VMSCompat(nxfile);
if (instrument.empty()) {
// Get the instrument name from the file instead
size_t n = nexusfilename.rfind('/');
if (n != std::string::npos) {
std::string temp =
nexusfilename.substr(n + 1, nexusfilename.size() - n - 1);
n = temp.find('_');
if (n != std::string::npos && n > 0) {
instrument = temp.substr(0, n);
}
}
}
}
if (instrument == "POWGEN3") // hack for powgen b/c of bad long name
instrument = "POWGEN";
if (instrument == "NOM") // hack for nomad
instrument = "NOMAD";
if (instrument.empty())
throw std::runtime_error("Could not find the instrument name in the NXS "
"file or using the filename. Cannot load "
"instrument!");
// Now let's close the file as we don't need it anymore to load the
// instrument.
nxfile.close();
// do the actual work
Mantid::API::IAlgorithm_sptr loadInst =
alg->createChildAlgorithm("LoadInstrument");
// Now execute the Child Algorithm. Catch and log any error, but don't stop.
bool executionSuccessful(true);
try {
loadInst->setPropertyValue("InstrumentName", instrument);
loadInst->setProperty<Mantid::API::MatrixWorkspace_sptr>("Workspace",
localWorkspace);
loadInst->setProperty("RewriteSpectraMap",
Mantid::Kernel::OptionalBool(false));
loadInst->execute();
// Populate the instrument parameters in this workspace - this works around
// a bug
localWorkspace->populateInstrumentParameters();
} catch (std::invalid_argument &e) {
alg->getLogger().information()
<< "Invalid argument to LoadInstrument Child Algorithm : " << e.what()
<< '\n';
executionSuccessful = false;
} catch (std::runtime_error &e) {
alg->getLogger().information(
"Unable to successfully run LoadInstrument Child Algorithm");
alg->getLogger().information(e.what());
executionSuccessful = false;
}
// If loading instrument definition file fails
if (!executionSuccessful) {
alg->getLogger().error() << "Error loading Instrument definition file\n";
return false;
}
// Ticket #2049: Cleanup all loadinstrument members to a single instance
// If requested update the instrument to positions in the data file
const auto &pmap = localWorkspace->constInstrumentParameters();
if (!pmap.contains(localWorkspace->getInstrument()->getComponentID(),
"det-pos-source"))
return executionSuccessful;
boost::shared_ptr<Geometry::Parameter> updateDets = pmap.get(
localWorkspace->getInstrument()->getComponentID(), "det-pos-source");
std::string value = updateDets->value<std::string>();
if (value.substr(0, 8) == "datafile") {
Mantid::API::IAlgorithm_sptr updateInst =
alg->createChildAlgorithm("UpdateInstrumentFromFile");
updateInst->setProperty<Mantid::API::MatrixWorkspace_sptr>("Workspace",
localWorkspace);
updateInst->setPropertyValue("Filename", nexusfilename);
if (value == "datafile-ignore-phi") {
updateInst->setProperty("IgnorePhi", true);
alg->getLogger().information("Detector positions in IDF updated with "
"positions in the data file except for the "
"phi values");
} else {
alg->getLogger().information(
"Detector positions in IDF updated with positions in the data file");
}
// We want this to throw if it fails to warn the user that the information
// is not correct.
updateInst->execute();
}
return executionSuccessful;
}
//-----------------------------------------------------------------------------
/** Load the run number and other meta data from the given bank */
template <typename T>
void LoadEventNexus::loadEntryMetadata(const std::string &nexusfilename, T WS,
const std::string &entry_name) {
// Open the file
::NeXus::File file(nexusfilename);
file.openGroup(entry_name, "NXentry");
// get the title
try {
file.openData("title");
if (file.getInfo().type == ::NeXus::CHAR) {
std::string title = file.getStrData();
if (!title.empty())
WS->setTitle(title);
}
file.closeData();
} catch (std::exception &) {
// don't set the title if the field is not loaded
}
// get the notes
try {
file.openData("notes");
if (file.getInfo().type == ::NeXus::CHAR) {
std::string notes = file.getStrData();
if (!notes.empty())
WS->mutableRun().addProperty("file_notes", notes);
}
file.closeData();
} catch (::NeXus::Exception &) {
// let it drop on floor
}
// Get the run number
file.openData("run_number");
std::string run;
if (file.getInfo().type == ::NeXus::CHAR) {
run = file.getStrData();
} else if (file.isDataInt()) {
// inside ISIS the run_number type is int32
std::vector<int> value;
file.getData(value);
if (!value.empty())
run = std::to_string(value[0]);
}
if (!run.empty()) {
WS->mutableRun().addProperty("run_number", run);
}
file.closeData();
// get the experiment identifier
try {
file.openData("experiment_identifier");
std::string expId;
if (file.getInfo().type == ::NeXus::CHAR) {
expId = file.getStrData();
}
if (!expId.empty()) {
WS->mutableRun().addProperty("experiment_identifier", expId);
}
file.closeData();
} catch (::NeXus::Exception &) {
// let it drop on floor
}
// get the sample name - nested try/catch to leave the handle in an
// appropriate state
try {
file.openGroup("sample", "NXsample");
try {
file.openData("name");
const auto info = file.getInfo();
std::string name;
if (info.type == ::NeXus::CHAR) {
if (info.dims.size() == 1) {
name = file.getStrData();
} else { // something special for 2-d array
const int64_t total_length = std::accumulate(
info.dims.begin(), info.dims.end(), static_cast<int64_t>(1),
std::multiplies<int64_t>());
boost::scoped_array<char> val_array(new char[total_length]);
file.getData(val_array.get());
file.closeData();
name = std::string(val_array.get(), total_length);
}
}
file.closeData();
if (!name.empty()) {
WS->mutableSample().setName(name);
}
} catch (::NeXus::Exception &) {
// let it drop on floor
}
file.closeGroup();
} catch (::NeXus::Exception &) {
// let it drop on floor
}
// get the duration
file.openData("duration");
std::vector<double> duration;
file.getDataCoerce(duration);
if (duration.size() == 1) {
// get the units
// clang-format off
std::vector< ::NeXus::AttrInfo> infos = file.getAttrInfos();
std::string units;
for (std::vector< ::NeXus::AttrInfo>::const_iterator it = infos.begin();
it != infos.end(); ++it) {
if (it->name == "units") {
units = file.getStrAttr(*it);
break;
}
}
// clang-format on
// set the property
WS->mutableRun().addProperty("duration", duration[0], units);
}
file.closeData();
// close the file
file.close();
}
//-----------------------------------------------------------------------------
/** Load the instrument from the nexus file or if not found from the IDF file
* specified by the info in the Nexus file
*
* @param nexusfilename :: The Nexus file name
* @param localWorkspace :: templated workspace in which to put the instrument
*geometry
* @param top_entry_name :: entry name at the top of the Nexus file
* @param alg :: Handle of the algorithm
* @return true if successful
*/
template <typename T>
bool LoadEventNexus::loadInstrument(const std::string &nexusfilename,
T localWorkspace,
const std::string &top_entry_name,
Algorithm *alg) {
bool foundInstrument = runLoadIDFFromNexus<T>(nexusfilename, localWorkspace,
top_entry_name, alg);
if (!foundInstrument)
foundInstrument = runLoadInstrument<T>(nexusfilename, localWorkspace,
top_entry_name, alg);
return foundInstrument;
}
//-----------------------------------------------------------------------------
/** Load the instrument from the nexus file
*
* @param nexusfilename :: The name of the nexus file being loaded
* @param localWorkspace :: templated workspace in which to put the instrument
*geometry
* @param top_entry_name :: entry name at the top of the Nexus file
* @param alg :: Handle of the algorithm
* @return true if successful
*/
template <typename T>
bool LoadEventNexus::runLoadIDFFromNexus(const std::string &nexusfilename,
T localWorkspace,
const std::string &top_entry_name,
Algorithm *alg) {
// Test if IDF exists in file, move on quickly if not
try {
::NeXus::File nxsfile(nexusfilename);
nxsfile.openPath(top_entry_name + "/instrument/instrument_xml");
} catch (::NeXus::Exception &) {
alg->getLogger().information("No instrument definition found in " +
nexusfilename + " at " + top_entry_name +
"/instrument");
return false;
}
Mantid::API::IAlgorithm_sptr loadInst =
alg->createChildAlgorithm("LoadIDFFromNexus");
// Now execute the Child Algorithm. Catch and log any error, but don't stop.
try {
loadInst->setPropertyValue("Filename", nexusfilename);
loadInst->setProperty<Mantid::API::MatrixWorkspace_sptr>("Workspace",
localWorkspace);
loadInst->setPropertyValue("InstrumentParentPath", top_entry_name);
loadInst->execute();
} catch (std::invalid_argument &) {
alg->getLogger().error(
"Invalid argument to LoadIDFFromNexus Child Algorithm ");
} catch (std::runtime_error &) {
alg->getLogger().debug("No instrument definition found in " +
nexusfilename + " at " + top_entry_name +
"/instrument");
}
if (!loadInst->isExecuted())
alg->getLogger().information("No IDF loaded from Nexus file.");
return loadInst->isExecuted();
}
} // namespace DataHandling
} // namespace Mantid
#endif /*MANTID_DATAHANDLING_LOADEVENTNEXUS_H_*/