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//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
#include "MantidNexus/LoadEventNexus.h"
#include "MantidGeometry/IInstrument.h"
#include "MantidGeometry/Instrument/CompAssembly.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidAPI/FileProperty.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/Timer.h"
#include "MantidAPI/MemoryManager.h"
#include "MantidAPI/LoadAlgorithmFactory.h" // For the DECLARE_LOADALGORITHM macro
#include <fstream>
#include <sstream>
#include <boost/algorithm/string/replace.hpp>
#include <Poco/File.h>
#include <Poco/Path.h>
using std::endl;
using std::map;
using std::string;
using std::vector;
using namespace ::NeXus;
using namespace Mantid::Geometry;
using namespace Mantid::DataObjects;
namespace Mantid
{
namespace NeXus
{
DECLARE_ALGORITHM(LoadEventNexus)
DECLARE_LOADALGORITHM(LoadEventNexus)
using namespace Kernel;
using namespace API;
using Geometry::Instrument;
/// Empty default constructor
LoadEventNexus::LoadEventNexus() : IDataFileChecker()
{}
/**
* Do a quick file type check by looking at the first 100 bytes of the file
* @param filePath :: path of the file including name.
* @param nread :: no.of bytes read
* @param header :: The first 100 bytes of the file as a union
* @return true if the given file is of type which can be loaded by this algorithm
*/
bool LoadEventNexus::quickFileCheck(const std::string& filePath,size_t nread, const file_header& header)
{
std::string ext = this->extension(filePath);
// If the extension is nxs then give it a go
if( ext.compare("nxs") == 0 ) return true;
// If not then let's see if it is a HDF file by checking for the magic cookie
if ( nread >= sizeof(int32_t) && (ntohl(header.four_bytes) == g_hdf_cookie) ) return true;
return false;
}
/**
* Checks the file by opening it and reading few lines
* @param filePath :: name of the file inluding its path
* @return an integer value how much this algorithm can load the file
*/
int LoadEventNexus::fileCheck(const std::string& filePath)
{
int confidence(0);
try
{
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::NeXus::File file = ::NeXus::File(filePath);
// Open the base group called 'entry'
file.openGroup("entry", "NXentry");
// If all this succeeded then we'll assume this is an SNS Event NeXus file
confidence = 80;
}
catch(::NeXus::Exception&)
{
}
return confidence;
}
/// Initialisation method.
void LoadEventNexus::init()
{
this->setOptionalMessage(
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"Optionally, you can filter out events falling outside a\n"
"range of times-of-flight and/or a time interval.");
this->declareProperty(new FileProperty("Filename", "", FileProperty::Load, ".nxs"),
"The name (including its full or relative path) of the Nexus file to\n"
"attempt to load. The file extension must either be .nxs or .NXS" );
this->declareProperty(
new WorkspaceProperty<IEventWorkspace>("OutputWorkspace", "", Direction::Output),
"The name of the output EventWorkspace in which to load the EventNexus file." );
declareProperty(
new PropertyWithValue<double>("FilterByTof_Min", EMPTY_DBL(), Direction::Input),
"Optional: To exclude events that do not fall within a range of times-of-flight.\n"\
"This is the minimum accepted value in microseconds." );
declareProperty(
new PropertyWithValue<double>("FilterByTof_Max", EMPTY_DBL(), Direction::Input),
"Optional: To exclude events that do not fall within a range of times-of-flight.\n"\
"This is the maximum accepted value in microseconds." );
declareProperty(
new PropertyWithValue<double>("FilterByTime_Start", EMPTY_DBL(), Direction::Input),
"Optional: To only include events after the provided start time, in seconds (relative to the start of the run).");
declareProperty(
new PropertyWithValue<double>("FilterByTime_Stop", EMPTY_DBL(), Direction::Input),
"Optional: To only include events before the provided stop time, in seconds (relative to the start of the run).");
declareProperty(
new PropertyWithValue<string>("BankName", "", Direction::Input),
"Optional: To only include events from one bank. Any bank whose name does not match the given string will have no events.");
declareProperty(
new PropertyWithValue<bool>("SingleBankPixelsOnly", true, Direction::Input),
"Optional: Only applies if you specified a single bank to load with BankName.\n"
"Only pixels in the specified bank will be created if true; all of the instrument's pixels will be created otherwise.");
declareProperty(
new PropertyWithValue<bool>("LoadMonitors", false, Direction::Input),
"Load the monitors from the file (optional, default False).");
//
// declareProperty(
// new PropertyWithValue<bool>("LoadLogs", true, Direction::Input),
// "Load the sample logs from the file (optional, default True).");
declareProperty(
new PropertyWithValue<bool>("Precount", false, Direction::Input),
"Pre-count the number of events in each pixel before allocating memory (optional, default False). \n"
"This can significantly reduce memory use and memory fragmentation; it may also speed up loading.");
}
//------------------------------------------------------------------------------------------------
/** Executes the algorithm. Reading in the file and creating and populating
* the output workspace
*/
void LoadEventNexus::exec()
{
// Retrieve the filename from the properties
m_filename = getPropertyValue("Filename");
precount = getProperty("Precount");
//loadlogs = getProperty("LoadLogs");
loadlogs = true;
//Get the limits to the filter
filter_tof_min = getProperty("FilterByTof_Min");
filter_tof_max = getProperty("FilterByTof_Max");
if ( (filter_tof_min == EMPTY_DBL()) || (filter_tof_max == EMPTY_DBL()))
{
//Nothing specified. Include everything
filter_tof_min = -1e20;
filter_tof_max = +1e20;
}
else if ( (filter_tof_min != EMPTY_DBL()) || (filter_tof_max != EMPTY_DBL()))
{
//Both specified. Keep these values
}
else
throw std::invalid_argument("You must specify both the min and max of time of flight to filter, or neither!");
// Check to see if the monitors need to be loaded later
bool load_monitors = this->getProperty("LoadMonitors");
// Create the output workspace
WS = EventWorkspace_sptr(new EventWorkspace());
//Make sure to initialize.
// We can use dummy numbers for arguments, for event workspace it doesn't matter
WS->initialize(1,1,1);
// Set the units
WS->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
WS->setYUnit("Counts");
//Initialize progress reporting.
//3 calls for the first part, 4 if monitors are loaded
int reports = 4;
if (load_monitors)
{
reports++;
}
Progress prog(this,0.0,0.3, reports);
if (loadlogs)
{
// --------------------- Load DAS Logs -----------------
prog.report("Loading DAS logs");
//The pulse times will be empty if not specified in the DAS logs.
pulseTimes.clear();
IAlgorithm_sptr loadLogs = createSubAlgorithm("LoadLogsFromSNSNexus");
// Now execute the sub-algorithm. Catch and log any error, but don't stop.
try
{
g_log.information() << "Loading logs from NeXus file..." << endl;
loadLogs->setPropertyValue("Filename", m_filename);
loadLogs->setProperty<MatrixWorkspace_sptr> ("Workspace", WS);
loadLogs->execute();
//If successful, we can try to load the pulse times
Kernel::TimeSeriesProperty<double> * log = dynamic_cast<Kernel::TimeSeriesProperty<double> *>( WS->mutableRun().getProperty("proton_charge") );
std::vector<Kernel::DateAndTime> temp = log->timesAsVector();
for (size_t i =0; i < temp.size(); i++)
pulseTimes.push_back( temp[i] );
// Use the first pulse as the run_start time.
if (temp.size() > 0)
{
// add the start of the run as a ISO8601 date/time string. The start = the first pulse.
// (this is used in LoadInstrumentHelper to find the right instrument file to use).
WS->mutableRun().addProperty("run_start", temp[0].to_ISO8601_string(), true );
}
}
catch (...)
{
g_log.error() << "Error while loading Logs from SNS Nexus. Some sample logs may be missing." << std::endl;
}
}
else
{
g_log.information() << "Skipping the loading of sample logs!" << endl;
}
prog.report("Loading instrument");
//Load the instrument
runLoadInstrument(m_filename, WS);
if (!this->instrument_loaded_correctly)
throw std::runtime_error("Instrument was not initialized correctly! Loading cannot continue.");
if (load_monitors)
{
prog.report("Loading monitors");
this->runLoadMonitors();
}
// Delete the output workspace name if it existed
std::string outName = getPropertyValue("OutputWorkspace");
if (AnalysisDataService::Instance().doesExist(outName))
AnalysisDataService::Instance().remove( outName );
// top level file information
::NeXus::File file(m_filename);
//Start with the base entry
file.openGroup("entry", "NXentry");
//Now we want to go through all the bankN_event entries
map<string, string> entries = file.getEntries();
std::vector<string> bankNames;
map<string,string>::const_iterator it = entries.begin();
for (; it != entries.end(); it++)
{
std::string entry_name(it->first);
std::string entry_class(it->second);
if ((entry_class == "NXevent_data"))
{
bankNames.push_back( entry_name );
}
}
//Close up the file
file.closeGroup();
file.close();
// --------- Loading only one bank ----------------------------------
std::string onebank = getProperty("BankName");
bool doOneBank = (onebank != "");
bool SingleBankPixelsOnly = getProperty("SingleBankPixelsOnly");
if (doOneBank)
{
bankNames.clear();
bankNames.push_back( onebank + "_events" );
}
prog.report("Initializing all pixels");
//----------------- Pad Empty Pixels -------------------------------
if (!this->instrument_loaded_correctly)
{
g_log.warning() << "Warning! Cannot pad empty pixels, since the instrument geometry did not load correctly or was not specified. Sorry!\n";
}
else
{
Timer tim1;
//Pad pixels; parallel flag is off because it is actually slower :(
if (doOneBank && SingleBankPixelsOnly)
{
// ---- Pad a pixel for each detector inside the bank -------
int wi = 0;
IInstrument_sptr inst = WS->getInstrument();
boost::shared_ptr<IComponent> comp = inst->getComponentByName(onebank);
boost::shared_ptr<ICompAssembly> bank = boost::dynamic_pointer_cast<ICompAssembly>(comp);
if (bank)
{
// Get a vector of children (recursively)
std::vector<boost::shared_ptr<IComponent> > children;
bank->getChildren(children, true);
std::vector<boost::shared_ptr<IComponent> >::iterator it;
for (it = children.begin(); it != children.end(); it++)
{
IDetector_sptr det = boost::dynamic_pointer_cast<IDetector>(*it);
if (det)
{
WS->getOrAddEventList(wi).addDetectorID( det->getID() );
wi++;
}
}
WS->doneAddingEventLists();
}
else
throw std::runtime_error("Could not find the bank named " + onebank + " as a component assembly in the instrument tree.");
}
else
{
WS->padPixels( false );
}
//std::cout << tim1.elapsed() << "seconds to pad pixels.\n";
}
// -- Time filtering --
double filter_time_start_sec, filter_time_stop_sec;
filter_time_start_sec = getProperty("FilterByTime_Start");
filter_time_stop_sec = getProperty("FilterByTime_Stop");
//Default to ALL pulse times
bool is_time_filtered = false;
filter_time_start = Kernel::DateAndTime::minimum();
filter_time_stop = Kernel::DateAndTime::maximum();
if (pulseTimes.size() > 0)
{
//If not specified, use the limits of doubles. Otherwise, convert from seconds to absolute PulseTime
if (filter_time_start_sec != EMPTY_DBL())
{
filter_time_start = pulseTimes[0] + filter_time_start_sec;
is_time_filtered = true;
}
if (filter_time_stop_sec != EMPTY_DBL())
{
filter_time_stop = pulseTimes[0] + filter_time_stop_sec;
is_time_filtered = true;
}
//Silly values?
if (filter_time_stop < filter_time_start)
throw std::invalid_argument("Your filter for time's Stop value is smaller than the Start value.");
}
//Count the limits to time of flight
shortest_tof = static_cast<double>(std::numeric_limits<uint32_t>::max()) * 0.1;
longest_tof = 0.;
Progress prog2(this,0.3,1.0, bankNames.size());
//This map will be used to find the workspace index
IndexToIndexMap * pixelID_to_wi_map = WS->getDetectorIDToWorkspaceIndexMap(false);
// Now go through each bank.
// This'll be parallelized - but you can't run it in parallel if you couldn't pad the pixels.
PARALLEL_FOR_IF( (this->instrument_loaded_correctly) )
for (int i=0; i < static_cast<int>(bankNames.size()); i++)
{
PARALLEL_START_INTERUPT_REGION
prog2.report("Loading " + bankNames[i]);
this->loadBankEventData(bankNames[i], pixelID_to_wi_map);
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
//Don't need the map anymore.
delete pixelID_to_wi_map;
if (is_time_filtered)
{
//Now filter out the run, using the DateAndTime type.
WS->mutableRun().filterByTime(filter_time_start, filter_time_stop);
}
//Info reporting
g_log.information() << "Read " << WS->getNumberEvents() << " events"
<< ". Shortest TOF: " << shortest_tof << " microsec; longest TOF: "
<< longest_tof << " microsec." << std::endl;
//Now, create a default X-vector for histogramming, with just 2 bins.
Kernel::cow_ptr<MantidVec> axis;
MantidVec& xRef = axis.access();
xRef.resize(2);
xRef[0] = shortest_tof - 1; //Just to make sure the bins hold it all
xRef[1] = longest_tof + 1;
//Set the binning axis using this.
WS->setAllX(axis);
// set more properties on the workspace
this->loadEntryMetadata("entry");
//Save output
this->setProperty<IEventWorkspace_sptr>("OutputWorkspace", WS);
// Clear any large vectors to free up memory.
this->pulseTimes.clear();
return;
}
void LoadEventNexus::loadEntryMetadata(const std::string &entry_name) {
// Open the file
::NeXus::File file(m_filename);
file.openGroup(entry_name, "NXentry");
// get the title
file.openData("title");
if (file.getInfo().type == ::NeXus::CHAR) {
string title = file.getStrData();
if (!title.empty())
WS->setTitle(title);
}
file.closeData();
// TODO get the run number
file.openData("run_number");
string run("");
if (file.getInfo().type == ::NeXus::CHAR) {
run = file.getStrData();
}
if (!run.empty()) {
WS->mutableRun().addProperty("run_number", run);
}
file.closeData();
// close the file
file.close();
}
//------------------------------------------------------------------------------------------------
/**
* Load one of the banks' event data from the nexus file
* @param entry_name :: The pathname of the bank to load
* @param pixelID_to_wi_map :: a map where key = pixelID and value = the workpsace index to use.
*/
void LoadEventNexus::loadBankEventData(const std::string entry_name, IndexToIndexMap * pixelID_to_wi_map)
{
//Local tof limits
double my_shortest_tof, my_longest_tof;
my_shortest_tof = static_cast<double>(std::numeric_limits<uint32_t>::max()) * 0.1;
my_longest_tof = 0.;
//The vectors we will be filling
std::vector<uint64_t> event_index;
std::vector<uint32_t> event_id;
std::vector<float> event_time_of_flight;
bool loadError = false ;
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PARALLEL_CRITICAL(LoadEventNexus_loadBankEventData_nexus_file_access)
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{
// Open the file
::NeXus::File file(m_filename);
file.openGroup("entry", "NXentry");
//Open the bankN_event group
file.openGroup(entry_name, "NXevent_data");
// Get the event_index (a list of size of # of pulses giving the index in the event list for that pulse)
file.openData("event_index");
//Must be uint64
if (file.getInfo().type == ::NeXus::UINT64)
file.getData(event_index);
else
{
g_log.warning() << "Entry " << entry_name << "'s event_index field is not UINT64! It will be skipped.\n";
loadError = true;
}
file.closeData();
// Look for the sign that the bank is empty
if (event_index.size()==1)
{
if (event_index[0] == 0)
{
//One entry, only zero. This means NO events in this bank.
loadError = true;
g_log.debug() << "Bank " << entry_name << " is empty.\n";
}
}
if (!loadError)
{
bool old_nexus_file_names = false;
// Get the list of pixel ID's
try
{
file.openData("event_id");
}
catch (::NeXus::Exception& )
{
//Older files (before Nov 5, 2010) used this field.
file.openData("event_pixel_id");
old_nexus_file_names = true;
}
//Must be uint32
if (file.getInfo().type == ::NeXus::UINT32)
file.getData(event_id);
else
{
g_log.warning() << "Entry " << entry_name << "'s event_id field is not UINT32! It will be skipped.\n";
loadError = true;
}
file.closeData();
if (!loadError)
{
// Get the list of event_time_of_flight's
if (!old_nexus_file_names)
file.openData("event_time_offset");
else
file.openData("event_time_of_flight");
//Check that the type is what it is supposed to be
if (file.getInfo().type == ::NeXus::FLOAT32)
file.getData(event_time_of_flight);
else
{
g_log.warning() << "Entry " << entry_name << "'s event_time_offset field is not FLOAT32! It will be skipped.\n";
loadError = true;
}
if (!loadError)
{
std::string units;
file.getAttr("units", units);
if (units != "microsecond")
{
g_log.warning() << "Entry " << entry_name << "'s event_time_offset field's units are not microsecond. It will be skipped.\n";
loadError = true;
}
file.closeData();
} //no error
} //no error
} //no error
//Close up the file
file.closeGroup();
file.close();
} // END of critical block.
//Abort if anything failed
if (loadError)
return;
// Two arrays must be the same size
if (event_id.size() != event_time_of_flight.size())
{
g_log.warning() << "Entry " << entry_name << "'s event_time_offset and event_id vectors are not the same size! It will be skipped.\n";
return;
}
// ---- Pre-counting events per pixel ID ----
if (precount)
{
std::map<uint32_t, size_t> counts; // key = pixel ID, value = count
std::vector<uint32_t>::const_iterator it;
for (it = event_id.begin(); it != event_id.end(); it++)
{
std::map<uint32_t, size_t>::iterator map_found = counts.find(*it);
if (map_found != counts.end())
{
map_found->second++;
}
else
{
counts[*it] = 1; // First entry
}
}
// Now we pre-allocate (reserve) the vectors of events in each pixel counted
std::map<uint32_t, size_t>::iterator pixID;
for (pixID = counts.begin(); pixID != counts.end(); pixID++)
{
//Find the the workspace index corresponding to that pixel ID
int wi((*pixelID_to_wi_map)[ pixID->first ]);
// Allocate it
WS->getEventList(wi).reserve( pixID->second );
}
}
//Default pulse time (if none are found)
Mantid::Kernel::DateAndTime pulsetime;
// Index into the pulse array
int pulse_i = 0;
// And there are this many pulses
int numPulses = static_cast<int>(pulseTimes.size());
if (numPulses > static_cast<int>(event_index.size()))
{
g_log.warning() << "Entry " << entry_name << "'s event_index vector is smaller than the proton_charge DAS log. This is inconsistent, so we cannot find pulse times for this entry.\n";
//This'll make the code skip looking for any pulse times.
pulse_i = numPulses + 1;
}
//Go through all events in the list
std::size_t numEvents = event_id.size();
for (std::size_t i = 0; i < numEvents; i++)
{
//Find the pulse time for this event index
if (pulse_i < numPulses-1)
{
//Go through event_index until you find where the index increases to encompass the current index. Your pulse = the one before.
while ( !((i >= event_index[pulse_i]) && (i < event_index[pulse_i+1])))
{
pulse_i++;
if (pulse_i >= (numPulses-1))
break;
}
//Save the pulse time at this index for creating those events
pulsetime = pulseTimes[pulse_i];
}
//Does this event pass the time filter?
if ((pulsetime < filter_time_stop) && (pulsetime >= filter_time_start))
{
//Create the tofevent
double tof = static_cast<double>( event_time_of_flight[i] );
if ((tof >= filter_tof_min) && (tof <= filter_tof_max))
{
//The event TOF passes the filter.
TofEvent event(tof, pulsetime);
//Find the the workspace index corresponding to that pixel ID
int wi((*pixelID_to_wi_map)[event_id[i]]);
// Add it to the list at that workspace index
WS->getEventList(wi).addEventQuickly( event );
//Local tof limits
if (tof < my_shortest_tof) { my_shortest_tof = tof;}
if (tof > my_longest_tof) { my_longest_tof = tof;}
}
}
}
//Join back up the tof limits to the global ones
PARALLEL_CRITICAL(tof_limits)
{
//This is not thread safe, so only one thread at a time runs this.
if (my_shortest_tof < shortest_tof) { shortest_tof = my_shortest_tof;}
if (my_longest_tof > longest_tof ) { longest_tof = my_longest_tof;}
}
}
//-----------------------------------------------------------------------------
/** Load the instrument geometry File
* @param nexusfilename :: Used to pick the instrument.
* @param localWorkspace :: MatrixWorkspace in which to put the instrument geometry
*/
void LoadEventNexus::runLoadInstrument(const std::string &nexusfilename, MatrixWorkspace_sptr localWorkspace)
{
string instrument;
// Get the instrument name
::NeXus::File nxfile(nexusfilename);
//Start with the base entry
nxfile.openGroup("entry", "NXentry");
// Open the instrument
nxfile.openGroup("instrument", "NXinstrument");
nxfile.openData("name");
instrument = nxfile.getStrData();
g_log.debug() << "Instrument name read from NeXus file is " << instrument << std::endl;
if (instrument.compare("POWGEN3") == 0) // hack for powgen b/c of bad long name
instrument = "POWGEN";
// Now let's close the file as we don't need it anymore to load the instrument.
nxfile.close();
// do the actual work
IAlgorithm_sptr loadInst= createSubAlgorithm("LoadInstrument");
// Now execute the sub-algorithm. Catch and log any error, but don't stop.
bool executionSuccessful(true);
try
{
loadInst->setPropertyValue("InstrumentName", instrument);
loadInst->setProperty<MatrixWorkspace_sptr> ("Workspace", localWorkspace);
loadInst->execute();
// Populate the instrument parameters in this workspace - this works around a bug
localWorkspace->populateInstrumentParameters();
} catch (std::invalid_argument& e)
{
g_log.information() << "Invalid argument to LoadInstrument sub-algorithm : " << e.what() << std::endl;
executionSuccessful = false;
} catch (std::runtime_error& e)
{
g_log.information("Unable to successfully run LoadInstrument sub-algorithm");
g_log.information(e.what());
executionSuccessful = false;
}
// If loading instrument definition file fails
if (!executionSuccessful)
{
g_log.error() << "Error loading Instrument definition file\n";
}
else
{
this->instrument_loaded_correctly = true;
}
}
/**
* Load the Monitors from the NeXus file into a workspace. The original
* workspace name is used and appended with _monitors.
*/
void LoadEventNexus::runLoadMonitors()
{
IAlgorithm_sptr loadMonitors = this->createSubAlgorithm("LoadNexusMonitors");
std::string mon_wsname = this->getProperty("OutputWorkspace");
mon_wsname.append("_monitors");
try
{
this->g_log.information() << "Loading monitors from NeXus file..."
<< std::endl;
loadMonitors->setPropertyValue("Filename", m_filename);
this->g_log.information() << "New workspace name for monitors: "
<< mon_wsname << std::endl;
loadMonitors->setPropertyValue("OutputWorkspace", mon_wsname);
loadMonitors->execute();
MatrixWorkspace_sptr mons = loadMonitors->getProperty("OutputWorkspace");
this->declareProperty(new WorkspaceProperty<>("MonitorWorkspace",
mon_wsname, Direction::Output), "Monitors from the Event NeXus file");
this->setProperty("MonitorWorkspace", mons);
}
catch (...)
{
this->g_log.error() << "Error while loading the monitors from the file. "
<< "File may contain no monitors." << std::endl;
}
}
} // namespace NeXus
} // namespace Mantid