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FilterEventsByLogValuePreNexus.cpp
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FilterEventsByLogValuePreNexus.cpp
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// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidDataHandling/FilterEventsByLogValuePreNexus.h"
#include "MantidAPI/Axis.h"
#include "MantidAPI/FileFinder.h"
#include "MantidAPI/FileProperty.h"
#include "MantidAPI/RegisterFileLoader.h"
#include "MantidAPI/Run.h"
#include "MantidAPI/TableRow.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/EventList.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/TableWorkspace.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidGeometry/IDetector.h"
#include "MantidGeometry/Instrument.h"
#include "MantidGeometry/Instrument/DetectorInfo.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/BinaryFile.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidKernel/CPUTimer.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/FileValidator.h"
#include "MantidKernel/Glob.h"
#include "MantidKernel/ListValidator.h"
#include "MantidKernel/OptionalBool.h"
#include "MantidKernel/System.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/VisibleWhenProperty.h"
#if BOOST_VERSION < 107100
#include <boost/timer.hpp>
#else
#include <boost/timer/timer.hpp>
#endif
#include <Poco/File.h>
#include <Poco/Path.h>
#include <algorithm>
#include <functional>
#include <set>
#include <sstream>
#include <stdexcept>
#include <vector>
// #define DBOUT
namespace Mantid::DataHandling {
DECLARE_FILELOADER_ALGORITHM(FilterEventsByLogValuePreNexus)
using namespace Kernel;
using namespace API;
using namespace DataObjects;
using namespace Geometry;
using DataObjects::EventList;
using DataObjects::EventWorkspace;
using DataObjects::EventWorkspace_sptr;
using std::ifstream;
using std::runtime_error;
using std::string;
using std::stringstream;
using std::vector;
using Types::Core::DateAndTime;
using Types::Event::TofEvent;
//----------------------------------------------------------------------------------------------
// constants for locating the parameters to use in execution
//----------------------------------------------------------------------------------------------
static const string EVENT_PARAM("EventFilename");
static const string PULSEID_PARAM("PulseidFilename");
static const string MAP_PARAM("MappingFilename");
static const string PID_PARAM("SpectrumList");
static const string PARALLEL_PARAM("UseParallelProcessing");
static const string BLOCK_SIZE_PARAM("LoadingBlockSize");
static const string OUT_PARAM("OutputWorkspace");
/// All pixel ids with matching this mask are errors.
static const PixelType ERROR_PID = 0x80000000;
/// The maximum possible tof as native type
static const uint32_t MAX_TOF_UINT32 = std::numeric_limits<uint32_t>::max();
/// Conversion factor between 100 nanoseconds and 1 microsecond.
static const double TOF_CONVERSION = .1;
/// Conversion factor between picoColumbs and microAmp*hours
static const double CURRENT_CONVERSION = 1.e-6 / 3600.;
/// Veto mask as 0xFF000000000
static const uint64_t VETOFLAG(72057594037927935);
static const string EVENT_EXTS[] = {"_neutron_event.dat", "_neutron0_event.dat", "_neutron1_event.dat",
"_neutron2_event.dat", "_neutron3_event.dat", "_live_neutron_event.dat"};
static const string PULSE_EXTS[] = {"_pulseid.dat", "_pulseid0.dat", "_pulseid1.dat",
"_pulseid2.dat", "_pulseid3.dat", "_live_pulseid.dat"};
static const int NUM_EXT = 6;
//----------------------------------------------------------------------------------------------
// Functions to deal with file name and run information
//----------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------
/** Get run number
*/
static string getRunnumber(const string &filename) {
// start by trimming the filename
string runnumber(Poco::Path(filename).getBaseName());
if (runnumber.find("neutron") >= string::npos)
return "0";
std::size_t left = runnumber.find('_');
std::size_t right = runnumber.find('_', left + 1);
return runnumber.substr(left + 1, right - left - 1);
}
//----------------------------------------------------------------------------------------------
/** Generate pulse ID
*/
static string generatePulseidName(string eventfile) {
// initialize vector of endings and put live at the beginning
vector<string> eventExts(EVENT_EXTS, EVENT_EXTS + NUM_EXT);
std::reverse(eventExts.begin(), eventExts.end());
vector<string> pulseExts(PULSE_EXTS, PULSE_EXTS + NUM_EXT);
std::reverse(pulseExts.begin(), pulseExts.end());
// look for the correct ending
for (std::size_t i = 0; i < eventExts.size(); ++i) {
size_t start = eventfile.find(eventExts[i]);
if (start != string::npos)
return eventfile.replace(start, eventExts[i].size(), pulseExts[i]);
}
// give up and return nothing
return "";
}
//----------------------------------------------------------------------------------------------
/** Generate mapping file name
*/
static string generateMappingfileName(EventWorkspace_sptr &wksp) {
// get the name of the mapping file as set in the parameter files
std::vector<string> temp = wksp->getInstrument()->getStringParameter("TS_mapping_file");
if (temp.empty())
return "";
string mapping = temp[0];
// Try to get it from the working directory
Poco::File localmap(mapping);
if (localmap.exists())
return mapping;
// Try to get it from the data directories
string dataversion = Mantid::API::FileFinder::Instance().getFullPath(mapping);
if (!dataversion.empty())
return dataversion;
// get a list of all proposal directories
string instrument = wksp->getInstrument()->getName();
Poco::File base("/SNS/" + instrument + "/");
// try short instrument name
if (!base.exists()) {
return "";
#if 0
instrument = Kernel::ConfigService::Instance().getInstrument(instrument).shortName();
base = Poco::File("/SNS/" + instrument + "/");
if (!base.exists())
return "";
#endif
}
vector<string> dirs; // poco won't let me reuse temp
base.list(dirs);
// check all of the proposals for the mapping file in the canonical place
const string CAL("_CAL");
const size_t CAL_LEN = CAL.length(); // cache to make life easier
vector<string> files;
for (auto &dir : dirs) {
if ((dir.length() > CAL_LEN) && (dir.compare(dir.length() - CAL.length(), CAL.length(), CAL) == 0)) {
std::string path = std::string(base.path()).append("/").append(dir).append("/calibrations/").append(mapping);
if (Poco::File(path).exists()) {
files.emplace_back(path);
}
}
}
if (files.empty())
return std::string();
else if (files.size() == 1)
return files[0];
else // just assume that the last one is the right one, this should never be
// fired
return *(files.rbegin());
}
//----------------------------------------------------------------------------------------------
// Member functions
//----------------------------------------------------------------------------------------------
//----------------------------------------------------------------------------------------------
/** Constructor
*/
FilterEventsByLogValuePreNexus::FilterEventsByLogValuePreNexus()
: Mantid::API::IFileLoader<Kernel::FileDescriptor>(), m_protonChargeTot(0), m_detid_max(0), m_eventFile(nullptr),
m_numEvents(0), m_numPulses(0), m_numPixel(0), m_numGoodEvents(0), m_numErrorEvents(0), m_numBadEvents(0),
m_numWrongdetidEvents(0), m_numIgnoredEvents(0), m_firstEvent(0), m_maxNumEvents(0), m_usingMappingFile(false),
m_loadOnlySomeSpectra(false), m_longestTof(0.0), m_shortestTof(0.0), m_parallelProcessing(false),
m_pulseTimesIncreasing(false), m_throwError(true), m_examEventLog(false), m_pixelid2exam(0), m_numevents2write(0),
m_freqHz(0), m_istep(0), m_dbPixelID(0), m_useDBOutput(false), m_corretctTOF(false) {}
//----------------------------------------------------------------------------------------------
/** Destructor
*/
FilterEventsByLogValuePreNexus::~FilterEventsByLogValuePreNexus() = default;
//----------------------------------------------------------------------------------------------
/** Return the confidence with with this algorithm can load the file
* @param descriptor A descriptor for the file
* @returns An integer specifying the confidence level. 0 indicates it will not
* be used
*/
int FilterEventsByLogValuePreNexus::confidence(Kernel::FileDescriptor &descriptor) const {
if (descriptor.extension().rfind("dat") == std::string::npos)
return 0;
// If this looks like a binary file where the exact file length is a multiple
// of the DasEvent struct then we're probably okay.
if (descriptor.isAscii())
return 0;
const size_t objSize = sizeof(DasEvent);
auto &handle = descriptor.data();
// get the size of the file in bytes and reset the handle back to the
// beginning
handle.seekg(0, std::ios::end);
const auto filesize = static_cast<size_t>(handle.tellg());
handle.seekg(0, std::ios::beg);
if (filesize % objSize == 0)
return 10;
else
return 0;
}
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm
*/
void FilterEventsByLogValuePreNexus::init() {
// File files to use
vector<string> eventExts(EVENT_EXTS, EVENT_EXTS + NUM_EXT);
declareProperty(std::make_unique<FileProperty>(EVENT_PARAM, "", FileProperty::Load, eventExts),
"The name of the neutron event file to read, including its full or "
"relative path. In most cases, the file typically ends in "
"neutron_event.dat (N.B. case sensitive if running on Linux).");
vector<string> pulseExts(PULSE_EXTS, PULSE_EXTS + NUM_EXT);
declareProperty(std::make_unique<FileProperty>(PULSEID_PARAM, "", FileProperty::OptionalLoad, pulseExts),
"File containing the accelerator pulse information; the "
"filename will be found automatically if not specified.");
declareProperty(std::make_unique<FileProperty>(MAP_PARAM, "", FileProperty::OptionalLoad, ".dat"),
"File containing the pixel mapping (DAS pixels to pixel IDs) file "
"(typically INSTRUMENT_TS_YYYY_MM_DD.dat). The filename will be found "
"automatically if not specified.");
// Pixels to load
declareProperty(std::make_unique<ArrayProperty<int64_t>>(PID_PARAM),
"A list of individual spectra (pixel IDs) to read, specified "
"as e.g. 10:20. Only used if set.");
auto mustBePositive = std::make_shared<BoundedValidator<int>>();
mustBePositive->setLower(1);
declareProperty("ChunkNumber", EMPTY_INT(), mustBePositive,
"If loading the file by sections ('chunks'), this is the "
"section number of this execution of the algorithm.");
declareProperty("TotalChunks", EMPTY_INT(), mustBePositive,
"If loading the file by sections ('chunks'), this is the "
"total number of sections.");
// TotalChunks is only meaningful if ChunkNumber is set
// Would be nice to be able to restrict ChunkNumber to be <= TotalChunks at
// validation
setPropertySettings("TotalChunks", std::make_unique<VisibleWhenProperty>("ChunkNumber", IS_NOT_DEFAULT));
// Loading option
std::vector<std::string> propOptions{"Auto", "Serial", "Parallel"};
declareProperty("UseParallelProcessing", "Auto", std::make_shared<StringListValidator>(propOptions),
"Use multiple cores for loading the data?\n"
" Auto: Use serial loading for small data sets, parallel "
"for large data sets.\n"
" Serial: Use a single core.\n"
" Parallel: Use all available cores.");
// the output workspace name
declareProperty(std::make_unique<WorkspaceProperty<IEventWorkspace>>(OUT_PARAM, "", Direction::Output),
"The name of the workspace that will be created, filled with the read-in "
"data and stored in the [[Analysis Data Service]].");
// Optional output table workspace
declareProperty(
std::make_unique<WorkspaceProperty<ITableWorkspace>>("EventLogTableWorkspace", "", PropertyMode::Optional),
"Optional output table workspace containing the event log "
"(pixel) information. ");
//
std::vector<std::string> vecfunmode{"LoadData", "Filter", "ExamineEventLog"};
declareProperty("FunctionMode", "LoadData", std::make_shared<StringListValidator>(vecfunmode),
"Function mode for different purpose. ");
declareProperty("PixelIDtoExamine", EMPTY_INT(), "Pixel ID for the events to be examined. ");
declareProperty("NumberOfEventsToExamine", EMPTY_INT(), "Number of events on the pixel ID to get examined. ");
declareProperty(std::make_unique<ArrayProperty<int>>("LogPixelIDs"),
"Pixel IDs for event log. Must have 2 (or more) entries. ");
declareProperty(std::make_unique<ArrayProperty<std::string>>("LogPIxelTags"),
"Pixel ID tags for event log. Must have same items as 'LogPixelIDs'. ");
declareProperty("AcceleratorFrequency", 60,
"Freuqency of the accelerator at "
"which the experiment runs. It "
"can 20, 30 or 60.");
declareProperty("CorrectTOFtoSample", false, "Correct TOF to sample position. ");
declareProperty("DBPixelID", EMPTY_INT(), "ID of the pixel (detector) for debug output. ");
}
//----------------------------------------------------------------------------------------------
/** Execute the algorithm
* 1. check all the inputs
* 2. create an EventWorkspace object
* 3. process events
* 4. set out output
*/
void FilterEventsByLogValuePreNexus::exec() {
// Process inputs
m_progress = std::make_unique<Progress>(this, 0.0, 1.0, 100);
processProperties();
// Read input files
m_progress->report("Loading Pulse ID file");
readPulseidFile(m_pulseIDFileName, m_throwError);
m_progress->report("Loading Event File");
openEventFile(m_eventFileName);
// Correct wrong event index in loaded eventindexes
unmaskVetoEventIndexes();
// Find out the frequency of the frequency
int runfreq = findRunFrequency();
if (m_freqHz != runfreq) {
if (m_freqHz % runfreq == 0) {
int frame = m_freqHz / runfreq;
g_log.warning() << "Input frequency " << m_freqHz << " is different from data. "
<< "It is forced to use input frequency, while all "
"events' pulse time will be "
<< "set to " << frame << "-th freme. "
<< "\n";
} else {
throw std::runtime_error("Operation frequency is not self-consistent");
}
}
m_istep = 60 / m_freqHz;
// Create and set up output EventWorkspace
m_localWorkspace = setupOutputEventWorkspace();
if (m_functionMode == "Filter")
m_localWorkspaceBA = setupOutputEventWorkspace();
// Process the events into pixels
if (m_functionMode == "Filter") {
filterEvents();
} else {
procEvents(m_localWorkspace);
}
// set that the sort order on the event lists
if (this->m_numPulses > 0 && this->m_pulseTimesIncreasing) {
const int64_t numberOfSpectra = m_localWorkspace->getNumberHistograms();
PARALLEL_FOR_NO_WSP_CHECK()
for (int64_t i = 0; i < numberOfSpectra; i++) {
PARALLEL_START_INTERRUPT_REGION
m_localWorkspace->getSpectrum(i).setSortOrder(DataObjects::PULSETIME_SORT);
PARALLEL_END_INTERRUPT_REGION
}
PARALLEL_CHECK_INTERRUPT_REGION
}
// Save output
setProperty<IEventWorkspace_sptr>(OUT_PARAM, m_localWorkspace);
if (m_functionMode == "Filter") {
declareProperty(
std::make_unique<WorkspaceProperty<IEventWorkspace>>("OutputFilteredWorkspace", "WS_A", Direction::Output), "");
setProperty<IEventWorkspace_sptr>("OutputFilteredWorkspace", m_localWorkspaceBA);
}
// Add fast frequency sample environment (events) data to workspace's log
processEventLogs();
} // exec()
//----------------------------------------------------------------------------------------------
/** Process input properties
*/
void FilterEventsByLogValuePreNexus::processProperties() {
// Process and check input properties
// Check 'chunk' properties are valid, if set
const int chunks = getProperty("TotalChunks");
if (!isEmpty(chunks) && int(getProperty("ChunkNumber")) > chunks) {
throw std::out_of_range("ChunkNumber cannot be larger than TotalChunks");
}
// What spectra (pixel ID's) to load
this->m_spectraList = this->getProperty(PID_PARAM);
// The event file is needed in case the pulseid fileanme is empty
m_eventFileName = this->getPropertyValue(EVENT_PARAM);
// Pulse ID file
m_pulseIDFileName = this->getPropertyValue(PULSEID_PARAM);
m_throwError = true;
if (m_pulseIDFileName.empty()) {
// Pulse ID file is not given: generate by routine
m_pulseIDFileName = generatePulseidName(m_eventFileName);
if (!m_pulseIDFileName.empty()) {
// Check existence of pulse ID file with generated name
if (Poco::File(m_pulseIDFileName).exists()) {
g_log.information() << "Found pulseid file " << m_pulseIDFileName << "\n";
m_throwError = false;
} else {
m_pulseIDFileName = "";
g_log.warning("Generated pulse ID file name does not point to an "
"existing file. ");
}
} else {
g_log.warning("Generated an empty pulse ID file. ");
}
}
m_functionMode = getPropertyValue("FunctionMode");
m_pixelid2exam = getProperty("PixelIDtoExamine");
m_numevents2write = getProperty("NumberOfEventsToExamine");
// Check whether option function mode is valid
m_examEventLog = false;
if (m_functionMode == "ExamineEventLog") {
bool nogo = false;
if (isEmpty(m_pixelid2exam)) {
nogo = true;
}
if (nogo) {
g_log.warning() << "In functional mode ExamineEventLog, pixel ID must be given!"
<< "\n";
throw std::runtime_error("Incorrect input.");
}
m_examEventLog = true;
} else if (m_functionMode == "Filter") {
m_vecLogPixelID = getProperty("LogPixelIDs");
m_vecLogPixelTag = getProperty("LogPIxelTags");
if (m_vecLogPixelID.size() < 2) {
throw std::runtime_error("Input log pixel IDs must have more than 2 entries. ");
} else if (m_vecLogPixelID.size() != m_vecLogPixelTag.size()) {
throw std::runtime_error("Input log pixel tags must have the same number of items as "
"log pixe IDs. ");
}
}
//---------------------------------------------------------------------------
// Load partial spectra
//---------------------------------------------------------------------------
// For slight speed up
m_loadOnlySomeSpectra = (!this->m_spectraList.empty());
// Turn the spectra list into a map, for speed of access
for (auto spectra : m_spectraList)
spectraLoadMap[spectra] = true;
//---------------------------------------------------------------------------
// Other features
//---------------------------------------------------------------------------
// Accelerator frquency
m_freqHz = getProperty("AcceleratorFrequency");
if (m_freqHz != 20 && m_freqHz != 30 && m_freqHz != 60)
throw runtime_error("Only 20, 30 and 60Hz are supported. ");
int tempint = getProperty("DBPixelID");
if (isEmpty(tempint))
m_useDBOutput = false;
else {
m_useDBOutput = true;
m_dbPixelID = static_cast<int64_t>(tempint);
}
m_corretctTOF = getProperty("CorrectTOFtoSample");
} // END of processProperties
//----------------------------------------------------------------------------------------------
/** Create, initialize and set up output EventWorkspace
*/
DataObjects::EventWorkspace_sptr FilterEventsByLogValuePreNexus::setupOutputEventWorkspace() {
// Create and initialize output EventWorkspace
m_progress->report("Creating output workspace");
EventWorkspace_sptr tempworkspace;
tempworkspace = EventWorkspace_sptr(new EventWorkspace());
// Make sure to initialize. We can use dummy numbers for arguments, for event
// workspace it doesn't matter
tempworkspace->initialize(1, 1, 1);
// Set the units and title
tempworkspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
tempworkspace->setYUnit("Counts");
tempworkspace->setTitle("Dummy Title");
// Add some properties to output workspace, including
// the run_start property (Use the first pulse as the run_start time)
if (this->m_numPulses > 0) {
// add the start of the run as a ISO8601 date/time string. The start = the first
// pulse.
// (this is used in LoadInstrument to find the right instrument file to use).
#if 0
DateAndTime pulse0 = pulsetimes[0];
g_log.notice() << "Pulse time 0 = " << pulse0.totalNanoseconds() << "\n";
#endif
tempworkspace->mutableRun().addProperty("run_start", pulsetimes[0].toISO8601String(), true);
}
// the run number and add it to the run object
tempworkspace->mutableRun().addProperty("run_number", getRunnumber(m_eventFileName));
// Add the instrument!
m_progress->report("Loading Instrument");
this->runLoadInstrument(m_eventFileName, tempworkspace);
// Load the mapping file
m_progress->report("Loading Mapping File");
string mapping_filename = this->getPropertyValue(MAP_PARAM);
if (mapping_filename.empty()) {
// No mapping file given: genrate mapping file name by routine
mapping_filename = generateMappingfileName(tempworkspace);
if (!mapping_filename.empty())
g_log.information() << "Found mapping file \"" << mapping_filename << "\""
<< "\n";
else
g_log.warning("No mapping file is generated. ");
}
// if (!mapping_filename.empty())
loadPixelMap(mapping_filename);
// Create workspace of correct size
// Number of non-monitors in instrument
size_t nSpec = tempworkspace->getInstrument()->getDetectorIDs(true).size();
if (!this->m_spectraList.empty())
nSpec = this->m_spectraList.size();
auto ws = createWorkspace<EventWorkspace>(nSpec, 2, 1);
WorkspaceFactory::Instance().initializeFromParent(*tempworkspace, *ws, true);
return ws;
}
//----------------------------------------------------------------------------------------------
/** Process imbed logs (marked by bad pixel IDs)
* (1) Add special event log to workspace log
* (2) (Optionally) do statistic to each pixel
* (3) (Optionally) write out information
*/
void FilterEventsByLogValuePreNexus::processEventLogs() {
std::map<PixelType, size_t>::iterator mit;
for (const auto pid : this->wrongdetids) {
// Convert Pixel ID to 'wrong detectors ID' map's index
mit = this->wrongdetidmap.find(pid);
size_t mindex = mit->second;
if (mindex > this->wrongdetid_pulsetimes.size()) {
g_log.error() << "Wrong Index " << mindex << " for Pixel " << pid << '\n';
throw std::invalid_argument("Wrong array index for pixel from map");
} else {
g_log.information() << "Processing imbed log marked by Pixel " << pid
<< " with size = " << this->wrongdetid_pulsetimes[mindex].size() << '\n';
}
// Generate the log name
std::stringstream ssname;
ssname << "Pixel" << pid;
std::string logname = ssname.str();
// Add this map entry to log
addToWorkspaceLog(logname, mindex);
// Do some statistic to this event log
doStatToEventLog(mindex);
g_log.information() << "Added Log " << logname << " to output workspace. \n";
} // ENDFOR pit
// Output table workspace
std::string evlog = getPropertyValue("EventLogTableWorkspace");
if (!evlog.empty()) {
// Initialize table workspace
TableWorkspace_sptr evtablews = std::make_shared<TableWorkspace>();
evtablews->addColumn("int", "Pixel-ID");
evtablews->addColumn("int", "NumberOfEvents");
// Add information rows
std::map<PixelType, size_t>::iterator git;
for (git = this->wrongdetidmap.begin(); git != this->wrongdetidmap.end(); ++git) {
PixelType tmpid = git->first;
size_t vindex = git->second;
TableRow temprow = evtablews->appendRow();
temprow << static_cast<int>(tmpid) << static_cast<int>(wrongdetid_pulsetimes[vindex].size());
}
// Set property
setProperty("EventLogTableWorkspace", std::dynamic_pointer_cast<ITableWorkspace>(evtablews));
}
}
//----------------------------------------------------------------------------------------------
/** Add absolute time series to log
* @param logtitle :: title of the log to be inserted to workspace
* @param mindex :: index of the the series in the wrong detectors map
*/
void FilterEventsByLogValuePreNexus::addToWorkspaceLog(const std::string &logtitle, size_t mindex) {
// Create TimeSeriesProperty
auto property = new TimeSeriesProperty<double>(logtitle);
// Add entries
size_t nbins = this->wrongdetid_pulsetimes[mindex].size();
for (size_t k = 0; k < nbins; k++) {
double tof = this->wrongdetid_tofs[mindex][k];
DateAndTime pulsetime = wrongdetid_pulsetimes[mindex][k];
int64_t abstime_ns = pulsetime.totalNanoseconds() + static_cast<int64_t>(tof * 1000);
DateAndTime abstime(abstime_ns);
double value = tof;
property->addValue(abstime, value);
} // ENDFOR
// Add property to workspace
m_localWorkspace->mutableRun().addProperty(property, false);
g_log.information() << "Size of Property " << property->name() << " = " << property->size()
<< " vs Original Log Size = " << nbins << "\n";
}
//----------------------------------------------------------------------------------------------
/** Perform statistics to event (wrong pixel ID) logs
* @param mindex :: index of the the series in the list
*/
void FilterEventsByLogValuePreNexus::doStatToEventLog(size_t mindex) {
// Create a vector of event log time entries
size_t nbins = this->wrongdetid_pulsetimes[mindex].size();
if (nbins <= 2) {
g_log.warning() << "Event log of map index " << mindex << " has " << nbins
<< " entries. There is no need to do statistic on it. "
<< "\n";
}
std::vector<int64_t> vec_logtime(nbins);
for (size_t i = 0; i < nbins; ++i) {
DateAndTime ptime = wrongdetid_pulsetimes[mindex][i];
int64_t templogtime = ptime.totalNanoseconds() + static_cast<int64_t>(wrongdetid_tofs[mindex][i] * 1000.);
vec_logtime[i] = templogtime;
} // ENDFOR
// Sort
std::sort(vec_logtime.begin(), vec_logtime.end());
// Do statistic
int64_t min_dt = vec_logtime[1] - vec_logtime[0];
int64_t max_dt = min_dt;
int64_t sum_dt = min_dt;
int64_t numzeros = 0;
for (size_t i = 2; i < nbins; ++i) {
int64_t temp_dt = vec_logtime[i] - vec_logtime[i - 1];
if (temp_dt == 0)
++numzeros;
sum_dt += temp_dt;
if (temp_dt < min_dt)
min_dt = temp_dt;
else if (temp_dt > max_dt)
max_dt = temp_dt;
}
if (nbins - 1) {
double avg_dt = static_cast<double>(sum_dt) / static_cast<double>(nbins - 1);
g_log.information() << "Event log of map index " << mindex << ": Avg(dt) = " << avg_dt * 1.0E-9
<< ", Min(dt) = " << static_cast<double>(min_dt) * 1.0E-9
<< ", Max(dt) = " << static_cast<double>(max_dt) * 1.0E-9 << "\n";
} else {
g_log.information() << "Event log of map index " << mindex << ": Avg(dt) = " << static_cast<double>(sum_dt) * 1.0E-9
<< ", Min(dt) = " << static_cast<double>(min_dt) * 1.0E-9
<< ", Max(dt) = " << static_cast<double>(max_dt) * 1.0E-9 << "\n";
}
g_log.information() << "Number of zero-interval eveng log = " << numzeros << "\n";
}
//-----------------------------------------------------------------------------
/** Load the instrument geometry File
* @param eventfilename :: Used to pick the instrument.
* @param localWorkspace :: MatrixWorkspace in which to put the instrument
* geometry
*/
void FilterEventsByLogValuePreNexus::runLoadInstrument(const std::string &eventfilename,
const MatrixWorkspace_sptr &localWorkspace) {
// start by getting just the filename
string instrument = Poco::Path(eventfilename).getFileName();
// initialize vector of endings and put live at the beginning
vector<string> eventExts(EVENT_EXTS, EVENT_EXTS + NUM_EXT);
std::reverse(eventExts.begin(), eventExts.end());
for (auto &eventExt : eventExts) {
size_t pos = instrument.find(eventExt);
if (pos != string::npos) {
instrument = instrument.substr(0, pos);
break;
}
}
// determine the instrument parameter file
size_t pos = instrument.rfind('_'); // get rid of the run number
instrument = instrument.substr(0, pos);
// do the actual work
auto loadInst = createChildAlgorithm("LoadInstrument");
// Now execute the Child Algorithm. Catch and log any error, but don't stop.
loadInst->setPropertyValue("InstrumentName", instrument);
loadInst->setProperty<MatrixWorkspace_sptr>("Workspace", localWorkspace);
loadInst->setProperty("RewriteSpectraMap", Mantid::Kernel::OptionalBool(false));
loadInst->executeAsChildAlg();
// Populate the instrument parameters in this workspace - this works around a
// bug
localWorkspace->populateInstrumentParameters();
}
//----------------------------------------------------------------------------------------------
/** Process the event file properly.
* @param workspace :: EventWorkspace to write to.
*/
void FilterEventsByLogValuePreNexus::procEvents(DataObjects::EventWorkspace_sptr &workspace) {
// Initialize stat parameters
this->m_numErrorEvents = 0;
this->m_numGoodEvents = 0;
this->m_numIgnoredEvents = 0;
this->m_numBadEvents = 0;
this->m_numWrongdetidEvents = 0;
m_shortestTof = static_cast<double>(MAX_TOF_UINT32) * TOF_CONVERSION;
m_longestTof = 0.;
// -------------------------------------------------------------------
// Set up instrument related parameters such as detector map and etc.
// We want to pad out empty pixels.
//--------------------------------------------------------------------
const auto &detectorInfo = workspace->detectorInfo();
const auto &detIDs = detectorInfo.detectorIDs();
// Determine maximum pixel id
const auto it = std::max_element(detIDs.cbegin(), detIDs.cend());
m_detid_max = it == detIDs.cend() ? 0 : *it; // in case detIDs is empty
// Pad all the pixels
m_progress->report("Padding Pixels");
this->m_pixelToWkspindex.reserve(m_detid_max + 1); // starting at zero up to and including m_detid_max
// Set to zero
this->m_pixelToWkspindex.assign(m_detid_max + 1, 0);
size_t workspaceIndex = 0;
specnum_t spectrumNumber = 1;
for (size_t i = 0; i < detectorInfo.size(); ++i) {
if (!detectorInfo.isMonitor(i)) {
if (!m_loadOnlySomeSpectra || (spectraLoadMap.find(detIDs[i]) != spectraLoadMap.end())) {
// Add non-monitor detector ID
this->m_pixelToWkspindex[detIDs[i]] = workspaceIndex;
EventList &spec = workspace->getSpectrum(workspaceIndex);
spec.addDetectorID(detIDs[i]);
// Start the spectrum number at 1
spec.setSpectrumNo(spectrumNumber);
workspaceIndex += 1;
++workspaceIndex;
} else {
this->m_pixelToWkspindex[detIDs[i]] = -1;
}
++spectrumNumber;
}
}
// ----------------------------------------------------------------
// Determine processing mode and file-loading parameters
//------------------------------------------------------------------
// Set up some default values in the case of no parallel
size_t loadBlockSize = Mantid::Kernel::DEFAULT_BLOCK_SIZE * 2;
size_t numBlocks = (m_maxNumEvents + loadBlockSize - 1) / loadBlockSize;
std::string procMode = getProperty("UseParallelProcessing");
if (procMode == "Serial") {
m_parallelProcessing = false;
} else if (procMode == "Parallel") {
m_parallelProcessing = true;
} else {
// Automatic determination. Loading serially (for me) is about 3 million
// events per second,
// (which is sped up by ~ x 3 with parallel processing, say 10 million per
// second, e.g. 7 million events more per seconds).
// compared to a setup time/merging time of about 10 seconds per million
// detectors.
double setUpTime = double(detectorInfo.size()) * 10e-6;
m_parallelProcessing = ((double(m_maxNumEvents) / 7e6) > setUpTime);
g_log.information() << (m_parallelProcessing ? "Using" : "Not using") << " parallel processing."
<< "\n";
}
if (m_functionMode == "ExamineEventLog" && m_parallelProcessing) {
m_parallelProcessing = false;
g_log.notice("In function mode 'ExamineEventLog', processing mode is "
"forced to serial. ");
}
#if 0
//For slight speed up
m_loadOnlySomeSpectra = (this->m_spectraList.size() > 0);
//Turn the spectra list into a map, for speed of access
for (std::vector<int64_t>::iterator it = m_spectraList.begin(); it != m_spectraList.end(); it++)
spectraLoadMap[*it] = true;
#endif
CPUTimer tim;
// -------------------------------------------------------------------
// Create the partial workspaces
//--------------------------------------------------------------------
// Vector of partial workspaces, for parallel processing.
std::vector<EventWorkspace_sptr> partWorkspaces;
std::vector<DasEvent *> buffers;
/// Pointer to the vector of events
using EventVector_pt = std::vector<TofEvent> *;
/// Bare array of arrays of pointers to the EventVectors
EventVector_pt **eventVectors;
/// How many threads will we use?
size_t numThreads = 1;
if (m_parallelProcessing)
numThreads = size_t(PARALLEL_GET_MAX_THREADS);
partWorkspaces.resize(numThreads);
buffers.resize(numThreads);
eventVectors = new EventVector_pt *[numThreads];
// Processing by number of threads
g_log.information() << "Processing input event preNexus by " << numThreads << " threads"
<< " in " << numBlocks << " blocks. "
<< "\n";
PRAGMA_OMP( parallel for schedule(dynamic, 1) if (m_parallelProcessing) )
for (int i = 0; i < int(numThreads); i++) {
// This is the partial workspace we are about to create (if in parallel)
EventWorkspace_sptr partWS;
if (m_parallelProcessing) {
m_progress->report("Creating Partial Workspace");
// Create a partial workspace, copy all the spectra numbers and stuff
// (no actual events to copy though).
partWS = workspace->clone();
// Push it in the array
partWorkspaces[i] = partWS;
} else
partWS = workspace;
// Allocate the buffers
buffers[i] = new DasEvent[loadBlockSize];
// For each partial workspace, make an array where index = detector ID and
// value = pointer to the events vector
eventVectors[i] = new EventVector_pt[m_detid_max + 1];
EventVector_pt *theseEventVectors = eventVectors[i];
for (detid_t j = 0; j < m_detid_max + 1; ++j) {
size_t wi = m_pixelToWkspindex[j];
// Save a POINTER to the vector<tofEvent>
theseEventVectors[j] = &partWS->getSpectrum(wi).getEvents();
}
} // END FOR [Threads]
g_log.information() << tim << " to create " << partWorkspaces.size() << " workspaces for parallel loading."
<< "\n";
m_progress->resetNumSteps(numBlocks, 0.1, 0.8);
// -------------------------------------------------------------------
// LOAD THE DATA
//--------------------------------------------------------------------
PRAGMA_OMP( parallel for schedule(dynamic, 1) if (m_parallelProcessing) )
for (int blockNum = 0; blockNum < int(numBlocks); blockNum++) {
PARALLEL_START_INTERRUPT_REGION
// Find the workspace for this particular thread
EventWorkspace_sptr ws;
size_t threadNum = 0;
if (m_parallelProcessing) {
threadNum = PARALLEL_THREAD_NUMBER;
ws = partWorkspaces[threadNum];
} else
ws = workspace;
// Get the buffer (for this thread)
DasEvent *event_buffer = buffers[threadNum];
// Get the speeding-up array of vector<tofEvent> where index = detid.
EventVector_pt *theseEventVectors = eventVectors[threadNum];
// Where to start in the file?
size_t fileOffset = m_firstEvent + (loadBlockSize * blockNum);
// May need to reduce size of last (or only) block
size_t current_event_buffer_size =
(blockNum == int(numBlocks - 1)) ? (m_maxNumEvents - (numBlocks - 1) * loadBlockSize) : loadBlockSize;
// Load this chunk of event data (critical block)
PARALLEL_CRITICAL(FilterEventsByLogValuePreNexus_fileAccess) {
current_event_buffer_size = m_eventFile->loadBlockAt(event_buffer, fileOffset, current_event_buffer_size);
}
// This processes the events. Can be done in parallel!
procEventsLinear(ws, theseEventVectors, event_buffer, current_event_buffer_size, fileOffset);
// Report progress
m_progress->report("Load Event PreNeXus");
PARALLEL_END_INTERRUPT_REGION
}
PARALLEL_CHECK_INTERRUPT_REGION
g_log.information() << tim << " to load the data.\n";
// -------------------------------------------------------------------
// MERGE WORKSPACES BACK TOGETHER
//--------------------------------------------------------------------
if (m_parallelProcessing) {
PARALLEL_START_INTERRUPT_REGION
m_progress->resetNumSteps(workspace->getNumberHistograms(), 0.8, 0.95);
// Merge all workspaces, index by index.
PARALLEL_FOR_NO_WSP_CHECK()
for (int iwi = 0; iwi < int(workspace->getNumberHistograms()); iwi++) {
auto wi = size_t(iwi);
// The output event list.
EventList &el = workspace->getSpectrum(wi);
el.clear(false);
// How many events will it have?
size_t numEvents = 0;
for (size_t i = 0; i < numThreads; i++)
numEvents += partWorkspaces[i]->getSpectrum(wi).getNumberEvents();
// This will avoid too much copying.
el.reserve(numEvents);
// Now merge the event lists
for (size_t i = 0; i < numThreads; i++) {
EventList &partEl = partWorkspaces[i]->getSpectrum(wi);
el += partEl.getEvents();
// Free up memory as you go along.
partEl.clear(false);
}
m_progress->report("Merging Workspaces");
}
g_log.debug() << tim << " to merge workspaces together.\n";
PARALLEL_END_INTERRUPT_REGION
}
PARALLEL_CHECK_INTERRUPT_REGION
// Delete the buffers for each thread.
for (size_t i = 0; i < numThreads; i++) {
delete[] buffers[i];
delete[] eventVectors[i];
}
delete[] eventVectors;
m_progress->resetNumSteps(3, 0.94, 1.00);
// finalize loading
m_progress->report("Setting proton charge");