/*WIKI*
The LoadEventPreNeXus algorithm stores data from the pre-nexus neutron event data file in an [[EventWorkspace]]. The default histogram bin boundaries consist of a single bin able to hold all events (in all pixels), and will have their [[units]] set to time-of-flight. Since it is an [[EventWorkspace]], it can be rebinned to finer bins with no loss of data.
=== Optional properties ===
Specific pulse ID and mapping files can be specified if needed; these are guessed at automatically from the neutron filename, if not specified.
*WIKI*/
#include "MantidDataHandling/LoadEventPreNexus2.h"
#include <algorithm>
#include <sstream>
#include <stdexcept>
#include <functional>
#include <iostream>
#include <set>
#include <vector>
#include <Poco/File.h>
#include <Poco/Path.h>
#include <boost/timer.hpp>
#include "MantidAPI/FileFinder.h"
#include "MantidAPI/LoadAlgorithmFactory.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/EventWorkspace.h"
#include "MantidDataObjects/EventList.h"
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/FileValidator.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidKernel/Glob.h"
#include "MantidAPI/FileProperty.h"
#include "MantidKernel/ConfigService.h"
#include "MantidKernel/BinaryFile.h"
#include "MantidKernel/System.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/UnitFactory.h"
#include "MantidKernel/DateAndTime.h"
#include "MantidGeometry/IDetector.h"
#include "MantidKernel/CPUTimer.h"
#include "MantidKernel/VisibleWhenProperty.h"
#include "MantidDataObjects/Workspace2D.h"
#include <algorithm>
#include <sstream>
namespace Mantid
{
namespace DataHandling
{
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(LoadEventPreNexus2)
DECLARE_LOADALGORITHM(LoadEventPreNexus2)
using namespace Kernel;
using namespace API;
using namespace Geometry;
using boost::posix_time::ptime;
using boost::posix_time::time_duration;
using DataObjects::EventList;
using DataObjects::EventWorkspace;
using DataObjects::EventWorkspace_sptr;
using DataObjects::TofEvent;
using std::cout;
using std::endl;
using std::ifstream;
using std::runtime_error;
using std::stringstream;
using std::string;
using std::vector;
/*
* 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");
static const string PULSE_EXT("pulseid.dat");
static const string EVENT_EXT("event.dat");
/// Default number of items to read in from any of the files.
static const size_t DEFAULT_BLOCK_SIZE = 1000000; // 100,000
/// 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.;
//-----------------------------------------------------------------------------
//Statistic Functions
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);
}
static string generatePulseidName(string eventfile)
{
size_t start;
string ending;
// normal ending
ending = "neutron_event.dat";
start = eventfile.find(ending);
if (start != string::npos)
return eventfile.replace(start, ending.size(), "pulseid.dat");
// split up event files - yes this is copy and pasted code
ending = "neutron0_event.dat";
start = eventfile.find(ending);
if (start != string::npos)
return eventfile.replace(start, ending.size(), "pulseid0.dat");
ending = "neutron1_event.dat";
start = eventfile.find(ending);
if (start != string::npos)
return eventfile.replace(start, ending.size(), "pulseid1.dat");
return "";
}
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())
{
instrument = Kernel::ConfigService::Instance().getInstrument(instrument).shortName();
base = Poco::File("/SNS/" + instrument + "/");
if (!base.exists())
return "";
}
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 (size_t i = 0; i < dirs.size(); ++i) {
if ( (dirs[i].length() > CAL_LEN)
&& (dirs[i].compare(dirs[i].length() - CAL.length(), CAL.length(), CAL) == 0) ) {
if (Poco::File(base.path() + "/" + dirs[i] + "/calibrations/" + mapping).exists())
files.push_back(base.path() + "/" + dirs[i] + "/calibrations/" + mapping);
}
}
if (files.empty())
return "";
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());
}
//-----------------------------------------------------------------------------
/*
* Constructor
*/
LoadEventPreNexus2::LoadEventPreNexus2() : Mantid::API::IDataFileChecker(), eventfile(NULL), max_events(0)
{
}
/*
* Desctructor
*/
LoadEventPreNexus2::~LoadEventPreNexus2()
{
delete this->eventfile;
}
/*
* Sets documentation strings for this algorithm
*/
void LoadEventPreNexus2::initDocs()
{
this->setWikiSummary("Loads SNS raw neutron event data format and stores it in a [[workspace]] ([[EventWorkspace]] class). ");
this->setOptionalMessage("Loads SNS raw neutron event data format and stores it in a workspace (EventWorkspace class).");
}
//-----------------------------------------------------------------------------
/*
* Initialize the algorithm
*/
void LoadEventPreNexus2::init()
{
// which files to use
declareProperty(new FileProperty(EVENT_PARAM, "", FileProperty::Load, EVENT_EXT),
"The name of the neutron event file to read, including its full or relative path. The file typically ends in neutron_event.dat (N.B. case sensitive if running on Linux).");
declareProperty(new FileProperty(PULSEID_PARAM, "", FileProperty::OptionalLoad, PULSE_EXT),
"File containing the accelerator pulse information; the filename will be found automatically if not specified.");
declareProperty(new 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.");
// which pixels to load
declareProperty(new ArrayProperty<int64_t>(PID_PARAM),
"A list of individual spectra (pixel IDs) to read, specified as e.g. 10:20. Only used if set.");
BoundedValidator<int> *mustBePositive = new 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->clone(),
"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", new VisibleWhenProperty(this, "ChunkNumber", IS_NOT_DEFAULT));
std::vector<std::string> propOptions;
propOptions.push_back("Auto");
propOptions.push_back("Serial");
propOptions.push_back("Parallel");
declareProperty("UseParallelProcessing", "Auto",new ListValidator(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(new 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]].");
return;
}
/*
* Execute the algorithm
* 1. check all the inputs
* 2. create an EventWorkspace object
* 3. process events
* 4. set out output
*/
void LoadEventPreNexus2::exec()
{
// 1. Check!
// a. 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");
}
prog = new Progress(this,0.0,1.0,100);
// b. what spectra (pixel ID's) to load
this->spectra_list = this->getProperty(PID_PARAM);
// c. the event file is needed in case the pulseid fileanme is empty
string event_filename = this->getPropertyValue(EVENT_PARAM);
string pulseid_filename = this->getPropertyValue(PULSEID_PARAM);
bool throwError = true;
if (pulseid_filename.empty())
{
pulseid_filename = generatePulseidName(event_filename);
if (!pulseid_filename.empty())
{
if (Poco::File(pulseid_filename).exists())
{
this->g_log.information() << "Found pulseid file " << pulseid_filename << std::endl;
throwError = false;
}
else
{
pulseid_filename = "";
}
}
}
// 2. Read input files
prog->report("Loading Pulse ID file");
this->readPulseidFile(pulseid_filename, throwError);
prog->report("Loading Event File");
this->openEventFile(event_filename);
// 3. Create otuput Workspace
prog->report("Creating output workspace");
// a. prep the output workspace
EventWorkspace_sptr localWorkspace = EventWorkspace_sptr(new EventWorkspace());
// b. Make sure to initialize. We can use dummy numbers for arguments, for event workspace it doesn't matter
localWorkspace->initialize(1,1,1);
// c. Set the units
localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
localWorkspace->setYUnit("Counts");
// d. Set title
localWorkspace->setTitle("Dummy Title");
// 4. Properties:
// a. Add the run_start property (Use the first pulse as the run_start time)
if (this->num_pulses > 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).
localWorkspace->mutableRun().addProperty("run_start", pulsetimes[0].to_ISO8601_string(), true );
}
// b. determine the run number and add it to the run object
localWorkspace->mutableRun().addProperty("run_number", getRunnumber(event_filename));
// 5. Get the instrument!
prog->report("Loading Instrument");
this->runLoadInstrument(event_filename, localWorkspace);
// 6. load the mapping file
prog->report("Loading Mapping File");
string mapping_filename = this->getPropertyValue(MAP_PARAM);
if (mapping_filename.empty()) {
mapping_filename = generateMappingfileName(localWorkspace);
if (!mapping_filename.empty())
this->g_log.information() << "Found mapping file \"" << mapping_filename << "\"" << std::endl;
}
this->loadPixelMap(mapping_filename);
// 7. Process the events into pixels
this->procEvents(localWorkspace);
// 8. Save output
this->setProperty<IEventWorkspace_sptr>(OUT_PARAM, localWorkspace);
// 9. Fast frequency sample environment data
std::vector<size_t> numpixels;
std::set<PixelType>::iterator pit;
std::map<PixelType, size_t>::iterator mit;
for (pit=this->wrongdetids.begin(); pit!=this->wrongdetids.end(); ++pit){
// a. pixel ID -> index
PixelType pid = *pit;
mit = this->wrongdetidmap.find(pid);
size_t mindex = mit->second;
if (mindex > this->wrongdetid_abstimes.size()){
g_log.error() << "Wrong Index " << mindex << " for Pixel " << pid << std::endl;
throw std::invalid_argument("Wrong array index for pixel from map");
}
// b. Create output workspace2D
// i. Output information in workspaces
size_t nbins = this->wrongdetid_abstimes[mindex].size();
// ii.Create workspace
DataObjects::Workspace2D_sptr ws2d = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", 1, nbins, nbins));
// iii. set data
double y0 = 0;
for (size_t k = 0; k < nbins; k ++){
ws2d->dataX(0)[k] = static_cast<double>(this->wrongdetid_abstimes[mindex][k]);
ws2d->dataY(0)[k] = y0;
y0 = 1.0-y0;
}
// c. Set up otuput Workspace2D
std::stringstream ssws;
ssws << "OutputPixel" << pid << "Workspace";
std::string outputtitle = ssws.str();
std::stringstream ssname;
ssname << "Pixel" << pid;
std::string wsname = ssname.str();
g_log.notice() << "Pixel " << pid << ": OutputWorkspace(" << outputtitle << ") <-- " << wsname << std::endl;
this->declareProperty(new WorkspaceProperty<DataObjects::Workspace2D>(outputtitle, wsname, Direction::Output),
"Set the output sample environment data record");
this->setProperty(outputtitle, ws2d);
// z. Check workspace
// TODO This will be removed later
g_log.error() << "Test Only! Delete this section later!" << std::endl;
size_t maxcounts = 3;
size_t counts = 0;
std::set<int64_t> deltas;
// i. do statistic
size_t numzerodeltat = 0;
size_t numfreq = 0;
int64_t sumdeltat = 0;
for (size_t k = 1; k < nbins; k ++){
int64_t deltat = this->wrongdetid_abstimes[mindex][k]-this->wrongdetid_abstimes[mindex][k-1];
deltas.insert(deltat);
if (deltat == 0){
numzerodeltat ++;
if (counts < maxcounts)
{
g_log.error() << "Delta T = 0: T = " << this->wrongdetid_abstimes[mindex][k] << std::endl;
counts ++;
}
} else {
numfreq ++;
sumdeltat += deltat;
}
}
double frequency = 1.0/(static_cast<double>(sumdeltat)/static_cast<double>(numfreq)*1.0E-9);
size_t numpt = this->wrongdetid_abstimes[mindex].size();
g_log.notice() << "Frequency = " << frequency << " Number of pixels with zero Delta T = " << numzerodeltat << std::endl;
int64_t t0 = this->wrongdetid_abstimes[mindex][0];
int64_t tf = this->wrongdetid_abstimes[mindex][numpt-1];
g_log.notice() << "T0 = " << t0 << ", Tf = " << tf << " Delta T = " << tf-t0 << " ns"<< std::endl;
g_log.notice() << "Theoretical number of events = " << static_cast<double>(tf-t0)*frequency*1.0E-9 << std::endl;
g_log.notice() << "Number of various delta T = " << deltas.size() << std::endl;
std::set<int64_t>::iterator dtit;
for (dtit=deltas.begin(); dtit!=deltas.end(); ++dtit){
g_log.notice() << *dtit <<", ";
}
g_log.notice() << std::endl;
} //ENDFOR pit
// -1. Cleanup
delete prog;
return;
} // exec()
/**
* Returns the name of the property to be considered as the Filename for Load
* @returns A character string containing the file property's name
*/
const char * LoadEventPreNexus2::filePropertyName() const
{
return EVENT_PARAM.c_str();
}
/**
* 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 LoadEventPreNexus2::quickFileCheck(const std::string& filePath,size_t,const file_header&)
{
std::string ext = extension(filePath);
return (ext.rfind("dat") != std::string::npos);
}
/**
* 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 LoadEventPreNexus2::fileCheck(const std::string& filePath)
{
int confidence(0);
try
{
// If this looks like a binary file where the exact file length is a multiple
// of the DasEvent struct then we're probably okay.
// NOTE: Putting this on the stack gives a segfault on Windows when for some reason
// the BinaryFile destructor is called twice! I'm sure there is something I don't understand there
// but heap allocation seems to work so go for that.
BinaryFile<DasEvent> *event_file = new BinaryFile<DasEvent>(filePath);
confidence = 80;
delete event_file;
}
catch(std::runtime_error &)
{
// This BinaryFile constructor throws if the file does not contain an
// exact multiple of the sizeof(DasEvent) objects.
}
return confidence;
}
//-----------------------------------------------------------------------------
/** Load the instrument geometry File
* @param eventfilename :: Used to pick the instrument.
* @param localWorkspace :: MatrixWorkspace in which to put the instrument geometry
*/
void LoadEventPreNexus2::runLoadInstrument(const std::string &eventfilename, MatrixWorkspace_sptr localWorkspace)
{
// determine the instrument parameter file
string instrument = Poco::Path(eventfilename).getFileName();
size_t pos = instrument.rfind("_"); // get rid of 'event.dat'
pos = instrument.rfind("_", pos-1); // get rid of 'neutron'
pos = instrument.rfind("_", pos-1); // get rid of the run number
instrument = instrument.substr(0, pos);
// do the actual work
IAlgorithm_sptr loadInst= createSubAlgorithm("LoadInstrument");
// Now execute the sub-algorithm. Catch and log any error, but don't stop.
loadInst->setPropertyValue("InstrumentName", instrument);
loadInst->setProperty<MatrixWorkspace_sptr> ("Workspace", localWorkspace);
loadInst->setProperty("RewriteSpectraMap", false);
loadInst->executeAsSubAlg();
// Populate the instrument parameters in this workspace - this works around a bug
localWorkspace->populateInstrumentParameters();
}
//-----------------------------------------------------------------------------
/** Turn a pixel id into a "corrected" pixelid and period.
*
*/
inline void LoadEventPreNexus2::fixPixelId(PixelType &pixel, uint32_t &period) const
{
if (!this->using_mapping_file) { // nothing to do here
period = 0;
return;
}
PixelType unmapped_pid = pixel % this->numpixel;
period = (pixel - unmapped_pid) / this->numpixel;
pixel = this->pixelmap[unmapped_pid];
}
//-----------------------------------------------------------------------------
/** Process the event file properly.
* @param workspace :: EventWorkspace to write to.
*/
void LoadEventPreNexus2::procEvents(DataObjects::EventWorkspace_sptr & workspace)
{
this->num_error_events = 0;
this->num_good_events = 0;
this->num_ignored_events = 0;
this->num_bad_events = 0;
this->num_wrongdetid_events = 0;
//Default values in the case of no parallel
size_t loadBlockSize = Mantid::Kernel::DEFAULT_BLOCK_SIZE * 2;
shortest_tof = static_cast<double>(MAX_TOF_UINT32) * TOF_CONVERSION;
longest_tof = 0.;
//Initialize progress reporting.
size_t numBlocks = (max_events + loadBlockSize - 1) / loadBlockSize;
// We want to pad out empty pixels.
detid2det_map detector_map;
workspace->getInstrument()->getDetectors(detector_map);
// -------------- Determine processing mode
std::string procMode = getProperty("UseParallelProcessing");
if (procMode == "Serial")
parallelProcessing = false;
else if (procMode == "Parallel")
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(detector_map.size()) * 10e-6;
parallelProcessing = ((double(max_events) / 7e6) > setUpTime);
g_log.debug() << (parallelProcessing ? "Using" : "Not using") << " parallel processing." << std::endl;
}
// determine maximum pixel id
detid2det_map::iterator it;
detid_max = 0; // seems like a safe lower bound
for (it = detector_map.begin(); it != detector_map.end(); it++)
if (it->first > detid_max)
detid_max = it->first;
// Pad all the pixels
prog->report("Padding Pixels");
this->pixel_to_wkspindex.reserve(detid_max+1); //starting at zero up to and including detid_max
// Set to zero
this->pixel_to_wkspindex.assign(detid_max+1, 0);
size_t workspaceIndex = 0;
for (it = detector_map.begin(); it != detector_map.end(); it++)
{
if (!it->second->isMonitor())
{
this->pixel_to_wkspindex[it->first] = workspaceIndex;
EventList & spec = workspace->getOrAddEventList(workspaceIndex);
spec.addDetectorID(it->first);
// Start the spectrum number at 1
spec.setSpectrumNo(specid_t(workspaceIndex+1));
workspaceIndex += 1;
}
}
workspace->doneAddingEventLists();
//For slight speed up
loadOnlySomeSpectra = (this->spectra_list.size() > 0);
//Turn the spectra list into a map, for speed of access
for (std::vector<int64_t>::iterator it = spectra_list.begin(); it != spectra_list.end(); it++)
spectraLoadMap[*it] = true;
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
typedef std::vector<TofEvent> * EventVector_pt;
/// Bare array of arrays of pointers to the EventVectors
EventVector_pt ** eventVectors;
/// How many threads will we use?
size_t numThreads = 1;
if (parallelProcessing)
numThreads = size_t(PARALLEL_GET_MAX_THREADS);
partWorkspaces.resize(numThreads);
buffers.resize(numThreads);
eventVectors = new EventVector_pt *[numThreads];
PRAGMA_OMP( parallel for if (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 (parallelProcessing)
{
prog->report("Creating Partial Workspace");
// Create a partial workspace
partWS = EventWorkspace_sptr(new EventWorkspace());
//Make sure to initialize.
partWS->initialize(1,1,1);
// Copy all the spectra numbers and stuff (no actual events to copy though).
partWS->copyDataFrom(*workspace);
// 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[detid_max+1];
EventVector_pt * theseEventVectors = eventVectors[i];
for (detid_t j=0; j<detid_max+1; j++)
{
size_t wi = pixel_to_wkspindex[j];
// Save a POINTER to the vector<tofEvent>
theseEventVectors[j] = &partWS->getEventList(wi).getEvents();
}
}
g_log.debug() << tim << " to create " << partWorkspaces.size() << " workspaces for parallel loading." << std::endl;
prog->resetNumSteps( numBlocks, 0.1, 0.8);
// ---------------------------------- LOAD THE DATA --------------------------
PRAGMA_OMP( parallel for schedule(dynamic, 1) if (parallelProcessing) )
for (int blockNum=0; blockNum<int(numBlocks); blockNum++)
{
PARALLEL_START_INTERUPT_REGION
// Find the workspace for this particular thread
EventWorkspace_sptr ws;
size_t threadNum = 0;
if (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 = first_event + (loadBlockSize * blockNum);
// May need to reduce size of last (or only) block
size_t current_event_buffer_size =
( blockNum == int(numBlocks-1) ) ? ( max_events - (numBlocks-1)*loadBlockSize ) : loadBlockSize;
// Load this chunk of event data (critical block)
PARALLEL_CRITICAL( LoadEventPreNexus2_fileAccess )
{
current_event_buffer_size = 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
prog->report("Load Event PreNeXus");
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
g_log.debug() << tim << " to load the data." << std::endl;
// ---------------------------------- MERGE WORKSPACES BACK TOGETHER --------------------------
if (parallelProcessing)
{
PARALLEL_START_INTERUPT_REGION
prog->resetNumSteps( workspace->getNumberHistograms(), 0.8, 0.95);
size_t memoryCleared = 0;
MemoryManager::Instance().releaseFreeMemory();
// Merge all workspaces, index by index.
PARALLEL_FOR_NO_WSP_CHECK()
for (int iwi=0; iwi<int(workspace->getNumberHistograms()); iwi++)
{
size_t wi = size_t(iwi);
// The output event list.
EventList & el = workspace->getEventList(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]->getEventList(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]->getEventList(wi);
el += partEl.getEvents();
// Free up memory as you go along.
partEl.clear(false);
}
// With TCMalloc, release memory when you accumulate enough to make sense
PARALLEL_CRITICAL( LoadEventPreNexus2_trackMemory )
{
memoryCleared += numEvents;
if (memoryCleared > 10000000) // ten million events = about 160 MB
{
MemoryManager::Instance().releaseFreeMemory();
memoryCleared = 0;
}
}
prog->report("Merging Workspaces");
}
// Final memory release
MemoryManager::Instance().releaseFreeMemory();
g_log.debug() << tim << " to merge workspaces together." << std::endl;
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Delete the buffers for each thread.
for (size_t i=0; i<numThreads; i++)
{
delete [] buffers[i];
delete [] eventVectors[i];
}
delete [] eventVectors;
//delete [] pulsetimes;
prog->resetNumSteps( 3, 0.94, 1.00);
//finalize loading
prog->report("Deleting Empty Lists");
if(loadOnlySomeSpectra)
workspace->deleteEmptyLists();
prog->report("Setting proton charge");
this->setProtonCharge(workspace);
g_log.debug() << tim << " to set the proton charge log." << std::endl;
//Make sure the MRU is cleared
workspace->clearMRU();
//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;
workspace->setAllX(axis);
this->pixel_to_wkspindex.clear();
// Final process on wrong detector id events
for (size_t vi = 0; vi < this->wrongdetid_abstimes.size(); vi ++){
std::sort(this->wrongdetid_abstimes[vi].begin(), this->wrongdetid_abstimes[vi].end());
}
// Final message output
g_log.notice() << "Read " << this->num_good_events << " events + "
<< this->num_error_events << " errors"
<< ". Shortest TOF: " << shortest_tof << " microsec; longest TOF: "
<< longest_tof << " microsec." << std::endl;
g_log.notice() << "Bad Events = " << this->num_bad_events << " Events of Wrong Detector = " << this->num_wrongdetid_events << std::endl;
g_log.notice() << "Number of Wrong Detector IDs = " << this->wrongdetids.size() << std::endl;
std::set<PixelType>::iterator wit;
for (wit=this->wrongdetids.begin(); wit!=this->wrongdetids.end(); ++wit){
g_log.notice() << "Wrong Detector ID : " << *wit << std::endl;
}
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;
g_log.notice() << "Pixel " << tmpid << ": Total number of events = " << this->wrongdetid_abstimes[vindex].size() << std::endl;
}
return;
} // End of procEvents
//-----------------------------------------------------------------------------
/** Linear-version of the procedure to process the event file properly.
* @param workspace :: EventWorkspace to write to.
* @param arrayOfVectors :: For speed up: this is an array, of size detid_max+1, where the
* index is a pixel ID, and the value is a pointer to the vector<tofEvent> in the given EventList.
* @param event_buffer :: The buffer containing the DAS events
* @param current_event_buffer_size :: The length of the given DAS buffer
* @param fileOffset :: Value for an offset into the binary file
*/
void LoadEventPreNexus2::procEventsLinear(DataObjects::EventWorkspace_sptr & /*workspace*/,
std::vector<TofEvent> ** arrayOfVectors, DasEvent * event_buffer,
size_t current_event_buffer_size, size_t fileOffset)
{
//Starting pulse time
DateAndTime pulsetime;
int64_t pulse_i = 0;
int64_t numPulses = static_cast<int64_t>(num_pulses);
if (event_indices.size() < num_pulses)
{
g_log.warning() << "Event_indices vector is smaller than the pulsetimes array.\n";
numPulses = static_cast<int64_t>(event_indices.size());
}
size_t local_num_error_events = 0;
size_t local_num_bad_events = 0;
size_t local_num_wrongdetid_events = 0;
size_t local_num_ignored_events = 0;
size_t local_num_good_events = 0;
double local_shortest_tof = static_cast<double>(MAX_TOF_UINT32) * TOF_CONVERSION;
double local_longest_tof = 0.;
std::map<PixelType, size_t> local_pidindexmap;
std::vector<std::vector<int64_t> > local_abstimes;
std::set<PixelType> local_wrongdetids;
// process the individual events
for (size_t i = 0; i < current_event_buffer_size; i++)
{
DasEvent & temp = *(event_buffer + i);
PixelType pid = temp.pid;
bool iswrongdetid = false;
if ((pid & ERROR_PID) == ERROR_PID) // marked as bad
{
local_num_error_events++;
local_num_bad_events ++;
continue;
}
//Covert the pixel ID from DAS pixel to our pixel ID
if (this->using_mapping_file)
{
PixelType unmapped_pid = pid % this->numpixel;
pid = this->pixelmap[unmapped_pid];
}
// Wrong pixel IDs
if (pid > static_cast<PixelType>(detid_max))
{
iswrongdetid = true;
local_num_error_events++;
local_num_wrongdetid_events++;
local_wrongdetids.insert(pid);
}
//Now check if this pid we want to load.
if (loadOnlySomeSpectra && !iswrongdetid)
{
std::map<int64_t, bool>::iterator it;
it = spectraLoadMap.find(pid);
if (it == spectraLoadMap.end())
{
//Pixel ID was not found, so the event is being ignored.
local_num_ignored_events++;
continue;
}
}
// work with the good guys
//Find the pulse time for this event index
if (pulse_i < numPulses-1)
{
//This is the total offset into the file
size_t total_i = i + fileOffset;
//Go through event_index until you find where the index increases to encompass the current index. Your pulse = the one before.
while (!((total_i >= event_indices[pulse_i]) && (total_i < event_indices[pulse_i+1])) )
{
pulse_i++;
if (pulse_i >= (numPulses-1))
break;
}
//if (pulsetimes[pulse_i] != pulsetime) std::cout << pulse_i << " at " << pulsetimes[pulse_i] << "\n";
//Save the pulse time at this index for creating those events
pulsetime = pulsetimes[pulse_i];
} // Find pulse time
double tof = static_cast<double>(temp.tof) * TOF_CONVERSION;
if (!iswrongdetid){
// a) Regular events
TofEvent event(tof, pulsetime);
//Find the overall max/min tof
if (tof < local_shortest_tof)
local_shortest_tof = tof;
if (tof > local_longest_tof)
local_longest_tof = tof;
//The addEventQuickly method does not clear the cache, making things slightly faster.
//workspace->getEventList(this->pixel_to_wkspindex[pid]).addEventQuickly(event);
// This is equivalent to workspace->getEventList(this->pixel_to_wkspindex[pid]).addEventQuickly(event);
// But should be faster as a bunch of these calls were cached.
arrayOfVectors[pid]->push_back(event);
// TODO work with period
local_num_good_events++;
} else {
// b) Special events/Wrong detector id
// i. get/add index of the entry in map
std::map<PixelType, size_t>::iterator it;
it = local_pidindexmap.find(pid);
size_t theindex = 0;
if (it == local_pidindexmap.end()){
// Initialize it!
size_t newindex = local_abstimes.size();
local_pidindexmap[pid] = newindex;
std::vector<int64_t> tempvectime;
local_abstimes.push_back(tempvectime);
theindex = newindex;
} else {
// existing
theindex = it->second;
}
// ii. calculate and add absolute time
int64_t abstime = (pulsetime.total_nanoseconds()+int64_t(tof*1000));
local_abstimes[theindex].push_back(abstime);
if (abstime == 666977093983629966)
g_log.error() << "Check Special Event: Pulse ID = " << pulse_i << " Tof = " << temp.tof << std::endl;
}
} // ENDFOR each event
PARALLEL_CRITICAL( LoadEventPreNexus2_global_statistics )
{
this->num_good_events += local_num_good_events;
this->num_ignored_events += local_num_ignored_events;
this->num_error_events += local_num_error_events;
this->num_bad_events += local_num_bad_events;
this->num_wrongdetid_events += local_num_wrongdetid_events;
std::set<PixelType>::iterator it;
for (it = local_wrongdetids.begin(); it != local_wrongdetids.end(); ++it){
PixelType tmpid = *it;
this->wrongdetids.insert(*it);
// 1. Create class map entry if not there
size_t mindex = 0;
std::map<PixelType, size_t>::iterator git = this->wrongdetidmap.find(tmpid);
if (git == this->wrongdetidmap.end()){
// create entry
size_t newindex = this->wrongdetid_abstimes.size();
this->wrongdetidmap[tmpid] = newindex;
std::vector<int64_t> temptimes;
this->wrongdetid_abstimes.push_back(temptimes);
mindex = newindex;
} else {
mindex = git->second;
}
// 2. Find local
std::map<PixelType, size_t>::iterator lit = local_pidindexmap.find(tmpid);
size_t localindex= lit->second;
// g_log.notice() << "Pixel " << tmpid << " Global index = " << mindex << " Local Index = " << localindex << std::endl;
// 3. Sort and merge
std::sort(local_abstimes[localindex].begin(), local_abstimes[localindex].end());
for (size_t iv = 0; iv < local_abstimes[localindex].size(); iv ++){
this->wrongdetid_abstimes[mindex].push_back(local_abstimes[localindex][iv]);
}
// std::sort(this->wrongdetid_abstimes[mindex].begin(), this->wrongdetid_abstimes[mindex].end());
}
if (local_shortest_tof < shortest_tof)
shortest_tof = local_shortest_tof;
if (local_longest_tof > longest_tof)
longest_tof = local_longest_tof;
}
}
//-----------------------------------------------------------------------------
/// Comparator for sorting dasevent lists
bool vzintermediatePixelIDComp(IntermediateEvent x, IntermediateEvent y)
{
return (x.pid < y.pid);
}
//-----------------------------------------------------------------------------
/**
* Add a sample environment log for the proton chage (charge of the pulse in picoCoulombs)
* and set the scalar value (total proton charge, microAmps*hours, on the sample)
*
* @param workspace :: Event workspace to set the proton charge on
*/
void LoadEventPreNexus2::setProtonCharge(DataObjects::EventWorkspace_sptr & workspace)
{
if (this->proton_charge.empty()) // nothing to do
return;
Run& run = workspace->mutableRun();
//Add the proton charge entries.
TimeSeriesProperty<double>* log = new TimeSeriesProperty<double>("proton_charge");
log->setUnits("picoCoulombs");
//Add the time and associated charge to the log
log->addValues(this->pulsetimes, this->proton_charge);
/// TODO set the units for the log
run.addLogData(log);
double integ = run.integrateProtonCharge();
//run.setProtonCharge(this->proton_charge_tot); //This is now redundant
this->g_log.information() << "Total proton charge of " << integ << " microAmp*hours found by integrating.\n";
}
//-----------------------------------------------------------------------------
/** Load a pixel mapping file
* @param filename :: Path to file.
*/
void LoadEventPreNexus2::loadPixelMap(const std::string &filename)
{
this->using_mapping_file = false;
this->pixelmap.clear();
// check that there is a mapping file
if (filename.empty()) {
this->g_log.information("NOT using a mapping file");
return;
}
// actually deal with the file
this->g_log.debug("Using mapping file \"" + filename + "\"");
//Open the file; will throw if there is any problem
BinaryFile<PixelType> pixelmapFile(filename);
PixelType max_pid = static_cast<PixelType>(pixelmapFile.getNumElements());
//Load all the data
pixelmapFile.loadAllInto( this->pixelmap );
//Check for funky file
if (std::find_if(pixelmap.begin(), pixelmap.end(), std::bind2nd(std::greater<PixelType>(), max_pid))
!= pixelmap.end())
{
this->g_log.warning("Pixel id in mapping file was out of bounds. Loading without mapping file");
this->numpixel = 0;
this->pixelmap.clear();
this->using_mapping_file = false;
return;
}
//If we got here, the mapping file was loaded correctly and we'll use it
this->using_mapping_file = true;
//Let's assume that the # of pixels in the instrument matches the mapping file length.
this->numpixel = static_cast<uint32_t>(pixelmapFile.getNumElements());
}
//-----------------------------------------------------------------------------
/** Open an event file
* @param filename :: file to open.
*/
void LoadEventPreNexus2::openEventFile(const std::string &filename)
{
//Open the file
eventfile = new BinaryFile<DasEvent>(filename);
num_events = eventfile->getNumElements();
g_log.debug() << "File contains " << num_events << " event records.\n";
// Check if we are only loading part of the event file
const int chunk = getProperty("ChunkNumber");
if ( isEmpty(chunk) ) // We are loading the whole file
{
first_event = 0;
max_events = num_events;
}
else // We are loading part - work out the event number range
{
const int totalChunks = getProperty("TotalChunks");
max_events = num_events/totalChunks;
first_event = (chunk - 1) * max_events;
// Need to add any remainder to the final chunk
if ( chunk == totalChunks ) max_events += num_events%totalChunks;
}
g_log.information()<< "Reading " << max_events << " event records\n";
}
//-----------------------------------------------------------------------------
/** Read a pulse ID file
* @param filename :: file to load.
* @param throwError :: Flag to trigger error throwing instead of just logging
*/
void LoadEventPreNexus2::readPulseidFile(const std::string &filename, const bool throwError)
{
this->proton_charge_tot = 0.;
this->num_pulses = 0;
// jump out early if there isn't a filename
if (filename.empty()) {
this->g_log.information("NOT using a pulseid file");
return;
}
std::vector<Pulse> * pulses;
// set up for reading
//Open the file; will throw if there is any problem
try {
BinaryFile<Pulse> pulseFile(filename);
//Get the # of pulse
this->num_pulses = pulseFile.getNumElements();
this->g_log.information() << "Using pulseid file \"" << filename << "\", with " << num_pulses
<< " pulses.\n";
//Load all the data
pulses = pulseFile.loadAll();
} catch (runtime_error &e) {
if (throwError)
{
throw;
}
else
{
this->g_log.information() << "Encountered error in pulseidfile (ignoring file): " << e.what() << "\n";
return;
}
}
double temp;
if (num_pulses > 0)
{
this->pulsetimes.reserve(num_pulses);
for (size_t i=0; i < num_pulses; i++)
{
Pulse & it = (*pulses)[i];
this->pulsetimes.push_back( DateAndTime( (int64_t) it.seconds, (int64_t) it.nanoseconds) );
this->event_indices.push_back(it.event_index);
temp = it.pCurrent;
this->proton_charge.push_back(temp);
if (temp < 0.)
this->g_log.warning("Individual proton charge < 0 being ignored");
else
this->proton_charge_tot += temp;
}
}
this->proton_charge_tot = this->proton_charge_tot * CURRENT_CONVERSION;
//Clear the vector
delete pulses;
}
} // namespace DataHandling
} // namespace Mantid