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#include <exception>
#include <fstream>
#include <Poco/Path.h>
#include <Poco/File.h>
#include <Poco/DOM/DOMParser.h>
#include <Poco/DOM/Document.h>
#include <Poco/DOM/Element.h>
#include <Poco/DOM/NodeIterator.h>
#include <Poco/DOM/NodeFilter.h>
#include <Poco/DOM/NodeList.h>
#include <Poco/DOM/AutoPtr.h>
#include <Poco/SAX/InputSource.h>
#include <set>
#include "MantidAPI/FileProperty.h"
#include "MantidDataHandling/DetermineChunking.h"
#include "MantidDataHandling/LoadPreNexus.h"
#include "MantidDataHandling/LoadEventNexus.h"
#include "MantidDataHandling/LoadTOFRawNexus.h"
#include "LoadRaw/isisraw.h"
#include "MantidDataHandling/LoadRawHelper.h"
#include "MantidKernel/System.h"
#include "MantidKernel/VisibleWhenProperty.h"
#include "MantidAPI/TableRow.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidKernel/BinaryFile.h"
#include "MantidKernel/BoundedValidator.h"
#include <boost/mpi.hpp>
namespace mpi = boost::mpi;
using namespace ::NeXus;
using namespace Mantid::Kernel;
using namespace Mantid::API;
using std::size_t;
using std::map;
using std::string;
using std::vector;
namespace Mantid {
namespace DataHandling {
const int NUM_EXT_PRENEXUS(1); ///< Number of prenexus extensions
/// Valid extensions for prenexus files
const std::string PRENEXUS_EXT[NUM_EXT_PRENEXUS] = {"_runinfo.xml"};
const int NUM_EXT_EVENT_NEXUS(3); ///< Number of event nexus extensions
/// Valid extensions for event nexus files
const std::string EVENT_NEXUS_EXT[NUM_EXT_EVENT_NEXUS] = {"_event.nxs", ".nxs",
".nxs.h5"};
const int NUM_EXT_HISTO_NEXUS(1); ///< Number of histogram nexus extensions
/// Valid extensions for histogram nexus files
const std::string HISTO_NEXUS_EXT[NUM_EXT_HISTO_NEXUS] = {"_histo.nxs"};
const int NUM_EXT_RAW(1); ///< Number of raw file extensions
/// Valid extensions for ISIS raw files
const std::string RAW_EXT[NUM_EXT_RAW] = {".raw"};
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(DetermineChunking)
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//----------------------------------------------------------------------------------------------
/// Constructor
DetermineChunking::DetermineChunking() {}
//----------------------------------------------------------------------------------------------
/// Destructor
DetermineChunking::~DetermineChunking() {}
//----------------------------------------------------------------------------------------------
/// @copydoc Mantid::API::IAlgorithm::name()
const std::string DetermineChunking::name() const {
return "DetermineChunking";
}
/// @copydoc Mantid::API::IAlgorithm::version()
int DetermineChunking::version() const { return 1; }
/// @copydoc Mantid::API::IAlgorithm::category()
const std::string DetermineChunking::category() const {
return "DataHandling\\PreNexus;Workflow\\DataHandling";
}
//----------------------------------------------------------------------------------------------
/// @copydoc Mantid::API::Algorithm::init()
void DetermineChunking::init() {
// runfile to read in
std::set<std::string> exts_set;
exts_set.insert(PRENEXUS_EXT, PRENEXUS_EXT + NUM_EXT_PRENEXUS);
exts_set.insert(EVENT_NEXUS_EXT, EVENT_NEXUS_EXT + NUM_EXT_EVENT_NEXUS);
exts_set.insert(HISTO_NEXUS_EXT, HISTO_NEXUS_EXT + NUM_EXT_HISTO_NEXUS);
exts_set.insert(RAW_EXT, RAW_EXT + NUM_EXT_RAW);
std::vector<std::string> exts(exts_set.begin(), exts_set.end());
this->declareProperty(
new FileProperty("Filename", "", FileProperty::Load, exts),
"The name of the event nexus, runinfo.xml, raw, or histo nexus file to "
"read, including its full or relative path. The Event NeXus file name is "
"typically of the form INST_####_event.nxs (N.B. case sensitive if "
"running on Linux).");
auto mustBePositive = boost::make_shared<BoundedValidator<double>>();
mustBePositive->setLower(0.0);
declareProperty("MaxChunkSize", EMPTY_DBL(), mustBePositive,
"Get chunking strategy for chunks with this number of "
"Gbytes. File will not be loaded if this option is set.");
declareProperty(new WorkspaceProperty<API::ITableWorkspace>(
"OutputWorkspace", "", Direction::Output),
"An output workspace.");
}
//----------------------------------------------------------------------------------------------
/// @copydoc Mantid::API::Algorithm::exec()
void DetermineChunking::exec() {
// get the chunking parameter and fix it up
double maxChunk = this->getProperty("MaxChunkSize");
if (maxChunk == 0) {
g_log.debug() << "Converting maxChunk=0 to maxChunk=EMPTY_DBL\n";
maxChunk = EMPTY_DBL();
// get the filename and determine the file type
double filesize = 0;
int m_numberOfSpectra = 0;
string filename = this->getPropertyValue("Filename");
FileType fileType = getFileType(filename);
// setup the chunking table with the correct column headings
Mantid::API::ITableWorkspace_sptr strategy =
Mantid::API::WorkspaceFactory::Instance().createTable("TableWorkspace");
if (fileType == PRENEXUS_FILE || fileType == EVENT_NEXUS_FILE) {
strategy->addColumn("int", "ChunkNumber");
strategy->addColumn("int", "TotalChunks");
} else if (fileType == RAW_FILE || fileType == HISTO_NEXUS_FILE) {
strategy->addColumn("int", "SpectrumMin");
strategy->addColumn("int", "SpectrumMax");
}
this->setProperty("OutputWorkspace", strategy);
// mpi needs work for every core, so don't do this
if (maxChunk == 0 || isEmpty(maxChunk)) {
return;
}
// --------------------- DETERMINE NUMBER OF CHUNKS
// PreNexus
if (fileType == PRENEXUS_FILE) {
vector<string> eventFilenames;
string dataDir;
LoadPreNexus lp;
lp.parseRuninfo(filename, dataDir, eventFilenames);
for (size_t i = 0; i < eventFilenames.size(); i++) {
BinaryFile<DasEvent> eventfile(dataDir + eventFilenames[i]);
// Factor of 2 for compression
filesize += static_cast<double>(eventfile.getNumElements()) * 48.0 /
(1024.0 * 1024.0 * 1024.0);
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}
// Event Nexus
else if (fileType == EVENT_NEXUS_FILE) {
// top level file information
::NeXus::File file(filename);
std::string m_top_entry_name = setTopEntryName(filename);
// Start with the base entry
file.openGroup(m_top_entry_name, "NXentry");
// Now we want to go through all the bankN_event entries
map<string, string> entries = file.getEntries();
map<string, string>::const_iterator it = entries.begin();
std::string classType = "NXevent_data";
size_t total_events = 0;
for (; it != entries.end(); ++it) {
std::string entry_name(it->first);
std::string entry_class(it->second);
if (entry_class == classType) {
if (!isEmpty(maxChunk)) {
try {
// Get total number of events for each bank
file.openGroup(entry_name, entry_class);
file.openData("total_counts");
if (file.getInfo().type == NX_UINT64) {
std::vector<uint64_t> bank_events;
file.getData(bank_events);
total_events += bank_events[0];
} else {
std::vector<int> bank_events;
file.getDataCoerce(bank_events);
total_events += bank_events[0];
file.closeData();
file.closeGroup();
} catch (::NeXus::Exception &) {
g_log.error()
<< "Unable to find total counts to determine chunking strategy."
<< std::endl;
// Close up the file
file.closeGroup();
file.close();
// Factor of 2 for compression
filesize =
static_cast<double>(total_events) * 48.0 / (1024.0 * 1024.0 * 1024.0);
} else if (fileType == RAW_FILE) {
// Check the size of the file loaded
Poco::File info(filename);
filesize = double(info.getSize()) * 24.0 / (1024.0 * 1024.0 * 1024.0);
g_log.notice() << "Wksp size is " << filesize << " GB" << std::endl;
LoadRawHelper helper;
FILE *file = helper.openRawFile(filename);
ISISRAW iraw;
iraw.ioRAW(file, true);
// Read in the number of spectra in the RAW file
m_numberOfSpectra = iraw.t_nsp1;
g_log.notice() << "Spectra size is " << m_numberOfSpectra << " spectra"
<< std::endl;
fclose(file);
}
// Histo Nexus
else if (fileType == HISTO_NEXUS_FILE) {
// Check the size of the file loaded
Poco::File info(filename);
filesize = double(info.getSize()) * 144.0 / (1024.0 * 1024.0 * 1024.0);
g_log.notice() << "Wksp size is " << filesize << " GB" << std::endl;
LoadTOFRawNexus lp;
lp.m_signalNo = 1;
// Find the entry name we want.
std::string entry_name = LoadTOFRawNexus::getEntryName(filename);
std::vector<std::string> bankNames;
lp.countPixels(filename, entry_name, bankNames);
m_numberOfSpectra = static_cast<int>(lp.m_numPixels);
g_log.notice() << "Spectra size is " << m_numberOfSpectra << " spectra"
<< std::endl;
} else {
throw(std::invalid_argument("unsupported file type"));
}
int numChunks = 0;
if (maxChunk) // protect from divide by zero
{
numChunks = static_cast<int>(filesize / maxChunk);
}
numChunks++; // So maxChunkSize is not exceeded
if (numChunks <= 1 || isEmpty(maxChunk)) {
g_log.information()
<< "Everything can be done in a single chunk returning empty table\n";
return;
// --------------------- FILL IN THE CHUNKING TABLE
// use all cores so number of chunks should be a multiple of cores
if (mpi::communicator().size() > 1) {
int imult = numChunks / mpi::communicator().size() + 1;
numChunks = imult * mpi::communicator().size();
}
for (int i = 1; i <= numChunks; i++) {
if (mpi::communicator().size() > 1) {
// chunk 1 should go to rank=0, chunk 2 to rank=1, etc.
if ((i - 1) % mpi::communicator().size() != mpi::communicator().rank())
continue;
}
Mantid::API::TableRow row = strategy->appendRow();
if (fileType == PRENEXUS_FILE || fileType == EVENT_NEXUS_FILE) {
row << i << numChunks;
} else if (fileType == RAW_FILE || fileType == HISTO_NEXUS_FILE) {
int spectraPerChunk = m_numberOfSpectra / numChunks;
int first = (i - 1) * spectraPerChunk + 1;
int last = first + spectraPerChunk - 1;
if (i == numChunks)
last = m_numberOfSpectra;
row << first << last;
/// set the name of the top level NXentry m_top_entry_name
std::string DetermineChunking::setTopEntryName(std::string filename) {
std::string top_entry_name;
typedef std::map<std::string, std::string> string_map_t;
try {
string_map_t::const_iterator it;
::NeXus::File file = ::NeXus::File(filename);
string_map_t entries = file.getEntries();
// Choose the first entry as the default
top_entry_name = entries.begin()->first;
for (it = entries.begin(); it != entries.end(); ++it) {
if (((it->first == "entry") || (it->first == "raw_data_1")) &&
(it->second == "NXentry")) {
top_entry_name = it->first;
break;
} catch (const std::exception &) {
g_log.error()
<< "Unable to determine name of top level NXentry - assuming \"entry\"."
<< std::endl;
top_entry_name = "entry";
/**
* Determine the file type using the filename. This throws an exception
* if the type cannot be determined.
*
* @param filename Name of the file to determine the type of.
* @return The file type.
*/
FileType DetermineChunking::getFileType(const string &filename) {
// check for prenexus
for (int i = 0; i < NUM_EXT_PRENEXUS; ++i) {
if (filename.find(PRENEXUS_EXT[i]) != std::string::npos) {
g_log.information() << "Determined \'" << filename
<< "\' is a prenexus file\n";
return PRENEXUS_FILE;
// check for histogram nexus
for (int i = 0; i < NUM_EXT_HISTO_NEXUS; ++i) {
if (filename.find(HISTO_NEXUS_EXT[i]) != std::string::npos) {
g_log.information() << "Determined \'" << filename
<< "\' is a histogram nexus file\n";
return HISTO_NEXUS_FILE;
// check for event nexus - must be last because a valid extension is ".nxs"
for (int i = 0; i < NUM_EXT_EVENT_NEXUS; ++i) {
if (filename.find(EVENT_NEXUS_EXT[i]) != std::string::npos) {
g_log.information() << "Determined \'" << filename
<< "\' is an event nexus file\n";
return EVENT_NEXUS_FILE;
// check for isis raw files
for (int i = 0; i < NUM_EXT_RAW; ++i) {
if (filename.find(RAW_EXT[i]) != std::string::npos) {
g_log.information() << "Determined \'" << filename
<< "\' is an ISIS raw file\n";
return RAW_FILE;
throw std::invalid_argument("Unsupported file type");
}
} // namespace Mantid
} // namespace DataHandling