From 6bba0d02452ca818af9bc49d2e2a6be976045d52 Mon Sep 17 00:00:00 2001
From: Martyn Gigg <martyn.gigg@stfc.ac.uk>
Date: Wed, 1 Jun 2011 12:46:29 +0000
Subject: [PATCH] Refs #3106. Created a new algorithm that replaces
LoadLogsFromSNSNexus and can be used for any of the NXlog and IXseblock
entries in a NeXus file. LoadEventNexus and LoadISISNexus2 now use these
also.
---
Code/Mantid/Framework/Nexus/CMakeLists.txt | 135 +++---
.../Nexus/inc/MantidNexus/LoadISISNexus2.h | 2 +-
.../inc/MantidNexus/LoadLogsFromSNSNexus.h | 4 +-
.../Nexus/inc/MantidNexus/LoadRunLogs.h | 100 +++++
.../Framework/Nexus/src/LoadEventNexus.cpp | 7 +-
.../Framework/Nexus/src/LoadISISNexus2.cpp | 112 ++---
.../Nexus/src/LoadLogsFromSNSNexus.cpp | 11 +-
.../Framework/Nexus/src/LoadRunLogs.cpp | 396 ++++++++++++++++++
.../Framework/Nexus/test/LoadISISNexusTest.h | 47 ++-
.../Framework/Nexus/test/LoadRunLogsTest.h | 76 ++++
10 files changed, 715 insertions(+), 175 deletions(-)
create mode 100644 Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadRunLogs.h
create mode 100644 Code/Mantid/Framework/Nexus/src/LoadRunLogs.cpp
create mode 100644 Code/Mantid/Framework/Nexus/test/LoadRunLogsTest.h
diff --git a/Code/Mantid/Framework/Nexus/CMakeLists.txt b/Code/Mantid/Framework/Nexus/CMakeLists.txt
index 53ec8d5c48b..f4fcc351433 100644
--- a/Code/Mantid/Framework/Nexus/CMakeLists.txt
+++ b/Code/Mantid/Framework/Nexus/CMakeLists.txt
@@ -1,79 +1,82 @@
set ( SRC_FILES
- src/LoadEventNexus.cpp
- src/LoadISISNexus.cpp
- src/LoadISISNexus2.cpp
- src/LoadInstrumentFromNexus.cpp
- src/LoadLogsFromSNSNexus.cpp
- src/LoadMuonLog.cpp
- src/LoadMuonNexus.cpp
- src/LoadMuonNexus2.cpp
- src/LoadNeXus.cpp
- src/LoadNexusMonitors.cpp
- src/LoadNexusProcessed.cpp
- src/LoadRaw/byte_rel_comp.cpp
- src/LoadRaw/isisraw.cpp
- src/LoadRaw/isisraw2.cpp
- src/LoadRaw/item_struct.cpp
- src/LoadRaw/vms_convert.cpp
- src/LoadSNSEventNexus.cpp
- src/LoadSNSNexus.cpp
- src/LoadTOFRawNeXus.cpp
- src/MuonNexusReader.cpp
- src/NeXusException.cpp
- src/NeXusFile.cpp
- src/NeXusStream.cpp
- src/NexusClasses.cpp
- src/NexusFileIO.cpp
- src/SaveISISNeXus.cpp
- src/SaveNeXus.cpp
- src/SaveNexusProcessed.cpp
- src/SaveToSNSHistogramNexus.cpp
+ src/LoadEventNexus.cpp
+ src/LoadISISNexus.cpp
+ src/LoadISISNexus2.cpp
+ src/LoadInstrumentFromNexus.cpp
+ src/LoadLogsFromSNSNexus.cpp
+ src/LoadMuonLog.cpp
+ src/LoadMuonNexus.cpp
+ src/LoadMuonNexus2.cpp
+ src/LoadNeXus.cpp
+ src/LoadNexusMonitors.cpp
+ src/LoadNexusProcessed.cpp
+ src/LoadRaw/byte_rel_comp.cpp
+ src/LoadRaw/isisraw.cpp
+ src/LoadRaw/isisraw2.cpp
+ src/LoadRaw/item_struct.cpp
+ src/LoadRaw/vms_convert.cpp
+ src/LoadRunLogs.cpp
+ src/LoadSNSEventNexus.cpp
+ src/LoadSNSNexus.cpp
+ src/LoadTOFRawNeXus.cpp
+ src/MuonNexusReader.cpp
+ src/NeXusException.cpp
+ src/NeXusFile.cpp
+ src/NeXusStream.cpp
+ src/NexusClasses.cpp
+ src/NexusFileIO.cpp
+ src/SaveISISNeXus.cpp
+ src/SaveNeXus.cpp
+ src/SaveNexusProcessed.cpp
+ src/SaveToSNSHistogramNexus.cpp
)
set ( SRC_UNITY_IGNORE_FILES src/NeXusFile.cpp)
set ( INC_FILES
- inc/MantidNexus/LoadEventNexus.h
- inc/MantidNexus/LoadISISNexus.h
- inc/MantidNexus/LoadISISNexus2.h
- inc/MantidNexus/LoadInstrumentFromNexus.h
- inc/MantidNexus/LoadLogsFromSNSNexus.h
- inc/MantidNexus/LoadMuonLog.h
- inc/MantidNexus/LoadMuonNexus.h
- inc/MantidNexus/LoadMuonNexus2.h
- inc/MantidNexus/LoadNeXus.h
- inc/MantidNexus/LoadNexusMonitors.h
- inc/MantidNexus/LoadNexusProcessed.h
- inc/MantidNexus/LoadSNSEventNexus.h
- inc/MantidNexus/LoadSNSNexus.h
- inc/MantidNexus/LoadTOFRawNeXus.h
- inc/MantidNexus/MuonNexusReader.h
- inc/MantidNexus/NexusClasses.h
- inc/MantidNexus/NexusFileIO.h
- inc/MantidNexus/SaveISISNeXus.h
- inc/MantidNexus/SaveNeXus.h
- inc/MantidNexus/SaveNexusProcessed.h
- inc/MantidNexus/SaveToSNSHistogramNexus.h
+ inc/MantidNexus/LoadEventNexus.h
+ inc/MantidNexus/LoadISISNexus.h
+ inc/MantidNexus/LoadISISNexus2.h
+ inc/MantidNexus/LoadInstrumentFromNexus.h
+ inc/MantidNexus/LoadLogsFromSNSNexus.h
+ inc/MantidNexus/LoadMuonLog.h
+ inc/MantidNexus/LoadMuonNexus.h
+ inc/MantidNexus/LoadMuonNexus2.h
+ inc/MantidNexus/LoadNeXus.h
+ inc/MantidNexus/LoadNexusMonitors.h
+ inc/MantidNexus/LoadNexusProcessed.h
+ inc/MantidNexus/LoadRunLogs.h
+ inc/MantidNexus/LoadSNSEventNexus.h
+ inc/MantidNexus/LoadSNSNexus.h
+ inc/MantidNexus/LoadTOFRawNeXus.h
+ inc/MantidNexus/MuonNexusReader.h
+ inc/MantidNexus/NexusClasses.h
+ inc/MantidNexus/NexusFileIO.h
+ inc/MantidNexus/SaveISISNeXus.h
+ inc/MantidNexus/SaveNeXus.h
+ inc/MantidNexus/SaveNexusProcessed.h
+ inc/MantidNexus/SaveToSNSHistogramNexus.h
)
set ( TEST_FILES
- #test/LoadSNSNexusTest.h # TODO has no active tests in it
- #test/LoadTOFRawNeXusTest.h # TODO has no active tests in it
- test/LoadEventNexusTest.h
- test/LoadISISNexusTest.h
- test/LoadLogsFromSNSNexusTest.h
- test/LoadMuonLogTest.h
- test/LoadMuonNexus2Test.h
- test/LoadMuonNexusTest.h
- test/LoadNeXusTest.h
- test/LoadNexusMonitorsTest.h
- test/LoadNexusProcessedTest.h
- test/LoadRSaveNLoadNcspTest.h
- test/LoadSNSEventNexusTest.h
- test/NexusAPITest.h
- test/SaveNeXusTest.h
- test/SaveNexusProcessedTest.h
+ #test/LoadSNSNexusTest.h # TODO has no active tests in it
+ #test/LoadTOFRawNeXusTest.h # TODO has no active tests in it
+ test/LoadEventNexusTest.h
+ test/LoadISISNexusTest.h
+ test/LoadLogsFromSNSNexusTest.h
+ test/LoadMuonLogTest.h
+ test/LoadMuonNexus2Test.h
+ test/LoadMuonNexusTest.h
+ test/LoadNeXusTest.h
+ test/LoadNexusMonitorsTest.h
+ test/LoadNexusProcessedTest.h
+ test/LoadRunLogsTest.h
+ test/LoadRSaveNLoadNcspTest.h
+ test/LoadSNSEventNexusTest.h
+ test/NexusAPITest.h
+ test/SaveNeXusTest.h
+ test/SaveNexusProcessedTest.h
)
if(UNITY_BUILD)
diff --git a/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadISISNexus2.h b/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadISISNexus2.h
index eff586312d0..3b7071054af 100644
--- a/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadISISNexus2.h
+++ b/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadISISNexus2.h
@@ -96,7 +96,7 @@ namespace Mantid
/// Load in details about the sample
void loadSampleData(DataObjects::Workspace2D_sptr, NXEntry & entry);
/// Load log data from the nexus file
- void loadLogs(DataObjects::Workspace2D_sptr, NXEntry & entry,int period = 1);
+ void loadLogs(DataObjects::Workspace2D_sptr, int period = 1);
// Load a given period into the workspace
void loadPeriodData(int64_t period, NXEntry & entry, DataObjects::Workspace2D_sptr local_workspace);
// Load a data block
diff --git a/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadLogsFromSNSNexus.h b/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadLogsFromSNSNexus.h
index 900c507b4f7..30b97117bc7 100644
--- a/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadLogsFromSNSNexus.h
+++ b/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadLogsFromSNSNexus.h
@@ -14,6 +14,7 @@
#include "MantidNexus/NeXusFile.hpp"
#include "MantidNexus/NeXusException.hpp"
+#include "MantidAPI/DeprecatedAlgorithm.h"
namespace Mantid
{
@@ -60,8 +61,9 @@ namespace Mantid
File change history is stored at: <https://svn.mantidproject.org/mantid/trunk/Code/Mantid>
*/
- class DLLExport LoadLogsFromSNSNexus : public API::Algorithm
+ class DLLExport LoadLogsFromSNSNexus : public API::Algorithm, public API::DeprecatedAlgorithm
{
+
public:
/// Default constructor
LoadLogsFromSNSNexus();
diff --git a/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadRunLogs.h b/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadRunLogs.h
new file mode 100644
index 00000000000..a6b3d84524f
--- /dev/null
+++ b/Code/Mantid/Framework/Nexus/inc/MantidNexus/LoadRunLogs.h
@@ -0,0 +1,100 @@
+#ifndef MANTID_DATAHANDLING_LOADRUNLOGS_H_
+#define MANTID_DATAHANDLING_LOADRUNLOGS_H_
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAPI/Algorithm.h"
+#include "MantidNexus/NeXusFile.hpp"
+
+namespace Mantid
+{
+ //----------------------------------------------------------------------
+ // Forward declaration
+ //----------------------------------------------------------------------
+ namespace Kernel
+ {
+ class Property;
+ }
+ namespace API
+ {
+ class MatrixWorkspace;
+ }
+
+ namespace NeXus
+ {
+
+ /**
+
+ Loads the run logs from a NeXus file.
+
+ Required Properties:
+ <UL>
+ <LI> Filename - The name of and path to the input Nexus file </LI>
+ <LI> Workspace - The name of the workspace in which to store the imported data.</LI>
+ </UL>
+
+ @author Martyn Gigg, Tessella plc
+
+ Copyright © 2011 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://svn.mantidproject.org/mantid/trunk/Code/Mantid>.
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+ */
+ class DLLExport LoadRunLogs : public API::Algorithm
+ {
+ public:
+ /// Default constructor
+ LoadRunLogs();
+ /// Destructor
+ virtual ~LoadRunLogs() {}
+ /// Algorithm's name for identification overriding a virtual method
+ virtual const std::string name() const { return "LoadRunLogs"; }
+ /// Algorithm's version for identification overriding a virtual method
+ virtual int version() const { return 1; }
+ /// Algorithm's category for identification overriding a virtual method
+ virtual const std::string category() const { return "DataHandling"; }
+
+ private:
+ /// Overwrites Algorithm method.
+ void initDocs();
+ /// Overwrites Algorithm method.
+ void init();
+ /// Overwrites Algorithm method
+ void exec();
+ /// Load log data from a group
+ void loadLogs(::NeXus::File & file, const std::string & entry_name,
+ const std::string & entry_class,
+ boost::shared_ptr<API::MatrixWorkspace> workspace) const;
+ /// Load an NXlog entry
+ void loadNXLog(::NeXus::File & file, const std::string & entry_name,
+ boost::shared_ptr<API::MatrixWorkspace> workspace) const;
+ /// Load an IXseblock entry
+ void loadSELog(::NeXus::File & file, const std::string & entry_name,
+ boost::shared_ptr<API::MatrixWorkspace> workspace) const;
+ /// Create a time series property
+ Kernel::Property * createTimeSeries(::NeXus::File & file,
+ const std::string & prop_name) const;
+ ///Progress reporting object
+ boost::shared_ptr<API::Progress> m_progress;
+ };
+
+ } // namespace NeXus
+} // namespace Mantid
+
+#endif /*MANTID_DATAHANDLING_LOADRUNLOGS_H_*/
diff --git a/Code/Mantid/Framework/Nexus/src/LoadEventNexus.cpp b/Code/Mantid/Framework/Nexus/src/LoadEventNexus.cpp
index 3f55662ea43..9c3f1fd3700 100644
--- a/Code/Mantid/Framework/Nexus/src/LoadEventNexus.cpp
+++ b/Code/Mantid/Framework/Nexus/src/LoadEventNexus.cpp
@@ -627,10 +627,6 @@ void LoadEventNexus::init()
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),
@@ -657,7 +653,6 @@ void LoadEventNexus::exec()
precount = getProperty("Precount");
compressTolerance = getProperty("CompressTolerance");
- //loadlogs = getProperty("LoadLogs");
loadlogs = true;
//Get the limits to the filter
@@ -709,7 +704,7 @@ void LoadEventNexus::exec()
prog.doReport("Loading DAS logs");
//The pulse times will be empty if not specified in the DAS logs.
pulseTimes.clear();
- IAlgorithm_sptr loadLogs = createSubAlgorithm("LoadLogsFromSNSNexus");
+ IAlgorithm_sptr loadLogs = createSubAlgorithm("LoadRunLogs");
// Now execute the sub-algorithm. Catch and log any error, but don't stop.
try
diff --git a/Code/Mantid/Framework/Nexus/src/LoadISISNexus2.cpp b/Code/Mantid/Framework/Nexus/src/LoadISISNexus2.cpp
index be1662f97d9..9234e7ec4c0 100644
--- a/Code/Mantid/Framework/Nexus/src/LoadISISNexus2.cpp
+++ b/Code/Mantid/Framework/Nexus/src/LoadISISNexus2.cpp
@@ -213,7 +213,7 @@ namespace Mantid
loadSampleData(local_workspace, entry);
m_progress->report("Loading logs");
- loadLogs(local_workspace, entry);
+ loadLogs(local_workspace);
// Load first period outside loop
m_progress->report("Loading data");
@@ -271,7 +271,7 @@ namespace Mantid
{
//Check the numbers supplied are not in the range and erase the ones that are
struct range_check
- {
+ {
range_check(int64_t min, int64_t max) : m_min(min), m_max(max) {}
bool operator()(int64_t x)
@@ -609,26 +609,26 @@ namespace Mantid
// RPB struct info
NXInt rpb_int = vms_compat.openNXInt("IRPB");
rpb_int.load();
- runDetails.addProperty("dur", rpb_int[0]); // actual run duration
- runDetails.addProperty("durunits", rpb_int[1]); // scaler for above (1=seconds)
+ runDetails.addProperty("dur", rpb_int[0]); // actual run duration
+ runDetails.addProperty("durunits", rpb_int[1]); // scaler for above (1=seconds)
runDetails.addProperty("dur_freq", rpb_int[2]); // testinterval for above (seconds)
runDetails.addProperty("dmp", rpb_int[3]); // dump interval
- runDetails.addProperty("dmp_units", rpb_int[4]); // scaler for above
- runDetails.addProperty("dmp_freq", rpb_int[5]); // interval for above
- runDetails.addProperty("freq", rpb_int[6]); // 2**k where source frequency = 50 / 2**k
+ runDetails.addProperty("dmp_units", rpb_int[4]); // scaler for above
+ runDetails.addProperty("dmp_freq", rpb_int[5]); // interval for above
+ runDetails.addProperty("freq", rpb_int[6]); // 2**k where source frequency = 50 / 2**k
// Now double data
NXFloat rpb_dbl = vms_compat.openNXFloat("RRPB");
rpb_dbl.load();
runDetails.addProperty("gd_prtn_chrg", static_cast<double>(rpb_dbl[7])); // good proton charge (uA.hour)
runDetails.addProperty("tot_prtn_chrg", static_cast<double>(rpb_dbl[8])); // total proton charge (uA.hour)
- runDetails.addProperty("goodfrm",rpb_int[9]); // good frames
- runDetails.addProperty("rawfrm", rpb_int[10]); // raw frames
+ runDetails.addProperty("goodfrm",rpb_int[9]); // good frames
+ runDetails.addProperty("rawfrm", rpb_int[10]); // raw frames
runDetails.addProperty("dur_wanted", rpb_int[11]); // requested run duration (units as for "duration" above)
- runDetails.addProperty("dur_secs", rpb_int[12]); // actual run duration in seconds
- runDetails.addProperty("mon_sum1", rpb_int[13]); // monitor sum 1
- runDetails.addProperty("mon_sum2", rpb_int[14]); // monitor sum 2
- runDetails.addProperty("mon_sum3",rpb_int[15]); // monitor sum 3
+ runDetails.addProperty("dur_secs", rpb_int[12]); // actual run duration in seconds
+ runDetails.addProperty("mon_sum1", rpb_int[13]); // monitor sum 1
+ runDetails.addProperty("mon_sum2", rpb_int[14]); // monitor sum 2
+ runDetails.addProperty("mon_sum3",rpb_int[15]); // monitor sum 3
// End date and time is stored separately in ISO format in the "raw_data1/endtime" class
char_data = entry.openNXChar("end_time");
@@ -699,78 +699,34 @@ namespace Mantid
* /raw_data_1/runlog group of the file. Call to this method must be done
* within /raw_data_1 group.
* @param ws :: The workspace to load the logs to.
- * @param entry :: The Nexus entry
* @param period :: The period of this workspace
*/
- void LoadISISNexus2::loadLogs(DataObjects::Workspace2D_sptr ws, NXEntry & entry,int period)
+ void LoadISISNexus2::loadLogs(DataObjects::Workspace2D_sptr ws, int period)
{
-
- NXMainClass runlogs = entry.openNXClass<NXMainClass>("runlog");
-
- for(std::vector<NXClassInfo>::const_iterator it=runlogs.groups().begin();it!=runlogs.groups().end();it++)
+ IAlgorithm_sptr alg = createSubAlgorithm("LoadRunLogs", 0.0, 0.5);
+ alg->setPropertyValue("Filename", this->getProperty("Filename"));
+ alg->setProperty<MatrixWorkspace_sptr>("Workspace", ws);
+ try
{
- if (it->nxclass == "NXlog")
- {
-
- NXLog nxLog(runlogs,it->nxname);
- nxLog.openLocal();
-
- Kernel::Property* logv = nxLog.createTimeSeries();
- if (!logv)
- {
- nxLog.close();
- continue;
- }
- ws->mutableRun().addLogData(logv);
- if (it->nxname == "icp_event")
- {
- LogParser parser(logv);
- ws->mutableRun().addLogData(parser.createPeriodLog(period));
- ws->mutableRun().addLogData(parser.createAllPeriodsLog());
- ws->mutableRun().addLogData(parser.createRunningLog());
- }
- nxLog.close();
- }
+ alg->executeAsSubAlg();
}
-
- NXMainClass selogs = entry.openNXClass<NXMainClass>("selog");
- for(std::vector<NXClassInfo>::const_iterator it=selogs.groups().begin();it!=selogs.groups().end();it++)
+ catch(std::runtime_error&)
{
- if (it->nxclass == "IXseblock")
- {
- NXMainClass selog(selogs,it->nxname);
- selog.openLocal("IXseblock");
- NXLog nxLog(selog,"value_log");
- bool ok = nxLog.openLocal();
- std::string propName = it->nxname;
- if (ws->run().hasProperty(propName))
- {
- propName = "selog_"+propName;
- }
-
- if (ok)
- {
- Kernel::Property* logv = nxLog.createTimeSeries("",propName);
- if (!logv)
- {
- nxLog.close();
- selog.close();
- continue;
- }
- ws->mutableRun().addLogData(logv);
- nxLog.close();
- }
- else
- {
- NXFloat value = selog.openNXFloat("value");
- value.load();
- ws->mutableRun().addProperty(propName,(double)*value());
- }
- selog.close();
- }
+ g_log.warning() << "Unable to load run logs. There will be no log "
+ << "data associated with this workspace\n";
+ return;
}
-
ws->populateInstrumentParameters();
+ // If we loaded an icp_event log then create the necessary period logs
+ if( ws->run().hasProperty("icp_event") )
+ {
+ Kernel::Property *log = ws->run().getProperty("icp_event");
+ LogParser parser(log);
+ ws->mutableRun().addProperty(parser.createPeriodLog(period));
+ ws->mutableRun().addProperty(parser.createAllPeriodsLog());
+ ws->mutableRun().addProperty(parser.createRunningLog());
+ }
+
}
double LoadISISNexus2::dblSqrt(double in)
@@ -798,7 +754,7 @@ namespace Mantid
return true;
}
else if ( (nread >= sizeof(g_hdf5_signature)) &&
- (!memcmp(header.full_hdr, g_hdf5_signature, sizeof(g_hdf5_signature))) )
+ (!memcmp(header.full_hdr, g_hdf5_signature, sizeof(g_hdf5_signature))) )
{
//hdf5
return true;
diff --git a/Code/Mantid/Framework/Nexus/src/LoadLogsFromSNSNexus.cpp b/Code/Mantid/Framework/Nexus/src/LoadLogsFromSNSNexus.cpp
index bce972d96c3..067180ef5f5 100644
--- a/Code/Mantid/Framework/Nexus/src/LoadLogsFromSNSNexus.cpp
+++ b/Code/Mantid/Framework/Nexus/src/LoadLogsFromSNSNexus.cpp
@@ -41,7 +41,10 @@ using Geometry::Instrument;
/// Empty default constructor
LoadLogsFromSNSNexus::LoadLogsFromSNSNexus()
-{}
+{
+ useAlgorithm("LoadRunLogs");
+ deprecatedDate("2011-06-01");
+}
/// Initialisation method.
void LoadLogsFromSNSNexus::init()
@@ -52,9 +55,9 @@ void LoadLogsFromSNSNexus::init()
"The name of the workspace in which to import the sample logs." );
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 instrument from. The file extension must either be\n"
- ".nxs or .NXS" );
+ "The name (including its full or relative path) of the Nexus file to\n"
+ "attempt to load the instrument from. The file extension must either be\n"
+ ".nxs or .NXS" );
declareProperty(new PropertyWithValue<bool>("OverwriteLogs", true, Direction::Input));
}
diff --git a/Code/Mantid/Framework/Nexus/src/LoadRunLogs.cpp b/Code/Mantid/Framework/Nexus/src/LoadRunLogs.cpp
new file mode 100644
index 00000000000..297d66953fa
--- /dev/null
+++ b/Code/Mantid/Framework/Nexus/src/LoadRunLogs.cpp
@@ -0,0 +1,396 @@
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidNexus/LoadRunLogs.h"
+#include "MantidNexus/NeXusException.hpp"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidAPI/FileProperty.h"
+#include <cctype>
+
+#include <Poco/Path.h>
+#include <Poco/DateTimeFormatter.h>
+#include <Poco/DateTimeParser.h>
+#include <Poco/DateTimeFormat.h>
+
+#include <boost/scoped_array.hpp>
+
+namespace Mantid
+{
+ namespace NeXus
+ {
+ // Register the algorithm into the algorithm factory
+ DECLARE_ALGORITHM(LoadRunLogs)
+
+ /// Sets documentation strings for this algorithm
+ void LoadRunLogs::initDocs()
+ {
+ this->setWikiSummary("Loads run logs (temperature, pulse charges, etc.) from a NeXus file and adds it to the run information in a [[workspace]].");
+ this->setOptionalMessage("Loads run logs (temperature, pulse charges, etc.) from a NeXus file and adds it to the run information in a workspace.");
+ }
+
+ using namespace Kernel;
+ using API::WorkspaceProperty;
+ using API::MatrixWorkspace;
+ using API::MatrixWorkspace_sptr;
+ using API::FileProperty;
+ using std::size_t;
+
+ /// Empty default constructor
+ LoadRunLogs::LoadRunLogs()
+ {}
+
+ /// Initialisation method.
+ void LoadRunLogs::init()
+ {
+ declareProperty(new WorkspaceProperty<MatrixWorkspace>("Workspace","Anonymous",Direction::InOut));
+ std::vector<std::string> exts;
+ exts.push_back(".nxs");
+ exts.push_back(".n*");
+ declareProperty(new FileProperty("Filename", "", FileProperty::Load, exts),
+ "The name of the Nexus file to load" );
+ declareProperty(new PropertyWithValue<bool>("OverwriteLogs", true, Direction::Input));
+
+
+ }
+
+ /** Executes the algorithm. Reading in the file and creating and populating
+ * the output workspace
+ *
+ * @throw Exception::FileError If the Nexus file cannot be found/opened
+ * @throw std::invalid_argument If the optional properties are set to invalid values
+ */
+ void LoadRunLogs::exec()
+ {
+ std::string filename = getPropertyValue("Filename");
+ ::NeXus::File file(filename);
+ MatrixWorkspace_sptr workspace = getProperty("Workspace");
+
+ // Find the root entry
+ try
+ {
+ file.openGroup("entry", "NXentry"); // SNS style root
+ }
+ catch(::NeXus::Exception&)
+ {
+ try
+ {
+ file.openGroup("raw_data_1", "NXentry"); //ISIS style root
+ }
+ catch(::NeXus::Exception&)
+ {
+ throw std::invalid_argument("Unknown NeXus file format found in file '" + filename + "'");
+ }
+ }
+ // print out the entry level fields
+ std::map<std::string,std::string> entries = file.getEntries();
+ std::map<std::string,std::string>::const_iterator iend = entries.end();
+ for(std::map<std::string,std::string>::const_iterator it = entries.begin();
+ it != iend; it++)
+ {
+ std::string entry_name(it->first);
+ std::string entry_class(it->second);
+ if( entry_name == "DASlogs" || entry_class == "IXrunlog" ||
+ entry_class == "IXselog" )
+ {
+ loadLogs(file, entry_name, entry_class, workspace);
+ }
+ }
+ file.close();
+ }
+
+ /**
+ * Load log entries from the given group
+ * @param file :: A reference to the NeXus file handle opened such that the
+ * next call can be to open the named group
+ * @param entry_name :: The name of the log entry
+ * @param_entry_class :: The class type of the log entry
+ * @param workspace :: A pointer to the workspace to store the logs
+ */
+ void LoadRunLogs::loadLogs(::NeXus::File & file, const std::string & entry_name,
+ const std::string & entry_class,
+ MatrixWorkspace_sptr workspace) const
+ {
+ file.openGroup(entry_name, entry_class);
+ std::map<std::string,std::string> entries = file.getEntries();
+ std::map<std::string,std::string>::const_iterator iend = entries.end();
+ for(std::map<std::string,std::string>::const_iterator itr = entries.begin();
+ itr != iend; itr++)
+ {
+ std::string log_class = itr->second;
+ if( log_class == "NXlog" || entry_class == "NXpositioner" )
+ {
+ loadNXLog(file, itr->first, workspace);
+ }
+ else if( log_class == "IXseblock" )
+ {
+ loadSELog(file, itr->first, workspace);
+ }
+ }
+
+ file.closeGroup();
+ }
+
+ /**
+ * Load an NX log entry
+ * @param file :: A reference to the NeXus file handle opened at the parent group
+ * @param entry_name :: The name of the log entry
+ * @param workspace :: A pointer to the workspace to store the logs
+ */
+ void LoadRunLogs::loadNXLog(::NeXus::File & file, const std::string & entry_name,
+ MatrixWorkspace_sptr workspace) const
+ {
+ file.openGroup(entry_name, "NXlog");
+ // Validate the NX log class.
+ std::map<std::string, std::string> entries = file.getEntries();
+ if ((entries.find("value") == entries.end()) ||
+ (entries.find("time") == entries.end()) )
+ {
+ g_log.warning() << "Invalid NXlog entry " << entry_name
+ << " found. Did not contain 'value' and 'time'.\n";
+ file.closeGroup();
+ return;
+ }
+ // whether or not to overwrite logs on workspace
+ bool overwritelogs = this->getProperty("OverwriteLogs");
+ try
+ {
+ Kernel::Property *logValue = createTimeSeries(file, entry_name);
+ workspace->mutableRun().addProperty(logValue, overwritelogs);
+ }
+ catch(::NeXus::Exception &e)
+ {
+ g_log.warning() << "NXlog entry " << entry_name
+ << " gave an error when loading:'" << e.what() << "'.\n";
+ }
+
+ file.closeGroup();
+ }
+
+ /**
+ * Load an SE log entry
+ * @param file :: A reference to the NeXus file handle opened at the parent group
+ * @param entry_name :: The name of the log entry
+ * @param workspace :: A pointer to the workspace to store the logs
+ */
+ void LoadRunLogs::loadSELog(::NeXus::File & file, const std::string & entry_name,
+ MatrixWorkspace_sptr workspace) const
+ {
+ // Open the entry
+ file.openGroup(entry_name, "IXseblock");
+ std::string propName = entry_name;
+ if (workspace->run().hasProperty(propName))
+ {
+ propName = "selog_" + propName;
+ }
+ // There are two possible entries:
+ // value_log - A time series entry
+ // value - A single value float entry
+ Kernel::Property *logValue(NULL);
+ std::map<std::string, std::string> entries = file.getEntries();
+ if( entries.find("value_log") != entries.end() )
+ {
+ try
+ {
+ try
+ {
+ file.openGroup("value_log", "NXlog");
+ }
+ catch(::NeXus::Exception&)
+ {
+ file.closeGroup();
+ throw;
+ }
+ logValue = createTimeSeries(file, propName);
+ file.closeGroup();
+ }
+ catch(::NeXus::Exception& e)
+ {
+ g_log.warning() << "IXseblock entry " << entry_name << " gave an error when loading "
+ << "a time series:'" << e.what() << "'.\n";
+ file.closeGroup();
+ return;
+ }
+ }
+ else if( entries.find("value") != entries.end() )
+ {
+ float val_array[1];
+ try
+ {
+ file.openData("value");
+ file.getData(val_array);
+ file.closeData();
+ }
+ catch(::NeXus::Exception& e)
+ {
+ g_log.warning() << "IXseblock entry " << entry_name << " gave an error when loading "
+ << "a single value:'" << e.what() << "'.\n";
+ file.closeData();
+ file.closeGroup();
+ return;
+ }
+ logValue = new Kernel::PropertyWithValue<double>(propName, static_cast<double>(val_array[0]), true);
+ }
+ else
+ {
+ g_log.warning() << "IXseblock entry " << entry_name
+ << " does not contain a value or value_log field, skipping entry.";
+ file.closeGroup();
+ return;
+ }
+ workspace->mutableRun().addProperty(logValue);
+ file.closeGroup();
+ }
+
+ /**
+ * Creates a time series property from the currently opened log entry. It is assumed to
+ * have been checked to have a time field and the value entry's name is given as an argument
+ * @param file :: A reference to the file handle
+ * @param prop_name :: The name of the property
+ * @returns A pointer to a new property containing the time series
+ */
+ Kernel::Property * LoadRunLogs::createTimeSeries(::NeXus::File & file,
+ const std::string & prop_name) const
+ {
+ file.openData("time");
+ //----- Start time is an ISO8601 string date and time. ------
+ std::string start;
+ try
+ {
+ file.getAttr("start", start);
+ }
+ catch (::NeXus::Exception &)
+ {
+ //Some logs have "offset" instead of start
+ try
+ {
+ file.getAttr("offset", start);
+ }
+ catch (::NeXus::Exception &)
+ {
+ g_log.warning() << "Log entry has no start time indicated.\n";
+ file.closeData();
+ throw;
+ }
+ }
+ //Convert to date and time
+ Kernel::DateAndTime start_time = Kernel::DateAndTime(start);
+ std::string time_units;
+ file.getAttr("units", time_units);
+ if( time_units.find("second") != 0 && time_units != "minutes" )
+ {
+ file.closeData();
+ throw ::NeXus::Exception("Unsupported time unit '" + time_units + "'");
+
+ }
+ //--- Load the seconds into a double array ---
+ std::vector<double> time_double;
+ try
+ {
+ file.getDataCoerce(time_double);
+ }
+ catch (::NeXus::Exception &e)
+ {
+ g_log.warning() << "Log entry 's time field could not be loaded: '" << e.what() << "'.\n";
+ file.closeData();
+ throw;
+ }
+ file.closeData(); // Close time data
+ // Convert to seconds if needed
+ if( time_units == "minutes" )
+ {
+ std::transform(time_double.begin(),time_double.end(), time_double.begin(),
+ std::bind2nd(std::multiplies<double>(),60.0));
+ }
+ // Now the values: Could be a string, int or double
+ file.openData("value");
+ // Get the units of the property
+ std::string value_units("");
+ try
+ {
+ file.getAttr("units", value_units);
+ }
+ catch (::NeXus::Exception &)
+ {
+ //Ignore missing units field.
+ value_units = "";
+ }
+
+ // Now the actual data
+ ::NeXus::Info info = file.getInfo();
+ if( file.isDataInt() ) // Int type
+ {
+ std::vector<int> values;
+ try
+ {
+ file.getDataCoerce(values);
+ file.closeData();
+ }
+ catch(::NeXus::Exception&)
+ {
+ file.closeData();
+ throw;
+ }
+ //Make an int TSP
+ TimeSeriesProperty<int> * tsp = new TimeSeriesProperty<int>(prop_name);
+ tsp->create(start_time, time_double, values);
+ tsp->setUnits(value_units);
+ return tsp;
+ }
+ else if( info.type == ::NeXus::CHAR )
+ {
+ std::string values;
+ const int item_length = info.dims[1];
+ try
+ {
+ const int nitems = info.dims[0];
+ boost::scoped_array<char> val_array(new char[nitems*item_length]);
+ file.getData(val_array.get());
+ file.closeData();
+ values = std::string(val_array.get());
+ }
+ catch(::NeXus::Exception&)
+ {
+ file.closeData();
+ throw;
+ }
+ // The string may contain non-printable (i.e. control) characters, replace these
+ std::replace_if(values.begin(), values.end(), iscntrl, ' ');
+ TimeSeriesProperty<std::string> * tsp = new TimeSeriesProperty<std::string>(prop_name);
+ std::vector<DateAndTime> times;
+ DateAndTime::createVector(start_time, time_double, times);
+ const size_t ntimes = times.size();
+ for(size_t i = 0; i < ntimes; ++i)
+ {
+ std::string value_i = std::string(values.data() + i*item_length, item_length);
+ tsp->addValue(times[i], value_i);
+ }
+ tsp->setUnits(value_units);
+ return tsp;
+ }
+ else if( info.type == ::NeXus::FLOAT32 || info.type == ::NeXus::FLOAT64 )
+ {
+ std::vector<double> values;
+ try
+ {
+ file.getDataCoerce(values);
+ file.closeData();
+ }
+ catch(::NeXus::Exception&)
+ {
+ file.closeData();
+ throw;
+ }
+ TimeSeriesProperty<double> * tsp = new TimeSeriesProperty<double>(prop_name);
+ tsp->create(start_time, time_double, values);
+ tsp->setUnits(value_units);
+ return tsp;
+ }
+ else
+ {
+ throw ::NeXus::Exception("Invalid value type for time series. Only int, double or strings are "
+ "supported");
+ }
+ }
+
+ } // namespace DataHandling
+} // namespace Mantid
diff --git a/Code/Mantid/Framework/Nexus/test/LoadISISNexusTest.h b/Code/Mantid/Framework/Nexus/test/LoadISISNexusTest.h
index 2118656d199..ccb2077e88f 100644
--- a/Code/Mantid/Framework/Nexus/test/LoadISISNexusTest.h
+++ b/Code/Mantid/Framework/Nexus/test/LoadISISNexusTest.h
@@ -56,18 +56,27 @@ public:
TS_ASSERT(slog);
TS_ASSERT_EQUALS(slog->size(),50);
- TimeSeriesProperty<double>* dlog = dynamic_cast<TimeSeriesProperty<double>*>(ws->run().getLogData("total_counts"));
- TS_ASSERT(dlog);
- TS_ASSERT_EQUALS(dlog->size(),172);
+ TimeSeriesProperty<int>* ilog = dynamic_cast<TimeSeriesProperty<int>*>(ws->run().getLogData("total_counts"));
+ TS_ASSERT(ilog);
+ TS_ASSERT_EQUALS(ilog->size(),172);
+
+ ilog = dynamic_cast<TimeSeriesProperty<int>*>(ws->run().getLogData("period"));
+ TS_ASSERT(ilog);
+ TS_ASSERT_EQUALS(ilog->size(),172);
- dlog = dynamic_cast<TimeSeriesProperty<double>*>(ws->run().getLogData("period"));
+ TimeSeriesProperty<double> *dlog = dynamic_cast<TimeSeriesProperty<double>*>(ws->run().getLogData("proton_charge"));
TS_ASSERT(dlog);
TS_ASSERT_EQUALS(dlog->size(),172);
+
TimeSeriesProperty<bool>* blog = dynamic_cast<TimeSeriesProperty<bool>*>(ws->run().getLogData("period 1"));
TS_ASSERT(blog);
TS_ASSERT_EQUALS(blog->size(),1);
+ blog = dynamic_cast<TimeSeriesProperty<bool>*>(ws->run().getLogData("running"));
+ TS_ASSERT(blog);
+ TS_ASSERT_EQUALS(blog->size(),2);
+
TS_ASSERT_EQUALS(ws->sample().getName(),"");
Property *l_property = ws->run().getLogData( "run_number" );
@@ -86,7 +95,7 @@ public:
TS_ASSERT_THROWS_NOTHING(ld.execute());
TS_ASSERT(ld.isExecuted());
- MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(AnalysisDataService::Instance().retrieve("outWS"));
+ MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(AnalysisDataService::Instance().retrieve("outWS"));
TS_ASSERT_EQUALS(ws->blocksize(),5);
TS_ASSERT_EQUALS(ws->getNumberHistograms(),14);
@@ -102,27 +111,27 @@ public:
TS_ASSERT_EQUALS(ws->readY(10)[3],1.);
TS_ASSERT_EQUALS(ws->readY(13)[4],1.);
}
- void testMultiPeriodEntryNumberZero()
+ void testMultiPeriodEntryNumberZero()
{
- Mantid::API::FrameworkManager::Instance();
+ Mantid::API::FrameworkManager::Instance();
LoadISISNexus2 ld;
ld.initialize();
ld.setPropertyValue("Filename","TEST00000008.nxs");
- ld.setPropertyValue("OutputWorkspace","outWS");
+ ld.setPropertyValue("OutputWorkspace","outWS");
ld.setPropertyValue("SpectrumMin","10");
ld.setPropertyValue("SpectrumMax","19");
- ld.setPropertyValue("EntryNumber","0");
- //ld.setPropertyValue("SpectrumList","30,31");
+ ld.setPropertyValue("EntryNumber","0");
+ //ld.setPropertyValue("SpectrumList","30,31");
TS_ASSERT_THROWS_NOTHING(ld.execute());
TS_ASSERT(ld.isExecuted());
-
- WorkspaceGroup_sptr grpout;//=WorkspaceGroup_sptr(new WorkspaceGroup);
- TS_ASSERT_THROWS_NOTHING(grpout=boost::dynamic_pointer_cast<WorkspaceGroup>(AnalysisDataService::Instance().retrieve("outWS")));
+
+ WorkspaceGroup_sptr grpout;//=WorkspaceGroup_sptr(new WorkspaceGroup);
+ TS_ASSERT_THROWS_NOTHING(grpout=boost::dynamic_pointer_cast<WorkspaceGroup>(AnalysisDataService::Instance().retrieve("outWS")));
MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(AnalysisDataService::Instance().retrieve("outWS_1"));
TS_ASSERT_EQUALS(ws->blocksize(),995);
TS_ASSERT_EQUALS(ws->getNumberHistograms(),10);
- TS_ASSERT_DELTA(ws->run().getProtonCharge(), 0.069991, 1e-6);
+ TS_ASSERT_DELTA(ws->run().getProtonCharge(), 0.069991, 1e-6);
TS_ASSERT_EQUALS(ws->readX(0)[0],5.);
TS_ASSERT_EQUALS(ws->readX(0)[1],6.);
@@ -136,7 +145,7 @@ public:
TS_ASSERT_EQUALS(ws->readY(9)[3],0.);
TS_ASSERT_EQUALS(ws->readY(9)[1],0.);
}
- void testMultiPeriodEntryNumberNonZero()
+ void testMultiPeriodEntryNumberNonZero()
{
Mantid::API::FrameworkManager::Instance();
LoadISISNexus2 ld;
@@ -145,17 +154,17 @@ public:
ld.setPropertyValue("OutputWorkspace","outWS");
ld.setPropertyValue("SpectrumMin","10");
ld.setPropertyValue("SpectrumMax","20");
- // ld.setPropertyValue("SpectrumList","29,30,31");
- ld.setPropertyValue("EntryNumber","5");
+ // ld.setPropertyValue("SpectrumList","29,30,31");
+ ld.setPropertyValue("EntryNumber","5");
TS_ASSERT_THROWS_NOTHING(ld.execute());
TS_ASSERT(ld.isExecuted());
-
+
MatrixWorkspace_sptr ws = boost::dynamic_pointer_cast<MatrixWorkspace>(AnalysisDataService::Instance().retrieve("outWS"));
TS_ASSERT_EQUALS(ws->blocksize(),995);
// TS_ASSERT_EQUALS(ws->getNumberHistograms(),14);
TS_ASSERT_EQUALS(ws->getTitle(), "hello\\0");
- TS_ASSERT_DELTA(ws->run().getProtonCharge(), 0.069991, 1e-6);
+ TS_ASSERT_DELTA(ws->run().getProtonCharge(), 0.069991, 1e-6);
TS_ASSERT_EQUALS(ws->readX(0)[0],5.);
TS_ASSERT_EQUALS(ws->readX(0)[1],6.);
TS_ASSERT_EQUALS(ws->readX(0)[2],7.);
diff --git a/Code/Mantid/Framework/Nexus/test/LoadRunLogsTest.h b/Code/Mantid/Framework/Nexus/test/LoadRunLogsTest.h
new file mode 100644
index 00000000000..2b6834bff89
--- /dev/null
+++ b/Code/Mantid/Framework/Nexus/test/LoadRunLogsTest.h
@@ -0,0 +1,76 @@
+#ifndef LOADLOGSFROMSNSNEXUSTEST_H_
+#define LOADLOGSFROMSNSNEXUSTEST_H_
+
+#include "MantidNexus/LoadRunLogs.h"
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidAPI/FrameworkManager.h"
+#include "MantidAPI/Workspace.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidKernel/PhysicalConstants.h"
+using namespace Mantid;
+using namespace Mantid::Geometry;
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+using namespace Mantid::NeXus;
+
+#include <cxxtest/TestSuite.h>
+#include "MantidAPI/WorkspaceGroup.h"
+#include <iostream>
+
+class LoadRunLogsTest : public CxxTest::TestSuite
+{
+public:
+
+ void testExec()
+ {
+ Mantid::API::FrameworkManager::Instance();
+ LoadRunLogs ld;
+ std::string outws_name = "CNCS_instrument";
+ ld.initialize();
+ ld.setPropertyValue("Filename","CNCS_7860.nxs");
+
+ //Create an empty workspace with some fake size, to start from.
+ DataObjects::Workspace2D_sptr ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
+ (WorkspaceFactory::Instance().create("Workspace2D",1000,18+1,18));
+ //Put it in the object.
+ ld.setProperty("Workspace", boost::dynamic_pointer_cast<MatrixWorkspace>(ws));
+
+ ld.execute();
+ TS_ASSERT( ld.isExecuted() );
+
+ double val;
+ Run& run = ws->mutableRun();
+ Property * prop;
+ TimeSeriesProperty<double> * dProp;
+
+ prop = run.getLogData("Speed3");
+ TS_ASSERT(prop);
+ //TS_ASSERT_EQUALS( prop->value(), "60");
+ TS_ASSERT_EQUALS( prop->units(), "Hz");
+
+ prop = run.getLogData("PhaseRequest1");
+ dProp = dynamic_cast< TimeSeriesProperty<double> * >(prop);
+ TS_ASSERT(dProp);
+ val = dProp->nthValue(0);
+ TS_ASSERT_DELTA( val, 8798.7236, 1e-2);
+ TS_ASSERT_EQUALS(prop->units(), "microsecond");
+
+ TimeSeriesProperty<double> * tsp;
+
+ prop = run.getLogData("Phase1");
+ tsp = dynamic_cast< TimeSeriesProperty<double> * >(prop);
+ TS_ASSERT(tsp);
+ TS_ASSERT_EQUALS(tsp->units(), "microsecond");
+ TS_ASSERT_DELTA( tsp->nthValue(1), 8798.99, 2);
+
+ //The time diff between the 0th and 1st entry is 2.328 seconds
+ TS_ASSERT_DELTA( Kernel::DateAndTime::seconds_from_duration(tsp->nthInterval(0).length()), 2.328, 0.01);
+
+ //Now the stats
+
+ }
+};
+
+#endif /*LOADRUNLOGS_H_*/
--
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