From 5c58a0d439bd54cf959c2f33ac2065e255151b32 Mon Sep 17 00:00:00 2001
From: Roman Tolchenov <roman.tolchenov@stfc.ac.uk>
Date: Wed, 16 Jan 2013 14:54:24 +0000
Subject: [PATCH] Re #6131. Implemented changes to version 2 muon nexus format.
---
.../Framework/Algorithms/test/AlphaCalcTest.h | 5 +-
.../Algorithms/test/ApplyDeadTimeCorrTest.h | 4 +-
.../Algorithms/test/MuonAsymmetryCalcTest.h | 4 +-
.../Algorithms/test/MuonRemoveExpDecayTest.h | 4 +-
.../Algorithms/test/RemoveBinsTest.h | 4 +-
.../Framework/DataHandling/CMakeLists.txt | 4 +-
.../inc/MantidDataHandling/LoadMuonNexus.h | 20 +-
.../inc/MantidDataHandling/LoadMuonNexus1.h | 101 +++
.../inc/MantidDataHandling/LoadMuonNexus2.h | 18 +-
.../DataHandling/src/LoadMuonNexus.cpp | 640 +---------------
.../DataHandling/src/LoadMuonNexus1.cpp | 696 ++++++++++++++++++
.../DataHandling/src/LoadMuonNexus2.cpp | 310 ++++----
.../DataHandling/test/GroupDetectors2Test.h | 8 +-
.../DataHandling/test/LoadMuonNexus1Test.h | 415 +++++++++++
.../DataHandling/test/LoadMuonNexus2Test.h | 64 +-
.../DataHandling/test/LoadMuonNexusTest.h | 381 +---------
.../Nexus/inc/MantidNexus/NexusClasses.h | 7 +-
.../Framework/Nexus/src/NexusClasses.cpp | 13 +
Test/AutoTestData/deltat_tdc_gpd_0900.nxs | Bin 0 -> 75276 bytes
19 files changed, 1466 insertions(+), 1232 deletions(-)
create mode 100644 Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus1.h
create mode 100644 Code/Mantid/Framework/DataHandling/src/LoadMuonNexus1.cpp
create mode 100644 Code/Mantid/Framework/DataHandling/test/LoadMuonNexus1Test.h
create mode 100644 Test/AutoTestData/deltat_tdc_gpd_0900.nxs
diff --git a/Code/Mantid/Framework/Algorithms/test/AlphaCalcTest.h b/Code/Mantid/Framework/Algorithms/test/AlphaCalcTest.h
index 80b2f9d2ac0..dbaede7f8ca 100644
--- a/Code/Mantid/Framework/Algorithms/test/AlphaCalcTest.h
+++ b/Code/Mantid/Framework/Algorithms/test/AlphaCalcTest.h
@@ -3,7 +3,7 @@
#include <cxxtest/TestSuite.h>
-#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataHandling/LoadMuonNexus2.h"
#include "MantidDataHandling/LoadInstrument.h"
#include "MantidDataHandling/GroupDetectors.h"
#include "MantidAPI/IAlgorithm.h"
@@ -38,6 +38,7 @@ public:
void testCalAlphaManySpectra()
{
+ //system("pause");
//Load the muon nexus file
loader.initialize();
loader.setPropertyValue("Filename", "emu00006473.nxs");
@@ -93,7 +94,7 @@ public:
private:
AlphaCalc alphaCalc;
- Mantid::DataHandling::LoadMuonNexus loader;
+ Mantid::DataHandling::LoadMuonNexus2 loader;
};
diff --git a/Code/Mantid/Framework/Algorithms/test/ApplyDeadTimeCorrTest.h b/Code/Mantid/Framework/Algorithms/test/ApplyDeadTimeCorrTest.h
index 230fd5576ff..d729719b217 100644
--- a/Code/Mantid/Framework/Algorithms/test/ApplyDeadTimeCorrTest.h
+++ b/Code/Mantid/Framework/Algorithms/test/ApplyDeadTimeCorrTest.h
@@ -3,7 +3,7 @@
#include <cxxtest/TestSuite.h>
-#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataHandling/LoadMuonNexus2.h"
#include "MantidDataHandling/LoadInstrument.h"
#include "MantidDataHandling/GroupDetectors.h"
#include "MantidAPI/IAlgorithm.h"
@@ -199,7 +199,7 @@ public:
private:
ApplyDeadTimeCorr applyDeadTime;
- Mantid::DataHandling::LoadMuonNexus loader;
+ Mantid::DataHandling::LoadMuonNexus2 loader;
};
diff --git a/Code/Mantid/Framework/Algorithms/test/MuonAsymmetryCalcTest.h b/Code/Mantid/Framework/Algorithms/test/MuonAsymmetryCalcTest.h
index b6a9857ba81..883b9f5256f 100644
--- a/Code/Mantid/Framework/Algorithms/test/MuonAsymmetryCalcTest.h
+++ b/Code/Mantid/Framework/Algorithms/test/MuonAsymmetryCalcTest.h
@@ -3,7 +3,7 @@
#include <cxxtest/TestSuite.h>
-#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataHandling/LoadMuonNexus2.h"
#include "MantidDataHandling/LoadInstrument.h"
#include "MantidDataHandling/GroupDetectors.h"
#include "MantidAPI/IAlgorithm.h"
@@ -91,7 +91,7 @@ public:
private:
MuonAsymmetryCalc asymCalc;
- Mantid::DataHandling::LoadMuonNexus loader;
+ Mantid::DataHandling::LoadMuonNexus2 loader;
Mantid::DataHandling::GroupDetectors group1;
Mantid::DataHandling::GroupDetectors group2;
diff --git a/Code/Mantid/Framework/Algorithms/test/MuonRemoveExpDecayTest.h b/Code/Mantid/Framework/Algorithms/test/MuonRemoveExpDecayTest.h
index a7b6d068e7d..6ad22942904 100644
--- a/Code/Mantid/Framework/Algorithms/test/MuonRemoveExpDecayTest.h
+++ b/Code/Mantid/Framework/Algorithms/test/MuonRemoveExpDecayTest.h
@@ -4,7 +4,7 @@
#include <cxxtest/TestSuite.h>
#include "MantidDataHandling/LoadInstrument.h"
-#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataHandling/LoadMuonNexus2.h"
#include "MantidAlgorithms/MuonRemoveExpDecay.h"
#include "MantidAPI/Workspace.h"
#include "MantidDataObjects/Workspace2D.h"
@@ -93,7 +93,7 @@ public:
private:
MuonRemoveExpDecay alg;
- Mantid::DataHandling::LoadMuonNexus loader;
+ Mantid::DataHandling::LoadMuonNexus2 loader;
};
diff --git a/Code/Mantid/Framework/Algorithms/test/RemoveBinsTest.h b/Code/Mantid/Framework/Algorithms/test/RemoveBinsTest.h
index 545b4331dd9..6e4886bdbcc 100644
--- a/Code/Mantid/Framework/Algorithms/test/RemoveBinsTest.h
+++ b/Code/Mantid/Framework/Algorithms/test/RemoveBinsTest.h
@@ -9,7 +9,7 @@
#include <stdexcept>
#include "MantidAlgorithms/RemoveBins.h"
-#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataHandling/LoadMuonNexus2.h"
#include "MantidDataHandling/LoadInstrument.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidKernel/UnitFactory.h"
@@ -177,7 +177,7 @@ public:
void xtestRealData()
{
- Mantid::DataHandling::LoadMuonNexus loader;
+ Mantid::DataHandling::LoadMuonNexus2 loader;
loader.initialize();
loader.setPropertyValue("Filename", "emu00006473.nxs");
loader.setPropertyValue("OutputWorkspace", "EMU6473");
diff --git a/Code/Mantid/Framework/DataHandling/CMakeLists.txt b/Code/Mantid/Framework/DataHandling/CMakeLists.txt
index 9f7787a4cde..74e4d8e267a 100644
--- a/Code/Mantid/Framework/DataHandling/CMakeLists.txt
+++ b/Code/Mantid/Framework/DataHandling/CMakeLists.txt
@@ -58,6 +58,7 @@ set ( SRC_FILES
src/LoadMaskingFile.cpp
src/LoadMuonLog.cpp
src/LoadMuonNexus.cpp
+ src/LoadMuonNexus1.cpp
src/LoadMuonNexus2.cpp
src/LoadNXSPE.cpp
src/LoadNexus.cpp
@@ -196,6 +197,7 @@ set ( INC_FILES
inc/MantidDataHandling/LoadMaskingFile.h
inc/MantidDataHandling/LoadMuonLog.h
inc/MantidDataHandling/LoadMuonNexus.h
+ inc/MantidDataHandling/LoadMuonNexus1.h
inc/MantidDataHandling/LoadMuonNexus2.h
inc/MantidDataHandling/LoadNXSPE.h
inc/MantidDataHandling/LoadNexus.h
@@ -322,8 +324,8 @@ set ( TEST_FILES
LoadMappingTableTest.h
LoadMaskTest.h
LoadMuonLogTest.h
+ LoadMuonNexus1Test.h
LoadMuonNexus2Test.h
- LoadMuonNexusTest.h
LoadNXSPETest.h
LoadNexusLogsTest.h
LoadNexusMonitorsTest.h
diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus.h
index 579b210cb9f..74ba34c15d3 100644
--- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus.h
+++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus.h
@@ -22,10 +22,8 @@ namespace Mantid
{
/** @class LoadMuonNexus LoadMuonNexus.h DataHandling/LoadMuonNexus.h
- Loads an file in Nexus Muon format and stores it in a 2D workspace
- (Workspace2D class). LoadMuonNexus is an algorithm and as such inherits
- from the Algorithm class, via DataHandlingCommand, and overrides
- the init() & exec() methods.
+ It is a base class for loadres for versions 1 and 2 of the muon nexus file format.
+ It implements property initialization and some common for both versions methods.
Required Properties:
<UL>
@@ -77,19 +75,20 @@ namespace Mantid
/// Algorithm's category for identification overriding a virtual method
virtual const std::string category() const { return "DataHandling\\Nexus;Muon"; }
- /// do a quick check that this file can be loaded
+ /// do a quick check that this file can be loaded
virtual bool quickFileCheck(const std::string& filePath,size_t nread,const file_header& header);
/// check the structure of the file and return a value between 0 and 100 of how much this file can be loaded
virtual int fileCheck(const std::string& filePath);
protected:
- /// Overwrites Algorithm method
- void exec();
+ virtual void runLoadInstrumentFromNexus(DataObjects::Workspace2D_sptr) {}
void checkOptionalProperties();
void runLoadInstrument(DataObjects::Workspace2D_sptr);
/// The name and path of the input file
std::string m_filename;
+ /// The first top-level entry name in the file
+ std::string m_entry_name;
/// The instrument name from Nexus
std::string m_instrument_name;
/// The sample name read from Nexus
@@ -120,13 +119,6 @@ namespace Mantid
virtual void initDocs();
/// Overwrites Algorithm method.
void init();
-
- void loadData(const MantidVecPtr::ptr_type& tcbs,size_t hist, specid_t& i,
- MuonNexusReader& nxload, const int64_t lengthIn, DataObjects::Workspace2D_sptr localWorkspace);
- void runLoadInstrumentFromNexus(DataObjects::Workspace2D_sptr);
- void runLoadMappingTable(DataObjects::Workspace2D_sptr);
- void runLoadLog(DataObjects::Workspace2D_sptr);
- void loadRunDetails(DataObjects::Workspace2D_sptr localWorkspace);
};
} // namespace DataHandling
diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus1.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus1.h
new file mode 100644
index 00000000000..671b0315371
--- /dev/null
+++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus1.h
@@ -0,0 +1,101 @@
+#ifndef MANTID_DATAHANDLING_LOADMUONNEXUS1_H_
+#define MANTID_DATAHANDLING_LOADMUONNEXUS1_H_
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidDataHandling/LoadMuonNexus.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidKernel/System.h"
+#include "MantidAPI/SpectraDetectorMap.h"
+
+#include <napi.h>
+//----------------------------------------------------------------------
+// Forward declaration
+//----------------------------------------------------------------------
+class MuonNexusReader;
+
+namespace Mantid
+{
+ namespace DataHandling
+ {
+ /** @class LoadMuonNexus LoadMuonNexus.h DataHandling/LoadMuonNexus.h
+
+ Loads an file in Nexus Muon format version 1 and stores it in a 2D workspace
+ (Workspace2D class). LoadMuonNexus is an algorithm and as such inherits
+ from the Algorithm class, via DataHandlingCommand, and overrides
+ the init() & exec() methods.
+
+ Required Properties:
+ <UL>
+ <LI> Filename - The name of and path to the input NeXus file </LI>
+ <LI> OutputWorkspace - The name of the workspace in which to store the imported data
+ (a multiperiod file will store higher periods in workspaces called OutputWorkspace_PeriodNo)
+ [ not yet implemented for Nexus ]</LI>
+ </UL>
+
+ Optional Properties: (note that these options are not available if reading a multiperiod file)
+ <UL>
+ <LI> spectrum_min - The spectrum to start loading from</LI>
+ <LI> spectrum_max - The spectrum to load to</LI>
+ <LI> spectrum_list - An ArrayProperty of spectra to load</LI>
+ <LI> auto_group - Determines whether the spectra are automatically grouped together based on the groupings in the NeXus file. </LI>
+ </UL>
+
+ Copyright © 2007-2010 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://github.com/mantidproject/mantid>.
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+ */
+ class DLLExport LoadMuonNexus1 : public LoadMuonNexus
+ {
+ public:
+ /// Default constructor
+ LoadMuonNexus1();
+ /// Destructor
+ virtual ~LoadMuonNexus1() {}
+ /// Algorithm's name for identification overriding a virtual method
+ virtual const std::string name() const { return "LoadMuonNexus"; }
+ /// 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\\Nexus;Muon"; }
+
+ /// check the structure of the file and return a value between 0 and 100 of how much this file can be loaded
+ virtual int fileCheck(const std::string& filePath);
+ protected:
+ /// Overwrites Algorithm method
+ void exec();
+ /// Implement the base class method
+ void runLoadInstrumentFromNexus(DataObjects::Workspace2D_sptr);
+
+ private:
+ /// Sets documentation strings for this algorithm
+ virtual void initDocs();
+
+ void loadData(const MantidVecPtr::ptr_type& tcbs,size_t hist, specid_t& i,
+ MuonNexusReader& nxload, const int64_t lengthIn, DataObjects::Workspace2D_sptr localWorkspace);
+ void runLoadMappingTable(DataObjects::Workspace2D_sptr);
+ void runLoadLog(DataObjects::Workspace2D_sptr);
+ void loadRunDetails(DataObjects::Workspace2D_sptr localWorkspace);
+ };
+
+ } // namespace DataHandling
+} // namespace Mantid
+
+#endif /*MANTID_DATAHANDLING_LOADMUONNEXUS1_H_*/
diff --git a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus2.h b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus2.h
index edd5b5ed44c..1094ac22d00 100644
--- a/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus2.h
+++ b/Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadMuonNexus2.h
@@ -10,24 +10,12 @@
namespace Mantid
{
-namespace NeXus
-{
- // Forward declarations
- template<class T>
- class NXDataSetTyped;
- typedef NXDataSetTyped<int> NXInt;
-}
-
namespace DataHandling
{
- // Forward declarations
- template<class T>
- class NXDataSetTyped;
- typedef NXDataSetTyped<int> NXInt;
/**
- Loads an file in NeXus Muon format and stores it in a 2D workspace
+ Loads an file in NeXus Muon format version 1 and 2 and stores it in a 2D workspace
(Workspace2D class). LoadMuonNexus is an algorithm and as such inherits
from the Algorithm class, via DataHandlingCommand, and overrides
the init() & exec() methods.
@@ -82,8 +70,6 @@ namespace NeXus
/// Algorithm's category for identification overriding a virtual method
virtual const std::string category() const { return "DataHandling\\Nexus;Muon"; }
- /// do a quick check that this file can be loaded
- virtual bool quickFileCheck(const std::string& filePath,size_t nread,const file_header& header);
/// check the structure of the file and return a value between 0 and 100 of how much this file can be loaded
virtual int fileCheck(const std::string& filePath);
private:
@@ -91,6 +77,8 @@ namespace NeXus
virtual void initDocs();
/// Overwrites Algorithm method
void exec();
+ /// Execute this version of the algorithm
+ void doExec();
void loadData(const Mantid::NeXus::NXInt& counts,const std::vector<double>& timeBins,int wsIndex,
int period,int spec,API::MatrixWorkspace_sptr localWorkspace);
diff --git a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp
index 53ea3c2f104..e043b3f973e 100644
--- a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp
+++ b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus.cpp
@@ -1,45 +1,3 @@
-/*WIKI*
-
-
-The algorithm LoadMuonNexus will read a Muon Nexus data file (original format) and place the data
-into the named workspace.
-The file name can be an absolute or relative path and should have the extension
-.nxs or .NXS.
-If the file contains data for more than one period, a separate workspace will be generated for each.
-After the first period the workspace names will have "_2", "_3", and so on, appended to the given workspace name.
-For single period data, the optional parameters can be used to control which spectra are loaded into the workspace.
-If spectrum_min and spectrum_max are given, then only that range to data will be loaded.
-If a spectrum_list is given than those values will be loaded.
-* TODO get XML descriptions of Muon instruments. This data is not in existing Muon Nexus files.
-* TODO load the spectra detector mapping. This may be very simple for Muon instruments.
-
-===Time series data===
-The log data in the Nexus file (NX_LOG sections) will be loaded as TimeSeriesProperty data within the workspace.
-Time is stored as seconds from the Unix epoch.
-
-===Errors===
-
-The error for each histogram count is set as the square root of the number of counts.
-
-===Time bin data===
-
-The ''corrected_times'' field of the Nexus file is used to provide time bin data and the bin edge values are calculated from these
-bin centre times.
-
-===Multiperiod data===
-
-To determine if a file contains data from more than one period the field ''switching_states'' is read from the Nexus file.
-If this value is greater than one it is taken to be the number of periods, <math>N_p</math> of the data.
-In this case the <math>N_s</math> spectra in the ''histogram_data'' field are split with <math>N_s/N_p</math> assigned to each period.
-
-===ChildAlgorithms used===
-
-The ChildAlgorithms used by LoadMuonNexus are:
-* LoadMuonLog - this reads log information from the Nexus file and uses it to create TimeSeriesProperty entries in the workspace.
-* LoadInstrument - this algorithm looks for an XML description of the instrument and if found reads it.
-* LoadIntstrumentFromNexus - this is called if the normal LoadInstrument fails. As the Nexus file has limited instrument data, this only populates a few fields.
-
-*WIKI*/
//----------------------------------------------------------------------
// Includes
//----------------------------------------------------------------------
@@ -70,8 +28,6 @@ namespace Mantid
{
namespace DataHandling
{
- // Register the algorithm into the algorithm factory
- DECLARE_ALGORITHM(LoadMuonNexus)
/// Sets documentation strings for this algorithm
void LoadMuonNexus::initDocs()
@@ -139,396 +95,6 @@ namespace Mantid
"The name of the vector in which to store the list of deadtimes for each spectrum", Direction::Output);
}
- /** 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 LoadMuonNexus::exec()
- {
- // Retrieve the filename from the properties
- m_filename = getPropertyValue("Filename");
- // Retrieve the entry number
- m_entrynumber = getProperty("EntryNumber");
-
-
-
- NXRoot root(m_filename);
- NXEntry entry = root.openEntry("run/histogram_data_1");
- try
- {
- NXInfo info = entry.getDataSetInfo("time_zero");
- if (info.stat != NX_ERROR)
- {
- double dum = root.getFloat("run/histogram_data_1/time_zero");
- setProperty("TimeZero", dum);
- }
- }
- catch (::NeXus::Exception&)
- {}
-
- try
- {
- NXInfo infoResolution = entry.getDataSetInfo("resolution");
- NXInt counts = root.openNXInt("run/histogram_data_1/counts");
- std::string firstGoodBin = counts.attributes("first_good_bin");
- if ( !firstGoodBin.empty() && infoResolution.stat != NX_ERROR )
- {
- double bin = static_cast<double>(boost::lexical_cast<int>(firstGoodBin));
- double bin_size = static_cast<double>(root.getInt("run/histogram_data_1/resolution"))/1000000.0;
- setProperty("FirstGoodData", bin*bin_size);
- }
- }
- catch (::NeXus::Exception&)
- {}
-
- try
- {
- std::vector<double>defaultDeadTimes;
- NXFloat deadTimes = root.openNXFloat("run/instrument/detector/deadtimes");
- deadTimes.load();
-
- int length = deadTimes.dim0();
- for (int i = 0; i < length; i++)
- {
- defaultDeadTimes.push_back(static_cast<double>(*(deadTimes() + i) ) );
- }
- setProperty("DeadTimes", defaultDeadTimes);
- }
- catch (::NeXus::Exception&)
- {}
-
- NXEntry nxRun = root.openEntry("run");
- std::string title;
- std::string notes;
- try
- {
- title = nxRun.getString("title");
- notes = nxRun.getString("notes");
- }
- catch (::NeXus::Exception&)
- {}
- std::string run_num;
- try
- {
- run_num = boost::lexical_cast<std::string>(nxRun.getInt("number"));
- }
- catch (::NeXus::Exception&)
- {}
-
- MuonNexusReader nxload;
- if (nxload.readFromFile(m_filename) != 0)
- {
- g_log.error("Unable to open file " + m_filename);
- throw Exception::FileError("Unable to open File:" , m_filename);
- }
-
- // Read in the instrument name from the Nexus file
- m_instrument_name = nxload.getInstrumentName();
- // Read in the number of spectra in the Nexus file
- m_numberOfSpectra = nxload.t_nsp1;
- if(m_entrynumber!=0)
- {
- m_numberOfPeriods=1;
- if(m_entrynumber>nxload.t_nper)
- {
- throw std::invalid_argument("Invalid Entry Number:Enter a valid number");
- }
- }
- else
- {
- // Read the number of periods in this file
- m_numberOfPeriods = nxload.t_nper;
- }
- // Need to extract the user-defined output workspace name
- Property *ws = getProperty("OutputWorkspace");
- std::string localWSName = ws->value();
- // If multiperiod, will need to hold the Instrument, Sample & SpectraDetectorMap for copying
- boost::shared_ptr<Instrument> instrument;
- boost::shared_ptr<Sample> sample;
-
- // Call private method to validate the optional parameters, if set
- checkOptionalProperties();
-
- // Read the number of time channels (i.e. bins) from the Nexus file
- const int channelsPerSpectrum = nxload.t_ntc1;
- // Read in the time bin boundaries
- const int lengthIn = channelsPerSpectrum + 1;
- float* timeChannels = new float[lengthIn];
- nxload.getTimeChannels(timeChannels, lengthIn);
- // Put the read in array into a vector (inside a shared pointer)
- boost::shared_ptr<MantidVec> timeChannelsVec
- (new MantidVec(timeChannels, timeChannels + lengthIn));
-
- // Calculate the size of a workspace, given its number of periods & spectra to read
- int64_t total_specs;
- if( m_interval || m_list)
- {
- total_specs = m_spec_list.size();
- if (m_interval)
- {
- total_specs += (m_spec_max-m_spec_min+1);
- m_spec_max += 1;
- }
- }
- else
- {
- total_specs = m_numberOfSpectra;
- // for nexus return all spectra
- m_spec_min = 0; // changed to 0 for NeXus, was 1 for Raw
- m_spec_max = m_numberOfSpectra; // was +1?
- }
-
- // Create the 2D workspace for the output
- DataObjects::Workspace2D_sptr localWorkspace = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
- (WorkspaceFactory::Instance().create("Workspace2D",total_specs,lengthIn,lengthIn-1));
- localWorkspace->setTitle(title);
- localWorkspace->setComment(notes);
- localWorkspace->mutableRun().addLogData(new PropertyWithValue<std::string>("run_number", run_num));
- // Set the unit on the workspace to muon time, for now in the form of a Label Unit
- boost::shared_ptr<Kernel::Units::Label> lblUnit =
- boost::dynamic_pointer_cast<Kernel::Units::Label>(UnitFactory::Instance().create("Label"));
- lblUnit->setLabel("Time","microsecond");
- localWorkspace->getAxis(0)->unit() = lblUnit;
- // Set y axis unit
- localWorkspace->setYUnit("Counts");
-
- WorkspaceGroup_sptr wsGrpSptr=WorkspaceGroup_sptr(new WorkspaceGroup);
- if(m_numberOfPeriods>1)
- {
- setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(wsGrpSptr));
- }
-
- API::Progress progress(this,0.,1.,m_numberOfPeriods * total_specs);
- // Loop over the number of periods in the Nexus file, putting each period in a separate workspace
- for (int64_t period = 0; period < m_numberOfPeriods; ++period) {
- if(m_entrynumber!=0)
- {
- period=m_entrynumber-1;
- if(period!=0)
- {
- loadRunDetails(localWorkspace);
- runLoadInstrument(localWorkspace );
- runLoadMappingTable(localWorkspace );
- }
- }
-
- if (period == 0)
- {
- // Only run the Child Algorithms once
- loadRunDetails(localWorkspace);
- runLoadInstrument(localWorkspace );
- runLoadMappingTable(localWorkspace );
- runLoadLog(localWorkspace );
- localWorkspace->populateInstrumentParameters();
- }
- else // We are working on a higher period of a multiperiod raw file
- {
- localWorkspace = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
- (WorkspaceFactory::Instance().create(localWorkspace));
- localWorkspace->setTitle(title);
- localWorkspace->setComment(notes);
- //localWorkspace->newInstrumentParameters(); ???
-
- }
-
-
- std::string outws("");
- if(m_numberOfPeriods>1)
- {
- std::string outputWorkspace = "OutputWorkspace";
- std::stringstream suffix;
- suffix << (period+1);
- outws =outputWorkspace+"_"+suffix.str();
- std::string WSName = localWSName + "_" + suffix.str();
- declareProperty(new WorkspaceProperty<Workspace>(outws,WSName,Direction::Output));
- if (wsGrpSptr)
- {
- wsGrpSptr->addWorkspace( localWorkspace );
- }
- }
-
- size_t counter = 0;
- for (int64_t i = m_spec_min; i < m_spec_max; ++i)
- {
- // Shift the histogram to read if we're not in the first period
- specid_t histToRead = static_cast<specid_t>(i + period*total_specs);
- loadData(timeChannelsVec,counter,histToRead,nxload,lengthIn-1,localWorkspace ); // added -1 for NeXus
- counter++;
- progress.report();
- }
- // Read in the spectra in the optional list parameter, if set
- if (m_list)
- {
- for(size_t i=0; i < m_spec_list.size(); ++i)
- {
- loadData(timeChannelsVec,counter,m_spec_list[i],nxload,lengthIn-1, localWorkspace );
- counter++;
- progress.report();
- }
- }
- // Just a sanity check
- assert(counter == size_t(total_specs) );
-
- bool autogroup = getProperty("AutoGroup");
-
- if (autogroup)
- {
-
- //Get the groupings
- int64_t max_group = 0;
- // use a map for mapping group number and output workspace index in case
- // there are group numbers > number of groups
- std::map<int64_t,int64_t> groups;
- m_groupings.resize(nxload.numDetectors);
- bool thereAreZeroes = false;
- for (int64_t i =0; i < static_cast<int64_t>(nxload.numDetectors); ++i)
- {
- int64_t ig = static_cast<int64_t>(nxload.detectorGroupings[i]);
- if (ig == 0)
- {
- thereAreZeroes = true;
- continue;
- }
- m_groupings[i] = static_cast<specid_t>(ig);
- if (groups.find(ig) == groups.end())
- groups[ig] = static_cast<int64_t>(groups.size());
- if (ig > max_group) max_group = ig;
- }
-
- if (thereAreZeroes)
- for (int64_t i =0; i < static_cast<int64_t>(nxload.numDetectors); ++i)
- {
- int64_t ig = static_cast<int64_t>(nxload.detectorGroupings[i]);
- if (ig == 0)
- {
- ig = ++max_group;
- m_groupings[i] = static_cast<specid_t>(ig);
- groups[ig] = groups.size();
- }
- }
-
- int numHists = static_cast<int>(localWorkspace->getNumberHistograms());
- size_t ngroups = groups.size(); // number of groups
-
- // to output groups in ascending order
- {
- int64_t i=0;
- for(std::map<int64_t,int64_t>::iterator it=groups.begin();it!=groups.end();++it,++i)
- {
- it->second = i;
- g_log.information()<<"group "<<it->first<<": ";
- bool first = true;
- int64_t first_i = -1 * std::numeric_limits<int64_t>::max();
- int64_t last_i = -1 * std::numeric_limits<int64_t>::max();
- for(int64_t i=0;i<static_cast<int64_t>(numHists);i++)
- if (m_groupings[i] == it->first)
- {
- if (first)
- {
- first = false;
- g_log.information()<<i;
- first_i = i;
- }
- else
- {
- if (first_i >= 0)
- {
- if (i > last_i + 1)
- {
- g_log.information()<<'-'<<i;
- first_i = -1;
- }
- }
- else
- {
- g_log.information()<<','<<i;
- first_i = i;
- }
- }
- last_i = i;
- }
- else
- {
- if (!first && first_i >= 0)
- {
- if (last_i > first_i)
- g_log.information()<<'-'<<last_i;
- first_i = -1;
- }
- }
- if (first_i >= 0 && last_i > first_i)
- g_log.information()<<'-'<<last_i;
- g_log.information()<<'\n';
- }
- }
-
- //Create a workspace with only two spectra for forward and back
- DataObjects::Workspace2D_sptr groupedWS = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
- (API::WorkspaceFactory::Instance().create(localWorkspace, ngroups, localWorkspace->dataX(0).size(), localWorkspace->blocksize()));
-
- boost::shared_array<specid_t> spec(new specid_t[numHists]);
- boost::shared_array<detid_t> dets(new detid_t[numHists]);
-
- //Compile the groups
- for (int i = 0; i < numHists; ++i)
- {
- specid_t k = static_cast<specid_t>(groups[ m_groupings[numHists*period + i] ]);
-
- for (detid_t j = 0; j < static_cast<detid_t>(localWorkspace->blocksize()); ++j)
- {
- groupedWS->dataY(k)[j] = groupedWS->dataY(k)[j] + localWorkspace->dataY(i)[j];
-
- //Add the errors in quadrature
- groupedWS->dataE(k)[j]
- = sqrt(pow(groupedWS->dataE(k)[j], 2) + pow(localWorkspace->dataE(i)[j], 2));
- }
-
- //Copy all the X data
- groupedWS->dataX(k) = localWorkspace->dataX(i);
- spec[i] = k + 1;
- dets[i] = i + 1;
- }
-
- m_groupings.clear();
-
- // All two spectra
- for(detid_t k=0; k<static_cast<detid_t>(ngroups); k++)
- {
- groupedWS->getAxis(1)->spectraNo(k)= k + 1;
- }
-
- groupedWS->replaceSpectraMap(new API::SpectraDetectorMap(spec.get(),dets.get(),numHists));
-
- // Assign the result to the output workspace property
- if(m_numberOfPeriods>1)
- setProperty(outws, boost::dynamic_pointer_cast<Workspace>(groupedWS));
- else
- {
- setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(groupedWS));
-
- }
-
- }
- else
- {
- // Assign the result to the output workspace property
- if(m_numberOfPeriods>1)
- setProperty(outws,boost::dynamic_pointer_cast<Workspace>(localWorkspace));
- else
- {
- setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(localWorkspace));
- }
-
- }
-
- } // loop over periods
-
- // Clean up
- delete[] timeChannels;
- }
-
/// Validates the optional 'spectra to read' properties, if they have been set
void LoadMuonNexus::checkOptionalProperties()
{
@@ -564,91 +130,6 @@ namespace Mantid
}
}
- /** Load in a single spectrum taken from a NeXus file
- * @param tcbs :: The vector containing the time bin boundaries
- * @param hist :: The workspace index
- * @param i :: The spectrum number
- * @param nxload :: A reference to the MuonNeXusReader object
- * @param lengthIn :: The number of elements in a spectrum
- * @param localWorkspace :: A pointer to the workspace in which the data will be stored
- */
- void LoadMuonNexus::loadData(const MantidVecPtr::ptr_type& tcbs,size_t hist, specid_t& i,
- MuonNexusReader& nxload, const int64_t lengthIn, DataObjects::Workspace2D_sptr localWorkspace)
- {
- // Read in a spectrum
- // Put it into a vector, discarding the 1st entry, which is rubbish
- // But note that the last (overflow) bin is kept
- // For Nexus, not sure if above is the case, hence give all data for now
- MantidVec& Y = localWorkspace->dataY(hist);
- Y.assign(nxload.counts + i * lengthIn, nxload.counts + i * lengthIn + lengthIn);
- // Create and fill another vector for the errors, containing sqrt(count)
- MantidVec& E = localWorkspace->dataE(hist);
- typedef double (*uf)(double);
- uf dblSqrt = std::sqrt;
- std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt);
- // Populate the workspace. Loop starts from 1, hence i-1
- localWorkspace->setX(hist, tcbs);
- localWorkspace->getAxis(1)->spectraNo(hist)= static_cast<int>(hist) + 1;
- }
-
-
- /** Log the run details from the file
- * @param localWorkspace :: The workspace details to use
- */
- void LoadMuonNexus::loadRunDetails(DataObjects::Workspace2D_sptr localWorkspace)
- {
- API::Run & runDetails = localWorkspace->mutableRun();
-
- runDetails.addProperty("run_title", localWorkspace->getTitle(), true);
-
- int numSpectra = static_cast<int>(localWorkspace->getNumberHistograms());
- runDetails.addProperty("nspectra", numSpectra);
-
- NXRoot root(m_filename);
- try
- {
- std::string start_time = root.getString("run/start_time");
- runDetails.addProperty("run_start", start_time);
- }
- catch (std::runtime_error &)
- {
- g_log.warning("run/start_time is not available, run_start log not added.");
- }
-
-
- try
- {
- std::string stop_time = root.getString("run/stop_time");
- runDetails.addProperty("run_end", stop_time);
- }
- catch (std::runtime_error &)
- {
- g_log.warning("run/stop_time is not available, run_end log not added.");
- }
-
- try
- {
- std::string dur = root.getString("run/duration");
- runDetails.addProperty("dur", dur);
- runDetails.addProperty("durunits", 1); // 1 means second here
- runDetails.addProperty("dur_secs", dur);
- }
- catch (std::runtime_error &)
- {
- g_log.warning("run/duration is not available, dur log not added.");
- }
-
- // Get number of good frames
- NXEntry runInstrumentBeam = root.openEntry("run/instrument/beam");
- NXInfo infoGoodTotalFrames = runInstrumentBeam.getDataSetInfo("frames_good");
- if (infoGoodTotalFrames.stat != NX_ERROR)
- {
- int dum = root.getInt("run/instrument/beam/frames_good");
- runDetails.addProperty("goodfrm", dum);
- }
-
- }
-
/// Run the Child Algorithm LoadInstrument (or LoadInstrumentFromNexus)
void LoadMuonNexus::runLoadInstrument(DataObjects::Workspace2D_sptr localWorkspace)
{
@@ -682,104 +163,6 @@ namespace Mantid
}
}
- /// Run LoadInstrumentFromNexus as a Child Algorithm (only if loading from instrument definition file fails)
- void LoadMuonNexus::runLoadInstrumentFromNexus(DataObjects::Workspace2D_sptr localWorkspace)
- {
- g_log.information() << "Instrument definition file not found. Attempt to load information about \n"
- << "the instrument from nexus data file.\n";
-
- IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrumentFromNexus");
-
- // Now execute the Child Algorithm. Catch and log any error, but don't stop.
- bool executionSuccessful(true);
- try
- {
- loadInst->setPropertyValue("Filename", m_filename);
- loadInst->setProperty<MatrixWorkspace_sptr> ("Workspace", localWorkspace);
- loadInst->execute();
- }
- catch( std::invalid_argument&)
- {
- g_log.information("Invalid argument to LoadInstrument Child Algorithm");
- executionSuccessful = false;
- }
- catch (std::runtime_error&)
- {
- g_log.information("Unable to successfully run LoadInstrument Child Algorithm");
- executionSuccessful = false;
- }
-
- if ( !executionSuccessful ) g_log.error("No instrument definition loaded");
- }
-
- /// Run the LoadMappingTable Child Algorithm to fill the SpectraToDetectorMap
- void LoadMuonNexus::runLoadMappingTable(DataObjects::Workspace2D_sptr localWorkspace)
- {
- NXRoot root(m_filename);
- NXInt number = root.openNXInt("run/instrument/detector/number");
- number.load();
- detid_t ndet = static_cast<detid_t>(number[0]/m_numberOfPeriods);
- boost::shared_array<detid_t> det(new detid_t[ndet]);
- for(detid_t i=0;i<ndet;i++)
- {
- det[i] = i + 1;
- }
- localWorkspace->replaceSpectraMap(new API::SpectraDetectorMap(det.get(),det.get(),ndet));
- }
-
- /// Run the LoadLog Child Algorithm
- void LoadMuonNexus::runLoadLog(DataObjects::Workspace2D_sptr localWorkspace)
- {
- IAlgorithm_sptr loadLog = createChildAlgorithm("LoadMuonLog");
- // Pass through the same input filename
- loadLog->setPropertyValue("Filename",m_filename);
- // Set the workspace property to be the same one filled above
- loadLog->setProperty<MatrixWorkspace_sptr>("Workspace",localWorkspace);
-
- // Now execute the Child Algorithm. Catch and log any error, but don't stop.
- try
- {
- loadLog->execute();
- }
- catch (std::runtime_error&)
- {
- g_log.error("Unable to successfully run LoadLog Child Algorithm");
- }
- catch (std::logic_error&)
- {
- g_log.error("Unable to successfully run LoadLog Child Algorithm");
- }
-
- if ( ! loadLog->isExecuted() ) g_log.error("Unable to successfully run LoadLog Child Algorithm");
-
-
- NXRoot root(m_filename);
-
- try
- {
- NXChar orientation = root.openNXChar("run/instrument/detector/orientation");
- // some files have no data there
- orientation.load();
-
- if (orientation[0] == 't')
- {
- Kernel::TimeSeriesProperty<double>* p = new Kernel::TimeSeriesProperty<double>("fromNexus");
- std::string start_time = root.getString("run/start_time");
- p->addValue(start_time,-90.0);
- localWorkspace->mutableRun().addLogData(p);
- setProperty("MainFieldDirection", "Transverse");
- }
- else
- {
- setProperty("MainFieldDirection", "Longitudinal");
- }
- }
- catch(...)
- {
- setProperty("MainFieldDirection", "Longitudinal");
- }
-
- }
/**This method does a quick file type check by looking at the first 100 bytes of the file
* @param filePath- path of the file including name.
@@ -807,7 +190,6 @@ namespace Mantid
return true;
}
return false;
-
}
/**checks the file by opening it and reading few lines
* @param filePath :: name of the file inluding its path
@@ -815,26 +197,8 @@ namespace Mantid
*/
int LoadMuonNexus::fileCheck(const std::string& filePath)
{
- using namespace ::NeXus;
- int confidence(0);
- try
- {
- ::NeXus::File file = ::NeXus::File(filePath);
- file.openPath("/run/analysis");
- std::string analysisType = file.getStrData();
- std::string compareString = "muon";
- if( analysisType.compare(0,compareString.length(),compareString) == 0 )
- {
- // If all this succeeded then we'll assume this is an ISIS Muon NeXus file
- confidence = 80;
- }
- file.close();
- }
- catch(::NeXus::Exception&)
- {
- }
- return confidence;
-
+ UNUSED_ARG( filePath );
+ throw Kernel::Exception::NotImplementedError("LoadMuonNexus cannot be used as a file checker.");
}
} // namespace DataHandling
diff --git a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus1.cpp b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus1.cpp
new file mode 100644
index 00000000000..ce959c6405d
--- /dev/null
+++ b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus1.cpp
@@ -0,0 +1,696 @@
+/*WIKI*
+
+
+The algorithm LoadMuonNexus will read a Muon Nexus data file (original format) and place the data
+into the named workspace.
+The file name can be an absolute or relative path and should have the extension
+.nxs or .NXS.
+If the file contains data for more than one period, a separate workspace will be generated for each.
+After the first period the workspace names will have "_2", "_3", and so on, appended to the given workspace name.
+For single period data, the optional parameters can be used to control which spectra are loaded into the workspace.
+If spectrum_min and spectrum_max are given, then only that range to data will be loaded.
+If a spectrum_list is given than those values will be loaded.
+* TODO get XML descriptions of Muon instruments. This data is not in existing Muon Nexus files.
+* TODO load the spectra detector mapping. This may be very simple for Muon instruments.
+
+===Time series data===
+The log data in the Nexus file (NX_LOG sections) will be loaded as TimeSeriesProperty data within the workspace.
+Time is stored as seconds from the Unix epoch.
+
+===Errors===
+
+The error for each histogram count is set as the square root of the number of counts.
+
+===Time bin data===
+
+The ''corrected_times'' field of the Nexus file is used to provide time bin data and the bin edge values are calculated from these
+bin centre times.
+
+===Multiperiod data===
+
+To determine if a file contains data from more than one period the field ''switching_states'' is read from the Nexus file.
+If this value is greater than one it is taken to be the number of periods, <math>N_p</math> of the data.
+In this case the <math>N_s</math> spectra in the ''histogram_data'' field are split with <math>N_s/N_p</math> assigned to each period.
+
+===ChildAlgorithms used===
+
+The ChildAlgorithms used by LoadMuonNexus are:
+* LoadMuonLog - this reads log information from the Nexus file and uses it to create TimeSeriesProperty entries in the workspace.
+* LoadInstrument - this algorithm looks for an XML description of the instrument and if found reads it.
+* LoadIntstrumentFromNexus - this is called if the normal LoadInstrument fails. As the Nexus file has limited instrument data, this only populates a few fields.
+
+*WIKI*/
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidDataHandling/LoadMuonNexus1.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidAPI/LoadAlgorithmFactory.h"
+#include "MantidAPI/FileProperty.h"
+#include "MantidAPI/Progress.h"
+#include "MantidAPI/SpectraDetectorMap.h"
+#include "MantidAPI/TableRow.h"
+#include "MantidGeometry/Instrument/Detector.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/ConfigService.h"
+#include "MantidKernel/ArrayProperty.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidKernel/BoundedValidator.h"
+#include "MantidKernel/ListValidator.h"
+#include "MantidNexus/MuonNexusReader.h"
+#include "MantidNexus/NexusClasses.h"
+
+#include <Poco/Path.h>
+#include <limits>
+#include <cmath>
+#include <boost/shared_ptr.hpp>
+
+namespace Mantid
+{
+ namespace DataHandling
+ {
+ // Register the algorithm into the algorithm factory
+ DECLARE_ALGORITHM(LoadMuonNexus1)
+ DECLARE_LOADALGORITHM(LoadMuonNexus1)
+
+ /// Sets documentation strings for this algorithm
+ void LoadMuonNexus1::initDocs()
+ {
+ this->setWikiSummary("The LoadMuonNexus algorithm will read the given NeXus Muon data file Version 1 and use the results to populate the named workspace. LoadMuonNexus may be invoked by [[LoadNexus]] if it is given a NeXus file of this type. ");
+ this->setOptionalMessage("The LoadMuonNexus algorithm will read the given NeXus Muon data file Version 1 and use the results to populate the named workspace. LoadMuonNexus may be invoked by LoadNexus if it is given a NeXus file of this type.");
+ }
+
+
+ using namespace Kernel;
+ using namespace API;
+ using Geometry::Instrument;
+ using namespace Mantid::NeXus;
+
+ /// Empty default constructor
+ LoadMuonNexus1::LoadMuonNexus1() : LoadMuonNexus() {}
+
+ /** 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 LoadMuonNexus1::exec()
+ {
+ // Retrieve the filename from the properties
+ m_filename = getPropertyValue("Filename");
+ // Retrieve the entry number
+ m_entrynumber = getProperty("EntryNumber");
+
+ NXRoot root(m_filename);
+ NXEntry entry = root.openEntry("run/histogram_data_1");
+ try
+ {
+ NXInfo info = entry.getDataSetInfo("time_zero");
+ if (info.stat != NX_ERROR)
+ {
+ double dum = root.getFloat("run/histogram_data_1/time_zero");
+ setProperty("TimeZero", dum);
+ }
+ }
+ catch (::NeXus::Exception&)
+ {}
+
+ try
+ {
+ NXInfo infoResolution = entry.getDataSetInfo("resolution");
+ NXInt counts = root.openNXInt("run/histogram_data_1/counts");
+ std::string firstGoodBin = counts.attributes("first_good_bin");
+ if ( !firstGoodBin.empty() && infoResolution.stat != NX_ERROR )
+ {
+ double bin = static_cast<double>(boost::lexical_cast<int>(firstGoodBin));
+ double bin_size = static_cast<double>(root.getInt("run/histogram_data_1/resolution"))/1000000.0;
+ setProperty("FirstGoodData", bin*bin_size);
+ }
+ }
+ catch (::NeXus::Exception&)
+ {}
+
+ try
+ {
+ std::vector<double>defaultDeadTimes;
+ NXFloat deadTimes = root.openNXFloat("run/instrument/detector/deadtimes");
+ deadTimes.load();
+
+ int length = deadTimes.dim0();
+ for (int i = 0; i < length; i++)
+ {
+ defaultDeadTimes.push_back(static_cast<double>(*(deadTimes() + i) ) );
+ }
+ setProperty("DeadTimes", defaultDeadTimes);
+ }
+ catch (::NeXus::Exception&)
+ {}
+
+ NXEntry nxRun = root.openEntry("run");
+ std::string title;
+ std::string notes;
+ try
+ {
+ title = nxRun.getString("title");
+ notes = nxRun.getString("notes");
+ }
+ catch (::NeXus::Exception&)
+ {}
+ std::string run_num;
+ try
+ {
+ run_num = boost::lexical_cast<std::string>(nxRun.getInt("number"));
+ }
+ catch (::NeXus::Exception&)
+ {}
+
+ MuonNexusReader nxload;
+ if (nxload.readFromFile(m_filename) != 0)
+ {
+ g_log.error("Unable to open file " + m_filename);
+ throw Exception::FileError("Unable to open File:" , m_filename);
+ }
+
+ // Read in the instrument name from the Nexus file
+ m_instrument_name = nxload.getInstrumentName();
+ // Read in the number of spectra in the Nexus file
+ m_numberOfSpectra = nxload.t_nsp1;
+ if(m_entrynumber!=0)
+ {
+ m_numberOfPeriods=1;
+ if(m_entrynumber>nxload.t_nper)
+ {
+ throw std::invalid_argument("Invalid Entry Number:Enter a valid number");
+ }
+ }
+ else
+ {
+ // Read the number of periods in this file
+ m_numberOfPeriods = nxload.t_nper;
+ }
+ // Need to extract the user-defined output workspace name
+ Property *ws = getProperty("OutputWorkspace");
+ std::string localWSName = ws->value();
+ // If multiperiod, will need to hold the Instrument, Sample & SpectraDetectorMap for copying
+ boost::shared_ptr<Instrument> instrument;
+ boost::shared_ptr<Sample> sample;
+
+ // Call private method to validate the optional parameters, if set
+ checkOptionalProperties();
+
+ // Read the number of time channels (i.e. bins) from the Nexus file
+ const int channelsPerSpectrum = nxload.t_ntc1;
+ // Read in the time bin boundaries
+ const int lengthIn = channelsPerSpectrum + 1;
+ float* timeChannels = new float[lengthIn];
+ nxload.getTimeChannels(timeChannels, lengthIn);
+ // Put the read in array into a vector (inside a shared pointer)
+ boost::shared_ptr<MantidVec> timeChannelsVec
+ (new MantidVec(timeChannels, timeChannels + lengthIn));
+
+ // Calculate the size of a workspace, given its number of periods & spectra to read
+ int64_t total_specs;
+ if( m_interval || m_list)
+ {
+ total_specs = m_spec_list.size();
+ if (m_interval)
+ {
+ total_specs += (m_spec_max-m_spec_min+1);
+ m_spec_max += 1;
+ }
+ }
+ else
+ {
+ total_specs = m_numberOfSpectra;
+ // for nexus return all spectra
+ m_spec_min = 0; // changed to 0 for NeXus, was 1 for Raw
+ m_spec_max = m_numberOfSpectra; // was +1?
+ }
+
+ // Create the 2D workspace for the output
+ DataObjects::Workspace2D_sptr localWorkspace = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
+ (WorkspaceFactory::Instance().create("Workspace2D",total_specs,lengthIn,lengthIn-1));
+ localWorkspace->setTitle(title);
+ localWorkspace->setComment(notes);
+ localWorkspace->mutableRun().addLogData(new PropertyWithValue<std::string>("run_number", run_num));
+ // Set the unit on the workspace to muon time, for now in the form of a Label Unit
+ boost::shared_ptr<Kernel::Units::Label> lblUnit =
+ boost::dynamic_pointer_cast<Kernel::Units::Label>(UnitFactory::Instance().create("Label"));
+ lblUnit->setLabel("Time","microsecond");
+ localWorkspace->getAxis(0)->unit() = lblUnit;
+ // Set y axis unit
+ localWorkspace->setYUnit("Counts");
+
+ WorkspaceGroup_sptr wsGrpSptr=WorkspaceGroup_sptr(new WorkspaceGroup);
+ if(m_numberOfPeriods>1)
+ {
+ setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(wsGrpSptr));
+ }
+
+ API::Progress progress(this,0.,1.,m_numberOfPeriods * total_specs);
+ // Loop over the number of periods in the Nexus file, putting each period in a separate workspace
+ for (int64_t period = 0; period < m_numberOfPeriods; ++period) {
+ if(m_entrynumber!=0)
+ {
+ period=m_entrynumber-1;
+ if(period!=0)
+ {
+ loadRunDetails(localWorkspace);
+ runLoadInstrument(localWorkspace );
+ runLoadMappingTable(localWorkspace );
+ }
+ }
+
+ if (period == 0)
+ {
+ // Only run the Child Algorithms once
+ loadRunDetails(localWorkspace);
+ runLoadInstrument(localWorkspace );
+ runLoadMappingTable(localWorkspace );
+ runLoadLog(localWorkspace );
+ localWorkspace->populateInstrumentParameters();
+ }
+ else // We are working on a higher period of a multiperiod raw file
+ {
+ localWorkspace = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
+ (WorkspaceFactory::Instance().create(localWorkspace));
+ localWorkspace->setTitle(title);
+ localWorkspace->setComment(notes);
+ //localWorkspace->newInstrumentParameters(); ???
+
+ }
+
+
+ std::string outws("");
+ if(m_numberOfPeriods>1)
+ {
+ std::string outputWorkspace = "OutputWorkspace";
+ std::stringstream suffix;
+ suffix << (period+1);
+ outws =outputWorkspace+"_"+suffix.str();
+ std::string WSName = localWSName + "_" + suffix.str();
+ declareProperty(new WorkspaceProperty<Workspace>(outws,WSName,Direction::Output));
+ if (wsGrpSptr)
+ {
+ wsGrpSptr->addWorkspace( localWorkspace );
+ }
+ }
+
+ size_t counter = 0;
+ for (int64_t i = m_spec_min; i < m_spec_max; ++i)
+ {
+ // Shift the histogram to read if we're not in the first period
+ specid_t histToRead = static_cast<specid_t>(i + period*total_specs);
+ loadData(timeChannelsVec,counter,histToRead,nxload,lengthIn-1,localWorkspace ); // added -1 for NeXus
+ counter++;
+ progress.report();
+ }
+ // Read in the spectra in the optional list parameter, if set
+ if (m_list)
+ {
+ for(size_t i=0; i < m_spec_list.size(); ++i)
+ {
+ loadData(timeChannelsVec,counter,m_spec_list[i],nxload,lengthIn-1, localWorkspace );
+ counter++;
+ progress.report();
+ }
+ }
+ // Just a sanity check
+ assert(counter == size_t(total_specs) );
+
+ bool autogroup = getProperty("AutoGroup");
+
+ if (autogroup)
+ {
+
+ //Get the groupings
+ int64_t max_group = 0;
+ // use a map for mapping group number and output workspace index in case
+ // there are group numbers > number of groups
+ std::map<int64_t,int64_t> groups;
+ m_groupings.resize(nxload.numDetectors);
+ bool thereAreZeroes = false;
+ for (int64_t i =0; i < static_cast<int64_t>(nxload.numDetectors); ++i)
+ {
+ int64_t ig = static_cast<int64_t>(nxload.detectorGroupings[i]);
+ if (ig == 0)
+ {
+ thereAreZeroes = true;
+ continue;
+ }
+ m_groupings[i] = static_cast<specid_t>(ig);
+ if (groups.find(ig) == groups.end())
+ groups[ig] = static_cast<int64_t>(groups.size());
+ if (ig > max_group) max_group = ig;
+ }
+
+ if (thereAreZeroes)
+ for (int64_t i =0; i < static_cast<int64_t>(nxload.numDetectors); ++i)
+ {
+ int64_t ig = static_cast<int64_t>(nxload.detectorGroupings[i]);
+ if (ig == 0)
+ {
+ ig = ++max_group;
+ m_groupings[i] = static_cast<specid_t>(ig);
+ groups[ig] = groups.size();
+ }
+ }
+
+ int numHists = static_cast<int>(localWorkspace->getNumberHistograms());
+ size_t ngroups = groups.size(); // number of groups
+
+ // to output groups in ascending order
+ {
+ int64_t i=0;
+ for(std::map<int64_t,int64_t>::iterator it=groups.begin();it!=groups.end();++it,++i)
+ {
+ it->second = i;
+ g_log.information()<<"group "<<it->first<<": ";
+ bool first = true;
+ int64_t first_i = -1 * std::numeric_limits<int64_t>::max();
+ int64_t last_i = -1 * std::numeric_limits<int64_t>::max();
+ for(int64_t i=0;i<static_cast<int64_t>(numHists);i++)
+ if (m_groupings[i] == it->first)
+ {
+ if (first)
+ {
+ first = false;
+ g_log.information()<<i;
+ first_i = i;
+ }
+ else
+ {
+ if (first_i >= 0)
+ {
+ if (i > last_i + 1)
+ {
+ g_log.information()<<'-'<<i;
+ first_i = -1;
+ }
+ }
+ else
+ {
+ g_log.information()<<','<<i;
+ first_i = i;
+ }
+ }
+ last_i = i;
+ }
+ else
+ {
+ if (!first && first_i >= 0)
+ {
+ if (last_i > first_i)
+ g_log.information()<<'-'<<last_i;
+ first_i = -1;
+ }
+ }
+ if (first_i >= 0 && last_i > first_i)
+ g_log.information()<<'-'<<last_i;
+ g_log.information()<<'\n';
+ }
+ }
+
+ //Create a workspace with only two spectra for forward and back
+ DataObjects::Workspace2D_sptr groupedWS = boost::dynamic_pointer_cast<DataObjects::Workspace2D>
+ (API::WorkspaceFactory::Instance().create(localWorkspace, ngroups, localWorkspace->dataX(0).size(), localWorkspace->blocksize()));
+
+ boost::shared_array<specid_t> spec(new specid_t[numHists]);
+ boost::shared_array<detid_t> dets(new detid_t[numHists]);
+
+ //Compile the groups
+ for (int i = 0; i < numHists; ++i)
+ {
+ specid_t k = static_cast<specid_t>(groups[ m_groupings[numHists*period + i] ]);
+
+ for (detid_t j = 0; j < static_cast<detid_t>(localWorkspace->blocksize()); ++j)
+ {
+ groupedWS->dataY(k)[j] = groupedWS->dataY(k)[j] + localWorkspace->dataY(i)[j];
+
+ //Add the errors in quadrature
+ groupedWS->dataE(k)[j]
+ = sqrt(pow(groupedWS->dataE(k)[j], 2) + pow(localWorkspace->dataE(i)[j], 2));
+ }
+
+ //Copy all the X data
+ groupedWS->dataX(k) = localWorkspace->dataX(i);
+ spec[i] = k + 1;
+ dets[i] = i + 1;
+ }
+
+ m_groupings.clear();
+
+ // All two spectra
+ for(detid_t k=0; k<static_cast<detid_t>(ngroups); k++)
+ {
+ groupedWS->getAxis(1)->spectraNo(k)= k + 1;
+ }
+
+ groupedWS->replaceSpectraMap(new API::SpectraDetectorMap(spec.get(),dets.get(),numHists));
+
+ // Assign the result to the output workspace property
+ if(m_numberOfPeriods>1)
+ setProperty(outws, boost::dynamic_pointer_cast<Workspace>(groupedWS));
+ else
+ {
+ setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(groupedWS));
+
+ }
+
+ }
+ else
+ {
+ // Assign the result to the output workspace property
+ if(m_numberOfPeriods>1)
+ setProperty(outws,boost::dynamic_pointer_cast<Workspace>(localWorkspace));
+ else
+ {
+ setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(localWorkspace));
+ }
+
+ }
+
+ } // loop over periods
+
+ // Clean up
+ delete[] timeChannels;
+ }
+
+ /** Load in a single spectrum taken from a NeXus file
+ * @param tcbs :: The vector containing the time bin boundaries
+ * @param hist :: The workspace index
+ * @param i :: The spectrum number
+ * @param nxload :: A reference to the MuonNeXusReader object
+ * @param lengthIn :: The number of elements in a spectrum
+ * @param localWorkspace :: A pointer to the workspace in which the data will be stored
+ */
+ void LoadMuonNexus1::loadData(const MantidVecPtr::ptr_type& tcbs,size_t hist, specid_t& i,
+ MuonNexusReader& nxload, const int64_t lengthIn, DataObjects::Workspace2D_sptr localWorkspace)
+ {
+ // Read in a spectrum
+ // Put it into a vector, discarding the 1st entry, which is rubbish
+ // But note that the last (overflow) bin is kept
+ // For Nexus, not sure if above is the case, hence give all data for now
+ MantidVec& Y = localWorkspace->dataY(hist);
+ Y.assign(nxload.counts + i * lengthIn, nxload.counts + i * lengthIn + lengthIn);
+ // Create and fill another vector for the errors, containing sqrt(count)
+ MantidVec& E = localWorkspace->dataE(hist);
+ typedef double (*uf)(double);
+ uf dblSqrt = std::sqrt;
+ std::transform(Y.begin(), Y.end(), E.begin(), dblSqrt);
+ // Populate the workspace. Loop starts from 1, hence i-1
+ localWorkspace->setX(hist, tcbs);
+ localWorkspace->getAxis(1)->spectraNo(hist)= static_cast<int>(hist) + 1;
+ }
+
+
+ /** Log the run details from the file
+ * @param localWorkspace :: The workspace details to use
+ */
+ void LoadMuonNexus1::loadRunDetails(DataObjects::Workspace2D_sptr localWorkspace)
+ {
+ API::Run & runDetails = localWorkspace->mutableRun();
+
+ runDetails.addProperty("run_title", localWorkspace->getTitle(), true);
+
+ int numSpectra = static_cast<int>(localWorkspace->getNumberHistograms());
+ runDetails.addProperty("nspectra", numSpectra);
+
+ NXRoot root(m_filename);
+ try
+ {
+ std::string start_time = root.getString("run/start_time");
+ runDetails.addProperty("run_start", start_time);
+ }
+ catch (std::runtime_error &)
+ {
+ g_log.warning("run/start_time is not available, run_start log not added.");
+ }
+
+
+ try
+ {
+ std::string stop_time = root.getString("run/stop_time");
+ runDetails.addProperty("run_end", stop_time);
+ }
+ catch (std::runtime_error &)
+ {
+ g_log.warning("run/stop_time is not available, run_end log not added.");
+ }
+
+ try
+ {
+ std::string dur = root.getString("run/duration");
+ runDetails.addProperty("dur", dur);
+ runDetails.addProperty("durunits", 1); // 1 means second here
+ runDetails.addProperty("dur_secs", dur);
+ }
+ catch (std::runtime_error &)
+ {
+ g_log.warning("run/duration is not available, dur log not added.");
+ }
+
+ // Get number of good frames
+ NXEntry runInstrumentBeam = root.openEntry("run/instrument/beam");
+ NXInfo infoGoodTotalFrames = runInstrumentBeam.getDataSetInfo("frames_good");
+ if (infoGoodTotalFrames.stat != NX_ERROR)
+ {
+ int dum = root.getInt("run/instrument/beam/frames_good");
+ runDetails.addProperty("goodfrm", dum);
+ }
+
+ }
+
+ /// Run LoadInstrumentFromNexus as a Child Algorithm (only if loading from instrument definition file fails)
+ void LoadMuonNexus1::runLoadInstrumentFromNexus(DataObjects::Workspace2D_sptr localWorkspace)
+ {
+ g_log.information() << "Instrument definition file not found. Attempt to load information about \n"
+ << "the instrument from nexus data file.\n";
+
+ IAlgorithm_sptr loadInst = createChildAlgorithm("LoadInstrumentFromNexus");
+
+ // Now execute the Child Algorithm. Catch and log any error, but don't stop.
+ bool executionSuccessful(true);
+ try
+ {
+ loadInst->setPropertyValue("Filename", m_filename);
+ loadInst->setProperty<MatrixWorkspace_sptr> ("Workspace", localWorkspace);
+ loadInst->execute();
+ }
+ catch( std::invalid_argument&)
+ {
+ g_log.information("Invalid argument to LoadInstrument Child Algorithm");
+ executionSuccessful = false;
+ }
+ catch (std::runtime_error&)
+ {
+ g_log.information("Unable to successfully run LoadInstrument Child Algorithm");
+ executionSuccessful = false;
+ }
+
+ if ( !executionSuccessful ) g_log.error("No instrument definition loaded");
+ }
+
+ /// Run the LoadMappingTable Child Algorithm to fill the SpectraToDetectorMap
+ void LoadMuonNexus1::runLoadMappingTable(DataObjects::Workspace2D_sptr localWorkspace)
+ {
+ NXRoot root(m_filename);
+ NXInt number = root.openNXInt("run/instrument/detector/number");
+ number.load();
+ detid_t ndet = static_cast<detid_t>(number[0]/m_numberOfPeriods);
+ boost::shared_array<detid_t> det(new detid_t[ndet]);
+ for(detid_t i=0;i<ndet;i++)
+ {
+ det[i] = i + 1;
+ }
+ localWorkspace->replaceSpectraMap(new API::SpectraDetectorMap(det.get(),det.get(),ndet));
+ }
+
+ /// Run the LoadLog Child Algorithm
+ void LoadMuonNexus1::runLoadLog(DataObjects::Workspace2D_sptr localWorkspace)
+ {
+ IAlgorithm_sptr loadLog = createChildAlgorithm("LoadMuonLog");
+ // Pass through the same input filename
+ loadLog->setPropertyValue("Filename",m_filename);
+ // Set the workspace property to be the same one filled above
+ loadLog->setProperty<MatrixWorkspace_sptr>("Workspace",localWorkspace);
+
+ // Now execute the Child Algorithm. Catch and log any error, but don't stop.
+ try
+ {
+ loadLog->execute();
+ }
+ catch (std::runtime_error&)
+ {
+ g_log.error("Unable to successfully run LoadLog Child Algorithm");
+ }
+ catch (std::logic_error&)
+ {
+ g_log.error("Unable to successfully run LoadLog Child Algorithm");
+ }
+
+ if ( ! loadLog->isExecuted() ) g_log.error("Unable to successfully run LoadLog Child Algorithm");
+
+
+ NXRoot root(m_filename);
+
+ try
+ {
+ NXChar orientation = root.openNXChar("run/instrument/detector/orientation");
+ // some files have no data there
+ orientation.load();
+
+ if (orientation[0] == 't')
+ {
+ Kernel::TimeSeriesProperty<double>* p = new Kernel::TimeSeriesProperty<double>("fromNexus");
+ std::string start_time = root.getString("run/start_time");
+ p->addValue(start_time,-90.0);
+ localWorkspace->mutableRun().addLogData(p);
+ setProperty("MainFieldDirection", "Transverse");
+ }
+ else
+ {
+ setProperty("MainFieldDirection", "Longitudinal");
+ }
+ }
+ catch(...)
+ {
+ setProperty("MainFieldDirection", "Longitudinal");
+ }
+
+ }
+
+ /**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 LoadMuonNexus1::fileCheck(const std::string& filePath)
+ {
+ try
+ {
+ NXRoot root(filePath);
+ NXEntry entry = root.openFirstEntry();
+ if ( ! entry.containsDataSet( "analysis" ) ) return 0;
+ std::string versionField = "IDF_version";
+ if ( ! entry.containsDataSet( versionField ) )
+ {
+ versionField = "idf_version";
+ if ( ! entry.containsDataSet( versionField ) ) return 0;
+ }
+ if ( entry.getInt( versionField ) != 1 ) return 0;
+ std::string definition = entry.getString( "analysis" );
+ if ( definition == "muonTD" || definition == "pulsedTD" )
+ {
+ // If all this succeeded then we'll assume this is an ISIS Muon NeXus file version 1
+ return 81;
+ }
+ }
+ catch(...)
+ {
+ }
+ return 0;
+ }
+
+ } // namespace DataHandling
+} // namespace Mantid
diff --git a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus2.cpp b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus2.cpp
index 0ad28d34e65..3a7eeba29f7 100644
--- a/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus2.cpp
+++ b/Code/Mantid/Framework/DataHandling/src/LoadMuonNexus2.cpp
@@ -2,21 +2,21 @@
// Includes
//----------------------------------------------------------------------
#include "MantidDataHandling/LoadMuonNexus2.h"
+#include "MantidDataHandling/LoadMuonNexus1.h"
#include "MantidDataObjects/Workspace2D.h"
-#include "MantidKernel/UnitFactory.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidKernel/ArrayProperty.h"
#include "MantidAPI/FileProperty.h"
-#include "MantidKernel/TimeSeriesProperty.h"
-#include "MantidGeometry/Instrument/Detector.h"
#include "MantidAPI/Progress.h"
#include "MantidAPI/SpectraDetectorMap.h"
+#include "MantidAPI/LoadAlgorithmFactory.h"
+#include "MantidGeometry/Instrument/Detector.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidKernel/ConfigService.h"
+#include "MantidKernel/ArrayProperty.h"
#include "MantidNexus/NexusClasses.h"
#include "MantidNexusCPP/NeXusFile.hpp"
#include "MantidNexusCPP/NeXusException.hpp"
-
-#include "MantidAPI/LoadAlgorithmFactory.h"
#include <Poco/Path.h>
#include <boost/lexical_cast.hpp>
#include <boost/shared_ptr.hpp>
@@ -40,8 +40,8 @@ namespace Mantid
/// Sets documentation strings for this algorithm
void LoadMuonNexus2::initDocs()
{
- this->setWikiSummary("The LoadMuonNexus algorithm will read the given NeXus Muon data file Version 1 and use the results to populate the named workspace. LoadMuonNexus may be invoked by [[LoadNexus]] if it is given a NeXus file of this type. ");
- this->setOptionalMessage("The LoadMuonNexus algorithm will read the given NeXus Muon data file Version 1 and use the results to populate the named workspace. LoadMuonNexus may be invoked by LoadNexus if it is given a NeXus file of this type.");
+ this->setWikiSummary("The LoadMuonNexus algorithm will read the given NeXus Muon data file Version 2 and use the results to populate the named workspace. LoadMuonNexus may be invoked by [[LoadNexus]] if it is given a NeXus file of this type. ");
+ this->setOptionalMessage("The LoadMuonNexus algorithm will read the given NeXus Muon data file Version 2 and use the results to populate the named workspace. LoadMuonNexus may be invoked by LoadNexus if it is given a NeXus file of this type.");
}
@@ -49,13 +49,49 @@ namespace Mantid
LoadMuonNexus2::LoadMuonNexus2() : LoadMuonNexus()
{}
- /** Executes the algorithm. Reading in the file and creating and populating
- * the output workspace
+ /** Executes the right version of the muon nexus loader: versions 1 or 2.
*
* @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 LoadMuonNexus2::exec()
+ {
+ std::string filePath = getPropertyValue("Filename");
+ LoadMuonNexus1 load1; load1.initialize();
+
+ int confidence1 = load1.fileCheck( filePath );
+ int confidence2 = this->fileCheck( filePath );
+
+ // if none can load the file throw
+ if ( confidence1 < 80 && confidence2 < 80)
+ {
+ throw Kernel::Exception::FileError("Cannot open the file ", filePath);
+ }
+
+ if ( confidence2 > confidence1 )
+ {
+ // this loader
+ doExec();
+ }
+ else
+ {
+ // version 1 loader
+ IAlgorithm_sptr childAlg = createChildAlgorithm("LoadMuonNexus",0,1,true,1);
+ auto version1Loader = boost::dynamic_pointer_cast<API::Algorithm>( childAlg );
+ version1Loader->copyPropertiesFrom( *this );
+ version1Loader->executeAsChildAlg();
+ this->copyPropertiesFrom( *version1Loader );
+ API::Workspace_sptr outWS = version1Loader->getProperty("OutputWorkspace");
+ setProperty("OutputWorkspace", outWS);
+ }
+ }
+
+ /** Read in a muon nexus file of the version 2.
+ *
+ * @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 LoadMuonNexus2::doExec()
{
// Create the root Nexus class
NXRoot root(getPropertyValue("Filename"));
@@ -67,45 +103,27 @@ namespace Mantid
}
// Open the data entry
- std::string entryName = root.groups()[iEntry].nxname;
- NXEntry entry = root.openEntry(entryName);
+ m_entry_name = root.groups()[iEntry].nxname;
+ NXEntry entry = root.openEntry(m_entry_name);
+
+ // Read in the instrument name from the Nexus file
+ m_instrument_name = entry.getString("instrument/name");
- NXInfo info = entry.getDataSetInfo("definition");
- if (info.stat == NX_ERROR)
+ // Read the number of periods in this file
+ if ( entry.containsGroup("run") )
{
- info = entry.getDataSetInfo("analysis");
- std::string compareString = "muon";
- if (info.stat == NX_OK && entry.getString("analysis").compare(0,compareString.length(),compareString) == 0)
+ try
{
- LoadMuonNexus::exec();
- return;
+ m_numberOfPeriods = entry.getInt("run/number_periods");
}
- else
+ catch (::NeXus::Exception&)
{
- g_log.debug()<<"analysis=|" << entry.getString("analysis") << "|" << std::endl;
- throw std::runtime_error("Unknown Muon NeXus file format");
+ //assume 1
+ m_numberOfPeriods = 1;
}
}
else
{
- std::string definition = entry.getString("definition");
- if (info.stat == NX_ERROR || definition != "pulsedTD")
- {
- throw std::runtime_error("Unknown Muon Nexus file format");
- }
- }
-
- // Read in the instrument name from the Nexus file
- m_instrument_name = entry.getString("instrument/name");
-
- // Read the number of periods in this file
- try
- {
- m_numberOfPeriods = entry.getInt("run/number_periods");
- }
- catch (::NeXus::Exception&)
- {
- //assume 1
m_numberOfPeriods = 1;
}
@@ -179,56 +197,44 @@ namespace Mantid
//g_log.error()<<" number of perioids= "<<m_numberOfPeriods<<std::endl;
WorkspaceGroup_sptr wsGrpSptr=WorkspaceGroup_sptr(new WorkspaceGroup);
- try
+ if ( entry.containsDataSet( "title" ) )
{
wsGrpSptr->setTitle(entry.getString("title"));
}
- catch (::NeXus::Exception&)
- {}
- try
+
+ if ( entry.containsDataSet( "notes" ) )
{
wsGrpSptr->setComment(entry.getString("notes"));
}
- catch (::NeXus::Exception&)
- {}
if(m_numberOfPeriods>1)
{
setProperty("OutputWorkspace",boost::dynamic_pointer_cast<Workspace>(wsGrpSptr));
}
- Mantid::NeXus::NXInt period_index = dataGroup.openNXInt("period_index");
- period_index.load();
+ // period_index is currently unused
+ //Mantid::NeXus::NXInt period_index = dataGroup.openNXInt("period_index");
+ //period_index.load();
Mantid::NeXus::NXInt counts = dataGroup.openIntData();
counts.load();
+ NXInstrument instr = entry.openNXInstrument("instrument");
- try
+ if ( instr.containsGroup( "detector_fb" ) )
{
- NXEntry entryTimeZero = root.openEntry("run/instrument/detector_fb");
- NXInfo infoTimeZero = entryTimeZero.getDataSetInfo("time_zero");
- if (infoTimeZero.stat != NX_ERROR)
+ NXDetector detector = instr.openNXDetector("detector_fb");
+ if (detector.containsDataSet("time_zero"))
{
- double dum = root.getFloat("run/instrument/detector_fb/time_zero");
+ double dum = detector.getFloat("time_zero");
setProperty("TimeZero", dum);
}
- }
- catch (::NeXus::Exception&)
- {}
-
- try
- {
- NXEntry entryFGB = root.openEntry("run/instrument/detector_fb");
- NXInfo infoFGB = entryFGB.getDataSetInfo("first_good_time");
- if (infoFGB.stat != NX_ERROR)
+ if (detector.containsDataSet("first_good_time"))
{
- double dum = root.getFloat("run/instrument/detector_fb/first_good_time");
+ double dum = detector.getFloat("first_good_time");
setProperty("FirstGoodData", dum);
}
}
- catch (::NeXus::Exception&)
- {}
API::Progress progress(this,0.,1.,m_numberOfPeriods * total_specs);
// Loop over the number of periods in the Nexus file, putting each period in a separate workspace
@@ -321,10 +327,27 @@ namespace Mantid
MantidVec& X = localWorkspace->dataX(wsIndex);
MantidVec& Y = localWorkspace->dataY(wsIndex);
MantidVec& E = localWorkspace->dataE(wsIndex);
- int nBins = counts.dim2();
- assert( nBins+1 == static_cast<int>(timeBins.size()) );
X.assign(timeBins.begin(),timeBins.end());
- int *data = &counts(period,spec,0);
+
+ int nBins = 0;
+ int *data = NULL;
+
+ if ( counts.rank() == 3 )
+ {
+ nBins = counts.dim2();
+ data = &counts(period,spec,0);
+ }
+ else if ( counts.rank() == 2 )
+ {
+ nBins = counts.dim1();
+ data = &counts(spec,0);
+ }
+ else
+ {
+ throw std::runtime_error("Data have unsupported dimansionality");
+ }
+ assert( nBins+1 == static_cast<int>(timeBins.size()) );
+
Y.assign(data,data+nBins);
typedef double (*uf)(double);
uf dblSqrt = std::sqrt;
@@ -357,7 +380,11 @@ namespace Mantid
}
ws->setTitle(entry.getString("title"));
- ws->setComment(entry.getString("notes"));
+
+ if ( entry.containsDataSet("notes") )
+ {
+ ws->setComment(entry.getString("notes"));
+ }
std::string run_num = boost::lexical_cast<std::string>(entry.getInt("run_number"));
//The sample is left to delete the property
@@ -366,86 +393,6 @@ namespace Mantid
ws->populateInstrumentParameters();
}
- /**This method does 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 LoadMuonNexus2::quickFileCheck(const std::string& filePath,size_t nread,const file_header& header)
- {
- std::string extn=extension(filePath);
- bool bnexs(false);
- (!extn.compare("nxs")||!extn.compare("nx5"))?bnexs=true:bnexs=false;
- /*
- * HDF files have magic cookie in the first 4 bytes
- */
- if ( ((nread >= sizeof(unsigned)) && (ntohl(header.four_bytes) == g_hdf_cookie)) || bnexs )
- {
- //hdf
- return true;
- }
- else if ( (nread >= sizeof(g_hdf5_signature)) && (!memcmp(header.full_hdr, g_hdf5_signature, sizeof(g_hdf5_signature))) )
- {
- //hdf5
- return true;
- }
- return false;
-
- }
- /**checks the file by opening it and reading few lines
- * @param filePath :: name of the file inluding its path
- * @return an integer value how much this algorithm can load the file
- */
- int LoadMuonNexus2::fileCheck(const std::string& filePath)
- {
- int confidence(0);
- std::string analysisType;
- try
- {
- ::NeXus::File file = ::NeXus::File(filePath);
- // Will throw if this doesn't exist
- file.openPath("/run/analysis");
- analysisType = file.getStrData();
- }
- catch(::NeXus::Exception&)
- {
- try
- {
- ::NeXus::File file = ::NeXus::File(filePath);
- file.openPath("/run/definition");
- analysisType = file.getStrData();
- }
- catch(::NeXus::Exception&)
- {
- //one last try - this is the area for PSI written files
- try
- {
- ::NeXus::File file = ::NeXus::File(filePath);
- file.openPath("/raw_data_1/definition");
- analysisType = file.getStrData();
- }
- catch(::NeXus::Exception&)
- {
- //no give up this doesn't look like a muon v2 file
- analysisType = "";
- }
- }
- }
- std::string compareString = "muon";
- if( analysisType == "pulsedTD" )
- {
- confidence = 85;
- }
- else if( analysisType.compare(0,compareString.length(),compareString) == 0 )
- {
- confidence = 50;
- }
- else confidence = 0;
-
- return confidence;
- }
-
/** Log the run details from the file
* @param localWorkspace :: The workspace details to use
*/
@@ -460,28 +407,29 @@ namespace Mantid
m_filename = getPropertyValue("Filename");
NXRoot root(m_filename);
+ NXEntry entry = root.openEntry(m_entry_name);
- std::string start_time = root.getString("run/start_time");
+ std::string start_time = entry.getString("start_time");
runDetails.addProperty("run_start", start_time);
- std::string stop_time = root.getString("run/end_time");
+ std::string stop_time = entry.getString("end_time");
runDetails.addProperty("run_end", stop_time);
-
- NXEntry runRun = root.openEntry("run/run");
-
- NXInfo infoGoodTotalFrames = runRun.getDataSetInfo("good_total_frames");
- if (infoGoodTotalFrames.stat != NX_ERROR)
+ if ( entry.containsGroup( "run" ) )
{
- int dum = root.getInt("run/run/good_total_frames");
- runDetails.addProperty("goodfrm", dum);
- }
+ NXClass runRun = entry.openNXGroup("run");
- NXInfo infoNumberPeriods = runRun.getDataSetInfo("number_periods");
- if (infoNumberPeriods.stat != NX_ERROR)
- {
- int dum = root.getInt("run/run/number_periods");
- runDetails.addProperty("nperiods", dum);
+ if ( runRun.containsDataSet("good_total_frames") )
+ {
+ int dum = runRun.getInt("good_total_frames");
+ runDetails.addProperty("goodfrm", dum);
+ }
+
+ if ( runRun.containsDataSet("number_periods") )
+ {
+ int dum = runRun.getInt("number_periods");
+ runDetails.addProperty("nperiods", dum);
+ }
}
{ // Duration taken to be stop_time minus stat_time
@@ -490,9 +438,37 @@ namespace Mantid
double duration_in_secs = DateAndTime::secondsFromDuration( end - start);
runDetails.addProperty("dur_secs",duration_in_secs);
}
+ }
-
-
+ /**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 LoadMuonNexus2::fileCheck(const std::string& filePath)
+ {
+ try
+ {
+ NXRoot root(filePath);
+ NXEntry entry = root.openFirstEntry();
+ if ( ! entry.containsDataSet( "definition" ) ) return 0;
+ std::string versionField = "IDF_version";
+ if ( ! entry.containsDataSet( versionField ) )
+ {
+ versionField = "idf_version";
+ if ( ! entry.containsDataSet( versionField ) ) return 0;
+ }
+ if ( entry.getInt( versionField ) != 2 ) return 0;
+ std::string definition = entry.getString( "definition" );
+ if ( definition == "muonTD" || definition == "pulsedTD" )
+ {
+ // If all this succeeded then we'll assume this is an ISIS Muon NeXus file version 2
+ return 81;
+ }
+ }
+ catch( ... )
+ {
+ }
+ return 0;
}
} // namespace DataHandling
diff --git a/Code/Mantid/Framework/DataHandling/test/GroupDetectors2Test.h b/Code/Mantid/Framework/DataHandling/test/GroupDetectors2Test.h
index c6f55455d95..70bf0c22b77 100644
--- a/Code/Mantid/Framework/DataHandling/test/GroupDetectors2Test.h
+++ b/Code/Mantid/Framework/DataHandling/test/GroupDetectors2Test.h
@@ -12,7 +12,7 @@
#include "MantidKernel/ArrayProperty.h"
#include "MantidKernel/Exception.h"
#include "MantidKernel/UnitFactory.h"
-#include "MantidDataHandling/LoadMuonNexus2.h"
+#include "MantidDataHandling/LoadMuonNexus1.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
#include <cxxtest/TestSuite.h>
#include <fstream>
@@ -351,7 +351,7 @@ public:
void testReadingFromXML()
{
- Mantid::DataHandling::LoadMuonNexus2 nxLoad;
+ Mantid::DataHandling::LoadMuonNexus1 nxLoad;
nxLoad.initialize();
// Now set required filename and output workspace name
@@ -391,7 +391,7 @@ public:
void testReadingFromXMLCheckDublicateIndex()
{
- Mantid::DataHandling::LoadMuonNexus2 nxLoad;
+ Mantid::DataHandling::LoadMuonNexus1 nxLoad;
nxLoad.initialize();
// Now set required filename and output workspace name
@@ -431,7 +431,7 @@ public:
void testReadingFromXMLCheckDublicateIndex2()
{
- Mantid::DataHandling::LoadMuonNexus2 nxLoad;
+ Mantid::DataHandling::LoadMuonNexus1 nxLoad;
nxLoad.initialize();
// Now set required filename and output workspace name
diff --git a/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus1Test.h b/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus1Test.h
new file mode 100644
index 00000000000..0e533d3d8cd
--- /dev/null
+++ b/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus1Test.h
@@ -0,0 +1,415 @@
+#ifndef LOADMUONNEXUS1TEST_H_
+#define LOADMUONNEXUS1TEST_H_
+
+
+
+// These includes seem to make the difference between initialization of the
+// workspace names (workspace2D/1D etc), instrument classes and not for this test case.
+#include "MantidDataObjects/WorkspaceSingleValue.h"
+#include "MantidDataHandling/LoadInstrument.h"
+//
+
+#include <fstream>
+#include <cxxtest/TestSuite.h>
+
+#include "MantidDataHandling/LoadMuonNexus1.h"
+#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidDataObjects/ManagedWorkspace2D.h"
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/FrameworkManager.h"
+#include "MantidKernel/ConfigService.h"
+#include "MantidKernel/TimeSeriesProperty.h"
+#include "MantidAPI/SpectraDetectorMap.h"
+#include <Poco/Path.h>
+
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+using namespace Mantid::DataHandling;
+using namespace Mantid::DataObjects;
+
+class LoadMuonNexus1Test : public CxxTest::TestSuite
+{
+public:
+
+
+ void testInit()
+ {
+ TS_ASSERT_THROWS_NOTHING(nxLoad.initialize());
+ TS_ASSERT( nxLoad.isInitialized() );
+ }
+
+
+ void testExec()
+ {
+ if ( !nxLoad.isInitialized() ) nxLoad.initialize();
+ // Should fail because mandatory parameter has not been set
+ TS_ASSERT_THROWS(nxLoad.execute(),std::runtime_error);
+
+ // Now set required filename and output workspace name
+ inputFile = "emu00006473.nxs";
+ nxLoad.setPropertyValue("FileName", inputFile);
+
+ outputSpace="outer";
+ nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
+
+ //
+ // Test execute to read file and populate workspace
+ //
+ TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
+ TS_ASSERT( nxLoad.isExecuted() );
+
+ // Test additional output parameters
+ std::string field = nxLoad.getProperty("MainFieldDirection");
+ TS_ASSERT( field == "Longitudinal" );
+
+ //
+ // Test workspace data (copied from LoadRawTest.h)
+ //
+ MatrixWorkspace_sptr output;
+ output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace);
+ Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
+ // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006473.nxs";
+ TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
+ // Check two X vectors are the same
+ TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
+ // Check two Y arrays have the same number of elements
+ TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
+ // Check one particular value
+ TS_ASSERT_EQUALS( output2D->dataY(11)[686], 81);
+ // Check that the error on that value is correct
+ TS_ASSERT_EQUALS( output2D->dataE(11)[686], 9);
+ // Check that the time is as expected from bin boundary update
+ TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
+
+ // Check the unit has been set correctly
+ TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
+ TS_ASSERT( ! output-> isDistribution() );
+
+ /* - other tests from LoadRawTest - These test data not in current Nexus files
+ //----------------------------------------------------------------------
+ // Tests taken from LoadInstrumentTest to check Child Algorithm is running properly
+ //----------------------------------------------------------------------
+ boost::shared_ptr<Instrument> i = output->getInstrument();
+ Mantid::Geometry::Component* source = i->getSource();
+
+ TS_ASSERT_EQUALS( source->getName(), "undulator");
+ TS_ASSERT_DELTA( source->getPos().Y(), 0.0,0.01);
+
+ Mantid::Geometry::Component* samplepos = i->getSample();
+ TS_ASSERT_EQUALS( samplepos->getName(), "nickel-holder");
+ TS_ASSERT_DELTA( samplepos->getPos().Y(), 10.0,0.01);
+
+ Mantid::Geometry::Detector *ptrDet103 = dynamic_cast<Mantid::Geometry::Detector*>(i->getDetector(103));
+ TS_ASSERT_EQUALS( ptrDet103->getID(), 103);
+ TS_ASSERT_EQUALS( ptrDet103->getName(), "pixel");
+ TS_ASSERT_DELTA( ptrDet103->getPos().X(), 0.4013,0.01);
+ TS_ASSERT_DELTA( ptrDet103->getPos().Z(), 2.4470,0.01);
+ */
+ //----------------------------------------------------------------------
+ // Test code copied from LoadLogTest to check Child Algorithm is running properly
+ //----------------------------------------------------------------------
+ //boost::shared_ptr<Sample> sample = output->getSample();
+ Property *l_property = output->run().getLogData( std::string("beamlog_current") );
+ TimeSeriesProperty<double> *l_timeSeriesDouble = dynamic_cast<TimeSeriesProperty<double>*>(l_property);
+ std::string timeSeriesString = l_timeSeriesDouble->value();
+ TS_ASSERT_EQUALS( timeSeriesString.substr(0,27), "2006-Nov-21 07:03:08 182.8" );
+ //check that sample name has been set correctly
+ TS_ASSERT_EQUALS(output->sample().getName(), "Cr2.7Co0.3Si");
+
+ /*
+ //----------------------------------------------------------------------
+ // Tests to check that Loading SpectraDetectorMap is done correctly
+ //----------------------------------------------------------------------
+ map= output->getSpectraMap();
+
+ // Check the total number of elements in the map for HET
+ TS_ASSERT_EQUALS(map->nElements(),24964);
+
+ // Test one to one mapping, for example spectra 6 has only 1 pixel
+ TS_ASSERT_EQUALS(map->ndet(6),1);
+
+ // Test one to many mapping, for example 10 pixels contribute to spectra 2084
+ TS_ASSERT_EQUALS(map->ndet(2084),10);
+ // Check the id number of all pixels contributing
+ std::vector<Mantid::Geometry::IDetector*> detectorgroup;
+ detectorgroup=map->getDetectors(2084);
+ std::vector<Mantid::Geometry::IDetector*>::iterator it;
+ int pixnum=101191;
+ for (it=detectorgroup.begin();it!=detectorgroup.end();it++)
+ TS_ASSERT_EQUALS((*it)->getID(),pixnum++);
+
+ // Test with spectra that does not exist
+ // Test that number of pixel=0
+ TS_ASSERT_EQUALS(map->ndet(5),0);
+ // Test that trying to get the Detector throws.
+ boost::shared_ptr<Mantid::Geometry::IDetector> test;
+ TS_ASSERT_THROWS(test=map->getDetector(5),std::runtime_error);
+ */
+
+ }
+// void testWithManagedWorkspace()
+// {
+// ConfigService::Instance().updateConfig("UseManagedWS.properties");
+// //LoadRaw loader4;
+// //loader4.initialize();
+// //loader4.setPropertyValue("Filename", inputFile);
+// //loader4.setPropertyValue("OutputWorkspace", "managedws");
+// // TS_ASSERT_THROWS_NOTHING( loader4.execute() )
+// //TS_ASSERT( loader4.isExecuted() )
+//
+// // Get back workspace and check it really is a ManagedWorkspace2D
+// MatrixWorkspace_sptr output;
+// TS_ASSERT_THROWS_NOTHING( output = AnalysisDataService::Instance().retrieve("managedws") );
+// TS_ASSERT( dynamic_cast<ManagedWorkspace2D*>(output.get()) )
+// }
+
+
+
+ void testTransvereDataset()
+ {
+ LoadMuonNexus1 nxL;
+ if ( !nxL.isInitialized() ) nxL.initialize();
+
+ // Now set required filename and output workspace name
+ std::string inputFile_musr00022725 = "MUSR00022725.nxs";
+ nxL.setPropertyValue("FileName", inputFile_musr00022725);
+
+ outputSpace="outermusr00022725";
+ nxL.setPropertyValue("OutputWorkspace", outputSpace);
+
+ TS_ASSERT_THROWS_NOTHING(nxL.execute());
+ TS_ASSERT( nxL.isExecuted() );
+
+ // Test additional output parameters
+ std::string field = nxL.getProperty("MainFieldDirection");
+ TS_ASSERT( field == "Transverse" );
+ double timeZero = nxL.getProperty("TimeZero");
+ TS_ASSERT_DELTA( timeZero, 0.55,0.001);
+ double firstgood = nxL.getProperty("FirstGoodData");
+ TS_ASSERT_DELTA( firstgood, 0.656,0.001);
+ std::vector<double> deadTimes = nxL.getProperty("DeadTimes");
+ TS_ASSERT_DELTA( deadTimes[0], 0.006,0.001);
+ TS_ASSERT_DELTA( deadTimes[deadTimes.size()-1], 0.011,0.001);
+ }
+
+ void testExec2()
+ {
+ //test for multi period
+ // Now set required filename and output workspace name
+ inputFile2 = "emu00006475.nxs";
+ nxLoad.setPropertyValue("FileName", inputFile2);
+
+ outputSpace="outer2";
+ nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
+ nxLoad.setPropertyValue("EntryNumber", "1");
+ int64_t entryNumber=nxLoad.getProperty("EntryNumber");
+
+ //
+ // Test execute to read file and populate workspace
+ //
+ TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
+ TS_ASSERT( nxLoad.isExecuted() );
+ //
+ // Test workspace data - should be 4 separate workspaces for this 4 period file
+ //
+ if(entryNumber==0)
+ {
+ WorkspaceGroup_sptr outGrp;
+ TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
+
+ }
+ //if entry number is given
+ if(entryNumber==1)
+ {
+ MatrixWorkspace_sptr output;
+ output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace);
+
+ Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
+ //Workspace2D_sptr output2D2 = boost::dynamic_pointer_cast<Workspace2D>(output2);
+ // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006475.nxs";
+ TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
+ // Check two X vectors are the same
+ TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
+ // Check two Y arrays have the same number of elements
+ TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
+ // Check that the time is as expected from bin boundary update
+ TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
+
+ // Check the unit has been set correctly
+ TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
+ TS_ASSERT( ! output-> isDistribution() );
+
+ //check that sample name has been set correctly
+ //boost::shared_ptr<Sample> sample,sample2;
+ //sample = output->getSample();
+ //sample2 = output2->getSample();
+ //TS_ASSERT_EQUALS(sample->getName(), sample2->getName());
+ TS_ASSERT_EQUALS(output->sample().getName(), "ptfe test");
+
+ }
+ MatrixWorkspace_sptr output,output2,output3,output4;
+ WorkspaceGroup_sptr outGrp;
+ //if no entry number load the group workspace
+ if(entryNumber==0)
+ {
+ TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
+
+ (output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_1"));
+ (output2 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_2"));
+ (output3 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_3"));
+ (output4 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_4"));
+
+ Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
+ Workspace2D_sptr output2D2 = boost::dynamic_pointer_cast<Workspace2D>(output2);
+ // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006475.nxs";
+ TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
+ // Check two X vectors are the same
+ TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
+ // Check two Y arrays have the same number of elements
+ TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
+ // Check one particular value
+ TS_ASSERT_EQUALS( output2D2->dataY(8)[502], 121);
+ // Check that the error on that value is correct
+ TS_ASSERT_EQUALS( output2D2->dataE(8)[502], 11);
+ // Check that the time is as expected from bin boundary update
+ TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
+
+ // Check the unit has been set correctly
+ TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
+ TS_ASSERT( ! output-> isDistribution() );
+
+ //check that sample name has been set correctly
+ // boost::shared_ptr<Sample> sample,sample2;
+ //sample = output->getSample();
+ // sample2 = output2->getSample();
+ TS_ASSERT_EQUALS(output->sample().getName(), output2->sample().getName());
+ TS_ASSERT_EQUALS(output->sample().getName(), "ptfe test");
+
+ }
+ }
+ void testExec2withZeroEntryNumber()
+ {
+ //test for multi period
+ // Now set required filename and output workspace name
+ inputFile2 = "emu00006475.nxs";
+ nxLoad.setPropertyValue("FileName", inputFile2);
+
+ outputSpace="outer2";
+ nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
+ nxLoad.setPropertyValue("EntryNumber", "0");
+ int64_t entryNumber=nxLoad.getProperty("EntryNumber");
+
+ //
+ // Test execute to read file and populate workspace
+ //
+ TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
+ TS_ASSERT( nxLoad.isExecuted() );
+ //
+ // Test workspace data - should be 4 separate workspaces for this 4 period file
+ //
+ WorkspaceGroup_sptr outGrp;
+ TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
+
+ MatrixWorkspace_sptr output,output2,output3,output4;
+ //WorkspaceGroup_sptr outGrp;
+ //if no entry number load the group workspace
+ if(entryNumber==0)
+ {
+ //TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
+
+ (output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_1"));
+ (output2 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_2"));
+ (output3 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_3"));
+ (output4 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_4"));
+
+ Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
+ Workspace2D_sptr output2D2 = boost::dynamic_pointer_cast<Workspace2D>(output2);
+ // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006475.nxs";
+ TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
+ // Check two X vectors are the same
+ TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
+ // Check two Y arrays have the same number of elements
+ TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
+ // Check one particular value
+ TS_ASSERT_EQUALS( output2D2->dataY(8)[502], 121);
+ // Check that the error on that value is correct
+ TS_ASSERT_EQUALS( output2D2->dataE(8)[502], 11);
+ // Check that the time is as expected from bin boundary update
+ TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
+
+ // Check the unit has been set correctly
+ TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
+ TS_ASSERT( ! output-> isDistribution() );
+
+ //check that sample name has been set correctly
+ //boost::shared_ptr<Sample> sample,sample2;
+ // sample = output->getSample();
+ // sample2 = output2->getSample();
+ TS_ASSERT_EQUALS(output->sample().getName(), output2->sample().getName());
+ TS_ASSERT_EQUALS(output->sample().getName(), "ptfe test");
+
+ }
+ }
+
+ void testarrayin()
+ {
+ if ( !nxload3.isInitialized() ) nxload3.initialize();
+
+ nxload3.setPropertyValue("Filename", inputFile);
+ nxload3.setPropertyValue("OutputWorkspace", "outWS");
+ nxload3.setPropertyValue("SpectrumList", "29,30,31");
+ nxload3.setPropertyValue("SpectrumMin", "5");
+ nxload3.setPropertyValue("SpectrumMax", "10");
+
+ TS_ASSERT_THROWS_NOTHING(nxload3.execute());
+ TS_ASSERT( nxload3.isExecuted() );
+
+ // Get back the saved workspace
+ MatrixWorkspace_sptr output;
+ (output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>("outWS"));
+ Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
+
+ // Should be 6 for selected input
+ TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 9);
+
+ // Check two X vectors are the same
+ TS_ASSERT( (output2D->dataX(1)) == (output2D->dataX(5)) );
+
+ // Check two Y arrays have the same number of elements
+ TS_ASSERT_EQUALS( output2D->dataY(2).size(), output2D->dataY(7).size() );
+
+ // Check one particular value
+ TS_ASSERT_EQUALS( output2D->dataY(8)[479], 144);
+ // Check that the error on that value is correct
+ TS_ASSERT_EQUALS( output2D->dataE(8)[479], 12);
+ // Check that the error on that value is correct
+ TS_ASSERT_DELTA( output2D->dataX(8)[479], 7.410, 0.0001);
+ }
+
+private:
+ LoadMuonNexus1 nxLoad,nxload2,nxload3;
+ std::string outputSpace;
+ std::string entryName;
+ std::string inputFile;
+ std::string inputFile2;
+ boost::shared_ptr<SpectraDetectorMap> map;
+};
+
+////------------------------------------------------------------------------------
+//// Performance test
+////------------------------------------------------------------------------------
+//
+//class LoadMuonNexus1TestPerformance : public CxxTest::TestSuite
+//{
+//public:
+// void testDefaultLoad()
+// {
+// LoadMuonNexus1 loader;
+// loader.initialize();
+// loader.setPropertyValue("Filename", "deltat_tdc_gpd_0900.nxs");
+// loader.setPropertyValue("OutputWorkspace", "ws");
+// TS_ASSERT( loader.execute() );
+// }
+//};
+//
+#endif /*LOADMUONNEXUS1TEST_H_*/
diff --git a/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus2Test.h b/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus2Test.h
index a3bb3d00845..17909c0d7de 100644
--- a/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus2Test.h
+++ b/Code/Mantid/Framework/DataHandling/test/LoadMuonNexus2Test.h
@@ -358,7 +358,7 @@ public:
check_spectra_and_detectors(output);
- AnalysisDataService::Instance().remove(outputSpace);
+ AnalysisDataService::Instance().clear();
}
void testExec2()
@@ -443,9 +443,69 @@ public:
check_spectra_and_detectors(output);
- AnalysisDataService::Instance().remove(outputSpace);
+ AnalysisDataService::Instance().clear();
}
+ void test_gpd_file()
+ {
+ LoadMuonNexus2 nxLoad;
+ nxLoad.initialize();
+
+ // Now set required filename and output workspace name
+ std::string inputFile = "deltat_tdc_gpd_0900.nxs";
+ nxLoad.setPropertyValue("FileName", inputFile);
+
+ std::string outputSpace="outer";
+ nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
+
+ //
+ // Test execute to read file and populate workspace
+ //
+ TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
+ TS_ASSERT( nxLoad.isExecuted() );
+
+ //
+ // Test additional output parameters
+ //
+ std::string field = nxLoad.getProperty("MainFieldDirection");
+ TS_ASSERT( field == "Transverse" );
+ // TimeZero and FirstGoodData are not read yet so they are 0
+ double timeZero = nxLoad.getProperty("TimeZero");
+ TS_ASSERT_DELTA( timeZero, 0.0,0.001);
+ double firstgood = nxLoad.getProperty("FirstGoodData");
+ TS_ASSERT_DELTA( firstgood, 0.0,0.001);
+
+ //
+ // Test workspace data
+ //
+ MatrixWorkspace_sptr output;
+ output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace);
+ Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
+ // Should be 192 for file inputFile = "argus0026287.nxs";
+ TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 2);
+ TS_ASSERT_EQUALS( output2D->blocksize(), 8192);
+ // Check two X vectors are the same
+ TS_ASSERT( (output2D->dataX(0)) == (output2D->dataX(1)) );
+ // Check two Y arrays have the same number of elements
+ TS_ASSERT_EQUALS( output2D->dataY(0).size(), output2D->dataY(1).size() );
+ // Check one particular value
+ TS_ASSERT_EQUALS( output2D->dataY(0)[686], 516);
+ TS_ASSERT_EQUALS( output2D->dataY(0)[687], 413);
+ TS_ASSERT_EQUALS( output2D->dataY(1)[686], 381);
+
+ // Check that the error on that value is correct
+ TS_ASSERT_DELTA( output2D->dataE(0)[686], 22.7156,0.001);
+ TS_ASSERT_DELTA( output2D->dataE(0)[687], 20.3224,0.001);
+ TS_ASSERT_DELTA( output2D->dataE(1)[686], 19.5192,0.001);
+ // Check that the time is as expected from bin boundary update
+ TS_ASSERT_DELTA( output2D->dataX(1)[687], 0.8050,0.001);
+
+ // Check the unit has been set correctly
+ TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
+ TS_ASSERT( ! output-> isDistribution() );
+
+ AnalysisDataService::Instance().remove(outputSpace);
+ }
};
//------------------------------------------------------------------------------
diff --git a/Code/Mantid/Framework/DataHandling/test/LoadMuonNexusTest.h b/Code/Mantid/Framework/DataHandling/test/LoadMuonNexusTest.h
index 6c62b27823a..3bbae100287 100644
--- a/Code/Mantid/Framework/DataHandling/test/LoadMuonNexusTest.h
+++ b/Code/Mantid/Framework/DataHandling/test/LoadMuonNexusTest.h
@@ -1,397 +1,20 @@
#ifndef LOADMUONNEXUSTEST_H_
#define LOADMUONNEXUSTEST_H_
-
-
-// These includes seem to make the difference between initialization of the
-// workspace names (workspace2D/1D etc), instrument classes and not for this test case.
-#include "MantidDataObjects/WorkspaceSingleValue.h"
-#include "MantidDataHandling/LoadInstrument.h"
-//
-
-#include <fstream>
#include <cxxtest/TestSuite.h>
-#include "MantidDataHandling/LoadMuonNexus.h"
-#include "MantidAPI/WorkspaceFactory.h"
-#include "MantidDataObjects/ManagedWorkspace2D.h"
-#include "MantidAPI/AnalysisDataService.h"
-#include "MantidAPI/FrameworkManager.h"
-#include "MantidKernel/ConfigService.h"
-#include "MantidKernel/TimeSeriesProperty.h"
-#include "MantidAPI/SpectraDetectorMap.h"
-#include <Poco/Path.h>
+#include "MantidDataHandling/LoadMuonNexus3.h"
-using namespace Mantid::API;
-using namespace Mantid::Kernel;
using namespace Mantid::DataHandling;
-using namespace Mantid::DataObjects;
class LoadMuonNexusTest : public CxxTest::TestSuite
{
public:
-
- void testInit()
- {
- TS_ASSERT_THROWS_NOTHING(nxLoad.initialize());
- TS_ASSERT( nxLoad.isInitialized() );
- }
-
-
void testExec()
{
- if ( !nxLoad.isInitialized() ) nxLoad.initialize();
- // Should fail because mandatory parameter has not been set
- TS_ASSERT_THROWS(nxLoad.execute(),std::runtime_error);
-
- // Now set required filename and output workspace name
- inputFile = "emu00006473.nxs";
- nxLoad.setPropertyValue("FileName", inputFile);
-
- outputSpace="outer";
- nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
-
- //
- // Test execute to read file and populate workspace
- //
- TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
- TS_ASSERT( nxLoad.isExecuted() );
-
- // Test additional output parameters
- std::string field = nxLoad.getProperty("MainFieldDirection");
- TS_ASSERT( field == "Longitudinal" );
-
- //
- // Test workspace data (copied from LoadRawTest.h)
- //
- MatrixWorkspace_sptr output;
- output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace);
- Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
- // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006473.nxs";
- TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
- // Check two X vectors are the same
- TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
- // Check two Y arrays have the same number of elements
- TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
- // Check one particular value
- TS_ASSERT_EQUALS( output2D->dataY(11)[686], 81);
- // Check that the error on that value is correct
- TS_ASSERT_EQUALS( output2D->dataE(11)[686], 9);
- // Check that the time is as expected from bin boundary update
- TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
-
- // Check the unit has been set correctly
- TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
- TS_ASSERT( ! output-> isDistribution() );
-
- /* - other tests from LoadRawTest - These test data not in current Nexus files
- //----------------------------------------------------------------------
- // Tests taken from LoadInstrumentTest to check Child Algorithm is running properly
- //----------------------------------------------------------------------
- boost::shared_ptr<Instrument> i = output->getInstrument();
- Mantid::Geometry::Component* source = i->getSource();
-
- TS_ASSERT_EQUALS( source->getName(), "undulator");
- TS_ASSERT_DELTA( source->getPos().Y(), 0.0,0.01);
-
- Mantid::Geometry::Component* samplepos = i->getSample();
- TS_ASSERT_EQUALS( samplepos->getName(), "nickel-holder");
- TS_ASSERT_DELTA( samplepos->getPos().Y(), 10.0,0.01);
-
- Mantid::Geometry::Detector *ptrDet103 = dynamic_cast<Mantid::Geometry::Detector*>(i->getDetector(103));
- TS_ASSERT_EQUALS( ptrDet103->getID(), 103);
- TS_ASSERT_EQUALS( ptrDet103->getName(), "pixel");
- TS_ASSERT_DELTA( ptrDet103->getPos().X(), 0.4013,0.01);
- TS_ASSERT_DELTA( ptrDet103->getPos().Z(), 2.4470,0.01);
- */
- //----------------------------------------------------------------------
- // Test code copied from LoadLogTest to check Child Algorithm is running properly
- //----------------------------------------------------------------------
- //boost::shared_ptr<Sample> sample = output->getSample();
- Property *l_property = output->run().getLogData( std::string("beamlog_current") );
- TimeSeriesProperty<double> *l_timeSeriesDouble = dynamic_cast<TimeSeriesProperty<double>*>(l_property);
- std::string timeSeriesString = l_timeSeriesDouble->value();
- TS_ASSERT_EQUALS( timeSeriesString.substr(0,27), "2006-Nov-21 07:03:08 182.8" );
- //check that sample name has been set correctly
- TS_ASSERT_EQUALS(output->sample().getName(), "Cr2.7Co0.3Si");
-
- /*
- //----------------------------------------------------------------------
- // Tests to check that Loading SpectraDetectorMap is done correctly
- //----------------------------------------------------------------------
- map= output->getSpectraMap();
-
- // Check the total number of elements in the map for HET
- TS_ASSERT_EQUALS(map->nElements(),24964);
-
- // Test one to one mapping, for example spectra 6 has only 1 pixel
- TS_ASSERT_EQUALS(map->ndet(6),1);
-
- // Test one to many mapping, for example 10 pixels contribute to spectra 2084
- TS_ASSERT_EQUALS(map->ndet(2084),10);
- // Check the id number of all pixels contributing
- std::vector<Mantid::Geometry::IDetector*> detectorgroup;
- detectorgroup=map->getDetectors(2084);
- std::vector<Mantid::Geometry::IDetector*>::iterator it;
- int pixnum=101191;
- for (it=detectorgroup.begin();it!=detectorgroup.end();it++)
- TS_ASSERT_EQUALS((*it)->getID(),pixnum++);
-
- // Test with spectra that does not exist
- // Test that number of pixel=0
- TS_ASSERT_EQUALS(map->ndet(5),0);
- // Test that trying to get the Detector throws.
- boost::shared_ptr<Mantid::Geometry::IDetector> test;
- TS_ASSERT_THROWS(test=map->getDetector(5),std::runtime_error);
- */
-
}
-// void testWithManagedWorkspace()
-// {
-// ConfigService::Instance().updateConfig("UseManagedWS.properties");
-// //LoadRaw loader4;
-// //loader4.initialize();
-// //loader4.setPropertyValue("Filename", inputFile);
-// //loader4.setPropertyValue("OutputWorkspace", "managedws");
-// // TS_ASSERT_THROWS_NOTHING( loader4.execute() )
-// //TS_ASSERT( loader4.isExecuted() )
-//
-// // Get back workspace and check it really is a ManagedWorkspace2D
-// MatrixWorkspace_sptr output;
-// TS_ASSERT_THROWS_NOTHING( output = AnalysisDataService::Instance().retrieve("managedws") );
-// TS_ASSERT( dynamic_cast<ManagedWorkspace2D*>(output.get()) )
-// }
-
-
- void testTransvereDataset()
- {
- LoadMuonNexus nxL;
- if ( !nxL.isInitialized() ) nxL.initialize();
-
- // Now set required filename and output workspace name
- std::string inputFile_musr00022725 = "MUSR00022725.nxs";
- nxL.setPropertyValue("FileName", inputFile_musr00022725);
-
- outputSpace="outermusr00022725";
- nxL.setPropertyValue("OutputWorkspace", outputSpace);
-
- TS_ASSERT_THROWS_NOTHING(nxL.execute());
- TS_ASSERT( nxL.isExecuted() );
-
- // Test additional output parameters
- std::string field = nxL.getProperty("MainFieldDirection");
- TS_ASSERT( field == "Transverse" );
- double timeZero = nxL.getProperty("TimeZero");
- TS_ASSERT_DELTA( timeZero, 0.55,0.001);
- double firstgood = nxL.getProperty("FirstGoodData");
- TS_ASSERT_DELTA( firstgood, 0.656,0.001);
- std::vector<double> deadTimes = nxL.getProperty("DeadTimes");
- TS_ASSERT_DELTA( deadTimes[0], 0.006,0.001);
- TS_ASSERT_DELTA( deadTimes[deadTimes.size()-1], 0.011,0.001);
- }
-
- void testExec2()
- {
- //test for multi period
- // Now set required filename and output workspace name
- inputFile2 = "emu00006475.nxs";
- nxLoad.setPropertyValue("FileName", inputFile2);
-
- outputSpace="outer2";
- nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
- nxLoad.setPropertyValue("EntryNumber", "1");
- int64_t entryNumber=nxLoad.getProperty("EntryNumber");
-
- //
- // Test execute to read file and populate workspace
- //
- TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
- TS_ASSERT( nxLoad.isExecuted() );
- //
- // Test workspace data - should be 4 separate workspaces for this 4 period file
- //
- if(entryNumber==0)
- {
- WorkspaceGroup_sptr outGrp;
- TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
-
- }
- //if entry number is given
- if(entryNumber==1)
- {
- MatrixWorkspace_sptr output;
- output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace);
-
- Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
- //Workspace2D_sptr output2D2 = boost::dynamic_pointer_cast<Workspace2D>(output2);
- // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006475.nxs";
- TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
- // Check two X vectors are the same
- TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
- // Check two Y arrays have the same number of elements
- TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
- // Check that the time is as expected from bin boundary update
- TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
-
- // Check the unit has been set correctly
- TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
- TS_ASSERT( ! output-> isDistribution() );
-
- //check that sample name has been set correctly
- //boost::shared_ptr<Sample> sample,sample2;
- //sample = output->getSample();
- //sample2 = output2->getSample();
- //TS_ASSERT_EQUALS(sample->getName(), sample2->getName());
- TS_ASSERT_EQUALS(output->sample().getName(), "ptfe test");
-
- }
- MatrixWorkspace_sptr output,output2,output3,output4;
- WorkspaceGroup_sptr outGrp;
- //if no entry number load the group workspace
- if(entryNumber==0)
- {
- TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
-
- (output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_1"));
- (output2 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_2"));
- (output3 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_3"));
- (output4 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_4"));
-
- Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
- Workspace2D_sptr output2D2 = boost::dynamic_pointer_cast<Workspace2D>(output2);
- // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006475.nxs";
- TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
- // Check two X vectors are the same
- TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
- // Check two Y arrays have the same number of elements
- TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
- // Check one particular value
- TS_ASSERT_EQUALS( output2D2->dataY(8)[502], 121);
- // Check that the error on that value is correct
- TS_ASSERT_EQUALS( output2D2->dataE(8)[502], 11);
- // Check that the time is as expected from bin boundary update
- TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
-
- // Check the unit has been set correctly
- TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
- TS_ASSERT( ! output-> isDistribution() );
-
- //check that sample name has been set correctly
- // boost::shared_ptr<Sample> sample,sample2;
- //sample = output->getSample();
- // sample2 = output2->getSample();
- TS_ASSERT_EQUALS(output->sample().getName(), output2->sample().getName());
- TS_ASSERT_EQUALS(output->sample().getName(), "ptfe test");
-
- }
- }
- void testExec2withZeroEntryNumber()
- {
- //test for multi period
- // Now set required filename and output workspace name
- inputFile2 = "emu00006475.nxs";
- nxLoad.setPropertyValue("FileName", inputFile2);
-
- outputSpace="outer2";
- nxLoad.setPropertyValue("OutputWorkspace", outputSpace);
- nxLoad.setPropertyValue("EntryNumber", "0");
- int64_t entryNumber=nxLoad.getProperty("EntryNumber");
-
- //
- // Test execute to read file and populate workspace
- //
- TS_ASSERT_THROWS_NOTHING(nxLoad.execute());
- TS_ASSERT( nxLoad.isExecuted() );
- //
- // Test workspace data - should be 4 separate workspaces for this 4 period file
- //
- WorkspaceGroup_sptr outGrp;
- TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
-
- MatrixWorkspace_sptr output,output2,output3,output4;
- //WorkspaceGroup_sptr outGrp;
- //if no entry number load the group workspace
- if(entryNumber==0)
- {
- //TS_ASSERT_THROWS_NOTHING(outGrp = AnalysisDataService::Instance().retrieveWS<WorkspaceGroup>(outputSpace));
-
- (output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_1"));
- (output2 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_2"));
- (output3 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_3"));
- (output4 = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(outputSpace+"_4"));
-
- Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
- Workspace2D_sptr output2D2 = boost::dynamic_pointer_cast<Workspace2D>(output2);
- // Should be 32 for file inputFile = "../../../../Test/Nexus/emu00006475.nxs";
- TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 32);
- // Check two X vectors are the same
- TS_ASSERT( (output2D->dataX(3)) == (output2D->dataX(31)) );
- // Check two Y arrays have the same number of elements
- TS_ASSERT_EQUALS( output2D->dataY(5).size(), output2D->dataY(17).size() );
- // Check one particular value
- TS_ASSERT_EQUALS( output2D2->dataY(8)[502], 121);
- // Check that the error on that value is correct
- TS_ASSERT_EQUALS( output2D2->dataE(8)[502], 11);
- // Check that the time is as expected from bin boundary update
- TS_ASSERT_DELTA( output2D->dataX(11)[687], 10.738,0.001);
-
- // Check the unit has been set correctly
- TS_ASSERT_EQUALS( output->getAxis(0)->unit()->unitID(), "Label" );
- TS_ASSERT( ! output-> isDistribution() );
-
- //check that sample name has been set correctly
- //boost::shared_ptr<Sample> sample,sample2;
- // sample = output->getSample();
- // sample2 = output2->getSample();
- TS_ASSERT_EQUALS(output->sample().getName(), output2->sample().getName());
- TS_ASSERT_EQUALS(output->sample().getName(), "ptfe test");
-
- }
- }
-
- void testarrayin()
- {
- if ( !nxload3.isInitialized() ) nxload3.initialize();
-
- nxload3.setPropertyValue("Filename", inputFile);
- nxload3.setPropertyValue("OutputWorkspace", "outWS");
- nxload3.setPropertyValue("SpectrumList", "29,30,31");
- nxload3.setPropertyValue("SpectrumMin", "5");
- nxload3.setPropertyValue("SpectrumMax", "10");
-
- TS_ASSERT_THROWS_NOTHING(nxload3.execute());
- TS_ASSERT( nxload3.isExecuted() );
-
- // Get back the saved workspace
- MatrixWorkspace_sptr output;
- (output = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>("outWS"));
- Workspace2D_sptr output2D = boost::dynamic_pointer_cast<Workspace2D>(output);
-
- // Should be 6 for selected input
- TS_ASSERT_EQUALS( output2D->getNumberHistograms(), 9);
-
- // Check two X vectors are the same
- TS_ASSERT( (output2D->dataX(1)) == (output2D->dataX(5)) );
-
- // Check two Y arrays have the same number of elements
- TS_ASSERT_EQUALS( output2D->dataY(2).size(), output2D->dataY(7).size() );
-
- // Check one particular value
- TS_ASSERT_EQUALS( output2D->dataY(8)[479], 144);
- // Check that the error on that value is correct
- TS_ASSERT_EQUALS( output2D->dataE(8)[479], 12);
- // Check that the error on that value is correct
- TS_ASSERT_DELTA( output2D->dataX(8)[479], 7.410, 0.0001);
- }
-
-private:
- LoadMuonNexus nxLoad,nxload2,nxload3;
- std::string outputSpace;
- std::string entryName;
- std::string inputFile;
- std::string inputFile2;
- boost::shared_ptr<SpectraDetectorMap> map;
};
+
#endif /*LOADMUONNEXUSTEST_H_*/
diff --git a/Code/Mantid/Framework/Nexus/inc/MantidNexus/NexusClasses.h b/Code/Mantid/Framework/Nexus/inc/MantidNexus/NexusClasses.h
index 1a215c19913..f63827b2aed 100644
--- a/Code/Mantid/Framework/Nexus/inc/MantidNexus/NexusClasses.h
+++ b/Code/Mantid/Framework/Nexus/inc/MantidNexus/NexusClasses.h
@@ -399,7 +399,7 @@ namespace Mantid
alloc(n);
getSlab(m_data.get(),start,m_size);
}
- protected:
+ private:
/** Allocates memory for the data buffer
* @param n :: The number of elements to allocate.
*/
@@ -559,7 +559,10 @@ namespace Mantid
* @return NXInfo::stat is set to NX_ERROR if the dataset does not exist
*/
NXInfo getDataSetInfo(const std::string& name)const;
- void close();///< Close this class
+ /// Returns whether an individual dataset is present
+ bool containsDataSet(const std::string & query) const;
+ /// Close this class
+ void close();
/// Opens this NXClass using NXopengrouppath. Can be slow (or is slow)
void open();
/// Opens this NXClass using NXopengroup. It is fast, but the parent of this class must be open at
diff --git a/Code/Mantid/Framework/Nexus/src/NexusClasses.cpp b/Code/Mantid/Framework/Nexus/src/NexusClasses.cpp
index ab7cf50613d..153924ee68d 100644
--- a/Code/Mantid/Framework/Nexus/src/NexusClasses.cpp
+++ b/Code/Mantid/Framework/Nexus/src/NexusClasses.cpp
@@ -307,6 +307,11 @@ bool NXClass::containsGroup(const std::string & query) const
return false;
}
+/**
+ * Returns NXInfo for a dataset
+ * @param name :: The name of the dataset
+ * @return NXInfo::stat is set to NX_ERROR if the dataset does not exist
+ */
NXInfo NXClass::getDataSetInfo(const std::string& name)const
{
NXInfo info;
@@ -318,6 +323,14 @@ NXInfo NXClass::getDataSetInfo(const std::string& name)const
return info;
}
+/**
+ * Returns whether an individual dataset is present.
+ */
+bool NXClass::containsDataSet(const std::string & query) const
+{
+ return getDataSetInfo( query ).stat != NX_ERROR;
+}
+
//---------------------------------------------------------
// NXNote methods
//---------------------------------------------------------
diff --git a/Test/AutoTestData/deltat_tdc_gpd_0900.nxs b/Test/AutoTestData/deltat_tdc_gpd_0900.nxs
new file mode 100644
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--
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