Refs #8590 Merge remote-tracking branch 'origin' into feature/8590

Conflicts:
	Code/Mantid/scripts/Interface/ui/reflectometer/refl_gui.py

Code/Mantid/Framework/API/inc/MantidAPI/ExperimentInfo.h

@@ -120,6 +120,8 @@ namespace API
     void saveExperimentInfoNexus(::NeXus::File * file) const;
     /// Loads an experiment description from the open NeXus file
     void loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr);
+    /// Load the sample and log info from an open NeXus file.
+    void loadSampleAndLogInfoNexus(::NeXus::File * file);
     /// Populate the parameter map given a string
     void readParameterMap(const std::string & parameterStr);
 

Code/Mantid/Framework/API/inc/MantidAPI/ICatalog.h

@@ -67,6 +67,8 @@ class DLLExport ICatalog
   virtual void getFileLocation(const long long&,std::string& )=0;
   /// get URLs of the files
   virtual void getDownloadURL(const long long& fileid,std::string&)=0;
+  /// get URL of where to PUT (publish) files.
+  virtual const std::string getUploadURL(const std::string &, const std::string &)=0;
   /// keep alive
   virtual void keepAlive()=0;
   ///keep alive in minutes

Code/Mantid/Framework/API/src/ExperimentInfo.cpp

@@ -864,19 +864,11 @@ namespace API
   }
 
   //--------------------------------------------------------------------------------------------
-  /** Load the object from an open NeXus file.
+  /** Load the sample and log info from an open NeXus file.
    * @param file :: open NeXus file
-   * @param[out] parameterStr :: special string for all the parameters.
-   *             Feed that to ExperimentInfo::readParameterMap() after the instrument is done.
-   * @throws Exception::NotFoundError If instrument definition is not in the nexus file and cannot
-   *                                  be loaded from the IDF.
    */
-  void ExperimentInfo::loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr)
+  void ExperimentInfo::loadSampleAndLogInfoNexus(::NeXus::File * file)
   {
-    std::string instrumentName;
-    std::string instrumentXml;
-    std::string instrumentFilename;
-
     // First, the sample and then the logs
     int sampleVersion = mutableSample().loadNexus(file, "sample");
     if (sampleVersion == 0)
@@ -892,6 +884,24 @@ namespace API
       // Newer style: separate "logs" field for the Run object
       this->mutableRun().loadNexus(file, "logs");
     }
+  }
+
+  //--------------------------------------------------------------------------------------------
+  /** Load the object from an open NeXus file.
+   * @param file :: open NeXus file
+   * @param[out] parameterStr :: special string for all the parameters.
+   *             Feed that to ExperimentInfo::readParameterMap() after the instrument is done.
+   * @throws Exception::NotFoundError If instrument definition is not in the nexus file and cannot
+   *                                  be loaded from the IDF.
+   */
+  void ExperimentInfo::loadExperimentInfoNexus(::NeXus::File * file, std::string & parameterStr)
+  {
+    // load sample and log info
+    loadSampleAndLogInfoNexus(file);
+
+    std::string instrumentName;
+    std::string instrumentXml;
+    std::string instrumentFilename;
 
     // Try to get the instrument file
     file->openGroup("instrument", "NXinstrument");

Code/Mantid/Framework/Algorithms/src/ExtractMaskToTable.cpp

@@ -1,9 +1,20 @@
 /*WIKI* 
-The masking from the InputWorkspace property is extracted by creating a new MatrixWorkspace with a single X bin where:
-* 0 = masked;
-* 1 = unmasked.
 
-The spectra containing 0 are also marked as masked and the instrument link is preserved so that the instrument view functions correctly.
+==== InputWorskpace ====
+It can be either a MaskWorkspace, containing the masking information, or a Data workspace (EventWorkspace or Workspace2D), having
+detectors masked.
+
+==== Optional MaskTableWorkspace ====
+If the optional input 'MaskTableWorkspace' is given, it must be a table workspace having the
+same format as output TableWorkspace such that it contains 3 columns, XMin, XMax and DetectorIDsList.
+
+The contents in this mask table workspace will be copied to output workspace.
+
+If a detector is masked in this input 'MaskTableWorkspace', and it is also masked in input MaskWorkspace or data workspace,
+the setup (Xmin and Xmax) in MaskTableWorkspace has higher priority, i.e., in the output mask table workspace,
+the masked detector will be recorded in the row copied from input MaskTableWrokspace.
+
+
 *WIKI*/
 
 #include "MantidAlgorithms/ExtractMaskToTable.h"
@@ -56,11 +67,11 @@ namespace Algorithms
     */
   void ExtractMaskToTable::init()
   {
-    auto inwsprop = new WorkspaceProperty<MatrixWorkspace>("InputWorkspace", "Anonymous", Direction::Input);
-    declareProperty(inwsprop, "A workspace whose masking is to be extracted");
+    auto inwsprop = new WorkspaceProperty<MatrixWorkspace>("InputWorkspace", "", Direction::Input);
+    declareProperty(inwsprop, "A workspace whose masking is to be extracted or a MaskWorkspace. ");
 
     auto intblprop = new WorkspaceProperty<TableWorkspace>("MaskTableWorkspace", "", Direction::Input, PropertyMode::Optional);
-    declareProperty(intblprop, "A workspace containing the masked spectra as zeroes and ones. ");
+    declareProperty(intblprop, "A mask table workspace containing 3 columns: XMin, XMax and DetectorIDsList. ");
 
     auto outwsprop = new WorkspaceProperty<TableWorkspace>("OutputWorkspace", "", Direction::Output);
     declareProperty(outwsprop, "A comma separated list or array containing a list of masked detector ID's ");
@@ -108,7 +119,7 @@ namespace Algorithms
     vector<detid_t> prevmaskeddetids;
     if (m_inputTableWS)
     {
-      g_log.notice("[To implement] Parse input table workspace.");
+      g_log.notice("Parse input masking table workspace.");
       parseMaskTable(m_inputTableWS, prevmaskeddetids);
     }
     else
@@ -143,12 +154,37 @@ namespace Algorithms
   //----------------------------------------------------------------------------------------------
   /** Parse input TableWorkspace to get a list of detectors IDs of which detector are already masked
     * @param masktablews :: TableWorkspace containing masking information
-    * @param maskeddetectorids :: List for holding masked detector IDs
+    * @param maskeddetectorids :: (output) vector of detector IDs that are masked
     */
   void ExtractMaskToTable::parseMaskTable(DataObjects::TableWorkspace_sptr masktablews, std::vector<detid_t>& maskeddetectorids)
   {
     // Clear input
-    maskeddetectorids.clear();;
+    maskeddetectorids.clear();
+
+    // Check format of mask table workspace
+    if (masktablews->columnCount() != 3)
+    {
+      g_log.error("Mask table workspace must have more than 3 columns.  First 3 must be Xmin, Xmax and Spectrum List.");
+      return;
+    }
+    else
+    {
+      vector<string> colnames = masktablews->getColumnNames();
+      vector<string> chkcolumans(3);
+      chkcolumans[0] = "XMin";
+      chkcolumans[1] = "XMax";
+      chkcolumans[2] = "DetectorIDsList";
+      for (int i = 0; i < 3; ++i)
+      {
+        if (colnames[i] != chkcolumans[i])
+        {
+          g_log.error() << "Mask table workspace " << masktablews->name() << "'s " << i << "-th column name is "
+                        << colnames[i] << ", while it should be " << chkcolumans[i] << ". MaskWorkspace is invalid"
+                        << " and thus not used.\n";
+          return;
+        }
+      }
+    }
 
     // Parse each row
     size_t numrows = masktablews->rowCount();
@@ -319,7 +355,8 @@ namespace Algorithms
   }
 
   //----------------------------------------------------------------------------------------------
-  /** Add a list of spectra (detector IDs) to the output table workspace
+  /** Add a list of spectra (detector IDs) to the output table workspace.
+    * If a detector is masked in input MaskTableWorkspace, then it will not be added to a new row
     * @param outws :: table workspace to write
     * @param maskeddetids :: vector of detector IDs of which detectors masked
     * @param xmin :: minumim x

Code/Mantid/Framework/Algorithms/src/GeneratePythonScript.cpp

@@ -1,22 +1,28 @@
 /*WIKI* 
 
-Accepts an input workspace and the name of a file.  Retrieves the algorithm history of the workspace, and then dumps it to file in the format of a Python script.  
+Retrieves the algorithm history of the workspace and saves it to a Python script file or Python variable.
 
-Example format:
+=== Example usage: ===
 
 <div style="border:1pt dashed black; background:#f9f9f9;padding: 1em 0;">
 <source lang="python">
- ######################################################################
- #Python Script Generated by GeneratePythonScript Algorithm
- ######################################################################
- LoadRaw(Filename='G:/Spencer/Science/Raw/irs26173.raw',OutputWorkspace='IPG',SpectrumMin='3',SpectrumMax='53')
- ConvertUnits(InputWorkspace='IPG',OutputWorkspace='Spec',Target='Wavelength')
- LoadRaw(Filename='G:/Spencer/Science/Raw/irs26173.raw',OutputWorkspace='Mon_in',SpectrumMax='1')
-</source></div>
+  # Optional: Store the contents of the workspace to a file to your desktop.
+  GeneratePythonScript("MUSR00022725", "/home/userName/Desktop/MUSR00022725.py")
 
-{{AlgorithmLinks|GeneratePythonScript}}
+  # Store the contents of the workspace history into the hist variable
+  wsHistory = GeneratePythonScript("MUSR00022725")
 
+  # Output the contents of the hist variable.
+  print wsHistory
 
+  ######################################################################
+  #Python Script Generated by GeneratePythonScript Algorithm
+  ######################################################################
+  Load(Filename=r'/home/userName/workspace/mantid/Test/AutoTestData/MUSR00022725.nxs',OutputWorkspace='MUSR00022725')
+  RenameWorkspace(InputWorkspace='MUSR00022725',OutputWorkspace='test')
+</source></div>
+
+{{AlgorithmLinks|GeneratePythonScript}}
 
 *WIKI*/
 #include "MantidAlgorithms/GeneratePythonScript.h"
@@ -38,13 +44,11 @@ namespace Algorithms
 // Register the algorithm into the AlgorithmFactory
 DECLARE_ALGORITHM(GeneratePythonScript)
 
-
-
 //----------------------------------------------------------------------------------------------
 /// Sets documentation strings for this algorithm
 void GeneratePythonScript::initDocs()
 {
-  this->setWikiSummary("Generate a Python script file to reproduce the history of a workspace.");
+  this->setWikiSummary("Reproduce the history of a workspace and save it to a Python script file or Python variable.");
   this->setOptionalMessage("An Algorithm to generate a Python script file to reproduce the history of a workspace.");
 }
 
@@ -59,8 +63,8 @@ void GeneratePythonScript::init()
   exts.push_back(".py");
 
   declareProperty(new API::FileProperty("Filename","", API::FileProperty::OptionalSave, exts),
-  "The file into which the Python script will be generated.");
-  declareProperty("ScriptText", "",Direction::Output);
+  "The name of the file into which the workspace history will be generated.");
+  declareProperty("ScriptText", std::string(""), "Saves the history of the workspace to a variable.",Direction::Output);
 }
 
 //----------------------------------------------------------------------------------------------

Code/Mantid/Framework/Algorithms/test/ExtractMaskToTableTest.h

@@ -31,7 +31,8 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
   static ExtractMaskToTableTest *createSuite() { return new ExtractMaskToTableTest(); }
   static void destroySuite( ExtractMaskToTableTest *suite ) { delete suite; }
 
-  /** Test a method
+  //----------------------------------------------------------------------------------------------
+  /** Test method 'subtractVector'
     */
   void test_method()
   {
@@ -40,7 +41,7 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
     vector<int> vecA;
     vector<int> vecB;
 
-    // All B's items are in A
+    // Case: A constains B
     for (size_t i = 0; i < 20; ++i)
     {
       vecA.push_back(static_cast<int>(i)+5);
@@ -52,13 +53,10 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
     }
 
     vector<int> vecC = alg.subtractVector(vecA, vecB);
-    for (size_t i = 0;i < vecC.size(); ++i)
-      cout << "Item " << i << "\t = \t" << vecC[i] << ".\n";
-    cout << "\n";
 
     TS_ASSERT_EQUALS(vecC.size(), vecA.size()-vecB.size());
 
-    // Not all B's item are in A
+    // Case: A does not contain B; but the intersection between A and B is not empty
     vecA.clear();
     vecB.clear();
 
@@ -70,13 +68,9 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
 
     vecC = alg.subtractVector(vecA, vecB);
 
-    for (size_t i = 0;i < vecC.size(); ++i)
-      cout << "Item " << i << "\t = \t" << vecC[i] << ".\n";
-    cout << "\n";
-
     TS_ASSERT_EQUALS(vecC.size(), 7);
 
-    // B has a large range than A
+    // Case: B has a larger range than A
     vecA.clear();
     vecB.clear();
 
@@ -91,14 +85,13 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
     vecB.push_back(30);
 
     vecC = alg.subtractVector(vecA, vecB);
-    for (size_t i = 0;i < vecC.size(); ++i)
-      cout << "Item " << i << "\t = \t" << vecC[i] << ".\n";
-    cout << "\n";
+
     TS_ASSERT_EQUALS(vecC.size(), 5);
 
     return;
   }
 
+  //----------------------------------------------------------------------------------------------
   /** Test initialization of the algorithm
     */
   void test_Init()
@@ -108,6 +101,7 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
     TS_ASSERT(alg.isInitialized());
   }
 
+  //----------------------------------------------------------------------------------------------
   /** Test for writing a new line to a new table workspace
     */
   void test_writeToNewTable()
@@ -130,27 +124,13 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
 
     AnalysisDataService::Instance().addOrReplace("TestWorkspace1", inputws);
 
-    /*
-    for (size_t i = 0; i < inputws->getNumberHistograms(); ++i)
-    {
-      IDetector_const_sptr det = inputws->getDetector(i);
-      cout << "WorkspaceIndex = " << i << "  X Size = " << inputws->readX(i).size()
-           << "; Detector ID = " << det->getID() << ".\n";
-    }
-    Instrument_const_sptr instrument = inputws->getInstrument();
-    vector<detid_t> detids = instrument->getDetectorIDs();
-    cout << "Number of detectors = " << detids.size() << ".\n";
-    for (size_t i = 0; i < detids.size(); ++i)
-      cout << "Detector " << i << ":  ID = " << detids[i] << ".\n";
-     */
-
     // Call algorithms
     ExtractMaskToTable alg;
     alg.initialize();
 
     // Set up properties
-    alg.setProperty("InputWorkspace", "TestWorkspace1");
-    alg.setProperty("OutputWorkspace", "MaskTable1");
+    alg.setPropertyValue("InputWorkspace", "TestWorkspace1");
+    alg.setPropertyValue("OutputWorkspace", "MaskTable1");
     alg.setProperty("XMin", 1234.0);
     alg.setProperty("XMax", 12345.6);
 
@@ -173,7 +153,6 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
     string specstr;
     therow >> xxmin >> xxmax >> specstr;
 
-    cout << "XMin = " << xxmin << ", XMax = " << xxmax << ", Spec list = " << specstr << ".\n";
     string expectedspec(" 1,  6-8,  11,  21,  31,  41");
     TS_ASSERT_EQUALS(specstr, expectedspec);
     TS_ASSERT_DELTA(xxmin, 1234.0, 0.0001);
@@ -186,6 +165,7 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
     return;
   }
 
+  //----------------------------------------------------------------------------------------------
   /** Test for appending a new line to an existing table workspace
     */
   void test_appendToExistingTable()
@@ -250,15 +230,15 @@ class ExtractMaskToTableTest : public CxxTest::TestSuite
 
     TableRow therow = outws->getRow(2);
     therow >> xxmin >> xxmax >> specstr;
-    cout << "XMin = " << xxmin << ", XMax = " << xxmax << ", Spec list = " << specstr << ".\n";
+
     string expectedspec(" 1,  6-8,  11,  21,  31,  41");
     TS_ASSERT_EQUALS(specstr, expectedspec);
     TS_ASSERT_DELTA(xxmin, 1234.0, 0.0001);
     TS_ASSERT_DELTA(xxmax, 12345.6, 0.0001);
 
     TableRow therow1 = outws->getRow(1);
     therow1 >> xxmin >> xxmax >> specstr;
-    cout << "XMin = " << xxmin << ", XMax = " << xxmax << ", Spec list = " << specstr << ".\n";
+
     string expectedspec2("43");
     TS_ASSERT_DELTA(xxmin, 2345.1, 0.0001);
     TS_ASSERT_DELTA(xxmax, 78910.5, 0.0001);