Fixes #3126: PeaksWorkspace algorithms use the Clone() method in order to give...

Fixes #3126: PeaksWorkspace algorithms use the Clone() method in order to give a different output workspace, if desired. Also added progress reporting to PeakIntegration.

Code/Mantid/Framework/Crystal/src/PeakIntegration.cpp

@@ -51,6 +51,8 @@ namespace Mantid
 
       declareProperty(new WorkspaceProperty<PeaksWorkspace>("InPeaksWorkspace", "", Direction::Input), "Name of the peaks workspace.");
 
+      declareProperty(new WorkspaceProperty<PeaksWorkspace>("OutPeaksWorkspace", "", Direction::Output), "Name of the output peaks workspace with integrated intensities.");
+
       declareProperty("XMin", -7, "Minimum of X (col) Range to integrate for peak");
       declareProperty("XMax", 7, "Maximum of X (col) Range to integrate for peak");
       declareProperty("YMin", -7, "Minimum of Y (row) Range to integrate for peak");
@@ -77,9 +79,15 @@ namespace Mantid
       Beta0 = 31.9;
       Kappa = 46.0;
   
-      PeaksWorkspace_sptr peaksW;
-      peaksW = boost::dynamic_pointer_cast<PeaksWorkspace>(AnalysisDataService::Instance().retrieve(getProperty("InPeaksWorkspace")));
+      /// Input peaks workspace
+      PeaksWorkspace_sptr inPeaksW = getProperty("InPeaksWorkspace");
+
+      /// Output peaks workspace, create if needed
+      PeaksWorkspace_sptr peaksW = getProperty("OutPeaksWorkspace");
+      if (peaksW != inPeaksW)
+        peaksW = inPeaksW->clone();
 
+      Progress prog(this, 0.0, 1.0, peaksW->getNumberPeaks());
 
       int i, XPeak, YPeak;
       double col, row, I, sigI;
@@ -144,7 +152,14 @@ namespace Mantid
         //std::cout << peak.getIntensity()<<"  " << I << "  " << peak.getSigmaIntensity() << "  "<< sigI << "\n";
         peak.setIntensity(I);
         peak.setSigmaIntensity(sigI);
+
+        std::ostringstream mess;
+        mess << "Peak " << peak.getHKL();
+        prog.report(mess.str());
       }
+
+      // Save the output
+      setProperty("OutPeaksWorkspace", peaksW);
     }
 
     void PeakIntegration::retrieveProperties()

Code/Mantid/Framework/Crystal/test/PeakIntegrationTest.h

@@ -173,6 +173,7 @@ public:
     alg.setProperty("InputWorkspace", inputW);
     alg.setProperty("OutputWorkspace", "tmp");
     alg.setProperty("InPeaksWorkspace", "TOPAZ");
+    alg.setProperty("OutPeaksWorkspace", "TOPAZ");
     alg.setProperty("XMin", -2);
     alg.setProperty("XMax", 2);
     alg.setProperty("YMin", -2);

Code/Mantid/Framework/MDEvents/src/MDCentroidPeaks.cpp

@@ -72,9 +72,12 @@ namespace MDEvents
     declareProperty(new PropertyWithValue<double>("PeakRadius",1.0,Direction::Input),
         "Fixed radius around each peak position in which to calculate the centroid.");
 
-    declareProperty(new WorkspaceProperty<PeaksWorkspace>("PeaksWorkspace","",Direction::InOut),
-        "A PeaksWorkspace containing the peaks to integrate. "
-        "The peaks' coordinates will be updated with the found centroids.");
+    declareProperty(new WorkspaceProperty<PeaksWorkspace>("PeaksWorkspace","",Direction::Input),
+        "A PeaksWorkspace containing the peaks to centroid.");
+
+    declareProperty(new WorkspaceProperty<PeaksWorkspace>("OutputWorkspace","",Direction::Output),
+        "The output PeaksWorkspace will be a copy of the input PeaksWorkspace "
+        "with the peaks' positions modified by the new found centroids.");
   }
 
   //----------------------------------------------------------------------------------------------
@@ -87,8 +90,13 @@ namespace MDEvents
     if (nd != 3)
       throw std::invalid_argument("For now, we expect the input MDEventWorkspace to have 3 dimensions only.");
 
-    /// Peak workspace to integrate
-    Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("PeaksWorkspace");
+    /// Peak workspace to centroid
+    Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS = getProperty("PeaksWorkspace");
+
+    /// Output peaks workspace, create if needed
+    Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("OutputWorkspace");
+    if (peakWS != inPeakWS)
+      peakWS = inPeakWS->clone();
 
     /// Value of the CoordinatesToUse property.
     std::string CoordinatesToUse = getPropertyValue("CoordinatesToUse");
@@ -162,6 +170,9 @@ namespace MDEvents
       }
     }
 
+    // Save the output
+    setProperty("OutputWorkspace", peakWS);
+
   }
 
   //----------------------------------------------------------------------------------------------

Code/Mantid/Framework/MDEvents/src/MDEWPeakIntegration.cpp

@@ -73,9 +73,12 @@ namespace MDEvents
         "The signal density around the peak (PeakRadius < r < BackgroundRadius) is used to estimate the background under the peak.\n"
         "If smaller than PeakRadius, no background measurement is done." );
 
-    declareProperty(new WorkspaceProperty<PeaksWorkspace>("PeaksWorkspace","",Direction::InOut),
-        "A PeaksWorkspace containing the peaks to integrate. The peaks' integrated intensities will be updated"
-        "with the new values.");
+    declareProperty(new WorkspaceProperty<PeaksWorkspace>("PeaksWorkspace","",Direction::Input),
+        "A PeaksWorkspace containing the peaks to integrate.");
+
+    declareProperty(new WorkspaceProperty<PeaksWorkspace>("OutputWorkspace","",Direction::Output),
+        "The output PeaksWorkspace will be a copy of the input PeaksWorkspace "
+        "with the peaks' integrated intensities.");
   }
 
   //----------------------------------------------------------------------------------------------
@@ -89,7 +92,12 @@ namespace MDEvents
       throw std::invalid_argument("For now, we expect the input MDEventWorkspace to have 3 dimensions only.");
 
     /// Peak workspace to integrate
-    Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("PeaksWorkspace");
+    Mantid::DataObjects::PeaksWorkspace_sptr inPeakWS = getProperty("PeaksWorkspace");
+
+    /// Output peaks workspace, create if needed
+    Mantid::DataObjects::PeaksWorkspace_sptr peakWS = getProperty("OutputWorkspace");
+    if (peakWS != inPeakWS)
+      peakWS = inPeakWS->clone();
 
     /// Value of the CoordinatesToUse property.
     std::string CoordinatesToUse = getPropertyValue("CoordinatesToUse");
@@ -169,6 +177,9 @@ namespace MDEvents
           << std::endl;
     }
 
+    // Save the output
+    setProperty("OutputWorkspace", peakWS);
+
   }
 
   //----------------------------------------------------------------------------------------------

Code/Mantid/Framework/MDEvents/test/MDCentroidPeaksTest.h

@@ -79,7 +79,8 @@ public:
 
   //-------------------------------------------------------------------------------
   /** Run the MDCentroidPeaks with the given peak radius param */
-  void doRun( V3D startPos, double PeakRadius, V3D expectedResult, std::string message)
+  void doRun( V3D startPos, double PeakRadius, V3D expectedResult, std::string message,
+      std::string OutputWorkspace = "MDCentroidPeaksTest_Peaks")
   {
     // Make a fake instrument - doesn't matter, we won't use it really
     IInstrument_sptr inst = ComponentCreationHelper::createTestInstrumentCylindrical(5);
@@ -105,10 +106,16 @@ public:
     TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("InputWorkspace", "MDCentroidPeaksTest_MDEWS" ) );
     TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("PeaksWorkspace", "MDCentroidPeaksTest_Peaks" ) );
     TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("CoordinatesToUse", CoordinatesToUse ) );
+    TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("OutputWorkspace", OutputWorkspace ) );
     TS_ASSERT_THROWS_NOTHING( alg.setProperty("PeakRadius", PeakRadius ) );
     TS_ASSERT_THROWS_NOTHING( alg.execute() );
     TS_ASSERT( alg.isExecuted() );
 
+    peakWS = boost::dynamic_pointer_cast<PeaksWorkspace>(
+        AnalysisDataService::Instance().retrieve(OutputWorkspace));
+    TS_ASSERT(peakWS);
+    if (!peakWS) return;
+
     // Compare the result to the expectation
     V3D result;
     Peak & p = peakWS->getPeak(0);
@@ -177,6 +184,16 @@ public:
     do_test_exec();
   }
 
+  void test_exec_HKL_NotInPlace()
+  {
+    CoordinatesToUse = "HKL";
+    createMDEW();
+    addPeak(1000, 0,0.,0., 1.0);
+    doRun(V3D( 0.,0.,0.), 1.0, V3D( 0.,0.,0.), "Start at the center, get the center",
+        "MDCentroidPeaksTest_MDEWS_outputCopy");
+
+  }
+
 private:
   std::string CoordinatesToUse;
 

Code/Mantid/Framework/MDEvents/test/MDEWPeakIntegrationTest.h

@@ -46,16 +46,18 @@ public:
 
   //-------------------------------------------------------------------------------
   /** Run the MDEWPeakIntegration with the given peak radius integration param */
-  static void doRun(double PeakRadius, double BackgroundRadius)
+  static void doRun(double PeakRadius, double BackgroundRadius,
+      std::string OutputWorkspace = "MDEWPeakIntegrationTest_peaks")
   {
     MDEWPeakIntegration alg;
     TS_ASSERT_THROWS_NOTHING( alg.initialize() )
     TS_ASSERT( alg.isInitialized() )
     TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("InputWorkspace", "MDEWPeakIntegrationTest_MDEWS" ) );
-    TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("PeaksWorkspace", "MDEWPeakIntegrationTest_peaks" ) );
     TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("CoordinatesToUse", "HKL" ) );
     TS_ASSERT_THROWS_NOTHING( alg.setProperty("PeakRadius", PeakRadius ) );
     TS_ASSERT_THROWS_NOTHING( alg.setProperty("BackgroundRadius", BackgroundRadius ) );
+    TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("PeaksWorkspace", "MDEWPeakIntegrationTest_peaks" ) );
+    TS_ASSERT_THROWS_NOTHING( alg.setPropertyValue("OutputWorkspace", OutputWorkspace) );
     TS_ASSERT_THROWS_NOTHING( alg.execute() );
     TS_ASSERT( alg.isExecuted() );
   }
@@ -182,6 +184,33 @@ public:
 
 
 
+  //-------------------------------------------------------------------------------
+  void test_exec_NotInPlace()
+  {
+    // --- Fake workspace with 3 peaks ------
+    createMDEW();
+    addPeak(1000, 0.,0.,0., 1.0);
+
+    // Make a fake instrument - doesn't matter, we won't use it really
+    IInstrument_sptr inst = ComponentCreationHelper::createTestInstrumentCylindrical(5);
+    // --- Make a fake PeaksWorkspace ---
+    PeaksWorkspace_sptr peakWS(new PeaksWorkspace());
+    peakWS->addPeak( Peak(inst, 1, 1.0, V3D(0., 0., 0.) ) );
+    AnalysisDataService::Instance().add("MDEWPeakIntegrationTest_peaks",peakWS);
+
+    // Integrate and copy to a new peaks workspace
+    doRun(1.0,0.0, "MDEWPeakIntegrationTest_peaks_out");
+
+    // Old workspace is unchanged
+    TS_ASSERT_EQUALS( peakWS->getPeak(0).getIntensity(), 0.0);
+
+    PeaksWorkspace_sptr newPW = boost::dynamic_pointer_cast<PeaksWorkspace>(
+        AnalysisDataService::Instance().retrieve("MDEWPeakIntegrationTest_peaks_out"));
+    TS_ASSERT( newPW );
+
+    TS_ASSERT_DELTA( newPW->getPeak(0).getIntensity(), 1000.0, 1e-2);
+  }
+