From a4db2b1f5410a65703dd33b46e00886164704764 Mon Sep 17 00:00:00 2001
From: Vickie Lynch <lynchve@ornl.gov>
Date: Thu, 17 Jan 2019 09:06:38 -0500
Subject: [PATCH] Refs #24333 optimize sample position for each run

---
 .../Crystal/src/OptimizeCrystalPlacement.cpp  |  2 +-
 .../OptimizeCrystalPlacementByRun.py          | 78 +++++++++++++++++++
 2 files changed, 79 insertions(+), 1 deletion(-)
 create mode 100644 Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py

diff --git a/Framework/Crystal/src/OptimizeCrystalPlacement.cpp b/Framework/Crystal/src/OptimizeCrystalPlacement.cpp
index 257a0f8129e..7a5eff13303 100644
--- a/Framework/Crystal/src/OptimizeCrystalPlacement.cpp
+++ b/Framework/Crystal/src/OptimizeCrystalPlacement.cpp
@@ -449,7 +449,7 @@ void OptimizeCrystalPlacement::exec() {
   UBinv.Invert();
   UBinv /= (2 * M_PI);
   for (int i = 0; i < outPeaks->getNumberPeaks(); ++i) {
-    auto peak = outPeaks->getPeak(i);
+    auto &peak = outPeaks->getPeak(i);
     peak.setSamplePos(peak.getSamplePos() + newSampPos);
     int RunNum = peak.getRunNumber();
     std::string RunNumStr = std::to_string(RunNum);
diff --git a/Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py b/Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py
new file mode 100644
index 00000000000..5a2907267b4
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py
@@ -0,0 +1,78 @@
+# Mantid Repository : https://github.com/mantidproject/mantid
+#
+# Copyright &copy; 2018 ISIS Rutherford Appleton Laboratory UKRI,
+#     NScD Oak Ridge National Laboratory, European Spallation Source
+#     & Institut Laue - Langevin
+# SPDX - License - Identifier: GPL - 3.0 +
+#pylint: disable=no-init
+from __future__ import (absolute_import, division, print_function)
+
+from mantid.api import PythonAlgorithm, AlgorithmFactory, ITableWorkspaceProperty, WorkspaceFactory
+from mantid.kernel import Direction
+from mantid.simpleapi import *
+from mantid import mtd
+
+# Create an empty table workspace to be populated by a python script.
+
+
+class OptimizeCrystalPlacementByRun(PythonAlgorithm):
+
+    def summary(self):
+        return "Optimizes the sample position for each run in a peaks workspace."
+
+    def category(self):
+        return 'Crystal\\Corrections'
+
+    def seeAlso(self):
+        return [ "OptimizeCrystalPlacement" ]
+
+    def PyInit(self):
+        # Declare properties
+        self.declareProperty(ITableWorkspaceProperty("InputWorkspace", "", Direction.Input),
+                             "The name of the peaks workspace that will be optimized.")
+        self.declareProperty("Tolerance", 0.15, "Tolerance of indexing of peaks.")
+        self.declareProperty(ITableWorkspaceProperty("OutputWorkspace", "", Direction.Output),
+                             "The name of the peaks workspace that will be created.")
+
+    def PyExec(self):
+        ws = self.getProperty("InputWorkspace").value
+        ws_append = self.getProperty("OutputWorkspace").value
+        ws_group = 'ws_group'
+        tolerance = self.getProperty("Tolerance").value
+        if not ws.sample().hasOrientedLattice():
+            FindUBUsingIndexedPeaks(PeaksWorkspace=ws,Tolerance=tolerance)
+        num,err=IndexPeaks(PeaksWorkspace=ws,Tolerance=tolerance)
+        print('Initial Number indexed: %s error: %s\n'%(num, err))
+        stats = StatisticsOfTableWorkspace(InputWorkspace=ws)
+        stat_col = stats.column('Statistic')
+        minR = int(stats.column('RunNumber')[stat_col.index('Minimum')])
+        maxR = int(stats.column('RunNumber')[stat_col.index('Maximum')]) + 1
+        
+        group = []
+        for run in range(minR, maxR):
+            FilterPeaks(InputWorkspace=ws, OutputWorkspace=str(run), FilterVariable='RunNumber', FilterValue=run, Operator='=')
+            run = mtd[str(run)]
+            peaks = run.getNumberPeaks()
+            if peaks == 0:
+                AnalysisDataService.remove( str(run))
+            else:
+                group.append(str(run))
+        GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=ws_group)
+        
+        OptimizeCrystalPlacement(PeaksWorkspace=ws_group, ModifiedPeaksWorkspace=ws_group, AdjustSampleOffsets=True, MaxSamplePositionChangeMeters=0.005,MaxIndexingError=tolerance)
+        
+        CloneWorkspace(InputWorkspace=str(minR),OutputWorkspace=ws_append)
+        for run in range(minR+1, maxR):
+            if AnalysisDataService.doesExist( str(run)):
+                CombinePeaksWorkspaces(LHSWorkspace=ws_append, RHSWorkspace=str(run),OutputWorkspace=ws_append)
+                print('Optimized %s sample position: %s\n'%(str(run),mtd[str(run)].getPeak(0).getSamplePos()))
+                AnalysisDataService.remove( str(run))
+        num,err=IndexPeaks(PeaksWorkspace=ws_append,Tolerance=tolerance)
+        print('After Optimization Number indexed: %s error: %s\n'%(num, err))
+        AnalysisDataService.remove(ws_group)
+    
+        self.setProperty("OutputWorkspace", ws_append)
+
+
+# Register algorithm with Mantid
+AlgorithmFactory.subscribe(OptimizeCrystalPlacementByRun)
-- 
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