diff --git a/Framework/Crystal/inc/MantidCrystal/PeakHKLErrors.h b/Framework/Crystal/inc/MantidCrystal/PeakHKLErrors.h
index 5d06df47752bebcc0526fb2e80191e2781596526..b4f7577491ad34528c464e34ad28579450976a58 100644
--- a/Framework/Crystal/inc/MantidCrystal/PeakHKLErrors.h
+++ b/Framework/Crystal/inc/MantidCrystal/PeakHKLErrors.h
@@ -153,6 +153,11 @@ private:
// OptRuns setup
void setUpOptRuns();
+
+ mutable boost::shared_ptr<Geometry::Instrument> instChange;
+ mutable bool hasParameterMap = false;
+ mutable Kernel::V3D sampPos;
+ mutable boost::shared_ptr<const Geometry::ParameterMap> pmapSv;
};
} // namespace Crystal
} // namespace Mantid
diff --git a/Framework/Crystal/src/FilterPeaks.cpp b/Framework/Crystal/src/FilterPeaks.cpp
index 3fa0520ff9b3a8216bfb444bc72a2788dd22b1d5..b1b1b7aef61de38d16b3bbdb6103e971ab154b5f 100644
--- a/Framework/Crystal/src/FilterPeaks.cpp
+++ b/Framework/Crystal/src/FilterPeaks.cpp
@@ -34,6 +34,8 @@ double QMOD(const Mantid::Geometry::IPeak &p) {
double SN(const Mantid::Geometry::IPeak &p) {
return p.getIntensity() / p.getSigmaIntensity();
}
+
+double RUN(const Mantid::Geometry::IPeak &p) { return p.getRunNumber(); }
} // namespace
namespace Mantid {
@@ -66,7 +68,7 @@ void FilterPeaks::init() {
std::vector<std::string> filters{"h+k+l", "h^2+k^2+l^2", "Intensity",
"Signal/Noise", "QMod", "Wavelength",
- "DSpacing", "TOF"};
+ "DSpacing", "TOF", "RunNumber"};
declareProperty("FilterVariable", "",
boost::make_shared<StringListValidator>(filters),
"The variable on which to filter the peaks");
@@ -150,6 +152,8 @@ FilterPeaks::FilterFunction FilterPeaks::getFilterVariableFunction(
filterFunction = &SN;
else if (filterVariable == "QMod")
filterFunction = &QMOD;
+ else if (filterVariable == "RunNumber")
+ filterFunction = &RUN;
else
throw std::invalid_argument("Unknown FilterVariable: " + filterVariable);
return filterFunction;
diff --git a/Framework/Crystal/src/PeakHKLErrors.cpp b/Framework/Crystal/src/PeakHKLErrors.cpp
index 3edfe24e37f5f5fc0a06130cca41282b3975c7ae..f7a32da50a7c93b372562836a1d15ee8ebc22294 100644
--- a/Framework/Crystal/src/PeakHKLErrors.cpp
+++ b/Framework/Crystal/src/PeakHKLErrors.cpp
@@ -190,26 +190,31 @@ boost::shared_ptr<Geometry::Instrument>
PeakHKLErrors::getNewInstrument(PeaksWorkspace_sptr Peaks) const {
Geometry::Instrument_const_sptr instSave = Peaks->getPeak(0).getInstrument();
auto pmap = boost::make_shared<Geometry::ParameterMap>();
- boost::shared_ptr<const Geometry::ParameterMap> pmapSv =
- instSave->getParameterMap();
if (!instSave) {
g_log.error(" Peaks workspace does not have an instrument");
throw std::invalid_argument(" Not all peaks have an instrument");
}
- auto instChange = boost::shared_ptr<Geometry::Instrument>();
- if (!instSave->isParametrized()) {
-
- boost::shared_ptr<Geometry::Instrument> instClone(instSave->clone());
- auto Pinsta = boost::make_shared<Geometry::Instrument>(instSave, pmap);
-
- instChange = Pinsta;
- } else // catch(... )
- {
- auto P1 = boost::make_shared<Geometry::Instrument>(
- instSave->baseInstrument(), instSave->makeLegacyParameterMap());
- instChange = P1;
+ if (!hasParameterMap) {
+ pmapSv = instSave->getParameterMap();
+ hasParameterMap = true;
+ if (!instSave->isParametrized()) {
+
+ boost::shared_ptr<Geometry::Instrument> instClone(instSave->clone());
+ auto Pinsta = boost::make_shared<Geometry::Instrument>(instSave, pmap);
+
+ instChange = Pinsta;
+ IComponent_const_sptr sample = instChange->getSample();
+ sampPos = sample->getRelativePos();
+ } else // catch(... )
+ {
+ auto P1 = boost::make_shared<Geometry::Instrument>(
+ instSave->baseInstrument(), instSave->makeLegacyParameterMap());
+ instChange = P1;
+ IComponent_const_sptr sample = instChange->getSample();
+ sampPos = sample->getRelativePos();
+ }
}
if (!instChange) {
@@ -219,11 +224,10 @@ PeakHKLErrors::getNewInstrument(PeaksWorkspace_sptr Peaks) const {
//------------------"clone" orig instruments pmap -------------------
cLone(pmap, instSave, pmapSv);
- IComponent_const_sptr sample = instChange->getSample();
- V3D sampPos = sample->getRelativePos();
V3D sampOffsets(getParameter("SampleXOffset"), getParameter("SampleYOffset"),
getParameter("SampleZOffset"));
+ IComponent_const_sptr sample = instChange->getSample();
pmap->addPositionCoordinate(sample.get(), std::string("x"),
sampPos.X() + sampOffsets.X());
pmap->addPositionCoordinate(sample.get(), std::string("y"),
diff --git a/Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py b/Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py
new file mode 100644
index 0000000000000000000000000000000000000000..0ab0361b4cae86e3c2e6443e5433ed6fb64d5f4a
--- /dev/null
+++ b/Framework/PythonInterface/plugins/algorithms/OptimizeCrystalPlacementByRun.py
@@ -0,0 +1,76 @@
+# Mantid Repository : https://github.com/mantidproject/mantid
+#
+# Copyright © 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 mantid.api import PythonAlgorithm, AlgorithmFactory, ITableWorkspaceProperty
+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("OutputWorkspace", "",
+ "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)
+ logger.notice('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
+ AnalysisDataService.remove(stats.getName())
+ 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)
+ RenameWorkspace(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)
+ logger.notice('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)
+ logger.notice('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)
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
index 0baa419f1c91d63c35bd654abca34a52f652acc7..4603c39cde4eec159288be26df141e29c8fc97de 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
@@ -79,6 +79,7 @@ set ( TEST_PY_FILES
MuonMaxEntTest.py
NMoldyn4InterpolationTest.py
NormaliseSpectraTest.py
+ OptimizeCrystalPlacementByRunTest.py
ReflectometryReductionOneLiveDataTest.py
ReflectometrySliceEventWorkspaceTest.py
RetrieveRunInfoTest.py
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/OptimizeCrystalPlacementByRunTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/OptimizeCrystalPlacementByRunTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..9429be6ff88a77351cf3ce73fff45f42079f8e5a
--- /dev/null
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/OptimizeCrystalPlacementByRunTest.py
@@ -0,0 +1,32 @@
+# Mantid Repository : https://github.com/mantidproject/mantid
+#
+# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
+# NScD Oak Ridge National Laboratory, European Spallation Source
+# & Institut Laue - Langevin
+# SPDX - License - Identifier: GPL - 3.0 +
+from __future__ import (absolute_import, division, print_function)
+
+import unittest
+from mantid.simpleapi import LoadIsawPeaks, FindUBUsingFFT, IndexPeaks, OptimizeCrystalPlacementByRun
+from mantid.api import mtd
+
+
+class OptimizeCrystalPlacementByRunTest(unittest.TestCase):
+ def test_simple(self):
+ ws=LoadIsawPeaks("calibrated.peaks")
+ FindUBUsingFFT(PeaksWorkspace=ws,MinD=2,MaxD=20,Tolerance=0.12)
+ IndexPeaks(PeaksWorkspace='ws',Tolerance=0.12)
+ wsd = OptimizeCrystalPlacementByRun(InputWorkspace=ws,OutputWorkspace='wsd',Tolerance=0.12)
+ result = mtd['wsd'].getPeak(0).getSamplePos()
+ self.assertAlmostEqual(result.getX(), -0.000678629)
+ self.assertAlmostEqual(result.getY(), -2.16033e-05)
+ self.assertAlmostEqual(result.getZ(), 0.00493278)
+ result = mtd['wsd'].getPeak(8).getSamplePos()
+ self.assertAlmostEqual(result.getX(), -0.0027929)
+ self.assertAlmostEqual(result.getY(), -0.00105681)
+ self.assertAlmostEqual(result.getZ(), 0.00497094)
+
+
+
+if __name__=="__main__":
+ unittest.main()
diff --git a/docs/source/algorithms/OptimizeCrystalPlacementByRun-v1.rst b/docs/source/algorithms/OptimizeCrystalPlacementByRun-v1.rst
new file mode 100644
index 0000000000000000000000000000000000000000..758e4c699cbc0ffd59b44ee0c1d41b3f669e54a1
--- /dev/null
+++ b/docs/source/algorithms/OptimizeCrystalPlacementByRun-v1.rst
@@ -0,0 +1,45 @@
+.. algorithm::
+
+.. summary::
+
+.. relatedalgorithms::
+
+.. properties::
+
+Description
+-----------
+
+This algorithm basically optimizes h,k, and l offsets from an integer by
+varying the parameters sample positions for each run in the peaks workspace.
+
+The crystal orientation matrix, :ref:`UB matrix <Lattice>`, from the
+PeaksWorkspace should index all the runs "very well". Otherwise iterations
+that slowly build a :ref:`UB matrix <Lattice>` with corrected sample
+orientations may be needed.
+
+
+Usage
+-----
+
+**Example:**
+
+.. testcode:: ExOptimizeCrystalPlacementByRun
+
+ ws=LoadIsawPeaks("calibrated.peaks")
+ FindUBUsingFFT(PeaksWorkspace=ws,MinD=2,MaxD=20,Tolerance=0.12)
+ IndexPeaks(PeaksWorkspace='ws',Tolerance=0.12)
+ wsd = OptimizeCrystalPlacementByRun(InputWorkspace=ws,OutputWorkspace='wsd',Tolerance=0.12)
+ print('Optimized %s sample position: %s'%(mtd['wsd'].getPeak(0).getRunNumber(),mtd['wsd'].getPeak(0).getSamplePos()))
+ print('Optimized %s sample position: %s'%(mtd['wsd'].getPeak(8).getRunNumber(),mtd['wsd'].getPeak(8).getSamplePos()))
+
+Output:
+
+.. testoutput:: ExOptimizeCrystalPlacementByRun
+
+ Optimized 71907 sample position: [-0.000678629,-2.16033e-05,0.00493278]
+ Optimized 72007 sample position: [-0.0027929,-0.00105681,0.00497094]
+
+
+.. categories::
+
+.. sourcelink::
diff --git a/docs/source/release/v3.14.0/diffraction.rst b/docs/source/release/v3.14.0/diffraction.rst
index 30df5d2faaeccedec9d20d8361829f72f8978756..131bbab7513af585788e1eb4ffb4d5e87798788c 100644
--- a/docs/source/release/v3.14.0/diffraction.rst
+++ b/docs/source/release/v3.14.0/diffraction.rst
@@ -49,6 +49,7 @@ Improvements
- :ref:`IntegratePeaksUsingClusters <algm-IntegratePeaksUsingClusters>` will now treat NaN's as background.
- SCD Event Data Reduction Diffraction Interface now adds goniometer for CORELLI and used proton charge as monitor count if no monitors are in input file.
- :ref:`SetCrystalLocation <algm-SetCrystalLocation>` is a new algorithm to set the sample location in events workspaces.
+- :ref:`OptimizeCrystalPlacementByRun <algm-OptimizeCrystalPlacementByRun>` is new algorithm to update the sample position for each run in a peaks workspace.
Bugfixes
########