Checkpointing work on PoldiIndexKnownCompounds.

Refs #10247.

Code/Mantid/Framework/SINQ/CMakeLists.txt

@@ -6,6 +6,7 @@ set ( SRC_FILES
         src/PoldiCalculateSpectrum2D.cpp
 	src/PoldiCreatePeaksFromCell.cpp
 	src/PoldiFitPeaks1D.cpp
+	src/PoldiIndexKnownCompounds.cpp
 	src/PoldiLoadChopperSlits.cpp
 	src/PoldiLoadIPP.cpp
 	src/PoldiLoadLog.cpp
@@ -49,6 +50,7 @@ set ( INC_FILES
         inc/MantidSINQ/PoldiCalculateSpectrum2D.h
 	inc/MantidSINQ/PoldiCreatePeaksFromCell.h
 	inc/MantidSINQ/PoldiFitPeaks1D.h
+	inc/MantidSINQ/PoldiIndexKnownCompounds.h
 	inc/MantidSINQ/PoldiLoadChopperSlits.h
 	inc/MantidSINQ/PoldiLoadIPP.h
 	inc/MantidSINQ/PoldiLoadLog.h
@@ -107,6 +109,7 @@ set ( TEST_FILES
 	PoldiDetectorFactoryTest.h
 	PoldiDetectorTest.h
 	PoldiFitPeaks1DTest.h
+	PoldiIndexKnownCompoundsTest.h
         PoldiInstrumentAdapterTest.h
         PoldiPeakCollectionTest.h
 	PoldiPeakSearchTest.h

Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiIndexKnownCompounds.h

@@ -0,0 +1,134 @@
+#ifndef MANTID_SINQ_POLDIINDEXKNOWNCOMPOUNDS_H_
+#define MANTID_SINQ_POLDIINDEXKNOWNCOMPOUNDS_H_
+
+#include "MantidSINQ/DllConfig.h"
+#include "MantidAPI/Algorithm.h"
+#include "MantidSINQ/PoldiUtilities/PoldiPeakCollection.h"
+
+namespace Mantid
+{
+namespace Poldi
+{
+
+struct PeakCandidate
+{
+    PeakCandidate() :
+        unindexed(),
+        candidate(),
+        score(0.0),
+        candidateCollection(0) { }
+
+    PeakCandidate(const PoldiPeak_sptr &unindexedPeak, const PoldiPeak_sptr &candidatePeak, size_t index) :
+        unindexed(unindexedPeak),
+        candidate(candidatePeak),
+        candidateCollection(index)
+    {
+        double peakD = unindexed->d();
+        double fwhm = candidate->fwhm(PoldiPeak::AbsoluteD);
+        double sigma = fwhm / (2.0 * sqrt(2.0 * log(2.0)));
+        double difference = (peakD - candidate->d()) / sigma;
+        score = candidate->intensity() / (sigma * sqrt(2.0 * M_PI)) * exp(-0.5*difference*difference);
+    }
+
+    bool operator <(const PeakCandidate &other) const
+    {
+        return score < other.score;
+    }
+
+    PoldiPeak_sptr unindexed;
+    PoldiPeak_sptr candidate;
+    double score;
+    size_t candidateCollection;
+};
+
+/** PoldiIndexKnownCompounds : TODO: DESCRIPTION
+
+    Copyright &copy; 2014 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 MANTID_SINQ_DLL PoldiIndexKnownCompounds  : public API::Algorithm
+{
+public:
+    PoldiIndexKnownCompounds();
+    virtual ~PoldiIndexKnownCompounds();
+
+    virtual const std::string name() const;
+    virtual int version() const;
+    virtual const std::string category() const;
+    virtual const std::string summary() const;
+
+    virtual std::map<std::string, std::string> validateInputs();
+
+    void setMeasuredPeaks(const PoldiPeakCollection_sptr &measuredPeaks);
+    void setExpectedPhases(const std::vector<PoldiPeakCollection_sptr> &expectedPhases);
+
+    void initializeUnindexedPeaks();
+    void initializeIndexedPeaks(const std::vector<PoldiPeakCollection_sptr> &expectedPhases);
+
+protected:
+    std::vector<API::Workspace_sptr> getWorkspaces(const std::vector<std::string> &workspaceNames) const;
+    std::vector<PoldiPeakCollection_sptr> getPeakCollections(const std::vector<API::Workspace_sptr> &workspaces) const;
+
+    std::vector<double> getTolerances(size_t size) const;
+    std::vector<double> getContributions(size_t size) const;
+    std::vector<double> getNormalizedContributions(const std::vector<double> &contributions) const;
+
+    void assignIntensityEstimates(const std::vector<PoldiPeakCollection_sptr> &peakCollections, const std::vector<double> &normalizedContributions) const;
+    void assignIntensityEstimates(const PoldiPeakCollection_sptr &peakCollection, double contribution) const;
+
+    double getMultiplicity(const PoldiPeakCollection_sptr &peakCollection, const Kernel::V3D &hkl) const;
+
+    void assignFwhmEstimates(const std::vector<PoldiPeakCollection_sptr> &peakCollections, const std::vector<double> &tolerances) const;
+    void assignFwhmEstimates(const PoldiPeakCollection_sptr &peakCollection, double tolerance) const;
+
+
+    void indexPeaks(const PoldiPeakCollection_sptr &unindexed, const std::vector<PoldiPeakCollection_sptr> &knownCompounds);
+    void assignCandidates(const std::vector<PeakCandidate> &candidates);
+
+    std::vector<PeakCandidate> getPeakCandidates(const PoldiPeak_sptr &peak, const std::vector<PoldiPeakCollection_sptr> &candidateCollections) const;
+    bool isCandidate(const PoldiPeak_sptr &measuredPeak, const PoldiPeak_sptr &possibleCandidate) const;
+
+    std::vector<PeakCandidate> getAllCandidates(const PoldiPeakCollection_sptr &unindexed, const std::vector<PoldiPeakCollection_sptr> &knownCompounds);
+
+    bool inPeakSet(const std::set<PoldiPeak_sptr> &peakSet, const PoldiPeak_sptr &peak) const;
+    double fwhmToSigma(double fwhm) const;
+    double sigmaToFwhm(double sigma) const;
+
+    void assignPeakIndex(const PeakCandidate &candidate);
+
+
+    PoldiPeakCollection_sptr m_measuredPeaks;
+    std::vector<PoldiPeakCollection_sptr> m_expectedPhases;
+
+    PoldiPeakCollection_sptr m_unindexedPeaks;
+    std::vector<PoldiPeakCollection_sptr> m_indexedPeaks;
+
+private:
+    void init();
+    void exec();
+
+
+};
+
+
+} // namespace Poldi
+} // namespace Mantid
+
+#endif  /* MANTID_SINQ_POLDIINDEXKNOWNCOMPOUNDS_H_ */