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Refs #10702. Adding unit cell to PoldiPeakCollection
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This will make InitialCell and CrystalSystem of PoldiFitPeaks2D obsolete, as PoldiIndexKnownCompounds now stores the cell and point group.
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Michael Wedel committed Apr 23, 2015
1 parent 0521e7c commit 6c8f861
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Showing 6 changed files with 93 additions and 9 deletions.
4 changes: 4 additions & 0 deletions Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiIndexKnownCompounds.h
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Expand Up @@ -151,6 +151,10 @@ class MANTID_SINQ_DLL PoldiIndexKnownCompounds : public API::Algorithm {
PoldiPeakCollection_sptr
getIntensitySortedPeakCollection(const PoldiPeakCollection_sptr &peaks) const;

void assignCrystalStructureParameters(
PoldiPeakCollection_sptr &indexedPeaks,
const PoldiPeakCollection_sptr &phasePeaks) const;

PoldiPeakCollection_sptr m_measuredPeaks;
std::vector<PoldiPeakCollection_sptr> m_expectedPhases;
std::vector<std::string> m_phaseNames;
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13 changes: 12 additions & 1 deletion Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiPeakCollection.h
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Expand Up @@ -46,7 +46,10 @@ typedef boost::shared_ptr<PoldiPeakCollection> PoldiPeakCollection_sptr;

class MANTID_SINQ_DLL PoldiPeakCollection {
public:
enum IntensityType { Maximum, Integral };
enum IntensityType {
Maximum,
Integral
};

PoldiPeakCollection(IntensityType intensityType = Maximum);
PoldiPeakCollection(const DataObjects::TableWorkspace_sptr &workspace);
Expand All @@ -72,6 +75,9 @@ class MANTID_SINQ_DLL PoldiPeakCollection {
void setPointGroup(const Geometry::PointGroup_sptr &pointGroup);
Geometry::PointGroup_sptr pointGroup() const;

void setUnitCell(const Geometry::UnitCell &unitCell);
Geometry::UnitCell unitCell() const;

DataObjects::TableWorkspace_sptr asTableWorkspace();

protected:
Expand All @@ -93,6 +99,7 @@ class MANTID_SINQ_DLL PoldiPeakCollection {
std::string
getProfileFunctionNameFromLog(const API::LogManager_sptr &tableLog);
std::string getPointGroupStringFromLog(const API::LogManager_sptr &tableLog);
std::string getUnitCellStringFromLog(const API::LogManager_sptr &tableLog);

std::string getStringValueFromLog(const API::LogManager_sptr &logManager,
std::string valueName);
Expand All @@ -105,11 +112,15 @@ class MANTID_SINQ_DLL PoldiPeakCollection {
Geometry::PointGroup_sptr
pointGroupFromString(const std::string &pointGroupString) const;

Geometry::UnitCell
unitCellFromString(const std::string &unitCellString) const;

std::vector<PoldiPeak_sptr> m_peaks;
IntensityType m_intensityType;
std::string m_profileFunctionName;

Geometry::PointGroup_sptr m_pointGroup;
Geometry::UnitCell m_unitCell;
};
}
}
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11 changes: 11 additions & 0 deletions Code/Mantid/Framework/SINQ/src/PoldiIndexKnownCompounds.cpp
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Expand Up @@ -747,6 +747,14 @@ PoldiIndexKnownCompounds::getIntensitySortedPeakCollection(
return sortedPeaks;
}

void PoldiIndexKnownCompounds::assignCrystalStructureParameters(
PoldiPeakCollection_sptr &indexedPeaks,
const PoldiPeakCollection_sptr &phasePeaks) const {

indexedPeaks->setPointGroup(phasePeaks->pointGroup());
indexedPeaks->setUnitCell(phasePeaks->unitCell());
}

/** Initialize the algorithm's properties.
*/
void PoldiIndexKnownCompounds::init() {
Expand Down Expand Up @@ -836,6 +844,9 @@ void PoldiIndexKnownCompounds::exec() {
for (size_t i = 0; i < m_indexedPeaks.size(); ++i) {
PoldiPeakCollection_sptr intensitySorted =
getIntensitySortedPeakCollection(m_indexedPeaks[i]);

assignCrystalStructureParameters(intensitySorted, m_expectedPhases[i]);

ITableWorkspace_sptr tableWs = intensitySorted->asTableWorkspace();
AnalysisDataService::Instance().addOrReplace("Indexed_" + m_phaseNames[i],
tableWs);
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35 changes: 33 additions & 2 deletions Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiPeakCollection.cpp
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Expand Up @@ -3,6 +3,7 @@
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidAPI/LogManager.h"
#include "MantidGeometry/Crystal/PointGroupFactory.h"

#include "boost/format.hpp"
#include "boost/algorithm/string/join.hpp"

Expand All @@ -19,11 +20,11 @@ using namespace Mantid::Kernel;

PoldiPeakCollection::PoldiPeakCollection(IntensityType intensityType)
: m_peaks(), m_intensityType(intensityType), m_profileFunctionName(),
m_pointGroup() {}
m_pointGroup(), m_unitCell() {}

PoldiPeakCollection::PoldiPeakCollection(const TableWorkspace_sptr &workspace)
: m_peaks(), m_intensityType(Maximum), m_profileFunctionName(),
m_pointGroup() {
m_pointGroup(), m_unitCell() {
if (workspace) {
constructFromTableWorkspace(workspace);
}
Expand All @@ -42,6 +43,8 @@ PoldiPeakCollection::PoldiPeakCollection(
m_pointGroup =
pointGroupFromString(pointGroupToString(crystalStructure->pointGroup()));

m_unitCell = crystalStructure->cell();

std::vector<V3D> uniqueHKL = crystalStructure->getUniqueHKLs(
dMin, dMax, Geometry::CrystalStructure::UseStructureFactor);
std::vector<double> dValues = crystalStructure->getDValues(uniqueHKL);
Expand Down Expand Up @@ -104,6 +107,12 @@ void PoldiPeakCollection::setPointGroup(const PointGroup_sptr &pointGroup) {

PointGroup_sptr PoldiPeakCollection::pointGroup() const { return m_pointGroup; }

void PoldiPeakCollection::setUnitCell(const UnitCell &unitCell) {
m_unitCell = unitCell;
}

UnitCell PoldiPeakCollection::unitCell() const { return m_unitCell; }

TableWorkspace_sptr PoldiPeakCollection::asTableWorkspace() {
TableWorkspace_sptr peaks = boost::dynamic_pointer_cast<TableWorkspace>(
WorkspaceFactory::Instance().createTable());
Expand Down Expand Up @@ -131,6 +140,8 @@ void PoldiPeakCollection::dataToTableLog(const TableWorkspace_sptr &table) {
m_profileFunctionName);
tableLog->addProperty<std::string>("PointGroup",
pointGroupToString(m_pointGroup));
tableLog->addProperty<std::string>("UnitCell",
Geometry::unitCellToStr(m_unitCell));
}

void PoldiPeakCollection::peaksToTable(const TableWorkspace_sptr &table) {
Expand Down Expand Up @@ -217,6 +228,7 @@ void PoldiPeakCollection::recoverDataFromLog(
m_intensityType = intensityTypeFromString(getIntensityTypeFromLog(tableLog));
m_profileFunctionName = getProfileFunctionNameFromLog(tableLog);
m_pointGroup = pointGroupFromString(getPointGroupStringFromLog(tableLog));
m_unitCell = unitCellFromString(getUnitCellStringFromLog(tableLog));
}

std::string
Expand All @@ -234,6 +246,11 @@ std::string PoldiPeakCollection::getPointGroupStringFromLog(
return getStringValueFromLog(tableLog, "PointGroup");
}

std::string
PoldiPeakCollection::getUnitCellStringFromLog(const LogManager_sptr &tableLog) {
return getStringValueFromLog(tableLog, "UnitCell");
}

std::string
PoldiPeakCollection::getStringValueFromLog(const LogManager_sptr &logManager,
std::string valueName) {
Expand Down Expand Up @@ -286,5 +303,19 @@ PointGroup_sptr PoldiPeakCollection::pointGroupFromString(

return PointGroup_sptr();
}

UnitCell PoldiPeakCollection::unitCellFromString(
const std::string &unitCellString) const {
UnitCell cell;

try {
cell = strToUnitCell(unitCellString);
}
catch (std::runtime_error) {
// do nothing
}

return cell;
}
}
}
7 changes: 7 additions & 0 deletions Code/Mantid/Framework/SINQ/test/PoldiIndexKnownCompoundsTest.h
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Expand Up @@ -76,6 +76,13 @@ class PoldiIndexKnownCompoundsTest : public CxxTest::TestSuite
TS_ASSERT_EQUALS(tableSi->getName(), "Indexed_Si");
TS_ASSERT_EQUALS(tableSi->rowCount(), 4);

// Make sure unit cell and point group is carried over from compound ws
ITableWorkspace_sptr si = AnalysisDataService::Instance().retrieveWS<ITableWorkspace>("Si");
TS_ASSERT_EQUALS(tableSi->getLogs()->getProperty("PointGroup")->value(),
si->getLogs()->getProperty("PointGroup")->value());
TS_ASSERT_EQUALS(tableSi->getLogs()->getProperty("UnitCell")->value(),
si->getLogs()->getProperty("UnitCell")->value());

Workspace_sptr unindexed = group->getItem(1);
TS_ASSERT(unindexed);

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32 changes: 26 additions & 6 deletions Code/Mantid/Framework/SINQ/test/PoldiPeakCollectionTest.h
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Expand Up @@ -194,18 +194,37 @@ class PoldiPeakCollectionTest : public CxxTest::TestSuite
TS_ASSERT_EQUALS(peaks.pointGroup()->getName(), m3m->getName());
}

void testUnitCell()
{
PoldiPeakCollection peaks;

UnitCell defaultCell;
TS_ASSERT_EQUALS(unitCellToStr(peaks.unitCell()), unitCellToStr(defaultCell));

UnitCell cell(1, 2, 3, 90, 91, 92);
peaks.setUnitCell(cell);

UnitCell newCell = peaks.unitCell();
TS_ASSERT_EQUALS(unitCellToStr(newCell), unitCellToStr(cell));
}

void testUnitCellFromLogs()
{
TableWorkspace_sptr newDummy(m_dummyData->clone());

UnitCell cell(1, 2, 3, 90, 91, 92);
newDummy->logs()->addProperty<std::string>("UnitCell", unitCellToStr(cell));

PoldiPeakCollection collection(newDummy);
TS_ASSERT_EQUALS(unitCellToStr(collection.unitCell()), unitCellToStr(cell));
}

void testPointGroupStringConversion()
{
TestablePoldiPeakCollection peaks;
PointGroup_sptr m3m = PointGroupFactory::Instance().createPointGroup("m-3m");

TS_ASSERT(peaks.pointGroupFromString(peaks.pointGroupToString(m3m)));

std::cout << m3m->getName() << std::endl;

std::vector<PointGroup_sptr> pgs = getAllPointGroups();
std::cout << "Size: " << pgs.size() << std::endl;

TS_ASSERT_EQUALS(m3m->getName(), peaks.pointGroupFromString(peaks.pointGroupToString(m3m))->getName());
}

Expand Down Expand Up @@ -276,6 +295,7 @@ class PoldiPeakCollectionTest : public CxxTest::TestSuite
TS_ASSERT_EQUALS(clone->getProfileFunctionName(), peaks->getProfileFunctionName());
TS_ASSERT_EQUALS(clone->intensityType(), peaks->intensityType());
TS_ASSERT_EQUALS(clone->peakCount(), peaks->peakCount());
TS_ASSERT_EQUALS(unitCellToStr(clone->unitCell()), unitCellToStr(peaks->unitCell()));

for(size_t i = 0; i < clone->peakCount(); ++i) {
PoldiPeak_sptr clonePeak = clone->peak(i);
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