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Refs #9564. Reversed direction of POLDI data.
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Unit tests had to be adjusted because of element ordering. While looking at the file,
made some performance improvements.
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Michael Wedel committed Jun 6, 2014
1 parent ff7108e commit 4eb1ba0
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Showing 4 changed files with 48 additions and 37 deletions.
11 changes: 11 additions & 0 deletions Code/Mantid/Framework/PythonInterface/plugins/algorithms/LoadSINQFile.py
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Expand Up @@ -11,6 +11,7 @@
import mantid.simpleapi
from mantid import config
import os.path
import numpy as np

#--------- place to look for dictionary files

Expand Down Expand Up @@ -65,6 +66,16 @@ def PyExec(self):
ws = mantid.simpleapi.GroupDetectors(InputWorkspace=ws,
OutputWorkspace=wname,
MapFile=grp_file, Behaviour="Sum")

# Reverse direction of POLDI data so that low index corresponds to low 2theta.
histogramCount = ws.getNumberHistograms()
oldYData = []
for i in range(histogramCount):
oldYData.append([x for x in ws.readY(i)])

for i in range(histogramCount):
ws.setY(i, np.array(oldYData[histogramCount - 1 - i]))

elif inst == "TRICS":
ws = mantid.simpleapi.LoadFlexiNexus(fname,dicname,OutputWorkspace=wname)
ws = mantid.simpleapi.SINQTranspose3D(ws,OutputWorkspace=wname)
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30 changes: 15 additions & 15 deletions Code/Mantid/Framework/SINQ/inc/MantidSINQ/PoldiUtilities/PoldiAutoCorrelationCore.h
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Expand Up @@ -49,36 +49,36 @@ class MANTID_SINQ_DLL PoldiAutoCorrelationCore
{
public:
PoldiAutoCorrelationCore(Kernel::Logger& g_log);
virtual ~PoldiAutoCorrelationCore() { }
~PoldiAutoCorrelationCore() { }

void setInstrument(boost::shared_ptr<PoldiAbstractDetector> detector, boost::shared_ptr<PoldiAbstractChopper> chopper);
void setWavelengthRange(double lambdaMin, double lambdaMax);

DataObjects::Workspace2D_sptr calculate(DataObjects::Workspace2D_sptr countData);

protected:
double getNormalizedTOFSum(std::vector<double> normalizedTofs);
std::vector<double> calculateDWeights(std::vector<double> tofsFor1Angstrom, double deltaT, double deltaD, size_t nd);
double getNormalizedTOFSum(const std::vector<double> &normalizedTofs) const;
std::vector<double> calculateDWeights(const std::vector<double> &tofsFor1Angstrom, double deltaT, double deltaD, size_t nd) const;

double getRawCorrelatedIntensity(double dValue, double weight);
virtual UncertainValue getCMessAndCSigma(double dValue, double slitTimeOffset, int index);
double reduceChopperSlitList(std::vector<UncertainValue> valuesWithSigma, double weight);
double getRawCorrelatedIntensity(double dValue, double weight) const;
UncertainValue getCMessAndCSigma(double dValue, double slitTimeOffset, int index) const;
double reduceChopperSlitList(const std::vector<UncertainValue> &valuesWithSigma, double weight) const;

std::vector<double> getDistances(std::vector<int> elements);
std::vector<double> getTofsFor1Angstrom(std::vector<int> elements);
std::vector<double> getDistances(const std::vector<int> &elements) const;
std::vector<double> getTofsFor1Angstrom(const std::vector<int> &elements) const;

virtual double getCounts(int x, int y);
virtual double getNormCounts(int x, int y);
double getCounts(int x, int y) const;
double getNormCounts(int x, int y) const;

virtual int getElementFromIndex(int index);
virtual double getTofFromIndex(int index);
double getSumOfCounts(int timeBinCount, std::vector<int> detectorElements);
int getElementFromIndex(int index) const;
double getTofFromIndex(int index) const;
double getSumOfCounts(int timeBinCount, const std::vector<int> &detectorElements) const;

virtual int cleanIndex(int index, int maximum);
int cleanIndex(int index, int maximum) const;

void setCountData(DataObjects::Workspace2D_sptr countData);

double correctedIntensity(double intensity, double weight);
double correctedIntensity(double intensity, double weight) const;


boost::shared_ptr<PoldiAbstractDetector> m_detector;
Expand Down
34 changes: 17 additions & 17 deletions Code/Mantid/Framework/SINQ/src/PoldiUtilities/PoldiAutoCorrelationCore.cpp
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Expand Up @@ -77,7 +77,7 @@ DataObjects::Workspace2D_sptr PoldiAutoCorrelationCore::calculate(DataObjects::W
* - d-resolution deltaD, which results directly from deltaT
* - number of time bins for each copper cycle
*/
std::vector<double> timeData = m_countData->dataX(0);
std::vector<double> timeData = m_countData->readX(0);

m_logger.information() << " Setting time data..." << std::endl;
m_deltaT = timeData[1] - timeData[0];
Expand Down Expand Up @@ -182,7 +182,7 @@ DataObjects::Workspace2D_sptr PoldiAutoCorrelationCore::calculate(DataObjects::W
* @param normalizedTofs :: Vector with dimensionless numbers (TOF/(time bin size)).
* @return Sum over all elements of given vector.
*/
double PoldiAutoCorrelationCore::getNormalizedTOFSum(std::vector<double> normalizedTofs)
double PoldiAutoCorrelationCore::getNormalizedTOFSum(const std::vector<double> &normalizedTofs) const
{
/* Regarding numerical differences to fortran version
*
Expand All @@ -203,7 +203,7 @@ double PoldiAutoCorrelationCore::getNormalizedTOFSum(std::vector<double> normali
* @param nd :: Number of d-values.
* @return Vector with nd elements, each containing the weight for the given d-Value
*/
std::vector<double> PoldiAutoCorrelationCore::calculateDWeights(std::vector<double> tofsFor1Angstrom, double deltaT, double deltaD, size_t nd)
std::vector<double> PoldiAutoCorrelationCore::calculateDWeights(const std::vector<double> &tofsFor1Angstrom, double deltaT, double deltaD, size_t nd) const
{
/* Currently, all d-values get the same weight, so in fact this calculation would is not really
* necessary. But since there are not too many calculations involved and in order to stay close
Expand All @@ -227,7 +227,7 @@ std::vector<double> PoldiAutoCorrelationCore::calculateDWeights(std::vector<doub
* @param weight :: Dimensionless weight used for reduction of intermediate result.
* @return Correlated intensity, not corrected for correlation background.
*/
double PoldiAutoCorrelationCore::getRawCorrelatedIntensity(double dValue, double weight)
double PoldiAutoCorrelationCore::getRawCorrelatedIntensity(double dValue, double weight) const
{
/* Analysis according to the POLDI paper.
*
Expand Down Expand Up @@ -277,7 +277,7 @@ double PoldiAutoCorrelationCore::getRawCorrelatedIntensity(double dValue, double
* @param index :: Index of detector element the calculation is performed for.
* @return Pair of intensity and error for given input.
*/
UncertainValue PoldiAutoCorrelationCore::getCMessAndCSigma(double dValue, double slitTimeOffset, int index)
UncertainValue PoldiAutoCorrelationCore::getCMessAndCSigma(double dValue, double slitTimeOffset, int index) const
{
/* Element index and TOF for 1 Angstrom from current setup. */
int element = getElementFromIndex(index);
Expand Down Expand Up @@ -363,7 +363,7 @@ UncertainValue PoldiAutoCorrelationCore::getCMessAndCSigma(double dValue, double
* @param maximum :: Number of indices.
* @return Index on interval [0, max - 1]
*/
int PoldiAutoCorrelationCore::cleanIndex(int index, int maximum)
int PoldiAutoCorrelationCore::cleanIndex(int index, int maximum) const
{
int cleanIndex = index % maximum;
if(cleanIndex < 0) {
Expand All @@ -383,7 +383,7 @@ void PoldiAutoCorrelationCore::setCountData(DataObjects::Workspace2D_sptr countD
m_elementsMaxIndex = static_cast<int>(countData->getNumberHistograms()) - 1;
}

double PoldiAutoCorrelationCore::correctedIntensity(double intensity, double weight)
double PoldiAutoCorrelationCore::correctedIntensity(double intensity, double weight) const
{
return intensity - m_correlationBackground * weight / m_sumOfWeights;
}
Expand All @@ -394,7 +394,7 @@ double PoldiAutoCorrelationCore::correctedIntensity(double intensity, double wei
* @param weight :: Dimensionless weight.
* @return Correlated intensity, multiplied by weight.
*/
double PoldiAutoCorrelationCore::reduceChopperSlitList(std::vector<UncertainValue> valuesWithSigma, double weight)
double PoldiAutoCorrelationCore::reduceChopperSlitList(const std::vector<UncertainValue> &valuesWithSigma, double weight) const
{
try {
std::vector<double> signalToNoise(valuesWithSigma.size());
Expand All @@ -413,7 +413,7 @@ double PoldiAutoCorrelationCore::reduceChopperSlitList(std::vector<UncertainValu
* @param elements :: Vector of element indices.
* @return Vector of total neutron flight paths in mm.
*/
std::vector<double> PoldiAutoCorrelationCore::getDistances(std::vector<int> elements)
std::vector<double> PoldiAutoCorrelationCore::getDistances(const std::vector<int> &elements) const
{
double chopperDistance = m_chopper->distanceFromSample();
std::vector<double> distances;
Expand All @@ -433,7 +433,7 @@ std::vector<double> PoldiAutoCorrelationCore::getDistances(std::vector<int> elem
* @param elements :: Vector of element indices.
* @return Vector of specific TOFs (microseconds/Angstrom).
*/
std::vector<double> PoldiAutoCorrelationCore::getTofsFor1Angstrom(std::vector<int> elements)
std::vector<double> PoldiAutoCorrelationCore::getTofsFor1Angstrom(const std::vector<int> &elements) const
{
// Map element indices to 2Theta-Values
std::vector<double> twoThetas(elements.size());
Expand Down Expand Up @@ -462,9 +462,9 @@ std::vector<double> PoldiAutoCorrelationCore::getTofsFor1Angstrom(std::vector<in
* @param y :: Time bin index.
* @return Counts at position.
*/
double PoldiAutoCorrelationCore::getCounts(int x, int y)
double PoldiAutoCorrelationCore::getCounts(int x, int y) const
{
return static_cast<double>(m_countData->dataY(m_elementsMaxIndex - x)[y]);
return m_countData->readY(x)[y];
}

/** Returns normalized counts for correlation method at given position - these may come from a different source than the counts
Expand All @@ -473,9 +473,9 @@ double PoldiAutoCorrelationCore::getCounts(int x, int y)
* @param y :: Time bin index.
* @return Normalized counts at position.
*/
double PoldiAutoCorrelationCore::getNormCounts(int x, int y)
double PoldiAutoCorrelationCore::getNormCounts(int x, int y) const
{
return std::max(1.0, static_cast<double>(m_countData->dataY(m_elementsMaxIndex - x)[y]));
return std::max(1.0, m_countData->readY(x)[y]);
}

/** Returns detector element index for given index
Expand All @@ -485,7 +485,7 @@ double PoldiAutoCorrelationCore::getNormCounts(int x, int y)
* @param index :: Detector element index.
* @return Detector element index.
*/
int PoldiAutoCorrelationCore::getElementFromIndex(int index)
int PoldiAutoCorrelationCore::getElementFromIndex(int index) const
{
if(index < 0 || index >= static_cast<int>(m_detectorElements.size())) {
throw(std::range_error("Index out of bounds on accessing m_detectorElements."));
Expand All @@ -499,7 +499,7 @@ int PoldiAutoCorrelationCore::getElementFromIndex(int index)
* @param index :: Specific TOF index.
* @return TOF at index.
*/
double PoldiAutoCorrelationCore::getTofFromIndex(int index)
double PoldiAutoCorrelationCore::getTofFromIndex(int index) const
{
if(index < 0 || index >= static_cast<int>(m_tofsFor1Angstrom.size())) {
throw(std::range_error("Index out of bounds on accessing m_tofsFor1Angstrom."));
Expand All @@ -514,7 +514,7 @@ double PoldiAutoCorrelationCore::getTofFromIndex(int index)
* @param detectorElements :: Vector with all detector elements to be considered for the summation.
* @return Sum of all counts.
*/
double PoldiAutoCorrelationCore::getSumOfCounts(int timeBinCount, std::vector<int> detectorElements)
double PoldiAutoCorrelationCore::getSumOfCounts(int timeBinCount, const std::vector<int> &detectorElements) const
{
double sum = 0.0;

Expand Down
10 changes: 5 additions & 5 deletions Code/Mantid/Framework/SINQ/test/PoldiAutoCorrelationCoreTest.h
View file
Expand Up @@ -214,10 +214,10 @@ class PoldiAutoCorrelationCoreTest : public CxxTest::TestSuite
TS_ASSERT_EQUALS(autoCorrelationCore.m_countData->getNumberHistograms(), 2);
TS_ASSERT_EQUALS(autoCorrelationCore.m_elementsMaxIndex, 1);

TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(0, 0), 1.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(0, 1), 1.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(1, 0), 0.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(1, 1), 0.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(0, 0), 0.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(0, 1), 0.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(1, 0), 1.0);
TS_ASSERT_EQUALS(autoCorrelationCore.getCounts(1, 1), 1.0);
}

void testgetNormCounts()
Expand Down Expand Up @@ -263,7 +263,7 @@ class PoldiAutoCorrelationCoreTest : public CxxTest::TestSuite
double tofElements[] = {1.0, 2.0};
autoCorrelationCore.m_tofsFor1Angstrom = std::vector<double>(tofElements, tofElements + 2);

int elements[] = {1, 2};
int elements[] = {0, 1};
autoCorrelationCore.m_detectorElements = std::vector<int>(elements, elements + 2);

TS_ASSERT_DELTA(autoCorrelationCore.getCMessAndCSigma(1.2, 0.0, 0).value(), 0.0, 1e-6);
Expand Down

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