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IntegratePeakTimeSlices.cpp
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IntegratePeakTimeSlices.cpp
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// 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 & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
/*
* IntegratePeakTimeSlices.cpp
*
* Created on: May 5, 2011
* Author: ruth
*
*
*
*/
#include "MantidCrystal/IntegratePeakTimeSlices.h"
#include "MantidAPI/ConstraintFactory.h"
#include "MantidAPI/FuncMinimizerFactory.h"
#include "MantidAPI/FunctionDomain1D.h"
#include "MantidAPI/FunctionFactory.h"
#include "MantidAPI/IFuncMinimizer.h"
#include "MantidAPI/IFunction.h"
#include "MantidAPI/WorkspaceFactory.h"
#include "MantidDataObjects/Workspace2D.h"
#include "MantidHistogramData/BinEdges.h"
#include <boost/math/special_functions/round.hpp>
#include <utility>
using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::DataObjects;
using namespace Mantid::Geometry;
using namespace Mantid::HistogramData;
using namespace std;
namespace Mantid {
namespace Crystal {
DECLARE_ALGORITHM(IntegratePeakTimeSlices)
// Attr, m_AttributeValues, and StatBase indicies
#define IStartRow 0
#define IStartCol 1
#define INRows 2
#define INCol 3
#define ISSIxx 4
#define ISSIyy 5
#define ISSIxy 6
#define ISSxx 7
#define ISSyy 8
#define ISSxy 9
#define ISSIx 10
#define ISSIy 11
#define ISSx 12
#define ISSy 13
#define IIntensities 14
#define ISS1 15
#define IVariance 16
#define ITotBoundary 17
#define INBoundary 18
#define IVarBoundary 19
#define NAttributes 20
// Parameter indicies
#define IBACK 0
#define ITINTENS 1
#define IXMEAN 2
#define IYMEAN 3
#define IVXX 4
#define IVYY 5
#define IVXY 6
// TODO: Edge Peaks-Return NoPeak(Intensity=0,variance=0) if any center on any
// slice is out of bounds
// TODO: Calc ratio for edge peaks, should use the slant of bivariate normal
// instead of assuming
// distribution axes are lined up with the row and col vectors
#define NParameters 7
namespace {
// # std sigs 0 .25 .5 .75 1 1.25 1.5 2 2.5
const double probs[9] = {.5f, .5987f, .6915f, .7734f, .8413f, .8944f, .9322f, .9599f, .9772f};
const int MinRowColSpan = 6;
const int MaxRowColSpan = 36;
const int MinTimeSpan = 3;
const double NeighborhoodRadiusDivPeakRadius = 1.5;
const double MaxNeighborhoodRadius = 10;
const double NStdDevPeakSpan = 2;
const double MaxGoodRatioFitvsExpIntenisites = 2.5;
const double MinGoodRatioFitvsExpIntenisites = .25;
const double MinGoodIoverSigI = 3.0;
const double MinVariationInXYvalues = .6; // Peak spans one pixel only
const double MaxCorrCoeffinXY = .9; // otherwise all data on one line
} // namespace
IntegratePeakTimeSlices::IntegratePeakTimeSlices()
: Algorithm(), m_R0(-1), m_ROW(0.), m_COL(0.), m_cellWidth(0.), m_cellHeight(0.), m_NROWS(0), m_NCOLS(0) {
m_debug = false;
if (m_debug)
g_log.setLevel(7);
m_EdgePeak = false;
m_NeighborIDs = new int[3];
m_NeighborIDs[0] = 3;
m_NeighborIDs[1] = 2;
m_AttributeNames[0] = "StartRow";
m_AttributeNames[1] = "StartCol";
m_AttributeNames[2] = "NRows";
m_AttributeNames[3] = "NCols";
m_AttributeNames[4] = "SSIxx";
m_AttributeNames[5] = "SSIyy";
m_AttributeNames[6] = "SSIxy";
m_AttributeNames[7] = "SSxx";
m_AttributeNames[8] = "SSyy";
m_AttributeNames[9] = "SSxy";
m_AttributeNames[10] = "SSIx";
m_AttributeNames[11] = "SSIy";
m_AttributeNames[12] = "SSx";
m_AttributeNames[13] = "SSy";
m_AttributeNames[14] = "Intensities";
m_AttributeNames[15] = " SS1";
m_AttributeNames[16] = "Variance";
m_AttributeNames[17] = "TotBoundary";
m_AttributeNames[18] = "NBoundary";
m_AttributeNames[19] = "VarianceBoundary";
m_ParameterNames[0] = "Background";
m_ParameterNames[1] = "Intensity";
m_ParameterNames[2] = "Mcol";
m_ParameterNames[3] = "Mrow";
m_ParameterNames[4] = "SScol";
m_ParameterNames[5] = "SSrow";
m_ParameterNames[6] = "SSrc";
std::fill(m_ParameterValues.begin(), m_ParameterValues.end(), 0.0);
}
double SQRT(double v) {
if (v < 0)
return -1;
return sqrt(v);
}
/// Destructor
IntegratePeakTimeSlices::~IntegratePeakTimeSlices() { delete[] m_NeighborIDs; }
void IntegratePeakTimeSlices::init() {
declareProperty(std::make_unique<WorkspaceProperty<MatrixWorkspace>>("InputWorkspace", "", Direction::Input),
"A 2D workspace with X values of time of flight");
declareProperty(std::make_unique<WorkspaceProperty<TableWorkspace>>("OutputWorkspace", "", Direction::Output),
"Name of the output table workspace with Log info");
declareProperty(std::make_unique<WorkspaceProperty<PeaksWorkspace>>("Peaks", "", Direction::Input),
"Workspace of Peaks");
declareProperty("PeakIndex", 0, "Index of peak in PeaksWorkspace to integrate");
declareProperty("PeakQspan", .06, "Max magnitude of Q of Peak to Q of Peak Center, where mod(Q)=1/d");
declareProperty("CalculateVariances", true, "Calc (co)variances given parameter values versus fit (co)Variances ");
declareProperty("Ties", "", "Tie parameters(Background,Intensity, Mrow,...) to values/formulas.");
declareProperty("NBadEdgePixels", 0, "Number of bad Edge Pixels");
declareProperty("Intensity", 0.0, "Peak Integrated Intensity", Direction::Output);
declareProperty("SigmaIntensity", 0.0, "Peak Integrated Intensity Error", Direction::Output);
}
/**
* Executes this algorithm
*
* Integrates one peak
* -First attempts to find row/col extents, time extents to fully get most of
*the peak
* -Integrate each time slice.
* -Report Results
*/
void IntegratePeakTimeSlices::exec() {
time_t seconds1;
seconds1 = time(nullptr);
double dQ = getProperty("PeakQspan");
g_log.debug("------------------Start Peak Integrate-------------------");
if (dQ <= 0) {
g_log.error("Negative PeakQspans are not allowed. Use .17/G where G is the "
"max unit cell length");
throw std::runtime_error("Negative PeakQspans are not allowed in IntegratePeakTimeSlices");
}
MatrixWorkspace_const_sptr inpWkSpace = getProperty("InputWorkspace");
if (!inpWkSpace) {
g_log.error("Improper Input Workspace");
throw std::runtime_error("Improper Input Workspace in IntegratePeakTimeSlices");
}
PeaksWorkspace_sptr peaksW;
peaksW = getProperty("Peaks");
if (!peaksW) {
g_log.error("Improper Peaks Input");
throw std::runtime_error("Improper Peaks Input");
}
int indx = getProperty("PeakIndex");
Peak &peak = peaksW->getPeak(indx);
//------------------------------- Get Panel
//--------------------------------------
std::shared_ptr<const Geometry::IComponent> panel_const =
peak.getInstrument()->getComponentByName(peak.getBankName());
std::shared_ptr<Geometry::IComponent> panel = std::const_pointer_cast<Geometry::IComponent>(panel_const);
if (!panel || !panel_const) {
g_log.error("Cannot get panel for a peak");
throw std::runtime_error("Cannot get panel for a peak");
}
BoundingBox box;
panel->getBoundingBox(box);
int detID = peak.getDetectorID();
if (!box.isPointInside(peak.getDetPos())) {
g_log.error("Detector pixel is NOT inside the Peaks Bank");
throw std::runtime_error("Detector pixel is NOT inside the Peaks Bank");
}
FindPlane(m_center, m_xvec, m_yvec, m_ROW, m_COL, m_NROWS, m_NCOLS, m_cellWidth, m_cellHeight, peak);
g_log.debug() << " Peak Index " << indx << '\n';
double TotVariance = 0;
double TotIntensity = 0;
double lastRow = m_ROW;
double Row0 = lastRow;
double lastCol = m_COL;
double Col0 = lastCol;
string spec_idList;
// For quickly looking up workspace index from det id
m_wi_to_detid_map = inpWkSpace->getDetectorIDToWorkspaceIndexMap();
TableWorkspace_sptr TabWS = std::make_shared<TableWorkspace>(0);
//----------------------------- get Peak extents
//------------------------------
try {
// Find the workspace index for this detector ID
detid2index_map::const_iterator it = m_wi_to_detid_map.find(detID);
size_t wsIndx = (it->second);
double R = CalculatePositionSpan(peak, dQ) / 2;
R = min<double>(MaxRowColSpan * max<double>(m_cellWidth, m_cellHeight), R);
R = max<double>(MinRowColSpan * max<double>(m_cellWidth, m_cellHeight), R);
R = 2 * R; // Gets a few more background cells.
int Chan;
const auto &X = inpWkSpace->x(wsIndx);
int dChan = CalculateTimeChannelSpan(peak, dQ, X, int(wsIndx), Chan);
dChan = max<int>(dChan, MinTimeSpan);
double Centy = Row0;
double Centx = Col0;
IDetector_const_sptr CenterDet = peak.getDetector();
double neighborRadius; // last radius for finding neighbors
neighborRadius = min<double>(MaxNeighborhoodRadius, NeighborhoodRadiusDivPeakRadius * R);
auto Nneighbors = static_cast<int>(neighborRadius * neighborRadius / m_cellWidth / m_cellHeight * 4);
Nneighbors = min<int>(Nneighbors, static_cast<int>(inpWkSpace->getNumberHistograms()) - 2);
delete[] m_NeighborIDs;
m_NeighborIDs = new int[Nneighbors + 2];
m_NeighborIDs[0] = Nneighbors + 2;
m_NeighborIDs[1] = 2;
Kernel::V3D Cent = (m_center + m_xvec * (Centx - m_COL) + m_yvec * (Centy - m_ROW));
getNeighborPixIDs(panel, Cent, neighborRadius, m_NeighborIDs);
if (m_NeighborIDs[1] < 10) {
g_log.error("Not enough neighboring pixels to fit ");
throw std::runtime_error("Not enough neighboring pixels to fit ");
}
int NBadEdgeCells = getProperty("NBadEdgePixels");
int MaxChan = -1;
double MaxCounts = -1;
// --------------- Find Time Chan with max counts----------------
for (int dir = 1; dir > -2; dir -= 2) {
bool done = false;
for (int t = 0; t < dChan && !done; t++)
if (dir < 0 && t == 0) {
Centy = Row0;
Centx = Col0;
} else if (Chan + dir * t < 0 || Chan + dir * t >= static_cast<int>(X.size()))
done = true;
else {
int NN = m_NeighborIDs[1];
MatrixWorkspace_sptr Data = WorkspaceFactory::Instance().create(std::string("Workspace2D"), 3, NN, NN);
auto XXX = std::make_shared<DataModeHandler>(R, R, Centy, Centx, m_cellWidth, m_cellHeight,
getProperty("CalculateVariances"), NBadEdgeCells,
m_NCOLS - NBadEdgeCells, NBadEdgeCells, m_NROWS - NBadEdgeCells);
m_AttributeValues = XXX;
XXX->setCurrentRadius(R);
SetUpData1(Data, inpWkSpace, Chan + dir * t, Chan + dir * t, R, CenterDet->getPos(), spec_idList);
if (m_AttributeValues->StatBaseVals(ISSIxx) > 0) {
if (m_AttributeValues->StatBaseVals(IIntensities) > MaxCounts) {
MaxCounts = m_AttributeValues->StatBaseVals(IIntensities);
MaxChan = Chan + dir * t;
}
if (m_AttributeValues->StatBaseVals(IIntensities) > 0) {
Centx = m_AttributeValues->StatBaseVals(ISSIx) / m_AttributeValues->StatBaseVals(IIntensities);
Centy = m_AttributeValues->StatBaseVals(ISSIy) / m_AttributeValues->StatBaseVals(IIntensities);
} else
done = true;
} else
done = true;
if (t >= 3 && (m_AttributeValues->StatBaseVals(IIntensities) < MaxCounts / 2.0) && MaxCounts >= 0)
done = true;
}
}
if (MaxChan > 0)
Chan = MaxChan;
g_log.debug() << " largest Channel,Radius,m_cellWidth,m_cellHeight = " << Chan << " " << R << " " << m_cellWidth
<< " " << m_cellHeight << '\n';
if (R < MinRowColSpan / 2 * max<double>(m_cellWidth, m_cellHeight) || dChan < MinTimeSpan) {
g_log.error("Not enough rows and cols or time channels ");
throw std::runtime_error("Not enough rows and cols or time channels ");
}
InitializeColumnNamesInTableWorkspace(TabWS);
//------------------------------------- Start the Integrating
//-------------------------------
double time;
int ncells;
Mantid::API::Progress prog(this, 0.0, 1.0, dChan);
// Set from attributes replace by m_R0
m_R0 = -1;
int LastTableRow = -1;
auto origAttributeList = std::make_shared<DataModeHandler>();
auto lastAttributeList = std::make_shared<DataModeHandler>();
for (int dir = 1; dir >= -1; dir -= 2) {
bool done = false;
for (int chan = 0; chan < dChan && !done; chan++)
if (dir < 0 && chan == 0) {
lastRow = Row0;
lastCol = Col0;
lastAttributeList = origAttributeList;
if (TabWS->rowCount() > 0)
LastTableRow = 0;
} else if (Chan + dir * chan < 0 || Chan + dir * chan >= static_cast<int>(X.size()))
done = true;
else {
int xchan = Chan + dir * chan;
size_t topIndex = xchan + 1;
if (topIndex >= X.size())
topIndex = X.size() - 1;
time = (X[xchan] + X[topIndex]) / 2.0;
double Radius = R;
if (m_R0 > 0)
Radius = m_R0;
MatrixWorkspace_sptr Data =
WorkspaceFactory::Instance().create(std::string("Workspace2D"), 3, m_NeighborIDs[1], m_NeighborIDs[1]);
g_log.debug() << " A:chan=" << xchan << " time=" << time << " Radius=" << Radius << "row= " << lastRow
<< " col=" << lastCol << '\n';
SetUpData(Data, inpWkSpace, panel, xchan, xchan, lastCol, lastRow, Cent, neighborRadius, Radius, spec_idList);
m_AttributeValues->setTime(time);
// if( dir==1 && chan ==0)
// origAttributeList= m_AttributeValues;
ncells = static_cast<int>(m_AttributeValues->StatBaseVals(ISS1));
std::vector<double> params;
std::vector<double> errs;
std::vector<std::string> names;
if (m_AttributeValues->StatBaseVals(ISSIxx) > 0 &&
m_AttributeValues->IsEnoughData(m_ParameterValues.data(), g_log) && m_ParameterValues[ITINTENS] > 0) {
double chisqOverDOF;
Fit(Data, chisqOverDOF, done, names, params, errs, lastRow, lastCol, neighborRadius);
if (!done) // Bivariate error happened
{
if (isGoodFit(params, errs, names, chisqOverDOF)) {
LastTableRow = UpdateOutputWS(TabWS, dir, xchan, params, errs, names, chisqOverDOF,
m_AttributeValues->time, spec_idList);
double TotSliceIntensity = m_AttributeValues->StatBaseVals(IIntensities);
double TotSliceVariance = m_AttributeValues->StatBaseVals(IVariance);
updatePeakInformation(params, errs, names, TotVariance, TotIntensity, TotSliceIntensity,
TotSliceVariance, chisqOverDOF, ncells);
lastAttributeList = m_AttributeValues;
if (dir == 1 && chan == 0)
origAttributeList = lastAttributeList;
} else
done = true;
}
} else //(!IsEnoughData() || ParameterValues[ITINTENS] <= 0
{
done = true;
}
if (done) // try to merge
{
done = false;
int chanMin, chanMax;
if ((dir == 1 && chan == 0) || lastAttributeList->CellHeight <= 0) {
chanMin = xchan;
chanMax = xchan + 1;
if (dir < 0)
chanMax++;
auto XXX = std::make_shared<DataModeHandler>(*m_AttributeValues);
m_AttributeValues = XXX;
if (!X.empty())
m_AttributeValues->setTime((X[chanMax] + X[chanMin]) / 2.0);
} else // lastAttributeList exists
{
chanMin = std::min<int>(xchan, xchan - dir);
chanMax = chanMin + 1;
if (lastAttributeList->case4)
chanMax++;
auto XXX = std::make_shared<DataModeHandler>(*lastAttributeList);
m_AttributeValues = XXX;
m_AttributeValues->setTime((time + m_AttributeValues->time) / 2.0);
}
if (updateNeighbors(panel, m_AttributeValues->getCurrentCenter(), Cent,
m_AttributeValues->getCurrentRadius(), neighborRadius))
Cent = m_AttributeValues->getCurrentCenter();
Data =
WorkspaceFactory::Instance().create(std::string("Workspace2D"), 3, m_NeighborIDs[1], m_NeighborIDs[1]);
SetUpData1(Data, inpWkSpace, chanMin, chanMax, m_AttributeValues->getCurrentRadius(),
m_AttributeValues->getCurrentCenter(), spec_idList);
double chisqOverDOF;
g_log.debug("Try Merge 2 time slices");
if (m_AttributeValues->StatBaseVals(ISSIxx) >= 0 &&
m_AttributeValues->IsEnoughData(m_ParameterValues.data(), g_log))
Fit(Data, chisqOverDOF, done, names, params, errs, lastRow, lastCol, neighborRadius);
else
chisqOverDOF = -1;
if (!done && isGoodFit(params, errs, names, chisqOverDOF)) {
if (LastTableRow >= 0 && LastTableRow < static_cast<int>(TabWS->rowCount()))
TabWS->removeRow(LastTableRow);
else
LastTableRow = -1;
LastTableRow = UpdateOutputWS(TabWS, dir, (chanMin + chanMax) / 2.0, params, errs, names, chisqOverDOF,
m_AttributeValues->time, spec_idList);
if (lastAttributeList->lastISAWVariance > 0 && lastAttributeList->CellHeight > 0) {
TotIntensity -= lastAttributeList->lastISAWIntensity;
TotVariance -= lastAttributeList->lastISAWVariance;
}
double TotSliceIntensity = m_AttributeValues->StatBaseVals(IIntensities);
double TotSliceVariance = m_AttributeValues->StatBaseVals(IVariance);
updatePeakInformation(params, errs, names, TotVariance, TotIntensity, TotSliceIntensity, TotSliceVariance,
chisqOverDOF, static_cast<int>(m_AttributeValues->StatBaseVals(ISS1)));
// lastAttributeList= m_AttributeValues;
if (dir == 1 && (chan == 0 || chan == 1)) {
m_AttributeValues->case4 = true;
origAttributeList = m_AttributeValues;
} else
LastTableRow = -1;
} else {
auto XXX = std::make_shared<DataModeHandler>();
lastAttributeList = XXX;
}
done = true;
}
// Get ready for the next round
Data.reset();
if (!done) {
// Now set up the center for this peak
int i = findNameInVector("Mrow", names);
if (i < 0) {
throw std::runtime_error("Inconsistency found in algorithm "
"execution. The index for the parameter "
"Mrow is negative.");
}
lastRow = boost::math::iround(params[i]);
i = findNameInVector("Mcol", names);
if (i >= 0)
lastCol = boost::math::iround(params[i]);
prog.report();
} else if (dir > 0)
prog.report(dChan / 2);
else
prog.report(dChan);
params.clear();
errs.clear();
names.clear();
}
}
} catch (std::exception &EE1) {
std::cout << "Error in main reason=" << EE1.what() << '\n';
throw std::runtime_error(" Error IntegratePeakTimeSlices:" + std::string(EE1.what()));
} catch (std::string &mess) {
throw std::runtime_error("Error IntegratePeakTimeSlices:" + mess);
} catch (...) {
throw std::runtime_error("Error IntegratePeakTimeSlices:");
}
try {
setProperty("OutputWorkspace", TabWS);
setProperty("Intensity", TotIntensity);
setProperty("SigmaIntensity", SQRT(TotVariance));
time_t seconds2;
seconds2 = time(nullptr);
double dif = difftime(seconds2, seconds1);
g_log.debug() << "Finished Integr peak number " << indx << " in " << dif << " seconds\n";
} catch (std::exception &ss) {
std::cout << "Error occurred XX " << ss.what() << '\n';
throw std::runtime_error(ss.what());
}
}
/**
* Finds all neighbors within a given Radius of the Center on the given
* component.
* @param comp -The component of interest
* @param Center- the center of the neighbors
* @param Radius - The radius from the center of neighbors to be included
* @param ArryofID -The detector ID's of the neighbors. The id of the pixel at
* the center may be included.
*/
bool IntegratePeakTimeSlices::getNeighborPixIDs(const std::shared_ptr<Geometry::IComponent> &comp, Kernel::V3D &Center,
double &Radius, int *&ArryofID) {
int N = ArryofID[1];
int MaxN = ArryofID[0];
if (N >= MaxN)
return false;
Geometry::BoundingBox box;
comp->getBoundingBox(box);
double minx = Center.X() - Radius;
double miny = Center.Y() - Radius;
double minz = Center.Z() - Radius;
double maxx = Center.X() + Radius;
double maxy = Center.Y() + Radius;
double maxz = Center.Z() + Radius;
if (box.xMin() >= maxx)
return true;
if (box.xMax() <= minx)
return true;
;
if (box.yMin() >= maxy)
return true;
if (box.yMax() <= miny)
return true;
if (box.zMin() >= maxz)
return true;
if (box.zMax() <= minz)
return true;
;
auto det = std::dynamic_pointer_cast<Geometry::Detector>(comp);
if (det) {
V3D pos = det->getPos() - Center;
if (pos.X() * pos.X() + pos.Y() * pos.Y() + pos.Z() * pos.Z() < Radius * Radius) {
ArryofID[N] = det->getID();
N++;
ArryofID[1] = N;
}
return true;
}
auto Assembly = std::dynamic_pointer_cast<const Geometry::ICompAssembly>(comp);
if (!Assembly)
return true;
bool b = true;
for (int i = 0; i < Assembly->nelements() && b; i++)
b = getNeighborPixIDs(Assembly->getChild(i), Center, Radius, ArryofID);
return b;
}
/**
* Checks and updates if needed the list of m_NeighborIDs
* @param comp Component with the neighboring pixels
* @param CentPos new Center
* @param oldCenter old Center
* @param NewRadius new Radius
* @param neighborRadius old the new neighborhood radius
*/
bool IntegratePeakTimeSlices::updateNeighbors(std::shared_ptr<Geometry::IComponent> &comp, V3D CentPos, V3D oldCenter,
double NewRadius, double &neighborRadius) {
double DD = (CentPos - oldCenter).norm();
bool changed = false;
if (DD + NewRadius > neighborRadius) {
auto NN = int(NStdDevPeakSpan * NeighborhoodRadiusDivPeakRadius * NewRadius / m_cellWidth * NStdDevPeakSpan *
NeighborhoodRadiusDivPeakRadius * NewRadius / m_cellHeight);
if (m_NeighborIDs[0] < NN) {
delete[] m_NeighborIDs;
m_NeighborIDs = new int[NN + 2];
m_NeighborIDs[0] = NN + 2;
}
m_NeighborIDs[1] = 2;
neighborRadius = NeighborhoodRadiusDivPeakRadius * NewRadius;
getNeighborPixIDs(comp, CentPos, neighborRadius, m_NeighborIDs);
changed = true;
} else // big enough neighborhood so
neighborRadius -= DD;
return changed;
}
/**
* Calculates the span in rows and columns needed to include all data within dQ
*of the
* specified peak
* @param peak The peak of interest
* @param dQ The offset from the peak's Q value for the data of interest
*
* NOTE: differentials of Q =mv*sin(scatAng/2)/2 were used to calculate this
* Also s=r*theta was used to transfer d ScatAng to distance on a bank.
*/
double IntegratePeakTimeSlices::CalculatePositionSpan(Peak const &peak, const double dQ) {
try {
double Q = 0, ScatAngle = 0, dScatAngle = 0, DetSpan = 0;
Q = peak.getQLabFrame().norm();
Geometry::Instrument_const_sptr instr = peak.getInstrument();
const Geometry::IComponent_const_sptr sample = instr->getSample();
V3D pos = peak.getDetPos() - sample->getPos();
ScatAngle = acos(pos.Z() / pos.norm());
dScatAngle = 2 * dQ / Q * tan(ScatAngle / 2);
DetSpan = pos.norm() * dScatAngle; // s=r*theta
DetSpan = fabs(DetSpan);
// IDetector_sptr det = peak.getDetector();
return DetSpan;
} catch (std::exception &s) {
std::cout << "err in getNRowsCols, reason=" << s.what() << '\n';
return 0;
}
}
/**
* Calculates the span of channels needed to encompass all data around the peak
*with Q values within dQ
* of this peak's Q value
*
* @param peak The peak of interest
* @param dQ The offset of peak's Q value whose data is considered part of
*the peak
* @param X The list of time channel values.
* @param specNum The spectral number for the pixel(Not Currently Used)
* @param Centerchan The center time channel number( from X)
*
* @return The number of time channels around Centerchan to use
*/
int IntegratePeakTimeSlices::CalculateTimeChannelSpan(Geometry::IPeak const &peak, const double dQ, const HistogramX &X,
const int specNum, int &Centerchan) {
UNUSED_ARG(specNum);
double Q = peak.getQLabFrame().norm(); // getQ( peak)/2/M_PI;
double time = peak.getTOF();
double dtime = dQ / Q * time;
int chanCenter = findTimeChannel(X, time);
Centerchan = chanCenter;
int chanLeft = findTimeChannel(X, time - dtime);
int chanRight = findTimeChannel(X, time + dtime);
int dchan = abs(chanCenter - chanLeft);
if (abs(chanRight - chanCenter) > dchan)
dchan = abs(chanRight - chanCenter);
dchan = max<int>(3, dchan);
return dchan + 5; // heuristic should be a lot more
}
/**
* For NonFlat banks, this determines the data of a small planar region
*approximating the instrument
* close to the peak
*
* @param center The position of the center of this plane
* @param xvec The direction the column values increase
* @param yvec The direction the row values increase
* @param ROW The row for this peak( 0 if undefined)
* @param COL The col for this peak( 0 if undefined)
* @param NROWS The number? of rows for this bANK
* @param NCOLS The number of columns for this bank
* @param pixWidthx The width of a pixel
* @param pixHeighty The height of a pixel
* @param peak
*/
void IntegratePeakTimeSlices::FindPlane(V3D ¢er, V3D &xvec, V3D &yvec, double &ROW, double &COL, int &NROWS,
int &NCOLS, double &pixWidthx, double &pixHeighty,
DataObjects::Peak const &peak) const {
NROWS = NCOLS = -1;
IDetector_const_sptr det = peak.getDetector();
V3D detPos = det->getPos();
center.setX(detPos.X());
center.setY(detPos.Y());
center.setZ(detPos.Z());
std::shared_ptr<const Detector> dett = std::dynamic_pointer_cast<const Detector>(det);
pixWidthx = dett->getWidth();
pixHeighty = dett->getHeight();
Kernel::Quat Qt = dett->getRotation();
V3D yaxis0(0.0, 1.0, 0.0);
Qt.rotate(yaxis0);
yaxis0.normalize();
V3D xaxis0(1, 0, 0);
Qt.rotate(xaxis0);
xaxis0.normalize();
xvec.setX(xaxis0.X());
xvec.setY(xaxis0.Y());
xvec.setZ(xaxis0.Z());
yvec.setX(yaxis0.X());
yvec.setY(yaxis0.Y());
yvec.setZ(yaxis0.Z());
ROW = peak.getRow();
COL = peak.getCol();
Geometry::Instrument_const_sptr inst = peak.getInstrument();
if (!inst)
throw std::invalid_argument("No instrument for peak");
std::shared_ptr<const IComponent> panel = inst->getComponentByName(peak.getBankName());
std::shared_ptr<const RectangularDetector> ddet = std::dynamic_pointer_cast<const RectangularDetector>(panel);
if (ddet) {
std::pair<int, int> CR = ddet->getXYForDetectorID(det->getID());
ROW = CR.second;
COL = CR.first;
pixWidthx = ddet->xstep();
pixHeighty = ddet->ystep();
NROWS = ddet->ypixels();
NCOLS = ddet->xpixels();
return;
}
// Get NROWS and NCOLS for other panels
NROWS = NCOLS = -1;
if (!inst)
return;
if (!panel)
return;
std::shared_ptr<const Component> compPanel = std::dynamic_pointer_cast<const Component>(panel);
std::shared_ptr<IComponent> panel1(compPanel->base()->clone());
BoundingBox B;
Quat rot = panel1->getRotation();
rot.inverse();
panel1->rotate(rot);
panel1->getBoundingBox(B);
NROWS = boost::math::iround((B.yMax() - B.yMin()) / pixHeighty);
NCOLS = boost::math::iround((B.xMax() - B.xMin()) / pixWidthx);
}
/**
* Updates the cumulative statistics for the data being considered
*
* @param intensity -The experimental intensity at the given pixel
* @param variance -The square of the errors in the above intensity
* @param row -The row of the given pixel
* @param col -The column of the given pixel
* @param StatBase -The data accumulator
*/
void IntegratePeakTimeSlices::updateStats(const double intensity, const double variance, const double row,
const double col, std::vector<double> &StatBase) {
StatBase[ISSIxx] += col * col * intensity;
StatBase[ISSIyy] += intensity * row * row;
StatBase[ISSIxy] += intensity * row * col;
StatBase[ISSxx] += col * col;
StatBase[ISSyy] += row * row;
StatBase[ISSxy] += row * col;
StatBase[ISSIx] += intensity * col;
StatBase[ISSIy] += intensity * row;
StatBase[ISSx] += col;
StatBase[ISSy] += row;
StatBase[IIntensities] += intensity;
StatBase[IVariance] += variance;
StatBase[ISS1] += 1;
}
/**
* Finds and saves the initial values and modes( like isEdge) for this data.
*
* @param Varx The Variance of the x(column) values
* @param Vary The Variance of the y(row) values
* @param b The background
*
* NOTE:Used only in GetParams which is used only in PreFit which is not
* currently used.
*/
std::vector<double> DataModeHandler::InitValues(double Varx, double Vary, double b) {
std::vector<double> Res(7);
Res[IVXX] = Varx;
Res[IVYY] = Vary;
Res[IVXY] = 0;
auto nCells = static_cast<int>(StatBase[ISS1]);
double Den = StatBase[IIntensities] - b * nCells;
Res[IXMEAN] = (StatBase[ISSIx] - b * StatBase[ISSx]) / Den;
Res[IYMEAN] = (StatBase[ISSIy] - b * StatBase[ISSy]) / Den;
Res[IBACK] = b;
Res[ITINTENS] = StatBase[IIntensities] - b * nCells;
//---- Is Edge Cell ???-------
double NstdX = 4 * (currentRadius / CellWidth - EdgeX) / sqrt(Varx);
double NstdY = 4 * (currentRadius / CellHeight - EdgeY) / sqrt(Vary);
double sigx = 1;
double sigy = 1;
if (NstdX < 0)
sigx = -1;
if (NstdY < 0)
sigy = -1;
double x = 1;
if (sigy * NstdY < 7 && sigy * NstdY >= 0) // is close to row edge
{
x = probs[std::lround(sigy * NstdY)];
if (sigy < 0)
x = 1 - x;
double My2 = StatBase[IStartRow];
if (Res[IYMEAN] - My2 > My2 + StatBase[INRows] - Res[IYMEAN])
My2 += StatBase[INRows];
Res[IYMEAN] = Res[IYMEAN] * x + (1 - x) * My2;
}
double x1 = 1;
if (sigx * NstdX < 7 && sigx * NstdX > 0) // is close to x edge
{
x1 = probs[std::lround(sigx * NstdX)];
if (sigx < 0)
x1 = 1 - x1;
double Mx2 = StatBase[IStartCol];
if (Res[IXMEAN] - Mx2 > Mx2 + StatBase[INCol] - Res[IXMEAN])
Mx2 += StatBase[INCol];
Res[IXMEAN] = Res[IXMEAN] * x1 + (1 - x1) * Mx2;
}
Res[ITINTENS] /= x * x1;
return Res;
}
/**
* Calculates the initial values of the parameters given background b.
* Used only in the PreFit method that is not used.
* @param b the background
*
* @return The vector of parameter values.
*/
std::vector<double> DataModeHandler::GetParams(double b) {
auto nCells = static_cast<int>(StatBase[ISS1]);
double Den = StatBase[IIntensities] - b * nCells;
double Varx, Vary;
Varx = VarxHW;
Vary = VaryHW;
double Rx = lastRCRadius / CellWidth - EdgeX;
double Ry = lastRCRadius / CellHeight - EdgeY;
if (Varx <= 0)
Varx = HalfWidthAtHalfHeightRadius * HalfWidthAtHalfHeightRadius;
if (Vary <= 0)
Vary = HalfWidthAtHalfHeightRadius * HalfWidthAtHalfHeightRadius;
// Use
if (Rx * Rx < 4 * Varx || Ry * Ry < 4 * Vary) {
return InitValues(Varx, Vary, b);
}
if (Den < 0)
return std::vector<double>();
double Mx = StatBase[ISSIx] - b * StatBase[ISSx];
double My = StatBase[ISSIy] - b * StatBase[ISSy];
double Sxx = (StatBase[ISSIxx] - b * StatBase[ISSxx] - Mx * Mx / Den) / Den;
double Syy = (StatBase[ISSIyy] - b * StatBase[ISSyy] - My * My / Den) / Den;
double Sxy = (StatBase[ISSIxy] - b * StatBase[ISSxy] - Mx * My / Den) / Den;
double Intensity = StatBase[IIntensities] - b * nCells;
double col = Mx / Den;
double row = My / Den;
std::vector<double> Result(7);
Result[IBACK] = b;
Result[ITINTENS] = Intensity;
Result[IXMEAN] = col;
Result[IYMEAN] = row;
Result[IVXX] = Sxx;
Result[IVYY] = Syy;
Result[IVXY] = Sxy;
return Result;
}