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Commit ea81f9ff authored by Yaroslav Gevorkov's avatar Yaroslav Gevorkov
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added center refinement ability

parent 0230c11f
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include/Backprojection.h
View file @ ea81f9ff
......@@ -8,7 +8,7 @@ class Backprojection
public:
Backprojection(const ExperimentSettings& experimentSettings);
void backProject(const Eigen::Matrix2Xf& detectorPeaks_m, Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms );
void backProject(const Eigen::Matrix2Xf& detectorPeaks_m, Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms ) const;
private:
ExperimentSettings experimentSettings;
......
include/PinkIndexer.h
View file @ ea81f9ff
......@@ -40,21 +40,23 @@ class PinkIndexer
variableLatticeParameters,
firstFixedThenVariableLatticeParameters,
firstFixedThenVariableLatticeParametersMultiSeedLengths,
firstFixedThenVariableLatticeParametersMultiSeed
firstFixedThenVariableLatticeParametersMultiSeed,
variableLatticeParametersCenterAdjustmentMultiSeed
};
PinkIndexer(const ExperimentSettings& experimentSettings, ConsideredPeaksCount consideredPeaksCount, AngleResolution angleResolution,
RefinementType refinementType, float maxResolutionForIndexing_1_per_A);
int indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
int indexPattern(Lattice& indexedLattice, Eigen::Vector2f& centerShift, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
const Eigen::Matrix2Xf& detectorPeaks_m, int threadCount);
int indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
int indexPattern(Lattice& indexedLattice, Eigen::Vector2f& centerShift, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
const Eigen::Matrix3Xf& meanReciprocalPeaks_1_per_A, int threadCount);
private:
void reducePeakCount(Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms, Eigen::RowVectorXf& intensities,
const Eigen::Matrix2Xf& detectorPeaks_m);
void refine(Lattice& indexedLattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms);
void refine(Lattice& indexedLattice, Eigen::Vector2f& centerShift, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms,
const Eigen::Matrix2Xf& detectorPeaks_m);
float getAngleResolution();
int getConsideredPeaksCount();
......
include/ReciprocalToRealProjection.h
View file @ ea81f9ff
......@@ -10,7 +10,7 @@ class ReciprocalToRealProjection
ReciprocalToRealProjection(const ExperimentSettings& experimentSettings);
virtual ~ReciprocalToRealProjection() = default;
virtual void project(Eigen::Matrix2Xf& projectedPoints, const Eigen::Matrix3Xf& reciprocalPoints) = 0;
virtual void project(Eigen::Matrix2Xf& projectedPoints, const Eigen::Matrix3Xf& reciprocalPoints) const = 0;
protected:
ExperimentSettings experimentSettings;
......
include/Refinement.h
View file @ ea81f9ff
#pragma once
#include "Backprojection.h"
#include "Lattice.h"
#include "ReciprocalToRealProjection.h"
#include <Eigen/Dense>
#include <vector>
......@@ -9,14 +11,18 @@ class Refinement
{
public:
Refinement(float tolerance);
Refinement(float tolerance, const Backprojection& backprojection);
void refineFixedLattice(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms);
void refineVariableLattice(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms);
void refineFixedLattice(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms);
void refineVariableLattice(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms);
int getFittedPeaksCount(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms);
void refineVariableLatticeWithCenter(Lattice& lattice, Eigen::Vector2f& centerShift, const Eigen::Matrix2Xf& detectorPeaks_m);
void refineCenter(Eigen::Vector2f& centerShift, const Lattice& lattice, const Eigen::Matrix2Xf& detectorPeaks_m, float startStepSize = 20e-6);
int getFittedPeaksCount(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms);
int getFittedPeaks(Lattice& lattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, const Eigen::Matrix3Xf& ucsDirections,
const Eigen::Matrix2Xf& ucsBorderNorms);
double getMeanDefect(const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms,
const Eigen::Array2Xf& ucsBorderNorms);
double getMeanDefect(const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms,
bool significantChangesToPreviousCall = true);
void setTolerance(float tolerance)
......@@ -29,14 +35,19 @@ class Refinement
}
private:
void getDefects(Eigen::ArrayXf& defects, const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms,
void getDefects(Eigen::ArrayXf& defects, const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms,
bool significantChangesToPreviousCall = true);
void getCenterShiftedBackprojection(Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms, const Eigen::Matrix2Xf& detectorPeaks_m,
const Eigen::Vector2f& centerShift);
float tolerance;
const Backprojection* backprojection;
// preallocation
Eigen::ArrayXf defects;
Eigen::Matrix2Xf ucsBorderNormsSquared;
Eigen::Array2Xf ucsBorderNormsSquared;
Eigen::Matrix3Xf millerIndices_close;
Eigen::Matrix3Xf millerIndices_far;
Eigen::Matrix3Xf candidatePeaks;
......@@ -48,4 +59,7 @@ class Refinement
Eigen::Array<bool, 1, Eigen::Dynamic> notPredictablePeaks;
Eigen::ArrayXf meanDefects;
int validCandidatePeaksCount;
Eigen::Matrix2Xf detectorPeaks_m_shifted;
Eigen::Matrix3Xf ucsDirections;
Eigen::Array2Xf ucsBorderNorms;
};
include/SimpleProjection.h
View file @ ea81f9ff
......@@ -8,5 +8,5 @@ class SimpleProjection : public ReciprocalToRealProjection
public:
SimpleProjection(const ExperimentSettings& experimentSettings);
void project(Eigen::Matrix2Xf& projectedPeaks, const Eigen::Matrix3Xf& reciprocalPeaks);
void project(Eigen::Matrix2Xf& projectedPeaks, const Eigen::Matrix3Xf& reciprocalPeaks) const;
};
include/adaptions/crystfel/PinkIndexer.h
View file @ ea81f9ff
......@@ -9,7 +9,8 @@
extern "C" {
#endif
typedef enum {
typedef enum
{
CONSIDERED_PEAKS_COUNT_veryFew = 0,
CONSIDERED_PEAKS_COUNT_few = 1,
CONSIDERED_PEAKS_COUNT_standard = 2,
......@@ -19,7 +20,8 @@ typedef enum {
CONSIDERED_PEAKS_COUNT_lastEnum
} consideredPeaksCount_t;
typedef enum {
typedef enum
{
ANGLE_RESOLUTION_extremelyLoose = 0,
ANGLE_RESOLUTION_loose = 1,
ANGLE_RESOLUTION_standard = 2,
......@@ -29,14 +31,14 @@ typedef enum {
ANGLE_RESOLUTION_lastEnum
} angleResolution_t;
typedef enum {
typedef enum
{
REFINEMENT_TYPE_none = 0,
REFINEMENT_TYPE_fixedLatticeParameters = 1,
REFINEMENT_TYPE_variableLatticeParameters = 2,
REFINEMENT_TYPE_firstFixedThenVariableLatticeParameters = 3,
REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeedLengths = 4,
REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeed = 5,
REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeed = 4,
REFINEMENT_TYPE_variableLatticeParametersCenterAdjustmentMultiSeed = 5,
REFINEMENT_TYPE_lastEnum
} refinementType_t;
......@@ -46,7 +48,7 @@ PinkIndexer* PinkIndexer_new(ExperimentSettings* experimentSettings, consideredP
refinementType_t refinementType, float maxResolutionForIndexing_1_per_A);
void PinkIndexer_delete(PinkIndexer* pinkIndexer);
int PinkIndexer_indexPattern(PinkIndexer* pinkIndexer, Lattice_t* indexedLattice, reciprocalPeaks_1_per_A_t* meanReciprocalPeaks_1_per_A,
int PinkIndexer_indexPattern(PinkIndexer* pinkIndexer, Lattice_t* indexedLattice, float centerShift[2], reciprocalPeaks_1_per_A_t* meanReciprocalPeaks_1_per_A,
const float* intensities, float maxRefinementDisbalance, int threadCount);
......
src/Backprojection.cpp
View file @ ea81f9ff
......@@ -10,7 +10,7 @@ Backprojection::Backprojection(const ExperimentSettings& experimentSettings)
{
}
void Backprojection::backProject(const Matrix2Xf& detectorPeaks_m, Matrix3Xf& ucsDirections, Array2Xf& ucsBorderNorms)
void Backprojection::backProject(const Matrix2Xf& detectorPeaks_m, Matrix3Xf& ucsDirections, Array2Xf& ucsBorderNorms) const
{
Matrix3Xf projectionDirections(3, detectorPeaks_m.cols());
projectionDirections << RowVectorXf::Constant(1, detectorPeaks_m.cols(), experimentSettings.getDetectorDistance_m()),
......
src/PinkIndexer.cpp
View file @ ea81f9ff
......@@ -25,15 +25,15 @@ PinkIndexer::PinkIndexer(const ExperimentSettings& experimentSettings, Considere
sinogram.setSinogramAngleResolution(angleResolution_deg);
}
int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
int PinkIndexer::indexPattern(Lattice& indexedLattice, Vector2f& centerShift, Array<bool, Dynamic, 1>& fittedPeaks, RowVectorXf& intensities,
const Matrix3Xf& meanReciprocalPeaks_1_per_A, int threadCount)
{
Matrix2Xf detectorPeaks_m;
reciprocalToRealProjection.project(detectorPeaks_m, meanReciprocalPeaks_1_per_A);
return indexPattern(indexedLattice, fittedPeaks, intensities, detectorPeaks_m, threadCount);
return indexPattern(indexedLattice, centerShift, fittedPeaks, intensities, detectorPeaks_m, threadCount);
}
int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, Eigen::RowVectorXf& intensities,
int PinkIndexer::indexPattern(Lattice& indexedLattice, Vector2f& centerShift, Array<bool, Dynamic, 1>& fittedPeaks, RowVectorXf& intensities,
const Matrix2Xf& detectorPeaks_m, int threadCount)
{
Matrix3Xf ucsDirections;
......@@ -64,7 +64,7 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
Matrix3f bestBasis = bestRotation * sampleLattice.getBasis();
indexedLattice = Lattice(bestBasis);
refine(indexedLattice, ucsDirections, ucsBorderNorms);
refine(indexedLattice, centerShift, ucsDirections, ucsBorderNorms, detectorPeaks_m);
indexedLattice.minimize();
......@@ -73,8 +73,11 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
// sinogram.saveToFile("C:\\DesyFiles\\workspaces\\VisualStudio_workspace\\pinkIndexer\\workfolder\\sinogram");
}
void PinkIndexer::refine(Lattice& indexedLattice, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms)
void PinkIndexer::refine(Lattice& indexedLattice, Vector2f& centerShift, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms,
const Matrix2Xf& detectorPeaks_m)
{
centerShift.setZero();
switch (refinementType)
{
case RefinementType::none:
......@@ -99,20 +102,21 @@ void PinkIndexer::refine(Lattice& indexedLattice, const Matrix3Xf& ucsDirections
refinement.setTolerance(finalRefinementTolerance);
refinement.refineVariableLattice(indexedLattice, ucsDirections, ucsBorderNorms);
break;
case RefinementType::firstFixedThenVariableLatticeParametersMultiSeedLengths:
case RefinementType::firstFixedThenVariableLatticeParametersMultiSeed:
{
constexpr int refinemenTries = 750;
int fittedNodesCount[refinemenTries];
double fittedNodesMeanDefects[refinemenTries];
Lattice fittedLattices[refinemenTries];
constexpr int refinementTries = 750;
int fittedNodesCount[refinementTries];
double fittedNodesMeanDefects[refinementTries];
Lattice fittedLattices[refinementTries];
float maxRelativeDeviation = 0.0125;
Array<float, 1, 3> columnDeviationNorms = indexedLattice.getBasis().colwise().norm() * maxRelativeDeviation;
#pragma omp parallel for
for (int i = 0; i < refinemenTries; ++i)
for (int i = 0; i < refinementTries; ++i)
{
Refinement refinement(finalRefinementTolerance);
Matrix3f currentBasis = (indexedLattice.getBasis().array().rowwise() * (Array<float, 1, 3>::Random() * maxRelativeDeviation + 1)).array();
Matrix3f currentBasis = indexedLattice.getBasis() + (Array33f::Random().rowwise() * columnDeviationNorms).matrix();
fittedLattices[i] = Lattice(currentBasis);
refinement.setTolerance(min(finalRefinementTolerance * 2.5, 0.12));
......@@ -128,7 +132,7 @@ void PinkIndexer::refine(Lattice& indexedLattice, const Matrix3Xf& ucsDirections
int maxFittedNodesCount = refinement.getFittedPeaksCount(indexedLattice, ucsDirections, ucsBorderNorms);
double minFittedNodesMeanDefect = refinement.getMeanDefect(indexedLattice.getBasis(), ucsDirections, ucsBorderNorms);
for (int i = 0; i < refinemenTries; ++i)
for (int i = 0; i < refinementTries; ++i)
{
if (fittedNodesCount[i] > maxFittedNodesCount ||
(fittedNodesCount[i] == maxFittedNodesCount && fittedNodesMeanDefects[i] < minFittedNodesMeanDefect))
......@@ -140,29 +144,28 @@ void PinkIndexer::refine(Lattice& indexedLattice, const Matrix3Xf& ucsDirections
}
}
break;
case RefinementType::firstFixedThenVariableLatticeParametersMultiSeed:
case RefinementType::variableLatticeParametersCenterAdjustmentMultiSeed:
{
constexpr int refinementTries = 750;
int fittedNodesCount[refinementTries];
double fittedNodesMeanDefects[refinementTries];
Lattice fittedLattices[refinementTries];
Vector2f centerShifts[refinementTries];
float maxRelativeDeviation = 0.0125;
Array<float, 1, 3> columnDeviationNorms = indexedLattice.getBasis().colwise().norm() * maxRelativeDeviation;
#pragma omp parallel for
for (int i = 0; i < refinementTries; ++i)
{
Refinement refinement(finalRefinementTolerance);
Backprojection backprojection(backprojection);
Refinement refinement(finalRefinementTolerance, backprojection);
Matrix3f currentBasis = indexedLattice.getBasis() + (Array33f::Random().rowwise() * columnDeviationNorms).matrix();
fittedLattices[i] = Lattice(currentBasis);
centerShifts[i] = Vector2f::Random() * 80e-6;
refinement.setTolerance(min(finalRefinementTolerance * 2.5, 0.12));
refinement.refineFixedLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
refinement.setTolerance(min(finalRefinementTolerance * 1.8, 0.10));
refinement.refineVariableLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
refinement.setTolerance(finalRefinementTolerance);
refinement.refineVariableLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
refinement.refineVariableLatticeWithCenter(fittedLattices[i], centerShifts[i], detectorPeaks_m);
fittedNodesCount[i] = refinement.getFittedPeaksCount(fittedLattices[i], ucsDirections, ucsBorderNorms);
fittedNodesMeanDefects[i] = refinement.getMeanDefect(fittedLattices[i].getBasis(), ucsDirections, ucsBorderNorms);
......@@ -178,6 +181,7 @@ void PinkIndexer::refine(Lattice& indexedLattice, const Matrix3Xf& ucsDirections
maxFittedNodesCount = fittedNodesCount[i];
minFittedNodesMeanDefect = fittedNodesMeanDefects[i];
indexedLattice = fittedLattices[i];
centerShift = centerShifts[i];
}
}
}
......
src/Refinement.cpp
View file @ ea81f9ff
......@@ -17,9 +17,17 @@ Refinement::Refinement(float tolerance)
: tolerance(tolerance)
{
millerIndices.reserve(500);
backprojection = NULL;
}
void Refinement::refineVariableLattice(Lattice& lattice, const Matrix3Xf& ucsDirections, const Matrix2Xf& ucsBorderNorms)
Refinement::Refinement(float tolerance, const Backprojection& backprojection)
: tolerance(tolerance)
, backprojection(&backprojection)
{
millerIndices.reserve(500);
}
void Refinement::refineVariableLattice(Lattice& lattice, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms)
{
Matrix3f basis = lattice.getBasis();
float delta = 1e-8;
......@@ -88,7 +96,7 @@ void Refinement::refineVariableLattice(Lattice& lattice, const Matrix3Xf& ucsDir
lattice = Lattice(basis);
}
void Refinement::refineFixedLattice(Lattice& lattice, const Matrix3Xf& ucsDirections, const Matrix2Xf& ucsBorderNorms)
void Refinement::refineFixedLattice(Lattice& lattice, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms)
{
Matrix3f basis = lattice.getBasis();
......@@ -132,7 +140,141 @@ void Refinement::refineFixedLattice(Lattice& lattice, const Matrix3Xf& ucsDirect
lattice = Lattice(basis);
}
int Refinement::getFittedPeaksCount(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms)
void Refinement::refineVariableLatticeWithCenter(Lattice& lattice, Vector2f& centerShift, const Eigen::Matrix2Xf& detectorPeaks_m)
{
Matrix3f basis = lattice.getBasis();
float delta = 1e-8;
float deltaCenterShift = 2e-7;
float stepSize_basis = lattice.getBasisVectorNorms().maxCoeff() * 0.002;
float minStepSize_basis = lattice.getBasisVectorNorms().minCoeff() * 0.00001;
float startStepSize_center = 20e-6;
float minStepSize_center = 1e-6;
int maxStepsCount = 200;
meanDefects.resize(maxStepsCount);
getCenterShiftedBackprojection(ucsDirections, ucsBorderNorms, detectorPeaks_m, centerShift);
meanDefects[0] = getMeanDefect(basis, ucsDirections, ucsBorderNorms);
for (int i = 0; i < maxStepsCount; i++)
{
// cout << meanDefects[i] << endl;
if (i % 3 == 0)
{
refineCenter(centerShift, lattice, detectorPeaks_m, startStepSize_center);
startStepSize_center *= 0.85;
getCenterShiftedBackprojection(ucsDirections, ucsBorderNorms, detectorPeaks_m, centerShift);
meanDefects[i] = getMeanDefect(basis, ucsDirections, ucsBorderNorms);
}
Array33f basisGradient;
Matrix3f offsetBasis = basis;
offsetBasis(0, 0) += delta;
basisGradient(0, 0) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];
offsetBasis(0, 0) = basis(0, 0);
offsetBasis(1, 0) += delta;
basisGradient(1, 0) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];
offsetBasis(1, 0) = basis(1, 0);
offsetBasis(2, 0) += delta;
basisGradient(2, 0) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];
offsetBasis(2, 0) = basis(2, 0);
offsetBasis(0, 1) += delta;
basisGradient(0, 1) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];
offsetBasis(0, 1) = basis(0, 1);
offsetBasis(1, 1) += delta;
basisGradient(1, 1) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];
offsetBasis(1, 1) = basis(1, 1);
offsetBasis(2, 1) += delta;
basisGradient(2, 1) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];
offsetBasis(2, 1) = basis(2, 1);
offsetBasis(0, 2) += delta;
basisGradient(0, 2) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms) - meanDefects[i];
offsetBasis(0, 2) = basis(0, 2);
offsetBasis(1, 2) += delta;
basisGradient(1, 2) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms) - meanDefects[i];
offsetBasis(1, 2) = basis(1, 2);
offsetBasis(2, 2) += delta;
basisGradient(2, 2) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms) - meanDefects[i];
float norm = basisGradient.matrix().norm();
basisGradient = basisGradient / norm * stepSize_basis;
if (norm == 0)
{
// throw WrongUsageException("Numerical problems! Delta has been chosen too small for current lattice!\n");
break;
}
basis = basis - basisGradient.matrix();
meanDefects[i + 1] = getMeanDefect(basis, ucsDirections, ucsBorderNorms);
if (meanDefects[i + 1] > meanDefects[i])
{
stepSize_basis = stepSize_basis * 0.9;
if (i > 10 && (meanDefects.segment(i - 4, 4).maxCoeff() - meanDefects.segment(i - 4, 4).minCoeff()) / meanDefects[i] < 0.01)
{ // settled down
stepSize_basis = stepSize_basis * 0.2;
}
if (stepSize_basis < minStepSize_basis)
break;
}
}
lattice = Lattice(basis);
}
void Refinement::refineCenter(Eigen::Vector2f& centerShift, const Lattice& lattice, const Eigen::Matrix2Xf& detectorPeaks_m, float startStepSize)
{
Matrix3f basis = lattice.getBasis();
float deltaCenterShift = 5e-7;
float minStepSize_center = 1e-6;
float stepSize_center = max(startStepSize, minStepSize_center);
int maxStepsCount = 25;
meanDefects.resize(maxStepsCount);
getCenterShiftedBackprojection(ucsDirections, ucsBorderNorms, detectorPeaks_m, centerShift);
meanDefects[0] = getMeanDefect(basis, ucsDirections, ucsBorderNorms);
for (int i = 0; i < maxStepsCount; i++)
{
// cout << meanDefects[i] << endl;
Vector2f centerOffsetGradient;
Vector2f offsetCenterShift = centerShift + Vector2f(deltaCenterShift, 0);
getCenterShiftedBackprojection(ucsDirections, ucsBorderNorms, detectorPeaks_m, offsetCenterShift);
centerOffsetGradient.x() = getMeanDefect(basis, ucsDirections, ucsBorderNorms) - meanDefects[i];
offsetCenterShift = centerShift + Vector2f(0, deltaCenterShift);
getCenterShiftedBackprojection(ucsDirections, ucsBorderNorms, detectorPeaks_m, offsetCenterShift);
centerOffsetGradient.x() = getMeanDefect(basis, ucsDirections, ucsBorderNorms) - meanDefects[i];
float norm = offsetCenterShift.norm();
centerOffsetGradient = centerOffsetGradient / norm * stepSize_center;
if (norm == 0)
{
// throw WrongUsageException("Numerical problems! Delta has been chosen too small for current lattice!\n");
break;
}
centerShift = centerShift - centerOffsetGradient;
getCenterShiftedBackprojection(ucsDirections, ucsBorderNorms, detectorPeaks_m, centerShift);
meanDefects[i + 1] = getMeanDefect(basis, ucsDirections, ucsBorderNorms);
if (meanDefects[i + 1] > meanDefects[i])
{
stepSize_center = stepSize_center * 0.8;
if (i > 5 && (meanDefects.segment(i - 4, 4).maxCoeff() - meanDefects.segment(i - 4, 4).minCoeff()) / meanDefects[i] < 0.01)
{ // settled down
stepSize_center = stepSize_center * 0.2;
}
if (stepSize_center < minStepSize_center)
break;
}
}
}
int Refinement::getFittedPeaksCount(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms)
{
getDefects(defects, lattice.getBasis(), ucsDirections, ucsBorderNorms);
int fittedPeaksCount = (defects < tolerance).count();
......@@ -141,7 +283,7 @@ int Refinement::getFittedPeaksCount(Lattice& lattice, const Eigen::Matrix3Xf& uc
}
int Refinement::getFittedPeaks(Lattice& lattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, const Eigen::Matrix3Xf& ucsDirections,
const Eigen::Matrix2Xf& ucsBorderNorms)
const Eigen::Array2Xf& ucsBorderNorms)
{
getDefects(defects, lattice.getBasis(), ucsDirections, ucsBorderNorms);
fittedPeaks = (defects < tolerance);
......@@ -150,7 +292,7 @@ int Refinement::getFittedPeaks(Lattice& lattice, Eigen::Array<bool, Eigen::Dynam
}
void Refinement::getDefects(ArrayXf& defects, const Matrix3f& basis, const Matrix3Xf& ucsDirections, const Matrix2Xf& ucsBorderNorms,
void Refinement::getDefects(ArrayXf& defects, const Matrix3f& basis, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms,
bool significantChangesToPreviousCall)
{
Matrix3f basis_inverse = basis.inverse();
......@@ -210,7 +352,7 @@ void Refinement::getDefects(ArrayXf& defects, const Matrix3f& basis, const Matri
}
}
double Refinement::getMeanDefect(const Matrix3f& basis, const Matrix3Xf& ucsDirections, const Matrix2Xf& ucsBorderNorms, bool significantChangesToPreviousCall)
double Refinement::getMeanDefect(const Matrix3f& basis, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms, bool significantChangesToPreviousCall)
{
getDefects(defects, basis, ucsDirections, ucsBorderNorms, significantChangesToPreviousCall);
......@@ -227,6 +369,13 @@ double Refinement::getMeanDefect(const Matrix3f& basis, const Matrix3Xf& ucsDire
return defects.head(round(0.9 * (defects.size() - notPredictablePeaksCount))).mean();
}
void Refinement::getCenterShiftedBackprojection(Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms, const Eigen::Matrix2Xf& detectorPeaks_m,
const Eigen::Vector2f& centerShift)
{
detectorPeaks_m_shifted = detectorPeaks_m.colwise() + centerShift;
backprojection->backProject(detectorPeaks_m_shifted, ucsDirections, ucsBorderNorms);
}
static void roundTowardsZero(Matrix3Xf& x)
{
x = x.array().abs().floor() * x.array().sign();
......
src/SimpleProjection.cpp
View file @ ea81f9ff
......@@ -9,7 +9,7 @@ SimpleProjection::SimpleProjection(const ExperimentSettings& experimentSettings)
}
void SimpleProjection::project(Matrix2Xf& projectedPeaks, const Matrix3Xf& reciprocalPeaks)
void SimpleProjection::project(Matrix2Xf& projectedPeaks, const Matrix3Xf& reciprocalPeaks) const
{
RowVectorXf yzSquaredNorms = reciprocalPeaks.bottomRows(2).colwise().squaredNorm();
RowVectorXf rayOriginsX = (reciprocalPeaks.row(0) + (yzSquaredNorms.array() / reciprocalPeaks.row(0).array()).matrix()) / 2;
......
src/adaptions/crystfel/PinkIndexer.cpp
View file @ ea81f9ff
......@@ -70,12 +70,12 @@ extern "C" PinkIndexer* PinkIndexer_new(ExperimentSettings* experimentSettings,
case REFINEMENT_TYPE_firstFixedThenVariableLatticeParameters:
refinementType_enumClass = PinkIndexer::RefinementType::firstFixedThenVariableLatticeParameters;
break;
case REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeedLengths:
refinementType_enumClass = PinkIndexer::RefinementType::firstFixedThenVariableLatticeParametersMultiSeedLengths;
break;
case REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeed:
refinementType_enumClass = PinkIndexer::RefinementType::firstFixedThenVariableLatticeParametersMultiSeed;
break;
case REFINEMENT_TYPE_variableLatticeParametersCenterAdjustmentMultiSeed:
refinementType_enumClass = PinkIndexer::RefinementType::variableLatticeParametersCenterAdjustmentMultiSeed;
break;
default:
refinementType_enumClass = PinkIndexer::RefinementType::fixedLatticeParameters;
......@@ -91,8 +91,9 @@ extern "C" void PinkIndexer_delete(PinkIndexer* pinkIndexer)
delete pinkIndexer;
}
extern "C" int PinkIndexer_indexPattern(PinkIndexer* pinkIndexer, Lattice_t* indexedLattice, reciprocalPeaks_1_per_A_t* meanReciprocalPeaks_1_per_A,
const float* intensities, float maxRefinementDisbalance, int threadCount)
extern "C" int PinkIndexer_indexPattern(PinkIndexer* pinkIndexer, Lattice_t* indexedLattice, float centerShift[2],
reciprocalPeaks_1_per_A_t* meanReciprocalPeaks_1_per_A, const float* intensities, float maxRefinementDisbalance,
int threadCount)
{
Eigen::Matrix3Xf meanReciprocalPeaks_1_per_A_matrix(3, meanReciprocalPeaks_1_per_A->peakCount);
for (int i = 0; i < meanReciprocalPeaks_1_per_A->peakCount; i++)
......@@ -102,9 +103,11 @@ extern "C" int PinkIndexer_indexPattern(PinkIndexer* pinkIndexer, Lattice_t* ind
}
Lattice indexedLattice_class;
Eigen::Vector2f centerShift_vector;
Eigen::RowVectorXf intensities_class = Eigen::Map<Eigen::RowVectorXf>((float*)intensities, 1, meanReciprocalPeaks_1_per_A->peakCount);
Eigen::Array<bool, Eigen::Dynamic, 1> fittedPeaks;
int matchedPeaksCount = pinkIndexer->indexPattern(indexedLattice_class, fittedPeaks, intensities_class, meanReciprocalPeaks_1_per_A_matrix, threadCount);
int matchedPeaksCount =
pinkIndexer->indexPattern(indexedLattice_class, centerShift_vector, fittedPeaks, intensities_class, meanReciprocalPeaks_1_per_A_matrix, threadCount);
Eigen::Matrix3f basis = indexedLattice_class.getBasis();
indexedLattice->ax = basis(0, 0);
......@@ -117,6 +120,9 @@ extern "C" int PinkIndexer_indexPattern(PinkIndexer* pinkIndexer, Lattice_t* ind
indexedLattice->cy = basis(1, 2);
indexedLattice->cz = basis(2, 2);
centerShift[0] = centerShift_vector.x();
centerShift[1] = centerShift_vector.y();
float refinementDisbalance = getRefinementDisbalance(fittedPeaks, meanReciprocalPeaks_1_per_A_matrix);
float refinementDisbalance2 = getRefinementDisbalance2(fittedPeaks, meanReciprocalPeaks_1_per_A_matrix);
if (refinementDisbalance > maxRefinementDisbalance || refinementDisbalance2 > maxRefinementDisbalance * 0.5)
......
src/tests.cpp
View file @ ea81f9ff
......@@ -57,7 +57,8 @@ void testPinkIndexer()
auto tmp = Chronometer("sinogram");
int threadCount = 6;
Eigen::Array<bool, Eigen::Dynamic, 1> fittedPeaks;
pinkIndexer.indexPattern(indexedLattice, fittedPeaks, intensities, peaksOnDetector_m, threadCount);
Vector2f centerShift;
pinkIndexer.indexPattern(indexedLattice, centerShift, fittedPeaks, intensities, peaksOnDetector_m, threadCount);
}
SimpleDiffractionPatternPrediction simpleDiffractionPatternPrediction(experimentSettings);
......
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