use of org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer in project GDSC-SMLM by aherbert.
the class ApacheLvmFitter method computeFit.
@Override
public FitStatus computeFit(double[] y, final double[] fx, double[] a, double[] parametersVariance) {
final int n = y.length;
try {
// Different convergence thresholds seem to have no effect on the resulting fit, only the
// number of
// iterations for convergence
final double initialStepBoundFactor = 100;
final double costRelativeTolerance = 1e-10;
final double parRelativeTolerance = 1e-10;
final double orthoTolerance = 1e-10;
final double threshold = Precision.SAFE_MIN;
// Extract the parameters to be fitted
final double[] initialSolution = getInitialSolution(a);
// TODO - Pass in more advanced stopping criteria.
// Create the target and weight arrays
final double[] yd = new double[n];
// final double[] w = new double[n];
for (int i = 0; i < n; i++) {
yd[i] = y[i];
// w[i] = 1;
}
final LevenbergMarquardtOptimizer optimizer = new LevenbergMarquardtOptimizer(initialStepBoundFactor, costRelativeTolerance, parRelativeTolerance, orthoTolerance, threshold);
// @formatter:off
final LeastSquaresBuilder builder = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(getMaxEvaluations()).start(initialSolution).target(yd);
if (function instanceof ExtendedNonLinearFunction && ((ExtendedNonLinearFunction) function).canComputeValuesAndJacobian()) {
// Compute together, or each individually
builder.model(new ValueAndJacobianFunction() {
final ExtendedNonLinearFunction fun = (ExtendedNonLinearFunction) function;
@Override
public Pair<RealVector, RealMatrix> value(RealVector point) {
final double[] p = point.toArray();
final org.apache.commons.lang3.tuple.Pair<double[], double[][]> result = fun.computeValuesAndJacobian(p);
return new Pair<>(new ArrayRealVector(result.getKey(), false), new Array2DRowRealMatrix(result.getValue(), false));
}
@Override
public RealVector computeValue(double[] params) {
return new ArrayRealVector(fun.computeValues(params), false);
}
@Override
public RealMatrix computeJacobian(double[] params) {
return new Array2DRowRealMatrix(fun.computeJacobian(params), false);
}
});
} else {
// Compute separately
builder.model(new MultivariateVectorFunctionWrapper((NonLinearFunction) function, a, n), new MultivariateMatrixFunctionWrapper((NonLinearFunction) function, a, n));
}
final LeastSquaresProblem problem = builder.build();
final Optimum optimum = optimizer.optimize(problem);
final double[] parameters = optimum.getPoint().toArray();
setSolution(a, parameters);
iterations = optimum.getIterations();
evaluations = optimum.getEvaluations();
if (parametersVariance != null) {
// Set up the Jacobian.
final RealMatrix j = optimum.getJacobian();
// Compute transpose(J)J.
final RealMatrix jTj = j.transpose().multiply(j);
final double[][] data = (jTj instanceof Array2DRowRealMatrix) ? ((Array2DRowRealMatrix) jTj).getDataRef() : jTj.getData();
final FisherInformationMatrix m = new FisherInformationMatrix(data);
setDeviations(parametersVariance, m);
}
// Compute function value
if (fx != null) {
final ValueFunction function = (ValueFunction) this.function;
function.initialise0(a);
function.forEach(new ValueProcedure() {
int index;
@Override
public void execute(double value) {
fx[index++] = value;
}
});
}
// As this is unweighted then we can do this to get the sum of squared residuals
// This is the same as optimum.getCost() * optimum.getCost(); The getCost() function
// just computes the dot product anyway.
value = optimum.getResiduals().dotProduct(optimum.getResiduals());
} catch (final TooManyEvaluationsException ex) {
return FitStatus.TOO_MANY_EVALUATIONS;
} catch (final TooManyIterationsException ex) {
return FitStatus.TOO_MANY_ITERATIONS;
} catch (final ConvergenceException ex) {
// Occurs when QR decomposition fails - mark as a singular non-linear model (no solution)
return FitStatus.SINGULAR_NON_LINEAR_MODEL;
} catch (final Exception ex) {
// TODO - Find out the other exceptions from the fitter and add return values to match.
return FitStatus.UNKNOWN;
}
return FitStatus.OK;
}
use of org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer in project GDSC-SMLM by aherbert.
the class TraceDiffusion method fitMsd.
/**
* Fit the MSD using a linear fit that must pass through 0,0.
*
* <p>Update the plot by adding the fit line.
*
* @param x the x
* @param y the y
* @param title the title
* @param plot the plot
* @return [D, precision]
*/
private double[] fitMsd(double[] x, double[] y, String title, Plot plot) {
// The Weimann paper (Plos One e64287) fits:
// MSD(n dt) = 4D n dt + 4s^2
// n = number of jumps
// dt = time difference between frames
// s = localisation precision
// Thus we should fit an intercept as well.
// From the fit D = gradient / (4*exposureTime)
// D
double diffCoeff = 0;
double intercept = 0;
double precision = 0;
final LevenbergMarquardtOptimizer optimizer = new LevenbergMarquardtOptimizer();
Optimum lvmSolution;
double ic = Double.NaN;
// Fit with no intercept
try {
final LinearFunction function = new LinearFunction(x, y, clusteringSettings.getFitLength());
final double[] parameters = new double[] { function.guess() };
// @formatter:off
final LeastSquaresProblem problem = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(3000).start(parameters).target(function.getY()).weight(new DiagonalMatrix(function.getWeights())).model(function, function::jacobian).build();
// @formatter:on
lvmSolution = optimizer.optimize(problem);
final double ss = lvmSolution.getResiduals().dotProduct(lvmSolution.getResiduals());
// double ss = 0;
// double[] obs = function.getY();
// double[] exp = lvmSolution.getValue();
// for (int i = 0; i < obs.length; i++)
// ss += (obs[i] - exp[i]) * (obs[i] - exp[i]);
ic = getAkaikeInformationCriterionFromResiduals(ss, function.getY().length, 1);
final double gradient = lvmSolution.getPoint().getEntry(0);
diffCoeff = gradient / 4;
ImageJUtils.log("Linear fit (%d points) : Gradient = %s, D = %s um^2/s, SS = %s, " + "IC = %s (%d evaluations)", function.getY().length, MathUtils.rounded(gradient, 4), MathUtils.rounded(diffCoeff, 4), MathUtils.rounded(ss), MathUtils.rounded(ic), lvmSolution.getEvaluations());
} catch (final TooManyIterationsException ex) {
ImageJUtils.log("Failed to fit : Too many iterations (%s)", ex.getMessage());
} catch (final ConvergenceException ex) {
ImageJUtils.log("Failed to fit : %s", ex.getMessage());
}
// Fit with intercept.
// Optionally include the intercept (which is the estimated precision).
final boolean fitIntercept = true;
try {
final LinearFunctionWithIntercept function = new LinearFunctionWithIntercept(x, y, clusteringSettings.getFitLength(), fitIntercept);
// @formatter:off
final LeastSquaresProblem problem = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(3000).start(function.guess()).target(function.getY()).weight(new DiagonalMatrix(function.getWeights())).model(function, function::jacobian).build();
// @formatter:on
lvmSolution = optimizer.optimize(problem);
final RealVector residuals = lvmSolution.getResiduals();
final double ss = residuals.dotProduct(residuals);
// double ss = 0;
// double[] obs = function.getY();
// double[] exp = lvmSolution.getValue();
// for (int i = 0; i < obs.length; i++)
// ss += (obs[i] - exp[i]) * (obs[i] - exp[i]);
final double ic2 = getAkaikeInformationCriterionFromResiduals(ss, function.getY().length, 2);
final double gradient = lvmSolution.getPoint().getEntry(0);
final double s = lvmSolution.getPoint().getEntry(1);
final double intercept2 = 4 * s * s;
if (ic2 < ic || Double.isNaN(ic)) {
if (settings.debugFitting) {
// Convert fitted precision in um to nm
ImageJUtils.log("Linear fit with intercept (%d points) : Gradient = %s, Intercept = %s, " + "D = %s um^2/s, precision = %s nm, SS = %s, IC = %s (%d evaluations)", function.getY().length, MathUtils.rounded(gradient, 4), MathUtils.rounded(intercept2, 4), MathUtils.rounded(gradient / 4, 4), MathUtils.rounded(s * 1000, 4), MathUtils.rounded(ss), MathUtils.rounded(ic2), lvmSolution.getEvaluations());
}
intercept = intercept2;
diffCoeff = gradient / 4;
precision = s;
}
} catch (final TooManyIterationsException ex) {
ImageJUtils.log("Failed to fit with intercept : Too many iterations (%s)", ex.getMessage());
} catch (final ConvergenceException ex) {
ImageJUtils.log("Failed to fit with intercept : %s", ex.getMessage());
}
if (clusteringSettings.getMsdCorrection()) {
// i.e. the intercept is allowed to be a small negative.
try {
// This function fits the jump distance (n) not the time (nt) so update x
final double[] x2 = new double[x.length];
for (int i = 0; i < x2.length; i++) {
x2[i] = x[i] / exposureTime;
}
final LinearFunctionWithMsdCorrectedIntercept function = new LinearFunctionWithMsdCorrectedIntercept(x2, y, clusteringSettings.getFitLength(), fitIntercept);
// @formatter:off
final LeastSquaresProblem problem = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(3000).start(function.guess()).target(function.getY()).weight(new DiagonalMatrix(function.getWeights())).model(function, function::jacobian).build();
// @formatter:on
lvmSolution = optimizer.optimize(problem);
final RealVector residuals = lvmSolution.getResiduals();
final double ss = residuals.dotProduct(residuals);
// double ss = 0;
// double[] obs = function.getY();
// double[] exp = lvmSolution.getValue();
// for (int i = 0; i < obs.length; i++)
// ss += (obs[i] - exp[i]) * (obs[i] - exp[i]);
final double ic2 = getAkaikeInformationCriterionFromResiduals(ss, function.getY().length, 2);
double gradient = lvmSolution.getPoint().getEntry(0);
final double s = lvmSolution.getPoint().getEntry(1);
final double intercept2 = 4 * s * s - gradient / 3;
// Q. Is this working?
// Try fixed precision fitting. Is the gradient correct?
// Revisit all the equations to see if they are wrong.
// Try adding the x[0] datapoint using the precision.
// Change the formula to not be linear at x[0] and to just fit the precision, i.e. the
// intercept2 = 4 * s * s - gradient / 3 is wrong as the
// equation is not linear below n=1.
// Incorporate the exposure time into the gradient to allow comparison to other fits
gradient /= exposureTime;
if (ic2 < ic || Double.isNaN(ic)) {
if (settings.debugFitting) {
// Convert fitted precision in um to nm
ImageJUtils.log("Linear fit with MSD corrected intercept (%d points) : Gradient = %s, " + "Intercept = %s, D = %s um^2/s, precision = %s nm, SS = %s, " + "IC = %s (%d evaluations)", function.getY().length, MathUtils.rounded(gradient, 4), MathUtils.rounded(intercept2, 4), MathUtils.rounded(gradient / 4, 4), MathUtils.rounded(s * 1000, 4), MathUtils.rounded(ss), MathUtils.rounded(ic2), lvmSolution.getEvaluations());
}
intercept = intercept2;
diffCoeff = gradient / 4;
precision = s;
}
} catch (final TooManyIterationsException ex) {
ImageJUtils.log("Failed to fit with intercept : Too many iterations (%s)", ex.getMessage());
} catch (final ConvergenceException ex) {
ImageJUtils.log("Failed to fit with intercept : %s", ex.getMessage());
}
}
// Add the fit to the plot
if (diffCoeff > 0) {
plot.setColor(Color.magenta);
plot.drawLine(0, intercept, x[x.length - 1], 4 * diffCoeff * x[x.length - 1] + intercept);
display(title, plot);
checkTraceSettings(diffCoeff);
}
return new double[] { diffCoeff, precision };
}
use of org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer in project GDSC-SMLM by aherbert.
the class AstigmatismModelManager method doCurveFit.
private boolean doCurveFit() {
// Estimate:
// Focal plane = where width is at a minimum
// s0x/s0y = the min width of x/y
// gamma = Half the distance between the focal planes
// z0 = half way between the two focal planes
// d = depth of focus
double[] smoothSx = fitSx;
double[] smoothSy = fitSy;
if (pluginSettings.getSmoothing() > 0) {
final LoessInterpolator loess = new LoessInterpolator(pluginSettings.getSmoothing(), 0);
smoothSx = loess.smooth(fitZ, fitSx);
smoothSy = loess.smooth(fitZ, fitSy);
final Plot plot = widthPlot.getPlot();
plot.setColor(Color.RED);
plot.addPoints(fitZ, smoothSx, Plot.LINE);
plot.setColor(Color.BLUE);
plot.addPoints(fitZ, smoothSy, Plot.LINE);
plot.setColor(Color.BLACK);
plot.updateImage();
}
final int focalPlaneXindex = SimpleArrayUtils.findMinIndex(smoothSx);
final int focalPlaneYindex = SimpleArrayUtils.findMinIndex(smoothSy);
final double s0x = smoothSx[focalPlaneXindex];
final double s0y = smoothSy[focalPlaneYindex];
final double focalPlaneX = fitZ[focalPlaneXindex];
final double focalPlaneY = fitZ[focalPlaneYindex];
double gamma = Math.abs(focalPlaneY - focalPlaneX) / 2;
final double z0 = (focalPlaneX + focalPlaneY) / 2;
final double d = (estimateD(focalPlaneXindex, fitZ, smoothSx) + estimateD(focalPlaneYindex, fitZ, smoothSy)) / 2;
// Start with Ax, Bx, Ay, By as zero.
final double Ax = 0;
final double Bx = 0;
final double Ay = 0;
final double By = 0;
// If this is not the case we can invert the gamma parameter.
if (focalPlaneXindex < focalPlaneYindex) {
gamma = -gamma;
}
// Use an LVM fitter with numerical gradients.
final double initialStepBoundFactor = 100;
final double costRelativeTolerance = 1e-10;
final double parRelativeTolerance = 1e-10;
final double orthoTolerance = 1e-10;
final double threshold = Precision.SAFE_MIN;
// We optimise against both sx and sy as a combined y-value.
final double[] y = new double[fitZ.length * 2];
System.arraycopy(fitSx, 0, y, 0, fitSx.length);
System.arraycopy(fitSy, 0, y, fitSx.length, fitSy.length);
final LevenbergMarquardtOptimizer optimizer = new LevenbergMarquardtOptimizer(initialStepBoundFactor, costRelativeTolerance, parRelativeTolerance, orthoTolerance, threshold);
parameters = new double[9];
parameters[P_GAMMA] = gamma;
parameters[P_Z0] = z0;
parameters[P_D] = d;
parameters[P_S0X] = s0x;
parameters[P_AX] = Ax;
parameters[P_BX] = Bx;
parameters[P_S0Y] = s0y;
parameters[P_AY] = Ay;
parameters[P_BY] = By;
record("Initial", parameters);
if (pluginSettings.getShowEstimatedCurve()) {
plotFit(parameters);
IJ.showMessage(TITLE, "Showing the estimated curve parameters.\nClick OK to continue.");
}
// @formatter:off
final LeastSquaresBuilder builder = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(3000).start(parameters).target(y);
if (pluginSettings.getWeightedFit()) {
builder.weight(new DiagonalMatrix(getWeights(smoothSx, smoothSy)));
}
final AstigmatismVectorFunction vf = new AstigmatismVectorFunction();
builder.model(vf, new AstigmatismMatrixFunction());
final LeastSquaresProblem problem = builder.build();
try {
final Optimum optimum = optimizer.optimize(problem);
parameters = optimum.getPoint().toArray();
record("Final", parameters);
plotFit(parameters);
saveResult(optimum);
} catch (final Exception ex) {
IJ.error(TITLE, "Failed to fit curve: " + ex.getMessage());
return false;
}
return true;
}
use of org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer in project GDSC-SMLM by aherbert.
the class BlinkEstimator method fit.
/**
* Fit the dark time to counts of molecules curve. Only use the first n fitted points.
* <p>
* Calculates:<br/>
* N = The number of photoblinking molecules in the sample<br/>
* nBlink = The average number of blinks per flourophore<br/>
* tOff = The off-time
*
* @param td
* The dark time
* @param ntd
* The counts of molecules
* @param nFittedPoints
* @param log
* Write the fitting results to the ImageJ log window
* @return The fitted parameters [N, nBlink, tOff], or null if no fit was possible
*/
public double[] fit(double[] td, double[] ntd, int nFittedPoints, boolean log) {
blinkingModel = new BlinkingFunction();
blinkingModel.setLogging(true);
for (int i = 0; i < nFittedPoints; i++) blinkingModel.addPoint(td[i], ntd[i]);
// Different convergence thresholds seem to have no effect on the resulting fit, only the number of
// iterations for convergence
double initialStepBoundFactor = 100;
double costRelativeTolerance = 1e-6;
double parRelativeTolerance = 1e-6;
double orthoTolerance = 1e-6;
double threshold = Precision.SAFE_MIN;
LevenbergMarquardtOptimizer optimiser = new LevenbergMarquardtOptimizer(initialStepBoundFactor, costRelativeTolerance, parRelativeTolerance, orthoTolerance, threshold);
try {
double[] obs = blinkingModel.getY();
//@formatter:off
LeastSquaresProblem problem = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(1000).start(new double[] { ntd[0], 0.1, td[1] }).target(obs).weight(new DiagonalMatrix(blinkingModel.getWeights())).model(blinkingModel, new MultivariateMatrixFunction() {
public double[][] value(double[] point) throws IllegalArgumentException {
return blinkingModel.jacobian(point);
}
}).build();
//@formatter:on
blinkingModel.setLogging(false);
Optimum optimum = optimiser.optimize(problem);
double[] parameters = optimum.getPoint().toArray();
//double[] exp = blinkingModel.value(parameters);
double mean = 0;
for (double d : obs) mean += d;
mean /= obs.length;
double ssResiduals = 0, ssTotal = 0;
for (int i = 0; i < obs.length; i++) {
//ssResiduals += (obs[i] - exp[i]) * (obs[i] - exp[i]);
ssTotal += (obs[i] - mean) * (obs[i] - mean);
}
// This is true if the weights are 1
ssResiduals = optimum.getResiduals().dotProduct(optimum.getResiduals());
r2 = 1 - ssResiduals / ssTotal;
adjustedR2 = getAdjustedCoefficientOfDetermination(ssResiduals, ssTotal, obs.length, parameters.length);
if (log) {
Utils.log(" Fit %d points. R^2 = %s. Adjusted R^2 = %s", obs.length, Utils.rounded(r2, 4), Utils.rounded(adjustedR2, 4));
Utils.log(" N=%s, nBlink=%s, tOff=%s (%s frames)", Utils.rounded(parameters[0], 4), Utils.rounded(parameters[1], 4), Utils.rounded(parameters[2], 4), Utils.rounded(parameters[2] / msPerFrame, 4));
}
return parameters;
} catch (TooManyIterationsException e) {
if (log)
Utils.log(" Failed to fit %d points: Too many iterations: (%s)", blinkingModel.size(), e.getMessage());
return null;
} catch (ConvergenceException e) {
if (log)
Utils.log(" Failed to fit %d points", blinkingModel.size());
return null;
}
}
use of org.apache.commons.math3.fitting.leastsquares.LevenbergMarquardtOptimizer in project GDSC-SMLM by aherbert.
the class PCPALMFitting method fitRandomModel.
/**
* Fits the correlation curve with r>0 to the random model using the estimated density and precision. Parameters
* must be fit within a tolerance of the starting values.
*
* @param gr
* @param sigmaS
* The estimated precision
* @param proteinDensity
* The estimate protein density
* @return The fitted parameters [precision, density]
*/
private double[] fitRandomModel(double[][] gr, double sigmaS, double proteinDensity, String resultColour) {
final RandomModelFunction function = new RandomModelFunction();
randomModel = function;
log("Fitting %s: Estimated precision = %f nm, estimated protein density = %g um^-2", randomModel.getName(), sigmaS, proteinDensity * 1e6);
randomModel.setLogging(true);
for (int i = offset; i < gr[0].length; i++) {
// Only fit the curve above the estimated resolution (points below it will be subject to error)
if (gr[0][i] > sigmaS * fitAboveEstimatedPrecision)
randomModel.addPoint(gr[0][i], gr[1][i]);
}
LevenbergMarquardtOptimizer optimizer = new LevenbergMarquardtOptimizer();
Optimum optimum;
try {
//@formatter:off
LeastSquaresProblem problem = new LeastSquaresBuilder().maxEvaluations(Integer.MAX_VALUE).maxIterations(3000).start(new double[] { sigmaS, proteinDensity }).target(function.getY()).weight(new DiagonalMatrix(function.getWeights())).model(function, new MultivariateMatrixFunction() {
public double[][] value(double[] point) throws IllegalArgumentException {
return function.jacobian(point);
}
}).build();
//@formatter:on
optimum = optimizer.optimize(problem);
} catch (TooManyIterationsException e) {
log("Failed to fit %s: Too many iterations (%s)", randomModel.getName(), e.getMessage());
return null;
} catch (ConvergenceException e) {
log("Failed to fit %s: %s", randomModel.getName(), e.getMessage());
return null;
}
randomModel.setLogging(false);
double[] parameters = optimum.getPoint().toArray();
// Ensure the width is positive
parameters[0] = Math.abs(parameters[0]);
double ss = optimum.getResiduals().dotProduct(optimum.getResiduals());
ic1 = Maths.getAkaikeInformationCriterionFromResiduals(ss, randomModel.size(), parameters.length);
final double fitSigmaS = parameters[0];
final double fitProteinDensity = parameters[1];
// Check the fitted parameters are within tolerance of the initial estimates
double e1 = parameterDrift(sigmaS, fitSigmaS);
double e2 = parameterDrift(proteinDensity, fitProteinDensity);
log(" %s fit: SS = %f. cAIC = %f. %d evaluations", randomModel.getName(), ss, ic1, optimum.getEvaluations());
log(" %s parameters:", randomModel.getName());
log(" Average precision = %s nm (%s%%)", Utils.rounded(fitSigmaS, 4), Utils.rounded(e1, 4));
log(" Average protein density = %s um^-2 (%s%%)", Utils.rounded(fitProteinDensity * 1e6, 4), Utils.rounded(e2, 4));
valid1 = true;
if (fittingTolerance > 0 && (Math.abs(e1) > fittingTolerance || Math.abs(e2) > fittingTolerance)) {
log(" Failed to fit %s within tolerance (%s%%): Average precision = %f nm (%s%%), average protein density = %g um^-2 (%s%%)", randomModel.getName(), Utils.rounded(fittingTolerance, 4), fitSigmaS, Utils.rounded(e1, 4), fitProteinDensity * 1e6, Utils.rounded(e2, 4));
valid1 = false;
}
if (valid1) {
// ---------
// TODO - My data does not comply with this criteria.
// This could be due to the PC-PALM Molecule code limiting the nmPerPixel to fit the images in memory
// thus removing correlations at small r.
// It could also be due to the nature of the random simulations being 3D not 2D membranes
// as per the PC-PALM paper.
// ---------
// Evaluate g(r)protein where:
// g(r)peaks = g(r)protein + g(r)stoch
// g(r)peaks ~ 1 + g(r)stoch
// Verify g(r)protein should be <1.5 for all r>0
double[] gr_stoch = randomModel.value(parameters);
double[] gr_peaks = randomModel.getY();
double[] gr_ = randomModel.getX();
//SummaryStatistics stats = new SummaryStatistics();
for (int i = 0; i < gr_peaks.length; i++) {
// Only evaluate above the fitted average precision
if (gr_[i] < fitSigmaS)
continue;
// Note the RandomModelFunction evaluates g(r)stoch + 1;
double gr_protein_i = gr_peaks[i] - (gr_stoch[i] - 1);
if (gr_protein_i > gr_protein_threshold) {
// Failed fit
log(" Failed to fit %s: g(r)protein %s > %s @ r=%s", randomModel.getName(), Utils.rounded(gr_protein_i, 4), Utils.rounded(gr_protein_threshold, 4), Utils.rounded(gr_[i], 4));
valid1 = false;
}
//stats.addValue(gr_i);
//System.out.printf("g(r)protein @ %f = %f\n", gr[0][i], gr_protein_i);
}
}
addResult(randomModel.getName(), resultColour, valid1, fitSigmaS, fitProteinDensity, 0, 0, 0, 0, ic1);
return parameters;
}
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