Java tutorial
/* * Data Structures and functions used to relate assymetry of a spot to Z position * * Based on Bo Huang et al., DOI: 10.1126/science.1153529 * * Create 6/28/2012 * * Nico Stuurman, nico@cmp.ucsf.edu * * Copyright UCSF 2012 * * Licensed under BSD version 2.0 * */ package edu.valelab.GaussianFit; import java.util.ArrayList; import org.apache.commons.math.FunctionEvaluationException; import org.apache.commons.math.optimization.GoalType; import org.apache.commons.math.optimization.OptimizationException; import org.apache.commons.math.optimization.RealPointValuePair; import org.apache.commons.math.optimization.SimpleScalarValueChecker; import org.apache.commons.math.optimization.direct.NelderMead; import org.jfree.data.xy.XYSeries; import ij.measure.ResultsTable; /** * * @author Nico Stuurman */ public class ZCalibrator { /* * Structure of arrays "fitFunction"; * 0: c_; // center z position * 1: w0_; // PSF width at center position * 2: d_; // focus depth of the microscope (not sure what this means) * 3: A // higher order factor * 4: B_; // second higher order factor */ private double[] fitFunctionWx_; private double[] fitFunctionWy_; final int maxIterations_ = 10000; public boolean hasFitFunctions() { return fitFunctionWx_ != null && fitFunctionWy_ != null; } public class DataPoint { public double wx_; // width in x public double wy_; // width in y public double z_; //z position public DataPoint(double wx, double wy, double z) { wx_ = wx; wy_ = wy; z_ = z; } } private ArrayList<DataPoint> data_; public void addDataPoint(double wx, double wy, double z) { if (data_ == null) data_ = new ArrayList<DataPoint>(); data_.add(new DataPoint(wx, wy, z)); } public void clearDataPoints() { if (data_ != null) data_.clear(); } public int nrDataPoints() { return data_.size(); } /** * returns a 2D array representation of the data: * either z - wx ( dim == 0) * or z - wy (dim == 1) * * @param dim 0-returns array z-wx, 1 return array w-wy * @return 2D array, z values in D0, w value in D2 */ public double[][] getDataAsArray(int dim) { double[][] output = new double[2][data_.size()]; for (int i = 0; i < data_.size(); i++) { DataPoint dp = data_.get(i); output[0][i] = dp.z_; if (dim == 0) output[1][i] = dp.wx_; if (dim == 1) output[1][i] = dp.wy_; } return output; } public void plotDataPoints() { String xAxis = "Z (um)"; XYSeries[] plotData = new XYSeries[2]; plotData[0] = new XYSeries("wx"); plotData[1] = new XYSeries("wy"); for (int i = 0; i < data_.size(); i++) { DataPoint d = data_.get(i); plotData[0].add(d.z_, d.wx_); plotData[1].add(d.z_, d.wy_); } GaussianUtils.plotDataN("Z-calibration Data Points", plotData, xAxis, "Width(nm)", 0, 400, true, false); } private void plotFitFunctions() { String xAxis = "Z (um)"; XYSeries[] plotData = new XYSeries[2]; plotData[0] = new XYSeries("wx"); plotData[1] = new XYSeries("wy"); for (int i = 0; i < data_.size(); i++) { DataPoint d = data_.get(i); plotData[0].add(d.z_, MultiVariateZCalibrationFunction.funcval(fitFunctionWx_, d.z_)); plotData[1].add(d.z_, MultiVariateZCalibrationFunction.funcval(fitFunctionWy_, d.z_)); } GaussianUtils.plotDataN("", plotData, xAxis, "Width(nm)", 0, 400, true, false); } /** * Creates fitFunctionWx_ and fitFunctionWy_ based on data in data_ * * */ public void fitFunction() throws FunctionEvaluationException, OptimizationException { NelderMead nmx = new NelderMead(); SimpleScalarValueChecker convergedChecker_ = new SimpleScalarValueChecker(1e-6, -1); double[][] wxData = getDataAsArray(0); MultiVariateZCalibrationFunction mvcx = new MultiVariateZCalibrationFunction(wxData); double[] params0_ = new double[5]; // initial estimates: params0_[0] = 37; // TODO: better estimate for c params0_[1] = 200; // Estimate for w0 params0_[2] = 10; // TODO: better estimate for d params0_[3] = 1; // TODO: better estimate for A params0_[4] = 1; // TODO: better estimate for B nmx.setStartConfiguration(params0_); nmx.setConvergenceChecker(convergedChecker_); nmx.setMaxIterations(maxIterations_); double[] paramsOut = { 0.0 }; RealPointValuePair result = nmx.optimize(mvcx, GoalType.MINIMIZE, params0_); paramsOut = result.getPoint(); //for (int i = 0; i < paramsOut.length; i++) { // System.out.println("Result " + i + " value: " + (int) paramsOut[i]); //} // write fit result to Results Table: ResultsTable res = new ResultsTable(); res.incrementCounter(); res.addValue("c", paramsOut[0]); res.addValue("w0", paramsOut[1]); res.addValue("d", paramsOut[2]); res.addValue("A", paramsOut[3]); res.addValue("B", paramsOut[4]); fitFunctionWx_ = paramsOut; double[][] yxData = getDataAsArray(1); MultiVariateZCalibrationFunction yvcx = new MultiVariateZCalibrationFunction(yxData); nmx.setStartConfiguration(params0_); result = nmx.optimize(yvcx, GoalType.MINIMIZE, params0_); paramsOut = result.getPoint(); System.out.println("Y:"); //for (int i = 0; i < paramsOut.length; i++) { // System.out.println("Result " + i + " value: " + (int) paramsOut[i]); //} res.incrementCounter(); res.addValue("c", paramsOut[0]); res.addValue("w0", paramsOut[1]); res.addValue("d", paramsOut[2]); res.addValue("A", paramsOut[3]); res.addValue("B", paramsOut[4]); res.show("Fit Parameters"); fitFunctionWy_ = paramsOut; plotFitFunctions(); } /** * Use the fitfunction to estimate the z position given width in x and y * * minimize the distance D in sqrt wx and sqrt wy space * D = sqrt ( square (sqrt wx - sqrt wx, calib) + sqr(sqrt wy - sqrt w, calib) ) * * */ public double getZ(double wx, double wy) { if (!hasFitFunctions()) return 0.0; NelderMead nmx = new NelderMead(); SimpleScalarValueChecker convergedChecker_ = new SimpleScalarValueChecker(1e-6, -1); MultiVariateZFunction mz = new MultiVariateZFunction(fitFunctionWx_, fitFunctionWy_, wx, wy); double[] params0_ = new double[1]; // initial estimates: params0_[0] = 15; // TODO: Need the middle z value of the stack here!!! nmx.setStartConfiguration(params0_); nmx.setConvergenceChecker(convergedChecker_); nmx.setMaxIterations(maxIterations_); double[] paramsOut = { 0.0 }; try { RealPointValuePair result = nmx.optimize(mz, GoalType.MINIMIZE, params0_); paramsOut = result.getPoint(); } catch (java.lang.OutOfMemoryError e) { throw (e); } catch (Exception e) { ij.IJ.log(" " + e.toString()); } return paramsOut[0]; } }