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From source file:mt.LengthDistribution.java
public static void GetLengthDistributionArray(ArrayList<File> AllMovies, double[] calibration) { ArrayList<Double> maxlist = new ArrayList<Double>(); for (int i = 0; i < AllMovies.size(); ++i) { double maxlength = LengthDistribution.Lengthdistro(AllMovies.get(i)); if (maxlength != Double.NaN && maxlength > 0) maxlist.add(maxlength);//from ww w . j a v a2 s .co m } Collections.sort(maxlist); int min = 0; int max = (int) Math.round(maxlist.get(maxlist.size() - 1)) + 1; XYSeries counterseries = new XYSeries("MT length distribution"); XYSeries Logcounterseries = new XYSeries("MT Log length distribution"); final ArrayList<Point> points = new ArrayList<Point>(); for (int length = 0; length < max; ++length) { HashMap<Integer, Integer> frameseed = new HashMap<Integer, Integer>(); int count = 0; for (int i = 0; i < AllMovies.size(); ++i) { File file = AllMovies.get(i); double currentlength = LengthDistribution.Lengthdistro(file); ArrayList<FLSobject> currentobject = Tracking.loadMTStat(file); if (currentlength > length) { for (int index = 0; index < currentobject.size(); ++index) { ArrayList<Integer> seedlist = new ArrayList<Integer>(); if (currentobject.get(index).length >= length) { seedlist.add(currentobject.get(index).seedID); if (frameseed.get(currentobject.get(index).Framenumber) != null && frameseed.get(currentobject.get(index).Framenumber) != Double.NaN) { int currentcount = frameseed.get(currentobject.get(index).Framenumber); frameseed.put(currentobject.get(index).Framenumber, seedlist.size() + currentcount); } else if (currentobject.get(index) != null) frameseed.put(currentobject.get(index).Framenumber, seedlist.size()); } } } } // Get maxima length, count int maxvalue = Integer.MIN_VALUE; for (int key : frameseed.keySet()) { int Count = frameseed.get(key); if (Count >= maxvalue) maxvalue = Count; } if (maxvalue != Integer.MIN_VALUE) { counterseries.add(length, maxvalue); if (maxvalue > 0) { Logcounterseries.add((length), Math.log(maxvalue)); points.add(new Point(new double[] { length, Math.log(maxvalue) })); } } } final XYSeriesCollection dataset = new XYSeriesCollection(); final XYSeriesCollection nofitdataset = new XYSeriesCollection(); dataset.addSeries(counterseries); nofitdataset.addSeries(counterseries); final XYSeriesCollection Logdataset = new XYSeriesCollection(); Logdataset.addSeries(Logcounterseries); final JFreeChart chart = ChartFactory.createScatterPlot("MT length distribution", "Number of MT", "Length (micrometer)", dataset); final JFreeChart nofitchart = ChartFactory.createScatterPlot("MT length distribution", "Number of MT", "Length (micrometer)", nofitdataset); // Fitting line to log of the length distribution interpolation.Polynomial poly = new interpolation.Polynomial(1); try { poly.fitFunction(points); } catch (NotEnoughDataPointsException e) { // TODO Auto-generated catch block e.printStackTrace(); } DisplayPoints.display(nofitchart, new Dimension(800, 500)); dataset.addSeries(Tracking.drawexpFunction(poly, counterseries.getMinX(), counterseries.getMaxX(), 0.5, "Exponential fit")); NumberFormat nf = NumberFormat.getInstance(Locale.ENGLISH); nf.setMaximumFractionDigits(3); TextTitle legendText = new TextTitle("Mean Length" + " : " + nf.format(-1.0 / poly.getCoefficients(1)) + " " + "Standard Deviation" + " : " + nf.format(poly.SSE)); legendText.setPosition(RectangleEdge.RIGHT); DisplayPoints.display(chart, new Dimension(800, 500)); chart.addSubtitle(legendText); final JFreeChart logchart = ChartFactory.createScatterPlot("MT Log length distribution", "Number of MT", "Length (micrometer)", Logdataset); // DisplayPoints.display(logchart, new Dimension(800, 500)); for (int i = 1; i >= 0; --i) System.out.println(poly.getCoefficients(i) + " " + "x" + " X to the power of " + i); // Logdataset.addSeries(Tracking.drawFunction(poly, counterseries.getMinX(), counterseries.getMaxX(), 0.5, "Straight line fit")); WriteLengthdistroFile(AllMovies, counterseries, 0); }
From source file:mt.LengthDistribution.java
public static void GetLengthDistributionArrayatTime(ArrayList<File> AllMovies, double[] calibration, final int framenumber) { ArrayList<Double> maxlist = new ArrayList<Double>(); for (int i = 0; i < AllMovies.size(); ++i) { ArrayList<Pair<Integer, Double>> lengthlist = LengthDistribution.LengthdistroatTime(AllMovies.get(i), framenumber);/*from ww w. j a v a2 s. c o m*/ for (int index = 0; index < lengthlist.size(); ++index) { if (lengthlist.get(index).getB() != Double.NaN && lengthlist.get(index).getB() > 0) maxlist.add(lengthlist.get(index).getB()); } } Collections.sort(maxlist); int min = 0; int max = 0; if (maxlist.size() > 0) max = (int) Math.round(maxlist.get(maxlist.size() - 1)) + 1; XYSeries counterseries = new XYSeries("MT length distribution"); XYSeries Logcounterseries = new XYSeries("MT Log length distribution"); final ArrayList<Point> points = new ArrayList<Point>(); for (int length = 0; length < max; ++length) { HashMap<Integer, Integer> frameseed = new HashMap<Integer, Integer>(); int count = 0; for (int i = 0; i < AllMovies.size(); ++i) { File file = AllMovies.get(i); ArrayList<FLSobject> currentobject = Tracking.loadMTStat(file); if (currentobject != null) for (int index = 0; index < currentobject.size(); ++index) { ArrayList<Integer> seedlist = new ArrayList<Integer>(); if (currentobject.get(index).length >= length && currentobject.get(index).Framenumber == framenumber) { seedlist.add(currentobject.get(index).seedID); if (frameseed.get(currentobject.get(index).Framenumber) != null && frameseed.get(currentobject.get(index).Framenumber) != Double.NaN) { int currentcount = frameseed.get(currentobject.get(index).Framenumber); frameseed.put(currentobject.get(index).Framenumber, seedlist.size() + currentcount); } else if (currentobject.get(index) != null) frameseed.put(currentobject.get(index).Framenumber, seedlist.size()); } } } // Get maxima length, count int maxvalue = Integer.MIN_VALUE; for (int key : frameseed.keySet()) { int Count = frameseed.get(key); if (Count >= maxvalue) maxvalue = Count; } if (maxvalue != Integer.MIN_VALUE) { counterseries.add(length, maxvalue); if (maxvalue > 0) { System.out.println("Max " + maxvalue); Logcounterseries.add((length), Math.log(maxvalue)); points.add(new Point(new double[] { length, Math.log(maxvalue) })); } } } final XYSeriesCollection dataset = new XYSeriesCollection(); final XYSeriesCollection nofitdataset = new XYSeriesCollection(); dataset.addSeries(counterseries); nofitdataset.addSeries(counterseries); final XYSeriesCollection Logdataset = new XYSeriesCollection(); Logdataset.addSeries(Logcounterseries); final JFreeChart chart = ChartFactory.createScatterPlot("MT length distribution", "Number of MT", "Length (micrometer)", dataset); final JFreeChart nofitchart = ChartFactory.createScatterPlot("MT length distribution", "Number of MT", "Length (micrometer)", nofitdataset); // Fitting line to log of the length distribution interpolation.Polynomial poly = new interpolation.Polynomial(1); try { poly.fitFunction(points); } catch (NotEnoughDataPointsException e) { } DisplayPoints.display(nofitchart, new Dimension(800, 500)); dataset.addSeries(Tracking.drawexpFunction(poly, counterseries.getMinX(), counterseries.getMaxX(), 0.5, "Exponential fit")); NumberFormat nf = NumberFormat.getInstance(Locale.ENGLISH); nf.setMaximumFractionDigits(3); TextTitle legendText = new TextTitle("Mean Length" + " : " + nf.format(-1.0 / poly.getCoefficients(1)) + " " + "Standard Deviation" + " : " + nf.format(poly.SSE)); legendText.setPosition(RectangleEdge.RIGHT); DisplayPoints.display(chart, new Dimension(800, 500)); chart.addSubtitle(legendText); System.out.println("Series count" + dataset.getSeriesCount()); final JFreeChart logchart = ChartFactory.createScatterPlot("MT Log length distribution", "Length (micrometer)", "Number of MT", Logdataset); // DisplayPoints.display(logchart, new Dimension(800, 500)); for (int i = 1; i >= 0; --i) System.out.println(poly.getCoefficients(i) + " " + "x" + " X to the power of " + i); // Logdataset.addSeries(Tracking.drawFunction(poly, counterseries.getMinX(), counterseries.getMaxX(), 0.5, "Straight line fit")); WriteLengthdistroFile(AllMovies, counterseries, framenumber); }