Package sc.fiji.snt.analysis.sholl.gui

Class ShollPlot

java.lang.Object
ij.gui.Plot
sc.fiji.snt.analysis.sholl.gui.ShollPlot
All Implemented Interfaces:
Cloneable
public class ShollPlot extends ij.gui.Plot
An ImageJ Plot for displaying Sholl analysis profiles, including sampled data, fitted curves, and descriptive statistics.
Author:
Tiago Ferreira

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    THICK_LINE
    Flag for plotting points with a thicker solid line

    Fields inherited from class ij.gui.Plot

    AUTO_POSITION, BAR, BOTTOM_LEFT, BOTTOM_MARGIN, BOTTOM_RIGHT, BOX, CENTER, CIRCLE, CONNECTED_CIRCLES, COPY_AXIS_STYLE, COPY_CONTENTS_STYLE, COPY_EXTRA_OBJECTS, COPY_LABELS, COPY_LEGEND, COPY_SIZE, CROSS, CUSTOM, DEFAULT_FLAGS, DIAMOND, DOT, FILLED, LEFT, LEFT_MARGIN, LEGEND_BOTTOM_UP, LEGEND_TRANSPARENT, LINE, MIN_FRAMEHEIGHT, MIN_FRAMEWIDTH, PROPERTY_KEY, RIGHT, RIGHT_MARGIN, SEPARATED_BAR, TOP_LEFT, TOP_MARGIN, TOP_RIGHT, TRIANGLE, X, X_FORCE2GRID, X_GRID, X_LOG_NUMBERS, X_LOG_TICKS, X_MINOR_TICKS, X_NUMBERS, X_RANGE, X_TICKS, Y_FORCE2GRID, Y_GRID, Y_LOG_NUMBERS, Y_LOG_TICKS, Y_MINOR_TICKS, Y_NUMBERS, Y_RANGE, Y_TICKS

  • Constructor Summary

    Constructors
    Constructor
    Description
    ShollPlot(String title, String xLabel, String yLabel)
    Constructs a new empty Plot.
    ShollPlot(String title, String xLabel, String yLabel, ShollStats stats, boolean annotate, boolean useCumulativeFrequencies)
     
    ShollPlot(ShollStats stats)
     
    ShollPlot(ShollStats.DataMode dataMode, Profile... profiles)
     
    ShollPlot(ShollStats stats, boolean cumulativeFrequencies)
     
    ShollPlot(Profile profile)
     
    ShollPlot(Profile... profiles)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addPoints(double[] x, double[] y, double[] yErrorBars, String label)
     
    void
    addPoints(double[] x, double[] y, int shape)
     
    void
    addPoints(double[] x, double[] y, String label)
     
    void
    addPoints(List<double[]> points, String label)
     
    void
    addPoints(List<Number> xValues, List<Number> yValues, String label)
     
    void
    addPoints(List<Number> xValues, List<Number> yValues, List<Number> yErrorBars, String label)
     
    static String
    defaultXtitle(Profile profile)
     
    void
    drawLabel(String label, Color color)
    Draws a label at the less crowded corner of an ImageJ plot.
    void
    enableLegend(boolean enable)
     
    ShollStats
    getStats()
     
    boolean
    isUsingCumulativeFrequencies()
     
    boolean
    isVisible()
     
    void
    markPoint(ShollPoint pCentroid, int markShape, int markSize)
    Highlights a point on a plot without listing it on the Plot's table.
    void
    markPoint(ShollPoint point, Color color)
    Highlights a point on a plot using the default marker.
    void
    rebuild()
     
    void
    rebuild(ShollStats stats)
     
    boolean
    save(File file)
     
    boolean
    save(String filepath)
     
    static void
    show(List<ShollPlot> plots, String title)
     

    Methods inherited from class ij.gui.Plot

    add, add, addErrorBars, addErrorBars, addErrorBars, addHistogram, addHistogram, addHistogram, addHorizontalErrorBars, addHorizontalErrorBars, addLabel, addLegend, addLegend, addObjectFromPlot, addPoints, addPoints, addPoints, addPoints, addPoints, addPoints, addText, addToStack, adjustCalibration, appendToStack, calculateDistance, changeFont, descaleX, descaleY, dispose, draw, drawArrow, drawDottedLine, drawLine, drawNormalizedLine, drawShapes, drawVectors, drawVectors, getCurrentFont, getDataObjectArrays, getDataObjectDesignations, getDefaultFlags, getDefaultFont, getDoubleFromArrayList, getDrawingFrame, getFlags, getFont, getImagePlus, getLabel, getLimits, getMinimumSize, getNumPlotObjects, getObjectFlags, getPlotObjectDesignations, getPlotObjectIndex, getPlotObjectLabel, getPlotObjectStyle, getProcessor, getResultsTable, getResultsTable, getResultsTableWithLabels, getSize, getStack, getTitle, getTypes, getXValues, getYValues, isFrozen, killPlotObjectsSnapshot, killPlotPropertiesSnapshot, makeHighResolution, redrawGrid, removeNaNs, replace, restorePlotObjects, restorePlotProperties, savePlotObjects, savePlotPlotProperties, scaleXtoPxl, scaleYtoPxl, setAntialiasedText, setAxes, setAxisLabelFont, setAxisXLog, setAxisYLog, setBackgroundColor, setBackgroundColor, setColor, setColor, setColor, setColor, setFont, setFont, setFont, setFontSize, setFormatFlags, setFrameSize, setFrozen, setImagePlus, setJustification, setLabel, setLegend, setLimits, setLimits, setLimitsToDefaults, setLimitsToFit, setLineWidth, setLineWidth, setLogScaleX, setLogScaleY, setMaxIntervals, setMinorTickLength, setOptions, setPlotMaker, setPlotObjectLabel, setPlotObjectStyle, setPreviousMinMax, setScale, setSize, setStyle, setTickLength, setWindowSize, setXLabelFont, setXMinorTicks, setXTicks, setXYLabels, setYLabelFont, setYMinorTicks, setYTicks, show, toByteArray, toShape, update, updateImage, useTemplate, useTemplate

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • THICK_LINE

      public static final int THICK_LINE
      Flag for plotting points with a thicker solid line
      See Also:

  • Constructor Details

    • ShollPlot

      public ShollPlot(String title, String xLabel, String yLabel)
      Constructs a new empty Plot.
      Parameters:
      title - the plot title
      xLabel - the x-axis label
      yLabel - the y-axis label

    • ShollPlot

      public ShollPlot(Profile profile)

    • ShollPlot

      public ShollPlot(ShollStats stats)

    • ShollPlot

      public ShollPlot(ShollStats stats, boolean cumulativeFrequencies)

    • ShollPlot

      public ShollPlot(ShollStats.DataMode dataMode, Profile... profiles)

    • ShollPlot

      public ShollPlot(Profile... profiles)

    • ShollPlot

      public ShollPlot(String title, String xLabel, String yLabel, ShollStats stats, boolean annotate, boolean useCumulativeFrequencies)

  • Method Details

    • rebuild

      public void rebuild()

    • rebuild

      public void rebuild(ShollStats stats)

    • enableLegend

      public void enableLegend(boolean enable)

    • defaultXtitle

      public static String defaultXtitle(Profile profile)

    • markPoint

      public void markPoint(ShollPoint pCentroid, int markShape, int markSize)
      Highlights a point on a plot without listing it on the Plot's table. Does nothing if point is null
      Parameters:
      pCentroid - the point to be drawn (defined in calibrated coordinates)
      markShape - either X, CROSS or DOT. Other shapes are not supported.
      markSize - the mark size in pixels

    • markPoint

      public void markPoint(ShollPoint point, Color color)
      Highlights a point on a plot using the default marker. Does nothing if point is null.
      Parameters:
      point - the point to be drawn (defined in calibrated coordinates).
      color - the drawing color. This will not affect consequent objects

    • drawLabel

      public void drawLabel(String label, Color color)
      Draws a label at the less crowded corner of an ImageJ plot. Height and width of label is measured so that text remains within the plot's frame. Text is added to the first free position in this sequence: NE, NW, SE, SW.
      Parameters:
      label - Label contents
      color - Foreground color of text. Note that this will also set the drawing color for the next objects to be added to the plot

    • isVisible

      public boolean isVisible()

    • isUsingCumulativeFrequencies

      public boolean isUsingCumulativeFrequencies()

    • save

      public boolean save(String filepath)

    • save

      public boolean save(File file)

    • getStats

      public ShollStats getStats()

    • addPoints

      public void addPoints(double[] x, double[] y, int shape)
      Overrides:
      addPoints in class ij.gui.Plot

    • addPoints

      public void addPoints(double[] x, double[] y, double[] yErrorBars, String label)

    • addPoints

      public void addPoints(double[] x, double[] y, String label)

    • addPoints

      public void addPoints(List<double[]> points, String label)

    • addPoints

      public void addPoints(List<Number> xValues, List<Number> yValues, String label)

    • addPoints

      public void addPoints(List<Number> xValues, List<Number> yValues, List<Number> yErrorBars, String label)

    • show

      public static void show(List<ShollPlot> plots, String title)