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Add imagej plugins to generate charts from tables
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‎src/main/java/tableplugins/BoxPlotPlugin.java‎

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package tableplugins;
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import net.imagej.plot.AbstractPlot;
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import net.imagej.plot.BoxSeries;
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import net.imagej.plot.CategoryChart;
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import net.imagej.plot.PlotService;
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import net.imagej.table.Column;
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import net.imagej.table.Table;
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import org.scijava.ItemIO;
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import org.scijava.ItemVisibility;
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import org.scijava.command.Command;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import net.imagej.ui.swing.widget.MultipleChoices;
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import net.imagej.ui.swing.widget.MutableChoices;
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import java.util.*;
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@Plugin(type = Command.class, menuPath="Table>BoxPlot")
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public class BoxPlotPlugin implements Command {
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@Parameter(label = "Select table", callback = "tableChanged")
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private Table<Column<?>,?> table;
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@Parameter(label = "Select columns", initializer = "tableChanged")
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public MultipleChoices<Column<Double>> valueColumns;
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@Parameter(visibility = ItemVisibility.MESSAGE)
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private final String LABEL_OPTIONAL = "optional";
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@Parameter(label = "Select key column", initializer = "tableChanged", required = false)
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public MutableChoices<Column<?>> keyColumn;
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@Parameter(label = "Boxplot", type = ItemIO.OUTPUT)
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public AbstractPlot output;
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@Parameter
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private PlotService plotService;
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@Override
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public void run() {
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createChart();
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}
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private void tableChanged() {
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if(keyColumn != null)
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keyColumn.setChoices(table, c -> c.getHeader());
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if(valueColumns != null) {
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Iterable<Column<Double>> choices = TablePluginUtils.filterDoubleColumns(table);
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valueColumns.setChoices(choices, c -> c.getHeader());
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for(Column<Double> choice : choices)
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valueColumns.set(choice, true);
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}
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}
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private void createChart() {
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if (keyColumn != null)
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buildChartWithKeys();
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else
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buildChartWithoutKeys();
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}
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private void buildChartWithKeys() {
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output = ChartBuilderWithKey.build(plotService, keyColumn.get(), valueColumns.get());
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buildTitle();
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}
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private void buildChartWithoutKeys() {
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CategoryChart<String> chart = plotService.newCategoryChart(String.class);
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chart.numberAxis().setAutoRange();
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chart.categoryAxis().setLabel("Column");
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Map<String, Collection<Double>> data = new TreeMap<>();
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for (Column<Double> valueColumn : valueColumns.get())
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data.put(valueColumn.getHeader(), valueColumn);
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BoxSeries<String> series = chart.addBoxSeries();
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series.setLabel("data");
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series.setLegendVisible(false);
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series.setValues(data);
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output = chart;
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buildTitle();
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}
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private void buildTitle() {
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String title = "Boxplot - ";
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for(Column<Double> col : valueColumns.get())
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title += col.getHeader() + ", ";
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output.setTitle(title.substring(0, title.length() - 2));
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}
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static private class ChartBuilderWithKey<K> {
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final PlotService plotService;
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private CategoryChart<K> chart;
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private ChartBuilderWithKey(PlotService plotService) {
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this.plotService = plotService;
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}
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private CategoryChart<K> getChart(Column<K> keyColumn, Iterable<Column<Double>> valueColumns) {
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chart = plotService.newCategoryChart(keyColumn.getType());
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chart.numberAxis().setAutoRange();
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chart.categoryAxis().setLabel(keyColumn.getHeader());
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for (Column<Double> valueColumn : valueColumns)
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addColumn(keyColumn, valueColumn);
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return chart;
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}
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private void addColumn(Column<K> keyColumn, Column<Double> valueColumn) {
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BoxSeries<K> series = chart.addBoxSeries();
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series.setLabel(valueColumn.getHeader());
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MyMultiMap<K, Double> map = new MyMultiMap<>(keyColumn, valueColumn);
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series.setValues(map.toMap());
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}
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static private <K> CategoryChart<K> build(PlotService plotService,
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Column<K> keyColumn, Iterable<Column<Double>> valueColumn) {
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return new ChartBuilderWithKey<K>(plotService).getChart(keyColumn, valueColumn);
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}
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}
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static private class MyMultiMap<K,V> {
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private Map<K, List<V>> map;
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public MyMultiMap(Collection<? extends K> keys, Collection<? extends V> values) {
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map = new HashMap<>();
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Iterator<? extends K> kIterator = keys.iterator();
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Iterator<? extends V> vIterator = values.iterator();
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while(kIterator.hasNext() && vIterator.hasNext())
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add(kIterator.next(), vIterator.next());
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}
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public void add(K k, V v) { get(k).add(v); }
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private List<V> get(K k) {
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List<V> list = map.get(k);
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if(list == null) {
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list = new ArrayList<>();
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map.put(k, list);
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}
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return list;
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}
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public Map<K, List<V>> toMap() { return map; }
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}
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}

‎src/main/java/tableplugins/DescriptiveStatisticsPlugIn.java‎

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package tableplugins;
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import net.imagej.table.*;
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import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
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import org.apache.commons.math3.stat.descriptive.rank.Median;
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import org.scijava.ItemIO;
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import org.scijava.command.Command;
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import org.scijava.display.Display;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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@Plugin(type = Command.class, menuPath="Table>Calculate Descriptive Statistics")
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public class DescriptiveStatisticsPlugIn implements Command {
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@Parameter
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public Display<Table<Column<?>,?>> activeTableDisplay;
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@Parameter(label = "Descriptive Statistics", type = ItemIO.OUTPUT)
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public Table<?,?> output;
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@Override
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public void run() {
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GenericTable table = setupResultTable();
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for(Column<Double> column : TablePluginUtils.filterDoubleColumns(activeTableDisplay.get(0)))
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table.add(setupStatisticsColumn(column));
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output = table;
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}
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static private GenericTable setupResultTable() {
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GenericTable table = new DefaultGenericTable();
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table.setRowCount(8);
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table.setRowHeader(0,"mean");
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table.setRowHeader(1,"standard deviation");
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table.setRowHeader(2,"variance");
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table.setRowHeader(3,"min");
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table.setRowHeader(4,"max");
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table.setRowHeader(5,"sum");
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table.setRowHeader(6,"median");
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table.setRowHeader(7,"N");
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return table;
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}
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private static DoubleColumn setupStatisticsColumn(Column<Double> column) {
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SummaryStatistics stat = calculateSummaryStatistics(column);
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double median = calculateMean(column);
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DoubleColumn c = new DoubleColumn();
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c.setHeader(column.getHeader());
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c.add(stat.getMean());
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c.add(stat.getStandardDeviation());
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c.add(stat.getVariance());
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c.add(stat.getMin());
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c.add(stat.getMax());
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c.add(stat.getSum());
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c.add(median);
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c.add((double) stat.getN());
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return c;
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}
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public static double calculateMean(Column<Double> column) {
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return new Median().evaluate(TablePluginUtils.toArray(column));
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}
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public static SummaryStatistics calculateSummaryStatistics(Column<Double> column) {
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SummaryStatistics stat = new SummaryStatistics();
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for(double x : column)
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stat.addValue(x);
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return stat;
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}
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}

‎src/main/java/tableplugins/ScatterPlotPlugin.java‎

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package tableplugins;/*
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* To the extent possible under law, the ImageJ developers have waived
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* all copyright and related or neighboring rights to this tutorial code.
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*
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* See the CC0 1.0 Universal license for details:
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* http://creativecommons.org/publicdomain/zero/1.0/
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*/
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import net.imagej.plot.*;
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import net.imagej.table.Column;
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import net.imagej.table.Table;
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import org.scijava.ItemIO;
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import org.scijava.command.Command;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.util.Colors;
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import net.imagej.ui.swing.widget.MutableChoices;
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import java.util.ArrayList;
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import java.util.List;
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@Plugin(type = Command.class, menuPath="Table>ScatterPlot")
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public class ScatterPlotPlugin implements Command {
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@Parameter(label = "Table", callback = "tableChanged")
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public Table<Column<?>, ?> table;
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@Parameter(label = "X Column", initializer = "tableChanged")
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public MutableChoices<Column<Double>> xColumn;
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@Parameter(label = "Y Column", initializer = "tableChanged")
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public MutableChoices<Column<Double>> yColumn;
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@Parameter(label = "Scatter Plot", type = ItemIO.OUTPUT)
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public AbstractPlot output;
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@Parameter
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private PlotService plotService;
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@Override
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public void run() {
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generateChart();
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}
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private void tableChanged() {
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Iterable<Column<Double>> l = TablePluginUtils.filterDoubleColumns(table);
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if(xColumn != null)
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xColumn.setChoices(l, c -> c.getHeader());
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if(yColumn != null)
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yColumn.setChoices(l, c -> c.getHeader());
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}
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private void generateChart() {
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final String xLabel = xColumn.get().getHeader();
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final String yLabel = yColumn.get().getHeader();
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final String chart_title = "ScatterPlot - " + xLabel + " - " + yLabel;
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XYPlot plot = plotService.newXYPlot();
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plot.setTitle("Line Styles");
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List<Double> xs = new ArrayList<>(xColumn.get());
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List<Double> ys = new ArrayList<>(yColumn.get());
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XYSeries series = plot.addXYSeries();
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series.setValues(xs,ys);
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series.setStyle(plot.newSeriesStyle(Colors.RED, LineStyle.NONE, MarkerStyle.CIRCLE));
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plot.setTitle(chart_title);
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plot.xAxis().setLabel(xLabel);
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plot.yAxis().setLabel(yLabel);
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output = plot;
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}
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}

‎src/main/java/tableplugins/TTestPlugIn.java‎

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package tableplugins;
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import net.imagej.table.Column;
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import net.imagej.table.Table;
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import org.apache.commons.math3.stat.inference.TTest;
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import org.scijava.ItemIO;
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import org.scijava.ItemVisibility;
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import org.scijava.command.Command;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import net.imagej.ui.swing.widget.MutableChoices;
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@Plugin(type = Command.class, menuPath="Table>Calculate t-Test")
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public class TTestPlugIn implements Command {
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static final private String UNPAIRED = "unpaired t-test";
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static final private String PAIRED = "paired t-test";
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static final private String HOMOSCEDASTIC = "homoscedastic t-test";
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@Parameter(label = "Select t-Test", choices = {UNPAIRED, PAIRED, HOMOSCEDASTIC})
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public String kindOfTTest = UNPAIRED;
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@Parameter(label = "Table", callback = "tableChanged")
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public Table<Column<?>, ?> table;
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@Parameter(label = "Column with first sample", initializer = "tableChanged")
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public MutableChoices<Column<Double>> firstColumn;
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@Parameter(label = "Second with second sample", initializer = "tableChanged")
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public MutableChoices<Column<Double>> secondColumn;
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@Parameter(label = "Properties", visibility = ItemVisibility.MESSAGE)
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private final String LABEL_PROPERTIES = "two-sampled, two-tailed t-tests comparing mean";
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@Parameter(label = "p-value", type = ItemIO.OUTPUT)
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public double p_value;
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private void tableChanged() {
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Iterable<Column<Double>> l = TablePluginUtils.filterDoubleColumns(table);
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if(firstColumn != null)
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firstColumn.setChoices(l, c -> c.getHeader());
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if(secondColumn != null)
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secondColumn.setChoices(l, c -> c.getHeader());
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}
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@Override
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public void run() {
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Column<Double> s1 = firstColumn.get();
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Column<Double> s2 = secondColumn.get();
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switch (kindOfTTest) {
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case UNPAIRED:
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p_value = tTest(s1,s2);
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return;
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case PAIRED:
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p_value = pairedTTest(s1,s2);
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return;
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case HOMOSCEDASTIC:
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p_value = homoscedasticTTest(s1,s2);
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return;
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default:
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throw new IllegalArgumentException();
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}
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}
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static public double tTest(Column<Double> sample1, Column<Double> sample2) {
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return new TTest().tTest(TablePluginUtils.toArray(sample1), TablePluginUtils.toArray(sample2));
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}
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static public double pairedTTest(Column<Double> sample1, Column<Double> sample2) {
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return new TTest().pairedTTest(TablePluginUtils.toArray(sample1), TablePluginUtils.toArray(sample2));
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}
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static public double homoscedasticTTest(Column<Double> sample1, Column<Double> sample2) {
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return new TTest().homoscedasticTTest(TablePluginUtils.toArray(sample1), TablePluginUtils.toArray(sample2));
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}
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}

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