Merge pull request #61 from shalinshah1993/working-branch

Merge added plotting features with master

licenses/AUTHORS.txt

@@ -41,6 +41,8 @@
             [email protected]
          Hannes Planatscher, NMI Reutlingen, Germany,
            [email protected]
+         Shalin Shah, Duke University USA,
+           [email protected]
 
                              -- Thanks to --
 

pom.xml

@@ -260,7 +260,6 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 			<version>${junit.version}</version>
-			<!--<scope>test</scope> -->
 		</dependency>
 		<dependency>
 			<groupId>org.sbml.jsbml</groupId>
@@ -304,25 +303,21 @@
 			<groupId>scpsolver</groupId>
 			<artifactId>SCPSolver</artifactId>
 			<version>1.0v2</version>
-			<!-- <scope>system</scope> <systemPath>${project.basedir}/src/lib/maven/scpsolver/SCPSolver/1.0/SCPSolver-1.0.jar</systemPath> -->
 		</dependency>
 		<dependency>
 			<groupId>scpsolver</groupId>
 			<artifactId>GLPKSolverPack</artifactId>
 			<version>4.35v2</version>
-			<!-- <scope>system</scope> <systemPath>${project.basedir}/src/lib/maven/scpsolver/GLPKSolverPack/4.35/GLPKSolverPack-4.35.jar</systemPath> -->
 		</dependency>
 		<dependency>
 			<groupId>scpsolver</groupId>
 			<artifactId>LPSOLVESolverPack</artifactId>
 			<version>5.5.2.5</version>
-			<!-- <scope>system</scope> <systemPath>${project.basedir}/src/lib/maven/scpsolver/LPSOLVESolverPack/5.5.2.5/LPSOLVESolverPack-5.5.2.5.jar</systemPath> -->
 		</dependency>
 		<dependency>
 			<groupId>kisao</groupId>
 			<artifactId>libkisao</artifactId>
 			<version>1.0.3.1-rc</version>
-			<!-- <scope>system</scope> <systemPath>${project.basedir}/src/lib/kisao/LibKiSAO/1.0.3.1/libkisao-1.0.3.1-rc.jar</systemPath> -->
 		</dependency>
 		<!-- OMEX archive -->
 		<dependency>

src/main/java/org/simulator/examples/SEDMLExample.java

@@ -1,20 +1,26 @@
 package org.simulator.examples;
 
-import de.binfalse.bflog.LOGGER;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
 import org.jfree.ui.RefineryUtilities;
-import org.jlibsedml.*;
+import org.jlibsedml.AbstractTask;
+import org.jlibsedml.Curve;
+import org.jlibsedml.Libsedml;
+import org.jlibsedml.Output;
+import org.jlibsedml.Plot2D;
+import org.jlibsedml.SedML;
+import org.jlibsedml.XMLException;
 import org.jlibsedml.execution.IProcessedSedMLSimulationResults;
 import org.jlibsedml.execution.IRawSedmlSimulationResults;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.simulator.math.odes.MultiTable;
-import org.simulator.plot.PlotMultiTable;
+import org.simulator.plot.PlotProcessedSedmlResults;
 import org.simulator.sedml.SedMLSBMLSimulatorExecutor;
 
-import java.io.File;
-import java.util.List;
-import java.util.Map;
-
-import static org.junit.Assert.fail;
+import de.binfalse.bflog.LOGGER;
 
 /**
  * This test class shows how a SED-ML file can be interpreted and executed using
@@ -43,7 +49,7 @@ public static void main(String[] args) throws XMLException, OWLOntologyCreationE
 
 		// in this SED-ML file there's just one output. If there were several,
 		// we could either iterate or get user to  decide what they want to run.
-		Output wanted = sedml.getOutputs().get(0);
+		Output wanted = sedml.getOutputs().get(2);
 		SedMLSBMLSimulatorExecutor exe = new SedMLSBMLSimulatorExecutor(sedml, wanted, sedmlDir);
 		// This gets the raw simulation results - one for each Task that was run.
 		LOGGER.warn("Collecting tasks...");
@@ -52,10 +58,22 @@ public static void main(String[] args) throws XMLException, OWLOntologyCreationE
 			fail ("Simulatation failed: " + exe.getFailureMessages().get(0));
 			return;
 		}
+
 		// now process.In this case, there's no processing performed - we're displaying the
 		// raw results.
-		LOGGER.warn("Outputs wanted: " + wanted.getAllDataGeneratorReferences());
-		IProcessedSedMLSimulationResults mt = exe.processSimulationResults(wanted, res);
+		LOGGER.warn("Outputs wanted: " + wanted.getId());
+		IProcessedSedMLSimulationResults prRes = exe.processSimulationResults(wanted, res);
+
+		if(wanted.isPlot2d()) {
+			Plot2D plots = (Plot2D) wanted;
+			List<Curve> curves = plots.getListOfCurves();
+
+			// plot all processed results as per curve descriptions
+			PlotProcessedSedmlResults p = new PlotProcessedSedmlResults(prRes, curves, plots.getElementName());
+			p.pack();
+			RefineryUtilities.centerFrameOnScreen(p);
+			p.setVisible( true );
+		}
 	}
 
 }

src/main/java/org/simulator/plot/PlotProcessedSedmlResults.java

@@ -0,0 +1,153 @@
+/*
+ * ---------------------------------------------------------------------
+ * This file is part of Simulation Core Library, a Java-based library
+ * for efficient numerical simulation of biological models.
+ *
+ * Copyright (C) 2007-2016 jointly by the following organizations:
+ * 1. University of Tuebingen, Germany
+ * 2. Keio University, Japan
+ * 3. Harvard University, USA
+ * 4. The University of Edinburgh, UK
+ * 5. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 6. The University of California, San Diego, La Jolla, CA, USA
+ * 7. The Babraham Institute, Cambridge, UK
+ * 8. Duke University, USA
+ *
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation. A copy of the license
+ * agreement is provided in the file named "LICENSE.txt" included with
+ * this software distribution and also available online as
+ * <http://www.gnu.org/licenses/lgpl-3.0-standalone.html>.
+ * ---------------------------------------------------------------------
+ */
+package org.simulator.plot;
+
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.ChartUtilities;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.JFreeChart;
+import org.jfree.ui.ApplicationFrame;
+import org.jlibsedml.Curve;
+import org.jlibsedml.execution.IProcessedSedMLSimulationResults;
+
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+/**
+ * This class adds output data-plot support to SBSCL
+ * 
+ * @author Shalin Shah
+ * @since 1.5
+ */
+@SuppressWarnings("serial")
+public class PlotProcessedSedmlResults extends ApplicationFrame {
+	private IProcessedSedMLSimulationResults species;
+	private XYSeriesCollection graphData;
+	private String title;
+	private List<Curve> curves;
+	private JFreeChart lineChart;
+	private static final int CHART_WIDTH = 1366;
+	private static final int CHART_HEIGHT = 768;
+
+	/**
+	 * Initializes the JFreeChart and dataSet for the chart using IProcessedSedMLSimulationResults
+	 * 
+	 * @param IProcessedSedMLSimulationResults
+	 *        The input data type to the plot API is 2D data wrapped with jsedmllib data structure
+	 *        which gets converted internally to XY line plot
+	 */
+	public PlotProcessedSedmlResults(IProcessedSedMLSimulationResults data, String title) {
+		super(title);
+
+		this.title = title;
+		this.species = data;
+		this.lineChart = ChartFactory.createXYLineChart(this.title, 
+				".", ".", createDataset(),
+				PlotOrientation.VERTICAL, true, true, false);
+
+		ChartPanel chartPanel = new ChartPanel( this.lineChart );
+		chartPanel.setPreferredSize( new java.awt.Dimension(CHART_WIDTH, CHART_HEIGHT));
+		setContentPane(chartPanel);
+
+	}
+
+	public PlotProcessedSedmlResults(IProcessedSedMLSimulationResults data, List<Curve> curves, String title) {
+		super(title);
+
+		this.title = title;
+		this.species = data;
+		this.curves = curves;
+
+		this.lineChart = ChartFactory.createXYLineChart(this.title, 
+				".", ".", createDataset(),
+				PlotOrientation.VERTICAL, true, true, false);
+
+
+		ChartPanel chartPanel = new ChartPanel( this.lineChart );
+		chartPanel.setPreferredSize( new java.awt.Dimension(CHART_WIDTH, CHART_HEIGHT));
+		setContentPane(chartPanel);
+	}
+
+	/**
+	 * Helper function that converts IProcessedSedMLSimulationResults to DataSet for LineChart
+	 */
+	private XYSeriesCollection createDataset() {
+		graphData = new XYSeriesCollection();
+
+		// For each curve in the current output element of sedml file
+		// simple extract data generators and plot them
+		for(Curve cur: this.curves) {
+			Double[] xData = species.getDataByColumnId(cur.getXDataReference());
+			Double[] yData = species.getDataByColumnId(cur.getYDataReference());
+			XYSeries series = new XYSeries(cur.getId(), false);
+
+			for(int row = 0; row < Math.min(xData.length, yData.length); row++) {
+				series.add(xData[row], yData[row]);
+			}
+			graphData.addSeries(series);
+		}
+
+		return graphData;
+	}
+
+	/**
+	 * Helper function that can save the generated plot (simulationPath sedml file) as a PNG image
+	 * with fileName in the results folder
+	 */
+	public void savePlot(String simulationPath, String fileName) throws IOException {
+		// Get full folder for sedml xml file
+		String outputPath = getFolderPathForTestResource(simulationPath);
+		// Store the plots in the results folder in the same directory
+		outputPath = outputPath + "/results/simulation_core/" + fileName + ".png";
+		OutputStream out = FileUtils.openOutputStream(new File(outputPath));
+		// Use default width and height for chart size and save as png
+	    ChartUtilities.writeChartAsPNG(out, this.lineChart, CHART_WIDTH, CHART_HEIGHT);
+	}
+
+	/**
+     * Get absolute parent path for given test resource.
+     * Due to the relative paths of SBML and SED-ML files the resource loading is not working
+     * in maven.
+     *
+     * Example:
+     *  resourcePath="/fba/e_coli_core.xml"
+     */
+	private static String getFolderPathForTestResource(String resourcePath) {
+
+        String path = null;
+        File currentDir = new File(System.getProperty("user.dir"));
+        path = currentDir.getAbsolutePath() + "/src/test/resources" + resourcePath;
+        File pwd = new File(path);
+
+        return pwd.getParentFile().getAbsolutePath();
+	}
+}

src/main/java/org/simulator/sedml/ProcessSedMLResults.java

@@ -351,7 +351,7 @@ private IRawSedmlSimulationResults flattenResultsList(List<IRawSedmlSimulationRe
 								mergeTimeCols(a, b),
 								mergeDataCols(a.getData(), b.getData()), 
 								results.get(0).getColumnHeaders()))).get();
-			return flat;
+		return flat;
 	}
 
 	/**
@@ -396,7 +396,9 @@ private double[][] extractNonTimeData(double[][] data) {
 	private double[] mergeTimeCols(IRawSedmlSimulationResults a, IRawSedmlSimulationResults b) {
 		// Get end time point for taskA
 		double[] timeA = ((MultTableSEDMLWrapper)a).getMultiTable().getTimePoints();
-		double timeBegin = timeA[timeA.length - 1];
+		// Following tellurim we concat all the iterations of repeated tasks
+		// so start time from 0
+		double timeBegin = 0d;
 
 		// Add end time point to taskB
 		double[] timeB = Arrays.stream(((MultTableSEDMLWrapper)b).getMultiTable().getTimePoints()).map(row -> row + timeBegin).toArray();