mirror of https://github.com/jlizier/jidt
First version of TE Auto Analyser Java Swing GUI
This commit is contained in:
joseph.lizier
parent
e727233bc0
commit
6951f52f68
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@ -191,6 +191,7 @@
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<zipfileset dir="javadocs" includes="**/*.*,**/*" prefix="javadocs"/>
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<zipfileset dir="notices" includes="**/*.*,**/*" prefix="notices"/>
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<zipfileset dir="tutorial" prefix="tutorial"/>
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<zipfileset dir="web" includes="JIDT-logo.png" prefix=""/>
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</zip>
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</target>
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</project>
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@ -0,0 +1,560 @@
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/*
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* Java Information Dynamics Toolkit (JIDT)
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* Copyright (C) 2015, Joseph T. Lizier
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*
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*/
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package infodynamics.demos.autoanalysis;
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import infodynamics.measures.continuous.ConditionalMutualInfoMultiVariateCommon;
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import infodynamics.measures.continuous.TransferEntropyCalculator;
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import infodynamics.measures.continuous.gaussian.TransferEntropyCalculatorGaussian;
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import infodynamics.measures.continuous.kernel.TransferEntropyCalculatorKernel;
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import infodynamics.measures.continuous.kraskov.ConditionalMutualInfoCalculatorMultiVariateKraskov;
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import infodynamics.measures.continuous.kraskov.TransferEntropyCalculatorKraskov;
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import infodynamics.utils.ArrayFileReader;
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import infodynamics.utils.MatrixUtils;
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import javax.swing.ImageIcon;
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import javax.swing.JFrame;
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import javax.swing.JOptionPane;
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import javax.swing.JPanel;
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import javax.swing.JComboBox;
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import javax.swing.JButton;
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import javax.swing.JLabel;
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import javax.swing.JFileChooser;
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import javax.swing.JTable;
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import javax.swing.JTextField;
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import javax.swing.event.DocumentEvent;
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import javax.swing.event.DocumentListener;
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import javax.swing.table.AbstractTableModel;
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import java.awt.EventQueue;
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import java.awt.GridBagConstraints;
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import java.awt.GridBagLayout;
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import java.awt.Image;
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import java.awt.MediaTracker;
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import java.awt.event.ActionListener;
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import java.awt.event.ActionEvent;
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import java.io.File;
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import java.util.HashMap;
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import java.util.Vector;
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public class AutoAnalyser extends JFrame implements ActionListener, DocumentListener {
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/**
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* Need serialVersionUID to be serializable
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*/
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private static final long serialVersionUID = 1L;
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// Set options for the TE Calculator type:
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public final static String CALC_TYPE_DISCRETE = "Discrete";
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public final static String CALC_TYPE_GAUSSIAN = "Gaussian";
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public final static String CALC_TYPE_KRASKOV = "Kraskov";
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public final static String CALC_TYPE_KERNEL = "Kernel";
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protected String[] calcTypes = {
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CALC_TYPE_DISCRETE, CALC_TYPE_GAUSSIAN,
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CALC_TYPE_KRASKOV, CALC_TYPE_KERNEL};
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protected String[] unitsForEachCalc = {"bits", "nats", "nats", "bits"};
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// Store the properties for each calculator
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protected String[] commonContProperties = {
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TransferEntropyCalculator.K_PROP_NAME,
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};
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protected String[] gaussianProperties = {
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TransferEntropyCalculator.K_TAU_PROP_NAME, // Not common to Kernel
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TransferEntropyCalculator.L_PROP_NAME, // Not common to Kernel
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TransferEntropyCalculator.L_TAU_PROP_NAME, // Not common to Kernel
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TransferEntropyCalculator.DELAY_PROP_NAME, // Not common to Kernel
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};
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protected String[] kernelProperties = {
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TransferEntropyCalculatorKernel.KERNEL_WIDTH_PROP_NAME,
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TransferEntropyCalculatorKernel.DYN_CORR_EXCL_TIME_NAME,
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TransferEntropyCalculatorKernel.NORMALISE_PROP_NAME,
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};
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protected String[] kraskovProperties = {
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TransferEntropyCalculator.K_TAU_PROP_NAME, // Not common to Kernel
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TransferEntropyCalculator.L_PROP_NAME, // Not common to Kernel
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TransferEntropyCalculator.L_TAU_PROP_NAME, // Not common to Kernel
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TransferEntropyCalculator.DELAY_PROP_NAME, // Not common to Kernel
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ConditionalMutualInfoMultiVariateCommon.PROP_NORMALISE,
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ConditionalMutualInfoCalculatorMultiVariateKraskov.PROP_K,
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ConditionalMutualInfoCalculatorMultiVariateKraskov.PROP_ADD_NOISE,
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ConditionalMutualInfoCalculatorMultiVariateKraskov.PROP_DYN_CORR_EXCL_TIME,
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ConditionalMutualInfoCalculatorMultiVariateKraskov.PROP_NORM_TYPE,
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ConditionalMutualInfoCalculatorMultiVariateKraskov.PROP_NUM_THREADS,
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TransferEntropyCalculatorKraskov.PROP_KRASKOV_ALG_NUM,
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TransferEntropyCalculatorKraskov.PROP_AUTO_EMBED_METHOD,
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TransferEntropyCalculatorKraskov.PROP_K_SEARCH_MAX,
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TransferEntropyCalculatorKraskov.PROP_TAU_SEARCH_MAX,
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TransferEntropyCalculatorKraskov.PROP_RAGWITZ_NUM_NNS
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};
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protected JButton computeButton;
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protected JButton openDataButton;
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// Stores the current data file
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protected File dataFile = null;
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// Combo box for selecting the calculator type
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protected JComboBox<String> calcTypeComboBox;
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// Displays the current data file
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protected JTextField dataFileTextField;
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// Descriptor of the data:
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protected JLabel dataFileDescriptorLabel;
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// The data we're working with
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protected double[][] data = null;
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// Number of rows and columns of the data:
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protected int dataRows = 0;
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protected int dataColumns = 0;
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// Source column field
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protected JTextField sourceColTextField;
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// Destination column field
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protected JTextField destColTextField;
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// Table for the properties
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protected JTable propertiesTable;
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// Table model (local class) for the table
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protected PropertiesTableModel propertiesTableModel;
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// Panel for the table
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protected JPanel propertiesPanel;
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// Names of the properties
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protected Vector<String> fieldNames;
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// Values of the properties
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protected HashMap<String,String> propertyValues;
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// Results text
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protected JLabel resultsLabel;
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/**
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* Constructor to generate the application windows
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*/
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public AutoAnalyser() {
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ImageIcon icon = new ImageIcon("../../JIDT-logo.png"); // Location for distributions
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if (icon.getImageLoadStatus() != MediaTracker.COMPLETE) {
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// Try the alternative image location for SVN checkouts
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icon = new ImageIcon("../../web/JIDT-logo.png");
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}
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setIconImage(icon.getImage());
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GridBagLayout gridbag = new GridBagLayout();
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GridBagConstraints c = new GridBagConstraints();
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setLayout(gridbag);
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c.fill = GridBagConstraints.BOTH;
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c.weightx = 1.0;
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setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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setSize(500,500);
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setTitle("JIDT Transfer Entropy Auto-Analyser");
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// Centre in the middle of the screen
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setLocationRelativeTo(null);
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// Create a panel for the calc type:
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JPanel calcTypePanel = new JPanel();
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JLabel calcTypeLabel = new JLabel("TE Calculator Type:");
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calcTypeComboBox = (JComboBox<String>) new JComboBox<String>(calcTypes);
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calcTypeComboBox.setSelectedIndex(2); // Select Kraskov by default
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calcTypeComboBox.addActionListener(this);
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calcTypePanel.add(calcTypeLabel);
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calcTypePanel.add(calcTypeComboBox);
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JPanel dataFileChooserPanel = new JPanel();
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JLabel fileLabel = new JLabel("Data file:");
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dataFileTextField = new JTextField(30);
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dataFileTextField.setEnabled(false);
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dataFileChooserPanel.add(fileLabel);
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dataFileChooserPanel.add(dataFileTextField);
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// Button to open data file
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openDataButton = new JButton("Select");
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openDataButton.addActionListener(this);
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dataFileChooserPanel.add(openDataButton);
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// From column:
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JPanel sourceChooserPanel = new JPanel();
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JLabel sourceLabel = new JLabel("Source column (first is 0):");
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sourceColTextField = new JTextField(5);
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sourceColTextField.setEnabled(true);
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sourceColTextField.setText("0");
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sourceColTextField.getDocument().addDocumentListener(this);
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sourceChooserPanel.add(sourceLabel);
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sourceChooserPanel.add(sourceColTextField);
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// To column:
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JPanel destChooserPanel = new JPanel();
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JLabel destLabel = new JLabel("Destination column (first is 0):");
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destColTextField = new JTextField(5);
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destColTextField.setEnabled(true);
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destColTextField.setText("1");
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destColTextField.addActionListener(this);
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destChooserPanel.add(destLabel);
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destChooserPanel.add(destColTextField);
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// Description about the data
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JPanel dataFileDescriptorPanel = new JPanel();
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dataFileDescriptorLabel = new JLabel("No data file selected yet ...");
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dataFileDescriptorPanel.add(dataFileDescriptorLabel);
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// TODO Need to set an appropriate width here
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propertiesPanel = new JPanel();
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putCalcPropertiesInTable();
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propertiesTableModel = new PropertiesTableModel();
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propertiesTable = new JTable(propertiesTableModel);
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// Make sure any properties are saved when the compute button is clicked
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propertiesTable.putClientProperty("terminateEditOnFocusLost", Boolean.TRUE);
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propertiesPanel.add(propertiesTable);
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// Button to compute
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computeButton = new JButton("Compute");
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computeButton.addActionListener(this);
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// Results label
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JPanel resultsPanel = new JPanel();
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resultsLabel = new JLabel(" ");
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resultsPanel.add(resultsLabel);
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// Add all the components in:
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/*
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add(calcTypePanel, BorderLayout.NORTH);
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add(dataFileChooserPanel, BorderLayout.EAST);
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add(dataFileDescriptorPanel, BorderLayout.WEST);
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add(computeButton, BorderLayout.SOUTH);
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*/
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// gridbag.setConstraints(calcTypePanel, c);
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// add(calcTypePanel);
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c.gridwidth = 1;
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c.gridx = 0;
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add(calcTypePanel, c);
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add(dataFileChooserPanel, c);
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add(dataFileDescriptorPanel, c);
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add(sourceChooserPanel, c);
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add(destChooserPanel, c);
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add(propertiesPanel, c);
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add(computeButton, c);
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c.gridwidth = GridBagConstraints.REMAINDER; //end row
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c.anchor = GridBagConstraints.PAGE_START; // top of cell
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add(resultsPanel, c);
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// TODO Add the JIDT logo somewhere
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// TODO Add a panel for auto generated code.
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setVisible(true);
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}
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@Override
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public void actionPerformed(ActionEvent e) {
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resultsLabel.setText(""); // Clear text for now if anything changes
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if (e.getSource() == computeButton) {
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computeTE();
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} else if (e.getSource() == openDataButton) {
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selectFileAction();
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} else if (e.getSource() == calcTypeComboBox) {
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putCalcPropertiesInTable();
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propertiesTableModel.fireTableDataChanged(); // Alerts to refresh the table contents
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System.out.println("Added properties for new calculator");
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}
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// Else nothing extra to do
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}
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public void repaint() {
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System.out.println("repainting ...");
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super.repaint();
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}
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protected void selectFileAction() {
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System.out.println("Open data button pressed ...");
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// Give user a choice of file, starting from the currently selected
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// one
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JFileChooser dataFileChooser;
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if (dataFile == null) {
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dataFileChooser = new JFileChooser(System.getProperty("user.dir"));
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} else {
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dataFileChooser = new JFileChooser(dataFile);
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}
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int returnVal = dataFileChooser.showOpenDialog(this);
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if (returnVal == JFileChooser.APPROVE_OPTION) {
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// File selection was approved:
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dataFile = dataFileChooser.getSelectedFile();
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dataFileTextField.setText(dataFile.getAbsolutePath());
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System.out.println("Data file selected: " + dataFile.getAbsolutePath());
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// Now load the file in:
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ArrayFileReader afr = new ArrayFileReader(dataFile);
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try {
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data = afr.getDouble2DMatrix();
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dataRows = data.length;
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if (dataRows > 0) {
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dataColumns = data[0].length;
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} else {
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dataColumns = 0;
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}
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dataFileDescriptorLabel.setText(
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String.format("Valid data file with %d rows and %d columns",
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dataRows, dataColumns));
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System.out.printf("Read in data with %d rows and %d columns\n",
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dataRows, dataColumns);
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} catch (Exception ex) {
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ex.printStackTrace(System.err);
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JOptionPane.showMessageDialog(this,
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ex.getMessage());
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dataFileDescriptorLabel.setText("Invalid data file, please load another");
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data = null;
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}
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}
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// Else do nothing
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}
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protected void computeTE() {
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System.out.println("Compute button pressed ...");
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if (data == null) {
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JOptionPane.showMessageDialog(this, "No valid data source selected");
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return;
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}
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int sourceColumn = Integer.parseInt(sourceColTextField.getText());
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int destColumn = Integer.parseInt(destColTextField.getText());
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if ((sourceColumn < 0) || (sourceColumn >= dataColumns)) {
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JOptionPane.showMessageDialog(this,
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String.format("Source column must be between 0 and %d for this data set",
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dataColumns-1));
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return;
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}
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if ((destColumn < 0) || (destColumn >= dataColumns)) {
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JOptionPane.showMessageDialog(this,
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String.format("Destination column must be between 0 and %d for this data set",
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dataColumns-1));
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return;
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}
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String selectedCalcType = (String)
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calcTypeComboBox.getSelectedItem();
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String units = unitsForEachCalc[calcTypeComboBox.getSelectedIndex()];
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StringBuffer code = new StringBuffer();
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code.append("\tString dataFile = \"" + dataFile.getAbsolutePath() + "\";\n");
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code.append("\tArrayFileReader afr = new ArrayFileReader(dataFile);\n");
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code.append("\tdouble[][] data = afr.getDouble2DMatrix();\n");
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// Create a Kraskov TE calculator:
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TransferEntropyCalculator teCalc;
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code.append("\tTransferEntropyCalculator teCalc;\n");
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try{
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// Construct an instance of the selected calculator:
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if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_DISCRETE)) {
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throw new Exception("Not implemented yet");
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} else if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_GAUSSIAN)) {
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teCalc = new TransferEntropyCalculatorGaussian();
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code.append("\tteCalc = new TransferEntropyCalculatorGaussian();\n");
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} else if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_KRASKOV)) {
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teCalc = new TransferEntropyCalculatorKraskov();
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code.append("\tteCalc = new TransferEntropyCalculatorKraskov();\n");
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} else if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_KERNEL)) {
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teCalc = new TransferEntropyCalculatorKernel();
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code.append("\tteCalc = new TransferEntropyCalculatorKernel();\n");
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} else {
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throw new Exception("No recognised calculator selected: " +
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selectedCalcType);
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}
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// Set properties
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for (String propName : fieldNames) {
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String propValue = null;
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try {
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propValue = propertyValues.get(propName);
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} catch (Exception ex) {
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ex.printStackTrace(System.err);
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JOptionPane.showMessageDialog(this,
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ex.getMessage());
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resultsLabel.setText("Cannot find a value for property " + propName);
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}
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// Check whether this property value is different to the default for
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// this calculator. This is more for generating the minimal code.
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if (!propValue.equalsIgnoreCase(teCalc.getProperty(propName))) {
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// We need to set this property:
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teCalc.setProperty(propName, propValue);
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code.append("\tteCalc.setProperty(\"" + propName + "\", \"" +
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propValue + "\");\n");
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}
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}
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teCalc.initialise();
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code.append("\tteCalc.initialise();\n");
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// Compute TE
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teCalc.setObservations(
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MatrixUtils.selectColumn(data, sourceColumn),
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MatrixUtils.selectColumn(data, destColumn));
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code.append("\tteCalc.setObservations(\n" +
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"\t\tMatrixUtils.selectColumn(data, " + sourceColumn + "),\n" +
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"\t\tMatrixUtils.selectColumn(data, " + destColumn + "));\n");
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double teResult = teCalc.computeAverageLocalOfObservations();
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code.append("\tdouble teResult = teCalc.computeAverageLocalOfObservations();\n");
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String resultsPrefixString = String.format("TE_%s(col_%d -> col_%d) = ",
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selectedCalcType, sourceColumn, destColumn);
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resultsLabel.setText(String.format(resultsPrefixString + "%.4f %s", teResult, units));
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code.append("\tSystem.out.printf(\"" + resultsPrefixString + "%.4f " + units + "\\n\", teResult);\n");
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System.out.println("Code to generate this result:");
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System.out.print(code);
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} catch (Exception ex) {
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ex.printStackTrace(System.err);
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JOptionPane.showMessageDialog(this,
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ex.getMessage());
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resultsLabel.setText("Calculation failed, please see console");
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}
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||||
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}
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protected class PropertiesTableModel extends AbstractTableModel {
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/**
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*
|
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*/
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private static final long serialVersionUID = 1L;
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public PropertiesTableModel() {
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super();
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}
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@Override
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public String getColumnName(int column) {
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if (column == 0) {
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return "Property name";
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} else {
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return "Property value";
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}
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}
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||||
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@Override
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public boolean isCellEditable(int rowIndex, int columnIndex) {
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if (columnIndex == 0) {
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return false;
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}
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return true;
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}
|
||||
|
||||
@Override
|
||||
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
|
||||
if (columnIndex == 0) {
|
||||
return;
|
||||
}
|
||||
// Else we've changed a property value -- which one?
|
||||
String propName = fieldNames.get(rowIndex);
|
||||
propertyValues.put(propName, (String) aValue);
|
||||
}
|
||||
|
||||
@Override
|
||||
public int getColumnCount() {
|
||||
return 2;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int getRowCount() {
|
||||
return fieldNames.size();
|
||||
}
|
||||
|
||||
@Override
|
||||
public Object getValueAt(int rowIndex, int columnIndex) {
|
||||
String propName = fieldNames.get(rowIndex);
|
||||
if (columnIndex == 0) {
|
||||
return propName;
|
||||
} else {
|
||||
return propertyValues.get(propName);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public void putCalcPropertiesInTable() {
|
||||
System.out.println("Getting calc properties");
|
||||
String selectedCalcType = (String)
|
||||
calcTypeComboBox.getSelectedItem();
|
||||
@SuppressWarnings("rawtypes")
|
||||
Class teCalcClass = null;
|
||||
String[] classSpecificProperties = null;
|
||||
TransferEntropyCalculator teCalc = null;
|
||||
try {
|
||||
if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_DISCRETE)) {
|
||||
throw new Exception("Not implemented yet");
|
||||
} else if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_GAUSSIAN)) {
|
||||
teCalcClass = TransferEntropyCalculatorGaussian.class;
|
||||
teCalc = new TransferEntropyCalculatorGaussian();
|
||||
classSpecificProperties = gaussianProperties;
|
||||
} else if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_KRASKOV)) {
|
||||
teCalcClass = TransferEntropyCalculatorKraskov.class;
|
||||
teCalc = new TransferEntropyCalculatorKraskov();
|
||||
classSpecificProperties = kraskovProperties;
|
||||
} else if (selectedCalcType.equalsIgnoreCase(CALC_TYPE_KERNEL)) {
|
||||
teCalcClass = TransferEntropyCalculatorKernel.class;
|
||||
teCalc = new TransferEntropyCalculatorKernel();
|
||||
classSpecificProperties = kernelProperties;
|
||||
} else {
|
||||
throw new Exception("No recognised calculator selected: " +
|
||||
selectedCalcType);
|
||||
}
|
||||
} catch (Exception ex) {
|
||||
ex.printStackTrace(System.err);
|
||||
JOptionPane.showMessageDialog(this,
|
||||
ex.getMessage());
|
||||
resultsLabel.setText("Cannot load requested calculator");
|
||||
}
|
||||
|
||||
// Now get all of the possible properties for this class:
|
||||
fieldNames = new Vector<String>();
|
||||
Vector<String> fieldDescriptions = new Vector<String>();
|
||||
for (int i = 0; i < commonContProperties.length; i++) {
|
||||
fieldNames.add(commonContProperties[i]);
|
||||
System.out.println("Adding property name " + commonContProperties[i]);
|
||||
}
|
||||
for (int i = 0; i < classSpecificProperties.length; i++) {
|
||||
fieldNames.add(classSpecificProperties[i]);
|
||||
System.out.println("Adding property name " + classSpecificProperties[i]);
|
||||
}
|
||||
// Now extract the default values for all of these properties:
|
||||
propertyValues = new HashMap<String,String>();
|
||||
for (String propName : fieldNames) {
|
||||
String defaultPropValue = null;
|
||||
try {
|
||||
defaultPropValue = teCalc.getProperty(propName);
|
||||
} catch (Exception ex) {
|
||||
ex.printStackTrace(System.err);
|
||||
JOptionPane.showMessageDialog(this,
|
||||
ex.getMessage());
|
||||
propertyValues.put(propName, "Cannot find a value");
|
||||
}
|
||||
propertyValues.put(propName, defaultPropValue);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* @param args
|
||||
*/
|
||||
public static void main(String[] args) {
|
||||
new AutoAnalyser();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void changedUpdate(DocumentEvent e) {
|
||||
// Source or dest col number updated
|
||||
resultsLabel.setText(""); // Clear text for now if anything changes
|
||||
}
|
||||
|
||||
@Override
|
||||
public void insertUpdate(DocumentEvent e) {
|
||||
// Source or dest col number updated
|
||||
resultsLabel.setText(""); // Clear text for now if anything changes
|
||||
}
|
||||
|
||||
@Override
|
||||
public void removeUpdate(DocumentEvent e) {
|
||||
// Source or dest col number updated
|
||||
resultsLabel.setText(""); // Clear text for now if anything changes
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue