mirror of https://github.com/jlizier/jidt
First full working version of the TE Auto Analyser, including scripts to run auto generated Java code
This commit is contained in:
joseph.lizier
parent
6951f52f68
commit
53a3cf129d
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@ -0,0 +1,13 @@
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#!/bin/bash
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# The demo is intended to be run from the parent directory
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cd ..
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# Make sure the latest example source file is compiled.
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javac -classpath "../../infodynamics.jar" "infodynamics/demos/autoanalysis/AutoAnalyser.java"
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# Run the example:
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java -classpath ".:../../infodynamics.jar" infodynamics.demos.autoanalysis.AutoAnalyser
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cd $OLDPWD
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@ -0,0 +1,8 @@
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#!/bin/bash
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# Make sure the latest example source file is compiled.
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javac -classpath "../../../infodynamics.jar:.." "../infodynamics/demos/autoanalysis/GeneratedTECalculator.java"
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# Run the example:
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java -classpath ".:../../../infodynamics.jar:.." infodynamics.demos.autoanalysis.GeneratedTECalculator
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@ -27,6 +27,7 @@ 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.BorderFactory;
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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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@ -35,20 +36,27 @@ 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.JScrollPane;
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import javax.swing.JTable;
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import javax.swing.JTextArea;
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import javax.swing.JTextField;
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import javax.swing.border.EtchedBorder;
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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 javax.swing.table.TableColumn;
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import java.awt.EventQueue;
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import java.awt.BorderLayout;
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import java.awt.Color;
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import java.awt.Dimension;
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import java.awt.Font;
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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.io.FileWriter;
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import java.util.HashMap;
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import java.util.Vector;
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@ -126,14 +134,16 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
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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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// Text area for the generated code
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protected JTextArea codeTextArea;
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protected String codeDefaultText = " ... Awaiting new parameter selection (press compute) ...";
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/**
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* Constructor to generate the application windows
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@ -146,82 +156,112 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
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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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setSize(1100,530);
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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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// Create the fields for the calc type:
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JLabel calcTypeLabel = new JLabel("TE Calculator Type:");
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calcTypeLabel.setToolTipText("Select estimator type. \"Discrete\" is for discrete or pre-binned data; all others for continuous data.");
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calcTypeLabel.setBorder(BorderFactory.createEmptyBorder(0,0,10,0));
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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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// Don't set an empty border as it becomes clickable as well,
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// we'll use an empty label instead
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//calcTypeComboBox.setBorder(BorderFactory.createEmptyBorder(0,0,10,0));
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JPanel dataFileChooserPanel = new JPanel();
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// Create the fields for the data file
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JLabel fileLabel = new JLabel("Data file:");
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fileLabel.setToolTipText("Must be a text file of time-series values with time increasing in rows, and variables along columns");
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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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// Don't set border around this text field as it doesn't look right
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// TODO set action listener for on click of this field
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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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// Description about the data
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dataFileDescriptorLabel = new JLabel("No data file selected yet ...");
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dataFileDescriptorLabel.setHorizontalAlignment(JLabel.RIGHT);
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dataFileDescriptorLabel.setBorder(BorderFactory.createEmptyBorder(0,0,10,0));
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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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JLabel sourceLabel = new JLabel("Source column:");
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sourceLabel.setToolTipText("(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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// Must add document listener, not add action listener
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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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JLabel destLabel = new JLabel("Destination column:");
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destLabel.setToolTipText("(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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destColTextField.getDocument().addDocumentListener(this);
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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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JLabel dummyLabel1 = new JLabel(" ");
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dummyLabel1.setSize(10, 10);
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JLabel dummyLabel2 = new JLabel(" ");
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dummyLabel2.setSize(10, 10);
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JLabel dummyLabel3 = new JLabel(" ");
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dummyLabel3.setSize(10, 10);
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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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Font headerFont = propertiesTable.getTableHeader().getFont();
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propertiesTable.getTableHeader().setFont(headerFont.deriveFont(Font.BOLD));
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TableColumn valueColumn = propertiesTable.getColumn("Property value");
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valueColumn.setMinWidth(130);
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valueColumn.setMaxWidth(130);
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JScrollPane propsTableScrollPane = new JScrollPane(propertiesTable);
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// Set up for ~18 rows maximum (the +6 is exact to fit all props
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// for KRaskov in without scrollbar)
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Dimension d = propertiesTable.getPreferredSize();
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propsTableScrollPane.setPreferredSize(
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new Dimension(d.width,propertiesTable.getRowHeight()*17+6));
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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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// Code panel
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JPanel codePanel = new JPanel();
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codePanel.setBorder(BorderFactory.createCompoundBorder(
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BorderFactory.createTitledBorder("Generated code"),
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BorderFactory.createEmptyBorder(5,5,5,5)));
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codeTextArea = new JTextArea(codeDefaultText);
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codeTextArea.setOpaque(false);
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codeTextArea.setEditable(false);
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//codeTextArea.setLineWrap(true); // This makes it all unreadable
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//codeTextArea.setWrapStyleWord(true);
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JScrollPane areaScrollPane = new JScrollPane(codeTextArea);
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areaScrollPane.setVerticalScrollBarPolicy(
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JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
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areaScrollPane.setHorizontalScrollBarPolicy(
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JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
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int codeTextAreaWidth = 560;
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int codeTextAreaHeight = 460;
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Dimension codeTextAreaDimension =
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new Dimension(codeTextAreaWidth, codeTextAreaHeight);
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areaScrollPane.setPreferredSize(codeTextAreaDimension);
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areaScrollPane.setMinimumSize(codeTextAreaDimension);
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areaScrollPane.setMaximumSize(codeTextAreaDimension);
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codePanel.add(areaScrollPane);
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codePanel.setSize(codeTextAreaWidth+10, codeTextAreaHeight+10);
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// Add all the components in:
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/*
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@ -232,27 +272,88 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
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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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JPanel paramsPanel = new JPanel();
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paramsPanel.setBorder(BorderFactory.createCompoundBorder(
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BorderFactory.createTitledBorder("Calculation parameters"),
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BorderFactory.createEmptyBorder(5,5,5,5)));
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GridBagLayout gridbag = new GridBagLayout();
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GridBagConstraints c = new GridBagConstraints();
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paramsPanel.setLayout(gridbag);
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c.anchor = GridBagConstraints.EAST; // Not sure what I put EAST for?
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// Add the CalcType label and combobox
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c.gridwidth = GridBagConstraints.RELATIVE; //next-to-last
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c.fill = GridBagConstraints.NONE; //reset to default
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c.weightx = 0.0; //reset to default
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paramsPanel.add(calcTypeLabel, c);
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c.gridwidth = GridBagConstraints.REMAINDER; //end row
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c.fill = GridBagConstraints.HORIZONTAL;
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c.weightx = 1.0;
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paramsPanel.add(calcTypeComboBox, c);
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// Add dummy label for spacing
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paramsPanel.add(dummyLabel3, c);
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// Add the data file chooser fields
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c.gridwidth = GridBagConstraints.RELATIVE; //next-to-last
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c.fill = GridBagConstraints.NONE; //reset to default
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c.weightx = 0.0; //reset to default
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paramsPanel.add(fileLabel, c);
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c.gridwidth = GridBagConstraints.REMAINDER; //end row
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c.fill = GridBagConstraints.HORIZONTAL;
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c.weightx = 1.0;
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paramsPanel.add(dataFileTextField, c);
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c.gridx = 1;
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paramsPanel.add(openDataButton, c);
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c.gridx = -1; // Reset to no indication
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paramsPanel.add(dataFileDescriptorLabel, c);
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// Add the source selector
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c.gridwidth = GridBagConstraints.RELATIVE; //next-to-last
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c.fill = GridBagConstraints.NONE; //reset to default
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c.weightx = 0.0; //reset to default
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paramsPanel.add(sourceLabel, c);
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c.gridwidth = GridBagConstraints.REMAINDER; //end row
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c.fill = GridBagConstraints.HORIZONTAL;
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c.weightx = 1.0;
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paramsPanel.add(sourceColTextField, c);
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// Add the destination selector
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c.gridwidth = GridBagConstraints.RELATIVE; //next-to-last
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c.fill = GridBagConstraints.NONE; //reset to default
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c.weightx = 0.0; //reset to default
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paramsPanel.add(destLabel, c);
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c.gridwidth = GridBagConstraints.REMAINDER; //end row
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c.fill = GridBagConstraints.HORIZONTAL;
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c.weightx = 1.0;
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paramsPanel.add(destColTextField, c);
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// Add dummy label for spacing
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paramsPanel.add(dummyLabel1, c);
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// Add the properties table
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paramsPanel.add(propsTableScrollPane, c);
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// Add dummy label for spacing
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paramsPanel.add(dummyLabel2, c);
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// Add the compute button
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paramsPanel.add(computeButton, c);
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// Add the results text
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paramsPanel.add(resultsLabel, 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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// Add both panels into the frame with Border layout
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add(paramsPanel, BorderLayout.WEST);
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add(codePanel);
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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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// Clear text fields for now if anything changes
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resultsLabel.setText(" ");
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codeTextArea.setText(codeDefaultText);
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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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@ -276,7 +377,7 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
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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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dataFileChooser = new JFileChooser(System.getProperty("user.dir") + "/../data/");
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} else {
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dataFileChooser = new JFileChooser(dataFile);
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}
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@ -338,33 +439,47 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
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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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StringBuffer javaCode = new StringBuffer();
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javaCode.append("package infodynamics.demos.autoanalysis;\n\n");
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javaCode.append("import infodynamics.utils.ArrayFileReader;\n");
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javaCode.append("import infodynamics.utils.MatrixUtils;\n\n");
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javaCode.append("import infodynamics.measures.continuous.TransferEntropyCalculator;\n");
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try{
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// Create a Kraskov TE calculator:
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TransferEntropyCalculator teCalc;
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// Construct an instance of the selected calculator:
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String javaConstructorLine = null;
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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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javaCode.append("import infodynamics.measures.continuous.gaussian.TransferEntropyCalculatorGaussian;\n");
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javaConstructorLine = " teCalc = 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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javaCode.append("import infodynamics.measures.continuous.kraskov.TransferEntropyCalculatorKraskov;\n");
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javaConstructorLine = " teCalc = 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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javaCode.append("import infodynamics.measures.continuous.kernel.TransferEntropyCalculatorKernel;\n");
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javaConstructorLine = " teCalc = 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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javaCode.append("\npublic class GeneratedTECalculator {\n\n");
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javaCode.append(" public static void main(String[] args) throws Exception {\n");
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javaCode.append(" String dataFile = \"" + dataFile.getAbsolutePath() + "\";\n");
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javaCode.append(" ArrayFileReader afr = new ArrayFileReader(dataFile);\n");
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javaCode.append(" double[][] data = afr.getDouble2DMatrix();\n");
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javaCode.append(" TransferEntropyCalculator teCalc;\n");
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javaCode.append(javaConstructorLine);
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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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@ -381,28 +496,36 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
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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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javaCode.append(" teCalc.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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javaCode.append(" teCalc.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");
|
||||
javaCode.append(" teCalc.setObservations(\n" +
|
||||
" MatrixUtils.selectColumn(data, " + sourceColumn + "),\n" +
|
||||
" MatrixUtils.selectColumn(data, " + destColumn + "));\n");
|
||||
double teResult = teCalc.computeAverageLocalOfObservations();
|
||||
code.append("\tdouble teResult = teCalc.computeAverageLocalOfObservations();\n");
|
||||
javaCode.append(" double teResult = teCalc.computeAverageLocalOfObservations();\n");
|
||||
String resultsPrefixString = String.format("TE_%s(col_%d -> col_%d) = ",
|
||||
selectedCalcType, sourceColumn, destColumn);
|
||||
resultsLabel.setText(String.format(resultsPrefixString + "%.4f %s", teResult, units));
|
||||
code.append("\tSystem.out.printf(\"" + resultsPrefixString + "%.4f " + units + "\\n\", teResult);\n");
|
||||
System.out.println("Code to generate this result:");
|
||||
System.out.print(code);
|
||||
javaCode.append(" System.out.printf(\"" + resultsPrefixString + "%.4f " + units + "\\n\", teResult);\n");
|
||||
javaCode.append(" }\n");
|
||||
javaCode.append("}\n\n");
|
||||
// System.out.println("Code to generate this result:");
|
||||
// System.out.print(code);
|
||||
codeTextArea.setText(javaCode.toString());
|
||||
|
||||
// Now write the Java code to a file
|
||||
FileWriter javaFileWriter = new FileWriter("infodynamics/demos/autoanalysis/GeneratedTECalculator.java");
|
||||
javaFileWriter.write(javaCode.toString());
|
||||
javaFileWriter.close();
|
||||
} catch (Exception ex) {
|
||||
ex.printStackTrace(System.err);
|
||||
JOptionPane.showMessageDialog(this,
|
||||
|
|
@ -532,6 +655,27 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
|
|||
propertyValues.put(propName, defaultPropValue);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void changedUpdate(DocumentEvent e) {
|
||||
// Source or dest col number updated
|
||||
resultsLabel.setText(" "); // Clear text for now if anything changes
|
||||
codeTextArea.setText(codeDefaultText);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void insertUpdate(DocumentEvent e) {
|
||||
// Source or dest col number updated
|
||||
resultsLabel.setText(" "); // Clear text for now if anything changes
|
||||
codeTextArea.setText(codeDefaultText);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void removeUpdate(DocumentEvent e) {
|
||||
// Source or dest col number updated
|
||||
resultsLabel.setText(" "); // Clear text for now if anything changes
|
||||
codeTextArea.setText(codeDefaultText);
|
||||
}
|
||||
|
||||
/**
|
||||
* @param args
|
||||
|
|
@ -539,22 +683,4 @@ public class AutoAnalyser extends JFrame implements ActionListener, DocumentList
|
|||
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