Merge pull request #1784 from cmu-phil/joe_work_2024_6_1

Joe work 2024 6 1
cmu-phil · Jun 13, 2024 · 6aa0340 · 6aa0340
2 parents ebaba1b + 7585c80
commit 6aa0340
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Showing 371 changed files with 5,951 additions and 2,455 deletions.
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java
@@ -20,7 +20,6 @@
 ///////////////////////////////////////////////////////////////////////////////
 package edu.cmu.tetradapp;
 
-import edu.cmu.tetrad.search.work_in_progress.DMSearch;
 import edu.cmu.tetrad.util.JOptionUtils;
 import edu.cmu.tetrad.util.TetradLogger;
 import edu.cmu.tetrad.util.Version;
@@ -122,7 +121,7 @@ private static void setLookAndFeel() {
                         UIManager.getSystemLookAndFeelClassName());
             }
         } catch (Exception e) {
-            TetradLogger.getInstance().forceLogMessage("Couldn't set look and feel.");
+            TetradLogger.getInstance().log("Couldn't set look and feel.");
         }
     }
 
@@ -271,7 +270,7 @@ public void componentMoved(ComponentEvent e) {
                     }
                 });
             } catch (Exception e) {
-                TetradLogger.getInstance().forceLogMessage("Could not set quit handler on this platform..");
+                TetradLogger.getInstance().log("Could not set quit handler on this platform..");
             }
         }
     }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LoadSessionAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LoadSessionAction.java
@@ -123,7 +123,7 @@ public void watch() {
                             throw e1;
                         } catch (Exception e2) {
                             e2.printStackTrace();
-                            TetradLogger.getInstance().forceLogMessage("Exception: " + e2.getMessage());
+                            TetradLogger.getInstance().log("Exception: " + e2.getMessage());
                         }
                     } else if (o instanceof SessionWrapper) {
                         sessionWrapper = (SessionWrapper) o;

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/TetradDesktop.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/TetradDesktop.java
@@ -532,7 +532,7 @@ public void setDisplayLogging(boolean displayLogging) {
             try {
                 TetradLogger.getInstance().setNextOutputStream();
             } catch (IllegalStateException e2) {
-                TetradLogger.getInstance().forceLogMessage(
+                TetradLogger.getInstance().log(
                         "Unable to setup logging, please restart Tetrad.");
                 return;
             }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/EdgewiseComparisonEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/EdgewiseComparisonEditor.java
@@ -78,6 +78,13 @@ private void setup() {
 
         area.setFont(font);
 
+        int position = area.getText().indexOf("True graph");
+
+        // If the word is found, scroll to it
+        if (position >= 0) {
+            area.setCaretPosition(position);
+        }
+
         JScrollPane scrollTextPane = new JScrollPane(area);
         scrollTextPane.setPreferredSize(new Dimension(500, 600));
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GeneralAlgorithmEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GeneralAlgorithmEditor.java
@@ -198,7 +198,7 @@ public void setAlgorithmResult(String jsonResult) {
         this.algorithmRunner.getGraphs().clear();
         this.algorithmRunner.getGraphs().add(graph);
 
-        TetradLogger.getInstance().forceLogMessage("Remote graph result assigned to algorithmRunner!");
+        TetradLogger.getInstance().log("Remote graph result assigned to algorithmRunner!");
         firePropertyChange("modelChanged", null, null);
 
         this.graphCard.refresh();

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GeneralizedTemplateEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GeneralizedTemplateEditor.java
@@ -542,7 +542,7 @@ private void setParseText(String text) {
                 expressionTextDoc.remove(0, expressionTextPane.getText().length());
                 expressionTextDoc.insertString(0, text, null);
             } catch (BadLocationException e) {
-                TetradLogger.getInstance().forceLogMessage(e.getMessage());
+                TetradLogger.getInstance().log(e.getMessage());
                 throw new RuntimeException(e);
             }
         });

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphEditor.java
@@ -511,6 +511,9 @@ private JMenu createGraphMenu() {
         JMenuItem randomGraph = new JMenuItem("Random Graph");
         graph.add(randomGraph);
 
+        randomGraph.setAccelerator(
+                KeyStroke.getKeyStroke(KeyEvent.VK_R, InputEvent.META_DOWN_MASK));
+
         graph.addSeparator();
 
         graph.add(new GraphPropertiesAction(getWorkbench()));

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GridSearchEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GridSearchEditor.java
@@ -6,12 +6,16 @@
 import edu.cmu.tetrad.algcomparison.score.ScoreWrapper;
 import edu.cmu.tetrad.algcomparison.simulation.Simulation;
 import edu.cmu.tetrad.algcomparison.simulation.Simulations;
+import edu.cmu.tetrad.algcomparison.simulation.SingleDatasetSimulation;
 import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
 import edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper;
 import edu.cmu.tetrad.annotation.AnnotatedClass;
 import edu.cmu.tetrad.annotation.Score;
 import edu.cmu.tetrad.annotation.TestOfIndependence;
+import edu.cmu.tetrad.data.DataSet;
 import edu.cmu.tetrad.data.DataType;
+import edu.cmu.tetrad.data.Knowledge;
+import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.util.*;
 import edu.cmu.tetradapp.editor.simulation.ParameterTab;
 import edu.cmu.tetradapp.model.GridSearchModel;
@@ -30,10 +34,7 @@
 import javax.swing.table.TableRowSorter;
 import javax.swing.text.BadLocationException;
 import java.awt.*;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintStream;
+import java.io.*;
 import java.lang.reflect.InvocationTargetException;
 import java.nio.charset.StandardCharsets;
 import java.text.DecimalFormat;
@@ -155,8 +156,6 @@ public GridSearchEditor(GridSearchModel model) {
         model.getParameters().set("algcomparisonSaveGraphs", model.getParameters().getBoolean("algcomparisonSaveGraphs", true));
         model.getParameters().set("algcomparisonSaveCPDAGs", model.getParameters().getBoolean("algcomparisonSaveCPDAGs", false));
         model.getParameters().set("algcomparisonSavePAGs", model.getParameters().getBoolean("algcomparisonSavePAGs", false));
-        model.getParameters().set("algcomparisonShowAlgorithmIndices", model.getParameters().getBoolean("algcomparisonShowAlgorithmIndices", true));
-        model.getParameters().set("algcomparisonShowSimulationIndices", model.getParameters().getBoolean("algcomparisonShowSimulationIndices", true));
         model.getParameters().set("algcomparisonSortByUtility", model.getParameters().getBoolean("algcomparisonSortByUtility", false));
         model.getParameters().set("algcomparisonShowUtilities", model.getParameters().getBoolean("algcomparisonShowUtilities", false));
         model.getParameters().set("algcomparisonSetAlgorithmKnowledge", model.getParameters().getBoolean("algcomparisonSetAlgorithmKnowledge", false));
@@ -1299,16 +1298,6 @@ private void addComparisonTab(JTabbedPane tabbedPane) {
             horiz2c.add(Box.createHorizontalGlue());
             horiz2c.add(getBooleanSelectionBox("algcomparisonSavePAGs", model.getParameters(), false));
 
-            Box horiz3 = Box.createHorizontalBox();
-            horiz3.add(new JLabel("Show Algorithm Indices:"));
-            horiz3.add(Box.createHorizontalGlue());
-            horiz3.add(getBooleanSelectionBox("algcomparisonShowAlgorithmIndices", model.getParameters(), false));
-
-            Box horiz4 = Box.createHorizontalBox();
-            horiz4.add(new JLabel("Show Simulation Indices:"));
-            horiz4.add(Box.createHorizontalGlue());
-            horiz4.add(getBooleanSelectionBox("algcomparisonShowSimulationIndices", model.getParameters(), false));
-
             Box horiz4a = Box.createHorizontalBox();
             horiz4a.add(new JLabel("Sort by Utility:"));
             horiz4a.add(Box.createHorizontalGlue());
@@ -1354,8 +1343,6 @@ private void addComparisonTab(JTabbedPane tabbedPane) {
             parameterBox.add(horiz2);
             parameterBox.add(horiz2b);
             parameterBox.add(horiz2c);
-            parameterBox.add(horiz3);
-            parameterBox.add(horiz4);
             parameterBox.add(horiz4a);
             parameterBox.add(horiz4b);
             parameterBox.add(horiz4c);
@@ -1435,6 +1422,41 @@ public void watch() {
 
                     try {
                         model.runComparison(ps);
+
+                        String resultsPath = model.getResultsPath();
+
+                        if (resultsPath != null && simulationChoiceTextArea != null) {
+                            // Write contents of simulation text area to a file at resultsPath + "/simulation.txt"
+                            try (PrintWriter writer = new PrintWriter(resultsPath + "/simulation.txt")) {
+                                writer.println(simulationChoiceTextArea.getText());
+                            } catch (FileNotFoundException ex) {
+                                throw new RuntimeException(ex);
+                            }
+
+                            // Write contents of algorithm text area to a file at resultsPath + "/algorithm.txt"
+                            try (PrintWriter writer = new PrintWriter(resultsPath + "/algorithm.txt")) {
+                                writer.println(algorithmChoiceTextArea.getText());
+                            } catch (FileNotFoundException ex) {
+                                throw new RuntimeException(ex);
+                            }
+
+                            // Write contents of table columns text area to a file at resultsPath + "/tableColumns.txt"
+                            try (PrintWriter writer = new PrintWriter(resultsPath + "/tableColumns.txt")) {
+                                writer.println(tableColumnsChoiceTextArea.getText());
+                            } catch (FileNotFoundException ex) {
+                                throw new RuntimeException(ex);
+                            }
+
+                            // Write contents of verbose output text area to a file at resultsPath + "/verboseOutput.txt"
+                            try (PrintWriter writer = new PrintWriter(resultsPath + "/verboseOutput.txt")) {
+                                writer.println(verboseOutputTextArea.getText());
+                            } catch (FileNotFoundException ex) {
+                                throw new RuntimeException(ex);
+                            }
+
+
+                        }
+
                     } catch (Exception ex) {
                         throw new RuntimeException(ex);
                     }
@@ -2032,13 +2054,34 @@ private void setSimulationText() {
         Simulations selectedSimulations = model.getSelectedSimulations();
         List<Simulation> simulations = selectedSimulations.getSimulations();
 
+        DataSet dataSet = model.getSuppliedData();
+
+        if (dataSet != null) {
+            simulationChoiceTextArea.append("A data set has been supplied with " + dataSet.getNumColumns() + " variables and " + dataSet.getNumRows() + " rows.");
+            simulationChoiceTextArea.append("\n\nThe variables for the data are as follow: " + dataSet.getVariableNames() + "\n\n");
+        }
+
+        Graph graph = model.getSuppliedGraph();
+
+        if (graph != null) {
+            simulationChoiceTextArea.append("A graph has been supplied with " + graph.getNumNodes() + " nodes and " + graph.getNumEdges() + " edges.");
+            simulationChoiceTextArea.append("\n\nThe nodes for the graph are as follow: " + graph.getNodeNames() + "\n\n");
+        }
+
+        Knowledge knowledge = model.getKnowledge();
+
+        if (knowledge != null) {
+            simulationChoiceTextArea.append("Knowledge has been set, as follows:");
+            simulationChoiceTextArea.append("\n\n" + knowledge + "\n\n");
+        }
+
         if (simulations.isEmpty()) {
             simulationChoiceTextArea.append("""
                      ** No simulations have been selected. Please select at least one simulation using the Add Simulation button below. **
                     """);
             return;
         } else if (simulations.size() == 1) {
-            simulationChoiceTextArea.setText("""
+            simulationChoiceTextArea.append("""
                     The following simulation has been selected. This simulations will be run with the selected algorithms.
                                         
                     """);
@@ -2049,7 +2092,7 @@ private void setSimulationText() {
             simulationChoiceTextArea.append("Selected graph type = " + (randomGraphClass == null ? "None" : randomGraphClass.getSimpleName() + "\n"));
             simulationChoiceTextArea.append("Selected simulation type = " + simulationClass.getSimpleName() + "\n");
         } else {
-            simulationChoiceTextArea.setText("""
+            simulationChoiceTextArea.append("""
                     The following simulations have been selected. These simulations will be run with the selected algorithms.
                     """);
             for (int i = 0; i < simulations.size(); i++) {
@@ -2075,7 +2118,7 @@ private void setAlgorithmText() {
                     """);
             return;
         } else if (selectedAlgorithms.size() == 1) {
-            algorithmChoiceTextArea.setText("""
+            algorithmChoiceTextArea.append("""
                     The following algorithm has been selected. This algorithm will be run with the selected simulations.
                                         
                     """);
@@ -2092,7 +2135,7 @@ private void setAlgorithmText() {
             }
 
         } else {
-            algorithmChoiceTextArea.setText("""
+            algorithmChoiceTextArea.append("""
                     The following algorithms have been selected. These algorithms will be run with the selected simulations.
                     """);
             for (int i = 0; i < selectedAlgorithms.size(); i++) {

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraph.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraph.java
@@ -81,7 +81,8 @@ public void actionPerformed(ActionEvent e) {
         File file = chooser.getSelectedFile();
 
         if (file == null) {
-            System.out.println("File was null.");
+            JOptionPane.showMessageDialog((Component) this.graphEditable,
+                    "No file was selected.", "Error", JOptionPane.ERROR_MESSAGE);
             return;
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphAmatCpdag.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphAmatCpdag.java
@@ -82,7 +82,8 @@ public void actionPerformed(ActionEvent e) {
         File file = chooser.getSelectedFile();
 
         if (file == null) {
-            System.out.println("File was null.");
+            JOptionPane.showMessageDialog((Component) this.graphEditable,
+                    "No file was selected.", "Error", JOptionPane.ERROR_MESSAGE);
             return;
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphAmatPag.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphAmatPag.java
@@ -89,7 +89,8 @@ public void actionPerformed(ActionEvent e) {
         File file = chooser.getSelectedFile();
 
         if (file == null) {
-            System.out.println("File was null.");
+            JOptionPane.showMessageDialog((Component) this.graphEditable,
+                    "No file was selected.", "Error", JOptionPane.ERROR_MESSAGE);
             return;
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphJson.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphJson.java
@@ -62,7 +62,8 @@ public void actionPerformed(ActionEvent e) {
         File file = chooser.getSelectedFile();
 
         if (file == null) {
-            System.out.println("File was null.");
+            JOptionPane.showMessageDialog((Component) this.graphEditable,
+                    "No file was selected.", "Error", JOptionPane.ERROR_MESSAGE);
             return;
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphTxt.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphTxt.java
@@ -82,7 +82,8 @@ public void actionPerformed(ActionEvent e) {
         File file = chooser.getSelectedFile();
 
         if (file == null) {
-            System.out.println("File was null.");
+            JOptionPane.showMessageDialog((Component) this.graphEditable,
+                    "No file was selected.", "Error", JOptionPane.ERROR_MESSAGE);
             return;
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LogisticRegressionEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LogisticRegressionEditor.java
@@ -144,7 +144,7 @@ public LogisticRegressionEditor(LogisticRegressionRunner regressionRunner) {
             LayoutUtil.fruchtermanReingoldLayout(outGraph);
             workbench.setGraph(outGraph);
             String message = this.modelParameters.getText();
-            TetradLogger.getInstance().forceLogMessage(message);
+            TetradLogger.getInstance().log(message);
         });
     }