From ccd0fc796537e54f0ba8fc61f07f85adb800e41d Mon Sep 17 00:00:00 2001
From: m2oswald <45486636+m2oswald@users.noreply.github.com>
Date: Mon, 14 Nov 2022 11:00:15 +0000
Subject: [PATCH] small updates to Rocca (#84)

* allow Rocca to run without classifiers

Fixed bug that threw an error if no classifier files were specified in Rocca Params dialog

* add rocca switch to enable dev mode

currently only shows/hides extra buttons in the Params dialog, but will
extend to more options in the future
---
 .classpath                           |   2 +-
 .gitignore                           |   1 +
 src/pamguard/Pamguard.java           |   8 +-
 src/rocca/RoccaClassifier.java       | 251 ++++++++++++++-------------
 src/rocca/RoccaDev.java              |  27 +++
 src/rocca/RoccaParametersDialog.java |  18 +-
 6 files changed, 174 insertions(+), 133 deletions(-)
 create mode 100644 src/rocca/RoccaDev.java

diff --git a/.classpath b/.classpath
index a5d40376..26c568d7 100644
--- a/.classpath
+++ b/.classpath
@@ -6,7 +6,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
diff --git a/.gitignore b/.gitignore
index 6df976a9..c9419840 100644
--- a/.gitignore
+++ b/.gitignore
@@ -39,3 +39,4 @@ settings.xml
 .classpath
 .classpath
 .classpath
+.classpath
diff --git a/src/pamguard/Pamguard.java b/src/pamguard/Pamguard.java
index f6865503..4a142c0b 100644
--- a/src/pamguard/Pamguard.java
+++ b/src/pamguard/Pamguard.java
@@ -23,17 +23,14 @@ package pamguard;
 import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 
-import Acquisition.AcquisitionControl;
 import Acquisition.FolderInputSystem;
 import PamController.PamController;
 import PamController.PamGUIManager;
 import PamController.PamSettingManager;
 import PamController.PamguardVersionInfo;
 import PamController.pamBuoyGlobals;
-import PamController.command.TerminalController;
 import PamModel.SMRUEnable;
 import PamUtils.FileFunctions;
-import PamUtils.PamCalendar;
 import PamUtils.PamExceptionHandler;
 import PamUtils.PlatformInfo;
 import PamUtils.Splash;
@@ -45,6 +42,7 @@ import PamguardMVC.debug.Debug;
 import binaryFileStorage.BinaryStore;
 import dataPlotsFX.JamieDev;
 import generalDatabase.DBControl;
+import rocca.RoccaDev;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -190,6 +188,10 @@ public class Pamguard {
 					JamieDev.setEnabled(true);
 					System.out.println("Enabling Jamie Macaulay modifications.");
 				}
+				else if (anArg.equalsIgnoreCase("-rocca")) {
+					RoccaDev.setEnabled(true);
+					System.out.println("Enabling Rocca development mode");
+				}
 				else if (anArg.equalsIgnoreCase(Debug.flag)) {
 					Debug.setPrintDebug(true);
 					Debug.out.println("Enabling debug terminal output.");
diff --git a/src/rocca/RoccaClassifier.java b/src/rocca/RoccaClassifier.java
index fe699137..20acb872 100644
--- a/src/rocca/RoccaClassifier.java
+++ b/src/rocca/RoccaClassifier.java
@@ -408,92 +408,102 @@ public class RoccaClassifier {
 
     	// load the whistle classifier
     	if (roccaControl.roccaParameters.isClassifyWhistles()) {
-	        String fname = roccaControl.roccaParameters.roccaClassifierModelFilename.getAbsolutePath();
-	        File f = new File(fname);
-	        if (f.exists() == false) {
-	        	WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca whistle classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
-	            roccaControl.roccaParameters.setClassifyWhistles(false);
-	        }
-	        else {
-	        	try {
-	        		BufferedInputStream input = new BufferedInputStream(
-	        				(new ProgressMonitorInputStream(null, "Loading Whistle Classifier - Please wait",
-	        						new FileInputStream(fname))));
-	        		Object[] modelParams = SerializationHelper.readAll(input);
-	        		// separate the classifier model from the training dataset info
-	        		// roccaClassifierModel = (AbstractClassifier) modelParams[0];
-	        		// trainedDataset = (Instances) modelParams[1];
-
-	        		// there are 2 different styles of model file, the original version and the version
-	        		// developed for the 2-stage classifier.  Both files contain 2 objects.
-	        		// The original version contained the classifier and the training dataset.  The newer
-	        		// version contains a String description and the classifier.  Test the first object;
-	        		// if it's a String, then this is the newer version and the String is the description.
-	        		// If it's not a String, assume this is the old version and create a RoccaRFModel
-	        		// object from the file contents.
-	        		if (modelParams[0] instanceof String) {
-	        			modelList = (RoccaRFModel) modelParams[1];
-	        		} else {
-	        			AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
-	        			Instances dataset = (Instances) modelParams[1];
-	        			RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
-	        			for (int i=0; i<dataset.numClasses(); i++) {
-	        				models[i]=null;
-	        			}
-	        			modelList = new RoccaRFModel(classifier, dataset, models);
-	        		}
-
-	        	} catch (Exception ex) {
-	        		System.err.println("Deserialization of Whistle Classifier failed: " + ex.getMessage());
-	        		ex.printStackTrace();
-	        		roccaControl.roccaParameters.setClassifyWhistles(false);
-	        	}
-	        }
+    		if (roccaControl.roccaParameters.roccaClassifierModelFilename==null) {
+    			roccaControl.roccaParameters.setClassifyWhistles(false);
+    		}
+    		else {
+		        String fname = roccaControl.roccaParameters.roccaClassifierModelFilename.getAbsolutePath();
+		        File f = new File(fname);
+		        if (f.exists() == false) {
+		        	WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca whistle classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
+		            roccaControl.roccaParameters.setClassifyWhistles(false);
+		        }
+		        else {
+		        	try {
+		        		BufferedInputStream input = new BufferedInputStream(
+		        				(new ProgressMonitorInputStream(null, "Loading Whistle Classifier - Please wait",
+		        						new FileInputStream(fname))));
+		        		Object[] modelParams = SerializationHelper.readAll(input);
+		        		// separate the classifier model from the training dataset info
+		        		// roccaClassifierModel = (AbstractClassifier) modelParams[0];
+		        		// trainedDataset = (Instances) modelParams[1];
+	
+		        		// there are 2 different styles of model file, the original version and the version
+		        		// developed for the 2-stage classifier.  Both files contain 2 objects.
+		        		// The original version contained the classifier and the training dataset.  The newer
+		        		// version contains a String description and the classifier.  Test the first object;
+		        		// if it's a String, then this is the newer version and the String is the description.
+		        		// If it's not a String, assume this is the old version and create a RoccaRFModel
+		        		// object from the file contents.
+		        		if (modelParams[0] instanceof String) {
+		        			modelList = (RoccaRFModel) modelParams[1];
+		        		} else {
+		        			AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
+		        			Instances dataset = (Instances) modelParams[1];
+		        			RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
+		        			for (int i=0; i<dataset.numClasses(); i++) {
+		        				models[i]=null;
+		        			}
+		        			modelList = new RoccaRFModel(classifier, dataset, models);
+		        		}
+	
+		        	} catch (Exception ex) {
+		        		System.err.println("Deserialization of Whistle Classifier failed: " + ex.getMessage());
+		        		ex.printStackTrace();
+		        		roccaControl.roccaParameters.setClassifyWhistles(false);
+		        	}
+		        }
+	    	}
     	}
         
         // serialVersionUID=24 2016/08/10 added to load click classifier
     	if (roccaControl.roccaParameters.isClassifyClicks()) {
-	        String fname = roccaControl.roccaParameters.roccaClickClassifierModelFilename.getAbsolutePath();
-	        File f = new File(fname);
-	        if (f.exists() == false) {
-	        	WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca click classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
-	            roccaControl.roccaParameters.setClassifyClicks(false);
-	        }
-	        else {
-	        	try {
-	        		BufferedInputStream input = new BufferedInputStream(
-	        				(new ProgressMonitorInputStream(null, "Loading Click Classifier - Please wait",
-	        						new FileInputStream(fname))));
-	        		Object[] modelParams = SerializationHelper.readAll(input);
-	        		// separate the classifier model from the training dataset info
-	        		// roccaClassifierModel = (AbstractClassifier) modelParams[0];
-	        		// trainedDataset = (Instances) modelParams[1];
-
-	        		// there are 2 different styles of model file, the original version and the version
-	        		// developed for the 2-stage classifier.  Both files contain 2 objects.
-	        		// The original version contained the classifier and the training dataset.  The newer
-	        		// version contains a String description and the classifier.  Test the first object;
-	        		// if it's a String, then this is the newer version and the String is the description.
-	        		// If it's not a String, assume this is the old version and create a RoccaRFModel
-	        		// object from the file contents.
-	        		if (modelParams[0] instanceof String) {
-	        			clickModelList = (RoccaRFModel) modelParams[1];
-	        		} else {
-	        			AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
-	        			Instances dataset = (Instances) modelParams[1];
-	        			RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
-	        			for (int i=0; i<dataset.numClasses(); i++) {
-	        				models[i]=null;
-	        			}
-	        			clickModelList = new RoccaRFModel(classifier, dataset, models);
-	        		}
-
-	        	} catch (Exception ex) {
-	        		System.err.println("Deserialization of Click Classifier failed: " + ex.getMessage());
-	        		ex.printStackTrace();
-	        		roccaControl.roccaParameters.setClassifyClicks(false);
-	        	}
+    		if (roccaControl.roccaParameters.roccaClickClassifierModelFilename==null) {
+    			roccaControl.roccaParameters.setClassifyClicks(false);
     		}
+    		else {
+		        String fname = roccaControl.roccaParameters.roccaClickClassifierModelFilename.getAbsolutePath();
+		        File f = new File(fname);
+		        if (f.exists() == false) {
+		        	WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca click classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
+		            roccaControl.roccaParameters.setClassifyClicks(false);
+		        }
+		        else {
+		        	try {
+		        		BufferedInputStream input = new BufferedInputStream(
+		        				(new ProgressMonitorInputStream(null, "Loading Click Classifier - Please wait",
+		        						new FileInputStream(fname))));
+		        		Object[] modelParams = SerializationHelper.readAll(input);
+		        		// separate the classifier model from the training dataset info
+		        		// roccaClassifierModel = (AbstractClassifier) modelParams[0];
+		        		// trainedDataset = (Instances) modelParams[1];
+	
+		        		// there are 2 different styles of model file, the original version and the version
+		        		// developed for the 2-stage classifier.  Both files contain 2 objects.
+		        		// The original version contained the classifier and the training dataset.  The newer
+		        		// version contains a String description and the classifier.  Test the first object;
+		        		// if it's a String, then this is the newer version and the String is the description.
+		        		// If it's not a String, assume this is the old version and create a RoccaRFModel
+		        		// object from the file contents.
+		        		if (modelParams[0] instanceof String) {
+		        			clickModelList = (RoccaRFModel) modelParams[1];
+		        		} else {
+		        			AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
+		        			Instances dataset = (Instances) modelParams[1];
+		        			RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
+		        			for (int i=0; i<dataset.numClasses(); i++) {
+		        				models[i]=null;
+		        			}
+		        			clickModelList = new RoccaRFModel(classifier, dataset, models);
+		        		}
+	
+		        	} catch (Exception ex) {
+		        		System.err.println("Deserialization of Click Classifier failed: " + ex.getMessage());
+		        		ex.printStackTrace();
+		        		roccaControl.roccaParameters.setClassifyClicks(false);
+		        	}
+	    		}
+	    	}
     	}
     	
         // if we didn't load either classifier, don't bother loading trying to load an encounter
@@ -505,43 +515,48 @@ public class RoccaClassifier {
         
         // serialVersionUID=24 2016/08/10 added to load event classifier
     	if (roccaControl.roccaParameters.isClassifyEvents()) {
-	        String fname = roccaControl.roccaParameters.roccaEventClassifierModelFilename.getAbsolutePath();
-	        File f = new File(fname);
-	        if (f.exists() == false) {
-	        	WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca events classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
-	            roccaControl.roccaParameters.setClassifyEvents(false);
-	        }
-	        else {
-	        	try {
-	        		BufferedInputStream input = new BufferedInputStream(
-	        				(new ProgressMonitorInputStream(null, "Loading Event Classifier - Please wait",
-	        						new FileInputStream(fname))));
-	        		Object[] modelParams = SerializationHelper.readAll(input);
-
-	        		// there are 2 different styles of model file, the original version and the version
-	        		// developed for the 2-stage classifier.  Both files contain 2 objects.
-	        		// The original version contained the classifier and the training dataset.  The newer
-	        		// version contains a String description and the classifier.  Test the first object;
-	        		// if it's a String, then this is the newer version and the String is the description.
-	        		// If it's not a String, assume this is the old version and create a RoccaRFModel
-	        		// object from the file contents.
-	        		if (modelParams[0] instanceof String) {
-	        			eventModelList = (RoccaRFModel) modelParams[1];
-	        		} else {
-	        			AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
-	        			Instances dataset = (Instances) modelParams[1];
-	        			RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
-	        			for (int i=0; i<dataset.numClasses(); i++) {
-	        				models[i]=null;
-	        			}
-	        			eventModelList = new RoccaRFModel(classifier, dataset, models);
-	        		}
-
-	        	} catch (Exception ex) {
-	        		System.err.println("Deserialization of Event Classifier failed: " + ex.getMessage());
-	        		roccaControl.roccaParameters.setClassifyEvents(false);
-	        	}
-	        }
+       		if (roccaControl.roccaParameters.roccaEventClassifierModelFilename==null) {
+    			roccaControl.roccaParameters.setClassifyEvents(false);
+    		}
+    		else {
+		        String fname = roccaControl.roccaParameters.roccaEventClassifierModelFilename.getAbsolutePath();
+		        File f = new File(fname);
+		        if (f.exists() == false) {
+		        	WarnOnce.showWarning(roccaControl.getUnitName(), "Rocca events classifier file cannot be found at " + fname, WarnOnce.WARNING_MESSAGE);
+		            roccaControl.roccaParameters.setClassifyEvents(false);
+		        }
+		        else {
+		        	try {
+		        		BufferedInputStream input = new BufferedInputStream(
+		        				(new ProgressMonitorInputStream(null, "Loading Event Classifier - Please wait",
+		        						new FileInputStream(fname))));
+		        		Object[] modelParams = SerializationHelper.readAll(input);
+	
+		        		// there are 2 different styles of model file, the original version and the version
+		        		// developed for the 2-stage classifier.  Both files contain 2 objects.
+		        		// The original version contained the classifier and the training dataset.  The newer
+		        		// version contains a String description and the classifier.  Test the first object;
+		        		// if it's a String, then this is the newer version and the String is the description.
+		        		// If it's not a String, assume this is the old version and create a RoccaRFModel
+		        		// object from the file contents.
+		        		if (modelParams[0] instanceof String) {
+		        			eventModelList = (RoccaRFModel) modelParams[1];
+		        		} else {
+		        			AbstractClassifier classifier = (AbstractClassifier) modelParams[0];
+		        			Instances dataset = (Instances) modelParams[1];
+		        			RoccaRFModel[] models = new RoccaRFModel[dataset.numClasses()];
+		        			for (int i=0; i<dataset.numClasses(); i++) {
+		        				models[i]=null;
+		        			}
+		        			eventModelList = new RoccaRFModel(classifier, dataset, models);
+		        		}
+	
+		        	} catch (Exception ex) {
+		        		System.err.println("Deserialization of Event Classifier failed: " + ex.getMessage());
+		        		roccaControl.roccaParameters.setClassifyEvents(false);
+		        	}
+		        }
+	    	}
     	}
 
         resetSidePanel();
diff --git a/src/rocca/RoccaDev.java b/src/rocca/RoccaDev.java
new file mode 100644
index 00000000..b1ea414b
--- /dev/null
+++ b/src/rocca/RoccaDev.java
@@ -0,0 +1,27 @@
+package rocca;
+
+/**
+ * Global flag set at runtime for Rocca development flags. 
+ * @author mo55
+ *
+ */
+public class RoccaDev {
+
+	
+	private static boolean enabled = false;
+
+	/**
+	 * @return the enabled
+	 */
+	public static boolean isEnabled() {
+		return enabled;
+	}
+
+	/**
+	 * @param enabled the enabled to set
+	 */
+	public static void setEnabled(boolean enabled) {
+		RoccaDev.enabled = enabled;
+	}
+
+}
diff --git a/src/rocca/RoccaParametersDialog.java b/src/rocca/RoccaParametersDialog.java
index 301dae66..2fd1f136 100644
--- a/src/rocca/RoccaParametersDialog.java
+++ b/src/rocca/RoccaParametersDialog.java
@@ -26,7 +26,6 @@ import java.awt.Frame;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.GridLayout;
-import java.awt.Point;
 import java.util.ArrayList;
 import java.util.Objects;
 import java.util.Vector;
@@ -48,8 +47,6 @@ import PamUtils.PamFileChooser;
 import PamView.dialog.PamDialog;
 import PamView.dialog.SourcePanel;
 import PamguardMVC.PamDataBlock;
-import PamguardMVC.PamDataUnit;
-
 import java.awt.Dimension;
 import java.awt.Insets;
 import java.awt.event.ActionEvent;
@@ -60,20 +57,14 @@ import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileReader;
-import java.io.IOException;
-
 import javax.swing.Box;
 import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
 import javax.swing.DefaultComboBoxModel;
 import javax.swing.GroupLayout;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JFrame;
 import javax.swing.JRadioButton;
 import javax.swing.JFileChooser;
 import javax.swing.JScrollPane;
@@ -87,7 +78,6 @@ import javax.swing.border.EtchedBorder;
 import clickDetector.ClickControl;
 import clickDetector.ClickDetection;
 import clickDetector.NoiseDataBlock;
-import weka.classifiers.AbstractClassifier;
 import weka.core.Attribute;
 import weka.core.Instances;
 import weka.core.SerializationHelper;
@@ -523,7 +513,13 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
         reclassifyButton.addActionListener(this);
         reclassifyButton.setToolTipText("Load the whistle data from the contour stats output file, and run it through the current Classifier");
         reclassifyButton.setVisible(true);
-        extraButtonsSubPanel.setVisible(true);		// ******** THIS LINES CONTROLS THE VISIBILITY ********
+        
+        // ******** THIS LINES CONTROLS THE VISIBILITY ********
+        if (RoccaDev.isEnabled()) {
+        	extraButtonsSubPanel.setVisible(true);
+        } else {
+        	extraButtonsSubPanel.setVisible(false);
+        }
         GroupLayout extraPanelLayout = new GroupLayout(extraButtonsSubPanel);
         extraButtonsSubPanel.setLayout(extraPanelLayout);
         extraPanelLayout.setAutoCreateGaps(true);