Update pom to use GitHub jpam repository

pom.xml

@@ -16,8 +16,8 @@
 
     <properties>
         <javafx.version>16</javafx.version>
-        <maven.compiler.source>11</maven.compiler.source>
-        <maven.compiler.target>11</maven.compiler.target>
+        <maven.compiler.source>16</maven.compiler.source>
+        <maven.compiler.target>16</maven.compiler.target>
     </properties>
 
   <build>
@@ -246,6 +246,17 @@
 			</snapshots>
 			<url>file://${project.basedir}/repo</url>
 		</repository>
+
+	  	<!-- Repo for jpam code- this used for deep learning-->
+		<repository>
+			<id>jdl4pam</id>
+			<url>https://raw.github.com/macster110/jpam/mvn-repo/</url>
+		</repository>
+		<repository>
+			<id>jpamutils</id>
+			<url>https://raw.github.com/macster110/jpam/mvn-repo/</url>
+		</repository>
+
 		
 	  	<!-- Repo for Jamie's code -->
 	  	<!-- IMPORTANT: SOMEHOW THIS REPO INTERFERES WITH THE
@@ -255,14 +266,14 @@
 	  		repository.  Let Maven download the JavaFX files, and
 	  		then uncomment this repo again.
 	  		Same thing seems to be occurring if I try to update the postgresql library. -->
-		<repository>
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-	        <id>central</id>
-            <name>a0u0ltozdsehx-artifactory-primary-0-releases</name>
-            <url>https://jmachund.jfrog.io/artifactory/jpam2</url>
-		</repository> 
+<!-- 		<repository> -->
+<!-- 			<snapshots> -->
+<!-- 				<enabled>false</enabled> -->
+<!-- 			</snapshots> -->
+<!-- 	        <id>central</id> -->
+<!--             <name>a0u0ltozdsehx-artifactory-primary-0-releases</name> -->
+<!--             <url>https://jmachund.jfrog.io/artifactory/jpam2</url> -->
+<!-- 		</repository>  -->
 		
 	    <!-- Repo for netCDF -->
 	    <repository>
@@ -321,7 +332,7 @@
 	<dependency>
 		<groupId>org.jamdev</groupId>
 		<artifactId>jdl4pam</artifactId>
-		<version>0.0.91</version>
+		<version>0.0.92</version>
 	</dependency>
 
 	<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->
@@ -660,11 +671,11 @@
 	<!-- https://mvnrepository.com/artifact/org.springframework/org.springframework.core -->
 
 	<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
-	<dependency>
+	<!--<dependency>
 	    <groupId>org.postgresql</groupId>
 	    <artifactId>postgresql</artifactId>
 	    <version>42.2.24</version>
-	</dependency>
+	</dependency>-->
 
 	<!-- https://mvnrepository.com/artifact/org.renjin/renjin-script-engine -->
 	<dependency>

src/binaryFileStorage/BinaryDataSource.java

@@ -255,6 +255,11 @@ public abstract class BinaryDataSource {
 				pamDataUnit.setDataUnitFileInformation(dataUnitFileInformation);
 			}
 		}
+		
+		//sometimes get a null pointer exception here when trying to close PAMGuard?
+		if (getBinaryStorageStream() == null) {
+			return false;
+		}
 				
 		return getBinaryStorageStream().storeData(data.getObjectType(), pamDataUnit.getBasicData(), data);
 	}

src/rawDeepLearningClassifier/dlClassification/genericModel/DLModelWorker.java

@@ -99,11 +99,11 @@ public abstract class DLModelWorker<T> {
 
 			}
 
-			//run the model. The output is the 
+			//run the model. 
 			float[] output = null; 
 			long time1 = System.currentTimeMillis();
 			output = runModel(transformedDataStack); 
-			//System.out.println("Out: " + PamArrayUtils.array2String(output, 2, ","));
+			//System.out.println("Model out: " + PamArrayUtils.array2String(output, 2, ","));
 			long time2 = System.currentTimeMillis();
 
 

src/rawDeepLearningClassifier/dlClassification/genericModel/GenericDLClassifier.java

@@ -127,8 +127,11 @@ public class GenericDLClassifier implements DLClassiferModel, PamSettings {
 		 */
 		if ((PamCalendar.isSoundFile() && !forceQueue) || dlControl.isViewer()) {
 			//run the model 
+			
+			//System.out.println("GENERICDLCLASSIFIER: Run here!!!"); 
 			ArrayList<GenericPrediction> modelResult = getGenericDLWorker().runModel(groupedRawData, 
 					groupedRawData.get(0).getParentDataBlock().getSampleRate(), 0); 
+			//System.out.println("GENERICDLCLASSIFIER: RESULTS!!!: " + modelResult); 
 			
 			if (modelResult==null) {
 				genericModelWarning.setWarningMessage("Generic deep learning model returned null");

src/rawDeepLearningClassifier/dlClassification/genericModel/GenericModelTest.java

@@ -18,12 +18,13 @@ public class GenericModelTest {
 	public static void rightWhaleTest() {
 
 		//the model path
-		String modelPath = "/Users/au671271/Desktop/model_lenet_dropout_input_conv_all/saved_model.pb";
+		String modelPath = "/Users/au671271/git/PAMGuard_resources/deep_learning/right_whale_tutorial/model_lenet_dropout_input_conv_all/saved_model.pb";
 
 		//the audio file to test
 		String wavFilePath = "/Users/au671271/Google Drive/PAMGuard_dev/Deep_Learning/Right_whales_DG/SouthernRightWhale001-v1/sar98_trk3_8000.wav";
 		
 		wavFilePath = "/Users/au671271/Google Drive/PAMGuard_dev/Deep_Learning/Right_whales_DG/SouthernRightWhale001-v1/wav_files_timestamp/PAM_20010327_113000.wav";
+		wavFilePath = "/Users/au671271/git/PAMGuard_resources/deep_learning/right_whale_tutorial/wav/wav_files_timestamp/PAM_20010327_113200.wav"; 
 
 		//define some bits and pieces we need for the classiifer. 
 		float sr = 2000; 

src/rawDeepLearningClassifier/dlClassification/genericModel/GenericModelWorker.java

@@ -24,6 +24,7 @@ public class GenericModelWorker extends DLModelWorker<GenericPrediction> {
 	@Override
 	public float[] runModel(float[][][] transformedDataStack) {
 		//System.out.println("RUN GENERIC MODEL: " + transformedDataStack.length +  "  " + transformedDataStack[0].length +  "  " + transformedDataStack[0][0].length);
+		//System.out.println("RUN GENERIC MODEL: " + transformedDataStack[0][0][0]);
 		float[]  results =  genericModel.runModel(transformedDataStack);
 		//System.out.println("GENERIC MODEL RESULTS: " + results== null ? null : results.length);
 		return results;

src/rawDeepLearningClassifier/dlClassification/ketos/KetosModelTest.java

@@ -0,0 +1,115 @@
+package rawDeepLearningClassifier.dlClassification.ketos;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import org.jamdev.jdl4pam.ketos.KetosModel;
+import org.jamdev.jdl4pam.ketos.KetosParams;
+import org.jamdev.jdl4pam.transforms.DLTransform;
+import org.jamdev.jdl4pam.transforms.DLTransformsFactory;
+import org.jamdev.jdl4pam.transforms.FreqTransform;
+import org.jamdev.jdl4pam.transforms.WaveTransform;
+import org.jamdev.jdl4pam.transforms.jsonfile.DLTransformsParser;
+import org.jamdev.jdl4pam.utils.DLUtils;
+import org.jamdev.jpamutils.wavFiles.AudioData;
+
+/**
+ * Test the Ketos models in PAMGuard. 
+ * <p>
+ * Note a similar class also exists in the JPAM repository but this test ensure PAMGuard dependencies are up to date 
+ * etc. 
+ * 
+ * @author Jamie Macaulay
+ *
+ */
+public class KetosModelTest {
+	
+	public static void main(String[] args) {
+
+		//test on a right whale. 
+		//File file = new File("/Volumes/GoogleDrive/My Drive/PAMGuard_dev/Deep_Learning/Meridian/right_whales/for_pamguard/narw.ktpb"); 
+		File file = new File("/Volumes/GoogleDrive-108005893101854397430/My Drive/PAMGuard_dev/Deep_Learning/Meridian/humpback_whales/SOCAL_Mn_Network.ktpb");
+		//File file = new File("/Volumes/GoogleDrive-108005893101854397430/My Drive/PAMGuard_dev/Deep_Learning/Meridian/orca/kw_detector_v11_5s.ktpb"); 
+
+		//the wav file to test.
+		String wavFilePath = "/Volumes/GoogleDrive/My Drive/PAMGuard_dev/Deep_Learning/Meridian/right_whales/for_pamguard/input.wav"; 
+
+		try {
+			//the ketos model. 
+			KetosModel  ketosModel = new KetosModel(file);
+
+			//read the JSOn string from the the file. 
+			String jsonString  = DLTransformsParser.readJSONString(new File(ketosModel.getAudioReprFile()));
+
+			//get the audio representation file. 
+			KetosParams ketosParams = new KetosParams(jsonString); 			
+
+			//System.out.println(ketosParams.toString());
+
+			//Open wav files. 
+			AudioData soundData = DLUtils.loadWavFile(wavFilePath);
+			soundData = soundData.trim(0, (int) (soundData.getSampleRate()*3.0)); 
+
+			//generate the transforms. 
+			ArrayList<DLTransform> transforms =	DLTransformsFactory.makeDLTransforms(ketosParams.dlTransforms); 
+
+
+			((WaveTransform) transforms.get(0)).setWaveData(soundData); 
+			
+			
+			DLTransform transform = transforms.get(0); 
+			for (int i=0; i<transforms.size(); i++) {
+				//				System.out.println(transforms); 
+				transform = transforms.get(i).transformData(transform); 
+				//				if (i==1) {
+				//					 transfromedData =  DLMatFile.array2Matrix(((FreqTransform) transform).getSpecTransfrom().getTransformedData());
+				//				}
+				//				if (transforms.get(i) instanceof FreqTransform) {
+				//				transformedData = ((FreqTransform) transform).getSpecTransfrom().getTransformedData(); 
+				//					System.out.println("Transform shape: " + i + " " +  transformedData.length + " " + transformedData[0].length); 
+				//				}
+			}
+
+			double[][] transformedData = ((FreqTransform) transform).getSpecTransfrom().getTransformedData();
+
+
+			float[] output = null; 
+			float[][][] data;
+			int nStack = 1; //number of specs to give to the classifier. 
+			for (int i=0; i<10; i++) {
+				long time1 = System.currentTimeMillis();
+				data = new float[nStack][][]; 
+				for (int j=0; j<nStack; j++) {
+					data[j] = DLUtils.toFloatArray(transformedData); 
+				}
+				output = ketosModel.runModel(data); 
+				long time2 = System.currentTimeMillis();
+				System.out.println("Time to run model: " + (time2-time1) + " ms"); 
+			}
+
+
+
+			double[] prob = new double[output.length]; 
+			for (int j=0; j<output.length; j++) {
+				//python code for this. 
+				//		    	prob = torch.nn.functional.softmax(out).numpy()[n, 1]
+				//	                    pred = int(prob >= ARGS.threshold)		    	
+				//softmax function
+				System.out.println("The output is: " + output[j]); 
+
+				prob[j] = DLUtils.softmax(output[j], output); 
+				System.out.println("The probability is: " + prob[j]); 
+			}
+
+
+
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} 
+	}
+
+
+}
+

src/rawDeepLearningClassifier/layoutFX/dlTransfroms/DLTransformsPane.java

@@ -6,6 +6,7 @@ import java.util.List;
 import org.jamdev.jdl4pam.transforms.DLTransform;
 import org.jamdev.jdl4pam.transforms.DLTransform.DLTransformType;
 import org.jamdev.jdl4pam.transforms.FreqTransform;
+import org.jamdev.jdl4pam.transforms.SimpleTransform;
 import org.jamdev.jdl4pam.transforms.WaveTransform;
 
 import javafx.geometry.Pos;
@@ -149,6 +150,10 @@ public class DLTransformsPane extends PamBorderPane {
 		ArrayList<DLTransformPane> dlTransformPanes = new ArrayList<DLTransformPane>(); 
 
 		sampleRate=-1; 
+		
+//		for (int i=0; i<dlTransforms.size() ; i++) {
+//			System.out.println("Set DL transfroms: " + dlTransforms.get(i).getDLTransformType() + " " + ((SimpleTransform) dlTransforms.get(i)).getParams()); 
+//		}
 
 		//create a pane for each transform
 		for (int i=0; i<dlTransforms.size() ; i++) {
@@ -157,7 +162,6 @@ public class DLTransformsPane extends PamBorderPane {
 				sampleRate = ((WaveTransform) dlTransforms.get(i)).getWaveData().getSampleRate(); 
 			}
 
-		//	System.out.println("Set DL transfroms: " + dlTransforms.get(i).getDLTransformType()); 
 			dlTransformPanes.add(DataTransformPaneFactory.getSettingsPane(dlTransforms.get(i))); 
 			dlTransformPanes.get(i).setParams(dlTransforms.get(i));
 			dlTransformPanes.get(i).addSettingsListener(()->{