nordic-dev.net/PAMGuard
nordic-dev.net/PAMGuard
2
0
Fork 0
mirror of https://github.com/PAMGuard/PAMGuard.git synced 2025-04-28 02:57:22 +00:00
Code Issues Packages Projects Releases Wiki Activity

Thomas click deep learning unit test

Browse Source
This commit is contained in:
Jamie Mac 2025-03-21 15:21:26 +00:00
parent d18137223a
commit 1fedbe6acd
12 changed files with 215 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.classpath
View File

@ -6,7 +6,7 @@
<attribute name="maven.pomderived" value="true"/> <attribute name="maven.pomderived" value="true"/>
</attributes> </attributes>
</classpathentry> </classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/ojdk-21.0.1"> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/java-21-openjdk-amd64">
<attributes> <attributes>
<attribute name="module" value="true"/> <attribute name="module" value="true"/>
<attribute name="maven.pomderived" value="true"/> <attribute name="maven.pomderived" value="true"/>

1
.settings/org.eclipse.core.resources.prefs
View File

@ -1,6 +1,7 @@
eclipse.preferences.version=1 eclipse.preferences.version=1
encoding//src/help/utilities/tethys/docs/connection.html=UTF-8 encoding//src/help/utilities/tethys/docs/connection.html=UTF-8
encoding//src/rawDeepLearningClassifer/segmenter/SegmenterProcess.java=UTF-8 encoding//src/rawDeepLearningClassifer/segmenter/SegmenterProcess.java=UTF-8
encoding//src/test=UTF-8
encoding//src/test/resources=UTF-8 encoding//src/test/resources=UTF-8
encoding/<project>=UTF-8 encoding/<project>=UTF-8
encoding/src=UTF-8 encoding/src=UTF-8

6
.settings/org.eclipse.jdt.core.prefs
View File

@ -11,9 +11,9 @@ org.eclipse.jdt.core.codeComplete.staticFinalFieldPrefixes=
org.eclipse.jdt.core.codeComplete.staticFinalFieldSuffixes= org.eclipse.jdt.core.codeComplete.staticFinalFieldSuffixes=
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=17 org.eclipse.jdt.core.compiler.codegen.targetPlatform=21
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=17 org.eclipse.jdt.core.compiler.compliance=21
org.eclipse.jdt.core.compiler.debug.lineNumber=generate org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate org.eclipse.jdt.core.compiler.debug.sourceFile=generate
@ -23,4 +23,4 @@ org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
org.eclipse.jdt.core.compiler.release=enabled org.eclipse.jdt.core.compiler.release=enabled
org.eclipse.jdt.core.compiler.source=17 org.eclipse.jdt.core.compiler.source=21

BIN
build/deb/PAMGuardIcon2.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 99 KiB

13
build/deb/control Normal file
View File

@ -0,0 +1,13 @@
Package: PAMGuard
Version: 2.0.1
Section: java
Priority: optional
Architecture: all
Maintainer: Jamie Macaulay <jdjm@st-andrews.ac.uk>
Description: A complex Java application with additional dependencies.
Icon: pamguard_icon.png
Depends: openjdk-21-jre
postinst script:
#!/bin/bash
# Set JVM options for the application
export JAVA_OPTS="-Xmx2g -Xms512m"

8
build/deb/pamguard.desktop Executable file
View File

@ -0,0 +1,8 @@
[Desktop Entry]
Name=PAMGuard
Comment=Application for passive acoustic monitoring v1
Exec=java -jar /usr/share/pamguard/Pamguard.jar -c
Icon=/usr/share/pamguard/PAMGuardIcon2.png
Terminal=true
Type=Application
Categories=Application;

8
build/deb/set-java-propery.sh Normal file
View File

@ -0,0 +1,8 @@
[Desktop Entry]
Name=PAMGuard
Comment=Application for passive acoustic monitoring
Exec=java -jar /usr/share/pamguard/Pamguard-2.02.14a.jar -c
Icon=/path/to/your/icon.png
Terminal=true
Type=Application
Categories=Application;

BIN
data.mat Normal file
View File

Binary file not shown.

122
pom.xml
View File

@ -311,11 +311,82 @@
</execution> </execution>
--> -->
</executions> </executions>
</plugin> </plugin>
<!--Creates a deb file for Linux-->
<plugin>
<artifactId>jdeb</artifactId>
<groupId>org.vafer</groupId>
<version>1.11</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>jdeb</goal>
</goals>
<configuration>
<controlDir>${basedir}/build/deb</controlDir>
<dataSet>
<data>
<!--TODO-really hte jar file should be named properly but thos would mean we would
have to change the anme in the desktop file too. For now create a link to the jar file
with correct version number-->
<src>${project.build.directory}/Pamguard.jar</src>
<type>file</type>
<mapper>
<type>perm</type>
<prefix>/usr/share/pamguard</prefix>
</mapper>
</data>
<data>
<src>${basedir}/liblinux</src>
<type>directory</type>
<includes>*.txt</includes>
<includes>*.so</includes>
<mapper>
<type>perm</type>
<prefix>/usr/share/pamguard/liblinux</prefix>
</mapper>
</data>
<data>
<src>${basedir}/build/deb/PAMGuardIcon2.png</src>
<type>file</type>
<mapper>
<type>perm</type>
<prefix>/usr/share/pamguard</prefix>
</mapper>
</data>
<data>
<src>${basedir}/build/deb/pamguard.desktop</src>
<type>file</type>
<mapper>
<type>perm</type>
<prefix>/usr/share/applications</prefix>
</mapper>
</data>
<data>
<type>link</type>
<linkName>/usr/share/pamguard/PAMGuard</linkName>
<linkTarget>/usr/share/pamguard/${project.build.finalName}.jar</linkTarget>
<symlink>true</symlink>
</data>
<!--<data>
<src>${project.basedir}/build/deb/set-java-property.sh</src>
<type>file</type>
<mapper>
<type>perm</type>
<prefix>/usr/bin</prefix>
<filemode>755</filemode>
</mapper>
</data>-->
</dataSet>
</configuration>
</execution>
</executions>
</plugin>
</plugins> </plugins>
<pluginManagement> <pluginManagement>
<plugins> <plugins>
<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.--> <!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
@ -359,6 +430,51 @@
</profiles> </profiles>
<!-- Plugin which creates a .dmg file for MacOS.
<plugin>
<groupId>de.perdian.maven.plugins</groupId>
<artifactId>macosappbundler-maven-plugin</artifactId>
<version>1.21.1</version>
<configuration>
<plist>
<JVMMainClassName>pamguard.Pamguard</JVMMainClassName>
<CFBundleIconFile>src/Resources/PamguardIcon2.icns</CFBundleIconFile>
<CFBundleDisplayName>PAMGuard</CFBundleDisplayName>
<CFBundleDevelopmentRegion>English</CFBundleDevelopmentRegion>
<CFBundleURLTypes>
<string>msa</string>
</CFBundleURLTypes>
<JVMVersion>21+</JVMVersion>
<JVMArguments>
<string>-c</string>
</JVMArguments>
</plist>
<dmg>
<generate>true</generate>
<additionalResources>
<additionalResource>
<directory>src/target/bundle/</directory>
</additionalResource>
</additionalResources>
</dmg>
<jdk>
<include>false</include>
<location>/Library/Java/JavaVirtualMachines/amazon-corretto-21.jdk</location>
</jdk>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
</execution>
</executions>
</plugin>-->
<reporting> <reporting>
@ -1065,7 +1181,7 @@
--> -->
<dependency> <dependency>
<groupId>org.pamguard</groupId> <groupId>org.pamguard</groupId>
<artifactId>x3</artifactId> <artifactId>X3</artifactId>
<version>2.2.8</version> <version>2.2.8</version>
</dependency> </dependency>

1
src/rawDeepLearningClassifier/dlClassification/genericModel/DLModelWorker.java
View File

@ -82,6 +82,7 @@ public abstract class DLModelWorker<T> {
DLTransform transform = modelTransforms.get(0); DLTransform transform = modelTransforms.get(0);
for (int i =0; i<modelTransforms.size(); i++) { for (int i =0; i<modelTransforms.size(); i++) {
transform = modelTransforms.get(i).transformData(transform); transform = modelTransforms.get(i).transformData(transform);
// //TEMP // //TEMP
// if (transform instanceof FreqTransform) { // if (transform instanceof FreqTransform) {
// transformedData = ((FreqTransform) transform).getSpecTransfrom().getTransformedData(); // transformedData = ((FreqTransform) transform).getSpecTransfrom().getTransformedData();

2
src/rawDeepLearningClassifier/dlClassification/genericModel/GenericModelWorker.java
View File

@ -49,7 +49,7 @@ public class GenericModelWorker extends DLModelWorker<StandardPrediction> {
waveStack[i] = transformedDataStack[i][0]; waveStack[i] = transformedDataStack[i][0];
} }
System.out.println("RUN GENERIC MODEL WAVE: " + waveStack.length + " " + waveStack[0].length + " " + waveStack[0][0] + " " + PamArrayUtils.max( waveStack[0])); // System.out.println("RUN GENERIC MODEL WAVE: " + waveStack.length + " " + waveStack[0].length + " " + waveStack[0][0] + " " + PamArrayUtils.max( waveStack[0]));
// PamArrayUtils.printArray(waveStack[0]); // PamArrayUtils.printArray(waveStack[0]);
results = getModel().runModel(waveStack); results = getModel().runModel(waveStack);
} }

74
src/test/rawDeepLearningClassifier/ClickDLTest.java
View File

@ -1,12 +1,18 @@
package test.rawDeepLearningClassifier; package test.rawDeepLearningClassifier;
import static org.junit.Assert.assertTrue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.nio.file.Path; import java.nio.file.Path;
import java.nio.file.Paths; import java.nio.file.Paths;
import java.util.ArrayList; import java.util.ArrayList;
import org.jamdev.jdl4pam.transforms.DLTransform;
import org.jamdev.jdl4pam.transforms.DLTransformsFactory; import org.jamdev.jdl4pam.transforms.DLTransformsFactory;
import org.jamdev.jdl4pam.transforms.DLTransfromParams; import org.jamdev.jdl4pam.transforms.DLTransfromParams;
import org.jamdev.jdl4pam.transforms.SimpleTransformParams; import org.jamdev.jdl4pam.transforms.SimpleTransformParams;
import org.jamdev.jdl4pam.transforms.WaveTransform;
import org.jamdev.jdl4pam.utils.DLMatFile; import org.jamdev.jdl4pam.utils.DLMatFile;
import org.jamdev.jpamutils.wavFiles.AudioData; import org.jamdev.jpamutils.wavFiles.AudioData;
import org.jamdev.jdl4pam.transforms.DLTransform.DLTransformType; import org.jamdev.jdl4pam.transforms.DLTransform.DLTransformType;
@ -19,6 +25,7 @@ import rawDeepLearningClassifier.dlClassification.genericModel.StandardPredictio
import rawDeepLearningClassifier.segmenter.GroupedRawData; import rawDeepLearningClassifier.segmenter.GroupedRawData;
import us.hebi.matlab.mat.format.Mat5; import us.hebi.matlab.mat.format.Mat5;
import us.hebi.matlab.mat.format.Mat5File; import us.hebi.matlab.mat.format.Mat5File;
import us.hebi.matlab.mat.types.MatFile;
import us.hebi.matlab.mat.types.Matrix; import us.hebi.matlab.mat.types.Matrix;
import us.hebi.matlab.mat.types.Struct; import us.hebi.matlab.mat.types.Struct;
@ -30,9 +37,10 @@ public class ClickDLTest {
/** /**
* Test just one click * Test just one click
* @throws
*/ */
@Test @Test
public void aclickDLTest() { public void aclickDLTest() {
System.out.println("CLickDLTest: Single click test"); System.out.println("CLickDLTest: Single click test");
@ -40,15 +48,22 @@ public class ClickDLTest {
//relative paths to the resource folders. //relative paths to the resource folders.
System.out.println("*****Click classification Deep Learning C*****"); System.out.println("*****Click classification Deep Learning C*****");
// //relative paths to the resource folders.
// String relModelPath = "/Users/jdjm/Library/CloudStorage/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/model_pb/saved_model.pb";
// String clicksPath = "/Users/jdjm/Library/CloudStorage/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/example_2000021.mat";
//relative paths to the resource folders. //relative paths to the resource folders.
String relModelPath = "/Users/jdjm/Library/CloudStorage/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/model_pb/saved_model.pb"; String relModelPath = "/home/jamiemac/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/model_pb/saved_model.pb";
String clicksPath = "/Users/jdjm/Library/CloudStorage/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/example_2000021.mat"; String clicksPath = "/home/jamiemac/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/example_2000021.mat";
//load the click up //load the click up
// String matout = "/home/jamiemac/MATLAB-Drive/MATLAB/PAMGUARD/deep_learning/generic_classifier/example_2000021_transforms.mat";
String matout=null;
// load the click data up. // load the click data up.
Path clkPath = Paths.get(clicksPath); Path clkPath = Paths.get(clicksPath);
PredGroupedRawData clickData = null; PredGroupedRawData clickData = null;
Struct matclkStruct = Mat5.newStruct();
try { try {
Mat5File mfr = Mat5.readFromFile(clkPath.toAbsolutePath().normalize().toString()); Mat5File mfr = Mat5.readFromFile(clkPath.toAbsolutePath().normalize().toString());
@ -60,6 +75,7 @@ public class ClickDLTest {
Matrix modelInputM= mlArrayRetrived.get("wave_pad", 0); Matrix modelInputM= mlArrayRetrived.get("wave_pad", 0);
double[][] clickWaveform= PamArrayUtils.matrix2array(clickWavM); double[][] clickWaveform= PamArrayUtils.matrix2array(clickWavM);
clickWaveform=PamArrayUtils.transposeMatrix(clickWaveform);
//get the raw model input so we can test the model directly. //get the raw model input so we can test the model directly.
double[][] pythonModelInput= PamArrayUtils.matrix2array(modelInputM); double[][] pythonModelInput= PamArrayUtils.matrix2array(modelInputM);
@ -90,12 +106,14 @@ public class ClickDLTest {
//waveform transforms. //waveform transforms.
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, 248000.)); dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, 248000.));
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.NORMALISE_WAV, 0., 1, AudioData.ZSCORE)); //needs to be here
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.PEAK_TRIM, 64, 1)); dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.PEAK_TRIM, 64, 1));
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.NORMALISE_WAV, 0., 1, AudioData.ZSCORE));
genericModelParams.dlTransfromParams = dlTransformParamsArr; genericModelParams.dlTransfromParams = dlTransformParamsArr;
genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams); genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams);
//create the clicks. //create the clicks.
path = Paths.get(clicksPath); path = Paths.get(clicksPath);
@ -107,28 +125,56 @@ public class ClickDLTest {
System.out.println("Waveform input: " + groupedData.get(0).getRawData().length + " " + groupedData.get(0).getRawData()[0].length); System.out.println("Waveform input: " + groupedData.get(0).getRawData().length + " " + groupedData.get(0).getRawData()[0].length);
ArrayList<StandardPrediction> genericPrediction = genericModelWorker.runModel(groupedData,SAMPLE_RATE, 0); ArrayList<StandardPrediction> genericPrediction = genericModelWorker.runModel(groupedData,248000, 0);
System.out.println("PAMGuard input len: " + pythonModelInputF.length); // System.out.println("PAMGuard input len: " + pythonModelInputF.length);
float[] outputPAMGuard = genericPrediction.get(0).getPrediction(); float[] outputPAMGuard = genericPrediction.get(0).getPrediction();
System.out.println("Model output PAMGuard: " + outputPAMGuard[0]); System.out.println("Model output PAMGuard: " + outputPAMGuard[0]);
//run the transforms so we can take a look at the inpout
((WaveTransform) genericModelParams.dlTransfroms.get(0)).setWaveData(new AudioData(groupedData.get(0).getRawData()[0], 248000));;
//create the transformed wave
DLTransform transform = genericModelParams.dlTransfroms.get(0);
double[] audioOut = null;
for (int i=0; i<genericModelParams.dlTransfroms .size(); i++) {
transform = genericModelParams.dlTransfroms.get(i).transformData(transform);
audioOut = ((WaveTransform) transform).getWaveData().getScaledSampleAmplitudes();
matclkStruct.set(transform.getDLTransformType().getJSONString(), DLMatFile.array2Matrix(audioOut));
}
//RUN THE RAW MODEL with Python transformed input //RUN THE RAW MODEL with Python transformed input
System.out.println("Python input len: " + pythonModelInputF.length); // System.out.println("Python input len: " + pythonModelInputF.length);
// float[] outPutPython = genericModelWorker.getModel().runModel(new float[][] {PamArrayUtils.double2Float(audioOut)});
float[] outPutPython = genericModelWorker.getModel().runModel(new float[][] {pythonModelInputF}); float[] outPutPython = genericModelWorker.getModel().runModel(new float[][] {pythonModelInputF});
System.out.println("Model output Python: " + outPutPython[0]); System.out.println("Model output Python: " + outPutPython[0]);
assertEquals(outputPAMGuard[0], outPutPython[0], 0.05);
} }
catch (Exception e) { catch (Exception e) {
// TODO Auto-generated catch block // TODO Auto-generated catch block
e.printStackTrace(); e.printStackTrace();
assertTrue(false); //make sure the unit test fails
return; return;
} }
if (matout!=null) {
// Create MAT file with a scalar in a nested struct
MatFile matFile = Mat5.newMatFile()
.addArray("click_transforms", matclkStruct);
// Serialize to disk using default configurations
try {
Mat5.writeToFile(matFile, matout);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
} }
@ -141,8 +187,8 @@ public class ClickDLTest {
System.out.println("*****Click classification Deep Learning C*****"); System.out.println("*****Click classification Deep Learning C*****");
//relative paths to the resource folders. //relative paths to the resource folders.
String relModelPath = "./src/test/resources/rawDeepLearningClassifier/Generic/risso_click/uniform_model/saved_model.pb"; String relModelPath = "/home/jamiemac/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/model_pb/saved_model.pb";
String clicksPath = "./src/test/resources/rawDeepLearningClassifier/Generic/risso_click/clicks.mat"; String clicksPath = "/home/jamiemac/Dropbox/PAMGuard_dev/Deep_Learning/click_classifier_Thomas/model_v2/Click_Detector_Click_Detector_Clicks_20220603_111000.mat";
Path path = Paths.get(relModelPath); Path path = Paths.get(relModelPath);
@ -157,8 +203,8 @@ public class ClickDLTest {
//waveform transforms. //waveform transforms.
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, 248000.)); dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, 248000.));
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.PEAK_TRIM, 128, 1));
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.NORMALISE_WAV, 0., 1, AudioData.ZSCORE)); dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.NORMALISE_WAV, 0., 1, AudioData.ZSCORE));
dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.PEAK_TRIM, 64, 1));
genericModelParams.dlTransfromParams = dlTransformParamsArr; genericModelParams.dlTransfromParams = dlTransformParamsArr;
genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams); genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams);
@ -203,7 +249,7 @@ public class ClickDLTest {
Mat5File mfr = Mat5.readFromFile(filePath); Mat5File mfr = Mat5.readFromFile(filePath);
// //get array of a name "my_array" from file // //get array of a name "my_array" from file
Struct mlArrayRetrived = mfr.getStruct( "clickpreds" ); Struct mlArrayRetrived = mfr.getStruct( "binarydata" );
int numClicks= mlArrayRetrived.getNumCols(); int numClicks= mlArrayRetrived.getNumCols();
ArrayList<PredGroupedRawData> clicks = new ArrayList<PredGroupedRawData>(numClicks); ArrayList<PredGroupedRawData> clicks = new ArrayList<PredGroupedRawData>(numClicks);