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Ketos model fixes

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Fixed bug in ketos models were, if no transforms were present, the model would not load. Also fixed an error when no class names were provided.
This commit is contained in:
Jamie Mac 2022-01-14 09:39:49 +00:00
parent 490daf4481
commit fd31d94aa9
6 changed files with 46 additions and 25 deletions
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2
src/binaryFileStorage/BinaryOutputStream.java
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@ -502,7 +502,7 @@ public class BinaryOutputStream {
*/
public synchronized boolean storeData(DataOutputStream outputStream, int objectId, DataUnitBaseData baseData, BinaryObjectData binaryObjectData) {
if (lastObjectType == BinaryTypes.MODULE_FOOTER) {
System.out.printf("Storing binary object type %d in file %s with no module header\n", objectId, outputStream.toString());
System.out.printf("Storing binary object type %d in file %s with no module header\n", objectId, outputStream == null ? null : outputStream.toString());
}
byte[] data = binaryObjectData.getData();
int objectLength = binaryObjectData.getDataLength();

7
src/rawDeepLearningClassifier/dlClassification/animalSpot/StandardModelPane.java
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@ -421,11 +421,16 @@ public abstract class StandardModelPane extends SettingsPane<StandardModelParams
//get class names from the paramClone as these may have been set by a loaded model
//instea of a use changing a control.
//instead of a using changing a control.
currParams.classNames = paramsClone.classNames;
currParams.numClasses = paramsClone.numClasses;
currParams.useDefaultSegLen = usedefaultSeg.isSelected();
//System.out.println("Get CLASS NAMES: currParams.classNames: " + currParams.classNames + " Num classes " + currParams.numClasses);
return currParams;
}

11
src/rawDeepLearningClassifier/dlClassification/animalSpot/StandardModelParams.java
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@ -49,6 +49,12 @@ public class StandardModelParams implements Serializable, Cloneable {
*/
public int numClasses = 0;
/**
* The class names. e.g. porpoise, noise, bat
*/
public DLClassName[] classNames;
/**
* List of transforms for the raw data e.g. filtering, spectrogram, spectrogram normalisation etc.
* This is only used for saving serialised settings
@ -74,10 +80,7 @@ public class StandardModelParams implements Serializable, Cloneable {
public boolean useDefaultSegLen = false;
/**
* The class names. e.g. porpoise, noise, bat
*/
public DLClassName[] classNames;
/**
* Which classes to apply binary classification to.

1
src/rawDeepLearningClassifier/dlClassification/ketos/KetosClassifier.java
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@ -224,7 +224,6 @@ public class KetosClassifier implements DLClassiferModel, PamSettings {
* @param ketosDLParams - the Ketos parameters.
*/
public KetosDLParams getKetosParams() {
// TODO Auto-generated method stub
return ketosDLParams;
}

10
src/rawDeepLearningClassifier/dlClassification/ketos/KetosModelTest.java
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@ -13,6 +13,8 @@ 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;
import org.jamdev.jpamutils.JamArr;
/**
* Test the Ketos models in PAMGuard.
@ -33,7 +35,8 @@ public class KetosModelTest {
//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";
//String wavFilePath = "/Volumes/GoogleDrive/My Drive/PAMGuard_dev/Deep_Learning/Meridian/right_whales/for_pamguard/input.wav";
String wavFilePath = "/Volumes/GoogleDrive-108005893101854397430/My Drive/PAMGuard_dev/Deep_Learning/Meridian/humpback_whales/wav/5353.210403161502.wav";
try {
//the ketos model.
@ -44,12 +47,14 @@ public class KetosModelTest {
//get the audio representation file.
KetosParams ketosParams = new KetosParams(jsonString);
ketosParams.defaultOutputShape = ketosModel.getOutShape();
//System.out.println(ketosParams.toString());
System.out.println("Output shape" + ketosParams.defaultOutputShape);
//Open wav files.
AudioData soundData = DLUtils.loadWavFile(wavFilePath);
soundData = soundData.trim(0, (int) (soundData.getSampleRate()*3.0));
soundData = soundData.trim(0, (int) (soundData.getSampleRate()*3.52));
//generate the transforms.
ArrayList<DLTransform> transforms = DLTransformsFactory.makeDLTransforms(ketosParams.dlTransforms);
@ -83,6 +88,7 @@ public class KetosModelTest {
for (int j=0; j<nStack; j++) {
data[j] = DLUtils.toFloatArray(transformedData);
}
System.out.println("Input len: " + data.length + " " + data[0].length + " " + data[0][0].length);
output = ketosModel.runModel(data);
long time2 = System.currentTimeMillis();
System.out.println("Time to run model: " + (time2-time1) + " ms");

32
src/rawDeepLearningClassifier/dlClassification/ketos/KetosWorker.java
View File

@ -70,6 +70,11 @@ public class KetosWorker extends DLModelWorker<KetosResult> {
//convert the JSON string to a parameters object.
KetosParams ketosParams = new KetosParams(jsonString);
//important to add this for Ketos models because the JSON string does not necessarily contain and output shape.
//System.out.println("----Default output shape: " + ketosParams.defaultOutputShape + " " + ketosModel.getOutShape());
if (ketosParams.defaultOutputShape==null) {
ketosParams.defaultOutputShape = ketosModel.getOutShape();
}
@ -110,18 +115,21 @@ public class KetosWorker extends DLModelWorker<KetosResult> {
}
// if (dlParams.classNames!=null) {
// for (int i = 0; i<dlParams.classNames.length; i++) {
// System.out.println("Class name " + i + " " + dlParams.classNames[i]);
// }
// }
// ketosDLParams.classNames = dlControl.getClassNameManager().makeClassNames(ketosParams.classNames);
//
// if (ketosParams.classNames!=null) {
// for (int i = 0; i<ketosDLParams.classNames.length; i++) {
// System.out.println("Class name " + i + " " + ketosDLParams.classNames[i].className + " ID " + ketosDLParams.classNames[i].ID );
// }
// }
// if (dlParams.classNames!=null) {
// for (int i = 0; i<dlParams.classNames.length; i++) {
// System.out.println("Class name " + i + " " + dlParams.classNames[i]);
// }
// }
// ketosDLParams.classNames = dlControl.getClassNameManager().makeClassNames(ketosParams.classNames);
// if (ketosParams.classNames!=null) {
// for (int i = 0; i<ketosDLParams.classNames.length; i++) {
// System.out.println("Class name " + i + " " + ketosDLParams.classNames[i].className + " ID " + ketosDLParams.classNames[i].ID );
// }
// }
}
catch (Exception e) {