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Make SoftMax application optional in runInference #70

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Make SoftMax application optional in runInference #70

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7 changes: 3 additions & 4 deletions src/main/java/qupath/ext/wsinfer/WSInfer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -193,8 +193,7 @@ public static void runInference(ImageData<BufferedImage> imageData, WSInferModel
}
}

boolean applySoftmax = true;
Translator translator = buildTranslator(wsiModel, pipeline, applySoftmax);
Translator translator = buildTranslator(wsiModel, pipeline);
Criteria<Image, Classifications> criteria = buildCriteria(wsiModel, translator, device);
List<String> classNames = wsiModel.getConfiguration().getClassNames();
long startTime = System.currentTimeMillis();
Expand Down Expand Up @@ -308,13 +307,13 @@ private static boolean isMPS(Device device) {
}


private static Translator<Image, Classifications> buildTranslator(WSInferModel wsiModel, Pipeline pipeline, boolean applySoftmax) {
private static Translator<Image, Classifications> buildTranslator(WSInferModel wsiModel, Pipeline pipeline) {
// We should use ImageClassificationTranslator.builder() in the future if this is updated to work with MPS
// (See javadocs for MpsSupport.WSInferClassificationTranslator for details)
// ImageClassificationTranslator.Builder builder = ImageClassificationTranslator.builder()
return MpsSupport.WSInferClassificationTranslator.builder()
.optSynset(wsiModel.getConfiguration().getClassNames())
.optApplySoftmax(applySoftmax)
.optApplySoftmax(wsiModel.getConfiguration().isApplySoftmax())
.setPipeline(pipeline)
.build();
}
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11 changes: 11 additions & 0 deletions src/main/java/qupath/ext/wsinfer/models/WSInferModelConfiguration.java
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Expand Up @@ -45,6 +45,9 @@ public class WSInferModelConfiguration {
@SerializedName("spacing_um_px")
private double spacingUmPx;

@SerializedName("apply_softmax")
private boolean applySoftmax = true;

private List<WSInferTransform> transform;

/**
Expand Down Expand Up @@ -78,4 +81,12 @@ public double getPatchSizePixels() {
public double getSpacingMicronPerPixel() {
return spacingUmPx;
}

/**
* Whether to apply softmax to model output
* @return
*/
public boolean isApplySoftmax() {
return applySoftmax;
}
}