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Implements Prediction Mask for Pixel Classification #65

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Implements Prediction Mask for Pixel Classification #65

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7 changes: 6 additions & 1 deletion src/main/java/org/ilastik/ilastik4ij/executors/PixelClassification.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,9 @@ public PixelClassification(File executableFilePath, File projectFileName, LogSer
}

public <T extends NativeType<T>> ImgPlus<T> classifyPixels(ImgPlus<? extends RealType<?>> rawInputImg,
ImgPlus<? extends RealType<?>> predictionMask,
PixelPredictionType pixelPredictionType) throws IOException {
return executeIlastik(rawInputImg, null, pixelPredictionType);
return executeIlastik(rawInputImg, predictionMask, pixelPredictionType);
}

@Override
Expand All @@ -36,6 +37,10 @@ else if (pixelPredictionType == PixelPredictionType.Probabilities) {
commandLine.add("--raw_data=" + tempFiles.get(rawInputTempFile));
commandLine.add("--output_filename_format=" + tempFiles.get(outputTempFile));

if(tempFiles.containsKey(secondInputTempFile)){
commandLine.add("--prediction_mask=" + tempFiles.get(secondInputTempFile));
}

return commandLine;
}
}
24 changes: 22 additions & 2 deletions src/main/java/org/ilastik/ilastik4ij/ui/IlastikPixelClassificationCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import org.scijava.ItemIO;
import org.scijava.app.StatusService;
import org.scijava.command.Command;
import org.scijava.command.DynamicCommand;
import org.scijava.log.LogService;
import org.scijava.options.OptionsService;
import org.scijava.plugin.Parameter;
Expand All @@ -19,7 +20,7 @@
import static org.ilastik.ilastik4ij.executors.AbstractIlastikExecutor.PixelPredictionType;

@Plugin(type = Command.class, headless = true, menuPath = "Plugins>ilastik>Run Pixel Classification Prediction")
public class IlastikPixelClassificationCommand implements Command {
public class IlastikPixelClassificationCommand extends DynamicCommand {

@Parameter
public LogService logService;
Expand All @@ -42,6 +43,21 @@ public class IlastikPixelClassificationCommand implements Command {
@Parameter(label = "Output type", choices = {UiConstants.PIXEL_PREDICTION_TYPE_PROBABILITIES, UiConstants.PIXEL_PREDICTION_TYPE_SEGMENTATION}, style = "radioButtonHorizontal")
public String pixelClassificationType;

@Parameter(label = "Use Mask?", persist=false, initializer = "initUseMask")
public boolean useMask=false;

protected void initUseMask(){
useMask = false;
//resolveInput("useMask"); //this makes the input not be rendered -.-
}

@Parameter(
label = "Prediction Mask",
required = false,
description = "An image with same dimensions as Raw Data, where the black pixels will be masked out of the predictions"
)
public Dataset predictionMask;
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Did you try:

Suggested change
public Dataset predictionMask;
public Dataset predictionMask = null;

to see whether that solves the issue with a default value?


@Parameter(type = ItemIO.OUTPUT)
private ImgPlus<? extends NativeType<?>> predictions;

Expand Down Expand Up @@ -69,7 +85,11 @@ private void runClassification() throws IOException {
projectFileName, logService, statusService, ilastikOptions.getNumThreads(), ilastikOptions.getMaxRamMb());

PixelPredictionType pixelPredictionType = PixelPredictionType.valueOf(pixelClassificationType);
this.predictions = pixelClassification.classifyPixels(inputImage.getImgPlus(), pixelPredictionType);
this.predictions = pixelClassification.classifyPixels(
inputImage.getImgPlus(),
useMask ? predictionMask.getImgPlus() : null,
pixelPredictionType
);

// DisplayUtils.showOutput(uiService, predictions);
}
Expand Down
2 changes: 1 addition & 1 deletion src/test/java/org/ilastik/ilastik4ij/PixelClassificationDemo.java
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Expand Up @@ -62,7 +62,7 @@ public static <T extends RealType<T> & NativeType<T>> void main(String[] args) t
1024
);

final ImgPlus<T> classifiedPixels = prediction.classifyPixels(inputDataset.getImgPlus(), PixelPredictionType.Probabilities);
final ImgPlus<T> classifiedPixels = prediction.classifyPixels(inputDataset.getImgPlus(), null, PixelPredictionType.Probabilities);

ImageJFunctions.show(classifiedPixels, "Probability maps");
}
Expand Down