Hi Ignacio, thanks for the quick response. I updated FiJi, as well as downloaded a fresh install and updated it, still get the same error.
That seems a bug that was fixed in the latest release. Can you please update your Fiji and let me know if the problem persists?
> I was trying to use an old script, was getting an error on the
> wekaSegmentation.trainClassifier() (ArrayIndexOutOfBoundsException).
> I switched to the webpage example (modified to handle an issue with
> pulling the clown.jpg) and get the same error. My FiJi is fully up to
> date. Any ideas?
>
> Sean
>
> importClass(Packages.ij.IJ);
> importClass(Packages.ij.ImagePlus);
> importClass(Packages.ij.ImageStack);
> importClass(Packages.ij.gui.PolygonRoi);
> importClass(Packages.ij.plugin.Duplicator);
> importClass(Packages.ij.process.FloatPolygon);
> importClass(Packages.ij.process.StackConverter);
> importClass(Packages.trainableSegmentation.FeatureStack);
> importClass(Packages.trainableSegmentation.FeatureStackArray);
> importClass(Packages.trainableSegmentation.WekaSegmentation);
> importClass(Packages.ij.WindowManager);
>
> var image=WindowManager.getCurrentImage();
>
> //var image = IJ.openImage(System.getProperty("ij.dir") +
> "/samples/clown.jpg"); if (image.getStackSize() > 1)
> new StackConverter(image).convertToGray32();
> else
> image.setProcessor(image.getProcessor().convertToFloat());
> var duplicator = new Duplicator();
> // process the image into different stacks, one per feature:
> var smoothed = duplicator.run(image);
> IJ.run(smoothed, "Gaussian Blur...", "radius=20"); var medianed =
> duplicator.run(image); IJ.run(medianed, "Median...", "radius=10"); //
> add new feature here (1/2) // the FeatureStackArray contains a
> FeatureStack for every slice in our original image var featuresArray =
> new FeatureStackArray(image.getStackSize(), 1, 16, false,
> 1, 19, null);
> // turn the list of stacks into FeatureStack instances, one per
> original // slice. Each FeatureStack contains exactly one slice per feature.
> for (var slice = 1; slice <= image.getStackSize(); slice++) {
> var stack = new ImageStack(image.getWidth(), image.getHeight());
> stack.addSlice("smoothed",
> smoothed.getStack().getProcessor(slice));
> stack.addSlice("medianed",
> medianed.getStack().getProcessor(slice));
> // add new feature here (2/2) and do not forget to add it with a
> // unique slice label!
> // create empty feature stack
> var features = new FeatureStack( stack.getWidth(),
> stack.getHeight(), false );
> // set my features to the feature stack
> features.setStack( stack );
> // put my feature stack into the array
> featuresArray.set(features, slice - 1);
>
> featuresArray.setEnabledFeatures(features.getEnabledFeatures());
> }
> var wekaSegmentation = new WekaSegmentation(image);
> wekaSegmentation.setFeatureStackArray(featuresArray);
> // set examples for class 1 (= foreground) and 0 (= background))
> function addExample(classNum, slice, xArray, yArray) {
> var polygon = new FloatPolygon(xArray, yArray);
> var roi = new PolygonRoi(polygon, PolygonRoi.FREELINE);
> IJ.log("roi: " + roi);
> wekaSegmentation.addExample(classNum, roi, slice); }
> /*
> * generate these with the macro:
> getSelectionCoordinates(x, y);
> print('['); Array.print(x); print('],");
> print('['); Array.print(y); print(']"); */ addExample(1, 1,
> [ 82,85,85,86,87,87,87,88,88,88,88,88,88,88,88,86,86,84,83,82,81,
> 80,80,78,76,75,74,74,73,72,71,70,70,68,65,63,62,60,58,57,55,55,
> 54,53,51,50,49,49,49,51,52,53,54,55,55,56,56 ],
> [ 141,137,136,134,133,132,130,129,128,127,126,125,124,123,122,121,
> 120,119,118,118,116,116,115,115,114,114,113,112,111,111,111,111,
> 110,110,110,110,111,112,113,114,114,115,116,117,118,119,119,120,
> 121,123,125,126,128,128,129,129,130 ] ); addExample(0, 1,
> [ 167,165,163,161,158,157,157,157,157,157,157,157,158 ],
> [ 30,29,29,29,29,29,28,26,25,24,23,22,21 ] ); // train
> classifier if (!wekaSegmentation.trainClassifier())
> throw new RuntimeException("Uh oh! No training today.");
> output = wekaSegmentation.applyClassifier(image);
> output.show();
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
Department of Brain and Cognitive Sciences Massachusetts Institute of Technology