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 * Image processing operations for SciJava Ops.
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package org.scijava.ops.image.filter.vesselness;

import io.scif.img.IO;

import java.net.URL;

import org.scijava.ops.image.AbstractOpTest;
import net.imglib2.Cursor;
import net.imglib2.RandomAccess;
import net.imglib2.img.Img;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.view.Views;

import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;

/**
 * Tests the Frangi Vesselness operation.
 *
 * @author Gabriel Selzer
 */
public class FrangiVesselnessTest extends AbstractOpTest {

	@Test
	public void testFrangiVesselness() {
		// create input image
		final Img<DoubleType> inputImg = ArrayImgs.doubles(8, 8);
		setVesselPosValues(inputImg, new DoubleType(1.), new DoubleType(0.));

		// create expected output image
		final Img<FloatType> expectedOutput = ArrayImgs.floats(8, 8);
		setVesselPosValues(expectedOutput, new FloatType(0.0031375182f),
			new FloatType(0));

		// create output image
		final long[] dims = new long[inputImg.numDimensions()];
		inputImg.dimensions(dims);
		final Img<FloatType> actualOutput = ArrayImgs.floats(dims);

		// scale over which the filter operates (sensitivity)
		final int scale = 1;

		// physical spacing between data points (1,1 since I got it from the
		// computer)
		final double[] spacing = { 1, 1 };

		// run the op
		ops.op("filter.frangiVesselness").input(inputImg, scale, spacing).output(
			actualOutput).compute();

		// compare the output image data to that stored in the file.
		final Cursor<FloatType> cursor = Views.iterable(actualOutput)
			.localizingCursor();
		final RandomAccess<FloatType> actualRA = actualOutput.randomAccess();
		final RandomAccess<FloatType> expectedRA = expectedOutput.randomAccess();

		while (cursor.hasNext()) {
			cursor.fwd();
			actualRA.setPosition(cursor);
			expectedRA.setPosition(cursor);
			assertEquals(expectedRA.get().get(), actualRA.get().get(), 0);
		}
	}

	private <T extends RealType<T>> void setVesselPosValues(Img<T> img,
		T vesselVal, T otherVal)
	{
		Cursor<T> inputCursor = img.localizingCursor();
		// for each position, set to one if column at vesselPos, 0 otherwise
		int vesselPos = 4;
		while (inputCursor.hasNext()) {
			inputCursor.fwd();
			double[] pos = inputCursor.positionAsDoubleArray();
			inputCursor.get().set(pos[1] == vesselPos ? vesselVal : otherVal);
		}
	}
}
