DeconvolutionScriptTest.java

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package net.imagej.scripting;

import static org.junit.Assert.assertEquals;

import io.scif.services.DatasetIOService;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.ExecutionException;

import javax.script.ScriptException;

import net.imagej.Dataset;
import net.imagej.ImgPlus;
import net.imglib2.type.numeric.RealType;

import org.junit.Test;
import org.scijava.plugin.Parameter;
import org.scijava.script.ScriptModule;

/**
 * @author Hadrien Mary
 */
public class DeconvolutionScriptTest extends AbstractScriptTest {

	@Parameter
	protected DatasetIOService datasetIOService;

	@Test
	@SuppressWarnings("unchecked")
	public <T extends RealType<T>> void testDeconWithGaussian()
		throws InterruptedException, ExecutionException, IOException,
		URISyntaxException, FileNotFoundException, ScriptException
	{

		final String testPath =
			"8bit-signed&pixelType=int8&axes=X,Y,Z,&lengths=100,100,50.fake";
		final Dataset data = datasetIOService.open(testPath);

		final Map<String, Object> parameters = new HashMap<>();

		parameters.put("img", data.getImgPlus());
		parameters.put("sxy", 2.0);
		parameters.put("sz", 6.0);
		parameters.put("numIterations", 3);

		final File scriptFile = new File(getClass().getResource(
			"/script_templates/Deconvolution/DeconWithGaussian.py").toURI());
		final ScriptModule m = scriptService.run(scriptFile, true, parameters)
			.get();

		final ImgPlus<T> output1 = (ImgPlus<T>) m.getOutput("deconvolved");
		assertEquals(3, output1.numDimensions());
		final double[] expected = { 378.56768798828125, 97.66587829589844,
			22.849470138549805, 1.997551679611206, 51.35069274902344,
			73.30968475341797, -193.34324645996094, -616.32958984375,
			-628.3247680664062, -180.4445037841797 };
		assertSamplesEqual(output1, 1000, expected);
	}
}