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77
view-simulation-results/src/test/java/org/vcell/N5/analysis/DataReductionTest.java
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| package org.vcell.N5.analysis; | ||
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| import com.amazonaws.services.s3.AmazonS3ClientBuilder; | ||
| import ij.ImagePlus; | ||
| import ij.gui.Roi; | ||
| import ij.io.RoiDecoder; | ||
| import org.junit.Assert; | ||
| import org.junit.BeforeClass; | ||
| import org.junit.Test; | ||
| import org.vcell.N5.N5ImageHandler; | ||
| import org.vcell.N5.retrieving.SimResultsLoader; | ||
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| import java.io.File; | ||
| import java.net.URISyntaxException; | ||
| import java.net.URL; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
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| public class DataReductionTest { | ||
| private final double[] labMeans2DLabROI = new double[]{6, 0, 6.489, 0, 7.247, 0}; //calculated through IJ measurement tool | ||
| private final double[] labMeans2DSimROI = new double[]{18, 0, 16.341, 0, 14.469, 0}; | ||
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| private final double[] threeDMeans = new double[]{2884.526,3102.159, 3884.279, 4668.205, 5016.744, 5524.792, 4794.329, 5624.351, | ||
| 4559.778, 5510.099 | ||
| }; | ||
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| private File getTestResourceFiles(String filePath){ | ||
| try { | ||
| URL url = ClassLoader.getSystemClassLoader().getResource(filePath); | ||
| return new File(url.toURI().getPath()); | ||
| } | ||
| catch (URISyntaxException e){ | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
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| @BeforeClass | ||
| public static void init(){ | ||
| N5ImageHandler.initializeLogService(); | ||
| SimResultsLoader.s3ClientBuilder = AmazonS3ClientBuilder.standard(); | ||
| } | ||
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| private void compareExpectedCalculations(ImagePlus imagePlus, ArrayList<Roi> roiList, HashMap<String, double[]> expectedResults){ | ||
| DataReductionGUI.DataReductionSubmission dataReductionSubmission = new DataReductionGUI.DataReductionSubmission( | ||
| false, roiList, roiList, imagePlus,4, null); | ||
| DataReduction dataReduction = new DataReduction(dataReductionSubmission); | ||
| HashMap<String, ArrayList<Double>> result = dataReduction.calculateMean(imagePlus, roiList, Double.MIN_VALUE); | ||
| for (Roi roi : roiList){ | ||
| for (int i = 0; i < expectedResults.get(roi.getName()).length; i++){ | ||
| Assert.assertEquals(expectedResults.get(roi.getName())[i], result.get(roi.getName()).get(i), 0.0009); | ||
| } | ||
| } | ||
| } | ||
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| @Test | ||
| public void testMean2DCalculation(){ | ||
| // Ensure the mean calculated for each ROI, and each time point is what's to be expected | ||
| SimResultsLoader simResultsLoader = new SimResultsLoader("https://vcell.cam.uchc.edu/n5Data/ezequiel23/ddf7f4f0c77dffd.n5?dataSetName=4864003788", "test1"); | ||
| simResultsLoader.createS3ClientAndReader(); | ||
| ImagePlus labResultImage2D = simResultsLoader.getImgPlusFromN5File(); | ||
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| Roi labRoi = RoiDecoder.open(getTestResourceFiles("ROIs/Lab ROI.roi").getAbsolutePath()); | ||
| Roi simROI = RoiDecoder.open(getTestResourceFiles("ROIs/Sim ROI.roi").getAbsolutePath()); | ||
| ArrayList<Roi> roiList = new ArrayList<Roi>(){{add(labRoi); add(simROI);}}; | ||
| HashMap<String, double[]> expectedResults = new HashMap<String, double[]>(){{put(labRoi.getName(), labMeans2DLabROI); put(simROI.getName(), labMeans2DSimROI);}}; | ||
| compareExpectedCalculations(labResultImage2D, roiList, expectedResults); | ||
| } | ||
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| @Test | ||
| public void testMean3DCalculation(){ | ||
| ImagePlus mitosis = new ImagePlus(getTestResourceFiles("mitosis.tif").getAbsolutePath()); | ||
| Roi mitosisROI = RoiDecoder.open(getTestResourceFiles("ROIs/Mitosis Center.roi").getAbsolutePath()); | ||
| ArrayList<Roi> roiList = new ArrayList<Roi>(){{add(mitosisROI);}}; | ||
| HashMap<String, double[]> expectedResults = new HashMap<String, double[]>(){{put(mitosisROI.getName(), threeDMeans);}}; | ||
| compareExpectedCalculations(mitosis, roiList, expectedResults); | ||
| } | ||
| } |
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