ThresholderTest.java

package cz.cuni.lf1.lge.ThunderSTORM.thresholding;

import cz.cuni.lf1.lge.ThunderSTORM.FormulaParser.FormulaParserException;
import cz.cuni.lf1.lge.ThunderSTORM.filters.EmptyFilter;
import cz.cuni.lf1.lge.ThunderSTORM.filters.ui.BoxFilterUI;
import cz.cuni.lf1.lge.ThunderSTORM.filters.ui.IFilterUI;
import ij.process.FloatProcessor;
import java.util.Vector;
import org.junit.Test;
import static org.junit.Assert.*;

public class ThresholderTest {

    @Test
    public void testSimpleNumber() {
        double thr = Thresholder.getThreshold("120.5");
        assertEquals(120.5, thr, 0.001);
    }

    @Test
    public void testFormula() {
        Vector<IFilterUI> filters = new Vector<IFilterUI>();
        IFilterUI filter = new EmptyFilter();
        filters.add(filter);
        Thresholder.loadFilters(filters);
        Thresholder.setActiveFilter(0);
        assertSame(filter.getThreadLocalImplementation(), Thresholder.getActiveFilter());

        FloatProcessor fp = new FloatProcessor(new float[][]{
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5}
        });
        Thresholder.setCurrentImage(fp);
        assertSame(fp, Thresholder.getCurrentImage());

        filter.getThreadLocalImplementation().filterImage(fp);
        float result = Thresholder.getThreshold("mean(I+F)+1");
        assertEquals(7, result, 1e-5);

        try {
            Thresholder.getThreshold("std(Wave.F)"); //unknown filter
            fail("should have thrown exception");
        } catch(FormulaParserException e) {
        }
    }

    @Test
    public void testStd() {
        setupThresholder();
        float calc = Thresholder.getThreshold("std(I)");
        float expected = 1.4434f;
        assertEquals(expected, calc, 1e-4);
    }

    @Test
    public void testMean() {
        setupThresholder();
        float calc = Thresholder.getThreshold("mean(I)");
        float expected = 3;
        assertEquals(expected, calc, 1e-5);
    }

    @Test
    public void testMedian() {
        setupThresholder();
        float calc = Thresholder.getThreshold("median(I)");
        float expected = 3;
        assertEquals(expected, calc, 1e-2);//imageJ calculates median from histogram and can be a little bit off
    }

    @Test
    public void testMax() {
        setupThresholder();
        float calc = Thresholder.getThreshold("max(I)");
        float expected = 5;
        assertEquals(expected, calc, 1e-5);
    }

    @Test
    public void testMin() {
        setupThresholder();
        float calc = Thresholder.getThreshold("min(I)");
        float expected = 1;
        assertEquals(expected, calc, 1e-5);
    }

    @Test
    public void testSum() {
        setupThresholder();
        float calc = Thresholder.getThreshold("sum(I)");
        float expected = 75;
        assertEquals(expected, calc, 1e-5);
    }

    @Test
    public void testAbs() {
        setupThresholder();
        float calc = Thresholder.getThreshold("sum(abs(-I))");
        float expected = 75;
        assertEquals(expected, calc, 1e-5);
    }

    @Test
    public void testOtherFilter() {
        setupThresholder();
        float calc = Thresholder.getThreshold("min(Box.F)");
        assertTrue(calc > 1);
    }

    @Test
    public void testMultiplication() {
        setupThresholder();
        float calc = Thresholder.getThreshold("sum(2*I)");
        float expected = 2 * 75;
        assertEquals(expected, calc, 1e-5);

        calc = Thresholder.getThreshold("2*sum(I)");
        expected = 2 * 75;
        assertEquals(expected, calc, 1e-5);
    }

    @Test
    public void testExponentiation() {
        setupThresholder();
        float calc = Thresholder.getThreshold("sum(I^2)");
        float expected = 275;
        assertEquals(expected, calc, 1e-5);

        calc = Thresholder.getThreshold("sum(I)^2");
        expected = 75 * 75;
        assertEquals(expected, calc, 1e-5);

        try {
            Thresholder.getThreshold("sum(2^I)");
            fail("should have thrown exception");
        } catch(FormulaParserException e) {
        }
        try {
            Thresholder.getThreshold("sum(I^I)");
            fail("should have thrown exception");
        } catch(FormulaParserException e) {
        }
    }

    @Test
    public void testDivision() {
        setupThresholder();
        float calc = Thresholder.getThreshold("sum(I/2)");
        float expected = 75f / 2;
        assertEquals(expected, calc, 1e-5);

        calc = Thresholder.getThreshold("sum(1/I)");
        expected = 11.416666666666666f;
        assertEquals(expected, calc, 1e-5);

        calc = Thresholder.getThreshold("sum(I)/2");
        expected = 75f / 2;
        assertEquals(expected, calc, 1e-5);

        calc = Thresholder.getThreshold("sum(I/I)");
        expected = 25;
        assertEquals(expected, calc, 1e-5);

        calc = Thresholder.getThreshold("sum(I-1)");
        expected = 50;
        assertEquals(expected, calc, 1e-5);
    }

    /**
     * Setups the thresholder with two filters: EmptyFilter and BoxFilter.
     * EmptyFilter is set as active. An image is set as current image and active
     * filter is used to filter the image.
     */
    private void setupThresholder() {
        //run from other thread to test behavior of thread locals
        Thread t = new Thread() {
            @Override
            public void run() {
                Vector<IFilterUI> filters = new Vector<IFilterUI>();
                IFilterUI filter = new EmptyFilter();
                IFilterUI filter2 = new BoxFilterUI();

                filters.add(filter);

                filters.add(filter2);

                Thresholder.loadFilters(filters);
            }
        };
        t.start();
        try {
            t.join();
        } catch(InterruptedException ex) {
            throw new RuntimeException(ex);
        }

        Thresholder.setActiveFilter(0);

        FloatProcessor fp = new FloatProcessor(new float[][]{
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5},
            {1, 2, 3, 4, 5}
        });
        Thresholder.setCurrentImage(fp);

        Thresholder.getActiveFilter().filterImage(fp);
    }
}