Java tutorial
/*- * Copyright 2016 Diamond Light Source Ltd. * * All rights reserved. This program and the accompanying materials * are made available under the terms of the Eclipse Public License v1.0 * which accompanies this distribution, and is available at * http://www.eclipse.org/legal/epl-v10.html */ package uk.ac.diamond.scisoft.xpdf.views; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; import org.apache.commons.lang.ArrayUtils; import org.eclipse.dawnsci.analysis.dataset.impl.DoubleDataset; import org.eclipse.dawnsci.analysis.dataset.impl.StringDataset; import org.eclipse.dawnsci.nexus.NXsample; import org.eclipse.dawnsci.nexus.builder.NexusFileBuilder; import org.eclipse.dawnsci.nexus.builder.impl.DefaultNexusFileBuilder; import org.junit.Before; import org.junit.Test; import uk.ac.diamond.scisoft.xpdf.XPDFSubstance; /** * A unit test class for the XPDFSampleParameters class, a package private * class in the XPDF views package * @author Timothy Spain, timothy.spain@diamond.ac.uk * */ public class SampleParametersTest { private XPDFSampleParameters sample; private XPDFSampleParameters cap; @Before public void setUp() { sample = new XPDFSampleParameters(true); // ceria, with a hint of beryllium sample.addPhase(SampleTestData.createTestPhase("ceria"), 0.95); // beryllium needs atoms added to it XPDFPhase beryllium = SampleTestData.createTestPhase("beryllium"); beryllium.addAtom(new XPDFAtom("Be1", 4, 1.0, new double[] { 0.0, 0.0, 0.0 }, "a")); sample.addPhase(beryllium, 0.05); sample.setName("Contaminated ceria"); sample.setPackingFraction(0.6); cap = new XPDFSampleParameters(false); } @Test public void testXPDFSampleParameters() { // Is it a good idea to use this test to instantiate a new object? // 'Cause that's what I am going to do. sample = new XPDFSampleParameters(); testBasicFieldCreation(); } private void testBasicFieldCreation() { assertTrue("XPDFSampleParameters was not successfully created", sample != null); assertTrue("Phases list not successfully created", sample.getPhases() != null); assertTrue("Fractions list not successfully created", sample.getPhaseWeightings() != null); } @Test public void testXPDFSampleParametersBoolean() { sample = new XPDFSampleParameters(true); testBasicFieldCreation(); assertTrue("XPDFSampleParameters sample parameter not set correctly on construction", sample.isSample()); sample = null; sample = new XPDFSampleParameters(false); testBasicFieldCreation(); assertTrue("XPDFSampleParameters sample parameter not unset correctly on construction", !sample.isSample()); } @Test public void testXPDFSampleParametersXPDFSampleParameters() { XPDFSampleParameters copy = new XPDFSampleParameters(sample); assertEquals(sample.getName(), copy.getName()); assertEquals(sample.getPhases(), copy.getPhases()); assertEquals(sample.getPhaseWeightings(), copy.getPhaseWeightings()); assertEquals(sample.isSample(), copy.isSample()); assertEquals(sample.getComposition(), copy.getComposition()); assertEquals(sample.getDensity(), copy.getDensity(), 1e-3); assertEquals(sample.getPackingFraction(), copy.getPackingFraction(), 1e-3); assertEquals(sample.getShapeName(), copy.getShapeName()); } @Test public void testSetGetName() { String newName = "Highly contaminated beryllium"; sample.setName(newName); assertEquals("New name not set/got correctly", newName, sample.getName()); } @Test public void testSetGetId() { int id = 1; sample.setId(id); assertEquals("New ID not set/got correctly", id, sample.getId()); } @Test public void testSetGetPhases() { List<XPDFPhase> newPhases = new ArrayList<XPDFPhase>(); newPhases.add(SampleTestData.createTestPhase("ilmenite")); sample.setPhases(newPhases); assertEquals(newPhases, sample.getPhases()); } @Test public void testClearPhases() { sample.clearPhases(); assertTrue("XPDFSampleParameters phase list not cleared", sample.getPhases().isEmpty()); } @Test public void testAddPhaseXPDFPhase() { XPDFPhase rutile = SampleTestData.createTestPhase("rutile"); sample.addPhase(rutile); assertTrue("New phase not successfully added", sample.getPhases().contains(rutile)); } @Test public void testAddPhaseXPDFPhaseDouble() { XPDFPhase rutile = SampleTestData.createTestPhase("rutile"); double rutileWeight = 0.1; sample.addPhase(rutile, rutileWeight); assertTrue("New weighted phase not successfully added", sample.getPhases().contains(rutile)); assertEquals("New phase weighting not successfully retrieved", sample.getPhaseWeighting(rutile), rutileWeight, 1e-3); } @Test public void testSetGetPhaseWeightings() { List<Double> newWeightings = Arrays.asList(new Double[] { 0.9, 0.1 }); sample.setPhaseWeightings(newWeightings); for (int i = 0; i < newWeightings.size(); i++) assertEquals("Phase " + i + " incorrectly weighted", newWeightings.get(i), sample.getPhaseWeightings().get(i), 1e-3); } @Test public void testSetGetPhaseWeighting() { XPDFPhase firstPhase = sample.getPhases().get(0); double newWeight = 0.9; sample.setPhaseWeighting(firstPhase, newWeight); assertEquals("Phase weighting not set/got correctly", newWeight, sample.getPhaseWeighting(firstPhase), 1e-3); } @Test public void testSetIsSample() { sample.setAsContainer(); sample.setAsSample(); assertTrue("Not successfully set as a sample", sample.isSample()); } @Test public void testSetAsContainer() { sample.setAsContainer(); assertFalse("Not successfully set as a container", sample.isSample()); } @Test public void testSetGetSubstance() { // For samples/containers without phases XPDFSubstance quartz = new XPDFSubstance("SiO2", "SiO2", 1.65, 1.0); cap.setSubstance(quartz); assertEquals("Substance not set/got correctly", quartz.getMaterialName(), cap.getSubstance().getMaterialName()); } @Test public void testSetGetComposition() { String silica = "SiO2"; cap.setComposition(silica); String silicaHall = "OSi"; assertEquals("Composition not set/got correctly", silicaHall, cap.getComposition()); } @Test public void testSetGetDensity() { testSetGetComposition(); double silicaDensity = 1.65; cap.setDensity(silicaDensity); assertEquals("Density not set/got correctly", silicaDensity, cap.getDensity(), 1e-3); } @Test public void testSetGetPackingFraction() { testSetGetComposition(); double silicaPack = 1.0; cap.setPackingFraction(silicaPack); assertEquals("Packing fraction not set/got correctly", silicaPack, cap.getPackingFraction(), 1e-3); } // @Test public void testGetMu() { fail("Not yet implemented"); } @Test public void testSetGetShapeName() { testSetGetComposition(); String cyl = "Cylinder", plat = "Plate"; for (String shape : new String[] { cyl, plat }) { cap.setShape(shape); assertEquals("Shape not set/got correctly", shape, cap.getShapeName()); } // check set by container sample.setShape(cyl); sample.setShape(null); assertEquals("Non-shape not set/got correctly", "Defined by container", sample.getShapeName()); } @Test public void testSetGetDimensions() { testSetGetComposition(); cap.setShape("cylinder"); double[] dims = new double[] { 0.15, 0.16 }; cap.setDimensions(dims); assertEquals("New dimensions not set/got correctly", Arrays.asList(ArrayUtils.toObject(dims)), Arrays.asList(ArrayUtils.toObject(cap.getDimensions()))); } @Test public void testSetDimensionsDoubleDouble() { testSetGetDimensions(); double newInner = 0.5, newOuter = 0.51; cap.setDimensions(newInner, newOuter); assertEquals("New dimension not set correctly", newInner, cap.getDimensions()[0], 1e-3); assertEquals("New dimension not set correctly", newOuter, cap.getDimensions()[1], 1e-3); } // @Test public void testToString() { int id = 1; cap.setId(id); String name = "Quartz capillary"; cap.setName(name); String silica = "SiO2"; cap.setComposition(silica); double density = 1.65; cap.setDensity(density); double pack = 0.6; cap.setPackingFraction(pack); } @Test public void testWriteNX() { String filename = "/tmp/sample.nxs"; NexusFileBuilder builder = new DefaultNexusFileBuilder(filename); NXsample nxample = sample.getNXsample(builder); int nCompo = sample.getPhases().size(); assertEquals("NX name incorrect", sample.getName(), nxample.getNameScalar()); assertEquals("NX description incorrect", sample.getName() + ", " + sample.getComposition() + ", " + sample.getShapeName(), nxample.getDescriptionScalar()); assertEquals("NX component names incorrect", new StringDataset(sample.getPhases().stream() .map(a -> a.getName()).collect(Collectors.toList()).toArray(new String[nCompo])), nxample.getComponent()); assertEquals("NX component formulae incorrect", new StringDataset(sample.getPhases().stream().map(a -> a.getComposition().getHallNotation(false)) .collect(Collectors.toList()).toArray(new String[nCompo]), new int[] { nCompo, 1 }), nxample.getChemical_formula()); assertEquals("NX formula weight incorrect", new DoubleDataset( ArrayUtils.toPrimitive( sample.getPhases().stream().map(a -> a.getComposition().getFormulaMass()) .collect(Collectors.toList()).toArray(new Double[nCompo])), new int[] { nCompo }), nxample.getDataset("chemical_formula_weight")); // unit cell parameters... assertEquals("NX unit cell volume incorrect", new DoubleDataset(ArrayUtils.toPrimitive(sample.getPhases().stream().map(a -> a.getUnitCellVolume()) .collect(Collectors.toList()).toArray(new Double[nCompo])), new int[] { nCompo }), nxample.getUnit_cell_volume()); assertEquals("NX unit cell class incorrect", new StringDataset(sample.getPhases().stream().map(a -> a.getCrystalSystem().getName()) .collect(Collectors.toList()).toArray(new String[nCompo]), new int[] { nCompo }), nxample.getUnit_cell_class()); assertEquals("NX unit cell space group incorrect", new StringDataset(sample.getPhases().stream() .map(a -> a.getSpaceGroup().getNumber() + ": " + a.getSpaceGroup().getName()) .collect(Collectors.toList()).toArray(new String[nCompo]), new int[] { nCompo }), nxample.getUnit_cell_group()); assertEquals("NX theoretical densities incorrect", new DoubleDataset(ArrayUtils.toPrimitive(sample.getPhases().stream().map(a -> a.getDensity()) .collect(Collectors.toList()).toArray(new Double[nCompo])), new int[] { nCompo }), nxample.getDataset("theoretical_density")); } }