Java tutorial
/* * Copyright (c) 2012 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.analysis.io; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.util.Collection; import org.apache.commons.lang.SerializationUtils; import org.eclipse.dawnsci.analysis.api.dataset.IDataset; import org.eclipse.dawnsci.analysis.api.dataset.ILazyDataset; import org.eclipse.dawnsci.analysis.api.io.IDataHolder; import org.eclipse.dawnsci.analysis.api.io.ScanFileHolderException; import org.eclipse.dawnsci.analysis.api.metadata.IMetadata; import org.eclipse.dawnsci.analysis.dataset.impl.AbstractDataset; import org.eclipse.dawnsci.analysis.dataset.impl.Dataset; import org.eclipse.dawnsci.analysis.dataset.impl.DatasetFactory; import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; import uk.ac.diamond.scisoft.analysis.IOTestUtils; /** * Test for SRS Loader */ public class SRSLoaderTest { private static String testScratchDirectoryName; /** * Creates an empty directory for use by test code. * * @throws Exception * if the directory is not created */ @BeforeClass static public void setUpClass() throws Exception { testScratchDirectoryName = IOTestUtils .generateDirectorynameFromClassname(SRSLoaderTest.class.getCanonicalName()); IOTestUtils.makeScratchDirectory(testScratchDirectoryName); } /** * Test Loader */ public SRSLoaderTest() { } /** * This method tests for SciSoft trac #496 */ @Test public void testSS49() { try { DataHolder dh; String testfile1 = "testfiles/gda/analysis/io/SRSLoaderTest/96356.dat"; dh = new SRSLoader(testfile1).loadFile(); // now the file is loaded, check to make sure that it holds the right data assertEquals("There is not the correct number of axis in the file", 7, dh.size()); int dt = dh.getDataset(6).getDtype(); if (dt == Dataset.FLOAT32) assertEquals("The file does not contain NANs", Float.NaN, dh.getDataset(6).getDouble(1), 10.); if (dt == Dataset.FLOAT64) assertEquals("The file does not contain NANs", Double.NaN, dh.getDataset(6).getDouble(1), 10.); assertEquals("The file does not contain data as well", 0.1, dh.getDataset(0).getDouble(1), 1.); } catch (ScanFileHolderException e) { fail("Couldn't load the file"); } } @Test public void testSRSLoaderLoop() { boolean success = false; try { String testfile1 = "testfiles/gda/analysis/io/SRSLoaderTest/optics_april20110402.dat"; // Dodgy old spec file, but now SRSLoader loads it! (And does not loop forever) DataHolder dh = new SRSLoader(testfile1).loadFile(); success = dh.size() != 0; } catch (Exception expected) { // do nothing } if (!success) fail("Test file optics_april20110402.dat should be parsed!"); } @Test public void testExtendedSRSLoaderLoop() { boolean success = false; try { String testfile1 = "testfiles/gda/analysis/io/SRSLoaderTest/optics_april20110402.dat"; // Dodgy old spec file, but now SRSLoader loads it! (And does not loop forever) DataHolder dh = new ExtendedSRSLoader(testfile1).loadFile(); success = dh.size() != 0; } catch (Exception expected) { } if (!success) fail("Test file optics_april20110402.dat should be parsed!"); } @Test public void testLoaderFactory() throws Exception { // clear state left over from any previous tests LoaderFactory.clear(); IDataHolder dh = LoaderFactory.getData("testfiles/gda/analysis/io/SRSLoaderTest/96356.dat", null); if (dh == null || dh.getNames().length < 1) throw new Exception(); assertEquals("There is not the correct number of axis in the file", 7, dh.size()); int dt = AbstractDataset.getDType(dh.getDataset(6)); if (dt == Dataset.FLOAT32) assertEquals("The file does not contain NANs", Float.NaN, dh.getDataset(6).getDouble(1), 10.); if (dt == Dataset.FLOAT64) assertEquals("The file does not contain NANs", Double.NaN, dh.getDataset(6).getDouble(1), 10.); assertEquals("The file does not contain data as well", 0.1, dh.getDataset(0).getDouble(1), 1.); } private DataHolder testStoringString(String testfile, boolean storeStrings) throws ScanFileHolderException { DataHolder dh; SRSLoader srsLoader = new SRSLoader(testfile); srsLoader.setStoreStringValues(storeStrings); dh = srsLoader.loadFile(); return dh; } private DataHolder testStoringStringNotValidImages(boolean storeStrings) throws ScanFileHolderException { return testStoringString("testfiles/gda/analysis/io/SRSLoaderTest/testStoringStringNotValidImages.dat", storeStrings); } private DataHolder testStoringStringValidImages(boolean storeStrings) throws ScanFileHolderException { return testStoringString("testfiles/gda/analysis/io/SRSLoaderTest/testStoringStringValidImages.dat", storeStrings); } @Test public void testStoringStringFalseNotValidImages() throws ScanFileHolderException { DataHolder dh = testStoringStringNotValidImages(false); ILazyDataset dataset = dh.getLazyDataset("filename"); assertNull(dataset); } @Test public void testStoringStringTrueNotValidImages() throws ScanFileHolderException { DataHolder dh = testStoringStringNotValidImages(true); IDataset dataset = (IDataset) dh.getLazyDataset("filename"); assertNotNull(dataset); assertEquals(3, dataset.getSize()); assertEquals(1, (dataset.getShape()).length); assertEquals(3, (dataset.getShape())[0]); assertEquals("testfiles/gda/analysis/io/SRSLoaderTest/NotValidImage3.tif", dataset.getObject(2)); } @Test public void testStoringStringFalseValidImages() throws ScanFileHolderException { DataHolder dh = testStoringStringValidImages(false); { ILazyDataset dataset = dh.getLazyDataset("filename"); assertNull(dataset); } ILazyDataset dataset_image = dh.getLazyDataset("filename_image"); assertNotNull(dataset_image); assertEquals(3, (dataset_image.getShape()).length); assertEquals(3, (dataset_image.getShape())[0]); { //take slice from first file IDataset slice = dataset_image.getSlice(new int[] { 0, 0, 0 }, new int[] { 1, 195, 1475 }, new int[] { 1, 1, 1 }); slice.squeeze(); int[] shape = slice.getShape(); assertNotNull(shape); } { //take slice from second file - which is of a different size. IDataset slice = dataset_image.getSlice(new int[] { 1, 0, 0 }, new int[] { 2, 195, 1024 }, new int[] { 1, 1, 1 }); slice.squeeze(); int[] shape = slice.getShape(); assertNotNull(shape); } } @Test public void testStoringStringTrueValidImages() throws ScanFileHolderException { DataHolder dh = testStoringStringValidImages(true); IDataset dataset = (IDataset) dh.getLazyDataset("filename"); assertNotNull(dataset); assertEquals(3, dataset.getSize()); assertEquals(1, (dataset.getShape()).length); assertEquals(3, (dataset.getShape())[0]); assertEquals("testfiles/gda/analysis/io/SRSLoaderTest/simple_data.dat", dataset.getObject(2)); } @Test public void testWhiteSpaceBeforeNumberss() throws ScanFileHolderException { DataHolder dh; String testfile1 = "testfiles/gda/analysis/io/SRSLoaderTest/16446.dat"; dh = new SRSLoader(testfile1).loadFile(); assertEquals(4, dh.size()); assertEquals("DCMFPitch", dh.getNames()[0]); } /** * This method tests for B16 data's new-fangled metadata */ @Test public void testB16data() { try { DataHolder dh; String testfile1 = "testfiles/gda/analysis/io/SRSLoaderTest/34146.dat"; dh = new SRSLoader(testfile1).loadFile(); // now the file is loaded, check to make sure that it holds the right data assertEquals("There is not the correct number of axis in the file", 2, dh.size()); assertEquals("The file does not contain correct data", 2.0, dh.getDataset(0).getDouble(1), 1e-5); IMetadata mdo = dh.getMetadata(); try { Collection<String> mdNames = mdo.getMetaNames(); assertEquals("Loaded incorrect number of metadata items", 11, mdNames.size()); assertTrue("Metadata item missing", mdo.getMetaValue("cmd") != null); assertTrue("Metadata item missing", mdo.getMetaValue("SRSTIM") != null); assertEquals("SRS metadata item wrong", "95827", mdo.getMetaValue("SRSTIM")); } catch (Exception e) { // TODO Auto-generated catch block Assert.fail("Could not find metadata"); } } catch (ScanFileHolderException e) { fail("Couldn't load the file"); } } @Test public void testSerializability() throws Exception { DataHolder dh = new SRSLoader("testfiles/gda/analysis/io/SRSLoaderTest/96356.dat").loadFile(); Dataset data = dh.getDataset(0); SerializationUtils.serialize(data.getMetadata()); } @Test public void testSpacesInNames() throws Exception { DataHolder dh = new DataHolder(); String fileName = "quoted.dat"; Dataset data1 = DatasetFactory.createRange(20, Dataset.INT32); Dataset data2 = DatasetFactory.createLinearSpace(0, 576000, 20, Dataset.FLOAT64); try { dh.addDataset("col1", data1); dh.addDataset("testing data", data2); new SRSLoader(testScratchDirectoryName + fileName).saveFile(dh); } catch (Exception e) { throw new ScanFileHolderException("Problem testing SRSLoader class", e); } dh = new SRSLoader(testScratchDirectoryName + fileName).loadFile(); assertEquals(2, dh.size()); assertEquals("col1", dh.getName(0)); assertEquals("testing data", dh.getName(1)); } }