//
// MetadataConfigurableTest.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.utests;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.fail;
import java.io.IOException;
import java.security.MessageDigest;
import java.util.Arrays;
import loci.common.DataTools;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.ImageReader;
import loci.formats.MetadataTools;
import loci.formats.in.DefaultMetadataOptions;
import loci.formats.in.MetadataLevel;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/test/loci/formats/utests/MetadataConfigurableTest.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/test/loci/formats/utests/MetadataConfigurableTest.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class MetadataConfigurableTest {
private static final String FILENAME_PROPERTY = "testng.filename";
private ImageReader pixelsOnly;
private ImageReader all;
private ImageReader noOverlays;
private String id;
@BeforeClass
public void setUp() {
pixelsOnly = new ImageReader();
pixelsOnly.setMetadataOptions(
new DefaultMetadataOptions(MetadataLevel.MINIMUM));
all = new ImageReader();
all.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));
noOverlays = new ImageReader();
noOverlays.setMetadataOptions(
new DefaultMetadataOptions(MetadataLevel.NO_OVERLAYS));
id = System.getProperty(FILENAME_PROPERTY);
}
@Test
public void testSetId() throws FormatException, IOException {
long t0 = System.currentTimeMillis();
pixelsOnly.setId(id);
assertEquals(MetadataLevel.MINIMUM,
pixelsOnly.getMetadataOptions().getMetadataLevel());
long t1 = System.currentTimeMillis();
all.setId(id);
assertEquals(MetadataLevel.ALL,
all.getMetadataOptions().getMetadataLevel());
assertFalse(0 ==
all.getSeriesMetadata().size() + all.getGlobalMetadata().size());
long t2 = System.currentTimeMillis();
System.err.println(String.format("Pixels only: %d -- All: %d",
t1 - t0, t2 - t1));
IMetadata metadata = null;
try {
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
metadata = service.createOMEXMLMetadata();
noOverlays.setMetadataStore(metadata);
} catch (Exception e) {
throw new FormatException("Cannot initialize OMEXML metadata store");
}
noOverlays.setId(id);
assertEquals(MetadataLevel.NO_OVERLAYS,
noOverlays.getMetadataOptions().getMetadataLevel());
assertEquals(metadata.getROICount(), 0);
}
@Test(dependsOnMethods={"testSetId"})
public void testDimensions() {
assertEquals(all.getSeriesCount(), pixelsOnly.getSeriesCount());
assertEquals(all.getSeriesCount(), noOverlays.getSeriesCount());
for (int i=0; i<pixelsOnly.getSeriesCount(); i++) {
all.setSeries(i);
pixelsOnly.setSeries(i);
noOverlays.setSeries(i);
assertEquals(all.getSizeX(), pixelsOnly.getSizeX());
assertEquals(all.getSizeY(), pixelsOnly.getSizeY());
assertEquals(all.getSizeZ(), pixelsOnly.getSizeZ());
assertEquals(all.getSizeC(), pixelsOnly.getSizeC());
assertEquals(all.getSizeT(), pixelsOnly.getSizeT());
assertEquals(all.getPixelType(), pixelsOnly.getPixelType());
assertEquals(all.isLittleEndian(), pixelsOnly.isLittleEndian());
assertEquals(all.isIndexed(), pixelsOnly.isIndexed());
assertEquals(all.getSizeX(), noOverlays.getSizeX());
assertEquals(all.getSizeY(), noOverlays.getSizeY());
assertEquals(all.getSizeZ(), noOverlays.getSizeZ());
assertEquals(all.getSizeC(), noOverlays.getSizeC());
assertEquals(all.getSizeT(), noOverlays.getSizeT());
assertEquals(all.getPixelType(), noOverlays.getPixelType());
assertEquals(all.isLittleEndian(), noOverlays.isLittleEndian());
assertEquals(all.isIndexed(), noOverlays.isIndexed());
}
}
@Test(dependsOnMethods={"testSetId"})
public void testPlaneData() throws FormatException, IOException {
for (int i=0; i<pixelsOnly.getSeriesCount(); i++) {
pixelsOnly.setSeries(i);
all.setSeries(i);
noOverlays.setSeries(i);
assertEquals(all.getImageCount(), pixelsOnly.getImageCount());
assertEquals(all.getImageCount(), noOverlays.getImageCount());
for (int j=0; j<pixelsOnly.getImageCount(); j++) {
byte[] pixelsOnlyPlane = pixelsOnly.openBytes(j);
String pixelsOnlySHA1 = sha1(pixelsOnlyPlane);
byte[] allPlane = all.openBytes(j);
String allSHA1 = sha1(allPlane);
byte[] noOverlaysPlane = noOverlays.openBytes(j);
String noOverlaysSHA1 = sha1(noOverlaysPlane);
if (!pixelsOnlySHA1.equals(allSHA1)) {
fail(String.format("MISMATCH: Series:%d Image:%d PixelsOnly%s All:%s",
i, j, pixelsOnlySHA1, allSHA1));
}
if (!noOverlaysSHA1.equals(allSHA1)) {
fail(String.format("MISMATCH: Series:%d Image:%d PixelsOnly%s All:%s",
i, j, noOverlaysSHA1, allSHA1));
}
}
}
}
@Test(dependsOnMethods={"testSetId"})
public void testUsedFiles() throws FormatException, IOException {
for (int i=0; i<pixelsOnly.getSeriesCount(); i++) {
pixelsOnly.setSeries(i);
all.setSeries(i);
noOverlays.setSeries(i);
String[] pixelsOnlyFiles = pixelsOnly.getSeriesUsedFiles();
String[] allFiles = all.getSeriesUsedFiles();
String[] noOverlaysFiles = noOverlays.getSeriesUsedFiles();
assertEquals(allFiles.length, pixelsOnlyFiles.length);
assertEquals(allFiles.length, noOverlaysFiles.length);
Arrays.sort(allFiles);
Arrays.sort(pixelsOnlyFiles);
Arrays.sort(noOverlaysFiles);
for (int j=0; j<pixelsOnlyFiles.length; j++) {
assertEquals(allFiles[j], pixelsOnlyFiles[j]);
assertEquals(allFiles[j], noOverlaysFiles[j]);
}
}
}
// -- Utility methods --
private String sha1(byte[] buf) {
try {
MessageDigest md = MessageDigest.getInstance("SHA-1");
return DataTools.bytesToHex(md.digest(buf));
}
catch (Exception e) {
throw new RuntimeException(e);
}
}
}