@AfterMethod public void tearDown() throws Exception { reader.close(); recursiveDeleteOnExit(idDir); }
@AfterMethod public void tearDown() throws Exception { reader.close(); deleteTemporaryDirectoryOnExit(new Location(wd.toFile())); }
@Test public void testWrappedReader() throws Exception { Memoizer memoizer = new Memoizer(reader, 0); File memoFile = memoizer.getMemoFile(id); assertFalse(memoFile.exists()); reader.setId(id); assertFalse(memoFile.exists()); reader.close(); checkMemo(memoizer, id); }
@Test(dataProvider = "annotations") public void testAnnotations(String key, String methodName) throws Exception { reader.setId("foo&series=5&" + key + "=10.fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); Method method = Class.forName("loci.formats.meta.MetadataRetrieve").getMethod(methodName); assertEquals(method.invoke(m), 50); for (int i = 0; i < 5; i++) { assertEquals(m.getImageAnnotationRefCount(0), 10); } reader.close(); testDefaultValues(); }
@Test(dataProvider = "annotations") public void testAnnotationsINI(String key, String methodName) throws Exception { mkIni("foo.fake.ini", "series = 5\n" + key + " = 10"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); Method method = Class.forName("loci.formats.meta.MetadataRetrieve").getMethod(methodName); assertEquals(method.invoke(m), 50); for (int i = 0; i < 5; i++) { assertEquals(m.getImageAnnotationRefCount(0), 10); } reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeXIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeX = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeX(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeZIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeZ = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeZ(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "acquisition dates") public void testAcquisitionDateIni(String value, Timestamp date) throws Exception { mkIni("foo.fake.ini", "acquisitionDate = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getImageAcquisitionDate(0), date); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeYIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeY = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeY(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "acquisition dates") public void testAcquisitionDateMultiSeries(String value, Timestamp date) throws Exception { reader.setId("foo&series=10&acquisitionDate=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); for (int i = 0; i < 10; i++) { assertEquals(m.getImageAcquisitionDate(i), date); } reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeZ(String value, Length length) throws Exception { reader.setId("foo&physicalSizeZ=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeZ(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeX(String value, Length length) throws Exception { reader.setId("foo&physicalSizeX=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeX(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeY(String value, Length length) throws Exception { reader.setId("foo&physicalSizeY=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeY(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "acquisition dates") public void testAcquisitionDate(String value, Timestamp date) throws Exception { reader.setId("foo&acquisitionDate=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getImageAcquisitionDate(0), date); reader.close(); testDefaultValues(); }
@Test public void testMicrobeamINI() throws Exception { mkIni("foo.fake.ini", "plates=1\nwithMicrobeam = true"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getExperimentCount(), 1); assertEquals(m.getMicrobeamManipulationCount(0), 1); reader.close(); mkIni("foo.fake.ini", "screens=2\nwithMicrobeam=true"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getExperimentCount(), 2); assertEquals(m.getMicrobeamManipulationCount(0), 1); assertEquals(m.getMicrobeamManipulationCount(1), 1); reader.close(); }
@Test public void testMicrobeam() throws Exception { reader.setId("foo&plates=1&withMicrobeam=true.fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getExperimentCount(), 1); assertEquals(m.getMicrobeamManipulationCount(0), 1); reader.close(); reader.setId("foo&screens=2&withMicrobeam=true.fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getExperimentCount(), 2); assertEquals(m.getMicrobeamManipulationCount(0), 1); assertEquals(m.getMicrobeamManipulationCount(1), 1); reader.close(); testDefaultValues(); }
@Test(dataProvider = "shapes") public void testShapesINI(String key, String type) throws Exception { mkIni("foo.fake.ini", "series = 5\n" + key + " = 10"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 5, 10, type, 0); reader.close(); mkIni("foo.fake.ini", "plateRows = 10\nplateCols = 10\n" + key + " = 5\nwithMicrobeam=true"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 100, 5, type, 1); reader.close(); mkIni("foo.fake.ini", "plateRows = 10\nplateCols = 10\n" + key + " = 5"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 100, 5, type, 0); reader.close(); mkIni("foo.fake.ini", "screens = 2\nplateRows = 10\nplateCols = 10\n" + key + " = 5"); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 200, 5, type, 0); reader.close(); testDefaultValues(); }
@Test(dataProvider = "shapes") public void testShapes(String key, String type) throws Exception { reader.setId("foo&series=5&" + key + "=10.fake"); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 5, 10, type, 0); reader.close(); reader.setId("foo&plateRows=10&plateCols=10&" + key + "=5&withMicrobeam=true.fake"); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 100, 5, type, 1); reader.close(); reader.setId("foo&plateRows=10&plateCols=10&" + key + "=5.fake"); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 100, 5, type, 0); reader.close(); reader.setId("foo&screens=2&plateRows=10&plateCols=10&" + key + "=5.fake"); m = service.asRetrieve(reader.getMetadataStore()); checkROIs(m, 200, 5, type, 0); reader.close(); testDefaultValues(); }