@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 public void testDefaultValues() throws Exception { reader.setId("default.fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(reader.getSizeX(), FakeReader.DEFAULT_SIZE_X); assertEquals(reader.getSizeY(), FakeReader.DEFAULT_SIZE_Y); assertEquals(reader.getSizeZ(), FakeReader.DEFAULT_SIZE_Z); assertEquals(reader.getSizeC(), FakeReader.DEFAULT_SIZE_C); assertEquals(reader.getSizeT(), FakeReader.DEFAULT_SIZE_T); assertEquals(reader.getPixelType(), FakeReader.DEFAULT_PIXEL_TYPE); assertEquals(reader.getRGBChannelCount(), FakeReader.DEFAULT_RGB_CHANNEL_COUNT); assertEquals(reader.getDimensionOrder(), FakeReader.DEFAULT_DIMENSION_ORDER); assertEquals(m.getImageAcquisitionDate(0), null); assertEquals(m.getPixelsPhysicalSizeX(0), null); assertEquals(m.getPixelsPhysicalSizeY(0), null); assertEquals(m.getPixelsPhysicalSizeZ(0), null); assertEquals(m.getROICount(), 0); assertEquals(m.getExperimentCount(), 0); }
@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(); }
@Test public void testPlaneMetadata() throws Exception { File fakeIni = mkIni("foo.fake.ini", "sizeC=2", "[series_0]", "ExposureTime_0=100.0", "ExposureTimeUnit_0=ms", "ExposureTime_1=50.0", "ExposureTimeUnit_1=ns", "PositionX_0=10.0", "PositionY_0=20.0", "PositionZ_0=30.0", "PositionXUnit_0=mm", "PositionYUnit_0=mm", "PositionZUnit_0=mm", "PositionX_1=5.0", "PositionY_1=10.0", "PositionZ_1=15.0", "PositionXUnit_1=nm", "PositionYUnit_1=nm", "PositionZUnit_1=nm"); reader.setId(fakeIni.getAbsolutePath()); m = service.asRetrieve(reader.getMetadataStore()); assertEquals(m.getPixelsSizeC(0).getNumberValue(), 2); assertEquals(m.getPlaneExposureTime(0, 0), new Time(100.0, UNITS.MILLISECOND)); assertEquals(m.getPlaneExposureTime(0, 1), new Time(50.0, UNITS.NANOSECOND)); assertEquals(m.getPlanePositionX(0, 0), new Length(10.0, UNITS.MM)); assertEquals(m.getPlanePositionY(0, 0), new Length(20.0, UNITS.MM)); assertEquals(m.getPlanePositionZ(0, 0), new Length(30.0, UNITS.MM)); assertEquals(m.getPlanePositionX(0, 1), new Length(5.0, UNITS.NM)); assertEquals(m.getPlanePositionY(0, 1), new Length(10.0, UNITS.NM)); assertEquals(m.getPlanePositionZ(0, 1), new Length(15.0, UNITS.NM)); }