@Test(expectedExceptions={FormatException.class}) public void testPyramidInvalidScale() throws Exception { reader.setId("test&sizeX=10000&sizeY=10000&resolutions=4&resolutionScale=0.fake"); }
@Test(expectedExceptions={FormatException.class}) public void testPyramidInvalidResolutions() throws Exception { reader.setId("test&sizeX=10000&sizeY=10000&resolutions=0.fake"); }
@Override public void setId(String id) throws FormatException, IOException { super.setId(id); // insert a single sub-resolution core.add(new CoreMetadata(core.get(0))); core.get(0).resolutionCount++; core.get(1).sizeX /= 2; core.get(1).sizeY /= 2; } }
@Test(expectedExceptions={ RuntimeException.class }) public void testPhysicalSizeZIniBadParsing() throws Exception { mkIni("foo.fake.ini", "physicalSizeZ = 1 1"); reader.setId(wd.resolve("foo.fake").toString()); }
@Test public void testValuesFromFilename() throws Exception { int sizeX = FakeReader.DEFAULT_SIZE_X + 1; reader.setId(String.format("foo&sizeX=%d.fake", sizeX)); assertEquals(reader.getSizeX(), sizeX); }
@Test public void testReopenFile() throws Exception { reader.setId("foo.fake"); reader.reopenFile(); }
@Test public void testValuesFromIni() throws Exception { int sizeX = FakeReader.DEFAULT_SIZE_X + 1; mkIni("foo.fake.ini", String.format("sizeX = %d", sizeX)); reader.setId(wd.resolve("foo.fake").toString()); assertEquals(reader.getSizeX(), sizeX); }
@Test public void testPyramidNoResolutions() throws Exception { reader.setId("test&sizeX=10000&sizeY=10000&resolutions=1.fake"); assertEquals(reader.getSeriesCount(), 1); assertEquals(reader.getResolutionCount(), 1); }
@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 public void testExtraMetadata() throws Exception { File fakeIni = mkIni("foo.fake.ini", "[GlobalMetadata]", "foo=bar"); reader.setId(fakeIni.getAbsolutePath()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(reader.getGlobalMetadata().get("foo"), "bar"); }
@Test public void testNoCompanionFile() throws Exception { reader.setId(Files.createFile(wd.resolve("foo.fake")).toString()); assertEquals(1, reader.getUsedFiles().length); assertEquals(1, reader.getSeriesUsedFiles().length); assertEquals(1, reader.getUsedFiles(false).length); assertEquals(1, reader.getSeriesUsedFiles(false).length); assertEquals(0, reader.getUsedFiles(true).length); assertEquals(0, reader.getSeriesUsedFiles(true).length); }
@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 public void testTwoFields() throws Exception { Location twoFields = new FakeImage( mkSubd(wd, "2F.fake") ).generateScreen(1, 1, 1, 1, 2); reader.setId(twoFields.getAbsolutePath()); assertEquals(reader.getSeriesCount(), 2); }
@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 = "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 = "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 = "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 testTwoPlates() throws Exception { Location twoPlates = new FakeImage( mkSubd(wd, "2P.fake") ).generateScreen(2, 2, 2, 2, 4); reader.setId(twoPlates.getAbsolutePath()); OMEXMLMetadata metadata = reader.getOmeXmlMetadata(); int i = reader.getImageCount(); while (i >= 0) { assertEquals(metadata.getChannelCount(i--), reader.getSizeC()); } }