/** * Constructs a FileStitcher around a new image reader. * @param patternIds Whether string ids given should be treated as file * patterns rather than single file paths. */ public FileStitcher(boolean patternIds) { this(new ImageReader(), patternIds); }
/** * Constructs a FileStitcher around a new image reader. * @param patternIds Whether string ids given should be treated as file * patterns rather than single file paths. */ public FileStitcher(boolean patternIds) { this(new ImageReader(), patternIds); }
public void getFormat(String id, String[] format) throws FormatException, IOException { try (ImageReader reader = new ImageReader()) { format[0] = reader.getFormat(id); } }
public void getFormat(String id, String[] format) throws FormatException, IOException { try (ImageReader reader = new ImageReader()) { format[0] = reader.getFormat(id); } }
/** * Set the ClassList object to use when constructing any helper readers. */ public void setReaderClassList(ClassList<IFormatReader> classList) { this.classList = classList; reader = DimensionSwapper.makeDimensionSwapper(new ImageReader(classList)); }
/** * Set the ClassList object to use when constructing any helper readers. */ public void setReaderClassList(ClassList<IFormatReader> classList) { this.classList = classList; reader = DimensionSwapper.makeDimensionSwapper(new ImageReader(classList)); }
public static void main(String[] args) throws IOException { System.out.println("Generating list of Bio-Formats supported suffixes..."); try (IFormatReader reader = new ImageReader()) { String[] suffixes = reader.getSuffixes(); PrintWriter fo = null; fo = new PrintWriter(new File("BioFormatsSuffixes.txt"), Constants.ENCODING); for (String s : suffixes) fo.println("*." + s); fo.close(); System.out.println(suffixes.length + " suffixes discovered."); } }
/** Creates a new Bio-Formats {@link ImageReader}. */ public ImageReader createImageReader() { // Check for updated reader classes cacheReaderClasses(); return new ImageReader(readerClasses); }
public static void main(String[] args) throws IOException { System.out.println("Generating list of Bio-Formats supported suffixes..."); try (IFormatReader reader = new ImageReader()) { String[] suffixes = reader.getSuffixes(); PrintWriter fo = null; fo = new PrintWriter(new File("BioFormatsSuffixes.txt"), Constants.ENCODING); for (String s : suffixes) fo.println("*." + s); fo.close(); System.out.println(suffixes.length + " suffixes discovered."); } }
@Parameters({"id"}) @BeforeClass public void init(String id) throws FormatException, IOException { this.id = id; reader = new ImageReader(); reader.setFlattenedResolutions(false); reader.setId(id); }
private IFormatReader getReader(int index) throws FormatException, IOException { ImageReader reader = new ImageReader(); reader.setFlattenedResolutions(false); reader.setId(files[index].getAbsolutePath()); return reader; }
@Parameters({"id"}) @BeforeClass public void parse(String id) throws Exception { ServiceFactory factory = new ServiceFactory(); service = factory.getInstance(OMEXMLService.class); metadata = service.createOMEXMLMetadata(); reader = new ImageReader(); reader.setMetadataStore(metadata); reader.setId(id); }
@Test public void testSetId() throws Exception { reader = new MinMaxCalculator(new ChannelSeparator( new ChannelFiller(new ImageReader()))); metadata = new OMEXMLMetadataImpl(); reader.setMetadataStore(metadata); reader.setId(temporaryFile.getAbsolutePath()); }
@Test public void testSetIdWithNoLightSources() throws Exception { readerWithNoLightSources = new MinMaxCalculator(new ChannelSeparator( new ChannelFiller(new ImageReader()))); metadataWithNoLightSources = new OMEXMLMetadataImpl(); readerWithNoLightSources.setMetadataStore(metadataWithNoLightSources); readerWithNoLightSources.setId( temporaryFileWithNoLightSources.getAbsolutePath()); }
@Test public void testSetId() throws Exception { reader = new MinMaxCalculator(new ChannelSeparator( new ChannelFiller(new ImageReader()))); metadata = new OMEXMLMetadataImpl(); reader.setMetadataStore(metadata); reader.setId(temporaryFile.getAbsolutePath()); }
public void checkImage() throws FormatException, IOException { IFormatReader r = new ImageReader(); r.setId(outFile.getAbsolutePath()); assertEquals(r.getSizeX(), 512); r.close(); }
@Test public void testSetId() throws Exception { reader = new MinMaxCalculator(new ChannelSeparator( new ChannelFiller(new ImageReader()))); metadata = new OMEXMLMetadataImpl(); reader.setMetadataStore(metadata); reader.setId(temporaryFile.getAbsolutePath()); }
@Test public void testEquivalentPixels8Bit() throws Exception { ImageReader reader = new ImageReader(); reader.setId(FILE_8); byte[] plane = reader.openBytes(0); assertEquals(plane.length, PIXELS_8.length); for (int q=0; q<plane.length; q++) { assertEquals(plane[q], PIXELS_8[q]); } reader.close(); }
@Test public void testEquivalentPixels16Bit() throws Exception { ImageReader reader = new ImageReader(); reader.setId(FILE_16); byte[] plane = reader.openBytes(0); assertEquals(plane.length, PIXELS_16.length); for (int q=0; q<plane.length; q++) { assertEquals(plane[q], PIXELS_16[q]); } reader.close(); }
@Test(dataProvider = "levels") public void testOptionsImplicit(MetadataLevel level) throws Exception { ImageReader reader = new ImageReader(); reader.getMetadataOptions().setMetadataLevel(level); reader.setId("test.fake"); MetadataLevel rLevel = reader.getReader().getMetadataOptions().getMetadataLevel(); assertEquals(rLevel, level); reader.close(); }