public static void time(String id) throws IOException, FormatException { System.out.print("Timing " + new File(id).getName() + ": "); long t1 = System.currentTimeMillis(); boolean result = reader.isThisType(id); long t2 = System.currentTimeMillis(); System.out.print((t2 - t1) + " ms to check type (" + result + "); "); long t3 = System.currentTimeMillis(); reader.setId(id); long t4 = System.currentTimeMillis(); System.out.println((t4 - t3) + " ms to initialize"); reader.close(); }
public static void main(String[] args) throws FormatException, IOException { if (args.length < 1) { LOGGER.info("Usage: java.loci.tests.SingularityTest /path/to/input-file"); System.exit(1); } LOGGER.info("Testing {}", args[0]); ImageReader reader = new ImageReader(); boolean isSingleFile = reader.isSingleFile(args[0]); reader.setId(args[0]); String[] usedFiles = reader.getUsedFiles(); if (isSingleFile && usedFiles.length > 1) { LOGGER.info(" Used files list contains more than one file, " + "but isSingleFile(String) returned true."); LOGGER.info("FAILURE"); } else if (!isSingleFile && usedFiles.length == 1) { LOGGER.info(" Used files list only contains one file, " + "but isSingleFile(String) returned false."); LOGGER.info("FAILURE"); } else LOGGER.info("SUCCESS"); }
/** * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */ @Override public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException { if (Location.getMappedFile(entryName) == null) { initFile(currentId); } reader.setId(entryName); return reader.openBytes(no, buf, x, y, w, h); }
/** * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */ @Override public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException { if (Location.getMappedFile(entryName) == null) { initFile(currentId); } reader.setId(entryName); return reader.openBytes(no, buf, x, y, w, h); }
private IFormatReader getReader(int index) throws FormatException, IOException { ImageReader reader = new ImageReader(); reader.setFlattenedResolutions(false); reader.setId(files[index].getAbsolutePath()); return reader; }
@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); }
public static void main(String[] args) { ImageReader reader = new ImageReader(); reader.setMetadataStore( new OMEXMLMetadataImpl()); try { reader.setId( new OpenDialog("pick file").getPath() ); for (int i = 0; i < reader.getSeriesCount(); i++) { reader.setSeries( i ); Arrays.asList( reader.getSeriesUsedFiles() ).forEach( s -> System.out.println( s ) ); System.out.println( ((OMEXMLMetadataImpl)reader.getMetadataStore()).dumpXML()); } reader.close(); } catch ( FormatException | IOException e ) { // TODO Auto-generated catch block e.printStackTrace(); } }
@Test public void testLosslessPixels() throws Exception { int failureCount = 0; for (int i=0; i<files.size(); i++) { ImageReader reader = new ImageReader(); reader.setId(files.get(i)); byte[] plane = reader.openBytes(0); if (plane[0] != pixels[i][0]) { LOGGER.debug("FAILED on {}", pixels[i][0]); failureCount++; } reader.close(); } assertEquals(failureCount, 0); }
reader.setId(entryName);
private void parseROIs(MetadataStore store) throws FormatException, IOException { String roiID = MetadataTools.createLSID("ROI", 0, 0); String maskID = MetadataTools.createLSID("Shape", 0, 0); store.setROIID(roiID, 0); store.setMaskID(maskID, 0, 0); String positionData = DataTools.readFile(roiDrawFile); String[] coordinates = positionData.split("[ ,]"); double x1 = Double.parseDouble(coordinates[1]); double y1 = Double.parseDouble(coordinates[2]); double x2 = Double.parseDouble(coordinates[3]); double y2 = Double.parseDouble(coordinates[5]); store.setMaskX(x1, 0, 0); store.setMaskY(y1, 0, 0); store.setMaskWidth(x2 - x1, 0, 0); store.setMaskHeight(y2 - y1, 0, 0); store.setImageROIRef(roiID, 0, 0); ImageReader roiReader = new ImageReader(); roiReader.setId(roiFile); byte[] roiPixels = roiReader.openBytes(0); roiReader.close(); BitWriter bits = new BitWriter(roiPixels.length / 8); for (int i=0; i<roiPixels.length; i++) { bits.write(roiPixels[i] == 0 ? 0 : 1, 1); } store.setMaskBinData(bits.toByteArray(), 0, 0); }
@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(); }
private void parseROIs(MetadataStore store) throws FormatException, IOException { String roiID = MetadataTools.createLSID("ROI", 0, 0); String maskID = MetadataTools.createLSID("Shape", 0, 0); store.setROIID(roiID, 0); store.setMaskID(maskID, 0, 0); String positionData = DataTools.readFile(roiDrawFile); String[] coordinates = positionData.split("[ ,]"); double x1 = Double.parseDouble(coordinates[1]); double y1 = Double.parseDouble(coordinates[2]); double x2 = Double.parseDouble(coordinates[3]); double y2 = Double.parseDouble(coordinates[5]); store.setMaskX(x1, 0, 0); store.setMaskY(y1, 0, 0); store.setMaskWidth(x2 - x1, 0, 0); store.setMaskHeight(y2 - y1, 0, 0); store.setImageROIRef(roiID, 0, 0); ImageReader roiReader = new ImageReader(); roiReader.setId(roiFile); byte[] roiPixels = roiReader.openBytes(0); roiReader.close(); BitWriter bits = new BitWriter(roiPixels.length / 8); for (int i=0; i<roiPixels.length; i++) { bits.write(roiPixels[i] == 0 ? 0 : 1, 1); } store.setMaskBinData(bits.toByteArray(), 0, 0); }
@Test public void testOptionsExplicit() throws Exception { DynamicMetadataOptions opt = new DynamicMetadataOptions(); opt.set(KEY, VALUE); ImageReader reader = new ImageReader(); reader.setMetadataOptions(opt); reader.setId("test.fake"); MetadataOptions rOpt = reader.getReader().getMetadataOptions(); assertTrue(rOpt instanceof DynamicMetadataOptions); String v = ((DynamicMetadataOptions) rOpt).get(KEY); assertNotNull(v); assertEquals(v, VALUE); 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(); }
public static void main(String[] args) throws Exception { OriginalMetadataRequestI omr = new OriginalMetadataRequestI(null); ImageReader reader = new ImageReader(); for (String file : args) { reader.setId(file); final Hashtable<String, Object> bfglobal = reader.getGlobalMetadata(); final Hashtable<String, Object> bfseries = reader.getSeriesMetadata(); Map<String, RType> global = omr.wrap(bfglobal); Map<String, RType> series = omr.wrap(bfseries); printMap("[GlobalMetadata]", global); printMap("[SeriesMetadata]", series); } reader.close(); }
@Test public void testImageWidthWrittenCorrectly() throws Exception { OMETiffWriter writer = new OMETiffWriter(); writer.setMetadataRetrieve(ms); writer.setId(target.getAbsolutePath()); writer.saveBytes(0, buf, 0, 0, buf.length, 1); writer.close(); ImageReader reader = new ImageReader(); reader.setId(target.getAbsolutePath()); assertEquals(reader.getFormat(), "OME-TIFF"); reader.close(); } }
@Override protected void typedParse(final RandomAccessInputStream stream, final Metadata meta, final SCIFIOConfig config) throws IOException, FormatException { try { final ImageReader reader = createImageReader(this); meta.setReader(reader); MetadataStore store = new OMEXMLMetadataImpl(); reader.setMetadataStore(store); reader.setOriginalMetadataPopulated(config.parserIsSaveOriginalMetadata()); reader.setMetadataFiltered(config.parserIsFiltered()); reader.setGroupFiles(config.groupableIsGroupFiles()); reader.setId(stream.getFileName()); meta.setTable(new DefaultMetaTable(reader.getGlobalMetadata())); } catch (final loci.formats.FormatException e) { throw new FormatException(e); } } }
reader.setId(tmp.getAbsolutePath());
reader.setId(file); byte[] plane = reader.openBytes(0); for (int q=0; q<plane.length; q++) {