/** * 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); }
/** * @return true if reader being used is LeicaReader */ public boolean isLeicaReader() { return iReader.getReader() instanceof LeicaReader; }
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(); } }
public void getFormat(String id, String[] format) throws FormatException, IOException { try (ImageReader reader = new ImageReader()) { format[0] = reader.getFormat(id); } }
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"); }
@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(); }
reader = new ImageReader(); reader.setMetadataStore( new OMEXMLMetadataImpl()); if (reader.getCurrentFile() == null || !(Arrays.asList( reader.getUsedFiles()).contains( file.getAbsolutePath()))) reader.setId( file.getAbsolutePath() ); final File currentFile = new File( reader.getCurrentFile() ); for (int i = 0 ; i < reader.getSeriesCount(); i++) reader.setSeries( i ); MetadataRetrieve meta = (MetadataRetrieve)reader.getMetadataStore(); if (!reader.isOrderCertain() && reader.getSizeZ() <= 1 && reader.getSizeT() > 1 ){ IOFunctions.println( new Date(System.currentTimeMillis()) + ": WARNING: Uncertain XZY/XZT order in File " + file.getAbsolutePath() + ", Image " + i); int dimX = reader.getSizeX(); int dimY = reader.getSizeY(); int dimZ = (!reader.isOrderCertain() && reader.getSizeZ() <= 1 && reader.getSizeT() > 1 ) ? reader.getSizeT() : reader.getSizeZ(); FinalDimensions finalDimensions = new FinalDimensions( dimX, dimY, dimZ ); for (int j = 0; j < reader.getSizeC(); j++) reader.close();
@Override protected void initFile(String id) throws FormatException, IOException { super.initFile(id); reader = new ImageReader(); reader.setMetadataOptions(getMetadataOptions()); reader.setMetadataFiltered(isMetadataFiltered()); reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated()); reader.setNormalized(isNormalized()); reader.setMetadataStore(getMetadataStore()); reader.setId(entryName); metadataStore = reader.getMetadataStore(); core = new ArrayList<CoreMetadata>(reader.getCoreMetadataList()); metadata = reader.getGlobalMetadata();
ImageReader reader = new ImageReader(); reader.setId(tmp.getAbsolutePath()); assertEquals(reader.getSeriesCount(), seriesCount); reader.setSeries(s); assertEquals(reader.getSizeC(), rgbChannels); assertTrue(reader.getImageCount() == rgbChannels || reader.isRGB()); byte[] readPlane = reader.openBytes(0); Plane newPlane = new Plane(readPlane, reader.isLittleEndian(), !reader.isInterleaved(), reader.getRGBChannelCount(), FormatTools.getPixelTypeString(reader.getPixelType())); reader.close();
reader = new ImageReader(); reader.setMetadataStore( new OMEXMLMetadataImpl()); if ( reader.getCurrentFile() == null || !Arrays.asList( reader.getUsedFiles() ).contains( file.getAbsolutePath() )) reader.setId( file.getAbsolutePath() ); final File currentFile = new File( reader.getCurrentFile() ); if (reader.getRGBChannelCount() > 1) usedFiles.addAll( Arrays.asList( reader.getUsedFiles() )); if (reader.getUsedFiles().length > 1) state.setGroupedFormat( true ); for (int i = 0; i < reader.getSeriesCount(); i ++) reader.setSeries( i ); for (String usedFileI : reader.getSeriesUsedFiles()) state.getGroupUsageMap().put( usedFileI , new ValuePair< File, Integer >( currentFile, i )); TileOrAngleRefiner refiner = tileOrAngleRefiners.get( ((ImageReader)reader).getReader().getClass() ); if (refiner != null) refiner.refineTileOrAngleInfo( reader, predictTilesAndAngles );
ImageReader.getDefaultReaderClasses(); Class<? extends IFormatReader>[] c = defaultClasses.getClasses(); if (on) enabledClasses.addClass(c[i]); ImageReader reader = new ImageReader(enabledClasses); MetadataOptions options = reader.getMetadataOptions(); if (options instanceof DynamicMetadataOptions) { ((DynamicMetadataOptions) options).setBoolean( ((DynamicMetadataOptions) options).setBoolean( CellSensReader.FAIL_ON_MISSING_KEY, isCellsensFailOnMissing()); reader.setMetadataOptions(options); boolean sdtIntensity = LociPrefs.isSDTIntensity(); boolean tiffImageIO = LociPrefs.isTiffImageIO(); IFormatReader[] r = reader.getReaders(); for (int i=0; i<r.length; i++) { if (r[i] instanceof ND2Reader) {
@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(); }
pixelsFile = new Location(parent, pixelsFile).getAbsolutePath(); ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses(); Class<? extends IFormatReader>[] classArray = classes.getClasses(); ClassList<IFormatReader> newClasses = helperReader = new ImageReader(newClasses); helperReader.setId(pixelsFile); core = new ArrayList<CoreMetadata>(helperReader.getCoreMetadataList());
ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses(); Class<? extends IFormatReader>[] classArray = classes.getClasses(); ClassList<IFormatReader> newClasses = helper = new ImageReader(newClasses); helper.setMetadataOptions( new DefaultMetadataOptions(MetadataLevel.MINIMUM));
/** Constructs a new pattern reader. */ public FilePatternReader() { super("File pattern", new String[] {"pattern"}); ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses(); Class<? extends IFormatReader>[] classArray = classes.getClasses(); ClassList<IFormatReader> newClasses = new ClassList<IFormatReader>(IFormatReader.class); for (Class<? extends IFormatReader> c : classArray) { if (!c.equals(FilePatternReader.class)) { newClasses.addClass(c); } } helper = new FileStitcher(new ImageReader(newClasses)); suffixSufficient = true; }
@Override protected void doCheck() { final List<String> formatNames = new ArrayList<String>(); for (final IFormatReader formatReader : new ImageReader().getReaders()) { String name = formatReader.getClass().getSimpleName(); if (name.endsWith("Reader")) { name = name.substring(0, name.length() - 6); if ("Fake".equals(name)) { continue; } formatNames.add(name); if (formatReader.hasCompanionFiles()) { formatNames.add("Companion/" + name); } } } ensureEnum.ensure(Format.class, formatNames); }
@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(); } }