/** Constructs a cache source that draws from the given file. */ public CacheSource(String id) throws CacheException { this(new FileStitcher()); try { reader.setId(id); } catch (FormatException exc) { throw new CacheException(exc); } catch (IOException exc) { throw new CacheException(exc); } }
/** Constructs a cache source that draws from the given file. */ public CacheSource(String id) throws CacheException { this(new FileStitcher()); try { reader.setId(id); } catch (FormatException exc) { throw new CacheException(exc); } catch (IOException exc) { throw new CacheException(exc); } }
if (flattened) { ir = new ImageReader(); ir = new BufferedImageReader(new FileStitcher(new Memoizer(ir, Memoizer.DEFAULT_MINIMUM_ELAPSED, new File("")))); ir.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.NO_OVERLAYS)); ir = new BufferedImageReader(new FileStitcher()); ir.setFlattenedResolutions(false);
/** 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; }
/** 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; }
IFormatReader check = new FileStitcher(); try { check.setId(newFile);
final IFormatReader reader = filesArePatterns ? new FileStitcher( true ) : new ImageReader(); if (filesArePatterns) ( (FileStitcher) reader ).setCanChangePattern( false );
@Test public void testUnderlyingReaders() throws IOException, FormatException { FakeReader reader = new FakeReader(); FileStitcher fs = new FileStitcher(reader); assertNotNull(fs.getUnderlyingReaders()); fs.setId("test_z<0-2>.fake"); assertNotNull(fs.getUnderlyingReaders()); fs.close(); }
public LociFunctions() { boolean groupFiles = true; try { ImporterOptions options = new ImporterOptions(); groupFiles = options.isGroupFiles(); } catch (IOException exc) { IJ.handleException(exc); } if (groupFiles) { r = new ImageProcessorReader(new ChannelSeparator( new FileStitcher(LociPrefs.makeImageReader(), true))); } else { r = new ImageProcessorReader(new ChannelSeparator( LociPrefs.makeImageReader())); } try { ServiceFactory factory = new ServiceFactory(); OMEXMLService service = factory.getInstance(OMEXMLService.class); r.setMetadataStore(service.createOMEXMLMetadata()); } catch (DependencyException de) { } catch (ServiceException se) { } }
public LociFunctions() { boolean groupFiles = true; try { ImporterOptions options = new ImporterOptions(); groupFiles = options.isGroupFiles(); } catch (IOException exc) { IJ.handleException(exc); } if (groupFiles) { r = new ImageProcessorReader(new ChannelSeparator( new FileStitcher(LociPrefs.makeImageReader(), true))); } else { r = new ImageProcessorReader(new ChannelSeparator( LociPrefs.makeImageReader())); } try { ServiceFactory factory = new ServiceFactory(); OMEXMLService service = factory.getInstance(OMEXMLService.class); r.setMetadataStore(service.createOMEXMLMetadata()); } catch (DependencyException de) { } catch (ServiceException se) { } }
@Test(dataProvider = "levels") public void testOptionsImplicit(MetadataLevel level) throws IOException, FormatException { FileStitcher fs = new FileStitcher(); fs.getMetadataOptions().setMetadataLevel(level); fs.setId("test_z<0-2>.fake"); for (IFormatReader r: fs.getUnderlyingReaders()) { assertEquals(r.getMetadataOptions().getMetadataLevel(), level); } fs.close(); }
private static void check(String pattern, String[] filenames, Integer[] dims) throws IOException, FormatException { FileStitcher fs = new FileStitcher(); fs.setId(pattern); assertEquals(fs.getFilePattern().getPattern(), pattern); assertEquals(fs.getImageCount(), SIZE_Z * SIZE_T * SIZE_C); assertEquals(fs.getSizeX(), SIZE_X); assertEquals(fs.getSizeY(), SIZE_Y); assertEquals(fs.getSizeZ(), SIZE_Z); assertEquals(fs.getSizeT(), SIZE_T); assertEquals(fs.getSizeC(), SIZE_C); assertEquals(fs.getPixelType(), PIXEL_TYPE); assertEqualsNoOrder(mkBasenames(fs.getUsedFiles()), filenames); checkPlanes(fs, dims); fs.close(); }
if (zGrouped) final FileStitcher fs = new FileStitcher(true); fs.setCanChangePattern( false ); reader = new Memoizer( fs , Memoizer.DEFAULT_MINIMUM_ELAPSED, tempDir);
if (zGrouped) final FileStitcher fs = new FileStitcher(true); fs.setCanChangePattern( false ); reader = new Memoizer( fs , Memoizer.DEFAULT_MINIMUM_ELAPSED, tempDir);
@DataProvider(name = "wrappers") public Object[][] createWrappers() { Location.mapId(TEST_FILE, TEST_FILE); Object[][] wrappers = new Object[][] { {new ChannelFiller()}, {new ChannelMerger()}, {new ChannelSeparator()}, {new DimensionSwapper()}, {new FileStitcher()}, {new ImageReader()}, {new MinMaxCalculator()}, {new Memoizer()} }; for (int i=0; i<wrappers.length; i++) { IFormatReader reader = (IFormatReader) wrappers[i][0]; try { reader.setId(TEST_FILE); } catch (FormatException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } return wrappers; }
if (zGrouped) final FileStitcher fs = new FileStitcher(true); fs.setCanChangePattern( false ); reader = new Memoizer( fs , Memoizer.DEFAULT_MINIMUM_ELAPSED, tempDir);
reader = new FileStitcher(reader, true); Location f = new Location(id); String pat = null;
@Test public void testOptionsExplicit() throws IOException, FormatException { DynamicMetadataOptions opt = new DynamicMetadataOptions(); opt.set(KEY, VALUE); FileStitcher fs = new FileStitcher(); fs.setMetadataOptions(opt); fs.setId("test_z<0-2>.fake"); checkKV(fs.getUnderlyingReaders(), KEY, VALUE); DynamicMetadataOptions newOpt = new DynamicMetadataOptions(); String newValue = VALUE + "_"; newOpt.set(KEY, newValue); fs.setMetadataOptions(newOpt); checkKV(fs.getUnderlyingReaders(), KEY, newValue); fs.close(); }
r = fileStitcher = new FileStitcher(baseReader);
r = fileStitcher = new FileStitcher(baseReader);