/** Converts the given reader into a ChannelSeparator, wrapping if needed. */ public static ChannelSeparator makeChannelSeparator(IFormatReader r) { if (r instanceof ChannelSeparator) return (ChannelSeparator) r; return new ChannelSeparator(r); }
public static IFormatReader instantiateImageReader() { // should I use the ZeissCZIReader here directly? return new ChannelSeparator();// new ZeissCZIReader(); }
/** Converts the given reader into a ChannelSeparator, wrapping if needed. */ public static ChannelSeparator makeChannelSeparator(IFormatReader r) { if (r instanceof ChannelSeparator) return (ChannelSeparator) r; return new ChannelSeparator(r); }
@Test public void setId() throws Exception { reader = new ImageReader(); reader = new ChannelFiller(reader); reader = new ChannelSeparator(reader); reader = new MinMaxCalculator(reader); if (memMap && reader.isSingleFile(id)) { TestTools.mapFile(id); } StopWatch stopWatch = new Slf4JStopWatch(); reader.setId(id); stopWatch.stop(String.format("%s.setId.%s", ((ReaderWrapper) reader).unwrap().getClass().getName(), filename)); seriesCount = reader.getSeriesCount(); }
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) { } }
public static double[] loadTileLocation( final File file, final int seriesOffset ) final IFormatReader r = new ChannelSeparator();
/** Read out the width,height of an image using LOCI BioFormats. */ static public Dimension getDimensions(final String path) { IFormatReader fr = null; try { fr = new ChannelSeparator(); fr.setGroupFiles(false); fr.setId(path); return new Dimension(fr.getSizeX(), fr.getSizeY()); } catch (final FormatException fe) { Utils.log("Error in reading image file at " + path + "\n" + fe); } catch (final Exception e) { IJError.print(e); } finally { if (null != fr) try { fr.close(); } catch (final IOException ioe) { Utils.log2("Could not close IFormatReader: " + ioe); } } return null; }
public OMEROWrapper(ImportConfig config, long elapsedTime, File cacheDirectory) { super(createReader(config)); this.config = config; this.iReader = (ImageReader) reader; // Save old value this.reader = null; filler = new ChannelFiller(iReader); separator = new ChannelSeparator(filler); memoizer = new Memoizer(separator, elapsedTime, cacheDirectory) { public Deser getDeser() { KryoDeser k = new KryoDeser(); k.kryo.register(OMEXMLModelComparator.class); return k; } }; reader = memoizer; // Force unreadable characters to be removed from metadata key/value pairs iReader.setMetadataFiltered(true); filler.setMetadataFiltered(true); separator.setMetadataFiltered(true); // Force images with multiple sub-resolutions to not "duplicate" their // series. iReader.setFlattenedResolutions(false); };
@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()); }
@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()); }
/** * Create an {@link IFormatReader} with the appropriate {@link loci.formats.ReaderWrapper} * instances and {@link IFormatReader#setFlattenedResolutions(boolean)} set to false. */ protected IFormatReader createBfReader() { IFormatReader reader = new ImageReader(); reader = new ChannelFiller(reader); reader = new ChannelSeparator(reader); if (memoizerDirectoryLocalRW == null) { reader = new Memoizer(reader, getMemoizerWait(), getMemoizerDirectory()); } else { reader = new MemoizerFallback(reader, getMemoizerWait(), memoizerDirectoryLocalRW, Collections.singleton( new MemoizerReadOnly(reader, getMemoizerWait(), getMemoizerDirectory()))); } reader.setFlattenedResolutions(false); reader.setMetadataFiltered(true); return reader; }
@DataProvider(name = "equalWrappers") public Object[][] createEqualWrappers() { Location.mapId(TEST_FILE_A, TEST_FILE_A); Location.mapId(TEST_FILE_B, TEST_FILE_B); Object[][] wrappers = new Object[][] { {new ImageReader(), new ImageReader()}, {new ImageReader(), new ImageReader()}, {new MinMaxCalculator(new ChannelSeparator(new ChannelFiller())), new MinMaxCalculator(new ChannelSeparator(new ChannelFiller()))}, {new DimensionSwapper(new ChannelMerger()), new DimensionSwapper(new ChannelMerger())} }; for (int i=1; i<wrappers.length; i++) { IFormatReader readerA = (IFormatReader) wrappers[i][0]; IFormatReader readerB = (IFormatReader) wrappers[i][1]; try { readerA.setId(TEST_FILE_A); readerB.setId(TEST_FILE_B); } catch (FormatException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } return wrappers; }
{new ImageReader(), new ImageReader()}, {new ImageReader(), new ImageReader()}, {new MinMaxCalculator(new ChannelSeparator(new ChannelFiller())), new MinMaxCalculator(new ChannelSeparator())}, {new DimensionSwapper(new ChannelMerger()), new DimensionSwapper(new ChannelMerger())}
@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; }
fr = new ChannelSeparator(); fr.setGroupFiles(false); try {
r = channelSeparator = new ChannelSeparator(r); r = dimensionSwapper = new DimensionSwapper(r);
r = channelSeparator = new ChannelSeparator(r); r = dimensionSwapper = new DimensionSwapper(r);