@Override public boolean isLittleEndian() { return reader.isLittleEndian(); }
@Override public boolean isLittleEndian() { return reader.isLittleEndian(); }
public boolean isLittleEndian() { return reader.isLittleEndian(); }
/** * Delegates to {@link IFormatReader#isLittleEndian()}. * @return See above. */ public boolean isLittleEndian() { // Ensure the reader has been initialized reader(); return bfReader.isLittleEndian(); }
@Override public boolean isLittleEndian() { return getReader().isLittleEndian(); }
@Override public boolean isLittleEndian() { return getReader().isLittleEndian(); }
return bytes; boolean isLittleEndian = reader.isLittleEndian(); ByteBuffer buffer = ByteBuffer.wrap(bytes); int length;
@Override public boolean isLittleEndian() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isLittleEndian() : getReader(getCoreIndex(), 0).isLittleEndian(); }
@Override public boolean isLittleEndian() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isLittleEndian() : getReader(getCoreIndex(), 0).isLittleEndian(); }
boolean floatingPoint = FormatTools.isFloatingPoint(pixelType); Object pix = DataTools.makeDataArray(buf, bpp, floatingPoint, reader.isLittleEndian()); byte[][] b = ImageTools.make24Bits(pix, width, height, reader.isInterleaved(), false, min, max);
int bpp = FormatTools.getBytesPerPixel(srcReader.getPixelType()); boolean flipEndian = bpp > 1 && (srcReader.isLittleEndian() != checkReader.isLittleEndian());
/** * Use the lookup table from the reader (if present) to set * the color model in the given writer * @param writer the {@link loci.formats.IFormatWriter} on which to set a color model * @throws FormatException * @throws IOException */ private void applyLUT(IFormatWriter writer) throws FormatException, IOException { if (lookup) { byte[][] lut = reader.get8BitLookupTable(); if (lut != null) { IndexColorModel model = new IndexColorModel(8, lut[0].length, lut[0], lut[1], lut[2]); writer.setColorModel(model); } else { short[][] lut16 = reader.get16BitLookupTable(); if (lut16 != null) { Index16ColorModel model = new Index16ColorModel(16, lut16[0].length, lut16, reader.isLittleEndian()); writer.setColorModel(model); } } } }
private byte[] getTile(IFormatReader reader, int resolution, int no, int x, int y, int w, int h) throws FormatException, IOException { if (resolution < reader.getResolutionCount()) { reader.setResolution(resolution); return reader.openBytes(no, x, y, w, h); } reader.setResolution(0); IImageScaler scaler = new SimpleImageScaler(); int scale = (int) Math.pow(pyramidScale, resolution); byte[] tile = reader.openBytes(no, x * scale, y * scale, w * scale, h * scale); int type = reader.getPixelType(); return scaler.downsample(tile, w * scale, h * scale, scale, FormatTools.getBytesPerPixel(type), reader.isLittleEndian(), FormatTools.isFloatingPoint(type), reader.getRGBChannelCount(), reader.isInterleaved()); }
public CoreMetadata(IFormatReader r, int coreIndex) { int currentIndex = r.getCoreIndex(); r.setCoreIndex(coreIndex); sizeX = r.getSizeX(); sizeY = r.getSizeY(); sizeZ = r.getSizeZ(); sizeC = r.getSizeC(); sizeT = r.getSizeT(); thumbSizeX = r.getThumbSizeX(); thumbSizeY = r.getThumbSizeY(); pixelType = r.getPixelType(); bitsPerPixel = r.getBitsPerPixel(); imageCount = r.getImageCount(); dimensionOrder = r.getDimensionOrder(); orderCertain = r.isOrderCertain(); rgb = r.isRGB(); littleEndian = r.isLittleEndian(); interleaved = r.isInterleaved(); indexed = r.isIndexed(); falseColor = r.isFalseColor(); metadataComplete = r.isMetadataComplete(); seriesMetadata = new Hashtable<String, Object>(); seriesMetadata.putAll(r.getSeriesMetadata()); thumbnail = r.isThumbnailSeries(); resolutionCount = r.getResolutionCount(); moduloZ = r.getModuloZ(); moduloC = r.getModuloC(); moduloT = r.getModuloT(); r.setCoreIndex(currentIndex); }
public static void populatePixelsOnly(MetadataStore store, IFormatReader r) { int oldSeries = r.getSeries(); for (int i=0; i<r.getSeriesCount(); i++) { r.setSeries(i); String pixelType = FormatTools.getPixelTypeString(r.getPixelType()); populatePixelsOnly(store, i, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount()); if (store instanceof IPyramidStore) { for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res); } r.setResolution(0); } } r.setSeries(oldSeries); }
public static void populatePixelsOnly(MetadataStore store, IFormatReader r) { int oldSeries = r.getSeries(); for (int i=0; i<r.getSeriesCount(); i++) { r.setSeries(i); String pixelType = FormatTools.getPixelTypeString(r.getPixelType()); populatePixelsOnly(store, i, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount()); if (store instanceof IPyramidStore) { for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res); } r.setResolution(0); } } r.setSeries(oldSeries); }
@Test(dataProvider = "wrappers") public void testCoreMetadata(IFormatReader reader) { assertNotNull(reader.getCurrentFile()); List<CoreMetadata> coreList = reader.getCoreMetadataList(); assertEquals(coreList.size(), reader.getSeriesCount()); for (int i=0; i<reader.getSeriesCount(); i++) { CoreMetadata core = coreList.get(i); reader.setSeries(i); assertEquals(core.sizeX, reader.getSizeX()); assertEquals(core.sizeY, reader.getSizeY()); assertEquals(core.sizeZ, reader.getSizeZ()); assertEquals(core.sizeC, reader.getSizeC()); assertEquals(core.sizeT, reader.getSizeT()); assertEquals(core.pixelType, reader.getPixelType()); assertEquals(core.imageCount, reader.getImageCount()); assertEquals(core.dimensionOrder, reader.getDimensionOrder()); assertEquals(core.littleEndian, reader.isLittleEndian()); assertEquals(core.rgb, reader.isRGB()); assertEquals(core.interleaved, reader.isInterleaved()); assertEquals(core.indexed, reader.isIndexed()); } } }
public CoreMetadata(IFormatReader r, int coreIndex) { int currentIndex = r.getCoreIndex(); r.setCoreIndex(coreIndex); sizeX = r.getSizeX(); sizeY = r.getSizeY(); sizeZ = r.getSizeZ(); sizeC = r.getSizeC(); sizeT = r.getSizeT(); thumbSizeX = r.getThumbSizeX(); thumbSizeY = r.getThumbSizeY(); pixelType = r.getPixelType(); bitsPerPixel = r.getBitsPerPixel(); imageCount = r.getImageCount(); dimensionOrder = r.getDimensionOrder(); orderCertain = r.isOrderCertain(); rgb = r.isRGB(); littleEndian = r.isLittleEndian(); interleaved = r.isInterleaved(); indexed = r.isIndexed(); falseColor = r.isFalseColor(); metadataComplete = r.isMetadataComplete(); seriesMetadata = r.getSeriesMetadata(); thumbnail = r.isThumbnailSeries(); resolutionCount = r.getResolutionCount(); moduloZ = r.getModuloZ(); moduloC = r.getModuloC(); moduloT = r.getModuloT(); r.setCoreIndex(currentIndex); }
@SuppressWarnings("unchecked") public <T extends RealType< T > & NativeType< T >> RandomAccessibleInterval< T > createVirtual( final IFormatReader reader, final File file, final int series, final int channel, final int timepoint, T type, Dimensions dim) throws IncompatibleTypeException { setReaderFileAndSeriesIfNecessary( reader, file, series ); final boolean isLittleEndian = reader.isLittleEndian(); final long[] dims = new long[]{reader.getSizeX(), reader.getSizeY(), reader.getSizeZ()}; if (dim != null) dim.dimensions( dims ); final int pixelType = reader.getPixelType(); if (pixelType == FormatTools.UINT8) return new VirtualRandomAccessibleIntervalLOCI< T >( reader, file, dims, series, channel, timepoint, type == null ? (T) new UnsignedByteType() : type, (t, buf, i) -> {t.setReal( (int) buf[i] & 0xff);} ); else if (pixelType == FormatTools.UINT16) return new VirtualRandomAccessibleIntervalLOCI< T >( reader, file, dims, series, channel, timepoint, type == null ? (T) new UnsignedShortType() : type, (t, buf, i) -> {t.setReal( LegacyStackImgLoaderLOCI.getShortValueInt( buf, i*2, isLittleEndian ) );} ); else if (pixelType == FormatTools.INT16) return new VirtualRandomAccessibleIntervalLOCI< T >( reader, file, dims, series, channel, timepoint, type == null ? (T) new ShortType() : type, (t, buf, i) -> {t.setReal( LegacyStackImgLoaderLOCI.getShortValue( buf, i*2, isLittleEndian ) );} ); else if (pixelType == FormatTools.UINT32) return new VirtualRandomAccessibleIntervalLOCI< T >( reader, file, dims, series, channel, timepoint, type == null ? (T) new UnsignedIntType() : type, (t, buf, i) -> {t.setReal( LegacyStackImgLoaderLOCI.getIntValue( buf, i*4, isLittleEndian ) );} ); else if (pixelType == FormatTools.FLOAT) return new VirtualRandomAccessibleIntervalLOCI< T >( reader, file, dims, series, channel, timepoint, type == null ? (T) new FloatType() : type, (t, buf, i) -> {t.setReal( LegacyStackImgLoaderLOCI.getFloatValue( buf, i*4, isLittleEndian ) );} ); else throw new IncompatibleTypeException( this, "cannot create virtual image for this pixel type" ); }
final boolean isLittleEndian = reader.isLittleEndian(); final long[] dims = new long[]{reader.getSizeX(), reader.getSizeY(), reader.getSizeZ()};