throw new RuntimeException(e); assertEquals(reader.getImageCount(), SIZE_Z * SIZE_C * SIZE_T); assertEquals(reader.getSeriesCount(), 6); short tileCount = (short) TestTools.forEachTile(new TileLoopIteration() {
/** * @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 { FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h); int n = no; for (int i=0; i<getSeries(); i++) { n += core.get(i).imageCount; } if (tiffReaders.length == 1) { return tiffReaders[0].openBytes(n, buf, x, y, w, h); } int plane = 0; if (tiffReaders[0].getImageCount() > 1) { n /= tiffReaders.length; plane = n % tiffReaders.length; } if (lastPlane != 0) { tiffReaders[lastPlane].close(); } lastPlane = n; tiffReaders[n].setId(tiffs.get(n)); return tiffReaders[n].openBytes(plane, 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 { FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h); int n = no; for (int i=0; i<getSeries(); i++) { n += core.get(i).imageCount; } if (tiffReaders.length == 1) { return tiffReaders[0].openBytes(n, buf, x, y, w, h); } int plane = 0; if (tiffReaders[0].getImageCount() > 1) { n /= tiffReaders.length; plane = n % tiffReaders.length; } if (lastPlane != 0) { tiffReaders[lastPlane].close(); } lastPlane = n; tiffReaders[n].setId(tiffs.get(n)); return tiffReaders[n].openBytes(plane, buf, x, y, w, h); }
public static void checkImage(TiffReader reader, Plane originalPlane, boolean interleaved, int rgbChannels, int seriesCount, int sizeT, String compression) throws FormatException, IOException { for (int s=0; s<reader.getSeriesCount(); s++) { reader.setSeries(s); assertEquals(reader.getSizeC(), rgbChannels); int imageCount = reader.isRGB() ? seriesCount * sizeT : rgbChannels * sizeT * seriesCount; assertEquals(reader.getImageCount(), imageCount); for (int image=0; image<reader.getImageCount(); image++) { byte[] readPlane = reader.openBytes(image); boolean lossy = compression.equals(COMPRESSION_JPEG) || compression.equals(COMPRESSION_J2K_LOSSY); boolean isJ2K = compression.equals(COMPRESSION_J2K) || compression.equals(COMPRESSION_J2K_LOSSY); boolean interleavedDiffs = interleaved || (isJ2K && !interleaved); if (!(lossy || interleavedDiffs)) { Plane newPlane = new Plane(readPlane, reader.isLittleEndian(), !reader.isInterleaved(), reader.getRGBChannelCount(), FormatTools.getPixelTypeString(reader.getPixelType())); assert(originalPlane.equals(newPlane)); } } } }
int imageCount = source.getImageCount(); setSeries(series); for (int i = 0; i < imageCount; i++)
r.setId(currentId); try { planes = new OMETiffPlane[r.getImageCount()]; for (int plane=0; plane<planes.length; plane++) { planes[plane] = new OMETiffPlane();
r.setId(currentId); try { planes = new OMETiffPlane[r.getImageCount()]; for (int plane=0; plane<planes.length; plane++) { planes[plane] = new OMETiffPlane();
for (int s = 0; s < series; s++) { outputReader.setSeries(s); count = outputReader.getImageCount(); h = outputReader.getSizeY()/m; w = outputReader.getSizeX()/n;
for (int s = 0; s < series; s++) { outputReader.setSeries(s); count = outputReader.getImageCount(); for (int k = 0; k < count; k++) { sizeX = outputReader.getSizeX();