@Override public boolean isInterleaved(int subC) { return reader.isInterleaved(subC); }
@Override public boolean isInterleaved(int subC) { return reader.isInterleaved(subC); }
@Override public boolean isInterleaved() { return reader.isInterleaved(); }
@Override public boolean isInterleaved() { return reader.isInterleaved(); }
@Override public boolean isInterleaved() { return getReader().isInterleaved(); }
@Override public boolean isInterleaved(int subC) { return getReader().isInterleaved(subC); }
@Override public boolean isInterleaved() { return getReader().isInterleaved(); }
@Override public boolean isInterleaved(int subC) { return getReader().isInterleaved(subC); }
@Override public boolean isInterleaved() { FormatTools.assertId(getCurrentFile(), true, 2); return canMerge() ? false : reader.isInterleaved(); }
@Override public boolean isInterleaved() { FormatTools.assertId(getCurrentFile(), true, 2); return canMerge() ? false : reader.isInterleaved(); }
@Override public boolean isInterleaved() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isInterleaved() : getReader(getCoreIndex(), 0).isInterleaved(); }
@Override public boolean isInterleaved(int subC) { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isInterleaved(subC) : getReader(getCoreIndex(), 0).isInterleaved(subC); }
@Override public boolean isInterleaved(int subC) { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isInterleaved(subC) : getReader(getCoreIndex(), 0).isInterleaved(subC); }
@Override public boolean isInterleaved() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.isInterleaved() : getReader(getCoreIndex(), 0).isInterleaved(); }
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); int source = getOriginalIndex(no); byte[] thumb = reader.openThumbBytes(source); int c = getSizeC() / reader.getEffectiveSizeC(); int channel = no % c; int bpp = FormatTools.getBytesPerPixel(getPixelType()); return ImageTools.splitChannels(thumb, channel, c, bpp, false, reader.isInterleaved()); }
private byte[] getWholePlane(int z, int c, int t, byte[] plane) throws IOException, FormatException { int planeNumber; if (reader.getRGBChannelCount() == 1) { planeNumber = reader.getIndex(z, c, t); reader.openBytes(planeNumber, plane); } else { int size = RomioPixelBuffer.safeLongToInteger(getPlaneSize()); byte[] fullPlane = new byte[size*reader.getRGBChannelCount()]; planeNumber = reader.getIndex(z, 0, t); reader.openBytes(planeNumber, fullPlane); if(reader.isInterleaved()) { for(int p = 0; p < size; p += getByteWidth()) { System.arraycopy(fullPlane, c*getByteWidth() + p*reader.getRGBChannelCount(), plane, p, getByteWidth()); } } else { System.arraycopy(fullPlane, c*size, plane, 0, size); } } return plane; }
@Override public byte[] openThumbBytes(int no) throws FormatException, IOException { FormatTools.assertId(getCurrentFile(), true, 2); int source = getOriginalIndex(no); byte[] thumb = reader.openThumbBytes(source); int c = getSizeC() / reader.getEffectiveSizeC(); int channel = no % c; int bpp = FormatTools.getBytesPerPixel(getPixelType()); return ImageTools.splitChannels(thumb, channel, c, bpp, false, reader.isInterleaved()); }
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()); }
@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); }