@Override public void setSeries(int no) { reader.setSeries(no); }
@Override public void setSeries(int no) { reader.setSeries(no); }
protected static int getWidth(IFormatReader r, String path, int series) throws FormatException, IOException { r.setSeries(series); return r.getSizeX(); }
protected static int getHeight(IFormatReader r, String path, int series) throws FormatException, IOException { r.setSeries(series); return r.getSizeY(); }
/** * Sets the current series in the underlying Bio-Formats reader. * @param series The series to set. */ public void setSeries(int series) { // Ensure the reader has been initialized reader(); bfReader.setSeries(series); seriesIndex = series; }
protected static int getWidth(IFormatReader r, String path, int series) throws FormatException, IOException { r.setSeries(series); return r.getSizeX(); }
@Override public void setSeries(int no) { getReader().setSeries(no); }
protected static int getHeight(IFormatReader r, String path, int series) throws FormatException, IOException { r.setSeries(series); return r.getSizeY(); }
@Override public void setSeries(int no) { getReader().setSeries(no); }
/** * Determines whether the given reader represents any floating point data. * @param reader the reader to check * @return true if any of the reader's series have a floating point pixel type * @see #isFloatingPoint(int) */ public static boolean isFloatingPoint(IFormatReader reader) { int originalSeries = reader.getSeries(); for (int s=0; s<reader.getSeriesCount(); s++) { reader.setSeries(s); if (isFloatingPoint(reader.getPixelType())) { reader.setSeries(originalSeries); return true; } } reader.setSeries(originalSeries); return false; }
public static String[] getFilenames(String pattern, IFormatReader r) throws FormatException, IOException { Vector<String> filenames = new Vector<String>(); String filename = null; for (int series=0; series<r.getSeriesCount(); series++) { r.setSeries(series); for (int image=0; image<r.getImageCount(); image++) { filename = getFilename(series, image, r, pattern); if (!filenames.contains(filename)) filenames.add(filename); } } return filenames.toArray(new String[0]); }
public static String[] getFilenames(String pattern, IFormatReader r) throws FormatException, IOException { Vector<String> filenames = new Vector<String>(); String filename = null; for (int series=0; series<r.getSeriesCount(); series++) { r.setSeries(series); for (int image=0; image<r.getImageCount(); image++) { filename = getFilename(series, image, r, pattern); if (!filenames.contains(filename)) filenames.add(filename); } } return filenames.toArray(new String[0]); }
public static int getImagesPerFile(String pattern, IFormatReader r) throws FormatException, IOException { String[] filenames = getFilenames(pattern, r); int totalPlanes = 0; for (int series=0; series<r.getSeriesCount(); series++) { r.setSeries(series); totalPlanes += r.getImageCount(); } return totalPlanes / filenames.length; }
public static int getImagesPerFile(String pattern, IFormatReader r) throws FormatException, IOException { String[] filenames = getFilenames(pattern, r); int totalPlanes = 0; for (int series=0; series<r.getSeriesCount(); series++) { r.setSeries(series); totalPlanes += r.getImageCount(); } return totalPlanes / filenames.length; }
@Override public void setSeries(int no) { FormatTools.assertId(getCurrentFile(), true, 2); int n = reader.getCoreMetadataList().size(); if (n > 1 || noStitch) { reader.setSeries(no); } setCoreIndex(seriesToCoreIndex(no)); reader.setResolution(0); }
@Override public void setSeries(int no) { FormatTools.assertId(getCurrentFile(), true, 2); int n = reader.getCoreMetadataList().size(); if (n > 1 || noStitch) { reader.setSeries(no); } setCoreIndex(seriesToCoreIndex(no)); reader.setResolution(0); }
/** * Short-cut in the FS case where we know that we are dealing with a FS-lite * file, and want to retrieve the actual file as opposed to a pyramid or anything * else. This may be used to access the original metadata. * @throws FormatException * @throws IOException */ public IFormatReader getBfReader(Pixels pixels) throws FormatException, IOException { // from getPixelBuffer final String originalFilePath = getOriginalFilePath(pixels); final int series = getSeries(pixels); final IFormatReader reader = createBfReader(); reader.setId(originalFilePath); // Called by BfPixelsBuffer elsewhere. reader.setSeries(series); return reader; }
@Test public void testSubResolutionCount() { int seriesCount = reader.getSeriesCount(); assertTrue(seriesCount > 0); for (int series=0; series<seriesCount; series++) { reader.setSeries(series); int resolutionCount = reader.getResolutionCount(); assertTrue(resolutionCount > 0); for (int resolution=0; resolution<resolutionCount; resolution++) { reader.setResolution(resolution); assertTrue(reader.getSizeX() > 0); assertTrue(reader.getSizeY() > 0); } } }