Examples with IFormatReader loci.formats.IFormatReader used on opensource projects

Example 36 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class FormatReaderTest method testUnflattenedPixelsHashes.

@Test(groups = { "all", "pixels", "automated" })
public void testUnflattenedPixelsHashes() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testUnflattenedPixelsHashes";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        IFormatReader resolutionReader = new BufferedImageReader(new FileStitcher());
        resolutionReader.setFlattenedResolutions(false);
        resolutionReader.setNormalized(true);
        resolutionReader.setOriginalMetadataPopulated(false);
        resolutionReader.setMetadataFiltered(true);
        resolutionReader.setId(id);
        // check the MD5 of the first plane in each resolution
        for (int i = 0; i < resolutionReader.getSeriesCount() && success; i++) {
            resolutionReader.setSeries(i);
            for (int r = 0; r < resolutionReader.getResolutionCount() && success; r++) {
                resolutionReader.setResolution(r);
                config.setSeries(resolutionReader.getCoreIndex());
                long planeSize = -1;
                try {
                    planeSize = DataTools.safeMultiply32(resolutionReader.getSizeX(), resolutionReader.getSizeY(), resolutionReader.getRGBChannelCount(), FormatTools.getBytesPerPixel(resolutionReader.getPixelType()));
                } catch (IllegalArgumentException e) {
                    continue;
                }
                if (planeSize < 0 || !TestTools.canFitInMemory(planeSize)) {
                    continue;
                }
                String md5 = TestTools.md5(resolutionReader.openBytes(0));
                String expected1 = config.getMD5();
                String expected2 = config.getAlternateMD5();
                if (expected1 == null && expected2 == null) {
                    continue;
                }
                if (!md5.equals(expected1) && !md5.equals(expected2)) {
                    success = false;
                    msg = "series " + i + ", resolution " + r;
                }
            }
        }
        resolutionReader.close();
    } catch (Throwable t) {
        if (TestTools.isOutOfMemory(t)) {
            result(testName, true, "Image too large");
            return;
        }
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 37 with IFormatReader

use of loci.formats.IFormatReader in project bioformats by openmicroscopy.

the class SubResolutionExample method main.

public static void main(String[] args) throws FormatException, IOException {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java SubResolutionExample imageFile");
        System.exit(1);
    }
    String id = args[0];
    // configure reader
    IFormatReader reader = new ImageReader();
    reader.setFlattenedResolutions(false);
    System.out.println("Initializing file: " + id);
    // parse metadata
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    System.out.println("  Series count = " + seriesCount);
    for (int series = 0; series < seriesCount; series++) {
        reader.setSeries(series);
        int resolutionCount = reader.getResolutionCount();
        System.out.println("    Resolution count for series #" + series + " = " + resolutionCount);
        for (int r = 0; r < resolutionCount; r++) {
            reader.setResolution(r);
            System.out.println("      Resolution #" + r + " dimensions = " + reader.getSizeX() + " x " + reader.getSizeY());
        }
    }
    reader.close();
}

Example 38 with IFormatReader

use of loci.formats.IFormatReader in project TrakEM2 by trakem2.

the class Loader method getDimensions.

/**
 * Read out the width,height of an image using LOCI BioFormats.
 */
public static 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;
}