Examples with IMetadata loci.formats.meta.IMetadata used on opensource projects

Example 16 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testEmissionWavelengths.

@Test(groups = { "all", "fast", "automated" })
public void testEmissionWavelengths() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "EmissionWavelengths";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int c = 0; c < config.getChannelCount(); c++) {
            Length realWavelength = retrieve.getChannelEmissionWavelength(i, c);
            Length expectedWavelength = config.getEmissionWavelength(c);
            if (realWavelength == null && expectedWavelength == null) {
                continue;
            }
            if (!isAlmostEqual(expectedWavelength, realWavelength)) {
                result(testName, false, "Series " + i + " channel " + c + " (expected " + expectedWavelength + ", actual " + realWavelength + ")");
            }
        }
    }
    result(testName, true);
}

Example 17 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testChannelNames.

@Test(groups = { "all", "fast", "automated" })
public void testChannelNames() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "ChannelNames";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int c = 0; c < config.getChannelCount(); c++) {
            String realName = retrieve.getChannelName(i, c);
            String expectedName = config.getChannelName(c);
            if (!expectedName.equals(realName) && (realName == null && !expectedName.equals("null"))) {
                result(testName, false, "Series " + i + " channel " + c + " (got '" + realName + "', expected '" + expectedName + "')");
            }
        }
    }
    result(testName, true);
}

Example 18 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testPhysicalSizeX.

@Test(groups = { "all", "fast", "automated" })
public void testPhysicalSizeX() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "PhysicalSizeX";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        Length expectedSize = config.getPhysicalSizeX();
        Length realSize = retrieve.getPixelsPhysicalSizeX(i);
        if (!isAlmostEqual(realSize, expectedSize)) {
            result(testName, false, "Series " + i + " (expected " + expectedSize + ", actual " + realSize + ")");
        }
    }
    result(testName, true);
}

Example 19 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testExcitationWavelengths.

@Test(groups = { "all", "fast", "automated" })
public void testExcitationWavelengths() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "ExcitationWavelengths";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int c = 0; c < config.getChannelCount(); c++) {
            Length realWavelength = retrieve.getChannelExcitationWavelength(i, c);
            Length expectedWavelength = config.getExcitationWavelength(c);
            if (!isAlmostEqual(expectedWavelength, realWavelength)) {
                result(testName, false, "Series " + i + " channel " + c + " (expected " + expectedWavelength + ", actual " + realWavelength + ")");
            }
        }
    }
    result(testName, true);
}

Example 20 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatWriterTest method testWriterConsistency.

// -- Tests --
@Test(groups = { "all" }, dataProvider = "getWriterList")
public void testWriterConsistency(IFormatWriter writer) {
    String testName = TestTools.shortClassName(writer) + " " + writer.getCompression() + " testWriterConsistency";
    boolean success = true;
    String msg = null;
    try {
        reader.close();
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        reader.setMetadataStore(service.createOMEXMLMetadata());
        reader.setId(id);
        int type = reader.getPixelType();
        if (!writer.isSupportedType(type)) {
            success = true;
            result(testName, success, msg);
            return;
        }
        config = configTree.get(id);
        String prefix = id.substring(id.lastIndexOf(File.separator) + 1, id.lastIndexOf("."));
        // will throw an exception
        while (prefix.length() < 3) prefix = "x" + prefix;
        String suffix = "." + writer.getSuffixes()[0];
        File tmpFile = File.createTempFile(prefix, suffix);
        tmpFile.deleteOnExit();
        String convertedFile = tmpFile.getAbsolutePath();
        IMetadata meta = (IMetadata) reader.getMetadataStore();
        writer.close();
        writer.setMetadataRetrieve((MetadataRetrieve) meta);
        // convert the input file
        writer.setId(convertedFile);
        int seriesCount = writer.canDoStacks() ? reader.getSeriesCount() : 1;
        for (int series = 0; series < seriesCount; series++) {
            reader.setSeries(series);
            writer.setSeries(series);
            int imageCount = writer.canDoStacks() ? reader.getImageCount() : 1;
            for (int image = 0; image < imageCount; image++) {
                writer.saveBytes(image, reader.openBytes(image));
            }
        }
        writer.close();
        // verify that the dimensions are accurate
        convertedReader.setId(convertedFile);
        boolean seriesMatch = convertedReader.getSeriesCount() == config.getSeriesCount();
        boolean expectRGB = config.isRGB();
        int expectedCount = config.getSizeZ() * config.getSizeT() * (expectRGB ? 1 : config.getSizeC());
        boolean imageMatch = convertedReader.getImageCount() == expectedCount;
        if (!seriesMatch && writer.canDoStacks()) {
            int totalImages = 0;
            for (int i = 0; i < reader.getSeriesCount(); i++) {
                reader.setSeries(i);
                totalImages += reader.getImageCount();
            }
            reader.setSeries(0);
            if (convertedReader.getImageCount() != totalImages) {
                success = false;
                msg = "Series counts do not match (found " + convertedReader.getSeriesCount() + ", expected " + config.getSeriesCount() + ")";
            } else
                imageMatch = true;
        }
        if (success) {
            for (int series = 0; series < seriesCount; series++) {
                if (series >= convertedReader.getSeriesCount()) {
                    break;
                }
                convertedReader.setSeries(series);
                config.setSeries(series);
                int expectedX = config.getSizeX();
                int expectedY = config.getSizeY();
                expectRGB = config.isRGB();
                if (TestTools.shortClassName(writer).equals("OMEXMLWriter")) {
                    expectRGB = false;
                } else if (TestTools.shortClassName(writer).equals("JPEGWriter")) {
                    expectRGB = expectRGB || config.isIndexed();
                }
                int expectedPixelType = FormatTools.pixelTypeFromString(config.getPixelType());
                expectedCount = config.getSizeZ() * config.getSizeT() * (expectRGB ? 1 : config.getSizeC());
                String expectedMD5 = config.getMD5();
                int x = convertedReader.getSizeX();
                int y = convertedReader.getSizeY();
                int count = convertedReader.getImageCount();
                boolean rgb = convertedReader.isRGB();
                int pixelType = convertedReader.getPixelType();
                boolean isQuicktime = TestTools.shortClassName(writer).equals("QTWriter");
                String md5 = TestTools.md5(convertedReader.openBytes(0));
                if (msg == null)
                    msg = checkMismatch(x, expectedX, series, "X");
                if (msg == null)
                    msg = checkMismatch(y, expectedY, series, "Y");
                if (msg == null && writer.canDoStacks() && !imageMatch) {
                    msg = checkMismatch(count, expectedCount, series, "Image count");
                }
                if (msg == null && !isQuicktime) {
                    msg = checkMismatch(rgb, expectRGB, series, "RGB");
                }
                if (msg == null && !isQuicktime) {
                    msg = checkMismatch(pixelType, expectedPixelType, series, "Pixel type");
                }
                if (msg == null && isLosslessWriter(writer) && config.isRGB() == expectRGB) {
                    msg = checkMismatch(md5, expectedMD5, series, "Pixels hash");
                }
                success = msg == null;
                if (!success)
                    break;
            }
        }
        convertedReader.close();
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}