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

Example 61 with MetadataRetrieve

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

the class FormatReaderTest method testSaneOMEXML.

@Test(groups = { "all", "xml", "automated" })
public void testSaneOMEXML() {
    String testName = "testSaneOMEXML";
    if (!initFile())
        result(testName, false, "initFile");
    if (!config.hasValidXML()) {
        LOGGER.debug("Skipping valid XML test");
        result(testName, true);
        return;
    }
    String msg = null;
    try {
        MetadataRetrieve retrieve = (MetadataRetrieve) reader.getMetadataStore();
        boolean success = omexmlService.isOMEXMLMetadata(retrieve);
        if (!success)
            msg = TestTools.shortClassName(retrieve);
        for (int i = 0; i < reader.getSeriesCount() && msg == null; i++) {
            // total number of ChannelComponents should match SizeC
            int sizeC = retrieve.getPixelsSizeC(i).getValue().intValue();
            int nChannelComponents = retrieve.getChannelCount(i);
            int samplesPerPixel = retrieve.getChannelSamplesPerPixel(i, 0).getValue();
            if (sizeC != nChannelComponents * samplesPerPixel) {
                msg = "ChannelComponent";
            }
            // Z, C and T indices should be populated if PlaneTiming is present
            Time deltaT = null;
            Time exposure = null;
            Integer z = null, c = null, t = null;
            if (retrieve.getPlaneCount(i) > 0) {
                deltaT = retrieve.getPlaneDeltaT(i, 0);
                exposure = retrieve.getPlaneExposureTime(i, 0);
                z = retrieve.getPlaneTheZ(i, 0).getValue();
                c = retrieve.getPlaneTheC(i, 0).getValue();
                t = retrieve.getPlaneTheT(i, 0).getValue();
            }
            if ((deltaT != null || exposure != null) && (z == null || c == null || t == null)) {
                msg = "PlaneTiming";
            }
            // if CreationDate is before 1990, it's probably invalid
            String date = null;
            if (retrieve.getImageAcquisitionDate(i) != null) {
                date = retrieve.getImageAcquisitionDate(i).getValue();
            }
            config.setSeries(i);
            String configDate = config.getDate();
            if (date != null && !date.equals(configDate)) {
                date = date.trim();
                long acquiredDate = new Timestamp(date).asInstant().getMillis();
                long saneDate = new Timestamp("1990-01-01T00:00:00").asInstant().getMillis();
                long fileDate = new Location(reader.getCurrentFile()).getAbsoluteFile().lastModified();
                if (acquiredDate < saneDate && fileDate >= saneDate) {
                    msg = "CreationDate (date=" + date + " acquiredDate=" + acquiredDate + " fileDate=" + fileDate + " saneDate=" + saneDate + ")";
                }
            }
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        msg = t.getMessage();
    }
    result(testName, msg == null, msg);
}

Example 62 with MetadataRetrieve

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

the class FormatReaderTest method testOMEXML.

@Test(groups = { "all", "xml", "fast", "automated" })
public void testOMEXML() {
    String testName = "testOMEXML";
    if (!initFile())
        result(testName, false, "initFile");
    String msg = null;
    try {
        MetadataRetrieve retrieve = (MetadataRetrieve) reader.getMetadataStore();
        boolean success = omexmlService.isOMEXMLMetadata(retrieve);
        if (!success)
            msg = TestTools.shortClassName(retrieve);
        for (int i = 0; i < reader.getSeriesCount() && msg == null; i++) {
            reader.setSeries(i);
            String type = FormatTools.getPixelTypeString(reader.getPixelType());
            if (reader.getSizeX() != retrieve.getPixelsSizeX(i).getValue().intValue()) {
                msg = "SizeX";
            }
            if (reader.getSizeY() != retrieve.getPixelsSizeY(i).getValue().intValue()) {
                msg = "SizeY";
            }
            if (reader.getSizeZ() != retrieve.getPixelsSizeZ(i).getValue().intValue()) {
                msg = "SizeZ";
            }
            if (reader.getSizeC() != retrieve.getPixelsSizeC(i).getValue().intValue()) {
                msg = "SizeC";
            }
            if (reader.getSizeT() != retrieve.getPixelsSizeT(i).getValue().intValue()) {
                msg = "SizeT";
            }
            // NB: OME-TIFF files do not have a BinData element under Pixels
            IFormatReader r = reader.unwrap();
            if (r instanceof FileStitcher)
                r = ((FileStitcher) r).getReader();
            if (r instanceof ReaderWrapper)
                r = ((ReaderWrapper) r).unwrap();
            if (!(r instanceof OMETiffReader)) {
                boolean littleEndian = false;
                if (retrieve.getPixelsBigEndian(i) != null) {
                    littleEndian = !retrieve.getPixelsBigEndian(i).booleanValue();
                } else if (retrieve.getPixelsBinDataCount(i) == 0) {
                    littleEndian = !retrieve.getPixelsBinDataBigEndian(i, 0).booleanValue();
                }
                if (reader.isLittleEndian() != littleEndian) {
                    msg = "BigEndian";
                }
            }
            if (!reader.getDimensionOrder().equals(retrieve.getPixelsDimensionOrder(i).toString())) {
                msg = "DimensionOrder";
            }
            if (!type.equalsIgnoreCase(retrieve.getPixelsType(i).toString())) {
                msg = "PixelType";
            }
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        msg = t.getMessage();
    }
    result(testName, msg == null, msg);
}

Example 63 with MetadataRetrieve

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

the class FormatReaderTest method testValidXML.

@Test(groups = { "all", "xml", "fast", "automated" })
public void testValidXML() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testValidXML";
    if (!initFile())
        result(testName, false, "initFile");
    if (!config.hasValidXML()) {
        LOGGER.debug("Skipping valid XML test");
        result(testName, true);
        return;
    }
    String format = config.getReader();
    boolean success = true;
    try {
        MetadataStore store = reader.getMetadataStore();
        MetadataRetrieve retrieve = omexmlService.asRetrieve(store);
        String xml = omexmlService.getOMEXML(retrieve);
        // javax.xml.validation.Validator as used during XML validation
        synchronized (configTree) {
            success = xml != null && omexmlService.validateOMEXML(xml);
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success);
    try {
        close();
    } catch (IOException e) {
        LOGGER.info("", e);
    }
}

Example 64 with MetadataRetrieve

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

the class FormatReaderTest method writeXML.

@Test(groups = { "config-xml" })
public void writeXML() {
    setupReader();
    if (!initFile(false))
        return;
    String file = reader.getCurrentFile();
    LOGGER.info("Generating XML: {}", file);
    try {
        Location l = new Location(file);
        File f = new File(l.getParent(), l.getName() + ".ome.xml");
        OutputStreamWriter writer = new OutputStreamWriter(new FileOutputStream(f), Constants.ENCODING);
        MetadataStore store = reader.getMetadataStore();
        MetadataRetrieve retrieve = omexmlService.asRetrieve(store);
        String xml = omexmlService.getOMEXML(retrieve);
        writer.write(xml);
        writer.close();
        reader.close();
    } catch (Throwable t) {
        LOGGER.info("", t);
        assert false;
    }
}