Examples with IFD loci.formats.tiff.IFD used on opensource projects

Example 36 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class VectraReader method initMetadataStore.

/* @see loci.formats.BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    for (int i = 0; i < getSeriesCount(); i++) {
        int coreIndex = seriesToCoreIndex(i);
        store.setImageName(getImageName(coreIndex), i);
        store.setImageDescription("", i);
        int ifdIndex = getIFDIndex(coreIndex, 0);
        IFD ifd = ifds.get(ifdIndex);
        double x = ifd.getXResolution();
        double y = ifd.getYResolution();
        store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(x), i);
        store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(y), i);
    }
    for (int c = 0; c < getSizeC(); c++) {
        String xml = getIFDComment(c);
        try {
            Element root = XMLTools.parseDOM(xml).getDocumentElement();
            NodeList children = root.getChildNodes();
            for (int i = 0; i < children.getLength(); i++) {
                if (!(children.item(i) instanceof Element)) {
                    continue;
                }
                Element e = (Element) children.item(i);
                String name = e.getNodeName();
                String value = e.getTextContent();
                if (name.equals("ScanProfile")) {
                    try {
                        Document profileRoot = XMLTools.createDocument();
                        Node tmp = profileRoot.importNode(e, true);
                        profileRoot.appendChild(tmp);
                        profileXML = XMLTools.getXML(profileRoot);
                        // scan profile XML is usually too long to be saved
                        // when original metadata filtering is enabled, but there
                        // is an API method below to retrieve it
                        addGlobalMeta(name, profileXML);
                    } catch (Exception ex) {
                        LOGGER.debug("Could not preserve scan profile metadata", ex);
                    }
                } else {
                    addGlobalMetaList(name, value);
                }
                if (name.equals("Name")) {
                    if (hasFlattenedResolutions()) {
                        for (int series = 0; series < pyramidDepth; series++) {
                            store.setChannelName(value, series, c);
                        }
                    } else {
                        store.setChannelName(value, 0, c);
                    }
                } else if (name.equals("Color")) {
                    String[] components = value.split(",");
                    Color color = new Color(Integer.parseInt(components[0]), Integer.parseInt(components[1]), Integer.parseInt(components[2]), 255);
                    if (hasFlattenedResolutions()) {
                        for (int series = 0; series < pyramidDepth; series++) {
                            store.setChannelColor(color, series, c);
                        }
                    } else {
                        store.setChannelColor(color, 0, c);
                    }
                } else if (name.equals("Objective") && c == 0) {
                    String instrument = MetadataTools.createLSID("Instrument", 0);
                    String objective = MetadataTools.createLSID("Objective", 0, 0);
                    store.setInstrumentID(instrument, 0);
                    store.setObjectiveID(objective, 0, 0);
                    store.setObjectiveModel(value, 0, 0);
                    try {
                        String mag = value.toLowerCase().replace("x", "");
                        Double magFactor = DataTools.parseDouble(mag);
                        store.setObjectiveNominalMagnification(magFactor, 0, 0);
                    } catch (NumberFormatException ex) {
                        LOGGER.info("Could not determine magnification: {}", value);
                    }
                    for (int series = 0; series < getSeriesCount(); series++) {
                        store.setImageInstrumentRef(instrument, series);
                        store.setObjectiveSettingsID(objective, series);
                    }
                } else if (name.equals("ExposureTime")) {
                    Time exposure = new Time(DataTools.parseDouble(value), UNITS.MICROSECOND);
                    store.setPlaneExposureTime(exposure, 0, c);
                    store.setPlaneTheZ(new NonNegativeInteger(0), 0, c);
                    store.setPlaneTheT(new NonNegativeInteger(0), 0, c);
                    store.setPlaneTheC(new NonNegativeInteger(c), 0, c);
                }
            }
        } catch (ParserConfigurationException | SAXException | IOException e) {
            LOGGER.warn("Could not parse XML for channel {}", c);
            LOGGER.debug("", e);
        }
    }
}

Example 37 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class VectraReader method isThisType.

// -- IFormatReader API methods --
/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(java.lang.String, boolean)
   */
@Override
public boolean isThisType(String name, boolean open) {
    if (!open) {
        return checkSuffix(name, "qptiff");
    }
    try (RandomAccessInputStream stream = new RandomAccessInputStream(name)) {
        TiffParser tiffParser = new TiffParser(stream);
        tiffParser.setDoCaching(false);
        if (!tiffParser.isValidHeader()) {
            return false;
        }
        IFD ifd = tiffParser.getFirstIFD();
        if (ifd == null) {
            return false;
        }
        tiffParser.fillInIFD(ifd);
        String software = ifd.getIFDTextValue(IFD.SOFTWARE);
        return software != null && software.startsWith(SOFTWARE_CHECK);
    } catch (IOException e) {
        LOGGER.debug("I/O exception during isThisType() evaluation.", e);
        return false;
    }
}

Example 38 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class SVSReader method isThisType.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(java.lang.String, boolean)
   */
@Override
public boolean isThisType(String name, boolean open) {
    boolean isThisType = super.isThisType(name, open);
    if (!isThisType && open) {
        RandomAccessInputStream stream = null;
        try {
            stream = new RandomAccessInputStream(name);
            TiffParser tiffParser = new TiffParser(stream);
            tiffParser.setDoCaching(false);
            if (!tiffParser.isValidHeader()) {
                return false;
            }
            IFD ifd = tiffParser.getFirstIFD();
            if (ifd == null) {
                return false;
            }
            Object description = ifd.get(IFD.IMAGE_DESCRIPTION);
            if (description != null) {
                String imageDescription = null;
                if (description instanceof TiffIFDEntry) {
                    Object value = tiffParser.getIFDValue((TiffIFDEntry) description);
                    if (value != null) {
                        imageDescription = value.toString();
                    }
                } else if (description instanceof String) {
                    imageDescription = (String) description;
                }
                if (imageDescription != null && imageDescription.startsWith(APERIO_IMAGE_DESCRIPTION_PREFIX)) {
                    return true;
                }
            }
            return false;
        } catch (IOException e) {
            LOGGER.debug("I/O exception during isThisType() evaluation.", e);
            return false;
        } finally {
            try {
                if (stream != null) {
                    stream.close();
                }
            } catch (IOException e) {
                LOGGER.debug("I/O exception during stream closure.", e);
            }
        }
    }
    return isThisType;
}

Example 39 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class SlidebookTiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    if (software == null)
        return false;
    return software.equals(SLIDEBOOK_MAGIC_STRING) && ifd.getComment().length() == 0 && (ifd.containsKey(X_POS_TAG) || ifd.containsKey(Y_POS_TAG) || ifd.containsKey(Z_POS_TAG) || ifd.containsKey(CHANNEL_TAG) || ifd.containsKey(PHYSICAL_SIZE_TAG) || ifd.containsKey(MAGNIFICATION_TAG));
}

Example 40 with IFD

use of loci.formats.tiff.IFD in project bioformats by openmicroscopy.

the class SlidebookTiffReader method getFirstChannel.

private String getFirstChannel(String path) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(path);
    TiffParser parser = new TiffParser(s);
    IFD ifd = parser.getFirstIFD();
    Object channel = ifd.getIFDValue(CHANNEL_TAG);
    s.close();
    parser.getStream().close();
    return channel == null ? null : channel.toString();
}