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

Example 46 with MetadataStore

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

the class WlzReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        wlz = factory.getInstance(WlzService.class);
    } catch (DependencyException e) {
        throw new FormatException(NO_WLZ_MSG, e);
    }
    if (wlz != null) {
        wlz.open(id, "r");
        CoreMetadata md = core.get(0);
        MetadataStore store = makeFilterMetadata();
        md.rgb = wlz.isRGB();
        md.interleaved = false;
        md.indexed = false;
        md.sizeX = wlz.getSizeX();
        md.sizeY = wlz.getSizeY();
        md.sizeZ = wlz.getSizeZ();
        md.sizeC = wlz.getSizeC();
        md.sizeT = wlz.getSizeT();
        md.dimensionOrder = "XYZCT";
        md.imageCount = wlz.getSizeZ();
        md.pixelType = wlz.getPixelType();
        PositiveFloat x = new PositiveFloat(Math.abs(wlz.getVoxSzX()));
        PositiveFloat y = new PositiveFloat(Math.abs(wlz.getVoxSzY()));
        PositiveFloat z = new PositiveFloat(Math.abs(wlz.getVoxSzZ()));
        store.setPixelsPhysicalSizeX(FormatTools.createLength(x, UNITS.MICROMETER), 0);
        store.setPixelsPhysicalSizeY(FormatTools.createLength(y, UNITS.MICROMETER), 0);
        store.setPixelsPhysicalSizeZ(FormatTools.createLength(z, UNITS.MICROMETER), 0);
        store.setStageLabelName(wlz.getWlzOrgLabelName(), 0);
        store.setStageLabelX(new Length(wlz.getOrgX(), UNITS.REFERENCEFRAME), 0);
        store.setStageLabelY(new Length(wlz.getOrgY(), UNITS.REFERENCEFRAME), 0);
        store.setStageLabelZ(new Length(wlz.getOrgZ(), UNITS.REFERENCEFRAME), 0);
        MetadataTools.populatePixels(store, this);
    }
}

Example 47 with MetadataStore

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

the class ZeissLMSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    CoreMetadata thumb = new CoreMetadata();
    m.littleEndian = true;
    thumb.littleEndian = true;
    in.order(m.littleEndian);
    in.seek(18);
    double magnification = in.readInt();
    // all assumed to be constant based upon the CSM 700 data sheet
    thumb.sizeX = 1280;
    thumb.sizeY = 1024;
    thumb.pixelType = FormatTools.UINT8;
    thumb.sizeC = 3;
    thumb.rgb = true;
    thumb.interleaved = true;
    thumb.dimensionOrder = "XYCZT";
    m.sizeX = 1280;
    m.sizeY = 1024;
    m.pixelType = FormatTools.UINT16;
    m.sizeC = 1;
    m.rgb = false;
    m.dimensionOrder = "XYCZT";
    m.indexed = true;
    // each image can be found using the "BM6" marker
    seekToNextMarker();
    in.skipBytes(50);
    offsets.add(in.getFilePointer());
    in.skipBytes(thumb.sizeX * thumb.sizeY * thumb.sizeC);
    seekToNextMarker();
    in.skipBytes(50);
    lut = new byte[3][256];
    for (int i = 0; i < lut[0].length; i++) {
        for (int j = 0; j < lut.length; j++) {
            lut[j][i] = in.readByte();
        }
        // skip alpha channel
        in.skipBytes(1);
    }
    offsets.add(in.getFilePointer());
    // again, Z stack is assumed based upon the CSM 700 data sheet
    thumb.sizeZ = 1;
    thumb.sizeT = 1;
    thumb.imageCount = thumb.sizeZ * thumb.sizeT;
    long availableBytes = in.length() - offsets.get(1);
    int planeSize = m.sizeX * m.sizeY * FormatTools.getBytesPerPixel(m.pixelType);
    m.sizeZ = (int) (availableBytes / planeSize);
    m.sizeT = 1;
    m.imageCount = m.sizeZ * m.sizeT;
    core.add(thumb);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
    String objective = MetadataTools.createLSID("Objective", 0, 0);
    store.setObjectiveID(objective, 0, 0);
    store.setObjectiveNominalMagnification(magnification, 0, 0);
    store.setObjectiveSettingsID(objective, 0);
    store.setObjectiveSettingsID(objective, 1);
}

Example 48 with MetadataStore

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

the class TrestleReader 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++) {
        store.setImageName("Series " + (i + 1), i);
    }
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        // will not be stored with the mask dimensions
        if (level != MetadataLevel.NO_OVERLAYS && !(getMetadataStore() instanceof OMEXMLMetadata)) {
            try {
                parseROIs(store);
            } catch (IOException e) {
                LOGGER.debug("Could not parse ROIs", e);
            }
        }
    }
}

Example 49 with MetadataStore

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

the class VGSAMReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    in.seek(348);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(4);
    int bpp = in.readInt();
    addGlobalMeta("Bytes per pixel", bpp);
    m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, bpp == 4);
    m.littleEndian = false;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.rgb = false;
    m.interleaved = false;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 50 with MetadataStore

use of loci.formats.meta.MetadataStore 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);
        }
    }
}