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

Example 16 with IFD

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

the class FlexReader method parseFlexFile.

/**
 * Parses XML metadata from the Flex file corresponding to the given well.
 * If the 'firstFile' flag is set, then the core metadata is also
 * populated.
 */
private void parseFlexFile(int currentWell, int wellRow, int wellCol, int field, boolean firstFile, MetadataStore store) throws FormatException, IOException {
    LOGGER.info("Parsing .flex file (well {}{}, field {})", (char) (wellRow + 'A'), wellCol + 1, field);
    FlexFile file = lookupFile(wellRow, wellCol, field < 0 ? 0 : field);
    if (file == null)
        return;
    int originalFieldCount = fieldCount;
    if (xPositions == null)
        xPositions = new ArrayList<Double>();
    if (yPositions == null)
        yPositions = new ArrayList<Double>();
    if (xSizes == null)
        xSizes = new ArrayList<Double>();
    if (ySizes == null)
        ySizes = new ArrayList<Double>();
    if (cameraIDs == null)
        cameraIDs = new ArrayList<String>();
    if (lightSourceIDs == null)
        lightSourceIDs = new ArrayList<String>();
    if (objectiveIDs == null)
        objectiveIDs = new ArrayList<String>();
    if (lightSourceCombinationIDs == null) {
        lightSourceCombinationIDs = new HashMap<String, List<String>>();
    }
    if (lightSourceCombinationRefs == null) {
        lightSourceCombinationRefs = new ArrayList<String>();
    }
    if (cameraRefs == null)
        cameraRefs = new ArrayList<String>();
    if (objectiveRefs == null)
        objectiveRefs = new ArrayList<String>();
    if (binnings == null)
        binnings = new ArrayList<String>();
    if (filterSets == null)
        filterSets = new ArrayList<String>();
    if (filterSetMap == null)
        filterSetMap = new HashMap<String, FilterGroup>();
    // parse factors from XML
    LOGGER.debug("Parsing XML from {}", file.file);
    int nOffsets = file.offsets != null ? file.offsets.length : 0;
    IFD ifd = null;
    if (nOffsets == 0) {
        ifd = file.ifds.get(0);
    } else {
        RandomAccessInputStream ras = new RandomAccessInputStream(file.file);
        try {
            TiffParser parser = new TiffParser(ras);
            ifd = parser.getFirstIFD();
        } finally {
            ras.close();
        }
    }
    String xml = XMLTools.sanitizeXML(ifd.getIFDStringValue(FLEX));
    final List<String> n = new ArrayList<String>();
    final List<String> f = new ArrayList<String>();
    DefaultHandler handler = new FlexHandler(n, f, store, firstFile, currentWell, field);
    LOGGER.info("Parsing XML in .flex file");
    xml = xml.trim();
    // some files have a trailing ">" or "%", which needs to be removed
    if (xml.endsWith(">>") || xml.endsWith("%")) {
        xml = xml.substring(0, xml.length() - 1);
    }
    XMLTools.parseXML(xml.getBytes(Constants.ENCODING), handler);
    channelNames = n.toArray(new String[n.size()]);
    if (firstFile) {
        populateCoreMetadata(wellRow, wellCol, field < 0 ? 0 : field, n);
    }
    int totalPlanes = getSeriesCount() * getImageCount();
    LOGGER.info("Populating pixel scaling factors");
    // verify factor count
    int nsize = n.size();
    int fsize = f.size();
    if (nsize != fsize || nsize != totalPlanes) {
        LOGGER.warn("mismatch between image count, names and factors " + "(count={}, names={}, factors={})", new Object[] { totalPlanes, nsize, fsize });
    }
    if (firstFile) {
        for (String ns : n) {
            addGlobalMetaList("Name", ns);
        }
        for (String fs : f) {
            addGlobalMetaList("Factor", fs);
        }
    }
    // parse factor values
    file.factors = new double[totalPlanes];
    int max = 0;
    boolean oneFactors = true;
    for (int i = 0; i < fsize; i++) {
        String factor = f.get(i);
        double q = 1;
        try {
            q = Double.parseDouble(factor);
        } catch (NumberFormatException exc) {
            LOGGER.warn("invalid factor #{}: {}", i, factor);
        }
        if (i < file.factors.length) {
            file.factors[i] = q;
            if (q > file.factors[max])
                max = i;
            if (oneFactors && q != 1d) {
                oneFactors = false;
            }
        }
    }
    if (fsize < file.factors.length) {
        Arrays.fill(file.factors, fsize, file.factors.length, 1);
    }
    // determine pixel type
    if (file.factors[max] > 256) {
        core.get(0).pixelType = FormatTools.UINT32;
    } else if (file.factors[max] > 1) {
        core.get(0).pixelType = FormatTools.UINT16;
    }
    for (int i = 1; i < core.size(); i++) {
        core.get(i).pixelType = getPixelType();
    }
    if (!firstFile) {
        fieldCount = originalFieldCount;
    }
    if (oneFactors) {
        file.factors = null;
    }
}

Example 17 with IFD

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

the class FlexReader method getOptimalTileHeight.

/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
    FormatTools.assertId(currentId, true, 1);
    FlexFile file = lookupFile(0);
    IFD ifd = file.ifds.get(0);
    try {
        return (int) ifd.getTileLength();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    }
    return super.getOptimalTileHeight();
}

Example 18 with IFD

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

the class ImaconReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser parser = new TiffParser(stream);
    parser.setDoCaching(false);
    IFD ifd = parser.getFirstIFD();
    if (ifd == null)
        return false;
    return ifd.containsKey(XML_TAG);
}

Example 19 with IFD

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

the class PCIReader method getOptimalTileWidth.

/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
    FormatTools.assertId(currentId, true, 1);
    String file = imageFiles.get(0);
    try {
        if (poi == null) {
            initPOIService();
        }
        RandomAccessInputStream s = poi.getDocumentStream(file);
        TiffParser tp = new TiffParser(s);
        if (tp.isValidHeader()) {
            IFD ifd = tp.getFirstIFD();
            s.close();
            return (int) ifd.getTileWidth();
        }
        s.close();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile width", e);
    }
    return super.getOptimalTileWidth();
}

Example 20 with IFD

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

the class PCIReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (poi == null) {
        initPOIService();
    }
    String file = imageFiles.get(no);
    RandomAccessInputStream s = poi.getDocumentStream(file);
    TiffParser tp = new TiffParser(s);
    if (tp.isValidHeader()) {
        IFD ifd = tp.getFirstIFD();
        tp.getSamples(ifd, buf, x, y, w, h);
    } else {
        s.seek(0);
        readPlane(s, x, y, w, h, buf);
    }
    s.close();
    return buf;
}