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

Example 51 with TiffParser

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

the class FlowSightReader method initFile.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#initFile(java.lang.String)
   */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    tiffParser = new TiffParser(in);
    tiffParser.setDoCaching(false);
    tiffParser.setUse64BitOffsets(false);
    final Boolean littleEndian = tiffParser.checkHeader();
    if (littleEndian == null) {
        throw new FormatException("Invalid FlowSight file");
    }
    final boolean little = littleEndian.booleanValue();
    in.order(little);
    LOGGER.info("Reading IFDs");
    ifdOffsets = tiffParser.getIFDOffsets();
    if (ifdOffsets.length < 2) {
        throw new FormatException("No IFDs found");
    }
    LOGGER.info("Populating metadata");
    /*
     * The first IFD contains file-scope metadata
     */
    final IFD ifd0 = tiffParser.getFirstIFD();
    tiffParser.fillInIFD(ifd0);
    int channelCount = ifd0.getIFDIntValue(CHANNEL_COUNT_TAG, 1);
    final String channelNamesString = ifd0.getIFDStringValue(CHANNEL_NAMES_TAG);
    if (channelNamesString != null) {
        channelNames = channelNamesString.split("\\|");
        if (channelNames.length != channelCount) {
            if (LOGGER.isDebugEnabled()) {
                LOGGER.debug("Channel count (%d) does not match number of " + "channel names (%d) in string \"%s\"", channelCount, channelNames.length, channelNamesString);
            }
            channelCount = channelNames.length;
        }
        LOGGER.debug("Found {} channels: {}", channelCount, channelNamesString.replace('|', ','));
    }
    final String channelDescsString = ifd0.getIFDStringValue(CHANNEL_DESCS_TAG);
    if (channelDescsString != null) {
        channelDescs = channelDescsString.split("\\|");
        if (channelDescs.length != channelCount) {
            throw new FormatException(String.format("Channel count (%d) does not match number of channel descriptions (%d) in string \"%s\"", channelCount, channelDescs.length, channelDescsString));
        }
    }
    String xml = ifd0.getIFDTextValue(METADATA_XML_TAG);
    xml = XMLTools.sanitizeXML(xml);
    try {
        Element xmlRoot = XMLTools.parseDOM(xml).getDocumentElement();
        NodeList imagingNodes = xmlRoot.getElementsByTagName("Imaging");
        if (imagingNodes.getLength() > 0) {
            Element imagingNode = (Element) imagingNodes.item(0);
            NodeList children = imagingNode.getChildNodes();
            for (int child = 0; child < children.getLength(); child++) {
                Node childNode = children.item(child);
                String name = childNode.getNodeName();
                if (name.startsWith("ChannelInUseIndicators")) {
                    channelCount = 0;
                    String text = childNode.getTextContent();
                    String[] tokens = text.split(" ");
                    for (String token : tokens) {
                        if (token.equals("1")) {
                            channelCount++;
                        }
                    }
                }
            }
        }
    } catch (ParserConfigurationException e) {
        LOGGER.debug("Could not parse XML", e);
    } catch (SAXException e) {
        LOGGER.debug("Could not parse XML", e);
    }
    /*
     * Scan the remaining IFDs
     * 
     * Unfortunately, each image can have a different width and height
     * and the images and masks have a different bit depth, so in the
     * OME scheme of things, we get one series per plane.
     */
    for (int idxOff = 1; idxOff < ifdOffsets.length; idxOff++) {
        // TODO: Record the channel names
        final long offset = ifdOffsets[idxOff];
        final boolean first = (idxOff == 1);
        final IFD ifd = tiffParser.getIFD(offset);
        tiffParser.fillInIFD(ifd);
        CoreMetadata ms = first ? core.get(0) : new CoreMetadata();
        ms.rgb = false;
        ms.interleaved = false;
        ms.littleEndian = ifd0.isLittleEndian();
        ms.sizeX = (int) ifd.getImageWidth() / channelCount;
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = 1;
        ms.sizeC = channelCount;
        ms.sizeT = 1;
        ms.indexed = false;
        ms.dimensionOrder = "XYCZT";
        ms.bitsPerPixel = ifd.getIFDIntValue(IFD.BITS_PER_SAMPLE);
        ms.pixelType = (ms.bitsPerPixel == 8) ? FormatTools.UINT8 : FormatTools.UINT16;
        ms.imageCount = channelCount;
        ms.resolutionCount = 1;
        ms.thumbnail = false;
        ms.metadataComplete = true;
        if (!first) {
            core.add(ms);
        }
    }
    /*
     * Run through the metadata store, setting the channel names
     * for all the series.
     */
    final MetadataStore store = getMetadataStore();
    MetadataTools.populatePixels(store, this);
    if (channelNames != null && channelDescs != null) {
        String[] maskDescs = new String[channelCount];
        for (int i = 0; i < channelCount; i++) {
            maskDescs[i] = channelDescs[i] + " Mask";
        }
        for (int series = 0; series < ifdOffsets.length - 1; series++) {
            final boolean isMask = core.get(series).pixelType == FormatTools.UINT8;
            String[] descs = isMask ? maskDescs : channelDescs;
            for (int channel = 0; channel < channelCount; channel++) {
                store.setChannelName(descs[channel], series, channel);
                String cid = MetadataTools.createLSID("Channel", series, channel) + ":";
                store.setChannelID(cid + channelNames[channel], series, channel);
            }
        }
    }
}

Example 52 with TiffParser

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

the class FlowSightReader method reopenFile.

@Override
public void reopenFile() throws IOException {
    super.reopenFile();
    tiffParser = new TiffParser(in);
    tiffParser.setDoCaching(false);
    tiffParser.setUse64BitOffsets(false);
}

Example 53 with TiffParser

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

the class MicromanagerReader method parsePosition.

// -- Helper methods --
private void parsePosition(int posIndex) throws IOException, FormatException {
    Position p = positions.get(posIndex);
    String s = DataTools.readFile(p.metadataFile);
    parsePosition(s, posIndex);
    buildTIFFList(posIndex);
    // parse original metadata from each TIFF's JSON
    p.positions = new Double[p.tiffs.size()][3];
    int digits = String.valueOf(p.tiffs.size() - 1).length();
    boolean parseMMJSONTag = true;
    for (int plane = 0; plane < p.tiffs.size(); ) {
        String path = p.tiffs.get(plane);
        // file ordering is correct
        if (p.tiffs.size() == p.fileNameMap.size() && plane < getImageCount()) {
            path = p.getFile(plane);
        }
        if (path == null || !new Location(path).exists()) {
            plane++;
            continue;
        }
        try {
            TiffParser parser = new TiffParser(path);
            int nIFDs = parser.getIFDs().size();
            IFD firstIFD = parser.getFirstIFD();
            parser.fillInIFD(firstIFD);
            // ensure that the plane dimensions and pixel type are correct
            CoreMetadata ms = core.get(posIndex);
            ms.sizeX = (int) firstIFD.getImageWidth();
            ms.sizeY = (int) firstIFD.getImageLength();
            ms.pixelType = firstIFD.getPixelType();
            ms.littleEndian = firstIFD.isLittleEndian();
            String json = firstIFD.getIFDTextValue(JSON_TAG);
            if (json != null) {
                String[] lines = json.split("\n");
                for (String line : lines) {
                    String toSplit = line.trim();
                    if (toSplit.length() == 0) {
                        continue;
                    }
                    toSplit = toSplit.substring(0, toSplit.length() - 1);
                    String[] values = toSplit.split("\": ");
                    if (values.length < 2) {
                        continue;
                    }
                    String key = values[0].replaceAll("\"", "");
                    String value = values[1].replaceAll("\"", "");
                    if (key.length() > 0 && value.length() > 0) {
                        parseKeyAndValue(key, value, digits, plane * nIFDs, nIFDs);
                    }
                }
            }
            IFDList ifds = parser.getIFDs();
            for (int i = 0; i < ifds.size(); i++) {
                if (!parseMMJSONTag) {
                    break;
                }
                IFD ifd = ifds.get(i);
                parser.fillInIFD(ifd);
                json = ifd.getIFDTextValue(MM_JSON_TAG);
                LOGGER.trace("JSON for IFD #{} = {}", i, json);
                if (json == null) {
                    // if one of the files is missing the per-plane JSON tag,
                    // assume all files are missing it (for performance)
                    parseMMJSONTag = false;
                    break;
                }
                String[] tokens = json.split("[\\{\\}:,\"]");
                String key = null, value = null, propType = null;
                int nEmptyTokens = 0;
                for (int q = 0; q < tokens.length; q++) {
                    String token = tokens[q];
                    if (token.length() == 0) {
                        nEmptyTokens++;
                        continue;
                    }
                    if (nEmptyTokens == 5 && value == null) {
                        key = null;
                    }
                    if (key == null && value == null && propType == null) {
                        // don't use completeCoords as a key, defer to child attributes
                        if (!token.equals("completeCoords")) {
                            key = token;
                        }
                        nEmptyTokens = 0;
                    } else if (token.equals("PropVal") || token.equals("[")) {
                        value = token;
                    } else if (token.equals("PropType")) {
                        propType = token;
                    } else if (value != null && value.equals("PropVal") && propType == null) {
                        value = token;
                    } else if (value != null && propType == null && value.startsWith("[") && !token.startsWith("]")) {
                        value += token;
                        value += ", ";
                    } else if (((propType != null && propType.equals("PropType")) || token.equals("]")) || (key != null && value == null)) {
                        if (value == null && (propType == null || !propType.equals("PropType"))) {
                            StringBuilder sb = new StringBuilder(token);
                            while (q + 1 < tokens.length && tokens[q + 1].trim().length() > 0) {
                                sb.append(':');
                                sb.append(tokens[q + 1]);
                                q++;
                            }
                            value = sb.toString();
                        }
                        if (!value.equals("PropVal")) {
                            parseKeyAndValue(key, value, digits, plane + i, 1);
                        }
                        propType = null;
                        key = null;
                        value = null;
                        nEmptyTokens = 0;
                    }
                }
            }
            plane += ifds.size();
            parser.getStream().close();
        } catch (IOException e) {
            LOGGER.debug("Failed to read metadata from " + path, e);
        }
    }
}

Example 54 with TiffParser

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

the class FV1000Reader method getOptimalTileWidth.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
    FormatTools.assertId(currentId, true, 1);
    RandomAccessInputStream plane = getPlane(getSeries(), 0);
    if (plane == null)
        return super.getOptimalTileWidth();
    try {
        TiffParser tp = new TiffParser(plane);
        IFD ifd = tp.getFirstIFD();
        plane.close();
        return (int) ifd.getTileWidth();
    } 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 55 with TiffParser

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

the class FV1000Reader method getOptimalTileHeight.

/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
    FormatTools.assertId(currentId, true, 1);
    RandomAccessInputStream plane = getPlane(getSeries(), 0);
    if (plane == null)
        return super.getOptimalTileHeight();
    try {
        TiffParser tp = new TiffParser(plane);
        IFD ifd = tp.getFirstIFD();
        plane.close();
        return (int) ifd.getTileLength();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    }
    return super.getOptimalTileHeight();
}