Examples with FormatException loci.formats.FormatException used on opensource projects

Example 46 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class ZeissCZIReader method checkPALM.

private boolean checkPALM(String xml) throws FormatException, IOException {
    Element root = null;
    try {
        ByteArrayInputStream s = new ByteArrayInputStream(xml.getBytes(Constants.ENCODING));
        root = parser.parse(s).getDocumentElement();
        s.close();
    } catch (SAXException e) {
        throw new FormatException(e);
    }
    if (root == null) {
        throw new FormatException("Could not parse the XML metadata.");
    }
    NodeList customAttributes = root.getElementsByTagName("CustomAttributes");
    if (customAttributes != null && customAttributes.getLength() > 0) {
        Element attributes = (Element) customAttributes.item(0);
        if (attributes != null) {
            NodeList lsmTags = attributes.getElementsByTagName("LsmTag");
            if (lsmTags != null) {
                for (int i = 0; i < lsmTags.getLength(); i++) {
                    Element tag = (Element) lsmTags.item(i);
                    String name = tag.getAttribute("Name");
                    if (name.toLowerCase().startsWith("palm")) {
                        return true;
                    }
                }
            }
        }
    }
    NodeList experiments = root.getElementsByTagName("Experiment");
    if (experiments == null || experiments.getLength() == 0) {
        return false;
    }
    Element experimentBlock = getFirstNode((Element) experiments.item(0), "ExperimentBlocks");
    Element acquisition = getFirstNode(experimentBlock, "AcquisitionBlock");
    if (acquisition == null) {
        return false;
    }
    Element multiTrack = getFirstNode(acquisition, "MultiTrackSetup");
    if (multiTrack == null) {
        return false;
    }
    Element trackSetup = getFirstNode(multiTrack, "TrackSetup");
    if (trackSetup == null) {
        return false;
    }
    Element palmSlider = getFirstNode(trackSetup, "PalmSlider");
    if (palmSlider == null) {
        return false;
    }
    return Boolean.parseBoolean(palmSlider.getTextContent());
}

Example 47 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class TillVisionReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "vws")) {
        Location pst = new Location(id).getAbsoluteFile();
        String name = pst.getParentFile().getName();
        Location parent = pst.getParentFile().getParentFile();
        Location vwsFile = new Location(parent, name.replaceAll(".pst", ".vws"));
        if (vwsFile.exists() && !vwsFile.isDirectory()) {
            id = vwsFile.getAbsolutePath();
        } else if (vwsFile.isDirectory()) {
            parent = pst.getParentFile();
            String[] list = parent.list(true);
            boolean foundVWS = false;
            for (String f : list) {
                if (checkSuffix(f, "vws")) {
                    id = new Location(parent, f).getAbsolutePath();
                    foundVWS = true;
                    break;
                }
            }
            if (!foundVWS) {
                throw new FormatException("Could not find .vws file.");
            }
        } else
            throw new FormatException("Could not find .vws file.");
    }
    super.initFile(id);
    exposureTimes = new HashMap<Integer, Double>();
    POIService poi = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        poi = factory.getInstance(POIService.class);
    } catch (DependencyException de) {
        throw new FormatException("POI library not found", de);
    }
    poi.initialize(id);
    Vector<String> documents = poi.getDocumentList();
    int nImages = 0;
    final Hashtable<String, Object> tmpSeriesMetadata = new Hashtable<String, Object>();
    for (String name : documents) {
        LOGGER.debug("Reading {}", name);
        if (name.equals("Root Entry" + File.separator + "Contents")) {
            RandomAccessInputStream s = poi.getDocumentStream(name);
            s.order(true);
            boolean specialCImage = false;
            int nFound = 0;
            Long[] cimages = null;
            Location dir = new Location(id).getAbsoluteFile().getParentFile();
            String[] list = dir.list(true);
            boolean hasPST = false;
            for (String f : list) {
                if (checkSuffix(f, "pst")) {
                    hasPST = true;
                    break;
                }
            }
            if (!hasPST) {
                cimages = findImages(s);
                nFound = cimages.length;
                if (nFound == 0) {
                    s.seek(13);
                    int len = s.readShort();
                    String type = s.readString(len);
                    if (type.equals("CImage")) {
                        nFound = 1;
                        cimages = new Long[] { s.getFilePointer() + 6 };
                        specialCImage = true;
                    }
                }
                embeddedImages = nFound > 0;
            }
            LOGGER.debug("Images are {}embedded", embeddedImages ? "" : "not ");
            if (embeddedImages) {
                core.clear();
                embeddedOffset = new long[nFound];
                for (int i = 0; i < nFound; i++) {
                    CoreMetadata ms = new CoreMetadata();
                    core.add(ms);
                    s.seek(cimages[i]);
                    int len = s.read();
                    String imageName = s.readString(len);
                    imageNames.add(imageName);
                    if (specialCImage) {
                        s.seek(1280);
                    } else {
                        while (true) {
                            if (s.readString(2).equals("sB")) {
                                break;
                            } else
                                s.seek(s.getFilePointer() - 1);
                        }
                    }
                    s.skipBytes(20);
                    ms.sizeX = s.readInt();
                    ms.sizeY = s.readInt();
                    ms.sizeZ = s.readInt();
                    ms.sizeC = s.readInt();
                    ms.sizeT = s.readInt();
                    ms.pixelType = convertPixelType(s.readInt());
                    if (specialCImage) {
                        embeddedOffset[i] = s.getFilePointer() + 27;
                    } else {
                        embeddedOffset[i] = s.getFilePointer() + 31;
                    }
                }
                if (in != null)
                    in.close();
                in = poi.getDocumentStream(name);
                s.close();
                break;
            }
            s.seek(0);
            int lowerBound = 0;
            int upperBound = 0x1000;
            while (s.getFilePointer() < s.length() - 2) {
                LOGGER.debug("  Looking for image at {}", s.getFilePointer());
                s.order(false);
                int nextOffset = findNextOffset(s);
                if (nextOffset < 0 || nextOffset >= s.length())
                    break;
                s.seek(nextOffset);
                s.skipBytes(3);
                int len = s.readShort();
                if (len <= 0)
                    continue;
                imageNames.add(s.readString(len));
                if (s.getFilePointer() + 8 >= s.length())
                    break;
                s.skipBytes(6);
                s.order(true);
                len = s.readShort();
                if (nImages == 0 && len > upperBound * 2 && len < upperBound * 4) {
                    lowerBound = 512;
                    upperBound = 0x4000;
                }
                if (len < lowerBound || len > upperBound)
                    continue;
                String description = s.readString(len);
                LOGGER.debug("Description: {}", description);
                // parse key/value pairs from description
                String dateTime = "";
                String[] lines = description.split("[\r\n]");
                for (String line : lines) {
                    line = line.trim();
                    int colon = line.indexOf(':');
                    if (colon != -1 && !line.startsWith(";")) {
                        String key = line.substring(0, colon).trim();
                        String value = line.substring(colon + 1).trim();
                        String metaKey = "Series " + nImages + " " + key;
                        addMeta(metaKey, value, tmpSeriesMetadata);
                        if (key.equals("Start time of experiment")) {
                            // HH:mm:ss aa OR HH:mm:ss.sss aa
                            dateTime += " " + value;
                        } else if (key.equals("Date")) {
                            // mm/dd/yy ?
                            dateTime = value + " " + dateTime;
                        } else if (key.equals("Exposure time [ms]")) {
                            double exp = Double.parseDouble(value) / 1000;
                            exposureTimes.put(nImages, exp);
                        } else if (key.equals("Image type")) {
                            types.add(value);
                        }
                    }
                }
                dateTime = dateTime.trim();
                if (!dateTime.equals("")) {
                    boolean success = false;
                    for (String format : DATE_FORMATS) {
                        try {
                            dateTime = DateTools.formatDate(dateTime, format, ".");
                            success = true;
                        } catch (NullPointerException e) {
                        }
                    }
                    dates.add(success ? dateTime : "");
                }
                nImages++;
            }
            s.close();
        }
    }
    Location directory = new Location(currentId).getAbsoluteFile().getParentFile();
    String[] pixelsFile = new String[nImages];
    if (!embeddedImages) {
        if (nImages == 0) {
            throw new FormatException("No images found.");
        }
        // look for appropriate pixels files
        String[] files = directory.list(true);
        String name = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
        int nextFile = 0;
        for (String f : files) {
            if (checkSuffix(f, "pst")) {
                Location pst = new Location(directory, f);
                if (pst.isDirectory() && f.startsWith(name)) {
                    String[] subfiles = pst.list(true);
                    Arrays.sort(subfiles);
                    for (String q : subfiles) {
                        if (checkSuffix(q, "pst") && nextFile < nImages) {
                            pixelsFile[nextFile++] = f + File.separator + q;
                        }
                    }
                }
            }
        }
        if (nextFile == 0) {
            for (String f : files) {
                if (checkSuffix(f, "pst")) {
                    pixelsFile[nextFile++] = new Location(directory, f).getAbsolutePath();
                }
            }
            if (nextFile == 0)
                throw new FormatException("No image files found.");
        }
    }
    Arrays.sort(pixelsFile);
    int nSeries = core.size();
    if (!embeddedImages) {
        core.clear();
        nSeries = nImages;
    }
    pixelsFiles = new String[nSeries];
    infFiles = new String[nSeries];
    Object[] metadataKeys = tmpSeriesMetadata.keySet().toArray();
    IniParser parser = new IniParser();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms;
        if (!embeddedImages) {
            ms = new CoreMetadata();
            core.add(ms);
            setSeries(i);
            // make sure that pixels file exists
            String file = pixelsFile[i];
            file = file.replace('/', File.separatorChar);
            file = file.replace('\\', File.separatorChar);
            String oldFile = file;
            Location f = new Location(directory, oldFile);
            if (!f.exists()) {
                oldFile = oldFile.substring(oldFile.lastIndexOf(File.separator) + 1);
                f = new Location(directory, oldFile);
                if (!f.exists()) {
                    throw new FormatException("Could not find pixels file '" + file);
                }
            }
            file = f.getAbsolutePath();
            pixelsFiles[i] = file;
            // read key/value pairs from .inf files
            int dot = file.lastIndexOf(".");
            String inf = file.substring(0, dot) + ".inf";
            infFiles[i] = inf;
            BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inf), Constants.ENCODING));
            IniList data = parser.parseINI(reader);
            reader.close();
            IniTable infoTable = data.getTable("Info");
            ms.sizeX = Integer.parseInt(infoTable.get("Width"));
            ms.sizeY = Integer.parseInt(infoTable.get("Height"));
            ms.sizeC = Integer.parseInt(infoTable.get("Bands"));
            ms.sizeZ = Integer.parseInt(infoTable.get("Slices"));
            ms.sizeT = Integer.parseInt(infoTable.get("Frames"));
            int dataType = Integer.parseInt(infoTable.get("Datatype"));
            ms.pixelType = convertPixelType(dataType);
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                HashMap<String, String> iniMap = data.flattenIntoHashMap();
                ms.seriesMetadata.putAll(iniMap);
            }
        } else {
            ms = core.get(i);
            setSeries(i);
        }
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
        ms.rgb = false;
        ms.littleEndian = true;
        ms.dimensionOrder = "XYCZT";
        ms.seriesMetadata = new Hashtable<String, Object>();
        for (Object key : metadataKeys) {
            String keyName = key.toString();
            if (keyName.startsWith("Series " + i + " ")) {
                keyName = keyName.replaceAll("Series " + i + " ", "");
                ms.seriesMetadata.put(keyName, tmpSeriesMetadata.get(key));
            }
        }
    }
    setSeries(0);
    populateMetadataStore();
    poi.close();
    poi = null;
}

Example 48 with FormatException

use of loci.formats.FormatException 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 49 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class VarianFDFReader method parseFDF.

// -- Helper methods --
private void parseFDF(String file) throws FormatException, IOException {
    in = new RandomAccessInputStream(file);
    CoreMetadata m = core.get(0);
    boolean storedFloats = false;
    boolean multifile = false;
    String data = in.readString(Character.toString((char) 0x0c));
    String[] lines = data.split("\n");
    for (String line : lines) {
        line = line.trim();
        if (line.length() == 0)
            break;
        if (line.startsWith("#"))
            continue;
        int space = line.indexOf(' ');
        int eq = line.indexOf('=');
        String type = line.substring(0, space).trim();
        String var = line.substring(space, eq).trim();
        String value = line.substring(eq + 1, line.indexOf(';')).trim();
        if (var.equals("*storage")) {
            storedFloats = value.equals("\"float\"");
        }
        if (var.equals("bits")) {
            m.bitsPerPixel = Integer.parseInt(value);
            if (value.equals("8")) {
                m.pixelType = FormatTools.UINT8;
            } else if (value.equals("16")) {
                m.pixelType = FormatTools.UINT16;
            } else if (value.equals("32")) {
                if (storedFloats) {
                    m.pixelType = FormatTools.FLOAT;
                } else
                    m.pixelType = FormatTools.UINT32;
            } else
                throw new FormatException("Unsupported bits: " + value);
        } else if (var.equals("matrix[]")) {
            String[] values = parseArray(value);
            m.sizeX = (int) Double.parseDouble(values[0]);
            m.sizeY = (int) Double.parseDouble(values[1]);
            if (values.length > 2) {
                m.sizeZ = (int) Double.parseDouble(values[2]);
            }
        } else if (var.equals("slices")) {
            m.sizeZ = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("echoes")) {
            m.sizeT = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("span[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                pixelSizeX = computePhysicalSize(getSizeX(), values[0], units[0]);
            }
            if (values.length > 1) {
                pixelSizeY = computePhysicalSize(getSizeY(), values[1], units[1]);
            }
            if (values.length > 2) {
                pixelSizeZ = computePhysicalSize(getSizeZ(), values[2], units[2]);
            }
        } else if (var.equals("origin[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                final double size = computePhysicalSize(1, values[0], units[0]);
                originX = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("X position for position #1", originX);
            }
            if (values.length > 1) {
                final double size = computePhysicalSize(1, values[1], units[1]);
                originY = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Y position for position #1", originY);
            }
            if (values.length > 2) {
                final double size = computePhysicalSize(1, values[2], units[2]);
                originZ = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Z position for position #1", originZ);
            }
        } else if (var.equals("*abscissa[]")) {
            units = parseArray(value);
        } else if (var.equals("bigendian")) {
            m.littleEndian = value.equals("0");
            in.order(isLittleEndian());
        }
        addGlobalMeta(var, value);
    }
    if (multifile && files.isEmpty()) {
        Location thisFile = new Location(file).getAbsoluteFile();
        Location parent = thisFile.getParentFile();
        String[] list = parent.list(true);
        Arrays.sort(list);
        for (String f : list) {
            if (checkSuffix(f, "fdf") && f.length() == thisFile.getName().length()) {
                files.add(new Location(parent, f).getAbsolutePath());
            }
        }
    }
}

Example 50 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class VolocityClippingReader 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);
    m.littleEndian = in.read() == 'I';
    in.order(isLittleEndian());
    in.skipBytes(4);
    String magicString = in.readString(4);
    if (!magicString.equals(CLIPPING_MAGIC_STRING)) {
        throw new FormatException("Found invalid magic string: " + magicString);
    }
    int check = in.readInt();
    while (check != 0x208 && check != AISF) {
        in.seek(in.getFilePointer() - 3);
        check = in.readInt();
    }
    if (check == AISF) {
        m.littleEndian = false;
        in.order(isLittleEndian());
        in.skipBytes(28);
    }
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    m.sizeZ = in.readInt();
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = getSizeZ() * getSizeT();
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT8;
    pixelOffset = in.getFilePointer() + 65;
    if (getSizeX() * getSizeY() * 100 >= in.length()) {
        while (in.getFilePointer() < in.length()) {
            try {
                byte[] b = new LZOCodec().decompress(in, null);
                if (b.length > 0 && (b.length % (getSizeX() * getSizeY())) == 0) {
                    int bytes = b.length / (getSizeX() * getSizeY());
                    m.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, false);
                    break;
                }
            } catch (EOFException e) {
            }
            pixelOffset++;
            in.seek(pixelOffset);
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}