Examples with RandomAccessInputStream loci.common.RandomAccessInputStream used on opensource projects

Example 51 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class ZeissLSMReader 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 (getSeriesCount() > 1) {
        in.close();
        in = new RandomAccessInputStream(getLSMFileFromSeries(getSeries()));
        in.order(!isLittleEndian());
        tiffParser = new TiffParser(in);
    } else if (tiffParser == null) {
        tiffParser = new TiffParser(in);
    }
    IFDList ifds = ifdsList.get(getSeries());
    if (splitPlanes && getSizeC() > 1 && ifds.size() == getSizeZ() * getSizeT()) {
        int bpp = FormatTools.getBytesPerPixel(getPixelType());
        int plane = no / getSizeC();
        int c = no % getSizeC();
        Region region = new Region(x, y, w, h);
        if (prevPlane != plane || prevBuf == null || prevBuf.length < w * h * bpp * getSizeC() || !region.equals(prevRegion)) {
            prevBuf = new byte[w * h * bpp * getSizeC()];
            tiffParser.getSamples(ifds.get(plane), prevBuf, x, y, w, h);
            prevPlane = plane;
            prevRegion = region;
        }
        ImageTools.splitChannels(prevBuf, buf, c, getSizeC(), bpp, false, false, w * h * bpp);
        prevChannel = c;
    } else {
        tiffParser.getSamples(ifds.get(no), buf, x, y, w, h);
        prevChannel = getZCTCoords(no)[1];
    }
    if (getSeriesCount() > 1)
        in.close();
    return buf;
}

Example 52 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class ZeissLSMReader method getExtraSeries.

private int getExtraSeries(String file) throws FormatException, IOException {
    if (in != null)
        in.close();
    in = new RandomAccessInputStream(file, 16);
    boolean littleEndian = in.read() == TiffConstants.LITTLE;
    in.order(littleEndian);
    tiffParser = new TiffParser(in);
    IFD ifd = tiffParser.getFirstIFD();
    RandomAccessInputStream ras = getCZTag(ifd);
    if (ras == null)
        return 1;
    ras.order(littleEndian);
    ras.seek(264);
    dimensionP = ras.readInt();
    dimensionM = ras.readInt();
    ras.close();
    int nSeries = dimensionM * dimensionP;
    return nSeries <= 0 ? 1 : nSeries;
}

Example 53 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream 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 54 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class UnisokuReader 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);
    RandomAccessInputStream dat = new RandomAccessInputStream(datFile);
    dat.order(isLittleEndian());
    readPlane(dat, x, y, w, h, buf);
    dat.close();
    return buf;
}

Example 55 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream 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);
}