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Example 76 with RandomAccessInputStream

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

the class FEIReader 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);
    in.order(true);
    CoreMetadata m = core.get(0);
    LOGGER.info("Reading file header");
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(44);
        float magnification = in.readFloat();
        float kV = in.readFloat() / 1000;
        float wd = in.readFloat();
        in.skipBytes(12);
        float spot = in.readFloat();
        addGlobalMeta("Magnification", magnification);
        addGlobalMeta("kV", kV);
        addGlobalMeta("Working distance", wd);
        addGlobalMeta("Spot", spot);
    }
    in.seek(514);
    m.sizeX = in.readShort() - INVALID_PIXELS;
    m.sizeY = in.readShort();
    in.skipBytes(4);
    headerSize = in.readShort();
    // always one grayscale plane per file
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.littleEndian = true;
    m.pixelType = FormatTools.UINT8;
    m.rgb = false;
    m.indexed = false;
    m.interleaved = false;
    m.dimensionOrder = "XYCZT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}
Also used : MetadataStore(loci.formats.meta.MetadataStore) RandomAccessInputStream(loci.common.RandomAccessInputStream) CoreMetadata(loci.formats.CoreMetadata)

Example 77 with RandomAccessInputStream

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

the class FV1000Reader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    parser.setCommentDelimiter(null);
    isOIB = checkSuffix(id, OIB_SUFFIX);
    if (isOIB) {
        initPOIService();
    }
    // mappedOIF is used to distinguish between datasets that are being read
    // directly (e.g. using ImageJ or showinf), and datasets that are being
    // imported through omebf. In the latter case, the necessary directory
    // structure is not preserved (only relative file names are stored in
    // OMEIS), so we will need to use slightly different logic to build the
    // list of associated files.
    boolean mappedOIF = !isOIB && !new File(id).getAbsoluteFile().exists();
    wavelengths = new ArrayList<Double>();
    illuminations = new ArrayList<String>();
    channels = new ArrayList<ChannelData>();
    planes = new ArrayList<PlaneData>();
    String oifName = null;
    if (isOIB) {
        oifName = mapOIBFiles();
    } else {
        // make sure we have the OIF file, not a TIFF
        if (!checkSuffix(id, OIF_SUFFIX)) {
            currentId = findOIFFile(id);
            initFile(currentId);
        }
        oifName = currentId;
    }
    String oifPath = new Location(oifName).getAbsoluteFile().getAbsolutePath();
    if (mappedOIF) {
        oifPath = oifName.substring(0, oifName.lastIndexOf(File.separator) + 1);
    }
    String path = isOIB ? "" : oifPath.substring(0, oifPath.lastIndexOf(File.separator) + 1);
    try {
        RandomAccessInputStream s = getFile(oifName);
        s.close();
    } catch (IOException e) {
        oifName = oifName.replaceAll(".oif", ".OIF");
    }
    // parse key/value pairs from the OIF file
    code = new String[NUM_DIMENSIONS];
    size = new String[NUM_DIMENSIONS];
    pixelSize = new Double[NUM_DIMENSIONS];
    previewNames = new ArrayList<String>();
    SortedMap<Integer, String> previewFileNames = new TreeMap<Integer, String>();
    boolean laserEnabled = true;
    IniList f = getIniFile(oifName);
    IniTable saveInfo = f.getTable("ProfileSaveInfo");
    String[] saveKeys = saveInfo.keySet().toArray(new String[saveInfo.size()]);
    for (String key : saveKeys) {
        String value = saveInfo.get(key).toString();
        value = sanitizeValue(value).trim();
        if (key.startsWith("IniFileName") && key.indexOf("Thumb") == -1 && !isPreviewName(value)) {
            filenames.put(new Integer(key.substring(11)), value);
        } else if (key.startsWith("RoiFileName") && key.indexOf("Thumb") == -1 && !isPreviewName(value)) {
            try {
                roiFilenames.put(new Integer(key.substring(11)), value);
            } catch (NumberFormatException e) {
            }
        } else if (key.equals("PtyFileNameS"))
            ptyStart = value;
        else if (key.equals("PtyFileNameE"))
            ptyEnd = value;
        else if (key.equals("PtyFileNameT2"))
            ptyPattern = value;
        else if (key.indexOf("Thumb") != -1) {
            if (thumbId == null)
                thumbId = value.trim();
        } else if (key.startsWith("LutFileName")) {
            lutNames.add(path + value);
        } else if (isPreviewName(value)) {
            try {
                RandomAccessInputStream s = getFile(path + value.trim());
                if (s != null) {
                    s.close();
                    Integer previewIndex = getPreviewNameIndex(key);
                    if (previewIndex != null) {
                        previewFileNames.put(previewIndex, path + value.trim());
                    } else {
                        previewNames.add(path + value.trim());
                    }
                }
            } catch (FormatException e) {
                LOGGER.debug("Preview file not found", e);
            } catch (IOException e) {
                LOGGER.debug("Preview file not found", e);
            }
        }
    }
    // Store sorted list of preview names
    previewNames.addAll(previewFileNames.values());
    if (filenames.isEmpty())
        addPtyFiles();
    for (int i = 0; i < NUM_DIMENSIONS; i++) {
        IniTable commonParams = f.getTable("Axis " + i + " Parameters Common");
        code[i] = commonParams.get("AxisCode");
        size[i] = commonParams.get("MaxSize");
        double end = Double.parseDouble(commonParams.get("EndPosition"));
        double start = Double.parseDouble(commonParams.get("StartPosition"));
        pixelSize[i] = end - start;
    }
    IniTable referenceParams = f.getTable("Reference Image Parameter");
    imageDepth = Integer.parseInt(referenceParams.get("ImageDepth"));
    pixelSizeX = referenceParams.get("WidthConvertValue");
    pixelSizeY = referenceParams.get("HeightConvertValue");
    String ripValidBitCounts = referenceParams.get("ValidBitCounts");
    if (ripValidBitCounts != null) {
        validBits = Integer.parseInt(ripValidBitCounts);
    }
    int index = 0;
    IniTable laser = f.getTable("Laser " + index + " Parameters");
    while (laser != null) {
        laserEnabled = laser.get("Laser Enable").equals("1");
        if (laserEnabled) {
            wavelengths.add(new Double(laser.get("LaserWavelength")));
        }
        creationDate = laser.get("ImageCaputreDate");
        if (creationDate == null) {
            creationDate = laser.get("ImageCaptureDate");
        }
        index++;
        laser = f.getTable("Laser " + index + " Parameters");
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        index = 1;
        IniTable guiChannel = f.getTable("GUI Channel " + index + " Parameters");
        while (guiChannel != null) {
            ChannelData channel = new ChannelData();
            channel.gain = DataTools.parseDouble(guiChannel.get("AnalogPMTGain"));
            channel.voltage = DataTools.parseDouble(guiChannel.get("AnalogPMTVoltage"));
            channel.barrierFilter = channel.getFilter(guiChannel.get("BF Name"));
            channel.active = Integer.parseInt(guiChannel.get("CH Activate")) != 0;
            channel.name = guiChannel.get("CH Name");
            channel.dyeName = guiChannel.get("DyeName");
            channel.emissionFilter = channel.getFilter(guiChannel.get("EmissionDM Name"));
            channel.emWave = DataTools.parseDouble(guiChannel.get("EmissionWavelength"));
            channel.excitationFilter = channel.getFilter(guiChannel.get("ExcitationDM Name"));
            channel.exWave = DataTools.parseDouble(guiChannel.get("ExcitationWavelength"));
            channels.add(channel);
            index++;
            guiChannel = f.getTable("GUI Channel " + index + " Parameters");
        }
        index = 1;
        IniTable channel = f.getTable("Channel " + index + " Parameters");
        while (channel != null) {
            String illumination = channel.get("LightType");
            if (illumination != null)
                illumination = illumination.toLowerCase();
            if (illumination == null) {
            // Ignored
            } else if (illumination.indexOf("fluorescence") != -1) {
                illumination = "Epifluorescence";
            } else if (illumination.indexOf("transmitted") != -1) {
                illumination = "Transmitted";
            } else
                illumination = null;
            illuminations.add(illumination);
            index++;
            channel = f.getTable("Channel " + index + " Parameters");
        }
        HashMap<String, String> iniMap = f.flattenIntoHashMap();
        metadata.putAll(iniMap);
    }
    LOGGER.info("Initializing helper readers");
    if (previewNames.size() > 0) {
        final List<String> v = new ArrayList<String>();
        for (int i = 0; i < previewNames.size(); i++) {
            String ss = previewNames.get(i);
            ss = replaceExtension(ss, "pty", "tif");
            if (ss.endsWith(".tif"))
                v.add(ss);
        }
        previewNames = v;
        if (previewNames.size() > 0) {
            core.clear();
            core.add(new CoreMetadata());
            core.add(new CoreMetadata());
            IFDList ifds = null;
            CoreMetadata ms1 = core.get(1);
            for (String previewName : previewNames) {
                RandomAccessInputStream preview = getFile(previewName);
                TiffParser tp = new TiffParser(preview);
                ifds = tp.getIFDs();
                preview.close();
                tp = null;
                ms1.imageCount += ifds.size();
            }
            ms1.sizeX = (int) ifds.get(0).getImageWidth();
            ms1.sizeY = (int) ifds.get(0).getImageLength();
            ms1.sizeZ = 1;
            ms1.sizeT = 1;
            ms1.sizeC = ms1.imageCount;
            ms1.rgb = false;
            int bits = ifds.get(0).getBitsPerSample()[0];
            while ((bits % 8) != 0) bits++;
            bits /= 8;
            ms1.pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
            ms1.dimensionOrder = "XYCZT";
            ms1.indexed = false;
        }
    }
    CoreMetadata ms0 = core.get(0);
    ms0.imageCount = filenames.size();
    tiffs = new ArrayList<String>(getImageCount());
    thumbReader = new BMPReader();
    if (thumbId != null) {
        thumbId = replaceExtension(thumbId, "pty", "bmp");
        thumbId = sanitizeFile(thumbId, path);
    }
    LOGGER.info("Reading additional metadata");
    // open each INI file (.pty extension) and build list of TIFF files
    String tiffPath = null;
    ms0.dimensionOrder = "XY";
    final Map<String, String> values = new HashMap<String, String>();
    final List<String> baseKeys = new ArrayList<String>();
    for (int i = 0, ii = 0; ii < getImageCount(); i++, ii++) {
        String file = filenames.get(i);
        while (file == null) file = filenames.get(++i);
        file = sanitizeFile(file, path);
        if (file.indexOf(File.separator) != -1) {
            tiffPath = file.substring(0, file.lastIndexOf(File.separator));
        } else
            tiffPath = file;
        Location ptyFile = new Location(file);
        if (!isOIB && !ptyFile.exists()) {
            LOGGER.warn("Could not find .pty file ({}); guessing at the " + "corresponding TIFF file.", file);
            String tiff = replaceExtension(file, "pty", "tif");
            Location tiffFile = new Location(tiff);
            if (tiffFile.exists()) {
                tiffs.add(ii, tiffFile.getAbsolutePath());
                continue;
            } else {
                if (!tiffFile.getParentFile().exists()) {
                    String realOIFName = new Location(currentId).getName();
                    String basePath = tiffFile.getParentFile().getParent();
                    if (mappedOIF) {
                        tiffPath = basePath + File.separator + realOIFName + ".files";
                        ptyFile = new Location(tiffPath, ptyFile.getName());
                        file = ptyFile.getAbsolutePath();
                    } else {
                        Location newFile = new Location(basePath, realOIFName + ".files");
                        ptyFile = new Location(newFile, ptyFile.getName());
                        file = ptyFile.getAbsolutePath();
                        tiffPath = newFile.getAbsolutePath();
                    }
                }
            }
        } else if (!isOIB) {
            file = ptyFile.getAbsolutePath();
        }
        IniList pty = getIniFile(file);
        IniTable fileInfo = pty.getTable("File Info");
        file = sanitizeValue(fileInfo.get("DataName"));
        if (!isPreviewName(file)) {
            while (file.indexOf("GST") != -1) {
                file = removeGST(file);
            }
            if (isOIB) {
                file = tiffPath + File.separator + file;
            } else
                file = new Location(tiffPath, file).getAbsolutePath();
            file = replaceExtension(file, "pty", "tif");
            tiffs.add(ii, file);
        }
        PlaneData plane = new PlaneData();
        for (int dim = 0; dim < NUM_DIMENSIONS; dim++) {
            IniTable axis = pty.getTable("Axis " + dim + " Parameters");
            if (axis == null)
                break;
            boolean addAxis = Integer.parseInt(axis.get("Number")) > 1;
            if (dim == 2) {
                if (addAxis && getDimensionOrder().indexOf('C') == -1) {
                    ms0.dimensionOrder += 'C';
                }
            } else if (dim == 3) {
                if (addAxis && getDimensionOrder().indexOf('Z') == -1) {
                    ms0.dimensionOrder += 'Z';
                }
                final Double number = Double.valueOf(axis.get("AbsPositionValue"));
                plane.positionZ = new Length(number, UNITS.REFERENCEFRAME);
            } else if (dim == 4) {
                if (addAxis && getDimensionOrder().indexOf('T') == -1) {
                    ms0.dimensionOrder += 'T';
                }
                // divide by 1000, as the position is in milliseconds
                // and DeltaT is in seconds
                plane.deltaT = Double.parseDouble(axis.get("AbsPositionValue")) / 1000;
            } else if (dim == 7) {
                try {
                    String xPos = axis.get("AbsPositionValueX");
                    if (xPos != null) {
                        final Double number = Double.valueOf(xPos);
                        plane.positionX = new Length(number, UNITS.REFERENCEFRAME);
                    }
                } catch (NumberFormatException e) {
                }
                try {
                    String yPos = axis.get("AbsPositionValueY");
                    if (yPos != null) {
                        final Double number = Double.valueOf(yPos);
                        plane.positionY = new Length(number, UNITS.REFERENCEFRAME);
                    }
                } catch (NumberFormatException e) {
                }
            }
        }
        ms0.bitsPerPixel = validBits;
        planes.add(plane);
        IniTable acquisition = pty.getTable("Acquisition Parameters Common");
        if (acquisition != null) {
            magnification = acquisition.get("Magnification");
            lensNA = acquisition.get("ObjectiveLens NAValue");
            objectiveName = acquisition.get("ObjectiveLens Name");
            workingDistance = acquisition.get("ObjectiveLens WDValue");
            pinholeSize = acquisition.get("PinholeDiameter");
            String validBitCounts = acquisition.get("ValidBitCounts");
            if (validBitCounts != null) {
                ms0.bitsPerPixel = Integer.parseInt(validBitCounts);
            }
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            for (IniTable table : pty) {
                String[] keys = table.keySet().toArray(new String[table.size()]);
                for (String key : keys) {
                    values.put("Image " + ii + " : " + key, table.get(key));
                    if (!baseKeys.contains(key))
                        baseKeys.add(key);
                }
            }
        }
    }
    for (String key : baseKeys) {
        if (key.equals("DataName") || key.indexOf("FileName") >= 0)
            break;
        boolean equal = true;
        String first = values.get("Image 0 : " + key);
        for (int i = 1; i < getImageCount(); i++) {
            if (!first.equals(values.get("Image " + i + " : " + key))) {
                equal = false;
                break;
            }
        }
        if (equal) {
            addGlobalMeta(key, first);
        } else {
            for (int i = 0; i < getImageCount(); i++) {
                String k = "Image " + i + " : " + key;
                addGlobalMeta(k, values.get(k));
            }
        }
    }
    if (tiffs.size() != getImageCount()) {
        ms0.imageCount = tiffs.size();
    }
    usedFiles = new ArrayList<String>();
    if (tiffPath != null) {
        usedFiles.add(isOIB ? id : oifName);
        if (!isOIB) {
            Location dir = new Location(tiffPath);
            if (!mappedOIF && !dir.exists()) {
                throw new FormatException("Required directory " + tiffPath + " was not found.");
            }
            String[] list = mappedOIF ? Location.getIdMap().keySet().toArray(new String[0]) : dir.list(true);
            for (int i = 0; i < list.length; i++) {
                if (mappedOIF)
                    usedFiles.add(list[i]);
                else {
                    String p = new Location(tiffPath, list[i]).getAbsolutePath();
                    String check = p.toLowerCase();
                    if (!check.endsWith(".tif") && !check.endsWith(".pty") && !check.endsWith(".roi") && !check.endsWith(".lut") && !check.endsWith(".bmp")) {
                        continue;
                    }
                    usedFiles.add(p);
                }
            }
        }
    }
    LOGGER.info("Populating metadata");
    // calculate axis sizes
    int realChannels = 0;
    for (int i = 0; i < NUM_DIMENSIONS; i++) {
        int ss = Integer.parseInt(size[i]);
        if (pixelSize[i] == null)
            pixelSize[i] = 1.0;
        if (code[i].equals("X"))
            ms0.sizeX = ss;
        else if (code[i].equals("Y") && ss > 1)
            ms0.sizeY = ss;
        else if (code[i].equals("Z")) {
            if (getSizeY() == 0) {
                ms0.sizeY = ss;
            } else {
                ms0.sizeZ = ss;
                // Z size stored in nm
                pixelSizeZ = Math.abs((pixelSize[i].doubleValue() / (getSizeZ() - 1)) / 1000);
            }
        } else if (code[i].equals("T")) {
            if (getSizeY() == 0) {
                ms0.sizeY = ss;
            } else {
                ms0.sizeT = ss;
                pixelSizeT = Math.abs((pixelSize[i].doubleValue() / (getSizeT() - 1)) / 1000);
            }
        } else if (ss > 0) {
            if (getSizeC() == 0)
                ms0.sizeC = ss;
            else
                ms0.sizeC *= ss;
            if (code[i].equals("C"))
                realChannels = ss;
        }
    }
    if (getSizeZ() == 0)
        ms0.sizeZ = 1;
    if (getSizeC() == 0)
        ms0.sizeC = 1;
    if (getSizeT() == 0)
        ms0.sizeT = 1;
    if (getImageCount() == getSizeC() && getSizeY() == 1) {
        ms0.imageCount *= getSizeZ() * getSizeT();
    } else if (getImageCount() == getSizeC()) {
        ms0.sizeZ = 1;
        ms0.sizeT = 1;
    }
    if (getSizeZ() * getSizeT() * getSizeC() != getImageCount()) {
        int diff = (getSizeZ() * getSizeC() * getSizeT()) - getImageCount();
        if (diff == previewNames.size() || diff < 0) {
            diff /= getSizeC();
            if (getSizeT() > 1 && getSizeZ() == 1)
                ms0.sizeT -= diff;
            else if (getSizeZ() > 1 && getSizeT() == 1)
                ms0.sizeZ -= diff;
        } else
            ms0.imageCount += diff;
    }
    if (getSizeC() > 1 && getSizeZ() == 1 && getSizeT() == 1) {
        if (getDimensionOrder().indexOf('C') == -1)
            ms0.dimensionOrder += 'C';
    }
    if (getDimensionOrder().indexOf('Z') == -1)
        ms0.dimensionOrder += 'Z';
    if (getDimensionOrder().indexOf('C') == -1)
        ms0.dimensionOrder += 'C';
    if (getDimensionOrder().indexOf('T') == -1)
        ms0.dimensionOrder += 'T';
    ms0.pixelType = FormatTools.pixelTypeFromBytes(imageDepth, false, false);
    try {
        RandomAccessInputStream thumb = getFile(thumbId);
        byte[] b = new byte[(int) thumb.length()];
        thumb.read(b);
        thumb.close();
        Location.mapFile("thumbnail.bmp", new ByteArrayHandle(b));
        thumbReader.setId("thumbnail.bmp");
        for (int i = 0; i < getSeriesCount(); i++) {
            core.get(i).thumbSizeX = thumbReader.getSizeX();
            core.get(i).thumbSizeY = thumbReader.getSizeY();
        }
        thumbReader.close();
        Location.mapFile("thumbnail.bmp", null);
    } catch (IOException e) {
        LOGGER.debug("Could not read thumbnail", e);
    } catch (FormatException e) {
        LOGGER.debug("Could not read thumbnail", e);
    }
    // initialize lookup table
    lut = new short[getSizeC()][3][65536];
    byte[] buffer = new byte[65536 * 4];
    int count = (int) Math.min(getSizeC(), lutNames.size());
    for (int c = 0; c < count; c++) {
        Exception exc = null;
        try {
            RandomAccessInputStream stream = getFile(lutNames.get(c));
            stream.seek(stream.length() - 65536 * 4);
            stream.read(buffer);
            stream.close();
            for (int q = 0; q < buffer.length; q += 4) {
                lut[c][0][q / 4] = (short) ((buffer[q + 2] & 0xff) * 257);
                lut[c][1][q / 4] = (short) ((buffer[q + 1] & 0xff) * 257);
                lut[c][2][q / 4] = (short) ((buffer[q] & 0xff) * 257);
            }
        } catch (IOException e) {
            exc = e;
        } catch (FormatException e) {
            exc = e;
        }
        if (exc != null) {
            LOGGER.debug("Could not read LUT", exc);
            lut = null;
            break;
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        CoreMetadata ms = core.get(i);
        ms.rgb = false;
        ms.littleEndian = true;
        ms.interleaved = false;
        ms.metadataComplete = true;
        ms.indexed = lut != null;
        ms.falseColor = true;
        int nFiles = i == 0 ? tiffs.size() : previewNames.size();
        for (int file = 0; file < nFiles; file++) {
            RandomAccessInputStream plane = getFile(i == 0 ? tiffs.get(file) : previewNames.get(file));
            if (plane == null) {
                ifds.add(null);
                continue;
            }
            try {
                TiffParser tp = new TiffParser(plane);
                IFDList ifd = tp.getIFDs();
                ifds.add(ifd);
            } finally {
                plane.close();
            }
        }
    }
    // populate MetadataStore
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        creationDate = creationDate.replaceAll("'", "");
        creationDate = DateTools.formatDate(creationDate, DATE_FORMAT);
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        // populate Image data
        store.setImageName("Series " + (i + 1), i);
        if (creationDate != null)
            store.setImageAcquisitionDate(new Timestamp(creationDate), i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        populateMetadataStore(store, path);
    }
}
Also used : IniList(loci.common.IniList) HashMap(java.util.HashMap) ArrayList(java.util.ArrayList) Timestamp(ome.xml.model.primitives.Timestamp) IOException(java.io.IOException) TreeMap(java.util.TreeMap) CoreMetadata(loci.formats.CoreMetadata) FormatException(loci.formats.FormatException) DependencyException(loci.common.services.DependencyException) FormatException(loci.formats.FormatException) IOException(java.io.IOException) NonNegativeInteger(ome.xml.model.primitives.NonNegativeInteger) MetadataStore(loci.formats.meta.MetadataStore) Length(ome.units.quantity.Length) IniTable(loci.common.IniTable) IFDList(loci.formats.tiff.IFDList) TiffParser(loci.formats.tiff.TiffParser) RandomAccessInputStream(loci.common.RandomAccessInputStream) ByteArrayHandle(loci.common.ByteArrayHandle) File(java.io.File) Location(loci.common.Location)

Example 78 with RandomAccessInputStream

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

the class FV1000Reader method getIniFile.

private IniList getIniFile(String filename) throws FormatException, IOException {
    LOGGER.debug("getIniFile procession: {}", filename);
    RandomAccessInputStream stream = getFile(filename);
    String data = stream.readString((int) stream.length());
    if (!data.startsWith("[")) {
        data = data.substring(data.indexOf('['), data.length());
    }
    data = DataTools.stripString(data);
    BufferedReader reader = new BufferedReader(new StringReader(data));
    stream.close();
    IniList list = parser.parseINI(reader);
    // most of the values will be wrapped in double quotes
    for (IniTable table : list) {
        LOGGER.debug("");
        LOGGER.debug("[" + table.get(IniTable.HEADER_KEY) + "]");
        String[] keys = table.keySet().toArray(new String[table.size()]);
        for (String key : keys) {
            String value = sanitizeValue(table.get(key));
            LOGGER.debug(key + " = " + value);
            table.put(key, value);
        }
    }
    reader.close();
    return list;
}
Also used : IniList(loci.common.IniList) IniTable(loci.common.IniTable) BufferedReader(java.io.BufferedReader) StringReader(java.io.StringReader) RandomAccessInputStream(loci.common.RandomAccessInputStream)

Example 79 with RandomAccessInputStream

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

the class FV1000Reader 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);
    int nFiles = getSeries() == 0 ? tiffs.size() : previewNames.size();
    int image = no % (getImageCount() / nFiles);
    int file = no / (getImageCount() / nFiles);
    int[] coords = getZCTCoords(image);
    lastChannel = coords[1];
    RandomAccessInputStream plane = getPlane(getSeries(), no);
    if (plane == null)
        return buf;
    TiffParser tp = new TiffParser(plane);
    int index = getSeries() == 0 ? file : tiffs.size() + file;
    IFDList ifdList = ifds.get(index);
    if (image >= ifdList.size())
        return buf;
    IFD ifd = ifdList.get(image);
    if (getSizeY() != ifd.getImageLength()) {
        tp.getSamples(ifd, buf, x, getIndex(coords[0], 0, coords[2]), w, 1);
    } else
        tp.getSamples(ifd, buf, x, y, w, h);
    plane.close();
    plane = null;
    tp = null;
    return buf;
}
Also used : IFD(loci.formats.tiff.IFD) IFDList(loci.formats.tiff.IFDList) TiffParser(loci.formats.tiff.TiffParser) RandomAccessInputStream(loci.common.RandomAccessInputStream)

Example 80 with RandomAccessInputStream

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

the class DNGReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    // reset image dimensions
    // the actual image data is stored in IFDs referenced by the SubIFD tag
    // in the 'real' IFD
    CoreMetadata m = core.get(0);
    m.imageCount = ifds.size();
    IFD firstIFD = ifds.get(0);
    PhotoInterp photo = firstIFD.getPhotometricInterpretation();
    int samples = firstIFD.getSamplesPerPixel();
    m.rgb = samples > 1 || photo == PhotoInterp.RGB || photo == PhotoInterp.CFA_ARRAY;
    if (photo == PhotoInterp.CFA_ARRAY)
        samples = 3;
    m.sizeX = (int) firstIFD.getImageWidth();
    m.sizeY = (int) firstIFD.getImageLength();
    m.sizeZ = 1;
    m.sizeC = isRGB() ? samples : 1;
    m.sizeT = ifds.size();
    m.pixelType = FormatTools.UINT16;
    m.indexed = false;
    // now look for the EXIF IFD pointer
    IFDList exifIFDs = tiffParser.getExifIFDs();
    if (exifIFDs.size() > 0) {
        IFD exifIFD = exifIFDs.get(0);
        tiffParser.fillInIFD(exifIFD);
        for (Integer key : exifIFD.keySet()) {
            int tag = key.intValue();
            String name = IFD.getIFDTagName(tag);
            if (tag == IFD.CFA_PATTERN) {
                byte[] cfa = (byte[]) exifIFD.get(key);
                int[] colorMap = new int[cfa.length];
                for (int i = 0; i < cfa.length; i++) colorMap[i] = (int) cfa[i];
                addGlobalMeta(name, colorMap);
                cfaPattern = colorMap;
            } else {
                addGlobalMeta(name, exifIFD.get(key));
                if (name.equals("MAKER_NOTE")) {
                    byte[] b = (byte[]) exifIFD.get(key);
                    int offset = DataTools.bytesToInt(b, b.length - 4, isLittleEndian());
                    byte[] buf = new byte[b.length + offset - 8];
                    System.arraycopy(b, b.length - 8, buf, 0, 8);
                    System.arraycopy(b, 0, buf, offset, b.length - 8);
                    RandomAccessInputStream makerNote = new RandomAccessInputStream(buf);
                    TiffParser tp = new TiffParser(makerNote);
                    IFD note = null;
                    try {
                        note = tp.getFirstIFD();
                    } catch (Exception e) {
                        LOGGER.debug("Failed to parse first IFD", e);
                    }
                    if (note != null) {
                        for (Integer nextKey : note.keySet()) {
                            int nextTag = nextKey.intValue();
                            addGlobalMeta(name, note.get(nextKey));
                            if (nextTag == WHITE_BALANCE_RGB_COEFFS) {
                                if (note.get(nextTag) instanceof TiffRational[]) {
                                    TiffRational[] wb = (TiffRational[]) note.get(nextTag);
                                    whiteBalance = new double[wb.length];
                                    for (int i = 0; i < wb.length; i++) {
                                        whiteBalance[i] = wb[i].doubleValue();
                                    }
                                } else {
                                    // use a default white balance table
                                    whiteBalance = new double[3];
                                    whiteBalance[0] = 2.391381;
                                    whiteBalance[1] = 0.929156;
                                    whiteBalance[2] = 1.298254;
                                }
                            }
                        }
                    }
                    makerNote.close();
                }
            }
        }
    }
}
Also used : IFD(loci.formats.tiff.IFD) PhotoInterp(loci.formats.tiff.PhotoInterp) TiffRational(loci.formats.tiff.TiffRational) CoreMetadata(loci.formats.CoreMetadata) FormatException(loci.formats.FormatException) IOException(java.io.IOException) IFDList(loci.formats.tiff.IFDList) TiffParser(loci.formats.tiff.TiffParser) RandomAccessInputStream(loci.common.RandomAccessInputStream)

Aggregations

RandomAccessInputStream (loci.common.RandomAccessInputStream)246 CoreMetadata (loci.formats.CoreMetadata)108 MetadataStore (loci.formats.meta.MetadataStore)97 FormatException (loci.formats.FormatException)75 TiffParser (loci.formats.tiff.TiffParser)56 IFD (loci.formats.tiff.IFD)51 Length (ome.units.quantity.Length)48 Location (loci.common.Location)47 IOException (java.io.IOException)46 ArrayList (java.util.ArrayList)30 Timestamp (ome.xml.model.primitives.Timestamp)28 Time (ome.units.quantity.Time)21 ByteArrayHandle (loci.common.ByteArrayHandle)18 IFDList (loci.formats.tiff.IFDList)16 CodecOptions (loci.formats.codec.CodecOptions)9 RandomAccessOutputStream (loci.common.RandomAccessOutputStream)8 ServiceException (loci.common.services.ServiceException)7 PhotoInterp (loci.formats.tiff.PhotoInterp)7 TiffSaver (loci.formats.tiff.TiffSaver)7 BufferedReader (java.io.BufferedReader)6