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

Example 1 with MissingLibraryException

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

the class LegacyND2Reader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        openFile(id);
        int numSeries = getNumSeries();
        core.clear();
        for (int i = 0; i < numSeries; i++) {
            CoreMetadata ms = new CoreMetadata();
            core.add(ms);
            ms.sizeX = getWidth(i);
            if (ms.sizeX % 2 != 0)
                ms.sizeX++;
            ms.sizeY = getHeight(i);
            ms.sizeZ = getZSlices(i);
            ms.sizeT = getTFrames(i);
            ms.sizeC = getChannels(i);
            int bytes = getBytesPerPixel(i);
            if (bytes % 3 == 0) {
                ms.sizeC *= 3;
                bytes /= 3;
                ms.rgb = true;
            } else
                ms.rgb = false;
            ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, true);
            ms.imageCount = ms.sizeZ * ms.sizeT;
            if (!ms.rgb)
                ms.imageCount *= ms.sizeC;
            ms.interleaved = true;
            ms.littleEndian = true;
            ms.dimensionOrder = "XYCZT";
            ms.indexed = false;
            ms.falseColor = false;
        }
    } catch (UnsatisfiedLinkError e) {
        throw new MissingLibraryException(NO_NIKON_MSG, e);
    } catch (Exception e) {
        throw new MissingLibraryException(NO_NIKON_MSG, e);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName("Series " + (i + 1), i);
    }
}

Example 2 with MissingLibraryException

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

the class MINCReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        netcdf = factory.getInstance(NetCDFService.class);
        netcdf.setFile(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(e);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Vector<String> variableList = netcdf.getVariableList();
        for (String variable : variableList) {
            Hashtable<String, Object> attributes = netcdf.getVariableAttributes(variable);
            String[] keys = attributes.keySet().toArray(new String[0]);
            Arrays.sort(keys);
            for (String key : keys) {
                if (attributes.get(key) instanceof Object[]) {
                    final StringBuilder sb = new StringBuilder();
                    Object[] o = (Object[]) attributes.get(key);
                    for (Object q : o) {
                        sb.append(q.toString());
                    }
                    addGlobalMeta(variable + " " + key, sb.toString());
                } else {
                    addGlobalMeta(variable + " " + key, attributes.get(key));
                }
            }
        }
    }
    CoreMetadata m = core.get(0);
    try {
        Object pixels = netcdf.getVariableValue("/image");
        if (pixels == null) {
            pixels = netcdf.getVariableValue("/minc-2.0/image/0/image");
            isMINC2 = true;
        }
        m.littleEndian = isMINC2;
        boolean signed = false;
        if (isMINC2) {
            Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/minc-2.0/image/0/image");
            String unsigned = attrs.get("_Unsigned").toString();
            if (!unsigned.startsWith("true")) {
                signed = true;
            }
        } else {
            Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/image");
            String signtype = attrs.get("signtype").toString();
            if (signtype.startsWith("signed")) {
                signed = true;
            }
        }
        if (pixels instanceof byte[][][]) {
            m.pixelType = signed ? FormatTools.INT8 : FormatTools.UINT8;
            pixelData = (byte[][][]) pixels;
        } else if (pixels instanceof byte[][][][]) {
            byte[][][][] actualPixels = (byte[][][][]) pixels;
            m.pixelType = signed ? FormatTools.INT8 : FormatTools.UINT8;
            pixelData = new byte[actualPixels.length * actualPixels[0].length][][];
            int nextPlane = 0;
            for (int t = 0; t < actualPixels.length; t++) {
                for (int z = 0; z < actualPixels[t].length; z++) {
                    pixelData[nextPlane++] = actualPixels[t][z];
                }
            }
        } else if (pixels instanceof short[][][]) {
            m.pixelType = signed ? FormatTools.INT16 : FormatTools.UINT16;
            short[][][] s = (short[][][]) pixels;
            pixelData = new byte[s.length][][];
            for (int i = 0; i < s.length; i++) {
                pixelData[i] = new byte[s[i].length][];
                for (int j = 0; j < s[i].length; j++) {
                    pixelData[i][j] = DataTools.shortsToBytes(s[i][j], isLittleEndian());
                }
            }
        } else if (pixels instanceof int[][][]) {
            m.pixelType = signed ? FormatTools.INT32 : FormatTools.UINT32;
            int[][][] s = (int[][][]) pixels;
            pixelData = new byte[s.length][][];
            for (int i = 0; i < s.length; i++) {
                pixelData[i] = new byte[s[i].length][];
                for (int j = 0; j < s[i].length; j++) {
                    pixelData[i][j] = DataTools.intsToBytes(s[i][j], isLittleEndian());
                }
            }
        } else if (pixels instanceof float[][][]) {
            m.pixelType = FormatTools.FLOAT;
            float[][][] s = (float[][][]) pixels;
            pixelData = new byte[s.length][][];
            for (int i = 0; i < s.length; i++) {
                pixelData[i] = new byte[s[i].length][];
                for (int j = 0; j < s[i].length; j++) {
                    pixelData[i][j] = DataTools.floatsToBytes(s[i][j], isLittleEndian());
                }
            }
        } else if (pixels instanceof double[][][]) {
            m.pixelType = FormatTools.DOUBLE;
            double[][][] s = (double[][][]) pixels;
            pixelData = new byte[s.length][][];
            for (int i = 0; i < s.length; i++) {
                pixelData[i] = new byte[s[i].length][];
                for (int j = 0; j < s[i].length; j++) {
                    pixelData[i][j] = DataTools.doublesToBytes(s[i][j], isLittleEndian());
                }
            }
        }
    } catch (ServiceException e) {
        throw new FormatException(e);
    }
    Length physicalX = null;
    Length physicalY = null;
    Length physicalZ = null;
    Length xPosition = null;
    Length yPosition = null;
    Length zPosition = null;
    if (isMINC2) {
        Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/xspace");
        m.sizeX = Integer.parseInt(attrs.get("length").toString());
        physicalX = getStepSize(attrs);
        xPosition = getStart(attrs);
        attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/yspace");
        m.sizeY = Integer.parseInt(attrs.get("length").toString());
        physicalY = getStepSize(attrs);
        yPosition = getStart(attrs);
        attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/zspace");
        m.sizeZ = Integer.parseInt(attrs.get("length").toString());
        physicalZ = getStepSize(attrs);
        zPosition = getStart(attrs);
    } else {
        m.sizeX = netcdf.getDimension("/xspace");
        m.sizeY = netcdf.getDimension("/yspace");
        m.sizeZ = netcdf.getDimension("/zspace");
        Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/xspace");
        physicalX = getStepSize(attrs);
        xPosition = getStart(attrs);
        attrs = netcdf.getVariableAttributes("/yspace");
        physicalY = getStepSize(attrs);
        yPosition = getStart(attrs);
        attrs = netcdf.getVariableAttributes("/zspace");
        physicalZ = getStepSize(attrs);
        zPosition = getStart(attrs);
    }
    try {
        m.sizeT = netcdf.getDimension("/time");
    } catch (NullPointerException e) {
        m.sizeT = 1;
    }
    m.sizeC = 1;
    m.imageCount = getSizeZ() * getSizeT() * getSizeC();
    m.rgb = false;
    m.indexed = false;
    m.dimensionOrder = "XYZCT";
    String history = null;
    if (isMINC2) {
        history = netcdf.getAttributeValue("/minc-2.0/ident");
    } else {
        history = netcdf.getAttributeValue("/history");
    }
    addGlobalMeta("Comment", history);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, xPosition != null || yPosition != null || zPosition != null);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        store.setImageDescription(history, 0);
        if (physicalX != null) {
            store.setPixelsPhysicalSizeX(physicalX, 0);
        }
        if (physicalY != null) {
            store.setPixelsPhysicalSizeY(physicalY, 0);
        }
        if (physicalZ != null) {
            store.setPixelsPhysicalSizeZ(physicalZ, 0);
        }
        for (int i = 0; i < getImageCount(); i++) {
            if (xPosition != null) {
                store.setPlanePositionX(xPosition, 0, i);
            }
            if (yPosition != null) {
                store.setPlanePositionY(yPosition, 0, i);
            }
            if (zPosition != null) {
                int z = getZCTCoords(i)[0];
                Double pos = zPosition.value().doubleValue();
                if (physicalZ != null && z > 0) {
                    pos += z * physicalZ.value().doubleValue();
                }
                store.setPlanePositionZ(FormatTools.createLength(pos, zPosition.unit()), 0, i);
            }
        }
    }
}

Example 3 with MissingLibraryException

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

the class ImarisHDFReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        ServiceFactory factory = new ServiceFactory();
        netcdf = factory.getInstance(NetCDFService.class);
        netcdf.setFile(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(NetCDFServiceImpl.NO_NETCDF_MSG, e);
    }
    pixelSizeX = pixelSizeY = pixelSizeZ = 1;
    emWave = new ArrayList<String>();
    exWave = new ArrayList<String>();
    channelMin = new ArrayList<String>();
    channelMax = new ArrayList<String>();
    gain = new ArrayList<String>();
    pinhole = new ArrayList<String>();
    channelName = new ArrayList<String>();
    microscopyMode = new ArrayList<String>();
    colors = new ArrayList<double[]>();
    seriesCount = 0;
    // read all of the metadata key/value pairs
    parseAttributes();
    CoreMetadata ms0 = core.get(0);
    if (seriesCount > 1) {
        for (int i = 1; i < seriesCount; i++) {
            core.add(new CoreMetadata());
        }
        for (int i = 1; i < seriesCount; i++) {
            CoreMetadata ms = core.get(i);
            String groupPath = "DataSet/ResolutionLevel_" + i + "/TimePoint_0/Channel_0";
            ms.sizeX = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeX"));
            ms.sizeY = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeY"));
            ms.sizeZ = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeZ"));
            ms.imageCount = ms.sizeZ * getSizeC() * getSizeT();
            ms.sizeC = getSizeC();
            ms.sizeT = getSizeT();
            ms.thumbnail = true;
            if (ms.sizeZ == ms0.sizeZ && ms.sizeC == ms0.sizeC && ms.sizeT == ms0.sizeT) {
                // do not assume that all series will have the same dimensions
                // if the Z, C or T size is different, then it cannot
                // be a subresolution
                ms0.resolutionCount++;
            }
        }
    }
    ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
    ms0.thumbnail = false;
    ms0.dimensionOrder = "XYZCT";
    // determine pixel type - this isn't stored in the metadata, so we need
    // to check the pixels themselves
    int type = -1;
    Object pix = getImageData(0, 0, 0, 1, 1);
    if (pix instanceof byte[][])
        type = FormatTools.UINT8;
    else if (pix instanceof short[][])
        type = FormatTools.UINT16;
    else if (pix instanceof int[][])
        type = FormatTools.UINT32;
    else if (pix instanceof float[][])
        type = FormatTools.FLOAT;
    else if (pix instanceof double[][])
        type = FormatTools.DOUBLE;
    else {
        throw new FormatException("Unknown pixel type: " + pix);
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        ms.pixelType = type;
        ms.dimensionOrder = "XYZCT";
        ms.rgb = false;
        ms.thumbSizeX = 128;
        ms.thumbSizeY = 128;
        ms.orderCertain = true;
        ms.littleEndian = true;
        ms.interleaved = false;
        ms.indexed = colors.size() >= getSizeC();
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String imageName = new Location(getCurrentFile()).getName();
    for (int s = 0; s < getSeriesCount(); s++) {
        store.setImageName(imageName + " Resolution Level " + (s + 1), s);
    }
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
        return;
    }
    int cIndex = 0;
    for (int s = 0; s < getSeriesCount(); s++) {
        setSeries(s);
        double px = pixelSizeX, py = pixelSizeY, pz = pixelSizeZ;
        if (px == 1)
            px = (maxX - minX) / getSizeX();
        if (py == 1)
            py = (maxY - minY) / getSizeY();
        if (pz == 1)
            pz = (maxZ - minZ) / getSizeZ();
        Length sizeX = FormatTools.getPhysicalSizeX(px);
        Length sizeY = FormatTools.getPhysicalSizeY(py);
        Length sizeZ = FormatTools.getPhysicalSizeZ(pz);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, s);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, s);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, s);
        }
        for (int i = 0; i < getSizeC(); i++, cIndex++) {
            Float gainValue = null;
            Integer pinholeValue = null, emWaveValue = null, exWaveValue;
            if (cIndex < gain.size()) {
                try {
                    gainValue = new Float(gain.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < pinhole.size()) {
                try {
                    pinholeValue = new Integer(pinhole.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < emWave.size()) {
                try {
                    emWaveValue = new Integer(emWave.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < exWave.size()) {
                try {
                    exWaveValue = new Integer(exWave.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            Double minValue = null, maxValue = null;
            if (cIndex < channelMin.size()) {
                try {
                    minValue = new Double(channelMin.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < channelMax.size()) {
                try {
                    maxValue = new Double(channelMax.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (i < colors.size()) {
                double[] color = colors.get(i);
                Color realColor = new Color((int) (color[0] * 255), (int) (color[1] * 255), (int) (color[2] * 255), 255);
                store.setChannelColor(realColor, s, i);
            }
        }
    }
    setSeries(0);
}

Example 4 with MissingLibraryException

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

the class VolocityReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "mvd2")) {
        Location file = new Location(id).getAbsoluteFile();
        Location parent = file.getParentFile().getParentFile();
        String[] files = parent.list(true);
        for (String f : files) {
            if (checkSuffix(f, "mvd2")) {
                id = new Location(parent, f).getAbsolutePath();
                break;
            }
        }
    }
    super.initFile(id);
    stacks = new ArrayList<Stack>();
    extraFiles = new ArrayList<String>();
    Location file = new Location(id).getAbsoluteFile();
    extraFiles.add(file.getAbsolutePath());
    Location parentDir = file.getParentFile();
    dir = new Location(parentDir, DATA_DIR);
    if (dir.exists()) {
        String[] files = dir.list(true);
        for (String f : files) {
            if (!checkSuffix(f, "aisf") && !checkSuffix(f, "atsf")) {
                extraFiles.add(new Location(dir, f).getAbsolutePath());
            }
        }
    }
    try {
        ServiceFactory factory = new ServiceFactory();
        MetakitService reader = factory.getInstance(MetakitService.class);
        reader.initialize(id);
        sampleTable = reader.getTableData(1);
        stringTable = reader.getTableData(2);
        reader.close();
    } catch (DependencyException e) {
        throw new MissingLibraryException("Could not find Metakit library", e);
    }
    ArrayList<String> stackNames = new ArrayList<String>();
    ArrayList<Integer> parentIDs = new ArrayList<Integer>();
    for (int i = 0; i < sampleTable.length; i++) {
        Integer stringID = (Integer) sampleTable[i][11];
        String name = getString(stringID);
        int channelIndex = getChildIndex((Integer) sampleTable[i][0], "Channels");
        if (i > 0 && (Integer) sampleTable[i][2] == 1 && (channelIndex >= 0 || (sampleTable[i][14] != null && !sampleTable[i][14].equals(0)) || ((byte[]) sampleTable[i][13]).length > 21)) {
            if (channelIndex < 0) {
                RandomAccessInputStream s = getStream(i);
                s.seek(0);
                if (s.read() != 'I') {
                    s.order(false);
                }
                s.seek(22);
                int x = s.readInt();
                int y = s.readInt();
                int z = s.readInt();
                if (x * y * z > 0 && x * y * z < (s.length() * 3)) {
                    stackNames.add(name);
                    parentIDs.add((Integer) sampleTable[i][0]);
                }
                s.close();
            } else {
                stackNames.add(name);
                parentIDs.add((Integer) sampleTable[i][0]);
            }
        }
    }
    for (int i = 0; i < parentIDs.size(); i++) {
        Stack stack = new Stack();
        stack.core = new CoreMetadata();
        Integer parent = parentIDs.get(i);
        int channelIndex = getChildIndex(parent, "Channels");
        if (channelIndex >= 0) {
            Integer[] channels = getAllChildren((Integer) sampleTable[channelIndex][0]);
            stack.core.sizeC = channels.length;
            stack.pixelsFiles = new String[stack.core.sizeC];
            stack.channelNames = new String[channels.length];
            for (int c = 0; c < channels.length; c++) {
                stack.channelNames[c] = getString((Integer) sampleTable[channels[c]][11]);
                RandomAccessInputStream data = getStream(channels[c]);
                if (data.length() > 22) {
                    data.seek(22);
                    int stackID = data.readInt();
                    Location f = new Location(dir, stackID + ".aisf");
                    if (!f.exists()) {
                        f = new Location(dir, DataTools.swap(stackID) + ".aisf");
                    }
                    stack.pixelsFiles[c] = f.getAbsolutePath();
                } else {
                    Integer child = getAllChildren((Integer) sampleTable[channels[c]][0])[0];
                    stack.pixelsFiles[c] = getFile((Integer) sampleTable[child][0], dir);
                }
                data.close();
            }
        } else {
            stack.pixelsFiles = new String[1];
            stack.pixelsFiles[0] = getFile(parent, dir);
            if (stack.pixelsFiles[0] == null || !new Location(stack.pixelsFiles[0]).exists()) {
                int row = -1;
                for (int r = 0; r < sampleTable.length; r++) {
                    if (sampleTable[r][0].equals(parent)) {
                        row = r;
                        break;
                    }
                }
                stack.pixelsFiles[0] = EMBEDDED_STREAM;
                IRandomAccess data = new ByteArrayHandle((byte[]) sampleTable[row][13]);
                Location.mapFile(stack.pixelsFiles[0], data);
            }
        }
        RandomAccessInputStream data = null;
        int timestampIndex = getChildIndex(parent, "Timepoint times stream");
        if (timestampIndex >= 0) {
            data = getStream(timestampIndex);
            data.seek(22);
            int timestampID = data.readInt();
            Location f = new Location(dir, timestampID + ".atsf");
            if (!f.exists()) {
                f = new Location(dir, DataTools.swap(timestampID) + ".atsf");
            }
            stack.timestampFile = f.getAbsolutePath();
            data.close();
        }
        int xIndex = getChildIndex(parent, "um/pixel (X)");
        if (xIndex >= 0) {
            data = getStream(xIndex);
            data.seek(SIGNATURE_SIZE);
            stack.physicalX = data.readDouble();
            data.close();
        }
        int yIndex = getChildIndex(parent, "um/pixel (Y)");
        if (yIndex >= 0) {
            data = getStream(yIndex);
            data.seek(SIGNATURE_SIZE);
            stack.physicalY = data.readDouble();
            data.close();
        }
        int zIndex = getChildIndex(parent, "um/pixel (Z)");
        if (zIndex >= 0) {
            data = getStream(zIndex);
            data.seek(SIGNATURE_SIZE);
            stack.physicalZ = data.readDouble();
            data.close();
        }
        timestampIndex = getChildIndex(parent, "TimepointTimes");
        if (timestampIndex >= 0) {
            data = getStream(timestampIndex);
            data.seek(SIGNATURE_SIZE);
            data.close();
        }
        int objectiveIndex = getChildIndex(parent, "Microscope Objective");
        if (objectiveIndex >= 0) {
            data = getStream(objectiveIndex);
            data.seek(SIGNATURE_SIZE);
            stack.magnification = data.readDouble();
            data.close();
        }
        int detectorIndex = getChildIndex(parent, "Camera/Detector");
        if (detectorIndex >= 0) {
            data = getStream(detectorIndex);
            data.seek(SIGNATURE_SIZE);
            int len = data.readInt();
            stack.detector = data.readString(len);
            data.close();
        }
        int descriptionIndex = getChildIndex(parent, "Experiment Description");
        if (descriptionIndex >= 0) {
            data = getStream(descriptionIndex);
            data.seek(SIGNATURE_SIZE);
            int len = data.readInt();
            stack.description = data.readString(len);
            data.close();
        }
        int xLocationIndex = getChildIndex(parent, "X Location");
        if (xLocationIndex >= 0) {
            data = getStream(xLocationIndex);
            data.seek(SIGNATURE_SIZE);
            stack.xLocation = data.readDouble();
            data.close();
        }
        int yLocationIndex = getChildIndex(parent, "Y Location");
        if (yLocationIndex >= 0) {
            data = getStream(yLocationIndex);
            data.seek(SIGNATURE_SIZE);
            stack.yLocation = data.readDouble();
            data.close();
        }
        int zLocationIndex = getChildIndex(parent, "Z Location");
        if (zLocationIndex >= 0) {
            data = getStream(zLocationIndex);
            data.seek(SIGNATURE_SIZE);
            stack.zLocation = data.readDouble();
            data.close();
        }
        stacks.add(stack);
    }
    for (int i = 0; i < stacks.size(); i++) {
        Stack stack = stacks.get(i);
        if (!new Location(stack.pixelsFiles[0]).exists()) {
            stacks.remove(i);
            i--;
            continue;
        }
        RandomAccessInputStream base = new RandomAccessInputStream(stack.pixelsFiles[0]);
        long baseLength = base.length();
        base.close();
        for (int q = 1; q < stack.pixelsFiles.length; q++) {
            if (!new Location(stack.pixelsFiles[q]).exists()) {
                continue;
            }
            base = new RandomAccessInputStream(stack.pixelsFiles[q]);
            long length = base.length();
            base.close();
            if (length > baseLength) {
                // split the stack
                Stack newStack = new Stack();
                newStack.timestampFile = stack.timestampFile;
                newStack.core = new CoreMetadata();
                newStack.physicalX = stack.physicalX;
                newStack.physicalY = stack.physicalY;
                newStack.physicalZ = stack.physicalZ;
                newStack.magnification = stack.magnification;
                newStack.detector = stack.detector;
                newStack.description = stack.description;
                newStack.xLocation = stack.xLocation;
                newStack.yLocation = stack.yLocation;
                newStack.zLocation = stack.zLocation;
                String[] pixels = stack.pixelsFiles;
                newStack.pixelsFiles = new String[pixels.length - q];
                System.arraycopy(pixels, q, newStack.pixelsFiles, 0, newStack.pixelsFiles.length);
                stack.pixelsFiles = new String[q];
                System.arraycopy(pixels, 0, stack.pixelsFiles, 0, q);
                String[] channels = stack.channelNames;
                newStack.channelNames = new String[channels.length - q];
                System.arraycopy(channels, q, newStack.channelNames, 0, newStack.channelNames.length);
                stack.channelNames = new String[q];
                System.arraycopy(channels, 0, stack.channelNames, 0, q);
                newStack.core.sizeC = newStack.channelNames.length;
                stack.core.sizeC = stack.channelNames.length;
                stacks.add(i + 1, newStack);
                stackNames.add(i + 1, stackNames.get(i));
            }
        }
    }
    int seriesCount = stacks.size();
    core.clear();
    for (int i = 0; i < seriesCount; i++) {
        Stack stack = stacks.get(i);
        CoreMetadata ms = stack.core;
        core.add(ms);
        setSeries(i);
        ms.littleEndian = true;
        if (stack.timestampFile != null) {
            RandomAccessInputStream s = new RandomAccessInputStream(stack.timestampFile);
            s.seek(0);
            if (s.read() != 'I') {
                ms.littleEndian = false;
            }
            s.seek(17);
            s.order(isLittleEndian());
            ms.sizeT = s.readInt();
            Double firstStamp = null;
            Double[] stamps = new Double[ms.sizeT];
            for (int t = 0; t < ms.sizeT; t++) {
                // timestamps are stored in microseconds
                double timestamp = s.readLong() / 1000000.0;
                if (firstStamp == null) {
                    firstStamp = timestamp;
                }
                stamps[t] = timestamp - firstStamp;
            }
            timestamps.add(stamps);
            s.close();
        } else {
            ms.sizeT = 1;
        }
        ms.rgb = false;
        ms.interleaved = true;
        ms.dimensionOrder = "XYCZT";
        RandomAccessInputStream s = new RandomAccessInputStream(stack.pixelsFiles[0]);
        s.order(isLittleEndian());
        if (checkSuffix(stack.pixelsFiles[0], "aisf")) {
            s.seek(18);
            stack.blockSize = s.readShort() * 256;
            s.skipBytes(5);
            int x = s.readInt();
            int y = s.readInt();
            int zStart = s.readInt();
            int w = s.readInt();
            int h = s.readInt();
            if (w - x < 0 || h - y < 0 || (w - x) * (h - y) < 0) {
                ms.littleEndian = !isLittleEndian();
                s.order(isLittleEndian());
                s.seek(s.getFilePointer() - 20);
                x = s.readInt();
                y = s.readInt();
                zStart = s.readInt();
                w = s.readInt();
                h = s.readInt();
            }
            ms.sizeX = w - x;
            ms.sizeY = h - y;
            ms.sizeZ = s.readInt() - zStart;
            ms.imageCount = getSizeZ() * getSizeC() * getSizeT();
            ms.pixelType = FormatTools.INT8;
            int planesPerFile = getSizeZ() * getSizeT();
            int planeSize = FormatTools.getPlaneSize(this);
            int bytesPerPlane = (int) ((s.length() - stack.blockSize) / planesPerFile);
            int bytesPerPixel = 0;
            while (bytesPerPlane >= planeSize) {
                bytesPerPixel++;
                bytesPerPlane -= planeSize;
            }
            if ((bytesPerPixel % 3) == 0) {
                ms.sizeC *= 3;
                ms.rgb = true;
                bytesPerPixel /= 3;
            }
            ms.pixelType = FormatTools.pixelTypeFromBytes(bytesPerPixel, false, bytesPerPixel > 2);
            // full timepoints are padded to have a multiple of 256 bytes
            int timepoint = FormatTools.getPlaneSize(this) * getSizeZ();
            stack.planePadding = stack.blockSize - (timepoint % stack.blockSize);
            if (stack.planePadding == stack.blockSize) {
                stack.planePadding = 0;
            }
        } else {
            boolean embedded = Location.getMappedFile(EMBEDDED_STREAM) != null;
            s.seek(0);
            if (s.read() != 'I') {
                ms.littleEndian = false;
                s.order(false);
            }
            s.seek(22);
            ms.sizeX = s.readInt();
            ms.sizeY = s.readInt();
            ms.sizeZ = s.readInt();
            ms.sizeC = embedded ? 1 : 4;
            ms.imageCount = getSizeZ() * getSizeT();
            ms.rgb = ms.sizeC > 1;
            ms.pixelType = FormatTools.UINT8;
            stack.blockSize = embedded ? (int) s.getFilePointer() : 99;
            stack.planePadding = 0;
            if (s.length() > ms.sizeX * ms.sizeY * ms.sizeZ * 6) {
                ms.pixelType = FormatTools.UINT16;
                ms.sizeC = 3;
                ms.rgb = true;
            }
            if (s.length() < (ms.sizeX * ms.sizeY * ms.sizeZ * ms.sizeC)) {
                ms.rgb = false;
                ms.sizeC = 1;
                long pixels = ms.sizeX * ms.sizeY * ms.sizeZ;
                double approximateBytes = (double) s.length() / pixels;
                int bytes = (int) Math.ceil(approximateBytes);
                if (bytes == 0) {
                    bytes = 1;
                } else if (bytes == 3) {
                    bytes = 2;
                }
                ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, false);
                s.seek(70);
                stack.blockSize = s.readInt();
                stack.clippingData = true;
            }
        }
        s.close();
    }
    setSeries(0);
    for (int i = 0; i < getSeriesCount(); i++) {
        setSeries(i);
        Stack stack = stacks.get(i);
        addSeriesMeta("Name", stackNames.get(i));
        addSeriesMeta("Pixel width (in microns)", stack.physicalX);
        addSeriesMeta("Pixel height (in microns)", stack.physicalY);
        addSeriesMeta("Z step (in microns)", stack.physicalZ);
        addSeriesMeta("Objective magnification", stack.magnification);
        addSeriesMeta("Camera/Detector", stack.detector);
        addSeriesMeta("Description", stack.description);
        addSeriesMeta("X Location", stack.xLocation);
        addSeriesMeta("Y Location", stack.yLocation);
        addSeriesMeta("Z Location", stack.zLocation);
        if (stack.channelNames != null) {
            for (int c = 0; c < stack.channelNames.length; c++) {
                addSeriesMetaList("Channel", stack.channelNames[c]);
            }
        }
    }
    setSeries(0);
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String instrument = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrument, 0);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageInstrumentRef(instrument, i);
        setSeries(i);
        Stack stack = stacks.get(i);
        store.setImageName(stackNames.get(i), i);
        store.setImageDescription(stack.description, i);
        if (stack.channelNames != null) {
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                store.setChannelName(stack.channelNames[c], i, c);
            }
        }
        Length sizeX = FormatTools.getPhysicalSizeX(stack.physicalX);
        Length sizeY = FormatTools.getPhysicalSizeY(stack.physicalY);
        Length sizeZ = FormatTools.getPhysicalSizeZ(stack.physicalZ);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, i);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, i);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        String objective = MetadataTools.createLSID("Objective", 0, i);
        store.setObjectiveID(objective, 0, i);
        store.setObjectiveNominalMagnification(stack.magnification, 0, i);
        store.setObjectiveCorrection(getCorrection("Other"), 0, i);
        store.setObjectiveImmersion(getImmersion("Other"), 0, i);
        store.setObjectiveSettingsID(objective, i);
        String detectorID = MetadataTools.createLSID("Detector", 0, i);
        store.setDetectorID(detectorID, 0, i);
        store.setDetectorModel(stack.detector, 0, i);
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            store.setDetectorSettingsID(detectorID, i, c);
        }
        for (int img = 0; img < getImageCount(); img++) {
            int[] coords = getZCTCoords(img);
            int z = coords[0];
            final Length xLoc = new Length(stack.xLocation, UNITS.REFERENCEFRAME);
            final Length yLoc = new Length(stack.yLocation, UNITS.REFERENCEFRAME);
            store.setPlanePositionX(xLoc, i, img);
            store.setPlanePositionY(yLoc, i, img);
            if (stack.physicalZ != null) {
                final double zLocNumber = stack.zLocation + z * stack.physicalZ;
                final Length zLoc = new Length(zLocNumber, UNITS.REFERENCEFRAME);
                store.setPlanePositionZ(zLoc, i, img);
            }
            if (i < timestamps.size() && coords[2] < timestamps.get(i).length && timestamps.get(i)[coords[2]] != null) {
                store.setPlaneDeltaT(new Time(timestamps.get(i)[coords[2]], UNITS.SECOND), i, img);
            }
        }
    }
    setSeries(0);
}

Example 5 with MissingLibraryException

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

the class CellH5Reader method initializeJHDFService.

// -- Helper methods --
private void initializeJHDFService(String id) throws IOException, MissingLibraryException {
    try {
        ServiceFactory factory = new ServiceFactory();
        jhdf = factory.getInstance(JHDFService.class);
        jhdf.setFile(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(JHDFServiceImpl.NO_JHDF_MSG, e);
    }
}