Examples with DependencyException loci.common.services.DependencyException used on opensource projects

Example 1 with DependencyException

use of loci.common.services.DependencyException in project bioformats by openmicroscopy.

the class ImportProcess method getOMEXML.

/**
 * Valid only after {@link ImportStep#READER}.
 */
public String getOMEXML() {
    if (omeXML == null) {
        // NB: Extract the OME-XML once, then keep it cached.
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            omeXML = service.getOMEXML(getOMEMetadata());
        } catch (DependencyException de) {
        } catch (ServiceException se) {
        }
    }
    return omeXML;
}

Example 2 with DependencyException

use of loci.common.services.DependencyException 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 DependencyException

use of loci.common.services.DependencyException in project bioformats by openmicroscopy.

the class PCIReader method initPOIService.

// -- Helper methods --
private void initPOIService() throws FormatException, IOException {
    try {
        ServiceFactory factory = new ServiceFactory();
        poi = factory.getInstance(POIService.class);
    } catch (DependencyException de) {
        throw new FormatException("POI library not found", de);
    }
    poi.initialize(Location.getMappedId(getCurrentFile()));
}

Example 4 with DependencyException

use of loci.common.services.DependencyException 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 5 with DependencyException

use of loci.common.services.DependencyException in project bioformats by openmicroscopy.

the class Memoizer method getService.

// Copied from OMETiffReader.
protected OMEXMLService getService() throws MissingLibraryException {
    if (service == null) {
        try {
            ServiceFactory factory = new ServiceFactory();
            service = factory.getInstance(OMEXMLService.class);
        } catch (DependencyException de) {
            throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
        }
    }
    return service;
}