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

Example 41 with FormatException

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

the class AWTImageTools method openImage.

/**
 * Creates an image from the given byte array, using the given
 * IFormatReader to retrieve additional information.
 * The floating point normalization setting is specified by 'normal',
 * which allows the reader's normalization setting to be overridden.
 */
public static BufferedImage openImage(byte[] buf, IFormatReader r, int w, int h, boolean normal) throws FormatException, IOException {
    int pixelType = r.getPixelType();
    boolean little = r.isLittleEndian();
    int rgbChanCount = r.getRGBChannelCount();
    boolean interleaved = r.isInterleaved();
    boolean indexed = r.isIndexed();
    if (pixelType == FormatTools.FLOAT) {
        float[] f = (float[]) DataTools.makeDataArray(buf, 4, true, little);
        if (normal)
            f = DataTools.normalizeFloats(f);
        return makeImage(f, w, h, rgbChanCount, interleaved);
    } else if (pixelType == FormatTools.DOUBLE) {
        double[] d = (double[]) DataTools.makeDataArray(buf, 8, true, little);
        if (normal)
            d = DataTools.normalizeDoubles(d);
        return makeImage(d, w, h, rgbChanCount, interleaved);
    }
    boolean signed = FormatTools.isSigned(pixelType);
    ColorModel model = null;
    if (signed) {
        if (pixelType == FormatTools.INT8) {
            model = new SignedColorModel(8, DataBuffer.TYPE_BYTE, rgbChanCount);
        } else if (pixelType == FormatTools.INT16) {
            model = new SignedColorModel(16, DataBuffer.TYPE_SHORT, rgbChanCount);
        } else if (pixelType == FormatTools.INT32) {
            model = new SignedColorModel(32, DataBuffer.TYPE_INT, rgbChanCount);
        }
    }
    int bpp = FormatTools.getBytesPerPixel(pixelType);
    BufferedImage b = makeImage(buf, w, h, rgbChanCount, interleaved, bpp, false, little, signed);
    if (b == null) {
        throw new FormatException("Could not construct BufferedImage");
    }
    if (indexed && rgbChanCount == 1) {
        if (pixelType == FormatTools.UINT8 || pixelType == FormatTools.INT8) {
            byte[][] table = r.get8BitLookupTable();
            if (table != null && table.length > 0 && table[0] != null) {
                int len = table[0].length;
                byte[] dummy = table.length < 3 ? new byte[len] : null;
                byte[] red = table.length >= 1 ? table[0] : dummy;
                byte[] green = table.length >= 2 ? table[1] : dummy;
                byte[] blue = table.length >= 3 ? table[2] : dummy;
                model = new IndexColorModel(8, len, red, green, blue);
            }
        } else if (pixelType == FormatTools.UINT16 || pixelType == FormatTools.INT16) {
            short[][] table = r.get16BitLookupTable();
            if (table != null && table.length > 0 && table[0] != null) {
                model = new Index16ColorModel(16, table[0].length, table, r.isLittleEndian());
            }
        }
    }
    if (model != null) {
        WritableRaster raster = Raster.createWritableRaster(b.getSampleModel(), b.getRaster().getDataBuffer(), null);
        b = new BufferedImage(model, raster, false, null);
    }
    return b;
}

Example 42 with FormatException

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

the class ImageViewer method open.

/**
 * Opens the given data source using the current format reader.
 */
public void open(String id) {
    wait(true);
    try {
        // Location f = new Location(id);
        // id = f.getAbsolutePath();
        IMetadata meta = null;
        if (omexmlService != null) {
            try {
                meta = omexmlService.createOMEXMLMetadata();
                myReader.setMetadataStore(meta);
            } catch (ServiceException exc) {
                LOGGER.debug("Could not create OME-XML metadata", exc);
            }
        }
        if (meta == null) {
            LOGGER.info("OME metadata unavailable");
        }
        myReader.setId(id);
        int num = myReader.getImageCount();
        ProgressMonitor progress = new ProgressMonitor(this, "Reading " + id, null, 0, num + 1);
        sizeZ = myReader.getSizeZ();
        sizeT = myReader.getSizeT();
        sizeC = myReader.getEffectiveSizeC();
        // if (myReader.isRGB(id)) sizeC = (sizeC + 2) / 3; // adjust for RGB
        progress.setProgress(1);
        BufferedImage[] img = new BufferedImage[num];
        for (int i = 0; i < num; i++) {
            if (progress.isCanceled())
                break;
            img[i] = myReader.openImage(i);
            if (i == 0)
                setImages(myReader, img);
            progress.setProgress(i + 2);
        }
        myReader.close(true);
    } catch (FormatException exc) {
        LOGGER.info("", exc);
        wait(false);
        return;
    } catch (IOException exc) {
        LOGGER.info("", exc);
        wait(false);
        return;
    }
    wait(false);
}

Example 43 with FormatException

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

the class EPSReader 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);
    LOGGER.info("Verifying EPS format");
    String line = readLine();
    if (!line.trim().startsWith("%!PS")) {
        // read the TIFF preview
        isTiff = true;
        in.order(true);
        in.seek(20);
        int offset = in.readInt();
        int len = in.readInt();
        byte[] b = new byte[len];
        in.seek(offset);
        in.read(b);
        in = new RandomAccessInputStream(b);
        TiffParser tp = new TiffParser(in);
        ifds = tp.getIFDs();
        IFD firstIFD = ifds.get(0);
        map = tp.getColorMap(firstIFD);
        m.sizeX = (int) firstIFD.getImageWidth();
        m.sizeY = (int) firstIFD.getImageLength();
        m.sizeZ = 1;
        m.sizeT = 1;
        m.sizeC = firstIFD.getSamplesPerPixel();
        if (map != null && getSizeC() == 1) {
            m.sizeC = 3;
        }
        if (getSizeC() == 2)
            m.sizeC = 4;
        m.littleEndian = firstIFD.isLittleEndian();
        m.interleaved = true;
        m.rgb = getSizeC() > 1;
        m.pixelType = firstIFD.getPixelType();
        m.imageCount = 1;
        m.dimensionOrder = "XYCZT";
        m.metadataComplete = true;
        m.indexed = false;
        m.falseColor = false;
        MetadataStore store = makeFilterMetadata();
        MetadataTools.populatePixels(store, this);
        return;
    }
    LOGGER.info("Finding image data");
    binary = false;
    String image = "image";
    int lineNum = 1;
    line = readLine().trim();
    while (line != null && !line.equals("%%EOF")) {
        if (line.endsWith(image)) {
            if (!line.startsWith(image)) {
                if (line.indexOf("colorimage") != -1)
                    m.sizeC = 3;
                String[] t = line.split(" ");
                try {
                    int newX = Integer.parseInt(t[0]);
                    int newY = Integer.parseInt(t[1]);
                    if (t.length > 2 && Integer.parseInt(t[2]) >= 8) {
                        m.sizeX = newX;
                        m.sizeY = newY;
                        start = lineNum;
                    }
                } catch (NumberFormatException exc) {
                    LOGGER.debug("Could not parse image dimensions", exc);
                    if (t.length > 3) {
                        m.sizeC = Integer.parseInt(t[3]);
                    }
                }
            }
            break;
        } else if (line.startsWith("%%")) {
            if (line.startsWith("%%BoundingBox:")) {
                line = line.substring(14).trim();
                String[] t = line.split(" ");
                try {
                    int originX = Integer.parseInt(t[0].trim());
                    int originY = Integer.parseInt(t[1].trim());
                    m.sizeX = Integer.parseInt(t[2].trim()) - originX;
                    m.sizeY = Integer.parseInt(t[3].trim()) - originY;
                    addGlobalMeta("X-coordinate of origin", originX);
                    addGlobalMeta("Y-coordinate of origin", originY);
                } catch (NumberFormatException e) {
                    throw new FormatException("Files without image data are not supported.");
                }
            } else if (line.startsWith("%%BeginBinary")) {
                binary = true;
            } else {
                // parse key/value pairs
                int ndx = line.indexOf(':');
                if (ndx != -1) {
                    String key = line.substring(0, ndx);
                    String value = line.substring(ndx + 1);
                    addGlobalMeta(key, value);
                }
            }
        } else if (line.startsWith("%ImageData:")) {
            line = line.substring(11);
            String[] t = line.split(" ");
            m.sizeX = Integer.parseInt(t[0]);
            m.sizeY = Integer.parseInt(t[1]);
            m.sizeC = Integer.parseInt(t[3]);
            for (int i = 4; i < t.length; i++) {
                image = t[i].trim();
                if (image.length() > 1) {
                    image = image.substring(1, image.length() - 1);
                }
            }
        }
        lineNum++;
        line = readLine().trim();
    }
    LOGGER.info("Populating metadata");
    if (getSizeC() == 0)
        m.sizeC = 1;
    m.sizeZ = 1;
    m.sizeT = 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT8;
    m.rgb = getSizeC() == 3;
    m.interleaved = true;
    m.littleEndian = true;
    m.imageCount = 1;
    // Populate metadata store
    // The metadata store we're working with.
    MetadataStore store = getMetadataStore();
    MetadataTools.populatePixels(store, this);
}

Example 44 with FormatException

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

the class WlzReader 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();
        wlz = factory.getInstance(WlzService.class);
    } catch (DependencyException e) {
        throw new FormatException(NO_WLZ_MSG, e);
    }
    if (wlz != null) {
        wlz.open(id, "r");
        CoreMetadata md = core.get(0);
        MetadataStore store = makeFilterMetadata();
        md.rgb = wlz.isRGB();
        md.interleaved = false;
        md.indexed = false;
        md.sizeX = wlz.getSizeX();
        md.sizeY = wlz.getSizeY();
        md.sizeZ = wlz.getSizeZ();
        md.sizeC = wlz.getSizeC();
        md.sizeT = wlz.getSizeT();
        md.dimensionOrder = "XYZCT";
        md.imageCount = wlz.getSizeZ();
        md.pixelType = wlz.getPixelType();
        PositiveFloat x = new PositiveFloat(Math.abs(wlz.getVoxSzX()));
        PositiveFloat y = new PositiveFloat(Math.abs(wlz.getVoxSzY()));
        PositiveFloat z = new PositiveFloat(Math.abs(wlz.getVoxSzZ()));
        store.setPixelsPhysicalSizeX(FormatTools.createLength(x, UNITS.MICROMETER), 0);
        store.setPixelsPhysicalSizeY(FormatTools.createLength(y, UNITS.MICROMETER), 0);
        store.setPixelsPhysicalSizeZ(FormatTools.createLength(z, UNITS.MICROMETER), 0);
        store.setStageLabelName(wlz.getWlzOrgLabelName(), 0);
        store.setStageLabelX(new Length(wlz.getOrgX(), UNITS.REFERENCEFRAME), 0);
        store.setStageLabelY(new Length(wlz.getOrgY(), UNITS.REFERENCEFRAME), 0);
        store.setStageLabelZ(new Length(wlz.getOrgZ(), UNITS.REFERENCEFRAME), 0);
        MetadataTools.populatePixels(store, this);
    }
}

Example 45 with FormatException

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

the class WlzReader 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 (wlz != null) {
        buf = wlz.readBytes(no, buf, x, y, w, h);
    } else {
        try {
            ServiceFactory factory = new ServiceFactory();
            wlz = factory.getInstance(WlzService.class);
        } catch (DependencyException e) {
            throw new FormatException(NO_WLZ_MSG, e);
        }
        if (wlz != null) {
            wlz.open(currentId, "r");
            buf = wlz.readBytes(no, buf, x, y, w, h);
        }
    }
    return buf;
}