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

Example 11 with FormatException

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

the class NiftiReader method populatePixelType.

// -- Helper methods --
private void populatePixelType(int dataType) throws FormatException {
    CoreMetadata m = core.get(0);
    switch(dataType) {
        case 1:
        case 2:
            m.pixelType = FormatTools.UINT8;
            break;
        case 4:
            m.pixelType = FormatTools.INT16;
            break;
        case 8:
            m.pixelType = FormatTools.INT32;
            break;
        case 16:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 64:
            m.pixelType = FormatTools.DOUBLE;
            break;
        case 128:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
        case 256:
            m.pixelType = FormatTools.INT8;
            break;
        case 512:
            m.pixelType = FormatTools.UINT16;
            break;
        case 768:
            m.pixelType = FormatTools.UINT32;
            break;
        case 2304:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 4;
        default:
            throw new FormatException("Unsupported data type: " + dataType);
    }
}

Example 12 with FormatException

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

the class NikonReader 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 = firstIFD.getPixelType();
    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 extra = new String(b, 0, 10, Constants.ENCODING).startsWith("Nikon") ? 10 : 0;
                    byte[] buf = new byte[b.length];
                    System.arraycopy(b, extra, buf, 0, buf.length - extra);
                    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 == 150) {
                                b = (byte[]) note.get(nextKey);
                                RandomAccessInputStream s = new RandomAccessInputStream(b);
                                byte check1 = s.readByte();
                                byte check2 = s.readByte();
                                lossyCompression = check1 != 0x46;
                                vPredictor = new int[4];
                                for (int q = 0; q < vPredictor.length; q++) {
                                    vPredictor[q] = s.readShort();
                                }
                                curve = new int[16385];
                                int bps = ifds.get(0).getBitsPerSample()[0];
                                int max = 1 << bps & 0x7fff;
                                int step = 0;
                                int csize = s.readShort();
                                if (csize > 1) {
                                    step = max / (csize - 1);
                                }
                                if (check1 == 0x44 && check2 == 0x20 && step > 0) {
                                    for (int i = 0; i < csize; i++) {
                                        curve[i * step] = s.readShort();
                                    }
                                    for (int i = 0; i < max; i++) {
                                        int n = i % step;
                                        curve[i] = (curve[i - n] * (step - n) + curve[i - n + step] * n) / step;
                                    }
                                    s.seek(562);
                                    split = s.readShort();
                                } else {
                                    int maxValue = (int) Math.pow(2, bps) - 1;
                                    Arrays.fill(curve, maxValue);
                                    int nElements = (int) (s.length() - s.getFilePointer()) / 2;
                                    if (nElements < 100) {
                                        for (int i = 0; i < curve.length; i++) {
                                            curve[i] = (short) i;
                                        }
                                    } else {
                                        for (int q = 0; q < nElements; q++) {
                                            curve[q] = s.readShort();
                                        }
                                    }
                                }
                                s.close();
                            } else if (nextTag == WHITE_BALANCE_RGB_COEFFS) {
                                whiteBalance = (TiffRational[]) note.get(nextKey);
                            }
                        }
                    }
                    makerNote.close();
                }
            }
        }
    }
}

Example 13 with FormatException

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

the class OpenlabRawReader 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);
    // read the 12 byte file header
    LOGGER.info("Verifying Openlab RAW format");
    if (!in.readString(4).equals("OLRW")) {
        throw new FormatException("Openlab RAW magic string not found.");
    }
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    int version = in.readInt();
    m.imageCount = in.readInt();
    offsets = new int[getImageCount()];
    offsets[0] = 12;
    in.skipBytes(8);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(1);
    m.sizeC = in.read();
    bytesPerPixel = in.read();
    in.skipBytes(1);
    long stampMs = in.readLong();
    if (stampMs > 0) {
        stampMs /= 1000000;
        stampMs -= (67 * 365.25 * 24 * 60 * 60);
    } else
        stampMs = System.currentTimeMillis();
    String stamp = DateTools.convertDate(stampMs, DateTools.UNIX);
    in.skipBytes(4);
    int len = in.read() & 0xff;
    String imageName = in.readString(len - 1).trim();
    if (getSizeC() <= 1)
        m.sizeC = 1;
    else
        m.sizeC = 3;
    int plane = getSizeX() * getSizeY() * bytesPerPixel;
    for (int i = 1; i < getImageCount(); i++) {
        offsets[i] = offsets[i - 1] + HEADER_SIZE + plane;
    }
    m.sizeZ = getImageCount();
    m.sizeT = 1;
    m.rgb = getSizeC() > 1;
    m.dimensionOrder = isRGB() ? "XYCZT" : "XYZTC";
    m.interleaved = false;
    m.littleEndian = false;
    m.metadataComplete = true;
    m.indexed = false;
    m.falseColor = false;
    switch(bytesPerPixel) {
        case 1:
        case 3:
            m.pixelType = FormatTools.UINT8;
            break;
        case 2:
            m.pixelType = FormatTools.UINT16;
            break;
        default:
            m.pixelType = FormatTools.FLOAT;
    }
    addGlobalMeta("Width", getSizeX());
    addGlobalMeta("Height", getSizeY());
    addGlobalMeta("Bytes per pixel", bytesPerPixel);
    addGlobalMeta("Image name", imageName);
    addGlobalMeta("Timestamp", stamp);
    addGlobalMeta("Version", version);
    // The metadata store we're working with.
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (stamp != null) {
        store.setImageAcquisitionDate(new Timestamp(stamp), 0);
    }
    store.setImageName(imageName, 0);
}

Example 14 with FormatException

use of loci.formats.FormatException 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 15 with FormatException

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

the class PCIReader method getOptimalTileHeight.

/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
    FormatTools.assertId(currentId, true, 1);
    String file = imageFiles.get(0);
    try {
        if (poi == null) {
            initPOIService();
        }
        RandomAccessInputStream s = poi.getDocumentStream(file);
        TiffParser tp = new TiffParser(s);
        if (tp.isValidHeader()) {
            IFD ifd = tp.getFirstIFD();
            s.close();
            return (int) ifd.getTileLength();
        }
        s.close();
    } catch (FormatException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    } catch (IOException e) {
        LOGGER.debug("Could not retrieve tile height", e);
    }
    return super.getOptimalTileHeight();
}