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

Example 96 with FormatException

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

the class FileExportSPW method export.

/**
 * Save a single uint16 plane of data.
 */
public void export() {
    int width = 4, height = 4;
    int pixelType = FormatTools.UINT16;
    Exception exception = null;
    IMetadata omexml = initializeMetadata(width, height, pixelType);
    int series = 0;
    int nSeries = rows * cols * fovPerWell;
    // only save data if the file writer was initialized successfully
    boolean initializationSuccess = initializeWriter(omexml);
    if (initializationSuccess) {
        while (series < nSeries) {
            for (int p = 0; p < sizeT; p++) {
                savePlane(width, height, pixelType, p, series);
            }
            series++;
            if (series < nSeries) {
                try {
                    writer.setSeries(series);
                } catch (FormatException e) {
                    System.err.println("Fatal error unable to select correct image in series! " + e.getMessage());
                    break;
                }
            }
        }
    // endwhile
    }
    // endif
    cleanup();
}

Example 97 with FormatException

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

the class FileExportSPW method initializeWriter.

/**
 * Set up the file writer.
 *
 * @param omexml
 *          the IMetadata object that is to be associated with the writer
 * @return true if the file writer was successfully initialized; false if an
 *         error occurred
 */
private boolean initializeWriter(IMetadata omexml) {
    // create the file writer and associate the OME-XML metadata with it
    writer = new ImageWriter();
    writer.setMetadataRetrieve(omexml);
    Exception exception = null;
    try {
        writer.setId(outputFile);
    } catch (FormatException e) {
        exception = e;
    } catch (IOException e) {
        exception = e;
    }
    if (exception != null) {
        System.err.println("Failed to initialize file writer.");
        exception.printStackTrace();
    }
    return exception == null;
}

Example 98 with FormatException

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

the class FitsReader 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);
    String line = in.readString(LINE_LENGTH);
    if (!line.startsWith("SIMPLE")) {
        throw new FormatException("Unsupported FITS file.");
    }
    String key = "", value = "";
    while (true) {
        line = in.readString(LINE_LENGTH);
        // parse key/value pair
        int ndx = line.indexOf('=');
        int comment = line.indexOf("/", ndx);
        if (comment < 0)
            comment = line.length();
        if (ndx >= 0) {
            key = line.substring(0, ndx).trim();
            value = line.substring(ndx + 1, comment).trim();
        } else
            key = line.trim();
        // image dimensions are only populated by the standard header
        if (key.equals("END") && getSizeX() > 0)
            break;
        if (key.equals("BITPIX")) {
            int bits = Integer.parseInt(value);
            boolean fp = bits < 0;
            boolean signed = bits != 8;
            bits = Math.abs(bits) / 8;
            m.pixelType = FormatTools.pixelTypeFromBytes(bits, signed, fp);
        } else if (key.equals("NAXIS1"))
            m.sizeX = Integer.parseInt(value);
        else if (key.equals("NAXIS2"))
            m.sizeY = Integer.parseInt(value);
        else if (key.equals("NAXIS3"))
            m.sizeZ = Integer.parseInt(value);
        addGlobalMeta(key, value);
    }
    while (in.read() == 0x20) ;
    pixelOffset = in.getFilePointer() - 1;
    m.sizeC = 1;
    m.sizeT = 1;
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    // correct for truncated files
    int planeSize = getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType());
    if (DataTools.safeMultiply64(planeSize, getSizeZ()) > (in.length() - pixelOffset)) {
        m.sizeZ = (int) ((in.length() - pixelOffset) / planeSize);
    }
    m.imageCount = m.sizeZ;
    m.rgb = false;
    m.littleEndian = false;
    m.interleaved = false;
    m.dimensionOrder = "XYZCT";
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 99 with FormatException

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

the class GIFReader method readImageBlock.

private void readImageBlock() throws FormatException, IOException {
    ix = in.readShort();
    iy = in.readShort();
    iw = in.readShort();
    ih = in.readShort();
    int packed = in.read();
    boolean lctFlag = (packed & 0x80) != 0;
    interlace = (packed & 0x40) != 0;
    int lctSize = 2 << (packed & 7);
    act = lctFlag ? readLut(lctSize) : gct;
    int save = 0;
    if (transparency) {
        save = act[transIndex];
        act[transIndex] = 0;
    }
    if (act == null)
        throw new FormatException("Color table not found.");
    decodeImageData();
    skipBlocks();
    core.get(0).imageCount++;
    if (transparency)
        act[transIndex] = save;
    lastDispose = dispose;
}

Example 100 with FormatException

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

the class IM3Reader method initFile.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#initFile(java.lang.String)
   */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    core.clear();
    IRandomAccess is = Location.getHandle(id, false);
    try {
        is.setOrder(ByteOrder.LITTLE_ENDIAN);
        final int cookie = is.readInt();
        if (cookie != COOKIE) {
            throw new FormatException(String.format("Expected file cookie of %d, but got %d.", COOKIE, cookie));
        }
        long fileLength = is.length();
        while (is.getFilePointer() < fileLength) {
            final IM3Record rec = parseRecord(is);
            if (rec == null) {
                if (is.getFilePointer() > fileLength - 16)
                    break;
                /*
           * # of bytes in chunk.
           */
                @SuppressWarnings("unused") final int chunkLength = is.readInt();
                /*
           * Is always zero? Chunk #?
           */
                @SuppressWarnings("unused") final int unknown = is.readInt();
                /*
           * Is always one? Chunk #?
           */
                @SuppressWarnings("unused") final int unknown1 = is.readInt();
                /*
           * # of records to follow
           */
                @SuppressWarnings("unused") final int nRecords = is.readInt();
            } else {
                if (rec instanceof ContainerRecord) {
                    final ContainerRecord bRec = (ContainerRecord) rec;
                    for (IM3Record subDS : bRec.parseChunks(is)) {
                        if ((subDS instanceof ContainerRecord) && (subDS.name.equals(FIELD_DATA_SET))) {
                            final ContainerRecord bSubDS = (ContainerRecord) subDS;
                            for (IM3Record subSubDS : bSubDS.parseChunks(is)) {
                                if (subSubDS instanceof ContainerRecord) {
                                    final ContainerRecord bDataSet = (ContainerRecord) subSubDS;
                                    dataSets.add(bDataSet);
                                    List<IM3Record> subRecs = bDataSet.parseChunks(is);
                                    final CoreMetadata cm = new CoreMetadata();
                                    cm.dimensionOrder = DimensionOrder.XYCZT.getValue();
                                    cm.littleEndian = true;
                                    // TODO: Detect pixel type
                                    cm.pixelType = FormatTools.UINT16;
                                    for (IM3Record subRec : subRecs) {
                                        if (subRec.name.equals(FIELD_SHAPE) && (subRec instanceof IntIM3Record)) {
                                            final IntIM3Record iRec = (IntIM3Record) subRec;
                                            cm.sizeX = iRec.getEntry(is, 0);
                                            cm.sizeY = iRec.getEntry(is, 1);
                                            cm.sizeC = iRec.getEntry(is, 2);
                                            cm.sizeZ = 1;
                                            cm.sizeT = 1;
                                            cm.imageCount = cm.sizeC;
                                            cm.metadataComplete = true;
                                        }
                                    }
                                    core.add(cm);
                                }
                            }
                        } else if ((subDS instanceof ContainerRecord) && subDS.name.equals(FIELD_SPECTRAL_LIBRARY)) {
                            /*
                 * SpectralLibrary
                 *   (unnamed container record)
                 *       Spectra
                 *           Keys (integers)
                 *           Values
                 *               (unnamed container record for spectrum #1)
                 *               (unnamed container record for spectrum #2)...
                 *
                 */
                            for (IM3Record slContainer : ((ContainerRecord) subDS).parseChunks(is)) {
                                /* unnamed container */
                                if (slContainer instanceof ContainerRecord) {
                                    for (IM3Record slSpectra : ((ContainerRecord) slContainer).parseChunks(is)) {
                                        if ((slSpectra instanceof ContainerRecord) && (slSpectra.name.equals(FIELD_SPECTRA))) {
                                            for (IM3Record slRec : ((ContainerRecord) slSpectra).parseChunks(is)) {
                                                if (slRec.name.equals(FIELD_VALUES) && (slRec instanceof ContainerRecord)) {
                                                    for (IM3Record spectrumRec : ((ContainerRecord) slRec).parseChunks(is)) {
                                                        if (spectrumRec instanceof ContainerRecord) {
                                                            spectra.add(new Spectrum(is, (ContainerRecord) spectrumRec));
                                                        }
                                                    }
                                                }
                                            }
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
                records.add(rec);
            }
        }
    } finally {
        is.close();
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}