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

Example 26 with ImageReader

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

the class WritePrecompressedPlanes method main.

public static void main(String[] args) throws FormatException, IOException {
    // print usage if no args specified
    if (args.length == 0) {
        System.out.println("Usage: java WritePrecompressedPlanes " + "[input file 1] ... [input file n] [output file]");
        System.exit(0);
    }
    // first n - 1 args are the input files
    String[] inputFiles = new String[args.length - 1];
    System.arraycopy(args, 0, inputFiles, 0, inputFiles.length);
    // last arg is the output file
    String outputFile = args[args.length - 1];
    // open up one of the input files so that we can read the metadata
    // this assumes that the dimensions of the input files are the same
    ImageReader reader = new ImageReader();
    reader.setId(inputFiles[0]);
    int pixelType = reader.getPixelType();
    // write the pixel data to the output file
    RandomAccessOutputStream out = new RandomAccessOutputStream(outputFile);
    TiffSaver saver = new TiffSaver(out, outputFile);
    saver.setWritingSequentially(true);
    saver.setLittleEndian(reader.isLittleEndian());
    saver.setBigTiff(false);
    saver.writeHeader();
    for (int i = 0; i < inputFiles.length; i++) {
        RandomAccessInputStream in = new RandomAccessInputStream(inputFiles[i]);
        byte[] buf = new byte[(int) in.length()];
        in.readFully(buf);
        in.close();
        IFD ifd = new IFD();
        ifd.put(IFD.IMAGE_WIDTH, reader.getSizeX());
        ifd.put(IFD.IMAGE_LENGTH, reader.getSizeY());
        ifd.put(IFD.LITTLE_ENDIAN, reader.isLittleEndian());
        ifd.put(IFD.SAMPLE_FORMAT, FormatTools.isSigned(pixelType) ? 2 : FormatTools.isFloatingPoint(pixelType) ? 3 : 1);
        ifd.put(IFD.PLANAR_CONFIGURATION, 1);
        ifd.put(IFD.REUSE, out.length());
        out.seek(out.length());
        // this is very important
        // the data is already compressed in a single chunk, so setting the
        // number of rows per strip to something smaller than the full height
        // will require us to re-compress the data
        ifd.put(IFD.ROWS_PER_STRIP, reader.getSizeY());
        saver.writeImage(buf, ifd, i, pixelType, 0, 0, reader.getSizeX(), reader.getSizeY(), i == inputFiles.length - 1, reader.getRGBChannelCount(), true);
    }
    reader.close();
    out.close();
    // reset the TIFF file's compression flag
    // you cannot do this before the pixel data is written, otherwise
    // the pixels will be re-compressed
    saver = new TiffSaver(outputFile);
    for (int i = 0; i < inputFiles.length; i++) {
        RandomAccessInputStream in = new RandomAccessInputStream(outputFile);
        saver.overwriteLastIFDOffset(in);
        saver.overwriteIFDValue(in, i, IFD.COMPRESSION, TiffCompression.JPEG.getCode());
        in.close();
    }
    saver.getStream().close();
}

Example 27 with ImageReader

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

the class SimpleTiledWriter method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 * @throws DependencyException thrown if failed to create an OMEXMLService
 * @throws IOException thrown if unable to setup input or output stream for reader or writer
 * @throws FormatException thrown if invalid ID set for reader or writer or invalid tile size set
 * @throws ServiceException thrown if unable to create OME-XML meta data
 */
private void initialize() throws DependencyException, FormatException, IOException, ServiceException {
    // construct the object that stores OME-XML metadata
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexml = service.createOMEXMLMetadata();
    // set up the reader and associate it with the input file
    reader = new ImageReader();
    reader.setMetadataStore(omexml);
    reader.setId(inputFile);
    /* initialize-tiling-writer-example-start */
    // set up the writer and associate it with the output file
    writer = new OMETiffWriter();
    writer.setMetadataRetrieve(omexml);
    writer.setInterleaved(reader.isInterleaved());
    // set the tile size height and width for writing
    this.tileSizeX = writer.setTileSizeX(tileSizeX);
    this.tileSizeY = writer.setTileSizeY(tileSizeY);
    writer.setId(outputFile);
/* initialize-tiling-writer-example-end */
}

Example 28 with ImageReader

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

the class NRRDReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    // make sure we actually have the .nrrd/.nhdr file
    if (!checkSuffix(id, "nhdr") && !checkSuffix(id, "nrrd")) {
        id += ".nhdr";
        if (!new Location(id).exists()) {
            id = id.substring(0, id.lastIndexOf("."));
            id = id.substring(0, id.lastIndexOf("."));
            id += ".nhdr";
        }
        id = new Location(id).getAbsolutePath();
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses();
    Class<? extends IFormatReader>[] classArray = classes.getClasses();
    ClassList<IFormatReader> newClasses = new ClassList<IFormatReader>(IFormatReader.class);
    for (Class<? extends IFormatReader> c : classArray) {
        if (!c.equals(NRRDReader.class)) {
            newClasses.addClass(c);
        }
    }
    helper = new ImageReader(newClasses);
    helper.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM));
    String key, v;
    String[] pixelSizeUnits = null;
    int numDimensions = 0;
    CoreMetadata m = core.get(0);
    m.sizeX = 1;
    m.sizeY = 1;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.dimensionOrder = "XYCZT";
    String line = in.readLine();
    while (line != null && line.length() > 0) {
        if (!line.startsWith("#") && !line.startsWith("NRRD")) {
            // parse key/value pair
            key = line.substring(0, line.indexOf(':')).trim();
            v = line.substring(line.indexOf(':') + 1).trim();
            addGlobalMeta(key, v);
            if (key.equals("type")) {
                if (v.indexOf("char") != -1 || v.indexOf('8') != -1) {
                    m.pixelType = FormatTools.UINT8;
                } else if (v.indexOf("short") != -1 || v.indexOf("16") != -1) {
                    m.pixelType = FormatTools.UINT16;
                } else if (v.equals("int") || v.equals("signed int") || v.equals("int32") || v.equals("int32_t") || v.equals("uint") || v.equals("unsigned int") || v.equals("uint32") || v.equals("uint32_t")) {
                    m.pixelType = FormatTools.UINT32;
                } else if (v.equals("float"))
                    m.pixelType = FormatTools.FLOAT;
                else if (v.equals("double"))
                    m.pixelType = FormatTools.DOUBLE;
                else
                    throw new FormatException("Unsupported data type: " + v);
            } else if (key.equals("dimension")) {
                numDimensions = Integer.parseInt(v);
            } else if (key.equals("sizes")) {
                String[] tokens = v.split(" ");
                for (int i = 0; i < numDimensions; i++) {
                    int size = Integer.parseInt(tokens[i]);
                    if (numDimensions >= 3 && i == 0 && size > 1 && size <= 16) {
                        m.sizeC = size;
                    } else if (i == 0 || (getSizeC() > 1 && i == 1)) {
                        m.sizeX = size;
                    } else if (i == 1 || (getSizeC() > 1 && i == 2)) {
                        m.sizeY = size;
                    } else if (i == 2 || (getSizeC() > 1 && i == 3)) {
                        m.sizeZ = size;
                    } else if (i == 3 || (getSizeC() > 1 && i == 4)) {
                        m.sizeT = size;
                    }
                }
            } else if (key.equals("data file") || key.equals("datafile")) {
                dataFile = v;
            } else if (key.equals("encoding"))
                encoding = v;
            else if (key.equals("endian")) {
                m.littleEndian = v.equals("little");
            } else if (key.equals("spacings") || key.equals("space directions")) {
                pixelSizes = v.split(" ");
            } else if (key.equals("space units")) {
                pixelSizeUnits = v.split(" ");
            } else if (key.equals("byte skip")) {
                offset = Long.parseLong(v);
            }
        }
        line = in.readLine();
        if (line != null)
            line = line.trim();
    }
    if (dataFile == null)
        offset = in.getFilePointer();
    else {
        Location f = new Location(currentId).getAbsoluteFile();
        Location parent = f.getParentFile();
        if (f.exists() && parent != null) {
            dataFile = dataFile.substring(dataFile.indexOf(File.separator) + 1);
            dataFile = new Location(parent, dataFile).getAbsolutePath();
        }
        initializeHelper = !encoding.equals("raw");
    }
    m.rgb = getSizeC() > 1;
    m.interleaved = true;
    m.imageCount = getSizeZ() * getSizeT();
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (pixelSizes != null) {
            for (int i = 0; i < pixelSizes.length; i++) {
                if (pixelSizes[i] == null)
                    continue;
                try {
                    Double d = parsePixelSize(i);
                    String unit = pixelSizeUnits == null || i >= pixelSizeUnits.length ? null : pixelSizeUnits[i].replaceAll("\"", "");
                    if (i == 0) {
                        Length x = FormatTools.getPhysicalSizeX(d, unit);
                        if (x != null) {
                            store.setPixelsPhysicalSizeX(x, 0);
                        }
                    } else if (i == 1) {
                        Length y = FormatTools.getPhysicalSizeY(d, unit);
                        if (y != null) {
                            store.setPixelsPhysicalSizeY(y, 0);
                        }
                    } else if (i == 2) {
                        Length z = FormatTools.getPhysicalSizeZ(d, unit);
                        if (z != null) {
                            store.setPixelsPhysicalSizeZ(z, 0);
                        }
                    }
                } catch (NumberFormatException e) {
                }
            }
        }
    }
}

Example 29 with ImageReader

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

the class ZipReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    reader = new ImageReader();
    reader.setMetadataOptions(getMetadataOptions());
    reader.setMetadataFiltered(isMetadataFiltered());
    reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated());
    reader.setNormalized(isNormalized());
    reader.setMetadataStore(getMetadataStore());
    String innerFile = id;
    if (checkSuffix(id, "zip")) {
        innerFile = id.substring(0, id.length() - 4);
    }
    int sep = innerFile.lastIndexOf(File.separator);
    if (sep < 0) {
        sep = innerFile.lastIndexOf("/");
    }
    if (sep >= 0) {
        innerFile = innerFile.substring(sep + 1);
    }
    // NB: We need a raw handle on the ZIP data itself, not a ZipHandle.
    IRandomAccess rawHandle = Location.getHandle(id, false, false);
    in = new RandomAccessInputStream(rawHandle, id);
    ZipInputStream zip = new ZipInputStream(in);
    ZipEntry ze = null;
    entryName = null;
    boolean matchFound = false;
    while (true) {
        ze = zip.getNextEntry();
        if (ze == null)
            break;
        if (entryName == null) {
            entryName = ze.getName();
        }
        if (!matchFound && ze.getName().startsWith(innerFile)) {
            entryName = ze.getName();
            matchFound = true;
        }
        ZipHandle handle = new ZipHandle(id, ze);
        Location.mapFile(ze.getName(), handle);
        mappedFiles.add(ze.getName());
    }
    if (entryName == null) {
        throw new FormatException("Zip file does not contain any valid files");
    }
    reader.setId(entryName);
    metadataStore = reader.getMetadataStore();
    core = new ArrayList<CoreMetadata>(reader.getCoreMetadataList());
    metadata = reader.getGlobalMetadata();
}

Example 30 with ImageReader

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

the class BioFormatsExtensionPrinter method main.

public static void main(String[] args) throws IOException {
    System.out.println("Generating list of Bio-Formats supported suffixes...");
    try (IFormatReader reader = new ImageReader()) {
        String[] suffixes = reader.getSuffixes();
        PrintWriter fo = null;
        fo = new PrintWriter(new File("BioFormatsSuffixes.txt"), Constants.ENCODING);
        for (String s : suffixes) fo.println("*." + s);
        fo.close();
        System.out.println(suffixes.length + " suffixes discovered.");
    }
}