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

Example 1 with ImageReader

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

the class MakeDatasetStructureTable method printTable.

/**
 * Write the table to the file specified using setOutputFile(String[])
 */
public void printTable() {
    ImageReader baseReader = new ImageReader();
    IFormatReader[] allReaders = baseReader.getReaders();
    Comparator<IFormatReader> comparator = new Comparator<IFormatReader>() {

        @Override
        public int compare(IFormatReader r1, IFormatReader r2) {
            String s1 = r1.getFormat();
            String s2 = r2.getFormat();
            return s1.compareTo(s2);
        }
    };
    Arrays.sort(allReaders, comparator);
    printHeader();
    for (IFormatReader reader : allReaders) {
        try {
            printFormatEntry(reader);
        } catch (IllegalStateException e) {
        }
    }
    printFooter();
}

Example 2 with ImageReader

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

the class HitachiReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "txt")) {
        String base = id;
        if (base.indexOf('.') >= 0) {
            base = base.substring(0, base.lastIndexOf("."));
        }
        id = base + ".txt";
        initFile(id);
        return;
    }
    super.initFile(id);
    String data = DataTools.readFile(id);
    IniParser parser = new IniParser();
    parser.setBackslashContinuesLine(false);
    IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
    IniTable image = ini.getTable("SemImageFile");
    if (image == null) {
        throw new FormatException("Could not find 'SemImageFile' table.");
    }
    for (String key : image.keySet()) {
        addGlobalMeta(key, image.get(key));
    }
    String imageName = image.get("SampleName");
    String pixelsFile = image.get("ImageName");
    String date = image.get("Date");
    String time = image.get("Time");
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    pixelsFile = new Location(parent, pixelsFile).getAbsolutePath();
    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(HitachiReader.class)) {
            newClasses.addClass(c);
        }
    }
    helperReader = new ImageReader(newClasses);
    helperReader.setId(pixelsFile);
    core = new ArrayList<CoreMetadata>(helperReader.getCoreMetadataList());
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM);
    store.setImageName(imageName, 0);
    date = DateTools.formatDate(date + " " + time, DATE_FORMAT);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    populateOMEMetadata(image, store);
}

Example 3 with ImageReader

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

the class GetPhysicalMetadata method main.

public static void main(String[] args) throws Exception {
    // parse command line arguments
    if (args.length < 1) {
        System.err.println("Usage: java GetMetadata imageFile [seriesNo]");
        System.exit(1);
    }
    String id = args[0];
    int series = args.length > 1 ? Integer.parseInt(args[1]) : 0;
    // create OME-XML metadata store
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata meta = service.createOMEXMLMetadata();
    // create format reader
    IFormatReader reader = new ImageReader();
    reader.setMetadataStore(meta);
    // initialize file
    System.out.println("Initializing " + id);
    reader.setId(id);
    int seriesCount = reader.getSeriesCount();
    if (series < seriesCount)
        reader.setSeries(series);
    series = reader.getSeries();
    System.out.println("\tImage series = " + series + " of " + seriesCount);
    printPixelDimensions(reader);
    printPhysicalDimensions(meta, series);
}

Example 4 with ImageReader

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

the class MultiFileExample method main.

public static void main(String[] args) throws FormatException, IOException {
    if (args.length < 2) {
        System.out.println("You must specify two files.");
        System.exit(1);
    }
    ImageReader[] readers = new ImageReader[args.length];
    for (int i = 0; i < readers.length; i++) {
        readers[i] = new ImageReader();
        readers[i].setId(args[i]);
    }
    // read plane #0 from file #0
    readers[0].openBytes(0);
    // read plane #0 from file #1
    readers[1].openBytes(0);
// the other option is to use a single reader for all of the files
// this will use a little less memory, but is substantially slower
// unless you read all of the planes from one file before moving on
// to the next file
// 
// if you want one reader total, uncomment the following:
/*
    ImageReader reader = new ImageReader();
    //read plane #0 from file #0
    reader.setId(args[0]);
    reader.openBytes(0);
    // read plane #0 from file #1
    reader.setId(args[1]);
    reader.openBytes(0);
    */
}

Example 5 with ImageReader

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

the class ParallelRead method run.

public void run() {
    try {
        ImageReader r = new ImageReader();
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        r.setMetadataStore(meta);
        r.setId(id);
        System.out.println(Thread.currentThread().getName() + ": id=" + id + ", sizeX=" + r.getSizeX() + ", sizeY=" + r.getSizeY() + ", sizeZ=" + r.getSizeZ() + ", sizeT=" + r.getSizeT() + ", sizeC=" + r.getSizeC() + ", imageName=" + meta.getImageName(0));
        r.close();
    } catch (Exception exc) {
        exc.printStackTrace();
    }
}