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

Example 6 with ImageReader

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

the class PrintROIs method main.

public static void main(String[] args) throws Exception {
    ImageReader reader = new ImageReader();
    IMetadata omexml;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        omexml = service.createOMEXMLMetadata();
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    reader.setMetadataStore(omexml);
    reader.setId(args[0]);
    printAllROIs(omexml);
    System.out.println();
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        printSeriesROIs(omexml, series);
    }
    reader.close();
}

Example 7 with ImageReader

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

the class DumpOMEXML method dumpOMEXML.

public static void dumpOMEXML(String path) throws FormatException, IOException, DependencyException, ServiceException {
    ServiceFactory serviceFactory = new ServiceFactory();
    OMEXMLService omexmlService = serviceFactory.getInstance(OMEXMLService.class);
    IMetadata meta = omexmlService.createOMEXMLMetadata();
    ImageReader r = new ImageReader();
    r.setMetadataStore(meta);
    r.setOriginalMetadataPopulated(true);
    r.setId(path);
    r.close();
    String xml = omexmlService.getOMEXML(meta);
    System.out.println(xml);
}

Example 8 with ImageReader

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

the class EditImageName method main.

public static void main(String[] args) throws Exception {
    if (args.length != 1) {
        System.out.println("Usage: java EditImageName file");
        return;
    }
    ImageReader reader = new ImageReader();
    // record metadata to OME-XML format
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexmlMeta = service.createOMEXMLMetadata();
    reader.setMetadataStore(omexmlMeta);
    String id = args[0];
    System.out.print("Reading metadata ");
    reader.setId(id);
    System.out.println(" [done]");
    // get image name
    String name = omexmlMeta.getImageName(0);
    System.out.println("Initial Image name = " + name);
    // change image name (reverse it)
    char[] arr = name.toCharArray();
    for (int i = 0; i < arr.length / 2; i++) {
        int i2 = arr.length - i - 1;
        char c = arr[i];
        char c2 = arr[i2];
        arr[i] = c2;
        arr[i2] = c;
    }
    name = new String(arr);
    // save altered name back to OME-XML structure
    omexmlMeta.setImageName(name, 0);
    System.out.println("Updated Image name = " + name);
    // output full OME-XML block
    System.out.println("Full OME-XML dump:");
    String xml = service.getOMEXML(omexmlMeta);
    System.out.println(xml);
}

Example 9 with ImageReader

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

the class LosslessJPEG2000Test method testEquivalentPixels8Bit.

@Test
public void testEquivalentPixels8Bit() throws Exception {
    ImageReader reader = new ImageReader();
    reader.setId(FILE_8);
    byte[] plane = reader.openBytes(0);
    assertEquals(plane.length, PIXELS_8.length);
    for (int q = 0; q < plane.length; q++) {
        assertEquals(plane[q], PIXELS_8[q]);
    }
    reader.close();
}

Example 10 with ImageReader

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

the class LosslessJPEG2000Test method testEquivalentPixels16Bit.

@Test
public void testEquivalentPixels16Bit() throws Exception {
    ImageReader reader = new ImageReader();
    reader.setId(FILE_16);
    byte[] plane = reader.openBytes(0);
    assertEquals(plane.length, PIXELS_16.length);
    for (int q = 0; q < plane.length; q++) {
        assertEquals(plane[q], PIXELS_16[q]);
    }
    reader.close();
}