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

Example 6 with IFormatWriter

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

the class SixteenBitLosslessJPEG2000Test method testLosslessPixels.

@Test
public void testLosslessPixels() throws Exception {
    int failureCount = 0;
    for (int v = Short.MIN_VALUE; v < Short.MAX_VALUE; v += increment) {
        int index = v + Short.MAX_VALUE + 1;
        byte[] pixels = DataTools.shortToBytes((short) v, false);
        String file = index + ".jp2";
        ByteArrayHandle tmpFile = new ByteArrayHandle(1);
        Location.mapFile(file, tmpFile);
        IMetadata metadata16;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata16 = 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);
        }
        MetadataTools.populateMetadata(metadata16, 0, "foo", false, "XYCZT", "uint16", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer16 = new JPEG2000Writer();
        writer16.setMetadataRetrieve(metadata16);
        writer16.setId(file);
        writer16.saveBytes(0, pixels);
        writer16.close();
        byte[] buf = tmpFile.getBytes();
        byte[] realData = new byte[(int) tmpFile.length()];
        System.arraycopy(buf, 0, realData, 0, realData.length);
        tmpFile.close();
        tmpFile = new ByteArrayHandle(realData);
        Location.mapFile(file, tmpFile);
        ImageReader reader = new ImageReader();
        reader.setId(file);
        byte[] plane = reader.openBytes(0);
        for (int q = 0; q < plane.length; q++) {
            if (plane[q] != pixels[q]) {
                LOGGER.debug("FAILED on {}", DataTools.bytesToShort(pixels, false));
                failureCount++;
                break;
            }
        }
        reader.close();
        tmpFile.close();
        Location.mapFile(file, null);
    }
    assertEquals(failureCount, 0);
}

Example 7 with IFormatWriter

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

the class EightBitLosslessJPEG2000Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    for (byte v = Byte.MIN_VALUE; v < Byte.MAX_VALUE; v++) {
        int index = v + Byte.MAX_VALUE + 1;
        pixels[index][0] = v;
        String file = index + ".jp2";
        File tempFile = File.createTempFile("test", ".jp2");
        tempFile.deleteOnExit();
        Location.mapId(file, tempFile.getAbsolutePath());
        files.add(file);
        IMetadata metadata;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata = 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);
        }
        MetadataTools.populateMetadata(metadata, 0, "foo", false, "XYCZT", "uint8", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer = new JPEG2000Writer();
        writer.setMetadataRetrieve(metadata);
        writer.setId(file);
        writer.saveBytes(0, pixels[index]);
        writer.close();
    }
}

Example 8 with IFormatWriter

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

the class FormatWriterTest method getWriterList.

// -- Data provider --
@DataProvider(name = "getWriterList")
public Object[][] getWriterList() {
    IFormatWriter[] writers = new ImageWriter().getWriters();
    List tmp = new ArrayList();
    for (int i = 0; i < writers.length; i++) {
        String[] compressionTypes = writers[i].getCompressionTypes();
        if (compressionTypes == null) {
            try {
                IFormatWriter w = (IFormatWriter) writers[i].getClass().newInstance();
                tmp.add(w);
            } catch (InstantiationException ie) {
            } catch (IllegalAccessException iae) {
            }
            continue;
        }
        for (int q = 0; q < compressionTypes.length; q++) {
            try {
                IFormatWriter w = (IFormatWriter) writers[i].getClass().newInstance();
                if (DataTools.containsValue(w.getPixelTypes(compressionTypes[q]), reader.getPixelType())) {
                    w.setCompression(compressionTypes[q]);
                    tmp.add(w);
                }
            } catch (FormatException fe) {
            } catch (InstantiationException ie) {
            } catch (IllegalAccessException iae) {
            }
        }
    }
    IFormatWriter[][] writersToUse = new IFormatWriter[tmp.size()][1];
    for (int i = 0; i < tmp.size(); i++) {
        writersToUse[i][0] = (IFormatWriter) tmp.get(i);
    }
    return writersToUse;
}