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JPEG-2000 #3

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9 changes: 8 additions & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,13 @@
<artifactId>jblosc</artifactId>
<version>1.0.1</version>
</dependency>

<dependency>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-codecs</artifactId>
<version>0.3.1</version>
</dependency>

<!-- <dependency>-->
<!-- <groupId>org.blosc</groupId>-->
<!-- <artifactId>jblosc</artifactId>-->
Expand Down Expand Up @@ -211,4 +218,4 @@
</plugins>
</build>

</project>
</project>
37 changes: 37 additions & 0 deletions src/main/java/com/bc/zarr/Compressor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,4 +50,41 @@ void passThrough(InputStream is, OutputStream os) throws IOException {
read = is.read(bytes);
}
}

public boolean booleanValue(Object v, boolean defaultValue) {
if (v == null) {
return defaultValue;
}
if (v instanceof Boolean) {
return (Boolean) v;
}
return Boolean.parseBoolean(v.toString());
}

public int intValue(Object v, int defaultValue) {
int value = defaultValue;
if (v != null) {
if (v instanceof String) {
value = Integer.parseInt((String) v);
}
else if (v instanceof Number) {
value = ((Number) v).intValue();
}
}
return value;
}

public double doubleValue(Object v, double defaultValue) {
double value = defaultValue;
if (v != null) {
if (v instanceof String) {
value = Double.parseDouble((String) v);
}
else if (v instanceof Number) {
value = ((Number) v).doubleValue();
}
}
return value;
}

}
119 changes: 119 additions & 0 deletions src/main/java/com/bc/zarr/CompressorFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
import org.blosc.IBloscDll;
import org.blosc.JBlosc;

import java.awt.image.WritableRaster;
import java.io.ByteArrayOutputStream;
import java.io.DataInput;
import java.io.DataInputStream;
Expand All @@ -47,6 +48,16 @@
import java.util.zip.Inflater;
import java.util.zip.InflaterInputStream;

import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import ome.codecs.CodecException;
import ome.codecs.JPEG2000Codec;
import ome.codecs.JPEG2000CodecOptions;
import ome.codecs.gui.AWTImageTools;
import ome.codecs.services.JAIIIOService;
import ome.codecs.services.JAIIIOServiceImpl;

public class CompressorFactory {

public final static Compressor nullCompressor = new NullCompressor();
Expand Down Expand Up @@ -120,6 +131,9 @@ public static Compressor create(String id, Map<String, Object> properties) {
if ("blosc".equals(id)) {
return new BloscCompressor(properties);
}
if ("j2k".equals(id)) {
return new J2KCompressor(properties);
}
throw new IllegalArgumentException("Compressor id:'" + id + "' not supported.");
}

Expand Down Expand Up @@ -356,5 +370,110 @@ private BufferSizes cbufferSizes(ByteBuffer cbuffer) {
return bs;
}
}

static class J2KCompressor extends Compressor {
public static final String littleEndianKey = "littleEndian";
public static final String interleavedKey = "interleaved";
public static final String losslessKey = "lossless";
public static final String widthKey = "imageWidth";
public static final String heightKey = "imageHeight";
public static final String bitsPerSampleKey = "bitsPerSample";
public static final String channelsKey = "channels";
public static final String qualityKey = "quality";

// TODO: any way to copy these options from array metadata?
private boolean littleEndian;
private boolean interleaved;
private int width;
private int height;
private int bitsPerSample;
private int channels;
// specify lossless or quality, not both
private boolean lossless;
private double quality;

private J2KCompressor(Map<String, Object> map) {
littleEndian = booleanValue(map.get(littleEndianKey), false);
interleaved = booleanValue(map.get(interleavedKey), false);
width = intValue(map.get(widthKey), -1);
height = intValue(map.get(heightKey), -1);
bitsPerSample = intValue(map.get(bitsPerSampleKey), 8);
channels = intValue(map.get(channelsKey), 1);

// if neither quality nor lossless is defined, do lossless compression
quality = doubleValue(map.get(qualityKey), -1);
lossless = booleanValue(map.get(losslessKey), quality < 0);
}

@Override
public String toString() {
return "compressor=" + getId();
}

@Override
public String getId() {
return "j2k";
}

@Override
public void compress(InputStream is, OutputStream os) throws IOException {
try (ByteArrayOutputStream tmpOut = new ByteArrayOutputStream()) {
passThrough(is, tmpOut);
byte[] buffer = tmpOut.toByteArray();
JPEG2000Codec codec = new JPEG2000Codec();
JPEG2000CodecOptions options = getCodecOptions();
byte[] compressed = codec.compress(buffer, options);
os.write(compressed);
}
catch (CodecException e) {
throw new IOException(e);
}
}

@Override
public void uncompress(InputStream is, OutputStream os) throws IOException {
try {
JAIIIOService service = getService();
WritableRaster raster = (WritableRaster) service.readRaster(is, getCodecOptions());
byte[][] raw = AWTImageTools.getPixelBytes(raster, littleEndian);
for (byte[] channel : raw) {
os.write(channel);
}
}
catch (ServiceException e) {
throw new IOException(e);
}
}

private JPEG2000CodecOptions getCodecOptions() {
JPEG2000CodecOptions options = new JPEG2000CodecOptions();
options.interleaved = interleaved;
options.littleEndian = littleEndian;
options.width = width;
options.height = height;
options.channels = channels;
options.bitsPerSample = bitsPerSample;
if (quality >= 0) {
options.quality = quality;
}
options.lossless = lossless;
options.numDecompositionLevels = 1;

return JPEG2000CodecOptions.getDefaultOptions(options);
}

private JAIIIOService getService() throws IOException {
try {
ServiceFactory factory = new ServiceFactory();
return factory.getInstance(JAIIIOService.class);
}
catch (DependencyException de) {
throw new IOException(JAIIIOServiceImpl.NO_J2K_MSG, de);
}
}

}


}

46 changes: 46 additions & 0 deletions src/test/java/com/bc/zarr/CompressorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@

import static org.hamcrest.Matchers.*;
import static org.hamcrest.MatcherAssert.*;
import static org.junit.Assert.assertNotNull;

import com.bc.zarr.chunk.ZarrInputStreamAdapter;

Expand Down Expand Up @@ -155,6 +156,51 @@ public void writeRead_BloscCompressor() throws IOException {
assertThat(input, is(equalTo(uncompressed)));
}

@Test
public void writeRead_J2KCompressor() throws IOException {
final Map<String, Object> j2kProperties = new LinkedHashMap<>();
j2kProperties.put(CompressorFactory.J2KCompressor.widthKey, 11);
j2kProperties.put(CompressorFactory.J2KCompressor.heightKey, 5);
j2kProperties.put(CompressorFactory.J2KCompressor.bitsPerSampleKey, 16);
j2kProperties.put(CompressorFactory.J2KCompressor.channelsKey, 1);
j2kProperties.put(CompressorFactory.J2KCompressor.interleavedKey, false);
j2kProperties.put(CompressorFactory.J2KCompressor.littleEndianKey, false);
j2kProperties.put(CompressorFactory.J2KCompressor.losslessKey, true);

final Compressor compressor = CompressorFactory.create("j2k", j2kProperties);
final ByteOrder byteOrder = ByteOrder.BIG_ENDIAN;
final short[] input = {
100, 22, 100, 22, 22, 22, 100, 100, 100, 22, 100,
100, 22, 100, 22, 22, 22, 100, 100, 100, 22, 100,
100, 22, 100, 22, 22, 22, 100, 100, 100, 22, 100,
100, 22, 100, 22, 22, 22, 100, 100, 100, 22, 100,
100, 22, 100, 22, 22, 22, 100, 100, 100, 22, 100
};
final MemoryCacheImageOutputStream iis = new MemoryCacheImageOutputStream(new ByteArrayOutputStream());
iis.setByteOrder(byteOrder);
iis.writeShorts(input, 0, input.length);
iis.seek(0);

ByteArrayOutputStream os;
ByteArrayInputStream is;

//write
os = new ByteArrayOutputStream();
compressor.compress(new ZarrInputStreamAdapter(iis), os);
final byte[] compressed = os.toByteArray();

//read
is = new ByteArrayInputStream(compressed);
os = new ByteArrayOutputStream();
compressor.uncompress(is, os);
final ByteArrayInputStream bais = new ByteArrayInputStream(os.toByteArray());
final MemoryCacheImageInputStream resultIis = new MemoryCacheImageInputStream(bais);
resultIis.setByteOrder(byteOrder);
final short[] uncompressed = new short[input.length];
resultIis.readFully(uncompressed, 0, uncompressed.length);
assertThat(input, is(equalTo(uncompressed)));
}

@Test
public void read_BloscCompressor_DefaultAvailable() throws IOException {
final Compressor compressor = CompressorFactory.create("blosc");
Expand Down