reformatting

added cbf support

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi.zmq</groupId>
 	<artifactId>ch.psi.zmq.imagej</artifactId>
-	<version>0.2.0</version>
+	<version>0.4.0</version>
 
 	<dependencies>
 		<dependency>
@@ -11,6 +11,11 @@
 			<artifactId>jeromq</artifactId>
 			<version>0.2.0</version>
 		</dependency>
+		<dependency>
+			<groupId>ch.psi.imagej</groupId>
+			<artifactId>ch.psi.imagej.cbf</artifactId>
+			<version>0.0.3</version>
+		</dependency>
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>

src/main/java/ch/psi/zmq/imagej/Collector.java

@@ -18,10 +18,16 @@
  */
 package ch.psi.zmq.imagej;
 
+import ij.IJ;
 import ij.ImagePlus;
+import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 import ij.process.ShortProcessor;
 
+import java.awt.image.BufferedImage;
+import java.awt.image.DataBuffer;
+import java.awt.image.DataBufferFloat;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
@@ -31,8 +37,15 @@ import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import javax.imageio.ImageIO;
+import javax.imageio.ImageReadParam;
+import javax.imageio.stream.ImageInputStream;
+
 import org.jeromq.ZMQ;
 
+import ch.psi.imagej.cbf.CbfImageReader;
+import ch.psi.imagej.cbf.CbfImageReaderSpi;
+
 import com.fasterxml.jackson.core.JsonFactory;
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -43,11 +56,16 @@ import com.fasterxml.jackson.databind.ObjectMapper;
  */
 public class Collector implements Runnable {
 
-	
 	private static final Logger logger = Logger.getLogger(Collector.class.getName());
 
 	private static final int HIGH_WATER_MARK = 10;
 
+	private enum HType {
+		ARRAY_1_0, PILATUS_1_0
+	};
+
+	private HType htype = HType.ARRAY_1_0;
+
 	private boolean flipX = false;
 	private boolean flipY = false;
 
@@ -60,7 +78,6 @@ public class Collector implements Runnable{
 
 	private ObjectMapper mapper = new ObjectMapper(new JsonFactory());
 
-	
 	private int numImageUpdates;
 
 	private HeaderInfo hinfo;
@@ -75,7 +92,9 @@ public class Collector implements Runnable{
 		this.method = method;
 	}
 
-	/* (non-Javadoc)
+	/*
+	 * (non-Javadoc)
+	 * 
 	 * @see java.lang.Runnable#run()
 	 */
 	public void run() {
@@ -86,7 +105,6 @@ public class Collector implements Runnable{
 			img = null;
 		}
 
-			
 		context = ZMQ.context();
 		if (method.equals("PULL")) {
 			socket = context.socket(ZMQ.PULL);
@@ -125,8 +143,9 @@ public class Collector implements Runnable{
 
 			socket.close();
 			context.term();
-		}
+		} catch (Exception ex) { // This exception can savely be ignored
-		catch(Exception ex){ // This exception can savely be ignored (somewhat most of the time an exception is expected)
+									// (somewhat most of the time an exception
+									// is expected)
 			ex.printStackTrace();
 		}
 
@@ -142,8 +161,16 @@ public class Collector implements Runnable{
 		try {
 			String header = new String(h);
 			// hinfo.setHeader(header);
-			Map<String,Object> m = mapper.readValue(header, new TypeReference<HashMap<String,Object>>(){});
+			Map<String, Object> m = mapper.readValue(header, new TypeReference<HashMap<String, Object>>() {
-			if(((List<String>) m.get("htype")).contains("array-1.0")){ // currently we only support array-1.0 message types
+			});
+			if (((List<String>) m.get("htype")).contains("array-1.0")) { // currently
+																			// we
+																			// only
+																			// support
+																			// array-1.0
+																			// message
+																			// types
+				htype = HType.ARRAY_1_0;
 				List<Integer> shape = (List<Integer>) m.get("shape");
 				int nImageSizeX = shape.get(1);
 				int nImageSizeY = shape.get(0);
@@ -166,6 +193,12 @@ public class Collector implements Runnable{
 				hinfo.setText(m);
 
 			}
+			else if (((List<String>) m.get("htype")).contains("pilatus-1.0")) { // pilatus
+																				// 1.0
+																				// message
+																				// support
+				htype = HType.PILATUS_1_0;
+			}
 			else {
 				logger.info("Header type is not supported ...");
 				if (img != null) {
@@ -173,8 +206,7 @@ public class Collector implements Runnable{
 					img = null;
 				}
 			}
-		}
+		} catch (IOException e) {
-		catch(IOException e){
 			logger.log(Level.SEVERE, "Unable to parse header", e);
 		}
 
@@ -183,6 +215,7 @@ public class Collector implements Runnable{
 
 	private void readContent(byte[] content) {
 		try {
+			if (htype == HType.ARRAY_1_0) {
 				if (content != null && img != null) {
 					// TODO Check whether this is needed
 					short[] shorts = new short[content.length / 2];
@@ -200,28 +233,101 @@ public class Collector implements Runnable{
 					img.updateAndDraw();
 					numImageUpdates++;
 				}
+			}
+			else if (htype == HType.PILATUS_1_0) {
+				CbfImageReaderSpi spi = new CbfImageReaderSpi();
+				ImageInputStream stream = ImageIO.createImageInputStream(new ByteArrayInputStream(content));
+				CbfImageReader reader = new CbfImageReader(spi);
+				reader.setInput(stream);
+				ImageReadParam param = reader.getDefaultReadParam();
+				int width = reader.getWidth(0);
+				int height = reader.getHeight(0);
+				BufferedImage image = reader.read(0, param);
+				DataBuffer buffer = image.getData().getDataBuffer();
+				int bufferType = buffer.getDataType();
+				float[] pixels;
+				ImageProcessor ip = null;
+				if (buffer instanceof DataBufferFloat) {
+					pixels = ((DataBufferFloat) buffer).getData();
+					ip = new FloatProcessor(width, height, pixels, null);
+					image.flush();
+					reader.dispose();
+					// TODO
+					// return new ImagePlus(cbfFile.getName(), ip);
+				} else if (bufferType == DataBuffer.TYPE_INT || bufferType == DataBuffer.TYPE_FLOAT) {
+					pixels = new float[width * height];
+					for (int i = 0; i < pixels.length; i++)
+						pixels[i] = buffer.getElemFloat(i);
+					ip = new FloatProcessor(width, height, pixels, null);
+					image.flush();
+					reader.dispose();
+					// TODO
+					// return new ImagePlus(cbfFile.getName(), ip);
+				} else if (bufferType == DataBuffer.TYPE_DOUBLE) {
+					pixels = new float[width * height];
+					boolean clipped = false;
+					for (int i = 0; i < pixels.length; i++) {
+						double doubleValue = buffer.getElemDouble(i);
+						float floatValue;
+						if (doubleValue < Float.MIN_VALUE) {
+							floatValue = Float.MIN_VALUE;
+							clipped = true;
+						} else if (doubleValue > Float.MAX_VALUE) {
+							floatValue = Float.MAX_VALUE;
+							clipped = true;
+						} else {
+							floatValue = (float) doubleValue;
+						}
+						pixels[i] = floatValue;
+					}
+					if (clipped) {
+						IJ.log("Warning: pixel value(s) clipped to fit in type float");
+					}
+					ip = new FloatProcessor(width, height, pixels, null);
+					image.flush();
+					reader.dispose();
+					// TODO
+					// return new ImagePlus(cbfFile.getName(), ip);
+				} else {
+					reader.dispose();
+					// TODO
+					// return new ImagePlus(cbfFile.getName(), image);
+				}
+				if(img==null){
+					img = new ImagePlus("", ip);
+					img.show();
+				}
+				else{
+					img.setProcessor(ip);
+					img.updateAndDraw();
+				}
+				
+			}
 		} catch (Exception ex) {
 			logger.log(Level.SEVERE, "UpdateImage got exception", ex);
 		}
 	}
 
-
-	
 	public boolean isFlipX() {
 		return flipX;
 	}
+
 	public void setFlipX(boolean flipX) {
 		this.flipX = flipX;
 	}
+
 	public boolean isFlipY() {
 		return flipY;
 	}
+
 	public void setFlipY(boolean flipY) {
 		this.flipY = flipY;
 	}
+
 	public int getNumImageUpdates() {
 		return numImageUpdates;
 	}
+
 	public void setNumImageUpdates(int numImageUpdates) {
 		this.numImageUpdates = numImageUpdates;
 	}