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ebner 2015-10-09 08:40:32 +02:00
parent 0b3ce96675
commit 0c2c2d21d3
7 changed files with 151 additions and 75 deletions
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13
.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_annotations_2_2_0.xml generated Normal file
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@ -0,0 +1,13 @@
<component name="libraryTable">
<library name="Maven: com.fasterxml.jackson.core:jackson-annotations:2.2.0">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-annotations/2.2.0/jackson-annotations-2.2.0.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-annotations/2.2.0/jackson-annotations-2.2.0-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-annotations/2.2.0/jackson-annotations-2.2.0-sources.jar!/" />
</SOURCES>
</library>
</component>

13
.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_core_2_2_0.xml generated Normal file
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@ -0,0 +1,13 @@
<component name="libraryTable">
<library name="Maven: com.fasterxml.jackson.core:jackson-core:2.2.0">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-core/2.2.0/jackson-core-2.2.0.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-core/2.2.0/jackson-core-2.2.0-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-core/2.2.0/jackson-core-2.2.0-sources.jar!/" />
</SOURCES>
</library>
</component>

13
.idea/libraries/Maven__com_fasterxml_jackson_core_jackson_databind_2_2_0.xml generated Normal file
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@ -0,0 +1,13 @@
<component name="libraryTable">
<library name="Maven: com.fasterxml.jackson.core:jackson-databind:2.2.0">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-databind/2.2.0/jackson-databind-2.2.0.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-databind/2.2.0/jackson-databind-2.2.0-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/fasterxml/jackson/core/jackson-databind/2.2.0/jackson-databind-2.2.0-sources.jar!/" />
</SOURCES>
</library>
</component>

13
.idea/libraries/Maven__gov_nih_imagej_imagej_1_46.xml generated Normal file
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@ -0,0 +1,13 @@
<component name="libraryTable">
<library name="Maven: gov.nih.imagej:imagej:1.46">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/gov/nih/imagej/imagej/1.46/imagej-1.46.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/gov/nih/imagej/imagej/1.46/imagej-1.46-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/gov/nih/imagej/imagej/1.46/imagej-1.46-sources.jar!/" />
</SOURCES>
</library>
</component>

13
.idea/libraries/Maven__org_jeromq_jeromq_0_2_0.xml generated Normal file
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@ -0,0 +1,13 @@
<component name="libraryTable">
<library name="Maven: org.jeromq:jeromq:0.2.0">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/jeromq/jeromq/0.2.0/jeromq-0.2.0.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/org/jeromq/jeromq/0.2.0/jeromq-0.2.0-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/org/jeromq/jeromq/0.2.0/jeromq-0.2.0-sources.jar!/" />
</SOURCES>
</library>
</component>

15
pom.xml
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@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ch.psi.zmq</groupId>
<artifactId>ch.psi.zmq.imagej</artifactId>
<version>0.4.0</version>
<version>0.5.0</version>
<dependencies>
<dependency>
@ -11,11 +11,11 @@
<artifactId>jeromq</artifactId>
<version>0.2.0</version>
</dependency>
<dependency>
<!-- <dependency>
<groupId>ch.psi.imagej</groupId>
<artifactId>ch.psi.imagej.cbf</artifactId>
<version>0.0.3</version>
</dependency>
</dependency> -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
@ -31,6 +31,15 @@
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<encoding>UTF-8</encoding>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4</version>

146
src/main/java/ch/psi/zmq/imagej/Collector.java
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@ -43,8 +43,8 @@ import javax.imageio.stream.ImageInputStream;
import org.jeromq.ZMQ;
import ch.psi.imagej.cbf.CbfImageReader;
import ch.psi.imagej.cbf.CbfImageReaderSpi;
//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;
@ -178,7 +178,9 @@ public class Collector implements Runnable {
imageSizeX = nImageSizeX;
imageSizeY = nImageSizeY;
img.close();
if(img !=null){
img.close();
}
img = null;
}
@ -234,75 +236,75 @@ public class Collector implements Runnable {
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();
}
}
// 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);
}