renamed packages to fit into psi structure

Added plugins.config file

Readme.md

@@ -1,6 +1,13 @@
+# Overview
 Jcbf ([J]ava [C]rystallographic [B]inary [F]ile) is a pure Java library for
 reading and writing minimal CBF (miniCBF) image files using the MIME
 "mini-header" and the "none" or "byte_offset" compression algorithm, as
 produced by DECTRIS PILATUS detectors.
+It was initially developed by J. Lewis Muir <jlmuir@imca.aps.anl.gov> (IMCA-CAT).
+
+
+# Development
+To build the code run following maven command/goals:
+`mvn clean compile assembly:single`
+
 
-Written in March 2011 by J. Lewis Muir <jlmuir@imca.aps.anl.gov> (IMCA-CAT).

src/main/java/ch/psi/imagej/cbf/Base64.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.nio.ByteBuffer;
 

src/main/java/ch/psi/imagej/cbf/ByteArrayCbfData.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;

src/main/java/ch/psi/imagej/cbf/CbfCompression.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.text.ParseException;
 

src/main/java/ch/psi/imagej/cbf/CbfData.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.io.IOException;
 import java.nio.ByteOrder;

src/main/java/ch/psi/imagej/cbf/CbfElementType.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.awt.image.DataBuffer;
 import java.text.ParseException;

src/main/java/ch/psi/imagej/cbf/CbfImageReadParam.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import javax.imageio.ImageReadParam;
 

src/main/java/ch/psi/imagej/cbf/CbfImageReader.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.awt.Rectangle;
 import java.awt.color.ColorSpace;

src/main/java/ch/psi/imagej/cbf/CbfImageReaderSpi.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.io.EOFException;
 import java.io.IOException;
@@ -39,7 +39,8 @@ public class CbfImageReaderSpi extends ImageReaderSpi {
   private static final String METADATA_FORMAT_NAME = "imcacat.jcbf.CbfMetadataFormat_1.0";
   private static final String METADATA_FORMAT_CLASS_NAME = "imcacat.jcbf.CbfMetadataFormat";
 
-  public CbfImageReaderSpi() {
+  @SuppressWarnings("deprecation")
+public CbfImageReaderSpi() {
     super(VENDOR_NAME, VERSION, FORMAT_NAMES, FORMAT_SUFFIXES, MIME_TYPES, READER_CLASS_NAME,
       STANDARD_INPUT_TYPE, WRITER_SPI_CLASS_NAMES, false, null, null, null, null, false,
       METADATA_FORMAT_NAME, METADATA_FORMAT_CLASS_NAME, null, null);

src/main/java/ch/psi/imagej/cbf/CbfImageWriteParam.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import javax.imageio.ImageWriteParam;
 

src/main/java/ch/psi/imagej/cbf/CbfImageWriter.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.awt.Rectangle;
 import java.awt.image.BufferedImage;

src/main/java/ch/psi/imagej/cbf/CbfImageWriterSpi.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.awt.image.BufferedImage;
 import java.io.IOException;
@@ -38,7 +38,8 @@ public class CbfImageWriterSpi extends ImageWriterSpi {
   private static final String METADATA_FORMAT_NAME = "imcacat.jcbf.CbfMetadata_1.0";
   private static final String METADATA_FORMAT_CLASS_NAME = "imcacat.jcbf.CbfMetadataFormat";
 
-  public CbfImageWriterSpi() {
+  @SuppressWarnings("deprecation")
+public CbfImageWriterSpi() {
     super(VENDOR_NAME, VERSION, FORMAT_NAMES, FORMAT_SUFFIXES, MIME_TYPES, WRITER_CLASS_NAME,
       STANDARD_OUTPUT_TYPE, READER_SPI_CLASS_NAMES, false, null, null, null, null, false,
       METADATA_FORMAT_NAME, METADATA_FORMAT_CLASS_NAME, null, null);

src/main/java/ch/psi/imagej/cbf/CbfMetadata.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.nio.ByteOrder;
 import java.text.DateFormat;

src/main/java/ch/psi/imagej/cbf/CbfMetadataFormat.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import javax.imageio.ImageTypeSpecifier;
 import javax.imageio.metadata.IIOMetadataFormatImpl;

src/main/java/ch/psi/imagej/cbf/ImageInputStreamCbfData.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.io.IOException;
 import java.nio.ByteOrder;

src/main/java/ch/psi/imagej/cbf/ImageJCbfReader.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import java.awt.image.BufferedImage;
 import java.awt.image.DataBuffer;

src/main/java/ch/psi/imagej/cbf/Version.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 /**
  * I provide the version identifier for this library.

src/main/resources/plugins.config

@@ -0,0 +1 @@
+File>Import, "CBF...", imcacat.jcbf.ImageJCbfReader

src/test/java/ch/psi/imagej/cbf/Base64Test.java

@@ -14,13 +14,15 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.Base64;
+
 /**
  * I test <code>Base64</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfCompressionTest.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertEquals;
 
@@ -22,6 +22,8 @@ import java.text.ParseException;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.CbfCompression;
+
 /**
  * I test <code>CbfCompression</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfElementTypeTest.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertEquals;
 
@@ -22,6 +22,8 @@ import java.text.ParseException;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.CbfElementType;
+
 /**
  * I test <code>CbfElementType</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfImageReaderSpiTest.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
@@ -25,6 +25,8 @@ import javax.imageio.stream.ImageInputStream;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.CbfImageReaderSpi;
+
 /**
  * I test <code>CbfImageReaderSpi</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfImageReaderTest.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
@@ -45,6 +45,13 @@ import javax.imageio.stream.ImageInputStream;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.Base64;
+import ch.psi.imagej.cbf.CbfCompression;
+import ch.psi.imagej.cbf.CbfElementType;
+import ch.psi.imagej.cbf.CbfImageReader;
+import ch.psi.imagej.cbf.CbfImageReaderSpi;
+import ch.psi.imagej.cbf.CbfMetadata;
+
 /**
  * I test <code>CbfImageReader</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfImageWriterSpiTest.java

@@ -14,12 +14,14 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertTrue;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.CbfImageWriterSpi;
+
 /**
  * I test <code>CbfImageWriterSpi</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfImageWriterTest.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
@@ -51,6 +51,14 @@ import javax.imageio.stream.MemoryCacheImageOutputStream;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.CbfCompression;
+import ch.psi.imagej.cbf.CbfElementType;
+import ch.psi.imagej.cbf.CbfImageReader;
+import ch.psi.imagej.cbf.CbfImageWriteParam;
+import ch.psi.imagej.cbf.CbfImageWriter;
+import ch.psi.imagej.cbf.CbfImageWriterSpi;
+import ch.psi.imagej.cbf.CbfMetadata;
+
 /**
  * I test <code>CbfImageWriter</code>.
  */

src/test/java/ch/psi/imagej/cbf/CbfMetadataTest.java

@@ -14,13 +14,15 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
-import static junit.framework.Assert.assertNull;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertEquals;
 
 import org.junit.Test;
 
+import ch.psi.imagej.cbf.CbfMetadata;
+
 /**
  * I test <code>CbfMetadata</code>.
  */

src/test/java/ch/psi/imagej/cbf/TestUtils.java

@@ -14,7 +14,7 @@
  * OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
 
-package imcacat.jcbf;
+package ch.psi.imagej.cbf;
 
 import static org.junit.Assert.fail;
 
@@ -39,6 +39,12 @@ import javax.imageio.stream.ImageOutputStream;
 import javax.imageio.stream.MemoryCacheImageInputStream;
 import javax.imageio.stream.MemoryCacheImageOutputStream;
 
+import ch.psi.imagej.cbf.CbfImageReader;
+import ch.psi.imagej.cbf.CbfImageReaderSpi;
+import ch.psi.imagej.cbf.CbfImageWriter;
+import ch.psi.imagej.cbf.CbfImageWriterSpi;
+import ch.psi.imagej.cbf.CbfMetadata;
+
 /**
  * I provide utility methods for use in testing.
  */