Fix bug in generic region decoding procedure, when MMR is 1

.gitignore

@@ -1 +1,2 @@
-/build
+/build
+/bin/

README.md

@@ -1,17 +1,80 @@
 JBIG2-Image-Decoder
 =============================
+This project fix bug in MMR decoding in Borisvl/JBIG2-Image-Decoder's fork JPedal's JBIG2 library.
 
-This is a fork of [JPedal's JBIG2 library](http://www.jpedal.org/support_JBIG.php), 
-which aims to improve the performance of the original code.
-
-Results
+Description
 -----------------------------
+A pdf [file](https://github.com/afila/JBIG2-Image-Decoder/blob/master/XeroxWorkCentre5230A_Huffman.pdf)
+(version 1.4) produced by Xerox WorkCentre 5230(A) with JBIG2 compression (MMR) give an error, when attept to decode an [image  stream](https://github.com/afila/JBIG2-Image-Decoder/blob/master/XeroxWorkCentre5230A_Huffman.jb2) from this file:
+
+    Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 30447
+	    at org.jpedal.jbig2.io.StreamReader.readByte(StreamReader.java:86)
+	    at org.jpedal.jbig2.decoders.JBIG2StreamDecoder.handleSegmentReferredToCountAndRententionFlags(JBIG2StreamDecoder.java:503)
+	    at org.jpedal.jbig2.decoders.JBIG2StreamDecoder.readSegmentHeader(JBIG2StreamDecoder.java:457)
+	    at org.jpedal.jbig2.decoders.JBIG2StreamDecoder.readSegments(JBIG2StreamDecoder.java:211)
+	    at org.jpedal.jbig2.decoders.JBIG2StreamDecoder.decodeJBIG2(JBIG2StreamDecoder.java:173)
+	    at org.jpedal.jbig2.JBIG2Decoder.decodeJBIG2(JBIG2Decoder.java:148)
+	    at org.jpedal.jbig2.JBIG2Decoder.decodeJBIG2(JBIG2Decoder.java:123)
+	    at org.jpedal.jbig2.JBIG2Decoder.decodeJBIG2(JBIG2Decoder.java:108)
+	    at org.jpedal.jbig2.JBIG2Decoder.decodeJBIG2(JBIG2Decoder.java:98)
+	    at org.jpedal.jbig2.examples.viewer.JBIG2Viewer.openFile(JBIG2Viewer.java:274)
+	    at org.jpedal.jbig2.examples.viewer.JBIG2Viewer.access$0(JBIG2Viewer.java:252)
+	    at org.jpedal.jbig2.examples.viewer.JBIG2Viewer$1.actionPerformed(JBIG2Viewer.java:163)
+	    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
+	    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
+	    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
+	    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
+	    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
+	    at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
+	    at java.awt.Component.processMouseEvent(Unknown Source)
+	    at javax.swing.JComponent.processMouseEvent(Unknown Source)
+	    at java.awt.Component.processEvent(Unknown Source)
+	    at java.awt.Container.processEvent(Unknown Source)
+	    at java.awt.Component.dispatchEventImpl(Unknown Source)
+	    at java.awt.Container.dispatchEventImpl(Unknown Source)
+	    at java.awt.Component.dispatchEvent(Unknown Source)
+	    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
+	    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
+	    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
+	    at java.awt.Container.dispatchEventImpl(Unknown Source)
+	    at java.awt.Window.dispatchEventImpl(Unknown Source)
+	    at java.awt.Component.dispatchEvent(Unknown Source)
+	    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
+	    at java.awt.EventQueue.access$200(Unknown Source)
+	    at java.awt.EventQueue$3.run(Unknown Source)
+	    at java.awt.EventQueue$3.run(Unknown Source)
+	    at java.security.AccessController.doPrivileged(Native Method)
+	    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
+	    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
+	    at java.awt.EventQueue$4.run(Unknown Source)
+	    at java.awt.EventQueue$4.run(Unknown Source)
+	    at java.security.AccessController.doPrivileged(Native Method)
+	    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
+	    at java.awt.EventQueue.dispatchEvent(Unknown Source)
+	    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
+	    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
+	    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
+	    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
+	    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
+	    at java.awt.EventDispatchThread.run(Unknown Source)
+
+
+Reason
+--------------------------------
+I think the reason in the 6.2.6 **Decoding using MMR coding** of [JBIG2 specification](http://www.hlevkin.com/Standards/fcd14492.pdf).
 
-Version 1 (09.10.2011):
+If MMR is 1, the generic region decoding procedure is identical to an MMR (ModifiedModified READ) decoder
+described in ITU-T Recommendation T.6, with the following exceptions:
+ An invocation of the generic region decoding procedure with MMR equal to 1 `shall consume an integral
+number of bytes, beginning and ending on a byte boundary`. This may involve skipping over some bits in
+the last byte read.
 
-In all samples we have tested, the decoding speed has increased at least by 
-factor 2.5.
-In some examples a speed up by factor 4.5 was observed.
+_Correct me if I wrong..._
 
-There is still lot of room for improvements especially in the combine method 
-in JBIG2Bitmap, which is most time consuming. 
+Fix
+--------------------------------
+```java
+//GenericRegionSegment.java
+//bitmap.readBitmap(useMMR, template, typicalPredictionGenericDecodingOn, false, null, genericBAdaptiveTemplateX, genericBAdaptiveTemplateY, useMMR ? 0 : length - 18);
+bitmap.readBitmap(useMMR, template, typicalPredictionGenericDecodingOn, false, null, genericBAdaptiveTemplateX, genericBAdaptiveTemplateY, useMMR ? bytesRead : length - 18);
+```

src/org/jpedal/jbig2/decoders/JBIG2StreamDecoder.java

@@ -90,7 +90,7 @@ public class JBIG2StreamDecoder {
 
 	private MMRDecoder mmrDecoder;
 
-	public static boolean debug = false;
+	public static boolean debug = true;// DEBUG	DEBUG DEBUG DEBUG
 
 	public void movePointer(int i){
 		reader.movePointer(i);

src/org/jpedal/jbig2/segment/region/generic/GenericRegionSegment.java

@@ -109,6 +109,11 @@ public void readSegment() throws IOException, JBIG2Exception {
 
         boolean typicalPredictionGenericDecodingOn = genericRegionFlags.getFlagValue(GenericRegionFlags.TPGDON) != 0;
         int length = segmentHeader.getSegmentDataLength();
+
+        /*---1 fix MMR ---*/
+    	int bytesRead = 0;
+    	/*- end 1 fix MMR -*/
+
 
         if(length == -1) { 
         	/** 
@@ -133,7 +138,10 @@ public void readSegment() throws IOException, JBIG2Exception {
         		match2 = 172;
         	}
 
-        	int bytesRead = 0;
+        	/*--- 2 fix MMR ---*/
+        	//int bytesRead = 0;
+        	/*- end 2 fix MMR -*/
+
     		while(true) {
     			short bite1 = decoder.readByte();
     			bytesRead++;
@@ -154,9 +162,15 @@ public void readSegment() throws IOException, JBIG2Exception {
 
         JBIG2Bitmap bitmap = new JBIG2Bitmap(regionBitmapWidth, regionBitmapHeight, arithmeticDecoder, huffmanDecoder, mmrDecoder);
         bitmap.clear(0);
-        bitmap.readBitmap(useMMR, template, typicalPredictionGenericDecodingOn, false, null, genericBAdaptiveTemplateX, genericBAdaptiveTemplateY, useMMR ? 0 : length - 18);
-
+        /*--- 3 fix MMR ---*/
+        	// See 6.2.6 Decoding using MMR coding
+        	// An invocation of the generic region decoding procedure with MMR equal to 1 shall consume an integral
+        	// number of bytes, beginning and ending on a byte boundary. This may involve skipping over some bits in the last byte read.
 
+        	//bitmap.readBitmap(useMMR, template, typicalPredictionGenericDecodingOn, false, null, genericBAdaptiveTemplateX, genericBAdaptiveTemplateY, useMMR ? 0 : length - 18);
+         	bitmap.readBitmap(useMMR, template, typicalPredictionGenericDecodingOn, false, null, genericBAdaptiveTemplateX, genericBAdaptiveTemplateY, useMMR ? bytesRead : length - 18);
+
+        /*- end 3 fix MMR -*/
 
         if (inlineImage) {
             PageInformationSegment pageSegment = decoder.findPageSegement(segmentHeader.getPageAssociation());