Add initial structure for decompressing JPEG XR images (assist #8493).

ant/toplevel.properties

@@ -29,6 +29,7 @@ merged-docs.source    = ${root.dir}/components/formats-common/build/src:\
                         ${root.dir}/components/formats-gpl/build/src:\
                         ${root.dir}/components/bio-formats-plugins/build/src:\
                         ${root.dir}/components/metakit/build/src:\
+                        ${root.dir}/components/ome-jxr/build/src:\
                         ${root.dir}/components/ome-xml/build/src:\
                         ${root.dir}/components/stubs/lwf-stubs/build/src:\
                         ${root.dir}/components/test-suite/build/src:\
@@ -87,6 +88,7 @@ loci-tools.libraries = formats-api.jar \
                        metakit.jar \
                        native-lib-loader-2.0-SNAPSHOT.jar \
                        netcdf-4.3.19.jar \
+                       ome-jxr.jar \
                        ome-xml.jar \
                        perf4j-0.9.13.jar \
                        ome-poi.jar \

ant/toplevel.xml

@@ -23,6 +23,7 @@ Type "ant -p" for a list of targets.
       compile-lwf-stubs,
       compile-mdbtools,
       compile-metakit,
+      compile-ome-jxr,
       compile-ome-xml,
       compile-ome-poi,
       compile-formats-api,
@@ -42,6 +43,7 @@ Type "ant -p" for a list of targets.
       jar-lwf-stubs,
       jar-mdbtools,
       jar-metakit,
+      jar-ome-jxr,
       jar-ome-xml,
       jar-ome-poi,
       jar-formats-api,
@@ -63,6 +65,7 @@ Type "ant -p" for a list of targets.
       osgi-lwf-stubs,
       osgi-mdbtools,
       osgi-metakit,
+      osgi-ome-jxr,
       osgi-ome-xml,
       osgi-ome-poi,
       osgi-formats-api,
@@ -89,6 +92,7 @@ Type "ant -p" for a list of targets.
       findbugs-formats-api,
       findbugs-formats-bsd,
       findbugs-bio-formats-tools,
+      findbugs-ome-jxr,
       findbugs-tests"
     description="run findbugs on most components"/>
 
@@ -102,6 +106,7 @@ Type "ant -p" for a list of targets.
       clean-lwf-stubs,
       clean-mdbtools,
       clean-metakit,
+      clean-ome-jxr,
       clean-ome-xml,
       clean-ome-poi,
       clean-formats-api,
@@ -125,6 +130,7 @@ Type "ant -p" for a list of targets.
       test-lwf-stubs,
       test-mdbtools,
       test-metakit,
+      test-ome-jxr,
       test-ome-xml,
       test-ome-poi,
       test-formats-api,
@@ -322,6 +328,42 @@ Type "ant -p" for a list of targets.
     <ant dir="components/metakit" target="test"/>
   </target>
 
+  <!-- OME JPEG XR library -->
+
+  <target name="deps-ome-jxr"
+    depends="jar-formats-common, jar-formats-bsd"/>
+
+  <target name="compile-ome-jxr" depends="deps-ome-jxr"
+    description="compile classes for OME JPEG XR Java library">
+    <ant dir="components/ome-jxr" target="ome-jxr.compile"/>
+  </target>
+
+  <target name="jar-ome-jxr" depends="deps-ome-jxr"
+    description="generate JAR file for OME JPEG XR Java library">
+    <ant dir="components/ome-jxr" target="ome-jxr.jar"/>
+  </target>
+
+  <target name="osgi-ome-jxr" depends="jar-ome-jxr"
+    description="generate OSGi bundle for OME JPEG XR Java library">
+    <ant dir="components/ome-jxr" target="ome-jxr.osgi"/>
+  </target>
+
+  <target name="findbugs-ome-jxr" depends="jar-ome-jxr"
+    description="run findbugs on OME JPEG XR Java library">
+    <ant dir="components/ome-jxr" target="ome-jxr.findbugs"/>
+  </target>
+
+  <target name="clean-ome-jxr"
+    depends="clean-formats-common"
+    description="remove build files for OME JPEG XR Java library">
+    <ant dir="components/ome-jxr" target="ome-jxr.clean"/>
+  </target>
+
+  <target name="test-ome-jxr" depends="jar-ome-jxr, testing-deps"
+    description="compile and run tests for OME JPEG XR Java library">
+    <ant dir="components/ome-jxr" target="test"/>
+  </target>
+
   <!-- OME-XML Java library -->
 
   <target name="deps-ome-xml" depends="copy-jars, jar-formats-common" />
@@ -541,6 +583,7 @@ Type "ant -p" for a list of targets.
     depends="copy-jars, jar-formats-common,
       jar-mdbtools,
       jar-metakit,
+      jar-ome-jxr,
       jar-ome-xml,
       jar-ome-poi,
       jar-formats-api,
@@ -570,6 +613,7 @@ Type "ant -p" for a list of targets.
     depends="clean-formats-common,
       clean-mdbtools,
       clean-metakit,
+      clean-ome-jxr,
       clean-ome-xml,
       clean-ome-poi,
       clean-formats-api,
@@ -784,6 +828,7 @@ Type "ant -p" for a list of targets.
       jar-bio-formats-plugins,
       jar-mdbtools,
       jar-metakit,
+      jar-ome-jxr,
       jar-ome-xml,
       jar-ome-poi,
       jar-formats-api,

components/formats-bsd/src/loci/formats/codec/BitBuffer.java

@@ -190,6 +190,16 @@ public int getBits(int bitsToRead) {
     return toStore;
   }
 
+  /**
+   * Checks if the current position is on a byte boundary, that is the next
+   * bit in the byte array is the first bit in a byte.
+   *
+   * @return true if bit is on byte boundary, false otherwise.
+   */
+  public boolean isBitOnByteBoundary() {
+    return currentBit % 8 == 0 ? true : false;
+  }
+
   /**
    * Testing method.
    * @param args Ignored.
@@ -239,6 +249,7 @@ public static void main(String[] args) {
         bb.skipBits(len[i]);
       }
     }
+
     // Test reading past end of buffer.
     LOGGER.info("Testing end of buffer");
     bb = new BitBuffer(bw.toByteArray());
@@ -248,5 +259,20 @@ public static void main(String[] args) {
     if (-1 != read) {
       LOGGER.info("-1 expected at end of buffer, {} received.", read);
     }
+
+    // Test byte boundary detection
+    LOGGER.info("Testing byte boundary detection");
+    bb = new BitBuffer(bw.toByteArray());
+    for (int i = 0; i < trials; i++) {
+      int c = r.nextInt(100);
+      if (c > 50) {
+        if (len[i] > 8) {
+          bb.getBits(8);
+          if (!bb.isBitOnByteBoundary()){
+            LOGGER.info("Bit on byte boundary expected, but not returned.");
+          }
+        }
+      }
+    }
   }
 }