Merge pull request ome#4040 from sbesson/lurawave_removal

Remove support for proprietary LuraWave license

.classpath-template

@@ -6,8 +6,6 @@
         <classpathentry kind="src" path="components/formats-bsd/src"/>
         <classpathentry kind="src" path="components/formats-gpl/build/src"/>
         <classpathentry kind="src" path="components/formats-gpl/src"/>
-        <classpathentry kind="src" path="components/stubs/lwf-stubs/build/src"/>
-        <classpathentry kind="src" path="components/stubs/lwf-stubs/src"/>
         <classpathentry kind="src" path="components/test-suite/build/src"/>
         <classpathentry kind="src" path="components/test-suite/src"/>
         <classpathentry kind="src" path="components/formats-api/test"/>

build.xml

@@ -16,8 +16,7 @@ Bio-Formats
     JAR file:      bio-formats.jar
     Path:          components/bio-formats
     Project deps:  Formats Common, OME-XML Java library, JAI Image I/O Tools,
-                   MDB Tools (Java port), Apache Jakarta POI,
-                   Luratech LuraWave stubs
+                   MDB Tools (Java port), Apache Jakarta POI
     Library deps:  JGoodies Forms, Logback, NetCDF,
                    Simple Logging Facade for Java API, TestNG
     Optional:      Xalan Serializer, Xalan
@@ -76,21 +75,6 @@ JAI Image I/O Tools
                    This component will be removed once our changes have been
                    added to the official JAI CVS repository.
 
-===============================================================================
-The following components are stubs of third party projects:
-
-Luratech LuraWave stubs
-    Stub of proprietary Java API to handle Luratech LWF compression
-    -=-
-    JAR file:      lwf-stubs.jar
-    Path:          components/stubs/lwf-stubs
-    Project deps:  (none)
-    Optional:      (none)
-    License:       BSD
-    Project URL:   http://www.luratech.com/
-    Notes:         required to compile Bio-Formats's support for Luratech LWF
-                   compression for the Opera Flex format
-
 ===============================================================================
 The following external dependencies (in the jar folder) may be required:
 Ant-Contrib

components/bio-formats-plugins/src/loci/plugins/config/libraries.txt

@@ -261,11 +261,3 @@ url = http://www.loci.wisc.edu/software/ome-notes
 license = GPL
 notes = OME Notes library for flexible organization and presentation
         of OME-XML metadata.
-
-[LuraWave decoder SDK]
-type = Java library
-class = com.luratech.lwf.lwfDecoder
-url = http://www.luratech.com/
-license = Commercial
-notes = Used by Bio-Formats to decode Flex files
-        compressed with the LuraWave JPEG2000 codec.

components/bio-formats-plugins/src/loci/plugins/in/ImagePlusReader.java

@@ -60,7 +60,6 @@
 import loci.plugins.util.BFVirtualStack;
 import loci.plugins.util.ImageProcessorReader;
 import loci.plugins.util.LociPrefs;
-import loci.plugins.util.LuraWave;
 import loci.plugins.util.VirtualImagePlus;
 import ome.units.UNITS;
 import ome.units.quantity.Time;
@@ -385,7 +384,13 @@ private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts,
       updateTiming(s, current, current++, total);
 
       // get image processor for ith plane
-      final ImageProcessor[] p = readProcessors(process, i, region, thumbnail);
+      ImageProcessor[] p;
+      if (thumbnail) {
+        p = reader.openThumbProcessors(i);
+      } else {
+        p = reader.openProcessors(i, region.x, region.y, region.width, region.height);
+      }
+
       if (p == null || p.length == 0) {
         throw new FormatException("Cannot read plane #" + i);
       }
@@ -401,40 +406,6 @@ private ImageStack readPlanes(ImportProcess process, int s, List<LUT> luts,
     return createStack(procs, labels, luts);
   }
 
-  /**
-   * HACK: This method mainly exists to prompt the user for a missing
-   * LuraWave license code, in the case of LWF-compressed Flex.
-   *
-   * @see ImportProcess#setId()
-   */
-  private ImageProcessor[] readProcessors(ImportProcess process,
-    int no, Region r, boolean thumbnail) throws FormatException, IOException
-  {
-    final ImageProcessorReader reader = process.getReader();
-    final ImporterOptions options = process.getOptions();
-
-    boolean first = true;
-    for (int i=0; i<LuraWave.MAX_TRIES; i++) {
-      String code = LuraWave.initLicenseCode();
-      try {
-        if (thumbnail) {
-          return reader.openThumbProcessors(no);
-        }
-        return reader.openProcessors(no, r.x, r.y, r.width, r.height);
-      }
-      catch (FormatException exc) {
-        if (options.isQuiet() || options.isWindowless()) throw exc;
-        if (!LuraWave.isLicenseCodeException(exc)) throw exc;
-
-        // prompt user for LuraWave license code
-        code = LuraWave.promptLicenseCode(code, first);
-        if (code == null) throw exc;
-        if (first) first = false;
-      }
-    }
-    throw new FormatException(LuraWave.TOO_MANY_TRIES);
-  }
-
   // -- Helper methods - image post processing --
 
   private List<ImagePlus> concatenate(List<ImagePlus> imps) {

components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java

@@ -62,7 +62,6 @@
 import loci.plugins.BF;
 import loci.plugins.util.ImageProcessorReader;
 import loci.plugins.util.LociPrefs;
-import loci.plugins.util.LuraWave;
 import loci.plugins.util.VirtualReader;
 import loci.plugins.util.WindowTools;
 import ome.xml.model.enums.DimensionOrder;
@@ -544,7 +543,7 @@ private void initializeStack() throws FormatException, IOException {
       baseReader.getMetadataOptions().setMetadataLevel(
           MetadataLevel.NO_OVERLAYS);
     }
-    setId();
+    reader.setId(options.getId());
 
     computeSeriesLabels(reader);
   }
@@ -687,34 +686,6 @@ private void saveDefaults() {
 
   // -- Helper methods -- ImportStep.STACK --
 
-  /**
-   * HACK: This method mainly exists to prompt the user for a missing
-   * LuraWave license code, in the case of LWF-compressed Flex.
-   *
-   * @see ImagePlusReader#readProcessors(ImportProcess, int, Region, boolean)
-   */
-  private void setId() throws FormatException, IOException {
-    boolean first = true;
-    for (int i=0; i<LuraWave.MAX_TRIES; i++) {
-      String code = LuraWave.initLicenseCode();
-      try {
-        reader.setId(options.getId());
-        return;
-      }
-      catch (FormatException exc) {
-        if (options.isQuiet() || options.isWindowless()) throw exc;
-        if (!LuraWave.isLicenseCodeException(exc)) throw exc;
-
-        // prompt user for LuraWave license code
-        code = LuraWave.promptLicenseCode(code, first);
-        if (code == null) throw exc;
-        if (first) first = false;
-        reader.close();
-      }
-    }
-    throw new FormatException(LuraWave.TOO_MANY_TRIES);
-  }
-
   private void computeSeriesLabels(IFormatReader r) {
     final int seriesCount = r.getSeriesCount();
     seriesLabels = new String[seriesCount];

components/bundles/bioformats_package/pom.xml

@@ -40,13 +40,6 @@
       <version>${project.version}</version>
     </dependency>
 
-    <dependency>
-      <groupId>org.openmicroscopy</groupId>
-      <artifactId>lwf-stubs</artifactId>
-      <version>${lwf-stubs.version}</version>
-      <scope>provided</scope>
-    </dependency>
-
     <dependency>
       <groupId>org.openmicroscopy</groupId>
       <artifactId>mipav-stubs</artifactId>