SP-606 CCS-34 improve performance of reading c01 files

SVN: 28993

image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java

@@ -32,11 +32,16 @@ import java.util.UUID;
 
 import loci.common.IRandomAccess;
 import loci.common.Location;
+import loci.common.RandomAccessInputStream;
 import loci.formats.FormatException;
+import loci.formats.FormatHandler;
 import loci.formats.IFormatHandler;
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
+import loci.formats.MetadataTools;
+import loci.formats.codec.ZlibCodec;
 import loci.formats.gui.BufferedImageReader;
+import loci.formats.in.CellomicsReader;
 import loci.formats.in.DefaultMetadataOptions;
 import loci.formats.in.MetadataLevel;
 import loci.formats.in.MetadataOptions;
@@ -55,6 +60,12 @@ final class BioFormatsImageUtils
 
     private static final IFormatReader[] READERS = new ImageReader().getReaders();
 
+    static
+    {
+        MetadataTools.setDefaultDateEnabled(false);
+        CellomicsReader.setNoHiddenFiles(true);
+    }
+
     /**
      * Tries to create a suitable reader for the file specified with <var>fileName</var>. This is a
      * factory method which returns for each invocation a new instance of a suitable reader. May
@@ -201,7 +212,7 @@ final class BioFormatsImageUtils
             throws IOExceptionUnchecked, IllegalArgumentException
     {
         String handleId = generateHandleId(reader, imageID);
-        
+
         // Add to static map.
         Location.mapFile(handleId, handle);
         try
@@ -286,7 +297,7 @@ final class BioFormatsImageUtils
     {
         // Add to static map.
         String handleId = generateHandleId(reader, imageID);
-        
+
         Location.mapFile(handleId, handle);
         try
         {
@@ -326,6 +337,11 @@ final class BioFormatsImageUtils
         Location.mapFile(handleId, handle);
         try
         {
+            if (reader instanceof CellomicsReader)
+            {
+                return CellomicsReaderUtil.readSize(handleId);
+            }
+
             // This does the actual parsing.
             reader.setId(handleId);
             reader.setSeries(imageID.getSeriesIndex());
@@ -346,6 +362,42 @@ final class BioFormatsImageUtils
         }
     }
 
+    public static class CellomicsReaderUtil
+    {
+        public static Dimension readSize(String id) throws FormatException, IOException
+        {
+            RandomAccessInputStream in = getDecompressedStream(id);
+
+            in.order(true);
+            in.skipBytes(4);
+
+            int x = in.readInt();
+            int y = in.readInt();
+
+            in.close();
+
+            return new Dimension(x, y);
+
+        }
+
+        private static RandomAccessInputStream getDecompressedStream(String filename)
+                throws FormatException, IOException
+        {
+            RandomAccessInputStream s = new RandomAccessInputStream(filename);
+            if (FormatHandler.checkSuffix(filename, "c01"))
+            {
+
+                s.seek(4);
+                ZlibCodec codec = new ZlibCodec();
+                byte[] file = codec.decompress(s, null);
+                s.close();
+
+                return new RandomAccessInputStream(file);
+            }
+            return s;
+        }
+    }
+
     static Integer readImageColorDepth(IFormatReader reader, IRandomAccess handle, ImageID imageID)
             throws IOExceptionUnchecked, IllegalArgumentException
     {