If -precompressed specified without -compression, use reader comp…

…ression type automatically

This doesn't yet completely support mixed compression types within the same dataset, but something like:

$ bfconvert -noflat -precompressed CMU-1.svs CMU-1.dcm

should run without error and convert the pyramid without recompressing.

components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java

@@ -62,6 +62,7 @@
 import loci.formats.FileStitcher;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
+import loci.formats.ICompressedTileReader;
 import loci.formats.IFormatReader;
 import loci.formats.IFormatWriter;
 import loci.formats.ImageReader;
@@ -71,7 +72,9 @@
 import loci.formats.MetadataTools;
 import loci.formats.MinMaxCalculator;
 import loci.formats.MissingLibraryException;
+import loci.formats.codec.Codec;
 import loci.formats.codec.CodecOptions;
+import loci.formats.codec.CompressionType;
 import loci.formats.codec.JPEG2000CodecOptions;
 import loci.formats.gui.Index16ColorModel;
 import loci.formats.in.DynamicMetadataOptions;
@@ -558,6 +561,11 @@ public boolean testConvert(IFormatWriter writer, String[] args)
 
     reader.setId(in);
 
+    if (compression == null && precompressed) {
+      compression = getReaderCodecName();
+      LOGGER.info("Implicitly using compression = {}", compression);
+    }
+
     if (swapOrder != null) {
        dimSwapper.swapDimensions(swapOrder);
     }
@@ -1308,6 +1316,18 @@ private void setCodecOptions(IFormatWriter writer) {
     }
   }
 
+  private String getReaderCodecName() throws FormatException, IOException {
+    if (reader instanceof ICompressedTileReader) {
+      ICompressedTileReader r = (ICompressedTileReader) reader;
+      Codec c = r.getTileCodec(0);
+      CompressionType type = CompressionType.get(c);
+      if (type != null) {
+        return type.getCompression();
+      }
+    }
+    return null;
+  }
+
   // -- Main method --
 
   public static void main(String[] args) throws FormatException, IOException {

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

@@ -115,5 +115,27 @@ public int getCode() {
   public String getCompression() {
     return compression;
   }
-
+
+  /**
+   * Look up the compression type by Codec instance.
+   */
+  public static CompressionType get(Codec c) {
+    if (c instanceof ZlibCodec) {
+      return ZLIB;
+    }
+    if (c instanceof LZWCodec) {
+      return LZW;
+    }
+    if (c instanceof JPEGCodec) {
+      return JPEG;
+    }
+    if (c instanceof JPEG2000Codec) {
+      return J2K;
+    }
+    if (c instanceof PassthroughCodec) {
+      return UNCOMPRESSED;
+    }
+    return null;
+  }
+
 }