Merge pull request #4190 from melissalinkert/dicom-reader-precompressed

Extend precompressed support to read DICOM and write TIFF/OME-TIFF

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);
     }
@@ -759,7 +767,9 @@ else if (writer instanceof ImageWriter) {
         int writerSeries = series == -1 ? q : 0;
         writer.setSeries(writerSeries);
         writer.setResolution(res);
+
         writer.setInterleaved(reader.isInterleaved() && !autoscale);
+
         writer.setValidBitsPerPixel(reader.getBitsPerPixel());
         int numImages = writer.canDoStacks() ? reader.getImageCount() : 1;
 
@@ -832,6 +842,12 @@ else if (saveTileWidth > 0 && saveTileHeight > 0) {
             }
           }
 
+          if (precompressed && FormatTools.canUsePrecompressedTiles(reader, writer, writer.getSeries(), writer.getResolution())) {
+            if (getReaderCodecName().startsWith("JPEG")) {
+              writer.setInterleaved(true);
+            }
+          }
+
           int outputIndex = 0;
           if (nextOutputIndex.containsKey(outputName)) {
             outputIndex = nextOutputIndex.get(outputName);
@@ -1260,19 +1276,21 @@ private boolean isTiledWriter(IFormatWriter writer, String outputFile)
   private boolean doTileConversion(IFormatWriter writer, String outputFile)
     throws FormatException
   {
-    if (writer instanceof DicomWriter ||
-      (writer instanceof ImageWriter && ((ImageWriter) writer).getWriter(outputFile) instanceof DicomWriter))
+    // if we asked to try a precompressed conversion,
+    // then the writer's tile sizes will have been set automatically
+    // according to the input data
+    // the conversion must then be performed tile-wise to match the tile sizes,
+    // even if precompression doesn't end up being possible
+    if (precompressed) {
+      return true;
+    }
+    // tile size has already been set in the writer,
+    // so tile-wise conversion should be performed
+    // independent of image size
+    if ((writer.getTileSizeX() > 0 && writer.getTileSizeX() < width) ||
+      (writer.getTileSizeY() > 0 && writer.getTileSizeY() < height))
     {
-      // if we asked to try a precompressed conversion,
-      // then the writer's tile sizes will have been set automatically
-      // according to the input data
-      // the conversion must then be performed tile-wise to match the tile sizes,
-      // even if precompression doesn't end up being possible
-      if (precompressed) {
-        return true;
-      }
-      MetadataStore r = reader.getMetadataStore();
-      return !(r instanceof IPyramidStore) || ((IPyramidStore) r).getResolutionCount(reader.getSeries()) > 1;
+      return true;
     }
     return DataTools.safeMultiply64(width, height) >= DataTools.safeMultiply64(4096, 4096) ||
       saveTileWidth > 0 || saveTileHeight > 0;
@@ -1318,6 +1336,18 @@ 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-api/src/loci/formats/ICompressedTileReader.java

@@ -66,7 +66,7 @@ default int getTileColumns(int no) {
    *
    * @param no plane index
    * @param x tile X index (indexed from 0, @see getTileColumns(int))
-   * @param y tile Y index (indexed frmo 0, @see getTileRows(int))
+   * @param y tile Y index (indexed from 0, @see getTileRows(int))
    * @return compressed tile bytes
    */
   default byte[] openCompressedBytes(int no, int x, int y) throws FormatException, IOException {
@@ -79,7 +79,7 @@ default byte[] openCompressedBytes(int no, int x, int y) throws FormatException,
    * @param no plane index
    * @param buf pre-allocated buffer in which to store compressed bytes
    * @param x tile X index (indexed from 0, @see getTileColumns(int))
-   * @param y tile Y index (indexed frmo 0, @see getTileRows(int))
+   * @param y tile Y index (indexed from 0, @see getTileRows(int))
    * @return compressed tile bytes
    */
   default byte[] openCompressedBytes(int no, byte[] buf, int x, int y) throws FormatException, IOException {
@@ -102,7 +102,7 @@ default Codec getTileCodec(int no) throws FormatException, IOException {
    *
    * @param no plane index
    * @param x tile X index (indexed from 0, @see getTileColumns(int))
-   * @param y tile Y index (indexed frmo 0, @see getTileRows(int))
+   * @param y tile Y index (indexed from 0, @see getTileRows(int))
    * @return codec options
    * @see getTileCodec(int)
    */

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;
+  }
+
 }