Add CodecOptions.disableChromaSubsampling

[melissalinkert]

Companion to ome/ome-codecs#29.

Note I do not see any actual difference between disableChromaSubsampling = false and disableChromaSubsampling = true with something like:

import loci.formats.MetadataTools;
import loci.formats.codec.CodecOptions;
import loci.formats.in.FakeReader;
import loci.formats.meta.IMetadata;
import loci.formats.out.TiffWriter;

public class Snippet {
  public static void main(String[] args) throws Exception {
    String fakeData = "test&sizeC=3&rgb=3.fake";
    IMetadata metadata = MetadataTools.createOMEXMLMetadata();
    try (FakeReader reader = new FakeReader()) {
      // read artificial 512x512 RGB image
      reader.setMetadataStore(metadata);
      reader.setId(fakeData);
      byte[] rgbPlane = reader.openBytes(0);

      // write JPEG in TIFF, using default settings (uses chroma subsampling)
      try (TiffWriter defaultWriter = new TiffWriter()) {
        defaultWriter.setMetadataRetrieve(metadata);
        defaultWriter.setInterleaved(reader.isInterleaved());
        defaultWriter.setId("default.tiff");
        defaultWriter.setCompression("JPEG");
        defaultWriter.saveBytes(0, rgbPlane);
      }

      // write JPEG in TIFF, explicitly disabling chroma subsampling
      try (TiffWriter noChromaWriter = new TiffWriter()) {
        noChromaWriter.setMetadataRetrieve(metadata);
        noChromaWriter.setInterleaved(reader.isInterleaved());

        CodecOptions options = CodecOptions.getDefaultOptions();
        options.disableChromaSubsampling = true;
        noChromaWriter.setCodecOptions(options);

        noChromaWriter.setId("no-chroma.tiff");
        noChromaWriter.setCompression("JPEG");

        noChromaWriter.saveBytes(0, rgbPlane);
      }
    }
  }
}

but as far as I can tell that's an issue with ome/ome-codecs#29 (review incoming).

[iwbh15]

In the structured fake data (where R = G = B) the effect of the disabled chroma subsampling is not huge.
Therefore I have use the image lena-std.tif for my test (available in the ImageJ example images zip archive).
(Of course you can use any other RGB tif image.)

I used the following modified snipped for the test:

import java.io.File;
import loci.formats.MetadataTools;
import loci.formats.codec.CodecOptions;
import loci.formats.in.FakeReader;
import loci.formats.in.TiffReader;
import loci.formats.meta.IMetadata;
import loci.formats.out.TiffWriter;

public class Snippet2 {

  public static void main(String[] args) throws Exception {
	    
    //String fakeData = "test&sizeC=3&rgb=3.fake";
    
    IMetadata metadata = MetadataTools.createOMEXMLMetadata();
	
    //try (FakeReader reader = new FakeReader()) {
    try (TiffReader reader = new TiffReader()) {
      reader.setMetadataStore(metadata);
	  
      // read artificial 512x512 RGB image
      //reader.setId(fakeData);
    	
      // read baboon.gif (available at e.g. https://imagej.nih.gov/ij/images/)
      reader.setId("lena-std.tif");
      
      int w = reader.getSizeX();
      int h = reader.getSizeY();
      byte[] buf = new byte[w*h*3];
      byte[] bufRGB = new byte[w*h*3];
      
      buf = reader.openBytes(0, buf, 0, 0, w, h);
      
      // re-ordered image buffer
      int idx;
      int offset1 = w*h;
      int offset2 = 2*w*h;
      for (int i=0; i<w*h; i++) {
    	  idx = 3*i;
    	  bufRGB[idx+2] = buf[i+offset2];
    	  bufRGB[idx+1] = buf[i+offset1];
    	  bufRGB[idx] = buf[i];
      }

      String compression = "JPEG";       // "Uncompressed"; // 
      
      // write JPEG in TIFF, using default settings (uses chroma subsampling)
      try (TiffWriter defaultWriter = new TiffWriter()) {
        defaultWriter.setMetadataRetrieve(metadata);
        defaultWriter.setInterleaved(true); //(reader.isInterleaved());
                
        // Image file has to be deleted, otherwise the new content will be append to the existing file
        String fName = "default.tif";
        File f = new File(fName);
        if (f.exists())
        	f.delete();
        
        defaultWriter.setId(fName);
        defaultWriter.setCompression(compression);
        
        defaultWriter.saveBytes(0, bufRGB);
      }
    
      // write JPEG in TIFF, explicitly disabling chroma subsampling
      try (TiffWriter noChromaWriter = new TiffWriter()) {
        noChromaWriter.setMetadataRetrieve(metadata);
        noChromaWriter.setInterleaved(true); //(reader.isInterleaved());

        CodecOptions options = CodecOptions.getDefaultOptions();

        options.disableChromaSubsampling = true;
        
        noChromaWriter.setCodecOptions(options);

        // Image file has to be deleted, otherwise the new content will be append to the existing file
        String fName = "no-chroma.tif";
        File f = new File(fName);
        if (f.exists())
        	f.delete();
        
        noChromaWriter.setId(fName);
        noChromaWriter.setCompression(compression);
      
        noChromaWriter.saveBytes(0, bufRGB);
      }
    }
  }
}

[melissalinkert]

Retested with the current state of this PR and ome/ome-codecs#29.

• With the code example in Add CodecOptions.disableChromaSubsampling #4057 (comment), there is no difference between the two output files. The MD5s are identical.
• With the code example in Add CodecOptions.disableChromaSubsampling #4057 (comment), there is a difference between the output files. The default (with subsampling) is slightly smaller than without subsampling.
• With the code example in Add CodecOptions.disableChromaSubsampling #4057 (comment) modified to use test&sizeC=3&rgb=3&interleaved=true.fake as the input, there is a difference between the output files. The default (with subsampling) is slightly larger than without subsampling.

In all cases, both output files can be read by showinf and ImageMagick's display.

Build failures here are expected, and should go away when the ome-codecs version is bumped.

[dgault]

Tested alongside the codecs PR. Looks good from my side. As soon as the codecs component has been bumped and builds are green then this should be ready to merge. I have held off bumping ome-codecs now as all of the components will need bumped as part of the sl4j-api updates.