set codec default options for tiffsaver

src/main/java/EyesisCorrectionParameters.java

@@ -285,7 +285,7 @@ public class EyesisCorrectionParameters {
     		gd.addCheckbox ("Save chroma denoise mask (white - use hi-res, black - low-res)", this.saveChromaDenoiseMask);
     		gd.addCheckbox ("Rotate result image",                              this.rotate);
     		gd.addCheckbox ("Crop result image to the original size",           this.crop);
-			String [] tiffCompressionChoices={"UNCOMPRESSED","LZW","JPEG_2000","ALT_JPEG2000"};
+			String [] tiffCompressionChoices={"UNCOMPRESSED","LZW","JPEG", "JPEG_2000","ALT_JPEG2000"};
 			int tiffCompressionIndex=0;
 			String [] equirectangularFormatChoices={"RGBA 8-bit","RGBA 16-bit","RGBA 32-bit integer","RGBA 32-bit float","ImageJ stack"};
 			int [] equirectangularFormats={0,1,2,3,4};

src/main/java/EyesisTiff.java

@@ -34,6 +34,7 @@ import java.util.Arrays;
 
 //import org.apache.log4j.Logger;
 
+
 import ij.IJ;
 import ij.ImagePlus;
 import ij.WindowManager;
@@ -42,6 +43,7 @@ import loci.common.RandomAccessInputStream;
 import loci.common.services.DependencyException;
 import loci.common.services.ServiceException;
 import loci.formats.FormatException;
+import loci.formats.codec.CodecOptions;
 import loci.formats.tiff.IFD;
 import loci.formats.tiff.IFDList;
 import loci.formats.tiff.TiffParser;
@@ -222,6 +224,7 @@ public EyesisTiff(String codec){
         TiffSaver tiffSaver = new TiffSaver(path);
         tiffSaver.setWritingSequentially(true);
         tiffSaver.setLittleEndian(false);
+        tiffSaver.setCodecOptions(TiffCompression.valueOf(codec).getCompressionCodecOptions(ifd));
         tiffSaver.writeHeader(); 
 //        tiffSaver.writeIFD(ifd,0); //* SHould not write here, some fields are calculated during writeImage, that writes IFD too
 //        System.out.println("bytes.length="+bytes.length);