Commit 2d359171 authored by Luc Deschenaux's avatar Luc Deschenaux
Browse files

test tiff lossless compression

parent 4e70902f

src/main/java/EyesisCorrectionParameters.java

+6 −0
Original line number Diff line number Diff line
@@ -61,6 +61,7 @@ public class EyesisCorrectionParameters { 
  		public double  outputRangeFP=          255.0; // 1.0 intensity will be saved as 255.0 (in float 32-bit mode)

  		public boolean imageJTags=             false; // encode ImageJ info data to the TIFF output header 

  		

  		public String tiffCompression =        "UNCOMPRESSED"; // tiff compression codec

  		public boolean jpeg =                  true;  // convert to RGB and save JPEG (if save is true)

  		public boolean save =                  true;

  		public boolean save16 =                false; // save 16-bit tiff also if the end result is 8 bit
@@ -201,6 +202,7 @@ public class EyesisCorrectionParameters { 
  		    if (properties.getProperty(prefix+"equirectangularFormat")!=null) this.equirectangularFormat=Integer.parseInt(properties.getProperty(prefix+"equirectangularFormat"));

  		    if (properties.getProperty(prefix+"outputRangeInt")!=null) this.outputRangeInt=Double.parseDouble(properties.getProperty(prefix+"outputRangeInt"));

  		    if (properties.getProperty(prefix+"outputRangeFP")!=null) this.outputRangeFP=Double.parseDouble(properties.getProperty(prefix+"outputRangeFP"));

  		    if (properties.getProperty(prefix+"tiffCompression")!=null) this.tiffCompression=properties.getProperty(prefix+"tiffCompression");

  		    if (properties.getProperty(prefix+"imageJTags")!=null) this.imageJTags=Boolean.parseBoolean(properties.getProperty(prefix+"imageJTags"));

  		    if (properties.getProperty(prefix+"jpeg")!=null) this.jpeg=Boolean.parseBoolean(properties.getProperty(prefix+"jpeg"));   // convert to RGB and save jpeg (if save is true)

  		    if (properties.getProperty(prefix+"save")!=null) this.save=Boolean.parseBoolean(properties.getProperty(prefix+"save"));
@@ -283,6 +285,8 @@ 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"};

			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};

			int equirectangularFormatIndex=0;
@@ -294,6 +298,7 @@ public class EyesisCorrectionParameters { 
    		gd.addNumericField("Map 1.0 intensity to this fraction of the full range 8/16/32-bit integer mode output", 100*this.outputRangeInt, 2,6,"%");

    		gd.addNumericField("Map 1.0 intensity to this value in 32-bit floating point output mode", this.outputRangeFP, 2,6,"");

    		gd.addCheckbox ("Encode ImageJ specific Info metadata to the output file TIFF header", this.imageJTags);

    		gd.addChoice("TIFF lossless compression codec",tiffCompressionChoices,tiffCompressionChoices[tiffCompressionIndex]);

   		

			gd.addCheckbox ("Convert to RGB48",                                 this.toRGB);

    		gd.addCheckbox ("Convert to 8 bit RGB (and save JPEG if save is enabled)", this.jpeg);
@@ -372,6 +377,7 @@ public class EyesisCorrectionParameters { 
    		this.outputRangeInt=0.01*gd.getNextNumber();

    		this.outputRangeFP=     gd.getNextNumber();

    		this.imageJTags=        gd.getNextBoolean();

    		this.tiffCompression=   tiffCompressionChoices[gd.getNextChoiceIndex()];

    		this.toRGB=             gd.getNextBoolean();

    		this.jpeg=              gd.getNextBoolean();

    		this.save=              gd.getNextBoolean();

src/main/java/EyesisCorrections.java

+2 −2
Original line number Diff line number Diff line
@@ -472,7 +472,7 @@ public class EyesisCorrections { 
						this.defectsDiff[srcChannel]=this.pixelMapping.getDefectsDiff(srcChannel);

						if (this.debugLevel>0){

							if (this.defectsXY[srcChannel]==null){

								System.out.println("No pixel defects info is availabele for channel "+srcChannel);

								System.out.println("No pixel defects info is available for channel "+srcChannel);

							} else {

								System.out.println("Extracted "+this.defectsXY[srcChannel].length+" pixel outlayers for channel "+srcChannel+

										" (x:y:difference");
@@ -700,7 +700,7 @@ public class EyesisCorrections { 
			if (path!=null){

				path+=Prefs.getFileSeparator()+imp.getTitle()+".tiff";

	 			 if (this.debugLevel>0) System.out.println("Saving equirectangular result to "+path);

				(new EyesisTiff()).saveTiff(

				(new EyesisTiff(correctionsParameters.tiffCompression)).saveTiff(

						imp,

						path,

						correctionsParameters.equirectangularFormat,

src/main/java/EyesisTiff.java

+12 −3
Original line number Diff line number Diff line
@@ -47,16 +47,25 @@ import loci.formats.tiff.IFDList; 
import loci.formats.tiff.TiffParser;

import loci.formats.tiff.TiffRational;

import loci.formats.tiff.TiffSaver;

import com.sun.media.imageio.plugins.tiff.BaselineTIFFTagSet;

import loci.formats.tiff.TiffCompression;





public class EyesisTiff {

//	private static org.apache.log4j.Logger log= Logger.getLogger(EyesisTiff.class); 

	

private String codec="UNCOMPRESSED";



public EyesisTiff(){

//	Please initialize the log4j system properly





}



public EyesisTiff(String codec){

//	Please initialize the log4j system properly

	this.codec=codec;

}



	public void saveTiff(

			ImagePlus imp,

			String path,
@@ -176,7 +185,7 @@ public EyesisTiff(){ 
        ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis"); 

        ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);

        // copy some other data?

        ifd.putIFDValue(IFD.COMPRESSION, BaselineTIFFTagSet.COMPRESSION_LZW);

        ifd.putIFDValue(IFD.COMPRESSION, TiffCompression.valueOf(codec).getCode());

        ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB

        ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // 0 = Unspecified data  1 = Associated alpha data (with pre-multiplied color) 2 = Unassociated alpha data

//        int [] bpsArray={8,8,8,8};
@@ -258,7 +267,7 @@ public EyesisTiff(){ 
        ifd.putIFDValue(IFD.SOFTWARE, "Elphel Eyesis"); 

        ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, description);

        // copy some other data?

        ifd.putIFDValue(IFD.COMPRESSION, BaselineTIFFTagSet.COMPRESSION_LZW);

        ifd.putIFDValue(IFD.COMPRESSION, TiffCompression.valueOf(codec).getCode());

        ifd.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION,2); // RGB

        ifd.putIFDValue(IFD.EXTRA_SAMPLES,2); // extra bytes (over 3) meaning Unassociated alpha data