extracting background (e0cc40c3) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Correction.java

+54 −22

Original line number	Diff line number	Diff line
		@@ -190,7 +190,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6;
		0.075, // b_min;
		1.0, // r_max;
		1.0, // g_max;
		1.0 // b_max;
		1.0, // b_max;
		0.0, // alpha_min;
		1.0 // alpha_max;
		);

		public static FilesParameters FILE_PARAMETERS= new FilesParameters (
		@@ -802,7 +804,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
		imp_colorStack.getTitle()+"-RGB24",
		0, 65536, // r range 0->0, 65536->256
		0, 65536, // g range
		0, 65536);// b range
		0, 65536, // b range
		0, 65536);// alpha range
		imp_RGB24.setTitle(imp_colorStack.getTitle()+"rgb24");
		imp_RGB24.show();
		return;
		@@ -1177,22 +1180,26 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
		int g_min,
		int g_max,
		int b_min,
		int b_max){
		int [] mins= {r_min,g_min,b_min};
		int [] maxs= {r_max,g_max,b_max};
		int b_max,
		int alpha_min,
		int alpha_max){
		int [] mins= {r_min,g_min,b_min,alpha_min};
		int [] maxs= {r_max,g_max,b_max,alpha_max};
		int i;
		int length=stack16.getWidth()*stack16.getHeight();
		short [][] spixels=new short[3][];
		int numSlices = stack16.getSize();
		if (numSlices > 4) numSlices = 4;
		short [][] spixels=new short[numSlices][];
		int [] pixels=new int[length];
		int c,d;
		double [] scale=new double[3];
		for (c=0;c<3;c++) {
		double [] scale=new double[numSlices];
		for (c = 0; c < numSlices; c++) {
		scale[c]=256.0/(maxs[c]-mins[c]);
		}
		for (i=0;i<3;i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (i = 0; i < numSlices; i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (i = 0; i < length; i++) {
		pixels[i]=0;
		for (c=0;c<3;c++) {
		for (c=0;c < numSlices;c++) {
		d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
		if (d > 255) d=255;
		else if (d < 0) d=0;
		@@ -1976,7 +1983,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
		title+"-RGB24",
		0, 65536, // r range 0->0, 65536->256
		0, 65536, // g range
		0, 65536);// b range
		0, 65536, // b range
		0, 65536);// alpha range
		if (processParameters.JPEG_scale!=1.0){
		ImageProcessor ip=imp_RGB24.getProcessor();
		ip.setInterpolationMethod(ImageProcessor.BICUBIC);
		@@ -3504,6 +3512,9 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
		gd.addNumericField("Red color white level", rgbParameters.r_max, 3);
		gd.addNumericField("Green color white level", rgbParameters.g_max, 3);
		gd.addNumericField("Blue color white level", rgbParameters.b_max, 3);
		gd.addNumericField("Alpha channel min", rgbParameters.alpha_min, 3);
		gd.addNumericField("Alpha channel max", rgbParameters.alpha_max, 3);

		gd.showDialog();
		if (gd.wasCanceled()) return false;
		rgbParameters.r_min= gd.getNextNumber();
		@@ -3512,6 +3523,8 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
		rgbParameters.r_max= gd.getNextNumber();
		rgbParameters.g_max= gd.getNextNumber();
		rgbParameters.b_max= gd.getNextNumber();
		rgbParameters.alpha_min= gd.getNextNumber();
		rgbParameters.alpha_max= gd.getNextNumber();
		return true;
		}

		@@ -4233,13 +4246,15 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg

		/* ======================================================================== */
		public static class RGBParameters {
		public double r_min;
		public double g_min;
		public double b_min;
		public double r_max;
		public double g_max;
		public double b_max;

		public double r_min = 0.075;
		public double g_min = 0.075;
		public double b_min = 0.075;
		public double r_max = 1.0;
		public double g_max = 1.0;
		public double b_max = 1.0;
		public double alpha_min = 0.0;
		public double alpha_max = 1.0;
		/*
		public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max) {
		this.r_min = r_min;
		this.g_min = g_min;
		@@ -4248,6 +4263,18 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
		this.g_max = g_max;
		this.b_max = b_max;
		}
		*/
		public RGBParameters(double r_min, double g_min, double b_min, double r_max, double g_max, double b_max, double alpha_min, double alpha_max) {
		this.r_min = r_min;
		this.g_min = g_min;
		this.b_min = b_min;
		this.r_max = r_max;
		this.g_max = g_max;
		this.b_max = b_max;
		this.alpha_min = alpha_min;
		this.alpha_max = alpha_max;
		}

		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"r_min",this.r_min+"");
		properties.setProperty(prefix+"g_min",this.g_min+"");
		@@ -4255,6 +4282,9 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
		properties.setProperty(prefix+"r_max",this.r_max+"");
		properties.setProperty(prefix+"g_max",this.g_max+"");
		properties.setProperty(prefix+"b_max",this.b_max+"");
		properties.setProperty(prefix+"alpha_min",this.alpha_min+"");
		properties.setProperty(prefix+"alpha_max",this.alpha_max+"");

		}
		public void getProperties(String prefix,Properties properties){
		this.r_min=Double.parseDouble(properties.getProperty(prefix+"r_min"));
		@@ -4263,6 +4293,8 @@ G= Y +Pr(- 2Kr(1-Kr))/Kg + Pb(-2Kb(1-Kb))/Kg
		this.r_max=Double.parseDouble(properties.getProperty(prefix+"r_max"));
		this.g_max=Double.parseDouble(properties.getProperty(prefix+"g_max"));
		this.b_max=Double.parseDouble(properties.getProperty(prefix+"b_max"));
		if (properties.getProperty(prefix+"alpha_min")!=null) this.alpha_min=Double.parseDouble(properties.getProperty(prefix+"alpha_min"));
		if (properties.getProperty(prefix+"alpha_max")!=null) this.alpha_max=Double.parseDouble(properties.getProperty(prefix+"alpha_max"));
		}

		}

src/main/java/EyesisCorrectionParameters.java

+133 −13

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/EyesisCorrections.java

+176 −65

Original line number	Diff line number	Diff line
		@@ -1285,7 +1285,8 @@ public class EyesisCorrections {
		title+"-RGB24",
		0, 65536, // r range 0->0, 65536->256
		0, 65536, // g range
		0, 65536);// b range
		0, 65536,// b range
		0, 65536);// alpha range
		if (JPEG_scale!=1.0){
		ImageProcessor ip=imp_RGB.getProcessor();
		ip.setInterpolationMethod(ImageProcessor.BICUBIC);
		@@ -1524,7 +1525,6 @@ public class EyesisCorrections {

		/* ======================================================================== */
		public CompositeImage convertToComposite( ImagePlus imp) {
		// if (imp.isComposite()) return imp;
		if (imp.isComposite()) return null;
		if (imp.getNChannels()>1) {
		return null; // number of channels should be just 1
		@@ -1532,8 +1532,6 @@ public class EyesisCorrections {
		int c = imp.getStackSize();
		imp.setDimensions(c, 1, 1);
		CompositeImage ci = new CompositeImage(imp, CompositeImage.COMPOSITE);
		// ci.show();
		// imp.hide();
		return ci;
		}

		@@ -1546,12 +1544,14 @@ public class EyesisCorrections {
		int i,j;
		float [] fpixels;
		short [] spixels;
		double [] mins= {rgbParameters.r_min,rgbParameters.g_min,rgbParameters.b_min};
		double [] maxs= {rgbParameters.r_max,rgbParameters.g_max,rgbParameters.b_max};
		if (stack32.getSize()<3) return null;
		int numSlices = stack32.getSize();
		if (numSlices > 4) numSlices = 4;
		if (numSlices < 3) return null;
		double [] mins= {rgbParameters.r_min, rgbParameters.g_min, rgbParameters.b_min, rgbParameters.alpha_min};
		double [] maxs= {rgbParameters.r_max, rgbParameters.g_max, rgbParameters.b_max, rgbParameters.alpha_max};
		double value;
		double scale;
		for (i=0;i<3;i++) {
		for (i = 0; i < numSlices; i++) {
		fpixels= (float[])stack32.getPixels(i + 1);
		scale=65535.0 / (maxs[i] - mins[i]);
		spixels=new short [length];
		@@ -1575,22 +1575,31 @@ public class EyesisCorrections {
		int g_min,
		int g_max,
		int b_min,
		int b_max){
		int [] mins= {r_min,g_min,b_min};
		int [] maxs= {r_max,g_max,b_max};
		int b_max,
		int alpha_min,
		int alpha_max){
		int [] mins= {r_min,g_min,b_min,alpha_min};
		int [] maxs= {r_max,g_max,b_max,alpha_max};
		int i;
		int length=stack16.getWidth()*stack16.getHeight();
		short [][] spixels=new short[3][];
		int numSlices = stack16.getSize();
		if (numSlices > 4) numSlices = 4;
		short [][] spixels=new short[numSlices][];
		int [] sliceSeq = new int [numSlices];
		for (int j = 0; j < numSlices; j++) sliceSeq[j] = (j + ((numSlices > 3)? 3:0)) % 4;

		int [] pixels=new int[length];
		int c,d;
		double [] scale=new double[3];
		for (c=0;c<3;c++) {

		double [] scale=new double[numSlices];
		for (c = 0; c < numSlices; c++) {
		scale[c]=256.0/(maxs[c]-mins[c]);
		}
		for (i=0;i<3;i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (i = 0; i < numSlices; i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (i = 0; i < length; i++) {
		pixels[i]=0;
		for (c=0;c<3;c++) {
		for (int j=0; j < numSlices; j++) {
		c = sliceSeq[j];
		d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
		if (d > 255) d=255;
		else if (d < 0) d=0;
		@@ -1603,6 +1612,47 @@ public class EyesisCorrections {
		return imp;
		}

		public ImageStack convertRGB48toRGBA24Stack(
		ImageStack stack16,
		double [] dalpha, // alpha pixel array 0..1.0 or null
		// String title,
		int r_min,
		int r_max,
		int g_min,
		int g_max,
		int b_min,
		int b_max){
		ImageStack stack8 = new ImageStack(stack16.getWidth(), stack16.getHeight());
		int [] mins= {r_min,g_min,b_min};
		int [] maxs= {r_max,g_max,b_max};
		int i;
		int length=stack16.getWidth()*stack16.getHeight();
		short [][] spixels=new short[3][];
		byte [][] bpixels=new byte [(dalpha != null)? 4: 3][length];
		int c,d;
		double [] scale=new double[3];
		for (c=0;c<3;c++) {
		scale[c]=256.0/(maxs[c]-mins[c]);
		}
		for (i = 0; i <3; i++) spixels[i]= (short[])stack16.getPixels(i+1);
		for (c = 0; c <3; c++) {
		for (i = 0; i < length; i++){
		d=(int)(((spixels[c][i]& 0xffff)-mins[c])*scale[c]);
		if (d>255) d=255;
		else if (d<0) d=0;
		bpixels[c][i]= (byte) d;
		}
		stack8.addSlice(stack16.getSliceLabel(c+1), bpixels[c]);
		}
		if (dalpha != null) {
		for (i = 0; i < length; i++){
		bpixels[3][i] = (byte) (255*dalpha[i]);
		}
		stack8.addSlice("alpha", bpixels[3]);
		}
		return stack8;
		}

		/* ======================================================================== */
		public ImagePlus Image32toGreyRGB24(
		ImagePlus imp){
		@@ -2312,16 +2362,77 @@ public class EyesisCorrections {

		if (path!=null) {
		path+=Prefs.getFileSeparator()+imp.getTitle();
		if (((imp.getStackSize()==1)) && (jpegQuality!=0) && ((imp.getFileInfo().fileType== FileInfo.RGB) \|\| (jpegQuality>0))) {
		boolean hasAlphaHighByte = false;
		if ((imp.getStackSize()==1) && (imp.getFileInfo().fileType== FileInfo.RGB)) {
		int [] pixels = (int []) imp.getProcessor().getPixels();
		for (int i = 0; i < pixels.length; i++){
		if ((pixels[i] & 0xff000000) != 0){
		hasAlphaHighByte = true;
		break;
		}
		}
		}

		if (hasAlphaHighByte){
		if (correctionsParameters.png){
		if (this.debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
		(new EyesisTiff()).savePNG_ARGB32(
		imp,
		path+".png"
		);

		} else {
		if (this.debugLevel > 0) System.out.println("Saving RGBA result to "+path+".tiff");
		try {
		(new EyesisTiff()).saveTiffARGB32(
		imp,
		path+".tiff",
		false, // correctionsParameters.imageJTags,
		debugLevel);
		} catch (IOException e) {
		e.printStackTrace();
		} catch (FormatException e) {
		e.printStackTrace();
		} catch (ServiceException e) {
		e.printStackTrace();
		} catch (DependencyException e) {
		e.printStackTrace();
		}
		}

		} else if (((imp.getStackSize()==1)) && (jpegQuality!=0) && ((imp.getFileInfo().fileType== FileInfo.RGB) \|\| (jpegQuality>0))) {
		if (this.debugLevel>0) System.out.println("Saving result to "+path+".jpeg");
		FileSaver fs=new FileSaver(imp);
		if (jpegQuality>0) FileSaver.setJpegQuality(jpegQuality);
		fs.saveAsJpeg(path+".jpeg");
		}
		else {
		} else {
		if (this.debugLevel>0) System.out.println("Saving result to "+path+".tiff");
		FileSaver fs=new FileSaver(imp);
		if (imp.getStackSize()>1) fs.saveAsTiffStack(path+".tiff");
		// Save as RGBA if it is RGBA
		int bytesPerPixel = imp.getBytesPerPixel();
		int mode = 0;
		if (bytesPerPixel > 1) mode = 1;
		if (bytesPerPixel > 3) mode = 3;// float, mode 2 not supported

		if ((imp.getStackSize() == 4) && imp.getStack().getSliceLabel(4).equals("alpha")){
		try {
		(new EyesisTiff()).saveTiff(
		imp,
		path+".tiff",
		mode, //
		1.0, // full scale, absolute
		false, // correctionsParameters.imageJTags,
		debugLevel);
		} catch (IOException e) {
		e.printStackTrace();
		} catch (FormatException e) {
		e.printStackTrace();
		} catch (ServiceException e) {
		e.printStackTrace();
		} catch (DependencyException e) {
		e.printStackTrace();
		}
		} else if (imp.getStackSize()>1) fs.saveAsTiffStack(path+".tiff");
		else fs.saveAsTiff(path+".tiff");
		}
		}

src/main/java/EyesisDCT.java

+1445 −351

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/EyesisTiff.java

+304 −247

Original line number	Diff line number	Diff line
		@@ -26,12 +26,19 @@
		**
		*/
		import java.awt.Frame;
		import java.awt.image.BufferedImage;
		import java.awt.image.ColorModel;
		import java.awt.image.DataBufferInt;
		import java.awt.image.Raster;
		import java.awt.image.WritableRaster;
		import java.io.File;
		import java.io.IOException;
		import java.io.UnsupportedEncodingException;
		import java.lang.reflect.Array;
		import java.util.Arrays;

		import javax.imageio.ImageIO;

		//import org.apache.log4j.Logger;

		import ij.IJ;
		@@ -56,6 +63,33 @@ public EyesisTiff(){


		}
		public void savePNG_ARGB32(
		ImagePlus imp,
		String path
		){
		int width = imp.getWidth();
		int height = imp.getHeight();
		int [] pixels = (int []) imp.getProcessor().getPixels();
		System.out.println("width="+width+", height="+height+" length="+pixels.length);

		DataBufferInt buffer = new DataBufferInt(pixels, pixels.length);

		int[] bandMasks = {0xFF0000, 0xFF00, 0xFF, 0xFF000000}; // ARGB (yes, ARGB, as the masks are R, G, B, A always) order
		WritableRaster raster = Raster.createPackedRaster(buffer, width, height, width, bandMasks, null);

		ColorModel cm = ColorModel.getRGBdefault();
		BufferedImage bimage = new BufferedImage(cm, raster, cm.isAlphaPremultiplied(), null);
		try{
		(new File(path)).delete(); // Otherwise TiffSaver appends! - is it the same for PNG?
		ImageIO.write(bimage, "PNG", (new File(path)));
		}
		catch(Exception e){
		e.printStackTrace();
		}
		}



		public void saveTiff(
		ImagePlus imp,
		String path,
		@@ -64,8 +98,8 @@ public EyesisTiff(){
		boolean imageJTags,
		int debugLevel
		) throws IOException, FormatException, ServiceException, DependencyException{
		if (imp.getType()==ImagePlus.COLOR_RGB) {
		if (debugLevel>1) System.out.println("Saving 8-bit TIFF with alpha-channel: "+path);
		if (imp.getType()==ImagePlus.COLOR_RGB) { // 4*8 bit - type = 0
		if (debugLevel>1) System.out.println("Saving 8-bit TIFF with alpha-channel: "+path); // is it possible to just add alpha to high bytes?
		saveTiffARGB32(imp, path, imageJTags, debugLevel);
		return;
		} else if (imp.getStackSize()==4) {
		@@ -96,7 +130,30 @@ public EyesisTiff(){
		String description=(imp.getProperty("description")!=null)?((String) imp.getProperty("description")):"Elphel Eyesis4pi";
		// int [] iPixels= (int []) imp.getProcessor().getPixels();
		final float [][] imagePixels= new float [4][];
		for (int c=0;c<imagePixels.length;c++) imagePixels[c]= (float []) imp.getStack().getPixels(c+1); // bytes are little endian
		try {
		for (int c=0;c<imagePixels.length;c++){
		imagePixels[c]= (float []) imp.getStack().getPixels(c+1); // bytes are little endian
		}
		} catch (ClassCastException e) {
		try {
		for (int c=0;c<imagePixels.length;c++) {
		byte [] bpixels = (byte []) imp.getStack().getPixels(c+1); // bytes are little endian
		imagePixels[c] = new float[bpixels.length];
		for (int i = 0; i <bpixels.length; i++)
		imagePixels[c][i]= ((float) bpixels[i])/255;
		}
		} catch (ClassCastException e1) {
		for (int c=0;c<imagePixels.length;c++) {
		short [] spixels = (short []) imp.getStack().getPixels(c+1); // bytes are little endian
		imagePixels[c] = new float[spixels.length];
		for (int i = 0; i < spixels.length; i++)
		imagePixels[c][i]= ((float) spixels[i])/65535;
		}
		}
		}
		// for (int i = 0; i < imagePixels[3].length; i++){
		// imagePixels[3][i] = 1.0f - imagePixels[3][i];
		// }
		int bw;
		byte [] bytes;
		int pIndex=0;