working on 14MP (fafa9362) · Commits · Elphel / imagej-elphel

src/main/java/JP46_Reader_camera0.java

+71 −18

Original line number	Original line	Diff line number	Diff line
	@@ -82,16 +82,21 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
	*		*
	*/		*/
	private static final long serialVersionUID = 390855361964415147L;		private static final long serialVersionUID = 390855361964415147L;
			public static int [][] BAYER_INDICES = {
			{0, 1, 2 ,3},
			{1, 0, 3 ,2},
			{2, 3, 0 ,1},
			{3, 2, 1 ,0}};
	Panel panel1;		Panel panel1;
	Panel confpanel;		Panel confpanel;
	Frame instance;		Frame instance;

	String arg;		String arg;

	static File dir;

	ImagejJp4Tiff imagejJp4Tiff = new ImagejJp4Tiff();		ImagejJp4Tiff imagejJp4Tiff = new ImagejJp4Tiff();

			static File dir;
			public boolean fix_bayer = true; // shift image (replacing last row/column) if (corrected for flips) BAYER_MODE != 0
	public String camera_url = "http://192.168.0.236:8081/";		public String camera_url = "http://192.168.0.236:8081/";
	public String camera_img = "bimg";		public String camera_img = "bimg";
	public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)		public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
	@@ -325,6 +330,7 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
	gd.addStringField("Image (new): ", camera_img_new, 20);		gd.addStringField("Image (new): ", camera_img_new, 20);
	gd.addStringField("JP46 Parameters: ", camera_jp46settings, 50);		gd.addStringField("JP46 Parameters: ", camera_jp46settings, 50);
	gd.addCheckbox("Demux composite frame? ", demux);		gd.addCheckbox("Demux composite frame? ", demux);
			gd.addCheckbox("Fix bayer (shift to standard GR/BG)? ", fix_bayer);
	gd.addCheckbox("Silent? ", IS_SILENT);		gd.addCheckbox("Silent? ", IS_SILENT);
	// gd.addCheckbox("JP4 (not JP46)? ", IS_JP4);		// gd.addCheckbox("JP4 (not JP46)? ", IS_JP4);

	@@ -346,6 +352,7 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
	camera_img_new = gd.getNextString();		camera_img_new = gd.getNextString();
	camera_jp46settings = gd.getNextString();		camera_jp46settings = gd.getNextString();
	demux= gd.getNextBoolean();		demux= gd.getNextBoolean();
			fix_bayer= gd.getNextBoolean();
	IS_SILENT= gd.getNextBoolean();		IS_SILENT= gd.getNextBoolean();
	return true;		return true;
	}		}
	@@ -523,6 +530,7 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
	double[][] rgammas=new double[4][];		double[][] rgammas=new double[4][];
	double min_gain;		double min_gain;
	long WOI_LEFT,WOI_WIDTH,WOI_TOP,WOI_HEIGHT,BAYER_MODE,DCM_HOR,DCM_VERT,BIN_HOR,BIN_VERT;		long WOI_LEFT,WOI_WIDTH,WOI_TOP,WOI_HEIGHT,BAYER_MODE,DCM_HOR,DCM_VERT,BIN_HOR,BIN_VERT;
			BAYER_MODE = 0;
	long COLOR_MODE=0;		long COLOR_MODE=0;
	long FLIPH=0;		long FLIPH=0;
	long FLIPV=0;		long FLIPV=0;
	@@ -794,35 +802,36 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
	}		}
	}		}
	/* apply gammas here */		/* apply gammas here */
			int[] bayer_indices= BAYER_INDICES[(int) BAYER_MODE];
	if (MakerNote !=null) {		if (MakerNote !=null) {

	if (scale) {		if (scale) {
	for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {		for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {
	i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x ]= (float) (((rgammas[1][i])-blacks256[1])/gains[1]);		macroblock[y ][x ]= (float) (((rgammas[bayer_indices[1]][i])-blacks256[bayer_indices[1]])/gains[bayer_indices[1]]);

	i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x+1]= (float) (((rgammas[0][i])-blacks256[0])/gains[0]);		macroblock[y ][x+1]= (float) (((rgammas[bayer_indices[0]][i])-blacks256[bayer_indices[0]])/gains[bayer_indices[0]]);

	i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x ]= (float) (((rgammas[3][i])-blacks256[3])/gains[3]);		macroblock[y+1][x ]= (float) (((rgammas[bayer_indices[3]][i])-blacks256[bayer_indices[3]])/gains[bayer_indices[3]]);

	i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x+1]= (float) (((rgammas[2][i])-blacks256[2])/gains[2]);		macroblock[y+1][x+1]= (float) (((rgammas[bayer_indices[2]][i])-blacks256[bayer_indices[2]])/gains[bayer_indices[2]]);
	}		}
	} else {		} else {
	for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {		for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {
	i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x ]= (float) ((rgammas[1][i])-blacks256[1]);		macroblock[y ][x ]= (float) ((rgammas[bayer_indices[1]][i])-blacks256[bayer_indices[1]]);

	i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x+1]= (float) ((rgammas[0][i])-blacks256[0]);		macroblock[y ][x+1]= (float) ((rgammas[bayer_indices[0]][i])-blacks256[bayer_indices[0]]);

	i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x ]= (float) ((rgammas[3][i])-blacks256[3]);		macroblock[y+1][x ]= (float) ((rgammas[bayer_indices[3]][i])-blacks256[bayer_indices[3]]);

	i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x+1]= (float) ((rgammas[2][i])-blacks256[2]);		macroblock[y+1][x+1]= (float) ((rgammas[bayer_indices[2]][i])-blacks256[bayer_indices[2]]);
	}		}
	}		}
	}		}
	@@ -835,16 +844,60 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
	}		}
	}		}
	}		}
	if (FLIPH!=0) ip_src.flipHorizontal(); /* To correct Bayer */
	if (FLIPV!=0) ip_src.flipVertical(); /* To correct Bayer */		if (FLIPH!=0) {
			ip_src.flipHorizontal(); /* To correct Bayer */
			}
			if (FLIPV!=0) {
			ip_src.flipVertical(); /* To correct Bayer */
			}

	/* Is it needed here ? */		/* Is it needed here ? */
	/* imp.draw();		/* imp.draw();
	imp.show(); **/		imp.show(); **/
	if (use_imp_src) copyProperties (imp, imp_src);		if (use_imp_src) copyProperties (imp, imp_src);

			if (fix_bayer) {
			shiftToBayer(use_imp_src? imp_src: imp);
			}

	return use_imp_src;		return use_imp_src;
	}		}

			/**
			* Shift image vertically and/or horizontally to make it with BAYER_MODE=0 (RG/GB)
			* @param imp_src image, will be modified
			* @return true if any changes were applied
			*/
			public boolean shiftToBayer( ImagePlus imp) {
			int bayer_mode = Integer.parseInt((String) imp.getProperty("BAYER_MODE"));
			int flip_vert = Integer.parseInt((String) imp.getProperty("FLIPV"));
			int flip_hor = Integer.parseInt((String) imp.getProperty("FLIPH"));
			bayer_mode ^= flip_hor + (flip_vert << 1);

			if (bayer_mode == 0) return false;
			int width = imp.getWidth();
			int height = imp.getHeight();
			float [] pixels = (float[]) imp.getProcessor().getPixels();

			if ((bayer_mode & 1) != 0) { // horizontal shift
			System.arraycopy(pixels, 1, pixels, 0, pixels.length-1); // shift left by 1 pixel (last column will be wrong)
			for (int row = 0; row < height; row++) {
			pixels[(row + 1) * width -1] = pixels[(row + 1) * width - 3]; // set the last column with the nearest of the same Bayer
			}
			}

			if ((bayer_mode & 2) != 0) { // vertical shift
			System.arraycopy(pixels, width, pixels, 0, pixels.length-width); // shift up by 1 row (last row will be wrong)
			System.arraycopy(pixels, width * (height - 3), pixels, width * (height-1), width); // set the row column with the nearest of the same Bayer
			}
			bayer_mode = flip_hor + (flip_vert << 1);
			imp.setProperty("BAYER_MODE",""+bayer_mode);
			return true;
			}



	/* reverses gamma calculations in the camera		/* reverses gamma calculations in the camera
	returns double[] table , in the range 0.0..255.996		returns double[] table , in the range 0.0..255.996
	*/		*/

src/main/java/com/elphel/imagej/calibration/LaserPointer.java

+27 −35

Original line number	Original line	Diff line number	Diff line
	@@ -542,7 +542,9 @@ public class LaserPointer{
	int width		int width
	){		){
	ShowDoubleFloatArrays sdfra_instance= null;		ShowDoubleFloatArrays sdfra_instance= null;
	if (this.debugLevel>1) sdfra_instance= new ShowDoubleFloatArrays(); // just for debugging?		// if (this.debugLevel>0) sdfra_instance= new ShowDoubleFloatArrays(); // just for debugging?
			if (this.debugLevel > 4) sdfra_instance= new ShowDoubleFloatArrays(); // just for debugging?
			boolean show_debug = sdfra_instance != null;
	DoubleGaussianBlur gb=new DoubleGaussianBlur();		DoubleGaussianBlur gb=new DoubleGaussianBlur();
	double initialScale=0.5;		double initialScale=0.5;
	int height=pixels.length/width;		int height=pixels.length/width;
	@@ -580,18 +582,6 @@ public class LaserPointer{
	}		}
	index+=width;		index+=width;
	}		}
	/*
	if (i*dwidth+j>=dpixels.length){
	System.out.println(
	"dpixels.length="+dpixels.length+"\n"+
	"width="+width+"\n"+
	"height="+height+"\n"+
	"dwidth="+dwidth+"\n"+
	"dheight="+dheight+"\n"+
	"i="+i+"\n"+
	"j="+j+"\n");
	}
	*/
	dpixels[idwidth+j]=dk;		dpixels[idwidth+j]=dk;
	}		}
	if (extraWidth>0){ // j==dWidth-1		if (extraWidth>0){ // j==dWidth-1
	@@ -631,10 +621,10 @@ public class LaserPointer{
	}		}
	}		}
	} else dpixels=pixels.clone();		} else dpixels=pixels.clone();
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels, dwidth, dheight, "decimated");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels, dwidth, dheight, "decimated");
	double [] dpixels_lp=dpixels.clone();		double [] dpixels_lp=dpixels.clone();
	gb.blurDouble(dpixels_lp, dwidth, dheight, scalethis.localContrastSigma, scalethis.localContrastSigma, 0.01);		gb.blurDouble(dpixels_lp, dwidth, dheight, scalethis.localContrastSigma, scalethis.localContrastSigma, 0.01);
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_lp");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_lp");
	double sum=0.0;		double sum=0.0;
	for (int i=0;i<dpixels.length;i++){		for (int i=0;i<dpixels.length;i++){
	dpixels[i]-=dpixels_lp[i];		dpixels[i]-=dpixels_lp[i];
	@@ -642,26 +632,26 @@ public class LaserPointer{
	sum+=dpixels_lp[i];		sum+=dpixels_lp[i];
	}		}
	double corr=(1.0-this.localToGlobalContrast)Math.sqrt(sum/(dwidthdheight));		double corr=(1.0-this.localToGlobalContrast)Math.sqrt(sum/(dwidthdheight));
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_var");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_var");
	gb.blurDouble(dpixels_lp, dwidth, dheight, scalethis.localContrastSigma, scalethis.localContrastSigma, 0.01);		gb.blurDouble(dpixels_lp, dwidth, dheight, scalethis.localContrastSigma, scalethis.localContrastSigma, 0.01);
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_var_blur");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_var_blur");
	for (int i=0;i<dpixels.length;i++){		for (int i=0;i<dpixels.length;i++){
	dpixels_lp[i]=this.localToGlobalContrast*Math.sqrt(dpixels_lp[i])+corr;		dpixels_lp[i]=this.localToGlobalContrast*Math.sqrt(dpixels_lp[i])+corr;
	dpixels[i]/=dpixels_lp[i];		dpixels[i]/=dpixels_lp[i];
	}		}
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_denom");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels_lp, dwidth, dheight, "dpixels_denom");
	if (this.patternLowPassSigma>0) {		if (this.patternLowPassSigma>0) {
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels, dwidth, dheight, "dpixels_normalized");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels, dwidth, dheight, "dpixels_normalized");
	gb.blurDouble(dpixels, dwidth, dheight, scalethis.patternLowPassSigma, scalethis.patternLowPassSigma, 0.01);		gb.blurDouble(dpixels, dwidth, dheight, scalethis.patternLowPassSigma, scalethis.patternLowPassSigma, 0.01);
	}		}
	if (this.debugLevel>1) sdfra_instance.showArrays(dpixels, dwidth, dheight, "dpixels_norm_blur");		if (show_debug && (this.debugLevel>1)) sdfra_instance.showArrays(dpixels, dwidth, dheight, "dpixels_norm_blur");
	int [] ipixels=new int [dpixels.length];		int [] ipixels=new int [dpixels.length];
	for (int i=0;i<dpixels.length;i++){		for (int i=0;i<dpixels.length;i++){
	if (dpixels[i]>this.patternThreshold) ipixels[i]=1;		if (dpixels[i]>this.patternThreshold) ipixels[i]=1;
	else if (dpixels[i]<-this.patternThreshold) ipixels[i]=-1;		else if (dpixels[i]<-this.patternThreshold) ipixels[i]=-1;
	else ipixels[i]=0;		else ipixels[i]=0;
	}		}
	if (this.debugLevel>1) sdfra_instance.showArrays(ipixels, dwidth, dheight, "ipixels_threshold");		if (show_debug && (this.debugLevel>1)) sdfra_instance.showArrays(ipixels, dwidth, dheight, "ipixels_threshold");

	int maxDist = (int) Math.round(scale*this.maximalCellSize);		int maxDist = (int) Math.round(scale*this.maximalCellSize);
	if (maxDist<1) maxDist=1;		if (maxDist<1) maxDist=1;
	@@ -672,28 +662,29 @@ public class LaserPointer{
	dwidth,		dwidth,
	(pass & 1)==0, // false, // each black cell should have white in all 4 quadrants		(pass & 1)==0, // false, // each black cell should have white in all 4 quadrants
	maxDist,		maxDist,
	this.bordersOK		this.bordersOK,
			show_debug
	);		);
	if (this.debugLevel>2) sdfra_instance.showArrays(ipixels, dwidth, dheight, "pass-"+pass);		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(ipixels, dwidth, dheight, "pass-"+pass);
	}		}
	//blur-threshold-grow		//blur-threshold-grow
	// convert to Double (white cells - 1.0, black and none - 0.0)		// convert to Double (white cells - 1.0, black and none - 0.0)
	for (int i=0;i<dpixels.length;i++) dpixels[i]= (ipixels[i]>0)?1.0:0.0;		for (int i=0;i<dpixels.length;i++) dpixels[i]= (ipixels[i]>0)?1.0:0.0;
	// blur result with sigma > cell period to find continuous pattern cell areas		// blur result with sigma > cell period to find continuous pattern cell areas
	gb.blurDouble(dpixels, dwidth, dheight, scalethis.localContrastSigma, scalethis.localContrastSigma, 0.01);		gb.blurDouble(dpixels, dwidth, dheight, scalethis.localContrastSigma, scalethis.localContrastSigma, 0.01);
	if (this.debugLevel>2) sdfra_instance.showArrays(dpixels, dwidth, dheight, "white_blurred");		if (show_debug && (this.debugLevel>2)) sdfra_instance.showArrays(dpixels, dwidth, dheight, "white_blurred");
	// Threshold to boolean mask		// Threshold to boolean mask
	boolean [] dmask=new boolean[dpixels.length];		boolean [] dmask=new boolean[dpixels.length];
	for (int i=0;i<dpixels.length;i++) dmask[i]= (dpixels[i]>=this.blurredMaskThreshold);		for (int i=0;i<dpixels.length;i++) dmask[i]= (dpixels[i]>=this.blurredMaskThreshold);
	if (this.debugLevel>1) sdfra_instance.showArrays(dmask, dwidth, dheight, "white_threshold");		if (show_debug && (this.debugLevel>1)) sdfra_instance.showArrays(dmask, dwidth, dheight, "white_threshold");
	int iBlurMaskGrow= (int) Math.round(scale*this.localContrastSigma); // does in need separate coefficient?		int iBlurMaskGrow= (int) Math.round(scale*this.localContrastSigma); // does in need separate coefficient?
	growMask( dmask, //boolean [] pixels,		growMask( dmask, //boolean [] pixels,
	dwidth, // int width,		dwidth, // int width,
	iBlurMaskGrow); //int grow);		iBlurMaskGrow); //int grow);
	if (this.debugLevel>1) sdfra_instance.showArrays(dmask, dwidth, dheight, "white_threshold_grown"+iBlurMaskGrow);		if (show_debug && (this.debugLevel>1)) sdfra_instance.showArrays(dmask, dwidth, dheight, "white_threshold_grown"+iBlurMaskGrow);
	// Mask out white cells outside of the compact areas just found		// Mask out white cells outside of the compact areas just found
	for (int i=0;i<dpixels.length;i++) if (!dmask[i]) ipixels[i]=0;		for (int i=0;i<dpixels.length;i++) if (!dmask[i]) ipixels[i]=0;
	if (this.debugLevel>1) sdfra_instance.showArrays(ipixels, dwidth, dheight, "ipixels_masked");		if (show_debug && ((this.debugLevel>1))) sdfra_instance.showArrays(ipixels, dwidth, dheight, "ipixels_masked");
	boolean [] mask=new boolean[pixels.length];		boolean [] mask=new boolean[pixels.length];
	if (this.decimatePatternFilter>1){		if (this.decimatePatternFilter>1){
	for (int i=0;i<pixels.length;i++){		for (int i=0;i<pixels.length;i++){
	@@ -764,11 +755,12 @@ public class LaserPointer{
	int width,		int width,
	boolean fromBlack,		boolean fromBlack,
	int maxDist,		int maxDist,
	boolean bordersOK		boolean bordersOK,
			boolean show_debug
	){		){
	int height=pixels.length/width;		int height=pixels.length/width;
	ShowDoubleFloatArrays sdfra_instance= null;		ShowDoubleFloatArrays sdfra_instance= null;
	if (this.debugLevel>1) sdfra_instance= new ShowDoubleFloatArrays(); // just for debugging?		if (show_debug) sdfra_instance= new ShowDoubleFloatArrays(); // just for debugging?

	int [] distLeft= new int [pixels.length];		int [] distLeft= new int [pixels.length];
	int [] distRight=new int [pixels.length]; // also used for down		int [] distRight=new int [pixels.length]; // also used for down
	@@ -789,14 +781,14 @@ public class LaserPointer{
	distRight[index2--]=v2;		distRight[index2--]=v2;
	}		}
	}		}
	if (this.debugLevel>3){		if (show_debug && (this.debugLevel>3)){
	sdfra_instance.showArrays(distLeft, width, height, "distLeft-"+fromBlack);		sdfra_instance.showArrays(distLeft, width, height, "distLeft-"+fromBlack);
	sdfra_instance.showArrays(distRight, width, height, "distRight-"+fromBlack);		sdfra_instance.showArrays(distRight, width, height, "distRight-"+fromBlack);

	}		}
	// combine two (max distance)		// combine two (max distance)
	for (int i=0;i<pixels.length;i++) if (distRight[i]>distLeft[i])distLeft[i]=distRight[i];		for (int i=0;i<pixels.length;i++) if (distRight[i]>distLeft[i])distLeft[i]=distRight[i];
	if (this.debugLevel>3) sdfra_instance.showArrays(distLeft, width, height, "comboLeftRight-"+fromBlack);		if (show_debug && (this.debugLevel>3)) sdfra_instance.showArrays(distLeft, width, height, "comboLeftRight-"+fromBlack);


	// Down		// Down
	@@ -807,7 +799,7 @@ public class LaserPointer{
	v1=distRight[index1++]+1;		v1=distRight[index1++]+1;
	distRight[i]= (v1>distLeft[i])?distLeft[i]:v1;		distRight[i]= (v1>distLeft[i])?distLeft[i]:v1;
	}		}
	if (this.debugLevel>3) sdfra_instance.showArrays(distRight, width, height, "distDown-"+fromBlack);		if (show_debug && (this.debugLevel>3)) sdfra_instance.showArrays(distRight, width, height, "distDown-"+fromBlack);
	// Up		// Up
	for (int j=pixels.length-width;j<pixels.length;j++) distUp[j]= bordersOK?0:distLeft[j];		for (int j=pixels.length-width;j<pixels.length;j++) distUp[j]= bordersOK?0:distLeft[j];
	index1=pixels.length-1;		index1=pixels.length-1;
	@@ -816,10 +808,10 @@ public class LaserPointer{
	v1=distUp[index1--]+1;		v1=distUp[index1--]+1;
	distUp[i]= (v1>distLeft[i])?distLeft[i]:v1;		distUp[i]= (v1>distLeft[i])?distLeft[i]:v1;
	}		}
	if (this.debugLevel>3) sdfra_instance.showArrays(distUp, width, height, "distUp-"+fromBlack);		if (show_debug && (this.debugLevel>3)) sdfra_instance.showArrays(distUp, width, height, "distUp-"+fromBlack);
	// combine two (max distance)		// combine two (max distance)
	for (int i=0;i<pixels.length;i++) if (distUp[i]>distRight[i])distRight[i]=distUp[i];		for (int i=0;i<pixels.length;i++) if (distUp[i]>distRight[i])distRight[i]=distUp[i];
	if (this.debugLevel>3) sdfra_instance.showArrays(distRight, width, height, "combo-"+fromBlack);		if (show_debug && (this.debugLevel>3)) sdfra_instance.showArrays(distRight, width, height, "combo-"+fromBlack);
	// Now distRight contains the longest of 4 quadrants distance from "good" pixels - remove bad opposite side ones		// Now distRight contains the longest of 4 quadrants distance from "good" pixels - remove bad opposite side ones
	for (int i=0;i<pixels.length;i++) if ((distRight[i]>maxDist) && (pixels[i]!=sign)) pixels[i]=0; // if opposite signe (or 0) make 0		for (int i=0;i<pixels.length;i++) if ((distRight[i]>maxDist) && (pixels[i]!=sign)) pixels[i]=0; // if opposite signe (or 0) make 0
	}		}
	@@ -898,7 +890,7 @@ public class LaserPointer{
	String title,		String title,
	int debugLevel // debug level (normal == 1)		int debugLevel // debug level (normal == 1)
	){		){
	int debugTiming=1;		int debugTiming=1; // used >3
	if (debugLevel>debugTiming) printTimingInit();		if (debugLevel>debugTiming) printTimingInit();
	boolean skipFirst=scaleExposureForLasers>0.0; // do not use no-pointer image (may have different exposure time)		boolean skipFirst=scaleExposureForLasers>0.0; // do not use no-pointer image (may have different exposure time)
	/// if (scaleExposureForLasers>0) saturationRed*=scaleExposureForLasers; // scaled to reduced exposure time		/// if (scaleExposureForLasers>0) saturationRed*=scaleExposureForLasers; // scaled to reduced exposure time

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

+10867 −10014

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src/main/java/com/elphel/imagej/calibration/hardware/CamerasInterface.java

+46 −7

Original line number	Original line	Diff line number	Diff line
	@@ -899,6 +899,7 @@ public class CamerasInterface{
	return setupCameraAcquisition(Double.NaN);		return setupCameraAcquisition(Double.NaN);
	}		}
	public boolean setupCameraAcquisition(final double exposureScale){		public boolean setupCameraAcquisition(final double exposureScale){
			final boolean mp14 = true;// FIXME: Modified for 14Mpix
	final int ipLength=this.resetURLs.length;		final int ipLength=this.resetURLs.length;
	final boolean [] results=new boolean[ipLength];		final boolean [] results=new boolean[ipLength];
	for (int chn=0;chn<ipLength;chn++) results[chn]=(this.sensorPresent[chn]!=null);		for (int chn=0;chn<ipLength;chn++) results[chn]=(this.sensorPresent[chn]!=null);
	@@ -917,14 +918,15 @@ public class CamerasInterface{
	}		}
	startAndJoin(threads);		startAndJoin(threads);
	if (Double.isNaN(exposureScale)){ // full init		if (Double.isNaN(exposureScale)){ // full init
	int nRepeat=this.setupTriggerMode?4:1;		// int nRepeat=this.setupTriggerMode?4:1;
			int nRepeat=this.setupTriggerMode?4:2; // FIXME: Modified for 14Mpix
	if (this.nc393) nRepeat++; // is it needed?		if (this.nc393) nRepeat++; // is it needed?
	for (int i=0;i<nRepeat;i++){		for (int i=0;i<nRepeat;i++){
	if (this.debugLevel>0) System.out.println((i+1)+" of "+nRepeat+": Triggering cameras to give parameters a chance to propagate");		if (this.debugLevel>0) System.out.println((i+1)+" of "+nRepeat+": Triggering cameras to give parameters a chance to propagate");
	trigger();		trigger();
	try		try
	{		{
	Thread.sleep( 1000 ); // ms		Thread.sleep( 2000 ); // ms // FIXME: Modified for 14Mpix
	}		}
	catch ( InterruptedException e )		catch ( InterruptedException e )
	{		{
	@@ -932,6 +934,16 @@ public class CamerasInterface{
	}		}
	}		}

			} else if (mp14) {
			try
			{
			Thread.sleep( 2000 ); // ms // FIXME: Modified for 14Mpix
			}
			catch ( InterruptedException e )
			{
			System.out.println( "awakened prematurely" );
			}
			trigger();
	}		}
	boolean result=true;		boolean result=true;
	for (int chn=0;chn<ipLength;chn++) if (this.sensorPresent[chn]!=null) result &=results[chn];		for (int chn=0;chn<ipLength;chn++) if (this.sensorPresent[chn]!=null) result &=results[chn];
	@@ -1290,7 +1302,8 @@ public class CamerasInterface{
	DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();		DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
	DocumentBuilder db = dbf.newDocumentBuilder();		DocumentBuilder db = dbf.newDocumentBuilder();
	String url=metaURLs[ipIndex];		String url=metaURLs[ipIndex];
	if (debugLevel>2) System.out.println("timestampIPs:" + url );		// if (debugLevel>2) System.out.println("timestampIPs:" + url );
			if (debugLevel>0) System.out.println("timestampIPs:" + url );
	dom = db.parse(url);		dom = db.parse(url);
	if (!dom.getDocumentElement().getNodeName().equals("meta")) {		if (!dom.getDocumentElement().getNodeName().equals("meta")) {
	System.out.println("Root element: expected 'meta', got'" + dom.getDocumentElement().getNodeName()+"'");		System.out.println("Root element: expected 'meta', got'" + dom.getDocumentElement().getNodeName()+"'");
	@@ -1383,7 +1396,13 @@ public class CamerasInterface{
	startAndJoin(threads);		startAndJoin(threads);
	}		}

			// public boolean preTrigger() { // mt9f002 fails if more than 1-3 sec between triggers
			// return true;
			// }


	public ImagePlus [] getImages(final boolean [] acquire, boolean resetAndTrigger, final boolean show){		public ImagePlus [] getImages(final boolean [] acquire, boolean resetAndTrigger, final boolean show){
			final boolean dual_trig = false;
	final boolean [] acquireIPs=selectIPs(acquire);		final boolean [] acquireIPs=selectIPs(acquire);
	if (this.debugLevel>2) {		if (this.debugLevel>2) {
	System.out.println("getImages(...) 2");		System.out.println("getImages(...) 2");
	@@ -1391,8 +1410,20 @@ public class CamerasInterface{
	}		}

	if (resetAndTrigger) {		if (resetAndTrigger) {
			try { // FIXME: Make conditional for 14MPix
			Thread.sleep(2000);
			} catch (InterruptedException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			}
	resetCameras();		resetCameras();
	trigger();		trigger();
			if (dual_trig) {
			timestampIPs(acquireIPs); // ignoring results, just wait
			resetCameras();
			// trigger();
			jp4_Instances[0].readDummyURL("http://192.168.0.236/parsedit.php?immediate&TRIG_PERIOD=1*0");
			}
	}		}
	final double [] timestamps= timestampIPs(acquireIPs);		final double [] timestamps= timestampIPs(acquireIPs);
	if (this.debugLevel>2) System.out.println("getImages(): this.imagesIP.length=" + this.imagesIP.length);		if (this.debugLevel>2) System.out.println("getImages(): this.imagesIP.length=" + this.imagesIP.length);
	@@ -1590,6 +1621,12 @@ public class CamerasInterface{
	if (debugLevel>2) System.out.println(String.format("this.laserPointers.setLasers (0x%x)", sequence[nSeqNum]));		if (debugLevel>2) System.out.println(String.format("this.laserPointers.setLasers (0x%x)", sequence[nSeqNum]));
	}		}
	resetIPs(selectIPs(lasersIPs)); // flush buffer		resetIPs(selectIPs(lasersIPs)); // flush buffer
			try { // FIXME: Make conditional for 14MPix
			Thread.sleep(2000);
			} catch (InterruptedException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			}
	trigger(); // trigger cameras		trigger(); // trigger cameras
	ipIndexAtomic.set(0);		ipIndexAtomic.set(0);
	final int fnSeqNum=nSeqNum;		final int fnSeqNum=nSeqNum;
	@@ -1613,6 +1650,8 @@ public class CamerasInterface{
	System.out.println("==== "+imageURLs[ipIndex]+ " opened in "+IJ.d2s(0.000000001*(System.nanoTime()-st),3)+" sec");		System.out.println("==== "+imageURLs[ipIndex]+ " opened in "+IJ.d2s(0.000000001*(System.nanoTime()-st),3)+" sec");
	}		}
	laserImagesIP[fnSeqNum-1][ipIndex].setProperty("MIRRORED","NO");		laserImagesIP[fnSeqNum-1][ipIndex].setProperty("MIRRORED","NO");
			// laserImagesIP[fnSeqNum-1][ipIndex].setTitle("raw"+fnSeqNum); //FIXME:Debugging
			// laserImagesIP[fnSeqNum-1][ipIndex].show(); //FIXME:Debugging
	}		}
	}		}
	};		};

src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java

+95 −13

Original line number	Original line	Diff line number	Diff line
	@@ -85,6 +85,11 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	*		*
	*/		*/
	private static final long serialVersionUID = 390855361964415147L;		private static final long serialVersionUID = 390855361964415147L;
			public static int [][] BAYER_INDICES = {
			{0, 1, 2 ,3},
			{1, 0, 3 ,2},
			{2, 3, 0 ,1},
			{3, 2, 1 ,0}};
	Panel panel1;		Panel panel1;
	Panel confpanel;		Panel confpanel;
	Frame instance;		Frame instance;
	@@ -93,7 +98,7 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	String arg;		String arg;

	static File dir;		static File dir;
			public boolean fix_bayer = true; // shift image (replacing last row/column) if (corrected for flips) BAYER_MODE != 0
	public String camera_url = "http://192.168.0.236:8081/";		public String camera_url = "http://192.168.0.236:8081/";
	public String camera_img = "bimg";		public String camera_img = "bimg";
	public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)		public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
	@@ -109,14 +114,26 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	public void run(String arg) {		public void run(String arg) {
	}		}

	public JP46_Reader_camera(Boolean showGui) {		public JP46_Reader_camera(Boolean showGui) { // default fix_bayer = true
			if (showGui) initGui();
			}

			public JP46_Reader_camera() { // default fix_bayer = true
			initGui();
			}

			public JP46_Reader_camera(Boolean showGui, int fix_bayer) {
	if (showGui) initGui();		if (showGui) initGui();
			this.fix_bayer = (fix_bayer !=0);
	}		}

	public JP46_Reader_camera() {		public JP46_Reader_camera(int fix_bayer) {
	initGui();		initGui();
			this.fix_bayer = (fix_bayer !=0);
	}		}

			// fix_bayer

	private void initGui() {		private void initGui() {
	if (headless) return;		if (headless) return;

	@@ -390,6 +407,8 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	if (imp == null) {		if (imp == null) {
	IJ.showMessage("JP46 Reader Error", "Could not open the URL: " + url + " as JPEG/JP46");		IJ.showMessage("JP46 Reader Error", "Could not open the URL: " + url + " as JPEG/JP46");
	} else {		} else {
			// imp.updateAndDraw();
			// imp.show(); // updateAndDraw();
	if ((imp_src==null) && showImage) {		if ((imp_src==null) && showImage) {
	// System.out.println("show() 1");		// System.out.println("show() 1");
	imp.show(); /* Shows before re-ordering*/		imp.show(); /* Shows before re-ordering*/
	@@ -450,6 +469,7 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	}		}
	boolean jp46Reorder(ImagePlus imp, long[] MakerNote, boolean scale, ImagePlus imp_src) {		boolean jp46Reorder(ImagePlus imp, long[] MakerNote, boolean scale, ImagePlus imp_src) {
	// int MARGIN=2; // 2 pixels in JP4/JP46 mode around WOI		// int MARGIN=2; // 2 pixels in JP4/JP46 mode around WOI

	double[] gains= new double[4];		double[] gains= new double[4];
	double[] blacks= new double[4];		double[] blacks= new double[4];
	double[] blacks256= new double[4];		double[] blacks256= new double[4];
	@@ -459,6 +479,7 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	double[][] rgammas=new double[4][];		double[][] rgammas=new double[4][];
	double min_gain;		double min_gain;
	long WOI_LEFT,WOI_WIDTH,WOI_TOP,WOI_HEIGHT,BAYER_MODE,DCM_HOR,DCM_VERT,BIN_HOR,BIN_VERT;		long WOI_LEFT,WOI_WIDTH,WOI_TOP,WOI_HEIGHT,BAYER_MODE,DCM_HOR,DCM_VERT,BIN_HOR,BIN_VERT;
			BAYER_MODE = 0;
	long COLOR_MODE=0;		long COLOR_MODE=0;
	long FLIPH=0;		long FLIPH=0;
	long FLIPV=0;		long FLIPV=0;
	@@ -730,35 +751,36 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	}		}
	}		}
	/* apply gammas here */		/* apply gammas here */
			int[] bayer_indices= BAYER_INDICES[(int) BAYER_MODE];
	if (MakerNote !=null) {		if (MakerNote !=null) {

	if (scale) {		if (scale) {
	for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {		for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {
	i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x ]= (float) (((rgammas[1][i])-blacks256[1])/gains[1]);		macroblock[y ][x ]= (float) (((rgammas[bayer_indices[1]][i])-blacks256[bayer_indices[1]])/gains[bayer_indices[1]]);

	i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x+1]= (float) (((rgammas[0][i])-blacks256[0])/gains[0]);		macroblock[y ][x+1]= (float) (((rgammas[bayer_indices[0]][i])-blacks256[bayer_indices[0]])/gains[bayer_indices[0]]);

	i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x ]= (float) (((rgammas[3][i])-blacks256[3])/gains[3]);		macroblock[y+1][x ]= (float) (((rgammas[bayer_indices[3]][i])-blacks256[bayer_indices[3]])/gains[bayer_indices[3]]);

	i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x+1]= (float) (((rgammas[2][i])-blacks256[2])/gains[2]);		macroblock[y+1][x+1]= (float) (((rgammas[bayer_indices[2]][i])-blacks256[bayer_indices[2]])/gains[bayer_indices[2]]);
	}		}
	} else {		} else {
	for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {		for (y=0;y<16;y+=2) for (x=0;x<16;x+=2) {
	i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x ]= (float) ((rgammas[1][i])-blacks256[1]);		macroblock[y ][x ]= (float) ((rgammas[bayer_indices[1]][i])-blacks256[bayer_indices[1]]);

	i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y ][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y ][x+1]= (float) ((rgammas[0][i])-blacks256[0]);		macroblock[y ][x+1]= (float) ((rgammas[bayer_indices[0]][i])-blacks256[bayer_indices[0]]);

	i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x ]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x ]= (float) ((rgammas[3][i])-blacks256[3]);		macroblock[y+1][x ]= (float) ((rgammas[bayer_indices[3]][i])-blacks256[bayer_indices[3]]);

	i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;		i=(int) macroblock[y+1][x+1]; if (i<0) i=0 ; else if (i>255) i=255;
	macroblock[y+1][x+1]= (float) ((rgammas[2][i])-blacks256[2]);		macroblock[y+1][x+1]= (float) ((rgammas[bayer_indices[2]][i])-blacks256[bayer_indices[2]]);
	}		}
	}		}
	}		}
	@@ -771,16 +793,60 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	}		}
	}		}
	}		}
	if (FLIPH!=0) ip_src.flipHorizontal(); /* To correct Bayer */
	if (FLIPV!=0) ip_src.flipVertical(); /* To correct Bayer */		if (FLIPH!=0) {
			ip_src.flipHorizontal(); /* To correct Bayer */
			}
			if (FLIPV!=0) {
			ip_src.flipVertical(); /* To correct Bayer */
			}

	/* Is it needed here ? */		/* Is it needed here ? */
	/* imp.draw();		/* imp.draw();
	imp.show(); **/		imp.show(); **/
	if (use_imp_src) copyProperties (imp, imp_src);		if (use_imp_src) copyProperties (imp, imp_src);

			if (fix_bayer) {
			shiftToBayer(use_imp_src? imp_src: imp);
			}

	return use_imp_src;		return use_imp_src;
	}		}

			/**
			* Shift image vertically and/or horizontally to make it with BAYER_MODE=0 (RG/GB)
			* @param imp_src image, will be modified
			* @return true if any changes were applied
			*/
			public boolean shiftToBayer( ImagePlus imp) {
			int bayer_mode = Integer.parseInt((String) imp.getProperty("BAYER_MODE"));
			int flip_vert = Integer.parseInt((String) imp.getProperty("FLIPV"));
			int flip_hor = Integer.parseInt((String) imp.getProperty("FLIPH"));
			bayer_mode ^= flip_hor + (flip_vert << 1);

			if (bayer_mode == 0) return false;
			int width = imp.getWidth();
			int height = imp.getHeight();
			float [] pixels = (float[]) imp.getProcessor().getPixels();

			if ((bayer_mode & 1) != 0) { // horizontal shift
			System.arraycopy(pixels, 1, pixels, 0, pixels.length-1); // shift left by 1 pixel (last column will be wrong)
			for (int row = 0; row < height; row++) {
			pixels[(row + 1) * width -1] = pixels[(row + 1) * width - 3]; // set the last column with the nearest of the same Bayer
			}
			}

			if ((bayer_mode & 2) != 0) { // vertical shift
			System.arraycopy(pixels, width, pixels, 0, pixels.length-width); // shift up by 1 row (last row will be wrong)
			System.arraycopy(pixels, width * (height - 3), pixels, width * (height-1), width); // set the row column with the nearest of the same Bayer
			}
			bayer_mode = flip_hor + (flip_vert << 1);
			imp.setProperty("BAYER_MODE",""+bayer_mode);
			return true;
			}



	/* reverses gamma calculations in the camera		/* reverses gamma calculations in the camera
	returns double[] table , in the range 0.0..255.996		returns double[] table , in the range 0.0..255.996
	*/		*/
	@@ -924,6 +990,22 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
	}		}
	return data;		return data;
	}		}
			public boolean readDummyURL(String url ) { // throws IOException {
			URL camURL = null;
			URLConnection urlConn = null;
			try {
			camURL = new URL(url);
			urlConn = camURL.openConnection();
			urlConn.getHeaderFields();
			} catch(MalformedURLException e){
			System.out.println("Please check the URL:" + e.toString() );
			return false;
			} catch(IOException e1){
			System.out.println("Can't read from the Internet: "+ e1.toString() );
			return false;
			}
			return true;
			}

	long[] readElphelMakerNoteURL(String url, int len, double [] xtraExif) throws IOException {		long[] readElphelMakerNoteURL(String url, int len, double [] xtraExif) throws IOException {
	URL camURL = null;		URL camURL = null;

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