testing witgh Eyesis

src/main/java/EyesisCorrectionParameters.java

@@ -101,7 +101,7 @@ public class EyesisCorrectionParameters {
     	public boolean planeAsJPEG=       true;   // save de-warped image as JPEG (only if equirectangularFormat==0)
 //    	public String equirectangularSuffixA="A.eqr-tiff"; // or the roll-over part
     	public String resultsDirectory="";
-    	public boolean removeUnusedSensorData=true;
+    	public boolean removeUnusedSensorData=false;
     	public int exposureCorrectionMode=2; // - 0 - none, 1 - absolute, 2 - relative
     	public double referenceExposure=0.0003; // 3/10000 sec, used in absolute mode only
     	public double relativeExposure=0.5; // 0.0 - use shortest (darken), 1.0 - use longest (brighten)
@@ -1795,7 +1795,6 @@ public class EyesisCorrectionParameters {
   		public double decimateSigma =   -1.0; // special mode for 2:1 deciamtion 
   		public int    tileX =            82;  // number of kernel tile (0..163) 
   		public int    tileY =            62;  // number of kernel tile (0..122) 
-  		public boolean subtract_dc =     false;// subtract/restore dc
   		public int    kernel_chn =      -1; // camera channel calibration to use for aberration correction ( < 0 - no correction)
   		public boolean normalize =       true; // normalize both sym and asym kernels (asym to have sum==1, sym to have sum = dct_size
   		public boolean normalize_sym =   true; // normalize sym kernels separately
@@ -1808,6 +1807,10 @@ public class EyesisCorrectionParameters {
   		public double novignetting_g    = 0.3733; // green gain in the center of sensor calibration G
   		public double novignetting_b    = 0.2034; // blue gain in the center of sensor calibration B
   		
+  		public double scale_r =           1.0; // extra gain correction after vignetting or nonvignetting, before other processing
+  		public double scale_g =           1.0;
+  		public double scale_b =           1.0;
+  		
   		public double vignetting_max    = 0.4; // value in vignetting data to correspond to 1x in the kernel
   		public double vignetting_range  = 5.0; // do not try to correct vignetting less than vignetting_max/vignetting_range
   		
@@ -1877,7 +1880,6 @@ public class EyesisCorrectionParameters {
   			properties.setProperty(prefix+"decimateSigma",      this.decimateSigma+"");
   			properties.setProperty(prefix+"tileX",              this.tileX+"");
   			properties.setProperty(prefix+"tileY",              this.tileY+"");
-  			properties.setProperty(prefix+"subtract_dc",   this.subtract_dc+"");
   			properties.setProperty(prefix+"kernel_chn",         this.kernel_chn+"");
   			properties.setProperty(prefix+"normalize",          this.normalize+"");
   			properties.setProperty(prefix+"normalize_sym",      this.normalize_sym+"");
@@ -1889,6 +1891,12 @@ public class EyesisCorrectionParameters {
   			properties.setProperty(prefix+"novignetting_g",     this.novignetting_g+"");
   			properties.setProperty(prefix+"novignetting_b",     this.novignetting_b+"");
   			
+  			
+  			properties.setProperty(prefix+"scale_r",            this.scale_r+"");
+  			properties.setProperty(prefix+"scale_g",            this.scale_g+"");
+  			properties.setProperty(prefix+"scale_b",            this.scale_b+"");
+  			
+  			
   			properties.setProperty(prefix+"vignetting_max",     this.vignetting_max+"");
   			properties.setProperty(prefix+"vignetting_range",   this.vignetting_range+"");
   			properties.setProperty(prefix+"color_DCT",          this.color_DCT+"");
@@ -1941,7 +1949,6 @@ public class EyesisCorrectionParameters {
   			if (properties.getProperty(prefix+"tileX")!=null) this.tileX=Integer.parseInt(properties.getProperty(prefix+"tileX"));
   			if (properties.getProperty(prefix+"tileY")!=null) this.tileY=Integer.parseInt(properties.getProperty(prefix+"tileY"));
   			if (properties.getProperty(prefix+"dbg_window_mode")!=null) this.dbg_window_mode=Integer.parseInt(properties.getProperty(prefix+"dbg_window_mode"));
-  			if (properties.getProperty(prefix+"subtract_dc")!=null) this.subtract_dc=Boolean.parseBoolean(properties.getProperty(prefix+"subtract_dc"));
   			if (properties.getProperty(prefix+"kernel_chn")!=null) this.kernel_chn=Integer.parseInt(properties.getProperty(prefix+"kernel_chn"));
   			if (properties.getProperty(prefix+"normalize")!=null) this.normalize=Boolean.parseBoolean(properties.getProperty(prefix+"normalize"));
   			if (properties.getProperty(prefix+"normalize_sym")!=null) this.normalize_sym=Boolean.parseBoolean(properties.getProperty(prefix+"normalize_sym"));
@@ -1953,6 +1960,11 @@ public class EyesisCorrectionParameters {
   			if (properties.getProperty(prefix+"novignetting_g")!=null) this.novignetting_g=Double.parseDouble(properties.getProperty(prefix+"novignetting_g"));
   			if (properties.getProperty(prefix+"novignetting_b")!=null) this.novignetting_b=Double.parseDouble(properties.getProperty(prefix+"novignetting_b"));
   			
+  			if (properties.getProperty(prefix+"scale_r")!=null)        this.scale_r=Double.parseDouble(properties.getProperty(prefix+"scale_r"));
+  			if (properties.getProperty(prefix+"scale_g")!=null)        this.scale_g=Double.parseDouble(properties.getProperty(prefix+"scale_g"));
+  			if (properties.getProperty(prefix+"scale_b")!=null)        this.scale_b=Double.parseDouble(properties.getProperty(prefix+"scale_b"));
+
+  			
   			if (properties.getProperty(prefix+"vignetting_max")!=null) this.vignetting_max=Double.parseDouble(properties.getProperty(prefix+"vignetting_max"));
   			if (properties.getProperty(prefix+"vignetting_range")!=null) this.vignetting_range=Double.parseDouble(properties.getProperty(prefix+"vignetting_range"));
   			if (properties.getProperty(prefix+"color_DCT")!=null)      this.color_DCT=Boolean.parseBoolean(properties.getProperty(prefix+"color_DCT"));
@@ -2004,7 +2016,6 @@ public class EyesisCorrectionParameters {
   			gd.addNumericField("Smooth convolution kernel before decimation",                    this.decimateSigma,       3);
   			gd.addNumericField("Tile X to extract (0..163)",                                     this.tileX,               0);
   			gd.addNumericField("Tile Y to extract (0..122)",                                     this.tileY,               0);
-  			gd.addCheckbox    ("Subtract avarege before dct, restore after idct",                this.subtract_dc);
   			gd.addNumericField("Calibration channel to use for aberration ( <0 - no correction)",this.kernel_chn,          0);
   			gd.addCheckbox    ("Normalize both sym and asym kernels ",                           this.normalize);
   			gd.addCheckbox    ("Normalize sym kernels separately",                               this.normalize_sym);
@@ -2016,9 +2027,13 @@ public class EyesisCorrectionParameters {
   			gd.addNumericField("Green gain in the center of sensor calibration G (instead of vignetting)",this.novignetting_g, 4);
   			gd.addNumericField("Blue gain in the center of sensor calibration B (instead of vignetting)",this.novignetting_b,  4);
 
-  			gd.addNumericField("Value (max) in vignetting data to correspond to 1x in the kernel",this.vignetting_max,      3);
-  			gd.addNumericField("Do not try to correct vignetting smaller than this fraction of max",this.vignetting_range,  3);
-  			gd.addCheckbox    ("Use DCT-base color conversion",                                   this.color_DCT             );
+  			gd.addNumericField("Extra red correction to compensate for light temperature",               this.scale_r,  4);
+  			gd.addNumericField("Extra green correction to compensate for light temperature",             this.scale_g,  4);
+  			gd.addNumericField("Extra blue correction to compensate for light temperature",              this.scale_b,  4);
+  			
+  			gd.addNumericField("Value (max) in vignetting data to correspond to 1x in the kernel",    this.vignetting_max,      3);
+  			gd.addNumericField("Do not try to correct vignetting smaller than this fraction of max",  this.vignetting_range,  3);
+  			gd.addCheckbox    ("Use DCT-based color conversion (false - just LPF RGB with dbg_sigma)",this.color_DCT             );
   			gd.addNumericField("Gaussian sigma to apply to R and B (in addition to G), pix",      this.sigma_rb,            3);
   			gd.addNumericField("Gaussian sigma to apply to Y in the MDCT domain, pix",            this.sigma_y,             3);
   			gd.addNumericField("Gaussian sigma to apply to Pr and Pb in the MDCT domain, pix",    this.sigma_color,         3);
@@ -2067,7 +2082,6 @@ public class EyesisCorrectionParameters {
   			this.decimateSigma=         gd.getNextNumber();
   			this.tileX=           (int) gd.getNextNumber();
   			this.tileY=           (int) gd.getNextNumber();
-  			this.subtract_dc=           gd.getNextBoolean();
   			this.kernel_chn=      (int) gd.getNextNumber();
   			this.normalize=             gd.getNextBoolean();
   			this.normalize_sym=         gd.getNextBoolean();
@@ -2077,6 +2091,12 @@ public class EyesisCorrectionParameters {
   			this.novignetting_r=        gd.getNextNumber();
   			this.novignetting_g=        gd.getNextNumber();
   			this.novignetting_b=        gd.getNextNumber();
+
+  			this.scale_r=               gd.getNextNumber();
+  			this.scale_g=               gd.getNextNumber();
+  			this.scale_b=               gd.getNextNumber();
+  			
+  			
   			this.vignetting_max=        gd.getNextNumber();
   			this.vignetting_range=      gd.getNextNumber();
   			this.color_DCT=             gd.getNextBoolean();

src/main/java/EyesisCorrections.java

@@ -107,16 +107,6 @@ public class EyesisCorrections {
 		//if ((this.debugLevel>1) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
 		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
 			testFF(correctionsParameters.sourcePaths[0]);
-//			this.channelVignettingCorrection[srcChannel]=this.pixelMapping.getBayerFlatFieldFloat(
-/*			
-			SDFA_INSTANCE.showArrays(
-					this.channelVignettingCorrection,
-					this.channelWidthHeight[srcChannel][0],
-					this.channelWidthHeight[srcChannel][1],
-					true,
-					"Flat-Field");
-					//LENS_DISTORTIONS.displayGridTitles());
-*/
 		}
 		
 	}

src/main/java/Eyesis_Correction.java

@@ -454,7 +454,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 			addButton("DCT test 1",                panelDct1, color_process);
 			addButton("select MDCT image",         panelDct1, color_configure);
 			addButton("MDCT stack",                panelDct1, color_process);
-			addButton("MDCT DC stack",             panelDct1, color_process);
 			addButton("DCT test 3",                panelDct1, color_process);
 			addButton("DCT test 4",                panelDct1, color_process);
 			addButton("Test Kernel Factorization", panelDct1, color_process);
@@ -462,6 +461,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 			addButton("Select kernels image",      panelDct1, color_configure);
 			addButton("Create DCT kernels",        panelDct1, color_process);
 			addButton("Read DCT kernels",          panelDct1, color_process);
+			addButton("Reset DCT kernels",         panelDct1, color_stop);
 			addButton("Setup DCT parameters",      panelDct1, color_configure);
 			addButton("DCT process files",         panelDct1, color_process);
 			add(panelDct1);
@@ -2627,70 +2627,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
            	DBG_IMP = imp_src;
            }
  /* ======================================================================== */
-    } else if (label.equals("MDCT stack")) {
-    	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
-//    	IJ.showMessage("DCT test 1");
-        if (!DCT_PARAMETERS.showDialog()) return;
-// process selected image stack
-        if (DBG_IMP == null) {
-        	ImagePlus imp_src = WindowManager.getCurrentImage();
-        	if (imp_src==null){
-        		IJ.showMessage("Error","JP4 image or Bayer image stack required");
-        		return;
-        	}
-//        	ImagePlus imp2;
-        	if (imp_src.getStackSize()<3){ // convert JP4 to image stack
-
-        		EyesisCorrectionParameters.SplitParameters split_parameters = new EyesisCorrectionParameters.SplitParameters(
-        				1,  // oversample;
-        				// Add just for mdct (N/2)
-        				DCT_PARAMETERS.dct_size/2, // addLeft
-        				DCT_PARAMETERS.dct_size/2, // addTop
-        				DCT_PARAMETERS.dct_size/2, // addRight
-        				DCT_PARAMETERS.dct_size/2  // addBottom
-        				);		   
-
-
-        		ImageStack sourceStack= bayerToStack(imp_src, // source Bayer image, linearized, 32-bit (float))
-        				split_parameters);
-        		DBG_IMP = new ImagePlus(imp_src.getTitle()+"-SPIT", sourceStack);
-        		DBG_IMP.getProcessor().resetMinAndMax();
-        		DBG_IMP.show();
-        	} else {
-        		DBG_IMP = imp_src;
-        	}
-        }
-        ImageDtt image_dtt = new ImageDtt();
-        double [][] dct_data = image_dtt.mdctStack(DBG_IMP.getStack(),
-        		                                   DCT_PARAMETERS,
-        		                                   THREADS_MAX, DEBUG_LEVEL, UPDATE_STATUS);
-        int tilesY = DBG_IMP.getHeight()/DCT_PARAMETERS.dct_size - 1;
-        int tilesX = DBG_IMP.getWidth()/DCT_PARAMETERS.dct_size - 1;
-        System.out.println("tilesX="+tilesX);
-        System.out.println("tilesY="+tilesY);
-        SDFA_INSTANCE.showArrays(dct_data,
-        		tilesX*DCT_PARAMETERS.dct_size,
-        		tilesY*DCT_PARAMETERS.dct_size,
-        		true,
-        		DBG_IMP.getTitle()+"-DCT");  
-        double [][] idct_data = new double [dct_data.length][];
-        for (int chn=0; chn<idct_data.length;chn++){
-        	idct_data[chn] = image_dtt.lapped_idct(
-        			dct_data[chn],                  // scanline representation of dcd data, organized as dct_size x dct_size tiles  
-        			tilesX*DCT_PARAMETERS.dct_size, //   dct_width,
-        			DCT_PARAMETERS.dct_size,        // final int
-        			DCT_PARAMETERS.dct_window,      //window_type
-        			THREADS_MAX,                    // maximal number of threads to launch                         
-        			DEBUG_LEVEL);                   //        globalDebugLevel)
-        }
-        SDFA_INSTANCE.showArrays(idct_data,
-        		(tilesX + 1) * DCT_PARAMETERS.dct_size,
-        		(tilesY + 1) * DCT_PARAMETERS.dct_size,
-        		true,
-        		DBG_IMP.getTitle()+"-IDCT");  
-    	return;
 /* ======================================================================== */
-    } else if (label.equals("MDCT DC stack")) {
+    } else if (label.equals("MDCT stack")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 //    	IJ.showMessage("DCT test 1");
         if (!DCT_PARAMETERS.showDialog()) return;
@@ -2725,8 +2663,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 
         }
         ImageDtt image_dtt = new ImageDtt();
-        double [][][][] dctdc_data = image_dtt.mdctDcStack(
+        double [][][][] dctdc_data = image_dtt.mdctStack(
         		DBG_IMP.getStack(),
+        		DCT_PARAMETERS.kernel_chn,
         		DCT_PARAMETERS,
         		EYESIS_DCT,
         		THREADS_MAX, DEBUG_LEVEL, UPDATE_STATUS);
@@ -2743,36 +2682,24 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
         int tilesX = DBG_IMP.getWidth()/DCT_PARAMETERS.dct_size - 1;
         System.out.println("tilesX="+tilesX);
         System.out.println("tilesY="+tilesY);
-        double [][] dct_dc = new double [dctdc_data.length][];
-        double [][] dct_ac = new double [dctdc_data.length][];
-        for (int chn = 0; chn < dct_dc.length; chn++) {
-        	dct_dc[chn] = image_dtt.lapped_dct_dcac(
-        			false, //       out_ac, // false - output DC, true - output AC
-        			dctdc_data [chn],
-        			THREADS_MAX,
-        			DEBUG_LEVEL);
-        	dct_ac[chn] = image_dtt.lapped_dct_dcac(
-        			true, //       out_ac, // false - output DC, true - output AC
+        double [][] dct = new double [dctdc_data.length][];
+        for (int chn = 0; chn < dct.length; chn++) {
+        	dct[chn] = image_dtt.lapped_dct_dbg(
         			dctdc_data [chn],
         			THREADS_MAX,
         			DEBUG_LEVEL);
         }
 //        System.out.println("dct_dc.length="+dct_dc.length+" dct_ac.length="+dct_ac.length);
         if (DEBUG_LEVEL > 0){
-        	SDFA_INSTANCE.showArrays(dct_ac,
+        	SDFA_INSTANCE.showArrays(dct,
         			tilesX*DCT_PARAMETERS.dct_size,
         			tilesY*DCT_PARAMETERS.dct_size,
         			true,
-        			DBG_IMP.getTitle()+"-DCT_AC");  
-        	SDFA_INSTANCE.showArrays(dct_dc,
-        			tilesX,
-        			tilesY,
-        			true,
-        			DBG_IMP.getTitle()+"-DCT_DC");
+        			DBG_IMP.getTitle()+"-DCT");  
         }
         double [][] idct_data = new double [dctdc_data.length][];
         for (int chn=0; chn<idct_data.length;chn++){
-        	idct_data[chn] = image_dtt.lapped_idctdc(
+        	idct_data[chn] = image_dtt.lapped_idct(
         			dctdc_data[chn],                  // scanline representation of dcd data, organized as dct_size x dct_size tiles  
         			DCT_PARAMETERS.dct_size,        // final int
         			DCT_PARAMETERS.dct_window,      //window_type
@@ -3503,14 +3430,15 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
         
         EYESIS_DCT.createDCTKernels(
         		DCT_PARAMETERS,
-/*        		
-        		EYESIS_CORRECTIONS.pixelMapping,
-*/        		
         		CONVOLVE_FFT_SIZE/2,
                 THREADS_MAX,
                 UPDATE_STATUS, // update status info
         		DEBUG_LEVEL);
-
+//"Reset DCT kernels"
+    } else if (label.equals("Reset DCT kernels")) {
+        if (EYESIS_DCT != null){
+        	EYESIS_DCT.resetDCTKernels();
+        }
     } else if (label.equals("Read DCT kernels")) {
         if (!DCT_PARAMETERS.showDialog()) return;
         if (EYESIS_DCT == null){

src/main/java/PixelMapping.java

@@ -151,23 +151,11 @@ public class PixelMapping {
     	return (this.sensors != null) && (channel>=0)  && (channel<this.sensors.length) && (this.sensors[channel]!=null);
     }
 
-/*
-    
-    public int [] channelsForSubCamera(int subCamera){
-    	if (this.sensors == null) return null;
-    	int numChannels=0;
-    	for (int i=0;i<this.sensors.length;i++) if ((this.sensors[i]!=null) &&(this.sensors[i].subcamera==subCamera)) numChannels++;
-    	int [] result=new int [numChannels];
-    	numChannels=0;
-    	for (int i=0;i<this.sensors.length;i++) if ((this.sensors[i]!=null) &&(this.sensors[i].subcamera==subCamera)) result[numChannels++]=i;
-    	return result;
-    }
-    
- */
     // Updating for nc393. subCamera here is 0..9 for Eyesis4pi393 - 0-based index of the file, so it combines physical camera (separate IP)
     // as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations
-    
+    //removeUnusedSensorData xshould be off!
     public int [] channelsForSubCamera(int subCamera){
+		System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);
 //    	ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>(); 
     	ArrayList<Point> cam_port = new ArrayList<Point>();
     	for (int i=0;i<this.sensors.length;i++)  if (this.sensors[i]!=null) {
@@ -175,6 +163,7 @@ public class PixelMapping {
     		if (!cam_port.contains(cp)){
     			cam_port.add(cp);
     		}
+    		System.out.println("this.sensors["+i+"]!=null, this.sensors[i].subcamera="+this.sensors[i].subcamera+", this.sensors[i].sensor_port="+this.sensors[i].sensor_port);
     	}
     	Point [] cam_port_arr = cam_port.toArray(new Point[0]);
 		Arrays.sort(cam_port_arr, new Comparator<Point>() {
@@ -183,9 +172,7 @@ public class PixelMapping {
 				return (o1.x>o2.x)? 1:((o1.x < o2.x)?-1:(o1.y > o2.y)? 1:((o1.y < o2.y)?-1:0)); 
 			}
 		});
-//		for (int i=0; i<cam_port_arr.length;i++){
-//			System.out.println("----- physical camera #"+cam_port_arr[i].x+", sensor_port="+cam_port_arr[i].y);
-//		}
+		// debugging:
 		System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);
 		if (subCamera >= cam_port_arr.length) {
 			System.out.println("Error: Subcamera "+subCamera+" > that total namera of sensor ports in the system = "+cam_port_arr.length);