Cleanup, improving photometry equalization

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -366,11 +366,16 @@ public class CLTParameters {
 	public double     fom_inf_range  =    0.8; // 0.5
 	
 	// Photometric calibration (move elsewhere)?
-	public boolean    photo_en =                      false; // perform photogrammetric calibration to equalize pixel values
+	public boolean    photo_en =                      false; // perform photogrammetric calibration to equalize pixel values and update config
+	public boolean    photo_each =                    true;  // perform photogrammetric calibration for each series ref scene and config
+	public boolean    photo_to_main =                 true;  // propagate scene sequence photometrics to the main instance to be applied
+	                                                         // to the next sequence and saved with corr-xml configuration. It is always
+	                                                         // propagated when calibration is run manually with photo_en = true
 	public int        photo_num_full =                3;     // Number of full recalibrations with re-processing of the images  
 	public int        photo_num_refines =             3;     // Calibrate, remove outliers, recalibrate, ... 
 	public double     photo_min_strength =            0.0;   // maybe add to filter out weak tiles
 	public double     photo_max_diff =                40.0;  // To filter mismatches. Normal (adjusted) have RMSE ~9
+	public int        photo_order =                   2;     // Approximation order: 0 - just offset, 1 - linear, 2 - quadratic
 	public boolean    photo_debug =                   false; // Generate images and text
 	
 	
@@ -1355,10 +1360,13 @@ public class CLTParameters {
 		properties.setProperty(prefix+"fom_inf_range",              this.fom_inf_range+"");
 		
 		properties.setProperty(prefix+"photo_en",                   this.photo_en+"");            // boolean
+		properties.setProperty(prefix+"photo_each",                 this.photo_each+"");          // boolean
+		properties.setProperty(prefix+"photo_to_main",              this.photo_to_main+"");       // boolean
 		properties.setProperty(prefix+"photo_num_full",             this.photo_num_full+"");      // int
 		properties.setProperty(prefix+"photo_num_refines",          this.photo_num_refines+"");   // int
 		properties.setProperty(prefix+"photo_min_strength",         this.photo_min_strength+"");  // double
 		properties.setProperty(prefix+"photo_max_diff",             this.photo_max_diff+"");      // double
+		properties.setProperty(prefix+"photo_order",                this.photo_order+"");         // int
 		properties.setProperty(prefix+"photo_debug",                this.photo_debug+"");         // boolean
 		
 		properties.setProperty(prefix+"show_textures",              this.show_textures+"");
@@ -2219,10 +2227,13 @@ public class CLTParameters {
 		if (properties.getProperty(prefix+"fom_inf_range")!=null)                 this.fom_inf_range=Double.parseDouble(properties.getProperty(prefix+"fom_inf_range"));
 		
 		if (properties.getProperty(prefix+"photo_en")!=null)             this.photo_en=Boolean.parseBoolean(properties.getProperty(prefix+"photo_en"));		
+		if (properties.getProperty(prefix+"photo_each")!=null)           this.photo_each=Boolean.parseBoolean(properties.getProperty(prefix+"photo_each"));		
+		if (properties.getProperty(prefix+"photo_to_main")!=null)        this.photo_to_main=Boolean.parseBoolean(properties.getProperty(prefix+"photo_to_main"));		
 		if (properties.getProperty(prefix+"photo_num_full")!=null)       this.photo_num_full=Integer.parseInt(properties.getProperty(prefix+"photo_num_full"));
 		if (properties.getProperty(prefix+"photo_num_refines")!=null)    this.photo_num_refines=Integer.parseInt(properties.getProperty(prefix+"photo_num_refines"));
 		if (properties.getProperty(prefix+"photo_min_strength")!=null)   this.photo_min_strength=Double.parseDouble(properties.getProperty(prefix+"photo_min_strength"));
 		if (properties.getProperty(prefix+"photo_max_diff")!=null)       this.photo_max_diff=Double.parseDouble(properties.getProperty(prefix+"photo_max_diff"));
+		if (properties.getProperty(prefix+"photo_order")!=null)          this.photo_order=Integer.parseInt(properties.getProperty(prefix+"photo_order"));		
 		if (properties.getProperty(prefix+"photo_debug")!=null)          this.photo_debug=Boolean.parseBoolean(properties.getProperty(prefix+"photo_debug"));		
 		
 		if (properties.getProperty(prefix+"show_textures")!=null)                 this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
@@ -3218,6 +3229,11 @@ public class CLTParameters {
  		gd.addMessage  ("It is applied when the source files are read.");
 		gd.addCheckbox ("Enable photometric calibration",            this.photo_en,
 				"Equalize per- sensor gains and offsets. Requires disparity map. Save to reference scene and with current scene (to .corr-zml).");
+		gd.addCheckbox ("Re-calibrate photometric for each series",  this.photo_each,
+				"Equalize per- sensor gains and offsets for each reference scene. Requires disparity map. Save to reference scene and with current scene (to .corr-xml).");
+		gd.addCheckbox ("Propagate per-series to main",              this.photo_to_main,
+				"Propagate scene sequence photometrics to the main instance to be applied to the next sequence and saved with corr-xml configuration."+
+				"\nIt is always propagated when calibration is run manually with photo_en = true.");
 		gd.addNumericField("Full photometric (re)calibrations",      this.photo_num_full, 0,3,"",
 				"Full recalibratrions include re-importing raw images with updated offsets/gains");
 		gd.addNumericField("Refines",                                this.photo_num_refines, 0,3,"",
@@ -3226,7 +3242,10 @@ public class CLTParameters {
 				"Do not use weak tiles.");
 		gd.addNumericField("Maximal channel mismatch",               this.photo_max_diff, 5,7,"",
 				"Detect (and remove outliers). Adjusted images have RMSE ~9 counts.");
-		gd.addCheckbox ("Debug pphotometric calibration",            this.photo_debug,
+
+		gd.addNumericField("Approximation polynomial order",         this.photo_order, 0,3,"",
+				"0 - only offset, 1 - linear, 2 - quadratic");
+		gd.addCheckbox ("Debug photometric calibration",             this.photo_debug,
 				"Generate debug images an text output.");
 		
 		
@@ -4225,10 +4244,13 @@ public class CLTParameters {
 		this.fom_inf_range=         gd.getNextNumber();
 		
  		this.photo_en =                 gd.getNextBoolean();
+ 		this.photo_each =               gd.getNextBoolean();
+ 		this.photo_to_main =            gd.getNextBoolean();
 		this.photo_num_full =     (int) gd.getNextNumber();
 		this.photo_num_refines =  (int) gd.getNextNumber();
 		this.photo_min_strength =       gd.getNextNumber();
 		this.photo_max_diff =           gd.getNextNumber();
+		this.photo_order =        (int) gd.getNextNumber();
 		this.photo_debug =              gd.getNextBoolean();
 		
 		this.show_textures=         gd.getNextBoolean();

src/main/java/com/elphel/imagej/readers/ImagejJp4Tiff.java

@@ -502,6 +502,35 @@ public class ImagejJp4Tiff {
 		return pixels;
 	}
 	
+	public static boolean needsFix000E6410C435(ImagePlus imp) {
+		String prefix = "STD_";
+		String serial = (String) imp.getProperty(prefix+"Serial_Number");
+		if ((serial == null) || !serial.equals(FIXCH6_SERIAL)) {
+			return false; // wrong camera 
+		}
+		String schannel = ((String) imp.getProperty(prefix+"PageNumber")).substring(0,1);
+		if ((schannel == null) || (Integer.parseInt(schannel) != FIXCH6_CHANNEL)) {
+			return false; // wrong channel
+		}		
+		String sfdate = (String) imp.getProperty(prefix+"DateTime");
+		sfdate = sfdate.replaceFirst(":", "-");
+		sfdate = sfdate.replaceFirst(":", "-")+".000";
+		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss.SSS");
+		try {
+			Date startDate = dateFormat.parse(FIXCH6_EARLIEST);
+			Date endDate =   dateFormat.parse(FIXCH6_LATEST);
+			Date fileDate =  dateFormat.parse(sfdate);
+			if (fileDate.before(startDate) || fileDate.after(endDate)) {
+				return false; // too early or too late 
+			}
+		} catch (ParseException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return true;
+	}
+	
+	
 	// fixing "00:0E:64:10:C4:35" camera
 	public int fix000E6410C435(
 			Hashtable<String, Object> meta_hash,

src/main/java/com/elphel/imagej/tileprocessor/CLTPass3d.java

@@ -1060,6 +1060,9 @@ public class CLTPass3d{
 		}
 		public int setTileOpDisparity(
 				double []  disparity) {
+			if (disparity== null) {
+				disparity=new double[tileProcessor.getTilesX() * tileProcessor.getTilesY()]; // all defined, infinity 
+			}
 			boolean [] selection = new boolean [disparity.length];
 			for (int i = 0; i < disparity.length; i++) {
 				selection[i] = !Double.isNaN(disparity[i]);

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

@@ -4039,10 +4039,14 @@ public class OpticalFlow {
 
     	//boolean calibrate_photometric =      true;
     	boolean  photo_en =                  clt_parameters.photo_en; //          false; // perform photogrammetric calibration to equalize pixel values
+    	boolean  photo_each =                clt_parameters.photo_each; //        true;  // perform photogrammetric calibration to equalize pixel values
+		boolean  photo_to_main=              clt_parameters.photo_to_main; // maybe it will not be needed, it will apply this calibration to the next scene sequence
+
     	int      photo_num_full =            clt_parameters.photo_num_full; //     1;    // Number of full recalibrations with re-processing of the images  
     	int      photo_num_refines =         clt_parameters.photo_num_refines; //  3;    // Calibrate, remove outliers, recalibrate, ... 
     	double   photo_min_strength =        clt_parameters.photo_min_strength; // 0.0;  // maybe add to filter out weak tiles
     	double   photo_max_diff =            clt_parameters.photo_max_diff; //    40.0;  // To filter mismatches. Normal (adjusted) have RMSE ~9
+    	int      photo_order =               clt_parameters.photo_order;
     	boolean  photo_debug =               clt_parameters.photo_debug; //       false; // Generate images and text
     	
     	boolean show_dsi_image =             clt_parameters.imp.show_ranges && !batch_mode;
@@ -4202,7 +4206,9 @@ public class OpticalFlow {
 				build_ref_dsi = true;
 			}
 		}
-		
+		if (!build_ref_dsi && (quadCLTs[ref_index] != null)) {
+			quadCLTs[ref_index].restoreInterProperties(null, false, debugLevel); //null
+		}
 		// 1. Reference scene DSI
 		while ((quadCLTs[ref_index] == null) || (quadCLTs[ref_index].getBlueSky() == null)) { // null
 			if (build_ref_dsi) {
@@ -4265,6 +4271,147 @@ public class OpticalFlow {
 				} else {
 					dsi[TwoQuadCLT.DSI_STRENGTH_AUX] =      aux_last_scan[1];
 				}
+				// perform photometric here, after first DSI
+				
+				
+
+				if (photo_each  && !quadCLTs[ref_index].isPhotometricThis()) {
+					if (debugLevel > -3) {
+						System.out.println("**** Running photometric equalization for "+quadCLTs[ref_index].getImageName()+
+								", current was from scene "+quadCLTs[ref_index].getPhotometricScene()+" ****");
+					}
+				
+					// preparing same format as after combo, filling in only needed data
+					double [][] ds_photo = new double[TwoQuadCLT.DSI_LENGTH][];
+					ds_photo[OpticalFlow.COMBO_DSN_INDX_DISP] =        dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA];
+					ds_photo[OpticalFlow.COMBO_DSN_INDX_DISP_BG_ALL] = dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA];
+					ds_photo[OpticalFlow.COMBO_DSN_INDX_STRENGTH] =    dsi[TwoQuadCLT.DSI_STRENGTH_AUX];
+						
+					boolean photo_each_debug = false; // true; // false;
+					boolean photo_each_debug2 = false; // true; // false;
+					for (int nrecalib = 0; nrecalib < photo_num_full; nrecalib++) { // maybe need to correct just offsets?
+						int poly_order = photo_order;
+						if ((poly_order > 1) && (nrecalib == 0)) {
+							poly_order = 1;
+						}
+						
+						QuadCLT.calibratePhotometric2(
+								clt_parameters,           // CLTParameters     clt_parameters,
+								quadCLTs[ref_index],      // final QuadCLT     ref_scene, will set photometric calibration to this scene
+								photo_min_strength,       // final double      min_strength,
+								photo_max_diff,           // final double      max_diff,    // 30.0
+								poly_order,               // final int         photo_order, // 0 - offset only, 1 - linear, 2 - quadratic
+								photo_num_refines,        // final int         num_refines, // 2
+								ds_photo,                 // combo_dsn_final_filtered, // final double [][] combo_dsn_final,     // double [][]    combo_dsn_final, // dls,			
+								threadsMax,               // int               threadsMax,
+								photo_each_debug);        //final boolean     debug)
+						// copy offsets to the current to be saved with other properties. Is it correct/needed?
+						quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
+								null, // String path,             // full name with extension or w/o path to use x3d directory
+								debugLevel+1);
+						quadCLTs[ref_index].setDSI(dsi); // try to avoid saving, will complain on restoring, but keep
+//						quadCLTs[ref_index].saveDSIAll ( // will reload during spawnQuadCLT
+//								"-DSI_MAIN", // String suffix, // "-DSI_MAIN"
+//								dsi);
+						
+//						quadCLT_main.setLwirOffsets(quadCLTs[ref_index].getLwirOffsets());
+//						quadCLT_main.setLwirScales (quadCLTs[ref_index].getLwirScales ());
+//						quadCLT_main.setLwirScales2(quadCLTs[ref_index].getLwirScales2());
+//						quadCLT_main.setPhotometricScene(quadCLTs[ref_index].getPhotometricScene());
+
+						// Re-read reference and other scenes using new offsets	
+//						quadCLTs[ref_index].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
+						quadCLTs[ref_index].setQuadClt(); // should work even when the data is new for the same scene
+						quadCLTs[ref_index] = (QuadCLT) quadCLT_main.spawnQuadCLT( // restores dsi from "DSI-MAIN"
+								set_channels[ref_index].set_name,
+								clt_parameters,
+								colorProcParameters, //
+								threadsMax,
+								debugLevel);
+						// Re-measure and update (is it needed?)
+						CLTPass3d scan = new CLTPass3d(quadCLTs[ref_index].tp);
+						scan.setTileOpDisparity(dsi[TwoQuadCLT.DSI_DISPARITY_AUX]);
+						quadCLTs[ref_index].setQuadClt(); // just in case ?
+						quadCLTs[ref_index].CLTMeas( // perform single pass according to prepared tiles operations and disparity
+								clt_parameters, // EyesisCorrectionParameters.CLTParameters           clt_parameters,
+								scan,           // final CLTPass3d   scan,
+								false,          // final boolean     save_textures,
+								false,          // final boolean       need_diffs,     // calculate diffs even if textures are not needed 
+								0,              // final int         clust_radius,
+								true,           // final boolean     save_corr,
+								true, // false,          // final boolean     run_lma, // =    true;
+								0.0,            // final double        max_chn_diff, // filter correlation results by maximum difference between channels
+								-1.0,           // final double        mismatch_override, // keep tile with large mismatch if there is LMA with really strong correlation
+								threadsMax,     // final int         threadsMax,  // maximal number of threads to launch
+								updateStatus,   // final boolean     updateStatus,
+								debugLevel-2);  // final int         debugLevel);
+						double [][] aux_new_scan = TileProcessor.getDSLMA(
+								scan,
+								false); // boolean force_final);
+						dsi[TwoQuadCLT.DSI_DISPARITY_AUX] =     aux_new_scan[0]; // compare diffs
+						dsi[TwoQuadCLT.DSI_STRENGTH_AUX] =      aux_new_scan[1];
+						dsi[TwoQuadCLT.DSI_DISPARITY_AUX_LMA] = aux_new_scan[2];
+						// Re-measure and update from BG spread and average in dsi
+						CLTPass3d bgscan = new CLTPass3d(quadCLTs[ref_index].tp);
+						bgscan.setTileOpDisparity(null);
+						quadCLTs[ref_index].setQuadClt(); // just in case ?
+						quadCLTs[ref_index].CLTMeas( // perform single pass according to prepared tiles operations and disparity
+								clt_parameters, // EyesisCorrectionParameters.CLTParameters           clt_parameters,
+								bgscan,           // final CLTPass3d   scan,
+								true, // false,          // final boolean     save_textures,
+								true, // false,          // final boolean       need_diffs,     // calculate diffs even if textures are not needed 
+								0,              // final int         clust_radius,
+								true,           // final boolean     save_corr, IS IT NEEDED?
+								false,          // final boolean     run_lma, // =    true;
+								0.0,            // final double        max_chn_diff, // filter correlation results by maximum difference between channels
+								-1.0,           // final double        mismatch_override, // keep tile with large mismatch if there is LMA with really strong correlation
+								threadsMax,     // final int         threadsMax,  // maximal number of threads to launch
+								updateStatus,   // final boolean     updateStatus,
+								debugLevel-2);  // final int         debugLevel);
+						
+						if (photo_each_debug2) {
+							quadCLTs[ref_index].tp.showScan(bgscan, quadCLTs[ref_index].getImageName()+"-bgscan-"+nrecalib); // nrecalib
+							quadCLTs[ref_index].tp.showScan(scan,   quadCLTs[ref_index].getImageName()+"-scan-"+nrecalib);
+						}
+						dsi[TwoQuadCLT.DSI_SPREAD_AUX] = bgscan.getSecondMax(); //    //aux_bg_scan[3];
+						dsi[TwoQuadCLT.DSI_AVGVAL_AUX] = bgscan.getAvgVal(); //aux_bg_scan[4];
+						
+						quadCLTs[ref_index].setDSI(dsi); // Restore known dsi
+						quadCLTs[ref_index].setBlueSky(ref_blue_sky);
+						quadCLTs[ref_index].setDSRBG(
+								clt_parameters, // CLTParameters  clt_parameters,
+								threadsMax,     // int            threadsMax,  // maximal number of threads to launch
+								updateStatus,   // boolean        updateStatus,
+								debugLevel);    // int            debugLevel)
+//						ers_reference = quadCLTs[ref_index].getErsCorrection();
+					}
+					/*
+					// propagate to other scenes in this sequence HERE THEY ARE NOT YET READ
+					for (int scene_index =  ref_index - 1; scene_index >= earliest_scene ; scene_index--) {
+						//						quadCLTs[scene_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // restores image data
+						// to include ref scene photometric calibration
+						quadCLTs[scene_index] = quadCLTs[ref_index].spawnNoModelQuadCLT( // restores image data
+								set_channels[scene_index].set_name,
+								clt_parameters,
+								colorProcParameters, //
+								threadsMax,
+								debugLevel-2);
+					}
+					*/
+				} else {
+					System.out.println("(Re)using photometric calibration from this sequence reference "+quadCLTs[ref_index].getPhotometricScene());
+					quadCLTs[ref_index].setQuadClt(); // just in case ?
+				}
+					
+				
+				
+				
+				
+				
+				
+				
+				
+				
 //				int tilesX = quadCLTs[ref_index].getTileProcessor().getTilesX();
 				boolean retry=false;
 				while (true) {
@@ -4321,6 +4468,23 @@ public class OpticalFlow {
 				quadCLTs[ref_index].set_accum(0);  // reset accumulations ("build_interscene") number
 				earliest_scene = 0;  // reset failures, try to use again all scenes
 			} else {// if (build_ref_dsi) {
+				// need to read photometric from reference scene -INTERFRAME.corr-xml, and if it exists - set and propagate to main?
+				if (photo_each  && !quadCLTs[ref_index].isPhotometricThis()) {
+					if (debugLevel > -3) {
+						System.out.println("Per-sequence photogrammetric calibration is required, but it does not exist");
+					}
+					if (photo_to_main) {
+						quadCLT_main.setLwirOffsets(quadCLTs[ref_index].getLwirOffsets());
+						quadCLT_main.setLwirScales (quadCLTs[ref_index].getLwirScales ());
+						quadCLT_main.setLwirScales2(quadCLTs[ref_index].getLwirScales2());
+						quadCLT_main.setPhotometricScene(quadCLTs[ref_index].getPhotometricScene());
+						if (debugLevel > -3) {
+							System.out.println("Propagating per-sequence photogrammetric calibration to main instance, will apply to next sequence and config file");
+						}
+					}
+				} else {
+					System.out.println("Without building reference DSI: (re)using photometric calibration from this sequence reference "+quadCLTs[ref_index].getPhotometricScene());
+				}
 				// read DSI_MAIN
 				double [][] dsi = quadCLTs[ref_index].readDsiMain();
 				if (dsi[TwoQuadCLT.DSI_SPREAD_AUX] == null) {
@@ -4362,6 +4526,7 @@ public class OpticalFlow {
 				colorProcParameters, //
 				threadsMax,
 				debugLevel);
+		quadCLTs[ref_index].setQuadClt(); // just in case ?
 		quadCLTs[ref_index].setBlueSky(ref_blue_sky);
 		
 		quadCLTs[ref_index].setDSRBG(
@@ -4387,7 +4552,9 @@ public class OpticalFlow {
 			double [] lma_rms = new double[2];
 			double [] use_atr = null;
 			for (int scene_index =  ref_index - 1; scene_index >= 0 ; scene_index--) {
-				quadCLTs[scene_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT(
+//				quadCLTs[scene_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT(
+				// to include ref scene photometric calibration
+				quadCLTs[scene_index] = quadCLTs[ref_index].spawnNoModelQuadCLT(
 						set_channels[scene_index].set_name,
 						clt_parameters,
 						colorProcParameters, //
@@ -4649,11 +4816,16 @@ public class OpticalFlow {
 							quadCLTs[ref_index], // QuadCLT        scene,
 							debugLevel); // int            debugLevel);// > 0
 			for (int nrecalib = 0; nrecalib < photo_num_full; nrecalib++) {
+				int poly_order = photo_order;
+				if ((poly_order > 1) && (nrecalib == 0)) {
+					poly_order = 1;
+				}
 				QuadCLT.calibratePhotometric2(
 						clt_parameters,           // CLTParameters     clt_parameters,
-						quadCLTs[ref_index],      // final QuadCLT     ref_scene, // now - may be null - for testing if scene is rotated ref
+						quadCLTs[ref_index],      // final QuadCLT     ref_scene, will set photometric calibration to this scene
 						photo_min_strength,       // final double      min_strength,
 						photo_max_diff,           // final double      max_diff,    // 30.0
+						poly_order,               // final int         photo_order, // 0 - offset only, 1 - linear, 2 - quadratic
 						photo_num_refines,        // final int         num_refines, // 2
 						combo_dsn_final_filtered, // final double [][] combo_dsn_final,     // double [][]    combo_dsn_final, // dls,			
 						threadsMax,               // int               threadsMax,
@@ -4662,13 +4834,13 @@ public class OpticalFlow {
 				quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
 						null, // String path,             // full name with extension or w/o path to use x3d directory
 						debugLevel+1);
-				quadCLT_main.setLwirOffsets(quadCLTs[ref_index].getLwirOffsets());
-				quadCLT_main.setLwirScales (quadCLTs[ref_index].getLwirScales ());
-				quadCLT_main.setLwirScales2(quadCLTs[ref_index].getLwirScales2());
-				quadCLT_main.setPhotometricScene(quadCLTs[ref_index].getPhotometricScene());
+//				quadCLT_main.setLwirOffsets(quadCLTs[ref_index].getLwirOffsets());
+//				quadCLT_main.setLwirScales (quadCLTs[ref_index].getLwirScales ());
+//				quadCLT_main.setLwirScales2(quadCLTs[ref_index].getLwirScales2());
+//				quadCLT_main.setPhotometricScene(quadCLTs[ref_index].getPhotometricScene());
 				
 				// Re-read reference and other scenes using new offsets	
-				quadCLTs[ref_index].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
+				quadCLTs[ref_index].setQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
 				quadCLTs[ref_index] = (QuadCLT) quadCLT_main.spawnQuadCLT( // restores dsi from "DSI-MAIN"
 						set_channels[ref_index].set_name,
 						clt_parameters,
@@ -4695,12 +4867,24 @@ public class OpticalFlow {
 						debugLevel-2);
 			}
 		} else {
+			if (debugLevel> -3) {
 				System.out.println("Using photometric calibration from scene "+quadCLTs[ref_index].getPhotometricScene());
 			}
+		}
+		// only now copy photometric to main instance
+		if (!reuse_video) {
+			quadCLT_main.setLwirOffsets(quadCLTs[ref_index].getLwirOffsets());
+			quadCLT_main.setLwirScales (quadCLTs[ref_index].getLwirScales ());
+			quadCLT_main.setLwirScales2(quadCLTs[ref_index].getLwirScales2());
+			quadCLT_main.setPhotometricScene(quadCLTs[ref_index].getPhotometricScene());
+			if (debugLevel> -3) {
+				System.out.println("Applied photometric calibration from scene "+quadCLTs[ref_index].getPhotometricScene()+
+						" to quadCLT_main, so it will be applied to the next sequences and saved in config file");
+			}
+		}
 		
 		if (test_ers) { // only debug feature
 			test_ers0 = quadCLTs.length -1; // make it always == reference !
-			
 			testERS(
 					clt_parameters, // CLTParameters clt_parameters,
 					test_ers0, // int           indx0, // reference scene in a pair
@@ -4708,7 +4892,6 @@ public class OpticalFlow {
 					//		    		double []     ref_disparity,			
 					quadCLTs, // QuadCLT []    quadCLTs,
 					debugLevel); // int           debugLevel)
-
 			System.out.println("buildSeries(): ABORTED after test_ers"); //
 			return quadCLTs[ref_index].getX3dTopDirectory();
 		}

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

@@ -2435,7 +2435,7 @@ public class QuadCLT extends QuadCLTCPU {
 				scales_new[n] = scales_old[n]/scales[n];
 				offsets_new[n] = offsets_old[n]  + offsets[n] / scales_old[n];
 			}
-			System.out.println("calibratePhotometric() Updated calibration:");
+			System.out.println("calibratePhotometric() Final calibration:");
 			for (int n = 0; n < num_sens; n++) {
 				System.out.println(String.format("%2d: %8.4f %8.6f %8.6f", n,offsets_new[n],scales_new[n], scales2_new[n]));
 			}
@@ -2452,6 +2452,7 @@ public class QuadCLT extends QuadCLTCPU {
 			final QuadCLT     ref_scene, // now - may be null - for testing if scene is rotated ref
 			final double      min_strength,
 			final double      max_diff,    // 30.0
+			final int         photo_order, // 0 - offset only, 1 - linear, 2 - quadratic
 			final int         num_refines, // 2
 			final double [][] combo_dsn_final,     // double [][]    combo_dsn_final, // dls,			
 			int               threadsMax,
@@ -2484,7 +2485,9 @@ public class QuadCLT extends QuadCLTCPU {
 					"PHOTOMETRIC",      // String            suffix,
 					threadsMax,         // int               threadsMax,
 					-2);        // final int         debugLevel);
+			if (debug) {
 				img_ref.show();
+			}
 			ImageStack imageStack = img_ref.getStack();
 			int num_sens=imageStack.getSize();
 			float [] fpixels;
@@ -2496,23 +2499,11 @@ public class QuadCLT extends QuadCLTCPU {
 					dpixels[n][i] = fpixels[i];
 				}
 			}
-			boolean quadratic = true;
-//			double [][] dpix_orig = new double[num_sens][];
-//			for (int n = 0; n < num_sens; n++) {
-//				dpix_orig[n] =  dpixels[n].clone();
-//			}					
+//			boolean quadratic = true;
 			int width =  img_ref.getWidth();
 			int height = img_ref.getHeight();
 			int len = width* height;
 			double [] avg_pix = new double [len];
-			double [] offsets = new double[dpixels.length];
-			double [] scales =  new double[dpixels.length];
-			double [] scales2 = new double[dpixels.length];
-			double    s0 =  0.0;
-			double    sx=   0.0;
-			double    sx2 = 0.0;
-			double [] sy = new double[num_sens];
-			double [] sxy = new double[num_sens];
 			boolean [] good_pix = new boolean[len];
 			double [][] pa_coeff = new double[num_sens][];
 			double min_abs_a = 1E-9;
@@ -2539,7 +2530,7 @@ public class QuadCLT extends QuadCLTCPU {
 						num_good++;
 					}
 				}
-				double [][] pa_data = new double [num_good][2];
+				double [][][] pa_data = new double [num_sens][num_good][2];
 				double [][] raw = new double [num_sens][len];
 				for (int nsens = 0; nsens < num_sens; nsens++) {
 					Arrays.fill(raw[nsens],Double.NaN); // debug only
@@ -2557,15 +2548,28 @@ public class QuadCLT extends QuadCLTCPU {
 							p= (-b + Math.sqrt(b*b - 4 * a * c))/(2 * a);
 						}
 						raw[nsens][i] = p;
-						pa_data[indx][0] = p; // dpixels[nsens][i]; 
-						pa_data[indx][1] = avg_pix[i];
+						pa_data[nsens][indx][0] = p; // dpixels[nsens][i]; 
+						pa_data[nsens][indx][1] = avg_pix[i];
 						indx++;
 					}
-					// quadratic
-					pa_coeff[nsens] =(new PolynomialApproximation(0)).polynomialApproximation1d(pa_data, quadratic ? 2 : 1);
-					double a = pa_coeff[nsens][2];
-					double b = pa_coeff[nsens][1];
-					double c = pa_coeff[nsens][0];
+					double c, b, a;
+					int poly_debug = 0;
+					if (photo_order < 1) { // zero out scales2, keep old scales (even if not normalized)
+						a = 0;
+						b = scales_old[nsens];
+						double s = 0.0;
+						for (int i = 0; i < num_good; i++) {
+							s += pa_data[nsens][i][0] - pa_data[nsens][i][1]/b; 
+						}
+						c = -s/num_good*b;
+					} else {
+					// need to balance quadratic so their average is 0	
+					// linear or quadratic
+						pa_coeff[nsens] =(new PolynomialApproximation(poly_debug)).polynomialApproximation1d(pa_data[nsens], photo_order);
+						c = pa_coeff[nsens][0];
+						b = pa_coeff[nsens][1];
+						a = (pa_coeff[nsens].length > 2) ? pa_coeff[nsens][2] : 0.0;
+					}
 					double A = a;
 					double C = -c/b;
 					if (Math.abs(a) >= min_abs_a) {
@@ -2576,17 +2580,48 @@ public class QuadCLT extends QuadCLTCPU {
 					scales_new [nsens] = B;
 					offs_new[nsens] =    C;
 				}
-				
-				if (debug) {
-					System.out.println("calibratePhotometric() nref="+nref);
-					/*
-					System.out.println(String.format("%3s %8s %8s %8s",
-							"chn","   c   ","   b   ", " 1e6*a "));
-					for (int n = 0; n < num_sens; n++) {
-						System.out.println(String.format("%2d: %8.4f %8.6f %8.6f", n,pa_coeff[n][0],pa_coeff[n][1], 1e6*pa_coeff[n][2]));
+				// Make scales_new to be (geometric) average 1.0 (except photo_order == 0), update pa_data to match
+				if (photo_order > 0) {
+					double scales_avg = 1.0;
+					for (int nsens = 0; nsens < num_sens; nsens++) {
+						scales_avg *= scales_new [nsens];
 					}
-					System.out.println();
-					*/
+					scales_avg = Math.pow(scales_avg, 1.0/num_sens);
+					for (int nsens = 0; nsens < num_sens; nsens++) {
+						scales_new [nsens] /= scales_avg;
+						scales2_new [nsens] /= scales_avg;
+						for (int i = 0; i < num_good; i++) {
+							pa_data[nsens][i][1] /= scales_avg;
+						}
+					}
+				}				
+				// make scales2 be average zero, re-run scales
+				if (photo_order > 1) {
+					double scales2_offset = 0;
+					for (int nsens = 0; nsens < num_sens; nsens++) {
+						scales2_offset += scales2_new[nsens];
+					}
+					scales2_offset /= num_sens;
+					for (int nsens = 0; nsens < num_sens; nsens++) {
+						scales2_new[nsens] -= scales2_offset;
+					}
+					// modify pa_data, re-run linear
+					for (int nsens = 0; nsens < num_sens; nsens++) {
+						for (int i = 0; i < num_good; i++) {
+							double poffs = pa_data[nsens][i][0] - offs_new[nsens];
+							pa_data[nsens][i][1] -=poffs*poffs*scales2_new[nsens];
+						}
+						pa_coeff[nsens] =(new PolynomialApproximation(0)).polynomialApproximation1d(
+								pa_data[nsens], 1);
+						double c = pa_coeff[nsens][0];
+						double b = pa_coeff[nsens][1];
+						scales_new [nsens] = b;
+						offs_new[nsens] =   -c/b;
+					}
+				}
+				
+				if (true) { // debug) { during debug,
+					System.out.println("DEBUG: calibratePhotometric() nref="+nref);
 					System.out.println(String.format("%3s %10s %8s %8s %10s %8s %8s",
 						//  "chn","   c   ","   b   ", " 1e6*a "));          
 							"chn","  offs0  ","scale0 ", "scale20","  offs "," scale ", " scale2"));
@@ -2596,9 +2631,8 @@ public class QuadCLT extends QuadCLTCPU {
 								offs_new[n],scales_new[n], 1e6*scales2_new[n]));
 					}
 					System.out.println();
-					
-					
-					
+				}
+				if (debug) {
 					double [][] diffs = new double [num_sens][len];
 					for (int n = 0; n < num_sens; n++) {
 						Arrays.fill(diffs[n], Double.NaN);
@@ -2746,10 +2780,12 @@ public class QuadCLT extends QuadCLTCPU {
 						dbg_img[i][nTile] = pXpYD[nTile][i];
 					}
 				}
+				if (mb_vectors!=null) {
 					for (int i = 0; i <2; i++) {
 						dbg_img[3 + i][nTile] =  mb_tau * mb_vectors[i][nTile];
 					}
 				}
+			}
 			(new ShowDoubleFloatArrays()).showArrays( // out of boundary 15
 					dbg_img,
 					dbg_width,

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -1253,10 +1253,11 @@ public class QuadCLTCPU {
 		if (!isLwir()) { // colorProcParameters.lwir_islwir) {
 			referenceExposures = eyesisCorrections.calcReferenceExposures(sourceFiles, debugLevel);
 		}
+		// move after restoring properties
+		/*
 		int [] channelFiles = set_channels[0].fileNumber();		
 		boolean [][] saturation_imp = (clt_parameters.sat_level > 0.0)? new boolean[channelFiles.length][] : null;
 		double []    scaleExposures = new double[channelFiles.length];
-//		ImagePlus [] imp_srcs = 
 		conditionImageSet(
 				clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
 				colorProcParameters,            //  ColorProcParameters                       colorProcParameters, //
@@ -1277,6 +1278,7 @@ public class QuadCLTCPU {
 					threadsMax,
 					1); // debugLevel); // final int       debug_level)
 		}
+		*/
 		// try to restore DSI generated from interscene if available, if not use single-scene -DSI_MAIN
 		int dsi_result = -1;
 		int max_length=OpticalFlow.COMBO_DSN_TITLES.length;
@@ -1302,11 +1304,35 @@ public class QuadCLTCPU {
 		if (dsi_result < 0) {
 				System.out.println("No DSI data for the scene "+this.getImageName()+", setting this.dsi=null");
 				setDSI(null);
-		} else {
+		}
+		// WAS: resore only if (dsi_result < 0)...  else 
 		restoreInterProperties( // restore properties for interscene processing (extrinsics, ers, ...) // get relative poses (98)
 				null, // String path,             // full name with extension or null to use x3d directory
 				false, // boolean all_properties,//				null, // Properties properties,   // if null - will only save extrinsics)
 				debugLevel);
+		
+		int [] channelFiles = set_channels[0].fileNumber();		
+		boolean [][] saturation_imp = (clt_parameters.sat_level > 0.0)? new boolean[channelFiles.length][] : null;
+		double []    scaleExposures = new double[channelFiles.length];
+		conditionImageSet(
+				clt_parameters,                 // EyesisCorrectionParameters.CLTParameters  clt_parameters,
+				colorProcParameters,            //  ColorProcParameters                       colorProcParameters, //
+				sourceFiles,                    // String []                                 sourceFiles,
+				this.image_name,                       // String                                    set_name,
+				referenceExposures,             // double []                                 referenceExposures,
+				channelFiles,                   // int []                                    channelFiles,
+				scaleExposures,                 // output  // double [] scaleExposures
+				saturation_imp,                 // output  // boolean [][]                              saturation_imp,
+				threadsMax,                     // int                                       threadsMax,
+				debugLevelInner);               // int                                       debugLevel);
+		if (noise_sigma_level != null) {
+			generateAddNoise(
+					"-NOISE",
+					ref_scene, // final QuadCLTCPU ref_scene, // may be null if scale_fpn <= 0
+					noise_sigma_level,
+					noise_variant, //final int       noise_variant, // <0 - no-variants, compatible with old code
+					threadsMax,
+					1); // debugLevel); // final int       debug_level)
 		}
 		return this; //  can only be QuadCLT instance
 	}
@@ -1933,6 +1959,14 @@ public class QuadCLTCPU {
     	setPhotometricScene(getImageName());
     }
     
+    public boolean isPhotometricThis() {
+    	if (this.photometric_scene == null) {
+    		return false;
+    	}
+    	return this.photometric_scene.equals(getImageName());
+    }
+    
+
     public void setLwirScales(double [] scales) {
     	lwir_scales = scales; // will need to update properties!
 //    	this.photometric_scene = getImageName();
@@ -2253,7 +2287,7 @@ public class QuadCLTCPU {
 			for (int d = 0; d < fine_corr[n].length; d++){
 				for (int i = 0; i < fine_corr[n][d].length; i++){
 					String name = prefix+"fine_corr_"+n+fine_corr_dir_names[d]+fine_corr_coeff_names[i];
-		  			if (properties.getProperty(name)!=null) this.fine_corr[n][d][i]=Double.parseDouble(properties.getProperty(name));
+		  			if (properties.getProperty(name)!=null) this.fine_corr[n][d][i]=Double.parseDouble(properties.getProperty(name));// null
 				}
 			}
 		}
@@ -5728,6 +5762,37 @@ public class QuadCLTCPU {
 			  double [] offsets =  getLwirOffsets();
 			  double [] scales =   getLwirScales();
 			  double [] scales2 =  getLwirScales2();
+			  int needs_fix = -1;
+			  for (int i = 0; i < imp_srcs.length; i++) {
+				  if (ImagejJp4Tiff.needsFix000E6410C435(imp_srcs[i])) {
+					  needs_fix = i;
+					  break; // only one, and always 6
+				  }
+			  }
+			  if (needs_fix >= 0) {
+				  double [] fix_offsets = channelLwirEqualize( // now only calculates offsets, does not apply
+						  channelFiles,
+						  imp_srcs,
+						  lwir_subtract_dc, // boolean      remove_dc,
+						  set_name, // just for debug messages == setNames.get(nSet)
+						  threadsMax,
+						  debugLevel);
+				  double avg_offs = 0.0;
+				  for (int i = 0; i < fix_offsets.length; i++) if (i != needs_fix) {
+					  avg_offs += fix_offsets[i];
+				  }
+				  avg_offs /= (fix_offsets.length - 1);
+				  int icorr =  (int) Math.round((avg_offs - fix_offsets[needs_fix])/4096);
+				  if (icorr != 0) {
+					  float fcorr = icorr*4096;
+					  System.out.println("Correcting "+imp_srcs[needs_fix].getTitle()+" by "+fcorr);
+					  float [] pixels = (float []) imp_srcs[needs_fix].getProcessor().getPixels();
+					  for (int i = 0; i < pixels.length; i++) {
+						  pixels[i] += fcorr;
+					  }
+				  }
+			  }
+			  
 			  channelLwirApplyEqualize( // now apply (was part of channelLwirEqualize() )
 					  channelFiles, // int [] channelFiles,
 					  imp_srcs,     // ImagePlus [] imp_srcs,
@@ -6295,16 +6360,10 @@ public class QuadCLTCPU {
 		  for (int ithread = 0; ithread < threads.length; ithread++) {
 			  threads[ithread] = new Thread() {
 				  public void run() {
-					  // for (int srcChannel=0; srcChannel < channelFiles.length; srcChannel++){
 					  for (int srcChannel = ai.getAndIncrement(); srcChannel < channelFiles.length; srcChannel = ai.getAndIncrement()) {
 						  int nFile=channelFiles[srcChannel];
 						  if (nFile >=0) {
 							  offsets[srcChannel]= avr_pix[srcChannel][0];
-//							  float fd = (float)offsets[srcChannel];
-//							  float [] pixels = (float []) imp_srcs[srcChannel].getProcessor().getPixels();
-//							  for (int i = 0; i < pixels.length; i++) {
-//								  pixels[i] -= fd;
-//							  }
 						  }
 					  }
 				  }

src/main/java/com/elphel/imagej/tileprocessor/TwoQuadCLT.java

@@ -84,6 +84,7 @@ public class TwoQuadCLT {
 	public static  int DSI_SPREAD_AUX =        10;
 	public static  int DSI_AVGVAL_MAIN =       11;
 	public static  int DSI_AVGVAL_AUX =        12;
+	public static  int DSI_LENGTH =            DSI_AVGVAL_AUX+1;
 
 	public static String DSI_COMBO_SUFFIX = "-DSI_COMBO";
 	public static String DSI_MAIN_SUFFIX =  "-DSI_MAIN";