Updated to restore first stage of the UAS detection

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

@@ -1724,6 +1724,7 @@ public class CalibrationIllustration {
 		int last_seq_size = 0;
 		double last_ts =    0.0;
 		String seq_name =   "";
+		int num_seqs = 1;
 		while (true) {
 			boolean some_left = false;
 			for (int si = 0; si < scenePaths.length;si++) {
@@ -1788,6 +1789,7 @@ public class CalibrationIllustration {
 						((seq_len > 0) && (last_seq_size >= seq_len)) ||
 						((seq_gap > 0.0) && ((cs.ts - last_ts) >= seq_gap))
 						) {
+					num_seqs++;
 					seq_name = cs.getName();
 				}
 				last_ts = cs.ts;
@@ -1799,7 +1801,7 @@ public class CalibrationIllustration {
 			filteredScenesList.add(cs); // modified version
 			
 		}
-		System.out.println("Selected "+(filteredScenesList.size())+" scenes");
+		System.out.println("Selected "+(filteredScenesList.size())+" scenes, "+num_seqs+" sequences=");
 		return filteredScenesList.toArray(new CapturedScene[0]);
 	}
 

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

@@ -55,6 +55,7 @@ import ij.gui.GenericDialog;
 
 public class EyesisCorrectionParameters {
     public static class CorrectionParameters{
+    	public static boolean MKDIRS_ALLOW = true; // make false for safer mode
     	public static final String [] KEY_DIRS= {
     			"rootDirectory",    // 0
     			"sourceDirectory",  // 1
@@ -1832,9 +1833,14 @@ public class EyesisCorrectionParameters {
             			File dir_file = new File(dir_path.toString());
             			if ((i != KEY_INDEX_UAS_LOGS) && (i != KEY_INDEX_SKY_MASK)) { // cuasUasLogs, cuasSkyMask are files, not directories
             				if (!dir_file.exists()) {
-            					System.out.println(KEY_DIRS[i]+" directory "+dir_path.toString()+" does not exist, ignoring "+seq_str);
-            					System.out.println("Please run:\nmkdir -p "+dir_path.toString());
-            					return null;
+            					if (MKDIRS_ALLOW) {
+            						dir_file.mkdirs();
+                					System.out.println("Created data dirtectory "+dir_path.toString());
+            					} else {
+            						System.out.println(KEY_DIRS[i]+" directory "+dir_path.toString()+" does not exist, ignoring "+seq_str);
+            						System.out.println("Please run:\nmkdir -p "+dir_path.toString());
+            						return null;
+            					}
             				}
             			}
             			dir_string =  dir_path.toString();

src/main/java/com/elphel/imagej/cuas/CorrectionFPN.java

@@ -760,7 +760,7 @@ public class CorrectionFPN {
 
 		for (int nscene =  first_index; nscene <= last_index ; nscene++) { // was reversed ***
 			if (debugLevel > -3) {
-				System.out.println ("Processing scene "+nscene+" ("+quadCLTs[nscene].getImageName()+"). Last is "+last_index);
+				System.out.println ("Processing scene "+nscene+" ("+quadCLTs[nscene].getImageName()+"). Last is "+last_index+ "(integer number of full rotations).");
 			}
 			double [][][] diff_src_synth_weights = backPropagate(
 					clt_parameters,        // CLTParameters     clt_parameters,

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

@@ -1506,7 +1506,7 @@ min_str_neib_fpn	0.35
 		gd.addNumericField("Master timestamp",                      this.ims_master_ts, 6,20,"s",
 				"Master timestamp (used in image names) corresponding to the local timestamp above.");
 		gd.addNumericField("Master clock correction",               1e6*this.ims_master_scale, 6,20,"ppm",
-				"Relastive master clock duration (master_period-local_period)/master_period, parts per million.");
+				"Relative master clock duration (master_period-local_period)/master_period, parts per million.");
 		
 		gd.addMessage  ("Extracting vertical from the IMS data");
 		gd.addCheckbox ("Calculate and set vertical direction (imsv_xyz)",this.imsv_calc,

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

@@ -3273,7 +3273,7 @@ public class OpticalFlow {
 			){
 		final int tilesX = tp.getTilesX();
 		final int tilesY = tp.getTilesY();
-		final int dbg_nTile = dbg_tileY * tilesX + dbg_tileX;
+		final int dbg_nTile = -(dbg_tileY * tilesX + dbg_tileX);
 		final int tileSize = tp.getTileSize();
 //		final double tileSize2 = tileSize * 2;
 		final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
@@ -5199,6 +5199,17 @@ public class OpticalFlow {
 		QuadCLT center_CLT = null; // used for CUAS - rotation center
 		// See if build_ref_dsi is needed
 		if (!build_ref_dsi) {
+			// Added 03.25.26 - for cuas ended up w/o jp4 copy, when processing the second sequence
+			TwoQuadCLT.copyJP4src( // actually there is no sense to process multiple image sets. Combine with other
+					// processing?
+					set_channels[last_index].set_name, // String set_name
+					quadCLT_main, // QuadCLT quadCLT_main,
+					null, // QuadCLT quadCLT_aux,
+					null, // QuadCLT quadCLT_this,
+					clt_parameters, // EyesisCorrectionParameters.DCTParameters dct_parameters,
+					true, // boolean                                  skip_existing,
+					true, // false, // boolean                                  search_KML,
+					debugLevel);
 			// try reading full
 			quadCLTs[last_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // will conditionImageSet copies quat_corr from this
 					set_channels[last_index].set_name,
@@ -5211,27 +5222,8 @@ public class OpticalFlow {
 				parent_clt_name = cuas_centers[0]; // may be ==""
 			}
 			if (use_cuas  && (cuas_centers != null)) { // (parent_clt_name != null)) { //  && (parent_clt_name.length() > 0)) {
-				if (quadCLTs[last_index] == null) {// happens if no files are copied (they were copied with build_ref_dsi, not needed now
-					TwoQuadCLT.copyJP4src( // actually there is no sense to process multiple image sets. Combine with other
-							// processing?
-							set_channels[last_index].set_name, // String set_name
-							quadCLT_main, // QuadCLT quadCLT_main,
-							null, // QuadCLT quadCLT_aux,
-							null, // QuadCLT quadCLT_this,
-							clt_parameters, // EyesisCorrectionParameters.DCTParameters dct_parameters,
-							true, // boolean                                  skip_existing,
-							true, // false, // boolean                                  search_KML,
-							debugLevel);
-					quadCLTs[last_index] = (QuadCLT) quadCLT_main.spawnNoModelQuadCLT( // will conditionImageSet
-							set_channels[last_index].set_name,
-							clt_parameters,
-							colorProcParameters, //
-							threadsMax,
-							debugLevel-2);
-					quadCLTs[last_index].saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU) and Geometry
-				}
 				System.out.println("cuas mode, verifying that all scenes have files copied - optimize"); // multithreaded?
-				int [] scene_range = {0, last_index - 1};
+				int [] scene_range = {0, last_index - 1}; // all but last
 				TwoQuadCLT.copyJP4src(
 						set_channels,   // final SetChannels []                     set_channels,
 						scene_range,    // final int []                             range, // [earlies, latest]
@@ -5241,15 +5233,6 @@ public class OpticalFlow {
 						true, // boolean                                  skip_existing,
 						true, // false, // boolean                                  search_KML,
 						debugLevel);
-/*
-				QuadCLT.copyJP4src(
-						clt_parameters, // final CLTParameters   clt_parameters,
-						quadCLTs,       // final QuadCLT []      quadCLTs,
-						scene_range,    // final int []          range, // [earlies, latest]
-						true,           // boolean                                  skip_existing,					
-						true,           // boolean                                  search_KML,
-						debugLevel);   // final int             debugLevel) { // throws Exception
-*/				
 				double []   dbg_weights = cuas_debug ? new double [quadCLTs[last_index].getTilesX() * quadCLTs[last_index].getTilesY()] : null;
 				String parent_or_null = ((parent_clt_name != null) && (parent_clt_name.length()>0)) ? parent_clt_name : null;  
 				boolean         ignore_this =    (parent_or_null != null) ? clt_parameters.imp.cuas_reset_first : false;
@@ -5269,8 +5252,8 @@ public class OpticalFlow {
 					if (cuas_debug) { // show_clt && !clt_parameters.batch_run) {
 						ImagePlus imp_weights = ShowDoubleFloatArrays.makeArrays( // all 0-s
 								dbg_weights,
-								quadCLTs[last_index].getTileProcessor().getTilesX(),
-								quadCLTs[last_index].getTileProcessor().getTilesY(),
+								quadCLTs[last_index].getTilesX(),
+								quadCLTs[last_index].getTilesY(),
 								quadCLTs[last_index].getImageName()+"-restoreCenterClt-weights");
 						if (imp_weights != null) {
 							String suffix ="-RESTORE_CENTER_CLT-WEIGHTHS";

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

@@ -181,10 +181,6 @@ public class QuadCLT extends QuadCLTCPU {
      */
 	public double [][] convertCenterClt(
 			float [][] fclt){ // may be null 
-//		if (getCenterClt() == null) {
-//			System.out.println("convertCenterClt(): not a center CLT");
-//			return null;
-//		}
 		int sensor_mask_clt = 1; // just one
 		setQuadClt();
 		int tilesX = getTilesX();
@@ -208,28 +204,21 @@ public class QuadCLT extends QuadCLTCPU {
 				sensor_mask_clt, // final int         sensor_mask,
                 wh,              // null, // int []  wh,
                 false);          // boolean use_reference
-/*		
-		float [][]  fpix = getComboFromTD(
-				-1, // final int                 sensor_mask, // only if merge_channels
-				false, // final boolean             merge_channels,
-				null, // final int []              whc, // if int[2], will return width, height
-				false); // final boolean             use_reference){
-				*/
-
-		
-		double [][] dbg = renderDoubleFromTDMono (
-				-1, // final int         sensor_mask,
-                wh,              // null, // int []  wh,
-                false);          // boolean use_reference
-
-		System.out.println("###  convertCenterClt(): result={"+result[0][0]+","+result[0][1]+","+result[0][2]+","+result[0][3]+", dbg.length="+dbg.length);
-		ShowDoubleFloatArrays.showArrays(
-				dbg,
-				wh[0],
-				wh[1],
-				true,
-				"convertCenterClt_test");
-		
+		boolean debug_convertCenterClt_test = false;
+		if (debug_convertCenterClt_test) {
+			double [][] dbg = renderDoubleFromTDMono (
+					-1, // final int         sensor_mask,
+					wh,              // null, // int []  wh,
+					false);          // boolean use_reference
+
+			System.out.println("###  convertCenterClt(): result={"+result[0][0]+","+result[0][1]+","+result[0][2]+","+result[0][3]+", dbg.length="+dbg.length);
+			ShowDoubleFloatArrays.showArrays(
+					dbg,
+					wh[0],
+					wh[1],
+					true,
+					"convertCenterClt_test");
+		}
 		return result;
 	}
 	

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

@@ -551,7 +551,11 @@ public class QuadCLTCPU {
 		}
 		// Read parent (cumulative if possible) data if full_path is provided
 		CuasData parentCuasData = null;
+		if (center_CLT == null) {
+			System.out.println("Gave up trying to read this CenterCLT, saved earlier");
+		}
 		if (full_path != null) { // if full path provided, but something went wrong with cuasData or dsi_parent - return null
+			System.out.println("Trying to read parent CenterCLT");
 			parentCuasData = CuasData.getCuasData( // need cumulative here!
 					true,            // boolean try_cumul,  // and save as such if only old style existed
 					full_path,       // String  full_path,  // ends with /vxx
@@ -1745,7 +1749,8 @@ public class QuadCLTCPU {
        		quat_ims_cam=Imx5.applyQuaternionToQuaternion(quat_corr, quat_ims_cam, false);
        	} 
        	if (did_ins_2 == null) {
-       		System.out.println("getDxyzatrIms(): did_ins_2=null");
+       		System.out.println("getDxyzatrIms(): did_ins_2=null for "+getImageName());
+       		return null;
        	}
     	double [] double_uvw =  did_ins_2.getUvw();
     	if ((double_uvw[0] == 0.0) && (double_uvw[1] == 0.0) && (double_uvw[2] == 0.0)) {
@@ -1985,6 +1990,9 @@ public class QuadCLTCPU {
     	return scenes_xyzatr;
     }
 
+    public boolean hasIns() {
+    	return (did_ins_2 != null);
+    }
 
     public double [] getLla() {
     	return did_ins_2.lla;
@@ -6292,6 +6300,16 @@ LogTee.clearSceneLog();   // stop per‑scene logging
 		return this; //  can only be QuadCLT instance
 	}
 	
+	public boolean hasSrcFiles() {
+		String jp4_copy_path= correctionsParameters.selectX3dDirectory(
+				this.image_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+				correctionsParameters.jp4SubDir,
+				true,  // smart,
+				true); // false); // true);  //newAllowed, // save
+		int num_src_files=correctionsParameters.selectSourceFileInSet(jp4_copy_path, -5).length;
+		return (num_src_files >= getNumSensors());
+	}
+	
 	public QuadCLTCPU restoreNoModel(
 			CLTParameters        clt_parameters,
 			ColorProcParameters  colorProcParameters,

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

@@ -2883,7 +2883,7 @@ if (debugLevel > -100) return true; // temporarily !
 	
 	public static void copyJP4src(
 			final SetChannels []                     set_channels,
-			final int []                             range, // [earlies, latest]
+			final int []                             range, // [earliest, latest]
 			final QuadCLT                            quadCLT_main,  // tiles should be set
 			final QuadCLT                            quadCLT_aux,
 			final CLTParameters                      clt_parameters,
@@ -8833,7 +8833,7 @@ if (debugLevel > -100) return true; // temporarily !
 
 						// trying re-using reference scenes list
 						int [] next_first_last_index = null;
-						if (keep_segments) {
+						if (keep_segments && !use_cuas) { // no segments for suas
 							if( (scene_names != null) && (index_scenes[0] != null)) {
 								if (ref_scene_names == null) { // proceesed first (latest by ts) segment
 									ref_scene_names = index_scenes[0].getRefScenes();
@@ -8864,7 +8864,7 @@ if (debugLevel > -100) return true; // temporarily !
 								}
 							}
 						}
-						if (next_first_last_index == null) {
+						if ((next_first_last_index == null) && !use_cuas) { 
 							// testing half-step
 							System.out.println("Calculating next segment's indices.");
 							if (start_ref_pointers[0] >= (min_num_scenes-1)) { // maybe just >=0 here?