Implementing batch mode for EO/LWIR images

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

@@ -169,6 +169,7 @@ public class EyesisCorrectionParameters {
 
     	public String mlDirectory="ml";
 
+    	public boolean  thumb_overwrite =     true;
     	public int      thumb_width =         200;
     	public int      thumb_height =        100;
     	public double   thumb_h_center =      0.5;
@@ -296,6 +297,17 @@ public class EyesisCorrectionParameters {
   			cp.clt_batch_dsi_aux=    	  this.clt_batch_dsi_aux;
   			cp.clt_batch_save_extrinsics= this.clt_batch_save_extrinsics;
   			cp.clt_batch_save_all=        this.clt_batch_save_all;
+
+
+    		cp.thumb_overwrite =        this.thumb_overwrite;
+    		cp.thumb_width =            this.thumb_width;
+    		cp.thumb_height =           this.thumb_height;
+    		cp.thumb_h_center =         this.thumb_h_center;
+    		cp.thumb_v_center =         this.thumb_v_center;
+    		cp.thumb_size =             this.thumb_size;
+    		cp.default_rating =         this.default_rating;
+
+
 		}
 
 
@@ -462,6 +474,7 @@ public class EyesisCorrectionParameters {
     		properties.setProperty(prefix+"clt_batch_save_extrinsics", this.clt_batch_save_extrinsics+"");
     		properties.setProperty(prefix+"clt_batch_save_all",        this.clt_batch_save_all+"");
 
+    		properties.setProperty(prefix+"thumb_overwrite",       this.thumb_overwrite+"");
     		properties.setProperty(prefix+"thumb_width",           this.thumb_width+"");
     		properties.setProperty(prefix+"thumb_height",          this.thumb_height+"");
     		properties.setProperty(prefix+"thumb_h_center",        this.thumb_h_center+"");
@@ -616,6 +629,7 @@ public class EyesisCorrectionParameters {
 			if (properties.getProperty(prefix+"clt_batch_save_extrinsics")!= null) this.clt_batch_save_extrinsics=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_save_extrinsics"));
 			if (properties.getProperty(prefix+"clt_batch_save_all")!= null)        this.clt_batch_save_all=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_save_all"));
 
+			if (properties.getProperty(prefix+"thumb_overwrite")!= null)     this.thumb_overwrite=Boolean.parseBoolean(properties.getProperty(prefix+"thumb_overwrite"));
 			if (properties.getProperty(prefix+"thumb_width")!=null)          this.thumb_width=Integer.parseInt(properties.getProperty(prefix+"thumb_width"));
   		    if (properties.getProperty(prefix+"thumb_height")!=null)         this.thumb_height=Integer.parseInt(properties.getProperty(prefix+"thumb_height"));
   		    if (properties.getProperty(prefix+"thumb_h_center")!=null)       this.thumb_h_center=   Double.parseDouble(properties.getProperty(prefix+"thumb_h_center"));
@@ -769,6 +783,7 @@ public class EyesisCorrectionParameters {
     		gd.addCheckbox   ("Swap top and equator images",     this.swapSubchannels01);
 
     		gd.addTab("Thumbnails","Thumbnail image generation");
+    		gd.addCheckbox("Overwrite existing thumbnail images",this.thumb_overwrite);
     		gd.addNumericField("Thumbnail image width",          this.thumb_width, 0,4,"pix",
     				"");
     		gd.addNumericField("Thumbnail image height",         this.thumb_height, 0,4,"pix",
@@ -871,6 +886,7 @@ public class EyesisCorrectionParameters {
     		this.removeUnusedSensorData= gd.getNextBoolean();
     		this.swapSubchannels01=      gd.getNextBoolean();
 
+    		this.thumb_overwrite =       gd.getNextBoolean();
     		this.thumb_width=      (int) gd.getNextNumber();
     		this.thumb_height=     (int) gd.getNextNumber();
     		this.thumb_h_center=         gd.getNextNumber();

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -705,6 +705,10 @@ private Panel panel1,
 			addButton("GPU files",                  panelClt_GPU, color_conf_process);
 			addButton("Rig8 gpu",                   panelClt_GPU, color_conf_process);
 			addButton("ShowGPU",                    panelClt_GPU, color_conf_process);
+
+			addButton("LWIR_TEST",                  panelClt_GPU, color_conf_process);
+			addButton("LWIR_ACQUIRE",               panelClt_GPU, color_conf_process);
+
 			plugInFrame.add(panelClt_GPU);
 		}
 		if (LWIR_MODE) {
@@ -730,13 +734,13 @@ private Panel panel1,
 			addButton("AUX OUT 3D",                 panelLWIR, color_process_aux);
 			addButton("Main img AUX",               panelLWIR, color_process_aux);
 			addButton("Main to AUX",                panelLWIR, color_process_aux);
-
-			addButton("LWIR_TEST",                  panelLWIR, color_conf_process);
-			addButton("LWIR_ACQUIRE",               panelLWIR, color_conf_process);
+			addButton("LWIR batch",                  panelClt4, color_process);
+//			addButton("LWIR_TEST",                  panelLWIR, color_conf_process);
+//			addButton("LWIR_ACQUIRE",               panelLWIR, color_conf_process);
 			plugInFrame.add(panelLWIR);
 		}
 		plugInFrame.pack();
-
+//"LWIR batch"
 		GUI.center(plugInFrame);
 		plugInFrame.setVisible(true);
 		FHT_INSTANCE=       new DoubleFHT();
@@ -3960,12 +3964,6 @@ private Panel panel1,
 			IJ.showMessage("Warning",msg);
 			return;
     	}
-/*
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL,
-        		true, // true - ignore missing files
-    			true, // boolean all_sensors,
-    			COLOR_PROC_PARAMETERS.correct_vignetting); //boolean correct_vignetting
-*/
         QUAD_CLT.resetGeometryCorrection();
         QUAD_CLT.initGeometryCorrection(DEBUG_LEVEL+2);
 
@@ -5016,6 +5014,14 @@ private Panel panel1,
     	batchRig();
     	return;
 
+/* ======================================================================== */
+    } else if (label.equals("LWIR batch")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+        CLT_PARAMETERS.batch_run = true;
+    	batchLwir();
+    	return;
+
 /* ======================================================================== */
     } else if (label.equals("CLT rig edit")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
@@ -5464,7 +5470,7 @@ private Panel panel1,
 
 		return true;
 	}
-
+// inverted false/true in initSensorFiles(), should work with LWIR also
 	public boolean prepareRigImages() {
         if (QUAD_CLT == null){
         	QUAD_CLT = new  QuadCLT (
@@ -5489,8 +5495,6 @@ private Panel panel1,
         		System.out.println("Created new QuadCLT instance, will need to read CLT kernels");
         	}
         }
-//        QuadCLT dbg_QUAD_CLT = QUAD_CLT;
-//        QuadCLT dbg_QUAD_CLT_AUX = QUAD_CLT_AUX;
     	String configPath=getSaveCongigPath();
     	if (configPath.equals("ABORT")) return false;
     	if (DEBUG_LEVEL > -2){
@@ -5498,15 +5502,15 @@ private Panel panel1,
     	}
         EYESIS_CORRECTIONS.initSensorFiles(
         		DEBUG_LEVEL+2,
-        		true,
-        		false,
+        		false, // true,
+        		true,  // false,
     			COLOR_PROC_PARAMETERS.correct_vignetting); //boolean correct_vignetting
     	if (DEBUG_LEVEL > -2){
     		System.out.println("++++++++++++++ Running initSensorFiles for the auxiliary camera ++++++++++++++");
     	}
         EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL+2,
-        		true,
-        		false,
+        		false, // true,
+        		true,  // false,
     			COLOR_PROC_PARAMETERS_AUX.correct_vignetting); //boolean correct_vignetting
 
 
@@ -6149,6 +6153,52 @@ private Panel panel1,
 		return true;
 	}
 
+	public boolean batchLwir() {
+		long startTime=System.nanoTime();
+		// load needed sensor and kernels files
+		if (!prepareRigImages()) return false;
+		String configPath=getSaveCongigPath();
+		if (configPath.equals("ABORT")) return false;
+		setAllProperties(PROPERTIES); // batchRig may save properties with the model. Extrinsics will be updated, others should be set here
+		if (DEBUG_LEVEL > -2){
+			System.out.println("++++++++++++++ Running batch processing of dual-quad EO/LWIR camera rig ++++++++++++++");
+		}
+		// parameters are different
+///		if (COLOR_PROC_PARAMETERS_AUX == null) {
+///			COLOR_PROC_PARAMETERS_AUX = COLOR_PROC_PARAMETERS.clone();
+///		}
+		try {
+			TWO_QUAD_CLT.batchLwirRig(
+					QUAD_CLT, // QuadCLT quadCLT_main,
+					QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
+					CLT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
+					DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
+					COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
+					COLOR_PROC_PARAMETERS_AUX, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters_aux,
+					CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters     channelGainParameters,
+					RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters             rgbParameters,
+					EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
+					PROPERTIES,  // Properties                                           properties,
+					THREADS_MAX, //final int          threadsMax,  // maximal number of threads to launch
+					UPDATE_STATUS, //final boolean    updateStatus,
+					DEBUG_LEVEL);
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		} //final int        debugLevel);
+		if (configPath!=null) {
+			saveTimestampedProperties( // save config again
+					configPath,      // full path or null
+					null, // use as default directory if path==null
+					true,
+					PROPERTIES);
+		}
+		System.out.println("batchRig(): Processing finished at "+
+				IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec, --- Free memory="+
+				Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+		return true;
+	}
+
 
 
 
@@ -6337,7 +6387,9 @@ private Panel panel1,
 
 		String mask = ".*EXTRINSICS\\.corr-xml";
 		String full_conf_suffix = ".corr-xml";
-		String dsi_suffix = "-DSI_COMBO.tiff";
+//		String dsi_suffix = "-DSI_COMBO.tiff";
+		String dsi_suffix = TwoQuadCLT.DSI_COMBO_SUFFIX+".tiff";
+
 		String correction_parameters_prefix = "CORRECTION_PARAMETERS.";
 
 		System.out.println("File mask = "+mask);

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

@@ -998,6 +998,9 @@ public class GeometryCorrection {
 	}
 
 	public void showRig() {
+		if (this.rigOffset == null) {
+			this.rigOffset = new RigOffset();
+		}
 		this.rigOffset.showRigOffsets();
 	}
 
@@ -1401,18 +1404,22 @@ public class GeometryCorrection {
 
 
 
-
-		public void incrementVector(double [] incr,
+		// returns false if any component is NaN, in that case do not increment
+		public boolean incrementVector(double [] incr,
 				double scale)
 		{
+			for (int i = 0; i < incr.length; i++){
+				if (Double.isNaN(vector[i])) return false;
+			}
 			for (int i = 0; i < incr.length; i++){
 				vector[i]+= incr[i] * scale;
 			}
+			return true;
 		}
 
-		public void incrementVector(CorrVector incr, double scale)
+		public boolean incrementVector(CorrVector incr, double scale)
 		{
-			incrementVector(incr.toArray(), scale);
+			return incrementVector(incr.toArray(), scale);
 		}
 
 		@Override

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

@@ -83,7 +83,8 @@ public class MLStats {
 		int    result_disparity_step =  10; // bins
 
 
-		String mask = ".*-DSI_COMBO\\.tiff";
+//		String mask = ".*-DSI_COMBO\\.tiff";
+		String mask = ".*"+TwoQuadCLT.DSI_COMBO_SUFFIX+"\\.tiff";
 
 		GenericDialog gd = new GenericDialog("Select file mask and histogram parameters");
 		gd.addStringField ("Combined DSI file mask: ",                       mask,                        40);
@@ -443,7 +444,8 @@ public class MLStats {
 	{
 		String mask = ".*EXTRINSICS\\.corr-xml";
 		String full_conf_suffix = ".corr-xml";
-		String dsi_suffix = "-DSI_COMBO.tiff";
+//		String dsi_suffix = "-DSI_COMBO.tiff";
+		String dsi_suffix = TwoQuadCLT.DSI_COMBO_SUFFIX+".tiff";
 		String correction_parameters_prefix = "CORRECTION_PARAMETERS.";
 
 		System.out.println("File mask = "+mask);

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

@@ -23,7 +23,6 @@ package com.elphel.imagej.tileprocessor;
  **
  */
 import java.awt.Point;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
@@ -4016,7 +4015,7 @@ public class TilePlanes {
 				System.out.println("getPlaneToThis(), px_py = {"+px_py[0]+", "+px_py[1]+"}, px_py_other = {"+px_py_other[0]+", "+px_py_other[1]+"}");
 				System.out.println("getPlaneToThis(), disp = "+disp);
 				System.out.println("getPlaneToThis(), pd="+ pd.toString());
-//				System.out.println("getPlaneToThis(), otherPd="+ otherPd.toString()); 
+//				System.out.println("getPlaneToThis(), otherPd="+ otherPd.toString());
 //				System.out.println("getPlaneToThis(), pd.getWorldXYZ(this.correctDistortions)="+ pd.getWorldXYZ(this.correctDistortions));
 //				System.out.println("getPlaneToThis(), wv1 = {"+ wv1[0]+", "+ wv1[1]+", "+ wv1[2]+"}");
 //				System.out.println("getPlaneToThis(), wv2 = {"+ wv2[0]+", "+ wv2[1]+", "+ wv2[2]+"}");
@@ -4216,7 +4215,9 @@ public class TilePlanes {
 			if (world_xyz != null) {
 				double l2 = world_xyz[0]*world_xyz[0] + world_xyz[1]*world_xyz[1]+world_xyz[2]*world_xyz[2];
 				if (l2 < 0.5) {
-					System.out.println("getWorldXYZ(): l2="+l2); // +" this=\n"+this.toString());
+					if (debugLevel > -1) {
+						System.out.println("getWorldXYZ(): l2="+l2); // +" this=\n"+this.toString());
+					}
 					world_xyz = null;
 				}
 			}
@@ -4316,7 +4317,9 @@ public class TilePlanes {
 			world_xyz = norm_xyz.times((xyz.transpose().times(norm_xyz).get(0,0))).getColumnPackedCopy();
 			double l2 = world_xyz[0]*world_xyz[0] + world_xyz[1]*world_xyz[1]+world_xyz[2]*world_xyz[2];
 			if (l2 < 0.5) {
-				System.out.println("getWorldXYZ(): l2="+l2); // +" this=\n"+this.toString());
+				if (debugLevel > -1) {
+					System.out.println("getWorldXYZ(): l2="+l2); // +" this=\n"+this.toString());
+				}
 			}
 			return world_xyz;
 		}