Set default directory, averaging to multithreaded

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

@@ -1102,24 +1102,25 @@ if (MORE_BUTTONS) {
 		Runtime runtime = Runtime.getRuntime();
 	    runtime.gc();
 		if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
-
 		if (label==null) return;
-	    String LOG_LEVEL;
-	    switch (MASTER_DEBUG_LEVEL) {
-	    case -2: LOG_LEVEL = "FATAL"; break;
-	    case -1: LOG_LEVEL = "ERROR"; break;
-	    case  0: LOG_LEVEL = "WARN";  break;
-	    case  1: LOG_LEVEL = "INFO";  break;
-	    case  2: LOG_LEVEL = "DEBUG"; break;
-	    default: LOG_LEVEL = "OFF";
-	    }
+	    if (LWIR_PARAMETERS !=null) {
+	    	String LOG_LEVEL;
+	    	switch (LWIR_PARAMETERS.getDebugLevel()) {
+	    	case -2: LOG_LEVEL = "FATAL"; break;
+	    	case -1: LOG_LEVEL = "ERROR"; break;
+	    	case  0: LOG_LEVEL = "WARN";  break;
+	    	case  1: LOG_LEVEL = "INFO";  break;
+	    	case  2: LOG_LEVEL = "DEBUG"; break;
+	    	default: LOG_LEVEL = "OFF";
+	    	}
 
-		boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
-		if (!LOG_LEVEL_SET) { // only first time true
-			loci.common.DebugTools.setRootLevel(LOG_LEVEL);
-		}
-	    System.out.println("DEBUG_LEVEL = "+DEBUG_LEVEL+", MASTER_DEBUG_LEVEL = "+MASTER_DEBUG_LEVEL+
-	    		" LOG_LEVEL="+LOG_LEVEL+"LOG_LEVEL_SET="+LOG_LEVEL_SET);
+	    	boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
+	    	if (!LOG_LEVEL_SET) { // only first time true
+	    		loci.common.DebugTools.setRootLevel(LOG_LEVEL);
+	    	}
+	    	System.out.println("DEBUG_LEVEL = "+DEBUG_LEVEL+", LWIR_PARAMETERS.getDebugLevel() = "+LWIR_PARAMETERS.getDebugLevel()+
+	    			" LOG_LEVEL="+LOG_LEVEL+"LOG_LEVEL_SET="+LOG_LEVEL_SET);
+	    }
 
 		if (FOCUSING_FIELD!=null) FOCUSING_FIELD.setThreads(THREADS_MAX);
 /* ======================================================================== */
@@ -9441,7 +9442,8 @@ if (MORE_BUTTONS) {
 		if (LWIR_READER == null) {
 			LWIR_READER =  new LwirReader(LWIR_PARAMETERS);
 		}
-        ImagePlus [] imps = LWIR_READER.acquire("/data_ssd/imagej-elphel/attic/camera_img/test-calib"); // directory to save
+//        ImagePlus [] imps = LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
+        ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save
 		if (imps != null) {
 //			for (ImagePlus imp: imps) {
 //				imp.show();

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

@@ -897,22 +897,24 @@ private Panel panel1,
 	if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
 	CLT_PARAMETERS.batch_run = false;
     if (label==null) return;
-    String LOG_LEVEL;
-    switch (MASTER_DEBUG_LEVEL) {
-    case -2: LOG_LEVEL = "FATAL"; break;
-    case -1: LOG_LEVEL = "ERROR"; break;
-    case  0: LOG_LEVEL = "WARN";  break;
-    case  1: LOG_LEVEL = "INFO";  break;
-    case  2: LOG_LEVEL = "DEBUG"; break;
-    default: LOG_LEVEL = "OFF";
-    }
+    if ((CLT_PARAMETERS !=null) && (CLT_PARAMETERS.lwir !=null)) {
+    	String LOG_LEVEL;
+    	switch (CLT_PARAMETERS.lwir.getDebugLevel()) {
+    	case -2: LOG_LEVEL = "FATAL"; break;
+    	case -1: LOG_LEVEL = "ERROR"; break;
+    	case  0: LOG_LEVEL = "WARN";  break;
+    	case  1: LOG_LEVEL = "INFO";  break;
+    	case  2: LOG_LEVEL = "DEBUG"; break;
+    	default: LOG_LEVEL = "OFF";
+    	}
 
-	boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
-	if (!LOG_LEVEL_SET) { // only first time true
-		loci.common.DebugTools.setRootLevel(LOG_LEVEL);
-	}
-    System.out.println("DEBUG_LEVEL = "+DEBUG_LEVEL+", MASTER_DEBUG_LEVEL = "+MASTER_DEBUG_LEVEL+
-    		" LOG_LEVEL="+LOG_LEVEL+"LOG_LEVEL_SET="+LOG_LEVEL_SET);
+    	boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
+    	if (!LOG_LEVEL_SET) { // only first time true
+    		loci.common.DebugTools.setRootLevel(LOG_LEVEL);
+    	}
+    	System.out.println("DEBUG_LEVEL = "+DEBUG_LEVEL+", CLT_PARAMETERS.lwir.getDebugLevel() = "+CLT_PARAMETERS.lwir.getDebugLevel()+
+    			" LOG_LEVEL="+LOG_LEVEL+"LOG_LEVEL_SET="+LOG_LEVEL_SET);
+    }
 
 /* ======================================================================== */
     if (label.equals("Configure spilt")) {
@@ -4873,7 +4875,7 @@ private Panel panel1,
 		if (LWIR_READER == null) {
 			LWIR_READER =  new LwirReader(CLT_PARAMETERS.lwir);
 		}
-        ImagePlus [] imps = LWIR_READER.acquire("/data_ssd/imagej-elphel/attic/camera_img/test"); // directory to save
+        ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save
 		if (imps != null) {
 			for (ImagePlus imp: imps) {
 //				imp.show();

src/main/java/com/elphel/imagej/lwir/LwirReader.java

@@ -208,12 +208,54 @@ public class LwirReader {
 		return imps;
 	}
 
-	public ImagePlus [] averageMultiFrames(ImagePlus [][] sets) {
-		//TODO: convert to multithreaded !
-		int num_frames = sets.length;
-		int num_channels = sets[0].length;
-		ImagePlus [] imps_avg = new ImagePlus [num_channels];
+	public ImagePlus [] averageMultiFrames(
+			final ImagePlus [][] sets) {
+		final int num_frames = sets.length;
+		final int num_channels = sets[0].length;
+		final ImagePlus [] imps_avg = new ImagePlus [num_channels];
+   		final Thread[] threads = newThreadArray(MAX_THREADS);
+   		final AtomicInteger indxAtomic = new AtomicInteger(0);
+
+   		for (int ithread = 0; ithread < threads.length; ithread++) {
+   			threads[ithread] = new Thread() {
+   				@Override
+				public void run() {
+   					for (int chn = indxAtomic.getAndIncrement(); chn < num_channels; chn = indxAtomic.getAndIncrement())
+   					{
+   						int width =  sets[0][chn].getWidth();
+   						int height = sets[0][chn].getHeight();
+   						String title = sets[0][chn].getTitle()+"_average"+num_frames;
+   						float [] pixels_avg = (float []) sets[0][chn].getProcessor().getPixels(); //null pointer
+   						for (int n = 1; n < num_frames; n++) {
+   							float [] pixels = (float []) sets[n][chn].getProcessor().getPixels();
+   							for (int i = 0; i < pixels_avg.length; i++) {
+   								pixels_avg[i] += pixels[i];
+   							}
+   						}
+   						double scale = 1.0/num_frames;
+   						for (int i = 0; i < pixels_avg.length; i++) {
+   							pixels_avg[i] *= scale;
+   						}
+   						ImageProcessor ip=new FloatProcessor(width,height);
+   						ip.setPixels(pixels_avg);
+   						ip.resetMinAndMax();
+   						imps_avg[chn]=  new ImagePlus(title, ip);
+   						Properties properties0 = sets[0][chn].getProperties();
+   						for (String key:properties0.stringPropertyNames()) {
+   							imps_avg[chn].setProperty(key, properties0.getProperty(key));
+   						}
+   						imps_avg[chn].setProperty("average", ""+num_frames);
+   						if (motorsPosition!=null) for (int m=0;m<motorsPosition.length;m++ ) {
+   							imps_avg[chn].setProperty("MOTOR"+(m+1), ""+motorsPosition[m]);
+   						}
+   						ImagejJp4Tiff.encodeProperiesToInfo(imps_avg[chn]);
+   					}
+   				}
+   			};
+   		}
+   		startAndJoin(threads);
 
+   		/*
 		for (int chn = 0; chn < num_channels; chn++) {
 			int width =  sets[0][chn].getWidth();
 			int height = sets[0][chn].getHeight();
@@ -244,7 +286,7 @@ public class LwirReader {
 			ImagejJp4Tiff.encodeProperiesToInfo(imps_avg[chn]);
 			// TODO: Overwrite some properties?
 		}
-
+   		 */
 		return imps_avg;
 	}
 
@@ -513,13 +555,14 @@ public class LwirReader {
 			String set_path = dirpath+Prefs.getFileSeparator()+set_name;
 			File  set_dir = new File(set_path);
 			set_dir.mkdirs(); // including parent
+			LOGGER.warn("Saving image set to: "+set_dir.getAbsolutePath());
 			for (ImagePlus imp:imps_avg) {
 				String fname = imp.getTitle();
 				fname = fname.substring(0, fname.lastIndexOf('_')) + ".tiff"; // remove _average
    				FileSaver fs=new FileSaver(imp);
    				String path=set_path+Prefs.getFileSeparator()+fname;
    				IJ.showStatus("Saving "+path);
-   				LOGGER.debug("LWIR_ACQUIRE: 'Saving "+path+ " (and other with the same timestamp)" );
+   				LOGGER.info("LWIR_ACQUIRE: 'Saving "+path );
    				fs.saveAsTiff(path);
 			}
 		}

src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java

@@ -49,6 +49,7 @@ public class LwirReaderParameters {
 	protected double  vnir_gain_g =           2.0;
 	protected double  vnir_gain_rg =          0.7705; // 1.116; halogen/fluorescent
 	protected double  vnir_gain_bg =          2.401;  // 1.476;
+
 /*
 	protected double [] vnir_exp_corr = {1.0, 1.0, 1.0, 1.0};
 	protected double [] vnir_gcorr_rbgb = {
@@ -69,9 +70,17 @@ public class LwirReaderParameters {
 	protected int     vnir_lag   =          1; // frames
 	protected double  max_mismatch_ms =     0.05;
 	protected int     max_frame_diff =      1; // 2;
+	protected int     debug_level =           0;//-3: OFF, -2:Fatal, -1:ERROR, 0:WARN, 1:INFO,2:DEBUG
 
 
 	// --- interface methods
+	public int getDebugLevel() {
+		return this.debug_level;
+	}
+	public void setDebugLevel(int level) {
+		this.debug_level = level;
+	}
+
 	public void setProperties(String prefix,Properties properties){
 		properties.setProperty(prefix+"avg_number",          this.avg_number+"");
 		properties.setProperty(prefix+"lwir_ffc",            this.lwir_ffc+"");
@@ -96,6 +105,8 @@ public class LwirReaderParameters {
 		properties.setProperty(prefix+"vnir_lag",            this.vnir_lag+"");
 		properties.setProperty(prefix+"max_mismatch_ms",     this.max_mismatch_ms+"");
 		properties.setProperty(prefix+"max_frame_diff",      this.max_frame_diff+"");
+		properties.setProperty(prefix+"debug_level",         this.debug_level+"");
+
 	}
 
 	public void getProperties(String prefix,Properties properties){
@@ -122,6 +133,7 @@ public class LwirReaderParameters {
 		if (properties.getProperty(prefix+"vnir_lag")!=null)            this.vnir_lag=Integer.parseInt(properties.getProperty(prefix+"vnir_lag"));
 		if (properties.getProperty(prefix+"max_mismatch_ms")!=null)     this.max_mismatch_ms=Double.parseDouble(properties.getProperty(prefix+"max_mismatch_ms"));
 		if (properties.getProperty(prefix+"max_frame_diff")!=null)      this.max_frame_diff=Integer.parseInt(properties.getProperty(prefix+"max_frame_diff"));
+		if (properties.getProperty(prefix+"debug_level")!=null)         this.debug_level=Integer.parseInt(properties.getProperty(prefix+"debug_level"));
 		parameters_updated = true;
 	}
 	@Override
@@ -150,6 +162,7 @@ public class LwirReaderParameters {
 		lrp.vnir_lag=                  this.vnir_lag;
 		lrp.max_mismatch_ms=           this.max_mismatch_ms;
 		lrp.max_frame_diff=            this.max_frame_diff;
+		lrp.debug_level=               this.debug_level;
 		return lrp;
 	}
 
@@ -184,7 +197,8 @@ public class LwirReaderParameters {
 				(lrp.lwir_trig_dly == this.lwir_trig_dly) &&
 				(lrp.vnir_lag == this.vnir_lag) &&
 				(lrp.max_mismatch_ms == this.max_mismatch_ms) &&
-				(lrp.max_frame_diff == this.max_frame_diff);
+				(lrp.max_frame_diff == this.max_frame_diff) &&
+				(lrp.debug_level ==    this.debug_level);
 	}
 
 	@Override
@@ -242,6 +256,7 @@ public class LwirReaderParameters {
 		gd.addNumericField("VNIR lag",      this.vnir_lag,     0,3,"","Visible camera lag (in frames) relative to LWIR one");
 		gd.addNumericField("Max mismatch",  this.max_mismatch_ms,    3,6,"ms","Maximal mismatch between image timestamps. Larger mismatch requires LWIR sinsor reinitialization");
 		gd.addNumericField("Max frame diff",this.max_frame_diff,     0,3,"","Maximal difference in frames between simultaneously acquired channels as calculated from the timestamps");
+		gd.addNumericField("Debug level",   this.debug_level,         0,3,"","Image acquisition log level: -3: OFF, -2:FATAL, -1:ERROR, 0:WARN, 1:INFO, 2:DEBUG");
 	}
 
 	public void dialogAnswers(GenericJTabbedDialog gd) {
@@ -268,6 +283,7 @@ public class LwirReaderParameters {
 		this.vnir_lag =               (int) gd.getNextNumber();
 		this.max_mismatch_ms =              gd.getNextNumber();
 		this.max_frame_diff =         (int) gd.getNextNumber();
+		this.debug_level =            (int) gd.getNextNumber();
 		parameters_updated = true;
 	}