Set default directory, averaging to multithreaded (632eb62e) · Commits · Elphel / imagej-elphel

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

+19 −17

Original line number	Diff line number	Diff line
		@@ -1102,10 +1102,10 @@ 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;
		if (LWIR_PARAMETERS !=null) {
		String LOG_LEVEL;
		switch (MASTER_DEBUG_LEVEL) {
		switch (LWIR_PARAMETERS.getDebugLevel()) {
		case -2: LOG_LEVEL = "FATAL"; break;
		case -1: LOG_LEVEL = "ERROR"; break;
		case 0: LOG_LEVEL = "WARN"; break;
		@@ -1118,8 +1118,9 @@ if (MORE_BUTTONS) {
		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+
		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

+18 −16

Original line number	Diff line number	Diff line
		@@ -897,8 +897,9 @@ 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;
		if ((CLT_PARAMETERS !=null) && (CLT_PARAMETERS.lwir !=null)) {
		String LOG_LEVEL;
		switch (MASTER_DEBUG_LEVEL) {
		switch (CLT_PARAMETERS.lwir.getDebugLevel()) {
		case -2: LOG_LEVEL = "FATAL"; break;
		case -1: LOG_LEVEL = "ERROR"; break;
		case 0: LOG_LEVEL = "WARN"; break;
		@@ -911,8 +912,9 @@ private Panel panel1,
		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+
		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

+50 −7

Original line number	Diff line number	Diff line
		@@ -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

+17 −1

Original line number	Diff line number	Diff line
		@@ -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;
		}

Admin message