Merge branch 'lwir' of git.elphel.com:Elphel/imagej-elphel into lwir (42ed650b) · Commits · Elphel / imagej-elphel

pom.xml

+6 −0

Original line number	Diff line number	Diff line
		@@ -90,6 +90,12 @@
		<artifactId>loci_tools</artifactId>
		<version>6.0.1</version>
		</dependency>
		<dependency>
		<groupId>com.drewnoakes</groupId>
		<artifactId>metadata-extractor</artifactId>
		<version>2.11.0</version>
		<type>java-source</type>
		</dependency>
		</dependencies>

		<build>

src/main/java/Eyesis_Correction.java

+45 −3

Original line number	Diff line number	Diff line
		@@ -70,6 +70,8 @@ import java.util.concurrent.atomic.AtomicInteger;
		import javax.swing.JFileChooser;
		import javax.swing.filechooser.FileFilter;

		import com.elphel.imagej.lwir.LwirReader;

		import ij.CompositeImage;
		import ij.IJ;
		import ij.ImageJ;
		@@ -118,7 +120,8 @@ private Panel panel1,
		panelClt3,
		panelClt4,
		panelClt5,
		panelClt_GPU
		panelClt_GPU,
		panelLWIR
		;
		JP46_Reader_camera JP4_INSTANCE=null;

		@@ -384,6 +387,7 @@ private Panel panel1,
		public static boolean DCT_MODE=false; //true; // show all buttons
		public static boolean MODE_3D=false; // 3D-related commands
		public static boolean GPU_MODE=false; // 3D-related commands
		public static boolean LWIR_MODE = false; // LWIR-related commands
		public PixelMapping.InterSensor.DisparityTiles DISPARITY_TILES=null;
		public ImagePlus DBG_IMP = null;
		public ImagePlus CORRELATE_IMP = null;
		@@ -420,7 +424,7 @@ private Panel panel1,

		instance = this;
		addKeyListener(IJ.getInstance());
		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?6:0) + (GPU_MODE?1:0);
		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?6:0) + (GPU_MODE?1:0) +(LWIR_MODE?1:0);
		setLayout(new GridLayout(menuRows, 1));

		panel6 = new Panel();
		@@ -645,7 +649,13 @@ private Panel panel1,
		addButton("ShowGPU", panelClt_GPU, color_conf_process);
		add(panelClt_GPU);
		}

		if (LWIR_MODE) {
		panelLWIR = new Panel();
		panelLWIR.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
		addButton("LWIR_ACQUIRE", panelLWIR, color_conf_process);
		add(panelLWIR);
		}
		//
		pack();

		GUI.center(this);
		@@ -740,6 +750,15 @@ private Panel panel1,
		IJ.showMessage("Error",msg);
		throw new IOException (msg);
		}
		sValue= this.prefsProperties.getProperty("LWIR_MODE");
		if (sValue!=null) {
		LWIR_MODE=Boolean.parseBoolean(sValue);
		System.out.println("Read LWIR_MODE="+LWIR_MODE);
		} else {
		String msg="LWIR_MODE is undefined in "+this.prefsPath;
		IJ.showMessage("Error",msg);
		throw new IOException (msg);
		}
		}

		public static String stack2string(Exception e) {
		@@ -4783,6 +4802,29 @@ private Panel panel1,
		}
		TENSORFLOW_INFER_MODEL.test_tensorflow(keep_empty);
		return;
		/* ======================================================================== */
		} else if (label.equals("LWIR_ACQUIRE")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		loci.common.DebugTools.enableLogging("ERROR"); // INFO"); // ERROR");
		LwirReader lwirReader = new LwirReader();
		ImagePlus [][] imps = lwirReader.readAllMultiple(
		10, // final int num_frames,
		true, // final boolean show,
		false); // true); // final boolean scale)
		for (ImagePlus imp: imps[0]) {
		imp.show();
		}

		System.out.println("LWIR_ACQUIRE: got "+imps.length+" image sets");
		ImagePlus [][] imps_sync = lwirReader.matchSets(imps, 0.001, 3); // double max_mismatch)
		if (imps_sync != null) {
		ImagePlus [] imps_avg = lwirReader.averageMultiFrames(imps_sync);
		for (ImagePlus imp: imps_avg) {
		imp.show();
		}
		}


		//JTabbedTest
		// End of buttons code
		}

src/main/java/JP46_Reader_camera.java

+1 −44

Original line number	Diff line number	Diff line
		@@ -1133,34 +1133,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		fi.fileFormat = isTiff?FileInfo.TIFF: FileInfo.GIF_OR_JPG; // even if set originally, it is lost after convertToGray32
		imp.setFileInfo(fi);

		FileInfo ofi = imp.getOriginalFileInfo();
		fi = imp.getFileInfo();

		// testing
		/*
		if ((ofi!=null) && (ofi.directory!=null) && (ofi.fileFormat == FileInfo.TIFF)) {
		String path = ofi.directory + ofi.fileName;
		EyesisTiff ET = new EyesisTiff();
		ImagePlus imptiff = ET.readTiff(path);
		if (imptiff!=null) {
		imptiff.show();
		}

		// IJ.error("TIFF Dumper", "File path not available or not TIFF file");
		IJ.log("\\Clear");
		IJ.log("PATH = "+path);
		try {
		dumpIFDs(path);
		} catch(IOException e) {
		IJ.error("Tiff Dumper", ""+e);
		}
		Frame log = WindowManager.getFrame("Log");
		if (log!=null) log.toFront();
		}
		*/
		}


		return imp;
		}

		@@ -1421,16 +1394,11 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		timestamp=imp.getProperty("timestamp");
		if (timestamp!=null);

		/*
		System.out.println("FLIPV="+FLIPGV+" FLIPH="+FLIPGH);
		for (i=0;i<3;i++) System.out.println("FLIPV["+i+"]= "+FLIPV[i]+" FLIPH["+i+"]= "+FLIPH[i]);
		for (i=0;i<3;i++) System.out.println("HEIGHTS["+i+"]="+HEIGHTS[i]);
		for (i=0;i<2;i++) System.out.println("BLANKS["+i+"]= "+BLANKS[i]);
		*/
		Rectangle [] r = new Rectangle[3];
		r[0]=new Rectangle(0, 0, width,HEIGHTS[0]);
		r[1]=new Rectangle(0, HEIGHTS[0]+BLANKS[0], width,HEIGHTS[1]);
		r[2]=new Rectangle(0, HEIGHTS[0]+BLANKS[0]+HEIGHTS[1]+BLANKS[1],width,HEIGHTS[2]);

		// assuming that (HEIGHTS[1]==0) && (HEIGHTS[2]!=0) == false
		if (FLIPGV!=0){
		if (HEIGHTS[1]>0) {
		@@ -1448,13 +1416,10 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		if (FLIPGV>0) for (i=0;i<3;i++) FLIPV[i]=1-FLIPV[i];
		if (FLIPGH>0) for (i=0;i<3;i++) FLIPH[i]=1-FLIPH[i];

		// for (i=0;i<3;i++) System.out.println("Final: FLIPV["+i+"]= "+FLIPV[i]+" FLIPH["+i+"]= "+FLIPH[i]);

		// if needed, we'll cut one pixel line. later can modify to add one extra, but then we need to duplicate the pre-last one (same Bayer),
		// not just add zeros - later before sliding FHT the two border lines are repeated for 16 times to reduce border effects.
		for (i=0;i<3;i++) {
		// System.out.println("before r["+i+"].x= "+r[i].x+" r["+i+"].width= "+r[i].width);
		// System.out.println("before r["+i+"].y= "+r[i].y+" r["+i+"].height= "+r[i].height);
		if (((r[i].height & 1)==0 ) & (((r[i].y+FLIPV[i])&1)!=0)) r[i].height-=2;
		r[i].height &=~1;
		if (((r[i].y+FLIPV[i])&1)!=0) r[i].y+=1;
		@@ -1462,16 +1427,8 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
		if (((r[i].width & 1)==0 ) & (((r[i].x+FLIPH[i])&1)!=0)) r[i].width-=2;
		r[i].width &=~1;
		if (((r[i].x+FLIPH[i])&1)!=0) r[i].x+=1;



		// System.out.println("after r["+i+"].x= "+r[i].x+" r["+i+"].width= "+r[i].width);
		// System.out.println("after r["+i+"].y= "+r[i].y+" r["+i+"].height= "+r[i].height);
		}
		if (r[numImg].height<=0) return null;
		// ImageProcessor ip=imp.getProcessor();
		// ip.setRoi(r[numImg]);
		// ImageProcessor ip_individual=ip.crop().duplicate(); //java.lang.NegativeArraySizeException
		/*
		* When using in multithreaded with (probably) the same composite image
		Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970912

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

0 → 100644

+274 −0

Original line number	Diff line number	Diff line
		/**
		-----------------------------------------------------------------------------
		** LwirReader.java
		**
		** Multithreaded reading cameras - visible and LWIR
		**
		**
		** Copyright (C) 2019 Elphel, Inc.
		**
		-----------------------------------------------------------------------------
		**
		** LwirReader.java is free software: you can redistribute it and/or modify
		** it under the terms of the GNU General Public License as published by
		** the Free Software Foundation, either version 3 of the License, or
		** (at your option) any later version.
		**
		** This program is distributed in the hope that it will be useful,
		** but WITHOUT ANY WARRANTY; without even the implied warranty of
		** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
		** GNU General Public License for more details.
		**
		** You should have received a copy of the GNU General Public License
		** along with this program. If not, see <http://www.gnu.org/licenses/>.
		-----------------------------------------------------------------------------
		**
		*/
		package com.elphel.imagej.lwir;

		import java.io.IOException;
		import java.util.Properties;

		import org.slf4j.Logger;
		import org.slf4j.LoggerFactory;

		import com.elphel.imagej.readers.ElphelTiffReader;
		import com.elphel.imagej.readers.ImagejJp4TiffMulti;

		import ij.ImagePlus;
		import ij.process.FloatProcessor;
		import ij.process.ImageProcessor;
		import loci.formats.FormatException;

		public class LwirReader {
		public static String [] BASE_URLS= {
		"http://192.168.0.36:2323/bchn0",
		"http://192.168.0.36:2324/bchn0",
		"http://192.168.0.36:2325/bchn0",
		"http://192.168.0.36:2326/bchn0",
		"http://192.168.0.38:2323/bchn4",
		"http://192.168.0.38:2324/bchn4",
		"http://192.168.0.38:2325/bchn4",
		"http://192.168.0.38:2326/bchn4",
		};
		// public static String IMAGE_URL_FIRST="/towp/wait/img/next/save";
		// public static String IMAGE_URL_NEXT= "/torp/wait/img/next/save";
		// public static String IMAGE_URL_FIRST="/towp/wait/img/save"; // next image name, same image number/time
		// public static String IMAGE_URL_NEXT= "/torp/wait/img/save"; // same image name, same image number/time

		public static String IMAGE_URL_FIRST="/towp/wait/img/save"; // next image name, same image number/time
		public static String IMAGE_URL_NEXT= "/torp/next/wait/img/save"; // same image name, same image number/time

		// public static String IMAGE_URL_FIRST="/towp/wait/bimg/save"; // next image name, same image number/time
		// public static String IMAGE_URL_NEXT= "/torp/next/wait/bimg/save"; // same image name, same image number/time

		/** Logger for this class. */
		private static final Logger LOGGER =
		LoggerFactory.getLogger(ElphelTiffReader.class);

		private ImagejJp4TiffMulti imagejJp4TiffMulti;

		public LwirReader() {
		imagejJp4TiffMulti = null;
		}


		public ImagePlus[][] readAllMultiple(
		final int num_frames,
		final boolean show,
		final boolean scale) {
		return readAllMultiple(num_frames, show, scale, "STD_");
		}

		public ImagePlus[][] readAllMultiple(
		final int num_frames,
		final boolean show,
		final boolean scale,
		final String std)
		{
		String [] urls0 = new String[BASE_URLS.length];
		String [] urls1 = new String[BASE_URLS.length];
		ImagePlus [][] imps = new ImagePlus[num_frames][BASE_URLS.length];
		for (int i = 0; i < BASE_URLS.length; i++) {
		urls0[i] = BASE_URLS[i] + IMAGE_URL_FIRST;
		urls1[i] = BASE_URLS[i] + IMAGE_URL_NEXT;
		}
		if (imagejJp4TiffMulti == null) {
		imagejJp4TiffMulti = new ImagejJp4TiffMulti();
		for (int i = 0; i < 2; i++) {
		try {
		imagejJp4TiffMulti.getMultiImages(urls0, imps[0], scale, std);
		} catch (IOException e) {
		LOGGER.error("readAllMultiple0: IOException, priming" );
		} catch (FormatException e) {
		LOGGER.error("readAllMultiple0:FormatException, priming");
		}
		LOGGER.error("priming..."+(i+1));
		try {
		Thread.sleep(1000);
		} catch (InterruptedException e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
		}
		}
		}
		for (int n = 0; n < num_frames; n++) {
		LOGGER.error("---- Acquiring frame set "+n);
		try {
		imagejJp4TiffMulti.getMultiImages( (n==0)? urls0:urls1, imps[n], scale, std);
		} catch (IOException e) {
		LOGGER.error("readAllMultiple0: IOException, n = " + n);
		} catch (FormatException e) {
		LOGGER.error("readAllMultiple0:FormatException, n = " + n);
		}
		}
		double [][] img_seconds = new double [num_frames][BASE_URLS.length];
		int [][] img_numbers = new int [num_frames][BASE_URLS.length];
		String [][] img_names = new String [num_frames][BASE_URLS.length];
		for (int n = 0; n < num_frames; n++) {
		for (int i = 0; i < imps[n].length; i++) {
		String dt = null;
		try {
		dt = (String) imps[n][i].getProperty("DATE_TIME");
		} catch (Exception e) {
		LOGGER.error("Something is wrong!");
		}

		img_seconds[n][i] = Double.parseDouble(dt.substring(dt.lastIndexOf(":")+1));
		try {
		img_numbers[n][i] = Integer.parseInt((String) imps[n][i].getProperty("STD_Image_Number"));
		} catch (Exception e) {
		img_numbers[n][i] = -1;
		}
		img_names[n][i] = (String) imps[n][i].getProperty("CONTENT_FILENAME");
		LOGGER.error("Seconds for" + n+":"+i+" - "+img_seconds[n][i]+", number"+img_numbers[n][i]+", name "+img_names[n][i]);
		}
		}


		for (ImagePlus [] imp_sets :imps) {
		for (ImagePlus imp: imp_sets) {
		// imp.show();
		}
		}
		return imps;
		}

		public ImagePlus [] averageMultiFrames(ImagePlus [][] sets) {
		int num_frames = sets.length;
		int num_channels = sets[0].length;
		ImagePlus [] imps_avg = new ImagePlus [num_channels];

		for (int chn = 0; chn < num_channels; chn++) {
		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));
		}
		// TODO: Overwrite some properties?
		}

		return imps_avg;
		}


		public ImagePlus [][] matchSets(ImagePlus [][] sets, double max_mismatch, int max_frame_diff){
		int num_frames = sets.length;
		int num_channels = sets[0].length;
		double [][] img_seconds = new double [num_frames][num_channels];
		int [] frame_offsets = new int[num_channels];
		double [] time_offsets = new double [num_channels];
		boolean some_notsynced = false;
		int fr_min = 0, fr_max = 0;
		for (int n = 0; n < num_frames; n++) {
		for (int i = 0; i < num_channels; i++) {
		String dt = (String) sets[n][i].getProperty("DATE_TIME");
		img_seconds[n][i] = Double.parseDouble(dt.substring(dt.lastIndexOf(":")+1));

		}
		}
		for (int i = 1; i < num_channels; i++) { // compare all to the first channel
		frame_offsets[i] = 0;
		time_offsets[i] = secOffs(img_seconds[0][0], img_seconds[0][i]);
		if (num_frames > max_frame_diff) {
		if (time_offsets[i] > max_mismatch) {
		for (int fr_diff = 1; fr_diff < max_frame_diff; fr_diff++) {
		double aoff = secOffs(img_seconds[fr_diff][0], img_seconds[0][i]);
		if (aoff < time_offsets[i]) {
		time_offsets[i] = aoff;
		frame_offsets[i] = fr_diff; // second channel starts later, than [0]
		}
		if (time_offsets[i] <=max_mismatch) break;
		aoff = secOffs(img_seconds[0][0], img_seconds[fr_diff][i]);
		if (aoff < time_offsets[i]) {
		time_offsets[i] = aoff;
		frame_offsets[i] = -fr_diff; // second channel starts earlier, than [0]
		}
		if (time_offsets[i] <=max_mismatch) break;
		}
		}
		}
		if (time_offsets[i] > max_mismatch) {
		some_notsynced = true;
		}
		if (frame_offsets[i] > 0) {
		fr_max = frame_offsets[i];
		}
		if (frame_offsets[i] < 0) {
		fr_min = frame_offsets[i];
		}
		}
		if (some_notsynced) {
		LOGGER.error("* Some channels are not synchronized, reboot or sensors re-start is needed *");
		for (int i = 0; i < num_channels; i++) {
		LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
		}
		return null;
		}
		if (((fr_max - fr_min) > max_frame_diff) \|\| ((fr_max - fr_min) > (num_frames - 1))) {
		LOGGER.error("* Earliest/latest channels differ by more than 1 frame, that should not happen! *");
		for (int i = 0; i < num_channels; i++) {
		LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
		}
		return null;
		}
		for (int i = 0; i < num_channels; i++) {
		// change to info later:
		LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
		}
		ImagePlus [][] imps_synced = new ImagePlus [num_frames - fr_max + fr_min][num_channels];
		for (int n = 0; n < imps_synced.length; n++) {
		imps_synced[n][0]= sets[n+fr_max][0];
		for (int i = 1; i < num_channels; i++) {
		imps_synced[n][i]= sets[n - fr_min][i];
		}
		}
		return imps_synced;
		}

		private double secOffs(double sec1, double sec2) {
		double aoff = Math.abs(sec2 - sec1);
		if (aoff > 30) {
		aoff = Math.abs(aoff - 30);
		}
		return aoff;
		}

		}

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