Implementing telemetry data for Letnon 3.5

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

@@ -4838,6 +4838,7 @@ private Panel panel1,
 		}
         ImagePlus [][] imps = LWIR_READER.readAllMultiple(
     			10, // final int     num_frames,
+//    			true, // use LWIR telemetry
     			true, // final boolean show,
     			false); // true); // final boolean scale)
 		for (ImagePlus imp: imps[0]) {

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

@@ -65,6 +65,9 @@ public class LwirReader {
 	public static final String SKIP_FRAME_URL= "/towp/wait/meta";          // Wit for the next frame, return meta data
 	public static final int COLOR_JP4 = 5;
 	public static final int COLOR_RAW = 15;
+	public static final int LWIR_HEIGHT = 120;
+	public static final int LWIR_TELEMETRY_LINES = 2;
+
 	public static final int FRAMES_SKIP = 3;
 	public static final int MAX_THREADS = 100; // combine from all classes?
 
@@ -103,13 +106,16 @@ public class LwirReader {
 
 	public ImagePlus[][] readAllMultiple(
 			final int     num_frames,
+//			final boolean telemetry,
 			final boolean show,
 			final boolean scale) {
 		return readAllMultiple(num_frames, show, scale, "STD_");
+//		return readAllMultiple(num_frames, telemetry, show, scale, "STD_");
 	}
 
 	public ImagePlus[][] readAllMultiple(
 			final int     num_frames,
+//			final boolean telemetry,
 			final boolean show,
 			final boolean scale,
 			final String  std)
@@ -125,6 +131,7 @@ public class LwirReader {
 			imagejJp4TiffMulti = new ImagejJp4TiffMulti();
 			for (int i = 0; i < 2; i++) {
 				try {
+//					imagejJp4TiffMulti.getMultiImages(urls0, imps[0],  telemetry, scale,  std);
 					imagejJp4TiffMulti.getMultiImages(urls0, imps[0],  scale,  std);
 				} catch (IOException e) {
 					LOGGER.error("readAllMultiple0: IOException, priming" );
@@ -143,6 +150,7 @@ public class LwirReader {
 		for (int n = 0; n < num_frames; n++) {
 			LOGGER.info("---- Acquiring frame set "+n);
 			try {
+//				imagejJp4TiffMulti.getMultiImages( (n==0)? urls0:urls1, imps[n], telemetry,  scale,  std);
 				imagejJp4TiffMulti.getMultiImages( (n==0)? urls0:urls1, imps[n],  scale,  std);
 			} catch (IOException e) {
 				LOGGER.error("readAllMultiple0: IOException, n = " + n);
@@ -365,6 +373,7 @@ public class LwirReader {
 		int num_frames = lrp.avg_number + lrp.vnir_lag + 2 * lrp.max_frame_diff;
 		ImagePlus [][] imps = readAllMultiple(
 				num_frames,
+//				lrp.lwir_telemetry,
 				false, // final boolean show,
 				lrp.vnir_scale);
 		if (imps == null) {
@@ -433,7 +442,8 @@ public class LwirReader {
 		for (int chn:lrp.lwir_channels) {
 			urls[chn] = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
 					"&BITS=16"+
-					"&COLOR="+COLOR_RAW; // +"*0"; // raw mode - delay 0 - breaks compressor
+					"&COLOR="+COLOR_RAW+ // +"*0"; // raw mode - delay 0 - breaks compressor
+					"&WOI_HEIGHT="+(LWIR_HEIGHT + (lrp.lwir_telemetry?LWIR_TELEMETRY_LINES:0));
 			if (chn == lwir_master_port) {
 				urls[chn] +="&TRIG=0*0"+
 						"&TRIG_DELAY="+lrp.lwir_trig_dly+"*0"+

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

@@ -32,21 +32,22 @@ import com.elphel.imagej.common.GenericJTabbedDialog;
 
 public class LwirReaderParameters {
 	private boolean parameters_updated = false;
-	protected int    avg_number =            4; // number of measurements to average
-	public boolean   avg_all =               true;
-	protected String lwir_ip =               "192.168.0.36";
-	protected String vnir_ip =               "192.168.0.38";
-	protected int [] lwir_channels =         {0, 1, 2 ,3};
-	protected int [] vnir_channels =         {0, 1, 2 ,3};
-	protected double vnir_quality =          98.0;
+	protected int     avg_number =            4; // number of measurements to average
+	protected boolean avg_all =               true;
+	protected String  lwir_ip =               "192.168.0.36";
+	protected String  vnir_ip =               "192.168.0.38";
+	protected int []  lwir_channels =         {0, 1, 2 ,3};
+	protected int []  vnir_channels =         {0, 1, 2 ,3};
+	protected boolean lwir_telemetry =        true;
+	protected double  vnir_quality =          98.0;
 	protected boolean vnir_scale =           false; // restore sensor pixel values, undo camera white balancing
 	protected boolean vnir_autoexp =         false;
-	protected double vnir_max_autoexp_ms =  20.0;
-	protected double vnir_exposure_ms =      5.0;
+	protected double  vnir_max_autoexp_ms =  20.0;
+	protected double  vnir_exposure_ms =      5.0;
 	protected boolean vnir_whitebal =        false;
-	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_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 = {
@@ -63,10 +64,10 @@ public class LwirReaderParameters {
 			1.0668, 1.1055, 1.0006,
 			1.1533, 1.0780, 1.0015,
 			0.9966, 1.0445, 1.0023};
-	protected int    lwir_trig_dly   =     1000; //in 100MHz clock cycle, current FPGA requires >0 (used 1000)
-	protected int    vnir_lag   =          1; // frames
-	protected double max_mismatch_ms =     0.05;
-	protected int    max_frame_diff =      1; // 2;
+	protected int     lwir_trig_dly   =     1000; //in 100MHz clock cycle, current FPGA requires >0 (used 1000)
+	protected int     vnir_lag   =          1; // frames
+	protected double  max_mismatch_ms =     0.05;
+	protected int     max_frame_diff =      1; // 2;
 
 
 	// --- interface methods
@@ -77,6 +78,7 @@ public class LwirReaderParameters {
 		properties.setProperty(prefix+"vnir_ip",             this.vnir_ip+"");
 		properties.setProperty(prefix+"lwir_channels",       arr_to_str(this.lwir_channels));
 		properties.setProperty(prefix+"vnir_channels",       arr_to_str(this.vnir_channels));
+		properties.setProperty(prefix+"lwir_telemetry",      this.lwir_telemetry+"");
 		properties.setProperty(prefix+"vnir_quality",        this.vnir_quality+"");
 		properties.setProperty(prefix+"vnir_scale",          this.vnir_scale+"");
 		properties.setProperty(prefix+"vnir_autoexp",        this.vnir_autoexp+"");
@@ -101,6 +103,7 @@ public class LwirReaderParameters {
 		if (properties.getProperty(prefix+"vnir_ip")!=null)             this.vnir_ip=      properties.getProperty(prefix+"vnir_ip");
 		if (properties.getProperty(prefix+"lwir_channels")!=null)       this.lwir_channels=str_to_iarr(properties.getProperty(prefix+"lwir_channels"));
 		if (properties.getProperty(prefix+"vnir_channels")!=null)       this.vnir_channels=str_to_iarr(properties.getProperty(prefix+"vnir_channels"));
+		if (properties.getProperty(prefix+"lwir_telemetry")!=null)      this.lwir_telemetry= Boolean.parseBoolean(properties.getProperty(prefix+"lwir_telemetry"));
 		if (properties.getProperty(prefix+"vnir_quality")!=null)        this.vnir_quality=Double.parseDouble(properties.getProperty(prefix+"vnir_quality"));
 		if (properties.getProperty(prefix+"vnir_scale")!=null)          this.vnir_scale= Boolean.parseBoolean(properties.getProperty(prefix+"vnir_scale"));
 		if (properties.getProperty(prefix+"vnir_autoexp")!=null)        this.vnir_autoexp= Boolean.parseBoolean(properties.getProperty(prefix+"vnir_autoexp"));
@@ -127,6 +130,7 @@ public class LwirReaderParameters {
 		lrp.vnir_ip=                   this.vnir_ip;
 		lrp.lwir_channels=             this.lwir_channels.clone();
 		lrp.vnir_channels=             this.vnir_channels.clone();
+		lrp.lwir_telemetry=            this.lwir_telemetry;
 		lrp.vnir_quality=              this.vnir_quality;
 		lrp.vnir_scale=                this.vnir_scale;
 		lrp.vnir_autoexp=              this.vnir_autoexp;
@@ -160,6 +164,7 @@ public class LwirReaderParameters {
 				(lrp.vnir_ip.equals(this.vnir_ip)) &&
 				(java.util.Arrays.equals(lrp.lwir_channels, this.lwir_channels)) &&
 				(java.util.Arrays.equals(lrp.vnir_channels, this.vnir_channels)) &&
+				(lrp.lwir_telemetry == this.lwir_telemetry) &&
 				(lrp.vnir_quality == this.vnir_quality) &&
 				(lrp.vnir_scale == this.vnir_scale) &&
 				(lrp.vnir_autoexp == this.vnir_autoexp) &&
@@ -187,6 +192,7 @@ public class LwirReaderParameters {
 		result = prime * result + vnir_ip.hashCode();
 		result = prime * result + arr_to_str(lwir_channels).hashCode();
 		result = prime * result + arr_to_str(vnir_channels).hashCode();
+		result = prime * result + (lwir_telemetry?1:0);
 		result = prime * result + (new Double(vnir_quality)).hashCode();
 		result = prime * result + (vnir_scale?1:0);
 		result = prime * result + (vnir_autoexp?1:0);
@@ -213,6 +219,7 @@ public class LwirReaderParameters {
 		gd.addStringField ("VNIR IP",       this.vnir_ip, 20, "Visible range high resolution camera IP address");
 		gd.addStringField ("LWIR channels", arr_to_str(this.lwir_channels), 20, "Space-separated list of used LWIR camera channels, such as '0 1 2 3'");
 		gd.addStringField ("VNIR channels", arr_to_str(this.vnir_channels), 20, "Space-separated list of used visible range camera channels, such as '0 1 2 3'");
+		gd.addCheckbox    ("LWIR telemetry",    this.lwir_telemetry, "Set LWIR sesnors to provide telemetry data in the last 2 lines (may become mandatory later)");
 		gd.addNumericField("VNIR quality",  this.vnir_quality,  3,6,"ms", "Visible range camera JPEG compression quality (all channels)");
 		gd.addCheckbox    ("VNIR undo white balance",    this.vnir_scale, "Undo in-camera white balancing");
 		gd.addCheckbox    ("VNIR autoexposure", this.vnir_autoexp, "Enable autoexposure for the visible range camera");
@@ -237,6 +244,7 @@ public class LwirReaderParameters {
 		this.vnir_ip =                      gd.getNextString();
 		this.lwir_channels =                str_to_iarr(gd.getNextString());
 		this.vnir_channels =                str_to_iarr(gd.getNextString());
+		this.lwir_telemetry =               gd.getNextBoolean();
 		this.vnir_quality =                 gd.getNextNumber();
 		this.vnir_scale =                   gd.getNextBoolean();
 		this.vnir_autoexp =                 gd.getNextBoolean();

src/main/java/com/elphel/imagej/readers/ImagejJp4Tiff.java

@@ -35,6 +35,7 @@ import java.net.URL;
 import java.net.URLConnection;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.Properties;
@@ -65,8 +66,10 @@ public class ImagejJp4Tiff {
 
 	private static final Logger LOGGER = LoggerFactory.getLogger(ClassList.class);
 	private static final boolean BYPASS_SERVICES = false; //  true;
+	private static final String TELEMETRY_PREFIX = "TLM_";
 	private static final String SERVICES_PATH = "services.properties.forelphel";
 	private static final boolean KEEP_EXTENSION = false; // remove extension for ImagePlus title
+	private static final boolean BOTTOM_TELEMETRY = true; // telemetry (if present) is at the bottom of the image
 
 	// -- Fields --
 
@@ -186,12 +189,13 @@ public class ImagejJp4Tiff {
 		boolean is_le = reader.isLittleEndian();
 		int bytes_per_pixel =  (bpp + 7) / 9;
 		float [] pixels = new float [bytes.length/bytes_per_pixel];
+		ByteBuffer bb = null;
 		if (bytes_per_pixel == 1) {
 			for (int i = 0; i < pixels.length; i++) {
 				pixels[i] = ((bytes[i])) & 0xff;
 			}
 		} else {
-			ByteBuffer bb = ByteBuffer.wrap(bytes);
+			bb = ByteBuffer.wrap(bytes);
 			if (is_le) {
 				bb.order( ByteOrder.LITTLE_ENDIAN);
 			} else {
@@ -208,9 +212,20 @@ public class ImagejJp4Tiff {
 			LOGGER.error("Problem degamma/scaling of "+content_fileName);
 
 		}
-
-		ImageProcessor ip=new FloatProcessor(reader.getSizeX(), reader.getSizeY());
-		ip.setPixels(pixels);
+		boolean telemetry = (bytes_per_pixel == 2);
+		Lepton3Telemetry lepton3Telemetry = null;
+		if (telemetry) {
+			lepton3Telemetry = new Lepton3Telemetry(bb,pixels, true); // bottom
+			telemetry = lepton3Telemetry.hasTelemetry();
+		}
+		ImageProcessor ip = null;
+		if (telemetry) {
+			ip=new FloatProcessor(Lepton3Telemetry.LEPTON3_IMAGE_WIDTH, Lepton3Telemetry.LEPTON3_IMAGE_HEIGHT);
+			ip.setPixels(lepton3Telemetry.getPixels()); // bo
+		} else {
+			ip=new FloatProcessor(reader.getSizeX(), reader.getSizeY());
+			ip.setPixels(pixels);
+		}
 		ip.resetMinAndMax();
 		String prefix = ElphelTiffReader.ELPHEL_PROPERTY_PREFIX;
 		String imageName = content_fileName; // path;
@@ -234,6 +249,12 @@ public class ImagejJp4Tiff {
 				imp.setProperty(std+(key.replace(" ","_").replace("/","_")), meta_hash.get(key).toString());
 			}
 		}
+		if (telemetry) {
+			HashMap<String, String> telemetryMap = lepton3Telemetry.parseTelemetry();
+			for (String key:telemetryMap.keySet()) {
+				imp.setProperty(TELEMETRY_PREFIX+key, telemetryMap.get(key));
+			}
+		}
 		encodeProperiesToInfo(imp);
 		Location.mapFile(content_fileName, null);
 		return imp;

src/main/java/com/elphel/imagej/readers/ImagejJp4TiffMulti.java

@@ -47,6 +47,7 @@ public class ImagejJp4TiffMulti {
 	public ImagePlus [] getMultiImages(
 			final String [] urls,
 			final ImagePlus [] imps,
+//			final boolean telemetry,
 			final boolean scale,
 			final String std) throws IOException, FormatException  // std - include non-elphel properties with prefix std
 	{

src/main/java/com/elphel/imagej/readers/Lepton3Telemetry.java

+/**
+ ** -----------------------------------------------------------------------------**
+ ** Lepton3Telemetry.java
+ **
+ ** Parses FLIR Lepton3 telemetry data
+ **
+ ** Copyright (C) 2019 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  Lepton3Telemetry.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.readers;
+
+import java.nio.ByteBuffer;
+import java.util.HashMap;
+
+public class Lepton3Telemetry {
+	public static final int LEPTON3_IMAGE_WIDTH =     160;
+	public static final int LEPTON3_IMAGE_HEIGHT =    120;
+	public static final int LEPTON3_TELEMETRY_LINES =   2;
+	public static final String REVISION =  "REVISION";   public static final int REVISION_OFFSET =   0;
+	public static final String UPTIME =    "UPTIME";     public static final int UPTIME_OFFSET =     1;
+	public static final String STATUS =    "STATUS";     public static final int STATUS_OFFSET =     3;
+	public static final String MOD_SER =   "MOD_SER";    public static final int MOD_SER_OFFSET =    5;
+	public static final String SOFT_REV =  "SOFT_REV";   public static final int SOFT_REV_OFFSET =  13;
+	public static final String FRAME =     "FRAME";      public static final int FRAME_OFFSET =     20;
+	public static final String MEAN =      "MEAN";       public static final int MEAN_OFFSET =      22;
+	public static final String FPA_TCNT =  "FPA_TCNT";   public static final int FPA_TCNT_OFFSET =  23;
+	public static final String FPA_KELV =  "FPA_KELV";   public static final int FPA_KELV_OFFSET =  24;
+	public static final String ENCL_TCNT = "ENCL_TCNT";  public static final int ENCL_TCNT_OFFSET = 25;
+	public static final String ENCL_KELV = "ENCL_KELV";  public static final int ENCL_KELV_OFFSET = 26;
+	public static final String FFC_KELV =  "FFC_KELV";   public static final int FFC_KELV_OFFSET =  29;
+
+
+	private float [] pixels =  null;
+	private byte  [] btm =     null;
+	private ByteBuffer bbtm  = null;
+
+	public Lepton3Telemetry(ByteBuffer bb, float [] pixels, boolean bottom) {
+		this.pixels = pixels;
+		int offset = 2*(bottom?(LEPTON3_IMAGE_WIDTH * LEPTON3_IMAGE_HEIGHT):0);
+		if (pixels.length > LEPTON3_IMAGE_WIDTH*LEPTON3_IMAGE_HEIGHT) {
+			this.btm = new byte [LEPTON3_IMAGE_WIDTH* LEPTON3_TELEMETRY_LINES * 2];
+			bb.position(offset);
+			this.bbtm = bb.get(btm, 0,btm.length);
+			this.bbtm.order( bb.order()); // or is it already same as in bb?
+			this.pixels = new float [LEPTON3_IMAGE_WIDTH * LEPTON3_IMAGE_HEIGHT];
+			System.arraycopy(
+					pixels,
+					(bottom? 0: LEPTON3_IMAGE_WIDTH * LEPTON3_TELEMETRY_LINES),
+					this.pixels,
+					0,
+					this.pixels.length);
+		}
+	}
+
+	public boolean hasTelemetry() {
+		return bbtm != null;
+	}
+
+	public float [] getPixels() {
+		return pixels;
+	}
+
+	public HashMap<String, String> parseTelemetry(){
+		HashMap<String, String> tm = new HashMap<String, String>();
+		byte [] bytes = getBytes(REVISION_OFFSET,2);
+		tm.put(REVISION,  ""+bytes[1]+"."+bytes[0]);
+		tm.put(UPTIME,    ""+getU32(UPTIME_OFFSET));
+		tm.put(STATUS,    ""+getU32(STATUS_OFFSET));
+		tm.put(MOD_SER,   ""+getHex(MOD_SER_OFFSET,8));
+		tm.put(SOFT_REV,  ""+getHex(SOFT_REV_OFFSET,4));
+		tm.put(FPA_TCNT,  ""+getU16(FPA_TCNT_OFFSET));
+		tm.put(FPA_KELV,  ""+getU16(FPA_KELV_OFFSET));
+		tm.put(ENCL_TCNT, ""+getU16(ENCL_TCNT_OFFSET));
+		tm.put(ENCL_KELV, ""+getU16(ENCL_KELV_OFFSET));
+		tm.put(FFC_KELV,  ""+getU16(FFC_KELV_OFFSET));
+
+/*
+	public static final String FPA_TCNT =  "FPA_TCNT";   public static final int FPA_TCNT_OFFSET =  23;
+	public static final String FPA_KELV =  "FPA_KELV";   public static final int FPA_KELV_OFFSET =  24;
+	public static final String ENCL_TCNT = "ENCL_TCNT";  public static final int ENCL_TCNT_OFFSET = 25;
+	public static final String ENCL_KELV = "ENCL_KELV";  public static final int ENCL_KELV_OFFSET = 26;
+	public static final String FFC_KELV =  "FFC_KELV";   public static final int FFC_KELV_OFFSET =  29;
+
+ */
+		return tm;
+	}
+	// internal methods
+	// input byte array depends on tiff endian for short (16-bit) words, but FLIR word sequence is little endian
+	private byte[] getBytes (int offset, int len) { // offset in shorts, len in shorts
+		byte [] bytes = new byte [2*len];
+		for (int i = 0; i<len; i++) {
+			int d = (bbtm.getShort(2 * (offset + i))) & 0xffff;
+			bytes[2*i+0] = (byte) (d & 0xff);
+			bytes[2*i+1] = (byte) ((d >> 8) & 0xff);
+		}
+		return bytes;
+	}
+
+	private String getString (int offset, int len) { // offset in shorts, len in shorts
+		return new String(getBytes(offset, len));
+	}
+	private String getHex (int offset, int len) { // offset in shorts, len in shorts
+		String s = "";
+		for (byte b :getBytes(offset, len)) {
+			s += String.format("%02x", b);
+		}
+		return s;
+	}
+
+	private int getU16(int offset) {
+		return (bbtm.getShort(2 * offset)) & 0xffff;
+	}
+
+	private long getU32(int offset) {
+		return ((long) (bbtm.getShort(2 * offset)) & 0xffff) + (((long) (bbtm.getShort(2 * (offset+1))) & 0xffff) << 16);
+	}
+
+
+}