preparing for the goniometer with LWIR

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

@@ -29,12 +29,10 @@ package com.elphel.imagej.calibration;
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import com.elphel.imagej.calibration.CalibrationHardwareInterface.CamerasInterface;
-import com.elphel.imagej.calibration.CalibrationHardwareInterface.GoniometerMotors;
-import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
 import com.elphel.imagej.cameras.EyesisCameraParameters;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.common.WindowTools;
+import com.elphel.imagej.lwir.LwirReader;
 
 import ij.IJ;
 import ij.ImagePlus;
@@ -53,6 +51,7 @@ horizontal axis:
 																				// for
 																				// debugging
 	public CalibrationHardwareInterface.CamerasInterface cameras = null;
+	LwirReader lwirReader = null;
 	// public CalibrationHardwareInterface.LaserPointers lasers = null;
 	// public static CalibrationHardwareInterface.FocusingMotors motorsS=null;
 	// public DistortionProcessConfiguration
@@ -81,7 +80,6 @@ horizontal axis:
 
 	public Goniometer(CalibrationHardwareInterface.CamerasInterface cameras,
 			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
-//			MatchSimulatedPattern.DistortionParameters distortion,
 			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
 			EyesisCameraParameters eyesisCameraParameters,
 			MatchSimulatedPattern.LaserPointer laserPointers,
@@ -98,9 +96,34 @@ horizontal axis:
 		this.simulParametersDefault=simulParametersDefault;
 		this.goniometerParameters=goniometerParameters;
 		this.distortionProcessConfiguration=distortionProcessConfiguration;
+	}
 
+	public Goniometer(
+			LwirReader lwirReader,
+//			CalibrationHardwareInterface.CamerasInterface cameras,
+			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
+			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+			EyesisCameraParameters eyesisCameraParameters,
+			MatchSimulatedPattern.LaserPointer laserPointers,
+			SimulationPattern.SimulParameters simulParametersDefault,
+			Goniometer.GoniometerParameters goniometerParameters,
+			DistortionProcessConfiguration distortionProcessConfiguration
+			) {
+		this.lwirReader= lwirReader;
+//		this.cameras = cameras;
+		this.distortionParametersDefault = distortionParametersDefault;
+//		this.distortion = distortion;
+		this.patternDetectParameters=patternDetectParameters;
+		this.eyesisCameraParameters = eyesisCameraParameters;
+		this.laserPointers = laserPointers;
+		this.simulParametersDefault=simulParametersDefault;
+		this.goniometerParameters=goniometerParameters;
+		this.distortionProcessConfiguration=distortionProcessConfiguration;
 	}
 
+
+
+
 	//goniometerMotors
 	private enum MOT_ACT {
 		MOVE_SPEC,
@@ -222,6 +245,8 @@ horizontal axis:
 		if (!OK) System.out.println("motorsMove()->false");
 		return true; // OK; // So will re-open dialog even after abort
 	}
+
+
 	public boolean scanAndAcquire(
 			double targetAngleHorizontal,
 			double targetAngleVertical,
@@ -276,7 +301,6 @@ horizontal axis:
 			double cosMinAbsTilt=Math.cos(minAbsTilt*Math.PI/180.0);
 			if (this.debugLevel>2) System.out.println("tilt="+IJ.d2s(tilt,2)+"tiltL="+IJ.d2s(tiltL,2)+", tiltH="+IJ.d2s(tiltH,2)+
 					", minAbsTilt="+IJ.d2s(minAbsTilt,2)+", cosMinAbsTilt="+IJ.d2s(cosMinAbsTilt,2));
-//			double axialRange=
 			double scanStep=scanStepAxial;
 			double overlap=scanOverlapHorizontal;
 			int numAxialSteps=(int) Math.ceil((scanLimitAxialHigh-scanLimitAxialLow)*cosMinAbsTilt/scanStepAxial);
@@ -296,8 +320,6 @@ horizontal axis:
 
 			// spread evenly
 			if (numAxialSteps>0){ // increase vertical overlap to make it same for all images
-//				scanStep=(scanLimitAxialHigh-scanLimitAxialLow)*cosMinAbsTilt/numAxialSteps;
-//				overlap=1.0-(scanStep/targetAngleHorizontal);
 				scanStep=(scanLimitAxialHigh-scanLimitAxialLow)/numAxialSteps;
 				overlap=1.0-(scanStep*cosMinAbsTilt/targetAngleHorizontal);
 			}
@@ -322,14 +344,8 @@ horizontal axis:
 			  System.out.println();
 		  }
 		}
-//		return true;
-		
-//	motorsSimultaneous	
-// show current tilt/axial
-//		double absTiltRange=Math.abs(this.goniometerParameters.scanLimitTiltStart-this.goniometerParameters.scanLimitTiltStart);
 
 		GenericDialog gd = new GenericDialog("Start scanning");
-		//	    		this.serialNumber, // camera serial number string
 		gd.addMessage("About to start scanning and recording images, parameters are set in the \"Configure Goniometer\" dialog");
 		gd.addMessage("Please make sure goniometer motors are set that 0,0 corresponds to the camera in the initial position -");
 		gd.addMessage("vertical and cables are not entangled, camera exposure is set correctly.");
@@ -389,7 +405,6 @@ horizontal axis:
 			if (this.debugLevel>0) System.out.println(status);
 			if (updateStatus) IJ.showStatus(status);
 			this.goniometerParameters.motorsSimultaneous=false; // not yet implemented
-			//			if (!this.goniometerParameters.motorsSimultaneous){
 			OK= this.goniometerParameters.goniometerMotors.moveMotorSetETA(tiltMotor, tiltMotorPosition);
 			if (!OK) {
 				String msg="Could not set motor "+(tiltMotor+1)+" to move to "+tiltMotorPosition+" - may be out of limit";
@@ -433,10 +448,19 @@ horizontal axis:
 				}
 				// update motor positions in the image properties, acquire and save images.
 				// TODO: Make acquisition/decoding/laser identification multi-threaded
+
+				if (cameras != null) {
 					this.cameras.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations
 					this.cameras.reportTiming=debugTiming;
-
 					this.cameras.acquire(this.distortionProcessConfiguration.sourceDirectory,true, updateStatus); // true - use lasers, updateStatus - make false?
+				} else if (lwirReader != null) {
+					this.lwirReader.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations
+					this.lwirReader.reportTiming=debugTiming;
+					this.lwirReader.acquire(this.distortionProcessConfiguration.sourceDirectory); // true - use lasers, updateStatus - make false?
+				} else {
+					System.out.println("Neignter traditional camera/rig, no LWIR rig are initialized, dry run");
+				}
+
 				this.lastScanStep++;
 				if (stopRequested.get()>1){
 					if (this.debugLevel>0) System.out.println("User interrupt");
@@ -1185,6 +1209,7 @@ horizontal axis:
 			this.scanBidirectional=scanBidirectional;
 			this.motorsSimultaneous=motorsSimultaneous;
     	}
+    	@Override
 		public GoniometerParameters clone(){
     		return new GoniometerParameters(
     				this.goniometerMotors,

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

@@ -4873,10 +4873,10 @@ private Panel panel1,
 		if (LWIR_READER == null) {
 			LWIR_READER =  new LwirReader(CLT_PARAMETERS.lwir);
 		}
-        ImagePlus [] imps = LWIR_READER.acquire();
+        ImagePlus [] imps = LWIR_READER.acquire("/data_ssd/imagej-elphel/attic/camera_img/test"); // directory to save
 		if (imps != null) {
 			for (ImagePlus imp: imps) {
-				imp.show();
+//				imp.show();
 			}
 		}
 

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

@@ -26,6 +26,7 @@
  */
 package com.elphel.imagej.lwir;
 
+import java.io.File;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.util.Properties;
@@ -40,9 +41,13 @@ import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
 import org.xml.sax.SAXException;
 
+import com.elphel.imagej.readers.ImagejJp4Tiff;
 import com.elphel.imagej.readers.ImagejJp4TiffMulti;
 
+import ij.IJ;
 import ij.ImagePlus;
+import ij.Prefs;
+import ij.io.FileSaver;
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 import loci.formats.FormatException;
@@ -68,7 +73,7 @@ public class LwirReader {
 	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 FRAMES_SKIP = 4;
 	public static final int MAX_THREADS = 100; // combine from all classes?
 
 	/** Logger for this class. */
@@ -82,6 +87,10 @@ public class LwirReader {
 	private LwirReaderParameters lwirReaderParameters = null;
 	private LwirReaderParameters last_programmed = null;
 
+
+	private int [] motorsPosition = null;
+	public boolean reportTiming=false;
+
 	// -- constructors
 
 	public LwirReader() {
@@ -99,6 +108,15 @@ public class LwirReader {
 	}
 
 
+   	public void setMotorsPosition (int [] position) {
+   		this.motorsPosition=position;
+   	}
+
+   	public int [] getMotorsPosition() {
+   		return this.motorsPosition;  // may be null
+   	}
+
+
 	// TODO: create
 	public boolean reSyncNeeded() {
 		return out_of_sync;
@@ -220,6 +238,10 @@ public class LwirReader {
 				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]);
 			// TODO: Overwrite some properties?
 		}
 
@@ -333,10 +355,12 @@ public class LwirReader {
 		for (int c : lrp.lwir_channels) {
 			channels |= 1 << c;
 		}
-		String hex_chan = String.format("%x", channels);
+		String hex_chan = String.format("0x%x", channels);
 
 		String url = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
 				"&SENSOR_REGS67=0!"+hex_chan;
+//		String url = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
+//				"&SENSOR_REGS67=0&*SENSOR_REGS67="+hex_chan;
 		Document dom=null;
 		LOGGER.warn("calibrate(): Perform calibration (instead of 15 frames), url="+url);
 		try {
@@ -415,12 +439,12 @@ public class LwirReader {
 		return true;
 	}
 
-	public ImagePlus [] acquire() {
-		return acquire(lwirReaderParameters);
+	public ImagePlus [] acquire(String dirpath) {
+		return acquire(lwirReaderParameters, dirpath);
 	}
 
 
-	public ImagePlus [] acquire(LwirReaderParameters lrp) {
+	public ImagePlus [] acquire(LwirReaderParameters lrp, String dirpath) {
 		if (!condProgramLWIRCamera(lrp)) {
 			LOGGER.error("acquire(): failed to program cameras");
 			return null;
@@ -439,6 +463,20 @@ public class LwirReader {
 			return null;
 		}
 		LOGGER.debug("LWIR_ACQUIRE: got "+imps.length+" image sets");
+// Verify fresh FFC for all channels
+		double [] after_ffc = new double [lrp.lwir_channels.length];
+		for (int chn = 0; chn < after_ffc.length; chn++) {
+			double uptime = Double.NaN, ffctime = Double.NaN;
+			try {
+				uptime =  Double.parseDouble(((String) imps[0][chn].getProperty("TLM_UPTIME")));
+				ffctime = Double.parseDouble(((String) imps[0][chn].getProperty("TLM_FFC_TIME")));
+				after_ffc[chn] = uptime-ffctime;
+			} catch (Exception e) {
+				LOGGER.warn("acquire(): TLM_UPTIME and/or TLM_FFC_TIME properties are not available for"+imps[0][chn].getTitle());
+			}
+			LOGGER.warn(String.format("LWIR channel %d time from FFC: %.3f", chn, after_ffc[chn]));
+		}
+
 		int [] lags = new int [lrp.lwir_channels.length + lrp.vnir_channels.length];
 		for (int i = 0; i < lags.length; i++) {
 			lags[i] = (i >= lrp.lwir_channels.length) ? lrp.vnir_lag : 0;
@@ -464,6 +502,27 @@ public class LwirReader {
 			}
 		}
 		ImagePlus [] imps_avg = averageMultiFrames(imps_sync);
+
+
+
+		if (dirpath != null) {
+			File  f_dir = new File(dirpath);
+			// get series path from the first channel file title
+			String first_name = imps_sync[0][0].getTitle();
+			String set_name = first_name.substring(0, first_name.lastIndexOf('_'));
+			String set_path = dirpath+Prefs.getFileSeparator()+set_name;
+			File  set_dir = new File(set_path);
+			set_dir.mkdirs(); // including parent
+			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)" );
+   				fs.saveAsTiff(path);
+			}
+		}
 		return imps_avg;
 	}