Merge branch 'lwir-distort' of git.elphel.com:Elphel/imagej-elphel into lwir-distort

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

@@ -96,6 +96,7 @@ import ij.text.TextWindow;
     		return (eyesisCameraParameters==null)?0:eyesisCameraParameters.getNumStations();
     	}
 
+    	
 		public double getPixelSize(int station, int channel) {
 			return this.eyesisCameraParameters.eyesisSubCameras[station][channel].getPixelSize();
 		}

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

@@ -1248,10 +1248,16 @@ public class EyesisAberrations {
 			if (debugLevel>0) System.out.println("Processing file #"+(imgNum+1)+ " ( of "+files.length+") :"+files[imgNum][0]);
         	ImagePlus imp=new ImagePlus(files[imgNum][0]); // read source file
         	JP4_INSTANCE.decodeProperiesFromInfo(imp);
-       		boolean is_lwir =      lwirReaderParameters.is_LWIR(imp);
-       	    int     fft_size =     is_lwir ? distortionParameters.FFTSize_lwir :    distortionParameters.FFTSize;
-       	    int     fft_overlap =  is_lwir ? distortionParameters.FFTOverlap_lwir : distortionParameters.FFTOverlap;
-       	    imp.setProperty("MONOCHROME",""+is_lwir);
+//       		boolean is_lwir =      lwirReaderParameters.is_LWIR(imp);
+       		int sensor_type =      LwirReaderParameters.sensorType(imp);
+//       	    int     fft_size =     is_lwir ? distortionParameters.FFTSize_lwir :    distortionParameters.FFTSize;
+//       	    int     fft_overlap =  is_lwir ? distortionParameters.FFTOverlap_lwir : distortionParameters.FFTOverlap;
+
+       	    int     fft_size =     distortionParameters.getFFTSize(sensor_type);
+       	    int     fft_overlap =  distortionParameters.getFFTOverlap(sensor_type);
+       	    
+       	    
+       	    imp.setProperty("MONOCHROME",""+(sensor_type == 1));
         	// pad image to full sensor size
 			int numGridImage=fileIndices[imgNum];
 			int chn = distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].getChannel();
@@ -1261,7 +1267,8 @@ public class EyesisAberrations {
 					  sensor_width_height, // eyesisCorrections.pixelMapping.sensors[srcChannel].getSensorWH(),
 					  true); // boolean replicate);
 // TODO: Add vignetting correction ?
-        	MatchSimulatedPattern matchSimulatedPattern= new MatchSimulatedPattern(distortionParameters.FFTSize);
+//        	MatchSimulatedPattern matchSimulatedPattern= new MatchSimulatedPattern(distortionParameters.FFTSize);
+        	MatchSimulatedPattern matchSimulatedPattern= new MatchSimulatedPattern(distortionParameters.getFFTSize(sensor_type));
 			boolean [] correlationSizesUsed=null;
 			float [][] simArray=         	null;
 
@@ -1348,7 +1355,7 @@ public class EyesisAberrations {
         					fft_size, // FFT_SIZE, // int               fft_size,
         					colorComponents, //COMPONENTS,   // ColorComponents colorComponents,
         					PSF_subpixel, //PSF_SUBPIXEL, // int           PSF_subpixel,
-        					(is_lwir?otfFilterParameters_lwir:otfFilterParameters),
+        					((sensor_type == 1) ?otfFilterParameters_lwir:otfFilterParameters),
 //        					otfFilterParameters, // OTF_FILTER, // OTFFilterParameters otfFilterParameters,
         					psfParameters, //PSF_PARS, // final PSFParameters psfParameters
         					psfParameters.minDefinedArea , //PSF_PARS.minDefinedArea, // final double       minDefinedArea,

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

@@ -632,6 +632,9 @@ horizontal axis:
 		int nImg=indices[index];
 
 		int subCam=        distortionCalibrationData.getImageChannel(images[nImg]);
+		int sensor_type =  eyesisCameraParameters.getSensorType(subCam);
+
+		
 //		int stationNumber= distortionCalibrationData.getImageStation(numGridImage), // station number
 		double timeStamp=  distortionCalibrationData.getImageTimestamp(images[nImg]);
 
@@ -673,7 +676,9 @@ horizontal axis:
 		if (this.debugLevel>1) lensDistortions.showHintGrid(hintGrid);
 
 
-		MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern(this.distortionParametersDefault.FFTSize); // new instance, all reset
+///		MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern(this.distortionParametersDefault.FFTSize); // new instance, all reset
+		MatchSimulatedPattern matchSimulatedPattern = new MatchSimulatedPattern(distortionParametersDefault.getFFTSize(sensor_type)); // new instance, all reset
+		//sensort_type
 		// next 2 lines are not needed for the new instance, but can be
 		// used alternatively if keeping it
 		matchSimulatedPattern.invalidateFlatFieldForGrid(); // Reset Flat Filed calibration - different image.
@@ -690,7 +695,7 @@ horizontal axis:
 					", initial number of pointers was "+numPointers);
 		}
 //matchSimulatedPatterns[numSensor].getChannel(images[numSensor])+" ");
-		MatchSimulatedPattern.DistortionParameters distortionParameters = modifyDistortionParameters();
+		MatchSimulatedPattern.DistortionParameters distortionParameters = modifyDistortionParameters(sensor_type);
 		SimulationPattern.SimulParameters simulParameters = modifySimulParameters();
 
 		boolean noMessageBoxes=true;
@@ -729,34 +734,13 @@ horizontal axis:
 
 	}
 
-	/*
-	 * 	private showDoubleFloatArrays SDFA_INSTANCE= new showDoubleFloatArrays(); // just for debugging?
-   		this.SDFA_INSTANCE.showArrays(gridXYZCorr, getGridWidth(), getGridHeight(),  true, "Grid corrections", titles);
-
-	 *
-					gd.addChoice( // ArrayIndexOutOfBoundsException: 21
-							this.distortionCalibrationData.getParameterName(parIndex)+
-							" ("+sValue+" "+
-							this.distortionCalibrationData.getParameterUnits(parIndex)+")"+
-							(this.distortionCalibrationData.isSubcameraParameter(parIndex)?(" s"+subCam):"com "),
-							this.definedModes, this.definedModes[this.parameterMode[numSeries][i]]);
-
-	 *
-	 * 					this.parameterMode[numSeries][i]=gd.getNextChoiceIndex();
-			PatternParameters patternParameters, // should not be  null
-			boolean equalizeGreens,
-			int threadsMax,
-			boolean updateStatus,
-			int debug_level) {// debug level used inside loops
-
-	 *
-	 *
-	 */
-	public MatchSimulatedPattern.DistortionParameters modifyDistortionParameters(){
+	public MatchSimulatedPattern.DistortionParameters modifyDistortionParameters(int sensor_type){
 		MatchSimulatedPattern.DistortionParameters distortionParameters = this.distortionParametersDefault.clone();
 		distortionParameters.refineInPlace = false;
 		distortionParameters.correlationMaxOffset = this.goniometerParameters.maxCorr;
-		distortionParameters.correlationSize = this.goniometerParameters.correlationSize;
+//		distortionParameters.correlationSize = this.goniometerParameters.correlationSize;
+		distortionParameters.setCorrelationSize(this.goniometerParameters.correlationSize, sensor_type);
+		
 		distortionParameters.correlationGaussWidth = this.goniometerParameters.correlationGaussWidth;
 		distortionParameters.refineCorrelations = false;
 		distortionParameters.fastCorrelationOnFirstPass = true;
@@ -767,7 +751,8 @@ horizontal axis:
 		distortionParameters.flatFieldExpand = this.goniometerParameters.flatFieldExpand;
 		distortionParameters.numberExtrapolated = 1; // measuring distortions -
 		distortionParameters.correlationMinInitialContrast=this.goniometerParameters.correlationMinInitialContrast;
-		distortionParameters.minimalPatternCluster=this.goniometerParameters.minimalPatternCluster;
+//		distortionParameters.minimalPatternCluster=this.goniometerParameters.minimalPatternCluster;
+		distortionParameters.setMinimalPatternCluster(this.goniometerParameters.minimalPatternCluster, sensor_type);
 		distortionParameters.scaleMinimalInitialContrast=this.goniometerParameters.scaleMinimalInitialContrast;
 		distortionParameters.searchOverlap=this.goniometerParameters.searchOverlap;
 		return distortionParameters;
@@ -781,7 +766,7 @@ horizontal axis:
 		return simulParameters;
 	}
 
-	public double[] estimateOrientation(
+	public double[] estimateOrientation( // FIXME: Does not use LWIR parameters, assumes EO!
 			ImagePlus[] images, // last acquire images with number of pointers
 								// detected>0
 			DistortionCalibrationData distortionCalibrationData,
@@ -792,6 +777,7 @@ horizontal axis:
 			int threadsMax,
 			boolean updateStatus,
 			int debug_level) {// debug level used inside loops
+		int sensor_type = 0; // EO
 		long startTime = System.nanoTime();
 		if (lensDistortions == null) {
 			String msg = "lensDistortions is not initialized";
@@ -801,7 +787,7 @@ horizontal axis:
 
 		// remove unneeded, copied from updateFocusGrid() Now it is not needed?
 		SimulationPattern.SimulParameters simulParameters = modifySimulParameters();
-		MatchSimulatedPattern.DistortionParameters distortionParameters = modifyDistortionParameters();
+		MatchSimulatedPattern.DistortionParameters distortionParameters = modifyDistortionParameters(sensor_type);
 
 		int numImages = 0;
 		for (int i = 0; i < images.length; i++)
@@ -834,8 +820,8 @@ horizontal axis:
 		for (int numSensor = 0; numSensor < images.length; numSensor++)
 			if (images[numSensor] != null) {
 				// reset matchSimulatedPattern, so it will start from scratch
-				this.matchSimulatedPatterns[numSensor] = new MatchSimulatedPattern(
-						this.distortionParametersDefault.FFTSize); // new instance, all reset
+//				this.matchSimulatedPatterns[numSensor] = new MatchSimulatedPattern(	this.distortionParametersDefault.FFTSize); // new instance, all reset
+				this.matchSimulatedPatterns[numSensor] = new MatchSimulatedPattern(distortionParametersDefault.getFFTSize(sensor_type)); // new instance, all reset
 				// next 2 lines are not needed for the new instance, but can be
 				// used alternatively if keeping it
 				this.matchSimulatedPatterns[numSensor].invalidateFlatFieldForGrid(); // Reset Flat Filed calibration - different image.

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

@@ -63,8 +63,9 @@ public class LensAdjustment {
 		distortionParameters.refineInPlace=false;
 
 		distortionParameters.correlationMaxOffset=focusMeasurementParameters.maxCorr;
-
-		distortionParameters.correlationSize=focusMeasurementParameters.correlationSize;
+ 		int sensor_type = 0; // EO
+//		distortionParameters.correlationSize=focusMeasurementParameters.correlationSize;
+		distortionParameters.setCorrelationSize(focusMeasurementParameters.correlationSize,sensor_type);
 		distortionParameters.correlationGaussWidth=focusMeasurementParameters.correlationGaussWidth;
 		distortionParameters.refineCorrelations=false;
 		distortionParameters.fastCorrelationOnFirstPass=true;

src/main/java/com/elphel/imagej/cameras/EyesisCameraParameters.java

@@ -1407,6 +1407,10 @@ import ij.gui.GenericDialog;
     		return eyesisSubCameras[0][ncam].isLWIR();
     	}
     	
+    	public int getSensorType(int ncam) {
+    		return eyesisSubCameras[0][ncam].isLWIR()? 1 : 0;
+    	}
+    	
     	/**
     	 * Setting default camera geometry parameters for LWIR16 prototype system
     	 * @return false if number of cameras is not 20

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

@@ -44,6 +44,7 @@ public class LwirReaderParameters {
 	public final static int []    FFC_GROUPS=          {1,2,4};
 	public static final String [] SENSOR_TYPES = {"EO","LWIR"};
 	public static final String    SENSOR_TYPE =  "SENSOR_TYPE";
+	protected static int MAX_LWIR_WIDTH =     1024; //
 	
 	private boolean parameters_updated =     false;
 	protected String  camera_name =          "Talon"; // "LWIR16";
@@ -73,7 +74,6 @@ public class LwirReaderParameters {
 	protected double  eo_gain_rg =           0.7705; // 1.116; halogen/fluorescent
 	protected double  eo_gain_bg =           2.401;  // 1.476;
 	protected boolean [] selected_channels = {true, true, true, true, true, true, true, true};
-	protected int     max_lwir_width =       1024; //
 /*
 	protected double [] eo_exp_corr = {1.0, 1.0, 1.0, 1.0};
 	protected double [] eo_gcorr_rbgb = {
@@ -145,11 +145,11 @@ public class LwirReaderParameters {
 		return 20;
 	}
 
-	public boolean is_LWIR(int width) {
-		return width <= max_lwir_width;
+	public static boolean is_LWIR(int width) {
+		return width <= MAX_LWIR_WIDTH;
 	}
 
-	public boolean is_LWIR(ImagePlus imp){
+	public static boolean is_LWIR(ImagePlus imp){
 		// See if image has LwirReaderParameters.SENSOR_TYPE property, then use is_LWIR(String property_value),
 		// if not - use old width property
 		if (imp.getProperty("WOI_WIDTH")==null) {
@@ -160,6 +160,16 @@ public class LwirReaderParameters {
 		}
 		return is_LWIR(imp.getWidth());
 	}
+	public static int sensorType(ImagePlus imp) {
+		if (imp.getProperty("WOI_WIDTH")==null) {
+			EyesisTiff.decodeProperiesFromInfo(imp);
+		}
+		if (imp.getProperty(SENSOR_TYPE)!=null) {
+			return (is_LWIR((String) imp.getProperty(SENSOR_TYPE)))? 1:0;
+		}
+		return is_LWIR(imp.getWidth())? 1 : 0;
+		
+	}
 
 	public int getDebugLevel() {
 		return this.debug_level;

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

@@ -51,6 +51,22 @@ public class ImagejJp4TiffMulti {
 			final boolean scale,
 			final String std) throws IOException, FormatException  // std - include non-elphel properties with prefix std
 	{
+		return 	getMultiImages(
+				urls,
+				imps,
+				0.0, // final double timeout_sec,
+				scale,
+				std);
+	}
+	
+	
+	public ImagePlus [] getMultiImages(
+			final String [] urls,
+			final ImagePlus [] imps,
+			final double timeout_sec,
+			final boolean scale,
+			final String std) throws IOException, FormatException  // std - include non-elphel properties with prefix std
+	{
 //		final ImagePlus [] imps = new ImagePlus [urls.length];
 		LOGGER.error("Please ignore 'File has length 0 and may be corrupt' - caused by bioformat reading memory file");
    		final Thread[] threads = newThreadArray(MAX_THREADS);