Debugging fitting strategies, initial image parameter setup

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

@@ -2634,6 +2634,7 @@ if (MORE_BUTTONS) {
 					parFilter,
 					""); //String defaultPath
 			if ((pathname==null) || (pathname=="")) return;
+			System.out.println("*** Will not work with different size senspors !!!");
 		    DISTORTION_CALIBRATION_DATA.setMaskFromImageStack(pathname);
 			if (LENS_DISTORTIONS!=null) LENS_DISTORTIONS.updateSensorMasks();
 			return;
@@ -3642,8 +3643,8 @@ if (MORE_BUTTONS) {
 
 
 				double threadPitch=0.35; // M1.6
-				double dPx0=camPars.eyesisSubCameras[stationNumber][0].px0-(camPars.sensorWidth/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaX;
-				double dPy0=camPars.eyesisSubCameras[stationNumber][0].py0-(camPars.sensorHeight/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaY;
+				double dPx0=camPars.eyesisSubCameras[stationNumber][0].px0-(camPars.getSensorWidth(0)/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaX;
+				double dPy0=camPars.eyesisSubCameras[stationNumber][0].py0-(camPars.getSensorHeight(0)/2)-FOCUS_MEASUREMENT_PARAMETERS.centerDeltaY;
 			   	double psi=camPars.eyesisSubCameras[stationNumber][0].psi;     // degrees, rotation (of the sensor) around the optical axis. Positive if camera is rotated clockwise looking to the target
 
 			   	FOCUS_MEASUREMENT_PARAMETERS.result_PX0=camPars.eyesisSubCameras[stationNumber][0].px0;
@@ -5026,8 +5027,8 @@ if (MORE_BUTTONS) {
 						if (DEBUG_LEVEL>2) System.out.println("sfeParameters["+numSFE+"].length="+sfeParameters[numSFE].length);
 						if (DEBUG_LEVEL>2) System.out.println("sfeParameters["+numSFE+"]["+iLens+"].length="+sfeParameters[numSFE][iLens].length);
 						sfeParameters[numSFE][iLens][iState]=FOCUS_MEASUREMENT_PARAMETERS.clone();
-						sensorDimensions[numSFE][0]=EYESIS_CAMERA_PARAMETERS.sensorWidth; // should be the same for all lenses/states
-						sensorDimensions[numSFE][1]=EYESIS_CAMERA_PARAMETERS.sensorHeight;
+						sensorDimensions[numSFE][0]=EYESIS_CAMERA_PARAMETERS.getSensorWidth(numSFE); // should be the same for all lenses/states
+						sensorDimensions[numSFE][1]=EYESIS_CAMERA_PARAMETERS.getSensorHeight(numSFE);
 						iState++;
 					}
 					iLens++;
@@ -5492,12 +5493,12 @@ if (MORE_BUTTONS) {
 				String path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+
 				(modeAverage?"-summary.csv":"-tempscan.csv");
 				if (MASTER_DEBUG_LEVEL>0) System.out.println ((modeAverage?"Saving averaged measurements to ":"Saving temperature measurement log data to ")+path);
-				int sensorWidth=2992,sensorHeight=1936;
+				int sensorWidth=2592,sensorHeight=1936;
 				if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)&&
 						(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData!=null) &&
 						(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters!=null)){
-					sensorWidth=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.sensorWidth;
-					sensorHeight=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.sensorHeight;
+					sensorWidth=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(0);
+					sensorHeight=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(0);
 				}
 				if (FOCUSING_FIELD!=null){
 					sensorWidth=FOCUSING_FIELD.sensorWidth;
@@ -5918,7 +5919,12 @@ if (MORE_BUTTONS) {
 				IJ.showMessage("LENS_DISTORTION.fittingStrategy is not set");
 				return;
 			}
-			LENS_DISTORTIONS.listImageSets();
+			GenericDialog gd=new GenericDialog ("Select list mode");
+    		gd.addNumericField("Mode 0 - old, 1 - shift/Rots", 0, 0);
+    		gd.showDialog();
+    		if (gd.wasCanceled()) return;
+    		int listMode=          (int) gd.getNextNumber();
+			LENS_DISTORTIONS.listImageSets(listMode);
 			return;
 		}
 /* ======================================================================== */
@@ -8986,12 +8992,20 @@ if (MORE_BUTTONS) {
     	    	for (int nChn=0;nChn<masks.length;nChn++) if ((nChn<selectedChannels.length)&&!selectedChannels[nChn]) masks[nChn]=null;
     	    }
 
-			if (showSensorMasks) this.SDFA_INSTANCE.showArrays( //java.lang.ArrayIndexOutOfBoundsException: 313632
+    	    if (showSensorMasks) {
+    	    	boolean same_size = true;
+    	    	for (int i = 1; i < masks.length; i++) same_size &= (masks[i].length == masks[0].length);
+    	    	if (same_size) {
+    	    		this.SDFA_INSTANCE.showArrays( //java.lang.ArrayIndexOutOfBoundsException: 313632
     	    				masks,
-					LENS_DISTORTIONS.pixelCorrectionWidth/ LENS_DISTORTIONS.pixelCorrectionDecimation,
-					LENS_DISTORTIONS.pixelCorrectionHeight/LENS_DISTORTIONS.pixelCorrectionDecimation,
+    	    				LENS_DISTORTIONS.getSensorWidth(0)/ LENS_DISTORTIONS.getDecimateMasks(0),
+    	    				LENS_DISTORTIONS.getSensorHeight(0)/LENS_DISTORTIONS.getDecimateMasks(0),
     	    				true,
     	    				"nonVinetting masks");
+    	    	} else {
+    	    		System.out.println("**** Can't show sesnor masks for different size sesnors as a stack! ");
+    	    	}
+    	    }
 			double [][][][] sensorGrids=LENS_DISTORTIONS.calculateGridFlatField(
 					serNumber,
 					masks,
@@ -9556,7 +9570,7 @@ if (MORE_BUTTONS) {
 				true,                    // boolean read_grids
 				MASTER_DEBUG_LEVEL);
 
-	    if (MASTER_DEBUG_LEVEL <100) return true;
+///	    if (MASTER_DEBUG_LEVEL <100) return true;
 	    // patterns are not yet read here!
 
 /*
@@ -9639,6 +9653,11 @@ if (MORE_BUTTONS) {
 				path,
 				PROCESS_PARAMETERS.useXML,
 				null); // Properties properties
+		if (LENS_DISTORTIONS==null) {
+			System.out.println("Creating new LENS_DISTORTIONS");
+			LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
+		}
+//		ABERRATIONS_PARAMETERS.selectCalibrationDirectory(true, ABERRATIONS_PARAMETERS.calibrationDirectory, true);
 		return EYESIS_CAMERA_PARAMETERS.importSystem(
 				properties,
 				prefix,

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

 package com.elphel.imagej.calibration;
+import java.awt.Rectangle;
+import java.util.Properties;
+
+import com.elphel.imagej.jp4.JP46_Reader_camera;
+
 /*
  **
  ** PatternParameters.java
@@ -28,12 +33,6 @@ import ij.ImageStack;
 import ij.gui.GenericDialog;
 import ij.io.FileSaver;
 import ij.io.Opener;
-
-import java.awt.Rectangle;
-import java.util.Properties;
-
-import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
-import com.elphel.imagej.jp4.JP46_Reader_camera;
 	/* gridGeometry:
 	 * [v][u][0] - x(mm) of the node(u,v), right (looking to the wall) - positive
 	 * [v][u][1] - y(mm) of the node(u,v), down - positive
@@ -260,6 +259,7 @@ import com.elphel.imagej.jp4.JP46_Reader_camera;
 			setPhotometric(viewMap);
 			calculateGridGeometryAndPhotometric(true);
 		}
+		@Override
 		public PatternParameters clone() {
 			PatternParameters patternParameters= new PatternParameters(
 					this.viewMap,
@@ -609,13 +609,15 @@ import com.elphel.imagej.jp4.JP46_Reader_camera;
 			GenericDialog gd = new GenericDialog("Initial Wall pattern parameters");
 			gd.addNumericField("Pattern full width",                  this.patternWidth, 1,6,"mm"); // pattern full width in mm
 			gd.addNumericField("Pattern full height",                 this.patternHeight, 1,6,"mm"); // pattern full width in mm
-			gd.addNumericField("Distance between opposite sign nodes",this.patternHalfPeriod, 4,8,"mm"); // istance between opposite sign nodes in mm
-			gd.addNumericField("Pattern tilt (clockwise)",            this.patternTilt, 1,5,"degrees"); //  pattern tilt (degrees) - U clockwise from X-right (V clockwise from Y-down)
+			gd.addNumericField("Distance between opposite sign nodes",this.patternHalfPeriod, 4,8,"mm"); // distance between opposite sign nodes in mm
+			gd.addNumericField("Pattern tilt (clockwise)",            this.patternTilt, 3,8,"degrees"); //  pattern tilt (degrees) - U clockwise from X-right (V clockwise from Y-down)
 			gd.addNumericField("Average grid RED   (1.0 for white)",  this.averageRGB[0], 3,5,"x"); //
 			gd.addNumericField("Average grid GREEN (1.0 for white)",  this.averageRGB[1], 3,5,"x"); //
 			gd.addNumericField("Average grid BLUE  (1.0 for white)",  this.averageRGB[2], 3,5,"x"); //
 
 			gd.addNumericField("Number of sensors (>24 - two groups, 0 - do not change)",this.defaultNumberOfChannels,0); //
+			gd.addCheckbox("Reset to standard fine pitch pattern" ,   false);
+			gd.addCheckbox("Reset to standard LWIR pattern" ,         false);
 
 			gd.addMessage("Pressing OK will recalculate grid and clear current grid calibration");
 			gd.showDialog();
@@ -628,6 +630,27 @@ import com.elphel.imagej.jp4.JP46_Reader_camera;
 			this.averageRGB[1]=        gd.getNextNumber();
 			this.averageRGB[2]=        gd.getNextNumber();
 			int numberOfChannels= (int)gd.getNextNumber();
+			boolean use_fine_pattern = gd.getNextBoolean();
+			boolean use_lwir_pattern = gd.getNextBoolean();
+
+			if (use_fine_pattern) {
+				this.patternWidth=         7010.0;
+				this.patternHeight=        3073.0;
+				this.patternHalfPeriod=      41.57;
+				this.patternTilt=             5.0;
+				this.averageRGB[0]=           1.0;
+				this.averageRGB[1]=           1.0;
+				this.averageRGB[2]=           1.0;
+
+			} else if (use_lwir_pattern) {
+				this.patternWidth=         7010.0; // 7192.0
+				this.patternHeight=        2997.2;
+				this.patternHalfPeriod=     178.65;
+				this.patternTilt=             14.036;
+				this.averageRGB[0]=           1.0;
+				this.averageRGB[1]=           1.0;
+				this.averageRGB[2]=           1.0;
+			}
 
 			if (numberOfChannels>0){
 				initDefaultChannels(numberOfChannels);

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

@@ -25,6 +25,9 @@ package com.elphel.imagej.cameras;
 import java.util.Properties;
 
     public class EyesisSubCameraParameters{
+    	public int sensorWidth=      2592; // moving here from the camera as a whole
+    	public int sensorHeight=     1936;
+    	public int decimateMasks=       1;
     	// origin is on the rotation axis of the tube body closest to the goniometer horizontal axis
     	public boolean cartesian = false; // cartesian coordinates mode (false - cylindrical)
     	public int    lensDistortionModel=0;
@@ -80,6 +83,9 @@ import java.util.Properties;
 		*/
 
     	public EyesisSubCameraParameters(
+    	    	int sensorWidth,
+    	    	int sensorHeight,
+    	    	int decimateMasks,
     			boolean cartesian,
     			int lensDistortionModel,
     			boolean enableNoLaser,
@@ -111,6 +117,9 @@ import java.util.Properties;
     			int sensor_port,
     			int subchannel
     	){
+    		this.decimateMasks = decimateMasks;
+        	this.sensorWidth= sensorWidth;
+        	this.sensorHeight=sensorHeight;
     		this.cartesian = cartesian;
     		this.lensDistortionModel=lensDistortionModel;
     		this.enableNoLaser=enableNoLaser;
@@ -156,6 +165,9 @@ import java.util.Properties;
     	@Override
 		public EyesisSubCameraParameters clone() {
     		return new EyesisSubCameraParameters(
+    				this.sensorWidth,
+    				this.sensorHeight,
+    				this.decimateMasks,
     	    		this.cartesian,
     				this.lensDistortionModel,
     				this.enableNoLaser,
@@ -196,6 +208,9 @@ import java.util.Properties;
     	}
 // TODO: add/restore new properties
     	public void setProperties(String prefix,Properties properties){
+    		properties.setProperty(prefix+"sensorWidth",         this.sensorWidth+"");
+    		properties.setProperty(prefix+"sensorHeight",        this.sensorHeight+"");
+      		properties.setProperty(prefix+"decimateMasks",       this.decimateMasks+"");
     		properties.setProperty(prefix+"cartesian",           this.cartesian+"");
     		properties.setProperty(prefix+"lensDistortionModel", this.lensDistortionModel+"");
     		properties.setProperty(prefix+"enableNoLaser",       this.enableNoLaser+"");
@@ -239,6 +254,12 @@ import java.util.Properties;
     		getProperties(prefix,properties, -1);
     	}
     	public void getProperties(String prefix,Properties properties, int channel){
+    		if (properties.getProperty(prefix+"sensorWidth")!=null)
+    			this.sensorWidth=Integer.parseInt(properties.getProperty(prefix+"sensorWidth"));
+    		if (properties.getProperty(prefix+"sensorHeight")!=null)
+    			this.sensorHeight=Integer.parseInt(properties.getProperty(prefix+"sensorHeight"));
+       		if (properties.getProperty(prefix+"decimateMasks")!=null)
+       			this.decimateMasks=Integer.parseInt(properties.getProperty(prefix+"decimateMasks"));
     		if (properties.getProperty(prefix+"cartesian")!=null)
     			this.cartesian=Boolean.parseBoolean(properties.getProperty(prefix+"cartesian"));
     		if (properties.getProperty(prefix+"lensDistortionModel")!=null)