addin illustration generation

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

+package com.elphel.imagej.calibration;
+
+import java.util.Properties;
+
+import com.elphel.imagej.common.GenericJTabbedDialog;
+import com.elphel.imagej.lwir.LwirReaderParameters;
+
+public class CalibrationIllustrationParameters {
+	double               dflt_lwir_lo = 22500.0;
+	double               dflt_lwir_hi = 23500.0;
+	LwirReaderParameters lwirReaderParameters;
+	double [][]          lwir_ranges; //  = new double [lwirReaderParameters.getLwirChannels(false).length][2];
+	int                  palette = 0; // 0 - white - hot, 1 - black - hot, 2+ - colored
+	String               src_chn_prefix="src_chn-";
+	boolean              save_png = true;
+	int                  JPEG_quality = 90;
+	String               channel_dir_prefix = "chn_";
+	
+	public CalibrationIllustrationParameters (LwirReaderParameters lwirReaderParameters) {
+		this.lwirReaderParameters = lwirReaderParameters;
+	}
+	public void setProperties(String prefix,Properties properties){
+//		properties.setProperty(prefix+"camera_name",         this.camera_name+"");
+		set_parameters();
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			properties.setProperty(prefix+"lwir_range_lo_"+i,         this.lwir_ranges[i][0]+"");
+			properties.setProperty(prefix+"lwir_range_hi_"+i,         this.lwir_ranges[i][1]+"");
+		}		
+		properties.setProperty(prefix+"palette",            this.palette+"");
+		properties.setProperty(prefix+"save_png",           this.save_png+"");
+		properties.setProperty(prefix+"JPEG_quality",       this.JPEG_quality+"");
+		properties.setProperty(prefix+"channel_dir_prefix", this.channel_dir_prefix);
+	}
+
+	public void getProperties(String prefix,Properties properties){
+		set_parameters();
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			if (properties.getProperty(prefix+"lwir_range_lo_"+i)!=null) {
+				this.lwir_ranges[i][0] = Double.parseDouble(properties.getProperty(prefix+"lwir_range_lo_"+i));
+			}
+			if (properties.getProperty(prefix+"lwir_range_hi_"+i)!=null) {
+				this.lwir_ranges[i][1] = Double.parseDouble(properties.getProperty(prefix+"lwir_range_hi_"+i));
+			}
+		}
+		if (properties.getProperty(prefix+"palette")!=null)      this.palette = Integer.parseInt(properties.getProperty(prefix+"palette"));
+		if (properties.getProperty(prefix+"save_png")!=null)     this.save_png = Boolean.parseBoolean(properties.getProperty(prefix+"save_png"));
+		if (properties.getProperty(prefix+"JPEG_quality")!=null) this.JPEG_quality = Integer.parseInt(properties.getProperty(prefix+"JPEG_quality"));
+		if (properties.getProperty(prefix+"channel_dir_prefix")!=null) this.channel_dir_prefix = (String) properties.getProperty(prefix+"channel_dir_prefix");
+
+	}
+	public void dialogQuestions(GenericJTabbedDialog gd) {
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			gd.addNumericField("LWIR chn:"+i+" low range", this.lwir_ranges[i][0],  0,8,"","LWIR sensor range low level ");
+			gd.addNumericField("LWIR chn:"+i+" high range", this.lwir_ranges[i][1],  0,8,"","LWIR sensor range high level ");
+		}
+		gd.addNumericField("Thermal color palette", this.palette,  0,3,"","0 - white-hot, 1 - black-hot, 2+ - colored");
+		gd.addCheckbox("Save as PNG instead of JPEG", save_png);
+		gd.addNumericField("JPEG quality", this.JPEG_quality,  0,3,"","Jpeg quality, 0 - use Tiff");
+    	gd.addStringField ("Channel directory prefix",this.channel_dir_prefix, 15,"prefix to a directory name to save channel annotated files");
+	}
+	
+	public void dialogAnswers(GenericJTabbedDialog gd) {
+		for (int i = 0; i < lwir_ranges.length; i++) {
+			this.lwir_ranges[i][0] = gd.getNextNumber();
+			this.lwir_ranges[i][1] = gd.getNextNumber();
+		}
+		this.palette =      (int) gd.getNextNumber();
+		this.save_png =           gd.getNextBoolean();
+		this.JPEG_quality = (int) gd.getNextNumber();
+		this.channel_dir_prefix = gd.getNextString();
+	}
+	public boolean showJDialog() {
+		set_parameters();
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set illustration parameters",800,900);
+		dialogQuestions(gd);
+		gd.showDialog();
+		if (gd.wasCanceled()) return false;
+		dialogAnswers(gd);
+		return true;
+	}
+	public void set_parameters () {
+		//		this.lwirReaderParameters = lwirReaderParameters;
+		if ((lwir_ranges == null) || (lwir_ranges.length != lwirReaderParameters.getLwirChannels(false).length)){
+			lwir_ranges = new double [lwirReaderParameters.getLwirChannels(false).length][2];
+			for (int i = 0; i < lwir_ranges.length; i++) {
+				this.lwir_ranges[i][0] = dflt_lwir_lo;
+				this.lwir_ranges[i][1] = dflt_lwir_hi;
+			}
+		}
+	}
+	
+	public int getPalette() {
+		return this.palette;
+	}
+	public double [] getLwirRange(int lwir_index) {
+		return lwir_ranges[lwir_index];
+	}
+	public LwirReaderParameters getLwirReaderParameters() {
+		return lwirReaderParameters;
+	}
+}

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

@@ -1039,16 +1039,6 @@ import ij.text.TextWindow;
         					System.out.println("sfiles == null");
         				}
         				for (String spath:sfiles) {
-        					/*
-        					int last_dash = spath.lastIndexOf('-');
-        					int last =      spath.lastIndexOf('_');
-        					if (last_dash >last) last = last_dash;
-        					int last_dot = spath.lastIndexOf('.');
-        					if (last_dot < 0) {
-        						last_dot = spath.length();
-        					}
-        					int chn = Integer.parseInt(spath.substring(last+1, last_dot));
-        					*/
             				int chn = pathToChannel(spath);
         					spaths[chn] = (new File(set_dir,spath)).getPath();
         				}

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

@@ -4784,6 +4784,7 @@ public class EyesisAberrations {
     public static class AberrationParameters{
     	public String sourceDirectory="";
     	public String partialKernelDirectory="";
+    	public String illustrationsDirectory="";
     	public String psfKernelDirectory="";
     	public String aberrationsKernelDirectory="";
     	public String calibrationDirectory="";
@@ -4821,6 +4822,7 @@ public class EyesisAberrations {
 		public void setProperties(String prefix,Properties properties){
 			properties.setProperty(prefix+"sourceDirectory",this.sourceDirectory);
 			properties.setProperty(prefix+"partialKernelDirectory",this.partialKernelDirectory);
+			properties.setProperty(prefix+"illustrationsDirectory",this.illustrationsDirectory);
 			properties.setProperty(prefix+"psfKernelDirectory",this.psfKernelDirectory);
 			properties.setProperty(prefix+"aberrationsKernelDirectory",this.aberrationsKernelDirectory);
 			properties.setProperty(prefix+"calibrationDirectory",this.calibrationDirectory);
@@ -4866,6 +4868,7 @@ public class EyesisAberrations {
 		public void getProperties(String prefix,Properties properties){
 			if (properties.getProperty(prefix+"sourceDirectory")!=null)	           this.sourceDirectory=properties.getProperty(prefix+"sourceDirectory");
 			if (properties.getProperty(prefix+"partialKernelDirectory")!=null)     this.partialKernelDirectory=properties.getProperty(prefix+"partialKernelDirectory");
+			if (properties.getProperty(prefix+"illustrationsDirectory")!=null)     this.illustrationsDirectory=properties.getProperty(prefix+"illustrationsDirectory");
 			if (properties.getProperty(prefix+"psfKernelDirectory")!=null)         this.psfKernelDirectory=properties.getProperty(prefix+"psfKernelDirectory");
 			if (properties.getProperty(prefix+"aberrationsKernelDirectory")!=null) this.aberrationsKernelDirectory=properties.getProperty(prefix+"aberrationsKernelDirectory");
 			if (properties.getProperty(prefix+"calibrationDirectory")!=null)       this.calibrationDirectory=properties.getProperty(prefix+"calibrationDirectory");
@@ -5018,6 +5021,8 @@ public class EyesisAberrations {
     		gd.addCheckbox("Select source directory", false);
     		gd.addStringField("Partial kernels directory", this.partialKernelDirectory, 60);
     		gd.addCheckbox("Select partial kernels directory", false);
+    		gd.addStringField("Illustrations directory", this.illustrationsDirectory, 60);
+    		gd.addCheckbox("Select illustrations directory", false);
     		gd.addStringField("Combined kernels directory", this.psfKernelDirectory, 60);
     		gd.addCheckbox("Select combined kernsls directory", false);
     		gd.addStringField("Aberrations kernels directory", this.aberrationsKernelDirectory, 60);
@@ -5071,6 +5076,8 @@ public class EyesisAberrations {
     		if (gd.getNextBoolean()) selectSourceDirectory(false, this.sourceDirectory, false);
     		this.partialKernelDirectory=gd.getNextString();
     		if (gd.getNextBoolean()) selectPartialKernelDirectory(false, this.partialKernelDirectory, false);
+    		this.illustrationsDirectory=gd.getNextString();
+    		if (gd.getNextBoolean()) selectIllustrationsDirectory(false, this.illustrationsDirectory, false);
     		this.psfKernelDirectory=gd.getNextString();
     		if (gd.getNextBoolean()) selectPSFKernelDirectory(false, this.psfKernelDirectory, false);
     		this.aberrationsKernelDirectory=gd.getNextString();
@@ -5133,6 +5140,19 @@ public class EyesisAberrations {
     		if (dir!=null) this.partialKernelDirectory=dir;
     		return dir;
     	}
+
+    	public String selectIllustrationsDirectory(boolean smart, String defaultPath, boolean newAllowed) {
+    		String dir= CalibrationFileManagement.selectDirectory(
+    				smart,
+    				newAllowed, // save
+    				"Illustrations directory", // title
+    				"Select illustrations directory", // button
+    				null, // filter
+    				defaultPath); //this.sourceDirectory);
+    		if (dir!=null) this.illustrationsDirectory=dir;
+    		return dir;
+    	}
+    	
     	public String selectPSFKernelDirectory(boolean smart, String defaultPath, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,

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

@@ -2696,7 +2696,7 @@ public class EyesisCorrections {
 	}
 
 
-	public void saveAndShow(
+	public static void saveAndShow(
 			ImagePlus             imp,
 			String                path,
 			boolean               png,
@@ -2716,12 +2716,12 @@ public class EyesisCorrections {
 				}
 			}
 
-			if (hasAlphaHighByte && (jpegQuality <= 0)){
+			if (hasAlphaHighByte && ((jpegQuality <= 0) || png)){
 				if (png){
 					if (debugLevel > 0) System.out.println("Saving RGBA result to "+path+".png");
 					(new EyesisTiff()).savePNG_ARGB32(
 							imp,
-							path+".png"
+							path +".png"
 							);
 
 				} else {
@@ -2729,7 +2729,7 @@ public class EyesisCorrections {
 					try {
 						(new EyesisTiff()).saveTiffARGB32(
 								imp,
-								path+".tiff",
+								path, // +".tiff",
 								false, // correctionsParameters.imageJTags,
 								debugLevel);
 					} catch (IOException e) {

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

@@ -102,6 +102,26 @@ public class LwirReaderParameters {
 	public LwirReaderParameters() {
 		
 	}
+	
+	public int [] getLwirChannels(boolean absolote) {
+		int [] absolute_chn = new int [lwir_channels.length];
+		for (int i = 0; i < absolute_chn.length; i++) {
+			absolute_chn[i] = lwir_channels[i] + (absolote? getLwirChn0() : 0);
+		}
+		return absolute_chn;
+	}
+
+	public int [] getAbsoluteEoChannels(boolean absolote) {
+		int [] absolute_chn = new int [eo_channels.length];
+		for (int i = 0; i < absolute_chn.length; i++) {
+			absolute_chn[i] = eo_channels[i] +  + (absolote? getEoChn0():0);
+		}
+		return absolute_chn;
+	}
+//	protected int []  lwir_channels =        {0, 1, 2 ,3};
+//	protected int []  eo_channels =          {0, 1, 2 ,3};
+	
+	
 	public LwirReaderParameters(String name) {
 		if (NAME_TALON.equals(name)) camera_name = NAME_TALON;
 		else if (NAME_LWIR16.equals(name)) camera_name = NAME_LWIR16;
@@ -133,11 +153,11 @@ public class LwirReaderParameters {
 	public int getNumFrames() {
 		return num_frames;
 	}
-	public int getLwirChn0 () {
+	public int getLwirChn0() {
 		return lwir_chn0;
 	}
 
-	public int getEoChn0 () {
+	public int getEoChn0() {
 		return isLwir16() ? 16:4;// eo_chn0;
 	}
 	

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

@@ -2191,7 +2191,7 @@ public class QuadCLT extends QuadCLTCPU {
 					true,  // smart,
 					true);  //newAllowed, // save
 			for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-				eyesisCorrections.saveAndShow(
+				EyesisCorrections.saveAndShow(
 						imps_RGB[sub_img],
 						x3d_path,
 						correctionsParameters.png && !clt_parameters.black_back,
@@ -2720,7 +2720,7 @@ public class QuadCLT extends QuadCLTCPU {
 					true,  // smart,
 					true);  //newAllowed, // save
 			for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-				quadCLT_main.eyesisCorrections.saveAndShow(
+				EyesisCorrections.saveAndShow(
 						imps_RGB[sub_img],
 						x3d_path,
 						quadCLT_main.correctionsParameters.png && !clt_parameters.black_back,

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -5159,7 +5159,7 @@ public class QuadCLTCPU {
 						  true,  // smart,
 						  true);  //newAllowed, // save
 				  for (int sub_img = 0; sub_img < 4; sub_img++){
-					  eyesisCorrections.saveAndShow(
+					  EyesisCorrections.saveAndShow(
 							  imps_RGB[sub_img],
 							  x3d_path,
 							  correctionsParameters.png && !clt_parameters.black_back,
@@ -12185,7 +12185,7 @@ public class QuadCLTCPU {
 
 		  }
 		  ImagePlus ip_thumb = new ImagePlus(name,ip);
-		  eyesisCorrections.saveAndShow(
+		  EyesisCorrections.saveAndShow(
 				  ip_thumb,
 				  dir,
 				  false,

src/main/java/com/elphel/imagej/tileprocessor/TwoQuadCLT.java

@@ -50,6 +50,7 @@ import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.CorrectionColorProc;
+import com.elphel.imagej.correction.EyesisCorrections;
 import com.elphel.imagej.gpu.GPUTileProcessor;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
 
@@ -1030,7 +1031,7 @@ public class TwoQuadCLT {
 						true,  // smart,
 						true);  //newAllowed, // save
 				for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-					quadCLT_main.eyesisCorrections.saveAndShow(
+					EyesisCorrections.saveAndShow(
 							imps_RGB[sub_img],
 							x3d_path,
 							quadCLT_main.correctionsParameters.png && !clt_parameters.black_back,
@@ -1916,7 +1917,7 @@ public class TwoQuadCLT {
 						true,  // smart,
 						true);  //newAllowed, // save
 				for (int sub_img = 0; sub_img < imps_RGB.length; sub_img++){
-					quadCLT_main.eyesisCorrections.saveAndShow(
+					EyesisCorrections.saveAndShow(
 							imps_RGB[sub_img],
 							x3d_path,
 							quadCLT_main.correctionsParameters.png && !clt_parameters.black_back,