Fixing conversion from calibration to correction.

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

@@ -84,6 +84,7 @@ public class CLTParameters {
 	public double     scale_b =           1.0;
 	public double     vignetting_max    = 0.4; // value in vignetting data to correspond to 1x in the kernel
 	public double     vignetting_range  = 5.0; // do not try to correct vignetting less than vignetting_max/vignetting_range
+	// NOT used !
 	public int        kernel_step =       16;  // source kernels step in pixels (have 1 kernel margin on each side)
 	public double     disparity  =        0.0; // nominal disparity between side of square cameras (pix)
 	public double     z_correction  =     0.0; // Inverse distance to infinity (misalignment correction)

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

@@ -14,6 +14,7 @@ public class ColorProcParameters {
 	public boolean lwir_autorange =      true;
 	public double  lwir_too_cold =       100.0; // discard this number of pixels too cold
 	public double  lwir_too_hot =          3.0; // discard this number of pixels too hot
+	public boolean lwir_pseudocolor =     true;
 	public int     lwir_palette =           0; // 0 - white - hot, 1 - black - hot, 2+ - colored
 	public boolean lwir_subtract_dc   = false;
 	public boolean lwir_eq_chn   =      true;  // adjust average temperature between channels
@@ -84,7 +85,7 @@ public class ColorProcParameters {
 			boolean lwir_autorange,     //  true;
 			double  lwir_too_cold,      //   100.0; // discard this number of pixels too cold
 			double  lwir_too_hot,       //     3.0; // discard this number of pixels too hot
-
+			boolean lwir_pseudocolor,
 			int     lwir_palette,       //  0 - white - hot, 1 - black - hot, 2+ - colored
 			boolean lwir_subtract_dc,   //   = false;
 			boolean lwir_eq_chn,        // true
@@ -144,6 +145,7 @@ public class ColorProcParameters {
 		this.lwir_too_cold =  lwir_too_cold;
 		this.lwir_too_hot =   lwir_too_hot;
 
+		this.lwir_pseudocolor = lwir_pseudocolor;
 		this.lwir_palette = lwir_palette;
 		this.lwir_subtract_dc = lwir_subtract_dc;
 		this.lwir_eq_chn =lwir_eq_chn;
@@ -204,6 +206,7 @@ public class ColorProcParameters {
 		properties.setProperty(prefix+"lwir_too_cold",      this.lwir_too_cold+"");
 		properties.setProperty(prefix+"lwir_too_hot",       this.lwir_too_hot+"");
 
+		properties.setProperty(prefix+"lwir_pseudocolor",   this.lwir_pseudocolor+"");
 		properties.setProperty(prefix+"lwir_palette",       this.lwir_palette+"");
 		properties.setProperty(prefix+"lwir_subtract_dc",   this.lwir_subtract_dc+"");
 		properties.setProperty(prefix+"lwir_eq_chn",        this.lwir_eq_chn+"");
@@ -273,6 +276,7 @@ public class ColorProcParameters {
 		if (properties.getProperty(prefix+"lwir_too_cold")!=null)  this.lwir_too_cold=Double.parseDouble(properties.getProperty(prefix+"lwir_too_cold"));
 		if (properties.getProperty(prefix+"lwir_too_hot")!=null)   this.lwir_too_hot=Double.parseDouble(properties.getProperty(prefix+"lwir_too_hot"));
 
+		if (properties.getProperty(prefix+"lwir_pseudocolor")!=null) this.lwir_pseudocolor=Boolean.parseBoolean(properties.getProperty(prefix+"lwir_pseudocolor"));
 		if (properties.getProperty(prefix+"lwir_palette")!=null) this.lwir_palette=Integer.parseInt(properties.getProperty(prefix+"lwir_palette"));
 		if (properties.getProperty(prefix+"lwir_subtract_dc")!=null) this.lwir_subtract_dc=Boolean.parseBoolean(properties.getProperty(prefix+"lwir_subtract_dc"));
 		if (properties.getProperty(prefix+"lwir_eq_chn")!=null) this.lwir_eq_chn=Boolean.parseBoolean(properties.getProperty(prefix+"lwir_eq_chn"));
@@ -349,7 +353,8 @@ public class ColorProcParameters {
 		gd.addNumericField("Number of too cold pixels/image to ignore during autorange",    this.lwir_too_cold, 4); // 100.0
 		gd.addNumericField("Number of too hot pixels/image to ignore during autorange",     this.lwir_too_hot,  4); //  0.53
 
-		gd.addNumericField("LWIR pallet (0-white hot, 1-black hot, 2+ - pseudo colors ",    this.lwir_palette,    0);
+		gd.addCheckbox    ("Use pseudocolors for LWIR (unchecked - floating point monochrome)", this.lwir_pseudocolor);
+		gd.addNumericField("LWIR pallete (0-white hot, 1-black hot, 2+ - pseudo colors ",   this.lwir_palette,    0);
 		gd.addCheckbox    ("Subtract each image DC when conditioning",                      this.lwir_subtract_dc);
 		gd.addCheckbox    ("Adjust average temperature between cameras",                    this.lwir_eq_chn);
 
@@ -437,6 +442,7 @@ public class ColorProcParameters {
 		this.lwir_too_cold=            gd.getNextNumber();
 		this.lwir_too_hot=             gd.getNextNumber();
 
+		this.lwir_pseudocolor=         gd.getNextBoolean();
 		this.lwir_palette=       (int) gd.getNextNumber();
 		this.lwir_subtract_dc=         gd.getNextBoolean();
 		this.lwir_eq_chn=              gd.getNextBoolean();
@@ -503,6 +509,7 @@ public class ColorProcParameters {
 		cp.lwir_too_cold =           this.lwir_too_cold;
 		cp.lwir_too_hot =            this.lwir_too_hot;
 
+		cp.lwir_pseudocolor =        this.lwir_pseudocolor;
 		cp.lwir_palette =            this.lwir_palette;
 		cp.lwir_subtract_dc =        this.lwir_subtract_dc;
 		cp.lwir_eq_chn =             this.lwir_eq_chn;
@@ -567,6 +574,7 @@ public class ColorProcParameters {
 		this.lwir_too_cold =           cp.lwir_too_cold;
 		this.lwir_too_hot =            cp.lwir_too_hot;
 
+		this.lwir_pseudocolor =        cp.lwir_pseudocolor;
 		this.lwir_palette =            cp.lwir_palette;
 		this.lwir_subtract_dc =        cp.lwir_subtract_dc;
 		this.lwir_eq_chn =             cp.lwir_eq_chn;

src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java

@@ -145,6 +145,9 @@ import ij.process.ImageProcessor;
 
   public void showArrays(float[][] pixels, int width, int height,  boolean asStack, String title, String [] titles) {
 	    int i,j;
+	    if (pixels == null) {
+	    	return;
+	    }
 	    if (asStack) {
 	      float [] fpixels;
 	      ImageStack array_stack=new ImageStack(width,height);

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

@@ -276,6 +276,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			true, // boolean lwir_autorange, // true;
 			100.0, // double lwir_too_cold, // 100.0; // discard this number of pixels too cold
 			3.0, // double lwir_too_hot, // 3.0; // discard this number of pixels too hot
+			true, // lwir_pseudocolor,
 			1, // int lwir_palette, // 0 - white - hot, 1 - black - hot, 2+ - pseudocolored
 			false, // boolean lwir_subtract_dc, // = false;
 			true, // boolean lwir_eq_chn = true; // adjust average temperature between channels
@@ -7381,6 +7382,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	 */
 	public boolean adjustLYSeries(boolean use_aux) {
 		MultisceneLY.MSLY_MODE adjust_mode = MultisceneLY.MSLY_MODE.INF_NOINF;
+		if (CLT_PARAMETERS.ofp.pattern_mode) {
+			adjust_mode = MultisceneLY.MSLY_MODE.NOINF_ONLY;	
+		}
 		long startTime = System.nanoTime();
 		// load needed sensor and kernels files
 		if (!prepareRigImages())

src/main/java/com/elphel/imagej/gpu/GPUTileProcessor.java

@@ -116,7 +116,7 @@ public class GPUTileProcessor {
 //	public static int IMG_HEIGHT =             1936;
 	static int        KERNELS_HOR =             164;
 	static int        KERNELS_VERT =            123;
-	static int        KERNELS_LSTEP =             4;
+	static int        KERNELS_LSTEP =             3; // 4;// FIXME: Make it dynamic: 3 for LWIR, 4 - for RGB?) 
 	static int        THREADS_PER_TILE =          8;
 	static int        TILES_PER_BLOCK =           4; // 8 - slower
 	static int        CORR_THREADS_PER_TILE =     8;

src/main/java/com/elphel/imagej/gpu/GpuQuad.java

@@ -3190,6 +3190,41 @@ public class GpuQuad{ // quad camera description
 	}
 
 	public float [][] getRBG (int ncam){
+		int gpu_height = (img_height + GPUTileProcessor.DTT_SIZE);
+		int gpu_width =  (img_width + GPUTileProcessor.DTT_SIZE);
+		int gpu_img_size =       gpu_width * gpu_height;
+		int rslt_img_size =      img_height * img_width; // width * height;
+		float [] cpu_corr_image = new float [ num_colors * gpu_img_size];
+		int gpu_width_in_bytes = gpu_width *Sizeof.FLOAT;
+
+		// for copying results to host
+		CUDA_MEMCPY2D copyD2H =   new CUDA_MEMCPY2D();
+		copyD2H.srcMemoryType =   CUmemorytype.CU_MEMORYTYPE_DEVICE;
+		copyD2H.srcDevice =       gpu_corr_images_h[ncam]; // ((test & 1) ==0) ? src_dpointer : dst_dpointer; // copy same data
+		copyD2H.srcPitch =        imclt_stride*Sizeof.FLOAT;
+
+		copyD2H.dstMemoryType =   CUmemorytype.CU_MEMORYTYPE_HOST;
+		copyD2H.dstHost =         Pointer.to(cpu_corr_image);
+		copyD2H.dstPitch =        gpu_width_in_bytes;
+
+		copyD2H.WidthInBytes =    gpu_width_in_bytes;
+		copyD2H.Height =          num_colors * gpu_height; // /2;
+
+		cuMemcpy2D(copyD2H); // run copy
+
+		float [][] fimg = new float [num_colors][ rslt_img_size];
+		for (int ncol = 0; ncol < num_colors; ncol++) {
+			int tl_offset = (GPUTileProcessor.DTT_SIZE/2) * (gpu_width + 1) + ncol*gpu_img_size;
+			for (int nrow=0; nrow < img_height; nrow++) {
+//				System.arraycopy(cpu_corr_image, ncol*gpu_img_size, fimg[ncol], 0, rslt_img_size);
+				System.arraycopy(cpu_corr_image, tl_offset + (gpu_width * nrow), fimg[ncol], img_width * nrow, img_width);
+			}
+		}
+		return fimg;
+	}
+
+	@Deprecated
+	public float [][] getRBGuntrimmed (int ncam){
 		int height = (img_height + GPUTileProcessor.DTT_SIZE);
 		int width =  (img_width + GPUTileProcessor.DTT_SIZE);
 		int rslt_img_size =      width * height;
@@ -3207,7 +3242,6 @@ public class GpuQuad{ // quad camera description
 		copyD2H.dstPitch =        width_in_bytes;
 
 		copyD2H.WidthInBytes =    width_in_bytes;
-//		copyD2H.Height =          3 * height; // /2;
 		copyD2H.Height =          num_colors * height; // /2;
 
 		cuMemcpy2D(copyD2H); // run copy
@@ -3218,7 +3252,9 @@ public class GpuQuad{ // quad camera description
 		}
 		return fimg;
 	}
-
+	
+	
+	
 	@Deprecated
 	public void  getTileSubcamOffsets(
 			final TpTask[]            tp_tasks,        // will use // modify to have offsets for 8 cameras

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

@@ -326,6 +326,9 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		          throw new ServiceException("Could not read EXIF data", e);
 		        }
 		      }
+		    if (directory==null) { // trying to read ImageJ file 640x512
+		    	return;
+		    }
 		    Date date =  directory.getDate(ExifSubIFDDirectory.TAG_DATETIME_ORIGINAL);
 
 		    if (date != null) {

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

@@ -31,6 +31,7 @@ package com.elphel.imagej.readers;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.StringReader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLConnection;
@@ -46,9 +47,17 @@ import java.util.Iterator;
 import java.util.Properties;
 import java.util.Set;
 
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
 import org.apache.commons.compress.utils.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
 
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.tileprocessor.TileNeibs;
@@ -213,6 +222,11 @@ public class ImagejJp4Tiff {
 		ImagePlus imp=  null;
 		bytes = reader.openBytes(0);
 		int bpp =   reader.getBitsPerPixel();
+		if (bpp == 32) { // already ImageJ file - just read it and decode properties
+			imp =  new ImagePlus(content_fileName);
+			decodeProperiesFromInfo(imp);
+			return imp;
+		}
 
 		boolean is_le = reader.isLittleEndian();
 		int bytes_per_pixel =  (bpp + 7) / 9;
@@ -350,6 +364,43 @@ public class ImagejJp4Tiff {
 		imp.setProperty("Info", info);
 		return imp;
 	}
+	
+	public static boolean decodeProperiesFromInfo(ImagePlus imp){
+		if (imp.getProperty("Info")==null) return false;
+		String xml= (String) imp.getProperty("Info");
+
+	    DocumentBuilder db=null;
+		try {
+			db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+		} catch (ParserConfigurationException e) {
+			return false;
+		}
+	    InputSource is = new InputSource();
+	    is.setCharacterStream(new StringReader(xml));
+    	Document doc = null;
+	    try {
+	    	doc = db.parse(is);
+	    } catch (SAXException e) {
+	    	return false;
+	    } catch (IOException e) {
+	    	return false;
+	    }
+	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
+	    for (int i=0;i<allNodes.getLength();i++) {
+	        String name= allNodes.item(i).getNodeName();
+	        String value="";
+	        try {
+	        	value=allNodes.item(i).getFirstChild().getNodeValue();
+	        } catch(Exception e) {
+
+	        }
+    		imp.setProperty(name, value);
+
+	    }
+
+		return true;
+	}
+	
 
 	public float [] deGammaScale(float [] pixels, int width, Hashtable<String, Object> meta_hash, boolean degamma, boolean scale) {
 		int height = pixels.length/width;

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

@@ -621,6 +621,10 @@ public class CorrVector{ // TODO: Update to non-quad (extract to a file first)?
 		return toString(false);
 	}
 	
+	public double getTiltAzPerPixel() {
+		return 1.0/1000.0*geometryCorrection.focalLength/geometryCorrection.pixelSize;
+	}
+	
 	public String toString(boolean short_out) {
 		String s;
 		double [] sym_vect = toSymArray(null);

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

@@ -360,7 +360,7 @@ public class ImageDtt extends ImageDttCPU {
 		if (iclt_fimg != null) {
 			gpuQuad.execImcltRbgAll(isMonochrome());  // execute GPU kernel
 			for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
-				iclt_fimg[ncam] = gpuQuad.getRBG(ncam); // retrieve data from GPU
+				iclt_fimg[ncam] = gpuQuad.getRBG(ncam); // retrieve data from GPU (not used !)
 			}
 		} else {gpuQuad.execImcltRbgAll(isMonochrome());} // just for testing
 		// does it need texture tiles to be output?
@@ -1554,7 +1554,7 @@ public class ImageDtt extends ImageDttCPU {
 		if (iclt_fimg != null) {
 			gpuQuad.execImcltRbgAll(isMonochrome());  // execute GPU kernel
 			for (int ncam = 0; ncam < iclt_fimg.length; ncam++) {
-				iclt_fimg[ncam] = gpuQuad.getRBG(ncam); // retrieve data from GPU
+				iclt_fimg[ncam] = gpuQuad.getRBG(ncam); // retrieve data from GPU not used, but now width/height are nominal, not increased 
 			}
 		} else {gpuQuad.execImcltRbgAll(isMonochrome());} // just for testing
 		// does it need texture tiles to be output?

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

@@ -93,18 +93,31 @@ public class IntersceneLma {
 	}
 
 	public String [] printOldNew(boolean allvectors, int w, int d) {
+		String fmt1 = String.format("%%%d.%df", w,d);
 		ArrayList<String> lines = new ArrayList<String>();
 		for (int n = ErsCorrection.DP_DVAZ; n < ErsCorrection.DP_NUM_PARS; n+=3) {
 			boolean adj = false;
 			for (int i = 0; i <3; i++) adj |= par_mask[n+i];
 			if (allvectors || adj) {
 				String line = printNameV3(n, false, w,d)+"  (was "+printNameV3(n, true, w,d)+")";
+				line += ", diff="+String.format(fmt1, getV3Diff(n));
 				lines.add(line);
 			}
 		}
 		return lines.toArray(new String[lines.size()]);
 	}
 	
+	public double getV3Diff(int indx) {
+		double [] v_new = new double[3], v_old = new double[3];
+		System.arraycopy(getFullVector(parameters_vector), indx, v_new, 0, 3);
+		System.arraycopy(backup_parameters_full, indx, v_old, 0, 3);
+		double l2 = 0;
+		for (int i = 0; i < 3; i++) {
+			l2 += (v_new[i]-v_old[i]) * (v_new[i]-v_old[i]); 
+		}
+		return Math.sqrt(l2);
+	}
+	
 	public String printNameV3(int indx, boolean initial, int w, int d) {
 		double [] full_vector = initial? backup_parameters_full: getFullVector(parameters_vector);
 		double [] vector = new double[3];
@@ -283,6 +296,11 @@ public class IntersceneLma {
 		if (show_intermediate && (debug_level > 0)) {
 			System.out.println("LMA: full RMS="+last_rms[0]+" ("+initial_rms[0]+"), pure RMS="+last_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
 		}
+		String [] lines1 = printOldNew(false); // boolean allvectors)
+		System.out.print("iteration="+iter);
+		for (String line : lines1) {
+			System.out.println(line);
+		}
 		if (debug_level > 0) {
 			if ((debug_level > 1) || (iter == 1) || last_run) {
 				if (!show_intermediate) {

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

@@ -339,7 +339,7 @@ public class MacroCorrelation {
 				geometryCorrection,            // final GeometryCorrection  geometryCorrection,
 				null,                          // final GeometryCorrection  geometryCorrection_main, // if not null correct this camera (aux) to the coordinates of the main
 				null,     // clt_kernels,                  // final double [][][][][][] clt_kernels, // [channel_in_quad][color][tileY][tileX][band][pixel] , size should match image (have 1 tile around)
-				clt_parameters.kernel_step,
+//				clt_parameters.kernel_step,
 ///				clt_parameters.transform_size,
 				clt_parameters.clt_window,
 				shiftXY, //

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

@@ -2080,8 +2080,8 @@ public class QuadCLT extends QuadCLTCPU {
 			iclt_fimg[ncam] = gpuQuad.getRBG(ncam);
 		}
 
-		int out_width =  gpuQuad.getImageWidth()  + gpuQuad.getDttSize();
-		int out_height = gpuQuad.getImageHeight() + gpuQuad.getDttSize();
+		int out_width =  gpuQuad.getImageWidth();//   + gpuQuad.getDttSize(); // 2022/05/12 removed margins from gpuQuad.getRBG(ncam);
+		int out_height = gpuQuad.getImageHeight(); // + gpuQuad.getDttSize(); // 2022/05/12 removed margins from gpuQuad.getRBG(ncam);
 		if (isLwir() && colorProcParameters.lwir_autorange) {
 			double rel_low =  colorProcParameters.lwir_low;
 			double rel_high = colorProcParameters.lwir_high;
@@ -2145,7 +2145,7 @@ public class QuadCLT extends QuadCLTCPU {
 				///					array_stack.addSlice("port_"+slice_seq[i], results[slice_seq[i]].getProcessor().getPixels());
 				///				}
 			}
-			ImagePlus imp_stack = new ImagePlus(image_name+sAux()+"-SHIFTED-D"+clt_parameters.disparity, array_stack);
+			ImagePlus imp_stack = new ImagePlus(image_name+sAux()+"GPU-SHIFTED-D"+clt_parameters.disparity, array_stack);
 			imp_stack.getProcessor().resetMinAndMax();
 			if (only4slice) {
 				return imp_stack;
@@ -2691,8 +2691,8 @@ public class QuadCLT extends QuadCLTCPU {
 			iclt_fimg[ncam] = quadCLT_main.getGPU().getRBG(ncam);
 		}
 
-		int out_width =  quadCLT_main.getGPU().getImageWidth()  + quadCLT_main.getGPU().getDttSize();
-		int out_height = quadCLT_main.getGPU().getImageHeight() + quadCLT_main.getGPU().getDttSize();
+		int out_width =  quadCLT_main.getGPU().getImageWidth(); //  + quadCLT_main.getGPU().getDttSize(); // 2022/05/12 removed margins from gpuQuad.getRBG(ncam);
+		int out_height = quadCLT_main.getGPU().getImageHeight(); // + quadCLT_main.getGPU().getDttSize();// 2022/05/12 removed margins from gpuQuad.getRBG(ncam);
 		int tilesX =     quadCLT_main.getGPU().getImageWidth()  / quadCLT_main.getGPU().getDttSize();
 		int tilesY =     quadCLT_main.getGPU().getImageHeight() / quadCLT_main.getGPU().getDttSize();
 		
@@ -2861,7 +2861,7 @@ public class QuadCLT extends QuadCLTCPU {
 					array_stack.addSlice("port_"+slice_seq[i], results[slice_seq[i]].getProcessor().getPixels());
 				}
 			}
-			ImagePlus imp_stack = new ImagePlus(name+"-SHIFTED-D"+clt_parameters.disparity, array_stack);
+			ImagePlus imp_stack = new ImagePlus(name+"GPU-SHIFTED-D"+clt_parameters.disparity, array_stack);
 			imp_stack.getProcessor().resetMinAndMax();
 			if (!batch_mode) {
 				imp_stack.updateAndDraw();
@@ -5338,7 +5338,7 @@ public class QuadCLT extends QuadCLTCPU {
 					  geometryCorrection,            // final GeometryCorrection  geometryCorrection,
 					  null,                          // final GeometryCorrection  geometryCorrection_main, // if not null correct this camera (aux) to the coordinates of the main
 					  clt_kernels,                   // final double [][][][][][] clt_kernels, // [channel_in_quad][color][tileY][tileX][band][pixel] , size should match image (have 1 tile around)
-					  clt_parameters.kernel_step,    // final int                 kernel_step,
+//					  clt_parameters.kernel_step,    // final int                 kernel_step,
 					  clt_parameters.clt_window,     // final int                 window_type,
 					  shiftXY,                       // final double [][]         shiftXY, // [port]{shiftX,shiftY}
 					  disparity_corr,                // final double              disparity_corr, // disparity at infinity