Working on extended window (more than reference scene sesnor view)

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

@@ -95,7 +95,7 @@ public class ImagejJp4Tiff {
 //	private static final int    FIXCH6_MAXVAL  = 23367; // higher - subtract 4096, <19271 -add 4096 
 	private static final int    FIXCH6_EXPECTED  = 21319; // expected value 
 	private static final String FIXCH6_EARLIEST = "2021-12-01 00:00:00.000";
-	private static final String FIXCH6_LATEST =   "2022-04-01 00:00:00.000";
+	private static final String FIXCH6_LATEST =   "2022-12-01 00:00:00.000";
 	
 	// -- Fields --
 

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

@@ -141,35 +141,16 @@ public class ImageDtt extends ImageDttCPU {
 
 
 		final boolean macro_mode = macro_scale != 1;      // correlate tile data instead of the pixel data
-//		final int quad = getNumSensors(); // 4;   // number of subcameras
-//		final int numcol = 3; // number of colors // keep the same, just do not use [0] and [1], [2] - green
 		final int numcol = isMonochrome()?1:3;
 
 		final int width =  gpuQuad.getImageWidth();
 		final int height = gpuQuad.getImageHeight();
 		final int tilesX=gpuQuad.getTilesX(); // width/transform_size;
 		final int tilesY=gpuQuad.getTilesY(); // final int tilesY=height/transform_size;
-////		final int nTilesInChn=tilesX*tilesY;
-////		final double [][][][][][] clt_data = new double[quad][numcol][tilesY][tilesX][][];
 		final Thread[] threads = newThreadArray(threadsMax);
 		final AtomicInteger ai = new AtomicInteger(0);
 		final double [] col_weights= new double [numcol]; // colors are RBG
 		final double [][] dbg_distort = debug_distort? (new double [4*getNumSensors()][tilesX*tilesY]) : null;
-		// not yet used with GPU
-/**		
-		final double [][] corr_wnd = Corr2dLMA.getCorrWnd(
-				transform_size,
-				imgdtt_params.lma_wnd);
-		final double [] corr_wnd_inv_limited = (imgdtt_params.lma_min_wnd <= 1.0)?  new double [corr_wnd.length * corr_wnd[0].length]: null;
-		if (corr_wnd_inv_limited != null) {
-			double inv_pwr = imgdtt_params.lma_wnd_pwr - (imgdtt_params.lma_wnd - 1.0); // compensate for lma_wnd
-			for (int i = imgdtt_params.lma_hard_marg; i < (corr_wnd.length - imgdtt_params.lma_hard_marg); i++) {
-				for (int j = imgdtt_params.lma_hard_marg; j < (corr_wnd.length - imgdtt_params.lma_hard_marg); j++) {
-					corr_wnd_inv_limited[i * (corr_wnd.length) + j] = 1.0/Math.max(Math.pow(corr_wnd[i][j],inv_pwr), imgdtt_params.lma_min_wnd);
-				}
-			}
-		}
-*/
 		// keep for now for mono, find out  what do they mean for macro mode
 		
 		if (isMonochrome()) {
@@ -1173,6 +1154,7 @@ public class ImageDtt extends ImageDttCPU {
 	 * @param globalDebugLevel
 	 */
 	public void setReferenceTD(
+			final int []              wh,               // null (use sensor dimensions) or pair {width, height} in pixels
 			final ImageDttParameters  imgdtt_params,    // Now just extra correlation parameters, later will include, most others
 			final boolean             use_reference_buffer,
 			final TpTask[]            tp_tasks,
@@ -1203,7 +1185,8 @@ public class ImageDtt extends ImageDttCPU {
 				tp_tasks,
 				false); // boolean use_aux    // while is it in class member? - just to be able to free
 		// Skipping if ((fdisp_dist != null) || (fpxpy != null)) {...
-		gpuQuad.execConvertDirect(use_reference_buffer); // put results into a "reference" buffer
+//		int [] wh = null;
+		gpuQuad.execConvertDirect(use_reference_buffer, wh); // put results into a "reference" buffer
 	}
 
 

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

@@ -33,8 +33,10 @@ public class IntersceneMatchParameters {
 	public  boolean force_ref_dsi =      false; // true;
 	public  boolean force_orientations = false;
 	public  boolean force_interscene =   false; // true;
-	public  boolean export_images =      true; // 16-slice images (same disparity, COMBO_DSN_INDX_DISP_FG and COMBO_DSN_INDX_DISP_BG_ALL,
-	public  boolean show_images =        false;
+	public  boolean export_images =      true;  // pseudo-color 16-slice images (same disparity, COMBO_DSN_INDX_DISP_FG and COMBO_DSN_INDX_DISP_BG_ALL,
+	public  boolean show_images =        false; // color, infinity
+	public  boolean show_images_bgfg =   false; // bg and fg
+	public  boolean show_images_mono =   false; // float, monochrome 16-slice images (same disparity, COMBO_DSN_INDX_DISP_FG and COMBO_DSN_INDX_DISP_BG_ALL,
 	public  boolean show_ranges =        true;
 	
 	public  double  range_disparity_offset =   -0.08;
@@ -112,8 +114,12 @@ public class IntersceneMatchParameters {
 				"Force interscene calculation (+ML export) even if it was performed before.");
 		gd.addCheckbox ("Export all-sensor images",                  this.export_images,
 				"Export multi-slice images: with constant disparity, with foreground disparity, and with background disparity");
-		gd.addCheckbox ("Show exported images",                      this.show_images,
-				"Display generated/saved images");
+		gd.addCheckbox ("Show exported images (same disparity)",     this.show_images,
+				"Display generated/saved image set, pseudocolors");
+		gd.addCheckbox ("Show exported FG/BG",                       this.show_images_bgfg,
+				"Show foreground and background exported images");
+		gd.addCheckbox ("Show floating-point monochrome images",     this.show_images_mono,
+				"Display generated/saved monochrome images");
 		gd.addCheckbox ("Show distances in meters",                  this.show_ranges,
 				"Calculate strength, distance, X, and Y in meters");
 		
@@ -226,6 +232,8 @@ public class IntersceneMatchParameters {
 		this.force_interscene =         gd.getNextBoolean();
 		this.export_images =            gd.getNextBoolean();
 		this.show_images =              gd.getNextBoolean();
+		this.show_images_bgfg =         gd.getNextBoolean();
+		this.show_images_mono =         gd.getNextBoolean();
 		this.show_ranges =              gd.getNextBoolean();
 		this.range_disparity_offset =   gd.getNextNumber();
 		this.range_min_strength =       gd.getNextNumber();
@@ -282,6 +290,8 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"force_interscene",     this.force_interscene + "");  // boolean
 		properties.setProperty(prefix+"export_images",        this.export_images + "");     // boolean
 		properties.setProperty(prefix+"show_images",          this.show_images + "");       // boolean
+		properties.setProperty(prefix+"show_images_bgfg",     this.show_images_bgfg + "");  // boolean
+		properties.setProperty(prefix+"show_images_mono",     this.show_images_mono + "");  // boolean
 		properties.setProperty(prefix+"show_ranges",          this.show_ranges + "");       // boolean
 
 		properties.setProperty(prefix+"range_disparity_offset",this.range_disparity_offset+""); // double
@@ -337,6 +347,8 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"force_interscene")!=null)     this.force_interscene=Boolean.parseBoolean(properties.getProperty(prefix+"force_interscene"));		
 		if (properties.getProperty(prefix+"export_images")!=null)        this.export_images=Boolean.parseBoolean(properties.getProperty(prefix+"export_images"));		
 		if (properties.getProperty(prefix+"show_images")!=null)          this.show_images=Boolean.parseBoolean(properties.getProperty(prefix+"show_images"));		
+		if (properties.getProperty(prefix+"show_images_bgfg")!=null)     this.show_images_bgfg=Boolean.parseBoolean(properties.getProperty(prefix+"show_images_bgfg"));		
+		if (properties.getProperty(prefix+"show_images_mono")!=null)     this.show_images_mono=Boolean.parseBoolean(properties.getProperty(prefix+"show_images_mono"));		
 		if (properties.getProperty(prefix+"show_ranges")!=null)          this.show_images=Boolean.parseBoolean(properties.getProperty(prefix+"show_ranges"));
 		if (properties.getProperty(prefix+"range_disparity_offset")!=null) this.range_disparity_offset=Double.parseDouble(properties.getProperty(prefix+"range_disparity_offset"));
 		if (properties.getProperty(prefix+"range_min_strength")!=null)   this.range_min_strength=Double.parseDouble(properties.getProperty(prefix+"range_min_strength"));
@@ -392,6 +404,8 @@ public class IntersceneMatchParameters {
 		imp.force_interscene      = this.force_interscene;
 		imp.export_images         = this.export_images;
 		imp.show_images           = this.show_images;
+		imp.show_images_bgfg      = this.show_images_bgfg;
+		imp.show_images_mono      = this.show_images_mono;
 		imp.show_ranges           = this.show_ranges;
 		imp.range_disparity_offset = this.range_disparity_offset;
 		imp.range_min_strength    = this.range_min_strength;

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

 package com.elphel.imagej.tileprocessor;
 
+import java.awt.Rectangle;
 import java.util.Arrays;
 import java.util.concurrent.atomic.AtomicInteger;
 
@@ -237,6 +238,7 @@ public class MultisceneLY {
 			String ts = scenes[nscene].getImageName();
 			if (nscene == last_scene_index) {
 				scenes_pXpYD[nscene] = OpticalFlow.transformToScenePxPyD(
+						null, // final Rectangle [] extra_woi,    // show larger than sensor WOI (or null)
 						disparity_ref,      // final double []   disparity_ref, // invalid tiles - NaN in disparity (maybe it should not be masked by margins?)
 						OpticalFlow.ZERO3,              // final double []   scene_xyz, // camera center in world coordinates
 						OpticalFlow.ZERO3,              // final double []   scene_atr, // camera orientation relative to world frame
@@ -253,6 +255,7 @@ public class MultisceneLY {
 						scene_ers_atr_dt); // double []    ers_atr_dt)(ers_scene_original_xyz_dt);
 				//setupERS() will be inside transformToScenePxPyD()
 				scenes_pXpYD[nscene] = OpticalFlow.transformToScenePxPyD( // will be null for disparity == NaN, total size - tilesX*tilesY
+						null, // final Rectangle [] extra_woi,    // show larger than sensor WOI (or null)
 						disparity_ref,      // final double []   disparity_ref, // invalid tiles - NaN in disparity (maybe it should not be masked by margins?)
 						scene_xyz,          // final double []   scene_xyz, // camera center in world coordinates
 						scene_atr,          // final double []   scene_atr, // camera orientation relative to world frame

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

@@ -1175,12 +1175,15 @@ public class QuadCLTCPU {
 	}
 	
 	public void saveImagePlusInModelDirectory(
-			String      suffix,
+			String      suffix, // null - use title from the imp
 			ImagePlus   imp)
 	{
 		String x3d_path = getX3dDirectory();
-		String file_name = image_name + suffix;
-		String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
+		String file_name = (suffix==null) ? imp.getTitle():(image_name + suffix);
+		String file_path = x3d_path + Prefs.getFileSeparator() + file_name; // + ".tiff";
+		if (!file_path.endsWith(".tiff")) {
+			file_path +=".tiff";
+		}
 		FileSaver fs=new FileSaver(imp);
 		fs.saveAsTiff(file_path);
 		System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
@@ -7122,7 +7125,8 @@ public class QuadCLTCPU {
 		  float []   alpha = null; // (0..1.0)
 		  if (iclt_data.length > 3) alpha = iclt_data[3];
 		  if (isLwir()) {
-			  if (!colorProcParameters.lwir_pseudocolor) {
+////			  if (!colorProcParameters.lwir_pseudocolor) {
+			  if (!toRGB) {
 				  ImageProcessor ip= new FloatProcessor(width,height);
 				  ip.setPixels(iclt_data[0]);
 				  ip.resetMinAndMax();