New ROI and save enables

src/main/java/com/elphel/imagej/cuas/rt/CuasDetectRT.java

 package com.elphel.imagej.cuas.rt;
 
+import java.awt.Rectangle;
 import java.nio.file.Path;
 
 import com.elphel.imagej.cameras.CLTParameters;
@@ -167,6 +168,10 @@ public class CuasDetectRT {
 		int      curt_vel_radius =   clt_parameters.imp.curt_vel_radius;
 		double[] curt_temp_weights = clt_parameters.imp.curt_temp_weights.clone();
       	
+		boolean  curt_save_c5full =  clt_parameters.imp.curt_save_c5full;
+		boolean  curt_save_c5rect =  clt_parameters.imp.curt_save_c5rect;
+		Rectangle curt_save_select =  clt_parameters.imp.curt_save_select;	
+		
 // Initialize LoG and other kernel parameters, calculate LoG first, show results
        	int      kernel3d3_rad = 1;
        	
@@ -278,7 +283,7 @@ public class CuasDetectRT {
 //   		System.arraycopy(dpixels_log, 1, dpixels_pyramid[0], 0, dpixels_pyramid[0].length);
    		int center9 = 4;
    		int num_hist_5d = cuasRTUtils.getNumHist();
-   		boolean save_5d_pixels = debugLevel > -4;
+   		boolean save_5d_pixels = curt_save_c5full; // debugLevel > -4;
    		String title_conv5d = getBaseName()+SUFFIX_CONV5D+"-PSF"+d2s(cuasRTUtils.getPsfRadius())+
    				"-KR"+d2s(cuasRTUtils.getKernel2dRadius())+"-NHIST"+num_hist_5d+
    				"-VELRAD"+curt_vel_radius+"-VELDEC"+curt_vel_decimate;

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

@@ -1145,6 +1145,11 @@ min_str_neib_fpn	0.35
 	public int      curt_vel_decimate =    4;     // decimate velocities
 	public int      curt_vel_radius =      5;     // velocities radius in decimated samples
 	public double[] curt_temp_weights =    {1,1,1,1,1}; // historic weights for 5D convolution ([0] is the latest sample) 
+
+	// debug/saving images
+	public boolean  curt_save_c5full =     false; // save fine velocities [direction][scene][subpixels]
+	public boolean  curt_save_c5rect =     true;  // save fine velocities for selected rectangle only [scene][flattened image]
+	public Rectangle curt_save_select =    new Rectangle(98, 265, 82, 24); // Example selection for 1773135527_803834
 	
 	// Airplane mode
 	public boolean  air_mode_en =          false; // enable airplane mode
@@ -1152,6 +1157,8 @@ min_str_neib_fpn	0.35
 	public boolean  air_disp_corr =        true;  // refine disparity offset from IMS movements  
 	public boolean  air_disp_corr_save =   false; // apply disparity correction to the geometry correction of the master_CLT   
 
+	
+	
 	// Flat ground detection
 	public double   fgnd_percent_low =     0.01; // Discard lowest outliers. Percentile to remove lowest elevation outliers during initial terrain filtering
 	public double   fgnd_percent_high=     0.2;  // Discard highest outliers. Percentile to remove highest elevation outliers during initial terrain filtering.
@@ -3407,8 +3414,13 @@ min_str_neib_fpn	0.35
 		gd.addStringField ("Historic weight for 5D convolution",  IntersceneMatchParameters.doublesToString(curt_temp_weights), 80,
 				"Historic weights for 5D convolution ([0] is the latest sample). Will be normalized");
 		
+		gd.addMessage("=== Debug, saving images ===");
+		gd.addCheckbox ("Save full velocities hyperstack",           this.curt_save_c5full,
+				"save fine velocities [direction][scene][subpixels].");
+		gd.addCheckbox ("Save velocities for rectangle",             this.curt_save_c5rect,
+				"save fine velocities for selected rectangle only [scene][flattened image].");
+		gd.addStringField ("Output selection Rectangle",             rectangleToString(curt_save_select), 40, "Selection Rectangle:left, top, width,height");
 		
-		//
 		gd.addTab("Airplane","Airplane mode (fast forward movement, low vertical speed");
 		gd.addCheckbox ("Enable airplane mode",                      this.air_mode_en,
 				"Apply algorithms specific to the airplane mode.");
@@ -4900,6 +4912,10 @@ min_str_neib_fpn	0.35
 		this.curt_vel_decimate =  (int) gd.getNextNumber();
 		this.curt_vel_radius =    (int) gd.getNextNumber();
 	    this.curt_temp_weights = IntersceneMatchParameters. StringToDoubles(gd.getNextString(), 0);
+	    
+		this.curt_save_c5full =         gd.getNextBoolean();
+		this.curt_save_c5rect =         gd.getNextBoolean();
+		this.curt_save_select =         stringToRectangle(gd.getNextString());// Rectangle
 		
 		this.air_mode_en =              gd.getNextBoolean();
 		this.air_sync_ims =             gd.getNextBoolean();
@@ -6223,6 +6239,10 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"curt_vel_radius",      this.curt_vel_radius+"");     // int
 		properties.setProperty(prefix+"curt_temp_weights", IntersceneMatchParameters.doublesToString(this.curt_temp_weights));
 		
+		properties.setProperty(prefix+"curt_save_c5full",     this.curt_save_c5full+"");    // boolean
+		properties.setProperty(prefix+"curt_save_c5rect",     this.curt_save_c5rect+"");    // boolean
+		properties.setProperty(prefix+"curt_save_select",     rectangleToString(curt_save_select)+"");  // Rectangle
+		
 		properties.setProperty(prefix+"air_mode_en",          this.air_mode_en+"");         // boolean
 		properties.setProperty(prefix+"air_sync_ims",         this.air_sync_ims+"");        // boolean
 		properties.setProperty(prefix+"air_disp_corr",        this.air_disp_corr+"");       // boolean
@@ -7530,6 +7550,10 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"curt_vel_radius")!=null)      this.curt_vel_radius=Integer.parseInt(properties.getProperty(prefix+"curt_vel_radius"));
 		if (properties.getProperty(prefix+"curt_temp_weights")!=null) this.curt_temp_weights= IntersceneMatchParameters.StringToDoubles(properties.getProperty(prefix+"curt_temp_weights"),0); // use 0
 		
+		if (properties.getProperty(prefix+"curt_save_c5full")!=null)     this.curt_save_c5full=Boolean.parseBoolean(properties.getProperty(prefix+"curt_save_c5full"));
+		if (properties.getProperty(prefix+"curt_save_c5rect")!=null)     this.curt_save_c5rect=Boolean.parseBoolean(properties.getProperty(prefix+"curt_save_c5rect"));
+		if (properties.getProperty(prefix+"curt_save_select")!=null)     this.curt_save_select=stringToRectangle((String) properties.getProperty(prefix+"curt_save_select"));
+	
 		if (properties.getProperty(prefix+"air_mode_en")!=null)          this.air_mode_en=Boolean.parseBoolean(properties.getProperty(prefix+"air_mode_en"));
 		if (properties.getProperty(prefix+"air_sync_ims")!=null)         this.air_sync_ims=Boolean.parseBoolean(properties.getProperty(prefix+"air_sync_ims"));
 		if (properties.getProperty(prefix+"air_disp_corr")!=null)        this.air_disp_corr=Boolean.parseBoolean(properties.getProperty(prefix+"air_disp_corr"));
@@ -8815,6 +8839,10 @@ min_str_neib_fpn	0.35
 		imp.curt_vel_radius =       this.curt_vel_radius;
 		imp.curt_temp_weights =     this.curt_temp_weights.clone();
 		
+		imp.curt_save_c5full =      this.curt_save_c5full;
+		imp.curt_save_c5rect =      this.curt_save_c5rect;
+		imp.curt_save_select =      new Rectangle(this.curt_save_select);		
+		
 		imp.air_mode_en =           this.air_mode_en;
 		imp.air_sync_ims =          this.air_sync_ims;
 		imp.air_disp_corr =         this.air_disp_corr;