Implemented 8bpp mode for ML output

src/main/java/BiQuadParameters.java

@@ -80,6 +80,7 @@ public class BiQuadParameters {
 	public boolean ml_keep_hor_vert =          true; // include combined horizontal and vertical pairs data in the ML output
 	public boolean ml_keep_debug=              true; // include debug layer(s) data in the ML output
 	public boolean ml_8bit=                    true; // output in 8-bit format (default - 32-bit TIFF
+	public double  ml_limit_extrim =           0.00001; // ignore lowest and highest values when converting to 8 bpp
 	public boolean ml_show_ml =                true; // show each generated MLoutput file
 
 
@@ -185,6 +186,8 @@ public class BiQuadParameters {
 				"Keep additional (debug) layers that may change for different file versions");
 		gd.addCheckbox    ("Use 8 bpp TIFF (default - 32 bpp)",                                                   this.ml_8bit,
 				"Reduce file size by lowering bpp");
+		gd.addNumericField("When converting to 8bpp, limit fraction of extreme values",                           1E6 * this.ml_limit_extrim,  1,8,"ppm",
+				"Use values histogram to find min/max values, ignoring(limiting) this fraction (parts per million) of pixels at both extremes");
 		gd.addCheckbox    ("Show each generated ML file",                                                         this.ml_show_ml,
 				"Use only for small number of generated files to reduce memory usage");
 
@@ -241,6 +244,7 @@ public class BiQuadParameters {
 		this.ml_keep_hor_vert=              gd.getNextBoolean();
 		this.ml_keep_debug=                 gd.getNextBoolean();
 		this.ml_8bit=                       gd.getNextBoolean();
+		this.ml_limit_extrim=               gd.getNextNumber() * 1E-6;
 		this.ml_show_ml=                    gd.getNextBoolean();
 	}
 
@@ -298,6 +302,7 @@ public class BiQuadParameters {
 		properties.setProperty(prefix+"ml_keep_hor_vert",          this.ml_keep_hor_vert+"");
 		properties.setProperty(prefix+"ml_keep_debug",             this.ml_keep_debug+"");
 		properties.setProperty(prefix+"ml_8bit",                   this.ml_8bit+"");
+		properties.setProperty(prefix+"ml_limit_extrim",           this.ml_limit_extrim+"");
 		properties.setProperty(prefix+"ml_show_ml",                this.ml_show_ml+"");
 
 
@@ -353,6 +358,7 @@ public class BiQuadParameters {
 		if (properties.getProperty(prefix+"ml_keep_hor_vert")!=null)        this.ml_keep_hor_vert=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_hor_vert"));
 		if (properties.getProperty(prefix+"ml_keep_debug")!=null)           this.ml_keep_debug=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_debug"));
 		if (properties.getProperty(prefix+"ml_8bit")!=null)                 this.ml_8bit=Boolean.parseBoolean(properties.getProperty(prefix+"ml_8bit"));
+		if (properties.getProperty(prefix+"ml_limit_extrim")!=null)         this.ml_limit_extrim=Double.parseDouble(properties.getProperty(prefix+"ml_limit_extrim"));
 		if (properties.getProperty(prefix+"ml_show_ml")!=null)              this.ml_show_ml=Boolean.parseBoolean(properties.getProperty(prefix+"ml_show_ml"));
 	}
 	@Override
@@ -408,9 +414,8 @@ public class BiQuadParameters {
 		bqp.ml_keep_hor_vert=           this.ml_keep_hor_vert;
 		bqp.ml_keep_debug=              this.ml_keep_debug;
 		bqp.ml_8bit=                    this.ml_8bit;
+		bqp.ml_limit_extrim=            this.ml_limit_extrim;
 		bqp.ml_show_ml=                 this.ml_show_ml;
 		return bqp;
-
-
 	}
 }

src/main/java/Correlation2d.java

@@ -1162,7 +1162,54 @@ public class Correlation2d {
     	int oindex = tileY *tile_width * full_width  + tileX * tile_width + (ml_index/tile_width)*full_width + (ml_index%tile_width) ;
     	ml_data[ml_layer][oindex] = ml_value;
     }
+    /**
+     * Get a single value from the combined multi-layer ML array, viewable as an image
+     * @param tileX horizontal tile index
+     * @param tileY vertical tile index
+     * @param ml_hwidth half-width of the preserved 2d correlation (0 - single point, 1 -> 3x3, 2 -> 5x5, 7 - all data)
+     * @param ml_data multi-layer array, each layer matches an image of ((2 * ml_hwidth + 1) * tilesX) by ((2 * ml_hwidth + 1) * tilesY) in scanline order
+     * Each tile corresponds to  (2 * ml_hwidth + 1) * (2 * ml_hwidth + 1) square in the image. Only selected tiles will be updated, so it is good to initialize array
+     * with all Double.NaN values
+     * @param ml_layer layer to save tile data
+     * @param ml_index data index within tile
+     * @param tilesX image width in tiles
+     * @return value indexed by tileX, tileY, ml_layer and ml_index
+     */
+    public double restoreMlTilePixel(
+    		int         tileX,
+    		int         tileY,
+    		int         ml_hwidth,
+    		double [][] ml_data,
+    		int         ml_layer,
+    		int         ml_index,
+    		int         tilesX) {
+    	int tile_width = 2 * ml_hwidth + 1;
+    	int full_width = tile_width * tilesX;
+    	int oindex = tileY *tile_width * full_width  + tileX * tile_width + (ml_index/tile_width)*full_width + (ml_index%tile_width) ;
+    	return ml_data[ml_layer][oindex];
+    }
+
+    /**
+     * Get an index of the selected tile+index in a ML array layer
+     * @param tileX horizontal tile index
+     * @param tileY vertical tile index
+     * @param ml_hwidth half-width of the preserved 2d correlation (0 - single point, 1 -> 3x3, 2 -> 5x5, 7 - all data)
+     * @param ml_index data index within tile
+     * @param tilesX image width in tiles
+     * @return index of teh selected pixel in thye whole image (specified by  tileX, tileY, and ml_index)
+     */
 
+    public  int getMlTilePixelIndex(
+    		int         tileX,
+    		int         tileY,
+    		int         ml_hwidth,
+    		int         ml_index,
+    		int         tilesX) {
+    	int tile_width = 2 * ml_hwidth + 1;
+    	int full_width = tile_width * tilesX;
+    	int oindex = tileY *tile_width * full_width  + tileX * tile_width + (ml_index/tile_width)*full_width + (ml_index%tile_width) ;
+    	return oindex;
+    }