snapshot before splitting EyesisDCT (ae48752e) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+60 −8

Original line number	Original line	Diff line number	Diff line
	@@ -1942,7 +1942,7 @@ public class EyesisCorrectionParameters {
	public boolean corr_show = false; // Show combined correlations		public boolean corr_show = false; // Show combined correlations
	public boolean corr_mismatch= false; // calculate per-pair X/Y variations of measured correlations		public boolean corr_mismatch= false; // calculate per-pair X/Y variations of measured correlations
	// TODO: what to do if some occlusion is present (only some channels correlate)		// TODO: what to do if some occlusion is present (only some channels correlate)
	public double corr_offset = -1.0; //0.1; // add to pair correlation before multiplying by other pairs (between sum and product)		public double corr_offset = 0.1; //0.1; // add to pair correlation before multiplying by other pairs (between sum and product)
	// negative - add, not mpy		// negative - add, not mpy
	public double corr_red = 0.5; // Red to green correlation weight		public double corr_red = 0.5; // Red to green correlation weight
	public double corr_blue = 0.2; // Blue to green correlation weight		public double corr_blue = 0.2; // Blue to green correlation weight
	@@ -2013,18 +2013,29 @@ public class EyesisCorrectionParameters {
	// 3d reconstruction		// 3d reconstruction
	public boolean show_textures = true; // show generated textures		public boolean show_textures = true; // show generated textures
	public boolean debug_filters = false;// show intermediate results of filtering		public boolean debug_filters = false;// show intermediate results of filtering
	public double min_smth = 0.5; // 0.25 minimal noise-normalized pixel difference in a channel to suspect something		public double min_smth = 0.25; // 0.25 minimal noise-normalized pixel difference in a channel to suspect something
	public double sure_smth = 2.0; // reliable noise-normalized pixel difference in a channel to have something		public double sure_smth = 2.0; // reliable noise-normalized pixel difference in a channel to have something
	public double bgnd_range = 0.3; // disparity range to be considered background		public double bgnd_range = 0.3; // disparity range to be considered background
	public double other_range = 2.0; // disparity difference from center (provided) disparity to trust		public double other_range = 2.0; // disparity difference from center (provided) disparity to trust

	public double bgnd_sure = 0.02; // minimal strength to be considered definitely background		public double bgnd_sure = 0.18; // minimal strength to be considered definitely background
	public double bgnd_maybe = 0.004; // maximal strength to ignore as non-background		public double bgnd_maybe = 0.1; // maximal strength to ignore as non-background
	// public double bgnd_2diff = 0.005; // maximal strength to ignore as non-background		// public double bgnd_2diff = 0.005; // maximal strength to ignore as non-background
	public int min_clstr_seed = 3; // number of tiles in a cluster to seed (just background?)		public int min_clstr_seed = 2; // number of tiles in a cluster to seed (just background?)
	public int min_clstr_block = 3; // number of tiles in a cluster to block (just non-background?)		public int min_clstr_block = 3; // number of tiles in a cluster to block (just non-background?)
	public int bgnd_grow = 2; // number of tiles to grow (1 - hor/vert, 2 - hor/vert/diagonal)		public int bgnd_grow = 2; // number of tiles to grow (1 - hor/vert, 2 - hor/vert/diagonal)

			// public double ortho_min = 0.09; // minimal strength of hor/vert correlation to be used instead of full 4-pair correlation
			public double ortho_min_hor = 0.07; // minimal strength of hor correlation to be used instead of full 4-pair correlation -
			public double ortho_min_vert = 0.15; // minimal strength of vert correlation to be used instead of full 4-pair correlation
			public double ortho_asym = 1.2; // vert/hor (or hor/vert) strength to be used instead of the full correlation
			public double ortho_sustain = 0.05; // minimal strength of hor/vert to bridge over
			public int ortho_run = 3; // minimal run of hor/vert tiles to be considered (at least from one side)
			public double ortho_minmax = 0.09; // minimal maximal strength in an ortho run
			public int ortho_bridge = 10; // number of tiles to bridge over hor/vert gaps
			public double ortho_rms = 0.3; // maximal disparity RMS in a run to replace by average
			public int ortho_half_length = 4; // convolve hor/vert strength by 3(2l+1) kernels to detect multi-tile features
			public double ortho_mix = 0.5; // Fraction ovf convolved ortho in a mix with raw



	@@ -2131,10 +2142,20 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"other_range", this.other_range +"");		properties.setProperty(prefix+"other_range", this.other_range +"");
	properties.setProperty(prefix+"bgnd_sure", this.bgnd_sure +"");		properties.setProperty(prefix+"bgnd_sure", this.bgnd_sure +"");
	properties.setProperty(prefix+"bgnd_maybe", this.bgnd_maybe +"");		properties.setProperty(prefix+"bgnd_maybe", this.bgnd_maybe +"");

	properties.setProperty(prefix+"min_clstr_seed", this.min_clstr_seed+"");		properties.setProperty(prefix+"min_clstr_seed", this.min_clstr_seed+"");
	properties.setProperty(prefix+"min_clstr_block", this.min_clstr_block+"");		properties.setProperty(prefix+"min_clstr_block", this.min_clstr_block+"");
	properties.setProperty(prefix+"bgnd_grow", this.bgnd_grow+"");		properties.setProperty(prefix+"bgnd_grow", this.bgnd_grow+"");
			properties.setProperty(prefix+"ortho_min_hor", this.ortho_min_hor +"");
			properties.setProperty(prefix+"ortho_min_vert", this.ortho_min_vert +"");
			properties.setProperty(prefix+"ortho_asym", this.ortho_asym +"");

			properties.setProperty(prefix+"ortho_sustain", this.ortho_sustain +"");
			properties.setProperty(prefix+"ortho_run", this.ortho_run+"");
			properties.setProperty(prefix+"ortho_minmax", this.ortho_minmax +"");
			properties.setProperty(prefix+"ortho_bridge", this.ortho_bridge+"");
			properties.setProperty(prefix+"ortho_rms", this.ortho_rms +"");
			properties.setProperty(prefix+"ortho_half_length",this.ortho_half_length+"");
			properties.setProperty(prefix+"ortho_mix", this.ortho_mix +"");
	}		}
	public void getProperties(String prefix,Properties properties){		public void getProperties(String prefix,Properties properties){
	if (properties.getProperty(prefix+"transform_size")!=null) this.transform_size=Integer.parseInt(properties.getProperty(prefix+"transform_size"));		if (properties.getProperty(prefix+"transform_size")!=null) this.transform_size=Integer.parseInt(properties.getProperty(prefix+"transform_size"));
	@@ -2233,11 +2254,20 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"other_range")!=null) this.other_range=Double.parseDouble(properties.getProperty(prefix+"other_range"));		if (properties.getProperty(prefix+"other_range")!=null) this.other_range=Double.parseDouble(properties.getProperty(prefix+"other_range"));
	if (properties.getProperty(prefix+"bgnd_sure")!=null) this.bgnd_sure=Double.parseDouble(properties.getProperty(prefix+"bgnd_sure"));		if (properties.getProperty(prefix+"bgnd_sure")!=null) this.bgnd_sure=Double.parseDouble(properties.getProperty(prefix+"bgnd_sure"));
	if (properties.getProperty(prefix+"bgnd_maybe")!=null) this.bgnd_maybe=Double.parseDouble(properties.getProperty(prefix+"bgnd_maybe"));		if (properties.getProperty(prefix+"bgnd_maybe")!=null) this.bgnd_maybe=Double.parseDouble(properties.getProperty(prefix+"bgnd_maybe"));

	if (properties.getProperty(prefix+"min_clstr_seed")!=null) this.min_clstr_seed=Integer.parseInt(properties.getProperty(prefix+"min_clstr_seed"));		if (properties.getProperty(prefix+"min_clstr_seed")!=null) this.min_clstr_seed=Integer.parseInt(properties.getProperty(prefix+"min_clstr_seed"));
	if (properties.getProperty(prefix+"min_clstr_block")!=null) this.min_clstr_block=Integer.parseInt(properties.getProperty(prefix+"min_clstr_block"));		if (properties.getProperty(prefix+"min_clstr_block")!=null) this.min_clstr_block=Integer.parseInt(properties.getProperty(prefix+"min_clstr_block"));
	if (properties.getProperty(prefix+"bgnd_grow")!=null) this.bgnd_grow=Integer.parseInt(properties.getProperty(prefix+"bgnd_grow"));		if (properties.getProperty(prefix+"bgnd_grow")!=null) this.bgnd_grow=Integer.parseInt(properties.getProperty(prefix+"bgnd_grow"));
			if (properties.getProperty(prefix+"ortho_min_hor")!=null) this.ortho_min_hor=Double.parseDouble(properties.getProperty(prefix+"ortho_min_hor"));
			if (properties.getProperty(prefix+"ortho_min_vert")!=null) this.ortho_min_vert=Double.parseDouble(properties.getProperty(prefix+"ortho_min_vert"));
			if (properties.getProperty(prefix+"ortho_asym")!=null) this.ortho_asym=Double.parseDouble(properties.getProperty(prefix+"ortho_asym"));

			if (properties.getProperty(prefix+"ortho_sustain")!=null) this.ortho_sustain=Double.parseDouble(properties.getProperty(prefix+"ortho_sustain"));
			if (properties.getProperty(prefix+"ortho_run")!=null) this.ortho_run=Integer.parseInt(properties.getProperty(prefix+"ortho_run"));
			if (properties.getProperty(prefix+"ortho_minmax")!=null) this.ortho_minmax=Double.parseDouble(properties.getProperty(prefix+"ortho_minmax"));
			if (properties.getProperty(prefix+"ortho_bridge")!=null) this.ortho_bridge=Integer.parseInt(properties.getProperty(prefix+"ortho_bridge"));
			if (properties.getProperty(prefix+"ortho_rms")!=null) this.ortho_rms=Double.parseDouble(properties.getProperty(prefix+"ortho_rms"));
			if (properties.getProperty(prefix+"ortho_half_length")!=null) this.ortho_half_length=Integer.parseInt(properties.getProperty(prefix+"ortho_half_length"));
			if (properties.getProperty(prefix+"ortho_mix")!=null) this.ortho_mix=Double.parseDouble(properties.getProperty(prefix+"ortho_mix"));
	}		}

	public boolean showDialog() {		public boolean showDialog() {
	@@ -2355,6 +2385,18 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("Number of tiles in a cluster to block (just non-background?)", this.min_clstr_block, 0);		gd.addNumericField("Number of tiles in a cluster to block (just non-background?)", this.min_clstr_block, 0);
	gd.addNumericField("Number of tiles to grow tile selection (1 - hor/vert, 2 - hor/vert/diagonal)", this.bgnd_grow, 0);		gd.addNumericField("Number of tiles to grow tile selection (1 - hor/vert, 2 - hor/vert/diagonal)", this.bgnd_grow, 0);

			gd.addNumericField("Minimal strength of hor correlation to be used instead of full 4-pair correlation", this.ortho_min_hor, 3);
			gd.addNumericField("Minimal strength of vert correlation to be used instead of full 4-pair correlation", this.ortho_min_vert, 3);
			gd.addNumericField("Vert/hor (or hor/vert) strength to be used instead of the full correlation", this.ortho_asym, 3);

			gd.addNumericField("Minimal strength of hor/vert to bridge over", this.ortho_sustain, 3);
			gd.addNumericField("minimal run of hor/vert tiles to be considered (at least from one side)", this.ortho_run, 0);
			gd.addNumericField("Minimal maximal strength in an ortho run (max. in run >=...)", this.ortho_minmax, 3);
			gd.addNumericField("Number of tiles to bridge over hor/vert gaps", this.ortho_bridge, 0);
			gd.addNumericField("Maximal disparity RMS in a run to replace by average)", this.ortho_rms, 3);
			gd.addNumericField("convolve hor/vert strength by 3(2l+1) kernels to detect multi-tile features",this.ortho_half_length, 0);
			gd.addNumericField("Fraction ovf convolved ortho in a mix with raw", this.ortho_mix, 3);

	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();

	@@ -2463,7 +2505,17 @@ public class EyesisCorrectionParameters {
	this.min_clstr_seed= (int) gd.getNextNumber();		this.min_clstr_seed= (int) gd.getNextNumber();
	this.min_clstr_block= (int) gd.getNextNumber();		this.min_clstr_block= (int) gd.getNextNumber();
	this.bgnd_grow= (int) gd.getNextNumber();		this.bgnd_grow= (int) gd.getNextNumber();
			this.ortho_min_hor= gd.getNextNumber();
			this.ortho_min_vert= gd.getNextNumber();
			this.ortho_asym= gd.getNextNumber();

			this.ortho_sustain= gd.getNextNumber();
			this.ortho_run= (int) gd.getNextNumber();
			this.ortho_minmax= gd.getNextNumber();
			this.ortho_bridge= (int) gd.getNextNumber();
			this.ortho_rms= gd.getNextNumber();
			this.ortho_half_length=(int)gd.getNextNumber();
			this.ortho_mix= gd.getNextNumber();
	return true;		return true;
	}		}
	}		}

src/main/java/EyesisDCT.java

+466 −27

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/ImageDtt.java

+33 −6

Original line number	Original line	Diff line number	Diff line
	@@ -1041,8 +1041,10 @@ public class ImageDtt {
	for (int i = 0; i < corr_size; i++){		for (int i = 0; i < corr_size; i++){
	if ((i < (transform_size - enhortho_width)) \|\| (i > (transform_size - 2 + enhortho_width))) enh_ortho_scale[i] = 1.0;		if ((i < (transform_size - enhortho_width)) \|\| (i > (transform_size - 2 + enhortho_width))) enh_ortho_scale[i] = 1.0;
	else enh_ortho_scale[i] = enhortho_scale;		else enh_ortho_scale[i] = enhortho_scale;
			if (i == (transform_size-1)) enh_ortho_scale[i] = 0.0 ; // hardwired 0 in the center
			enh_ortho_scale[i] = Math.sin(Math.PI(i+1.0)/(2*transform_size));
	}		}
	if (globalDebugLevel > 0){		if (globalDebugLevel > -1){
	System.out.println("enhortho_width="+ enhortho_width+" enhortho_scale="+ enhortho_scale);		System.out.println("enhortho_width="+ enhortho_width+" enhortho_scale="+ enhortho_scale);
	for (int i = 0; i < corr_size; i++){		for (int i = 0; i < corr_size; i++){
	System.out.println(" enh_ortho_scale["+i+"]="+ enh_ortho_scale[i]);		System.out.println(" enh_ortho_scale["+i+"]="+ enh_ortho_scale[i]);
	@@ -1380,16 +1382,23 @@ public class ImageDtt {
	} // all pairs calculated		} // all pairs calculated
	tcorr_combo = new double [TCORR_TITLES.length][corr_size * corr_size];		tcorr_combo = new double [TCORR_TITLES.length][corr_size * corr_size];

	int numPairs = 0;		int numPairs = 0, numPairsHor = 0, numPairsVert = 0;
	for (int pair = 0; pair < corr_pairs.length; pair++) if (((corr_mask >> pair) & 1) != 0){		for (int pair = 0; pair < corr_pairs.length; pair++) if (((corr_mask >> pair) & 1) != 0){
	numPairs++;		numPairs++;
			if (corr_pairs[pair][2] == 0) { // horizontal pair)
			numPairsHor++;
			} else {
			numPairsVert++;
			}
	}		}
	double avScale = 0.0;		double avScale = 0.0, avScaleHor = 0.0, avScaleVert = 0.0;
	if (numPairs > 0) {		if (numPairs > 0) {
	boolean debugMax = (globalDebugLevel > 0) && (tileX == debug_tileX) && (tileY == debug_tileY);		boolean debugMax = (globalDebugLevel > 0) && (tileX == debug_tileX) && (tileY == debug_tileY);
	avScale = 1.0/numPairs;		avScale = 1.0/numPairs;
			if (numPairsHor > 0) avScaleHor = 1.0/numPairsHor;
			if (numPairsVert > 0) avScaleVert = 1.0/numPairsVert;
	if (debugMax) {		if (debugMax) {
	System.out.println("avScale="+avScale+", corr_offset="+corr_offset);		System.out.println("avScale = "+avScale+", avScaleHor = "+avScaleHor+", avScaleVert = "+avScaleVert+", corr_offset = "+corr_offset);
	}		}
	if (corr_offset < 0) { // just add all partial correlations for composite color		if (corr_offset < 0) { // just add all partial correlations for composite color
	for (int i = 0; i < tcorr_combo[TCORR_COMBO_RSLT].length; i++){		for (int i = 0; i < tcorr_combo[TCORR_COMBO_RSLT].length; i++){
	@@ -1399,9 +1408,9 @@ public class ImageDtt {
	for (int pair = 0; pair < corr_pairs.length; pair++) if (((corr_mask >> pair) & 1) != 0){		for (int pair = 0; pair < corr_pairs.length; pair++) if (((corr_mask >> pair) & 1) != 0){
	tcorr_combo[TCORR_COMBO_RSLT][i] += avScale*tcorr_partial[pair][numcol][i]; // only composite color channel		tcorr_combo[TCORR_COMBO_RSLT][i] += avScale*tcorr_partial[pair][numcol][i]; // only composite color channel
	if (corr_pairs[pair][2] == 0) { // horizontal pair		if (corr_pairs[pair][2] == 0) { // horizontal pair
	tcorr_combo[TCORR_COMBO_HOR][i] += avScale*tcorr_partial[pair][numcol][i]; // only composite color channel		tcorr_combo[TCORR_COMBO_HOR][i] += avScaleHor*tcorr_partial[pair][numcol][i]; // only composite color channel
	} else { //vertical pair		} else { //vertical pair
	tcorr_combo[TCORR_COMBO_VERT][i] += avScale*tcorr_partial[pair][numcol][i]; // only composite color channel		tcorr_combo[TCORR_COMBO_VERT][i] += avScaleVert*tcorr_partial[pair][numcol][i]; // only composite color channel
	}		}
	if (debugMax) {		if (debugMax) {
	System.out.println("tcorr_combo[TCORR_COMBO_RSLT]["+i+"]="+tcorr_combo[TCORR_COMBO_RSLT][i]+" tcorr_partial["+pair+"]["+numcol+"]["+i+"]="+tcorr_partial[pair][numcol][i]);		System.out.println("tcorr_combo[TCORR_COMBO_RSLT]["+i+"]="+tcorr_combo[TCORR_COMBO_RSLT][i]+" tcorr_partial["+pair+"]["+numcol+"]["+i+"]="+tcorr_partial[pair][numcol][i]);
	@@ -1428,7 +1437,25 @@ public class ImageDtt {
	}		}
	// tcorr_combo[TCORR_COMBO_HOR][i] *= tcorr_combo[TCORR_COMBO_HOR][i]; // no have the same scale as tcorr_combo[TCORR_COMBO_RSLT]		// tcorr_combo[TCORR_COMBO_HOR][i] *= tcorr_combo[TCORR_COMBO_HOR][i]; // no have the same scale as tcorr_combo[TCORR_COMBO_RSLT]
	// tcorr_combo[TCORR_COMBO_VERT][i] *= tcorr_combo[TCORR_COMBO_VERT][i];		// tcorr_combo[TCORR_COMBO_VERT][i] *= tcorr_combo[TCORR_COMBO_VERT][i];
			if (corr_normalize) {
			if (tcorr_combo[TCORR_COMBO_RSLT][i] > 0.0){
			tcorr_combo[TCORR_COMBO_RSLT][i] = Math.pow(tcorr_combo[TCORR_COMBO_RSLT][i],avScale) - corr_offset;
			} else {
			tcorr_combo[TCORR_COMBO_RSLT][i] = -corr_offset;
			}

			if (tcorr_combo[TCORR_COMBO_HOR][i] > 0.0){
			tcorr_combo[TCORR_COMBO_HOR][i] = Math.pow(tcorr_combo[TCORR_COMBO_HOR][i],avScaleHor) - corr_offset;
			} else {
			tcorr_combo[TCORR_COMBO_HOR][i] = -corr_offset;
			}

			if (tcorr_combo[TCORR_COMBO_VERT][i] > 0.0){
			tcorr_combo[TCORR_COMBO_VERT][i] = Math.pow(tcorr_combo[TCORR_COMBO_VERT][i],avScaleVert) - corr_offset;
			} else {
			tcorr_combo[TCORR_COMBO_VERT][i] = -corr_offset;
			}
			}
	}		}
	}		}
	// calculate sum also		// calculate sum also