Commit 4ec177ed authored by Andrey Filippov's avatar Andrey Filippov
Browse files

added denoise, debugging window influence

parent 271830ae

src/main/java/EyesisCorrectionParameters.java

+42 −4
Original line number Diff line number Diff line
@@ -1809,11 +1809,17 @@ public class EyesisCorrectionParameters { 
  		public double  sigma_y =          0.7; // blur for G contribution to Y

  		public double  sigma_color =      0.7; // blur for Pb and Pr in addition to that of Y

  		public double  line_thershold =   1.0; // line detection amplitude to apply line enhancement - not used?

  		public boolean nonlin =           true; // enable nonlinear processing (including denoise

  		public double  nonlin_max_y =     1.0; // maximal amount of nonlinear line/edge emphasis for Y component

  		public double  nonlin_max_c =     1.0; // maximal amount of nonlinear line/edge emphasis for C component

  		public double  nonlin_y =         0.1; // amount of nonlinear line/edge emphasis for Y component

  		public double  nonlin_c =         0.01; // amount of nonlinear line/edge emphasis for C component

  		public double  nonlin_corn =      0.5;  // relative weight for nonlinear corner elements

  		public boolean denoise =          true; // suppress noise during nonlinear processing

  		public double  denoise_y =        1.0;  // maximal total smoothing of the Y post-kernel (will compete with edge emphasis)

  		public double  denoise_c =        1.0;  // maximal total smoothing of the color differences post-kernel (will compete with edge emphasis)

  		public double  denoise_y_corn =   0.3;  // weight of the 4 corner pixels during denoise y (straight - 1-denoise_y_corn)

  		public double  denoise_c_corn =   0.3;  // weight of the 4 corner pixels during denoise y (straight - 1-denoise_c_corn)

  		



  		public DCTParameters(){}
@@ -1877,11 +1883,21 @@ public class EyesisCorrectionParameters { 
  			properties.setProperty(prefix+"sigma_color",        this.sigma_color+"");

  			properties.setProperty(prefix+"line_thershold",     this.line_thershold+"");

  			

  			properties.setProperty(prefix+"nonlin",             this.nonlin+"");

  			properties.setProperty(prefix+"nonlin_max_y",       this.nonlin_max_y+"");

  			properties.setProperty(prefix+"nonlin_max_c",       this.nonlin_max_c+"");

  			properties.setProperty(prefix+"nonlin_y",           this.nonlin_y+"");

  			properties.setProperty(prefix+"nonlin_c",           this.nonlin_c+"");

  			properties.setProperty(prefix+"nonlin_corn",        this.nonlin_corn+"");



  			properties.setProperty(prefix+"denoise",            this.denoise+"");

  			properties.setProperty(prefix+"denoise_y",          this.denoise_y+"");

  			properties.setProperty(prefix+"denoise_c",          this.denoise_c+"");

  			properties.setProperty(prefix+"denoise_y_corn",     this.denoise_y_corn+"");

  			properties.setProperty(prefix+"denoise_c_corn",     this.denoise_c_corn+"");

  			

  			

  			

  		}

  		public void getProperties(String prefix,Properties properties){

  			if (properties.getProperty(prefix+"dct_size")!=null) this.dct_size=Integer.parseInt(properties.getProperty(prefix+"dct_size"));
@@ -1924,11 +1940,19 @@ public class EyesisCorrectionParameters { 
  			if (properties.getProperty(prefix+"sigma_color")!=null)    this.sigma_color=Double.parseDouble(properties.getProperty(prefix+"sigma_color"));

  			if (properties.getProperty(prefix+"line_thershold")!=null) this.line_thershold=Double.parseDouble(properties.getProperty(prefix+"line_thershold"));



  			if (properties.getProperty(prefix+"nonlin")!=null)         this.nonlin=Boolean.parseBoolean(properties.getProperty(prefix+"nonlin"));

  			if (properties.getProperty(prefix+"nonlin_max_y")!=null)   this.nonlin_max_y=Double.parseDouble(properties.getProperty(prefix+"nonlin_max_y"));

  			if (properties.getProperty(prefix+"nonlin_max_c")!=null)   this.nonlin_max_c=Double.parseDouble(properties.getProperty(prefix+"nonlin_max_c"));

  			if (properties.getProperty(prefix+"nonlin_y")!=null)       this.nonlin_y=Double.parseDouble(properties.getProperty(prefix+"nonlin_y"));

  			if (properties.getProperty(prefix+"nonlin_c")!=null)       this.nonlin_c=Double.parseDouble(properties.getProperty(prefix+"nonlin_c"));

  			if (properties.getProperty(prefix+"nonlin_corn")!=null)    this.nonlin_corn=Double.parseDouble(properties.getProperty(prefix+"nonlin_corn"));

  			

  			if (properties.getProperty(prefix+"denoise")!=null)        this.denoise=Boolean.parseBoolean(properties.getProperty(prefix+"denoise"));

  			if (properties.getProperty(prefix+"denoise_y")!=null)      this.denoise_y=Double.parseDouble(properties.getProperty(prefix+"denoise_y"));

  			if (properties.getProperty(prefix+"denoise_c")!=null)      this.denoise_c=Double.parseDouble(properties.getProperty(prefix+"denoise_c"));

  			if (properties.getProperty(prefix+"denoise_y_corn")!=null) this.denoise_y_corn=Double.parseDouble(properties.getProperty(prefix+"denoise_y_corn"));

  			if (properties.getProperty(prefix+"denoise_c_corn")!=null) this.denoise_c_corn=Double.parseDouble(properties.getProperty(prefix+"denoise_c_corn"));

  			

  		}

  		public boolean showDialog() {

  			GenericDialog gd = new GenericDialog("Set DCT parameters");
@@ -1972,11 +1996,17 @@ public class EyesisCorrectionParameters { 
  			gd.addNumericField("Gaussian sigma to apply to Pr and Pb in the MDCT domain, pix",    this.sigma_color,         3);

  			gd.addNumericField("Threshold for line detection (not yet used)",                     this.line_thershold,      3);



  			gd.addCheckbox    ("Use non-linear line emphasis and denoise",                        this.nonlin             );

  			gd.addNumericField("Maximal amount of non-linear emphasis for linear edges for Y component",  this.nonlin_max_y,3);

  			gd.addNumericField("Maximal amount of non-linear emphasis for linear edges for color diffs.", this.nonlin_max_c,3);

  			gd.addNumericField("Sensitivity of non-linear emphasis for linear edges for Y component",  this.nonlin_y,       3);

  			gd.addNumericField("Sensitivity of non-linear emphasis for linear edges for color diffs.", this.nonlin_c,       3);

  			gd.addNumericField("Corretion for diagonal/corner emphasis elements",                 this.nonlin_corn,         3);

  			gd.addCheckbox    ("Suppress noise during nonlinear processing",                      this.denoise             );

  			gd.addNumericField("Maximal total smoothing of the Y post-kernel (will compete with edge emphasis)",  this.denoise_y,3);

  			gd.addNumericField("Maximal total smoothing of the color differences post-kernel (will compete with edge emphasis)",  this.denoise_c,3);

  			gd.addNumericField("Weight of the 4 corner pixels during denoising y (straight - 1.0-denoise_y_corn)",  this.denoise_y_corn,3);

  			gd.addNumericField("Weight of the 4 corner pixels during denoising color ((straight - 1.0-denoise_c_corn))",  this.denoise_c_corn,3);

  			

  			WindowTools.addScrollBars(gd);

  			gd.showDialog();
@@ -2022,11 +2052,19 @@ public class EyesisCorrectionParameters { 
  			this.sigma_color=           gd.getNextNumber();

  			this.line_thershold=        gd.getNextNumber();

  			

  			this.nonlin=             gd.getNextBoolean();

  			this.nonlin_max_y=          gd.getNextNumber();

  			this.nonlin_max_c=          gd.getNextNumber();

  			this.nonlin_y=              gd.getNextNumber();

  			this.nonlin_c=              gd.getNextNumber();

  			this.nonlin_corn=           gd.getNextNumber();

  			

  			this.denoise=             gd.getNextBoolean();

  			this.denoise_y=          gd.getNextNumber();

  			this.denoise_c=          gd.getNextNumber();

  			this.denoise_y_corn=          gd.getNextNumber();

  			this.denoise_c_corn=          gd.getNextNumber();

  			

  			//  	    MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();

  			return true;

  		}

src/main/java/EyesisDCT.java

+310 −181
Original line number Diff line number Diff line
@@ -1139,9 +1139,9 @@ public class EyesisDCT { 
				return result;

			}

// =================

			

	        ImageDtt image_dtt = new ImageDtt();

			showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

			if (this.correctionsParameters.deconvolve) { // process with DCT, otherwise use simple debayer

				ImageDtt image_dtt = new ImageDtt();

				double [][][][] dctdc_data = image_dtt.mdctDcStack(

						stack,

						dct_parameters,
@@ -1224,7 +1224,7 @@ public class EyesisDCT { 
							(tilesY + 1) * dct_parameters.dct_size,

							true,

							result.getTitle()+"-IDCTDC-YPrPb");

				if ((dct_parameters.nonlin_y != 0.0) || (dct_parameters.nonlin_c != 0.0)) {

					if (dct_parameters.nonlin && ((dct_parameters.nonlin_y != 0.0) || (dct_parameters.nonlin_c != 0.0))) {

						System.out.println("Applying edge emphasis, nonlin_y="+dct_parameters.nonlin_y+

								", nonlin_c="+dct_parameters.nonlin_c+", nonlin_corn="+dct_parameters.nonlin_corn);

						idct_data = edge_emphasis(
@@ -1236,6 +1236,10 @@ public class EyesisDCT { 
								dct_parameters.nonlin_y,                // final double      nonlin_y,         //  =        0.01; // amount of nonlinear line/edge emphasis for Y component

								dct_parameters.nonlin_c,                // final double      nonlin_c,         //  =        0.01; // amount of nonlinear line/edge emphasis for C component

								dct_parameters.nonlin_corn,             // final double      nonlin_corn,      // =     0.5;  // relative weight for nonlinear corner elements

								(dct_parameters.denoise? dct_parameters.denoise_y:0.0), // final double      denoise_y,        // =        1.0;  // maximal total smoothing of the Y post-kernel (will compete with edge emphasis)

								(dct_parameters.denoise? dct_parameters.denoise_c:0.0), // final double      denoise_c,        //  =        1.0;  // maximal total smoothing of the color differences post-kernel (will compete with edge emphasis)

								dct_parameters.denoise_y_corn,          // final double      denoise_y_corn,   // =   0.5;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)

								dct_parameters.denoise_c_corn,          // final double      denoise_c_corn,   // =   0.5;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)

								threadsMax,                             // final int         threadsMax,       // maximal number of threads to launch                         

								debugLevel);                            // final int         globalDebugLevel)

						sdfa_instance.showArrays(
@@ -1252,7 +1256,10 @@ public class EyesisDCT { 
							colorProcParameters.kb,        // 0.114;

							(tilesX + 1) * dct_parameters.dct_size);



				} else {

					System.out.println("Bypassing nonlinear correction");

				}



				sdfa_instance.showArrays(idct_data,

						(tilesX + 1) * dct_parameters.dct_size,

						(tilesY + 1) * dct_parameters.dct_size,
@@ -1266,6 +1273,13 @@ public class EyesisDCT { 
						(tilesX + 1) * dct_parameters.dct_size,

						(tilesY + 1) * dct_parameters.dct_size,

						sliceNames); // or use null to get chn-nn slice names





			} else { // if (this.correctionsParameters.deconvolve) - here use a simple debayer

				System.out.println("Bypassing DCTR-based aberration correction");

				debayer_rbg(stack, 0.25); // simple standard 3x3 kernel debayer

			}



			if (!this.correctionsParameters.colorProc){

				result= new ImagePlus(titleFull, stack);    			  

				eyesisCorrections.saveAndShow(
@@ -1321,6 +1335,7 @@ public class EyesisDCT { 
				for (int i = 0; i < fpixels.length; i++) yPrPb[n][i] = fpixels[i];

			}

			//			}

			/*

			String [] slice_names_YPrPb={"Y","Pr","Pb"};

			sdfa_instance.showArrays(idct_data,

					stack.getWidth(), // (tilesX + 1) * dct_parameters.dct_size,
@@ -1328,6 +1343,7 @@ public class EyesisDCT { 
					true,

					result.getTitle()+"-YPrPb",

					slice_names_YPrPb);

			*/		





			if (toRGB) {
@@ -1481,7 +1497,7 @@ public class EyesisDCT { 
				int width

				) {

			int length = yPrPb[0].length;

			int height = length/width;

//			int height = length/width;

			

			double [][]rbg = new double[3][length];

			double Kg=1.0-Kr-Kb;
@@ -1518,6 +1534,10 @@ public class EyesisDCT { 
				final double      nonlin_y,         //  =        0.01; // amount of nonlinear line/edge emphasis for Y component

				final double      nonlin_c,         //  =        0.01; // amount of nonlinear line/edge emphasis for C component

				final double      nonlin_corn,      // =     0.5;  // relative weight for nonlinear corner elements

				final double      denoise_y,        // =        1.0;  // maximal total smoothing of the Y post-kernel (will compete with edge emphasis)

				final double      denoise_c,        //  =        1.0;  // maximal total smoothing of the color differences post-kernel (will compete with edge emphasis)

				final double      denoise_y_corn,   // =   0.3;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)

				final double      denoise_c_corn,   // =   0.3;  // weight of the 4 corner pixels during denoise y (relative to 4 straight)

				final int         threadsMax,       // maximal number of threads to launch                         

				final int         globalDebugLevel)

		{
@@ -1532,6 +1552,15 @@ public class EyesisDCT { 
			final int    []   neib_indices = {-width-1,-width,-width+1,-1,0,1,width-1,width,width+1};       

			final double [][] kernsw_y = new double [kernsw.length][];

			final double [][] kernsw_c = new double [kernsw.length][];

			final double []   denoise_kern_y = {

					0.125*denoise_y*denoise_y_corn,         0.125*denoise_y*(1.0-denoise_y_corn), 0.125*denoise_y*denoise_y_corn,

					0.125*denoise_y*(1.0-denoise_y_corn),  -0.5*  denoise_y,                      0.125*denoise_y*(1.0-denoise_y_corn),

					0.125*denoise_y*denoise_y_corn,         0.125*denoise_y*(1.0-denoise_y_corn), 0.125*denoise_y*denoise_y_corn};

			final double []   denoise_kern_c = {

					0.125*denoise_c*denoise_c_corn,         0.125*denoise_c*(1.0-denoise_c_corn), 0.125*denoise_c*denoise_c_corn,

					0.125*denoise_c*(1.0-denoise_c_corn),  -0.5*  denoise_c,                      0.125*denoise_c*(1.0-denoise_c_corn),

					0.125*denoise_c*denoise_c_corn,         0.125*denoise_c*(1.0-denoise_c_corn), 0.125*denoise_c*denoise_c_corn};

			

			for (int n = 0; n < kernsw.length; n++){

				kernsw_y[n] = new double [kernsw[n].length];

				kernsw_c[n] = new double [kernsw[n].length];
@@ -1617,6 +1646,16 @@ public class EyesisDCT { 
												kern_c[ni]+= squared*kernsw_c[n][i];

											}

										}

										if (denoise_y > 0.0){

											for (int i = 0; i < kern_y.length; i++){

												kern_y[i]+= denoise_kern_y[i];

											}

										}

										if (denoise_c > 0.0){

											for (int i = 0; i < kern_y.length; i++){

												kern_c[i]+= denoise_kern_c[i];

											}

										}



										if (nonlin_max_y != 0){

											double sum = 0;
@@ -1662,7 +1701,97 @@ public class EyesisDCT { 
			ImageDtt.startAndJoin(threads);

			return yPrPb_new;

		}

		public void debayer_rbg(

				ImageStack stack_rbg){

			debayer_rbg(stack_rbg, 1.0);

		}

		

		// Simple in-place debayer by (bi) linear approximation, assumes [0R/00], [00/B0], [G0/0G] slices

		public void debayer_rbg(

				ImageStack stack_rbg,

				double scale)

		{

			int width = stack_rbg.getWidth();

			int height = stack_rbg.getHeight();

			float [] fpixels_r = (float[]) stack_rbg.getPixels(1);

			float [] fpixels_b = (float[]) stack_rbg.getPixels(2);

			float [] fpixels_g = (float[]) stack_rbg.getPixels(3);

			int [][][] av_row = {

					{{1,1},{-1,1},{-1,-1}},

					{{1,1},{-1,1},{-1,-1}},

					{{1,1},{-1,1},{-1,-1}}};

			int [][][] av_col =  {

					{{ width, width},{ width, width},{ width, width}},

					{{-width, width},{-width, width},{-width, width}},

					{{-width,-width},{-width,-width},{-width,-width}}};



			int [][][] av_xcross =  {

					{{ width+1, width+1, width+1, width+1}, { width-1, width+1, width-1, width+1}, { width-1, width-1, width-1, width-1}},

					{{-width+1, width+1,-width+1, width+1}, {-width-1,-width+1, width-1, width+1}, {-width-1,-width-1, width-1, width-1}},

					{{-width+1,-width+1,-width+1,-width+1}, {-width-1,-width+1,-width-1,-width+1}, {-width-1,-width-1,-width-1,-width-1}}};

			int [][][] av_plus =  {

					{{ width,         1,       1, width},   { width,        -1,       1, width  }, { width,        -1,      -1, width  }},

					{{-width,         1,       1, width},   {-width,        -1,       1, width  }, {-width,        -1,      -1, width  }},

					{{-width,         1,       1,-width},   {-width,        -1,       1,-width  }, {-width,        -1,      -1,-width  }}};

			for (int y = 0; y < height; y++){

				boolean odd_row = (y & 1) != 0;

				int row_type = (y==0)? 0: ((y==(height-1))?2:1);

				for (int x = 0; x < width; x++){

					int indx = y*width+x;

					boolean odd_col =   (x & 1) != 0;

					int col_type = (x==0)? 0: ((x==(width-1))?2:1);

					if (odd_row){

						if (odd_col){ // GB site

							fpixels_r[indx] = 0.5f*(

									fpixels_r[indx+av_col[row_type][col_type][0]]+

									fpixels_r[indx+av_col[row_type][col_type][1]]); 

							fpixels_b[indx] = 0.5f*(

									fpixels_b[indx+av_row[row_type][col_type][0]]+

									fpixels_b[indx+av_row[row_type][col_type][1]]); 

						} else { // !odd col  // B site

							fpixels_r[indx] = 0.25f*(

									fpixels_r[indx+av_xcross[row_type][col_type][0]]+

									fpixels_r[indx+av_xcross[row_type][col_type][1]]+

									fpixels_r[indx+av_xcross[row_type][col_type][2]]+

									fpixels_r[indx+av_xcross[row_type][col_type][3]]);

							fpixels_g[indx] = 0.25f*(

									fpixels_g[indx+av_plus[row_type][col_type][0]]+

									fpixels_g[indx+av_plus[row_type][col_type][1]]+

									fpixels_g[indx+av_plus[row_type][col_type][2]]+

									fpixels_g[indx+av_plus[row_type][col_type][3]]); 

						}

						

					} else { // !odd_row 

						if (odd_col){  // R site

							fpixels_b[indx] = 0.25f*(

									fpixels_b[indx+av_xcross[row_type][col_type][0]]+

									fpixels_b[indx+av_xcross[row_type][col_type][1]]+

									fpixels_b[indx+av_xcross[row_type][col_type][2]]+

									fpixels_b[indx+av_xcross[row_type][col_type][3]]);

							fpixels_g[indx] = 0.25f*(

									fpixels_g[indx+av_plus[row_type][col_type][0]]+

									fpixels_g[indx+av_plus[row_type][col_type][1]]+

									fpixels_g[indx+av_plus[row_type][col_type][2]]+

									fpixels_g[indx+av_plus[row_type][col_type][3]]); 

						} else { // !odd col  // G site

							fpixels_r[indx] = 0.5f*(

									fpixels_r[indx+av_row[row_type][col_type][0]]+

									fpixels_r[indx+av_row[row_type][col_type][1]]); 

							fpixels_b[indx] = 0.5f*(

									fpixels_b[indx+av_col[row_type][col_type][0]]+

									fpixels_b[indx+av_col[row_type][col_type][1]]); 

						}

					}

				}				

			}

			if (scale !=1.0){

				for (int i = 0; i< fpixels_r.length; i++){

					fpixels_r[i] *= scale;

					fpixels_b[i] *= scale;

					fpixels_g[i] *= scale;

				}

			}

		}

src/main/java/ImageDtt.java

+20 −3
Original line number Diff line number Diff line
@@ -583,6 +583,21 @@ public class ImageDtt { 
				}

			}

		}

		// normalize

		double sum = 0;

		for (int i = 0; i < dct_size; i++){

			for (int j = 0; j < dct_size; j++){

				double d = 	filter_direct[i*dct_size+j];

				d*=Math.cos(Math.PI*i/(2*dct_size))*Math.cos(Math.PI*j/(2*dct_size));

				if (i > 0) d*= 2.0;

				if (j > 0) d*= 2.0;

				sum +=d;

			}

		}

		for (int i = 0; i<filter_direct.length; i++){

			filter_direct[i] /= sum;

		}

		

		if (globalDebugLevel > -1) {

			for (int i=0; i<filter_direct.length;i++){

				System.out.println("dct_lpf_psf() "+i+": "+filter_direct[i]);
@@ -591,6 +606,8 @@ public class ImageDtt { 
		DttRad2 dtt = new DttRad2(dct_size);

//		final double [] filter= dtt.dttt_iii(filter_direct);

		final double [] filter= dtt.dttt_iiie(filter_direct);

		final double [] dbg_filter= dtt.dttt_ii(filter);

		

		for (int i=0; i < filter.length;i++) filter[i] *= dct_size;  

		

		if (globalDebugLevel > -1) {
@@ -598,7 +615,7 @@ public class ImageDtt { 
				System.out.println("dct_lpf_psf() "+i+": "+filter[i]); 

			}

			showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

			double [][] ff = {filter_direct,filter};

			double [][] ff = {filter_direct,filter,dbg_filter};

			sdfa_instance.showArrays(ff,  dct_size,dct_size, true, "filter_lpf");

		}
@@ -671,7 +688,7 @@ public class ImageDtt { 
			for (int j=0; j < dct_len; j++) filters_proto[i][j] *= 2*dct_size;  



		}

		if (globalDebugLevel > -1) {

		if (globalDebugLevel > 0) {

			showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

			double [][] ff = {filters_proto_direct[0],filters_proto_direct[1],filters_proto_direct[2],filters_proto[0],filters_proto[1],filters_proto[2]};

			sdfa_instance.showArrays(ff,  dct_size,dct_size, true, "filters_proto");
@@ -695,7 +712,7 @@ public class ImageDtt { 
				}

			}

		}

		if (globalDebugLevel > -1) {

		if (globalDebugLevel > 0) {

			showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?

			double [][] ff = {

					filters[0][0], filters[0][1], filters[0][2],