Commit b15f9feb authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Merge remote-tracking branch 'origin/dct'

parents c7e1de46 7c36f258

src/main/java/Aberration_Calibration.java

+10 −2
Original line number Diff line number Diff line
@@ -12003,7 +12003,11 @@ if (MORE_BUTTONS) { 
			int       loopDebugLevel){

		boolean noMove=false;

		if (newMotorPos==null) {

			try {

				newMotorPos=focusingMotors.readElphel10364Motors().clone();

			} catch (Exception e){

				System.out.println("moveAndMaybeProbe(): Failed to read motors");

			}

			justMove=true;

			noMove=true;

		}
@@ -12098,7 +12102,11 @@ if (MORE_BUTTONS) { 
//		System.out.println(">"+focusingMotors.historySize()+": "+focusingMotors.curpos[0]+", "+focusingMotors.curpos[1]+", "+focusingMotors.curpos[2]);

		boolean noMove=false;

		if (newMotorPos==null) {

			try {

				newMotorPos=focusingMotors.readElphel10364Motors().clone();

			} catch (Exception e){

				System.out.println("moveMeasureAndSave(): motors unreachable.");

			}

			noMove=true;

		}

		if (!noMove)focusingMotors.moveElphel10364Motors(

src/main/java/CalibrationHardwareInterface.java

+8 −3
Original line number Diff line number Diff line
@@ -2671,7 +2671,7 @@ public class CalibrationHardwareInterface { 
    		}

    		

    		boolean result=commandToDevice(command);

    		updateCurrents();

    		if (result)	updateCurrents();

    		return result;



    	}
@@ -2718,7 +2718,8 @@ public class CalibrationHardwareInterface { 
    				String msg = e1.getMessage();

    				if (msg==null || msg.equals(""))  msg = ""+e1;

					IJ.showMessage("Error",msg); 

					throw new IllegalArgumentException (msg);

					return false;

//					throw new IllegalArgumentException (msg);

    			}catch(ParserConfigurationException pce) {

    				pce.printStackTrace();

    				return false;
@@ -3471,7 +3472,9 @@ public class CalibrationHardwareInterface { 
    		IJ.showStatus("");

    		String error = e1.getMessage();

    		if (error==null || error.equals(""))  error = ""+e1;

    		IJ.showMessage("commandElphel10364Motors ERRROR", ""+error);

    		System.out.println("commandElphel10364Motors ERRROR: "+error);

    		// *********** Temporary removed message box (usually "HOST UNREACHABLE") *************

//    		IJ.showMessage("commandElphel10364Motors ERRROR", ""+error);

    		return null;

    	}catch(ParserConfigurationException pce) {

    		pce.printStackTrace();
@@ -6529,7 +6532,9 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" " 
    	}

    	public double distFromProbed(int [] position){

    		double minDist=Double.NaN;

    		if (this.history.size() <1) return Double.NaN;

    		if (position==null) position= this.history.get(this.history.size()-1).motorsPos;

    		

    		if (this.history.size()>0){

    			for (int i=0;i<this.history.size();i++) if (this.history.get(i).isProbed) {

    				int [] probedPosition=this.history.get(i).motorsPos;

src/main/java/DistortionCalibrationData.java

+18 −8
Original line number Diff line number Diff line
@@ -1691,15 +1691,25 @@ import org.apache.commons.configuration.XMLConfiguration; 
			if (gridImages!=null) {

//				this.pathName="";  // modified, keep the path anyway

// overwrite saved paths with the provided images, number of images{ should match

				if (this.gIP.length!=gridImages.length){

				if (this.gIP.length == gridImages.length){

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

						this.gIP[i].gridImage=gridImages[i];

						this.gIP[i].path=null; // not needed, just in case

						this.gIP[i].enabled=true;// enable all (actually just one) acquired images

					}

				} else {

					String msg="Number of provided images ("+gridImages.length+") does not match parameters restored from the "+pathname+" ("+this.gIP.length+")";

		    		IJ.showMessage("Error",msg);

		    		throw new IllegalArgumentException (msg);

				}

//		    		throw new IllegalArgumentException (msg);

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

					this.gIP[i].gridImage=gridImages[i];

						this.gIP[i].path=null; // not needed, just in case

						this.gIP[i].enabled=true;// enable all (actually just one) acquired images

						if (i < gridImages.length) {

							this.gIP[i].gridImage=gridImages[i];

						} else {

							this.gIP[i].gridImage=null;

						}

					}

				}

//				setGridImages(gridImages);

			}
@@ -2080,7 +2090,7 @@ import org.apache.commons.configuration.XMLConfiguration; 
        			imp_grid=this.gIP[numGridImg].gridImage;

        		} else {

        			if (this.updateStatus) IJ.showStatus("Reading grid file "+(fileNumber+1)+" (of "+(numImages)+"): "+this.gIP[fileNumber].path);

        			if (this.debugLevel>1) System.out.print(fileNumber+" ("+this.gIP[fileNumber].getStationNumber()+"): "+this.gIP[fileNumber].path);

        			if (this.debugLevel>-1) System.out.print(fileNumber+" ("+this.gIP[fileNumber].getStationNumber()+"): "+this.gIP[fileNumber].path);

        			imp_grid=opener.openImage("", this.gIP[fileNumber].path);  // or (path+filenames[nFile])

        			if (imp_grid==null) {

        				String msg="Failed to read grid file "+this.gIP[fileNumber].path;

src/main/java/DttRad2.java

+182 −30
Original line number Diff line number Diff line
@@ -44,10 +44,10 @@ public class DttRad2 { 
	double [] hwindow = null; // half window

	int    [][] fold_index = null; // index of the source item in 2nx2n array input to mdct_2d.

	                               // First index (0..n^2-1) index in the folded array (dct-iV input) 

	                               // Second index(0..3) - item to add (2 vertiacl, 2 - horizontal)  

	double [][] fold_k = null; // Matching fold_index items. Each is a product of 2 window coefficients and sign  

	                               // Second index(0..3) - item to add (2 vertical, 2 - horizontal)  

	double [][][] fold_k = null; // First index - mode: 0 - CC 1: SC, 2: CS, 3: SS. Other indices matching fold_index items. Each is a product of 2 window coefficients and sign  

	int    [] unfold_index = null;  // index  for each element of idct(2nx2n)

	double [] unfold_k = null; // Matching unfold_index items. Each is a product of 2 window coefficients and sign  

	double [][] unfold_k = null; // First index - mode: 0 - CC 1: SC, 2: CS, 3: SS. Other indices matching unfold_index items. Each is a product of 2 window coefficients and sign  

	

	public DttRad2 (int maxN){ // n - maximal

		setup_arrays(maxN); // always setup arrays for fast calculations
@@ -87,25 +87,31 @@ public class DttRad2 { 
	// For index in dct-iv input (0..n-1) get 2 variants of index in mdct input array (0..2*n-1)

	// second index : 0 - index in X array 2*n long

	//                1 - window index (0..n-1), [0] - minimal, [n-1] - max

	//                2 - sign of the term

	//                2 - sign of the C term  (-~c - d, +a -~b)

	//                3 - sign of the S term  (+~c - d, +a +~b)

	private int [][] get_fold_indices(int x, int n){

		int n1 = n>>1;

		int [][] ind = new int[2][3];

		int [][] ind = new int[2][4];

		if (x <n1) {

			ind[0][0] = n + n1 - x - 1; // -cR

			ind[0][0] = n + n1 - x - 1; // C: -cR, S: +cR

			ind[0][1] = n1     + x;

			ind[0][2] = -1;

			ind[1][0] = n + n1 + x;     // -d

			ind[0][3] =  1;

			ind[1][0] = n + n1 + x;     // C: -d,  S: -d

			ind[1][1] = n1     - x - 1;

			ind[1][2] = -1;

			ind[1][3] = -1;

		} else {

			x-=n1;

			ind[0][0] =          x;     // +a

			ind[0][0] =          x;     // C: +a, S: +a

			ind[0][1] =          x;

			ind[0][2] = 1;

			ind[1][0] = n      - x - 1; // -bR

			ind[0][3] = 1;

			

			ind[1][0] = n      - x - 1; // C: -bR, S: +bR

			ind[1][1] = n      - x - 1;

			ind[1][2] = -1;

			ind[1][3] =  1;

		}

		

		return ind;
@@ -114,45 +120,120 @@ public class DttRad2 { 
	private void set_fold_2d(int n){ // n - DCT and window size

		if ((fold_index != null) && (fold_index.length == n*n)) return;

		fold_index = new int[n*n][4];

		fold_k =     new double[n*n][4];

		fold_k =     new double[4][n*n][4];

		int []    vert_ind = new int[2];

		double [] vert_k = new double[2];

		double [][] vert_k = new double[2][2];

		int    [] hor_ind = new int[2];

		double [] hor_k = new double[2];

		double [][] hor_k = new double[2][2];

		int [][] fi;

		int n2 = 2*n;

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

			fi = get_fold_indices(i,n);

			vert_ind[0] = fi[0][0];

			vert_ind[1] = fi[1][0];

			vert_k[0] =   fi[0][2] * hwindow[fi[0][1]];

			vert_k[1] =   fi[1][2] * hwindow[fi[1][1]];

			vert_k[0][0] =   fi[0][2] * hwindow[fi[0][1]]; // use cosine sign

			vert_k[0][1] =   fi[1][2] * hwindow[fi[1][1]]; // use cosine sign

			vert_k[1][0] =   fi[0][3] * hwindow[fi[0][1]]; // use sine sign

			vert_k[1][1] =   fi[1][3] * hwindow[fi[1][1]]; // use sine sign

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

				fi = get_fold_indices(j,n);

				hor_ind[0] = fi[0][0];

				hor_ind[1] = fi[1][0];

				hor_k[0] =   fi[0][2] * hwindow[fi[0][1]];

				hor_k[1] =   fi[1][2] * hwindow[fi[1][1]];

				hor_k[0][0] =   fi[0][2] * hwindow[fi[0][1]]; // use cosine sign

				hor_k[0][1] =   fi[1][2] * hwindow[fi[1][1]]; // use cosine sign

				hor_k[1][0] =   fi[0][3] * hwindow[fi[0][1]]; // use sine sign

				hor_k[1][1] =   fi[1][3] * hwindow[fi[1][1]]; // use sine sign

				int indx = n*i + j;

				for (int k = 0; k<4;k++) {

					fold_index[indx][k] = n2 * vert_ind[(k>>1) & 1] + hor_ind[k & 1];

					fold_k[indx][k] =     vert_k[(k>>1) & 1] * hor_k[k & 1]; 

				}

				for (int mode = 0; mode<4; mode++){

					for (int k = 0; k<4;k++) {

						fold_k[mode][indx][k] =     vert_k[(mode>>1) &1][(k>>1) & 1] * hor_k[mode &1][k & 1]; 

					}

				}

			}

		}

		if (n < 8) {

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

				fi = get_fold_indices(i,n);

				System.out.println(i+"->"+String.format("[%2d % 2d % 2d] [%2d %2d %2d] %f %f",

						fi[0][0],fi[0][1],fi[0][2],

						fi[1][0],fi[1][1],fi[1][2], hwindow[fi[0][1]], hwindow[fi[1][1]]));

				System.out.println(i+"->"+String.format("?[%2d %2d %2d %2d] [%2d %2d %2d %2d] %f %f",

						fi[0][0],fi[0][1],fi[0][2],fi[0][3],

						fi[1][0],fi[1][1],fi[1][2],fi[1][3], hwindow[fi[0][1]], hwindow[fi[1][1]]));

			}

		}

	}

	

	public double [][][] get_fold_2d(

			double scale_hor,

			double scale_vert)

	{

		return get_fold_2d( this.N, scale_hor, scale_vert);

	}

	public double [][][] get_fold_2d(

			int n,

			double scale_hor,

			double scale_vert

			){ // n - DCT and window size

//		if ((fold_index != null) && (fold_index.length == n*n)) return;

//		fold_index = new int[n*n][4];

		

			double [] hwindow_h = new double[n];

			double [] hwindow_v = new double[n];

			double f = Math.PI/(2.0*n);

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

				double ah = f*scale_hor * (n-i-0.5);

				double av = f*scale_vert * (n-i-0.5);

				hwindow_h[i] = (ah > (Math.PI/2))? 0.0: Math.cos(ah);

				hwindow_v[i] = (av > (Math.PI/2))? 0.0: Math.cos(av);

			}

		double [][][] fold_sk = new double[2][n*n][4];

		int []    vert_ind =    new int[2];

		double [][] vert_k =    new double[2][2];

		int    [] hor_ind =     new int[2];

		double [][] hor_k =     new double[2][2];

		int [][] fi;

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

			fi = get_fold_indices(i,n);

			vert_ind[0] = fi[0][0];

			vert_ind[1] = fi[1][0];

//			vert_k[0] =   fi[0][2] * hwindow_v[fi[0][1]];

//			vert_k[1] =   fi[1][2] * hwindow_v[fi[1][1]];

			vert_k[0][0] =   fi[0][2] * hwindow_v[fi[0][1]]; // use cosine sign

			vert_k[0][1] =   fi[1][2] * hwindow_v[fi[1][1]]; // use cosine sign

			vert_k[1][0] =   fi[0][3] * hwindow_v[fi[0][1]]; // use sine sign

			vert_k[1][1] =   fi[1][3] * hwindow_v[fi[1][1]]; // use sine sign

			

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

				fi = get_fold_indices(j,n);

				hor_ind[0] = fi[0][0];

				hor_ind[1] = fi[1][0];

//				hor_k[0] =   fi[0][2] * hwindow_h[fi[0][1]];

//				hor_k[1] =   fi[1][2] * hwindow_h[fi[1][1]];

				hor_k[0][0] =   fi[0][2] * hwindow_h[fi[0][1]]; // use cosine sign

				hor_k[0][1] =   fi[1][2] * hwindow_h[fi[1][1]]; // use cosine sign

				hor_k[1][0] =   fi[0][3] * hwindow_h[fi[0][1]]; // use sine sign

				hor_k[1][1] =   fi[1][3] * hwindow_h[fi[1][1]]; // use sine sign

				

				int indx = n*i + j;

//				for (int k = 0; k<4;k++) {

//					fold_sk[indx][k] =     vert_k[(k>>1) & 1] * hor_k[k & 1]; 

//				}

				

				for (int mode = 0; mode<4; mode++){

					for (int k = 0; k<4;k++) {

						fold_sk[mode][indx][k] =     vert_k[(mode>>1) &1][(k>>1) & 1] * hor_k[mode &1][k & 1]; 

					}

				}

			}

		}

		return fold_sk;

	}

	

/*	

	// return index+1 and sign for 1-d imdct. x is index (0..2*n-1) of the imdct array, value is sign * (idct_index+1),

	// where idct_index (0..n-1) is index in the dct-iv array

	private int get_unfold_index(int x, int n){

	private int get_unfold_index_signes(int x, int n){

		int n1 = n>>1;

		int segm = x / n1;

		x = x % n1;
@@ -167,7 +248,7 @@ public class DttRad2 { 
	private void set_unfold_2d(int n){ // n - DCT size

		if ((unfold_index != null) && (unfold_index.length == 4*n*n)) return;

		unfold_index = new int[4*n*n];

		unfold_k = new double[4*n*n];

		unfold_k = new double[4][4*n*n];

		int n2 = 2*n;

		for (int i = 0; i < 2*n; i++ ){

			int index_vert = get_unfold_index(i,n);
@@ -202,6 +283,52 @@ public class DttRad2 { 
			}

		}

	}	

*/

	// return index and two signs (c,s) for 1-d imdct. x is index (0..2*n-1) of the imdct array, value is sign * (idct_index+1),

	// where idct_index (0..n-1) is index in the dct-iv array

	private int [] get_unfold_index_signs(int x, int n){

		int n1 = n>>1;

		int segm = x / n1;

		x = x % n1;

		int [] is2  = new int[3]; 

		switch (segm){

		case 0: is2[0] =  x + n1;     is2[1]=  1; is2[2] =  1; return is2; // return 1+ (x + n1);

		case 1: is2[0] =  n -  x - 1; is2[1]= -1; is2[2] =  1; return is2; // return -(n - x);

		case 2: is2[0] =  n1 - x - 1; is2[1]= -1; is2[2] =  1; return is2; // return -(n1 - x);

		case 3: is2[0] =  x;          is2[1]= -1; is2[2] = -1; return is2; // return -(1 + x);

		}

		return null; //should never happen

	}

	private void set_unfold_2d(int n){ // n - DCT size

		if ((unfold_index != null) && (unfold_index.length == 4*n*n)) return;

		unfold_index = new int[4*n*n];

		unfold_k = new double[4][4*n*n];

		int n2 = 2*n;

		for (int i = 0; i < 2*n; i++ ){

			int [] is2_vert = get_unfold_index_signs(i,n);

			double [] k_vert = {is2_vert[1]*hwindow[(i < n)?i:n2 -i -1], is2_vert[2]*hwindow[(i < n)?i:n2 -i -1]};

			int index_vert = is2_vert[0] * n;

			

			for (int j = 0; j < 2*n; j++ ){

				int [] is2_hor = get_unfold_index_signs(j,n);

				int index_hor = is2_hor[0];

				double [] k_hor = {is2_hor[1] * hwindow[(j < n)?j:n2 -j -1], is2_hor[2] * hwindow[(j < n)?j:n2 -j -1]};

				unfold_index[n2*i+j]=(index_vert+index_hor);

				for (int mode = 0; mode < 4; mode++){

					unfold_k[mode][n2*i+j] = k_vert[(mode>>1) &1]*k_hor[mode &1]; 

				}

				

				if (n < 8) System.out.print(String.format("%4d", unfold_index[n2*i+j]));

				

			}

			if (n < 8) System.out.println();

		}

		if (n < 8) {

			for (int i = 0; i < 2*n; i++ ){

				System.out.println(i+"=>"+get_unfold_index_signs(i,n)[0]+", "+get_unfold_index_signs(i,n)[1]+", "+get_unfold_index_signs(i,n)[2]);

			}

		}

	}	

	

	public double [] dttt_iv(double [] x){

		return dttt_iv(x, 0, 1 << (ilog2(x.length)/2));
@@ -347,28 +474,53 @@ public class DttRad2 { 
	}

	

	// Convert 2nx2n overlapping tile to n*n for dct-iv

	public double [] fold_tile(double [] x) { // x should be 2n*2n

	public double [] fold_tile(double [] x, int mode) { // x should be 2n*2n

		return fold_tile(x, 1 << (ilog2(x.length/4)/2));

	}

	public double [] fold_tile(double [] x, int n) { // x should be 2n*2n

	public double [] fold_tile(double [] x, int n, int mode) { // x should be 2n*2n

		return fold_tile(x,n, mode,this.fold_k);

//		double [] y = new double [n*n];

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

//			y[i] = 0;

//			for (int k = 0; k < 4; k++){

//				y[i] += x[fold_index[i][k]] * fold_k[i][k];

//			}

//		}

//		return y;

	}



	public double [] fold_tile(

			double [] x,

			int n,

			int mode, //////

			double [][][] fold_k

			) { // x should be 2n*2n

		double [] y = new double [n*n];

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

			y[i] = 0;

			for (int k = 0; k < 4; k++){

				y[i] += x[fold_index[i][k]] * fold_k[i][k];

				y[i] += x[fold_index[i][k]] * fold_k[mode][i][k];

			}

		}

		return y;

	}

	

	public double [] unfold_tile(double [] x) { // x should be n*n

		return unfold_tile(x, 1 << (ilog2(x.length)/2));

	

	public double [] unfold_tile(

			double [] x,  // x should be n*n

			int mode)

	{

		return unfold_tile(x, 1 << (ilog2(x.length)/2), mode);

		

	}

	public double [] unfold_tile(double [] x, int n) { // x should be 2n*2n

	public double [] unfold_tile(

			double [] x,  // x should be 2n*2n

			int n,

			int mode) 

	{

		double [] y = new double [4*n*n];

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

			y[i] = unfold_k[i]* x[unfold_index[i]];

			y[i] = unfold_k[mode][i]* x[unfold_index[i]];

		}

		return y;

	}

src/main/java/EyesisCorrectionParameters.java

+139 −29

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