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imagej-elphel
Commit 37cad36d authored by Andrey Filippov's avatar Andrey Filippov
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more debugging

parent 09416a86
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Showing with 172 additions and 18 deletions
src/main/java/EyesisCorrectionParameters.java
View file @ 37cad36d
......@@ -1797,6 +1797,7 @@ public class EyesisCorrectionParameters {
public int kernel_chn = -1; //camera channel calibration to use for aberration correction ( < 0 - no correction)
public boolean normalize = true; //normalize both sym and asym kernels (asym to have sum==1, sym to have sum = dct_size
public boolean skip_sym = false; // do not apply symmetrical correction
public boolean convolve_direct = false; // do not apply symmetrical correction
public DCTParameters(
int dct_size,
......@@ -1846,6 +1847,7 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"kernel_chn", this.kernel_chn+"");
properties.setProperty(prefix+"normalize", this.normalize+"");
properties.setProperty(prefix+"skip_sym", this.skip_sym+"");
properties.setProperty(prefix+"convolve_direct", this.convolve_direct+"");
}
public void getProperties(String prefix,Properties properties){
......@@ -1878,6 +1880,7 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"kernel_chn")!=null) this.kernel_chn=Integer.parseInt(properties.getProperty(prefix+"kernel_chn"));
if (properties.getProperty(prefix+"normalize")!=null) this.normalize=Boolean.parseBoolean(properties.getProperty(prefix+"normalize"));
if (properties.getProperty(prefix+"skip_sym")!=null) this.skip_sym=Boolean.parseBoolean(properties.getProperty(prefix+"skip_sym"));
if (properties.getProperty(prefix+"convolve_direct")!=null) this.convolve_direct=Boolean.parseBoolean(properties.getProperty(prefix+"convolve_direct"));
}
public boolean showDialog() {
......@@ -1911,6 +1914,7 @@ public class EyesisCorrectionParameters {
gd.addNumericField("Calibration channel to use for aberration ( <0 - no correction)",this.kernel_chn, 0);
gd.addCheckbox ("Normalize both sym and asym kernels ", this.normalize);
gd.addCheckbox ("Do not apply symmetrical (DCT) correction ", this.skip_sym);
gd.addCheckbox ("Convolve directly with symmetrical kernel (debug feature) ", this.convolve_direct);
gd.showDialog();
......@@ -1944,6 +1948,7 @@ public class EyesisCorrectionParameters {
this.kernel_chn= (int) gd.getNextNumber();
this.normalize= gd.getNextBoolean();
this.skip_sym= gd.getNextBoolean();
this.convolve_direct= gd.getNextBoolean();
// MASTER_DEBUG_LEVEL= (int) gd.getNextNumber();
return true;
}
......
src/main/java/EyesisDCT.java
View file @ 37cad36d
......@@ -56,8 +56,10 @@ public class EyesisDCT {
public int asym_size = 15; // asymmetrical convolution limits, odd
public int asym_nonzero = 4; // maximal number of non-zero elements in the asymmetrical kernels
public double [][] sym_kernels = null; // per-color channel, DCT kernels in linescan order
public double [][] sym_direct = null; // per-color channel, DCT kernels in linescan order (direct, not dct-iii transformed) - debug feature
public double [][] asym_kernels = null; // per-color channel, asymmetrical kernels (all but asym_nonzero elements are strictly 0)
public double [][][][] st_kernels = null; // [color][tileY][tileX][pixel]
public double [][][][] st_direct = null; // [color][tileY][tileX][pixel] - direct, not converted with DCT-III - debug feature
public double [][][][] asym_val = null; // [color][tileY][tileX][index] // value - asym kernel for elements
public int [][][][] asym_indx = null; // [color][tileY][tileX][index] // value - index of non-zero elements in the list
}
......@@ -204,6 +206,18 @@ public class EyesisDCT {
dct_parameters.decimateSigma,
gb);
}
if (dct_parameters.normalize) {
double s =0.0;
for (int i = 0; i <target_kernel.length; i++){
s+=target_kernel[i];
}
for (int i = 0; i <target_kernel.length; i++){
target_kernel[i]/=s;
}
if (globalDebugLevel>0){
System.out.println(tileX+"/"+tileY+ " s="+s);
}
}
// int numAsym =
factorConvKernel.calcKernels(
target_kernel,
......@@ -603,10 +617,8 @@ public class EyesisDCT {
// sdfa_instance.showArrays(kernels[chn].asym_kernels, asym_width, asym_height, true, asymKernelPaths[chn]);
int numHor = kernels[chn].numHor;
int numVert = kernels[chn].sym_kernels[0].length / (dct_size * dct_size * numHor);
// public double [][][][] st_kernels = null; // [color][tileY][tileX][pixel]
// public double [][][][] asym_val = null; // [color][tileY][tileX][index] // value - asym kernel for elements
// public int [][][][] asym_indx = null; // [color][tileY][tileX][index] // value - index of non-zero elements in the list
kernels[chn].st_kernels = new double [nColors][numVert][numHor][dct_size * dct_size];
kernels[chn].st_direct = new double [nColors][numVert][numHor][dct_size * dct_size];
kernels[chn].asym_val = new double [nColors][numVert][numHor][asym_nonzero];
kernels[chn].asym_indx = new int [nColors][numVert][numHor][asym_nonzero];
int sym_kernel_inc_index = numHor * dct_size;
......@@ -637,19 +649,37 @@ public class EyesisDCT {
double sum = 0.0;
for (int i=0; i < dct_size;i++) {
for (int j=0; j < dct_size;j++) {
double d = kernels[chn].st_kernels[nc][tileY][tileX][i];
double d = kernels[chn].st_kernels[nc][tileY][tileX][i*dct_size+j];
if (i > 0) d *= 2.0;
if (j > 0) d *= 2.0;
sum += d;
}
}
scale /= sum;
if ((tileY == ((dct_parameters.tileY+1)/2)) && (tileX ==((dct_parameters.tileX+1)/2)) && (nc == 2)) {
System.out.println("(kernel) tileY="+tileY+"(kernel) tileX="+tileX+" sum="+sum + " scale="+scale);
}
kernels[chn].st_kernels[nc][tileY][tileX]= dtt.dttt_iii(kernels[chn].st_kernels[nc][tileY][tileX]);
}
for (int i=0; i < kernels[chn].st_kernels[nc][tileY][tileX].length;i++) {
kernels[chn].st_kernels[nc][tileY][tileX][i] *= scale;
}
// Make a copy of direct kernels (debug feature, may be removed later)
for (int i = 0; i < dct_size;i++){
System.arraycopy( // copy one kernel line
kernels[chn].st_kernels[nc][tileY][tileX],
i * dct_size,
kernels[chn].st_direct[nc][tileY][tileX],
i * dct_size,
dct_size);
}
// scale st_direct back to ~original
for (int i=0; i < kernels[chn].st_kernels[nc][tileY][tileX].length;i++) {
kernels[chn].st_direct[nc][tileY][tileX][i] /= dct_size;
}
kernels[chn].st_kernels[nc][tileY][tileX]= dtt.dttt_iii(kernels[chn].st_kernels[nc][tileY][tileX]);
// extract asymmetrical kernel and convert it to list of values and indices (as arrays as the length is known)
int asym_kernel_start_index = (asym_kernel_inc_index * tileY + tileX)* asym_size;
......@@ -731,6 +761,9 @@ public class EyesisDCT {
int asym_width = numHor * kernels[chn].asym_size;
int asym_height = numVert * kernels[chn].asym_size;
kernels[chn].sym_kernels = new double [nColors][sym_width*sym_height];
if (kernels[chn].st_direct != null) {
kernels[chn].sym_direct = new double [nColors][sym_width*sym_height];
}
kernels[chn].asym_kernels = new double [nColors][asym_width*asym_height];
int sym_kernel_inc_index = numHor * dct_size;
int asym_kernel_inc_index = numHor * asym_size;
......@@ -748,6 +781,16 @@ public class EyesisDCT {
sym_kernel_start_index + i * sym_kernel_inc_index,
dct_size);
}
if (kernels[chn].st_direct != null){
for (int i = 0; i < dct_size;i++){
System.arraycopy( // copy one kernel line
kernels[chn].st_direct[nc][tileY][tileX],
i * dct_size,
kernels[chn].sym_direct[nc],
sym_kernel_start_index + i * sym_kernel_inc_index,
dct_size);
}
}
// set asymmetrical kernel from the list of values and indices
double [] asym_kernel = new double[asym_size*asym_size];
......@@ -780,7 +823,11 @@ public class EyesisDCT {
System.out.println("kernels["+chn+"][0].asym_kernels.length="+kernels[chn].asym_kernels[0].length);
sdfa_instance.showArrays(kernels[chn].sym_kernels, sym_width, sym_height, true, "restored-sym-"+chn);
sdfa_instance.showArrays(kernels[chn].asym_kernels, asym_width, asym_height, true, "restored-asym-"+chn);
if (kernels[chn].st_direct != null){
sdfa_instance.showArrays(kernels[chn].sym_direct, sym_width, sym_height, true, "restored-direct-"+chn);
}
kernels[chn].sym_kernels = null; // not needed anymore
kernels[chn].asym_kernels = null; // not needed anymore
kernels[chn].sym_direct = null; // not needed anymore
}
}
src/main/java/ImageDtt.java
View file @ 37cad36d
......@@ -235,6 +235,9 @@ public class ImageDtt {
chn,
dct_kernels,
dctParameters.skip_sym,
dctParameters.convolve_direct,
dctParameters.tileX,
dctParameters.tileY,
threadsMax, // maximal number of threads to launch
debugLevel);
}
......@@ -252,6 +255,9 @@ public class ImageDtt {
final int color,
final EyesisDCT.DCTKernels dct_kernels,
final boolean skip_sym,
final boolean convolve_direct, // test feature - convolve directly with the symmetrical kernel
final int debug_tileX,
final int debug_tileY,
final int threadsMax, // maximal number of threads to launch
final int globalDebugLevel)
{
......@@ -276,11 +282,18 @@ public class ImageDtt {
DttRad2 dtt = new DttRad2(dct_size);
dtt.set_window(window_type);
double [] tile_in = new double[4*dct_size * dct_size];
double [] sym_conv= null;
if ((dct_kernels != null) && convolve_direct){ // debug feature - directly convolve with symmetrical kernel
sym_conv = new double[4*dct_size * dct_size];
}
double [] tile_folded;
double [] tile_out; // = new double[dct_size * dct_size];
int tileY,tileX;
int n2 = dct_size * 2;
double dc;
showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
for (int nTile = ai.getAndIncrement(); nTile < nTiles; nTile = ai.getAndIncrement()) {
tileY = nTile/tilesX;
tileX = nTile - tileY * tilesX;
......@@ -291,7 +304,7 @@ public class ImageDtt {
int asym_center = dct_kernels.asym_size/2; // 7 for 15
kernelTileY = kernel_margin + (tileY * dct_size) / dct_kernels.img_step;
kernelTileX = kernel_margin + (tileX * dct_size) / dct_kernels.img_step;
if ((tileY <2) && (tileX <2) && (color ==0)) {
if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
System.out.println("kernelTileY="+kernelTileY+" kernelTileX="+kernelTileX+" width="+width);
}
for (int i = 0; i < n2; i++){
......@@ -302,7 +315,7 @@ public class ImageDtt {
double [] asym_val = dct_kernels.asym_val[color][kernelTileY][kernelTileX];
for (int indx = 0; indx < asym_indx.length; indx++){
int xy = asym_indx[indx];
if ((tileY <2) && (tileX <2) && (color ==0)) {
if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
System.out.println("i="+i+" j="+j+" indx="+indx+" xy="+xy);
}
if (xy >= 0) {
......@@ -315,7 +328,7 @@ public class ImageDtt {
if (y >= height) y = (height - 2) + (y & 1);
if (x >= width) x = (width - 2) + (x & 1);
tile_in[i*n2 + j] += asym_val[indx] * dpixels[ y * width + x];
if ((tileY <2) && (tileX <2) && (color ==0)) {
if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
System.out.println("dy= "+dy+" dx="+dx+" x = "+x+" y="+y+" y*width + x="+(y*width + x));
System.out.println("asym_val["+indx+"]="+asym_val[indx]+
" dpixels["+(y * width + x)+"]="+ dpixels[ y * width + x]+
......@@ -325,6 +338,95 @@ public class ImageDtt {
}
}
}
// directly convolve with symmetrical kernel (debug feature
if ((dct_kernels != null) && convolve_direct){
double [] dir_sym = dct_kernels.st_direct[color][kernelTileY][kernelTileX];
double s0 = 0;
for (int i = 0; i < n2; i++){
for (int j = 0; j < n2; j++){
int indx = i*n2+j;
sym_conv[indx] = 0.0; // dir_sym[0]* tile_in[indx];
for (int dy = -dct_size +1; dy < dct_size; dy++){
int ady = (dy>=0)?dy:-dy;
int sgny = 1;
int y = i - dy;
if (y < 0){
y = -1 -y;
sgny = -sgny;
if (y < 0) {
y = 0;
sgny = 0;
}
}
if (y >= n2){
y = 2*n2 - y;
sgny = -sgny;
if (y >= n2) {
y = n2-1;
sgny = 0;
}
}
for (int dx = -dct_size +1; dx < dct_size; dx++){
int adx = (dx >= 0)? dx:-dx;
int sgn = sgny;
int x = j - dx;
if (x < 0){
x = -1 -x;
sgn = -sgn;
if (x <0) {
x = 0;
sgn = 0;
}
}
if (x >= n2){
x = 2*n2 - x;
sgn = -sgn;
if (x >= n2) {
x = n2-1;
sgn = 0;
}
}
sym_conv[indx] += sgn*dir_sym[ady * dct_size + adx] * tile_in[y * n2 + x];
s0+=dir_sym[ady * dct_size + adx];
if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2) &&
(i == dct_size) && (j== dct_size)) {
System.out.println("i="+i+" j="+j+" dy="+dy+" dx="+dx+" ady="+ady+" adx="+adx+
" y="+y+" x="+x+" sgny="+sgny+" sgn="+sgn+
"sym_conv["+indx+"] += "+sgn+"* dir_sym["+(ady * dct_size + adx)+"] * tile_in["+(y * n2 + x)+"] +="+
sgn+"* "+ dir_sym[ady * dct_size + adx]+" * "+tile_in[y * n2 + x]+" +="+
(sgn*dir_sym[ady * dct_size + adx] * tile_in[y * n2 + x])+" ="+sym_conv[indx]);
}
}
}
}
}
if ((tileY == debug_tileY) && (tileX == debug_tileX) && (color == 2)) {
// if ((tileY == debug_tileY) && (tileX == debug_tileX)) {
double [][] pair = {tile_in, sym_conv};
sdfa_instance.showArrays(pair, n2, n2, true, "dconv-X"+tileX+"Y"+tileY+"C"+color);
sdfa_instance.showArrays(dir_sym, dct_size, dct_size, "dk-X"+tileX+"Y"+tileY+"C"+color);
double s1=0,s2=0;
for (int i = 0; i<tile_in.length; i++){
s1 +=tile_in[i];
s2 +=sym_conv[i];
}
double s3 = 0.0;
for (int i=0; i<dct_size;i++){
for (int j=0; j<dct_size;j++){
double d = dir_sym[i*dct_size+j];
if (i > 0) d*=2;
if (j > 0) d*=2;
s3+=d;
}
}
System.out.println("s1="+s1+" s2="+s2+" s1/s2="+(s1/s2)+" s0="+s0+" s3="+s3);
}
// tile_in = sym_conv.clone();
System.arraycopy(sym_conv, 0, tile_in, 0, n2*n2);
}
} else { // no aberration correction, just copy data
for (int i = 0; i < n2;i++){
System.arraycopy(dpixels, (tileY*width+tileX)*dct_size + i*width, tile_in, i*n2, n2);
......
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