Commit 29e261ef authored by Andrey Filippov's avatar Andrey Filippov

Adding filtering by absolute contrast

parent 6cbc4b32
...@@ -777,7 +777,7 @@ public class ObjectLocation { ...@@ -777,7 +777,7 @@ public class ObjectLocation {
} }
// min_weight = 10.0 // min_weight = 10.0
// Starting from very center remove fartherst (first or last) pixel, // Starting from very center remove farthest (first or last) pixel,
// until remaining weight drops below min_weight or sw0[]*(1-frac_outliers). // until remaining weight drops below min_weight or sw0[]*(1-frac_outliers).
// weight of the previous radius may fall also, but likely not too much // weight of the previous radius may fall also, but likely not too much
for (int nr = 1; nr < sw.length; nr++) { for (int nr = 1; nr < sw.length; nr++) {
......
...@@ -18,6 +18,8 @@ import java.time.LocalDateTime; ...@@ -18,6 +18,8 @@ import java.time.LocalDateTime;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.Calendar; import java.util.Calendar;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Properties; import java.util.Properties;
...@@ -1855,6 +1857,248 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{ ...@@ -1855,6 +1857,248 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
return convolved; return convolved;
} }
/**
* Calculate absolute contrast of the pattern
* @param data extracted square image with the object exactly
* in the center
* @param ipattern square pattern array corresponding to data. 1 means
* average (w/o outliers) and add, 2 - average and subtract
* @param outliers_frac - fraction of outliers to remove while averaging
* @param debug show debug images
* @return difference between average in-pattern (1) and outside (2) average
* values
*/
public static double getAbsoluteContrast(
double [] data,
int [] ipattern,
double outliers_frac,
boolean debug) {
if (debug) {
int size = (int) Math.sqrt(data.length);
ShowDoubleFloatArrays.showArrays(
data,
size,
size,
"extracted_data");
}
ArrayList<ArrayList<Integer>> lists = new ArrayList<ArrayList<Integer>>();
for (int i = 0; i < 2; i++) {
lists.add(new ArrayList<Integer>());
}
double [] swd = new double [2],sw = new double [2], avg= new double[2], fracw=new double[2];
for (int n = 0; n < swd.length; n++) {
ArrayList<Integer> list = lists.get(n);
int n1 = n+1;
for (int i = 0; i < ipattern.length; i++) if (ipattern[i] == n1){
sw[n] += 1;
swd[n]+= data[i];
list.add(i);
}
avg[n] = swd[n]/sw[n];
fracw[n] = (1.0-outliers_frac) * sw[n];
}
if (debug) {
System.out.println("getAbsoluteContrast() before outliers: avg[0] ="+avg[0]+", avg[1]="+avg[1]+", avg[0]-avg[1]="+(avg[0]-avg[1]));
}
if (outliers_frac > 0) {
for (int n = 0; n < swd.length; n++) {
ArrayList<Integer> list = lists.get(n);
Collections.sort(list, new Comparator<Integer>() {
@Override
public int compare(Integer lhs, Integer rhs) {
double rhsd = data[rhs];
double lhsd = data[lhs];
return (rhsd > lhsd) ? -1 : (rhsd < lhsd) ? 1 : 0;
}
});
while (sw[n] >= fracw[n]) {
int indx_first = list.get(0);
int indx_last = list.get(list.size()-1);
boolean remove_first = Math.abs(data[indx_first] - avg[n]) > Math.abs(data[indx_last] - avg[n]);
int indx_worst = remove_first? indx_first : indx_last;
double d = data[indx_worst];
double sw_new = sw[n] - 1.0;
avg[n] = (avg[n] * sw[n] - d)/sw_new;
sw[n] = sw_new;
list.remove(remove_first ? 0 : list.size()-1);
}
}
}
if (debug) {
int [] ipattern1 = new int [ipattern.length];
for (int n = 0; n < lists.size(); n++) {
ArrayList<Integer> list = lists.get(n);
for (Integer i: list) {
ipattern1[i] = n+1;
}
}
int [][] ipatterns = {ipattern, ipattern1};
double [][] dbg_img = new double [2][ipattern.length];
for (int n = 0; n < ipatterns.length; n++) {
for (int i= 0; i < ipatterns[n].length; i++) if (ipatterns[n][i] != 0){
switch (ipatterns[n][i]) {
case 1: dbg_img[n][i] = 1.0; break;
case 2: dbg_img[n][i] = -1.0; break;
}
}
}
int size = (int) Math.sqrt(ipattern.length);
ShowDoubleFloatArrays.showArrays(
dbg_img,
size,
size,
true,
"integer_patterns_before_after");
}
if (debug) {
System.out.println("getAbsoluteContrast() after outliers: avg[0] ="+avg[0]+", avg[1]="+avg[1]+", avg[0]-avg[1]="+(avg[0]-avg[1]));
}
return avg[0]-avg[1];
}
/**
* From existing pattern (only for simple dark main scene)
* create two zones to calculate average (w/o outliers) inside
* the pattern and around it. Mark inner with 1, outer - 2, keep
* other 0. Then later find 2 averages (removing outliers) and their
* difference - absolute contrast.
* @param patterns set of square patterns, first [0] for full pattern,
* others - for half-patterns cut in different directions.
* @param edge_frac consider in-pattern if normalized value (normalized by
* the value with maximal absolute value) is above
* 1-edge_frac, completely out if it is below edge_frac.
* @param oversize scale patterns by this value to create outer area (marked 2)
* @param debug show debug images
* @return integer array corresponding to the original patterns. 1 means
* "in-patter" (average w/o outliers and add), 2 means "around pattern"-
* average w/o outliers and subtract.
*/
public static int[][] getIntPatterns(
double [][] patterns,
double edge_frac, // 0.15
double oversize,
boolean debug) {
double low_thresh = edge_frac;
double high_thresh = 1.0 - edge_frac;
int size = (int) Math.sqrt(patterns[0].length);
double xc = size/2;
double yc = size/2;
int [][] ipatterns = new int [patterns.length][patterns[0].length];
double amax = 0;
double absmax = 0;
for (int i = 0; i < patterns[0].length; i++) {
double d = patterns[0][i];
double ad = Math.abs(d);
if (ad > absmax) {
absmax = ad;
amax = d;
}
}
double scale = 1.0/amax;
double [][] npatterns = new double [patterns.length][patterns[0].length];
for (int n = 0; n < patterns.length; n++) {
for (int i = 0; i < patterns[n].length; i++) {
npatterns[n][i] = patterns[n][i] * scale;
}
}
// create full pattern first
int num_1 = 0, num_2=0;
for (int y=0; y < size; y++) {
double ys= yc+ (y-yc)/oversize;
for (int x=0; x < size; x++) {
int indx = y*size+x;
if (npatterns[0][indx] > high_thresh) {
ipatterns[0][indx] = 1;
num_1++;
} else if (npatterns[0][indx] <= low_thresh) {// interpolate scaled version, between - keep zero
double xs = xc+ (x-xc)/oversize;
// interpolate
int iys = (int) Math.floor(ys);
double fys = ys-iys;
int ixs = (int) Math.floor(xs);
double fxs = xs-ixs;
int sindx = iys*size+ixs;
double sd0 =
(1-fys)*(1-fxs)*npatterns[0][sindx] +
(1-fys)*( fxs)*npatterns[0][sindx+1] +
( fys)*(1-fxs)*npatterns[0][sindx+size] +
( fys)*( fxs)*npatterns[0][sindx+size+1];
if (sd0 > high_thresh) {
ipatterns[0][indx] = 2;
num_2++;
}
}
}
}
if ((num_1 == 0) || (num_2==0)) {
System.out.println("getIntPatterns(): wrong pattern or parameters: num_1="+num_1+", num2="+num_2);
return null;
}
// Other patterns
for (int n = 1; n < npatterns.length; n++) {
for (int y=0; y < size; y++) {
double ys= yc+ (y-yc)/oversize;
for (int x=0; x < size; x++) {
int indx = y*size+x;
if (ipatterns[0][indx] == 1) {
if (npatterns[n][indx]/npatterns[0][indx] > 0.5) {
ipatterns[n][indx] = ipatterns[0][indx]; //= 1
}
} else if (ipatterns[0][indx] == 2) {
double xs = xc+ (x-xc)/oversize;
// interpolate
int iys = (int) Math.floor(ys);
double fys = ys-iys;
int ixs = (int) Math.floor(xs);
double fxs = xs-ixs;
int sindx = iys*size+ixs;
double sd0 =
(1-fys)*(1-fxs)*npatterns[0][sindx] +
(1-fys)*( fxs)*npatterns[0][sindx+1] +
( fys)*(1-fxs)*npatterns[0][sindx+size] +
( fys)*( fxs)*npatterns[0][sindx+size+1];
double sdn =
(1-fys)*(1-fxs)*npatterns[n][sindx] +
(1-fys)*( fxs)*npatterns[n][sindx+1] +
( fys)*(1-fxs)*npatterns[n][sindx+size] +
( fys)*( fxs)*npatterns[n][sindx+size+1];
if (sdn/sd0 > 0.5) {
ipatterns[n][indx] = ipatterns[0][indx]; // =2
}
}
}
}
}
if (debug) {
ShowDoubleFloatArrays.showArrays(
npatterns,
size,
size,
true,
"normalized_patterns");
double [][] dbg_img = new double [ipatterns.length][ipatterns[0].length];
for (int n = 0; n < ipatterns.length; n++) {
for (int i= 0; i < ipatterns[n].length; i++) if (ipatterns[n][i] != 0){
switch (ipatterns[n][i]) {
case 1: dbg_img[n][i] = 1.0; break;
case 2: dbg_img[n][i] = -1.0; break;
}
}
}
ShowDoubleFloatArrays.showArrays(
dbg_img,
size,
size,
true,
"integer_patterns");
}
return ipatterns;
}
public static double [] extractKernel( public static double [] extractKernel(
double [] data, double [] data,
int kernel_radius, int kernel_radius,
......
...@@ -1976,6 +1976,8 @@ public class OrthoMapsCollection implements Serializable{ ...@@ -1976,6 +1976,8 @@ public class OrthoMapsCollection implements Serializable{
double [][][] corrs_out = new double[indices.length][][]; double [][][] corrs_out = new double[indices.length][][];
double [][][] convolve_out = new double[indices.length][][]; double [][][] convolve_out = new double[indices.length][][];
double [][][] corr_patterns = new double[indices.length][][]; double [][][] corr_patterns = new double[indices.length][][];
int [][][] icorr_patterns= new int[indices.length][][]; // will only be used for main !
double [][][] filtered_corrs = new double[indices.length][][]; double [][][] filtered_corrs = new double[indices.length][][];
int [] zoomout = new int[indices.length]; int [] zoomout = new int[indices.length];
ImagePlus [] imp_corrs = new ImagePlus[indices.length]; ImagePlus [] imp_corrs = new ImagePlus[indices.length];
...@@ -2066,8 +2068,17 @@ public class OrthoMapsCollection implements Serializable{ ...@@ -2066,8 +2068,17 @@ public class OrthoMapsCollection implements Serializable{
kernels_all[scene_num], // final double [] kernel, kernels_all[scene_num], // final double [] kernel,
corr_size); // final int width) corr_size); // final int width)
} }
} }
if (scene_num == 0) {
double oversize = 1.8;
double edge_frac = 0.25;
icorr_patterns[scene_num] = OrthoMap.getIntPatterns(
corr_patterns[scene_num], // double [][] patterns,
edge_frac, // double edge_frac, // 0.15
oversize, // double oversize,
true); // boolean debug);
}
} }
// Splitting - above done for both scenes, below - just for the main one // Splitting - above done for both scenes, below - just for the main one
for (int scene_num = 0; scene_num < indices.length; scene_num++) { // will probably just use first one, second - derivative for (int scene_num = 0; scene_num < indices.length; scene_num++) { // will probably just use first one, second - derivative
...@@ -2200,6 +2211,7 @@ public class OrthoMapsCollection implements Serializable{ ...@@ -2200,6 +2211,7 @@ public class OrthoMapsCollection implements Serializable{
num_non_overlap++; num_non_overlap++;
} }
} }
if (num_non_overlap > 0) { if (num_non_overlap > 0) {
System.out.println("Removed "+num_non_overlap+" objects outside of the scenes overlap, "+match_sort.size()+" remain"); System.out.println("Removed "+num_non_overlap+" objects outside of the scenes overlap, "+match_sort.size()+" remain");
} }
...@@ -2226,6 +2238,7 @@ public class OrthoMapsCollection implements Serializable{ ...@@ -2226,6 +2238,7 @@ public class OrthoMapsCollection implements Serializable{
System.out.print(","); System.out.print(",");
} }
} }
} }
// boolean remove_dc = true; // boolean remove_dc = true;
if (scene_num == 0) { if (scene_num == 0) {
...@@ -2353,6 +2366,18 @@ public class OrthoMapsCollection implements Serializable{ ...@@ -2353,6 +2366,18 @@ public class OrthoMapsCollection implements Serializable{
imps_extracted_corr, // ImagePlus[] imps_extracted_corr, // may be null - will not be displayed imps_extracted_corr, // ImagePlus[] imps_extracted_corr, // may be null - will not be displayed
imps_extracted_corr_half); // ImagePlus[] imps_extracted_corr_half imps_extracted_corr_half); // ImagePlus[] imps_extracted_corr_half
} }
double [] abs_contrast = new double [match_sort.size()];
double outliers_frac = 0.3;
for (int i = 0; i < match_sort.size(); i++) {
int indx =match_sort.get(i);
ItemMatch match = matches_list.get(indx);
int best_patt= match.getPatternMatch(gops[scene_num]).getBestSub();
abs_contrast[i] = OrthoMap.getAbsoluteContrast(
extracted_objects[scene_num][i], // double [] data,
icorr_patterns[scene_num][best_patt-1], //int [] ipattern,
outliers_frac, // double outliers_frac,
true); // boolean debug);
}
// Correlate second scene only for selected fragments // Correlate second scene only for selected fragments
for (int scene_other = 1; scene_other < indices.length; scene_other++) { // normally just 1 for (int scene_other = 1; scene_other < indices.length; scene_other++) { // normally just 1
filter_data[scene_other] = new double[match_sort.size()][2][]; // [scene][max][0-full, 1 - half][0- max, 1 - area, 2 - distance] filter_data[scene_other] = new double[match_sort.size()][2][]; // [scene][max][0-full, 1 - half][0- max, 1 - area, 2 - distance]
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment