Skip to content

I
imagej-elphel
Commit cc9dbf30 authored by Andrey Filippov's avatar Andrey Filippov
Browse files
Options

Cleaning up, improving results

parent 99126b30
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 408 additions and 71 deletions
src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java
View file @ cc9dbf30
......@@ -327,7 +327,29 @@ public class ComboMatch {
"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or40.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif"
"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
"patterns_r30.0_e15.0_ir15.0ie8.0_is-0.05_h8_w0.6_s-200.0_200x200.tiff", // morning used
"--- 30, 28 edge 10 --",
"patterns_r30.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r30.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r28.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r28.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"--- 26, 32 edge 10 --",
"patterns_r26.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r26.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
// "patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-170.0_200x200.tif",
"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r32.0_e10.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"---- 30, 26 edge 6 ---",
"patterns_r30.0_e6.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r30.0_e6.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r26.0_e6.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r26.0_e6.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"---- 30, 26 edge 8 ---",
"patterns_r30.0_e8.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r30.0_e8.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r26.0_e8.0_ir15.0_ie8.0_is-0.05_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif",
"patterns_r26.0_e8.0_ir15.0_ie8.0_is-0.3_or42.0_oe6.0_os0.0_h8_w0.6_s-200.0_200x200.tif"
};
......@@ -399,9 +421,39 @@ public class ComboMatch {
for (ObjectLocation ol: object_list) {
System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);
}
int [] indices = null;
int [][] bounds = maps_collection.getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
zool_lev_objects,
indices);
int width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
int height = bounds[1][1] - bounds[1][0];
if ((width != imp_sel.getWidth()) || (height != imp_sel.getHeight())) {
System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does not match the full map size ("+
width+"x"+height+"), will try just for a pair of the first two slices");
String [] labels = imp_sel.getStack().getSliceLabels();
indices = new int [2];
for (int i = 0; i < indices.length; i++) {
indices[i] = maps_collection.getIndex(labels[i].substring(0, 17));
}
bounds = maps_collection.getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
zool_lev_objects,
indices);
width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
height = bounds[1][1] - bounds[1][0];
if ((width != imp_sel.getWidth()) || (height != imp_sel.getHeight())) {
System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does not match the 2-image map size ("+
width+"x"+height+") either.Giving up");
return false;
} else {
System.out.println("Marked image ("+imp_sel.getWidth()+"x"+imp_sel.getHeight()+") does match the 2-image map size ("+
width+"x"+height+"). Using it.");
}
}
maps_collection.reverseRender(
object_list, // ArrayList<ObjectLocation> objects,
zool_lev_objects); // int zoom_level){
object_list, // ArrayList<ObjectLocation> objects,
zool_lev_objects, // int zoom_level){
indices); // int [] indices){ // null or selected image indices
System.out.println("Object coordinates in source images: ");
for (ObjectLocation ol: object_list) {
System.out.println(ol.name+": "+ol.getPixels()[0]+"/"+ol.getPixels()[1]);
......@@ -416,11 +468,14 @@ public class ComboMatch {
extr_size);
}
ImagePlus imp_obj = ShowDoubleFloatArrays.makeArrays(
object_stack,
extr_size,
extr_size,
OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-OBJECT_"+extr_size+"x"+extr_size+".tiff",
OrthoMap.removeKnownExtension(imp_sel.getTitle())+
OrthoMap.removeKnownExtension(pattern_file)+":"+sub_pattern_index+
"-OBJECT_"+extr_size+"x"+extr_size+".tiff",
object_titles); // test_titles,
imp_obj.show();
......@@ -448,8 +503,10 @@ public class ComboMatch {
}
double [] kernel = OrthoMap.getConvolutionKernel(default_kernel);
double [][] centers = new double [object_stack.length][];
double [][] corr_ret = new double [object_stack.length][corr_size*corr_size];
for (int i = 0; i < object_stack.length; i++) {
String dbg_prefix = "corr_patt_"+i;
String dbg_prefix = "corr_patt_"+i+"-"+OrthoMap.removeKnownExtension(pattern_file)+":"+sub_pattern_index;
ObjectLocation ol = object_list.get(i);
centers[i] = ObjectLocation.getPatternCenter(
object_stack[i], // double [] data,
......@@ -460,6 +517,7 @@ public class ComboMatch {
min_corr, // double min_corr,
radius_search, // int radius_search,
radius_centroid, // int radius_centroid,
corr_ret[i], //double [] corr_ret, // null or double[corr_size*corr_size]
dbg_prefix, // String dbg_prefix,
debugLevel); // int debugLevel)
System.out.println(i+": center at "+centers[i][0]+"/"+centers[i][1]+", strength="+centers[i][2]);
......@@ -470,6 +528,35 @@ public class ComboMatch {
roi.addPoint(centers[i][0]+extr_size/2, centers[i][1]+extr_size/2, i+1); // ,1);
}
imp_obj.setRoi(roi);
// calculate statistics for cor_ret[i]
double [][] stats = new double [object_stack.length][];
double search_rad = 15.0;
double frac_max = 0.5;
double other_rad = 25;
for (int i = 0; i < object_stack.length; i++) {
double [] a_cent= {corr_size/2+centers[i][0],corr_size/2+centers[i][1]};
stats[i]=ObjectLocation.getMaxLocArea(
corr_ret[i], // double [] data, // square data
a_cent, // centers[i], // double [] cent_xy, // if null, use center of the square
search_rad, // double radius, // search for maximum within this radius
frac_max, // double frac_max,
other_rad,
0); // int debugLevel)
}
System.out.println("\nUsing pattern file: "+pattern_path+", subpattern="+sub_pattern_index);
System.out.println(String.format("%2s (%9s): %7s %7s %7s %7s %7s %7s %17s",
"#"," X/Y ","strengh", "radius", " elong ", " dist ", " dx "," dy ",
"image timestamp"));
for (int i = 0; i < object_stack.length; i++) {
ObjectLocation ol = object_list.get(i);
System.out.println(String.format("%2d (%4d/%4d): %7.5f %7.3f %7.3f %7.3f %7.3f %7.3f %17s",
i, ol.getPixels()[0], ol.getPixels()[1],
stats[i][0],stats[i][1],stats[i][2],stats[i][3],stats[i][4]+centers[i][0],stats[i][5]+centers[i][1],
ol.getName()));
}
System.out.println();
if (only_correlate) {
System.out.println("testPatternCorrelate(): correlation DONE, only_correlate is set to true, exiting");
return true;
......@@ -797,7 +884,8 @@ public class ComboMatch {
}
if (render_match) {
ImagePlus imp_img_pair = maps_collection.renderMulti (
"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"-zoom_"+min_zoom_lev+"_"+zoom_lev, // String title,
//_zoom<integer> is needed for opening with "Extract Objects" command
"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"_zoom"+min_zoom_lev+"_"+zoom_lev, // String title,
false, // boolean use_alt,
gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
bounds_to_indices, // boolean bounds_to_indices,
......@@ -823,7 +911,12 @@ public class ComboMatch {
}
return true;
}
public void printSceneStats() {
}
/*
double [][] affine1 = {
{1,0,0},
......@@ -1056,7 +1149,10 @@ adjusted affines[1] for a pair: 1694564291_293695/1694564778_589341
int nSlices = stack_scenes.getSize();
String [] scene_names = new String [nSlices];
for (int n = 0; n < scene_names.length; n++) {
scene_names[n] = stack_scenes.getSliceLabel(n+1).substring(0,17);
scene_names[n] = stack_scenes.getSliceLabel(n+1);
if (scene_names[n].length() >= 17) {
scene_names[n] = scene_names[n].substring(0,17);
}
}
PointRoi pRoi = (PointRoi) imp.getRoi();
FloatPolygon fp = pRoi.getContainedFloatPoints();
......
src/main/java/com/elphel/imagej/orthomosaic/ObjectLocation.java
View file @ cc9dbf30
......@@ -125,6 +125,7 @@ public class ObjectLocation {
* @param cent_xy offset from the square center to search
* @param radius search for maximum within this radius
* @param frac_max fraction of maximum to measure area
* @param other_radius measure maximal disconnected pixel fraction of the maximum within this radius
* @return {maximum, area, dist, x, y}. No interpolation yet, each returned value is integer.
* Returns null if no local maximum within area. x,y are offsets from the (provided) center
*/
......@@ -133,12 +134,14 @@ public class ObjectLocation {
double [] cent_xy, // if null, use center of the square
double radius, // search for maximum within this radius
double frac_max,
double other_radius,
int debugLevel) {
double [] rslt = getMaxLocArea(
data, // square data
cent_xy, // if null, use center of the square
radius, // search for maximum within this radius
frac_max,
other_radius,
debugLevel);
if (rslt != null) {
return rslt;
......@@ -152,6 +155,7 @@ public class ObjectLocation {
double [] cent_xy, // if null, use center of the square
double radius, // search for maximum within this radius
double frac_max,
double other_radius,
int debugLevel) {
boolean debug = debugLevel > 1;
int size = (int) Math.sqrt(data.length);
......@@ -201,8 +205,11 @@ public class ObjectLocation {
false); // boolean ordered)
int center_cluster = clusters[best_indx];
double xc = best_indx % size - cent_xy[0];
double yc = best_indx / size - cent_xy[1];
int best_x = best_indx % size;
int best_y = best_indx / size;
double xc = best_x - cent_xy[0];
double yc = best_y - cent_xy[1];
double s0=0, sx=0, sy=0, sx2 = 0, sy2=0, sxy = 0;
for (int i = 0; i < clusters.length; i++) {
......@@ -233,6 +240,35 @@ public class ObjectLocation {
double elong = Math.sqrt(eigval[1]/eigval[0]);
double eff_rad = Math.sqrt(Math.sqrt(eigval[1]*eigval[0]));
double dist = Math.sqrt(cent_offs[0]*cent_offs[0] + cent_offs[1]*cent_offs[1]);
double max_other = 0.0;
if (other_radius > 0) { // only calculate if asked for
double or2 = other_radius*other_radius;
min_x = Math.max(1, (int) Math.floor(best_x-other_radius));
min_y = Math.max(1, (int) Math.floor(best_y-other_radius));
max_x = Math.min(size-2, (int) Math.ceil(best_x+other_radius));
max_y = Math.min(size-2, (int) Math.ceil(best_y+other_radius));
for (int y = min_y; y <= max_y; y++) { // do not search on very edges
double dy = (y-best_y);
double y2 = dy*dy;
if (y2 < or2) {
for (int x = min_x; x <= max_x; x++) {
double dx = x - best_x;
double r2 = y2 + dx*dx;
if (r2 < or2) {
int indx = y * size + x;
if (clusters[indx] != center_cluster) { // only disconnected from the central area
double d = data[indx];
if (d > max_other) {
max_other = d;
}
}
}
}
}
}
max_other /= best_d;
}
if (debug) {
System.out.println("\ncenter offset ["+(sx/s0)+","+(sy/s0)+"] , from center: ["+cent_offs[0]+","+cent_offs[1]+"]");
System.out.println("Covariance matrix:");
......@@ -241,11 +277,11 @@ public class ObjectLocation {
eig.getV().print(8, 6);
System.out.println("eig.getD()");
eig.getD().print(8, 6);
System.out.println(String.format("best_d=%7.5f, rad=%6.3f, elong=%6.3f, dist=%6.3f, dx=%6.3f, dy=%6.3f",
best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1]));
System.out.println(String.format("best_d=%7.5f, rad=%6.3f, elong=%6.3f, dist=%6.3f, dx=%6.3f, dy=%6.3f, mo=%5.3f",
best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1], max_other));
}
return new double [] {best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1]} ;
return new double [] {best_d, eff_rad, elong, dist, cent_offs[0], cent_offs[1], max_other} ;
}
......@@ -326,6 +362,7 @@ public class ObjectLocation {
double min_corr,
int radius_search,
int radius_centroid,
double [] corr_ret, // null or double[corr_size*corr_size]
String dbg_prefix,
int debugLevel){
int refine = 1;
......@@ -393,6 +430,9 @@ public class ObjectLocation {
false, // final boolean convolve, // convolve, not correlate
phaseCoeff, // final double phaseCoeff,
debugLevel); // final int debugLevel)
if (corr_ret != null) {
System.arraycopy(corr_out, 0, corr_ret, 0, corr_out.length);
}
int data_width = 2 *radius_search + 1;
int offs = corr_size/2 - radius_search;
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java
View file @ cc9dbf30
......@@ -3841,7 +3841,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
if (ipix1 >= 0) {
bestcorr[ipix1] = corrs[patt][ipix1];
if (combine_full) {
bestcorr[ipix1] *= corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix];
bestcorr[ipix1] *= Math.max(0, corrs[full_patt_indx][ipix1]/corrs[full_patt_indx][ipix]);
}
bestpatt[ipix1] = patt;
}
......
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