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Commit c4df622d authored by Andrey Filippov's avatar Andrey Filippov
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Fixing bugs, making OrthoMultiLMA run

parent b8b1f945
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Showing with 303 additions and 19 deletions
src/main/java/com/elphel/imagej/orthomosaic/OrthoMapsCollection.java
View file @ c4df622d
......@@ -345,10 +345,25 @@ public class OrthoMapsCollection implements Serializable{
}
return bounds_pix;
}
public int [][] getBoundsPixels(
int zoom_level, // maps[0] as a reference
int [] indices,
double [][][] affines) {
double [][] bounds_meters = (affines == null) ? getBoundsMeters(indices):getBoundsMeters(indices,affines);
double pix_size = OrthoMap.getPixelSizeMeters (zoom_level);
int [][] bounds_pix = new int[2][2];
for (int n = 0; n < bounds_pix.length; n++) {
bounds_pix[n][0] = (int) Math.floor(bounds_meters[n][0]/pix_size);
bounds_pix[n][1] = (int) Math.ceil (bounds_meters[n][1]/pix_size);
}
return bounds_pix;
}
public int [][] getBoundsPixels(
int zoom_level) { // maps[0] as a reference
return getBoundsPixels(zoom_level, null);
}
//double [][][] affines
/**
* Get rectified bounds of all provided ortho images relative to the origin (vertical
* point) of the first one in meters
......@@ -403,6 +418,36 @@ public class OrthoMapsCollection implements Serializable{
return bounds;
}
public double [][] getBoundsMeters(
int [] indices,
double [][][] affines){ // maps[0] as a reference
if (indices == null) {
indices = new int [ortho_maps.length];
for (int i = 0; i < indices.length; i++) {
indices[i] = i;
}
}
if (affines == null) {
affines = new double [ortho_maps.length][][];
for (int i = 0; i < affines.length; i++) {
affines[i] = ortho_maps[indices[i]].affine;
}
}
double [][] bounds = ortho_maps[indices[0]].getBoundsMeters(true,affines[0]);
for (int imap = 1; imap < indices.length; imap++) {
int nmap = indices[imap];
double [][] bounds_other = ortho_maps[nmap].getBoundsMeters(true,affines[imap]);
double [] enuOffset = ortho_maps[indices[0]].enuOffsetTo(ortho_maps[nmap]);
double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
for (int n = 0; n < bounds.length; n++) {
bounds[n][0] = Math.min(bounds[n][0],bounds_other[n][0]+ rd[n]);
bounds[n][1] = Math.max(bounds[n][1],bounds_other[n][1]+ rd[n]);
}
}
return bounds;
}
/**
* Get rectified overlap bounds of two provided ortho images relative to the origin (vertical
* point) of the first one in meters. Use specified affine transforms, not saved with the orto map
......@@ -783,10 +828,18 @@ public class OrthoMapsCollection implements Serializable{
int [] origin, // maps[0] as a reference
double [][] centers){
boolean use_alt = ground_planes != null;
final int dbg_x=2783, dbg_y=-5228;
int [][] bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
zoom_level,
bounds_to_indices? indices: null);
final int dbg_x=707, dbg_y=615;
int [][] bounds;
if (affines == null) {
bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
zoom_level,
bounds_to_indices? indices: null);
} else {
bounds = getBoundsPixels( // should be for rectified, {-bounds[0][0], -bounds[0][1]} - exact center
zoom_level,
bounds_to_indices? indices: null,
affines);
}
int width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
int height = bounds[1][1] - bounds[1][0];
if (wh != null) {
......@@ -808,20 +861,22 @@ public class OrthoMapsCollection implements Serializable{
for (int indx = 0; indx < indices.length; indx++) { //:indices) { // = 0; nmap< ortho_maps.length; nmap++) {
final int findx= indx;
final int nmap = indices[indx]; // nmap;
final double [][] affine = (affines !=null) ? affines[indx]: ortho_maps[nmap].affine; // only here use provided
Arrays.fill(dpixels[findx], Float.NaN);
final double scale = 1.0/OrthoMap.getPixelSizeMeters(zoom_level);
final double src_scale = 1.0/OrthoMap.getPixelSizeMeters(ortho_maps[nmap].orig_zoom_level); // pix per meter
// metric bounds of the rectified image relative to its origin
double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
/// double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true); // keep original bounds
double [][] mbounds = ortho_maps[nmap].getBoundsMeters(true,affine); // keep original bounds
double [] enu_offset = ortho_maps[indices[0]].enuOffsetTo(ortho_maps[nmap]);
final double [] scaled_out_center = { // xy center to apply affine to
final double [] scaled_out_center = { // xy center to apply affine to in output pixels
-bounds[0][0] + scale * enu_offset[0],
-bounds[1][0] - scale * enu_offset[1]};
if (centers != null) {
centers[findx] = scaled_out_center;
}
final int [][] obounds = new int [2][2]; // output (rectified, combined) image bounds, relative to thje top-left
for (int n = 0; n< 2; n++) {
final int [][] obounds = new int [2][2]; // output (rectified, combined) image bounds, relative to the top-left
for (int n = 0; n< 2; n++) { // output pixels
obounds[n][0] = (int) Math.floor(scaled_out_center[n] + scale*mbounds[n][0]);
obounds[n][1] = (int) Math.ceil (scaled_out_center[n] + scale*mbounds[n][1]);
}
......@@ -829,9 +884,10 @@ public class OrthoMapsCollection implements Serializable{
final int ownd_width = obounds[0][1] - obounds[0][0];
final int ownd_height = obounds[1][1] - obounds[1][0];
final int ownd_len = ownd_width * ownd_height;
double [][] src_bounds=ortho_maps[nmap].getBoundsMeters (true); // using original affines
/// final double [][] affine = (affines !=null) ? affines[indx]: ortho_maps[nmap].affine; // only here use provided
/// double [][] src_bounds=ortho_maps[nmap].getBoundsMeters (true); // using original affines
double [][] src_bounds=ortho_maps[nmap].getBoundsMeters (false,affine); // using provided affines
final double [] src_center = {-src_bounds[0][0],-src_bounds[1][0]}; // x,y center offset in the source image
final double [][] affine = (affines !=null) ? affines[indx]: ortho_maps[nmap].affine; // only here use provided
final int src_width = use_alt? ortho_maps[nmap].getAltData().width: ortho_maps[nmap].getImageData().width;
final int src_height = use_alt? ortho_maps[nmap].getAltData().height : ortho_maps[nmap].getImageData().height;
// final float [] src_img = use_alt? ortho_maps[nmap].getAltData().data : ortho_maps[nmap].getImageData().data;
......@@ -876,16 +932,16 @@ public class OrthoMapsCollection implements Serializable{
for (int nPix = ai.getAndIncrement(); nPix < ownd_len; nPix = ai.getAndIncrement()) {
int opX = nPix % ownd_width + obounds[0][0]; // absolute output pX, pY
int opY = nPix / ownd_width + obounds[1][0];
double dX = (opX - scaled_out_center[0]) /scale; // in original image scale
double dX = (opX - scaled_out_center[0]) /scale; // in meters
double dY = (opY - scaled_out_center[1]) /scale;
double [] xy_src = { // pixels of the source image
src_scale * (affine[0][0]*dX + affine[0][1]*dY + affine[0][2] + src_center[0]),
src_scale * (affine[1][0]*dX + affine[1][1]*dY + affine[1][2] + src_center[1])};
// limit to the source image
if ((((int) opX)==dbg_x) && (((int) opY)==dbg_y)) {
System.out.println("opX="+opX+", opy="+opY);
}
if ((warp_woi != null) && (warp_woi.contains(opX,opY))) {
if ((opX==dbg_x) && (opY==dbg_y)) {
System.out.println("opX="+opX+", opy="+opY);
}
double [] dxy = warp.getWarp(opX,opY);
xy_src[0] += dxy[0];
xy_src[1] += dxy[1];
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMultiLMA.java
View file @ c4df622d
......@@ -26,14 +26,18 @@
package com.elphel.imagej.orthomosaic;
import java.awt.Point;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.concurrent.atomic.AtomicInteger;
import com.elphel.imagej.cameras.CLTParameters;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.tileprocessor.ImageDtt;
import Jama.Matrix;
import ij.ImagePlus;
import ij.gui.PointRoi;
public class OrthoMultiLMA {
final boolean move_only;
......@@ -80,6 +84,99 @@ public class OrthoMultiLMA {
affine1[i][j] = 0.5 * (direct.getAffine()[i][j]+E[i][j]);
}
}
String [] titles = new String [indices.length];
for (int i = 0; i < indices.length; i++) {
titles[i] = indices[i]+"-"+maps_collection.ortho_maps[indices[i]].getName();
}
double [][][] affines_0d = {E,direct.getAffine()};
double [][][] affines_sym = {affine0, affine1};
double [][] affine0a = new double [2][3]; // keep b[] ==0
for (int i = 0; i < 2; i++) {
for (int j = 0; j < 2; j++) {
affine0a[i][j] = 0.5* affine0[i][j];
}
}
double [][] affine1a = PairwiseOrthoMatch.combineAffines(
affine0a, // double [][] affine0,
direct.getAffine(), //double [][] affine, // differential
rd); // double [] rd);
PairwiseOrthoMatch test_match = new PairwiseOrthoMatch (
affine0a, // double [][] affine0,
affine1a, // double [][] affine1,
rd); // double [] rd);
double [][][] affines_a = {affine0a,affine1a};
// show as intended (E, diff)
int zoom_level = -2;
int [] wh = new int[2];
int [] origin = new int[2];
double [][] centers = new double [indices.length][];
double [][] dmulti = maps_collection.renderMultiDouble (
null, // double [][] ground_planes, // null - images, non-null altitudes. use new double[2][3] for old way alt
indices, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
true, // boolean bounds_to_indices,
affines_a, // affines_0d, // affines, // double [][][] affines, // null or [indices.length][2][3]
null, // warp, // FineXYCorr warp,,
zoom_level, // int zoom_level,
wh, // int [] wh,
origin, // int [] origin){ // maps[0] as a reference
centers); // double [][] centers)
ImagePlus imp_multi = ShowDoubleFloatArrays.makeArrays(
dmulti,
wh[0],
wh[1],
"scaled.tiff", //"direct_diff.tiff",
titles); // test_titles,
PointRoi roi = new PointRoi();
for (int i = 0; i < centers.length; i++) {
roi.addPoint(centers[i][0],centers[i][1], 1+i);
}
roi.setOptions("label");
imp_multi.setRoi(roi);
imp_multi.show();
// show half_offsets
double [][] dmulti_sym = maps_collection.renderMultiDouble (
null, // double [][] ground_planes, // null - images, non-null altitudes. use new double[2][3] for old way alt
indices, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
true, // boolean bounds_to_indices,
affines_sym,// affines, // double [][][] affines, // null or [indices.length][2][3]
null, // warp, // FineXYCorr warp,,
zoom_level, // int zoom_level,
wh, // int [] wh,
origin, // int [] origin){ // maps[0] as a reference
centers); // double [][] centers)
ImagePlus imp_sym = ShowDoubleFloatArrays.makeArrays(
dmulti_sym,
wh[0],
wh[1],
"direct_sym.tiff",
titles); // test_titles,
PointRoi roi_sym = new PointRoi();
for (int i = 0; i < centers.length; i++) {
roi_sym.addPoint(centers[i][0],centers[i][1], 1+i);
}
roi_sym.setOptions("label");
imp_sym.setRoi(roi_sym);
imp_sym.show();
double [][][] derivs = new double [12][][];
double [][][] derivs_delta = new double [12][][];
double delta = 1E-7;
......@@ -111,12 +208,12 @@ public class OrthoMultiLMA {
public static int buildOrthoMap(
CLTParameters clt_parameters,
OrthoMapsCollection maps_collection,
String orthoMapsCollection_path
String orthoMapsCollection_path
) {
int debugLevel = 3;
int debugLevel = 1;
boolean move_only = false;
double [] val_coord = null; // 1 - valid, 0 - invalid, minimize coordinates errors
double position_pull = 0.1;
double position_pull = 0.001;
boolean use_inv = false;
double overlap_pow = 2.0; // match weight as overlap fraction to this power
int [] indices = maps_collection.getScenesSelection(
......@@ -127,7 +224,7 @@ public class OrthoMultiLMA {
double lambda_scale_good = 0.5;
double lambda_scale_bad = 8.0;
double lambda_max = 100;
double rms_diff = 0.0001;
double rms_diff = 0.000001;
int num_iter = 20;
boolean last_run = false;
oml.prepareLMA (
......@@ -155,6 +252,87 @@ public class OrthoMultiLMA {
if (debugLevel > 0) {
System.out.println("LMA: full RMS="+rms[0]+" ("+initial_rms[0]+"), pure RMS="+rms[1]+" ("+initial_rms[1]+")");
}
//Get and apply affines
//oml.updateAffines(maps_collection);
double [][][] affines = oml.getAffines();
// test
/*
PairwiseOrthoMatch match = maps_collection.ortho_maps[indices[0]].getMatch(maps_collection.ortho_maps[indices[1]].getName());
double [][] match_affine = match.getAffine();
double [] enuOffset = maps_collection.ortho_maps[indices[1]].enuOffsetTo(maps_collection.ortho_maps[indices[0]]);
double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
double [][] affine1a = PairwiseOrthoMatch.combineAffines(
affines[0], // double [][] affine0,
match_affine, //double [][] affine, // differential
rd); // double [] rd);
PairwiseOrthoMatch test_match = new PairwiseOrthoMatch (
affines[0], // double [][] affine0,
affines[1], // double [][] affine1,
rd); // double [] rd);
*/
int zoom_level = -2;
int [] wh = new int[2];
int [] origin = new int[2];
double [][] centers = new double [indices.length][];
double [][] dmulti = maps_collection.renderMultiDouble (
null, // double [][] ground_planes, // null - images, non-null altitudes. use new double[2][3] for old way alt
indices, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
true, // boolean bounds_to_indices,
affines, // null, // affines, // double [][][] affines, // null or [indices.length][2][3]
null, // warp, // FineXYCorr warp,,
zoom_level, // int zoom_level,
wh, // int [] wh,
origin, // int [] origin){ // maps[0] as a reference
centers); // double [][] centers)
String [] titles = new String [dmulti.length];
for (int i = 0; i < dmulti.length; i++) {
titles[i] = indices[i]+"-"+maps_collection.ortho_maps[indices[i]].getName();
}
ImagePlus imp_multi = ShowDoubleFloatArrays.makeArrays(
dmulti,
wh[0],
wh[1],
"matched_multi.tiff",
titles); // test_titles,
PointRoi roi = new PointRoi();
for (int i = 0; i < centers.length; i++) {
roi.addPoint(centers[i][0],centers[i][1], 1+i);
}
roi.setOptions("label");
imp_multi.setRoi(roi);
imp_multi.show();
double [][] affine = getAffineAndDerivatives(
move_only, //boolean move_only,
affines[0], // double [][] affine00,
affines[1], // double [][] affine10,
oml.offsets[0], // double [] rd,
null); // double [][][] derivs)
PairwiseOrthoMatch pom = new PairwiseOrthoMatch (
affines[0],
affines[1],
oml.offsets[0]);
/*
if (orthoMapsCollection_path != null) {
try {
maps_collection.writeOrthoMapsCollection(orthoMapsCollection_path);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (debugLevel > -4) {
System.out.println("Saved data to "+ orthoMapsCollection_path);
}
}
*/
return 0;
}
......@@ -205,7 +383,8 @@ public class OrthoMultiLMA {
for (int np = 0; np < num_pairs; np++) {
Point pair = pairs_list.get(np);
pairs[np] = new int[] {pair.x, pair.y};
double [] enuOffset = maps_collection.ortho_maps[indices[pair.x]].enuOffsetTo(maps_collection.ortho_maps[indices[pair.y]]);
// double [] enuOffset = maps_collection.ortho_maps[indices[pair.x]].enuOffsetTo(maps_collection.ortho_maps[indices[pair.y]]);
double [] enuOffset = maps_collection.ortho_maps[indices[pair.y]].enuOffsetTo(maps_collection.ortho_maps[indices[pair.x]]);
offsets[np] = new double[] {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
}
pairs_ni = createNonIntersectingPairs(pairs);
......@@ -272,6 +451,37 @@ public class OrthoMultiLMA {
return weights.length;
}
public void updateAffines(OrthoMapsCollection maps_collection) {
for (int n = 0; n < num_scenes; n++) {
double [][] affine = maps_collection.ortho_maps[indices[n]].getAffine();
if (move_only) {
System.arraycopy(parameters_vector, 2*n, affine[0], 2, 1);
System.arraycopy(parameters_vector, 2*n + 1, affine[1], 2, 1);
} else {
System.arraycopy(parameters_vector, 6*n, affine[0], 0, 3);
System.arraycopy(parameters_vector, 6*n + 3, affine[1], 0, 3);
}
}
}
public double [][][] getAffines(){
double [][][] affines = new double [num_scenes][2][3];
for (int n = 0; n < num_scenes; n++) {
if (move_only) {
affines[n][0][0] = 1.0;
affines[n][1][1] = 1.0;
System.arraycopy(parameters_vector, 2*n, affines[n][0], 2, 1);
System.arraycopy(parameters_vector, 2*n + 1, affines[n][1], 2, 1);
} else {
System.arraycopy(parameters_vector, 6*n, affines[n][0], 0, 3);
System.arraycopy(parameters_vector, 6*n + 3, affines[n][1], 0, 3);
}
}
return affines;
}
public static double [][] getAffineAndDerivetives_delta(
boolean move_only,
double delta,
......
src/main/java/com/elphel/imagej/orthomosaic/PairwiseOrthoMatch.java
View file @ c4df622d
......@@ -172,6 +172,24 @@ public class PairwiseOrthoMatch implements Serializable {
// rms = Double.NaN; // double rms,
// zoom_lev = 0; // int zoom_lev)
}
public static double [][] combineAffines(
double [][] affine0,
double [][] affine, // differential
double [] rd) {
Matrix A0 = new Matrix (
new double [][] {{affine0[0][0],affine0[0][1]},{affine0[1][0],affine0[1][1]}});
Matrix B0 = new Matrix(new double [][] {{affine0[0][2]},{affine0[1][2]}});
Matrix A = new Matrix (
new double [][] {{affine[0][0],affine[0][1]},{affine[1][0],affine[1][1]}});
Matrix B = new Matrix(new double [][] {{affine[0][2]},{affine[1][2]}});
Matrix V = new Matrix(new double [][] {{-rd[0]},{-rd[1]}});
Matrix A1 = A.times(A0);
Matrix B1 = B.minus(A.times(V.minus(B0).minus(A0.times(V))));
double[][] affine1 = new double[][] {
{A1.get(0,0),A1.get(0,1), B1.get(0,0)},
{A1.get(1,0),A1.get(1,1), B1.get(1,0)}};
return affine1;
}
public double [][] getAffine(){
return affine;
......
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