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Commit 6c7e3422 authored by Andrey Filippov's avatar Andrey Filippov
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working snapshot for VegetationLMA, some debug tools

parent 8aa4bef7
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Showing with 356 additions and 65 deletions
src/main/java/com/elphel/imagej/vegetation/VegetationLMA.java
View file @ 6c7e3422
......@@ -7,8 +7,12 @@ import java.util.concurrent.atomic.AtomicInteger;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
import com.elphel.imagej.tileprocessor.ImageDtt;
import com.elphel.imagej.tileprocessor.QuadCLT;
import com.elphel.imagej.tileprocessor.TileNeibs;
import Jama.Matrix;
import ij.ImagePlus;
import ij.ImageStack;
import ij.io.FileSaver;
public class VegetationLMA {
public static final int TVAO_TERRAIN = 0;
......@@ -34,6 +38,7 @@ public class VegetationLMA {
public double [][] tvao; // [0][image_length] - terrain, [1][image_length] - vegetation,
//[2][image_length] - alpha, [3][num_scenes] - per-scene offset (mostly for vignetting. MAYBE add per-scene pair of tilts
public int [][] par_index; // indices - [0..3][full_pixel] - same as for tvao, value - parameter index
public int [][] par_rindex; // parameter -> pair of type (0..3) and full window pixel index
// private double default_alpha;
private int num_pars_terrain;
private int num_pars_vegetation;
......@@ -55,11 +60,17 @@ public class VegetationLMA {
private double [] weights; // normalized so sum is 1.0 for all - samples and extra regularization
public double alpha_loss;
public double alpha_offset = 0; // if >0, start losses above 0.0 and below 1.0;
public double alpha_lpf = 0;
// data used to calculate lpf pull of the alpha pixel to average of four neighbors
public int [][] alpha_neibs; // corresponds to parameters for alpha (num_pars_vegetation_alpha), each has 4 ortho neibs, -1 - border, >= 0
// - parameter index, <=-2 -2-full_pixel_index
public double delta= 1e-5; // 7;
public int debug_index;
public double [][] debug_image;
public static double [] debug_alpha_scales = {100,150};
public String debug_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/lma/";
public int [] indices;
public int [][] cpairs = null;
......@@ -105,18 +116,23 @@ public class VegetationLMA {
}
public int prepareLMA(
final boolean keep_parameters,
final Rectangle woi,
final int min_scenes, // minimal number of scenes (inside woi) vegetation pixel must influence
final double default_alpha,
final double [] scene_weights, // null or per-scene weights (higher for larger offsets)?
final double reg_weights, // fraction of the total weight used for regularization
final double alpha_loss, // quadratic loss when alpha reaches -1.0 or 2.0
final double alpha_offset, // quadratic loss when alpha reaches -1.0 or 2.0
final double alpha_lpf, // pull to average of 4 neighbors
final double boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
final String parameters_read_path,
final int debugLevel) {
this.woi = woi;
this.alpha_loss = alpha_loss;
this.alpha_offset = alpha_offset;
// this.default_alpha = default_alpha;
this.alpha_lpf = alpha_lpf;
final double [] scene_weights = setupSceneWeights(
boost_parallax); // double boost_parallax)
int min_scenes_uses = min_scenes;
int min_scenes_used = min_scenes * 4;
boolean [][] valid_woi = filterValidWoi (
......@@ -124,7 +140,19 @@ public class VegetationLMA {
min_scenes_used, // int min_scenes_used,
debugLevel > 3); // boolean debug_img){ // 4x?
setupParametersIndices(valid_woi);
alpha_neibs = getAlphaNeighbors();
if (!keep_parameters) {
setupParametersVector (default_alpha); // areas where both terrain and vegetation are available
}
if (parameters_read_path != null) {
readParametersFromImage(
parameters_read_path, // String path,
parameters_vector, // double [] vector,
1) ;// int gap)
}
setupDataSource(); // condensed
setupYVector();
setupWeights( // after setupParametersIndices
......@@ -134,6 +162,45 @@ public class VegetationLMA {
return weights.length;
}
private double [] setupSceneWeights(
double boost_parallax) {
// find max parallax
final double [] scene_weights = new double[vegetation_offsets.length];
if (boost_parallax == 0) {
for (int nscene = 0; nscene < vegetation_offsets.length; nscene++) {
scene_weights[nscene] = 1.0;
}
} else {
final double [] max_parallax2 = new double [vegetation_offsets.length];
double super_max_parallax2 = 0;
for (int nscene = 0; nscene < vegetation_offsets.length; nscene++) {
// only compare for selected window!
for (int drow = 0; drow < woi.height; drow++) {
int row = woi.y + drow;
for (int dcol = 0; dcol < woi.width; dcol++) {
int col = woi.x + dcol;
int windx =dcol + drow * woi.width;
int indx = row*full.width + col;
double [] d = vegetation_offsets[nscene][indx];
if (d != null) {
double d2 = d[0]*d[0] + d[1]*d[1];
/*
if (d2 > max_parallax2[nscene]) {
System.out.println("setupSceneWeights(): nscene="+nscene+", pix = ("+(i%640)+","+(i/640)+") ="+i+" d2="+d2);
}
*/
max_parallax2[nscene] = Math.max(max_parallax2[nscene], d2);
}
}
}
super_max_parallax2 = Math.max(super_max_parallax2, max_parallax2[nscene]);
}
for (int nscene = 0; nscene < vegetation_offsets.length; nscene++) {
scene_weights[nscene] = 1.0+(boost_parallax - 1) * Math.sqrt(max_parallax2[nscene]/super_max_parallax2);
}
}
return scene_weights;
}
private double [] getYminusFxWeighted(
final double [] fx,
......@@ -226,7 +293,7 @@ public class VegetationLMA {
if (rslt == null) {
return -1; // false; // need to check
}
if (debug_level > 1) {
if (debug_level > -2) { // 1) {
System.out.println("LMA step"+String.format("%3d",iter)+": {"+rslt[0]+","+rslt[1]+"} full RMS= "+good_or_bad_rms[0]+
" ("+initial_rms[0]+"), pure RMS="+good_or_bad_rms[1]+" ("+initial_rms[1]+") + lambda="+lambda);
}
......@@ -420,28 +487,18 @@ public class VegetationLMA {
rslt[1] = rms[0] >=(this.last_rms[0] * (1.0 - rms_diff));
this.last_rms = rms.clone();
this.parameters_vector = new_vector.clone();
if (debug_level > 2) {
String title = (debug_level > 3)? "parameters.vector":null;
int [] wh = new int [2];
double [] debug_img = parametersImage (
parameters_vector, // double [] vector,
1, // int gap)
wh,
title);
if ((debug_image != null) && (debug_index < debug_image.length)) {
debug_image[debug_index++] = debug_img;
}
if (debug_level > 4) {
ShowDoubleFloatArrays.showArrays(
debug_image,
wh[0],
wh[1],
true,
"parameters_vector_live.tiff");
}
// print vectors in some format
if (debug_level > -2) { //
String save_dir = debug_path;
String debug_title = "parameters_vector-x"+woi.x+"-y"+woi.y+"-w"+woi.width+"-h"+woi.height;
boolean save_all = (debug_image != null);
boolean show_this = debug_level > 3;
boolean show_all = debug_level > 4;
debugImageSaveShow(
save_dir, // String save_dir, // save if not null
debug_title, // String title, // not null
save_all, // boolean save_all,
show_this, // boolean show_this,
show_all); // boolean show_all)
/*
System.out.print("delta: "+corr_delta.toString()+"\n");
System.out.print("New vector: "+new_vector.toString()+"\n");
......@@ -474,6 +531,57 @@ public class VegetationLMA {
return rslt;
}
public void debugImageSaveShow(
String save_dir, // save if not null
String title, // not null
boolean save_all,
boolean show_this,
boolean show_all) {
int [] wh = new int [2];
double [] debug_img = parametersImage (
parameters_vector, // double [] vector,
1, // int gap)
wh,
null); // title);
String title_all = title+"-live";
if ((debug_image != null) && (debug_index < debug_image.length)) {
title += "-"+debug_index;
debug_image[debug_index++] = debug_img;
}
if (show_this) {
ShowDoubleFloatArrays.showArrays(
debug_img,
wh[0],
wh[1],
title);
}
if (save_all || show_all) {
double [][] dbg_img = new double [debug_index][];
String [] titles = new String[debug_index];
for (int i = 0; i < debug_index; i++) {
titles[i] = ""+i;
dbg_img[i] = debug_image[i];
}
if (show_all) {
ShowDoubleFloatArrays.showArrays(
debug_image,
wh[0],
wh[1],
true,
title_all,
titles);
}
if (save_all) {
String file_path = save_dir+title_all+".tiff";
ImageStack imageStack = ShowDoubleFloatArrays.makeStack(dbg_img, wh[0], wh[1], titles);
ImagePlus imp = new ImagePlus( title, imageStack);
FileSaver fs=new FileSaver(imp);
fs.saveAsTiff(file_path);
System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
}
}
}
private double [][] getWJtJlambda(
......@@ -617,6 +725,35 @@ public class VegetationLMA {
jt[np][nx] = 2 * alpha_loss * d; // d/dalpha[i]
}
}
// add cost for difference between this alpha and average of 4 neighbors (when they exist
if (alpha_lpf > 0) {
double avg = 0;
int nn = 0;
for (int i = 0; i < alpha_neibs[n].length; i++) { // now 4, may be increased
int di = alpha_neibs[n][i];
d=0;
if (di >= 0) {
d = vector[di]; // d - full parameter index
avg+=d;
nn++;
} else if (di < -1) {
d = tvao[TVAO_VEGETATION_ALPHA][-di - 2];
avg+=d;
nn++;
}
}
avg /= nn; // average
fX[nx] += alpha_lpf * (vector[np] - avg);
if (jt != null) {
jt[np][nx] += alpha_lpf;
for (int i = 0; i < alpha_neibs[n].length; i++) { // now 4, may be increased
int di = alpha_neibs[n][i];
if (di > 0) {
jt[di][nx] -= alpha_lpf/nn;
}
}
}
}
}
}
};
......@@ -681,6 +818,58 @@ public class VegetationLMA {
return indices;
}
public void showYfX(
double [] vector,
String title) {
if (vector == null) {
vector = parameters_vector;
}
double [][][] img_data = new double [3][num_scenes][woi.width*woi.height];
for (int n = 0; n < img_data.length; n++) {
for (int nscene = 0; nscene < num_scenes; nscene++) {
Arrays.fill(img_data[n][nscene], Double.NaN);
}
}
double [] fX = getFxDerivs( // longer than y_vector
vector, // final double [] vector,
null, // final double [][] jt, // should be null or initialized with [vector.length][]
-1); // final int debug_level)
final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int ny = ai.getAndIncrement(); ny < data_source.length; ny = ai.getAndIncrement()) {
int nscene = data_source[ny][0][0];
int indx = data_source[ny][0][1];
int wx = (indx % full.width) - woi.x;
int wy = (indx / full.width) - woi.y;
int windx = wx + wy * woi.width;
img_data[0][nscene][windx] = y_vector[ny];
img_data[1][nscene][windx] = fX[ny];
img_data[2][nscene][windx] = y_vector[ny]-fX[ny];
}
}
};
}
ImageDtt.startAndJoin(threads);
String [] top_titles = {"Y", "fX", "Y-fX"};
String [] scene_titles = new String[num_scenes];
for (int i = 0; i < num_scenes; i++) {
scene_titles[i] = ""+i;
}
ShowDoubleFloatArrays.showArraysHyperstack(
img_data, // double[][][] pixels,
woi.width, // int width,
title, // "terrain_vegetation_render.tiff", // String title, "time_derivs-rt"+diff_time_rt+"-rxy"+diff_time_rxy,
scene_titles, // String [] titles, // all slices*frames titles or just slice titles or null
top_titles, // String [] frame_titles, // frame titles or null
true); // boolean show)
return;
}
public double [] parametersImage (
double [] vector,
int gap,
......@@ -696,7 +885,8 @@ public class VegetationLMA {
dbg_img[i]= vector[indices[i]];
// scale alpha for the same image
int w = i % woi_width3;
if (w > 2 *( woi.width+ gap)) {
int h = i / woi_width3;
if ((w > 2 *( woi.width+ gap)) && (h < woi.height)) {
dbg_img[i] = debug_alpha_scales[0] + (debug_alpha_scales[1] - debug_alpha_scales[0]) * dbg_img[i];
}
}
......@@ -715,6 +905,40 @@ public class VegetationLMA {
return dbg_img;
}
public void readParametersFromImage(
String path,
double [] vector,
int gap) {
int [] indices = getParamDebugIndices (gap);
ImagePlus imp_pars = new ImagePlus (path);
if (imp_pars.getWidth()==0) {
throw new IllegalArgumentException("Could not read "+path);
}
int woi_width3=woi.width*3 + 2 * gap;
int height = indices.length/woi_width3;
if ((woi_width3 != imp_pars.getWidth()) || (height != imp_pars.getHeight())) {
throw new IllegalArgumentException("Read image size does not match required: ("+imp_pars.getWidth()+"x"+imp_pars.getHeight()+
") != ("+woi_width3+"x"+height+")");
}
float [] pixels = (float[]) imp_pars.getProcessor().getPixels();
for (int i = 0; i < indices.length; i++) {
if (indices[i] >= 0) {
double d = pixels[i];
// scale alpha for the same image
int w = i % woi_width3;
int h = i / woi_width3;
if ((w > 2 *( woi.width+ gap)) && (h < woi.height)) {
d = (d- debug_alpha_scales[0])/(debug_alpha_scales[1] - debug_alpha_scales[0]);
}
vector[indices[i]] = d;
}
}
return;
}
public double debugDerivs (
double [] vector,
......@@ -810,6 +1034,37 @@ public class VegetationLMA {
ImageDtt.startAndJoin(threads);
return;
}
private int [][] getAlphaNeighbors(){
final int [][] alpha_neibs = new int[num_pars_vegetation_alpha][4];
final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
TileNeibs tn = new TileNeibs(full.width, full.height);
public void run() {
for (int i = ai.getAndIncrement(); i < num_pars_vegetation_alpha; i = ai.getAndIncrement()) {
int pindx = ind_pars_vegetation_alpha + i; // full parameter index
int indx = par_rindex[pindx][1]; // full pixel index
for (int dir4 = 0; dir4 < 4; dir4++) { // ortho only
int dir = 2 * dir4;
int nindx = tn.getNeibIndex(indx, dir);
if (nindx < 0) {
alpha_neibs[i][dir4] = -1;
} else if (par_index[TVAO_VEGETATION_ALPHA][nindx] >= 0) {
alpha_neibs[i][dir4] = par_index[TVAO_VEGETATION_ALPHA][nindx];
} else { // pull to fixed alpha value
alpha_neibs[i][dir4] = -2 -indx; // OFFSET by 2 !
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
//ind_pars_vegetation_alpha
return alpha_neibs;
}
private void setupDataSource() {
final int woi_length = woi.width*woi.height;
......@@ -939,6 +1194,12 @@ public class VegetationLMA {
par_index[TVAO_VEGETATION] = new int [image_length];
par_index[TVAO_VEGETATION_ALPHA] = new int [image_length];
par_index[TVAO_SCENE_OFFSET] = new int [num_scenes];
int max_pars = 0;
for (int i = 0; i < par_index.length; i++) {
max_pars += par_index[i].length;
}
int [][] par_rindex = new int [max_pars][2];
Arrays.fill(par_index[TVAO_TERRAIN], -1);
Arrays.fill(par_index[TVAO_VEGETATION], -1);
Arrays.fill(par_index[TVAO_VEGETATION_ALPHA], -1);
......@@ -951,6 +1212,8 @@ public class VegetationLMA {
int windx =dcol + drow * woi.width;
if (valid_woi[0][windx]) {
int indx = row*full.width + col;
par_rindex[par_num][0] = 0;
par_rindex[par_num][1] = indx;
par_index[TVAO_TERRAIN][indx] = par_num++;
}
}
......@@ -964,6 +1227,8 @@ public class VegetationLMA {
int windx =dcol + drow * woi.width;
if (valid_woi[1][windx]) {
int indx = row*full.width + col;
par_rindex[par_num][0] = 1;
par_rindex[par_num][1] = indx;
par_index[TVAO_VEGETATION][indx] = par_num++;
}
}
......@@ -977,6 +1242,8 @@ public class VegetationLMA {
int windx =dcol + drow * woi.width;
if (valid_woi[1][windx]) {
int indx = row*full.width + col;
par_rindex[par_num][0] = 2;
par_rindex[par_num][1] = indx;
par_index[TVAO_VEGETATION_ALPHA][indx] = par_num++;
}
}
......@@ -985,8 +1252,12 @@ public class VegetationLMA {
// int num_pars_pixel = par_num;
ind_pars_scenes = par_num;
for (int i = 0; i < par_index[TVAO_SCENE_OFFSET].length; i++) {
par_rindex[par_num][0] = 1;
par_rindex[par_num][1] = i;
par_index[TVAO_SCENE_OFFSET][i] = par_num++;
}
this.par_rindex = new int [par_num][2];
System.arraycopy(par_rindex, 0, this.par_rindex, 0, par_num);
num_pars_scenes = par_num - ind_pars_scenes;
parameters_vector = new double [par_num];
}
......
src/main/java/com/elphel/imagej/vegetation/VegetationModel.java
View file @ 6c7e3422
......@@ -697,27 +697,41 @@ public class VegetationModel {
Rectangle woi50 = new Rectangle(143,317,35,35);
int min_scenes = 10;
double default_alpha = 0.8;
double [] scene_weights = null;
double reg_weights = 0.25; // fraction of the total weight used for regularization
double alpha_loss = 1.0; // quadratic loss when alpha reaches -1.0 or 2.0
double alpha_loss = 1000.0; // 100.; // 10.0; // quadratic loss when alpha reaches -1.0 or 2.0
double alpha_offset = 0.0; // if >0, start losses above 0.0 and below 1.0;
double alpha_lpf = 2.0; // 1.5; // 5.0; // 0.5; // pull to average of 4 neighbors
double boost_parallax = 5;
boolean exit_loop = debugLevel < 1000;
boolean next_run = false;
boolean read_pars = true;
String parameters_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/lma/parameters_vector_data.tiff";
do {
String par_path = (read_pars && !next_run)? parameters_path : null;
int num_samples = vegetationLMA.prepareLMA(
next_run, // final boolean keep_parameters,
woi50, // final Rectangle woi,
min_scenes, // final int min_scenes, // minimal number of scenes (inside woi) vegetation pixel must influence
default_alpha, // final double default_alpha,
scene_weights, // final double [] scene_weights, // null or per-scene weights (higher for larger offsets)?
reg_weights, // final double reg_weights, // fraction of the total weight used for regularization
alpha_loss, // final double alpha_loss, // quadratic loss when alpha reaches -1.0 or 2.0
alpha_offset, // final double alpha_offset, // quadratic loss when alpha reaches -1.0 or 2.0
alpha_lpf, // final double alpha_lpf, // pull to average of 4 neighbors
boost_parallax, // final double boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
par_path, // final String parameters_read_path,
debugLevel); // final int debugLevel);
double lambda = 0.1;
if (debugLevel >-2) {
vegetationLMA.showYfX(
null, // double [] vector,
"reconstructed_model"); // String title)
}
next_run = true;
double lambda = 5.0; // 0.1;
double lambda_scale_good = 0.5;
double lambda_scale_bad = 8.0;
double lambda_max = 1000;
boolean last_run = false;
double rms_diff = 0.0001;
double rms_diff = 1e-8; // 0.0001; virtually forever
int num_iter = 100;
vegetationLMA.debug_index = 0;
vegetationLMA.debug_image = new double [num_iter][];
......@@ -732,6 +746,12 @@ public class VegetationModel {
last_run, // boolean last_run,
null, // String dbg_prefix,
debugLevel); // int debug_level)
} while (!exit_loop);
if (debugLevel >-2) {
vegetationLMA.showYfX(
null, // double [] vector,
"reconstructed_model_adjusted"); // String title)
}
return; //
}
......
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