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Commit 9ba553bb authored by Andrey Filippov's avatar Andrey Filippov
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prepared elevation data, starting elevation LMA fitting

parent 5980d194
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src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java
View file @ 9ba553bb
......@@ -5802,11 +5802,11 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
} else if (label.equals("Process Merged")) {
OrangeTest.processMerged();
} else if (label.equals("Vegetation LMA")) {
VegetationModel.testVegetationLMA(
VegetationModel.processVegetationLMA(
CLT_PARAMETERS, //CLTParameters clt_parameters,
false); //boolean combine_segments);
} else if (label.equals("Combine LMA Segments")) {
VegetationModel.testVegetationLMA(
VegetationModel.processVegetationLMA(
CLT_PARAMETERS, //CLTParameters clt_parameters,
true); //boolean combine_segments);
}
......
src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java
View file @ 9ba553bb
......@@ -760,7 +760,9 @@ min_str_neib_fpn 0.35
public double terr_difference = 100.0; // vegetation is 100 warmer (target)
public double terr_pull_cold = 0.001; // pull vegetations to warm, terrain to cold
public double terr_alpha_dflt = 0.5;
public double terr_alpha_contrast = 1.0; // initial alpha contrast (>=1.0)
public double terr_alpha_dflt = 0.5; // now unused
public double terr_alpha_loss = 100.0;
public double terr_alpha_offset = 0.0;
public double terr_alpha_lpf = 2.5; // pull to average of 4 neighbors
......@@ -775,6 +777,7 @@ min_str_neib_fpn 0.35
public double terr_veget_lpf = 0.2; // pull vegetation to average of 4 neighbors (very small - maybe not needed)
public double terr_terr_pull0 = 0.05; // pull terrain to zero (makes sense with UM
public double terr_veget_pull0 = 0.05; // pull vegetation to zero (makes sense with UM
public double terr_scenes_pull0 = 1.0; // pull average scene offset to zero
// LMA parameters
public double terr_boost_parallax = 3.0; //
......@@ -2013,15 +2016,19 @@ min_str_neib_fpn 0.35
gd.addNumericField("Min influenced scenes",terr_min_scenes, 0,3, "", "Minimal number of scenes (inside woi) vegetation pixel must influence.");
gd.addNumericField("Minimal samples/scene",terr_min_samples_scene, 0,3,"","Minimal samples per scene used for fitting (skip scene if less).");
gd.addNumericField("Minimum scenes used", terr_min_total_scenes, 0,3,"", "Minimal total number of scenes used (skip segment if less).");
gd.addNumericField("Minimal pixels fitted",terr_min_pixels, 0,3,"", "Minimal number of terrain and vegetation pixels used for fitting in this segment(skip segment if less).");
gd.addCheckbox ("Start by temperature", terr_warm_veget, "Start with vegetation warmer than terrain.");
gd.addNumericField("Warmest terrain", terr_warmest, 5,7,"", "Above - vegetation. below - terrain.");
gd.addNumericField("Initial split", terr_initial_split, 5,7,"", "Initial alpha: terrain 0.0+, vegetation 1.0-.");
gd.addNumericField("Min. split fraction", terr_min_split_frac, 5,7,"", "minimal modality fraction to use split by temperature (otherwise use default alpha).");
gd.addNumericField("Vegetation warmer", terr_difference, 5,7,"", "Pull vegetation to be this warmer.");
gd.addNumericField("Pull terrain cold", terr_pull_cold, 5,7,"", "Pull vegetations to warm, terrain to cold.");
gd.addNumericField("Alpha initial contrast",terr_alpha_contrast, 5,7,"","Initial alpha contrast (>= 1.0).");
gd.addNumericField("Defalt alpha", terr_alpha_dflt, 5,7,"", "Default vegetation alpha.");
gd.addNumericField("Alpha loss", terr_alpha_loss, 5,7,"", "Alpha quadratic growing loss for when out of [0,1] range");
gd.addNumericField("Alpha offset", terr_alpha_offset, 5,7,"", "Start alpha losses above 0.0 and below 1.0 by this value.");
gd.addNumericField("Alpha diffusion", terr_alpha_lpf, 5,7,"", "Alpha diffusion to 4 ortho neighbors.");
gd.addCheckbox ("Alpha piece-linear", terr_alpha_piece_linear, "Piece-linear alpha (_/\u203E, false - 0.0-cosine-1.0.");
......@@ -2035,6 +2042,7 @@ min_str_neib_fpn 0.35
gd.addNumericField("Vegetation diffusion", terr_veget_lpf, 5,7,"", "LPF for vegetation pixels (diffusion to 4 neighbors).");
gd.addNumericField("Terrain pull zero", terr_terr_pull0, 5,7,"", "Terrain pixels pull to 0 (makes sense with UM).");
gd.addNumericField("Vegetation pull zero", terr_veget_pull0, 5,7,"", "Vegetation pixels pull to 0 (makes sense with UM).");
gd.addNumericField("Pull scene offset", terr_scenes_pull0, 5,7,"", "Pull average scene offset to zero.");
gd.addMessage ("LMA parameters");
gd.addNumericField("Boost parallax", terr_boost_parallax, 5,7,"", "Increase weight of scenes that have high parallax to the reference one.");
......@@ -2721,6 +2729,7 @@ min_str_neib_fpn 0.35
terr_min_split_frac = gd.getNextNumber();// double
terr_difference = gd.getNextNumber();// double
terr_pull_cold = gd.getNextNumber();// double
terr_alpha_contrast = gd.getNextNumber();// double
terr_alpha_dflt = gd.getNextNumber();// double
terr_alpha_loss = gd.getNextNumber();// double
terr_alpha_offset = gd.getNextNumber();// double
......@@ -2737,7 +2746,7 @@ min_str_neib_fpn 0.35
terr_veget_lpf = gd.getNextNumber();// double
terr_terr_pull0 = gd.getNextNumber();// double
terr_veget_pull0 = gd.getNextNumber();// double
terr_scenes_pull0 = gd.getNextNumber();// double
terr_boost_parallax = gd.getNextNumber();// double
terr_max_parallax = gd.getNextNumber();// double
terr_hifreq_weight = gd.getNextNumber();// double
......@@ -3392,6 +3401,8 @@ min_str_neib_fpn 0.35
properties.setProperty(prefix+"terr_difference", terr_difference+""); // double
properties.setProperty(prefix+"terr_pull_cold", terr_pull_cold+""); // double
properties.setProperty(prefix+"terr_alpha_contrast", terr_alpha_contrast+""); // double
properties.setProperty(prefix+"terr_alpha_dflt", terr_alpha_dflt+""); // double
properties.setProperty(prefix+"terr_alpha_loss", terr_alpha_loss+""); // double
properties.setProperty(prefix+"terr_alpha_offset", terr_alpha_offset+""); // double
......@@ -3405,7 +3416,8 @@ min_str_neib_fpn 0.35
properties.setProperty(prefix+"terr_terr_lpf", terr_terr_lpf+""); // double
properties.setProperty(prefix+"terr_veget_lpf", terr_veget_lpf+""); // double
properties.setProperty(prefix+"terr_terr_pull0", terr_terr_pull0+""); // double
properties.setProperty(prefix+"terr_veget_pull0", terr_veget_pull0+""); // double
properties.setProperty(prefix+"terr_veget_pull0", terr_veget_pull0+""); // double
properties.setProperty(prefix+"terr_scenes_pull0", terr_scenes_pull0+""); // double
properties.setProperty(prefix+"terr_boost_parallax", terr_boost_parallax+""); // double
properties.setProperty(prefix+"terr_max_parallax", terr_max_parallax+""); // double
......@@ -4082,6 +4094,8 @@ min_str_neib_fpn 0.35
if (properties.getProperty(prefix+"terr_difference")!= null) terr_difference=Double.parseDouble(properties.getProperty(prefix+"terr_difference"));
if (properties.getProperty(prefix+"terr_pull_cold")!= null) terr_pull_cold=Double.parseDouble(properties.getProperty(prefix+"terr_pull_cold"));
if (properties.getProperty(prefix+"terr_alpha_contrast")!= null) terr_alpha_contrast=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_contrast"));
if (properties.getProperty(prefix+"terr_alpha_dflt")!= null) terr_alpha_dflt=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_dflt"));
if (properties.getProperty(prefix+"terr_alpha_loss")!= null) terr_alpha_loss=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_loss"));
if (properties.getProperty(prefix+"terr_alpha_offset")!= null) terr_alpha_offset=Double.parseDouble(properties.getProperty(prefix+"terr_alpha_offset"));
......@@ -4097,6 +4111,7 @@ min_str_neib_fpn 0.35
if (properties.getProperty(prefix+"terr_veget_lpf")!= null) terr_veget_lpf=Double.parseDouble(properties.getProperty(prefix+"terr_veget_lpf"));
if (properties.getProperty(prefix+"terr_terr_pull0")!= null) terr_terr_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_terr_pull0"));
if (properties.getProperty(prefix+"terr_veget_pull0")!= null) terr_veget_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_veget_pull0"));
if (properties.getProperty(prefix+"terr_scenes_pull0")!= null) terr_scenes_pull0=Double.parseDouble(properties.getProperty(prefix+"terr_scenes_pull0"));
if (properties.getProperty(prefix+"terr_boost_parallax")!= null) terr_boost_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_boost_parallax"));
if (properties.getProperty(prefix+"terr_max_parallax")!= null) terr_max_parallax=Double.parseDouble(properties.getProperty(prefix+"terr_max_parallax"));
......@@ -4740,7 +4755,8 @@ min_str_neib_fpn 0.35
imp.terr_initial_split = this.terr_initial_split;
imp.terr_min_split_frac = this.terr_min_split_frac;
imp.terr_difference = this.terr_difference;
imp.terr_pull_cold = this.terr_pull_cold;
imp.terr_pull_cold = this.terr_pull_cold;
imp.terr_alpha_contrast = this.terr_alpha_contrast;
imp.terr_alpha_dflt = this.terr_alpha_dflt;
imp.terr_alpha_loss = this.terr_alpha_loss;
imp.terr_alpha_offset = this.terr_alpha_offset;
......@@ -4755,7 +4771,8 @@ min_str_neib_fpn 0.35
imp.terr_terr_lpf = this.terr_terr_lpf;
imp.terr_veget_lpf = this.terr_veget_lpf;
imp.terr_terr_pull0 = this.terr_terr_pull0;
imp.terr_veget_pull0 = this.terr_veget_pull0;
imp.terr_veget_pull0 = this.terr_veget_pull0;
imp.terr_scenes_pull0 = this.terr_scenes_pull0;
imp.terr_boost_parallax = this.terr_boost_parallax;
imp.terr_max_parallax = this.terr_max_parallax;
......
src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java
View file @ 9ba553bb
......@@ -6368,7 +6368,7 @@ public class OpticalFlow {
// int [] first_last = quadCLTs[ref_index].getFirstLastIndex(quadCLTs);
QuadCLT [] quadCLT_tail = new QuadCLT [quadCLTs.length - earliest_scene];
System.arraycopy(quadCLTs, earliest_scene, quadCLT_tail, 0, quadCLT_tail.length);
VegetationModel.test_vegetation(
VegetationModel.prepareVegetationData(
clt_parameters, // CLTParameters clt_parameters,
quadCLT_tail, // QuadCLT [] quadCLTs,
ref_index-earliest_scene, // int ref_index,
......
src/main/java/com/elphel/imagej/tileprocessor/TileProcessor.java
View file @ 9ba553bb
......@@ -8786,6 +8786,27 @@ ImageDtt.startAndJoin(threads);
* @return data array made of input data with replaced NaN limited by
* optional prohibit array and amount of growth.
*/
public static double [] fillNaNs(
final double [] data,
final boolean [] prohibit,
int width,
final int grow,
double diagonal_weight, // relative to ortho
int num_passes,
final double max_rchange) // = 0.01
{
return fillNaNs(
data, // final double [] data,
null, // final double [] data_nan,
prohibit, // final boolean [] prohibit_in,
width, // int width,
grow, // final int grow,
diagonal_weight, //double diagonal_weight, // relative to ortho
num_passes, // int num_passes,
max_rchange, // final double max_rchange, // = 0.01
ImageDtt.THREADS_MAX); // final int threadsMax)
}
public static double [] fillNaNs(
final double [] data,
final boolean [] prohibit,
......
src/main/java/com/elphel/imagej/vegetation/VegetationLMA.java
View file @ 9ba553bb
......@@ -61,7 +61,7 @@ public class VegetationLMA {
public double [][] tvao; // [0][image_length] - terrain, [1][image_length] - vegetation,
// public double [][] tva_hf; // [0][image_length] - terrain, [1][image_length] - vegetation, - laplacian
public double [][][] scales_xy; // [scene][pixel{scale_x,scale_y}
public VegetationModel vegetationModel = null;
/*
// copy from Vegetation model
......@@ -99,7 +99,7 @@ public class VegetationLMA {
// private int num_used_scenes; // -> num_par_scenes
private boolean [] used_scenes; // encode unused as NaN
// private int [] used_scenes_indices;
public final double [] scene_weights;
private double [] parameters_vector = null;
......@@ -126,7 +126,7 @@ public class VegetationLMA {
public boolean fit_scenes = true;
public boolean fit_elevations = false;
*/
public double alpha_initial_contrast = 1.0; // >=1.0
public double alpha_loss = 0; // not used with cosine alpha
public double alpha_offset = 0; // if >0, start losses above 0.0 and below 1.0;
public double alpha_lpf = 0;
......@@ -149,6 +149,9 @@ public class VegetationLMA {
// when unsharp mask is applied , pulling to 0 (when alpha is 0 (for vegetation) or 1.0 (for terrain) makes sense
public double terr_pull0 = 0; // now - pull to filled terrain - terrain_average
public double veget_pull0 = 0; // now - pull to vegetation_pull (extended vegetation)
public double scenes_pull0 = 0; // pull average scene offset to 0;
public boolean use_scenes_pull0 = true; // derivative, set in setWeights
public double scale_scenes_pull = 0; // used in getFxDerivs to scale scene offsets as their weight will be reg_weights / extra_samples
public double boost_parallax = 1;
......@@ -176,6 +179,8 @@ public class VegetationLMA {
private double [] last_ymfx = null;
private double [][] last_jt = null;
public boolean skip_ref_scene = false;
public boolean debug_deriv = true;
public int debug_width = 12;
public int debug_decimals = 9;
......@@ -206,9 +211,14 @@ public class VegetationLMA {
tvao[TVAO_SCENE_OFFSET] = new double [num_scenes];
setupLaplacians(0.0); // double weight_diag)
scene_weights = new double [num_scenes];
}
public VegetationLMA (VegetationModel vegetationModel) {
public VegetationLMA (
VegetationModel vegetationModel,
double alpha_initial_contrast) {
this.alpha_initial_contrast = alpha_initial_contrast;
full = vegetationModel.full;
image_length = full.width * full.height;
num_scenes = vegetationModel.terrain_scenes_render.length;
......@@ -221,17 +231,53 @@ public class VegetationLMA {
tvao = new double[TVAO_TYPES][];
tvao[TVAO_TERRAIN] = this.terrain_average.clone();
tvao[TVAO_VEGETATION] = this.vegetation_average.clone();
// tvao[TVAO_ALPHA] = new double [image_length]; // 0 - use terrain
tvao[TVAO_SCENE_OFFSET] = new double [num_scenes];
setupInitialTerrainVegetationAlpha(
alpha_initial_contrast, // double alpha_contrast,
vegetationModel.terrain_filled, // double [] terrain_filled,
vegetationModel.vegetation_pull, // double [] vegetation_extended,
vegetationModel.vegetation_full); // double [] vegetation) { // best guess
/*
tvao[TVAO_ALPHA] =getInitialAlpha(
vegetation_filtered, // double [] vegetation_filtered,
vegetationModel.initial_transparent, // double transparent,
vegetationModel.initial_opaque); // double opaque)
*/
setupLaplacians(0.0); // double weight_diag)
diff_offsets = vegetationModel.diff_mode;
this.vegetationModel = vegetationModel; // to access scene names, directories, reference index
scene_weights = new double [num_scenes];
scales_xy = getScalesXY(vegetationModel.scale_dirs);
tvao[TVAO_ELEVATION] = vegetationModel.elevations.clone();
return;
}
private static double [][][] getScalesXY(
final double [][][] scales_mag_dir) {
final int num_scenes = scales_mag_dir.length;
final int num_pixels = scales_mag_dir[0].length;
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0);
final double [][][] scales_xy = new double [num_scenes][num_pixels][];
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int nScene = ai.getAndIncrement(); nScene < num_scenes; nScene = ai.getAndIncrement()) {
for (int npix = 0; npix < num_pixels; npix++) if (scales_mag_dir[nScene][npix] != null) {
double scale = scales_mag_dir[nScene][npix][0];
double angle = scales_mag_dir[nScene][npix][1];
scales_xy[nScene][npix] = new double [] {
scale*Math.cos(angle),
scale*Math.sin(angle)};
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return scales_xy;
}
private void setupLaplacians(double weight_diag) {
terrain_rendered_hf = new double [terrain_rendered.length][];
......@@ -243,7 +289,46 @@ public class VegetationLMA {
weight_diag); // final double weight_diag)
}
}
private void setupInitialTerrainVegetationAlpha(
double alpha_contrast,
double [] terrain_filled,
double [] vegetation_extended,
double [] vegetation) { // best guess
double dbg_lim = 0.01;
tvao[TVAO_TERRAIN] = terrain_filled.clone(); // == vegetationModel.terrain_filled
tvao[TVAO_VEGETATION] = vegetation_extended.clone();
tvao[TVAO_ALPHA] = new double [image_length];
for (int npix = 0; npix < image_length; npix++) {
double t = terrain_filled[npix];
double v = vegetation[npix];
double vp = vegetation_extended[npix];
double a = 0; // Double.NaN; // .isNaN(vegetation_filtered[npix])? 0.0:1.0; // not needed
if (!Double.isNaN(t) && !Double.isNaN(v) && !Double.isNaN(vp)) {
if (v < t) {
a = 0.0;
} else if (v > vp) {
a = 1.0;
} else {
a = (v-t)/(vp-t);
if (alpha_contrast != 1.0) {
a = 0.5 + (a - 0.5)*alpha_contrast;
if (a < 0) a = 0;
else if (a > 1.0) a = 1;
}
}
// if (a < dbg_lim) a = dbg_lim;
// if ( a > 1.0-dbg_lim) a = 1.0-dbg_lim;
// tvao[TVAO_ALPHA][npix] = a;
}
if (a < dbg_lim) a = dbg_lim;
if ( a > 1.0-dbg_lim) a = 1.0-dbg_lim;
tvao[TVAO_ALPHA][npix] = a;
}
}
@SuppressWarnings("unused")
private static double [] getInitialAlpha(
double [] vegetation_filtered,
double transparent,
......@@ -305,6 +390,7 @@ public class VegetationLMA {
final double veget_lpf, // pull vegetation to average of 4 neighbors (very small - maybe not needed)
final double terr_pull0, // pull terrain to zero (makes sense with UM
final double veget_pull0, // pull vegetation to zero (makes sense with UM
final double scenes_pull0,
final double boost_parallax, // increase weight of scene with maximal parallax relative to the reference scene
final double max_parallax, // do not consider maximal parallax above this (consider it a glitch)
final double um_sigma, // just use in debug image names
......@@ -343,6 +429,7 @@ public class VegetationLMA {
this.veget_lpf = veget_lpf;
this.terr_pull0 = terr_pull0;
this.veget_pull0 = veget_pull0;
this.scenes_pull0 = scenes_pull0;
this.boost_parallax = boost_parallax;
this.um_sigma = um_sigma; // just use in debug image names
this.um_weight = um_weight;
......@@ -367,6 +454,9 @@ public class VegetationLMA {
int min_scenes_uses = min_scenes;
int min_scenes_used = min_scenes * 4;
boolean all_terrain = true; // use all terrain tiles even not used with vegetation
boolean [][] valid_woi = filterValidWoi (
min_scenes_uses, // int min_scenes_uses,
min_scenes_used, // int min_scenes_used,
......@@ -377,7 +467,9 @@ public class VegetationLMA {
return -1;
}
setupParametersIndices(valid_woi); // needs to know number of used scenes // all but scenes
setupParametersIndices(
valid_woi, // needs to know number of used scenes // all but scenes
all_terrain); // boolean all_terrain
alpha_neibs = getNeighbors(
TVAO_ALPHA, // final int tvao, // TVAO_VEGETATION_ALPHA
......@@ -413,11 +505,14 @@ public class VegetationLMA {
default_alpha); // final double default_alpha // use in areas where both terrain and vegetation are available
*/
// new version - uses preset alpha for the full image
setupParametersVector (); // moved tweaking to constructor;
/*
if (alpha_contrast == 0) {
setupParametersVector ();
} else {
setupParametersVector(alpha_contrast); // double alpha_contrast);
}
*/
}
from_file = false;
if (parameters_read_path != null) {
......@@ -1354,9 +1449,22 @@ public class VegetationLMA {
// TODO: calculate high-frequency (laplacians)
// regularization weights and derivatives
// splitting alpha_lpf from alpha_loss+alpha_push
int ind_next = y_vector.length;
if (use_scenes_pull0) { // single sample after differences
fX[ind_next] =0.0;
for (int n = 0; n < num_pars_scenes; n++) { // only count adjustable scene offsets
int np = ind_pars_scenes + n; // index of the alpha parameter
int nscene = par_rindex[np][1];
double sw=scene_weights[nscene] * scale_scenes_pull;
fX[ind_next] += sw * vector[np];
if (jt != null) {
jt[np][ind_next] = sw;
}
}
ind_next++;
}
// splitting alpha_lpf from alpha_loss+alpha_push
if (fits[TVAO_ALPHA] && ((alpha_loss > 0) || (alpha_push > 0))) {
int dbg_nx = -76340;
final int ind_y_alpha_loss = ind_next;
......@@ -1679,7 +1787,7 @@ public class VegetationLMA {
double [] vector,
final double delta,
final int debug_level) {
int dbg_n = -2486;
int dbg_n = -2256; // 1698; // -2486;
double [][] jt = new double [vector.length][weights.length];
for (int nv = 0; nv < vector.length; nv++) {
if (nv == dbg_n) {
......@@ -2698,6 +2806,9 @@ public class VegetationLMA {
if (Math.abs(jt_diff[n][w]) > max_err) {
System.out.println("debugDerivs(): n="+n+", w = "+w +", diff="+jt_diff[n][w]);
}
if (Math.abs(jt_diff[n][w]) > .1) {
System.out.println("debugDerivs(): n="+n+", w = "+w +", diff="+jt_diff[n][w]+" jt="+jt[n][w]+" jt_delta="+jt_delta[n][w]);
}
max_err = Math.max(max_err, Math.abs(jt_diff[n][w]));
}
}
......@@ -2714,47 +2825,71 @@ public class VegetationLMA {
private void setupWeights( // after setupParametersIndices
final double [] scene_weights,
final double [] scene_weights_in,
final double reg_weights,
final double hifreq_weight) {
boolean use_hf = (hifreq_weight > 0);
use_scenes_pull0 = (scenes_pull0 >=0);
// int extra_samples = num_pars_vegetation_alpha; // in the future may be more regularization
// int hf_samples = use_hf ? data_source.length : 0;
int extra_samples = 0;
// using >=0 no use 0 as NOP but reserve space, <0 - do not reserve space
//(alpha_loss > 0)
if (use_scenes_pull0) extra_samples += 1;
if ((alpha_loss > 0) || (alpha_push > 0)) extra_samples+= num_pars_alpha; // need to split loss (always positive) from alpha_lpf
if (alpha_lpf >= 0) extra_samples+= num_pars_alpha;
if (terr_lpf >= 0) extra_samples+= num_pars_terrain;
if (veget_lpf >= 0) extra_samples+= num_pars_vegetation;
double reg_sample_weight = reg_weights/extra_samples; // weight of each regularization sample
final double [] sw = (scene_weights != null) ? scene_weights : new double [num_scenes];
if (scene_weights == null) {
Arrays.fill (sw, 1.0);
if (scene_weights_in != null) {
System.arraycopy(
scene_weights_in,
0,
scene_weights,
0,
num_scenes);
} else {
Arrays.fill (scene_weights, 1.0);
}
// weights = new double [data_source.length + extra_samples];
weights = new double [y_vector.length + extra_samples];
double s = 0;
for (int ny = 0; ny < data_source.length; ny++) {
int nscene = data_source[ny][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SCENE];
s += sw[nscene];
if (data_source[ny][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SINDEX] >=0) {
s += scene_weights[nscene];
}
}
double s_scenes = s; // sum of all scene weight. Maybe skip scenes that do not exist?
if (use_hf) { // second pass, repeating for possible future modifications
for (int ny = 0; ny < data_source.length; ny++) {
int nscene = data_source[ny][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SCENE];
s += sw[nscene] * hifreq_weight ;
if (data_source[ny][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SINDEX] >=0) {
s += scene_weights[nscene] * hifreq_weight ;
}
}
}
double s_pull_0 = s_scenes * scenes_pull0 * woi.width*woi.height;
final double s0 = s;
// final double s0 = s + s_pull_0;
s *= (1+ reg_weights);
final double k = 1.0/s;
weight_pure = s0/s;
// scale_scenes_pull = scenes_pull0 * woi.width*woi.height / s_scenes; // or use extra_samples instead of woi.width*woi.height ?
scale_scenes_pull = scenes_pull0 * extra_samples / s_scenes; // or use extra_samples instead of woi.width*woi.height ?
//scale_scenes_pull = 0; // used in getFxDerivs to scale scene offsets as their weight will be reg_weights / extra_samples
// weight of pull0 will be 1/(3*woi area) * reg_weight
// in fX will be multiplied by scene_weight*scene_offset. should be additionally multiplied by scene_pull0 * (3*woi_area) / sum scene weights
// for (int i = 0; i < extra_samples; i++) {
// s+=extra_weights;
// }
final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) {
......@@ -2762,13 +2897,13 @@ public class VegetationLMA {
public void run() {
for (int nw = ai.getAndIncrement(); nw < weights.length; nw = ai.getAndIncrement()) {
if (nw < data_source.length) { // DC differences
weights[nw] = sw[data_source[nw][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SCENE]] * k;
weights[nw] = scene_weights[data_source[nw][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SCENE]] * k;
if (Double.isNaN(weights[nw])) {
System.out.println("weights["+nw+"]=NaN");
}
} else if (nw < y_vector.length) { // HF differences if exist
weights[nw] = sw[data_source[nw-data_source.length][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SCENE]] * k * hifreq_weight;
weights[nw] = scene_weights[data_source[nw-data_source.length][DATA_SOURCE_HEAD][DATA_SOURCE_HEAD_SCENE]] * k * hifreq_weight;
if (Double.isNaN(weights[nw])) {
System.out.println("weights["+nw+"]=NaN");
}
......@@ -2786,7 +2921,8 @@ public class VegetationLMA {
return;
}
private void setupYVector(boolean use_hf) {
private void setupYVector(
boolean use_hf) {
int ds_length = (use_hf? 2 : 1) * data_source.length;
y_vector = new double [ds_length];
final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
......@@ -3013,7 +3149,7 @@ public class VegetationLMA {
used_scenes[nscene] = true;
num_samples+= scene_samples[nscene];
scene_samples[nscene] = num_prev; // start index
if (nscene != vegetationModel.reference_index) {
if (keepScene(nscene)) {
num_used_scenes++;
} else {
used_scene_indices[nscene] = -1;
......@@ -3293,7 +3429,8 @@ public class VegetationLMA {
private void setupParametersIndices(
boolean [][] valid_woi) { // [0] - valid terrain pixels, [1] valid vegetation and alpha pixels;
boolean [][] valid_woi, // [0] - valid terrain pixels, [1] valid vegetation and alpha pixels;
boolean all_terrain) {
par_index = new int [TVAO_TYPES][];
par_index[TVAO_TERRAIN] = new int [image_length];
par_index[TVAO_VEGETATION] = new int [image_length];
......@@ -3327,8 +3464,8 @@ public class VegetationLMA {
for (int dcol = 0; dcol < woi.width; dcol++) {
int col = woi.x + dcol;
int windx =dcol + drow * woi.width;
if (valid_woi[0][windx]) {
int indx = row*full.width + col;
int indx = row*full.width + col;
if ((all_terrain && !Double.isNaN(tvao[TVAO_TERRAIN][indx])) || valid_woi[0][windx]) {
par_rindex[par_num][0] = TVAO_TERRAIN;
par_rindex[par_num][1] = indx;
par_index[TVAO_TERRAIN][indx] = par_num++;
......@@ -3411,7 +3548,7 @@ public class VegetationLMA {
int par_num = ind_pars_scenes;
int [][] par_rindex = this.par_rindex;
for (int i = 0; i < par_index[TVAO_SCENE_OFFSET].length; i++) {
if (used_scenes[i] && !isReferenceScene(i)) {
if (used_scenes[i] && keepScene(i)) {
par_rindex[par_num][0] = TVAO_SCENE_OFFSET;
par_rindex[par_num][1] = i;
par_index[TVAO_SCENE_OFFSET][i] = par_num++;
......@@ -3430,6 +3567,15 @@ public class VegetationLMA {
return vegetationModel.reference_index == scene;
}
/**
* Keep scene as it is not a reference one or do not need to skip it
* @param scene
* @return
*/
private boolean keepScene(int scene) {
return !skip_ref_scene || !isReferenceScene(scene);
}
private boolean [][] filterValidWoi (
int min_scenes_uses,
int min_scenes_used,
......
src/main/java/com/elphel/imagej/vegetation/VegetationModel.java
View file @ 9ba553bb
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