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imagej-elphel
Commit ef8c6ac2 authored by Andrey Filippov's avatar Andrey Filippov
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preparing for adding pairwise matching after single-connected are 

subject to LMA
parent 099bf912
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Showing with 760 additions and 297 deletions
src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java
View file @ ef8c6ac2
......@@ -850,6 +850,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
addButton("Warp pair", panelLWIRWorld, color_process);
addButton("Read Tiff", panelLWIRWorld, color_process);
addButton("Test video", panelLWIRWorld, color_process);
addButton("Ortho", panelLWIRWorld, color_process);
addButton("Ortho Pairs", panelLWIRWorld, color_process);
addButton("Manual pair", panelLWIRWorld, color_process);
addButton("Extract Objects", panelLWIRWorld, color_process);
......@@ -5718,7 +5719,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
e.printStackTrace();
}
// ComboMatch.testReadTiff();
} else if (label.equals("Ortho Pairs") || label.equals("Extract Objects") || label.equals("Manual pair")) {
} else if (label.equals("Ortho") || label.equals("Ortho Pairs") || label.equals("Extract Objects") || label.equals("Manual pair")) {
DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
if (GPU_TILE_PROCESSOR == null) {
......@@ -5739,6 +5740,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
ComboMatch.openTestPairGps(
CLT_PARAMETERS, // CLTParameters clt_parameters,
GPU_TILE_PROCESSOR,
label.equals("Ortho"),// boolean dflt_options,
label.equals("Extract Objects"), // boolean extract_mines,
label.equals("Manual pair"), // boolean manual_pair,
DEBUG_LEVEL);
......
src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java
View file @ ef8c6ac2
......@@ -236,7 +236,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
if (undefined_only) {
String [] matches = pairwise_matches.keySet().toArray(new String[0]);
for (String match:matches) {
if (!getMatch(match).isDefined()) {
PairwiseOrthoMatch pm = getMatch(match);
if ((pm == null) || !pm.isDefined()) {
unsetMatch(match);
}
}
......@@ -483,7 +484,14 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
// TODO Auto-generated catch block
e.printStackTrace();
}
try {
lla = ElphelTiffReader.getLLA(imp_prop);
} catch (NullPointerException e) {
System.out.println("No GPS data in "+path);
// TODO Auto-generated catch block
e.printStackTrace();
}
dt = ElphelTiffReader.getLocalDateTime(imp_prop);
vert_meters = ElphelTiffReader.getXYOffsetMeters(imp_prop);
orig_pix_meters = ElphelTiffReader.getPixelSize(imp_prop)[0];
......
src/main/java/com/elphel/imagej/orthomosaic/PairwiseOrthoMatch.java
View file @ ef8c6ac2
......@@ -16,6 +16,7 @@ public class PairwiseOrthoMatch implements Serializable {
public transient int [] nxy = null; // not saved, just to communicate for logging
public transient double overlap = 0.0;
public transient double [] equalize1to0 = {1,0}; // value1 = equalize2to1[0]*value2+equalize2to1[1]
public transient boolean ok = false;
// public PairwiseOrthoMatch() {}
public double getOverlap() {
......@@ -75,6 +76,7 @@ public class PairwiseOrthoMatch implements Serializable {
pom.nxy = nxy.clone();
}
pom.equalize1to0 = this.equalize1to0.clone();
pom.ok = this.ok;
return pom;
}
/**
......
src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java
View file @ ef8c6ac2
......@@ -4631,6 +4631,8 @@ public class OpticalFlow {
int min_num_interscene = clt_parameters.imp.min_num_interscene; // 2; // make from parameters, should be >= 1
int min_num_orient = clt_parameters.imp.min_num_orient; // 2; // make from parameters, should be >= 1
boolean sfm_only = clt_parameters.imp.sfm_only; // process only data with SfM
boolean export_images = clt_parameters.imp.export_images;
boolean export_dsi_image = clt_parameters.imp.export_ranges;
boolean debug_ranges = clt_parameters.imp.debug_ranges && !batch_mode;
......@@ -5171,10 +5173,17 @@ public class OpticalFlow {
System.out.println("BUG: saved reference scene "+quadCLTs[ref_index].getImageName()+
" is not really a reference");
System.out.println();
start_ref_pointers[0] = 0;
start_ref_pointers[1] = 0;
return quadCLTs[ref_index].getX3dTopDirectory(); //bailing out
} else if ((first_last_index [0] < 0) || (first_last_index [1] < 0)) {
System.out.println("BUG: saved reference scene "+quadCLTs[ref_index].getImageName()+
" does not have both first/last scenes defined: ["+first_last_index [0]+", "+first_last_index [1]+"]");
System.out.println();
start_ref_pointers[0] = 0;
start_ref_pointers[1] = 0;
return quadCLTs[ref_index].getX3dTopDirectory(); //bailing out
} else {
earliest_scene = first_last_index[0];
last_index = first_last_index[1];
......@@ -5185,7 +5194,8 @@ public class OpticalFlow {
// earliest_scene = getEarliestScene(quadCLTs);
// below ref_index is not necessary the last (fix all where it is supposed to be the last
ErsCorrection ers_reference = quadCLTs[ref_index].getErsCorrection(); // only used in ml_export
while (!reuse_video && ((quadCLTs[ref_index].getNumOrient() < min_num_orient) || (quadCLTs[ref_index].getNumAccum() < min_num_interscene))) {
if (!reuse_video) {
while ((quadCLTs[ref_index].getNumOrient() < min_num_orient) || (quadCLTs[ref_index].getNumAccum() < min_num_interscene)) {
if (debugLevel > -3) {
System.out.println("quadCLTs["+ref_index+"].getNumOrient()="+quadCLTs[ref_index].getNumOrient()+
" of "+min_num_orient+", quadCLTs["+ref_index+"].getNumAccum()="+quadCLTs[ref_index].getNumAccum()+
......@@ -5210,9 +5220,9 @@ public class OpticalFlow {
" is more than half-range. Reducing to "+num_avg_pairs);
}
}
// if (num_avg_pairs > (last_index - ref_index)) {
// num_avg_pairs = last_index - ref_index;
// }
// if (num_avg_pairs > (last_index - ref_index)) {
// num_avg_pairs = last_index - ref_index;
// }
QuadCLT[][][] scenes_seq_pairs = new QuadCLT[3][num_avg_pairs][2];
int ref_index_mod1 = Math.max(ref_index, earliest_scene + num_avg_pairs - 1);
int ref_index_mod2 = Math.min(ref_index, last_index-num_avg_pairs + 1);
......@@ -5228,6 +5238,7 @@ public class OpticalFlow {
scenes_seq_pairs[2][i][0] = quadCLTs[ref_index_mod2 + num_avg_pairs - 1 - i];
scenes_seq_pairs[2][i][1] = quadCLTs[earliest_scene + num_avg_pairs - 1 - i];
}
double [][] sfm_dsn = StructureFromMotion.sfmPairsSet(
clt_parameters, // final CLTParameters clt_parameters,
quadCLTs[ref_index], // final QuadCLT ref_scene,
......@@ -5239,6 +5250,14 @@ public class OpticalFlow {
combo_dsn_final = sfm_dsn;
done_sfm = true;
}
if (!done_sfm && sfm_only) {
System.out.println("\nsfm_only is set and no SfM is available, skipping farther processing of this scene series.");
System.out.println("quadCLTs["+ref_index+"].getNumOrient()="+quadCLTs[ref_index].getNumOrient()+
" of "+min_num_orient+", quadCLTs["+ref_index+"].getNumAccum()="+quadCLTs[ref_index].getNumAccum()+
" of "+min_num_interscene+"\n");
break;
}
}
if (!done_sfm) { // first pass or sfm failed
boolean compensate_dsi = true;
......@@ -5400,46 +5419,10 @@ public class OpticalFlow {
if (debugLevel> -3) {
System.out.println("Egomotion table saved to "+ego_path);
}
/*
// reference to earliest
String ego_path_early = quadCLTs[ref_index].getX3dDirectory()+Prefs.getFileSeparator()+
quadCLTs[ref_index].getImageName()+
"-ego_early-"+quadCLTs[ref_index].getNumOrient()+".csv";
Interscene.invertInitialOrientation(
clt_parameters, // final CLTParameters clt_parameters,
batch_mode, // final boolean batch_mode,
false, // final boolean readjust,
true, // final int set_self, // set record for the new reference to new reference
quadCLTs, // final QuadCLT[] quadCLTs, //
quadCLTs.length-1,// final int last_index, // last to process (normally old reference)
earliest_scene, // final int ref_index, // new reference index (center)
ref_index, // final int ref_old, // original ref_index (normally == last_index)
earliest_scene, // final int earliest_index// first to process
debugLevel); // final int debugLevel
Interscene.generateEgomotionTable(
clt_parameters, // CLTParameters clt_parameters,
quadCLTs, // QuadCLT [] quadCLTs,
earliest_scene,// ref_indx,
earliest_scene, // int earliest_scene,
ego_path_early, // String path,
ego_comment); // String comment);
if (debugLevel> -3) {
System.out.println("Egomotion referenced to earliest scene table saved to "+ego_path_early);
}
*/
}
}
}
/*
boolean calc_smooth_ground = clt_parameters.gsmth_enable;
if (calc_smooth_ground) {
double [] smooth_ground = quadCLTs[ref_index].getSmoothGround(clt_parameters, debugLevel);
quadCLTs[ref_index].setSmoothGround(
clt_parameters, // CLTParameters clt_parameters,
smooth_ground, // double [] smooth_ground,
debugLevel); // int debugLevel)
}
*/
} // if (!reuse_video) {
// later move to the right place
if (adjust_imu_orient) { // (quadCLTs[ref_index].getNumOrient() >= clt_parameters.imp.mb_all_index)) {
boolean orient_combo = clt_parameters.imp.orient_combo; // use combined rotation+orientation for IMU/camera matching
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java
View file @ ef8c6ac2
......@@ -223,6 +223,9 @@ public class QuadCLTCPU {
enu_corr_metric = corr;
}
public String toString() {
return this.image_name;
}
// find best rotation between IMU XYZ and camera XYZ
/**
......
src/main/java/com/elphel/imagej/tileprocessor/TwoQuadCLT.java
View file @ ef8c6ac2
......@@ -8636,7 +8636,7 @@ if (debugLevel > -100) return true; // temporarily !
updateStatus, // final boolean updateStatus,
debugLevel+2); // final int debugLevel)
if (model_directory == null) {
// TODO: Save continueation after failure not to retry each run
// TODO: Save continuation after failure not to retry each run
System.out.println("Failed to build sequence for series "+ref_index);
if (start_ref_pointers[0] < (min_num_scenes-1)) {
break;
......@@ -8645,6 +8645,12 @@ if (debugLevel > -100) return true; // temporarily !
System.out.println("Continue from index "+ref_index);
continue; // and go to the to next scene sequence from the list
}
if ((start_ref_pointers[0]==0) && (start_ref_pointers[1]==0)) { // bail out for debug
System.out.println("\n ----- PROCESSING SCENE SEQUENCE "+nseq+" (last is "+(num_seq-1)+") ABORTED in "+
IJ.d2s(0.000000001*(System.nanoTime()-start_time_seq),3)+" sec ("+
IJ.d2s(0.000000001*(System.nanoTime()-start_time_all),3)+" sec from the overall start\n");
break;
}
first_in_series = false; // at least once success in this series
System.out.println("adding to video_sets_list start="+start_ref_pointers[0]+", end="+ref_index); // start_ref_pointers[1]);
for (int i= 0; i < video_list[0].length; i++) {
......
src/main/java/com/elphel/imagej/tileprocessor/sfm/StructureFromMotion.java
View file @ ef8c6ac2
......@@ -790,6 +790,76 @@ public class StructureFromMotion {
return combo_dsn_final;
}
/**
* Filter reference disparity from NaN (average immediate neighbors), dips and bumps
* @param disp_in
* @param max_dip maximal dip relative to lowest neighbor (0 - any)
* @param max_bump maximal bump relative to highest neighbor (0 - any)
* @param filter_nan replace NaN by neighbors average
* @param tilesX
* @return filtered disparity
*/
public static double [] filterRefDisparity(
final double [] disp_in,
final double max_dip,
final double max_bump,
final boolean filter_nan,
final int tilesX ) {
final double [] disp_out = disp_in.clone();
final int tilesY = disp_in.length / tilesX;
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() {
TileNeibs tn = new TileNeibs(tilesX,tilesY);
for (int nTile = ai.getAndIncrement(); nTile < disp_in.length; nTile = ai.getAndIncrement()) {
int navg = 0;
double s = 0;
if (Double.isNaN(disp_in[nTile])) {
for (int dir = 0; dir < TileNeibs.DIRS; dir++) {
int tile1 = tn.getNeibIndex(nTile, dir);
if ((tile1 >=0) && !Double.isNaN(disp_in[tile1])){
s += disp_in[tile1];
navg++;
}
}
if (navg > 0) {
disp_out[nTile] = s/navg;
}
} else {
double mn = Double.NaN, mx = Double.NaN;
for (int dir = 0; dir < TileNeibs.DIRS; dir++) {
int tile1 = tn.getNeibIndex(nTile, dir);
if (tile1 >=0){
double d = disp_in[tile1];
if (!Double.isNaN(d)) {
if (Double.isNaN(mn)) {
mn = d;
mx = d;
} else {
mn = Math.min(mn, d);
mx = Math.max(mn, d);
}
s += d;
navg++;
}
}
}
if (navg > 0) {
if ( ((max_dip > 0) && (disp_in[nTile] < (mn - max_dip))) ||
((max_bump > 0) && (disp_in[nTile] > (mx + max_bump)))) {
disp_out[nTile] = s/navg;
}
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return disp_out;
}
public static double [][] sfmPairsSet(
final CLTParameters clt_parameters,
......@@ -798,6 +868,7 @@ public class StructureFromMotion {
final double mb_max_gain,
final boolean batch_mode,
final int debugLevel) {
boolean save_disp_seq = clt_parameters.imp.sfm_save_seq; //true;
boolean show_disp_seq = clt_parameters.imp.sfm_show_seq &= !batch_mode; //true;
boolean show_disp_corr_ind = clt_parameters.imp.sfm_show_corr_ind &= !batch_mode; //false; //true;
......@@ -836,6 +907,10 @@ public class StructureFromMotion {
final boolean fill_weak = clt_parameters.imp.sfm_fill_weak; // false;
final boolean extrapolate = clt_parameters.imp.sfm_extrapolate; // false;
final double max_dip = clt_parameters.imp.sfm_max_dip; // 0.1;
final double max_bump = clt_parameters.imp.sfm_max_bump; // 0.5;
final boolean filter_nan = clt_parameters.imp.sfm_filter_nan; // true;
final int tilesX = ref_scene.getTileProcessor().getTilesX();
final int tilesY = ref_scene.getTileProcessor().getTilesY();
......@@ -882,7 +957,7 @@ public class StructureFromMotion {
debugLevel);
double [] interscene_ref_disparity = null; // keep null to use old single-scene disparity for interscene matching
if (use_combo_dsi) {
interscene_ref_disparity = ds[0].clone(); // use_lma_dsi ?
interscene_ref_disparity = ds[0]; // .clone(); // use_lma_dsi ?
/* use conditioned!
if (use_lma_dsi) {
for (int i = 0; i < interscene_ref_disparity.length; i++) {
......@@ -897,7 +972,15 @@ public class StructureFromMotion {
if (interscene_ref_disparity == null) {
interscene_ref_disparity =ref_scene.getDLS()[use_lma_dsi?1:0];
}
final double [] ref_disparity = interscene_ref_disparity;
boolean filter_ref = filter_nan || (max_dip > 0) || (max_bump > 0);
final double [] ref_disparity = filter_ref ?
filterRefDisparity(
interscene_ref_disparity, // final double [] disp_in,
max_dip, // final double max_dip,
max_bump, // final double max_bump,
filter_nan, // final boolean filter_nan,
tilesX ): // final int tilesX)
interscene_ref_disparity.clone();
double [][] disp_adj = (show_disp_seq || save_disp_seq)? (new double [num_readjust+2][]):null;
if (disp_adj != null) {
disp_adj[0] = ref_disparity.clone();
......@@ -1076,6 +1159,7 @@ public class StructureFromMotion {
if (sfmCorrCombo[nTile].corr_ind == null) {
sfmCorrCombo[nTile].corr_ind= new double[2];
}
if (!Double.isNaN(sfmCorr[nTile].corr_ind[0]) && (sfmCorr[nTile].corr_ind[1] > 0)) {
sfmCorrCombo[nTile].corr_ind[0]+= sfmCorr[nTile].corr_ind[0] * sfmCorr[nTile].sfm_gain;
sfmCorrCombo[nTile].corr_ind[1]+= sfmCorr[nTile].corr_ind[1] * sfmCorr[nTile].sfm_gain;
sum_weights_ind[nTile]+=sfmCorr[nTile].sfm_gain;
......@@ -1083,10 +1167,12 @@ public class StructureFromMotion {
sfmCorrCombo[nTile].sfm_gain = sfmCorr[nTile].sfm_gain;
}
}
}
if (sfmCorr[nTile].corr_neib != null) {
if (sfmCorrCombo[nTile].corr_neib == null) {
sfmCorrCombo[nTile].corr_neib= new double[2];
}
if (!Double.isNaN(sfmCorr[nTile].corr_neib[0]) && (sfmCorr[nTile].corr_neib[1] > 0)) {
sfmCorrCombo[nTile].corr_neib[0]+= sfmCorr[nTile].corr_neib[0] * sfmCorr[nTile].sfm_gain;
sfmCorrCombo[nTile].corr_neib[1]+= sfmCorr[nTile].corr_neib[1] * sfmCorr[nTile].sfm_gain;
sum_weights_neib[nTile]+=sfmCorr[nTile].sfm_gain;
......@@ -1097,6 +1183,7 @@ public class StructureFromMotion {
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
......
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