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Commit 17265194 authored by Andrey Filippov's avatar Andrey Filippov
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debugging and fine tuning detection

parent 673cd8a6
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Showing with 100 additions and 69 deletions
src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java
View file @ 17265194
......@@ -1091,6 +1091,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
int num_slices, // (0 - all)
int [] wh) {
ImagePlus imp = null;
System.out.println("readFloatArray(): reading "+file_path);
try {
imp = new ImagePlus(file_path);
} catch (Exception e) {
......@@ -1111,6 +1112,7 @@ G= Y +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
int [] wh, // should be null or int[2]
String [][] ptop_titles, // should be null or String [1][]
String [][] pslice_titles){// should be null or String [1][]
System.out.println("readDoubleHyperstack(): reading "+path);
ImagePlus imp = new ImagePlus(path);
if (imp.getWidth() == 0) {
System.out.println("testSynthetic(): Failed reading Vector field from: " + path);
......
src/main/java/com/elphel/imagej/cuas/CuasMotion.java
View file @ 17265194
......@@ -3183,7 +3183,7 @@ public class CuasMotion {
// duplicate first/last, interpolate middle
if (Double.isNaN(temp_line[x])) {
int i;
for (i = 1; Double.isNaN(temp_line[i * width+x]) && (i < num_scenes); i++);
for (i = 1; (i < num_scenes) && Double.isNaN(temp_line[i * width+x]) ; i++); //Index 318080 out of bounds for length 318080
temp_line[x] = temp_line[i * width+x];
}
if (Double.isNaN(temp_line[(num_scenes-1)*width + x])) {
......@@ -6989,8 +6989,12 @@ public class CuasMotion {
public static void calcMathingTargetsLengths( // calculate number of consecutive keyframes connected to each target
final double [][][][] targets_multi,
final double max_mismatch, // if <=0, do not calculate mismatch_ba and filter
// final double good_mismatch, // 0.4; // do not add to score if worse
final double slow_fast_mismatch,
final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
final double seq_travel,
final int tilesX) {
final double good_mismatch = max_mismatch;
final double max_mismatch2 = max_mismatch * max_mismatch;
final double slow_fast_mismatch2 = slow_fast_mismatch * slow_fast_mismatch;
// Will only consider not-failed targets
......@@ -7133,19 +7137,33 @@ public class CuasMotion {
for (int ntarg = 0; ntarg < targets.length; ntarg++) {
double [] target = targets[ntarg];
if ((target != null) && (target[CuasMotionLMA.RSLT_FAIL] == CuasMotionLMA.FAIL_NONE)) {
target[CuasMotionLMA.RSLT_BEFORE_LENGTH] = len_ba[0][nSeq][ntile][ntarg];
target[CuasMotionLMA.RSLT_AFTER_LENGTH] = len_ba[1][nSeq][ntile][ntarg];
target[CuasMotionLMA.RSLT_MATCH_LENGTH] = 0;
for (int ba = 0; ba < len_ba.length; ba++) {
if (len_ba[ba][nSeq][ntile] != null) {
target[CuasMotionLMA.RSLT_MATCH_LENGTH]+= len_ba[ba][nSeq][ntile][ntarg];
}
}
target[CuasMotionLMA.RSLT_BEFORE_LENGTH] = len_ba[0][nSeq][ntile][ntarg];
target[CuasMotionLMA.RSLT_AFTER_LENGTH] = len_ba[1][nSeq][ntile][ntarg];
double [] bbox = getBbox(
bbox_ba[0][nSeq][ntile][ntarg], // double [] bbox1,
bbox_ba[1][nSeq][ntile][ntarg]); //double [] bbox2);
target[CuasMotionLMA.RSLT_SEQ_TRAVEL] = Math.sqrt(getDiagonal2(bbox));
// calculate related quality factors (moved from getEffective...())
target[CuasMotionLMA.RSLT_QMATCH_LEN] = Math.pow(target[CuasMotionLMA.RSLT_MATCH_LENGTH], match_len_pwr);// 1.0 if in every scene;
target[CuasMotionLMA.RSLT_QTRAVEL] = Math.max((target[CuasMotionLMA.RSLT_SEQ_TRAVEL] - seq_travel)/seq_travel, 0);
double MM_BEFORE = target[CuasMotionLMA.RSLT_MISMATCH_BEFORE];
double MM_AFTER = target[CuasMotionLMA.RSLT_MISMATCH_AFTER];
target[CuasMotionLMA.RSLT_QMATCH] = 0;
if (MM_BEFORE <= good_mismatch) {
target[CuasMotionLMA.RSLT_QMATCH] += Math.max(0,(good_mismatch - MM_BEFORE)/good_mismatch); // 0 .. 1
}
if (MM_AFTER <= good_mismatch) {
target[CuasMotionLMA.RSLT_QMATCH] += Math.max(0,(good_mismatch - MM_AFTER)/good_mismatch); // 0 .. 1
}
if (ntile == dbg_tile) {
System.out.println("calcMathingTargetsLengths().4 nSeq = "+nSeq+", targets["+ntarg+"][CuasMotionLMA.RSLT_MATCH_LENGTH]="+
target[CuasMotionLMA.RSLT_MATCH_LENGTH]+", travel="+target[CuasMotionLMA.RSLT_SEQ_TRAVEL]);
......@@ -7982,10 +8000,10 @@ public class CuasMotion {
lma_maxk, // final double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0// final double lma_a2a,
lma_a2a, // final double lma_a2a,
0, // max_mismatch, // final double max_mismatch, apply only during final, when mismatch scores are calculated
good_mismatch, // final double good_mismatch, //do not add to score if worse
/// good_mismatch, // final double good_mismatch, //do not add to score if worse
slow_fast_mismatch, // final double slow_fast_mismatch, // // 1.5; allow larger mismatch between slow and fast
match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
seq_travel, // final double seq_travel,
/// match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
/// seq_travel, // final double seq_travel,
fail_mismatch, // final boolean fail_mismatch,
target_horizon, // final double lma_horizon, // horizon as maximal pixel Y
cuasMotion.tilesX); // final int tilesX,
......@@ -8060,7 +8078,6 @@ public class CuasMotion {
if (debugLevel > -4) {
System.out.println("\n========================== Starting centered iterations =============================.\n");
}
// second pass, using non-centered targets
int niter_lim = niter+ num_cycles;
int iter_show1 = iter_show + niter;
......@@ -8291,10 +8308,10 @@ public class CuasMotion {
lma_maxk, // final double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0// final double lma_a2a,
lma_a2a, // final double lma_a2a,
0, // max_mismatch, // final double max_mismatch, apply only during final, when mismatch scores are calculated
good_mismatch, // final double good_mismatch, //do not add to score if worse
/// good_mismatch, // final double good_mismatch, //do not add to score if worse
slow_fast_mismatch, // final double slow_fast_mismatch, // // 1.5; allow larger mismatch between slow and fast
match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
seq_travel, // final double seq_travel,
/// match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
/// seq_travel, // final double seq_travel,
fail_mismatch, // final boolean fail_mismatch,
target_horizon, // final double lma_horizon, // horizon as maximal pixel Y
cuasMotion.tilesX); // final int tilesX,
......@@ -8353,6 +8370,7 @@ public class CuasMotion {
boolean good_only= false;
boolean show_empty = true; // false; // show scenes with no (valid) targets
if (intermed_low) { // targets_good now has
ImagePlus imp_good = showTargetSequence(
target_sequence_multi, // double [][][] vector_fields_sequence,
......@@ -8635,6 +8653,35 @@ public class CuasMotion {
}
return filter5;
}
// mark all "used" targets (non-centered, after all centered are added) as failed
public static void failUsed(
final double [][][][] target_sequence) {
final int num_seq = target_sequence.length;
final int num_tiles = target_sequence[0].length;
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0);
ai.set(0);
// mark selected (non-centered) targets as "used"
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
for (int nSeq = ai.getAndIncrement(); nSeq < num_seq; nSeq = ai.getAndIncrement()) {
for (int ntile = 0; ntile < num_tiles; ntile++) if (target_sequence[nSeq][ntile] != null) {
for (int ntarg = 0; ntarg < target_sequence[nSeq][ntile].length; ntarg++) {
double [] target = target_sequence[nSeq][ntile][ntarg];
if ((target != null) && (target[CuasMotionLMA.RSLT_FAIL] == CuasMotionLMA.FAIL_NONE) && (target[CuasMotionLMA.RSLT_CENTERED] == CuasMotionLMA.CENTERED_USED)) {
target[CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_USED;
}
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
}
public static void getEffectiveStrengthLMA(
final double [][][][] target_sequence_multi, // modifies certain fields (scores)
......@@ -8650,10 +8697,10 @@ public class CuasMotion {
final double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0
final double lma_a2a,
final double max_mismatch,
final double good_mismatch, // 0.4; // do not add to score if worse
/// final double good_mismatch, // 0.4; // do not add to score if worse
final double slow_fast_mismatch,
final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
final double seq_travel,
/// final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
/// final double seq_travel,
final boolean fail_mismatch,
final double lma_horizon, // horizon as maximal pixel Y
final int tilesX ) {
......@@ -8678,7 +8725,10 @@ public class CuasMotion {
if (targets != null) {
for (int ntarg = 0; ntarg < targets.length; ntarg++) if (targets[ntarg] != null){
double [] lma_rslts = targets[ntarg];
if (lma_rslts != null) {
// if ((lma_rslts != null) && (Double.isNaN(lma_rslts[CuasMotionLMA.RSLT_FAIL]) || (lma_rslts[CuasMotionLMA.RSLT_FAIL] == CuasMotionLMA.FAIL_NONE))) {
// this method should be called only when [CuasMotionLMA.RSLT_FAIL] is not yet defined, only for the new LMA data is calculated
if ((lma_rslts != null) && Double.isNaN(lma_rslts[CuasMotionLMA.RSLT_FAIL])) {
lma_rslts[CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_NONE;
double CENT_STR = lma_rslts[CuasMotionLMA.RSLT_CENT_MX];
double CENT_FRAC= lma_rslts[CuasMotionLMA.RSLT_CENT_F];
......@@ -8780,7 +8830,7 @@ public class CuasMotion {
double [] quality_factors = new double [IMPORTANCE_LENGTH];
if (!failed) {
lma_rslts[CuasMotionLMA.RSLT_FAIL] = 0;
lma_rslts[CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_NONE;
double inv_rms = 1.0 / RMSE;
double inv_rms_lim = 1.0 / lma_arms;
double inv_rel_rms = 1.0 / RMSE_A; // A/RMSE;
......@@ -8790,15 +8840,19 @@ public class CuasMotion {
quality_factors[IMPORTANCE_RMS] = Math.max(0,(inv_rms - inv_rms_lim)/ inv_rms_lim); // only >0 for small max-es
quality_factors[IMPORTANCE_RMS_A] = Math.max(0,(inv_rel_rms - inv_rel_rms_lim)/ inv_rel_rms_lim); // only >0 for small max-es
if (MM_BEFORE <= good_mismatch) {
quality_factors[IMPORTANCE_MISMATCH] += Math.max(0,(good_mismatch - MM_BEFORE)/good_mismatch); // 0 .. 1
}
if (MM_AFTER <= good_mismatch) {
quality_factors[IMPORTANCE_MISMATCH] += Math.max(0,(good_mismatch - MM_AFTER)/good_mismatch); // 0 .. 1
}
quality_factors[IMPORTANCE_MATCH_LEN] = Math.pow(lma_rslts[CuasMotionLMA.RSLT_MATCH_LENGTH], match_len_pwr);// 1.0 if in every scene
quality_factors[IMPORTANCE_CENTER] = cxy*cxy;
quality_factors[IMPORTANCE_TRAVEL] = Math.max((lma_rslts[CuasMotionLMA.RSLT_SEQ_TRAVEL] - seq_travel)/seq_travel, 0);
quality_factors[IMPORTANCE_CENTER] = cxy*cxy;
// if (MM_BEFORE <= good_mismatch) {
// quality_factors[IMPORTANCE_MISMATCH] += Math.max(0,(good_mismatch - MM_BEFORE)/good_mismatch); // 0 .. 1
// }
// if (MM_AFTER <= good_mismatch) {
// quality_factors[IMPORTANCE_MISMATCH] += Math.max(0,(good_mismatch - MM_AFTER)/good_mismatch); // 0 .. 1
// }
/// quality_factors[IMPORTANCE_MATCH_LEN] = Math.pow(lma_rslts[CuasMotionLMA.RSLT_MATCH_LENGTH], match_len_pwr);// 1.0 if in every scene
/// quality_factors[IMPORTANCE_TRAVEL] = Math.max((lma_rslts[CuasMotionLMA.RSLT_SEQ_TRAVEL] - seq_travel)/seq_travel, 0);
// final double seq_travel,
}
......@@ -8806,10 +8860,10 @@ public class CuasMotion {
lma_rslts[CuasMotionLMA.RSLT_QA] = quality_factors[IMPORTANCE_A];
lma_rslts[CuasMotionLMA.RSLT_QRMS] = quality_factors[IMPORTANCE_RMS];
lma_rslts[CuasMotionLMA.RSLT_QRMS_A] = quality_factors[IMPORTANCE_RMS_A];
lma_rslts[CuasMotionLMA.RSLT_QMATCH] = quality_factors[IMPORTANCE_MISMATCH];
/// lma_rslts[CuasMotionLMA.RSLT_QMATCH] = quality_factors[IMPORTANCE_MISMATCH];
lma_rslts[CuasMotionLMA.RSLT_QCENTER] = quality_factors[IMPORTANCE_CENTER];
lma_rslts[CuasMotionLMA.RSLT_QMATCH_LEN] = quality_factors[IMPORTANCE_MATCH_LEN];
lma_rslts[CuasMotionLMA.RSLT_QTRAVEL] = quality_factors[IMPORTANCE_TRAVEL];
/// lma_rslts[CuasMotionLMA.RSLT_QMATCH_LEN] = quality_factors[IMPORTANCE_MATCH_LEN];
/// lma_rslts[CuasMotionLMA.RSLT_QTRAVEL] = quality_factors[IMPORTANCE_TRAVEL];
}
}
}
......@@ -9367,6 +9421,9 @@ public class CuasMotion {
parentCLT.saveImagePlusInModelDirectory(imp_in);
}
// Used non-centered tiles are not needed anymore, mark them as failed to simplify processing
failUsed(targets_multi); // final double [][][][] target_sequence) {
sortMultiTargets(
targets_multi, // final double [][][][] target_multi,
trim_nulls); // final boolean trim_nulls) { // trim null targets
......@@ -9412,6 +9469,8 @@ public class CuasMotion {
// which is better here?
good_mismatch, // max_mismatch, // final double max_mismatch, // if <=0, do not calculate mismatch_ba and filter
slow_fast_mismatch, // final double slow_fast_mismatch,
match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
seq_travel, // final double seq_travel,
cuasMotion.tilesX); //final int tilesX)
if (intermed_low && debug_more) {
ImagePlus imp_lengths = showTargetSequence(
......@@ -9425,7 +9484,7 @@ public class CuasMotion {
parentCLT.saveImagePlusInModelDirectory(imp_lengths);
}
/*
getEffectiveStrengthLMA(
targets_multi, // final double [][][][] target_sequence_multi, // modifies certain fields (scores)
target_strength, // final double target_strength,
......@@ -9442,14 +9501,16 @@ public class CuasMotion {
max_mismatch, // final double max_mismatch,
good_mismatch, // final double good_mismatch, //do not add to score if worse
slow_fast_mismatch, // final double slow_fast_mismatch, // // 1.5; allow larger mismatch between slow and fast
match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
seq_travel, // final double seq_travel,
/// match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
/// seq_travel, // final double seq_travel,
fail_mismatch, // final boolean fail_mismatch,
target_horizon, // final double lma_horizon, // target below horizon
cuasMotion.tilesX); // final int tilesX,
*/
// order/auto order with getEffectiveStrengthLMA()?
// int [] remain_es =
getScore( // calculates composite sceres
getScore( // calculates composite sceres
targets_multi, // final double [][][][] target_sequence_multi, // modifies certain fields (scores)
factor_lim, // final double importance_limit,
factor_pow, // final double importance_power, // Raise each factor to this power before combining
......@@ -9576,6 +9637,8 @@ public class CuasMotion {
// which is better here?
good_mismatch, // max_mismatch, // final double max_mismatch, // if <=0, do not calculate mismatch_ba and filter
slow_fast_mismatch, // final double slow_fast_mismatch,
match_len_pwr, // final double match_len_pwr, // 0.5; // raise matching length to this power for calculating score
seq_travel, // final double seq_travel,
cuasMotion.tilesX); //final int tilesX)
if (intermed_low) { // && debug_more) {
ImagePlus imp_lengths = showTargetSequence(
......@@ -9632,8 +9695,7 @@ public class CuasMotion {
if (targets != null) {
for (int ntarg = 0; ntarg < targets.length; ntarg++) if (targets[ntarg] != null){
double [] target = targets[ntarg];
if ((target != null) && (target[CuasMotionLMA.RSLT_FAIL] == CuasMotionLMA.FAIL_NONE) &&
(target[CuasMotionLMA.RSLT_CENTERED] != CuasMotionLMA.CENTERED_USED)) {
if ((target != null) && (target[CuasMotionLMA.RSLT_FAIL] == CuasMotionLMA.FAIL_NONE)) { // && (target[CuasMotionLMA.RSLT_CENTERED] != CuasMotionLMA.CENTERED_USED)) {
if (filter5[nSeq][ntile] >=0) {
if (filter5[nSeq][ntile] == ntarg) {
targets[ntarg][CuasMotionLMA.RSLT_STRONGER] = Double.NaN;
......
src/main/java/com/elphel/imagej/cuas/CuasMotionLMA.java
View file @ 17265194
......@@ -124,6 +124,7 @@ public class CuasMotionLMA {
public static final int FAIL_MISMATCH = 17; // Mismatch on both ends is too high
public static final int FAIL_NEIGHBOR = 18; // failed because some neighbor is stronger
public static final int FAIL_DUPLICATE= 19; // coordinate are (almost) the same as those of a stronger tile
public static final int FAIL_USED= 20; // non-centered used to generate centered, remove this
public static final int CENTERED_NO = 0;
public static final int CENTERED_YES = 1;
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java
View file @ 17265194
......@@ -6171,6 +6171,7 @@ public class QuadCLTCPU {
String x3d_path = readX3dDirectory(correctionsParameters.getModelName(image_name));
String file_name = image_name + suffix;
String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
System.out.println("readImagePlusFromModelDirectory(): reading "+file_path);
ImagePlus imp = null;
try {
imp = new ImagePlus(file_path);
......@@ -6184,41 +6185,6 @@ public class QuadCLTCPU {
}
/*
public float [][] readFloatArrayFromThisModelDirectory(
String suffix,
int num_slices, // (0 - all)
int [] wh)
{
String x3d_path = getImagePath(); // getX3dDirectory();
String file_name = image_name + suffix;
String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
ImagePlus imp = null;
try {
imp = new ImagePlus(file_path);
} catch (Exception e) {
System.out.println ("Failed to open "+file_path+", will generate it");
}
if ((imp == null) || (imp.getTitle() == null) || (imp.getTitle().equals(""))) {
return null;
}
ImageStack imageStack = imp.getStack();
int nChn=imageStack.getSize();
if ((num_slices > 0) && (num_slices < nChn)) {
nChn = num_slices;
}
float [][] result = new float [nChn][];
for (int n = 0; n < nChn; n++) {
result[n] = (float[]) imageStack.getPixels(n + 1);
}
if (wh != null) {
wh[0] = imp.getWidth();
wh[1] = imp.getHeight();
}
return result;
}*/
public void saveDSI() { saveDSI(this.dsi);}
......
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