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Commit b56ba447 authored by Andrey Filippov's avatar Andrey Filippov
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Adding "importance"

parent 97bfc4bf
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src/main/java/com/elphel/imagej/cuas/CuasMotion.java
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...@@ -57,9 +57,20 @@ public class CuasMotion { ...@@ -57,9 +57,20 @@ public class CuasMotion {
final static public int TARGET_VY = 3; final static public int TARGET_VY = 3;
final static public int TARGET_STRENGTH = 4; final static public int TARGET_STRENGTH = 4;
final static public int TARGET_NTILE = 5; final static public int TARGET_NTILE = 5;
final static public int TARGET_LENGTH = TARGET_NTILE+1; final static public int TARGET_LENGTH = TARGET_NTILE+1;
final static public int IMPORTANCE_A = 0;
final static public int IMPORTANCE_RMS = 1;
final static public int IMPORTANCE_RMS_A = 2;
final static public int IMPORTANCE_LENGTH = IMPORTANCE_RMS_A+ 1;
/*
final double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
*/
public static String RESOURCE_GRAPICS_DIR ="graphics"; public static String RESOURCE_GRAPICS_DIR ="graphics";
public static String ICON_TARGET_1X = "TDbox_dashed21x21_bold.png"; public static String ICON_TARGET_1X = "TDbox_dashed21x21_bold.png";
public static String ICON_TARGET_2X = "TDbox_dashed43x43_2px.png"; public static String ICON_TARGET_2X = "TDbox_dashed43x43_2px.png";
...@@ -319,8 +330,13 @@ public class CuasMotion { ...@@ -319,8 +330,13 @@ public class CuasMotion {
double lma_rrms = clt_parameters.imp.cuas_lma_rrms; // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) double lma_rrms = clt_parameters.imp.cuas_lma_rrms; // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
double lma_mina = clt_parameters.imp.cuas_lma_mina; // = 1.0; // Minimal A (amplitude) double lma_mina = clt_parameters.imp.cuas_lma_mina; // = 1.0; // Minimal A (amplitude)
double lma_maxr = clt_parameters.imp.cuas_lma_maxr; // = 5.0; // Maximal radius (>3.8) double lma_maxr = clt_parameters.imp.cuas_lma_maxr; // = 5.0; // Maximal radius (>3.8)
double lma_minr1 = clt_parameters.imp.cuas_lma_minr1; // = 1.0; // Maximal inner radius
double lma_mink = clt_parameters.imp.cuas_lma_mink; // = 0.0; // Minimal K (overshoot) <0.007 double lma_mink = clt_parameters.imp.cuas_lma_mink; // = 0.0; // Minimal K (overshoot) <0.007
double lma_maxk = clt_parameters.imp.cuas_lma_maxk; // = 5.0; // Minimal K (overshoot) > 3.8 double lma_maxk = clt_parameters.imp.cuas_lma_maxk; // = 5.0; // Minimal K (overshoot) > 3.8
double lma_a2a = clt_parameters.imp.cuas_lma_a2a; // = 0.7; // Minimal ratio of the maximal pixel to the amplitude
boolean remove_isolated= clt_parameters.imp.cuas_isolated; // true; boolean remove_isolated= clt_parameters.imp.cuas_isolated; // true;
double max_mismatch = clt_parameters.imp.cuas_max_mismatch; // 2; double max_mismatch = clt_parameters.imp.cuas_max_mismatch; // 2;
...@@ -908,21 +924,47 @@ public class CuasMotion { ...@@ -908,21 +924,47 @@ public class CuasMotion {
public static double[][][] filterAndShowTargetsLMA( public static double[][][] filterAndShowTargetsLMA(
double [][][] coord_data, double [][][] coord_data,
double importance_limit,
double importance_power, // Raise each factor to this power before combining
double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A) double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
double lma_arms, // = 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484) double lma_arms, // = 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484)
double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
double lma_mina, // = 1.0; // Minimal A (amplitude) double lma_mina, // = 1.0; // Minimal A (amplitude)
double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0 double lma_maxr, // = 5.0; // Minimal K (overshoot) = 5.0
double lma_mink, // = 0.0; // Minimal K (overshoot) = 1.0 double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0 double lma_mink, // = 0.0; // Minimal K (overshoot) = 0.0
double lma_maxk, // = 5.0; // Minimal K (overshoot) = 5.0
double lma_a2a,
String [] slice_titles, // String [] slice_titles, //
String title_targets_filt, String title_targets_filt,
double [][][] failures_debug,
int [] targets_remain, int [] targets_remain,
int tilesX, int tilesX,
boolean show, boolean show,
QuadCLT parentCLT) { QuadCLT parentCLT) {
boolean save = (parentCLT != null); boolean save = (parentCLT != null);
double lma_minxy = 0.8; double lma_minxy = 0.8;
double [][] target_scores = getEffectiveStrengthLMA(
coord_data, // final double [][][] target_coords, // LMA
importance_limit, // final double importance_limit,
importance_power, // final double importance_power, // Raise each factor to this power before combining
importance, // final double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
lma_rms, // final double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
lma_arms, // final double lma_arms, // = 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484)
lma_rrms, // final double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
lma_mina, // final double lma_mina, // = 1.0; // Minimal A (amplitude)
lma_maxr, // final double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
lma_minr1, // final double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
lma_mink, // final double lma_mink, // = 0.0; // Minimal K (overshoot) = 1.0
lma_maxk, // final double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0// final double lma_a2a,
lma_a2a, // final double lma_a2a,
lma_minxy, // final double lma_minxy, // 0.8
tilesX, // final int tilesX,
failures_debug, // final double failures_debug,
null); // remain); // final int [] remain)
/*
boolean [][] good_targets = filterTargetsLMA( boolean [][] good_targets = filterTargetsLMA(
coord_data, // final double [][][] target_coords, coord_data, // final double [][][] target_coords,
lma_rms, // double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A) lma_rms, // double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
...@@ -930,6 +972,7 @@ public class CuasMotion { ...@@ -930,6 +972,7 @@ public class CuasMotion {
lma_rrms, // double lma_rrms, // = 0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) lma_rrms, // double lma_rrms, // = 0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
lma_mina, // double lma_mina, // = 1.0; // Minimal A (amplitude) lma_mina, // double lma_mina, // = 1.0; // Minimal A (amplitude)
lma_maxr, // double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0 lma_maxr, // double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
lma_minr1, //double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
lma_mink, // double lma_mink, // = 1.0; // Minimal K (overshoot) = 1.0 lma_mink, // double lma_mink, // = 1.0; // Minimal K (overshoot) = 1.0
lma_maxk, // double lma_maxk, // = 1.0; // Minimal K (overshoot) = 3.0 lma_maxk, // double lma_maxk, // = 1.0; // Minimal K (overshoot) = 3.0
lma_minxy, // final double lma_minxy, // 0.8 lma_minxy, // final double lma_minxy, // 0.8
...@@ -938,6 +981,10 @@ public class CuasMotion { ...@@ -938,6 +981,10 @@ public class CuasMotion {
double [][][] coord_data_filtered = applyFilter( double [][][] coord_data_filtered = applyFilter(
coord_data, // double [][][] motion_scan, coord_data, // double [][][] motion_scan,
good_targets); // boolean [][] filter5) good_targets); // boolean [][] filter5)
*/
double [][][] coord_data_filtered = applyFilter(
coord_data, // double [][][] motion_scan,
target_scores); // double [][] filter5)
if (save || show) { if (save || show) {
ImagePlus imp = showVectorFieldsSequenceLMA( ImagePlus imp = showVectorFieldsSequenceLMA(
coord_data_filtered, // double [][][] target_scene_sequence, coord_data_filtered, // double [][][] target_scene_sequence,
...@@ -1065,7 +1112,7 @@ public class CuasMotion { ...@@ -1065,7 +1112,7 @@ public class CuasMotion {
param_select[CuasMotionLMA.INDX_C] = lma_fit_c; param_select[CuasMotionLMA.INDX_C] = lma_fit_c;
param_select[CuasMotionLMA.INDX_RR0] = lma_fit_r; param_select[CuasMotionLMA.INDX_RR0] = lma_fit_r;
param_select[CuasMotionLMA.INDX_K] = lma_fit_k; param_select[CuasMotionLMA.INDX_K] = lma_fit_k;
final int dbg_tile = (38 + 45 * 80); final int dbg_tile = (33 + 34 * 80); //(38 + 45 * 80);
final int dbg_seq = -15; final int dbg_seq = -15;
// final boolean[] fpn_mask= no_border? (new boolean[0]) : null; // final boolean[] fpn_mask= no_border? (new boolean[0]) : null;
for (int ithread = 0; ithread < threads.length; ithread++) { for (int ithread = 0; ithread < threads.length; ithread++) {
...@@ -1106,6 +1153,7 @@ public class CuasMotion { ...@@ -1106,6 +1153,7 @@ public class CuasMotion {
int ntile_amax = TileNeibs.getAmaxTile( int ntile_amax = TileNeibs.getAmaxTile(
pix_tile); //double [] data) pix_tile); //double [] data)
double amax_val = pix_tile[ntile_amax]; double amax_val = pix_tile[ntile_amax];
double lmax_val = amax_val;
int use_max = -1; int use_max = -1;
if (!tn.isEdge(ntile_amax)) { if (!tn.isEdge(ntile_amax)) {
boolean isolated = tn.isMaxIsolated( boolean isolated = tn.isMaxIsolated(
...@@ -1138,6 +1186,7 @@ public class CuasMotion { ...@@ -1138,6 +1186,7 @@ public class CuasMotion {
} }
} }
} }
lmax_val = best_val;
} }
if (use_max < 0){ if (use_max < 0){
// no candidate for the centroid/lma // no candidate for the centroid/lma
...@@ -1197,6 +1246,7 @@ public class CuasMotion { ...@@ -1197,6 +1246,7 @@ public class CuasMotion {
mv[1], // double yc, // relative to center =width/2 mv[1], // double yc, // relative to center =width/2
lma_r0, // double r0, lma_r0, // double r0,
lma_ovrsht, // double k, lma_ovrsht, // double k,
lmax_val, // double lmax_val,
debugLevel); // int debugLevel) debugLevel); // int debugLevel)
int rslt = cuasMotionLMA. runLma( // <0 - failed, >=0 iteration number (1 - immediately) int rslt = cuasMotionLMA. runLma( // <0 - failed, >=0 iteration number (1 - immediately)
lambda, // double lambda, // 0.1 lambda, // double lambda, // 0.1
...@@ -1283,6 +1333,24 @@ public class CuasMotion { ...@@ -1283,6 +1333,24 @@ public class CuasMotion {
} }
public static double [][][] applyFilter(
double [][][] motion_scan,
double [][] scores){
double [][][] filtered_scan = new double [motion_scan.length][motion_scan[0].length][];
for (int nscan = 0; nscan < motion_scan.length; nscan++) {
for (int t=0; t<motion_scan[nscan].length; t++) {
if ((motion_scan[nscan][t] != null) && (scores[nscan][t] > 0)) {
filtered_scan[nscan][t] = motion_scan[nscan][t].clone();
}
}
}
return filtered_scan;
}
public static ImagePlus showVectorFieldsSequence( public static ImagePlus showVectorFieldsSequence(
double [][][] vector_fields_sequence, double [][][] vector_fields_sequence,
double speed_min, double speed_min,
...@@ -1451,6 +1519,7 @@ public class CuasMotion { ...@@ -1451,6 +1519,7 @@ public class CuasMotion {
return filter_target; return filter_target;
} }
@Deprecated
public static boolean [][] filterTargetsLMA( public static boolean [][] filterTargetsLMA(
final double [][][] target_coords, final double [][][] target_coords,
double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A) double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
...@@ -1458,6 +1527,7 @@ public class CuasMotion { ...@@ -1458,6 +1527,7 @@ public class CuasMotion {
double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
double lma_mina, // = 1.0; // Minimal A (amplitude) double lma_mina, // = 1.0; // Minimal A (amplitude)
double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0 double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
double lma_mink, // = 0.0; // Minimal K (overshoot) = 1.0 double lma_mink, // = 0.0; // Minimal K (overshoot) = 1.0
double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0 double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0
final double lma_minxy, // 0.8 final double lma_minxy, // 0.8
...@@ -1469,7 +1539,7 @@ public class CuasMotion { ...@@ -1469,7 +1539,7 @@ public class CuasMotion {
final boolean [][] filter_target = new boolean [num_seq][num_tiles]; final boolean [][] filter_target = new boolean [num_seq][num_tiles];
final double maxxy = GPUTileProcessor.DTT_SIZE - 1 -lma_minxy; // lma_minxy=1 - prevent bottom row/righth column final double maxxy = GPUTileProcessor.DTT_SIZE - 1 -lma_minxy; // lma_minxy=1 - prevent bottom row/righth column
final double minxy = -GPUTileProcessor.DTT_SIZE +lma_minxy; // lma_minxy=1 - prevent top row/left column final double minxy = -GPUTileProcessor.DTT_SIZE +lma_minxy; // lma_minxy=1 - prevent top row/left column
final int dbg_tile = -(33 + 34*80); final int dbg_tile = -(33 + 34*80);
final Thread[] threads = ImageDtt.newThreadArray(); final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0); final AtomicInteger ai = new AtomicInteger(0);
for (int ithread = 0; ithread < threads.length; ithread++) { for (int ithread = 0; ithread < threads.length; ithread++) {
...@@ -1489,20 +1559,39 @@ public class CuasMotion { ...@@ -1489,20 +1559,39 @@ public class CuasMotion {
if (lma_rslts[CuasMotionLMA.RSLT_ITERS] < 0) { // fitting has not failed if (lma_rslts[CuasMotionLMA.RSLT_ITERS] < 0) { // fitting has not failed
continue; // LMA failed continue; // LMA failed
} }
double A = lma_rslts[CuasMotionLMA.RSLT_A]; double A = lma_rslts[CuasMotionLMA.RSLT_A];
double RMSE = lma_rslts[CuasMotionLMA.RSLT_RMS];
double RMSE_A = lma_rslts[CuasMotionLMA.RSLT_RMS_A];
double R1 = lma_rslts[CuasMotionLMA.RSLT_R1];
if (A < lma_mina) { if (A < lma_mina) {
continue; // too weak continue; // too weak
} }
if (lma_rslts[CuasMotionLMA.RSLT_RMS] > lma_rms) {
if (RMSE > lma_rms) {
continue; // too high RMSE regardless of A continue; // too high RMSE regardless of A
} }
if ((RMSE > lma_arms) && (RMSE_A > lma_rrms)) {
continue; // too high RMSE
}
/*
double max_RMS = Math.max(lma_arms, A * lma_rrms); double max_RMS = Math.max(lma_arms, A * lma_rrms);
if (lma_rslts[CuasMotionLMA.RSLT_RMS] > max_RMS) { if (RMSE > max_RMS) {
continue; // too high RMSE
}
*/
double max_RMS = Math.max(lma_arms, A * lma_rrms);
if (RMSE > max_RMS) {
continue; // too high RMSE continue; // too high RMSE
} }
if (lma_rslts[CuasMotionLMA.RSLT_R0] > lma_maxr) { if (lma_rslts[CuasMotionLMA.RSLT_R0] > lma_maxr) {
continue; // Radius is too high continue; // Radius is too high
} }
if (R1 < lma_minr1) {
continue; // Inner radius too small
}
if (lma_rslts[CuasMotionLMA.RSLT_K] < lma_mink) { if (lma_rslts[CuasMotionLMA.RSLT_K] < lma_mink) {
continue; // K is too low continue; // K is too low
} }
...@@ -1530,17 +1619,282 @@ public class CuasMotion { ...@@ -1530,17 +1619,282 @@ public class CuasMotion {
return filter_target; return filter_target;
} }
public static double [][] getEffectiveStrengthLMA(
final double [][][] target_coords, // LMA
final double importance_limit,
final double importance_power, // Raise each factor to this power before combining
final double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
final double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
final double lma_arms, // = 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484)
final double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
final double lma_mina, // = 1.0; // Minimal A (amplitude)
final double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
final double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
final double lma_mink, // = 0.0; // Minimal K (overshoot) = 1.0
final double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0
final double lma_a2a,
final double lma_minxy, // 0.8
final int tilesX,
final double [][][] failures_debug, // if not null, should be [num_scenes][][], fill contain a copy of original target_coords with failure reason
final int [] remain) {
final int num_seq = target_coords.length;
final int num_tiles = target_coords[0].length;
final double [][] effective_strength = new double [num_seq][num_tiles];
final double maxxy = GPUTileProcessor.DTT_SIZE - 1 -lma_minxy; // lma_minxy=1 - prevent bottom row/righth column
final double minxy = -GPUTileProcessor.DTT_SIZE +lma_minxy; // lma_minxy=1 - prevent top row/left column
final int dbg_tile = -(33 + 34*80);
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0);
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()) {
if (failures_debug != null) {
failures_debug[nSeq] = new double [num_tiles][];
}
int num = 0;
for (int ntile = 0; ntile < num_tiles; ntile++) {
if (ntile == dbg_tile) {
System.out.println("filterTargetsLMA(): ntile = "+ntile);
}
double [] lma_rslts = target_coords[nSeq][ntile];
if (lma_rslts != null) {
if (failures_debug != null) {
failures_debug[nSeq][ntile] = lma_rslts.clone();
}
if (lma_rslts[CuasMotionLMA.RSLT_ITERS] < 0) { // fitting has not failed
continue; // LMA failed
}
double A = lma_rslts[CuasMotionLMA.RSLT_A];
double RMSE = lma_rslts[CuasMotionLMA.RSLT_RMS];
double RMSE_A = lma_rslts[CuasMotionLMA.RSLT_RMS_A];
double R1 = lma_rslts[CuasMotionLMA.RSLT_R1];
double MAX2A = lma_rslts[CuasMotionLMA.RSLT_MAX2A];
if (A < lma_mina) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_A_LOW;
continue; // too weak
}
if (MAX2A < lma_a2a) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_ACENT;
continue; // ratio of maximal value to A is too low
}
if (RMSE > lma_rms) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_RMSE;
continue; // too high RMSE regardless of A
}
if ((RMSE > lma_arms) && (RMSE_A > lma_rrms)) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_RMSE_R;
continue; // too high RMSE
}
if (lma_rslts[CuasMotionLMA.RSLT_R0] > lma_maxr) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_R0_HIGH;
continue; // Radius is too high
}
if (R1 < lma_minr1) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_R1_LOW;
continue; // Inner radius too small
}
if (lma_rslts[CuasMotionLMA.RSLT_K] < lma_mink) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_K_LOW;
continue; // K is too low
}
if (lma_rslts[CuasMotionLMA.RSLT_K] > lma_maxk) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_K_HIGH;
continue; // K is too high
}
double x = lma_rslts[CuasMotionLMA.RSLT_X];
double y = lma_rslts[CuasMotionLMA.RSLT_Y];
if ((x < minxy) || (y < minxy) || (x > maxxy) || (y > maxxy)) {
if (failures_debug != null) failures_debug[nSeq][ntile][CuasMotionLMA.RSLT_FAIL] = CuasMotionLMA.FAIL_FAR;
continue; // center outside of allowed range (on the very edges)
}
// filter_target[nSeq][ntile] = true;
// Now calculate overall quality
double [] quality_factors = new double [IMPORTANCE_LENGTH];
double inv_rms = 1.0 / RMSE;
double inv_rms_lim = 1.0 / lma_arms;
double inv_rel_rms = 1.0 / RMSE_A; // A/RMSE;
double inv_rel_rms_lim = 1.0 / lma_rrms;
quality_factors[IMPORTANCE_A] = (A- lma_mina)/ lma_mina;
quality_factors[IMPORTANCE_RMS] = (inv_rms - inv_rms_lim)/ inv_rms_lim; // only >0 for small max-es
quality_factors[IMPORTANCE_RMS_A] = (inv_rel_rms - inv_rel_rms_lim)/ inv_rel_rms_lim; // only >0 for small max-es
double sw = 0;
for (int i = 0; i < importance.length; i++) {
sw += importance[i];
}
for (int i = 0; i < importance.length; i++) {
quality_factors[i] = Math.min(quality_factors[i], importance_limit);
}
// importance_limit
double quality = 0;
for (int i = 0; i < importance.length; i++) {
double factor_contrib = Math.pow(quality_factors[i], importance_power);
quality += (importance[i]/sw) * factor_contrib;
}
quality = Math.pow(quality, 1.0/importance_power);
effective_strength[nSeq][ntile] = quality;
num++;
}
}
if (remain != null) {
remain[nSeq] = num;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return effective_strength;
}
public static double [][] getEffectiveStrengthMV( // calculate tiles effective strength by the motion vectors. Combine with the target LMA?
final double [][][] motion_scan,
final int tilesX,
final int range, // 1 or 2
double speed_min,
double speed_pref,
double speed_boost ){
final int num_seq = motion_scan.length;
final int num_tiles = motion_scan[0].length;
final double [][] effective_strength = new double [num_seq][num_tiles];
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0);
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()) {
double [][] ms = motion_scan[nSeq];
for (int ntile = 0; ntile < num_tiles; ntile++) {
if (ms[ntile] != null) {
effective_strength[nSeq][ntile] = getEffectiveStrength(
ms[ntile], // double [] mv_tile, // 4
speed_min, // double speed_min,
speed_pref, // double speed_pref,
speed_boost); //double speed_boost)
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return effective_strength;
}
public static boolean [][] filterMotionScanTarget( // should work for motion vectors and target coordinates
double [][] confidence,
double min_confidence,
final int tilesX,
final int range, // 1 or 2
final int [] remain,
final int [] passes, // debugging - numer of passes required
final int debugLevel){
final int num_seq = confidence.length;
final int num_tiles = confidence[0].length;
final int tilesY = num_tiles/ tilesX;
final boolean [][] filter5 = new boolean [num_seq][num_tiles];
final Thread[] threads = ImageDtt.newThreadArray();
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);
boolean [] prohibit = new boolean [num_tiles];
for (int nSeq = ai.getAndIncrement(); nSeq < num_seq; nSeq = ai.getAndIncrement()) {
int num_total = 0;
Arrays.fill(prohibit, false);
double [] conf = confidence[nSeq];
int num_this_pass = 0;
int npass = 0;
do {
npass++;
num_this_pass = 0;
for (int tileY = 0; tileY < tilesY; tileY++) {
for (int tileX = 0; tileX < tilesX; tileX++) {
int ntile = tileX + tilesX * tileY;
if ((conf[ntile] > 0.0) && !prohibit[ntile]) {
boolean ismax = true;
check_max:{
double cval = conf[ntile]- min_confidence;
if (cval <= 0) {
ismax = false;
prohibit[ntile] = true; // not needed
break check_max;
}
for (int dy = -range; dy <= range; dy++) {
for (int dx = -range; dx <= range; dx++) {
int indx = tn.getNeibIndex(ntile, dx, dy);
if ((indx >= 0) && !prohibit[indx]) {
double val = conf[indx]- min_confidence;
if (val > cval) {
ismax = false;
break check_max;
}
}
}
}
}
if (ismax) {
filter5[nSeq][ntile] = true; // ismax;
// prohibit all around, including this one
for (int dy = -range; dy <= range; dy++) {
for (int dx = -range; dx <= range; dx++) {
int indx = tn.getNeibIndex(ntile, dx, dy);
if (indx >= 0) { // && ((filtered == null) || !filtered[nSeq][indx])){
prohibit[indx] = true;
}
}
}
num_this_pass++;
}
}
}
}
num_total+=num_this_pass;
} while (num_this_pass > 0);
if (remain != null) {
remain[nSeq] = num_total;
}
if (passes != null) {
passes[nSeq] = npass;
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return filter5;
}
public static boolean [][] filterMotionScan( public static boolean [][] filterMotionScan(
final double [][][] motion_scan, final double [][][] motion_scan,
final int tilesX, final int tilesX,
final int range, // 1 or 2 final int range, // 1 or 2
final boolean [][] filtered, // same format as output, previously selected // final boolean [][] filtered, // same format as output, previously selected
final int [] remain, final int [] remain,
double speed_min, double speed_min,
double speed_pref, double speed_pref,
double speed_boost ){ double speed_boost ){
final boolean [][] filtered = null;
final int num_seq = motion_scan.length; final int num_seq = motion_scan.length;
final int num_tiles = motion_scan[0].length; final int num_tiles = motion_scan[0].length;
final int tilesY = num_tiles/ tilesX; final int tilesY = num_tiles/ tilesX;
...@@ -1557,7 +1911,7 @@ public class CuasMotion { ...@@ -1557,7 +1911,7 @@ public class CuasMotion {
for (int tileY = 0; tileY < tilesY; tileY++) { for (int tileY = 0; tileY < tilesY; tileY++) {
for (int tileX = 0; tileX < tilesX; tileX++) { for (int tileX = 0; tileX < tilesX; tileX++) {
int ntile = tileX + tilesX * tileY; int ntile = tileX + tilesX * tileY;
if ((ms[ntile] != null) && ((filtered == null) || !filtered[nSeq][ntile])) { if ((ms[ntile] != null)) { // && ((filtered == null) || !filtered[nSeq][ntile])) {
boolean ismax = true; boolean ismax = true;
check_max:{ check_max:{
// double cval = ms[ntile][INDX_STRENGTH]*ms[ntile][INDX_FRAC]; // quality // double cval = ms[ntile][INDX_STRENGTH]*ms[ntile][INDX_FRAC]; // quality
...@@ -1573,8 +1927,9 @@ public class CuasMotion { ...@@ -1573,8 +1927,9 @@ public class CuasMotion {
for (int dy = -range; dy <= range; dy++) { for (int dy = -range; dy <= range; dy++) {
for (int dx = -range; dx <= range; dx++) { for (int dx = -range; dx <= range; dx++) {
int indx = tn.getNeibIndex(ntile, dx, dy); int indx = tn.getNeibIndex(ntile, dx, dy);
if ((indx >= 0) && (ms[indx] != null) && ((filtered == null) || !filtered[nSeq][indx])){ if ((filtered == null) || !filtered[nSeq][indx]) { // if ((indx >= 0) && (ms[indx] != null) && ((filtered == null) || !filtered[nSeq][indx])){ if ((filtered == null) || !filtered[nSeq][indx]) {
// double val = ms[indx][INDX_STRENGTH]*ms[indx][INDX_FRAC]; // quality if ((indx >= 0) && (ms[indx] != null)) { // && ((filtered == null) || !filtered[nSeq][indx])){
// if ((filtered == null) || !filtered[nSeq][indx]) {
// FIXME: calculate once all values before this cycle // FIXME: calculate once all values before this cycle
double val = getEffectiveStrength( double val = getEffectiveStrength(
ms[indx], // double [] mv_tile, // 4 ms[indx], // double [] mv_tile, // 4
...@@ -1585,7 +1940,7 @@ public class CuasMotion { ...@@ -1585,7 +1940,7 @@ public class CuasMotion {
ismax = false; ismax = false;
break check_max; break check_max;
} }
} // }
} }
} }
} }
...@@ -3379,8 +3734,19 @@ public class CuasMotion { ...@@ -3379,8 +3734,19 @@ public class CuasMotion {
double lma_rrms = clt_parameters.imp.cuas_lma_rrms; // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) double lma_rrms = clt_parameters.imp.cuas_lma_rrms; // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
double lma_mina = clt_parameters.imp.cuas_lma_mina; // = 1.0; // Minimal A (amplitude) double lma_mina = clt_parameters.imp.cuas_lma_mina; // = 1.0; // Minimal A (amplitude)
double lma_maxr = clt_parameters.imp.cuas_lma_maxr; // = 5.0; // Maximal radius (>3.8) double lma_maxr = clt_parameters.imp.cuas_lma_maxr; // = 5.0; // Maximal radius (>3.8)
double lma_minr1 = clt_parameters.imp.cuas_lma_minr1; // = 1.0; // Maximal inner radius
double lma_mink = clt_parameters.imp.cuas_lma_mink; // = 0.0; // Minimal K (overshoot) <0.007 double lma_mink = clt_parameters.imp.cuas_lma_mink; // = 0.0; // Minimal K (overshoot) <0.007
double lma_maxk = clt_parameters.imp.cuas_lma_maxk; // = 5.0; // Minimal K (overshoot) > 3.8 double lma_maxk = clt_parameters.imp.cuas_lma_maxk; // = 5.0; // Minimal K (overshoot) > 3.8
double lma_a2a = clt_parameters.imp.cuas_lma_a2a; // = 0.7; // Minimal ratio of the maximal pixel to the amplitude
// Handling overall target scores
double min_score_mv = clt_parameters.imp.cuas_score_mv;
double min_score_lma = clt_parameters.imp.cuas_score_lma;
double factor_lim = clt_parameters.imp.cuas_factor_lim;
double factor_pow = clt_parameters.imp.cuas_factor_pow;
double [] score_coeff = clt_parameters.imp.cuas_score_coeff;
// boolean remove_isolated= clt_parameters.imp.cuas_isolated; // boolean remove_isolated= clt_parameters.imp.cuas_isolated;
double input_range = clt_parameters.imp.cuas_input_range; // 5; double input_range = clt_parameters.imp.cuas_input_range; // 5;
int iter_show = clt_parameters.imp.cuas_iter_show; //1; // Maximal enhancement iteration to show intermediate result (0 - none) int iter_show = clt_parameters.imp.cuas_iter_show; //1; // Maximal enhancement iteration to show intermediate result (0 - none)
...@@ -3405,6 +3771,8 @@ public class CuasMotion { ...@@ -3405,6 +3771,8 @@ public class CuasMotion {
final int frame0 = start_frame + seq_length/2; final int frame0 = start_frame + seq_length/2;
final int half_accum_range = corr_pairs/2; final int half_accum_range = corr_pairs/2;
int [] remain = new int [num_corr_samples]; int [] remain = new int [num_corr_samples];
int [] passes = new int [num_corr_samples]; // debugging filter5
boolean debug_tum= true; // false; boolean debug_tum= true; // false;
String model_prefix = parentCLT.getImageName()+getParametersSuffix(clt_parameters,null); String model_prefix = parentCLT.getImageName()+getParametersSuffix(clt_parameters,null);
float [][] fpixels_tum = fpixels; float [][] fpixels_tum = fpixels;
...@@ -3637,16 +4005,49 @@ public class CuasMotion { ...@@ -3637,16 +4005,49 @@ public class CuasMotion {
if (debugLevel > -4) printRemain(remain, "motion_scan wo bad", true); if (debugLevel > -4) printRemain(remain, "motion_scan wo bad", true);
// filter remaining (no known bad ones) // filter remaining (no known bad ones)
boolean[][] filter5 = filterMotionScan(
double [][] effective_strength = getEffectiveStrengthMV( // calculate tiles effective strength by the motion vectors. Combine with the target LMA?
motion_scan, // final double [][][] motion_scan, motion_scan, // final double [][][] motion_scan,
cuasMotion.tilesX, // final int tilesX) cuasMotion.tilesX, // final int tilesX)
max_range, // final int range, // 1 or 2 max_range, // final int range, // 1 or 2
null, // final boolean [][] filtered, // same format as output, previously selected speed_min, // double speed_min,
speed_pref, // double speed_pref,
speed_boost); // double speed_boost);
if (save_filtered_low) {
ImagePlus imp_effective_strength = ShowDoubleFloatArrays.makeArrays(
effective_strength, // double[][] pixels,
cuasMotion.tilesX,
cuasMotion.tilesY,
model_prefix+"-EFFECTIVE_STRENGTH-n"+niter, // String title,
slice_titles);
if (!batch_mode) {
imp_effective_strength.show();
}
parentCLT.saveImagePlusInModelDirectory(imp_effective_strength); // ImagePlus imp)
}
boolean[][] filter5 = filterMotionScanTarget(
effective_strength, // double [][] confidence,
min_score_mv, // double min_confidence,
cuasMotion.tilesX, // final int tilesX,
max_range, // final int range, // 1 or 2
remain, // final int [] remain){
passes, // final int [] passes, // debugging - numer of passes required
debugLevel); // final int debugLevel)
/*
boolean[][] filter50 = filterMotionScan(
motion_scan, // final double [][][] motion_scan,
cuasMotion.tilesX, // final int tilesX)
max_range, // final int range, // 1 or 2
// null, // final boolean [][] filtered, // same format as output, previously selected
remain, // final int [] remain){ remain, // final int [] remain){
speed_min, // double speed_min, speed_min, // double speed_min,
speed_pref, // double speed_pref, speed_pref, // double speed_pref,
speed_boost); // double speed_boost); speed_boost); // double speed_boost);
*/
if (debugLevel > -4) printRemain(remain, "filter5", true); if (debugLevel > -4) printRemain(remain, "filter5", true);
if (debugLevel > -4) printRemain(passes, "filter5 passes", true);
if (save_filtered_low) { if (save_filtered_low) {
ImagePlus imp_filter5 = ShowDoubleFloatArrays.makeArrays( ImagePlus imp_filter5 = ShowDoubleFloatArrays.makeArrays(
filter5, // double[][] pixels, filter5, // double[][] pixels,
...@@ -3661,9 +4062,6 @@ public class CuasMotion { ...@@ -3661,9 +4062,6 @@ public class CuasMotion {
} }
double [][][] motion_scan_filtered = applyFilter( // motion vectors double [][][] motion_scan_filtered = applyFilter( // motion vectors
motion_scan, // double [][][] motion_scan, motion_scan, // double [][][] motion_scan,
filter5); // boolean [][] filter5) filter5); // boolean [][] filter5)
...@@ -3861,12 +4259,12 @@ public class CuasMotion { ...@@ -3861,12 +4259,12 @@ public class CuasMotion {
cuasMotion.tilesX); // int tilesX) { cuasMotion.tilesX); // int tilesX) {
parentCLT.saveImagePlusInModelDirectory(imp_lma); // ImagePlus imp) parentCLT.saveImagePlusInModelDirectory(imp_lma); // ImagePlus imp)
} }
double [][][] coord_centroids_filtered = filterAndShowTargets( // generates motion vectors? double [][][] coord_centroids_filtered = filterAndShowTargets( // generates motion vectors? Not used?
coord_centroid, // double [][][] coord_data, coord_centroid, // double [][][] coord_data,
target_strength, // double target_strength, target_strength, // double target_strength,
target_frac, // double [][] target_frac, target_frac, // double [][] target_frac,
slice_titles, // String [] slice_titles, // slice_titles, // String [] slice_titles, //
model_prefix+"-CENTROIDS-FILTERED-n"+niter, // String title_targets_filt, model_prefix+"-CENTROIDS-FILTERED-n"+niter, // String title_targets_filt, OK
remain, // int [] targets_remain, remain, // int [] targets_remain,
cuasMotion.tilesX, // int tilesX) cuasMotion.tilesX, // int tilesX)
save_filtered_low && !batch_mode, // boolean show) save_filtered_low && !batch_mode, // boolean show)
...@@ -3880,23 +4278,38 @@ public class CuasMotion { ...@@ -3880,23 +4278,38 @@ public class CuasMotion {
break; break;
// } // }
} }
double [][][] failures_debug = (intermed_low) ? (new double [targets_good.length][][]) : null;
double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA( double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA(
coord_lma, // double [][][] coord_data, coord_lma, // double [][][] coord_data,
lma_rms, // double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A) factor_lim, // final double importance_limit,
lma_arms, // double lma_arms, // = 0.03; // Maximal absolutre RMS factor_pow, // final double importance_power, // Raise each factor to this power before combining
lma_rrms, // double lma_rrms, // = 0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) score_coeff, // final double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
lma_mina, // double lma_mina, // = 1.0; // Minimal A (amplitude) lma_rms, // double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
lma_maxr, // double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0 lma_arms, // double lma_arms, // = 0.03; // Maximal absolutre RMS
lma_mink, // double lma_mink, // = 1.0; // Minimal K (overshoot) = 1.0 lma_rrms, // double lma_rrms, // = 0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
lma_maxk, // double lma_maxk, // = 1.0; // Minimal K (overshoot) = 3.0 lma_mina, // double lma_mina, // = 1.0; // Minimal A (amplitude)
lma_maxr, // double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
lma_minr1, // double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
lma_mink, // double lma_mink, // = 1.0; // Minimal K (overshoot) = 1.0
lma_maxk, // double lma_maxk, // = 1.0; // Minimal K (overshoot) = 3.0
lma_a2a, // double lma_a2a,
slice_titles, // String [] slice_titles, // slice_titles, // String [] slice_titles, //
model_prefix+"-TARGETS-FILTERED-LMA-n"+niter, // String title_targets_filt, model_prefix+"-TARGETS-FILTERED-LMA-n"+niter, // String title_targets_filt, // empty
remain, // int [] targets_remain, failures_debug, // double [][][] failures_debug,
remain, // int [] targets_remain,
cuasMotion.tilesX, // int tilesX) cuasMotion.tilesX, // int tilesX)
save_filtered_low && !batch_mode, // boolean show) save_filtered_low && !batch_mode, // boolean show)
(save_filtered_low? parentCLT : null)); // do not save //QuadCLT parentCLT) (save_filtered_low? parentCLT : null)); // do not save //QuadCLT parentCLT)
if (debugLevel > -4) remained_total = printRemain(remain, "coord_data_filtered_lma: Total new targets", true); if (debugLevel > -4) remained_total = printRemain(remain, "coord_data_filtered_lma: Total new targets", true);
if (failures_debug != null) { // last slice show reason of failure
ImagePlus imp_failures = showVectorFieldsSequenceLMA(
failures_debug, // double [][][] vector_fields_sequence,
slice_titles, // String [] titles, // all slices*frames titles or just slice titles or null
model_prefix+"-FAILURES-n"+niter,// String title,
!batch_mode, // boolean show,
cuasMotion.tilesX); // int tilesX) {
parentCLT.saveImagePlusInModelDirectory(imp_failures);
}
// add good targets to targets_good // add good targets to targets_good
targets_good = combineMotionScans( // lma-vectors targets_good = combineMotionScans( // lma-vectors
...@@ -3945,42 +4358,101 @@ public class CuasMotion { ...@@ -3945,42 +4358,101 @@ public class CuasMotion {
} }
// TODO See if they are needed here at all
/*
fpixels_accumulated_filtered = getTargetImages(
coord_centroids_filtered, // final double [][][] vector_fields, // centers , just null/not null
fpixels_accumulated, // final float [][] accum_data, // should be around 0, no low-freq
cuasMotion.tilesX); // final int tilesX)
if (save_filtered_high) {
ImagePlus imp_acc_filt = ShowDoubleFloatArrays.makeArrays(
fpixels_accumulated_filtered, // double[][] pixels,
cuasMotion.gpu_max_width,
cuasMotion.gpu_max_height,
model_prefix+"-ACCUMULATED-FILTERED-n"+niter, // String title,
slice_titles);
imp_acc_filt.getProcessor().setMinAndMax(-input_range/2, input_range/2);
if (!batch_mode) {
imp_acc_filt.show();
}
parentCLT.saveImagePlusInModelDirectory(imp_acc_filt); // ImagePlus imp)
}
*/
if (debugLevel > -4) { if (debugLevel > -4) {
System.out.println("Iteration "+niter+" DONE."); System.out.println("Iteration "+niter+" DONE.");
} }
// if (no_improve) {
// if (debugLevel > -4) {
// System.out.println("There was no improvement, exiting the loop, iteration "+niter+" .");
// }
// }
} //for (niter=0; niter < max_iter; niter++) } //for (niter=0; niter < max_iter; niter++)
// there could be conflicting tiles in targets_good. Calculate scores and then filter to keep the best ones that do not conflict
double lma_minxy = 0.8;
double [][][] failures_debug = (intermed_low) ? (new double [targets_good.length][][]) : null;
double [][] target_scores = getEffectiveStrengthLMA(
targets_good, // final double [][][] target_coords, // LMA
factor_lim, // final double importance_limit,
factor_pow, // final double importance_power, // Raise each factor to this power before combining
score_coeff, // final double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
lma_rms, // final double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
lma_arms, // final double lma_arms, // = 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484)
lma_rrms, // final double lma_rrms, // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
lma_mina, // final double lma_mina, // = 1.0; // Minimal A (amplitude)
lma_maxr, // final double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
lma_minr1, // final double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
lma_mink, // final double lma_mink, // = 0.0; // Minimal K (overshoot) = 1.0
lma_maxk, // final double lma_maxk, // = 5.0; // Minimal K (overshoot) = 3.0
lma_a2a, // final double lma_a2a,
lma_minxy, // final double lma_minxy, // 0.8
cuasMotion.tilesX, // final int tilesX,
failures_debug, // final double [][][] failures_debug,
remain); // final int [] remain)
if (debugLevel > -4) printRemain(remain, "remaining good targets", true);
if (intermed_low) {
ImagePlus imp_target_scores = ShowDoubleFloatArrays.makeArrays(
target_scores, // double[][] pixels,
cuasMotion.tilesX,
cuasMotion.tilesY,
model_prefix+"-TARGET_SCORES", // String title,
slice_titles);
if (!batch_mode) {
imp_target_scores.show();
}
parentCLT.saveImagePlusInModelDirectory(imp_target_scores); // ImagePlus imp)
}
if (failures_debug != null) { // last slice show reason of failure
ImagePlus imp_failures = showVectorFieldsSequenceLMA(
failures_debug, // double [][][] vector_fields_sequence,
slice_titles, // String [] titles, // all slices*frames titles or just slice titles or null
model_prefix+"-FAILURES",// String title,
!batch_mode, // boolean show,
cuasMotion.tilesX); // int tilesX) {
parentCLT.saveImagePlusInModelDirectory(imp_failures);
}
boolean[][] filter5 = filterMotionScanTarget(
target_scores, // double [][] confidence,
min_score_lma, // min_mv_strength, // double min_confidence,
cuasMotion.tilesX, // final int tilesX,
max_range, // final int range, // 1 or 2
remain, // final int [] remain){
passes, // final int [] passes, // debugging - numer of passes required
debugLevel); // final int debugLevel)
if (debugLevel > -4) printRemain(remain, "filter5 lma", true);
if (debugLevel > -4) printRemain(passes, "filter5 passes", true);
if (intermed_low) {
ImagePlus imp_filter5_lma = ShowDoubleFloatArrays.makeArrays(
filter5, // double[][] pixels,
cuasMotion.tilesX,
cuasMotion.tilesY,
model_prefix+"-FILTER5_LMA", // String title,
slice_titles);
if (!batch_mode) {
imp_filter5_lma.show();
}
parentCLT.saveImagePlusInModelDirectory(imp_filter5_lma);
}
if (intermed_low) { // save final
ImagePlus imp_good = showVectorFieldsSequenceLMA(
targets_good, // double [][][] vector_fields_sequence,
slice_titles, // String [] titles, // all slices*frames titles or just slice titles or null
model_prefix+"-TARGETS-GOOD-ALL",// String title,
!batch_mode, // boolean show,
cuasMotion.tilesX); // int tilesX) {
parentCLT.saveImagePlusInModelDirectory(imp_good); // ImagePlus imp)
}
// apply filter5 to targets_good
targets_good = applyFilter( // motion vectors
targets_good, // double [][][] motion_scan,
filter5); // boolean [][] filter5)
double [][][] motion_good = filterMotionScans( double [][][] motion_good = filterMotionScans(
motion_scan_original, // double [][][] scan1 // or just use motion_scan - it has only bad removed motion_scan_original, // double [][][] scan1 // or just use motion_scan - it has only bad removed
targets_good, // double [][][] scan1){ // keep scan0 that is in scan1 targets_good, // double [][][] scan1){ // keep scan0 that is in scan1
remain); remain);
if (debugLevel > -4) printRemain(remain, "All done: motion_good", true); if (debugLevel > -4) printRemain(remain, "motion_good final", true);
if (intermed_low) { // save final if (intermed_low) { // save final
ImagePlus imp_good = showVectorFieldsSequenceLMA( ImagePlus imp_good = showVectorFieldsSequenceLMA(
...@@ -3991,7 +4463,7 @@ public class CuasMotion { ...@@ -3991,7 +4463,7 @@ public class CuasMotion {
cuasMotion.tilesX); // int tilesX) { cuasMotion.tilesX); // int tilesX) {
parentCLT.saveImagePlusInModelDirectory(imp_good); // ImagePlus imp) parentCLT.saveImagePlusInModelDirectory(imp_good); // ImagePlus imp)
ImagePlus imp_mv_good = showVectorFieldsSequence( ImagePlus imp_mv_good = showVectorFieldsSequence(
targets_good, // double [][][] vector_fields_sequence, motion_good, // double [][][] vector_fields_sequence,
speed_min, // double speed_min, speed_min, // double speed_min,
speed_pref, // double speed_pref, speed_pref, // double speed_pref,
speed_boost, // double speed_boost, speed_boost, // double speed_boost,
...@@ -4068,11 +4540,22 @@ public class CuasMotion { ...@@ -4068,11 +4540,22 @@ public class CuasMotion {
double lma_rrms = clt_parameters.imp.cuas_lma_rrms; // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) double lma_rrms = clt_parameters.imp.cuas_lma_rrms; // = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
double lma_mina = clt_parameters.imp.cuas_lma_mina; // = 1.0; // Minimal A (amplitude) double lma_mina = clt_parameters.imp.cuas_lma_mina; // = 1.0; // Minimal A (amplitude)
double lma_maxr = clt_parameters.imp.cuas_lma_maxr; // = 5.0; // Maximal radius (>3.8) double lma_maxr = clt_parameters.imp.cuas_lma_maxr; // = 5.0; // Maximal radius (>3.8)
double lma_minr1 = clt_parameters.imp.cuas_lma_minr1; // = 1.0; // Maximal inner radius
double lma_mink = clt_parameters.imp.cuas_lma_mink; // = 0.0; // Minimal K (overshoot) <0.007 double lma_mink = clt_parameters.imp.cuas_lma_mink; // = 0.0; // Minimal K (overshoot) <0.007
double lma_maxk = clt_parameters.imp.cuas_lma_maxk; // = 5.0; // Minimal K (overshoot) > 3.8 double lma_maxk = clt_parameters.imp.cuas_lma_maxk; // = 5.0; // Minimal K (overshoot) > 3.8
double lma_a2a = clt_parameters.imp.cuas_lma_a2a; // = 0.7; // Minimal ratio of the maximal pixel to the amplitude
double factor_lim = clt_parameters.imp.cuas_factor_lim;
double factor_pow = clt_parameters.imp.cuas_factor_pow;
double [] score_coeff = clt_parameters.imp.cuas_score_coeff;
boolean remove_isolated= clt_parameters.imp.cuas_isolated; boolean remove_isolated= clt_parameters.imp.cuas_isolated;
double max_mismatch = clt_parameters.imp.cuas_max_mismatch; // 2; double max_mismatch = clt_parameters.imp.cuas_max_mismatch; // 2;
boolean ignore_mismatch= clt_parameters.imp.cuas_ignore_mismatch; boolean ignore_mismatch= clt_parameters.imp.cuas_ignore_mismatch;
boolean target_by_horizon = clt_parameters.imp.cuas_by_horizon; // true;
double target_horizon= clt_parameters.imp.cuas_horizon; // a90
int target_type = clt_parameters.imp.cuas_target_type; //0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe int target_type = clt_parameters.imp.cuas_target_type; //0; // 0 - unknown, 1 - known, 2 - friend, 3 - foe
double input_range = clt_parameters.imp.cuas_input_range; // 5; double input_range = clt_parameters.imp.cuas_input_range; // 5;
...@@ -4213,15 +4696,21 @@ public class CuasMotion { ...@@ -4213,15 +4696,21 @@ public class CuasMotion {
double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA( double [][][] coord_data_filtered_lma = filterAndShowTargetsLMA(
coord_lma,// double [][][] coord_data, coord_lma,// double [][][] coord_data,
lma_rms, // double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A) factor_lim, // final double importance_limit,
lma_arms, // double lma_arms, // = 0.03; // Maximal absolutre RMS factor_pow, // final double importance_power, // Raise each factor to this power before combining
lma_rrms, // double lma_rrms, // = 0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) score_coeff, // final double [] importance, // for now (each - squared?): [0] - Amplitude (A/A0), 1 - RMS (RMS0/RMS), 2 - RRMS((RMS/A0) / (RMS/A)
lma_mina, // double lma_mina, // = 1.0; // Minimal A (amplitude) lma_rms, // double lma_rms, // = 1.5; // Maximal RMS (should always match, regardless if A)
lma_maxr, // double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0 lma_arms, // double lma_arms, // = 0.03; // Maximal absolutre RMS
lma_mink, // double lma_mink, // = 1.0; // Minimal K (overshoot) = 1.0 lma_rrms, // double lma_rrms, // = 0.03; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
lma_maxk, // double lma_maxk, // = 1.0; // Minimal K (overshoot) = 3.0 lma_mina, // double lma_mina, // = 1.0; // Minimal A (amplitude)
lma_maxr, // double lma_maxr, // = 5.0; // Minimal K (overshoot) = 3.0
lma_minr1, // double lma_minr1,// = 1.0; // Minimal R1 (radius of positive peak)
lma_mink, // double lma_mink, // = 1.0; // Minimal K (overshoot) = 1.0
lma_maxk, // double lma_maxk, // = 1.0; // Minimal K (overshoot) = 3.0
lma_a2a, // double lma_a2a,
slice_titles, // String [] slice_titles, // slice_titles, // String [] slice_titles, //
model_prefix+"-LMA-FILTERED", // String title_targets_filt, model_prefix+"-LMA-FILTERED", // String title_targets_filt,
null, // double [][][] failures_debug,
remain, // int [] targets_remain, remain, // int [] targets_remain,
cuasMotion.tilesX, // int tilesX) cuasMotion.tilesX, // int tilesX)
intermed_low && !batch_mode, // show_vector_field); // boolean show) intermed_low && !batch_mode, // show_vector_field); // boolean show)
...@@ -4266,6 +4755,22 @@ public class CuasMotion { ...@@ -4266,6 +4755,22 @@ public class CuasMotion {
parentCLT.saveImagePlusInModelDirectory(imp_filtered_combo); // ImagePlus imp) parentCLT.saveImagePlusInModelDirectory(imp_filtered_combo); // ImagePlus imp)
} }
double [][][] mismatch_ba = null; double [][][] mismatch_ba = null;
if (target_by_horizon) {
if (target_by_horizon) {
targets_lma_combo = filterByHorizon(
targets_lma_combo, // final double [][][] target_positions,
target_horizon, // final double horizon,
remain, // final int [] remain,
cuasMotion.tilesX); // int tilesX) {
}
if (debugLevel > -4) printRemain(remain, "Remained after target_by_horizon", true);
targets_vf_combo = filterMotionScans( // duplicate removal to motion vectors
targets_vf_combo, // double [][][] scan0,
targets_lma_combo, // double [][][] scan1)
remain);
}
if (remove_isolated) { if (remove_isolated) {
double interseq_scale = 0.5* corr_inc/corr_offset; // multiply target velocity to get offset in the middle between the key frames double interseq_scale = 0.5* corr_inc/corr_offset; // multiply target velocity to get offset in the middle between the key frames
double [][][][] ba_xy = getHalfBeforeAfterPixXY( double [][][][] ba_xy = getHalfBeforeAfterPixXY(
...@@ -4549,6 +5054,52 @@ public class CuasMotion { ...@@ -4549,6 +5054,52 @@ public class CuasMotion {
return filtered_tiles; return filtered_tiles;
} }
public static double [][][] filterByHorizon(
final double [][][] target_positions,
final double horizon,
final int [] remain,
final int tilesX) {
final int num_seq = target_positions.length;
final int num_tiles = target_positions[0].length;
final double [][][] filtered_tiles = new double [num_seq][num_tiles][];
final int tileSize = GPUTileProcessor.DTT_SIZE;
final Thread[] threads = ImageDtt.newThreadArray();
final AtomicInteger ai = new AtomicInteger(0);
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()) {
if (remain != null) {
remain[nSeq] = 0;
}
for (int ntile = 0; ntile < num_tiles; ntile++) {
double [] target_pos = target_positions[nSeq][ntile];
if (target_pos != null) { // should be always
// int tileX = ntile % tilesX;
int tileY = ntile / tilesX;
// double xc = tileSize * tileX + tileSize/2;
double yc = tileSize * tileY + tileSize/2;
// double xtk = xc + target_pos[CuasMotionLMA.RSLT_X];
double ytk = yc + target_pos[CuasMotionLMA.RSLT_Y];
if (ytk <= horizon) {
filtered_tiles[nSeq][ntile] = target_pos;
if (remain != null) {
remain[nSeq]++;
}
}
}
}
}
}
};
}
ImageDtt.startAndJoin(threads);
return filtered_tiles;
}
public static String getParametersSuffix( public static String getParametersSuffix(
CLTParameters clt_parameters, CLTParameters clt_parameters,
......
src/main/java/com/elphel/imagej/cuas/CuasMotionLMA.java
View file @ b56ba447
...@@ -39,14 +39,27 @@ public class CuasMotionLMA { ...@@ -39,14 +39,27 @@ public class CuasMotionLMA {
public static final int RSLT_Y = 1; public static final int RSLT_Y = 1;
public static final int RSLT_A = 2; public static final int RSLT_A = 2;
public static final int RSLT_R0 = 3; public static final int RSLT_R0 = 3;
public static final int RSLT_K = 4; public static final int RSLT_R1 = 4;
public static final int RSLT_C = 5; public static final int RSLT_K = 5;
public static final int RSLT_RMS = 6; public static final int RSLT_C = 6;
public static final int RSLT_ITERS = 7; public static final int RSLT_RMS = 7;
public static final int RSLT_LEN = RSLT_ITERS+1; public static final int RSLT_RMS_A = 8;
public static final int RSLT_MAX2A = 9;
public static final String [] LMA_TITLES = {"X-OFFS","Y-OFFS", "AMPLITUDE","RADIUS","OVERSHOOT","OFFSET","RMSE","ITERATIONS"}; public static final int RSLT_ITERS =10;
public static final int RSLT_FAIL = 11;
public static final int RSLT_LEN = RSLT_FAIL+1;
public static final String [] LMA_TITLES = {"X-OFFS","Y-OFFS", "AMPLITUDE","RADIUS","RAD_POS", "OVERSHOOT","OFFSET","RMSE","RMSE/A","MAX2A","ITERATIONS","FAILURE"};
public static final int FAIL_NONE = 0;
public static final int FAIL_A_LOW = 1; // amplitude is too low
public static final int FAIL_ACENT = 2; // ratio of maximal pixel to amplitude is too low
public static final int FAIL_RMSE = 3; // RMSE is too high
public static final int FAIL_RMSE_R = 4; // BOTH RMSE is not sufficient and RMSE/A is too high
public static final int FAIL_R0_HIGH = 5; // Full radius (including negative overshoot) is too high
public static final int FAIL_R1_LOW = 6; // Inner (positive) peak radius is too low
public static final int FAIL_K_LOW = 7; // Overshoot is too low (not used, it can be down to 0)
public static final int FAIL_K_HIGH = 8; // Overshoot is too high
public static final int FAIL_FAR = 9; // Peak is too far from the center
private int width; private int width;
private double [][] window; private double [][] window;
...@@ -62,6 +75,7 @@ public class CuasMotionLMA { ...@@ -62,6 +75,7 @@ public class CuasMotionLMA {
private double [] last_ymfx = null; private double [] last_ymfx = null;
private double [][] last_jt = null; private double [][] last_jt = null;
private int iters = -2; // never ran private int iters = -2; // never ran
private double max_val = 0;
public CuasMotionLMA( public CuasMotionLMA(
int width, int width,
...@@ -110,10 +124,13 @@ public class CuasMotionLMA { ...@@ -110,10 +124,13 @@ public class CuasMotionLMA {
double yc, // relative to center =width/2 double yc, // relative to center =width/2
double r0, double r0,
double k, double k,
double lmax_val, // maximal pixel value near the centroid maximum to be used for comparison with A
int debugLevel) { int debugLevel) {
max_val = lmax_val;
y_vector = tile_data; y_vector = tile_data;
double x0 = Math.min(Math.max(xc + width/2, 0), width-1); double x0 = Math.min(Math.max(xc + width/2, 0), width-1);
double y0 = Math.min(Math.max(yc + width/2, 0), width-1); double y0 = Math.min(Math.max(yc + width/2, 0), width-1);
int ix0 = (int) Math.round(x0); int ix0 = (int) Math.round(x0);
int iy0 = (int) Math.round(y0); int iy0 = (int) Math.round(y0);
...@@ -182,9 +199,12 @@ public class CuasMotionLMA { ...@@ -182,9 +199,12 @@ public class CuasMotionLMA {
rslt[RSLT_Y] = getCenter()[1]; rslt[RSLT_Y] = getCenter()[1];
rslt[RSLT_A] = getA(); rslt[RSLT_A] = getA();
rslt[RSLT_R0] = getR0(); rslt[RSLT_R0] = getR0();
rslt[RSLT_R1] = getR0() / ((getK()>1) ? getK() : 1.0);
rslt[RSLT_K] = getK(); rslt[RSLT_K] = getK();
rslt[RSLT_C] = getC(); rslt[RSLT_C] = getC();
rslt[RSLT_RMS] = getRMS(); rslt[RSLT_RMS] = getRMS();
rslt[RSLT_RMS_A] = getRMS()/getA();
rslt[RSLT_MAX2A] = max_val/getA(); // ratio of maximal value to LMA amplitude
rslt[RSLT_ITERS] = getIters(); rslt[RSLT_ITERS] = getIters();
return rslt; return rslt;
} }
......
src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java
View file @ b56ba447
...@@ -30,6 +30,7 @@ import java.util.Properties; ...@@ -30,6 +30,7 @@ import java.util.Properties;
import java.util.StringTokenizer; import java.util.StringTokenizer;
import com.elphel.imagej.common.GenericJTabbedDialog; import com.elphel.imagej.common.GenericJTabbedDialog;
import com.elphel.imagej.cuas.CuasMotion;
import com.elphel.imagej.orthomosaic.ComboMatch; import com.elphel.imagej.orthomosaic.ComboMatch;
import com.elphel.imagej.vegetation.VegetationLMA; import com.elphel.imagej.vegetation.VegetationLMA;
...@@ -659,11 +660,11 @@ min_str_neib_fpn 0.35 ...@@ -659,11 +660,11 @@ min_str_neib_fpn 0.35
public int cuas_discard_border = 8; // Discard this number of pixels from each side when merging public int cuas_discard_border = 8; // Discard this number of pixels from each side when merging
public double cuas_max_fold = 50; public double cuas_max_fold = 50;
public int cuas_min_in_row_col = 4; // Minimal number of defined tiles in a row/column public int cuas_min_in_row_col = 4; // Minimal number of defined tiles in a row/column
public double cuas_clt_variant = 10; // threshold from the nearest to create a variant for the tile public double cuas_clt_variant = 50; // 10; // threshold from the nearest to create a variant for the tile
public double cuas_clt_threshold = 20; // threshold for CLT tile difference not merged when selecting the best public double cuas_clt_threshold = 70; // 20; // threshold for CLT tile difference not merged when selecting the best
public double cuas_clt_decrease = 0.01; // Scale CLT outliers weight public double cuas_clt_decrease = 0.01; // Scale CLT outliers weight
public double cuas_decay_average = 100.0; // Decay in seconds for cimulative CLT public double cuas_decay_average = 30.0; // Decay in seconds for cimulative CLT
public double cuas_keep_fraction = 0.9; // Filter CLT variants for tiles keeping at least this fraction of the total weight public double cuas_keep_fraction = 0.75; // Filter CLT variants for tiles keeping at least this fraction of the total weight
public boolean cuas_step = true; // recalculate template image after each fitting step public boolean cuas_step = true; // recalculate template image after each fitting step
public boolean cuas_subtract_fpn= true; // Subtract FPN public boolean cuas_subtract_fpn= true; // Subtract FPN
...@@ -671,11 +672,11 @@ min_str_neib_fpn 0.35 ...@@ -671,11 +672,11 @@ min_str_neib_fpn 0.35
public double cuas_rot_period = 175.0; // rotation period of te gimbal mount (in scenes) public double cuas_rot_period = 175.0; // rotation period of te gimbal mount (in scenes)
public double cuas_min_series = 180.0; // discard shorter series // FIXME: allow shorter, but modify FPN/row_col to copy parent's files if less than cuas_rot_period public double cuas_min_series = 180.0; // discard shorter series // FIXME: allow shorter, but modify FPN/row_col to copy parent's files if less than cuas_rot_period
public boolean cuas_subtract_rowcol= true; // Subtract row/column noise public boolean cuas_subtract_rowcol= true; // Subtract row/column noise
public boolean cuas_calc_rowcol= true; // Recalculate+save row/column noise, if false - try to read saved one first public boolean cuas_calc_rowcol= false; // Recalculate+save row/column noise, if false - try to read saved one first
public double cuas_um_sigma = 20.0; // Apply Unsharp Mask filter sigma when calculating row/column noise public double cuas_um_sigma = 10.0; // Apply Unsharp Mask filter sigma when calculating row/column noise
public double cuas_max_abs_rowcol = 100.0; // consider pixels with abs(UM difference) does not exceed this value public double cuas_max_abs_rowcol = 50.0; // consider pixels with abs(UM difference) does not exceed this value
public double cuas_outliers_rowcol = 0.001; // scale weight of the outliers with high difference (to prevent undefined values public double cuas_outliers_rowcol = 0.001; // scale weight of the outliers with high difference (to prevent undefined values
public boolean cuas_reset_first= false; // Reset average in first scene (for large diffirence in unfinished row/col) public boolean cuas_reset_first= true; // false; // Reset average in first scene (for large diffirence in unfinished row/col)
public int cuas_invert_margins = 0; // Expand image each side when inverting tasks public int cuas_invert_margins = 0; // Expand image each side when inverting tasks
public int cuas_invert_iters = 4; // Enhance inversion iterations public int cuas_invert_iters = 4; // Enhance inversion iterations
public double cuas_invert_tolerance = 0.001; // Finish enhancing when last change was lower than public double cuas_invert_tolerance = 0.001; // Finish enhancing when last change was lower than
...@@ -700,7 +701,7 @@ min_str_neib_fpn 0.35 ...@@ -700,7 +701,7 @@ min_str_neib_fpn 0.35
public double cuas_multi_strength = 0.45; // maximal strength to use multi-tile DSI public double cuas_multi_strength = 0.45; // maximal strength to use multi-tile DSI
public double cuas_reliable_str = 0.8; // use for relaible tiles if INTER-INTRA-LMA is available, not just DSI_MAIN public double cuas_reliable_str = 0.8; // use for relaible tiles if INTER-INTRA-LMA is available, not just DSI_MAIN
public double cuas_fat_zero = 100.0; // phase correlation fat zero public double cuas_fat_zero = 25.0; // phase correlation fat zero
public double cuas_cent_radius = 3.0; // centroids center radius public double cuas_cent_radius = 3.0; // centroids center radius
public int cuas_n_recenter = 2; // when cosine window, re-center window these many times public int cuas_n_recenter = 2; // when cosine window, re-center window these many times
public double cuas_rstr = 0.01; // minimal phase correlation maximums relative to max str public double cuas_rstr = 0.01; // minimal phase correlation maximums relative to max str
...@@ -724,7 +725,7 @@ min_str_neib_fpn 0.35 ...@@ -724,7 +725,7 @@ min_str_neib_fpn 0.35
public double cuas_speed_boost = 1.0; // speed boost limit public double cuas_speed_boost = 1.0; // speed boost limit
// target filtering after constant velocity accumulation // target filtering after constant velocity accumulation
public double cuas_lmax_fraction = 0.6; // Check if local maximum is separated from tye surrounding by this fraction of the maximum value public double cuas_lmax_fraction = 0.7; // Check if local maximum is separated from the surrounding by this fraction of the maximum value
public double cuas_lmax_radius = 4.5; // look inside ((int)cuas_lmax_radius) * 2 + 1 square for the local maximum isolation public double cuas_lmax_radius = 4.5; // look inside ((int)cuas_lmax_radius) * 2 + 1 square for the local maximum isolation
public boolean cuas_lmax_zero = false; // true; // zero all data outside this radius from the maximum public boolean cuas_lmax_zero = false; // true; // zero all data outside this radius from the maximum
...@@ -734,10 +735,10 @@ min_str_neib_fpn 0.35 ...@@ -734,10 +735,10 @@ min_str_neib_fpn 0.35
public double [][] cuas_target_frac = {{0,0.15},{2.5,0.18},{5,0.3}}; public double [][] cuas_target_frac = {{0,0.15},{2.5,0.18},{5,0.3}};
public boolean cuas_no_border = true; // exclude targets with centers on the 16x16 tile edges public boolean cuas_no_border = true; // exclude targets with centers on the 16x16 tile edges
// CUAS Motion LMA parameters // CUAS Motion LMA parameters
public double cuas_lma_sigma = 3.0; public double cuas_lma_sigma = 2.5;
public double cuas_wnd_pedestal = 0.1; // Add constant to Gaussian weights public double cuas_wnd_pedestal = 0.1; // Add constant to Gaussian weights
public double cuas_lma_r0 = 3.0; //maximum with with overshoot public double cuas_lma_r0 = 3.0; //maximum with with overshoot
public double cuas_lma_ovrsht = 2.0; public double cuas_lma_ovrsht = 1.75;
public boolean cuas_lma_fit_xy = true; public boolean cuas_lma_fit_xy = true;
public boolean cuas_lma_fit_a = true; public boolean cuas_lma_fit_a = true;
...@@ -752,19 +753,28 @@ min_str_neib_fpn 0.35 ...@@ -752,19 +753,28 @@ min_str_neib_fpn 0.35
public int cuas_num_iter = 20; public int cuas_num_iter = 20;
// CUAS Motion LMA filter parameters // CUAS Motion LMA filter parameters
public double cuas_lma_rms = 1.5; // Maximal RMS (should always match, regardless if A) public double cuas_lma_rms = 2.5; // 1.5; // Maximal RMS (should always match, regardless if A)
public double cuas_lma_arms = 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484) public double cuas_lma_arms = 0.4; // 0.06; // Maximal absolute RMS (should match one of cuas_lma_arms OR cuas_lma_rrms (0.484)
public double cuas_lma_rrms = 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A) public double cuas_lma_rrms = 0.2; // 0.15; // Maximal relative to A rms. OK is when (RMS < cuas_lma_arms) || (RMS < cuas_lma_rrms * A)
public double cuas_lma_mina = 1.0; // Minimal A (amplitude) = 1.0 (< 2.0) public double cuas_lma_mina = 0.7; // 1.0; // Minimal A (amplitude) = 1.0 (< 2.0)
public double cuas_lma_maxr = 5.0; // Maximal R (radius) =5.0 (> 3.8) public double cuas_lma_maxr = 5.0; // Maximal R (radius) =5.0 (> 3.8)
public double cuas_lma_minr1 = 1.0; // Minimal R1 (radius of positive peak)
public double cuas_lma_mink = 0.0; // Minimal K (overshoot) = 0.0 (<0.007) public double cuas_lma_mink = 0.0; // Minimal K (overshoot) = 0.0 (<0.007)
public double cuas_lma_maxk = 5.0; // Maximal K (overshoot) = 5.0 (>3.8) public double cuas_lma_maxk = 5.0; // Maximal K (overshoot) = 5.0 (>3.8)
public double cuas_lma_a2a = 0.7; // Minimal ratio of the maximal pixel to the amplitude
public double cuas_score_mv = 0.0; // minimal score for the motion vectors
public double cuas_score_lma = 0.0; // minimal score for the target LMA
public double cuas_factor_lim = 5.0; // limit each individual score factor
public double cuas_factor_pow = 1.0; // raise score factor to this power before combining
public double [] cuas_score_coeff = {1.0, 0.5, 1.0}; //weights of amplitude, RMSE and RMSE/amplitude
public boolean cuas_isolated = true; // remove targets that do not have neighbors before/after public boolean cuas_isolated = true; // remove targets that do not have neighbors before/after
public double cuas_max_mismatch = 2.0; // maximal position error between consecutive scene sequences public double cuas_max_mismatch = 2.0; // maximal position error between consecutive scene sequences
public boolean cuas_ignore_mismatch = false; // calculate mismatch but do not remove public boolean cuas_ignore_mismatch = false; // calculate mismatch but do not remove
public boolean cuas_by_horizon = true; // remove targets that are below horizon
public double cuas_horizon = 390.0; // maximal Y - position of the sky
public double cuas_mask_width = 9; public double cuas_mask_width = 9;
public double cuas_mask_blur = 3; public double cuas_mask_blur = 3;
...@@ -790,7 +800,7 @@ min_str_neib_fpn 0.35 ...@@ -790,7 +800,7 @@ min_str_neib_fpn 0.35
public boolean cuas_annotate = true; // save color rendered images (same as videos) public boolean cuas_annotate = true; // save color rendered images (same as videos)
public Color cuas_text_color = new Color (0, 255, 255);// 220); public Color cuas_text_color = new Color (0, 255, 255);// 220);
public String cuas_font_name = "Monospaced"; public String cuas_font_name = "Monospaced";
public int cuas_font_size = 6; // before scaling public int cuas_font_size = 7; // before scaling
public int cuas_font_type = 1; // 0 - PLAIN, 1 - BOLD, 2 - ITALIC public int cuas_font_type = 1; // 0 - PLAIN, 1 - BOLD, 2 - ITALIC
// AZ/EL calibration // AZ/EL calibration
public double cuas_ifov = 0.05; // degree per pixel public double cuas_ifov = 0.05; // degree per pixel
...@@ -801,8 +811,8 @@ min_str_neib_fpn 0.35 ...@@ -801,8 +811,8 @@ min_str_neib_fpn 0.35
public boolean cuas_debug = false; // save debug images (and show them if not in batch mode) public boolean cuas_debug = true; // save debug images (and show them if not in batch mode)
public boolean cuas_step_debug = false; // save debug images during per-step cuas recalculation (and show them if not in batch mode) public boolean cuas_step_debug = true; // save debug images during per-step cuas recalculation (and show them if not in batch mode)
public boolean cuas_target_debug = false; // save debug images during per-step cuas recalculation (and show them if not in batch mode) public boolean cuas_target_debug = false; // save debug images during per-step cuas recalculation (and show them if not in batch mode)
public boolean cuas_overwrite = false; // overwrite num_orient and num_accum public boolean cuas_overwrite = false; // overwrite num_orient and num_accum
public int cuas_num_orient = 2; // initial value for num_orient public int cuas_num_orient = 2; // initial value for num_orient
...@@ -2136,7 +2146,7 @@ min_str_neib_fpn 0.35 ...@@ -2136,7 +2146,7 @@ min_str_neib_fpn 0.35
"Discards rows then columns that have less defined tiles (noticed in a diagonal after folds removal)."); "Discards rows then columns that have less defined tiles (noticed in a diagonal after folds removal).");
gd.addNumericField("CLT tile variant thershold", this.cuas_clt_variant, 5,7,"", gd.addNumericField("CLT tile variant thershold", this.cuas_clt_variant, 5,7,"",
"Threshold from the nearest in teplate to create a variant for the tile (RMS)."); "Threshold from the nearest in teplate to create a variant for the tile (RMS).");
gd.addNumericField("CLT tile diff merge", this.cuas_clt_threshold, 5,7,"", gd.addNumericField("CLT tile diff merge", this.cuas_clt_threshold, 5,7,"",
"Threshold to the CLT tile difference to a template (RMS) when selectin a single best."); "Threshold to the CLT tile difference to a template (RMS) when selectin a single best.");
gd.addNumericField("CLT outliers scale", this.cuas_clt_decrease, 5,7,"x", gd.addNumericField("CLT outliers scale", this.cuas_clt_decrease, 5,7,"x",
"Scale CLT outliers tiles weight when averaging."); "Scale CLT outliers tiles weight when averaging.");
...@@ -2315,18 +2325,45 @@ min_str_neib_fpn 0.35 ...@@ -2315,18 +2325,45 @@ min_str_neib_fpn 0.35
"Filter out weak targets."); "Filter out weak targets.");
gd.addNumericField("Maximal radius", this.cuas_lma_maxr, 5,8,"pix", gd.addNumericField("Maximal radius", this.cuas_lma_maxr, 5,8,"pix",
"Maximal target radius including negative overshoot."); "Maximal target radius including negative overshoot.");
gd.addNumericField("Mimimal inner radius", this.cuas_lma_minr1, 5,8,"pix",
"Minimal radius of positive peak.");
gd.addNumericField("Minimal overshoot ratio", this.cuas_lma_mink, 5,8,"", gd.addNumericField("Minimal overshoot ratio", this.cuas_lma_mink, 5,8,"",
"Minimal ratio of the overshoot radius to the first 0 radius (typical 1.0)."); "Minimal ratio of the overshoot radius to the first 0 radius (typical 1.0).");
gd.addNumericField("Maximal overshoot ratio", this.cuas_lma_maxk, 5,8,"", gd.addNumericField("Maximal overshoot ratio", this.cuas_lma_maxk, 5,8,"",
"Maximal ratio of the overshoot radius to the first 0 radius (typical 3.0)."); "Maximal ratio of the overshoot radius to the first 0 radius (typical 3.0).");
gd.addNumericField("Minimal max pixel to amplitude ratio", this.cuas_lma_a2a, 5,8,"",
"Minimal ratio of the maximal pixel near fitted maximum to the LMA amplitude.");
gd.addMessage("=== Handling overall target scores ===");
gd.addNumericField("Minimal MV score", this.cuas_score_mv, 5,8,"",
"Remove potential motion tiles that have lower scores.");
gd.addNumericField("Minimal target LMA score", this.cuas_score_lma, 5,8,"",
"Remove potential target LMA tiles that have lower scores.");
gd.addNumericField("Limit each individual score factor", this.cuas_factor_lim, 5,8,"",
"Limit each contributing score factor by this value.");
gd.addNumericField("Raise score factor to this power", this.cuas_factor_pow, 5,8,"",
"Raise each score factor to this power before combining them.");
gd.addStringField ("Score factors weights", IntersceneMatchParameters.doublesToString(cuas_score_coeff), 80,
"Relative importance of LMA amplitude, RMSE and RMSE/ampitude.");
gd.addMessage("=== Post-processing targets filtering ===");
gd.addCheckbox ("Remove single-frame targets", this.cuas_isolated, gd.addCheckbox ("Remove single-frame targets", this.cuas_isolated,
"Remove targets that do not have neighbors before/afte."); "Remove targets that do not have neighbors before/afte.");
gd.addNumericField("Remove by mismatch", this.cuas_max_mismatch, 5,8,"pix", gd.addNumericField("Remove by mismatch", this.cuas_max_mismatch, 5,8,"pix",
"Maximal position error between consecutive scene sequences."); "Maximal position error between consecutive scene sequences.");
gd.addCheckbox ("Ignore mismatch", this.cuas_ignore_mismatch, gd.addCheckbox ("Ignore mismatch", this.cuas_ignore_mismatch,
"Calculate mismatch, but keep targets for debugging (see cuas_target_debug)."); "Calculate mismatch, but keep targets for debugging (see cuas_target_debug).");
gd.addCheckbox ("Filter by horizon", this.cuas_by_horizon,
"Remove targets that are below the horizon.");
gd.addNumericField("Pixel Y of the horizon", this.cuas_horizon, 5,8,"pix",
"Pixel Y of the horizon.");
gd.addMessage("=== Targets video generation (see also Vidoe/Stereo tab) ==="); gd.addMessage("=== Targets video generation (see also Vidoe/Stereo tab) ===");
...@@ -3398,12 +3435,23 @@ min_str_neib_fpn 0.35 ...@@ -3398,12 +3435,23 @@ min_str_neib_fpn 0.35
this.cuas_lma_rrms = gd.getNextNumber(); this.cuas_lma_rrms = gd.getNextNumber();
this.cuas_lma_mina = gd.getNextNumber(); this.cuas_lma_mina = gd.getNextNumber();
this.cuas_lma_maxr = gd.getNextNumber(); this.cuas_lma_maxr = gd.getNextNumber();
this.cuas_lma_minr1 = gd.getNextNumber();
this.cuas_lma_mink = gd.getNextNumber(); this.cuas_lma_mink = gd.getNextNumber();
this.cuas_lma_maxk = gd.getNextNumber(); this.cuas_lma_maxk = gd.getNextNumber();
this.cuas_lma_a2a = gd.getNextNumber();
this.cuas_score_mv = gd.getNextNumber();
this.cuas_score_lma = gd.getNextNumber();
this.cuas_factor_lim = gd.getNextNumber();
this.cuas_factor_pow = gd.getNextNumber();
this.cuas_score_coeff = IntersceneMatchParameters. StringToDoubles(gd.getNextString(), CuasMotion.IMPORTANCE_LENGTH);
this.cuas_isolated = gd.getNextBoolean(); this.cuas_isolated = gd.getNextBoolean();
this.cuas_max_mismatch= gd.getNextNumber(); this.cuas_max_mismatch= gd.getNextNumber();
this.cuas_ignore_mismatch = gd.getNextBoolean(); this.cuas_ignore_mismatch = gd.getNextBoolean();
this.cuas_by_horizon = gd.getNextBoolean();
this.cuas_horizon= gd.getNextNumber();
this.cuas_mask_width = gd.getNextNumber(); this.cuas_mask_width = gd.getNextNumber();
this.cuas_mask_blur = gd.getNextNumber(); this.cuas_mask_blur = gd.getNextNumber();
...@@ -4371,12 +4419,23 @@ min_str_neib_fpn 0.35 ...@@ -4371,12 +4419,23 @@ min_str_neib_fpn 0.35
properties.setProperty(prefix+"cuas_lma_rrms", this.cuas_lma_rrms+""); // double properties.setProperty(prefix+"cuas_lma_rrms", this.cuas_lma_rrms+""); // double
properties.setProperty(prefix+"cuas_lma_mina", this.cuas_lma_mina+""); // double properties.setProperty(prefix+"cuas_lma_mina", this.cuas_lma_mina+""); // double
properties.setProperty(prefix+"cuas_lma_maxr", this.cuas_lma_maxr+""); // double properties.setProperty(prefix+"cuas_lma_maxr", this.cuas_lma_maxr+""); // double
properties.setProperty(prefix+"cuas_lma_minr1", this.cuas_lma_minr1+""); // double
properties.setProperty(prefix+"cuas_lma_mink", this.cuas_lma_mink+""); // double properties.setProperty(prefix+"cuas_lma_mink", this.cuas_lma_mink+""); // double
properties.setProperty(prefix+"cuas_lma_maxk", this.cuas_lma_maxk+""); // double properties.setProperty(prefix+"cuas_lma_maxk", this.cuas_lma_maxk+""); // double
properties.setProperty(prefix+"cuas_lma_a2a", this.cuas_lma_a2a+""); // double
properties.setProperty(prefix+"cuas_score_mv", this.cuas_score_mv+""); // double
properties.setProperty(prefix+"cuas_score_lma", this.cuas_score_lma+""); // double
properties.setProperty(prefix+"cuas_factor_lim", this.cuas_factor_lim+""); // double
properties.setProperty(prefix+"cuas_factor_pow", this.cuas_factor_pow+""); // double
properties.setProperty(prefix+"cuas_score_coeff", IntersceneMatchParameters.doublesToString(this.cuas_score_coeff));
properties.setProperty(prefix+"cuas_isolated", this.cuas_isolated+""); // boolean properties.setProperty(prefix+"cuas_isolated", this.cuas_isolated+""); // boolean
properties.setProperty(prefix+"cuas_max_mismatch", this.cuas_max_mismatch+""); // double properties.setProperty(prefix+"cuas_max_mismatch", this.cuas_max_mismatch+""); // double
properties.setProperty(prefix+"cuas_ignore_mismatch", this.cuas_ignore_mismatch+"");// boolean properties.setProperty(prefix+"cuas_ignore_mismatch", this.cuas_ignore_mismatch+"");// boolean
properties.setProperty(prefix+"cuas_by_horizon", this.cuas_by_horizon+""); // boolean
properties.setProperty(prefix+"cuas_horizon", this.cuas_horizon+""); // double
properties.setProperty(prefix+"cuas_mask_width", this.cuas_mask_width+""); // double properties.setProperty(prefix+"cuas_mask_width", this.cuas_mask_width+""); // double
properties.setProperty(prefix+"cuas_mask_blur", this.cuas_mask_blur+""); // double properties.setProperty(prefix+"cuas_mask_blur", this.cuas_mask_blur+""); // double
...@@ -5312,12 +5371,23 @@ min_str_neib_fpn 0.35 ...@@ -5312,12 +5371,23 @@ min_str_neib_fpn 0.35
if (properties.getProperty(prefix+"cuas_lma_rrms")!=null) this.cuas_lma_rrms=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_rrms")); if (properties.getProperty(prefix+"cuas_lma_rrms")!=null) this.cuas_lma_rrms=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_rrms"));
if (properties.getProperty(prefix+"cuas_lma_mina")!=null) this.cuas_lma_mina=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_mina")); if (properties.getProperty(prefix+"cuas_lma_mina")!=null) this.cuas_lma_mina=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_mina"));
if (properties.getProperty(prefix+"cuas_lma_maxr")!=null) this.cuas_lma_maxr=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_maxr")); if (properties.getProperty(prefix+"cuas_lma_maxr")!=null) this.cuas_lma_maxr=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_maxr"));
if (properties.getProperty(prefix+"cuas_lma_minr1")!=null) this.cuas_lma_minr1=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_minr1"));
if (properties.getProperty(prefix+"cuas_lma_mink")!=null) this.cuas_lma_mink=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_mink")); if (properties.getProperty(prefix+"cuas_lma_mink")!=null) this.cuas_lma_mink=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_mink"));
if (properties.getProperty(prefix+"cuas_lma_maxk")!=null) this.cuas_lma_maxk=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_maxk")); if (properties.getProperty(prefix+"cuas_lma_maxk")!=null) this.cuas_lma_maxk=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_maxk"));
if (properties.getProperty(prefix+"cuas_lma_a2a")!=null) this.cuas_lma_a2a=Double.parseDouble(properties.getProperty(prefix+"cuas_lma_a2a"));
if (properties.getProperty(prefix+"cuas_score_mv")!=null) this.cuas_score_mv=Double.parseDouble(properties.getProperty(prefix+"cuas_score_mv"));
if (properties.getProperty(prefix+"cuas_score_lma")!=null) this.cuas_score_lma=Double.parseDouble(properties.getProperty(prefix+"cuas_score_lma"));
if (properties.getProperty(prefix+"cuas_factor_lim")!=null) this.cuas_factor_lim=Double.parseDouble(properties.getProperty(prefix+"cuas_factor_lim"));
if (properties.getProperty(prefix+"cuas_factor_pow")!=null) this.cuas_factor_pow=Double.parseDouble(properties.getProperty(prefix+"cuas_factor_pow"));
if (properties.getProperty(prefix+"cuas_score_coeff")!=null) this.cuas_score_coeff= IntersceneMatchParameters.StringToDoubles(properties.getProperty(prefix+"cuas_score_coeff"),3);
if (properties.getProperty(prefix+"cuas_isolated")!=null) this.cuas_isolated=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_isolated")); if (properties.getProperty(prefix+"cuas_isolated")!=null) this.cuas_isolated=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_isolated"));
if (properties.getProperty(prefix+"cuas_max_mismatch")!=null) this.cuas_max_mismatch=Double.parseDouble(properties.getProperty(prefix+"cuas_max_mismatch")); if (properties.getProperty(prefix+"cuas_max_mismatch")!=null) this.cuas_max_mismatch=Double.parseDouble(properties.getProperty(prefix+"cuas_max_mismatch"));
if (properties.getProperty(prefix+"cuas_ignore_mismatch")!=null) this.cuas_ignore_mismatch=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_ignore_mismatch")); if (properties.getProperty(prefix+"cuas_ignore_mismatch")!=null) this.cuas_ignore_mismatch=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_ignore_mismatch"));
if (properties.getProperty(prefix+"cuas_by_horizon")!=null) this.cuas_by_horizon=Boolean.parseBoolean(properties.getProperty(prefix+"cuas_by_horizon"));
if (properties.getProperty(prefix+"cuas_horizon")!=null) this.cuas_horizon=Double.parseDouble(properties.getProperty(prefix+"cuas_horizon"));
if (properties.getProperty(prefix+"cuas_mask_width")!=null) this.cuas_mask_width=Double.parseDouble(properties.getProperty(prefix+"cuas_mask_width")); if (properties.getProperty(prefix+"cuas_mask_width")!=null) this.cuas_mask_width=Double.parseDouble(properties.getProperty(prefix+"cuas_mask_width"));
if (properties.getProperty(prefix+"cuas_mask_blur")!=null) this.cuas_mask_blur=Double.parseDouble(properties.getProperty(prefix+"cuas_mask_blur")); if (properties.getProperty(prefix+"cuas_mask_blur")!=null) this.cuas_mask_blur=Double.parseDouble(properties.getProperty(prefix+"cuas_mask_blur"));
...@@ -6253,12 +6323,22 @@ min_str_neib_fpn 0.35 ...@@ -6253,12 +6323,22 @@ min_str_neib_fpn 0.35
imp.cuas_lma_rrms = this.cuas_lma_rrms; imp.cuas_lma_rrms = this.cuas_lma_rrms;
imp.cuas_lma_mina = this.cuas_lma_mina; imp.cuas_lma_mina = this.cuas_lma_mina;
imp.cuas_lma_maxr = this.cuas_lma_maxr; imp.cuas_lma_maxr = this.cuas_lma_maxr;
imp.cuas_lma_minr1 = this.cuas_lma_minr1;
imp.cuas_lma_mink = this.cuas_lma_mink; imp.cuas_lma_mink = this.cuas_lma_mink;
imp.cuas_lma_maxk = this.cuas_lma_maxk; imp.cuas_lma_maxk = this.cuas_lma_maxk;
imp.cuas_lma_a2a = this.cuas_lma_a2a;
imp.cuas_score_mv = this.cuas_score_mv;
imp.cuas_score_lma = this.cuas_score_lma;
imp.cuas_factor_lim = this.cuas_factor_lim;
imp.cuas_factor_pow = this.cuas_factor_pow;
imp.cuas_score_coeff = this.cuas_score_coeff.clone();
imp.cuas_isolated = this.cuas_isolated; imp.cuas_isolated = this.cuas_isolated;
imp.cuas_max_mismatch = this.cuas_max_mismatch; imp.cuas_max_mismatch = this.cuas_max_mismatch;
imp.cuas_ignore_mismatch = this.cuas_ignore_mismatch; imp.cuas_ignore_mismatch = this.cuas_ignore_mismatch;
imp.cuas_by_horizon = this.cuas_by_horizon;
imp.cuas_horizon = this.cuas_horizon;
imp.cuas_mask_width = this.cuas_mask_width; imp.cuas_mask_width = this.cuas_mask_width;
imp.cuas_mask_blur = this.cuas_mask_blur; imp.cuas_mask_blur = this.cuas_mask_blur;
......
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