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imagej-elphel
Commit 4e7653fe authored by Andrey Filippov's avatar Andrey Filippov
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fixed goodSamples variations

parent 0c488df6
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Showing with 80 additions and 16 deletions
src/main/java/FocusingField.java
View file @ 4e7653fe
...@@ -220,6 +220,9 @@ public class FocusingField { ...@@ -220,6 +220,9 @@ public class FocusingField {
double [] nextVector=null; double [] nextVector=null;
double [] savedVector=null; double [] savedVector=null;
boolean [][] goodCalibratedSamples=null;
private LMAArrays lMAArrays=null; private LMAArrays lMAArrays=null;
private LMAArrays savedLMAArrays=null; private LMAArrays savedLMAArrays=null;
// temporarily changing visibility of currentfX // temporarily changing visibility of currentfX
...@@ -235,6 +238,7 @@ public class FocusingField { ...@@ -235,6 +238,7 @@ public class FocusingField {
public void setDefaults(){ public void setDefaults(){
goodCalibratedSamples=null;
sensorWidth= 2592; sensorWidth= 2592;
sensorHeight= 1936; sensorHeight= 1936;
PIXEL_SIZE= 0.0022; // mm PIXEL_SIZE= 0.0022; // mm
...@@ -482,6 +486,15 @@ public class FocusingField { ...@@ -482,6 +486,15 @@ public class FocusingField {
} }
} }
} }
if (goodCalibratedSamples !=null){
properties.setProperty(prefix+"goodCalibratedSamples_length",goodCalibratedSamples.length+"");
for (int chn=0;chn<goodCalibratedSamples.length;chn++){
String s="";
if (goodCalibratedSamples[chn]!=null) for (int j=0;j<goodCalibratedSamples[chn].length;j++) s+=goodCalibratedSamples[chn][j]?"+":"-";
properties.setProperty(prefix+"goodCalibratedSamples_"+chn,s);
}
}
} }
} }
...@@ -682,6 +695,20 @@ public class FocusingField { ...@@ -682,6 +695,20 @@ public class FocusingField {
} }
} }
} }
if (properties.getProperty(prefix+"goodCalibratedSamples_length")!=null){
goodCalibratedSamples=new boolean [Integer.parseInt(properties.getProperty(prefix+"goodCalibratedSamples_length"))][];
for (int chn=0;chn<goodCalibratedSamples.length;chn++){
String s=properties.getProperty(prefix+"goodCalibratedSamples_"+chn);
if ((s==null) || (s.length()==0)){
goodCalibratedSamples[chn]=null;
} else {
goodCalibratedSamples[chn]=new boolean [s.length()];
for (int i=0;i<goodCalibratedSamples[chn].length;i++){
goodCalibratedSamples[chn][i]=s.charAt(i)=='+';
}
}
}
}
} }
public void setDebugLevel(int debugLevel){ public void setDebugLevel(int debugLevel){
this.debugLevel=debugLevel; this.debugLevel=debugLevel;
...@@ -3950,6 +3977,19 @@ public double [] findAdjustZ( ...@@ -3950,6 +3977,19 @@ public double [] findAdjustZ(
return result; return result;
} }
public void calculateGoodSamples(){
this.goodCalibratedSamples=new boolean[getNumChannels()][getNumSamples()];
for (int chn=0;chn<this.goodCalibratedSamples.length;chn++)
for (int sample=0;sample<this.goodCalibratedSamples[0].length;sample++)
this.goodCalibratedSamples[chn][sample]=false;
for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
this.goodCalibratedSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
}
if (debugLevel>0) {
System.out.println("Calculated good samples:");
System.out.println(showSamples(this.goodCalibratedSamples));
}
}
public boolean LevenbergMarquardt( public boolean LevenbergMarquardt(
...@@ -4201,9 +4241,12 @@ public boolean LevenbergMarquardt( ...@@ -4201,9 +4241,12 @@ public boolean LevenbergMarquardt(
} }
this.savedVector=this.currentVector.clone(); this.savedVector=this.currentVector.clone();
commitParameterVector(this.savedVector); commitParameterVector(this.savedVector);
if (calibrate) zRanges=calcZRanges( if (calibrate){
true, // boolean scanOnly, // do not use non-scan samples zRanges=calcZRanges(
dataWeightsToBoolean()); true, // boolean scanOnly, // do not use non-scan samples
dataWeightsToBoolean());
calculateGoodSamples();
}
return true; // all series done return true; // all series done
} }
...@@ -4766,6 +4809,10 @@ public boolean LevenbergMarquardt( ...@@ -4766,6 +4809,10 @@ public boolean LevenbergMarquardt(
for (int i=0;i<dataVector.length;i++) if (dataWeights[i]>0.0){ for (int i=0;i<dataVector.length;i++) if (dataWeights[i]>0.0){
usedSamples[dataVector[i].channel][dataVector[i].sampleIndex]=true; usedSamples[dataVector[i].channel][dataVector[i].sampleIndex]=true;
} }
return showSamples(usedSamples);
}
public String showSamples(boolean [][] usedSamples){
int height=sampleCoord.length; int height=sampleCoord.length;
int width= sampleCoord[0].length; int width= sampleCoord[0].length;
String s=""; String s="";
...@@ -5465,17 +5512,18 @@ public boolean LevenbergMarquardt( ...@@ -5465,17 +5512,18 @@ public boolean LevenbergMarquardt(
){ ){
double [] sampleCorrRadius=getSampleRadiuses(); double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length; int numSamples=sampleCorrRadius.length;
boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()]; // boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()];
for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false; // for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false;
for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){ // for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true; // goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
} // }
double [][] result=new double [6][]; double [][] result=new double [6][];
for (int chn=0;chn<result.length;chn++) { for (int chn=0;chn<result.length;chn++) {
if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){ if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){
result[chn]=new double [numSamples]; result[chn]=new double [numSamples];
for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) { for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {
if (goodSamples[chn][sampleIndex]) { if ((goodCalibratedSamples==null) || ((goodCalibratedSamples[chn]!=null) && goodCalibratedSamples[chn][sampleIndex])) {
// if (goodSamples[chn][sampleIndex]) {
/* /*
result[chn][sampleIndex]=curvatureModel[chn].getAr( result[chn][sampleIndex]=curvatureModel[chn].getAr(
sampleCorrRadius[sampleIndex], sampleCorrRadius[sampleIndex],
...@@ -5512,17 +5560,20 @@ public boolean LevenbergMarquardt( ...@@ -5512,17 +5560,20 @@ public boolean LevenbergMarquardt(
){ ){
double [] sampleCorrRadius=getSampleRadiuses(); double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length; int numSamples=sampleCorrRadius.length;
/*
boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()]; boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()];
for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false; for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false;
for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){ for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true; goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
} }
*/
double [][] result=new double [6][]; double [][] result=new double [6][];
for (int chn=0;chn<result.length;chn++) { for (int chn=0;chn<result.length;chn++) {
if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){ if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){
result[chn]=new double [numSamples]; result[chn]=new double [numSamples];
for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) { for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++) {
if (goodSamples[chn][sampleIndex]) { if ((goodCalibratedSamples==null) || ((goodCalibratedSamples[chn]!=null) && goodCalibratedSamples[chn][sampleIndex])) {
// if (goodSamples[chn][sampleIndex]) {
result[chn][sampleIndex]=getChannelBestFWHM( result[chn][sampleIndex]=getChannelBestFWHM(
chn, // int channel, chn, // int channel,
sampleIndex, // int sampleIndex, sampleIndex, // int sampleIndex,
...@@ -5563,18 +5614,23 @@ public boolean LevenbergMarquardt( ...@@ -5563,18 +5614,23 @@ public boolean LevenbergMarquardt(
double [] qualB = {0.0,0.0,0.0}; double [] qualB = {0.0,0.0,0.0};
double [] sampleCorrRadius=getSampleRadiuses(); double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length; int numSamples=sampleCorrRadius.length;
if (goodCalibratedSamples==null) calculateGoodSamples();
/*
boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()]; boolean [][] goodSamples=new boolean[getNumChannels()][getNumSamples()];
for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false; for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false;
for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){ for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true; goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
} }
*/
for (int c=0;c<3;c++) { for (int c=0;c<3;c++) {
if ((data[2*c]!=null) && (data[2*c+1]!=null)){ if ((data[2*c]!=null) && (data[2*c+1]!=null)){
int nSamp=0; int nSamp=0;
qualB[c]=0.0; qualB[c]=0.0;
for (int i=0;i<numSamples;i++){ for (int i=0;i<numSamples;i++){
for (int dir=0;dir<2;dir++) { for (int dir=0;dir<2;dir++) {
if (goodSamples[2*c+dir][i]){ // if (goodSamples[2*c+dir][i]){
int chn=2*c+dir;
if ((goodCalibratedSamples[chn]!=null) && goodCalibratedSamples[chn][i]) {
qualB[c]+=data[2*c+dir][i]*data[2*c+dir][i]*data[2*c+dir][i]*data[2*c+dir][i]; qualB[c]+=data[2*c+dir][i]*data[2*c+dir][i]*data[2*c+dir][i]*data[2*c+dir][i];
nSamp++; nSamp++;
} }
...@@ -5591,9 +5647,17 @@ public boolean LevenbergMarquardt( ...@@ -5591,9 +5647,17 @@ public boolean LevenbergMarquardt(
//TODO: Move to a separate function //TODO: Move to a separate function
int [] numBad={0,0,0,0,0,0}; int [] numBad={0,0,0,0,0,0};
boolean hasBad=false; boolean hasBad=false;
for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) if (!goodSamples[i][j]){ // for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) if (!goodSamples[i][j]){
numBad[i]++; for (int i=0;i<goodCalibratedSamples.length;i++){
hasBad=true; if (goodCalibratedSamples[i]==null) {
numBad[i]+=getNumSamples();
hasBad=true;
} else {
for (int j=0;j<goodCalibratedSamples[i].length;j++) if (!goodCalibratedSamples[i][j]){
numBad[i]++;
hasBad=true;
}
}
} }
if ((debugLevel>1) && hasBad){ // was 0 if ((debugLevel>1) && hasBad){ // was 0
for (int i=0;i<numBad.length;i++) if (numBad[i]>0){ for (int i=0;i<numBad.length;i++) if (numBad[i]>0){
...@@ -8577,7 +8641,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8577,7 +8641,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
this.k_blue, this.k_blue,
this.k_sag, this.k_sag,
this.k_tan, this.k_tan,
goodSamples, this.qualBRemoveBadSamples?this.goodCalibratedSamples:null, //goodSamples,
sampleWeights); sampleWeights);
qualBOptimize.initQPars( qualBOptimize.initQPars(
zTxTy, zTxTy,
...@@ -8678,7 +8742,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8678,7 +8742,7 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
int chn=c*dirWeights.length+d; int chn=c*dirWeights.length+d;
for (int sample=0;sample<numSamples;sample++){ for (int sample=0;sample<numSamples;sample++){
double w=0.0; double w=0.0;
if ((goodSamples==null) || goodSamples[chn][sample]) { if ((goodSamples==null) || ((goodSamples[chn]!=null) && goodSamples[chn][sample])) {
w=colorWeights[c]*dirWeights[d]; w=colorWeights[c]*dirWeights[d];
} }
if (sampleWeights!=null){ if (sampleWeights!=null){
......
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