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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 {
double [] nextVector=null;
double [] savedVector=null;
boolean [][] goodCalibratedSamples=null;
private LMAArrays lMAArrays=null;
private LMAArrays savedLMAArrays=null;
// temporarily changing visibility of currentfX
......@@ -235,6 +238,7 @@ public class FocusingField {
public void setDefaults(){
goodCalibratedSamples=null;
sensorWidth= 2592;
sensorHeight= 1936;
PIXEL_SIZE= 0.0022; // mm
......@@ -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 {
}
}
}
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){
this.debugLevel=debugLevel;
......@@ -3950,6 +3977,19 @@ public double [] findAdjustZ(
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(
......@@ -4201,9 +4241,12 @@ public boolean LevenbergMarquardt(
}
this.savedVector=this.currentVector.clone();
commitParameterVector(this.savedVector);
if (calibrate) zRanges=calcZRanges(
if (calibrate){
zRanges=calcZRanges(
true, // boolean scanOnly, // do not use non-scan samples
dataWeightsToBoolean());
calculateGoodSamples();
}
return true; // all series done
}
......@@ -4766,6 +4809,10 @@ public boolean LevenbergMarquardt(
for (int i=0;i<dataVector.length;i++) if (dataWeights[i]>0.0){
usedSamples[dataVector[i].channel][dataVector[i].sampleIndex]=true;
}
return showSamples(usedSamples);
}
public String showSamples(boolean [][] usedSamples){
int height=sampleCoord.length;
int width= sampleCoord[0].length;
String s="";
......@@ -5465,17 +5512,18 @@ public boolean LevenbergMarquardt(
){
double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length;
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 n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
}
// 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 n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
// goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
// }
double [][] result=new double [6][];
for (int chn=0;chn<result.length;chn++) {
if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){
result[chn]=new double [numSamples];
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(
sampleCorrRadius[sampleIndex],
......@@ -5512,17 +5560,20 @@ public boolean LevenbergMarquardt(
){
double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length;
/*
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 n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
}
*/
double [][] result=new double [6][];
for (int chn=0;chn<result.length;chn++) {
if ((curvatureModel[chn]!=null) && (allChannels || channelSelect[chn])){
result[chn]=new double [numSamples];
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(
chn, // int channel,
sampleIndex, // int sampleIndex,
......@@ -5563,18 +5614,23 @@ public boolean LevenbergMarquardt(
double [] qualB = {0.0,0.0,0.0};
double [] sampleCorrRadius=getSampleRadiuses();
int numSamples=sampleCorrRadius.length;
if (goodCalibratedSamples==null) calculateGoodSamples();
/*
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 n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
}
*/
for (int c=0;c<3;c++) {
if ((data[2*c]!=null) && (data[2*c+1]!=null)){
int nSamp=0;
qualB[c]=0.0;
for (int i=0;i<numSamples;i++){
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];
nSamp++;
}
......@@ -5591,10 +5647,18 @@ public boolean LevenbergMarquardt(
//TODO: Move to a separate function
int [] numBad={0,0,0,0,0,0};
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]){
for (int i=0;i<goodCalibratedSamples.length;i++){
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
for (int i=0;i<numBad.length;i++) if (numBad[i]>0){
System.out.println(numBad[i]+" sample locations are missing data for "+fieldFitting.getDescription(i));
......@@ -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_sag,
this.k_tan,
goodSamples,
this.qualBRemoveBadSamples?this.goodCalibratedSamples:null, //goodSamples,
sampleWeights);
qualBOptimize.initQPars(
zTxTy,
......@@ -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;
for (int sample=0;sample<numSamples;sample++){
double w=0.0;
if ((goodSamples==null) || goodSamples[chn][sample]) {
if ((goodSamples==null) || ((goodSamples[chn]!=null) && goodSamples[chn][sample])) {
w=colorWeights[c]*dirWeights[d];
}
if (sampleWeights!=null){
......
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