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imagej-elphel
Commit bb1ed3e1 authored by Andrey Filippov's avatar Andrey Filippov
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more software bug fixes after the broken mechanical parts were replaced

parent 6f8671a4
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Showing with 250 additions and 70 deletions
src/main/java/FocusingField.java
View file @ bb1ed3e1
......@@ -80,7 +80,11 @@ public class FocusingField {
int filterInputConcaveMinSeries;
double filterInputConcaveScale;
boolean filterZ; // (adjustment mode)filter samples by Z
boolean filterTiltedZ; // remove tilted measurements using Z range determined by non-tilted LMA
double filterByValueScale;
double filterTiltedByValueScale; // filter tilted measurement samples if the spot FWHM is higher than scaled best FWHM
boolean filterByScanValue; // filter adjustment samples if fwhm exceeds maximal used in focal scan mode
boolean filterTiltedByScanValue; // filter tilted samples if fwhm exceeds maximal used in focal scan mode
int minLeftSamples; // minimal number of samples (channel/dir/location) for adjustment
int minCenterSamplesBest; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
int minCenterSamplesTotal; // minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
......@@ -229,7 +233,12 @@ public class FocusingField {
filterInputConcaveMinSeries=5;
filterInputConcaveScale=0.9;
filterZ=true; // (adjustment mode)filter samples by Z
filterTiltedZ=true;
filterByValueScale=1.5; // (adjustment mode)filter samples by value - remove higher than scaled best FWHM
filterTiltedByValueScale=1.5;
filterByScanValue=true; // filter adjustment samples if fwhm exceeds maximal used in focal scan mode
filterTiltedByScanValue=true; // filter tilted samples if fwhm exceeds maximal used in focal scan mode
minLeftSamples=10; // minimal number of samples (channel/dir/location) for adjustment
minCenterSamplesBest=4; // minimal number of samples (channel/dir/location) for adjustment in the center, best channel
minCenterSamplesTotal=0;// minimal number of samples (channel/dir/location) for adjustment in the center, all channels total
......@@ -351,11 +360,14 @@ public class FocusingField {
properties.setProperty(prefix+"filterInputConcaveMinSeries",filterInputConcaveMinSeries+"");
properties.setProperty(prefix+"filterInputConcaveScale",filterInputConcaveScale+"");
properties.setProperty(prefix+"filterZ",filterZ+"");
properties.setProperty(prefix+"filterTiltedZ",filterTiltedZ+"");
properties.setProperty(prefix+"filterByValueScale",filterByValueScale+"");
properties.setProperty(prefix+"filterTiltedByValueScale",filterTiltedByValueScale+"");
properties.setProperty(prefix+"filterByScanValue",filterByScanValue+"");
properties.setProperty(prefix+"filterTiltedByScanValue",filterTiltedByScanValue+"");
properties.setProperty(prefix+"minLeftSamples",minLeftSamples+"");
properties.setProperty(prefix+"minCenterSamplesBest",minCenterSamplesBest+"");
properties.setProperty(prefix+"minCenterSamplesTotal",minCenterSamplesTotal+"");
properties.setProperty(prefix+"centerSamples",centerSamples+"");
properties.setProperty(prefix+"maxRMS",maxRMS+"");
properties.setProperty(prefix+"zMin",zMin+"");
......@@ -395,14 +407,14 @@ public class FocusingField {
properties.setProperty(prefix+"rslt_mtf50_mode",rslt_mtf50_mode+"");
properties.setProperty(prefix+"rslt_solve",rslt_solve+"");
for (int chn=0; chn<rslt_show_chn.length; chn++) properties.setProperty(prefix+"rslt_show_chn_"+chn,rslt_show_chn[chn]+"");
// always re-calculate here?
zRanges=calcZRanges(dataWeightsToBoolean());
// always re-calculate here? - only in calibration mode or restore calibration mode? No, only in LMA in calibration mode
// zRanges=calcZRanges(dataWeightsToBoolean());
if (zRanges!=null){
properties.setProperty(prefix+"zRanges_length",zRanges.length+"");
for (int chn=0;chn<zRanges.length;chn++) if (zRanges[chn]!=null) {
properties.setProperty(prefix+"zRanges_"+chn+"_length",zRanges[chn].length+"");
for (int sample=0;sample<zRanges[chn].length;sample++) if (zRanges[chn][sample]!=null) {
properties.setProperty(prefix+"zRanges_"+chn+"_"+sample,zRanges[chn][sample][0]+","+zRanges[chn][sample][1]);
properties.setProperty(prefix+"zRanges_"+chn+"_"+sample,zRanges[chn][sample][0]+","+zRanges[chn][sample][1]+","+zRanges[chn][sample][2]);
}
}
}
......@@ -456,8 +468,16 @@ public class FocusingField {
filterInputConcaveScale=Double.parseDouble(properties.getProperty(prefix+"filterInputConcaveScale"));
if (properties.getProperty(prefix+"filterZ")!=null)
filterZ=Boolean.parseBoolean(properties.getProperty(prefix+"filterZ"));
if (properties.getProperty(prefix+"filterTiltedZ")!=null)
filterTiltedZ=Boolean.parseBoolean(properties.getProperty(prefix+"filterTiltedZ"));
if (properties.getProperty(prefix+"filterByValueScale")!=null)
filterByValueScale=Double.parseDouble(properties.getProperty(prefix+"filterByValueScale"));
if (properties.getProperty(prefix+"filterTiltedByValueScale")!=null)
filterTiltedByValueScale=Double.parseDouble(properties.getProperty(prefix+"filterTiltedByValueScale"));
if (properties.getProperty(prefix+"filterByScanValue")!=null)
filterByScanValue=Boolean.parseBoolean(properties.getProperty(prefix+"filterByScanValue"));
if (properties.getProperty(prefix+"filterTiltedByScanValue")!=null)
filterTiltedByScanValue=Boolean.parseBoolean(properties.getProperty(prefix+"filterTiltedByScanValue"));
if (properties.getProperty(prefix+"minLeftSamples")!=null)
minLeftSamples=Integer.parseInt(properties.getProperty(prefix+"minLeftSamples"));
if (properties.getProperty(prefix+"minCenterSamplesBest")!=null)
......@@ -551,10 +571,12 @@ public class FocusingField {
zRanges[chn][sample]=null;
String s=properties.getProperty(prefix+"zRanges_"+chn+"_"+sample);
if (s!=null){
zRanges[chn][sample]=new double[2];
zRanges[chn][sample]=new double[3];
String [] ss=s.split(",");
zRanges[chn][sample][0]=Double.parseDouble(ss[0]);
zRanges[chn][sample][1]=Double.parseDouble(ss[1]);
if (ss.length>2) zRanges[chn][sample][2]=Double.parseDouble(ss[2]);
else zRanges[chn][sample][2]=0.0;
}
}
}
......@@ -623,6 +645,7 @@ public class MeasuredSample{
public int channel;
public double value;
public double [] dPxyc=new double[2]; // derivative of the value by optical (aberration) center pixel X,Y
public boolean scan=false; // sample belongs to focal distance scanning series
// public double weight;
// public MeasuredSample(){}
......@@ -635,7 +658,8 @@ public class MeasuredSample{
int channel,
double value,
double dPxc,
double dPyc
double dPyc,
boolean scan
){
this.motors = motors;
this.timestamp=timestamp;
......@@ -646,6 +670,7 @@ public class MeasuredSample{
this.dPxyc[0]=dPxc;
this.dPxyc[1]=dPyc;
this.sampleIndex=sampleIndex;
this.scan=scan;
}
}
public boolean configureDataVector(String title, boolean forcenew, boolean enableReset){
......@@ -659,7 +684,7 @@ public boolean configureDataVector(String title, boolean forcenew, boolean enabl
GenericDialog gd = new GenericDialog(title+(forcenew?" RESETTING DATA":""));
gd.addCheckbox("Only use measurements acquired during parallel moves (false - use all)",parallelOnly);
gd.addCheckbox("Remove \"crazy\" input data (samll motor move causing large variations of FWHM)",filterInput);
gd.addCheckbox("Remove \"crazy\" input data (small motor move causing large variations of FWHM)",filterInput);
gd.addNumericField("Maximal motor move to be considered small",filterInputMotorDiff,0,5,"steps (~90um/step)");
gd.addNumericField("Maximal allowed PSF FWHM variations fro the move above",filterInputDiff,3,5,"um");
gd.addCheckbox("Remove first/last in a series of measuremnts separated by small (see above) steps",filterInputFirstLast);
......@@ -672,6 +697,10 @@ public boolean configureDataVector(String title, boolean forcenew, boolean enabl
gd.addNumericField("Minimal number of samples (to remove / apply concave filter) ",filterInputConcaveMinSeries,3,5,"samples");
gd.addNumericField("Concave filter scale",filterInputConcaveScale,3,5,"<=1.0");
gd.addCheckbox("Filter tilted samples/channels by Z",filterTiltedZ);
gd.addCheckbox("Filter tilted samples by value (leave lower than maximal fwhm used in focal scan mode)",filterTiltedByScanValue);
gd.addNumericField("Filter tilted samples by value (remove samples above scaled best FWHM for channel/location)",filterTiltedByValueScale,2,5,"x");
gd.addCheckbox("Sagittal channels are master channels (false - tangential are masters)",sagittalMaster);
gd.addMessage("=== Setting minimal measured PSF radius for different colors/directions ===");
......@@ -730,6 +759,10 @@ public boolean configureDataVector(String title, boolean forcenew, boolean enabl
filterInputConcaveMinSeries= (int) gd.getNextNumber();
filterInputConcaveScale= gd.getNextNumber();
filterTiltedZ= gd.getNextBoolean();
filterTiltedByScanValue= gd.getNextBoolean();
filterTiltedByValueScale= gd.getNextNumber();
sagittalMaster= gd.getNextBoolean();
for (int i=0;i<minMeas.length;i++)this.minMeas[i]= gd.getNextNumber();
useMinMeas= gd.getNextBoolean();
......@@ -809,41 +842,58 @@ public double [][] getSeriesWeights(){
}
private double [][][] calcZRanges(
boolean scanOnly,
boolean [] enable){
double [][][] zRanges=new double[getNumChannels()][getNumSamples()][];
for (int chn=0;chn<zRanges.length;chn++) for (int sample=0;sample<zRanges[chn].length;sample++) zRanges[chn][sample]=null;
double [][] sCoord= flattenSampleCoord();
for (int index=0;index<dataVector.length;index++) if ((index>=enable.length) ||enable[index]){
for (int index=0;index<dataVector.length;index++) if ((!scanOnly || dataVector[index].scan) && ((index>=enable.length) ||enable[index])){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
double z= fieldFitting.getMotorsZ(
dataVector[index].motors, // 3 motor coordinates
sCoord[sample][0], // pixel x
sCoord[sample][1]); // pixel y
double fwhm=dataVector[index].value;
if (zRanges[chn][sample]==null){
zRanges[chn][sample]=new double[2];
zRanges[chn][sample][0]=z;
zRanges[chn][sample][1]=z;
zRanges[chn][sample]=new double[3];
zRanges[chn][sample][0]=z; // low limit
zRanges[chn][sample][1]=z; // high limit
zRanges[chn][sample][2]=0.0; // maximal used value
} else {
if (z<zRanges[chn][sample][0]) zRanges[chn][sample][0]=z;
if (z>zRanges[chn][sample][1]) zRanges[chn][sample][1]=z;
if (fwhm>zRanges[chn][sample][2]) zRanges[chn][sample][2]=fwhm;
}
}
if (debugLevel>0) System.out.println("calcZRanges()");
if (debugLevel>0) System.out.println("***** calcZRanges() *****");
return zRanges;
}
private boolean [] filterByZRanges (
double [][][] zRanges,
boolean [] enable_in){
boolean [] enable_out=enable_in.clone();
boolean [] enable_in,
boolean [] scanMask){
if (enable_in==null) {
enable_in=new boolean [dataVector.length];
for (int i=0;i<enable_in.length;i++)enable_in[i]=true;
}
// if (scanMask==null) {
// scanMask=new boolean [dataVector.length];
// for (int i=0;i<scanMask.length;i++) scanMask[i]=true;
// }
boolean [] enable_masked=enable_in.clone();
if (scanMask!=null) {
for (int i=0;i<enable_masked.length;i++) if ((i<scanMask.length) && scanMask[i]) enable_masked[i]=false;
}
boolean [] enable_out=enable_masked.clone();
// boolean [] enable_out=enable_in.clone();
double [][] sCoord= flattenSampleCoord();
int numFiltered=0;
int numLeft=0;
if (zRanges!=null) {
for (int index=0;index<dataVector.length;index++) if ((index>=enable_in.length) || enable_in[index]){
for (int index=0;index<dataVector.length;index++) if ((index>=enable_masked.length) || enable_masked[index]){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
double z= fieldFitting.getMotorsZ(
......@@ -854,39 +904,123 @@ private boolean [] filterByZRanges (
if ((z<zRanges[chn][sample][0]) || (z>zRanges[chn][sample][1])) {
enable_out[index]=false;
numFiltered++;
} else {
numLeft++;
// } else {
// numLeft++;
}
}
}
}
// restore masked out data
if (scanMask!=null) {
for (int i=0;i<enable_out.length;i++) if (
(i<scanMask.length) &&
scanMask[i] &&
enable_in[i]) enable_out[i]=true;
}
if ((debugLevel+((scanMask!=null)?1:0))>1) {
int numLeft=0;
for (int i=0;i<enable_out.length;i++) if (enable_out[i]) numLeft++;
System.out.println("filterByZRanges(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
return enable_out;
}
private boolean [] filterByScanValues (
double [][][] zRanges,
boolean [] enable_in,
boolean [] scanMask){
if (enable_in==null) {
enable_in=new boolean [dataVector.length];
for (int i=0;i<enable_in.length;i++)enable_in[i]=true;
}
boolean [] enable_masked=enable_in.clone();
if (scanMask!=null) {
for (int i=0;i<enable_masked.length;i++) if ((i<scanMask.length) && scanMask[i]) enable_masked[i]=false;
}
boolean [] enable_out=enable_masked.clone();
int numFiltered=0;
if (zRanges!=null) {
for (int index=0;index<dataVector.length;index++) if ((index>=enable_masked.length) || enable_masked[index]){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
double fwhm=dataVector[index].value;
if ((zRanges[chn]!=null) && (zRanges[chn][sample]!=null)){
if (fwhm>zRanges[chn][sample][2]){
enable_out[index]=false;
numFiltered++;
}
}
if (debugLevel>1) System.out.println("filterByZRanges(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
}
// restore masked out data
if (scanMask!=null) {
for (int i=0;i<enable_out.length;i++) if (
(i<scanMask.length) &&
scanMask[i] &&
enable_in[i]) enable_out[i]=true;
}
if ((debugLevel+((scanMask!=null)?1:0))>1) {
int numLeft=0;
for (int i=0;i<enable_out.length;i++) if (enable_out[i]) numLeft++;
System.out.println("filterByScanValues(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
return enable_out;
}
private boolean [] filterByValue (
double scale, // scale to best FWHM - larger are ignored
boolean [] enable_in){
boolean [] enable_out=enable_in.clone();
boolean [] enable_in,
boolean [] scanMask){
// boolean [] enable_out=enable_in.clone();
if (enable_in==null) {
enable_in=new boolean [dataVector.length];
for (int i=0;i<enable_in.length;i++)enable_in[i]=true;
}
// if (scanMask==null) {
// scanMask=new boolean [dataVector.length];
// for (int i=0;i<scanMask.length;i++) scanMask[i]=true;
// }
boolean [] enable_masked=enable_in.clone();
if (scanMask!=null) {
for (int i=0;i<enable_masked.length;i++) if ((i<scanMask.length) && scanMask[i]) enable_masked[i]=false;
}
boolean [] enable_out=enable_masked.clone();
double [][] fwhm = fieldFitting.getFWHM(
true, // boolean corrected,
true //boolean allChannels
);
int numFiltered=0;
int numLeft=0;
// int numLeft=0;
if (scale>0.0) {
for (int index=0;index<dataVector.length;index++) if ((index>=enable_in.length) || enable_in[index]){
for (int index=0;index<dataVector.length;index++) if ((index>=enable_masked.length) || enable_masked[index]){
int chn=dataVector[index].channel;
int sample=dataVector[index].sampleIndex;
if (dataVector[index].value > scale*fwhm[chn][sample]){
enable_out[index]=false;
numFiltered++;
} else {
numLeft++;
// } else {
// numLeft++;
}
}
}
if (debugLevel>1) System.out.println("filterByValue(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
// restore masked out data
if (scanMask!=null) {
for (int i=0;i<enable_out.length;i++) if (
(i<scanMask.length) &&
scanMask[i] &&
enable_in[i]) enable_out[i]=true;
}
if ((debugLevel+((scanMask!=null)?1:0))>1) {
int numLeft=0;
for (int i=0;i<enable_out.length;i++) if (enable_out[i]) numLeft++;
System.out.println("filterByValue(): Filtered "+numFiltered+" samples, left "+numLeft+" samples");
}
return enable_out;
}
......@@ -1378,18 +1512,12 @@ public void setDataVector(
boolean calibrateMode,
MeasuredSample [] vector){ // remove unused channels if any. vector is already corrected from input data, FWHM psf
if (debugLevel>1) System.out.println("+++++ (Re)calculating sample weights +++++");
// int [] diffs=null;
// if (calibrateMode && parallelOnly) diffs=getParallelDiff(vector);
boolean [] chanSel=fieldFitting.getSelectedChannels();
boolean [] fullScanMask=createScanMask(vector);
int numSamples=0;
// int index=0;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]){
if (calibrateMode && parallelOnly && !fullScanMask[i]) continue; // skip non-scan
// if ((diffs!=null) && (
// ((vector[i].motors[1]-vector[i].motors[0]) != diffs[0]) ||
// ((vector[i].motors[2]-vector[i].motors[0]) != diffs[1]))) continue;
numSamples++;
}
dataVector=new MeasuredSample [numSamples];
......@@ -1397,21 +1525,10 @@ public void setDataVector(
int n=0;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) {
if (calibrateMode && parallelOnly && !fullScanMask[i]) continue;
// if ((diffs!=null) && (
// ((vector[i].motors[1]-vector[i].motors[0]) != diffs[0]) ||
// ((vector[i].motors[2]-vector[i].motors[0]) != diffs[1]))) continue;
scanMask[n]=fullScanMask[i];
vector[i].scan=fullScanMask[i];
dataVector[n++]=vector[i];
}
// if (calibrateMode) {
// if (parallelOnly){
// scanMask=new boolean [numSamples];
// for (int i=0;i<scanMask.length;i++) scanMask[i]=true;
// }
// } else {
// scanMask=new boolean [numSamples];
// for (int i=0;i<scanMask.length;i++) scanMask[i]=false;
// }
int corrLength=fieldFitting.getNumberOfCorrParameters();
dataValues = new double [dataVector.length+corrLength];
dataWeights = new double [dataVector.length+corrLength];
......@@ -1459,8 +1576,35 @@ public void setDataVector(
filterInputConcaveScale,
en);
maskDataWeights(en);
}
if (calibrateMode && filterTiltedZ){
boolean [] en=dataWeightsToBoolean();
en= filterByZRanges(
zRanges,
en,
scanMask);
maskDataWeights(en);
}
if (calibrateMode && filterTiltedByScanValue){
boolean [] en=dataWeightsToBoolean();
en= filterByScanValues(
zRanges,
en,
scanMask);
maskDataWeights(en);
}
if (calibrateMode && !Double.isNaN(filterTiltedByValueScale) && (filterTiltedByValueScale>0.0)){
boolean [] en=dataWeightsToBoolean();
en= filterByValue(
filterByValueScale,
en,
scanMask);
maskDataWeights(en);
}
// TODO: add filtering for tilt motor calibration
fieldFitting.initSampleCorrVector(
......@@ -2051,7 +2195,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
chn,
value,
value_dx0, //double dPxc; // derivative of the value by optical (aberration) center pixel X
value_dy0 //double dPyc; // derivative of the value by optical (aberration) center pixel Y
value_dy0, //double dPyc; // derivative of the value by optical (aberration) center pixel Y
false // scan (scan mode sample)
));
if (debugLevel>3) System.out.print(" E "+value);
if (updateSelection) sampleMask[nMeas][i][j][c][d]=true;
......@@ -3350,6 +3495,7 @@ public boolean dialogLMAStep(boolean [] state){
public double getAdjustRMS(
FocusingFieldMeasurement measurement,
boolean filterZ,
boolean filterByScanValue,
double filterByValueScale,
double z,
double tx,
......@@ -3364,7 +3510,19 @@ public double getAdjustRMS(
boolean [] en=dataWeightsToBoolean();
en= filterByZRanges(
zRanges,
en);
en,
null);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return Double.NaN;
}
if (filterByScanValue) {
boolean [] en=dataWeightsToBoolean();
en= filterByScanValues(
zRanges,
en,
null);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
......@@ -3374,7 +3532,8 @@ public double getAdjustRMS(
boolean [] en=dataWeightsToBoolean();
en= filterByValue(
filterByValueScale,
en);
en,
null);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
......@@ -3392,10 +3551,11 @@ public double getAdjustRMS(
int [] numSamples=getNumCenterSamples( // per channel
centerSampesMask,
en);
System.out.println("Not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
// System.out.println("Not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
System.out.print("Got:");
for (int n:numSamples) System.out.print(" "+n);
System.out.println();
System.out.println(" - not enough center samples, requested "+minCenterSamplesBest+" best channel and "+minCenterSamplesTotal+" total.");
// System.out.println();
}
return Double.NaN;
}
......@@ -3409,6 +3569,7 @@ public double getAdjustRMS(
public double [] findAdjustZ(
FocusingFieldMeasurement measurement,
boolean filterZ,
boolean filterByScanValue,
double filterByValueScale,
double zMin,
double zMax,
......@@ -3425,6 +3586,7 @@ public double [] findAdjustZ(
double rms=getAdjustRMS(
measurement,
filterZ,
filterByScanValue,
filterByValueScale,
z,
tx,
......@@ -3509,7 +3671,19 @@ public boolean LevenbergMarquardt(
boolean [] en=dataWeightsToBoolean();
en= filterByZRanges(
zRanges,
en);
en,
null);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
if (numEn<minLeftSamples) return false;
}
if (filterByScanValue) {
boolean [] en=dataWeightsToBoolean();
en= filterByScanValues(
zRanges,
en,
null);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
......@@ -3519,7 +3693,8 @@ public boolean LevenbergMarquardt(
boolean [] en=dataWeightsToBoolean();
en= filterByValue(
filterByValueScale,
en);
en,
null);
maskDataWeights(en);
prevEnable=en;
int numEn=getNumEnabledSamples(en);
......@@ -3672,7 +3847,9 @@ public boolean LevenbergMarquardt(
}
this.savedVector=this.currentVector.clone();
commitParameterVector(this.savedVector);
if (calibrate) zRanges=calcZRanges(dataWeightsToBoolean());
if (calibrate) zRanges=calcZRanges(
true, // boolean scanOnly, // do not use non-scan samples
dataWeightsToBoolean());
return true; // all series done
}
......@@ -3961,6 +4138,7 @@ public boolean LevenbergMarquardt(
gd.addCheckbox("Filter samples/channels by Z",filterZ);
gd.addCheckbox("Filter by value (leave lower than maximal fwhm used in focal scan mode)",filterByScanValue);
gd.addNumericField("Filter by value (remove samples above scaled best FWHM for channel/location)",filterByValueScale,2,5,"x");
gd.addNumericField("Minimal required number of channels/samples",minLeftSamples,0,3,"samples");
gd.addNumericField("... of them closest to the center, best channel",minCenterSamplesBest,0,3,"samples");
......@@ -3989,8 +4167,8 @@ public boolean LevenbergMarquardt(
for (int i=0;i<fieldFitting.channelSelect.length;i++) {
fieldFitting.channelSelect[i]=gd.getNextBoolean();
}
filterZ=gd.getNextBoolean();
filterZ= gd.getNextBoolean();
filterByScanValue= gd.getNextBoolean();
filterByValueScale=gd.getNextNumber();
minLeftSamples=(int) gd.getNextNumber();
minCenterSamplesBest=(int) gd.getNextNumber();
......@@ -4206,6 +4384,7 @@ public boolean LevenbergMarquardt(
// measurements.get(nMeas),
measurement,
filterZ, //boolean filterZ,
filterByScanValue,
filterByValueScale,
zMin,
zMax,
......@@ -6058,8 +6237,8 @@ public boolean LevenbergMarquardt(
d2Z/dX/dm2=-ps/(4*Lx)* kM2 *( m2 + sM2*P/(2*pi)*sin(2pi*m2/P) + cM2*P/(2*pi)*cos(2pi*m2/P))
d2Z/dX/dm3= ps/(2*Lx)* kM3 * (m3 + sM3*P/(2*pi)*sin(2pi*m3/P) + cM3*P/(2*pi)*cos(2pi*m3/P))
d2Z/dY/dm1=+ps/(2*Ly)* kM1 * (m1 + sM1*P/(2*pi)*sin(2pi*m1/P) + cM1*P/(2*pi)*cos(2pi*m1/P))
d2Z/dY/dm2= -ps/(2*Ly)* kM2 * (m2 + sM2*P/(2*pi)*sin(2pi*m2/P) + cM2*P/(2*pi)*cos(2pi*m2/P))
d2Z/dY/dm1= -ps/(2*Ly)* kM1 * (m1 + sM1*P/(2*pi)*sin(2pi*m1/P) + cM1*P/(2*pi)*cos(2pi*m1/P)) //!
d2Z/dY/dm2= +ps/(2*Ly)* kM2 * (m2 + sM2*P/(2*pi)*sin(2pi*m2/P) + cM2*P/(2*pi)*cos(2pi*m2/P)) //!
d2Z/dY/dm3= 0
*/
......@@ -6080,8 +6259,8 @@ public boolean LevenbergMarquardt(
double dx=PIXEL_SIZE*(px-getValue(MECH_PAR.mpX0));
double dy=PIXEL_SIZE*(py-getValue(MECH_PAR.mpY0));
double zx=dx*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
// double zy=dy*(getValue(MECH_PAR.ty)+(zM1-zM2)/(2*getValue(MECH_PAR.Ly)));
double zy=dy*(getValue(MECH_PAR.ty)+(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));
// double zy=dy*(getValue(MECH_PAR.ty)-(zM1-zM2)/(2*getValue(MECH_PAR.Ly))); //!
double zy=dy*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))); //!
double z=zc+zx+zy;
if (dbg) if ((Math.abs(m1)==debugMot)&& (Math.abs(m2)==debugMot)){
System.out.print ("M: "+((int)m1)+":"+((int)m2)+":"+((int)m3)+
......@@ -6140,8 +6319,8 @@ public boolean LevenbergMarquardt(
double zx_mpX0=dx_mpX0*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))); // double zx_mpX0=dx_mpX0/(4*getValue(MECH_PAR.Lx));
double zx_tx= dx;
double zx_Lx= -dx*(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx)*getValue(MECH_PAR.Lx));
// double zy=dy*(getValue(MECH_PAR.ty)+(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));
double zy_a=dy/(2*getValue(MECH_PAR.Ly));
// double zy=dy*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly))); //!
double zy_a= -dy/(2*getValue(MECH_PAR.Ly)); //!
double zy_K0= (zM2_K0- zM1_K0) *zy_a;
double zy_KD1= (zM2_KD1-zM1_KD1)*zy_a;
double zy_KD3= (zM2_KD3-zM1_KD3)*zy_a;
......@@ -6151,10 +6330,11 @@ public boolean LevenbergMarquardt(
double zy_cM2= (zM2_cM2)*zy_a;
double zy_sM3= 0.0;
double zy_cM3= 0.0;
double zy_mpY0=dy_mpY0*(getValue(MECH_PAR.ty)+(zM2-zM1)/(2*getValue(MECH_PAR.Ly))); // double zy_mpY0=dy_mpY0/(2*getValue(MECH_PAR.Ly));
double zy_mpY0=dy_mpY0*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));//! // double zy_mpY0=-dy_mpY0/(2*getValue(MECH_PAR.Ly));//!
double zy_ty= dy;
// double zy_Ly= -dy*(zM1-zM2)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly));
double zy_Ly= -dy*(zM2-zM1)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly));
// double zy_Ly= dy*(zM1-zM2)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly)); //!
// double zy_Ly= -dy*(zM2-zM1)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly)); //!
double zy_Ly= dy*(zM2-zM1)/(2*getValue(MECH_PAR.Ly)*getValue(MECH_PAR.Ly)); //!
deriv[getIndex(MECH_PAR.K0)]= zc_K0+zx_K0+zy_K0;
deriv[getIndex(MECH_PAR.KD1)]=zc_KD1+zx_KD1+zy_KD1;
......@@ -6322,22 +6502,22 @@ public boolean LevenbergMarquardt(
double dy=PIXEL_SIZE*(py-getValue(MECH_PAR.mpY0));
// double zc= 0.25* zM1+ 0.25* zM2+ 0.5 * zM3+getValue(MECH_PAR.z0);
// double zx=dx*(getValue(MECH_PAR.tx)+(2*zM3-zM1-zM2)/(4*getValue(MECH_PAR.Lx))) ;
// double zy=dy*(getValue(MECH_PAR.ty)+(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));
// double zy=dy*(getValue(MECH_PAR.ty)-(zM2-zM1)/(2*getValue(MECH_PAR.Ly)));//!
// double z=zc+zx+zy
// A*{zM1,zM2,zM3}={targetZ,targetTx,targetTy}
// A*{zM1,zM2,zM3}={targetZ-getValue(MECH_PAR.z0),targetTx-dx*getValue(MECH_PAR.tx),targetTy-dy*getValue(MECH_PAR.ty)}
double [][] A={
{
0.25 - dx/(4*getValue(MECH_PAR.Lx)) -dy/(2*getValue(MECH_PAR.Ly)),
0.25 - dx/(4*getValue(MECH_PAR.Lx)) +dy/(2*getValue(MECH_PAR.Ly)),
0.25 - dx/(4*getValue(MECH_PAR.Lx)) +dy/(2*getValue(MECH_PAR.Ly)), //!
0.25 - dx/(4*getValue(MECH_PAR.Lx)) -dy/(2*getValue(MECH_PAR.Ly)), //!
0.5 + dx/(2*getValue(MECH_PAR.Lx))
} , {
-1.0/(4*getValue(MECH_PAR.Lx)),
-1.0/(4*getValue(MECH_PAR.Lx)),
1.0/ (2*getValue(MECH_PAR.Lx))
} , {
-1.0/(2*getValue(MECH_PAR.Ly)),
1.0/ (2*getValue(MECH_PAR.Ly)),
1.0/(2*getValue(MECH_PAR.Ly)), //!
-1.0/ (2*getValue(MECH_PAR.Ly)), //!
0.0
}
};
......
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