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Commit 348b8ec1 authored by Andrey Filippov's avatar Andrey Filippov
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src/main/java/Aberration_Calibration.java
View file @ 348b8ec1
...@@ -55,6 +55,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene ...@@ -55,6 +55,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
private Panel panelConf1,panelConf2,panelRun, panelDistortions, panelFitDistortions, panelProcessDistortions,panelAberrations ; private Panel panelConf1,panelConf2,panelRun, panelDistortions, panelFitDistortions, panelProcessDistortions,panelAberrations ;
private Panel panelCorrectGrid; private Panel panelCorrectGrid;
private Panel panelFocusing,panelFocusing1; private Panel panelFocusing,panelFocusing1;
private Panel panelCurvature;
private Panel panelGoniometer; private Panel panelGoniometer;
private Panel panelPixelMapping, panelStereo,panelStereo1; private Panel panelPixelMapping, panelStereo,panelStereo1;
...@@ -556,7 +557,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi ...@@ -556,7 +557,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
addKeyListener(IJ.getInstance()); addKeyListener(IJ.getInstance());
// setLayout(new GridLayout(ADVANCED_MODE?8:5, 1)); // setLayout(new GridLayout(ADVANCED_MODE?8:5, 1));
// setLayout(new GridLayout(ADVANCED_MODE?9:6, 1)); // setLayout(new GridLayout(ADVANCED_MODE?9:6, 1));
setLayout(new GridLayout(ADVANCED_MODE?19:19, 1)); setLayout(new GridLayout(ADVANCED_MODE?20:20, 1));
Color color_configure= new Color(200, 200,160); Color color_configure= new Color(200, 200,160);
Color color_process= new Color(180, 180, 240); Color color_process= new Color(180, 180, 240);
Color color_conf_process= new Color(180, 240, 240); Color color_conf_process= new Color(180, 240, 240);
...@@ -777,14 +778,23 @@ if (MORE_BUTTONS) { ...@@ -777,14 +778,23 @@ if (MORE_BUTTONS) {
addButton("Temp. Scan",panelFocusing,color_process); addButton("Temp. Scan",panelFocusing,color_process);
// //
addButton("List History",panelFocusing,color_report); addButton("List History",panelFocusing,color_report);
addButton("Save History",panelFocusing,color_debug);
addButton("Restore History",panelFocusing,color_debug);
addButton("Modify LMA",panelFocusing,color_debug);
addButton("LMA History",panelFocusing,color_debug);
addButton("List curv pars",panelFocusing,color_debug);
addButton("List curv data",panelFocusing,color_debug);
addButton("Show PSF",panelFocusing,color_report); addButton("Show PSF",panelFocusing,color_report);
add(panelFocusing); add(panelFocusing);
// panelCurvature
panelCurvature=new Panel();
panelCurvature.setLayout(new GridLayout(1, 0, 5, 5));
addButton("Save History", panelCurvature,color_debug);
addButton("Restore History",panelCurvature,color_debug);
addButton("Modify LMA", panelCurvature,color_debug);
addButton("LMA History", panelCurvature,color_process);
addButton("List curv pars", panelCurvature,color_debug);
addButton("List curv data", panelCurvature,color_debug);
addButton("List qualB", panelCurvature,color_report);
addButton("List curv", panelCurvature,color_report);
addButton("Show curv corr", panelCurvature,color_report);
add(panelCurvature);
//panelGoniometer //panelGoniometer
panelGoniometer = new Panel(); panelGoniometer = new Panel();
...@@ -4300,10 +4310,10 @@ if (MORE_BUTTONS) { ...@@ -4300,10 +4310,10 @@ if (MORE_BUTTONS) {
this.SYNC_COMMAND.stopRequested); this.SYNC_COMMAND.stopRequested);
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL); FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
System.out.println("Loaded FocusingField"); System.out.println("Loaded FocusingField");
FOCUSING_FIELD.configureDataVector("Configure curvature",true); if (!FOCUSING_FIELD.configureDataVector("Configure curvature",true)) return;
FOCUSING_FIELD.setDataVector(FOCUSING_FIELD.createDataVector()); FOCUSING_FIELD.setDataVector(FOCUSING_FIELD.createDataVector());
double []focusing_fx=FOCUSING_FIELD.createFXandJacobian(true); double []focusing_fx=FOCUSING_FIELD.createFXandJacobian(true);
double rms= FOCUSING_FIELD.getRMS(focusing_fx); double rms= FOCUSING_FIELD.getRMS(focusing_fx,false);
System.out.println("rms="+rms); System.out.println("rms="+rms);
return; return;
} }
...@@ -4312,7 +4322,7 @@ if (MORE_BUTTONS) { ...@@ -4312,7 +4322,7 @@ if (MORE_BUTTONS) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return; if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL); FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.configureDataVector("Re-configure curvature parameters",false); if (!FOCUSING_FIELD.configureDataVector("Re-configure curvature parameters",false)) return;
FOCUSING_FIELD.setDataVector(FOCUSING_FIELD.createDataVector()); FOCUSING_FIELD.setDataVector(FOCUSING_FIELD.createDataVector());
return; return;
} }
...@@ -4341,8 +4351,31 @@ if (MORE_BUTTONS) { ...@@ -4341,8 +4351,31 @@ if (MORE_BUTTONS) {
return; return;
} }
//"LMA History" /* ======================================================================== */
if (label.equals("List qualB")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.listScanQB(); // to screen
return;
}
/* ======================================================================== */
if (label.equals("List curv")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.listCombinedResults(); // to screen
return;
}
/* ======================================================================== */
if (label.equals("Show curv corr")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.showCurvCorr(); // to screen
return;
}
//
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("Show PSF")) { if (label.equals("Show PSF")) {
......
src/main/java/FocusingField.java
View file @ 348b8ec1
...@@ -32,6 +32,7 @@ import java.io.File; ...@@ -32,6 +32,7 @@ import java.io.File;
import java.io.FileWriter; import java.io.FileWriter;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.concurrent.atomic.AtomicInteger; import java.util.concurrent.atomic.AtomicInteger;
import org.apache.commons.configuration.ConfigurationException; import org.apache.commons.configuration.ConfigurationException;
...@@ -42,6 +43,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -42,6 +43,7 @@ import org.apache.commons.configuration.XMLConfiguration;
//import Distortions.LMAArrays; // may still reuse? //import Distortions.LMAArrays; // may still reuse?
import Jama.LUDecomposition; import Jama.LUDecomposition;
import Jama.Matrix; import Jama.Matrix;
...@@ -71,8 +73,8 @@ public class FocusingField { ...@@ -71,8 +73,8 @@ public class FocusingField {
boolean useMaxMeas= true; boolean useMaxMeas= true;
boolean useThresholdMax=true; boolean useThresholdMax=true;
FieldFitting fieldFitting=null; FieldFitting fieldFitting=null;
int weighMode=2; // 0; // 0 - same weight, 1 - linear threshold difference, 2 - quadratic thershold difference int weighMode=1; // 0; // 0 - same weight, 1 - linear threshold difference, 2 - quadratic thershold difference
double weightRadius=2.0; // Gaussian sigma in mm double weightRadius=0.0; //2.0; // Gaussian sigma in mm
MeasuredSample [] dataVector; MeasuredSample [] dataVector;
double [] dataValues; double [] dataValues;
double [] dataWeights; double [] dataWeights;
...@@ -86,8 +88,12 @@ public class FocusingField { ...@@ -86,8 +88,12 @@ public class FocusingField {
private double [] currentfX=null; // array of "f(x)" - simulated data for all images, combining pixel-X and pixel-Y (odd/even) private double [] currentfX=null; // array of "f(x)" - simulated data for all images, combining pixel-X and pixel-Y (odd/even)
private double [] nextfX=null; // array of "f(x)" - simulated data for all images, combining pixel-X and pixel-Y (odd/even) private double [] nextfX=null; // array of "f(x)" - simulated data for all images, combining pixel-X and pixel-Y (odd/even)
private double currentRMS=-1.0; // calculated RMS for the currentVector->currentfX private double currentRMS=-1.0; // calculated RMS for the currentVector->currentfX
private double currentRMSPure=-1.0; // calculated RMS for the currentVector->currentfX
private double nextRMS=-1.0; // calculated RMS for the nextVector->nextfX private double nextRMS=-1.0; // calculated RMS for the nextVector->nextfX
private double nextRMSPure=-1.0; // calculated RMS for the nextVector->nextfX
private double firstRMS=-1.0; // RMS before current series of LMA started private double firstRMS=-1.0; // RMS before current series of LMA started
private double firstRMSPure=-1.0; // RMS before current series of LMA started
private double lambdaStepUp= 8.0; // multiply lambda by this if result is worse private double lambdaStepUp= 8.0; // multiply lambda by this if result is worse
private double lambdaStepDown= 0.5; // multiply lambda by this if result is better private double lambdaStepDown= 0.5; // multiply lambda by this if result is better
private double thresholdFinish=0.001; // (copied from series) stop iterations if 2 last steps had less improvement (but not worsening ) private double thresholdFinish=0.001; // (copied from series) stop iterations if 2 last steps had less improvement (but not worsening )
...@@ -101,6 +107,7 @@ public class FocusingField { ...@@ -101,6 +107,7 @@ public class FocusingField {
private boolean stopOnFailure= true; // open dialog when fitting series failed private boolean stopOnFailure= true; // open dialog when fitting series failed
private boolean showParams= false; // show modified parameters private boolean showParams= false; // show modified parameters
private boolean showDisabledParams = false; private boolean showDisabledParams = false;
private boolean showCorrectionParams = false;
private long startTime=0; private long startTime=0;
private AtomicInteger stopRequested=null; // 1 - stop now, 2 - when convenient private AtomicInteger stopRequested=null; // 1 - stop now, 2 - when convenient
private boolean saveSeries=false; // just for the dialog private boolean saveSeries=false; // just for the dialog
...@@ -122,6 +129,29 @@ public class FocusingField { ...@@ -122,6 +129,29 @@ public class FocusingField {
public boolean debugDerivatives; public boolean debugDerivatives;
public boolean debugDerivativesFxDxDy=false; public boolean debugDerivativesFxDxDy=false;
private double k_red=0.7;
private double k_blue=0.4;
private double qb_scan_below=-20.0; // um
private double qb_scan_above= 60.0; // um
private double qb_scan_step= 0.5; // um
private boolean qb_use_corrected=true;
private boolean qb_invert=true;
private boolean rslt_show_z_axial=true;
private boolean rslt_show_z_individual=true;
private boolean rslt_show_f_axial=true;
private boolean rslt_show_f_individual=true;
private double rslt_scan_below=-10.0;
private double rslt_scan_above= 10.0;
private double rslt_scan_step= 5.0;
private boolean rslt_mtf50_mode= true;
private boolean [] rslt_show_chn={true,true,true,true,true,true};
// public double fwhm_to_mtf50=500.0; // put actual number
public double fwhm_to_mtf50=2*Math.log(2.0)/Math.PI*1000; //pi/0.004
public void setDebugLevel(int debugLevel){ public void setDebugLevel(int debugLevel){
this.debugLevel=debugLevel; this.debugLevel=debugLevel;
} }
...@@ -157,12 +187,22 @@ public class FocusingField { ...@@ -157,12 +187,22 @@ public class FocusingField {
} }
public static double getPixelMM(){return PIXEL_SIZE;} public static double getPixelMM(){return PIXEL_SIZE;}
public static double getPixelUM(){return PIXEL_SIZE*1000;} public static double getPixelUM(){return PIXEL_SIZE*1000;}
public int flattenIndex(int i, int j){return j+i*sampleCoord[0].length;}
public int getNumSamples(){return sampleCoord.length*sampleCoord[0].length;}
public int getSampleWidth(){return sampleCoord[0].length;}
public double [][] flattenSampleCoord(){
///sampleCoord
double [][] flatSampleCoord=new double [sampleCoord.length*sampleCoord[0].length][2];
int index=0;
for (int i=0;i<sampleCoord.length;i++) for (int j=0;j<sampleCoord[0].length;j++) flatSampleCoord[index++]= sampleCoord[i][j];
return flatSampleCoord; // last dimension is not cloned
}
public class MeasuredSample{ public class MeasuredSample{
public int [] motors = new int[3]; public int [] motors = new int[3];
public String timestamp; public String timestamp;
public double px; public double px;
public double py; public double py;
public int sampleIndex=0;
public int channel; public int channel;
public double value; public double value;
public double [] dPxyc=new double[2]; // derivative of the value by optical (aberration) center pixel X,Y public double [] dPxyc=new double[2]; // derivative of the value by optical (aberration) center pixel X,Y
...@@ -174,6 +214,7 @@ public class FocusingField { ...@@ -174,6 +214,7 @@ public class FocusingField {
String timestamp, String timestamp,
double px, double px,
double py, double py,
int sampleIndex,
int channel, int channel,
double value, double value,
double dPxc, double dPxc,
...@@ -187,6 +228,7 @@ public class FocusingField { ...@@ -187,6 +228,7 @@ public class FocusingField {
this.value = value; this.value = value;
this.dPxyc[0]=dPxc; this.dPxyc[0]=dPxc;
this.dPxyc[1]=dPyc; this.dPxyc[1]=dPyc;
this.sampleIndex=sampleIndex;
} }
} }
public boolean configureDataVector(String title, boolean forcenew){ public boolean configureDataVector(String title, boolean forcenew){
...@@ -259,8 +301,12 @@ public class FocusingField { ...@@ -259,8 +301,12 @@ public class FocusingField {
numCurvPars[0], numCurvPars[0],
numCurvPars[1]); numCurvPars[1]);
} }
if (setupMasks) fieldFitting.maskSetDialog("Setup parameter masks"); if (setupMasks) {
if (setupParameters) fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled); if (!fieldFitting.maskSetDialog("Setup parameter masks")) return false;
}
if (setupParameters) {
if (!fieldFitting.showModifyParameterValues("Setup parameter values",showDisabled)) return false;
}
double [] centerXY=fieldFitting.getCenterXY(); double [] centerXY=fieldFitting.getCenterXY();
currentPX0=centerXY[0]; currentPX0=centerXY[0];
currentPY0=centerXY[1]; currentPY0=centerXY[1];
...@@ -281,8 +327,9 @@ public class FocusingField { ...@@ -281,8 +327,9 @@ public class FocusingField {
dataVector=new MeasuredSample [numSamples]; dataVector=new MeasuredSample [numSamples];
int n=0; int n=0;
for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) dataVector[n++]=vector[i]; for (int i=0;i<vector.length;i++) if (chanSel[vector[i].channel]) dataVector[n++]=vector[i];
dataValues = new double [dataVector.length]; int corrLength=fieldFitting.getNumberOfCorrParameters();
dataWeights = new double [dataVector.length]; dataValues = new double [dataVector.length+corrLength];
dataWeights = new double [dataVector.length+corrLength];
// sumWeights=0.0; // sumWeights=0.0;
int mode=weighMode; int mode=weighMode;
double kw= (weightRadius>0.0)?(-0.5*getPixelMM()*getPixelMM()/(weightRadius*weightRadius)):0; double kw= (weightRadius>0.0)?(-0.5*getPixelMM()*getPixelMM()/(weightRadius*weightRadius)):0;
...@@ -305,6 +352,10 @@ public class FocusingField { ...@@ -305,6 +352,10 @@ public class FocusingField {
} }
// sumWeights+=dataWeights[i]; // sumWeights+=dataWeights[i];
} }
for (int i=0;i<corrLength;i++){
dataValues[i+dataVector.length]=0.0; // correction target is always 0
dataWeights[i+dataVector.length]=1.0; // improve?
}
} }
// for compatibility with Distortions class\ // for compatibility with Distortions class\
...@@ -336,7 +387,8 @@ public class FocusingField { ...@@ -336,7 +387,8 @@ public class FocusingField {
public double [] createFXandJacobian(boolean createJacobian){ public double [] createFXandJacobian(boolean createJacobian){
double [] fx=new double[dataVector.length]; int numCorrPar=fieldFitting.getNumberOfCorrParameters();
double [] fx=new double[dataVector.length + numCorrPar ];
double [][] derivs=null; double [][] derivs=null;
double [] subData=null; double [] subData=null;
boolean [] selChannels=fieldFitting.getSelectedChannels(); boolean [] selChannels=fieldFitting.getSelectedChannels();
...@@ -346,8 +398,11 @@ public class FocusingField { ...@@ -346,8 +398,11 @@ public class FocusingField {
selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0); selChanIndices[i]= selChanIndices[i-1]+(selChannels[i-1]?1:0);
} }
int numPars=fieldFitting.getNumberOfParameters(sagittalMaster); int numPars=fieldFitting.getNumberOfParameters(sagittalMaster);
int numRegPars=fieldFitting.getNumberOfRegularParameters(sagittalMaster);
if (createJacobian) { if (createJacobian) {
jacobian=new double [numPars][dataVector.length]; jacobian=new double [numPars][dataVector.length+numCorrPar];
for (double [] row : jacobian)
Arrays.fill(row, 0.0);
derivs=new double [fieldFitting.getNumberOfChannels()][]; derivs=new double [fieldFitting.getNumberOfChannels()][];
} }
String prevTimeStamp=""; String prevTimeStamp="";
...@@ -356,6 +411,7 @@ public class FocusingField { ...@@ -356,6 +411,7 @@ public class FocusingField {
MeasuredSample ms=dataVector[n]; MeasuredSample ms=dataVector[n];
if (!ms.timestamp.equals(prevTimeStamp) || (ms.px!=prevPx) || (ms.py!=prevPy)){ if (!ms.timestamp.equals(prevTimeStamp) || (ms.px!=prevPx) || (ms.py!=prevPy)){
subData=fieldFitting.getValsDerivatives( subData=fieldFitting.getValsDerivatives(
ms.sampleIndex,
sagittalMaster, sagittalMaster,
ms.motors, // 3 motor coordinates ms.motors, // 3 motor coordinates
ms.px, // pixel x ms.px, // pixel x
...@@ -367,9 +423,23 @@ public class FocusingField { ...@@ -367,9 +423,23 @@ public class FocusingField {
} }
fx[n]=subData[selChanIndices[ms.channel]]; fx[n]=subData[selChanIndices[ms.channel]];
if (createJacobian) { if (createJacobian) {
double [] thisDerivs=derivs[selChanIndices[ms.channel]];
// for (int i=0;i<numRegPars;i++){
// contains derivatives for normal and correction parameters
for (int i=0;i<numPars;i++){ for (int i=0;i<numPars;i++){
jacobian[i][n]=derivs[selChanIndices[ms.channel]][i]; // jacobian[i][n]=derivs[selChanIndices[ms.channel]][i];
jacobian[i][n]=thisDerivs[i];
} }
/*
if ((fieldFitting.sampleCorrChnParIndex!=null) && (fieldFitting.sampleCorrChnParIndex[ms.channel]!=null)){
for (int i=0;i<fieldFitting.getNumCurvars()[0];i++){
if (fieldFitting.sampleCorrChnParIndex[ms.channel][i]>=0){
jacobian[i][n]
}
}
}
*/
//TODO: correct /dpx, /dpy to compensate for measured S,T calcualtion //TODO: correct /dpx, /dpy to compensate for measured S,T calcualtion
boolean [] centerSelect=fieldFitting.getCenterSelect(); boolean [] centerSelect=fieldFitting.getCenterSelect();
if (correct_measurement_ST && (centerSelect[0] || centerSelect[1])){ // do not do that if both X and Y are disabled if (correct_measurement_ST && (centerSelect[0] || centerSelect[1])){ // do not do that if both X and Y are disabled
...@@ -379,23 +449,59 @@ public class FocusingField { ...@@ -379,23 +449,59 @@ public class FocusingField {
} }
} }
} }
// add mutual dependence of correction parameters. first - values (fx)
int index=dataVector.length; // add to the end of vector
if (fieldFitting.sampleCorrChnParIndex!=null){
int numSamples=getNumSamples();
for (int chn=0;chn<fieldFitting.sampleCorrChnParIndex.length;chn++) if (fieldFitting.sampleCorrChnParIndex[chn]!=null) {
for (int np=0;np<fieldFitting.sampleCorrChnParIndex[chn].length;np++){
int pindex=fieldFitting.sampleCorrChnParIndex[chn][np];
if (pindex>=0) {
for (int i=0;i<numSamples;i++){
double f=0.0;
for (int j=0;j<numSamples;j++){
f+=fieldFitting.sampleCorr[pindex+j]*fieldFitting.sampleCorrCrossWeights[chn][np][i][j];
}
fx[index]=f;
// f+=fieldFitting.sampleCorr[pindex+i]
if (createJacobian) {
for (int j=0;j<numSamples;j++){
jacobian[numRegPars+pindex+j][index]=fieldFitting.sampleCorrCrossWeights[chn][np][i][j];
}
}
index++;
}
}
}
}
}
} }
return fx; return fx;
} }
public double getRMS(double [] fx){ public double getRMS(double [] fx, boolean pure){
int len=pure?dataVector.length:fx.length;
double sum=0.0; double sum=0.0;
double sum_w=0.0; double sum_w=0.0;
for (int i=0;i<fx.length;i++){ if (dataWeights!=null){
for (int i=0;i<len;i++){
double d=fx[i]-dataValues[i]; double d=fx[i]-dataValues[i];
sum+=dataWeights[i]*d*d; sum+=dataWeights[i]*d*d;
sum_w+=dataWeights[i]; sum_w+=dataWeights[i];
} }
} else {
for (int i=0;i<len;i++){
double d=fx[i]-dataValues[i];
sum+=d*d;
sum_w+=1.0;
}
}
if (sum_w>0) { if (sum_w>0) {
sum/=sum_w; sum/=sum_w;
} }
return Math.sqrt(sum); return Math.sqrt(sum);
} }
public MeasuredSample [] createDataVector(){ public MeasuredSample [] createDataVector(){
return createDataVector( return createDataVector(
true, // boolean updateSelection, true, // boolean updateSelection,
...@@ -759,6 +865,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -759,6 +865,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
ffm.timestamp, ffm.timestamp,
sampleCoord[i][j][0], // px, sampleCoord[i][j][0], // px,
sampleCoord[i][j][1], // py, sampleCoord[i][j][1], // py,
flattenIndex(i,j),
chn, chn,
value, value,
value_dx0, //double dPxc; // derivative of the value by optical (aberration) center pixel X value_dx0, //double dPxc; // derivative of the value by optical (aberration) center pixel X
...@@ -787,11 +894,12 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -787,11 +894,12 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
for (int i=0;i<result.length;i++) result[i]-=fX[i]; for (int i=0;i<result.length;i++) result[i]-=fX[i];
return result; return result;
} }
public double calcErrorDiffY(double [] fX){ public double calcErrorDiffY(double [] fX, boolean pure){
int len=pure?dataVector.length:fX.length;
double result=0; double result=0;
double sumWeights=0; double sumWeights=0;
if (this.dataWeights!=null) { if (this.dataWeights!=null) {
for (int i=0;i<fX.length;i++){ for (int i=0;i<len;i++){ //
double diff=this.dataValues[i]-fX[i]; double diff=this.dataValues[i]-fX[i];
result+=diff*diff*this.dataWeights[i]; result+=diff*diff*this.dataWeights[i];
if (debugLevel>2) System.out.println(""+i+"fx="+fX[i]+" data="+this.dataValues[i]+" diff="+diff+" w="+this.dataWeights[i]); if (debugLevel>2) System.out.println(""+i+"fx="+fX[i]+" data="+this.dataValues[i]+" diff="+diff+" w="+this.dataWeights[i]);
...@@ -799,7 +907,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -799,7 +907,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
if (sumWeights>0) result/=sumWeights; if (sumWeights>0) result/=sumWeights;
} else { } else {
for (int i=0;i<fX.length;i++){ for (int i=0;i<len;i++){
double diff=this.dataValues[i]-fX[i]; double diff=this.dataValues[i]-fX[i];
result+=diff*diff; result+=diff*diff;
} }
...@@ -933,18 +1041,21 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -933,18 +1041,21 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
this.currentfX=createFXandJacobian(this.currentVector, true); // is it always true here (this.jacobian==null) this.currentfX=createFXandJacobian(this.currentVector, true); // is it always true here (this.jacobian==null)
this.lMAArrays=calculateJacobianArrays(this.currentfX); this.lMAArrays=calculateJacobianArrays(this.currentfX);
this.currentRMS=calcErrorDiffY(this.currentfX); this.currentRMS= calcErrorDiffY(this.currentfX,false);
this.currentRMSPure=calcErrorDiffY(this.currentfX, true);
if (debugLevel>1) { if (debugLevel>1) {
System.out.println(": initial RMS="+IJ.d2s(this.currentRMS,8)+ System.out.println(": initial RMS="+IJ.d2s(this.currentRMS,8)+" (pure RMS"+IJ.d2s(this.currentRMSPure,8)+")"+
". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length); ". Calculating next Jacobian. Points:"+this.dataValues.length+" Parameters:"+this.currentVector.length);
} }
} else { } else {
// continuing, but need to re-build Y vector to match this.currentVector // continuing, but need to re-build Y vector to match this.currentVector
commitParameterVector(this.currentVector); // may be extra job? commitParameterVector(this.currentVector); // may be extra job?
this.currentRMS= calcErrorDiffY(this.currentfX); // Verify - currentfX is correct, but Y vector is modified! Yes, it is so this.currentRMS= calcErrorDiffY(this.currentfX, false); // Verify - currentfX is correct, but Y vector is modified! Yes, it is so
this.currentRMSPure=calcErrorDiffY(this.currentfX, true);
} }
if (this.firstRMS<0) { if (this.firstRMS<0) {
this.firstRMS=this.currentRMS; this.firstRMS=this.currentRMS;
this.firstRMSPure=this.currentRMSPure;
} }
...@@ -979,12 +1090,15 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -979,12 +1090,15 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
this.jacobian=null; // not needed, just to catch bugs this.jacobian=null; // not needed, just to catch bugs
this.nextfX=createFXandJacobian(this.nextVector,true); this.nextfX=createFXandJacobian(this.nextVector,true);
this.lMAArrays=calculateJacobianArrays(this.nextfX); this.lMAArrays=calculateJacobianArrays(this.nextfX);
this.nextRMS= calcErrorDiffY(this.nextfX); this.nextRMS= calcErrorDiffY(this.nextfX,false);
this.nextRMSPure= calcErrorDiffY(this.nextfX,true);
this.lastImprovements[1]=this.lastImprovements[0]; this.lastImprovements[1]=this.lastImprovements[0];
this.lastImprovements[0]=this.currentRMS-this.nextRMS; this.lastImprovements[0]=this.currentRMS-this.nextRMS;
if (debugLevel>2) { if (debugLevel>2) {
System.out.println("stepLMA this.currentRMS="+this.currentRMS+ System.out.println("stepLMA this.currentRMS="+this.currentRMS+
", this.currentRMSPure="+this.currentRMSPure+
", this.nextRMS="+this.nextRMS+ ", this.nextRMS="+this.nextRMS+
", this.nextRMSPure="+this.nextRMSPure+
", delta="+(this.currentRMS-this.nextRMS)); ", delta="+(this.currentRMS-this.nextRMS));
} }
boolean [] status={matrixNonSingular && (this.nextRMS<=this.currentRMS),!matrixNonSingular}; boolean [] status={matrixNonSingular && (this.nextRMS<=this.currentRMS),!matrixNonSingular};
...@@ -1001,7 +1115,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1001,7 +1115,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
System.out.println("New RMS error is larger than the old one, but the difference is too small to be trusted "); System.out.println("New RMS error is larger than the old one, but the difference is too small to be trusted ");
System.out.println( System.out.println(
"stepLMA this.currentRMS="+this.currentRMS+ "stepLMA this.currentRMS="+this.currentRMS+
", this.currentRMSPure="+this.currentRMSPure+
", this.nextRMS="+this.nextRMS+ ", this.nextRMS="+this.nextRMS+
", this.nextRMSPure="+this.nextRMSPure+
", delta="+(this.currentRMS-this.nextRMS)); ", delta="+(this.currentRMS-this.nextRMS));
} }
...@@ -1035,7 +1151,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1035,7 +1151,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
System.out.println( System.out.println(
"stepLevenbergMarquardtAction() step="+this.iterationStepNumber+ "stepLevenbergMarquardtAction() step="+this.iterationStepNumber+
", this.currentRMS="+this.currentRMS+ ", this.currentRMS="+this.currentRMS+
", this.currentRMSPure="+this.currentRMSPure+
", this.nextRMS="+this.nextRMS+ ", this.nextRMS="+this.nextRMS+
", this.nextRMSPure="+this.nextRMSPure+
" lambda="+this.lambda); //+" at "+IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec"); " lambda="+this.lambda); //+" at "+IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec");
} }
if (this.nextRMS<this.currentRMS) { //improved if (this.nextRMS<this.currentRMS) { //improved
...@@ -1072,6 +1190,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1072,6 +1190,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
gd.addCheckbox("Show modified parameters", this.showParams); gd.addCheckbox("Show modified parameters", this.showParams);
gd.addCheckbox("Show disabled parameters", this.showDisabledParams); gd.addCheckbox("Show disabled parameters", this.showDisabledParams);
gd.addCheckbox("Show per-sample correction parameters", this.showCorrectionParams);
// gd.addCheckbox("Show debug images before correction",this.showThisImages); // gd.addCheckbox("Show debug images before correction",this.showThisImages);
// gd.addCheckbox("Show debug images after correction", this.showNextImages); // gd.addCheckbox("Show debug images after correction", this.showNextImages);
...@@ -1093,6 +1213,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1093,6 +1213,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
// this.askFilter= gd.getNextBoolean(); // this.askFilter= gd.getNextBoolean();
this.showParams= gd.getNextBoolean(); this.showParams= gd.getNextBoolean();
this.showDisabledParams= gd.getNextBoolean(); this.showDisabledParams= gd.getNextBoolean();
this.showCorrectionParams= gd.getNextBoolean();
// this.showThisImages= gd.getNextBoolean(); // this.showThisImages= gd.getNextBoolean();
// this.showNextImages= gd.getNextBoolean(); // this.showNextImages= gd.getNextBoolean();
// this.threadsMax= (int) gd.getNextNumber(); // this.threadsMax= (int) gd.getNextNumber();
...@@ -1103,7 +1224,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1103,7 +1224,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
public void listParameters(String title, String path){ public void listParameters(String title, String path){
String header="State\tDescription\tValue\tUnits"; String header="State\tDescription\tValue\tUnits";
StringBuffer sb = new StringBuffer(); StringBuffer sb = new StringBuffer();
for (String s:this.fieldFitting.getParameterValueStrings(true)){ //this.showDisabledParams)){ // for (String s:this.fieldFitting.getParameterValueStrings(true,true)){ //this.showDisabledParams)){ //
sb.append(s+"\n"); sb.append(s+"\n");
} }
if (path!=null) { if (path!=null) {
...@@ -1308,6 +1429,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1308,6 +1429,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
for (int i=0;i<sampleCoord.length;i++) for (int i=0;i<sampleCoord.length;i++)
for (int j=0;j<sampleCoord[0].length;j++) { for (int j=0;j<sampleCoord[0].length;j++) {
double [] subData=fieldFitting.getValsDerivatives( double [] subData=fieldFitting.getValsDerivatives(
flattenIndex(i,j),
sagittalMaster, // dependent channel does not have center parameters, but that is only used for derivs. sagittalMaster, // dependent channel does not have center parameters, but that is only used for derivs.
ffm.motors, // 3 motor coordinates ffm.motors, // 3 motor coordinates
sampleCoord[i][j][0], // pixel x sampleCoord[i][j][0], // pixel x
...@@ -1391,6 +1513,260 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1391,6 +1513,260 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
} }
public void showCurvCorr(){
fieldFitting.showCurvCorr("curv_corr");
}
public void listCombinedResults(){
// private boolean rslt_show_z_axial=true;
// private boolean rslt_show_z_individual=true;
// private boolean rslt_show_f_axial=true;
// private boolean rslt_show_f_individual=true;
// private double rslt_scan_below=-10.0;
// private double rslt_scan_above= 10.0;
// private double rslt_scan_step= 5.0;
// private boolean rslt_mtf50_mode= true;
// public double fwhm_to_mtf50=500.0; // put actual number
double [] center_z=fieldFitting.getZCenters();
GenericDialog gd = new GenericDialog("Setup results table");
double best_qb_axial= fieldFitting.getBestQualB(
k_red,
k_blue,
false);
double best_qb_corr= fieldFitting.getBestQualB(
k_red,
k_blue,
true);
gd.addMessage("Best center focus for Red "+ IJ.d2s(center_z[0],3)+" um");
gd.addMessage("Best center focus for Green "+ IJ.d2s(center_z[1],3)+" um");
gd.addMessage("Best center focus for Blue "+ IJ.d2s(center_z[2],3)+" um");
gd.addMessage("Best composite distance for FWHM^4, axial model "+ IJ.d2s(best_qb_axial,3)+" um");
gd.addMessage("Best composite distance for FWHM^4, individual "+ IJ.d2s(best_qb_corr,3)+" um");
for (int i=0;i<rslt_show_chn.length;i++){
gd.addCheckbox("Show results for "+fieldFitting.getDescription(i), this.rslt_show_chn[i]);
}
gd.addCheckbox("Show best focus distance (axial model)", this.rslt_show_z_axial);
gd.addCheckbox("Show best focus distance (per-sample adjusted)", this.rslt_show_z_individual);
gd.addCheckbox("Show constant-z sections (axial model)", this.rslt_show_f_axial);
gd.addCheckbox("Show constant-z sections (per-sample adjusted)", this.rslt_show_f_individual);
gd.addCheckbox("Show mtf50 (false - PSF FWHM)", this.rslt_mtf50_mode);
gd.addMessage("Multiple section setup:");
gd.addNumericField("Scan from (relative to green center)", this.rslt_scan_below, 3,7,"um");
gd.addNumericField("Scan to (relative to green center)", this.rslt_scan_above, 3,7,"um");
gd.addNumericField("Scan step", this.rslt_scan_step, 3,7,"um");
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
for (int i=0;i<rslt_show_chn.length;i++){
this.rslt_show_chn[i]=gd.getNextBoolean();
}
this.rslt_show_z_axial= gd.getNextBoolean();
this.rslt_show_z_individual= gd.getNextBoolean();
this.rslt_show_f_axial= gd.getNextBoolean();
this.rslt_show_f_individual= gd.getNextBoolean();
this.rslt_mtf50_mode= gd.getNextBoolean();
this.rslt_scan_below= gd.getNextNumber();
this.rslt_scan_above= gd.getNextNumber();
this.rslt_scan_step= gd.getNextNumber();
listCombinedResults(
"Field curvature measuremnts results", //String title,
null, //String path,
rslt_show_chn, //boolean [] show_chn,
rslt_show_z_axial, //boolean show_z_axial,
rslt_show_z_individual, //boolean show_z_individual,
rslt_show_f_axial, //boolean show_f_axial,
rslt_show_f_individual, //boolean show_f_individual,
center_z[1]+rslt_scan_below, // double scan_below,
center_z[1]+rslt_scan_above, //double scan_above,
rslt_scan_step, //double scan_step,
rslt_mtf50_mode); //boolean freq_mode)
}
public void listCombinedResults(
String title,
String path,
boolean [] show_chn,
boolean show_z_axial,
boolean show_z_individual,
boolean show_f_axial,
boolean show_f_individual,
double scan_below,
double scan_above,
double scan_step,
boolean freq_mode){
String [] chnNames={"RS","RT","GS","GT","BS","BT"};
// double k=this.fwhm_to_mtf50; //TODO: correct psf fwhm to mtf50 conversion
double k=2*Math.log(2.0)/Math.PI*1000;
// String header="Z(um)\tComposite\tRed\tGreen\tBlue";
String header="radius(mm)";
if (show_z_axial){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i];
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\tZ"+chnNames[i]+"*";
}
}
int numSect=0;
if (show_f_axial || show_f_individual) for (double z=scan_below;z<=scan_above;z+=scan_step){
if (show_f_axial) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z,1);
}
}
if (show_f_individual) {
for (int i=0;i<show_chn.length;i++){
if (show_chn[i])header+="\t"+chnNames[i]+IJ.d2s(z,1)+"*";
}
}
numSect++;
}
double [] radiuses=fieldFitting.getSampleRadiuses();
double [][][][] f_values=new double [numSect][2][][];
double [][][] z_values={
(show_z_axial?fieldFitting.getCalcZ(false,true):null),
(show_z_individual?fieldFitting.getCalcZ(true,true):null)};
int sect=0;
for (double z=scan_below;z<=scan_above;z+=scan_step){
f_values[sect][0]=show_f_axial?fieldFitting.getCalcValuesForZ(z, false,true):null;
f_values[sect][1]=show_f_individual?fieldFitting.getCalcValuesForZ(z, true,true):null;
sect++;
}
StringBuffer sb = new StringBuffer();
for (int n=0;n<radiuses.length;n++){
sb.append(IJ.d2s(radiuses[n],3));
if (show_z_axial){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[0][i][n],3));
}
}
if (show_z_individual){
for (int i=0;i<show_chn.length;i++){
if (show_chn[i]) sb.append("\t"+IJ.d2s(z_values[1][i][n],3));
}
}
if (show_f_axial || show_f_individual) for (int s=0;s<numSect;s++){
if (show_f_axial) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][0][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][0][i][n],3));
}
}
if (show_f_individual) for (int i=0;i<show_chn.length;i++) if (show_chn[i]) {
if (freq_mode){
sb.append("\t"+IJ.d2s(k/f_values[s][1][i][n],3));
} else {
sb.append("\t"+IJ.d2s(f_values[s][1][i][n],3));
}
}
}
sb.append("\n");
}
if (path!=null) {
CalibrationFileManagement.saveStringToFile (
path,
header+"\n"+sb.toString());
} else {
new TextWindow(title, header, sb.toString(), 800,1000);
}
}
public void listScanQB(){
double [] center_z=fieldFitting.getZCenters();
double best_qb_axial= fieldFitting.getBestQualB(
k_red,
k_blue,
false);
double best_qb_corr= fieldFitting.getBestQualB(
k_red,
k_blue,
true);
GenericDialog gd = new GenericDialog("Setup quality-B table");
gd.addMessage("Best center focus for Red "+ IJ.d2s(center_z[0],3)+" um");
gd.addMessage("Best center focus for Green "+ IJ.d2s(center_z[1],3)+" um");
gd.addMessage("Best center focus for Blue "+ IJ.d2s(center_z[2],3)+" um");
gd.addMessage("Best composite distance for FWHM^4, axial model "+ IJ.d2s(best_qb_axial,3)+" um");
gd.addMessage("Best composite distance for FWHM^4, individual "+ IJ.d2s(best_qb_corr,3)+" um");
gd.addNumericField("Scan from (relative to green center)", this.qb_scan_below, 3,7,"um");
gd.addNumericField("Scan to (relative to green center)", this.qb_scan_above, 3,7,"um");
gd.addNumericField("Scan step", this.qb_scan_step, 3,7,"um");
gd.addNumericField("Relative (to green) weight of red channel",100* this.k_red, 3,7,"%");
gd.addNumericField("Relative (to green) weight of blue channel",100* this.k_blue, 3,7,"%");
gd.addCheckbox("Use per-sample location corrected data", this.qb_use_corrected);
gd.addCheckbox("Use per-sample location corrected data", this.qb_invert);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
this.qb_scan_below= gd.getNextNumber();
this.qb_scan_above= gd.getNextNumber();
this.qb_scan_step= gd.getNextNumber();
this.k_red= 0.01*gd.getNextNumber();
this.k_blue= 0.01*gd.getNextNumber();
this.qb_use_corrected= gd.getNextBoolean();
this.qb_invert= gd.getNextBoolean();
listScanQB(
"Focus quality vs. distance", // String title,
null, //String path,
center_z[1]+this.qb_scan_below, //double min_z, // absolute
center_z[1]+this.qb_scan_above, //double max_z,
this.qb_scan_step , //double step_z,
this.k_red, //double kr,
this.k_blue, //double kb,
this.qb_use_corrected, //boolean corrected,
this.qb_invert); //boolean freq_mode)
}
public void listScanQB(
String title,
String path,
double min_z, // absolute
double max_z,
double step_z,
double kr,
double kb,
boolean corrected,
boolean freq_mode){
double k=this.fwhm_to_mtf50; //TODO: correct psf fwhm to mtf50 conversion
String header="Z(um)\tComposite\tRed\tGreen\tBlue";
StringBuffer sb = new StringBuffer();
for (double z=min_z; z<=max_z;z+=step_z){
double qb_w= fieldFitting.getQualB(
z,
kr,
kb,
corrected);
double [] qb_rgb=fieldFitting.getQualB(
z,
corrected);
if (freq_mode){
sb.append(z+"\t"+IJ.d2s(k/qb_w,3)+"\t"+IJ.d2s(k/qb_rgb[0],3)+"\t"+IJ.d2s(k/qb_rgb[1],3)+"\t"+IJ.d2s(k/qb_rgb[2],3) +"\n");
} else {
sb.append(z+"\t"+IJ.d2s(qb_w,3)+"\t"+IJ.d2s(qb_rgb[0],3)+"\t"+IJ.d2s(qb_rgb[1],3)+"\t"+IJ.d2s(qb_rgb[2],3) +"\n");
}
}
// for (String s:this.fieldFitting.getParameterValueStrings(true,true)){ //this.showDisabledParams)){ //
// sb.append(s+"\n");
// }
if (path!=null) {
CalibrationFileManagement.saveStringToFile (
path,
header+"\n"+sb.toString());
} else {
new TextWindow(title, header, sb.toString(), 800,1000);
}
}
public boolean dialogLMAStep(boolean [] state){ public boolean dialogLMAStep(boolean [] state){
...@@ -1407,11 +1783,11 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1407,11 +1783,11 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
gd.addMessage("Iteration step="+this.iterationStepNumber); gd.addMessage("Iteration step="+this.iterationStepNumber);
gd.addMessage("Initial RMS="+IJ.d2s(this.firstRMS,6)+", Current RMS="+IJ.d2s(this.currentRMS,6)+", new RMS="+IJ.d2s(this.nextRMS,6)); gd.addMessage("Initial RMS="+IJ.d2s(this.firstRMS,6)+", Current RMS="+IJ.d2s(this.currentRMS,6)+", new RMS="+IJ.d2s(this.nextRMS,6));
// gd.addMessage("Pure initial RMS="+IJ.d2s(this.firstRMSPure,6)+", Current RMS="+IJ.d2s(this.currentRMSPure,6)+", new RMS="+IJ.d2s(this.nextRMSPure,6)); gd.addMessage("Pure initial RMS="+IJ.d2s(this.firstRMSPure,6)+", Current RMS="+IJ.d2s(this.currentRMSPure,6)+", new RMS="+IJ.d2s(this.nextRMSPure,6));
if (this.showParams) { if (this.showParams) {
gd.addMessage("==== Current parameter values ==="); gd.addMessage("==== Current parameter values ===");
for (String s:this.fieldFitting.getParameterValueStrings(this.showDisabledParams)){ // for (String s:this.fieldFitting.getParameterValueStrings(this.showDisabledParams, this.showCorrectionParams)){ //
gd.addMessage(s); gd.addMessage(s);
} }
gd.addMessage(""); gd.addMessage("");
...@@ -1430,6 +1806,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1430,6 +1806,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
gd.addCheckbox("Dialog after each failure", this.stopOnFailure); gd.addCheckbox("Dialog after each failure", this.stopOnFailure);
gd.addCheckbox("Show modified parameters", this.showParams); gd.addCheckbox("Show modified parameters", this.showParams);
gd.addCheckbox("Show disabled parameters", this.showDisabledParams); gd.addCheckbox("Show disabled parameters", this.showDisabledParams);
gd.addCheckbox("Show per-sample correction parameters", this.showCorrectionParams);
// gd.addCheckbox("Show debug images before correction",this.showThisImages); // gd.addCheckbox("Show debug images before correction",this.showThisImages);
// gd.addCheckbox("Show debug images after correction", this.showNextImages); // gd.addCheckbox("Show debug images after correction", this.showNextImages);
gd.addMessage("Done will save the current (not new!) state and exit, Continue will proceed according to LMA"); gd.addMessage("Done will save the current (not new!) state and exit, Continue will proceed according to LMA");
...@@ -1452,6 +1830,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1452,6 +1830,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
this.stopOnFailure= gd.getNextBoolean(); this.stopOnFailure= gd.getNextBoolean();
this.showParams= gd.getNextBoolean(); this.showParams= gd.getNextBoolean();
this.showDisabledParams= gd.getNextBoolean(); this.showDisabledParams= gd.getNextBoolean();
this.showCorrectionParams= gd.getNextBoolean();
// this.showThisImages= gd.getNextBoolean(); // this.showThisImages= gd.getNextBoolean();
// this.showNextImages= gd.getNextBoolean(); // this.showNextImages= gd.getNextBoolean();
...@@ -1492,7 +1871,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1492,7 +1871,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
boolean cont=true; boolean cont=true;
// Make it success if this.currentRMS<this.firstRMS even if LMA failed to converge // Make it success if this.currentRMS<this.firstRMS even if LMA failed to converge
if (state[1] && !state[0] && (this.firstRMS>this.currentRMS)){ if (state[1] && !state[0] && (this.firstRMS>this.currentRMS)){
if (debugLevel>1) System.out.println("LMA failed to converge, but RMS improved from the initial value ("+this.currentRMS+" < "+this.firstRMS+")"); if (debugLevel>1) System.out.println("LMA failed to converge, but RMS improved from the initial value ("+
this.currentRMS+" < "+this.firstRMS+"), currentRMSPure="+currentRMSPure+", firstRMSPure="+firstRMSPure);
state[0]=true; state[0]=true;
} }
if ( if (
...@@ -1811,18 +2191,259 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1811,18 +2191,259 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
} }
public class FieldFitting{ public class FieldFitting{
public double [] pXY=null; private double [] pXY=null;
public boolean [] centerSelect=null; private boolean [] centerSelect=null;
public boolean [] centerSelectDefault={true,true}; private boolean [] centerSelectDefault={true,true};
MechanicalFocusingModel mechanicalFocusingModel; private MechanicalFocusingModel mechanicalFocusingModel;
CurvatureModel [] curvatureModel=new CurvatureModel[6]; // 3 colors, sagittal+tangential each private CurvatureModel [] curvatureModel=new CurvatureModel[6]; // 3 colors, sagittal+tangential each
boolean [] channelSelect=null; private boolean [] channelSelect=null;
boolean [] mechanicalSelect=null; private boolean [] mechanicalSelect=null;
boolean [][] curvatureSelect=new boolean[6][]; private boolean [][] curvatureSelect=new boolean[6][];
private boolean [][] sampleCorrSelect= new boolean[6][]; // enable individual (per sample coordinates) correction of parameters
private double [][] sampleCorrCost= new double[6][]; // equivalent cost of one unit of parameter value (in result units, um)
private double [][] sampleCorrSigma= new double[6][]; // sigma (in mm) for neighbors influence
private double [][] sampleCorrPullZero=new double[6][]; // 1.0 - only difference from neighbors matters, 0.0 - only difference from 0
private double [] sampleCorrRadius=null;
private double [][][][] sampleCorrCrossWeights= new double[6][][][];
private double [] sampleCorr=null;
private int [][] sampleCorrChnParIndex=null;
private boolean [] dflt_sampleCorrSelect= {false,false,false,false};
private double [] dflt_sampleCorrCost= {0.2,100.0,2.0,1.0};
private double dflt_sampleCorrSigma= 1.0; // mm
private double dflt_sampleCorrPullZero= 0.25; // fraction
public final String [] channelDescriptions={ public final String [] channelDescriptions={
"Red, sagittal","Red, tangential", "Red, sagittal","Red, tangential",
"Green, sagittal","Green, tangential", "Green, sagittal","Green, tangential",
"Blue, sagittal","Blue, tangential"}; "Blue, sagittal","Blue, tangential"};
public double [] getSampleRadiuses(){ // distance from the current center to each each sample
return sampleCorrRadius;
}
public void showCurvCorr(String title){
int width=getSampleWidth();
int numSamples=getNumSamples();
String [] chnShortNames={"RS","RT","GS","GT","BRS","BT"};
if ((sampleCorr==null) || (sampleCorr.length==0)) {
String msg="No correction parameters are enabled";
IJ.showMessage(msg);
System.out.println(msg);
return;
}
int numCorrPar=0;
int maxNumPars=0;
for (int chn=0;chn<sampleCorrChnParIndex.length;chn++)
if (sampleCorrChnParIndex[chn]!=null)
for (int np=0;np<sampleCorrChnParIndex[chn].length;np++)
if (sampleCorrChnParIndex[chn][np]>=0) {
numCorrPar++;
if (np>maxNumPars) maxNumPars=np;
}
maxNumPars++;
if (numCorrPar==0){
String msg="Still no correction parameters are enabled";
IJ.showMessage(msg);
System.out.println(msg);
return;
}
double [][] pixels=new double [numCorrPar][numSamples];
String [] titles=new String[numCorrPar];
int index=0;
/*
for (int chn=0;chn<sampleCorrChnParIndex.length;chn++)
if (sampleCorrChnParIndex[chn]!=null)
for (int np=0;np<sampleCorrChnParIndex[chn].length;np++)
if (sampleCorrChnParIndex[chn][np]>=0) {
titles[index]=chnShortNames[chn]+"-"+curvatureModel[chn].getZName(np);
for (int nSample=0;nSample<numSamples;nSample++) {
pixels[index][nSample]=sampleCorr[sampleCorrChnParIndex[chn][np]+nSample];
}
index++;
}
*/
for (int np=0;np<maxNumPars;np++)
for (int chn=0;chn<sampleCorrChnParIndex.length;chn++)
if ((sampleCorrChnParIndex[chn]!=null) && (sampleCorrChnParIndex[chn].length>np) && (sampleCorrChnParIndex[chn][np]>=0)) {
titles[index]=chnShortNames[chn]+"-"+curvatureModel[chn].getZName(np);
for (int nSample=0;nSample<numSamples;nSample++) {
pixels[index][nSample]=sampleCorr[sampleCorrChnParIndex[chn][np]+nSample];
}
index++;
}
(new showDoubleFloatArrays()). showArrays(
pixels,
width,
numSamples/width,
true, //boolean asStack,
title,
titles);
}
/**
* Calculate values (saggital and tangential PSF FWHM in um for each of color channels) for specified z
* @param z distance from lens (from some zero point), image plane is perpendicular to the axis
* @param corrected when false - provide averaged (axial model) for radius, if true - with individual correction applied
* @param allChannels calculate for all (even disabled) channels, false - only for currently selected
* @return outer dimension - number of channel, inner - number of sample (use getSampleRadiuses for radius of each)
*/
public double [][] getCalcValuesForZ(double z, boolean corrected, boolean allChannels){
int numSamples=sampleCorrRadius.length;
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++) {
result[chn][sampleIndex]=curvatureModel[chn].getFdF(
corrected?getCorrPar(chn,sampleIndex):null,
sampleCorrRadius[sampleIndex], //px,
Double.NaN, // py,
z, //mot_z,
null); //deriv_curv[c]);
}
} else {
result[chn]=null;
}
}
return result;
}
/**
* calculate distance to "best focus" for each channel (color and S/T) for each sample
* @param corrected when false - provide averaged (axial model) for radius, if true - with individual correction applied
* @param allChannels calculate for all (even disabled) channels, false - only for currently selected
* @return outer dimension - number of channel, inner - number of sample (use getSampleRadiuses for radius of each)
*/
public double [][] getCalcZ(boolean corrected, boolean allChannels){
int numSamples=sampleCorrRadius.length;
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++) {
result[chn][sampleIndex]=curvatureModel[chn].getAr(
sampleCorrRadius[sampleIndex],
corrected?getCorrPar(chn,sampleIndex):null
)[0];
}
} else {
result[chn]=null;
}
}
return result;
}
public double getGreenZCenter(){
int chn=3; // Green, Tangential
return curvatureModel[chn].getCenterVector()[0];
}
public double [] getZCenters(){
// int chn=3; // Green, Tangential
double [] result = {
curvatureModel[1].getCenterVector()[0], // Red, Tangential
curvatureModel[3].getCenterVector()[0], // Green, Tangential
curvatureModel[5].getCenterVector()[0]}; // Blue, Tangential
return result;
}
public double [] getQualB(double z, boolean corrected){
double [][] data=getCalcValuesForZ(z,corrected, true );
double [] qualB = {0.0,0.0,0.0};
int numSamples=sampleCorrRadius.length;
for (int c=0;c<3;c++) {
if ((data[2*c]!=null) && (data[2*c+1]!=null)){
qualB[c]=0.0;
for (int i=0;i<numSamples;i++){
qualB[c]+=data[2*c][i]*data[2*c][i]*data[2*c][i]*data[2*c][i]+
data[2*c+1][i]*data[2*c+1][i]*data[2*c+1][i]*data[2*c+1][i];
}
qualB[c]/=2.0*numSamples;
qualB[c]=Math.sqrt(Math.sqrt(qualB[c]));
} else {
qualB[c]=Double.NaN;
}
}
return qualB;
}
public double getQualB(
double z,
double kr,
double kb,
boolean corrected){
double [] k={kr,1.0,kb};
double [] qualB=getQualB(z,corrected);
for (int i=0;i<qualB.length;i++) if (Double.isNaN(qualB[i])){
qualB[i]=0.0;
k[i]=0.0;
}
return Math.sqrt(Math.sqrt((
k[0]*qualB[0]*qualB[0]*qualB[0]*qualB[0]+
k[1]*qualB[1]*qualB[1]*qualB[1]*qualB[1]+
k[2]*qualB[2]*qualB[2]*qualB[2]*qualB[2])/
(k[0]+k[1]+k[2])));
}
public double getBestQualB(
double kr,
double kb,
boolean corrected){
return getBestQualB(kr,kb,corrected,1.0,0.001);
}
public double getBestQualB( // find minimum
double kr,
double kb,
boolean corrected,
double iniStep,
double precision){
int maxSteps=100;
double z0=getGreenZCenter();
double qb0=getQualB(z0,kr,kb,corrected);
double z1=z0+iniStep;
double qb1=getQualB(z1,kr,kb,corrected);
double dir = (qb1<qb0)?1.0:-1.0;
double z_prev,qb_prev;
if (dir>0) {
z_prev=z0;
qb_prev=qb0;
z0=z1;
qb0=qb1;
} else {
z_prev=z1;
qb_prev=qb1;
}
int step;
for (step=0;step<maxSteps;step++) {
z1=z0+dir*iniStep;
qb1=getQualB(z1,kr,kb,corrected);
if (qb1>qb0) break;
z_prev=z0;
qb_prev=qb0;
z0=z1;
qb0=qb1;
}
if (step>=maxSteps){
System.out.println("Failed to find minimum in "+maxSteps+" steps");
return Double.NaN;
}
// now dividing z_prev - z0 - z1 range
for (step=0;step<maxSteps;step++) {
if (qb_prev>qb1){
z_prev=z0;
qb_prev=qb0;
} else {
z1=z0;
qb1=qb0;
}
z0=(z_prev+z1)/2;
qb0=getQualB(z1,kr,kb,corrected);
if (Math.abs(z0-z_prev)<precision) break;
}
return z0;
}
public String getDescription(int i){ public String getDescription(int i){
return channelDescriptions[i]; return channelDescriptions[i];
} }
...@@ -1833,7 +2454,176 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1833,7 +2454,176 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
public double[] getCenterXY(){ public double[] getCenterXY(){
return pXY; return pXY;
} }
public void setDefaultSampleCorr(){
int numPars= getNumCurvars()[0]; // number of Z parameters ( [1] - numbnr of radial parameters).
for (int n=0;n<channelDescriptions.length;n++){
sampleCorrSelect[n]=new boolean[numPars];
sampleCorrCost[n]=new double [numPars];
sampleCorrSigma[n]=new double [numPars];
sampleCorrPullZero[n]=new double [numPars];
for (int i=0;i<numPars;i++){
sampleCorrSelect[n][i]=(i<dflt_sampleCorrSelect.length)?dflt_sampleCorrSelect[i]:false;
sampleCorrCost[n][i]=(i<dflt_sampleCorrCost.length)?dflt_sampleCorrCost[i]:1.0;
sampleCorrSigma[n][i]=dflt_sampleCorrSigma;
sampleCorrPullZero[n][i]=dflt_sampleCorrPullZero;
}
}
}
/**
* Dialog to setup per-sample (coordinate) corrections
* @param title Dialog title
* @param individualChannels configure each of the six color/dir channels separately (false - apply to all)
* @param disabledPars enable use of the parameters that are currently disabled from fitting
* @return true if OK was pressed, false - if cancel
*/
public boolean setupSampleCorr(String title, boolean individualChannels, boolean disabledPars){
int firstChn=0;
for (int i=0;i<channelSelect.length;i++) if (channelSelect[i]){
firstChn=i;
break;
}
if (!channelSelect[firstChn]){
String msg="No channels selected, please select at least one";
IJ.showMessage(msg);
System.out.println(msg);
}
int fromChn=individualChannels?0:firstChn;
int toChn=individualChannels?channelSelect.length:(firstChn+1);
GenericDialog gd = new GenericDialog(title);
int numParsZR[] = getNumCurvars(); // [0] - Z, [1] - r,
for (int nChn=fromChn;nChn<toChn;nChn++) if (channelSelect[nChn]){
String chnName=individualChannels?channelDescriptions[nChn]:"All selected Channels";
for (int i=0;i<sampleCorrSelect[nChn].length;i++) if (disabledPars || curvatureSelect[nChn][i*numParsZR[1]]){
gd.addMessage("===== "+chnName+", "+curvatureModel[nChn].getZDescription(i)+" =====");
gd.addCheckbox("Enable per-sample correction for \""+curvatureModel[nChn].getZDescription(i)+"\"", sampleCorrSelect[nChn][i]);
gd.addNumericField("Correction cost",sampleCorrCost[nChn][i],5,8,"um");
gd.addNumericField("Correction sigma",sampleCorrSigma[nChn][i],5,8,"mm");
gd.addNumericField("Pull to zero fraction",100*sampleCorrPullZero[nChn][i],4,8,"%");
}
}
gd.enableYesNoCancel("Apply","Keep"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return false;
if (gd.wasOKed()) { // selected non-default "Apply"
for (int nChn=fromChn;nChn<toChn;nChn++) if (channelSelect[nChn]){
for (int i=0;i<sampleCorrSelect[nChn].length;i++) if (disabledPars || curvatureSelect[nChn][i*numParsZR[1]]){
sampleCorrSelect[nChn][i]= gd.getNextBoolean();
sampleCorrCost[nChn][i]= gd.getNextNumber();
sampleCorrSigma[nChn][i]= gd.getNextNumber();
sampleCorrPullZero[nChn][i]= 0.01*gd.getNextNumber();
} else {
sampleCorrSelect[nChn][i]= false;
}
}
if (!individualChannels){ // copy settings to other channels
for (int nChn=0;nChn<channelSelect.length;nChn++) if (channelSelect[nChn] && (nChn!=fromChn) ){
for (int i=0;i<sampleCorrSelect[nChn].length;i++){
sampleCorrSelect[nChn][i]= sampleCorrSelect[fromChn][i];
sampleCorrCost[nChn][i]= sampleCorrCost[fromChn][i];
sampleCorrSigma[nChn][i]= sampleCorrSigma[fromChn][i];
sampleCorrPullZero[nChn][i]= sampleCorrPullZero[fromChn][i];
}
}
}
}
return true;
}
/**
* create matrix of weights of the other parameters influence
* @param sampleCoordinates [sample number]{x,y} - flattened array of sample coordinates
* Run in the beginning of fitting series (zeroes the values)
*/
public void initSampleCorr(double [][] sampleCoordinates){
int numSamples=sampleCoordinates.length;
for (int nChn=0; nChn< sampleCorrSelect.length;nChn++) {
if (channelSelect[nChn]){
int numPars=sampleCorrSelect[nChn].length;
sampleCorrCrossWeights[nChn]=new double[numPars][][];
for (int nPar=0;nPar<numPars;nPar++){
if (sampleCorrSelect[nChn][nPar]){
sampleCorrCrossWeights[nChn][nPar]=new double[numSamples][numSamples];
double k=-getPixelMM()*getPixelMM()/(sampleCorrSigma[nChn][nPar]*sampleCorrSigma[nChn][nPar]);
for (int i=0;i<numSamples;i++){
double sw=0.0;
for (int j=0;j<numSamples;j++) {
if (i!=j){
double dx=sampleCoordinates[i][0]-sampleCoordinates[i][0];
double dy=sampleCoordinates[i][1]-sampleCoordinates[i][1];
double a= Math.exp(k*(dx*dx+dy*dy));
sampleCorrCrossWeights[nChn][nPar][i][j]=a;
sw+=a;
}
}
if ((sampleCorrPullZero[nChn][nPar]==0) ||(sampleCorrCost[nChn][nPar]==0)) sw=0.0;
else if (sw!=0.0) sw=-sampleCorrCost[nChn][nPar]*sampleCorrPullZero[nChn][nPar]/sw;
for (int j=0;j<numSamples;j++) {
if (i!=j){
sampleCorrCrossWeights[nChn][nPar][i][j]*=sw;
} else {
sampleCorrCrossWeights[nChn][nPar][i][j]=sampleCorrCost[nChn][nPar];
}
}
}
} else {
sampleCorrCrossWeights[nChn][nPar]=null;
}
}
} else {
sampleCorrCrossWeights[nChn]=null;
}
}
sampleCorrChnParIndex=new int [sampleCorrSelect.length][];
int numPars=0;
for (int nChn=0; nChn< sampleCorrCrossWeights.length;nChn++) {
if (sampleCorrCrossWeights[nChn]!=null){
sampleCorrChnParIndex[nChn]=new int [sampleCorrCrossWeights[nChn].length];
for (int nPar=0;nPar< sampleCorrCrossWeights[nChn].length;nPar++) {
if (sampleCorrCrossWeights[nChn][nPar]!=null){
sampleCorrChnParIndex[nChn][nPar]=numPars; // pointer to the first sample
numPars+=sampleCorrCrossWeights[nChn][nPar].length;
} else {
sampleCorrChnParIndex[nChn][nPar]=-1;
}
}
} else {
sampleCorrChnParIndex[nChn]=null;
}
}
// currently all correction parameters are initialized as zeros.
sampleCorr=new double [numPars];
for (int i=0;i<numPars;i++)sampleCorr[i]=0.0;
sampleCorrRadius=new double [numSamples];
//pXY
for (int i=0;i<numSamples;i++){
double dx=sampleCoordinates[i][0]-pXY[0];
double dy=sampleCoordinates[i][1]-pXY[0];
sampleCorrRadius[i]=getPixelMM()*Math.sqrt(dx*dx+dy*dy);
}
}
public double [] getCorrPar(int chn, int sampleIndex){
if ((sampleCorrChnParIndex==null) || (sampleCorrChnParIndex[chn]==null)) return null;
double [] corr =new double [sampleCorrChnParIndex[chn].length];
for (int i=0;i<corr.length;i++){
if (sampleCorrChnParIndex[chn][i]<0) corr[i]=0.0;
else corr[i]=sampleCorr[sampleCorrChnParIndex[chn][i]+sampleIndex];
}
return corr;
}
public double [][] getCorrPar(int sampleIndex){
if (sampleCorrChnParIndex==null) return null;
double [][] result=new double [sampleCorrChnParIndex.length][];
boolean non_null=false;
for (int i=0;i<sampleCorrChnParIndex.length;i++){
result[i]=getCorrPar(i, sampleIndex);
non_null |= (result[i]!=null);
}
return non_null?result:null;
}
public boolean[] getDefaultMask(){ public boolean[] getDefaultMask(){
boolean [] mask = {true,true,true,true,true,true}; boolean [] mask = {true,true,true,true,true,true};
return mask; return mask;
...@@ -1861,6 +2651,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1861,6 +2651,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
radialParametersNumber); radialParametersNumber);
curvatureSelect[i]=curvatureModel[i].getDefaultMask(); curvatureSelect[i]=curvatureModel[i].getDefaultMask();
} }
setDefaultSampleCorr(); // should be after curvatureModel
} }
public boolean [] getSelectedChannels(){ public boolean [] getSelectedChannels(){
...@@ -1881,6 +2672,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1881,6 +2672,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
boolean editCurvMask=false; boolean editCurvMask=false;
boolean commonCurvMask=true; boolean commonCurvMask=true;
boolean detailedCurvMask=false; boolean detailedCurvMask=false;
boolean setupCorrectionPars=false;
boolean commonCorrectionPars=true;
boolean disabledCorrectionPars=false;
if (centerSelect==null) centerSelect=centerSelectDefault.clone(); if (centerSelect==null) centerSelect=centerSelectDefault.clone();
gd.addCheckbox("Adjust aberration center (pX0)", centerSelect[0]); gd.addCheckbox("Adjust aberration center (pX0)", centerSelect[0]);
gd.addCheckbox("Adjust aberration center (pY0)", centerSelect[1]); gd.addCheckbox("Adjust aberration center (pY0)", centerSelect[1]);
...@@ -1893,6 +2687,11 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1893,6 +2687,11 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
gd.addCheckbox("Edit curvature model parameters mask(s)", editCurvMask); gd.addCheckbox("Edit curvature model parameters mask(s)", editCurvMask);
gd.addCheckbox("Apply same curvature model parameters mask to all channels", commonCurvMask); gd.addCheckbox("Apply same curvature model parameters mask to all channels", commonCurvMask);
gd.addCheckbox("Edit full matrix of the curvature model parameters masks", detailedCurvMask); gd.addCheckbox("Edit full matrix of the curvature model parameters masks", detailedCurvMask);
gd.addMessage("");
gd.addCheckbox("Setup per-sample correction", setupCorrectionPars);
gd.addCheckbox("Apply same per-sample corrections to all channels", commonCorrectionPars);
gd.addCheckbox("Setup correction parameters when the parameter itself is disabled", disabledCorrectionPars);
// gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep" // gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep"
gd.showDialog(); gd.showDialog();
...@@ -1906,6 +2705,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1906,6 +2705,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
editCurvMask=gd.getNextBoolean(); editCurvMask=gd.getNextBoolean();
commonCurvMask=gd.getNextBoolean(); commonCurvMask=gd.getNextBoolean();
detailedCurvMask=gd.getNextBoolean(); detailedCurvMask=gd.getNextBoolean();
setupCorrectionPars=gd.getNextBoolean();
commonCorrectionPars=gd.getNextBoolean();
disabledCorrectionPars=gd.getNextBoolean();
// boolean OK; // boolean OK;
if (editMechMask){ if (editMechMask){
boolean [] mask=mechanicalFocusingModel.maskSetDialog("Focusing mechanical parameters mask", mechanicalSelect); boolean [] mask=mechanicalFocusingModel.maskSetDialog("Focusing mechanical parameters mask", mechanicalSelect);
...@@ -1943,9 +2745,16 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1943,9 +2745,16 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
} }
} }
if (setupCorrectionPars) {
if (!setupSampleCorr("Setup per-sample correction parameters",
!commonCorrectionPars,
disabledCorrectionPars)) return false;
// initSampleCorr(flattenSampleCoord());
}
initSampleCorr(flattenSampleCoord()); // run always regardless of configured or not (to create zero-length array of corr)
return true; return true;
} }
ArrayList<String> getParameterValueStrings(boolean showDisabled){ ArrayList<String> getParameterValueStrings(boolean showDisabled, boolean showCorrection){
ArrayList<String> parList=new ArrayList<String>(); ArrayList<String> parList=new ArrayList<String>();
parList.add("\t ===== Aberrations center =====\t\t"); parList.add("\t ===== Aberrations center =====\t\t");
String [] centerDescriptions={"Aberrations center X","Aberrations center Y"}; String [] centerDescriptions={"Aberrations center X","Aberrations center Y"};
...@@ -1993,6 +2802,18 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -1993,6 +2802,18 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
index++; index++;
} }
} }
if (showCorrection && (getNumberOfCorrParameters()>0)){
parList.add("\t ===== Per-sample correction parameters =====\t\t");
for (int n=0;n<sampleCorrChnParIndex.length;n++) if (sampleCorrChnParIndex[n]!=null){
for (int np=0;np<sampleCorrChnParIndex[n].length;np++) if (sampleCorrChnParIndex[n][np]>=0){
int numSamples=sampleCorrCrossWeights[n][np].length;
parList.add("\t ----- correction parameters for \""+ getDescription(n)+" "+curvatureModel[n].getZDescription(np)+"\" -----\t\t");
for (int i=0;i<numSamples;i++){
parList.add(i+"\t"+curvatureModel[n].getZDescription(np)+":\t"+sampleCorr[sampleCorrChnParIndex[n][np]+i]+"\t");
}
}
}
}
return parList; return parList;
} }
// Show/modify all parameters in a single window. // Show/modify all parameters in a single window.
...@@ -2043,11 +2864,11 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2043,11 +2864,11 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
} }
gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep" gd.enableYesNoCancel("Apply","Keep"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
if (!gd.wasOKed()) { // selected non-default "Apply" if (gd.wasOKed()) { // selected default "Apply"
for (int i=0;i<2;i++){ for (int i=0;i<2;i++){
if (centerSelect[i] || showDisabled) { if (centerSelect[i] || showDisabled) {
pXY[i]=gd.getNextNumber(); pXY[i]=gd.getNextNumber();
...@@ -2071,10 +2892,17 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2071,10 +2892,17 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
return true; return true;
} }
public int getNumberOfCorrParameters(){
return (sampleCorr!=null)?sampleCorr.length:0;
}
public int getNumberOfParameters(boolean sagittalMaster){
return getNumberOfRegularParameters(sagittalMaster)+getNumberOfCorrParameters();
}
/** /**
* @return number of selected parameters (including center, mechanical and each selected - up to 6 - curvature) * @return number of selected parameters (including center, mechanical and each selected - up to 6 - curvature)
*/ */
public int getNumberOfParameters(boolean sagittalMaster){ public int getNumberOfRegularParameters(boolean sagittalMaster){
int np=0; int np=0;
for (int i=0;i<2;i++){ for (int i=0;i<2;i++){
if ( centerSelect[i]) np++; if ( centerSelect[i]) np++;
...@@ -2125,6 +2953,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2125,6 +2953,8 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
index++; index++;
} }
} }
int nCorrPars=getNumberOfCorrParameters();
for (int i=0;i<nCorrPars;i++) pars[np++]=sampleCorr[i];
return pars; return pars;
} }
...@@ -2150,6 +2980,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2150,6 +2980,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
index++; index++;
} }
} }
// copy correction parameters
int nCorrPars=getNumberOfCorrParameters();
for (int i=0;i<nCorrPars;i++) sampleCorr[i]=pars[np++];
// copy center parameters to dependent // copy center parameters to dependent
// copy if master is selected, regardless of is dependent selected or not // copy if master is selected, regardless of is dependent selected or not
for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){ for (int n=0;n<channelSelect.length;n++) if (channelSelect[n]){
...@@ -2199,12 +3033,16 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2199,12 +3033,16 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
* @return array of [getNumberOfChannels()] calculated function values * @return array of [getNumberOfChannels()] calculated function values
*/ */
public double [] getValsDerivatives( public double [] getValsDerivatives(
int sampleIndex, // double [][] corrPars, // [6][nParZ]
boolean sagittalMaster, // false - tangential master, true - sagittal master (for center coefficients) boolean sagittalMaster, // false - tangential master, true - sagittal master (for center coefficients)
int [] motors, // 3 motor coordinates int [] motors, // 3 motor coordinates
double px, // pixel x double px, // pixel x
double py, // pixel y double py, // pixel y
double [][] deriv // array of (1..6[][], matching getNumberOfChannels) or null if derivatives are not required double [][] deriv // array of (1..6[][], matching getNumberOfChannels) or null if derivatives are not required
){ ){
double [][] corrPars=getCorrPar(sampleIndex);
double [] motorDerivs=(deriv==null)? null:(new double [mechanicalFocusingModel.getNumPars()]); double [] motorDerivs=(deriv==null)? null:(new double [mechanicalFocusingModel.getNumPars()]);
double [] chnValues=new double [getNumberOfChannels()]; double [] chnValues=new double [getNumberOfChannels()];
double mot_z=mechanicalFocusingModel.calc_ZdZ( double mot_z=mechanicalFocusingModel.calc_ZdZ(
...@@ -2216,8 +3054,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2216,8 +3054,9 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
double [][] deriv_curv = new double [channelSelect.length][]; double [][] deriv_curv = new double [channelSelect.length][];
for (int c=0;c<channelSelect.length;c++) deriv_curv[c]=null; for (int c=0;c<channelSelect.length;c++) deriv_curv[c]=null;
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){ for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
deriv_curv[c]=(deriv==null)?null:(new double [curvatureModel[c].getSize()]); deriv_curv[c]=(deriv==null)?null:(new double [curvatureModel[c].getSize()]); // nr*nz+1
chnValues[nChn++]=curvatureModel[c].getFdF( chnValues[nChn++]=curvatureModel[c].getFdF(
(corrPars==null)?null:corrPars[c], // param_corr
px, px,
py, py,
mot_z, mot_z,
...@@ -2235,12 +3074,12 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2235,12 +3074,12 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
nChn=0; nChn=0;
for (int i=0;i<2;i++){ for (int i=0;i<2;i++){
dr_dxy[i]*=getPixelMM(); // radius in mm, dx, dy - in pixels dr_dxy[i]*=getPixelMM(); // radius in mm, dx, dy - in pixels
// dr_dxy[i]*=2; //?????
} }
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){ for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
boolean isMasterDir=(c%2) == (sagittalMaster?0:1); boolean isMasterDir=(c%2) == (sagittalMaster?0:1);
int otherChannel= c ^ 1; int otherChannel= c ^ 1;
deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)]; // deriv[nChn]=new double [getNumberOfRegularParameters(sagittalMaster)]; //???????????
deriv[nChn]=new double [getNumberOfParameters(sagittalMaster)]; //???????????
int np=0; int np=0;
for (int i=0;i<2;i++){ for (int i=0;i<2;i++){
if (centerSelect[i] ) { if (centerSelect[i] ) {
...@@ -2268,12 +3107,24 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2268,12 +3107,24 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
} }
} }
// add correction parameters?
// now np points to the first correction parameter
// correction parameters do not depend on sagittalMaster - each mayy have own shift
if ((corrPars!=null) && (sampleCorrChnParIndex!=null)){
for (int n=0;n<channelSelect.length;n++) if (sampleCorrChnParIndex[n]!=null){
int [] ncp=curvatureModel[n].getNumPars(); // {(z),(r)}
for (int i=0;i<ncp[0];i++) if (sampleCorrChnParIndex[n][i]>=0){
// np now points to the first corr parameter
deriv[nChn][np+sampleCorrChnParIndex[n][i]+sampleIndex]=deriv_curv[n][i*ncp[1]];
}
}
}
nChn++; nChn++;
} }
} }
return chnValues; return chnValues;
} }
/*
public double [] getValsDerivativesOld( public double [] getValsDerivativesOld(
boolean sagittalMaster, boolean sagittalMaster,
int [] motors, // 3 motor coordinates int [] motors, // 3 motor coordinates
...@@ -2292,6 +3143,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2292,6 +3143,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){ for (int c=0;c<channelSelect.length;c++) if (channelSelect[c]){
double [] deriv_curv=(deriv==null)?null:(new double [curvatureModel[c].getSize()]); double [] deriv_curv=(deriv==null)?null:(new double [curvatureModel[c].getSize()]);
chnValues[nChn]=curvatureModel[c].getFdF( chnValues[nChn]=curvatureModel[c].getFdF(
null, // param_corr
px, px,
py, py,
mot_z, mot_z,
...@@ -2314,7 +3166,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2314,7 +3166,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
} }
return chnValues; return chnValues;
} }
*/
} }
...@@ -2549,10 +3401,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2549,10 +3401,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
mask[i]=currentMask[i]; mask[i]=currentMask[i];
gd.addCheckbox(getDescription(i), mask[i]); gd.addCheckbox(getDescription(i), mask[i]);
} }
gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep" gd.enableYesNoCancel("Apply","Keep"); // default OK (on enter) - "Apply"
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return null; if (gd.wasCanceled()) return null;
if (!gd.wasOKed()) { // selected non-default "Apply" if (gd.wasOKed()) { // selected default "Apply"
for (int i=0;i<mask.length;i++) { for (int i=0;i<mask.length;i++) {
mask[i]=gd.getNextBoolean(); mask[i]=gd.getNextBoolean();
} }
...@@ -2569,10 +3421,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2569,10 +3421,10 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
gd.addNumericField("(disabled) "+getDescription(i),this.paramValues[i],5,8,getUnits(i)); gd.addNumericField("(disabled) "+getDescription(i),this.paramValues[i],5,8,getUnits(i));
} }
} }
gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep" gd.enableYesNoCancel("Apply","Keep"); // default OK (on enter) - "Apply"
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
if (!gd.wasOKed()) { // selected non-default "Apply" if (gd.wasOKed()) { // selected default "Apply"
for (int i=0;i<this.paramValues.length;i++){ for (int i=0;i<this.paramValues.length;i++){
if ((mask==null) || mask[i] || showDisabled) { if ((mask==null) || mask[i] || showDisabled) {
this.paramValues[i]=gd.getNextNumber(); this.paramValues[i]=gd.getNextNumber();
...@@ -2588,7 +3440,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2588,7 +3440,7 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
private double dflt_r0=4.0; //3.3; // um (1.5 pix) private double dflt_r0=4.0; //3.3; // um (1.5 pix)
private double [][] modelParams=null; private double [][] modelParams=null;
public static final int dflt_distanceParametersNumber=5; public static final int dflt_distanceParametersNumber=5;
public static final int dflt_radialParametersNumber=3; public static final int dflt_radialParametersNumber=4;
private static final int min_distanceParametersNumber=4; private static final int min_distanceParametersNumber=4;
private static final int min_radialParametersNumber=1; private static final int min_radialParametersNumber=1;
private double pX0,pY0; private double pX0,pY0;
...@@ -2654,19 +3506,39 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2 ...@@ -2654,19 +3506,39 @@ d_s2/d_x0= 2*delta_x*delta_y^2/r2^2
return 0; return 0;
} }
} }
double [] getAr(
double r,
double [] param_corr
){
double [] ar= new double [this.modelParams.length];
for (int i=0;i<this.modelParams.length;i++){
ar[i]=this.modelParams[i][0];
if (param_corr!=null) ar[i]+=param_corr[i];
// double rp=1.0;
double rp=r;
for (int j=1;j<this.modelParams[i].length;j++){
// rp*=r2;
rp*=r;
ar[i]+=this.modelParams[i][j]*rp;
}
}
return ar;
}
/** /**
* Calculate function value and (optionally) partial derivatives over all parameters as 1d array * Calculate function value and (optionally) partial derivatives over all parameters as 1d array
* inner scanning by radial coefficient (for even powers of radius), outer - for f(z) parameters * inner scanning by radial coefficient (for even powers of radius), outer - for f(z) parameters
* first parameter - z0 (shift), then scale (related to numeric aperture), then r0 (related to minimal PSF radius), * first parameter - z0 (shift), then scale (related to numeric aperture), then r0 (related to minimal PSF radius),
* other parameters - just polynomial coefficients for (z_in-z0)^n * other parameters - just polynomial coefficients for (z_in-z0)^n
* @param pX - sample pixel x coordinate (currently just for radius calculation) * @param param_corr - per-sample corrections, added to this.modelParams[i][0] - or null
* @param pY - sample pixel y coordinate (currently just for radius calculation) * @param pX - sample pixel x coordinate (currently just for radius calculation) or radius in mm (if pY is NaN)
* @param pY - sample pixel y coordinate (currently just for radius calculation) or NaN, then pX - radius in mm
* @param z_in - z (from mechanical) before subtracting of z0 * @param z_in - z (from mechanical) before subtracting of z0
* @param deriv array to accommodate all partial derivatives or null (should have modelParams.length*modelParams[0].length+1 * @param deriv array to accommodate all partial derivatives or null (should have modelParams.length*modelParams[0].length+1
* @return function value * @return function value
*/ */
public double getFdF( public double getFdF(
double pX, double [] param_corr,
double pX, // if isNaN(pY), then pX is radius in mm
double pY, double pY,
double z_in, double z_in,
double [] deriv){ double [] deriv){
...@@ -2686,11 +3558,12 @@ k - ar[3] ...@@ -2686,11 +3558,12 @@ k - ar[3]
ar1 - ar[4] ar1 - ar[4]
*/ */
double r=Math.sqrt((pX-pX0)*(pX-pX0)+(pY-pY0)*(pY-pY0))*PIXEL_SIZE; // in mm double r=Double.isNaN(pY)?pX:Math.sqrt((pX-pX0)*(pX-pX0)+(pY-pY0)*(pY-pY0))*PIXEL_SIZE; // in mm
// double r2=r*r; // double r2=r*r;
double [] ar= new double [this.modelParams.length]; double [] ar= new double [this.modelParams.length];
for (int i=0;i<this.modelParams.length;i++){ for (int i=0;i<this.modelParams.length;i++){
ar[i]=this.modelParams[i][0]; ar[i]=this.modelParams[i][0];
if (param_corr!=null) ar[i]+=param_corr[i];
// double rp=1.0; // double rp=1.0;
double rp=r; double rp=r;
for (int j=1;j<this.modelParams[i].length;j++){ for (int j=1;j<this.modelParams[i].length;j++){
...@@ -2838,11 +3711,11 @@ ar1 - ar[4] ...@@ -2838,11 +3711,11 @@ ar1 - ar[4]
} }
} }
gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep" gd.enableYesNoCancel("Apply","Keep"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return null; if (gd.wasCanceled()) return null;
if (!gd.wasOKed()) { // selected non-default "Apply" if (gd.wasOKed()) { // selected non-default "Apply"
if (detailed){ if (detailed){
int index=0; int index=0;
for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){ for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){
...@@ -2882,11 +3755,11 @@ ar1 - ar[4] ...@@ -2882,11 +3755,11 @@ ar1 - ar[4]
} }
index++; index++;
} }
gd.enableYesNoCancel("Keep","Apply"); // default OK (on enter) - "Keep" gd.enableYesNoCancel("Apply","Keep"); // default OK (on enter) - "Apply"
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
if (!gd.wasOKed()) { // selected non-default "Apply" if (gd.wasOKed()) { // selected default "Apply"
index=0; index=0;
for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){ for (int i=0;i<this.modelParams.length;i++) for (int j=0;j<this.modelParams[0].length;j++){
if ((mask==null) || mask[index] || showDisabled) { if ((mask==null) || mask[index] || showDisabled) {
......
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