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Commit e757252a authored by Andrey Filippov's avatar Andrey Filippov
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optimizing focus/tilt for qualB best tilt is different from the acis

parent 996dd2fd
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Showing with 864 additions and 93 deletions
src/main/java/Aberration_Calibration.java
View file @ e757252a
...@@ -809,6 +809,7 @@ if (MORE_BUTTONS) { ...@@ -809,6 +809,7 @@ if (MORE_BUTTONS) {
addButton("List curv", panelCurvature,color_report); addButton("List curv", panelCurvature,color_report);
addButton("Show curv corr", panelCurvature,color_report); addButton("Show curv corr", panelCurvature,color_report);
addButton("Test measurement", panelCurvature,color_debug); addButton("Test measurement", panelCurvature,color_debug);
addButton("Optimize qualB", panelCurvature,color_debug);
addButton("Focus/Tilt LMA", panelCurvature,color_process); addButton("Focus/Tilt LMA", panelCurvature,color_process);
add(panelCurvature); add(panelCurvature);
...@@ -4075,6 +4076,9 @@ if (MORE_BUTTONS) { ...@@ -4075,6 +4076,9 @@ if (MORE_BUTTONS) {
} }
path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml"; path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml";
FOCUSING_FIELD= new FocusingField( FOCUSING_FIELD= new FocusingField(
EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
EYESIS_CAMERA_PARAMETERS.getSensorHeight(),
0.001*EYESIS_CAMERA_PARAMETERS.getPixelSize(0), //subCamera_0.pixelSize,
FOCUS_MEASUREMENT_PARAMETERS.serialNumber, FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment, FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
...@@ -4402,6 +4406,9 @@ if (MORE_BUTTONS) { ...@@ -4402,6 +4406,9 @@ if (MORE_BUTTONS) {
} }
path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml"; path=dFile+Prefs.getFileSeparator()+lensPrefix+CAMERAS.getLastTimestampUnderscored()+".history-xml";
FOCUSING_FIELD= new FocusingField( FOCUSING_FIELD= new FocusingField(
EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
EYESIS_CAMERA_PARAMETERS.getSensorHeight(),
0.001*EYESIS_CAMERA_PARAMETERS.getPixelSize(0), //subCamera_0.pixelSize,
FOCUS_MEASUREMENT_PARAMETERS.serialNumber, FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment, FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
...@@ -4568,6 +4575,17 @@ if (MORE_BUTTONS) { ...@@ -4568,6 +4575,17 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.testMeasurement(); FOCUSING_FIELD.testMeasurement();
return; return;
} }
/* ======================================================================== */
if (label.equals("Optimize qualB")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (FOCUSING_FIELD==null) return;
FOCUSING_FIELD.setDebugLevel(DEBUG_LEVEL);
FOCUSING_FIELD.testQualB(true); // public double[] testQualB(boolean interactive)
return;
}
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("Focus/Tilt LMA")) { if (label.equals("Focus/Tilt LMA")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
...@@ -5131,6 +5149,9 @@ if (MORE_BUTTONS) { ...@@ -5131,6 +5149,9 @@ if (MORE_BUTTONS) {
FocusingField ff= null; FocusingField ff= null;
if (useLMA){ if (useLMA){
ff= new FocusingField( ff= new FocusingField(
EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
EYESIS_CAMERA_PARAMETERS.getSensorHeight(),
0.001*EYESIS_CAMERA_PARAMETERS.getPixelSize(0), //subCamera_0.pixelSize,
FOCUS_MEASUREMENT_PARAMETERS.serialNumber, FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment, FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
...@@ -5232,6 +5253,9 @@ if (MORE_BUTTONS) { ...@@ -5232,6 +5253,9 @@ if (MORE_BUTTONS) {
// Now in LMA mode - recalculate and overwrite // Now in LMA mode - recalculate and overwrite
if (useLMA){ if (useLMA){
ff= new FocusingField( ff= new FocusingField(
EYESIS_CAMERA_PARAMETERS.getSensorWidth(),
EYESIS_CAMERA_PARAMETERS.getSensorHeight(),
0.001*EYESIS_CAMERA_PARAMETERS.getPixelSize(0), //subCamera_0.pixelSize,
FOCUS_MEASUREMENT_PARAMETERS.serialNumber, FOCUS_MEASUREMENT_PARAMETERS.serialNumber,
FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average FOCUS_MEASUREMENT_PARAMETERS.lensSerial, // String lensSerial, // if null - do not add average
FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment, FOCUS_MEASUREMENT_PARAMETERS.comment, // String comment,
...@@ -8885,7 +8909,7 @@ if (MORE_BUTTONS) { ...@@ -8885,7 +8909,7 @@ if (MORE_BUTTONS) {
double [] targetTilts={0.0,0.0}; double [] targetTilts={0.0,0.0};
double [] manualScrewsCW=null; double [] manualScrewsCW=null;
if (zTxTyM1M2M3!=null){ if (zTxTyM1M2M3!=null){
manualScrewsCW=FOCUSING_FIELD.fieldFitting.mechanicalFocusingModel. getManualScrews( manualScrewsCW=FOCUSING_FIELD.fieldFitting.mechanicalFocusingModel.getManualScrews(
zTxTy[0]-FOCUSING_FIELD.targetRelFocalShift, //double zErr, // positive - away from lens zTxTy[0]-FOCUSING_FIELD.targetRelFocalShift, //double zErr, // positive - away from lens
zTxTy[1]-targetTilts[0], // double tXErr,// positive - 1,2 away from lens, 3 - to the lens zTxTy[1]-targetTilts[0], // double tXErr,// positive - 1,2 away from lens, 3 - to the lens
zTxTy[2]-targetTilts[1]); // double tYErr); zTxTy[2]-targetTilts[1]); // double tYErr);
...@@ -8916,9 +8940,15 @@ if (MORE_BUTTONS) { ...@@ -8916,9 +8940,15 @@ if (MORE_BUTTONS) {
gd.addMessage("**** Failed to determine focus/tilt, probably too far out of focus. ****"); gd.addMessage("**** Failed to determine focus/tilt, probably too far out of focus. ****");
gd.addMessage("**** You may cancel the command and try \"Auto pre-focus\" first. ****"); gd.addMessage("**** You may cancel the command and try \"Auto pre-focus\" first. ****");
} }
gd.addNumericField("Target focus (relative to best composirte)",FOCUSING_FIELD.targetRelFocalShift,2,5,"um ("+IJ.d2s(zTxTy[0],3)+")"); gd.addNumericField("Target focus (relative to best composite)",FOCUSING_FIELD.targetRelFocalShift,2,5,"um ("+IJ.d2s(zTxTy[0],3)+")");
gd.addNumericField("Target horizontal tilt (normally 0)",targetTilts[0],2,5,"um/mm ("+IJ.d2s(zTxTy[1],3)+")"); gd.addNumericField("Target horizontal tilt relative to optimal (normally 0)",targetTilts[0],2,5,"um/mm ("+IJ.d2s(zTxTy[1],3)+")");
gd.addNumericField("Target vertical tilt (normally 0)",targetTilts[1],2,5,"um/mm ("+IJ.d2s(zTxTy[2],3)+")"); gd.addNumericField("Target vertical tilt relative to optimal (normally 0)",targetTilts[1],2,5,"um/mm ("+IJ.d2s(zTxTy[2],3)+")");
gd.addCheckbox("Optimize focal distance",(FOCUSING_FIELD.qualBOptimizeMode & 1) != 0);
gd.addCheckbox("Optimize tiltX", (FOCUSING_FIELD.qualBOptimizeMode & 2) != 0);
gd.addCheckbox("Optimize tiltY", (FOCUSING_FIELD.qualBOptimizeMode & 4) != 0);
gd.addNumericField("Motor 1",newMotors[0],0,5,"steps ("+currentMotors[0]+")"); gd.addNumericField("Motor 1",newMotors[0],0,5,"steps ("+currentMotors[0]+")");
gd.addNumericField("Motor 2",newMotors[1],0,5,"steps ("+currentMotors[1]+")"); gd.addNumericField("Motor 2",newMotors[1],0,5,"steps ("+currentMotors[1]+")");
gd.addNumericField("Motor 3",newMotors[2],0,5,"steps ("+currentMotors[2]+")"); gd.addNumericField("Motor 3",newMotors[2],0,5,"steps ("+currentMotors[2]+")");
...@@ -8952,6 +8982,12 @@ if (MORE_BUTTONS) { ...@@ -8952,6 +8982,12 @@ if (MORE_BUTTONS) {
FOCUSING_FIELD.targetRelFocalShift=gd.getNextNumber(); FOCUSING_FIELD.targetRelFocalShift=gd.getNextNumber();
targetTilts[0]= gd.getNextNumber(); targetTilts[0]= gd.getNextNumber();
targetTilts[1]= gd.getNextNumber(); targetTilts[1]= gd.getNextNumber();
FOCUSING_FIELD.qualBOptimizeMode=0;
FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?1:0;
FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?2:0;
FOCUSING_FIELD.qualBOptimizeMode+= gd.getNextBoolean()?4:0;
newMotors[0]= (int) gd.getNextNumber(); newMotors[0]= (int) gd.getNextNumber();
newMotors[1]= (int) gd.getNextNumber(); newMotors[1]= (int) gd.getNextNumber();
newMotors[2]= (int) gd.getNextNumber(); newMotors[2]= (int) gd.getNextNumber();
......
src/main/java/FocusingField.java
View file @ e757252a
...@@ -53,6 +53,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -53,6 +53,7 @@ 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;
...@@ -116,6 +117,15 @@ public class FocusingField { ...@@ -116,6 +117,15 @@ public class FocusingField {
double weightRadius; //2.0; // Gaussian sigma in mm double weightRadius; //2.0; // Gaussian sigma in mm
private double k_red; private double k_red;
private double k_blue; private double k_blue;
private double k_sag;
private double k_tan;
private double k_qualBFractionPeripheral; // relative weight of peripheral areas when optimizing qualB
private double k_qualBFractionHor; // reduce weight of peripheral areas when optimizing qualB (linear, reaching k_qualBFractionPeripheral at the sensor margins)
private double k_qualBFractionVert; // reduce weight of peripheral areas when optimizing qualB (linear, reaching k_qualBFractionPeripheral at the sensor margins)
private boolean qualBRemoveBadSamples;
public int qualBOptimizeMode; // 0 - none, +1 - optimize Zc, +2 - optimize Tx, +4 - optimize Ty
public double [] qualBOptimizationResults=null; // not saved, re-calculated when needed
private double qb_scan_below; // um private double qb_scan_below; // um
private double qb_scan_above; // um private double qb_scan_above; // um
private double qb_scan_step; // um private double qb_scan_step; // um
...@@ -184,12 +194,15 @@ public class FocusingField { ...@@ -184,12 +194,15 @@ public class FocusingField {
private int iterationStepNumber=0; private int iterationStepNumber=0;
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
public static final double PIXEL_SIZE=0.0022; // mm
public static final String sep = " "; public static final String sep = " ";
public static final String regSep = "\\s"; public static final String regSep = "\\s";
public String serialNumber; public String serialNumber;
public String lensSerial; // if null - do not add average public String lensSerial; // if null - do not add average
public String comment; public String comment;
public int sensorWidth;
public int sensorHeight;
// public static final double PIXEL_SIZE=0.0022; // mm
public double PIXEL_SIZE; // mm
public double [][][] sampleCoord; public double [][][] sampleCoord;
public ArrayList<FocusingFieldMeasurement> measurements; public ArrayList<FocusingFieldMeasurement> measurements;
...@@ -222,6 +235,9 @@ public class FocusingField { ...@@ -222,6 +235,9 @@ public class FocusingField {
public void setDefaults(){ public void setDefaults(){
sensorWidth= 2592;
sensorHeight= 1936;
PIXEL_SIZE= 0.0022; // mm
pX0_distortions=Double.NaN; pX0_distortions=Double.NaN;
pY0_distortions=Double.NaN; pY0_distortions=Double.NaN;
zRanges=null; zRanges=null;
...@@ -281,6 +297,15 @@ public class FocusingField { ...@@ -281,6 +297,15 @@ public class FocusingField {
weightRadius=0.0; //2.0; // Gaussian sigma in mm weightRadius=0.0; //2.0; // Gaussian sigma in mm
k_red=0.7; k_red=0.7;
k_blue=0.4; k_blue=0.4;
k_sag=1.0;
k_tan=1.0;
k_qualBFractionPeripheral=0.5; // relative weight of peripheral areas when optimizing qualB
k_qualBFractionHor=0.8; // reduce weight of peripheral areas when optimizing qualB (linear, reaching k_qualBFractionPeripheral at the sensor margins)
k_qualBFractionVert=0.8; // reduce weight of peripheral areas when optimizing qualB (linear, reaching k_qualBFractionPeripheral at the sensor margins)
qualBRemoveBadSamples=true;
qualBOptimizeMode=7; // 0 - none, +1 - optimize Zc, +2 - optimize Tx, +4 - optimize Ty
qb_scan_below=-40.0; // um qb_scan_below=-40.0; // um
qb_scan_above= 80.0; // um qb_scan_above= 80.0; // um
qb_scan_step= 0.5; // um qb_scan_step= 0.5; // um
...@@ -420,6 +445,13 @@ public class FocusingField { ...@@ -420,6 +445,13 @@ public class FocusingField {
properties.setProperty(prefix+"weightRadius",weightRadius+""); properties.setProperty(prefix+"weightRadius",weightRadius+"");
properties.setProperty(prefix+"k_red",k_red+""); properties.setProperty(prefix+"k_red",k_red+"");
properties.setProperty(prefix+"k_blue",k_blue+""); properties.setProperty(prefix+"k_blue",k_blue+"");
properties.setProperty(prefix+"k_sag",k_sag+"");
properties.setProperty(prefix+"k_tan",k_tan+"");
properties.setProperty(prefix+"k_qualBFractionPeripheral",k_qualBFractionPeripheral+"");
properties.setProperty(prefix+"k_qualBFractionHor",k_qualBFractionHor+"");
properties.setProperty(prefix+"k_qualBFractionVert",k_qualBFractionVert+"");
properties.setProperty(prefix+"qualBRemoveBadSamples",qualBRemoveBadSamples+"");
properties.setProperty(prefix+"qualBOptimizeMode",qualBOptimizeMode+"");
properties.setProperty(prefix+"qb_scan_below",qb_scan_below+""); properties.setProperty(prefix+"qb_scan_below",qb_scan_below+"");
properties.setProperty(prefix+"qb_scan_above",qb_scan_above+""); properties.setProperty(prefix+"qb_scan_above",qb_scan_above+"");
properties.setProperty(prefix+"qb_scan_step",qb_scan_step+""); properties.setProperty(prefix+"qb_scan_step",qb_scan_step+"");
...@@ -575,6 +607,21 @@ public class FocusingField { ...@@ -575,6 +607,21 @@ public class FocusingField {
k_red=Double.parseDouble(properties.getProperty(prefix+"k_red")); k_red=Double.parseDouble(properties.getProperty(prefix+"k_red"));
if (properties.getProperty(prefix+"k_blue")!=null) if (properties.getProperty(prefix+"k_blue")!=null)
k_blue=Double.parseDouble(properties.getProperty(prefix+"k_blue")); k_blue=Double.parseDouble(properties.getProperty(prefix+"k_blue"));
if (properties.getProperty(prefix+"k_sag")!=null)
k_sag=Double.parseDouble(properties.getProperty(prefix+"k_sag"));
if (properties.getProperty(prefix+"k_tan")!=null)
k_tan=Double.parseDouble(properties.getProperty(prefix+"k_tan"));
if (properties.getProperty(prefix+"k_qualBFractionPeripheral")!=null)
k_qualBFractionPeripheral=Double.parseDouble(properties.getProperty(prefix+"k_qualBFractionPeripheral"));
if (properties.getProperty(prefix+"k_qualBFractionHor")!=null)
k_qualBFractionHor=Double.parseDouble(properties.getProperty(prefix+"k_qualBFractionHor"));
if (properties.getProperty(prefix+"k_qualBFractionVert")!=null)
k_qualBFractionVert=Double.parseDouble(properties.getProperty(prefix+"k_qualBFractionVert"));
if (properties.getProperty(prefix+"qualBRemoveBadSamples")!=null)
qualBRemoveBadSamples=Boolean.parseBoolean(properties.getProperty(prefix+"qualBRemoveBadSamples"));
if (properties.getProperty(prefix+"qualBOptimizeMode")!=null)
qualBOptimizeMode=Integer.parseInt(properties.getProperty(prefix+"qualBOptimizeMode"));
if (properties.getProperty(prefix+"qb_scan_below")!=null) if (properties.getProperty(prefix+"qb_scan_below")!=null)
qb_scan_below=Double.parseDouble(properties.getProperty(prefix+"qb_scan_below")); qb_scan_below=Double.parseDouble(properties.getProperty(prefix+"qb_scan_below"));
if (properties.getProperty(prefix+"qb_scan_above")!=null) if (properties.getProperty(prefix+"qb_scan_above")!=null)
...@@ -675,8 +722,10 @@ public enum MECH_PAR { ...@@ -675,8 +722,10 @@ public enum MECH_PAR {
tx, // horizontal tilt", "um/pix","0.0"}, tx, // horizontal tilt", "um/pix","0.0"},
ty // vertical tilt", "um/pix","0.0"}}; ty // vertical tilt", "um/pix","0.0"}};
} }
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 double getPixelMM(){return PIXEL_SIZE;}
public double getPixelUM(){return PIXEL_SIZE*1000;}
public int flattenIndex(int i, int j){return j+i*sampleCoord[0].length;} public int flattenIndex(int i, int j){return j+i*sampleCoord[0].length;}
public int getNumSamples(){return sampleCoord.length*sampleCoord[0].length;} public int getNumSamples(){return sampleCoord.length*sampleCoord[0].length;}
public int getNumChannels(){return 6;} public int getNumChannels(){return 6;}
...@@ -2819,7 +2868,7 @@ public void stepLevenbergMarquardtAction(int debugLevel){// ...@@ -2819,7 +2868,7 @@ public void stepLevenbergMarquardtAction(int debugLevel){//
public boolean selectLMAParameters(){ public boolean selectLMAParameters(){
// int numSeries=fittingStrategy.getNumSeries(); // int numSeries=fittingStrategy.getNumSeries();
// boolean resetCorrections=false; // boolean resetCorrections=false;
GenericDialog gd = new GenericDialog("Levenberg-Marquardt algorithm parameters for cameras distortions/locations"); GenericDialog gd = new GenericDialog("Levenberg-Marquardt algorithm parameters lens aberrations approxiamtion");
//TODO: change to selection using series comments //TODO: change to selection using series comments
// gd.addNumericField("Fitting series number", this.currentStrategyStep, 0, 3," (-1 - current)"); // gd.addNumericField("Fitting series number", this.currentStrategyStep, 0, 3," (-1 - current)");
...@@ -4268,6 +4317,9 @@ public boolean LevenbergMarquardt( ...@@ -4268,6 +4317,9 @@ public boolean LevenbergMarquardt(
} }
public FocusingField( public FocusingField(
int sensorWidth,
int sensorHeight,
double PIXEL_SIZE, //=0.0022; // mm
String serialNumber, String serialNumber,
String lensSerial, // if null - do not add average String lensSerial, // if null - do not add average
String comment, String comment,
...@@ -4287,6 +4339,9 @@ public boolean LevenbergMarquardt( ...@@ -4287,6 +4339,9 @@ public boolean LevenbergMarquardt(
this.sampleCoord=sampleCoord; this.sampleCoord=sampleCoord;
this.measurements=new ArrayList<FocusingFieldMeasurement>(); this.measurements=new ArrayList<FocusingFieldMeasurement>();
this.stopRequested=stopRequested; this.stopRequested=stopRequested;
this.sensorWidth=sensorWidth;
this.sensorHeight=sensorHeight;
this.PIXEL_SIZE=PIXEL_SIZE; //=0.0022; // mm
} }
public FocusingField( public FocusingField(
...@@ -4334,6 +4389,10 @@ public boolean LevenbergMarquardt( ...@@ -4334,6 +4389,10 @@ public boolean LevenbergMarquardt(
comment= hConfig.getString("comment","no comments"); comment= hConfig.getString("comment","no comments");
// if ((comment.length()>10) && comment.substring(0,9).equals("<![CDATA[")) comment=comment.substring(9,comment.length()-3); // if ((comment.length()>10) && comment.substring(0,9).equals("<![CDATA[")) comment=comment.substring(9,comment.length()-3);
PIXEL_SIZE=Double.parseDouble(hConfig.getString("PIXEL_SIZE",PIXEL_SIZE+""));
sensorWidth=Integer.parseInt(hConfig.getString("sensorWidth","0"));
sensorHeight=Integer.parseInt(hConfig.getString("sensorHeight","0"));
serialNumber= hConfig.getString("serialNumber","???"); serialNumber= hConfig.getString("serialNumber","???");
lensSerial= hConfig.getString("lensSerial","???"); lensSerial= hConfig.getString("lensSerial","???");
pX0_distortions=Double.parseDouble(hConfig.getString("lens_center_x","0.0")); pX0_distortions=Double.parseDouble(hConfig.getString("lens_center_x","0.0"));
...@@ -4369,48 +4428,53 @@ public boolean LevenbergMarquardt( ...@@ -4369,48 +4428,53 @@ public boolean LevenbergMarquardt(
return true; return true;
} }
public void saveXML( public void saveXML(
String path){ // x,y,r String path){ // x,y,r
XMLConfiguration hConfig=new XMLConfiguration(); XMLConfiguration hConfig=new XMLConfiguration();
hConfig.setRootElementName("focusingHistory"); hConfig.setRootElementName("focusingHistory");
if (comment!=null){ if (comment!=null){
String comment_esc=comment.replace(",","\\,"); String comment_esc=comment.replace(",","\\,");
// hConfig.addProperty("comment","<![CDATA["+comment_esc+ "]]>"); // hConfig.addProperty("comment","<![CDATA["+comment_esc+ "]]>");
hConfig.addProperty("comment",comment_esc); hConfig.addProperty("comment",comment_esc);
} }
if (serialNumber!=null) hConfig.addProperty("serialNumber",serialNumber); if (serialNumber!=null) hConfig.addProperty("serialNumber",serialNumber);
if (lensSerial!=null) hConfig.addProperty("lensSerial",lensSerial); if (lensSerial!=null) hConfig.addProperty("lensSerial",lensSerial);
hConfig.addProperty("lens_center_x",pX0_distortions); // distortions center, not aberrations! hConfig.addProperty("lens_center_x",pX0_distortions); // distortions center, not aberrations!
hConfig.addProperty("lens_center_y",pY0_distortions); hConfig.addProperty("lens_center_y",pY0_distortions);
if ((sampleCoord!=null) && (sampleCoord.length>0) && (sampleCoord[0] != null) && (sampleCoord[0].length>0)){
hConfig.addProperty("samples_x",sampleCoord[0].length); hConfig.addProperty("PIXEL_SIZE",PIXEL_SIZE);
hConfig.addProperty("samples_y",sampleCoord.length); hConfig.addProperty("sensorWidth", sensorWidth);
for (int i=0;i<sampleCoord.length;i++) hConfig.addProperty("sensorHeight",sensorHeight);
for (int j=0;j<sampleCoord[i].length;j++){
// double coord[] = {sampleCoord[i][j][0],sampleCoord[i][j][1]}; if ((sampleCoord!=null) && (sampleCoord.length>0) && (sampleCoord[0] != null) && (sampleCoord[0].length>0)){
hConfig.addProperty("sample_"+i+"_"+j,sampleCoord[i][j][0]+sep+sampleCoord[i][j][1]); hConfig.addProperty("samples_x",sampleCoord[0].length);
} hConfig.addProperty("samples_y",sampleCoord.length);
} for (int i=0;i<sampleCoord.length;i++)
hConfig.addProperty("measurements",this.measurements.size()); for (int j=0;j<sampleCoord[i].length;j++){
for (int i=0;i<this.measurements.size();i++){ // double coord[] = {sampleCoord[i][j][0],sampleCoord[i][j][1]};
FocusingFieldMeasurement meas=this.measurements.get(i); hConfig.addProperty("sample_"+i+"_"+j,sampleCoord[i][j][0]+sep+sampleCoord[i][j][1]);
String prefix="measurement_"+i+"."; }
if (meas.timestamp!=null) hConfig.addProperty(prefix+"timestamp",meas.timestamp); }
hConfig.addProperty(prefix+"temperature",meas.temperature); hConfig.addProperty("measurements",this.measurements.size());
hConfig.addProperty(prefix+"motors",meas.motors[0]+sep+meas.motors[1]+sep+meas.motors[2]); for (int i=0;i<this.measurements.size();i++){
hConfig.addProperty(prefix+"sample",meas.asListString()); FocusingFieldMeasurement meas=this.measurements.get(i);
} String prefix="measurement_"+i+".";
File file=new File (path); if (meas.timestamp!=null) hConfig.addProperty(prefix+"timestamp",meas.timestamp);
BufferedWriter writer; hConfig.addProperty(prefix+"temperature",meas.temperature);
try { hConfig.addProperty(prefix+"motors",meas.motors[0]+sep+meas.motors[1]+sep+meas.motors[2]);
writer = new BufferedWriter(new FileWriter(file)); hConfig.addProperty(prefix+"sample",meas.asListString());
hConfig.save(writer); }
} catch (IOException e) { File file=new File (path);
// TODO Auto-generated catch block BufferedWriter writer;
e.printStackTrace(); try {
} catch (ConfigurationException e) { writer = new BufferedWriter(new FileWriter(file));
// TODO Auto-generated catch block hConfig.save(writer);
e.printStackTrace(); } catch (IOException e) {
} // TODO Auto-generated catch block
e.printStackTrace();
} catch (ConfigurationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} }
public void testMeasurement(){ public void testMeasurement(){
GenericDialog gd = new GenericDialog("Select measurement"); GenericDialog gd = new GenericDialog("Select measurement");
...@@ -4759,14 +4823,23 @@ public boolean LevenbergMarquardt( ...@@ -4759,14 +4823,23 @@ public boolean LevenbergMarquardt(
return null; return null;
} }
double [] result=new double [6]; double [] result=new double [6];
double [] best_qb_corr= fieldFitting.getBestQualB( if (debugLevel>0) System.out.println("Calculating optimal focal/tilt, qualBOptimizeMode="+this.qualBOptimizeMode);
k_red, testQualB(false); // optimize qualB, store results in this.qualBOptimizationResults
k_blue, if (debugLevel>0) {
true); System.out.println("Target Zc="+this.qualBOptimizationResults[0]);
System.out.println("Target Tx="+this.qualBOptimizationResults[1]);
System.out.println("Target Ty="+this.qualBOptimizationResults[2]);
}
// double [] best_qb_corr= fieldFitting.getBestQualB(
// k_red,
// k_blue,
// true);
double [] zTilts=getCenterZTxTy(measurement); double [] zTilts=getCenterZTxTy(measurement);
result[0]=zTilts[0]-best_qb_corr[0]; result[0]=zTilts[0]-this.qualBOptimizationResults[0]; //best_qb_corr[0];
result[1]=zTilts[1]; result[1]=zTilts[1]-this.qualBOptimizationResults[1];
result[2]=zTilts[2]; result[2]=zTilts[2]-this.qualBOptimizationResults[2];
double [] zm=null; double [] zm=null;
if (parallelMove){ if (parallelMove){
zm=new double [3]; zm=new double [3];
...@@ -4774,9 +4847,9 @@ public boolean LevenbergMarquardt( ...@@ -4774,9 +4847,9 @@ public boolean LevenbergMarquardt(
} }
double [] dm= getAdjustedMotors( double [] dm= getAdjustedMotors(
zm, zm,
targetRelFocalShift+best_qb_corr[0], targetRelFocalShift+this.qualBOptimizationResults[0] , //targetRelFocalShift+best_qb_corr[0],
0.0, // targetTiltX, // for testing, normally should be 0 um/mm this.qualBOptimizationResults[1], //0.0, // targetTiltX, // for testing, normally should be 0 um/mm
0.0, // targetTiltY, this.qualBOptimizationResults[2], //0.0, // targetTiltY,
true); // motor steps true); // motor steps
if ((dm!=null) && (debugLevel>1)){ if ((dm!=null) && (debugLevel>1)){
System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0)); System.out.println("Suggested motor positions: "+IJ.d2s(dm[0],0)+":"+IJ.d2s(dm[1],0)+":"+IJ.d2s(dm[2],0));
...@@ -5987,6 +6060,17 @@ public boolean LevenbergMarquardt( ...@@ -5987,6 +6060,17 @@ public boolean LevenbergMarquardt(
} }
return non_null?result:null; return non_null?result:null;
} }
/**
* Generate correction parameter arrays for each sample
* @return array of [chn][parameter] arrays or nulls when the particualr sample does not have corrections
*/
public double [][][] getCorrPar(){
double [][][] result = new double [getNumSamples()][][];
for (int sampleIndex=0;sampleIndex<result.length;sampleIndex++) result[sampleIndex]=getCorrPar(sampleIndex);
return result;
}
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;
...@@ -6658,6 +6742,22 @@ public boolean LevenbergMarquardt( ...@@ -6658,6 +6742,22 @@ public boolean LevenbergMarquardt(
paramValues[getIndex(MECH_PAR.ty)]}; paramValues[getIndex(MECH_PAR.ty)]};
return vector; return vector;
} }
public String [] getZTxTyDescriptions(){
String [] descriptions={
getDescription(getIndex(MECH_PAR.z0)),
getDescription(getIndex(MECH_PAR.tx)),
getDescription(getIndex(MECH_PAR.ty))
};
return descriptions;
}
public String [] getZTxTyNames(){
String [] names={
getName(getIndex(MECH_PAR.z0)),
getName(getIndex(MECH_PAR.tx)),
getName(getIndex(MECH_PAR.ty))
};
return names;
}
public void setVector(double[] vector, boolean [] mask){ public void setVector(double[] vector, boolean [] mask){
for (int i=0;i<vector.length;i++) if (mask[i]) paramValues[i]=vector[i]; for (int i=0;i<vector.length;i++) if (mask[i]) paramValues[i]=vector[i];
...@@ -6754,8 +6854,8 @@ public boolean LevenbergMarquardt( ...@@ -6754,8 +6854,8 @@ public boolean LevenbergMarquardt(
derivs); derivs);
if (calDerivs){ if (calDerivs){
result[1]=derivs[getIndex(MECH_PAR.z0)]; result[1]=derivs[getIndex(MECH_PAR.z0)];
result[1]=derivs[getIndex(MECH_PAR.tx)]; result[2]=derivs[getIndex(MECH_PAR.tx)];
result[1]=derivs[getIndex(MECH_PAR.ty)]; result[3]=derivs[getIndex(MECH_PAR.ty)];
} }
return result; return result;
} }
...@@ -8369,18 +8469,179 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8369,18 +8469,179 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
} }
} }
} }
// qualBOptimizeMode; // 0 - none, +1 - optimize Zc, +2 - optimize Tx, +4 - optimize Ty
public double[] testQualB(boolean interactive){
double [] targetZTxTy={0.0,0.0,0.0};
if (interactive){
GenericDialog gd = new GenericDialog("Calculate optimal focus/tilt");
gd.addNumericField("Initial focus (relative to best composirte)",targetZTxTy[0],2,5,"um");
gd.addNumericField("Initial tiltX",targetZTxTy[1],2,5,"um/mm");
gd.addNumericField("Initial tiltY",targetZTxTy[2],2,5,"um/mm");
// gd.addCheckbox("Optimize focal distance",selectQualBPars[0]);
// gd.addCheckbox("Optimize tiltX", selectQualBPars[1]);
// gd.addCheckbox("Optimize tiltY", selectQualBPars[2]);
gd.addCheckbox("Optimize focal distance",(this.qualBOptimizeMode & 1) != 0);
gd.addCheckbox("Optimize tiltX", (this.qualBOptimizeMode & 2) != 0);
gd.addCheckbox("Optimize tiltY", (this.qualBOptimizeMode & 4) != 0);
gd.addNumericField("Relative (to green) weight of red channels",100* this.k_red, 1,7,"%");
gd.addNumericField("Relative (to green) weight of blue channels",100* this.k_blue, 1,7,"%");
gd.addNumericField("weight of sagittal channels",this.k_sag, 3,7,"");
gd.addNumericField("weight of tangential channels",this.k_tan, 3,7,"");
gd.addCheckbox("Remove channels with no data", this.qualBRemoveBadSamples);
gd.addNumericField("Relative weight of peripheral areas",100*this.k_qualBFractionPeripheral, 1,7,"%");
gd.addNumericField("Reduce weight of peripheral areas outside of this fraction, linear, large sensor dimension",100*this.k_qualBFractionHor, 1,5,"%");
gd.addNumericField("Reduce weight of peripheral areas outside of this fraction, linear, small sensor dimension",100*this.k_qualBFractionVert, 1,5,"%");
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) return null;
targetZTxTy[0]= gd.getNextNumber();
targetZTxTy[1]= gd.getNextNumber();
targetZTxTy[2]= gd.getNextNumber();
// selectQualBPars[0]= gd.getNextBoolean();
// selectQualBPars[1]= gd.getNextBoolean();
// selectQualBPars[2]= gd.getNextBoolean();
// this.qualBOptimizeMode=(selectQualBPars[0]?1:0)+(selectQualBPars[1]?2:0)+(selectQualBPars[2]?4:0);
this.qualBOptimizeMode=0;
this.qualBOptimizeMode+= gd.getNextBoolean()?1:0;
this.qualBOptimizeMode+= gd.getNextBoolean()?2:0;
this.qualBOptimizeMode+= gd.getNextBoolean()?4:0;
this.k_red= 0.01*gd.getNextNumber();
this.k_blue= 0.01*gd.getNextNumber();
this.k_sag= gd.getNextNumber();
this.k_tan= gd.getNextNumber();
this.qualBRemoveBadSamples=gd.getNextBoolean();
this.k_qualBFractionPeripheral= 0.01*gd.getNextNumber();
this.k_qualBFractionHor= 0.01*gd.getNextNumber();
this.k_qualBFractionVert= 0.01*gd.getNextNumber();
}
boolean [] selectQualBPars={
((this.qualBOptimizeMode & 1) != 0),
((this.qualBOptimizeMode & 2) != 0),
((this.qualBOptimizeMode & 4) != 0)};
double [] best_qb_corr= fieldFitting.getBestQualB(
this.k_red,
this.k_blue,
true);
double [] zTxTy={targetZTxTy[0]+best_qb_corr[0],targetZTxTy[1],targetZTxTy[2]};
if (!selectQualBPars[0] && !selectQualBPars[1] &&!selectQualBPars[2]){
this.qualBOptimizationResults=zTxTy;
return zTxTy; // no LMA, return zc for optimal qualB, zero tilts
}
fieldFitting.mechanicalFocusingModel.setAdjustMode(true);
qualBOptimize.initCorrPars();
double [][] sampleCoord=flattenSampleCoord();
double [] sampleWeights=new double [sampleCoord.length];
for (int i=0;i<sampleCoord.length;i++){
double fractHor= Math.abs((2*sampleCoord[i][0]-(this.sensorWidth-1.0))/(this.sensorWidth-1.0));
double fractVert=Math.abs((2*sampleCoord[i][1]-(this.sensorHeight-1.0))/(this.sensorHeight-1.0));
System.out.println(i+": "+sampleCoord[i][0]+":"+sampleCoord[i][1]+" fractHor="+fractHor+" fractVert="+fractVert);
sampleWeights[i]=1.0;
if (fractHor>this.k_qualBFractionHor){
double w=(this.k_qualBFractionPeripheral*(fractHor-this.k_qualBFractionHor)+1.0*(1.0-fractHor))/(1.0-this.k_qualBFractionHor);
if (w<sampleWeights[i]) sampleWeights[i]=w;
System.out.println("fractHor>this.k_qualBFractionHor, w="+w);
}
if (fractVert>this.k_qualBFractionVert){
double w=(this.k_qualBFractionPeripheral*(fractVert-this.k_qualBFractionVert)+1.0*(1.0-fractVert))/(1.0-this.k_qualBFractionVert);
if (w<sampleWeights[i]) sampleWeights[i]=w;
System.out.println("fractVert>this.k_qualBFractionVert, w="+w);
}
}
if (interactive && (debugLevel>3)){
for (int i=0;i<sampleCoord.length;i++){
System.out.print(" "+IJ.d2s(sampleWeights[i],3));
if (((i+1)%this.sampleCoord[0].length) == 0) System.out.println();
}
}
boolean [][] goodSamples=null;
if (this.qualBRemoveBadSamples){
goodSamples=new boolean[getNumChannels()][getNumSamples()];
for (int i=0;i<goodSamples.length;i++) for (int j=0;j<goodSamples[0].length;j++) goodSamples[i][j]=false;
for (int n=0;n<dataVector.length;n++) if (dataWeights[n]>0.0){
goodSamples[dataVector[n].channel][dataVector[n].sampleIndex]=true;
}
}
qualBOptimize.initWeights(
flattenSampleCoord(), //double [][] sampleCoord,
this.k_red,
this.k_blue,
this.k_sag,
this.k_tan,
goodSamples,
sampleWeights);
qualBOptimize.initQPars(
zTxTy,
selectQualBPars);
// Set all 3 parameter values, even if some are not selected
fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy);
boolean OK= qualBOptimize.qLevenbergMarquardt(
interactive, // boolean openDialog,
debugLevel+1);
if (OK){
zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy();
System.out.println("qualBOptimize returned:\n"+
"zc="+IJ.d2s((zTxTy[0]-best_qb_corr[0]),3)+"um\n"+
"tX="+IJ.d2s(zTxTy[1],3)+"um/mm\n"+
"tY="+IJ.d2s(zTxTy[2],3)+"um/mm");
} else {
System.out.println("qualBOptimize LMA failed");
}
// zTxTy[0]-=best_qb_corr[0]; - absolute, no need to calculate best_qb_corr;
this.qualBOptimizationResults=zTxTy;
return zTxTy;
}
public class QualBOptimize{ public class QualBOptimize{
// public double [] saveZcTxTy=null; // save Zc, Tx, Ty to be restored in the end (just save calibration?) public double [] qCurrentVector=null; // vector of 1..3 elements - parameters used in fitting (of Zc, Tx, Ty)
public double [] qVector=null; // vector of 1..3 elements - parameters used in fitting (of Zc, Tx, Ty) public int [] qIndices=null; // parameter index for each of qCurrentVector elements (0 - Zc, 1 - Tx, 2 - Ty)
public int [] qIndices=null; // parameter index for each of qVector elements (0 - Zc, 1 - Tx, 2 - Ty) public double [] qSavedVector;
public double [] qSaveVector;
public double qFirstRMS;
public double qInitialLambda=0.001;
public double qLambda;
public double [] qWeights=null; public double [] qWeights=null;
double [][] sampleCoord; double [][] sampleCoord;
double [][] jacobian=null; // rows - parameters, columns - samples double [][] qJacobian=null; // rows - parameters, columns - samples
public double [][][] corrPars=null;
int debugLevel=0;
//
private double qLambdaStepUp=8.0; // multiply lambda by this if result is worse
private double qLambdaStepDown=0.5; // multiply lambda by this if result is better
public double qInitialLambda=1.0; //0.001;
public double qThresholdFinish=0.001;
public int qNumIterations= 100; // maximal number of iterations
public double qMaxLambda= 100.0; // max lambda to fail
public double qLambda;
int iterationStepNumber=0;
double currentQualB=-1.0;
double nextQualB=-1.0;
double firstQualB=-1.0;
double [] qCurrentfX=null;
double [] qNextfX=null;
public double [] qNextVector=null;
private LMAArrays qLMAArrays=null;
private LMAArrays savedQLMAArrays=null;
private double [] qLastImprovements= {-1.0,-1.0}; // {last improvement, previous improvement}. If both >0 and < thresholdFinish - done
private boolean showQParams=true;
private boolean showDisabledQParams=true;
private boolean qSaveSeries=false; // just for the dialog
private boolean qStopEachStep=false; // stop after each series
private boolean qStopOnFailure=true; // open dialog when fitting series failed
private boolean debugQDerivatives=false;
private int debugQPoint=-1;
private int debugQParameter=-1;
public long qStartTime=0;
public void initCorrPars(){ // double [][][] corrPars){ // use getCorrPar() to provide corrPars
this.corrPars=fieldFitting.getCorrPar();
}
/** /**
* Generate weighs array for samples * Generate weighs array for samples
...@@ -8391,13 +8652,14 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8391,13 +8652,14 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
* @param kt weight of tangential components * @param kt weight of tangential components
* @param goodSamples array [channel][sample] of all samples taken into account, or null to use all * @param goodSamples array [channel][sample] of all samples taken into account, or null to use all
*/ */
public void initWeighs( public void initWeights(
double [][] sampleCoord, double [][] sampleCoord,
double kr, double kr,
double kb, double kb,
double ks, double ks,
double kt, double kt,
boolean [][] goodSamples){ boolean [][] goodSamples,
double [] sampleWeights){
int numSamples=sampleCoord.length; int numSamples=sampleCoord.length;
this.sampleCoord=new double [numSamples][]; this.sampleCoord=new double [numSamples][];
for (int i=0;i<numSamples;i++) this.sampleCoord[i]=sampleCoord[i].clone(); for (int i=0;i<numSamples;i++) this.sampleCoord[i]=sampleCoord[i].clone();
...@@ -8413,7 +8675,10 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8413,7 +8675,10 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
if ((goodSamples==null) || goodSamples[chn][sample]) { if ((goodSamples==null) || goodSamples[chn][sample]) {
w=colorWeights[c]*dirWeights[d]; w=colorWeights[c]*dirWeights[d];
} }
qWeights[numSamples*chn+sample]=w; if (sampleWeights!=null){
w*=sampleWeights[sample];
}
qWeights[chn+sample*numChannels]=w;
sumWeights+=w; sumWeights+=w;
} }
} }
...@@ -8423,25 +8688,25 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8423,25 +8688,25 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
} }
/** /**
* Init parameter vextr (subset of Zc, Tx, Ty) using provided mask and values * Init parameter vectr (subset of Zc, Tx, Ty) using provided mask and values
* @param selectedPars boolean array of selected parameters {select_zc, select_tx, select_ty} or null for all
* @param vector parameter vector {zc,tx,ty} or null to use current values * @param vector parameter vector {zc,tx,ty} or null to use current values
* @param selectedPars boolean array of selected parameters {select_zc, select_tx, select_ty} or null for all
* @return vector of 1..3 elements of selected parameter values * @return vector of 1..3 elements of selected parameter values
*/ */
public double [] initQPars( public double [] initQPars(
boolean [] selectedPars, double [] vector,
double [] vector){ boolean [] selectedPars){
if (vector==null) vector=fieldFitting.mechanicalFocusingModel.getZTxTy(); if (vector==null) vector=fieldFitting.mechanicalFocusingModel.getZTxTy();
int numPars=0; int numPars=0;
for (int i=0;i<vector.length;i++) if ((selectedPars==null) || selectedPars[i]) numPars++; for (int i=0;i<vector.length;i++) if ((selectedPars==null) || selectedPars[i]) numPars++;
qIndices=new int[numPars]; qIndices=new int[numPars];
qVector=new double[numPars]; qCurrentVector=new double[numPars];
int index=0; int index=0;
for (int i=0;i<vector.length;i++) if ((selectedPars==null) || selectedPars[i]) { for (int i=0;i<vector.length;i++) if ((selectedPars==null) || selectedPars[i]) {
qIndices[index]=i; qIndices[index]=i;
qVector[index++]=vector[i]; qCurrentVector[index++]=vector[i];
} }
return qVector; return qCurrentVector;
} }
public double [] initQPars( public double [] initQPars(
...@@ -8451,30 +8716,30 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8451,30 +8716,30 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
double [] vector={zc,tx,ty}; double [] vector={zc,tx,ty};
boolean [] selectedPars={true,true,true}; boolean [] selectedPars={true,true,true};
for (int i=0;i<vector.length;i++) if (Double.isNaN(vector[i]))selectedPars[i]=false; for (int i=0;i<vector.length;i++) if (Double.isNaN(vector[i]))selectedPars[i]=false;
return initQPars(selectedPars,vector); return initQPars(vector,selectedPars);
} }
public void commitQPars(double [] vector){ public void commitQPars(double [] vector){ // should not modify qCurrentVector
if (vector!=null) qVector=vector.clone(); // if (vector!=null) qCurrentVector=vector.clone();
if (vector==null) vector=qCurrentVector.clone();
double [] zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy(); // current values double [] zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy(); // current values
for (int i=0;i<qIndices.length;i++){ for (int i=0;i<qIndices.length;i++){
zTxTy[qIndices[i]]=qVector[i]; // overwrite selected zTxTy[qIndices[i]]=vector[i]; // overwrite selected
} }
fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy); fieldFitting.mechanicalFocusingModel.setZTxTy(zTxTy);
} }
public void saveQPars(){ // may need to call public void saveQPars(){ // may need to call
qSaveVector=qVector.clone(); qSavedVector=qCurrentVector.clone();
} }
public void restoreQPars(){ // may need to call public void restoreQPars(){ // may need to call
qVector=qSaveVector.clone(); qCurrentVector=qSavedVector.clone();
commitQPars(null); commitQPars(null);
} }
// fX here - FWHM^2, then instaed of rms will be weighted average qualB // fX here - FWHM^2, then instaed of rms will be weighted average qualB
/* public double [] createFXandJacobian(double [] vector, boolean createJacobian){
public double [] createFXandJacobian(double [] vector, boolean createJacobian){
commitQPars(vector); commitQPars(vector);
return createFXandJacobian(createJacobian); return createFXandJacobian(createJacobian);
...@@ -8483,13 +8748,483 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4] ...@@ -8483,13 +8748,483 @@ f_corr: d_fcorr/d_zcorr=0, other: a, reff, kx -> ar[1], ar[2], ar[3], ar[4]
public double [] createFXandJacobian(boolean createJacobian){ public double [] createFXandJacobian(boolean createJacobian){
int numSamples=sampleCoord.length; int numSamples=sampleCoord.length;
int numChannels=qWeights.length/numSamples; int numChannels=qWeights.length/numSamples;
for (int sample=0;sample<numSamples;sample++){ double [] fX=new double [qWeights.length];
if (createJacobian) this.qJacobian=new double [qIndices.length][qWeights.length];
for (int sampleIndex=0;sampleIndex<numSamples;sampleIndex++){
double [] zdZ=fieldFitting.mechanicalFocusingModel.getZdZ3(
sampleCoord[sampleIndex][0], //double px,
sampleCoord[sampleIndex][1], //double py,
createJacobian); //boolean calDerivs)
double [][] deriv_curv = createJacobian?(new double [numChannels][]): null;
double [] chnValues=new double [numChannels];
for (int chn=0;chn<numChannels;chn++){
if (createJacobian){
deriv_curv[chn]= new double [fieldFitting.curvatureModel[chn].getSize()]; // nr*nz+1
}
chnValues[chn]=fieldFitting.curvatureModel[chn].getFdF(
((corrPars==null)?null:((corrPars[sampleIndex]==null)?null:corrPars[sampleIndex][chn])), // (corrPars==null)?null:corrPars[c], // param_corr
sampleCoord[sampleIndex][0], //px,
sampleCoord[sampleIndex][1], //py,
zdZ[0], // mot_z,
createJacobian? deriv_curv[chn]:null);
fX[chn+sampleIndex*numChannels]=chnValues[chn]*chnValues[chn]; // squared FWHM value for qualB
if (createJacobian){
for (int i=0;i<qIndices.length;i++){
// "-" because mot Z is opposite to z0,
// 2*chnValues[chn] - because fX= chnValues ^ 2
this.qJacobian[i][chn+sampleIndex*numChannels]=-2*chnValues[chn]*zdZ[qIndices[i]+1]*deriv_curv[chn][0];
}
}
}
} }
} return fX;
*/ }
public double getQualB(){
return getQualB(createFXandJacobian(false));
}
public double getQualB(double [] fX){
double q=0;
for (int i=0;i<fX.length;i++){
q+=qWeights[i]*fX[i]*fX[i];
}
return Math.sqrt(Math.sqrt(q));
}
public LMAArrays calculateJacobianArrays(double [] fX){
// calculate JtJ
// here Y is zero vector, so just usxe -fX[i] instead of diff[i]
// double [] diff=calcYminusFx(fX);
int numPars=this.qJacobian.length; // number of parameters to be adjusted
int length=fX.length; // should be the same as this.jacobian[0].length
double [][] JtByJmod=new double [numPars][numPars]; //Transposed Jacobian multiplied by Jacobian
double [] JtByDiff=new double [numPars];
for (int i=0;i<numPars;i++) for (int j=i;j<numPars;j++){
JtByJmod[i][j]=0.0;
for (int k=0;k<length;k++) JtByJmod[i][j]+=this.qJacobian[i][k]*this.qJacobian[j][k]*this.qWeights[k];
}
for (int i=0;i<numPars;i++) { // subtract lambda*diagonal , fill the symmetrical half below the diagonal
for (int j=0;j<i;j++) JtByJmod[i][j]= JtByJmod[j][i]; // it is symmetrical matrix, just copy
}
for (int i=0;i<numPars;i++) {
JtByDiff[i]=0.0;
// for (int k=0;k<length;k++) JtByDiff[i]+=this.jacobian[i][k]*diff[k]*this.qWeights[k];
for (int k=0;k<length;k++) JtByDiff[i]-=this.qJacobian[i][k]*fX[k]*this.qWeights[k];// here Y is zero vector, so just usxe -fX[i] instead of diff[i]
}
LMAArrays lMAArrays = new LMAArrays();
lMAArrays.jTByJ=JtByJmod;
lMAArrays.jTByDiff=JtByDiff;
return lMAArrays;
}
public double [] solveLMA(
LMAArrays lMAArrays,
double lambda,
int debugLevel){
this.debugLevel=debugLevel;
double [][] JtByJmod= lMAArrays.jTByJ.clone();
int numPars=JtByJmod.length;
for (int i=0;i<numPars;i++){
JtByJmod[i]=lMAArrays.jTByJ[i].clone();
JtByJmod[i][i]+=lambda*JtByJmod[i][i]; //Marquardt mod
}
// M*Ma=Mb
Matrix M=new Matrix(JtByJmod);
if (debugLevel>2) {
System.out.println("qLMA Jt*J -lambda* diag(Jt*J), lambda="+lambda+":");
M.print(10, 5);
}
Matrix Mb=new Matrix(lMAArrays.jTByDiff,numPars); // single column
if (!(new LUDecomposition(M)).isNonsingular()){
double [][] arr=M.getArray();
System.out.println("qLMA Singular Matrix "+arr.length+"x"+arr[0].length);
// any rowsx off all 0.0?
for (int n=0;n<arr.length;n++){
boolean zeroRow=true;
for (int i=0;i<arr[n].length;i++) if (arr[n][i]!=0.0){
zeroRow=false;
break;
}
if (zeroRow){
System.out.println("qLMA Row of all zeros: "+n);
}
}
// M.print(10, 5);
return null;
}
Matrix Ma=M.solve(Mb); // singular
return Ma.getColumnPackedCopy();
}
public void qStepLevenbergMarquardtAction(int debugLevel){//
this.iterationStepNumber++;
// apply/revert,modify lambda
String msg="currentQualB="+this.currentQualB+
", nextQualB="+this.nextQualB+
", delta="+(this.currentQualB-this.nextQualB)+
", lambda="+this.qLambda;
if (debugLevel>1) System.out.println("stepLevenbergMarquardtAction() "+msg);
// if (this.updateStatus) IJ.showStatus(msg);
if (this.nextQualB<this.currentQualB) { //improved
this.qLambda*=this.qLambdaStepDown;
this.currentQualB=this.nextQualB;
this.qCurrentfX=this.qNextfX;
this.qCurrentVector=this.qNextVector;
} else {
this.qLambda*=this.qLambdaStepUp;
this.qLMAArrays=this.savedQLMAArrays; // restore Jt*J and Jt*diff
// restoreQPars();
}
}
/**
* Calculates next parameters vector, holds some arrays
* @param numSeries
* @return array of two booleans: { improved, finished}
*/
public boolean [] stepQLevenbergMarquardtFirst(int debugLevel){
double [] deltas=null;
if (this.qCurrentVector==null) {
this.qCurrentVector=this.qSavedVector.clone();
this.currentQualB=-1;
this.qCurrentfX=null; // invalidate
this.qJacobian=null; // invalidate
this.qLMAArrays=null;
this.qLastImprovements[0]=-1.0;
this.qLastImprovements[1]=-1.0;
}
this.debugLevel=debugLevel;
// calculate this.currentfX, this.jacobian if needed
if (debugLevel>2) {
System.out.println("this.qCurrentVector");
for (int i=0;i<this.qCurrentVector.length;i++){
System.out.println(i+": "+ this.qCurrentVector[i]);
}
}
// if ((this.currentfX==null)|| ((this.jacobian==null) && !this.threadedLMA )) {
if ((this.qCurrentfX==null)|| (this.qLMAArrays==null)) {
String msg="qLMA: initial Jacobian matrix calculation. Points:"+this.qWeights.length+" Parameters:"+this.qCurrentVector.length;
if (debugLevel>1) System.out.println(msg);
if (updateStatus) IJ.showStatus(msg);
this.qCurrentfX=createFXandJacobian(this.qCurrentVector, true); // is it always true here (this.jacobian==null)
this.qLMAArrays=calculateJacobianArrays(this.qCurrentfX);
this.currentQualB= getQualB(this.qCurrentfX);
msg="qLMA: initial qualB="+IJ.d2s(this.currentQualB,8)+
". Calculating next Jacobian. Points:"+this.qWeights.length+" Parameters:"+this.qCurrentVector.length;
if (debugLevel>1) System.out.println(msg);
if (updateStatus) IJ.showStatus(msg);
}
if (this.firstQualB<0) {
this.firstQualB=this.currentQualB;
}
deltas=solveLMA(this.qLMAArrays, this.qLambda, debugLevel);
boolean matrixNonSingular=true;
if (deltas==null) {
deltas=new double[this.qCurrentVector.length];
for (int i=0;i<deltas.length;i++) deltas[i]=0.0;
matrixNonSingular=false;
}
if (debugLevel>1) {
System.out.println("deltas");
for (int i=0;i<deltas.length;i++){
System.out.println(i+": "+ deltas[i]);
}
}
// apply deltas
this.qNextVector=this.qCurrentVector.clone();
for (int i=0;i<this.qNextVector.length;i++) this.qNextVector[i]+=deltas[i];
// another option - do not calculate J now, just fX. and late - calculate both if it was improvement
// save current Jacobian
if (debugLevel>1) {
System.out.println("qLMA: this.qNextVector");
for (int i=0;i<this.qNextVector.length;i++){
System.out.println(i+": "+ this.qNextVector[i]);
}
}
// this.savedJacobian=this.jacobian;
this.savedQLMAArrays=this.qLMAArrays.clone();
this.qJacobian=null; // not needed, just to catch bugs
this.qNextfX=createFXandJacobian(this.qNextVector,true);
this.qLMAArrays=calculateJacobianArrays(this.qNextfX);
this.nextQualB= getQualB(this.qNextfX);
this.qLastImprovements[1]=this.qLastImprovements[0];
this.qLastImprovements[0]=this.currentQualB-this.nextQualB;
String msg="currentQualB="+this.currentQualB+
", nextQualB="+this.nextQualB+
", delta="+(this.currentQualB-this.nextQualB);
if (debugLevel>1) System.out.println("qLMA: stepLMA "+msg);
if (updateStatus) IJ.showStatus(msg);
boolean [] status={matrixNonSingular && (this.nextQualB<=this.currentQualB),!matrixNonSingular};
// additional test if "worse" but the difference is too small, it was be caused by computation error, like here:
//stepLevenbergMarquardtAction() step=27, this.currentRMS=0.17068403807026408, this.nextRMS=0.1706840380702647
if (!status[0] && matrixNonSingular) {
if (this.nextQualB<(this.currentQualB+this.currentQualB*this.qThresholdFinish*0.01)) {
this.nextQualB=this.currentQualB;
status[0]=true;
status[1]=true;
this.qLastImprovements[0]=0.0;
if (debugLevel>1) {
System.out.println("qLMA: New RMS error is larger than the old one, but the difference is too small to be trusted ");
System.out.println(
"stepQLMA this.currentQualB="+this.currentQualB+
", this.nextQualB="+this.nextQualB+
", delta="+(this.currentQualB-this.nextQualB));
}
}
}
if (status[0] && matrixNonSingular) { //improved
status[1]=(this.iterationStepNumber>this.qNumIterations) || ( // done
(this.qLastImprovements[0]>=0.0) &&
(this.qLastImprovements[0]<this.qThresholdFinish*this.currentQualB) &&
(this.qLastImprovements[1]>=0.0) &&
(this.qLastImprovements[1]<this.qThresholdFinish*this.currentQualB));
} else if (matrixNonSingular){
// this.jacobian=this.savedJacobian;// restore saved Jacobian
this.qLMAArrays=this.savedQLMAArrays; // restore Jt*J and Jt*diff
status[1]=(this.iterationStepNumber>this.qNumIterations) || // failed
((this.qLambda*this.qLambdaStepUp)>this.qMaxLambda);
}
///this.currentRMS
//TODO: add other failures leading to result failure?
if (debugLevel>2) {
System.out.println("qLMA: stepLevenbergMarquardtFirst("+debugLevel+")=>"+status[0]+","+status[1]);
}
return status;
}
public boolean dialogQLMAStep(boolean [] state){
String [] states={
"Worse, increase lambda",
"Better, decrease lambda",
"Failed to fit",
"Fitting Successful"};
String [] descriptions=fieldFitting.mechanicalFocusingModel.getZTxTyDescriptions();
double [] zTxTy=fieldFitting.mechanicalFocusingModel.getZTxTy(); // current values
boolean [] paramSelect={false,false,false};
for (int i:qIndices) paramSelect[i]=true;
int iState=(state[0]?1:0)+(state[1]?2:0);
GenericDialog gd = new GenericDialog("(qualB) Levenberg-Marquardt algorithm step");
gd.addMessage("Current state="+states[iState]);
gd.addMessage("Iteration step="+this.iterationStepNumber);
gd.addMessage("Initial qualB="+IJ.d2s(this.firstQualB,6)+", Current qualB="+IJ.d2s(this.currentQualB,6)+", new qualB="+IJ.d2s(this.nextQualB,6));
if (this.showQParams) {
gd.addMessage("==== Current parameter values ===");
for (int i=0;i<zTxTy.length;i++) if (this.showDisabledQParams || paramSelect[i]){
gd.addMessage( (paramSelect[i]?"(+) ":"(-) ")+descriptions[i]+": "+IJ.d2s(zTxTy[i],6));
}
gd.addMessage("");
gd.addMessage("Lambda="+this.qLambda);
}
gd.addNumericField("Lambda ", this.qLambda, 5);
gd.addNumericField("Multiply lambda on success", this.qLambdaStepDown, 5);
gd.addNumericField("Threshold RMS to exit LMA", this.qThresholdFinish, 7,9,"pix");
gd.addNumericField("Multiply lambda on failure", this.qLambdaStepUp, 5);
gd.addNumericField("Threshold lambda to fail", this.qMaxLambda, 5);
gd.addNumericField("Maximal number of iterations", this.qNumIterations, 0);
gd.addCheckbox("Dialog after each iteration step", this.qStopEachStep);
gd.addCheckbox("Dialog after each failure", this.qStopOnFailure);
gd.addCheckbox("Show modified parameters", this.showQParams);
gd.addCheckbox("Show disabled parameters", this.showDisabledQParams);
gd.addMessage("Done will save the current (not new!) state and exit, Continue will proceed according to LMA");
gd.enableYesNoCancel("Continue", "Done");
WindowTools.addScrollBars(gd);
gd.showDialog();
if (gd.wasCanceled()) {
this.qSaveSeries=false;
return false;
}
this.qLambda= gd.getNextNumber();
this.qLambdaStepDown= gd.getNextNumber();
this.qThresholdFinish= gd.getNextNumber();
this.qLambdaStepUp= gd.getNextNumber();
this.qMaxLambda= gd.getNextNumber();
this.qNumIterations= (int) gd.getNextNumber();
this.qStopEachStep= gd.getNextBoolean();
this.qStopOnFailure= gd.getNextBoolean();
this.showQParams= gd.getNextBoolean();
this.showDisabledQParams= gd.getNextBoolean();
this.qSaveSeries=true;
return gd.wasOKed();
}
public boolean selectQLMAParameters(){
GenericDialog gd = new GenericDialog("Levenberg-Marquardt algorithm parameters for finding the optimal tilt/distance");
gd.addCheckbox("Debug derivatives", false);
gd.addNumericField("Debug Jacobian for point number", this.debugQPoint, 0, 5,"(-1 - none)");
gd.addNumericField("Debug Jacobian for parameter number", this.debugQParameter, 0, 5,"(-1 - none)");
gd.addNumericField("Initial LMA Lambda ", this.qInitialLambda, 5, 8, " last was "+this.qLambda);
gd.addNumericField("Multiply lambda on success", this.qLambdaStepDown, 5);
gd.addNumericField("Threshold RMS to exit LMA", this.qThresholdFinish, 7,9,"pix");
gd.addNumericField("Multiply lambda on failure", this.qLambdaStepUp, 5);
gd.addNumericField("Threshold lambda to fail", this.qMaxLambda, 5);
gd.addNumericField("Maximal number of iterations", this.qNumIterations, 0);
gd.addCheckbox("Dialog after each iteration step", this.qStopEachStep);
gd.addCheckbox("Dialog after each failure", this.qStopOnFailure);
gd.addCheckbox("Show modified parameters", this.showQParams);
gd.addCheckbox("Show disabled parameters", this.showDisabledQParams);
gd.showDialog();
if (gd.wasCanceled()) return false;
this.debugQDerivatives=gd.getNextBoolean();
this.debugQPoint= (int) gd.getNextNumber();
this.debugQParameter= (int) gd.getNextNumber();
this.qInitialLambda= gd.getNextNumber();
this.qLambdaStepDown= gd.getNextNumber();
this.qThresholdFinish= gd.getNextNumber();
this.qLambdaStepUp= gd.getNextNumber();
this.qMaxLambda= gd.getNextNumber();
this.qNumIterations= (int) gd.getNextNumber();
this.qStopEachStep= gd.getNextBoolean();
this.qStopOnFailure= gd.getNextBoolean();
this.showQParams= gd.getNextBoolean();
this.showDisabledQParams= gd.getNextBoolean();
return true;
}
public boolean qLevenbergMarquardt(
boolean openDialog,
int debugLevel){
double savedLambda=this.qLambda;
this.debugLevel=debugLevel;
if (openDialog && !selectQLMAParameters()) return false;
this.qLambda=this.qInitialLambda;
this.qStartTime=System.nanoTime();
// TODO: ASet ZTxTy, mask,
//initCorrPars(double [][][] corrPars)
// initWeights...
if (!openDialog) stopEachStep=false;
this.iterationStepNumber=0;
this.firstQualB=-1; //undefined
saveQPars();
if (debugQDerivatives){
qCompareDrDerivatives(this.qSavedVector);
}
this.qCurrentVector=null; // invalidate for the new series
while (true) { // loop for the same series
boolean [] state=stepQLevenbergMarquardtFirst(debugLevel);
if (state==null) {
String msg="Calculation aborted by user request, restoring saved parameter vector";
IJ.showMessage(msg);
System.out.println(msg);
restoreQPars();
// commitParameterVector(this.savedVector);
this.qLambda=savedLambda;
return false;
}
if (debugLevel>1) System.out.println(this.iterationStepNumber+": stepQLevenbergMarquardtFirst("+debugLevel+")==>"+state[1]+":"+state[0]);
boolean cont=true;
// Make it success if this.currentRMS<this.firstRMS even if LMA failed to converge
if (state[1] && !state[0] && (this.firstQualB>this.currentQualB)){
if (debugLevel>1) System.out.println("qLMA failed to converge, but RMS improved from the initial value ("+
this.currentQualB+" < "+this.firstQualB+")");
state[0]=true;
}
if (
(stopRequested.get()>0) || // graceful stop requested
(this.qStopEachStep) ||
// (this.stopEachSeries && state[1]) ||
(this.qStopOnFailure && state[1] && !state[0])){
// if (state[1] && !state[0] && !calibrate){
// return false;
// }
if (debugLevel>0){
if (stopRequested.get()>0) System.out.println("User requested stop");
System.out.println("qLevenbergMarquardt(): step ="+this.iterationStepNumber+
", QualB="+IJ.d2s(this.currentQualB,8)+
" ("+IJ.d2s(this.firstQualB,8)+") "+
") at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.qStartTime),3));
}
long startDialogTime=System.nanoTime();
cont=dialogQLMAStep(state);
stopRequested.set(0); // Will not stop each run
this.qStartTime+=(System.nanoTime()-startDialogTime); // do not count time used by the User.
}
qStepLevenbergMarquardtAction(debugLevel); // apply step - in any case?
if (updateStatus){
IJ.showStatus("Step #"+this.iterationStepNumber+
" QualB="+IJ.d2s(this.currentQualB,8)+
" ("+IJ.d2s(this.firstQualB,8)+")"+
" ");
}
if (!cont){
if (this.qSaveSeries) {
savedLambda=this.qLambda;
// this.qSavedVector=this.qCurrentVector.clone();
saveQPars();
}
// if RMS was decreased. this.saveSeries==false after dialogQLMAStep(state) only if "cancel" was pressed
// commitParameterVector(this.savedVector); // either new or original
commitQPars(this.qSavedVector);
this.qLambda=savedLambda;
return this.qSaveSeries; // TODO: Maybe change result?
}
//stepLevenbergMarquardtAction();
if (state[1]) {
if (!state[0]) {
// commitParameterVector(this.savedVector);
commitQPars(this.qSavedVector);
this.qLambda=savedLambda;
return false; // sequence failed
}
// this.savedVector=this.currentVector.clone();
saveQPars();
break; // while (true), proceed to the next series
}
} // while true - same series
String msg="QualB="+this.currentQualB+" ("+this.firstQualB+") "+
" at "+ IJ.d2s(0.000000001*(System.nanoTime()-this.qStartTime),3);
if (debugLevel>0) System.out.println("qStepLevenbergMarquardtAction() "+msg);
// if (this.updateStatus) IJ.showStatus(msg);
if (updateStatus){
IJ.showStatus("Done: Step #"+this.iterationStepNumber+
" QualB="+IJ.d2s(this.currentQualB,8)+
" ("+IJ.d2s(this.firstQualB,8)+")"+
" ");
}
// this.savedVector=this.currentVector.clone();
// commitParameterVector(this.savedVector);
saveQPars();
commitQPars(this.qSavedVector);
return true; // all series done
}
public void qCompareDrDerivatives(double [] vector){
double delta=0.00010; // make configurable
if (this.debugQParameter>=0){
String parName="";
// if ((debugParameterNames!=null) && (debugParameterNames.length>debugParameter)) parName=debugParameterNames[debugParameter];
System.out.println("Debugging derivatives for parameter #"+this.debugQParameter+" ("+parName+")");
//debugParameterNames
double [] vector_dp=vector.clone();
vector_dp[this.debugQParameter]+=delta;
double [] fx_dp=createFXandJacobian(vector_dp,false);
double [] fx= createFXandJacobian(vector,true);
for (int i=0;i<fx.length;i++){
if ((this.debugQPoint>=0) && (this.debugQPoint!=i)) continue; // debug only single point
int sample=i/6;
int chn=i%6;
String pointName="";
pointName="chn"+chn+":"+sample;
System.out.println(i+": "+pointName+" fx= "+fx[i]+" delta_fx= "+((fx_dp[i]-fx[i])/delta)+" df/dp= "+
this.qJacobian[this.debugQParameter][i]);
}
}
}
} }
} }
......
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