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imagej-elphel
Commit ec11a1dd authored by Andrey Filippov's avatar Andrey Filippov
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fixed bugs in hinted match

parent 2c684497
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Showing with 54 additions and 10 deletions
src/main/java/Aberration_Calibration.java
View file @ ec11a1dd
...@@ -6193,7 +6193,7 @@ if (MORE_BUTTONS) { ...@@ -6193,7 +6193,7 @@ if (MORE_BUTTONS) {
return; return;
} }
GenericDialog gd=new GenericDialog ("Parameters of the filter by predicted grid"); GenericDialog gd=new GenericDialog ("Parameters of the filter by predicted grid");
gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", 5.0, 1,4,"pix"); gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", 0.5, 1,4,"fraction of grid half-period");
gd.addCheckbox ("Calibrate by translation (false - orientation only)", true); gd.addCheckbox ("Calibrate by translation (false - orientation only)", true);
gd.addCheckbox ("Process all images (false - only not yet enabled)", false); gd.addCheckbox ("Process all images (false - only not yet enabled)", false);
gd.addCheckbox ("Ignore laser pointers", false); gd.addCheckbox ("Ignore laser pointers", false);
...@@ -6272,7 +6272,7 @@ if (MORE_BUTTONS) { ...@@ -6272,7 +6272,7 @@ if (MORE_BUTTONS) {
gd=new GenericDialog ("Image set # "+imageSetNumber+" re-calibration without laser pointers"); gd=new GenericDialog ("Image set # "+imageSetNumber+" re-calibration without laser pointers");
gd.addMessage("Strategy 0 should have all parameters but 2 goniometer axes disabled"); gd.addMessage("Strategy 0 should have all parameters but 2 goniometer axes disabled");
gd.addMessage("Imgages belonging to the set will be selected, possible to check with \"Remove Outlayers\" for strategy 0"); gd.addMessage("Imgages belonging to the set will be selected, possible to check with \"Remove Outlayers\" for strategy 0");
gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", hintGridTolerance, 1,4,"pix"); gd.addNumericField("Mismatch tolerance of match between the predicted and acquired grid", hintGridTolerance, 1,4,"fraction of grid half-period");
gd.addCheckbox("Ignore laser pointers", ignoreLaserPointers); gd.addCheckbox("Ignore laser pointers", ignoreLaserPointers);
gd.addNumericField("Image set tilt", tiltCenter, 2,6,"degrees"); gd.addNumericField("Image set tilt", tiltCenter, 2,6,"degrees");
gd.addNumericField("Image set axial", axialCenter, 2,6,"degrees"); gd.addNumericField("Image set axial", axialCenter, 2,6,"degrees");
......
src/main/java/MatchSimulatedPattern.java
View file @ ec11a1dd
...@@ -6625,15 +6625,16 @@ public class MatchSimulatedPattern { ...@@ -6625,15 +6625,16 @@ public class MatchSimulatedPattern {
public double [][] calcGridMatchMatrix (double [][][] hintGrid, double searchAround){ public double [][] calcGridMatchMatrix (double [][][] hintGrid, double searchAround){
double [][][] measuredUV=mapEstimatedToMeasured(hintGrid, searchAround); double [][][] measuredUV=mapEstimatedToMeasured(hintGrid, searchAround);
if (this.debugLevel>2){ if (this.debugLevel>2){
double [][] pixels=new double[7][measuredUV.length*measuredUV[0].length]; double [][] pixels=new double[9][measuredUV.length*measuredUV[0].length];
int index=0; int index=0;
String [] titles={"grid-U","grid-V","contrast","hint-X","hint-Y","hint-U","hint-V"}; String [] titles={"grid-U","grid-V","contrast","hint-X","hint-Y","hint-U","hint-V","grid-hint-U","grid-hint-V"}; // last 2 only valid for rotation==0
for (int v=0; v<measuredUV.length;v++) for (int u=0;u<measuredUV[v].length;u++){ for (int v=0; v<measuredUV.length;v++) for (int u=0;u<measuredUV[v].length;u++){
if (measuredUV[v][u]!=null){ if (measuredUV[v][u]!=null){
for (int i=0; i<3;i++) pixels[i][index]=measuredUV[v][u][i]; for (int i=0; i<3;i++) pixels[i][index]=measuredUV[v][u][i];
for (int i=0; i<4;i++) pixels[i+3][index]=hintGrid[v][u][i]; for (int i=0; i<4;i++) pixels[i+3][index]=hintGrid[v][u][i];
for (int i=0; i<2;i++) pixels[i+7][index]=measuredUV[v][u][i]-hintGrid[v][u][i+2];
} else { } else {
for (int i=0; i<7;i++) pixels[i][index]=Double.NaN; for (int i=0; i<9;i++) pixels[i][index]=Double.NaN;
} }
index++; index++;
} }
...@@ -6656,14 +6657,56 @@ public class MatchSimulatedPattern { ...@@ -6656,14 +6657,56 @@ public class MatchSimulatedPattern {
data [index][2][0]=measuredUV[v][u][2]; // contrast data [index][2][0]=measuredUV[v][u][2]; // contrast
index++; index++;
} }
if (this.debugLevel>0) System.out.println("calcGridMatchMatrix(), data.length="+data.length+" measuredUV.length="+measuredUV.length+ if (this.debugLevel>0) {
System.out.println("calcGridMatchMatrix(), data.length="+data.length+" measuredUV.length="+measuredUV.length+
((measuredUV.length>0)?(", measuredUV[0].length="+measuredUV[0].length):"")); ((measuredUV.length>0)?(", measuredUV[0].length="+measuredUV[0].length):""));
if (this.debugLevel>3) for (index=0;index<data.length;index++){
System.out.println(data[index][0][0]+","+data[index][0][1]+","+data[index][1][0]+","+data[index][1][1]+","+data[index][2][0]);
}
}
// int gridRotation=-1; //undefined
if (data.length<3){ if (data.length<3){
// if (this.debugLevel>0) System.out.println("calcGridMatchMatrix(), data.length="+data.length+" measuredUV.length="+measuredUV.length+ /// if (this.debugLevel>0) System.out.println("calcGridMatchMatrix(), data.length="+data.length+" measuredUV.length="+measuredUV.length+
// ((measuredUV.length>0)?(", measuredUV[0].length="+measuredUV[0].length):"")); /// ((measuredUV.length>0)?(", measuredUV[0].length="+measuredUV[0].length):""));
return null; return null;
} }
double [][] coeff=new PolynomialApproximation(this.debugLevel).quadraticApproximation(data, true); double [][] coeff=new PolynomialApproximation(this.debugLevel).quadraticApproximation(data, true);
if (coeff!=null) {
// gridRotation=matrixToRot(coeff);
int rot=matrixToRot(coeff);
boolean [] flips=rotToFlips(rot);
double [][] aI={{1,0},{0,1}};
double [][] aSwap= {{ 0,1},{1,0}};
double [][] aFlipU={{-1,0},{0,1}};
double [][] aFlipV={{ 1,0},{0,-1}};
Matrix M=new Matrix(aI);
if (flips[0]) M=M.times((new Matrix(aSwap)));
if (flips[1]) M=M.times((new Matrix(aFlipU)));
if (flips[2]) M=M.times((new Matrix(aFlipV)));
// now M reconstructs coeff
double [][]aM=M.getArray();
double SMU=0.0,SMV=0.0,SW=0.0;
for (int i=0;i<data.length;i++){
SMU+=data[i][2][0]*(data[i][1][0]-(aM[0][0]*data[i][0][0]+aM[0][1]*data[i][0][1]));
SMV+=data[i][2][0]*(data[i][1][1]-(aM[1][0]*data[i][0][0]+aM[1][1]*data[i][0][1]));
SW+=data[i][2][0];
}
SMU/=SW;
SMV/=SW;
if (this.debugLevel>0) {
System.out.println("coeff[0][0]="+coeff[0][0]+" coeff[0][1]="+coeff[0][1]+" coeff[0][2]="+coeff[0][2]);
System.out.println("coeff[1][0]="+coeff[1][0]+" coeff[1][1]="+coeff[1][1]+" coeff[1][2]="+coeff[1][2]);
System.out.println("aM[0][0]="+aM[0][0]+" aM[0][1]="+aM[0][1]+" SMU="+SMU);
System.out.println("aM[1][0]="+aM[1][0]+" aM[1][1]="+aM[1][1]+" SMV="+SMV);
}
coeff[0][0]=aM[0][0];
coeff[0][1]=aM[0][1];
coeff[1][0]=aM[1][0];
coeff[1][1]=aM[1][1];
coeff[0][2]=SMU;
coeff[1][2]=SMV;
}
return coeff; return coeff;
} }
public int matrixToRot(double [][] coeff){ public int matrixToRot(double [][] coeff){
...@@ -6744,7 +6787,7 @@ public class MatchSimulatedPattern { ...@@ -6744,7 +6787,7 @@ public class MatchSimulatedPattern {
} }
return worst; return worst;
} }
public double worstGridMatchTranslate(double [][] coeff){ public double worstGridMatchTranslate(double [][] coeff){ // in grids half-periods, not pixels!
int [][] iCoeff=gridMatrixApproximate(coeff); int [][] iCoeff=gridMatrixApproximate(coeff);
double worst=0; double worst=0;
for (int i=0;i<2;i++){ for (int i=0;i<2;i++){
...@@ -7117,6 +7160,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1]) ...@@ -7117,6 +7160,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
int [] iGridTranslateUV=null; // translate UV grid by these integer numbers int [] iGridTranslateUV=null; // translate UV grid by these integer numbers
if (hintGrid!=null){ if (hintGrid!=null){
gridMatchCoeff=calcGridMatchMatrix (hintGrid, searchAround); gridMatchCoeff=calcGridMatchMatrix (hintGrid, searchAround);
// now already rounds rotate and re-replaces gridMatchCoeff with approximated, refines gridMatchCoeff[0][2] and gridMatchCoeff[1][2]
if (gridMatchCoeff!=null) { if (gridMatchCoeff!=null) {
gridRotation=matrixToRot(gridMatchCoeff); gridRotation=matrixToRot(gridMatchCoeff);
this.debugLevel=global_debug_level; this.debugLevel=global_debug_level;
...@@ -7132,7 +7176,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1]) ...@@ -7132,7 +7176,7 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
} }
// hintGridTolerance==0 - do not try to determine shift from the hint (not reliable yet) // hintGridTolerance==0 - do not try to determine shift from the hint (not reliable yet)
if (hintGridTolerance>0) { if (hintGridTolerance>0) {
if (worstGridMatchTranslate(gridMatchCoeff)<=hintGridTolerance){ if (worstGridMatchTranslate(gridMatchCoeff)<=hintGridTolerance){ // convert to pixels from halfperiods (or just chnage definition of hintGridTolerance)
if (global_debug_level>1) System.out.println("worstGridMatchTranslate(gridMatchCoeff)= "+worstGridMatchTranslate(gridMatchCoeff)+", hintGridTolerance="+hintGridTolerance); if (global_debug_level>1) System.out.println("worstGridMatchTranslate(gridMatchCoeff)= "+worstGridMatchTranslate(gridMatchCoeff)+", hintGridTolerance="+hintGridTolerance);
iGridTranslateUV=new int[2]; iGridTranslateUV=new int[2];
iGridTranslateUV[0]=iGridMatchCoeff[0][2]; iGridTranslateUV[0]=iGridMatchCoeff[0][2];
......
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