Bug fixes (c26bdeca) · Commits · Elphel / imagej-elphel

src/main/java/FocusingField.java

+26 −0

Original line number	Original line	Diff line number	Diff line
	@@ -1596,6 +1596,9 @@ private boolean [] filterLowNeighbors(
	boolean [] left=usedSamples[chn].clone();		boolean [] left=usedSamples[chn].clone();
	for (int y=0;y<height;y++) for (int x=0;x<width;x++) if (usedSamples[chn][y*width+x]){		for (int y=0;y<height;y++) for (int x=0;x<width;x++) if (usedSamples[chn][y*width+x]){
	int n=0;		int n=0;
			// if ((chn==2) && (y==4) && (x==0)){ // debugging
			// n=0;
			// }
	for (int d=0;d<dirs.length;d++){		for (int d=0;d<dirs.length;d++){
	int [] dXY=dirs[d].clone();		int [] dXY=dirs[d].clone();
	if (((x==0) && (dXY[0]<0)) \|\| ((x==(width-1)) && (dXY[0]>0))) dXY[0]=-dXY[0];		if (((x==0) && (dXY[0]<0)) \|\| ((x==(width-1)) && (dXY[0]>0))) dXY[0]=-dXY[0];
	@@ -1794,6 +1797,9 @@ public void setDataVector(
	}		}

	if (calibrateMode && (filterSetsByRMS>0)){		if (calibrateMode && (filterSetsByRMS>0)){
			fieldFitting.initSampleCorrVector(
			flattenSampleCoord(), //double [][] sampleCoordinates,
			getSeriesWeights()); //double [][] sampleSeriesWeights);
	boolean [] en=dataWeightsToBoolean();		boolean [] en=dataWeightsToBoolean();
	en= filterSets(		en= filterSets(
	en,		en,
	@@ -4485,6 +4491,7 @@ public boolean LevenbergMarquardt(
	}		}
	}		}
	header+="\tRMS";		header+="\tRMS";
			header+="\tZc\tTiltX\tTiltY";
	for (int i=0;i<3;i++) header+="\tmz"+i;		for (int i=0;i<3;i++) header+="\tmz"+i;
	for (int i=0;i<3;i++) header+="\tm"+i;		for (int i=0;i<3;i++) header+="\tm"+i;
	StringBuffer sb = new StringBuffer();		StringBuffer sb = new StringBuffer();
	@@ -4519,6 +4526,8 @@ public boolean LevenbergMarquardt(
	fieldFitting.mechanicalFocusingModel.getUnits(i));		fieldFitting.mechanicalFocusingModel.getUnits(i));
	}		}
	}		}
			double [] zTilts=getCenterZTxTy(measurements.get(nMeas));

	double [] dmz= getAdjustedMotors(		double [] dmz= getAdjustedMotors(
	null, // double [] zM0, // current linearized motors (or null for full adjustment)		null, // double [] zM0, // current linearized motors (or null for full adjustment)
	targetRelFocalShift+best_qb_corr[0],		targetRelFocalShift+best_qb_corr[0],
	@@ -4544,6 +4553,14 @@ public boolean LevenbergMarquardt(
	}		}
	}		}
	sb.append("\t"+IJ.d2s(currentRMSPure,3));		sb.append("\t"+IJ.d2s(currentRMSPure,3));
			if (zTilts!=null){
			sb.append("\t"+IJ.d2s(zTilts[0]-best_qb_corr[0],3));
			sb.append("\t"+IJ.d2s(zTilts[1],3));
			sb.append("\t"+IJ.d2s(zTilts[2],3));
			System.out.println("Z center="+IJ.d2s(zTilts[0]-best_qb_corr[0],3)+"um, TiltX="+IJ.d2s(zTilts[1],3)+"um/mm, TiltY="+IJ.d2s(zTilts[2],3)+"um/mm");
			}else {
			sb.append("\t---\t---\t---");
			}
	if (dmz!=null){		if (dmz!=null){
	for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));		for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));
	} else {		} else {
	@@ -4582,6 +4599,7 @@ public boolean LevenbergMarquardt(
	fieldFitting.mechanicalFocusingModel.getUnits(i));		fieldFitting.mechanicalFocusingModel.getUnits(i));
	}		}
	}		}
			double [] zTilts=getCenterZTxTy(measurements.get(nMeas));
	double [] dmz= getAdjustedMotors(		double [] dmz= getAdjustedMotors(
	null, // double [] zM0, // current linearized motors (or null for full adjustment)		null, // double [] zM0, // current linearized motors (or null for full adjustment)
	targetRelFocalShift+best_qb_corr[0],		targetRelFocalShift+best_qb_corr[0],
	@@ -4614,6 +4632,14 @@ public boolean LevenbergMarquardt(
	}		}
	}		}
	sb.append("\t"+IJ.d2s(currentRMSPure,3));		sb.append("\t"+IJ.d2s(currentRMSPure,3));
			if (zTilts!=null){
			sb.append("\t"+IJ.d2s(zTilts[0]-best_qb_corr[0],3));
			sb.append("\t"+IJ.d2s(zTilts[1],3));
			sb.append("\t"+IJ.d2s(zTilts[2],3));
			System.out.println("Z center="+IJ.d2s(zTilts[0]-best_qb_corr[0],3)+"um, TiltX="+IJ.d2s(zTilts[1],3)+"um/mm, TiltY="+IJ.d2s(zTilts[2],3)+"um/mm");
			}else {
			sb.append("\t---\t---\t---");
			}
	if (dmz!=null){		if (dmz!=null){
	for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));		for (int i=0;i<dmz.length;i++) sb.append("\t"+IJ.d2s(dmz[i],1));
	} else {		} else {

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