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Commit 3272bf8a authored by Andrey Filippov's avatar Andrey Filippov
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X-cam alignment calculation

parent 739921ca
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src/main/java/Aberration_Calibration.java
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src/main/java/DistortionCalibrationData.java
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...@@ -5,7 +5,7 @@ ...@@ -5,7 +5,7 @@
** Copyright (C) 2011-2014 Elphel, Inc. ** Copyright (C) 2011-2014 Elphel, Inc.
** **
** -----------------------------------------------------------------------------** ** -----------------------------------------------------------------------------**
** **
** DistortionCalibrationData.java is free software: you can redistribute it and/or modify ** DistortionCalibrationData.java is free software: you can redistribute it and/or modify
** it under the terms of the GNU General Public License as published by ** it under the terms of the GNU General Public License as published by
** the Free Software Foundation, either version 3 of the License, or ** the Free Software Foundation, either version 3 of the License, or
...@@ -22,17 +22,6 @@ ...@@ -22,17 +22,6 @@
** **
*/ */
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
import java.io.FileWriter; import java.io.FileWriter;
...@@ -45,6 +34,17 @@ import org.apache.commons.configuration.ConfigurationException; ...@@ -45,6 +34,17 @@ import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.HierarchicalConfiguration; import org.apache.commons.configuration.HierarchicalConfiguration;
import org.apache.commons.configuration.XMLConfiguration; import org.apache.commons.configuration.XMLConfiguration;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import ij.text.TextWindow;
//import EyesisCameraParameters; //import EyesisCameraParameters;
//import Distortions.EyesisSubCameraParameters; //import Distortions.EyesisSubCameraParameters;
//import LensDistortionParameters; //import LensDistortionParameters;
...@@ -61,7 +61,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -61,7 +61,7 @@ import org.apache.commons.configuration.XMLConfiguration;
public int numPointers=4; // maximal number of pointers to look for public int numPointers=4; // maximal number of pointers to look for
public int numMotors =3; // maximal number of motors to look for public int numMotors =3; // maximal number of motors to look for
public GridImageParameters [] gIP= null; // per-grid image parameters public GridImageParameters [] gIP= null; // per-grid image parameters
public GridImageSet [] gIS= null; // sets of images with the same timestamp public GridImageSet [] gIS= null; // sets of images with the same timestamp
// public String [] paths=null; // public String [] paths=null;
// private ImagePlus [] gridImages=null; // array of grid images (to be used instead of files) // private ImagePlus [] gridImages=null; // array of grid images (to be used instead of files)
// public double [] timestamps=null; // public double [] timestamps=null;
...@@ -71,7 +71,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -71,7 +71,7 @@ import org.apache.commons.configuration.XMLConfiguration;
// public double [][][] pixelsXY=null; // for each image, each grid node - a pair of {px,py} // public double [][][] pixelsXY=null; // for each image, each grid node - a pair of {px,py}
// public int [][][] pixelsUV=null; // for each image, each grid node - a pair of {gridU, gridV} // public int [][][] pixelsUV=null; // for each image, each grid node - a pair of {gridU, gridV}
public double [][] sensorMasks= null; // per-channel (not image) mask public double [][] sensorMasks= null; // per-channel (not image) mask
//pixelsXY, pixelsUV should match, second dimension is variable //pixelsXY, pixelsUV should match, second dimension is variable
public boolean updateStatus=true; public boolean updateStatus=true;
public int debugLevel=2; public int debugLevel=2;
...@@ -102,9 +102,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -102,9 +102,9 @@ import org.apache.commons.configuration.XMLConfiguration;
public double [][] pixelsXY= null; // for each image, each grid node - a set of of {px,py,contrast,vignR,vignG,vignB} vign* is in the 0..1.0 range public double [][] pixelsXY= null; // for each image, each grid node - a set of of {px,py,contrast,vignR,vignG,vignB} vign* is in the 0..1.0 range
public double [] pixelsMask= null; // for each image, each grid node - weight function derived from contrast and 3 parameters public double [] pixelsMask= null; // for each image, each grid node - weight function derived from contrast and 3 parameters
public int [][] pixelsUV= null; // for each image, each grid node - a pair of {gridU, gridV} public int [][] pixelsUV= null; // for each image, each grid node - a pair of {gridU, gridV}
public boolean [] badNodes= null; // if not null, marks node with excessive errors public boolean [] badNodes= null; // if not null, marks node with excessive errors
public double [][] pixelsXY_extra= null; // extra data, for nodes that are out of the physical grid (may be needed after re-calibration) public double [][] pixelsXY_extra= null; // extra data, for nodes that are out of the physical grid (may be needed after re-calibration)
public int [][] pixelsUV_extra= null; public int [][] pixelsUV_extra= null;
public double gridPeriod=0.0; // average grid period, in pixels (to filter out (double-) reflected images public double gridPeriod=0.0; // average grid period, in pixels (to filter out (double-) reflected images
public boolean noUsefulPSFKernels=false; // used to mark images w/o good PSF data public boolean noUsefulPSFKernels=false; // used to mark images w/o good PSF data
public double diameter=0.0; public double diameter=0.0;
...@@ -152,7 +152,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -152,7 +152,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
public int getNumContrastNodes(double minContrast){ public int getNumContrastNodes(double minContrast){
int num=0; int num=0;
for (int i=0;i<this.pixelsXY.length;i++) if (this.pixelsXY[i][contrastIndex]>=minContrast) num++; for (int i=0;i<this.pixelsXY.length;i++) if (this.pixelsXY[i][contrastIndex]>=minContrast) num++;
return num; return num;
} }
...@@ -163,7 +163,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -163,7 +163,7 @@ import org.apache.commons.configuration.XMLConfiguration;
* @param r0 reference diameter * @param r0 reference diameter
* @param minContrast minimal contrast to count the node * @param minContrast minimal contrast to count the node
*/ */
public void setImageDiameter( // need to get image center px,py. Maybe r0 - use to normalize result diameter public void setImageDiameter( // need to get image center px,py. Maybe r0 - use to normalize result diameter
double xc, double xc,
double yc, double yc,
...@@ -222,10 +222,10 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -222,10 +222,10 @@ import org.apache.commons.configuration.XMLConfiguration;
double minContrast, double minContrast,
double shrinkBlurSigma, double shrinkBlurSigma,
double shrinkBlurLevel){ double shrinkBlurLevel){
if (this.pixelsMask!=null) return; // need to reset ro re-calculate if (this.pixelsMask!=null) return; // need to reset ro re-calculate
if (this.pixelsUV==null) {this.pixelsMask=null; return; } if (this.pixelsUV==null) {this.pixelsMask=null; return; }
if (this.pixelsUV.length==0){ this.pixelsMask=new double[0]; return; } if (this.pixelsUV.length==0){ this.pixelsMask=new double[0]; return; }
this.pixelsMask=new double [this.pixelsUV.length]; this.pixelsMask=new double [this.pixelsUV.length];
if (shrinkBlurSigma<=0){ if (shrinkBlurSigma<=0){
for (int i=0;i<this.pixelsUV.length;i++){ for (int i=0;i<this.pixelsUV.length;i++){
...@@ -242,7 +242,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -242,7 +242,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (this.pixelsUV[i][1]>maxV) maxV=this.pixelsUV[i][1]; if (this.pixelsUV[i][1]>maxV) maxV=this.pixelsUV[i][1];
if (this.pixelsUV[i][1]<minV) minV=this.pixelsUV[i][1]; if (this.pixelsUV[i][1]<minV) minV=this.pixelsUV[i][1];
} }
int U0=minU-margin; int U0=minU-margin;
int V0=minV-margin; int V0=minV-margin;
int width= (maxU-minU+1+2*margin); int width= (maxU-minU+1+2*margin);
...@@ -252,7 +252,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -252,7 +252,7 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<this.pixelsUV.length;i++){ for (int i=0;i<this.pixelsUV.length;i++){
int index=(this.pixelsUV[i][0]-U0)+width*(this.pixelsUV[i][1]-V0); int index=(this.pixelsUV[i][0]-U0)+width*(this.pixelsUV[i][1]-V0);
mask[index]=(this.pixelsXY[i][contrastIndex]>=minContrast)?1.0:-1.0; // java.lang.ArrayIndexOutOfBoundsException: 2230 mask[index]=(this.pixelsXY[i][contrastIndex]>=minContrast)?1.0:-1.0; // java.lang.ArrayIndexOutOfBoundsException: 2230
} }
(new DoubleGaussianBlur()).blurDouble( (new DoubleGaussianBlur()).blurDouble(
mask, mask,
width, width,
...@@ -288,7 +288,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -288,7 +288,7 @@ import org.apache.commons.configuration.XMLConfiguration;
public double horAxisErrPsi; //11 angle in degrees "horizontal" goniometer axis is rotated around moving X axis (up) public double horAxisErrPsi; //11 angle in degrees "horizontal" goniometer axis is rotated around moving X axis (up)
public double entrancePupilForward; //12 common to all lenses - distance from the sensor to the lens entrance pupil public double entrancePupilForward; //12 common to all lenses - distance from the sensor to the lens entrance pupil
public double centerAboveHorizontal;//13 camera center distance along camera axis above the closest point to horizontal rotation axis (adds to height of each public double centerAboveHorizontal;//13 camera center distance along camera axis above the closest point to horizontal rotation axis (adds to height of each
public double [] GXYZ=new double [3]; //14 (12) coordinates (in mm) of the goniometer horizontal axis closest to the moving one in target system public double [] GXYZ=new double [3]; //14 (12) coordinates (in mm) of the goniometer horizontal axis closest to the moving one in target system
// this.GXYZ[stationNumber][1], //15 (13) y // this.GXYZ[stationNumber][1], //15 (13) y
// this.GXYZ[stationNumber][2], //16 (14) z // this.GXYZ[stationNumber][2], //16 (14) z
public boolean orientationEstimated=true; // orientation is estimated from other stes, notr adjusted by LMA public boolean orientationEstimated=true; // orientation is estimated from other stes, notr adjusted by LMA
...@@ -302,7 +302,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -302,7 +302,7 @@ import org.apache.commons.configuration.XMLConfiguration;
public int getMaxIndexPlusOne(){ public int getMaxIndexPlusOne(){
return this.thisParsStartIndex+getSetVector().length; return this.thisParsStartIndex+getSetVector().length;
} }
public double [] getSetVector(){ public double [] getSetVector(){
double [] sv={ double [] sv={
this.goniometerTilt, this.goniometerTilt,
...@@ -313,9 +313,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -313,9 +313,9 @@ import org.apache.commons.configuration.XMLConfiguration;
this.horAxisErrPsi, this.horAxisErrPsi,
this.entrancePupilForward, this.entrancePupilForward,
this.centerAboveHorizontal, this.centerAboveHorizontal,
this.GXYZ[0], this.GXYZ[0],
this.GXYZ[1], this.GXYZ[1],
this.GXYZ[2] this.GXYZ[2]
}; };
return sv; return sv;
} }
...@@ -333,9 +333,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -333,9 +333,9 @@ import org.apache.commons.configuration.XMLConfiguration;
this.horAxisErrPsi= vector[ 5]; this.horAxisErrPsi= vector[ 5];
this.entrancePupilForward= vector[ 6]; this.entrancePupilForward= vector[ 6];
this.centerAboveHorizontal=vector[ 7]; this.centerAboveHorizontal=vector[ 7];
this.GXYZ[0]= vector[ 8]; this.GXYZ[0]= vector[ 8];
this.GXYZ[1]= vector[ 9]; this.GXYZ[1]= vector[ 9];
this.GXYZ[2]= vector[10]; this.GXYZ[2]= vector[10];
} }
public double getParameterValue(int index){ public double getParameterValue(int index){
...@@ -343,7 +343,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -343,7 +343,7 @@ import org.apache.commons.configuration.XMLConfiguration;
double [] sv=getSetVector(); double [] sv=getSetVector();
if ((thisIndex<0) || (index >sv.length)) return Double.NaN; if ((thisIndex<0) || (index >sv.length)) return Double.NaN;
return sv[thisIndex]; return sv[thisIndex];
} }
public void setParameterValue(int index, public void setParameterValue(int index,
double value, double value,
...@@ -364,9 +364,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -364,9 +364,9 @@ import org.apache.commons.configuration.XMLConfiguration;
case 5: this.horAxisErrPsi= value; break; case 5: this.horAxisErrPsi= value; break;
case 6: this.entrancePupilForward= value; break; case 6: this.entrancePupilForward= value; break;
case 7: this.centerAboveHorizontal=value; break; case 7: this.centerAboveHorizontal=value; break;
case 8: this.GXYZ[0]= value; break; case 8: this.GXYZ[0]= value; break;
case 9: this.GXYZ[1]= value; break; case 9: this.GXYZ[1]= value; break;
case 10: this.GXYZ[2]= value; break; case 10: this.GXYZ[2]= value; break;
} }
} }
...@@ -398,7 +398,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -398,7 +398,7 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<sv.length;i++) if (!Double.isNaN(sv[i]) && mask[this.thisParsStartIndex+ i]) vector[i+this.thisParsStartIndex]=sv[i]; for (int i=0;i<sv.length;i++) if (!Double.isNaN(sv[i]) && mask[this.thisParsStartIndex+ i]) vector[i+this.thisParsStartIndex]=sv[i];
return vector; return vector;
} }
public void updateSetFromParameterVector(double [] vector){ public void updateSetFromParameterVector(double [] vector){
if (vector.length!=this.numPars){ if (vector.length!=this.numPars){
String msg="Wrong parameter vector length - got:"+vector.length+", expected: "+this.numPars; String msg="Wrong parameter vector length - got:"+vector.length+", expected: "+this.numPars;
...@@ -413,9 +413,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -413,9 +413,9 @@ import org.apache.commons.configuration.XMLConfiguration;
this.horAxisErrPsi= vector[this.thisParsStartIndex+ 5]; this.horAxisErrPsi= vector[this.thisParsStartIndex+ 5];
this.entrancePupilForward= vector[this.thisParsStartIndex+ 6]; this.entrancePupilForward= vector[this.thisParsStartIndex+ 6];
this.centerAboveHorizontal=vector[this.thisParsStartIndex+ 7]; this.centerAboveHorizontal=vector[this.thisParsStartIndex+ 7];
this.GXYZ[0]= vector[this.thisParsStartIndex+ 8]; this.GXYZ[0]= vector[this.thisParsStartIndex+ 8];
this.GXYZ[1]= vector[this.thisParsStartIndex+ 9]; this.GXYZ[1]= vector[this.thisParsStartIndex+ 9];
this.GXYZ[2]= vector[this.thisParsStartIndex+10]; this.GXYZ[2]= vector[this.thisParsStartIndex+10];
} }
public void updateSetFromParameterVector(double [] vector, boolean [] mask){ public void updateSetFromParameterVector(double [] vector, boolean [] mask){
...@@ -432,9 +432,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -432,9 +432,9 @@ import org.apache.commons.configuration.XMLConfiguration;
if (mask[this.thisParsStartIndex+ 5]) this.horAxisErrPsi= vector[this.thisParsStartIndex+ 5]; if (mask[this.thisParsStartIndex+ 5]) this.horAxisErrPsi= vector[this.thisParsStartIndex+ 5];
if (mask[this.thisParsStartIndex+ 6]) this.entrancePupilForward= vector[this.thisParsStartIndex+ 6]; if (mask[this.thisParsStartIndex+ 6]) this.entrancePupilForward= vector[this.thisParsStartIndex+ 6];
if (mask[this.thisParsStartIndex+ 7]) this.centerAboveHorizontal=vector[this.thisParsStartIndex+ 7]; if (mask[this.thisParsStartIndex+ 7]) this.centerAboveHorizontal=vector[this.thisParsStartIndex+ 7];
if (mask[this.thisParsStartIndex+ 8]) this.GXYZ[0]= vector[this.thisParsStartIndex+ 8]; if (mask[this.thisParsStartIndex+ 8]) this.GXYZ[0]= vector[this.thisParsStartIndex+ 8];
if (mask[this.thisParsStartIndex+ 9]) this.GXYZ[1]= vector[this.thisParsStartIndex+ 9]; if (mask[this.thisParsStartIndex+ 9]) this.GXYZ[1]= vector[this.thisParsStartIndex+ 9];
if (mask[this.thisParsStartIndex+10]) this.GXYZ[2]= vector[this.thisParsStartIndex+10]; if (mask[this.thisParsStartIndex+10]) this.GXYZ[2]= vector[this.thisParsStartIndex+10];
} }
public double getSetWeight(){return this.setWeight;} public double getSetWeight(){return this.setWeight;}
...@@ -445,7 +445,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -445,7 +445,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.stationNumber=stationNumber; this.stationNumber=stationNumber;
} }
} }
public int index_right; // = getParameterIndexByName("subcamRight"); // 0 public int index_right; // = getParameterIndexByName("subcamRight"); // 0
public int index_forward; // = getParameterIndexByName("subcamForward"); // 1 public int index_forward; // = getParameterIndexByName("subcamForward"); // 1
public int index_azimuth; // = getParameterIndexByName("subcamAzimuth"); // 0 public int index_azimuth; // = getParameterIndexByName("subcamAzimuth"); // 0
...@@ -453,13 +453,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -453,13 +453,13 @@ import org.apache.commons.configuration.XMLConfiguration;
public int index_elevation; // = getParameterIndexByName("subcamElevation"); // 4 public int index_elevation; // = getParameterIndexByName("subcamElevation"); // 4
public int index_gh; //= getParameterIndexByName("goniometerHorizontal"); // 6 public int index_gh; //= getParameterIndexByName("goniometerHorizontal"); // 6
public int index_ga; //= getParameterIndexByName("goniometerAxial"); // 7 public int index_ga; //= getParameterIndexByName("goniometerAxial"); // 7
public String [][] parameterDescriptionsCartesian ={ // may be shorter, have null rows, shorter rows - will use parameterDescriptions for missing data public String [][] parameterDescriptionsCartesian ={ // may be shorter, have null rows, shorter rows - will use parameterDescriptions for missing data
{"subcamRight", "Subcamera distance from the vertical rotation axis, positive - right looking to the target","mm","S","E"}, // 0 {"subcamRight", "Subcamera distance from the vertical rotation axis, positive - right looking to the target","mm","S","E"}, // 0
{"subcamForward", "Subcamera distance from the vertical rotation axis, positive - towards the target","mm","S","E"}, // 1 {"subcamForward", "Subcamera distance from the vertical rotation axis, positive - towards the target","mm","S","E"}, // 1
null, // 2 null, // 2
{"subcamHeading", "Optical axis heading (0 - to the target, positive - CW looking from top)","degrees","S","E"}}; // 3 {"subcamHeading", "Optical axis heading (0 - to the target, positive - CW looking from top)","degrees","S","E"}}; // 3
public String [][] parameterDescriptions ={ public String [][] parameterDescriptions ={
{"subcamAzimuth", "Subcamera azimuth, clockwise looking from top","degrees","S","E"}, // 0 {"subcamAzimuth", "Subcamera azimuth, clockwise looking from top","degrees","S","E"}, // 0
{"subcamDistance", "Subcamera distance from the axis","mm","S","E"}, // 1 {"subcamDistance", "Subcamera distance from the axis","mm","S","E"}, // 1
...@@ -468,14 +468,14 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -468,14 +468,14 @@ import org.apache.commons.configuration.XMLConfiguration;
{"subcamElevation", "Optical axis elevation (up from equator)","degrees","S","E"}, // 4 {"subcamElevation", "Optical axis elevation (up from equator)","degrees","S","E"}, // 4
{"subcamRoll", "Subcamera roll, positive CW looking to the target","degrees","S","E"}, // 5 {"subcamRoll", "Subcamera roll, positive CW looking to the target","degrees","S","E"}, // 5
{"goniometerHorizontal", "Goniometer rotation around 'horizontal' axis (tilting from the target - positive)","degrees","R","E"},// 6 {"goniometerHorizontal", "Goniometer rotation around 'horizontal' axis (tilting from the target - positive)","degrees","R","E"},// 6
{"goniometerAxial", "Rotation around Eyesis main axis (clockwise in plan - positive)","degrees","R","E"}, // 7 {"goniometerAxial", "Rotation around Eyesis main axis (clockwise in plan - positive)","degrees","R","E"}, // 7
{"interAxisDistance", "Distance between goniometer axes","mm","C","E"}, // 8 {"interAxisDistance", "Distance between goniometer axes","mm","C","E"}, // 8
{"interAxisAngle", "Angle error between goniometer axes (<0 if vertical axis rotated CW )","degrees","C","E"}, // 9 {"interAxisAngle", "Angle error between goniometer axes (<0 if vertical axis rotated CW )","degrees","C","E"}, // 9
{"horAxisErrPhi", "Horizontal axis azimuth error (CW in plan)","degrees","C","E"}, //10 {"horAxisErrPhi", "Horizontal axis azimuth error (CW in plan)","degrees","C","E"}, //10
{"horAxisErrPsi", "Horizontal axis roll error (CW looking to target)","degrees","C","E"}, //11 {"horAxisErrPsi", "Horizontal axis roll error (CW looking to target)","degrees","C","E"}, //11
{"entrancePupilForward", "Distance from the sensor to the lens entrance pupil","mm","C","E"}, //12 {"entrancePupilForward", "Distance from the sensor to the lens entrance pupil","mm","C","E"}, //12
{"centerAboveHorizontal","CenterAboveHorizontal","mm","C","E"}, //13 {"centerAboveHorizontal","CenterAboveHorizontal","mm","C","E"}, //13
{"GXYZ0", "Goniometer reference point position X (target coordinates, left)","mm","T","E"}, //14 (12) {"GXYZ0", "Goniometer reference point position X (target coordinates, left)","mm","T","E"}, //14 (12)
{"GXYZ1", "Goniometer reference point position Y (target coordinates, up)","mm","T","E"}, //15 (13) {"GXYZ1", "Goniometer reference point position Y (target coordinates, up)","mm","T","E"}, //15 (13)
{"GXYZ2", "Goniometer reference point position Z (target coordinates, away)","mm","T","E"} , //16 (14) {"GXYZ2", "Goniometer reference point position Z (target coordinates, away)","mm","T","E"} , //16 (14)
{"subcamFocalLength", "Lens focal length","mm","S","I"}, //17 (15) {"subcamFocalLength", "Lens focal length","mm","S","I"}, //17 (15)
...@@ -488,7 +488,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -488,7 +488,7 @@ import org.apache.commons.configuration.XMLConfiguration;
{"subcamDistortionA", "Distortion A (r^4)","relative","S","I"}, //24 (22) {"subcamDistortionA", "Distortion A (r^4)","relative","S","I"}, //24 (22)
{"subcamDistortionB", "Distortion B (r^3)","relative","S","I"}, //25 (23) {"subcamDistortionB", "Distortion B (r^3)","relative","S","I"}, //25 (23)
{"subcamDistortionC", "Distortion C (r^2)","relative","S","I"}, //26 (24) {"subcamDistortionC", "Distortion C (r^2)","relative","S","I"}, //26 (24)
{"subcamElong_C_o", "Orthogonal elongation for r^2","relative","S","I"}, // 27 39 (37) {"subcamElong_C_o", "Orthogonal elongation for r^2","relative","S","I"}, // 27 39 (37)
{"subcamElong_C_d", "Diagonal elongation for r^2","relative","S","I"}, // 28 40 (38) {"subcamElong_C_d", "Diagonal elongation for r^2","relative","S","I"}, // 28 40 (38)
...@@ -522,7 +522,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -522,7 +522,7 @@ import org.apache.commons.configuration.XMLConfiguration;
{"subcamElong_A8_o", "Orthogonal elongation for r^8","relative","S","I"}, // 51 51 (49) {"subcamElong_A8_o", "Orthogonal elongation for r^8","relative","S","I"}, // 51 51 (49)
{"subcamElong_A8_d", "Diagonal elongation for r^8","relative","S","I"} // 52 52 (50) {"subcamElong_A8_d", "Diagonal elongation for r^8","relative","S","I"} // 52 52 (50)
}; };
public String [] channelSuffixes={ // natural order (same as array indices, may be modified to camera/subcamera public String [] channelSuffixes={ // natural order (same as array indices, may be modified to camera/subcamera
"00","01","02","03","04","05","06","07","08","09", "00","01","02","03","04","05","06","07","08","09",
"10","11","12","13","14","15","16","17","18","19", "10","11","12","13","14","15","16","17","18","19",
...@@ -536,8 +536,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -536,8 +536,8 @@ import org.apache.commons.configuration.XMLConfiguration;
this.index_elevation = getParameterIndexByName("subcamElevation"); // 4 this.index_elevation = getParameterIndexByName("subcamElevation"); // 4
this.index_gh= getParameterIndexByName("goniometerHorizontal"); // 6 this.index_gh= getParameterIndexByName("goniometerHorizontal"); // 6
this.index_ga= getParameterIndexByName("goniometerAxial"); // 7 this.index_ga= getParameterIndexByName("goniometerAxial"); // 7
} }
public boolean isCartesian(){ public boolean isCartesian(){
return (eyesisCameraParameters !=null) && eyesisCameraParameters.cartesian; return (eyesisCameraParameters !=null) && eyesisCameraParameters.cartesian;
} }
...@@ -552,11 +552,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -552,11 +552,11 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return this.parameterDescriptions[i][j]; return this.parameterDescriptions[i][j];
} }
public boolean isNonRadial(int index){ public boolean isNonRadial(int index){
return parameterDescriptions[index][0].startsWith("subcamEccen_") || parameterDescriptions[index][0].startsWith("subcamElong_"); return parameterDescriptions[index][0].startsWith("subcamEccen_") || parameterDescriptions[index][0].startsWith("subcamElong_");
} }
public int getParameterIndexByName(String name){ public int getParameterIndexByName(String name){
if (isCartesian()){ if (isCartesian()){
for (int i=0;i<this.parameterDescriptionsCartesian.length;i++) if ((this.parameterDescriptionsCartesian[i]!=null) && this.parameterDescriptionsCartesian[i][0].equals(name)){ for (int i=0;i<this.parameterDescriptionsCartesian.length;i++) if ((this.parameterDescriptionsCartesian[i]!=null) && this.parameterDescriptionsCartesian[i][0].equals(name)){
...@@ -568,13 +568,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -568,13 +568,13 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return -1; return -1;
} }
public int getNumDescriptions(){ public int getNumDescriptions(){
return this.parameterDescriptions.length; return this.parameterDescriptions.length;
} }
/** /**
* Initialize data from scratch using filenames "grid-<timestamp-seconds>_<timestamp-microseconds>-<channel-number>.tiff * Initialize data from scratch using filenames "grid-<timestamp-seconds>_<timestamp-microseconds>-<channel-number>.tiff
* @param filenames List of grid filenames (2-slice TIFFs) * @param filenames List of grid filenames (2-slice TIFFs)
*/ */
...@@ -633,11 +633,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -633,11 +633,11 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<stationFilenames.length;i++) numFiles+=stationFilenames[i].length; for (int i=0;i<stationFilenames.length;i++) numFiles+=stationFilenames[i].length;
this.gIP=new GridImageParameters[numFiles]; this.gIP=new GridImageParameters[numFiles];
int numFile=0; int numFile=0;
for (int numStation=0;numStation<stationFilenames.length;numStation++){ for (int numStation=0;numStation<stationFilenames.length;numStation++){
for (int index=0;index<stationFilenames[numStation].length;index++){ for (int index=0;index<stationFilenames[numStation].length;index++){
System.out.println(numFile+" ("+numStation+":"+index+"): "+stationFilenames[numStation][index]); System.out.println(numFile+" ("+numStation+":"+index+"): "+stationFilenames[numStation][index]);
this.gIP[numFile]=new GridImageParameters(numFile); this.gIP[numFile]=new GridImageParameters(numFile);
this.gIP[numFile].path=stationFilenames[numStation][index]; //Exception in thread "Run$_AWT-EventQueue-0" java.lang.NullPointerException at Distortions$DistortionCalibrationData.<init>(Distortions.java:5987) this.gIP[numFile].path=stationFilenames[numStation][index]; //Exception in thread "Run$_AWT-EventQueue-0" java.lang.NullPointerException at Distortions$DistortionCalibrationData.<init>(Distortions.java:5987)
...@@ -645,13 +645,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -645,13 +645,13 @@ import org.apache.commons.configuration.XMLConfiguration;
int i1=stationFilenames[numStation][index].indexOf('-',stationFilenames[numStation][index].lastIndexOf(Prefs.getFileSeparator())); int i1=stationFilenames[numStation][index].indexOf('-',stationFilenames[numStation][index].lastIndexOf(Prefs.getFileSeparator()));
int i2=stationFilenames[numStation][index].indexOf('-',i1+1); int i2=stationFilenames[numStation][index].indexOf('-',i1+1);
int i3=stationFilenames[numStation][index].indexOf('.',i2+1); int i3=stationFilenames[numStation][index].indexOf('.',i2+1);
// Extract timestamp from the filename // Extract timestamp from the filename
if ((i1<0) || (i2<0)) { if ((i1<0) || (i2<0)) {
String msg="invalid file format - '"+stationFilenames[numStation][index]+"', should be '<timestamp-seconds>_<timestamp-microseconds>-<channel-number>.tiff'"; String msg="invalid file format - '"+stationFilenames[numStation][index]+"', should be '<timestamp-seconds>_<timestamp-microseconds>-<channel-number>.tiff'";
IJ.showMessage("Error",msg); IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
// Extract channel number from the filename // Extract channel number from the filename
this.gIP[numFile].timestamp=Double.parseDouble(stationFilenames[numStation][index].substring(i1+1,i2).replace('_','.')); this.gIP[numFile].timestamp=Double.parseDouble(stationFilenames[numStation][index].substring(i1+1,i2).replace('_','.'));
String channelSuffix=stationFilenames[numStation][index].substring(i2+1,i3); String channelSuffix=stationFilenames[numStation][index].substring(i2+1,i3);
...@@ -673,23 +673,23 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -673,23 +673,23 @@ import org.apache.commons.configuration.XMLConfiguration;
// Create parameters array // Create parameters array
initPars (this.gIP.length,parameterDescriptions.length); initPars (this.gIP.length,parameterDescriptions.length);
if (this.debugLevel>1) System.out.println("setupDistortionCalibrationData(): Resetting this.gIS"); if (this.debugLevel>1) System.out.println("setupDistortionCalibrationData(): Resetting this.gIS");
this.gIS=null; // so it will be initialized in readAllGrids() this.gIS=null; // so it will be initialized in readAllGrids()
readAllGrids(patternParameters); // prepare grid parameters for LMA readAllGrids(patternParameters); // prepare grid parameters for LMA
// no orientation // no orientation
} }
public DistortionCalibrationData ( public DistortionCalibrationData (
EyesisCameraParameters eyesisCameraParameters EyesisCameraParameters eyesisCameraParameters
) { ) {
setupIndices(); setupIndices();
int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length; int numSubCameras=(eyesisCameraParameters==null)?1:eyesisCameraParameters.eyesisSubCameras[0].length;
this.numSubCameras=numSubCameras; this.numSubCameras=numSubCameras;
this.eyesisCameraParameters=eyesisCameraParameters; this.eyesisCameraParameters=eyesisCameraParameters;
} }
public DistortionCalibrationData ( public DistortionCalibrationData (
ImagePlus [] images, // images in the memory ImagePlus [] images, // images in the memory
PatternParameters patternParameters, PatternParameters patternParameters,
...@@ -701,7 +701,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -701,7 +701,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.eyesisCameraParameters=eyesisCameraParameters; this.eyesisCameraParameters=eyesisCameraParameters;
setImages(images,patternParameters); setImages(images,patternParameters);
} }
public int get_gIS_index(int numImg){ public int get_gIS_index(int numImg){
if (this.gIS==null) return -1; if (this.gIS==null) return -1;
for (int i=0;i<this.gIS.length;i++) for (int i=0;i<this.gIS.length;i++)
...@@ -709,9 +709,25 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -709,9 +709,25 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int j=0;j<this.gIS[i].imageSet.length;j++) for (int j=0;j<this.gIS[i].imageSet.length;j++)
if ((this.gIS[i].imageSet[j]!=null) &&(this.gIS[i].imageSet[j].imgNumber==numImg)) return i; if ((this.gIS[i].imageSet[j]!=null) &&(this.gIS[i].imageSet[j].imgNumber==numImg)) return i;
return -1; return -1;
}
public void listCameraParameters(boolean xcam){
int numSubCameras=getNumSubCameras();
if (this.gIP!=null) {
int maxChn=0;
for (int i=0;i<this.gIP.length;i++) if ((this.gIP[i]!=null) && (this.gIP[i].channel>maxChn)){
maxChn=this.gIP[i].channel;
}
numSubCameras=maxChn+1;
}
if (xcam && (numSubCameras == 4)) {
listCameraParametersXcam();
} else {
listCameraParameters();
}
} }
public void listCameraParameters(){ public void listCameraParameters(){
int numSubCameras=getNumSubCameras(); int numSubCameras=getNumSubCameras();
if (this.gIP!=null) { if (this.gIP!=null) {
...@@ -728,21 +744,199 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -728,21 +744,199 @@ import org.apache.commons.configuration.XMLConfiguration;
if (this.eyesisCameraParameters.numStations>1){ if (this.eyesisCameraParameters.numStations>1){
sb.append("Station "+stationNumber+" W="+(100*this.eyesisCameraParameters.stationWeight[stationNumber])+"%"); for (int i=-1;i<numSubCameras;i++) sb.append("\t==="); sb.append("\n"); sb.append("Station "+stationNumber+" W="+(100*this.eyesisCameraParameters.stationWeight[stationNumber])+"%"); for (int i=-1;i<numSubCameras;i++) sb.append("\t==="); sb.append("\n");
} }
int [] lensDistortionModels=new int [numSubCameras]; int [] lensDistortionModels=new int [numSubCameras];
for (int i=0;i<numSubCameras;i++) lensDistortionModels[i]=eyesisCameraParameters.getLensDistortionModel(stationNumber,i); for (int i=0;i<numSubCameras;i++) lensDistortionModels[i]=eyesisCameraParameters.getLensDistortionModel(stationNumber,i);
sb.append("Lens Distortion Model\t"); sb.append("Lens Distortion Model\t");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]); for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
sb.append("\n"); sb.append("\n");
double [][] cameraPars=new double [numSubCameras][]; double [][] cameraPars=new double [numSubCameras][];
for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
// parameters same order as in this
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3));
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && !isIntrinsicParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3));
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (
!isSubcameraParameter(n)&&
!isLocationParameter(n)&&
!isOrientationParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
sb.append("\t"+IJ.d2s(cameraPars[0][n],3));
for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isLocationParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
sb.append("\t"+IJ.d2s(cameraPars[0][n],3));
for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n");
}
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isOrientationParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
sb.append("\t"+IJ.d2s(cameraPars[0][n],3));
for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n");
}
}
new TextWindow("Camera parameters", header, sb.toString(), 85*(numSubCameras+3),600);
}
public void listCameraParametersXcam(){ // getNumSubCameras() should be 4!
double rollDegPerTurn = -0.45/33.5*180/Math.PI; // -0.769644799429464 deg/turn, CW screw increases roll, degrees per 1 screw turn
double headDegPerTurn = 0.45/34.5*180/Math.PI; // 0.7473362545184652 deg/turn, both screws CW decreases heading (degree/turn)
double elevDegPerTurn = 0.45/14*180/Math.PI; // 1.8416500557776463 deg/turn, top CW, bottom CCW decreases elevation (degree/turn)
int numSubCameras=getNumSubCameras();
if (this.gIP!=null) {
int maxChn=0;
for (int i=0;i<this.gIP.length;i++) if ((this.gIP[i]!=null) && (this.gIP[i].channel>maxChn)){
maxChn=this.gIP[i].channel;
}
numSubCameras=maxChn+1;
}
String header="Name\tUnits";
StringBuffer sb = new StringBuffer();
for (int i=0;i<numSubCameras;i++) header+="\t"+i;
for (int stationNumber=0;stationNumber<this.eyesisCameraParameters.numStations;stationNumber++){
if (this.eyesisCameraParameters.numStations>1){
sb.append("Station "+stationNumber+" W="+(100*this.eyesisCameraParameters.stationWeight[stationNumber])+"%"); for (int i=-1;i<numSubCameras;i++) sb.append("\t==="); sb.append("\n");
}
int [] lensDistortionModels=new int [numSubCameras];
for (int i=0;i<numSubCameras;i++) lensDistortionModels[i]=eyesisCameraParameters.getLensDistortionModel(stationNumber,i);
// sb.append("Lens Distortion Model\t");
// for (int i=0;i<numSubCameras;i++) sb.append("\t"+lensDistortionModels[i]);
// sb.append("\n");
double [][] cameraPars=new double [numSubCameras][];
for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i); for (int i=0;i<numSubCameras;i++) cameraPars[i]=eyesisCameraParameters.getParametersVector(stationNumber,i);
// calculate average height average right
double [] subcamRight = new double[numSubCameras];
double [] subcamHeight = new double[numSubCameras];
double [] subcamCorrRight = new double[numSubCameras]; // in rotated C.S.
double [] subcamCorrHeight = new double[numSubCameras]; // in rotated C.S.
double [] subcamHeading = new double[numSubCameras];
double [] subcamElevation = new double[numSubCameras];
double subcamRightCenter = 0.0;
double subcamHeightCenter = 0.0;
double subcamHeadingCenter = 0.0;
double subcamElevationCenter = 0.0;
double [] subcamRelRot = new double[numSubCameras];
double [] subcamRelHeading = new double[numSubCameras];
double [] subcamRelElevation = new double[numSubCameras];
double [] rollCorrTurns = new double[numSubCameras];
double [] topCorrTurns = new double[numSubCameras];
double [] botCorrTurns = new double[numSubCameras];
for (int i=0;i<numSubCameras;i++) {
subcamRight[i] = cameraPars[i][getParameterIndexByName("subcamRight")];
subcamHeight[i] = cameraPars[i][getParameterIndexByName("subcamHeight")];
subcamHeading[i] = cameraPars[i][getParameterIndexByName("subcamHeading")];
subcamElevation[i] = cameraPars[i][getParameterIndexByName("subcamElevation")];
subcamRightCenter += subcamRight[i];
subcamHeightCenter += subcamHeight[i];
subcamHeadingCenter += subcamHeading[i];
subcamElevationCenter += subcamElevation[i];
}
subcamRightCenter /= numSubCameras;
subcamHeightCenter /= numSubCameras;
subcamHeadingCenter /= numSubCameras;
subcamElevationCenter /= numSubCameras;
double [] subcamNominalDirs = {135.0,45.0, -135.0, -45.0};
double [] subcamDirsDeg = new double[numSubCameras];
double commonRot = 0.0;
for (int i=0;i<numSubCameras;i++) {
subcamDirsDeg[i]=180.0/Math.PI*Math.atan2(subcamHeight[i]-subcamHeightCenter, subcamRight[i]-subcamRightCenter);
commonRot += subcamNominalDirs[i]-subcamDirsDeg[i];
}
commonRot /= numSubCameras;
for (int i=0;i<numSubCameras;i++) {
subcamRelRot[i] = cameraPars[i][getParameterIndexByName("subcamRoll")] - commonRot;
subcamRelHeading[i] = subcamHeading[i] - subcamHeadingCenter;
subcamRelElevation[i] = subcamElevation[i] - subcamElevationCenter;
double r = Math.sqrt((subcamHeight[i]-subcamHeightCenter)*(subcamHeight[i]-subcamHeightCenter)+
(subcamRight[i]-subcamRightCenter)*(subcamRight[i]-subcamRightCenter));
subcamCorrRight[i] = r*Math.cos(Math.PI/180.0*(subcamDirsDeg[i]+commonRot));
subcamCorrHeight[i] = r*Math.sin(Math.PI/180.0*(subcamDirsDeg[i]+commonRot));
rollCorrTurns[i] = subcamRelRot[i] * rollDegPerTurn;
topCorrTurns[i] = subcamRelHeading[i] * headDegPerTurn + subcamRelElevation[i] * elevDegPerTurn;
botCorrTurns[i] = subcamRelHeading[i] * headDegPerTurn - subcamRelElevation[i] * elevDegPerTurn;
}
/*
// parameters same order as in this // parameters same order as in this
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){ for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && isIntrinsicParameter(n)){
sb.append(getParameterName(n)+"\t"+getParameterUnits(n)); sb.append(getParameterName(n)+"\t"+getParameterUnits(n));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3)); for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][n],3));
sb.append("\n"); sb.append("\n");
} }
*/
// sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
int flindex =getParameterIndexByName("subcamFocalLength");
sb.append(getParameterName(flindex)+"\t"+getParameterUnits(flindex));
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(cameraPars[i][flindex],3));
sb.append("\n");
sb.append("Camera roll"+"\t"+"degrees"+"\t"+IJ.d2s(commonRot,3));
for (int i=1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Camera heading"+"\t"+"degrees"+"\t"+IJ.d2s(subcamHeadingCenter,3));
for (int i=1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Camera elevation"+"\t"+"degrees"+"\t"+IJ.d2s(subcamElevationCenter,3));
for (int i=1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Rel roll"+"\t"+"degrees");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamRelRot[i],3));
sb.append("\n");
sb.append("Rel heading"+"\t"+"degrees");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamRelHeading[i],3));
sb.append("\n");
sb.append("Rel elevation"+"\t"+"degrees");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamRelElevation[i],3));
sb.append("\n");
sb.append("Corr right"+"\t"+"mm");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamCorrRight[i],3));
sb.append("\n");
sb.append("Corr height"+"\t"+"mm");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(subcamCorrHeight[i],3));
sb.append("\n");
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
sb.append("Screw roll"+"\t"+"turns CW");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(rollCorrTurns[i],2));
sb.append("\n");
sb.append("Screw top"+"\t"+"turns CW");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(topCorrTurns[i],2));
sb.append("\n");
sb.append("Screw bottom"+"\t"+"turns CW");
for (int i=0;i<numSubCameras;i++) sb.append("\t"+IJ.d2s(botCorrTurns[i],2));
sb.append("\n");
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n"); sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && !isIntrinsicParameter(n)){ for (int n=0;n<cameraPars[0].length;n++) if (isSubcameraParameter(n) && !isIntrinsicParameter(n)){
...@@ -751,6 +945,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -751,6 +945,7 @@ import org.apache.commons.configuration.XMLConfiguration;
sb.append("\n"); sb.append("\n");
} }
sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n"); sb.append("---"); for (int i=-1;i<numSubCameras;i++) sb.append("\t"); sb.append("\n");
/*
for (int n=0;n<cameraPars[0].length;n++) if ( for (int n=0;n<cameraPars[0].length;n++) if (
!isSubcameraParameter(n)&& !isSubcameraParameter(n)&&
!isLocationParameter(n)&& !isLocationParameter(n)&&
...@@ -774,6 +969,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -774,6 +969,7 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=1;i<numSubCameras;i++) sb.append("\t---"); for (int i=1;i<numSubCameras;i++) sb.append("\t---");
sb.append("\n"); sb.append("\n");
} }
*/
} }
new TextWindow("Camera parameters", header, sb.toString(), 85*(numSubCameras+3),600); new TextWindow("Camera parameters", header, sb.toString(), 85*(numSubCameras+3),600);
} }
...@@ -798,11 +994,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -798,11 +994,11 @@ import org.apache.commons.configuration.XMLConfiguration;
readAllGrids(patternParameters); // prepare grid parameters for LMA readAllGrids(patternParameters); // prepare grid parameters for LMA
// no orientation // no orientation
} }
public void listImageSet(){ public void listImageSet(){
listImageSet(null,null, null); listImageSet(null,null, null);
} }
public void listImageSet( public void listImageSet(
int [] numPoints, int [] numPoints,
double [] setRMS, double [] setRMS,
...@@ -819,7 +1015,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -819,7 +1015,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (setRMS!=null) header+="\tRMS\tWeight"; if (setRMS!=null) header+="\tRMS\tWeight";
for (int n=0;n<this.gIS[0].imageSet.length;n++) header+="\t"+n; for (int n=0;n<this.gIS[0].imageSet.length;n++) header+="\t"+n;
StringBuffer sb = new StringBuffer(); StringBuffer sb = new StringBuffer();
for (int i=0;i<this.gIS.length;i++){ for (int i=0;i<this.gIS.length;i++){
double axial_corr_sign=this.gIS[i].goniometerAxial; // correct sign of rotation beyond +/-180 according to motor steps double axial_corr_sign=this.gIS[i].goniometerAxial; // correct sign of rotation beyond +/-180 according to motor steps
if (this.gIS[i].motors != null) { if (this.gIS[i].motors != null) {
...@@ -831,7 +1027,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -831,7 +1027,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (axial_corr_sign > 90.0) { if (axial_corr_sign > 90.0) {
axial_corr_sign -= 360.0; axial_corr_sign -= 360.0;
} }
} }
} }
// calculate average tilt for this tilt motor and difference of the current tilt from average // calculate average tilt for this tilt motor and difference of the current tilt from average
...@@ -839,11 +1035,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -839,11 +1035,11 @@ import org.apache.commons.configuration.XMLConfiguration;
if (!Double.isNaN(this.gIS[i].goniometerTilt) && (this.gIS[i].motors != null)){ if (!Double.isNaN(this.gIS[i].goniometerTilt) && (this.gIS[i].motors != null)){
int i_low,i_high; int i_low,i_high;
for (i_low=i-1;i_low>=0;i_low--){ for (i_low=i-1;i_low>=0;i_low--){
if ((this.gIS[i_low].motors != null) && (this.gIS[i_low].motors[2] != this.gIS[i].motors[2])) break; if ((this.gIS[i_low].motors != null) && (this.gIS[i_low].motors[2] != this.gIS[i].motors[2])) break;
} }
i_low++; i_low++;
for (i_high=i+1;i_high < this.gIS.length;i_high++){ for (i_high=i+1;i_high < this.gIS.length;i_high++){
if ((this.gIS[i_high].motors != null) && (this.gIS[i_high].motors[2] != this.gIS[i].motors[2])) break; if ((this.gIS[i_high].motors != null) && (this.gIS[i_high].motors[2] != this.gIS[i].motors[2])) break;
} }
int num_avg=0; int num_avg=0;
double sum_avg=0.0; double sum_avg=0.0;
...@@ -853,8 +1049,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -853,8 +1049,8 @@ import org.apache.commons.configuration.XMLConfiguration;
sum_avg += this.gIS[i_avg].goniometerTilt; sum_avg += this.gIS[i_avg].goniometerTilt;
} }
} }
if (num_avg>0) dTilt = this.gIS[i].goniometerTilt - (sum_avg/num_avg); if (num_avg>0) dTilt = this.gIS[i].goniometerTilt - (sum_avg/num_avg);
} }
// double firstHorAxisErrPhi=Double.NaN; // double firstHorAxisErrPhi=Double.NaN;
// double firstHorAxisErrPsi=Double.NaN; // double firstHorAxisErrPsi=Double.NaN;
...@@ -868,7 +1064,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -868,7 +1064,7 @@ import org.apache.commons.configuration.XMLConfiguration;
// firstGXYZ1=this.gIS[i].GXYZ[1]; // firstGXYZ1=this.gIS[i].GXYZ[1];
// firstGXYZ2=this.gIS[i].GXYZ[2]; // firstGXYZ2=this.gIS[i].GXYZ[2];
firstInterAxisAngle = this.gIS[i].interAxisAngle; firstInterAxisAngle = this.gIS[i].interAxisAngle;
sb.append(i+"\t"+IJ.d2s(this.gIS[i].timeStamp,6)); sb.append(i+"\t"+IJ.d2s(this.gIS[i].timeStamp,6));
if (this.eyesisCameraParameters.numStations>1) sb.append(i+"\t"+ this.gIS[i].getStationNumber()); if (this.eyesisCameraParameters.numStations>1) sb.append(i+"\t"+ this.gIS[i].getStationNumber());
sb.append("\t"+(Double.isNaN(this.gIS[i].goniometerAxial)?"---":((this.gIS[i].orientationEstimated?"(":"")+IJ.d2s(axial_corr_sign,3)+(this.gIS[i].orientationEstimated?")":"")))); sb.append("\t"+(Double.isNaN(this.gIS[i].goniometerAxial)?"---":((this.gIS[i].orientationEstimated?"(":"")+IJ.d2s(axial_corr_sign,3)+(this.gIS[i].orientationEstimated?")":""))));
...@@ -879,7 +1075,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -879,7 +1075,7 @@ import org.apache.commons.configuration.XMLConfiguration;
// sb.append("\t"+(Double.isNaN(firstGXYZ0)?"---":IJ.d2s(firstGXYZ0,3))); // sb.append("\t"+(Double.isNaN(firstGXYZ0)?"---":IJ.d2s(firstGXYZ0,3)));
// sb.append("\t"+(Double.isNaN(firstGXYZ1)?"---":IJ.d2s(firstGXYZ1,3))); // sb.append("\t"+(Double.isNaN(firstGXYZ1)?"---":IJ.d2s(firstGXYZ1,3)));
// sb.append("\t"+(Double.isNaN(firstGXYZ2)?"---":IJ.d2s(firstGXYZ2,3))); // sb.append("\t"+(Double.isNaN(firstGXYZ2)?"---":IJ.d2s(firstGXYZ2,3)));
sb.append("\t"+(Double.isNaN(dTilt)?"---":IJ.d2s(dTilt,3))); sb.append("\t"+(Double.isNaN(dTilt)?"---":IJ.d2s(dTilt,3)));
sb.append("\t"+(Double.isNaN(firstInterAxisAngle)?"---":IJ.d2s(firstInterAxisAngle,3))); sb.append("\t"+(Double.isNaN(firstInterAxisAngle)?"---":IJ.d2s(firstInterAxisAngle,3)));
...@@ -892,12 +1088,12 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -892,12 +1088,12 @@ import org.apache.commons.configuration.XMLConfiguration;
int numEnImages=0; int numEnImages=0;
for (int n=0;n<this.gIS[i].imageSet.length;n++)if (this.gIS[i].imageSet[n]!=null){ for (int n=0;n<this.gIS[i].imageSet.length;n++)if (this.gIS[i].imageSet[n]!=null){
if (this.gIS[i].imageSet[n].enabled) numEnImages++; if (this.gIS[i].imageSet[n].enabled) numEnImages++;
} }
sb.append("\t"+numEnImages); sb.append("\t"+numEnImages);
int matchedPointersInSet=0; int matchedPointersInSet=0;
for (int n=0;n<this.gIS[i].imageSet.length;n++){ for (int n=0;n<this.gIS[i].imageSet.length;n++){
if (this.gIS[i].imageSet[n]!=null){ if (this.gIS[i].imageSet[n]!=null){
matchedPointersInSet+=this.gIS[i].imageSet[n].matchedPointers; matchedPointersInSet+=this.gIS[i].imageSet[n].matchedPointers;
} }
} }
sb.append("\t"+matchedPointersInSet); sb.append("\t"+matchedPointersInSet);
...@@ -916,7 +1112,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -916,7 +1112,7 @@ import org.apache.commons.configuration.XMLConfiguration;
sb.append(numPointers+"("+this.gIS[i].imageSet[n].matchedPointers+"):"+this.gIS[i].imageSet[n].hintedMatch + sb.append(numPointers+"("+this.gIS[i].imageSet[n].matchedPointers+"):"+this.gIS[i].imageSet[n].hintedMatch +
" "+IJ.d2s(this.gIS[i].imageSet[n].gridPeriod,1)); " "+IJ.d2s(this.gIS[i].imageSet[n].gridPeriod,1));
if (!this.gIS[i].imageSet[n].enabled) sb.append(")"); if (!this.gIS[i].imageSet[n].enabled) sb.append(")");
} }
} }
sb.append("\n"); sb.append("\n");
...@@ -925,7 +1121,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -925,7 +1121,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
/** /**
* crete list of image indices per image set * crete list of image indices per image set
* @return array of image indices for each image set * @return array of image indices for each image set
*/ */
public int [][] listImages(boolean enabledOnly){ public int [][] listImages(boolean enabledOnly){
int [][] imageSets = new int [this.gIS.length][]; int [][] imageSets = new int [this.gIS.length][];
...@@ -940,7 +1136,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -940,7 +1136,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return imageSets; return imageSets;
} }
/** /**
* Filter images (grids) by calibration status with laser pointers and "hinted" from the camera orientation * Filter images (grids) by calibration status with laser pointers and "hinted" from the camera orientation
* buildImageSets may be needed to be re-ran (if it was ran with all=false) * buildImageSets may be needed to be re-ran (if it was ran with all=false)
...@@ -1015,7 +1211,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1015,7 +1211,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (resetHinted) this.gIP[i].hintedMatch=-1; // undefined if (resetHinted) this.gIP[i].hintedMatch=-1; // undefined
if (Double.isNaN(this.gIP[i].gridPeriod) || if (Double.isNaN(this.gIP[i].gridPeriod) ||
((minGridPeriodFraction>0) && ((this.gIP[i].gridPeriod<minGridPeriod[stationNumber]) || (this.gIP[i].gridPeriod>maxGridPeriod[stationNumber])))){ ((minGridPeriodFraction>0) && ((this.gIP[i].gridPeriod<minGridPeriod[stationNumber]) || (this.gIP[i].gridPeriod>maxGridPeriod[stationNumber])))){
this.gIP[i].hintedMatch=0; // is it needed? this.gIP[i].hintedMatch=0; // is it needed?
this.gIP[i].enabled=false; // failed against minimal grid period (too far) - probably double reflection in the windows this.gIP[i].enabled=false; // failed against minimal grid period (too far) - probably double reflection in the windows
} }
if (this.gIP[i].hintedMatch==0) this.gIP[i].enabled=false; // failed against predicted grid if (this.gIP[i].hintedMatch==0) this.gIP[i].enabled=false; // failed against predicted grid
...@@ -1024,8 +1220,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1024,8 +1220,8 @@ import org.apache.commons.configuration.XMLConfiguration;
(this.gIP[i].matchedPointers>=minPointers) || (this.gIP[i].matchedPointers>=minPointers) ||
((this.gIP[i].matchedPointers>0) && (this.gIP[i].hintedMatch>0)) || // orientation and one pointer ((this.gIP[i].matchedPointers>0) && (this.gIP[i].hintedMatch>0)) || // orientation and one pointer
((this.gIP[i].hintedMatch>1) && enableNoLaser)) { // do not use bottom images w/o matched pointers ((this.gIP[i].hintedMatch>1) && enableNoLaser)) { // do not use bottom images w/o matched pointers
// before enabling - copy orientation from gIS // before enabling - copy orientation from gIS
if (!this.gIP[i].enabled && (gIS_index[i]>=0)){ if (!this.gIP[i].enabled && (gIS_index[i]>=0)){
if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerTilt)) setGH(i,this.gIS[gIS_index[i]].goniometerTilt ); if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerTilt)) setGH(i,this.gIS[gIS_index[i]].goniometerTilt );
if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerAxial)) setGA(i,this.gIS[gIS_index[i]].goniometerAxial ); if (!Double.isNaN(this.gIS[gIS_index[i]].goniometerAxial)) setGA(i,this.gIS[gIS_index[i]].goniometerAxial );
} }
...@@ -1035,7 +1231,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1035,7 +1231,7 @@ import org.apache.commons.configuration.XMLConfiguration;
disabledNoLaser++; disabledNoLaser++;
} }
} }
if (disableNoVignetting) { if (disableNoVignetting) {
if (this.gIP[i].enabled &!this.gIP[i].flatFieldAvailable) numNoVignetting++; if (this.gIP[i].enabled &!this.gIP[i].flatFieldAvailable) numNoVignetting++;
this.gIP[i].enabled &= this.gIP[i].flatFieldAvailable; this.gIP[i].enabled &= this.gIP[i].flatFieldAvailable;
...@@ -1050,13 +1246,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1050,13 +1246,13 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
if (hasMotors) this.gIP[i].enabled=false; // got some no-motor images made without scanning if (hasMotors) this.gIP[i].enabled=false; // got some no-motor images made without scanning
} }
/* Disable no-pointer, new, number of points less than required */ /* Disable no-pointer, new, number of points less than required */
if (this.gIP[i].enabled && !wasEnabled && (this.gIP[i].matchedPointers==0) && (this.gIP[i].pixelsXY.length<minGridNodes)){ if (this.gIP[i].enabled && !wasEnabled && (this.gIP[i].matchedPointers==0) && (this.gIP[i].pixelsXY.length<minGridNodes)){
this.gIP[i].enabled=false; this.gIP[i].enabled=false;
notEnoughNodes++; notEnoughNodes++;
} }
if (this.gIP[i].enabled) numEnabled++; if (this.gIP[i].enabled) numEnabled++;
this.gIP[i].newEnabled=this.gIP[i].enabled&&!wasEnabled; this.gIP[i].newEnabled=this.gIP[i].enabled&&!wasEnabled;
if (this.gIP[i].newEnabled) newEnabled++; if (this.gIP[i].newEnabled) newEnabled++;
...@@ -1070,8 +1266,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1070,8 +1266,8 @@ import org.apache.commons.configuration.XMLConfiguration;
// 2 - recalculate hinted // 2 - recalculate hinted
// connect "enabled" to strategies (not done yet) // connect "enabled" to strategies (not done yet)
// applyHintedGrids90 - moved to the parent class // applyHintedGrids90 - moved to the parent class
/** /**
* Create array of image sets ("panoramas"), sorted by timestamps * Create array of image sets ("panoramas"), sorted by timestamps
* @return number of sets * @return number of sets
...@@ -1129,13 +1325,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1129,13 +1325,13 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return this.gIS.length; return this.gIS.length;
} }
/** /**
* Create array of image sets ("panoramas"), sorted by timestamps * Create array of image sets ("panoramas"), sorted by timestamps
* @param all // use all images (false - only enabled) * @param all // use all images (false - only enabled)
* @return number of sets * @return number of sets
*/ */
public int buildImageSetsOld(boolean all){ public int buildImageSetsOld(boolean all){
List <Double> timeStampList=new ArrayList<Double>(this.gIP.length); List <Double> timeStampList=new ArrayList<Double>(this.gIP.length);
int numChannels=0; int numChannels=0;
...@@ -1169,7 +1365,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1169,7 +1365,7 @@ import org.apache.commons.configuration.XMLConfiguration;
/** /**
* Set goniometer initial orientation from the image with maximal number of laser pointers (make averaging later?) * Set goniometer initial orientation from the image with maximal number of laser pointers (make averaging later?)
* Needed before LMA to have some reasonable initial orientation * Needed before LMA to have some reasonable initial orientation
* @param overwriteAll if true, overwrite orientation data even if it is alredy not NaN, false -skipp those that have orientation set * @param overwriteAll if true, overwrite orientation data even if it is alredy not NaN, false -skipp those that have orientation set
*/ */
public void setInitialOrientation(boolean overwriteAll){ public void setInitialOrientation(boolean overwriteAll){
if (this.debugLevel>0) { if (this.debugLevel>0) {
...@@ -1191,7 +1387,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1191,7 +1387,7 @@ import org.apache.commons.configuration.XMLConfiguration;
EyesisSubCameraParameters esp = this.eyesisCameraParameters.eyesisSubCameras[stationNumber][bestChannel]; EyesisSubCameraParameters esp = this.eyesisCameraParameters.eyesisSubCameras[stationNumber][bestChannel];
if (overwriteAll || Double.isNaN(this.gIS[i].goniometerAxial)){ if (overwriteAll || Double.isNaN(this.gIS[i].goniometerAxial)){
// System.out.println("setInitialOrientation("+overwriteAll+"), Double.isNaN(this.gIS["+i+"].goniometerAxial)="+Double.isNaN(this.gIS[i].goniometerAxial)); // System.out.println("setInitialOrientation("+overwriteAll+"), Double.isNaN(this.gIS["+i+"].goniometerAxial)="+Double.isNaN(this.gIS[i].goniometerAxial));
double subcam_heading = (esp.heading + (esp.cartesian? 0: esp.azimuth)); double subcam_heading = (esp.heading + (esp.cartesian? 0: esp.azimuth));
this.gIS[i].goniometerAxial=-subcam_heading; this.gIS[i].goniometerAxial=-subcam_heading;
for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial); for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial);
...@@ -1213,7 +1409,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1213,7 +1409,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
} }
/** /**
* update image set (panorama, set of simultaneous images) goniometer orientation from the image parameters, do after running LMA * update image set (panorama, set of simultaneous images) goniometer orientation from the image parameters, do after running LMA
* @param selectedImages boolean array of selected images (in current strategy) or null (all selected) * @param selectedImages boolean array of selected images (in current strategy) or null (all selected)
*/ */
// TODO: potential problem here if only some images were enabled in the strategy -- FIXED // TODO: potential problem here if only some images were enabled in the strategy -- FIXED
...@@ -1221,7 +1417,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1221,7 +1417,7 @@ import org.apache.commons.configuration.XMLConfiguration;
/** /**
* Updated version - only flag as orientationEstimated if no enabled images exist in the set or any of the angles is NaN * Updated version - only flag as orientationEstimated if no enabled images exist in the set or any of the angles is NaN
* Temporarily duplicate image parameters from those of the set (should not be needed) * Temporarily duplicate image parameters from those of the set (should not be needed)
* selectedImages will not be used * selectedImages will not be used
*/ */
public void updateSetOrientation(boolean [] selectedImages){ // if selectedImages[] is not null will set orientationEstimated for unselected images public void updateSetOrientation(boolean [] selectedImages){ // if selectedImages[] is not null will set orientationEstimated for unselected images
if (this.gIS==null){ if (this.gIS==null){
...@@ -1229,7 +1425,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1229,7 +1425,7 @@ import org.apache.commons.configuration.XMLConfiguration;
System.out.println(msg); System.out.println(msg);
IJ.showMessage(msg); IJ.showMessage(msg);
} }
for (int i=0; i<this.gIS.length;i++){ for (int i=0; i<this.gIS.length;i++){
this.gIS[i].orientationEstimated=true; this.gIS[i].orientationEstimated=true;
if (!Double.isNaN(this.gIS[i].goniometerAxial) && !Double.isNaN(this.gIS[i].goniometerTilt)) { if (!Double.isNaN(this.gIS[i].goniometerAxial) && !Double.isNaN(this.gIS[i].goniometerTilt)) {
...@@ -1243,7 +1439,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1243,7 +1439,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
if (!this.gIS[i].orientationEstimated){ if (!this.gIS[i].orientationEstimated){
// now fill that data to all disabled images of the same set (just for listing RMS errors and debugging) // now fill that data to all disabled images of the same set (just for listing RMS errors and debugging)
for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { // fill even those that are enabled for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { // fill even those that are enabled
setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial ); setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial );
setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt ); setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt );
} }
...@@ -1254,7 +1450,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1254,7 +1450,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
} }
} }
public void updateSetOrientationOld(boolean [] selectedImages){ public void updateSetOrientationOld(boolean [] selectedImages){
if (this.gIS==null){ if (this.gIS==null){
String msg="Image set is not initilaized"; String msg="Image set is not initilaized";
...@@ -1266,7 +1462,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1266,7 +1462,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.gIS[i].goniometerAxial=Double.NaN; this.gIS[i].goniometerAxial=Double.NaN;
this.gIS[i].goniometerTilt= Double.NaN; this.gIS[i].goniometerTilt= Double.NaN;
this.gIS[i].orientationEstimated=true; this.gIS[i].orientationEstimated=true;
} }
for (int j=0;j<this.gIS[i].imageSet.length;j++) if ((this.gIS[i].imageSet[j]!=null) && this.gIS[i].imageSet[j].enabled){ for (int j=0;j<this.gIS[i].imageSet.length;j++) if ((this.gIS[i].imageSet[j]!=null) && this.gIS[i].imageSet[j].enabled){
if ((selectedImages==null) || selectedImages[this.gIS[i].imageSet[j].imgNumber]) { if ((selectedImages==null) || selectedImages[this.gIS[i].imageSet[j].imgNumber]) {
...@@ -1279,14 +1475,14 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1279,14 +1475,14 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
// now fill that data to all disabled images of the same set (just for listing RMS errors and debugging) // now fill that data to all disabled images of the same set (just for listing RMS errors and debugging)
if (!Double.isNaN(this.gIS[i].goniometerAxial) && !Double.isNaN(this.gIS[i].goniometerTilt)){ if (!Double.isNaN(this.gIS[i].goniometerAxial) && !Double.isNaN(this.gIS[i].goniometerTilt)){
for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { // fill even those that are enabled for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { // fill even those that are enabled
setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial ); setGA(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerAxial );
setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt ); setGH(this.gIS[i].imageSet[j].imgNumber,this.gIS[i].goniometerTilt );
} }
} }
} }
} }
public boolean isEstimated(int imgNum){ public boolean isEstimated(int imgNum){
if (this.gIS==null) { if (this.gIS==null) {
String msg="Image sets are not initialized"; String msg="Image sets are not initialized";
...@@ -1294,7 +1490,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1294,7 +1490,7 @@ import org.apache.commons.configuration.XMLConfiguration;
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
if (this.gIP[imgNum].gridImageSet!=null) return this.gIP[imgNum].gridImageSet.orientationEstimated; if (this.gIP[imgNum].gridImageSet!=null) return this.gIP[imgNum].gridImageSet.orientationEstimated;
// should not get here // should not get here
System.out.println("FIXME: isEstimated("+imgNum+"): this.gIP["+imgNum+"].gridImageSet==null"); System.out.println("FIXME: isEstimated("+imgNum+"): this.gIP["+imgNum+"].gridImageSet==null");
for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){ for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){
for (int j=0;j<this.gIS[i].imageSet.length;j++) if ((this.gIS[i].imageSet[j]!=null) && (this.gIS[i].imageSet[j].imgNumber==imgNum)){ for (int j=0;j<this.gIS[i].imageSet.length;j++) if ((this.gIS[i].imageSet[j]!=null) && (this.gIS[i].imageSet[j].imgNumber==imgNum)){
...@@ -1326,7 +1522,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1326,7 +1522,7 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){ for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){
for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) {
if ((!enabledOnly || this.gIS[i].imageSet[j].enabled) && this.gIS[i].orientationEstimated) numEstimated++; if ((!enabledOnly || this.gIS[i].imageSet[j].enabled) && this.gIS[i].orientationEstimated) numEstimated++;
} }
} }
return numEstimated; return numEstimated;
...@@ -1345,7 +1541,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1345,7 +1541,7 @@ import org.apache.commons.configuration.XMLConfiguration;
return numEstimated; return numEstimated;
} }
int getNumEnabled(){ int getNumEnabled(){
int num=0; int num=0;
for (int i=0;i<this.gIP.length;i++) if ((this.gIP[i]!=null) && this.gIP[i].enabled) num++; for (int i=0;i<this.gIP.length;i++) if ((this.gIP[i]!=null) && this.gIP[i].enabled) num++;
...@@ -1385,7 +1581,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1385,7 +1581,7 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<result.length;i++) result[i]=(this.gIP[i]!=null)?this.gIP[i].hintedMatch:-1; for (int i=0;i<result.length;i++) result[i]=(this.gIP[i]!=null)?this.gIP[i].hintedMatch:-1;
return result; return result;
} }
boolean [] selectNewEnabled () { boolean [] selectNewEnabled () {
boolean [] newEnabled=new boolean [this.gIP.length] ; boolean [] newEnabled=new boolean [this.gIP.length] ;
for (int i=0;i<this.gIP.length;i++) newEnabled[i]= (this.gIP[i]!=null) && this.gIP[i].enabled && this.gIP[i].newEnabled; for (int i=0;i<this.gIP.length;i++) newEnabled[i]= (this.gIP[i]!=null) && this.gIP[i].enabled && this.gIP[i].newEnabled;
...@@ -1407,12 +1603,12 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1407,12 +1603,12 @@ import org.apache.commons.configuration.XMLConfiguration;
Arrays.fill(estimated, true); Arrays.fill(estimated, true);
return estimated; return estimated;
} }
for (int i=0;i<estimated.length;i++) estimated[i]=false; for (int i=0;i<estimated.length;i++) estimated[i]=false;
for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){ for (int i=0;i<this.gIS.length;i++) if (this.gIS[i].imageSet!=null){
for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) { for (int j=0;j<this.gIS[i].imageSet.length;j++) if (this.gIS[i].imageSet[j]!=null) {
if ((!enabledOnly || this.gIS[i].imageSet[j].enabled) ) estimated[this.gIS[i].imageSet[j].imgNumber]= this.gIS[i].orientationEstimated; if ((!enabledOnly || this.gIS[i].imageSet[j].enabled) ) estimated[this.gIS[i].imageSet[j].imgNumber]= this.gIS[i].orientationEstimated;
} }
} }
return estimated; return estimated;
...@@ -1440,7 +1636,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1440,7 +1636,7 @@ import org.apache.commons.configuration.XMLConfiguration;
* Now 3-rd term - interAxisAngle - with goniometerTilt it is used for correction of non-pure axial movement of the camera. * Now 3-rd term - interAxisAngle - with goniometerTilt it is used for correction of non-pure axial movement of the camera.
*/ */
public double [] getImagesetTiltAxial(double timeStamp){ public double [] getImagesetTiltAxial(double timeStamp){
int mAxial=1; // m2 int mAxial=1; // m2
int mHorizontal=2;// m3 int mHorizontal=2;// m3
// this is probably already set // this is probably already set
for (int i=0;i<this.gIS.length;i++){ for (int i=0;i<this.gIS.length;i++){
...@@ -1464,7 +1660,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1464,7 +1660,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if ((early_set<0) || (this.gIS[j].timeStamp >this.gIS[early_set].timeStamp)) early_set = j; if ((early_set<0) || (this.gIS[j].timeStamp >this.gIS[early_set].timeStamp)) early_set = j;
} }
} }
if ((late_set <0) && (early_set<0)) { if ((late_set <0) && (early_set<0)) {
if (this.debugLevel>0) System.out.println("Failed to find any known orientation"); if (this.debugLevel>0) System.out.println("Failed to find any known orientation");
return null; return null;
...@@ -1482,7 +1678,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1482,7 +1678,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (axialCenter>0) axialCenter-=180.0; if (axialCenter>0) axialCenter-=180.0;
else axialCenter+=180.0; else axialCenter+=180.0;
} }
double interEarly=this.gIS[early_set].interAxisAngle; double interEarly=this.gIS[early_set].interAxisAngle;
double interLate= this.gIS[late_set].interAxisAngle; double interLate= this.gIS[late_set].interAxisAngle;
interEarly-=360.0*Math.floor((interEarly+180.0)/360.0); interEarly-=360.0*Math.floor((interEarly+180.0)/360.0);
...@@ -1492,7 +1688,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1492,7 +1688,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (interCenter>0) interCenter-=180.0; if (interCenter>0) interCenter-=180.0;
else interCenter+=180.0; else interCenter+=180.0;
} }
double tiltEarly=this.gIS[early_set].goniometerTilt; double tiltEarly=this.gIS[early_set].goniometerTilt;
double tiltLate= this.gIS[late_set].goniometerTilt; double tiltLate= this.gIS[late_set].goniometerTilt;
tiltEarly-=360.0*Math.floor((tiltEarly+180.0)/360.0); tiltEarly-=360.0*Math.floor((tiltEarly+180.0)/360.0);
...@@ -1566,12 +1762,12 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1566,12 +1762,12 @@ import org.apache.commons.configuration.XMLConfiguration;
int indexSecond=-1; int indexSecond=-1;
for (int j=0;j<setList.size();j++) { for (int j=0;j<setList.size();j++) {
if (((this.gIS[indexClosest].motors[mAxial]-thisMotorAxial)* if (((this.gIS[indexClosest].motors[mAxial]-thisMotorAxial)*
(this.gIS[setList.get(j)].motors[mAxial]-thisMotorAxial)<0) && // different side (this.gIS[setList.get(j)].motors[mAxial]-thisMotorAxial)<0) && // different side
((indexSecond<0) || (Math.abs(this.gIS[setList.get(j)].motors[mAxial]-thisMotorAxial)<dClosest))){ ((indexSecond<0) || (Math.abs(this.gIS[setList.get(j)].motors[mAxial]-thisMotorAxial)<dClosest))){
indexSecond=setList.get(j); indexSecond=setList.get(j);
dClosest=Math.abs(this.gIS[indexSecond].motors[mAxial]-thisMotorAxial); dClosest=Math.abs(this.gIS[indexSecond].motors[mAxial]-thisMotorAxial);
} }
} }
if (this.debugLevel>2) System.out.println("indexSecond="+indexSecond); if (this.debugLevel>2) System.out.println("indexSecond="+indexSecond);
if (indexSecond<0){ // no sets on the opposite side from the indexClosest, use second closest on the same side as indexClosest if (indexSecond<0){ // no sets on the opposite side from the indexClosest, use second closest on the same side as indexClosest
for (int j=0;j<setList.size();j++) { for (int j=0;j<setList.size();j++) {
...@@ -1580,8 +1776,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1580,8 +1776,8 @@ import org.apache.commons.configuration.XMLConfiguration;
indexSecond=setList.get(j); indexSecond=setList.get(j);
dClosest=Math.abs(this.gIS[indexSecond].motors[mAxial]-thisMotorAxial); dClosest=Math.abs(this.gIS[indexSecond].motors[mAxial]-thisMotorAxial);
} }
} }
} }
if (indexSecond<0){ // no second sets at all if (indexSecond<0){ // no second sets at all
System.out.println("getImagesetTiltAxial("+timeStamp+") - this is a BUG "); System.out.println("getImagesetTiltAxial("+timeStamp+") - this is a BUG ");
...@@ -1661,7 +1857,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1661,7 +1857,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return null; return null;
} }
public double getImageTimestamp(ImagePlus image){ public double getImageTimestamp(ImagePlus image){
if ((image.getProperty("timestamp")==null) || (((String) image.getProperty("timestamp")).length()==0)) { if ((image.getProperty("timestamp")==null) || (((String) image.getProperty("timestamp")).length()==0)) {
(new JP46_Reader_camera(false)).decodeProperiesFromInfo(image); (new JP46_Reader_camera(false)).decodeProperiesFromInfo(image);
...@@ -1691,9 +1887,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1691,9 +1887,9 @@ import org.apache.commons.configuration.XMLConfiguration;
IJ.showMessage("Error",msg); IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
return channel; return channel;
} }
/** /**
* initialize image data with camera defaults * initialize image data with camera defaults
* @param distortionCalibrationData grid distortionCalibrationData * @param distortionCalibrationData grid distortionCalibrationData
...@@ -1701,7 +1897,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1701,7 +1897,7 @@ import org.apache.commons.configuration.XMLConfiguration;
* @return * @return
*/ */
// Used in Goniometer // Used in Goniometer
public void initImageSet( public void initImageSet(
EyesisCameraParameters eyesisCameraParameters) { EyesisCameraParameters eyesisCameraParameters) {
for (int i=0;i<this.getNumImages();i++){ for (int i=0;i<this.getNumImages();i++){
int subCam=this.getImageSubcamera(i); int subCam=this.getImageSubcamera(i);
...@@ -1709,11 +1905,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1709,11 +1905,11 @@ import org.apache.commons.configuration.XMLConfiguration;
this.setParameters(eyesisCameraParameters.getParametersVector(stationNumber,subCam), i); this.setParameters(eyesisCameraParameters.getParametersVector(stationNumber,subCam), i);
} }
} }
// constructor from XML file // constructor from XML file
public DistortionCalibrationData ( public DistortionCalibrationData (
boolean smart, boolean smart,
String defaultPath, String defaultPath,
...@@ -1733,8 +1929,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1733,8 +1929,8 @@ import org.apache.commons.configuration.XMLConfiguration;
defaultPath); //String defaultPath defaultPath); //String defaultPath
if ((pathname==null) || (pathname=="")) return; if ((pathname==null) || (pathname=="")) return;
// setGridImages(gridImages); // setGridImages(gridImages);
//TODO: these images will be overwritten by setFromXML !!!!!!!!! //TODO: these images will be overwritten by setFromXML !!!!!!!!!
this.gIS=null; // So readAllGrids will create it this.gIS=null; // So readAllGrids will create it
setFromXML( setFromXML(
pathname, pathname,
eyesisCameraParameters, eyesisCameraParameters,
...@@ -1781,7 +1977,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1781,7 +1977,7 @@ import org.apache.commons.configuration.XMLConfiguration;
System.out.println("DistortionCalibrationData("+pathname+",eyesisCameraParameters) 2 -> this.gIS.length="+((this.gIS==null)?"null":this.gIS.length)); System.out.println("DistortionCalibrationData("+pathname+",eyesisCameraParameters) 2 -> this.gIS.length="+((this.gIS==null)?"null":this.gIS.length));
updateSetOrientation(null); // update orientation of image sets (built in readAllGrids()) updateSetOrientation(null); // update orientation of image sets (built in readAllGrids())
} }
*/ */
public void setFromXML(String pathname, public void setFromXML(String pathname,
EyesisCameraParameters eyesisCameraParameters, // should have cartesian set EyesisCameraParameters eyesisCameraParameters, // should have cartesian set
EyesisAberrations.AberrationParameters aberrationParameters) { EyesisAberrations.AberrationParameters aberrationParameters) {
...@@ -1794,14 +1990,14 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1794,14 +1990,14 @@ import org.apache.commons.configuration.XMLConfiguration;
// TODO Auto-generated catch block // TODO Auto-generated catch block
e.printStackTrace(); e.printStackTrace();
} }
this.numSubCameras=Integer.parseInt(hConfig.getString("subcameras","1")); this.numSubCameras=Integer.parseInt(hConfig.getString("subcameras","1"));
System.out.println("Number of subcameras is "+this.numSubCameras); System.out.println("Number of subcameras is "+this.numSubCameras);
int num=hConfig.getMaxIndex("file"); int num=hConfig.getMaxIndex("file");
num++; num++;
this.gIP=new GridImageParameters[num]; this.gIP=new GridImageParameters[num];
this.pars=new double[num][parameterDescriptions.length]; this.pars=new double[num][parameterDescriptions.length];
System.out.println("Number of pattern grid images in "+pathname+" is "+num); System.out.println("Number of pattern grid images in "+pathname+" is "+num);
int numSets=hConfig.getMaxIndex("set")+1; // see if it returns -1 for none int numSets=hConfig.getMaxIndex("set")+1; // see if it returns -1 for none
System.out.println("Number of image sets in "+pathname+" is "+numSets); System.out.println("Number of image sets in "+pathname+" is "+numSets);
if (numSets>0){ if (numSets>0){
...@@ -1820,7 +2016,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1820,7 +2016,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.gIS[index].setParameterValue(j,Double.parseDouble(sub.getString(descrField(j,0))), false); this.gIS[index].setParameterValue(j,Double.parseDouble(sub.getString(descrField(j,0))), false);
} }
} }
if (sub.getString("orientationEstimated")!=null) { if (sub.getString("orientationEstimated")!=null) {
this.gIS[i].orientationEstimated=Boolean.parseBoolean(sub.getString("orientationEstimated")); this.gIS[i].orientationEstimated=Boolean.parseBoolean(sub.getString("orientationEstimated"));
/* System.out.println(i+": restored orientationEstimated="+this.gIS[i].orientationEstimated+ /* System.out.println(i+": restored orientationEstimated="+this.gIS[i].orientationEstimated+
...@@ -1832,19 +2028,19 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1832,19 +2028,19 @@ import org.apache.commons.configuration.XMLConfiguration;
" tilt="+this.gIS[i].goniometerTilt+ " tilt="+this.gIS[i].goniometerTilt+
" axial="+this.gIS[i].goniometerAxial);*/ " axial="+this.gIS[i].goniometerAxial);*/
} }
} }
} else { } else {
this.gIS=null; // has to be build later this.gIS=null; // has to be build later
} }
for (int i=0;i<num;i++) { for (int i=0;i<num;i++) {
this.gIP[i]=new GridImageParameters(i); this.gIP[i]=new GridImageParameters(i);
HierarchicalConfiguration sub = hConfig.configurationAt("file("+i+")"); HierarchicalConfiguration sub = hConfig.configurationAt("file("+i+")");
this.gIP[i].imgNumber=i; this.gIP[i].imgNumber=i;
this.gIP[i].path=sub.getString("name"); this.gIP[i].path=sub.getString("name");
this.gIP[i].timestamp=Double.parseDouble(sub.getString("timestamp")); this.gIP[i].timestamp=Double.parseDouble(sub.getString("timestamp"));
this.gIP[i].channel=Integer.parseInt(sub.getString("channel")); this.gIP[i].channel=Integer.parseInt(sub.getString("channel"));
if (sub.getString("stationNumber")!=null) this.gIP[i].setStationNumber(Integer.parseInt(sub.getString("stationNumber"))); if (sub.getString("stationNumber")!=null) this.gIP[i].setStationNumber(Integer.parseInt(sub.getString("stationNumber")));
else this.gIP[i].setStationNumber(0); else this.gIP[i].setStationNumber(0);
...@@ -1856,7 +2052,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1856,7 +2052,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.gIP[i].enabled=sub.getBoolean("enabled",false); this.gIP[i].enabled=sub.getBoolean("enabled",false);
// if (aberrationParameters.trustEnabled && this.gIP[i].enabled) this.gIP[i].hintedMatch=2; // trusted // if (aberrationParameters.trustEnabled && this.gIP[i].enabled) this.gIP[i].hintedMatch=2; // trusted
if (aberrationParameters.trustEnabled) this.gIP[i].hintedMatch= this.gIP[i].enabled?2:-1; // trusted and only trusted to enabled if (aberrationParameters.trustEnabled) this.gIP[i].hintedMatch= this.gIP[i].enabled?2:-1; // trusted and only trusted to enabled
for (int j=0;j<this.parameterDescriptions.length;j++){ for (int j=0;j<this.parameterDescriptions.length;j++){
// if (sub.getString(parameterDescriptions[j][0])!=null) // if (sub.getString(parameterDescriptions[j][0])!=null)
if (sub.getString(descrField(j,0))!=null) if (sub.getString(descrField(j,0))!=null)
...@@ -1886,7 +2082,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1886,7 +2082,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.gIP[ip].gridImageSet=this.gIS[this.gIP[ip].setNumber]; this.gIP[ip].gridImageSet=this.gIS[this.gIP[ip].setNumber];
//this.gIP[i].channel //this.gIP[i].channel
} }
} else { } else {
System.out.println("Re-creating image set data from individual images (old format)"); System.out.println("Re-creating image set data from individual images (old format)");
System.out.println("WARNING: Some parameters may get from unused images and so have wrong values"); System.out.println("WARNING: Some parameters may get from unused images and so have wrong values");
...@@ -1950,10 +2146,10 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1950,10 +2146,10 @@ import org.apache.commons.configuration.XMLConfiguration;
public boolean saveTimestampedToXML(String pathname, String comment) { public boolean saveTimestampedToXML(String pathname, String comment) {
return saveToXML(pathname+"_"+IJ.d2s(0.000001*(System.nanoTime()/1000),6).replace('.', '_')+".dcal-xml", // full path or null return saveToXML(pathname+"_"+IJ.d2s(0.000001*(System.nanoTime()/1000),6).replace('.', '_')+".dcal-xml", // full path or null
null); null);
} }
public boolean saveToXML(String pathname) { public boolean saveToXML(String pathname) {
return saveToXML(pathname,null); return saveToXML(pathname,null);
} }
public boolean saveToXML(String pathname, String comment) { public boolean saveToXML(String pathname, String comment) {
XMLConfiguration hConfig=new XMLConfiguration(); XMLConfiguration hConfig=new XMLConfiguration();
if (comment!=null) hConfig.addProperty("comment",comment); if (comment!=null) hConfig.addProperty("comment",comment);
...@@ -1989,7 +2185,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -1989,7 +2185,7 @@ import org.apache.commons.configuration.XMLConfiguration;
hConfig.addProperty("set."+descrField(j,0),vector[j]); hConfig.addProperty("set."+descrField(j,0),vector[j]);
} }
} }
// hConfig.addProperty("grids",""); // hConfig.addProperty("grids","");
File file=new File (pathname); File file=new File (pathname);
BufferedWriter writer; BufferedWriter writer;
...@@ -2006,7 +2202,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2006,7 +2202,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.pathName=pathname; this.pathName=pathname;
return true; return true;
} }
// public double gridPeriod=0.0; // average grid period, in pixels (to filter out (double-) reflected images // public double gridPeriod=0.0; // average grid period, in pixels (to filter out (double-) reflected images
public double calcGridPeriod(int fileNumber){ public double calcGridPeriod(int fileNumber){
if ((this.gIP[fileNumber].pixelsXY==null) || (this.gIP[fileNumber].pixelsXY.length<3)) { if ((this.gIP[fileNumber].pixelsXY==null) || (this.gIP[fileNumber].pixelsXY.length<3)) {
...@@ -2040,13 +2236,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2040,13 +2236,13 @@ import org.apache.commons.configuration.XMLConfiguration;
return this.gIP[fileNumber].gridPeriod; return this.gIP[fileNumber].gridPeriod;
} }
public int [] setGridsWithRemap( public int [] setGridsWithRemap(
int fileNumber, int fileNumber,
int [][] reMap, int [][] reMap,
float [][] pixels, float [][] pixels,
PatternParameters patternParameters){ PatternParameters patternParameters){
// boolean disableNoFlatfield=false; // true only for processing transitional images - mixture of ff/ no-ff // boolean disableNoFlatfield=false; // true only for processing transitional images - mixture of ff/ no-ff
int sensorWidth=this.eyesisCameraParameters.getSensorWidth(this.gIP[fileNumber].channel); int sensorWidth=this.eyesisCameraParameters.getSensorWidth(this.gIP[fileNumber].channel);
int sensorHeight=this.eyesisCameraParameters.getSensorHeight(this.gIP[fileNumber].channel); int sensorHeight=this.eyesisCameraParameters.getSensorHeight(this.gIP[fileNumber].channel);
int station=this.gIP[fileNumber].getStationNumber(); int station=this.gIP[fileNumber].getStationNumber();
...@@ -2055,16 +2251,16 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2055,16 +2251,16 @@ import org.apache.commons.configuration.XMLConfiguration;
// int numOfGridNodes=0; // int numOfGridNodes=0;
// int numOfGridNodes_extra=0; // int numOfGridNodes_extra=0;
for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)){ for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)){
int u=(int) Math.round(pixels[2][i]); int u=Math.round(pixels[2][i]);
int v=(int) Math.round(pixels[3][i]); int v=Math.round(pixels[3][i]);
int u1= reMap[0][0]*u + reMap[0][1]*v + reMap[0][2]; // u int u1= reMap[0][0]*u + reMap[0][1]*v + reMap[0][2]; // u
int v1= reMap[1][0]*u + reMap[1][1]*v + reMap[1][2]; // v; int v1= reMap[1][0]*u + reMap[1][1]*v + reMap[1][2]; // v;
// if (patternParameters.getXYZM(u,v,this.debugLevel>1)!=null) size++; // if (patternParameters.getXYZM(u,v,this.debugLevel>1)!=null) size++;
if (patternParameters.getXYZM(u1,v1,false,station)!=null) size++; // already assumes correct uv? if (patternParameters.getXYZM(u1,v1,false,station)!=null) size++; // already assumes correct uv?
else size_extra++; else size_extra++;
} }
this.gIP[fileNumber].resetMask(); this.gIP[fileNumber].resetMask();
this.gIP[fileNumber].pixelsXY=new double [size][6]; this.gIP[fileNumber].pixelsXY=new double [size][6];
this.gIP[fileNumber].pixelsUV=new int [size][2]; this.gIP[fileNumber].pixelsUV=new int [size][2];
...@@ -2079,14 +2275,14 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2079,14 +2275,14 @@ import org.apache.commons.configuration.XMLConfiguration;
// this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8; // this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8;
// if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data // if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data
for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)) { for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)) {
int u=(int) Math.round(pixels[2][i]); int u=Math.round(pixels[2][i]);
int v=(int) Math.round(pixels[3][i]); int v=Math.round(pixels[3][i]);
int u1= reMap[0][0]*u + reMap[0][1]*v + reMap[0][2]; // u int u1= reMap[0][0]*u + reMap[0][1]*v + reMap[0][2]; // u
int v1= reMap[1][0]*u + reMap[1][1]*v + reMap[1][2]; // v; int v1= reMap[1][0]*u + reMap[1][1]*v + reMap[1][2]; // v;
// if (patternParameters.getXYZM(u,v,this.debugLevel>1)!=null) { // if (patternParameters.getXYZM(u,v,this.debugLevel>1)!=null) {
if (patternParameters.getXYZM(u1,v1,false,station)!=null) { if (patternParameters.getXYZM(u1,v1,false,station)!=null) {
this.gIP[fileNumber].pixelsXY[index][0]=pixels[0][i]; this.gIP[fileNumber].pixelsXY[index][0]=pixels[0][i];
this.gIP[fileNumber].pixelsXY[index][1]=pixels[1][i]; this.gIP[fileNumber].pixelsXY[index][1]=pixels[1][i];
...@@ -2118,11 +2314,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2118,11 +2314,11 @@ import org.apache.commons.configuration.XMLConfiguration;
int [] result = {size,size_extra}; int [] result = {size,size_extra};
return result; return result;
} }
public boolean readAllGrids(PatternParameters patternParameters){ public boolean readAllGrids(PatternParameters patternParameters){
boolean disableNoFlatfield=false; // true only for processing transitional images - mixture of ff/ no-ff boolean disableNoFlatfield=false; // true only for processing transitional images - mixture of ff/ no-ff
System.out.println("readAllGrids(), this.debugLevel="+this.debugLevel+" this.gIS is "+((this.gIS==null)?"null":"not null")); System.out.println("readAllGrids(), this.debugLevel="+this.debugLevel+" this.gIS is "+((this.gIS==null)?"null":"not null"));
int numImages=getNumImages(); int numImages=getNumImages();
// this.pixelsXY=new double[numImages][][]; // this.pixelsXY=new double[numImages][][];
// this.pixelsUV=new int[numImages][][]; // this.pixelsUV=new int[numImages][][];
...@@ -2157,11 +2353,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2157,11 +2353,11 @@ import org.apache.commons.configuration.XMLConfiguration;
this.gIP[fileNumber].matchedPointers=getUsedPonters(imp_grid); this.gIP[fileNumber].matchedPointers=getUsedPonters(imp_grid);
// this.gIP[fileNumber].enabled=true; // will filter separately // this.gIP[fileNumber].enabled=true; // will filter separately
// this.gIP[fileNumber].hintedMatch=-1; // unknown yet - now read from the calibration file // this.gIP[fileNumber].hintedMatch=-1; // unknown yet - now read from the calibration file
double [] saturations=new double [4]; double [] saturations=new double [4];
for (int i=0;i<saturations.length;i++) { for (int i=0;i<saturations.length;i++) {
saturations[i]=Double.NaN; saturations[i]=Double.NaN;
if (imp_grid.getProperty("saturation_" + i) !=null) saturations[i]=Double.parseDouble((String) imp_grid.getProperty("saturation_" + i)); if (imp_grid.getProperty("saturation_" + i) !=null) saturations[i]=Double.parseDouble((String) imp_grid.getProperty("saturation_" + i));
} }
if (!Double.isNaN(saturations[1])) this.gIP[fileNumber].saturation[0]=saturations[1]; if (!Double.isNaN(saturations[1])) this.gIP[fileNumber].saturation[0]=saturations[1];
if (!Double.isNaN(saturations[2])) this.gIP[fileNumber].saturation[2]=saturations[2]; if (!Double.isNaN(saturations[2])) this.gIP[fileNumber].saturation[2]=saturations[2];
...@@ -2170,7 +2366,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2170,7 +2366,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (!Double.isNaN(saturations[0])) this.gIP[fileNumber].saturation[1]=saturations[0]; if (!Double.isNaN(saturations[0])) this.gIP[fileNumber].saturation[1]=saturations[0];
if (!Double.isNaN(saturations[3])) this.gIP[fileNumber].saturation[1]=saturations[3]; if (!Double.isNaN(saturations[3])) this.gIP[fileNumber].saturation[1]=saturations[3];
} }
stack=imp_grid.getStack(); stack=imp_grid.getStack();
if ((stack==null) || (stack.getSize()<4)) { if ((stack==null) || (stack.getSize()<4)) {
String msg="Expected a 8-slice stack in "+this.gIP[fileNumber].path; String msg="Expected a 8-slice stack in "+this.gIP[fileNumber].path;
...@@ -2180,7 +2376,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2180,7 +2376,7 @@ import org.apache.commons.configuration.XMLConfiguration;
float [][] pixels=new float[stack.getSize()][]; // now - 8 (x,y,u,v,contrast, vignR,vignG,vignB float [][] pixels=new float[stack.getSize()][]; // now - 8 (x,y,u,v,contrast, vignR,vignG,vignB
for (int i=0;i<pixels.length;i++) pixels[i]= (float[]) stack.getPixels(i+1); // pixel X : negative - no grid here for (int i=0;i<pixels.length;i++) pixels[i]= (float[]) stack.getPixels(i+1); // pixel X : negative - no grid here
if (this.eyesisCameraParameters.badNodeThreshold>0.0){ if (this.eyesisCameraParameters.badNodeThreshold>0.0){
boolean thisDebug =false; boolean thisDebug =false;
// thisDebug|= (fileNumber== 720); // chn 25 // thisDebug|= (fileNumber== 720); // chn 25
...@@ -2191,8 +2387,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2191,8 +2387,8 @@ import org.apache.commons.configuration.XMLConfiguration;
// thisDebug|= (fileNumber==1081); // chn 14 // thisDebug|= (fileNumber==1081); // chn 14
// int maxBadNeighb=1; // 7 of 8 shold be good // int maxBadNeighb=1; // 7 of 8 shold be good
int numBadNodes=fixBadGridNodes( int numBadNodes=fixBadGridNodes(
pixels, pixels,
stack.getWidth(), stack.getWidth(),
...@@ -2209,7 +2405,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2209,7 +2405,7 @@ import org.apache.commons.configuration.XMLConfiguration;
" enabled="+this.gIP[fileNumber].enabled+" hintedMatch="+this.gIP[fileNumber].hintedMatch); " enabled="+this.gIP[fileNumber].enabled+" hintedMatch="+this.gIP[fileNumber].hintedMatch);
} }
} }
this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8; this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8;
if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data
// start new code: // start new code:
...@@ -2227,7 +2423,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2227,7 +2423,7 @@ import org.apache.commons.configuration.XMLConfiguration;
numOfGridNodes+=sizeSizeExtra[0]; numOfGridNodes+=sizeSizeExtra[0];
numOfGridNodes_extra+=sizeSizeExtra[1]; numOfGridNodes_extra+=sizeSizeExtra[1];
/* /*
int sensorWidth=this.eyesisCameraParameters.getSensorWidth(this.gIP[fileNumber].channel); int sensorWidth=this.eyesisCameraParameters.getSensorWidth(this.gIP[fileNumber].channel);
int sensorHeight=this.eyesisCameraParameters.getSensorHeight(this.gIP[fileNumber].channel); int sensorHeight=this.eyesisCameraParameters.getSensorHeight(this.gIP[fileNumber].channel);
int station=this.gIP[fileNumber].getStationNumber(); int station=this.gIP[fileNumber].getStationNumber();
...@@ -2245,8 +2441,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2245,8 +2441,8 @@ import org.apache.commons.configuration.XMLConfiguration;
this.gIP[fileNumber].pixelsUV=new int [size][2]; this.gIP[fileNumber].pixelsUV=new int [size][2];
this.gIP[fileNumber].pixelsXY_extra=new double [size_extra][6]; this.gIP[fileNumber].pixelsXY_extra=new double [size_extra][6];
this.gIP[fileNumber].pixelsUV_extra=new int [size_extra][2]; this.gIP[fileNumber].pixelsUV_extra=new int [size_extra][2];
numOfGridNodes+=size; numOfGridNodes+=size;
numOfGridNodes_extra+=size_extra; numOfGridNodes_extra+=size_extra;
int index=0; int index=0;
...@@ -2255,9 +2451,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2255,9 +2451,9 @@ import org.apache.commons.configuration.XMLConfiguration;
// this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8; // this.gIP[fileNumber].flatFieldAvailable=pixels.length>=8;
// if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data // if (disableNoFlatfield && !this.gIP[fileNumber].flatFieldAvailable) this.gIP[fileNumber].enabled=false; // just to use old mixed data
for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)) { for (int i=0;i<pixels[0].length;i++) if ((pixels[0][i]>=0) && (pixels[1][i]>=0) && (pixels[0][i]<sensorWidth) && (pixels[1][i]<sensorHeight)) {
int u=(int) Math.round(pixels[2][i]); int u=(int) Math.round(pixels[2][i]);
int v=(int) Math.round(pixels[3][i]); int v=(int) Math.round(pixels[3][i]);
...@@ -2290,9 +2486,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2290,9 +2486,9 @@ import org.apache.commons.configuration.XMLConfiguration;
index_extra++; index_extra++;
} }
} }
*/ */
calcGridPeriod(fileNumber); // will be used to filter out reflections calcGridPeriod(fileNumber); // will be used to filter out reflections
//System.out.println ("pixelsXY["+fileNumber+"]length="+pixelsXY[fileNumber].length); //System.out.println ("pixelsXY["+fileNumber+"]length="+pixelsXY[fileNumber].length);
} }
if (this.debugLevel>3) { if (this.debugLevel>3) {
...@@ -2314,7 +2510,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2314,7 +2510,7 @@ import org.apache.commons.configuration.XMLConfiguration;
System.out.println("readAllGrids(), numImages="+numImages+", total number of grid nodes="+numOfGridNodes+", unused nodes "+numOfGridNodes_extra); System.out.println("readAllGrids(), numImages="+numImages+", total number of grid nodes="+numOfGridNodes+", unused nodes "+numOfGridNodes_extra);
} }
// probably - do not need to verify that this.gIS is null - should do that anyway. UPDATE: no, now reading config file creates gIS // probably - do not need to verify that this.gIS is null - should do that anyway. UPDATE: no, now reading config file creates gIS
/* /*
if (this.gIS!=null){ if (this.gIS!=null){
System.out.println("readAllGrids() 1: "); System.out.println("readAllGrids() 1: ");
for (int is=0;is<this.gIS.length;is++){ for (int is=0;is<this.gIS.length;is++){
...@@ -2426,16 +2622,16 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2426,16 +2622,16 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
if (numBad==0) { if (numBad==0) {
System.out.println("fixBadGridNodes() BUG - should not get here."); System.out.println("fixBadGridNodes() BUG - should not get here.");
return 0; // should not get here - return 0; // should not get here -
} }
double [][] dbgData=null; double [][] dbgData=null;
if (debugLevel>debugThreshold){ if (debugLevel>debugThreshold){
dbgData=new double[9][]; dbgData=new double[9][];
dbgData[0]=diffs2.clone(); dbgData[0]=diffs2.clone();
dbgData[2]=dbgData[0].clone(); dbgData[2]=dbgData[0].clone();
for (int i=0;i< dbgData[2].length;i++) if (!localWorst[i]) dbgData[2][i]=-1.0; for (int i=0;i< dbgData[2].length;i++) if (!localWorst[i]) dbgData[2][i]=-1.0;
// (new showDoubleFloatArrays()).showArrays(diffs2, width, height, "diffs2"); // (new showDoubleFloatArrays()).showArrays(diffs2, width, height, "diffs2");
} }
// Trying to eliminate all non local worst (may that is just extra as there anot too many bad nodes) // Trying to eliminate all non local worst (may that is just extra as there anot too many bad nodes)
int numStillBad=0; int numStillBad=0;
for (int i=0;i<localWorst.length;i++) if (localWorst[i]){ for (int i=0;i<localWorst.length;i++) if (localWorst[i]){
...@@ -2517,10 +2713,10 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2517,10 +2713,10 @@ import org.apache.commons.configuration.XMLConfiguration;
dbgData[3][i]=fpixels[0][i]; dbgData[3][i]=fpixels[0][i];
dbgData[4][i]=fpixels[1][i]; dbgData[4][i]=fpixels[1][i];
} }
} }
// TODO - try to fix some around pixels first?
// TODO - try to fix some around pixels first?
// Actually patching locally worst nodes // Actually patching locally worst nodes
for (int index=0;index<localWorst.length;index++) if (localWorst[index]){ for (int index=0;index<localWorst.length;index++) if (localWorst[index]){
int numNonZero=0; int numNonZero=0;
...@@ -2592,16 +2788,16 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2592,16 +2788,16 @@ import org.apache.commons.configuration.XMLConfiguration;
dbgData[7][i]=dbgData[3][i]-fpixels[0][i]; dbgData[7][i]=dbgData[3][i]-fpixels[0][i];
dbgData[8][i]=dbgData[4][i]-fpixels[1][i]; dbgData[8][i]=dbgData[4][i]-fpixels[1][i];
} }
String [] dbgTitles={"diff20","diff2Mod","localWorst", "old-X", "old-Y", "new-X", "new-Y","old-new-X","old-new-Y"}; String [] dbgTitles={"diff20","diff2Mod","localWorst", "old-X", "old-Y", "new-X", "new-Y","old-new-X","old-new-Y"};
if (dbgTitle!=null) (new showDoubleFloatArrays()).showArrays(dbgData, width, height, true, dbgTitle, dbgTitles); if (dbgTitle!=null) (new showDoubleFloatArrays()).showArrays(dbgData, width, height, true, dbgTitle, dbgTitles);
} }
return numBad; return numBad;
} }
// TODO: Move all custom image properties (including encode/decode from JP4_reader_camera) to a separate class. // TODO: Move all custom image properties (including encode/decode from JP4_reader_camera) to a separate class.
// below is a duplicatie from MatchSimulatedPattern // below is a duplicatie from MatchSimulatedPattern
public double[][] getPointersXY(ImagePlus imp, int numPointers){ public double[][] getPointersXY(ImagePlus imp, int numPointers){
// read image info to properties (if it was not done yet - should it? // read image info to properties (if it was not done yet - should it?
if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) { if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) {
...@@ -2622,7 +2818,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2622,7 +2818,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (numPointerDetected>0) return pointersXY; if (numPointerDetected>0) return pointersXY;
else return null; else return null;
} }
public int [] getMotorPositions(ImagePlus imp, int numMotors){ public int [] getMotorPositions(ImagePlus imp, int numMotors){
// read image info to properties (if it was not done yet - should it? // read image info to properties (if it was not done yet - should it?
if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) { if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) {
...@@ -2641,7 +2837,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2641,7 +2837,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (numMotorsDetected>0) return motorPos; if (numMotorsDetected>0) return motorPos;
else return null; else return null;
} }
public int getUsedPonters(ImagePlus imp){ public int getUsedPonters(ImagePlus imp){
// read image info to properties (if it was not done yet - should it? // read image info to properties (if it was not done yet - should it?
if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) { if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) {
...@@ -2653,12 +2849,12 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2653,12 +2849,12 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return 0; return 0;
} }
public int getImageNumPoints(int numImg){ public int getImageNumPoints(int numImg){
return this.gIP[numImg].pixelsUV.length; return this.gIP[numImg].pixelsUV.length;
} }
public void initPars(int numImages, int numPars) { public void initPars(int numImages, int numPars) {
this.pars=new double [numImages][numPars]; this.pars=new double [numImages][numPars];
for (int i=0;i<numImages;i++) for (int j=0;j<numPars;j++) this.pars[i][j]=Double.NaN; for (int i=0;i<numImages;i++) for (int j=0;j<numPars;j++) this.pars[i][j]=Double.NaN;
...@@ -2722,8 +2918,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2722,8 +2918,8 @@ import org.apache.commons.configuration.XMLConfiguration;
public GridImageParameters getGridImageParameters(int numImg){ public GridImageParameters getGridImageParameters(int numImg){
return this.gIP[numImg]; return this.gIP[numImg];
} }
// next is just for goniometer - use elevation and heading for cartesian mode? // next is just for goniometer - use elevation and heading for cartesian mode?
public double [] getHeadEl(int imgNum){ // get sensor heading +(azimuth) and elevation public double [] getHeadEl(int imgNum){ // get sensor heading +(azimuth) and elevation
if ((imgNum<0) || (imgNum>=this.pars.length)) { if ((imgNum<0) || (imgNum>=this.pars.length)) {
String msg="There are only "+this.pars.length+" images defined, requested #"+imgNum; String msg="There are only "+this.pars.length+" images defined, requested #"+imgNum;
...@@ -2738,7 +2934,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2738,7 +2934,7 @@ import org.apache.commons.configuration.XMLConfiguration;
this.pars[imgNum][index_heading]+", "+this.pars[imgNum][index_elevation]); this.pars[imgNum][index_heading]+", "+this.pars[imgNum][index_elevation]);
return headel; return headel;
} }
// set goniometer horizontal axis angle and goniometer axial angles in all images // set goniometer horizontal axis angle and goniometer axial angles in all images
public void setGHGA(double gh, double ga){ public void setGHGA(double gh, double ga){
for (int imgNum=0;imgNum<this.pars.length;imgNum++) setGHGA( imgNum, gh,ga); for (int imgNum=0;imgNum<this.pars.length;imgNum++) setGHGA( imgNum, gh,ga);
} }
...@@ -2758,12 +2954,12 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2758,12 +2954,12 @@ import org.apache.commons.configuration.XMLConfiguration;
if (this.gIP[numImg].gridImageSet!=null) return this.gIP[numImg].gridImageSet.goniometerTilt; if (this.gIP[numImg].gridImageSet!=null) return this.gIP[numImg].gridImageSet.goniometerTilt;
return this.pars[numImg][index_gh]; return this.pars[numImg][index_gh];
} }
public double getGA(int numImg){ public double getGA(int numImg){
if (this.gIP[numImg].gridImageSet!=null) return this.gIP[numImg].gridImageSet.goniometerAxial; if (this.gIP[numImg].gridImageSet!=null) return this.gIP[numImg].gridImageSet.goniometerAxial;
return this.pars[numImg][index_ga]; return this.pars[numImg][index_ga];
} }
public void setParameters(double [] parameters, int numImg, boolean[] mask){ public void setParameters(double [] parameters, int numImg, boolean[] mask){
if ((numImg<0) || (numImg>=this.pars.length)) { if ((numImg<0) || (numImg>=this.pars.length)) {
String msg="There are only "+this.pars.length+" images defined, requested #"+numImg; String msg="There are only "+this.pars.length+" images defined, requested #"+numImg;
...@@ -2782,7 +2978,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2782,7 +2978,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (this.gIP[numImg].gridImageSet!=null) this.gIP[numImg].gridImageSet.updateSetFromParameterVector(parameters,mask); if (this.gIP[numImg].gridImageSet!=null) this.gIP[numImg].gridImageSet.updateSetFromParameterVector(parameters,mask);
} }
public void setIntrinsicParameters(double [] parameters, int num){ public void setIntrinsicParameters(double [] parameters, int num){
if ((num<0) || (num>=this.pars.length)) { if ((num<0) || (num>=this.pars.length)) {
String msg="There are only "+this.pars.length+" images defined, requested #"+num; String msg="There are only "+this.pars.length+" images defined, requested #"+num;
...@@ -2815,8 +3011,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2815,8 +3011,8 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<parameters.length;i++) if (isSubcameraParameter(i))this.pars[num][i]=parameters[i]; for (int i=0;i<parameters.length;i++) if (isSubcameraParameter(i))this.pars[num][i]=parameters[i];
// no need to update image sets // no need to update image sets
} }
public String getParameterName(int num){ public String getParameterName(int num){
if ((num<0) || (num>=this.parameterDescriptions.length)) { if ((num<0) || (num>=this.parameterDescriptions.length)) {
String msg="There are only "+this.parameterDescriptions.length+" parameters defined, requested #"+num; String msg="There are only "+this.parameterDescriptions.length+" parameters defined, requested #"+num;
...@@ -2824,7 +3020,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2824,7 +3020,7 @@ import org.apache.commons.configuration.XMLConfiguration;
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
return descrField(num,0); return descrField(num,0);
} }
public String getParameterDescription(int num){ public String getParameterDescription(int num){
if ((num<0) || (num>=this.parameterDescriptions.length)) { if ((num<0) || (num>=this.parameterDescriptions.length)) {
...@@ -2833,7 +3029,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2833,7 +3029,7 @@ import org.apache.commons.configuration.XMLConfiguration;
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
return descrField(num,1); return descrField(num,1);
} }
public String getParameterUnits(int num){ public String getParameterUnits(int num){
if ((num<0) || (num>=this.parameterDescriptions.length)) { if ((num<0) || (num>=this.parameterDescriptions.length)) {
...@@ -2850,7 +3046,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2850,7 +3046,7 @@ import org.apache.commons.configuration.XMLConfiguration;
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
return (descrField(num,3).equals("S")); return (descrField(num,3).equals("S"));
} }
public boolean isLocationParameter(int num){ //X,Y or Z location of the camera public boolean isLocationParameter(int num){ //X,Y or Z location of the camera
if ((num<0) || (num>=this.parameterDescriptions.length)) { if ((num<0) || (num>=this.parameterDescriptions.length)) {
...@@ -2877,7 +3073,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2877,7 +3073,7 @@ import org.apache.commons.configuration.XMLConfiguration;
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
return (descrField(num,4).equals("I")); return (descrField(num,4).equals("I"));
} }
public String getImagePath(int num) { public String getImagePath(int num) {
if ((num<0) || (num>=this.gIP.length)) { if ((num<0) || (num>=this.gIP.length)) {
...@@ -2921,7 +3117,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2921,7 +3117,7 @@ import org.apache.commons.configuration.XMLConfiguration;
return this.numSubCameras; return this.numSubCameras;
} }
/** /**
* *
* @param imgNumber number of grid image to edit parameters (location, distortion) for * @param imgNumber number of grid image to edit parameters (location, distortion) for
* @return <2 - canceled, -1 - done, els - number of the next image to edit * @return <2 - canceled, -1 - done, els - number of the next image to edit
*/ */
...@@ -2983,7 +3179,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -2983,7 +3179,7 @@ import org.apache.commons.configuration.XMLConfiguration;
for (int i=0;i<this.gIP.length;i++) if (this.gIP[i].channel>nChn) nChn=this.gIP[i].channel; for (int i=0;i<this.gIP.length;i++) if (this.gIP[i].channel>nChn) nChn=this.gIP[i].channel;
return nChn+1; return nChn+1;
} }
public double getMask(int chnNum, double px, double py){ public double getMask(int chnNum, double px, double py){
int width= eyesisCameraParameters.sensorWidth/eyesisCameraParameters.decimateMasks; int width= eyesisCameraParameters.sensorWidth/eyesisCameraParameters.decimateMasks;
int height=eyesisCameraParameters.sensorHeight/eyesisCameraParameters.decimateMasks; int height=eyesisCameraParameters.sensorHeight/eyesisCameraParameters.decimateMasks;
...@@ -3002,8 +3198,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3002,8 +3198,8 @@ import org.apache.commons.configuration.XMLConfiguration;
if ((iPX<0) || (iPY<0) || (iPX>=width) || (iPY>=height)) return 0.0; if ((iPX<0) || (iPY<0) || (iPX>=width) || (iPY>=height)) return 0.0;
return mask[iPY*width+iPX]; // null ponter return mask[iPY*width+iPX]; // null ponter
} }
public void setMaskFromImageStack(ImagePlus imp){ public void setMaskFromImageStack(ImagePlus imp){
if (imp == null){ if (imp == null){
String msg="sensors mask image is null"; String msg="sensors mask image is null";
...@@ -3018,7 +3214,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3018,7 +3214,7 @@ import org.apache.commons.configuration.XMLConfiguration;
eyesisCameraParameters.sensorWidth=Integer.parseInt((String) imp.getProperty("sensorWidth")); eyesisCameraParameters.sensorWidth=Integer.parseInt((String) imp.getProperty("sensorWidth"));
if (imp.getProperty("sensorHeight")!=null) if (imp.getProperty("sensorHeight")!=null)
eyesisCameraParameters.sensorHeight=Integer.parseInt((String) imp.getProperty("sensorHeight")); eyesisCameraParameters.sensorHeight=Integer.parseInt((String) imp.getProperty("sensorHeight"));
if (this.sensorMasks==null) { if (this.sensorMasks==null) {
this.sensorMasks=new double[getNumChannels()][]; this.sensorMasks=new double[getNumChannels()][];
for (int i=0;i<this.sensorMasks.length;i++) this.sensorMasks[i]=null; for (int i=0;i<this.sensorMasks.length;i++) this.sensorMasks[i]=null;
...@@ -3049,7 +3245,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3049,7 +3245,7 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
} }
} }
public ImagePlus saveMaskAsImageStack(String title, String path){ public ImagePlus saveMaskAsImageStack(String title, String path){
ImagePlus imp=getMaskAsImageStack(title); ImagePlus imp=getMaskAsImageStack(title);
if (imp==null) return null; if (imp==null) return null;
...@@ -3086,13 +3282,13 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3086,13 +3282,13 @@ import org.apache.commons.configuration.XMLConfiguration;
ip.setPixels(pixels[0]); ip.setPixels(pixels[0]);
imp=new ImagePlus(title, ip); imp=new ImagePlus(title, ip);
} }
// TODO: add more properties here (MAC+channel)? preserve other properties? // TODO: add more properties here (MAC+channel)? preserve other properties?
imp.setProperty("sensorWidth", ""+eyesisCameraParameters.sensorWidth); imp.setProperty("sensorWidth", ""+eyesisCameraParameters.sensorWidth);
imp.setProperty("sensorHeight", ""+eyesisCameraParameters.sensorHeight); imp.setProperty("sensorHeight", ""+eyesisCameraParameters.sensorHeight);
imp.setProperty("shrinkGridForMask", ""+eyesisCameraParameters.shrinkGridForMask); imp.setProperty("shrinkGridForMask", ""+eyesisCameraParameters.shrinkGridForMask);
imp.setProperty("maskBlurSigma", ""+eyesisCameraParameters.maskBlurSigma); imp.setProperty("maskBlurSigma", ""+eyesisCameraParameters.maskBlurSigma);
imp.setProperty("decimateMasks", ""+eyesisCameraParameters.decimateMasks); imp.setProperty("decimateMasks", ""+eyesisCameraParameters.decimateMasks);
(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp); (new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
imp.getProcessor().resetMinAndMax(); imp.getProcessor().resetMinAndMax();
return imp; return imp;
...@@ -3103,9 +3299,9 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3103,9 +3299,9 @@ import org.apache.commons.configuration.XMLConfiguration;
* @param width sensor width, pixels * @param width sensor width, pixels
* @param height sensor height, pixels * @param height sensor height, pixels
* @param shrink shrink sensor mask by this amount (sensor, non-decimated pixels) * @param shrink shrink sensor mask by this amount (sensor, non-decimated pixels)
* @param radius radial mask - zero if farther than radius, 0.5*(cos(pi*r/radius)+1.0) if less * @param radius radial mask - zero if farther than radius, 0.5*(cos(pi*r/radius)+1.0) if less
* @param minimalAlpha - zero mask below this threshold * @param minimalAlpha - zero mask below this threshold
* @return returns arrray with the same size as sensorMask that corresponds to low-vignetting areas of the sensor/lens * @return returns arrray with the same size as sensorMask that corresponds to low-vignetting areas of the sensor/lens
*/ */
public double [] nonVignettedMask( public double [] nonVignettedMask(
...@@ -3140,7 +3336,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3140,7 +3336,7 @@ import org.apache.commons.configuration.XMLConfiguration;
if (minimalAlpha>0.0) for (int i=0;i<mask.length;i++) if (mask[i]<minimalAlpha) mask[i]=0.0; if (minimalAlpha>0.0) for (int i=0;i<mask.length;i++) if (mask[i]<minimalAlpha) mask[i]=0.0;
return mask; return mask;
} }
public double [][] calculateSensorMasks() { public double [][] calculateSensorMasks() {
return calculateSensorMasks( return calculateSensorMasks(
eyesisCameraParameters.decimateMasks, eyesisCameraParameters.decimateMasks,
...@@ -3150,7 +3346,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3150,7 +3346,7 @@ import org.apache.commons.configuration.XMLConfiguration;
eyesisCameraParameters.maskBlurSigma); eyesisCameraParameters.maskBlurSigma);
} }
/** /**
* *
* @param width image width, in pixels (pixel X coordinates are between 0 and width-1, inclusive) * @param width image width, in pixels (pixel X coordinates are between 0 and width-1, inclusive)
* @param height image height, in pixels (pixel Y coordinates are between 0 and height-1, inclusive) * @param height image height, in pixels (pixel Y coordinates are between 0 and height-1, inclusive)
* @param shrinkGridForMask shrink detected grids by this number of nodes in each direction before bluring * @param shrinkGridForMask shrink detected grids by this number of nodes in each direction before bluring
...@@ -3190,8 +3386,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3190,8 +3386,8 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return this.sensorMasks; return this.sensorMasks;
} }
/** /**
* Create round mask inside the actual one, with the provided center. Blur result with the same sigma as original * Create round mask inside the actual one, with the provided center. Blur result with the same sigma as original
* @param chn sensor number * @param chn sensor number
...@@ -3217,7 +3413,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3217,7 +3413,7 @@ import org.apache.commons.configuration.XMLConfiguration;
System.out.println("iYC="+iYC); System.out.println("iYC="+iYC);
System.out.println("initial ir02="+ir02+ "("+Math.sqrt(ir02)+")"); System.out.println("initial ir02="+ir02+ "("+Math.sqrt(ir02)+")");
for (int i = 0; i < this.sensorMasks[chn].length; i++) if (this.sensorMasks[chn][i]<0.5) { for (int i = 0; i < this.sensorMasks[chn].length; i++) if (this.sensorMasks[chn][i]<0.5) {
int ix = (i % dWidth) - iXC; int ix = (i % dWidth) - iXC;
int iy = (i / dWidth) - iYC; int iy = (i / dWidth) - iYC;
int ir2=ix*ix + iy*iy; int ir2=ix*ix + iy*iy;
if (ir2 < ir02) ir02 = ir2; if (ir2 < ir02) ir02 = ir2;
...@@ -3225,7 +3421,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3225,7 +3421,7 @@ import org.apache.commons.configuration.XMLConfiguration;
System.out.println("second ir02="+ir02+ "("+Math.sqrt(ir02)+")"); System.out.println("second ir02="+ir02+ "("+Math.sqrt(ir02)+")");
double [] mask= new double[this.sensorMasks[chn].length]; double [] mask= new double[this.sensorMasks[chn].length];
for (int i = 0; i < mask.length; i++) { for (int i = 0; i < mask.length; i++) {
int ix = (i % dWidth) - iXC; int ix = (i % dWidth) - iXC;
int iy = (i / dWidth) - iYC; int iy = (i / dWidth) - iYC;
mask[i]=((ix*ix + iy*iy) > ir02)?0.0:1.0; mask[i]=((ix*ix + iy*iy) > ir02)?0.0:1.0;
} }
...@@ -3249,8 +3445,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3249,8 +3445,8 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return this.sensorMasks[chn]; return this.sensorMasks[chn];
} }
public double [] calculateImageGridMask(int imgNum) { public double [] calculateImageGridMask(int imgNum) {
return calculateImageGridMask( return calculateImageGridMask(
imgNum, imgNum,
...@@ -3275,7 +3471,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3275,7 +3471,7 @@ import org.apache.commons.configuration.XMLConfiguration;
rAverage/=rAverageNum; // average distance to the fartherst node from the current rAverage/=rAverageNum; // average distance to the fartherst node from the current
double sigma=sigmaUV; double sigma=sigmaUV;
if(sigma<0) sigma*=-rAverage; if(sigma<0) sigma*=-rAverage;
// old version, trying new - will influence all sensor masks!! // old version, trying new - will influence all sensor masks!!
// gb.blurDouble(preMask[1], dWidth, dHeight, sigma/decimate, sigma/decimate, 0.01); // gb.blurDouble(preMask[1], dWidth, dHeight, sigma/decimate, sigma/decimate, 0.01);
double [] mask0=preMask[1].clone(); double [] mask0=preMask[1].clone();
gb.blurDouble(preMask[1], dWidth, dHeight, sigma/decimate, sigma/decimate, 0.01); gb.blurDouble(preMask[1], dWidth, dHeight, sigma/decimate, sigma/decimate, 0.01);
...@@ -3285,11 +3481,11 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3285,11 +3481,11 @@ import org.apache.commons.configuration.XMLConfiguration;
} }
return preMask[1]; return preMask[1];
} }
/** /**
* *
* @param imgNum number of image to process * @param imgNum number of image to process
* @param decimate - reduce image resolution for the mask * @param decimate - reduce image resolution for the mask
* @param width - image width (actual will be divided by decimate * @param width - image width (actual will be divided by decimate
...@@ -3349,8 +3545,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3349,8 +3545,8 @@ import org.apache.commons.configuration.XMLConfiguration;
double [][] testArray=new double[3][pXY.length*pXY[0].length]; double [][] testArray=new double[3][pXY.length*pXY[0].length];
int index=0; int index=0;
for (int v=0;v<iMask.length;v++) for (int u=0;u<iMask[0].length;u++){ for (int v=0;v<iMask.length;v++) for (int u=0;u<iMask[0].length;u++){
testArray[0][index]=pXY[v][u][0]; testArray[0][index]=pXY[v][u][0];
testArray[1][index]=pXY[v][u][1]; testArray[1][index]=pXY[v][u][1];
testArray[2][index++]=iMask[v][u]; testArray[2][index++]=iMask[v][u];
} }
...@@ -3375,8 +3571,8 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3375,8 +3571,8 @@ import org.apache.commons.configuration.XMLConfiguration;
double [][] testArray1=new double[3][pXY.length*pXY[0].length]; double [][] testArray1=new double[3][pXY.length*pXY[0].length];
int index=0; int index=0;
for (int v=0;v<iMask.length;v++) for (int u=0;u<iMask[0].length;u++){ for (int v=0;v<iMask.length;v++) for (int u=0;u<iMask[0].length;u++){
testArray1[0][index]=pXY[v][u][0]; testArray1[0][index]=pXY[v][u][0];
testArray1[1][index]=pXY[v][u][1]; testArray1[1][index]=pXY[v][u][1];
testArray1[2][index++]=iMask[v][u]; testArray1[2][index++]=iMask[v][u];
} }
...@@ -3403,7 +3599,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3403,7 +3599,7 @@ import org.apache.commons.configuration.XMLConfiguration;
// calculate average radius (for bluring) // calculate average radius (for bluring)
double r=Math.sqrt(r2Max); double r=Math.sqrt(r2Max);
rAverage+=r; rAverage+=r;
rAverageNum++; rAverageNum++;
int iR= (int) Math.round(r); int iR= (int) Math.round(r);
int iX0= (int) Math.round (pXY[v][u][0]); int iX0= (int) Math.round (pXY[v][u][0]);
...@@ -3413,7 +3609,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3413,7 +3609,7 @@ import org.apache.commons.configuration.XMLConfiguration;
int yLowLim=iY0-iR; int yLowLim=iY0-iR;
int yHighLim=iY0+iR; int yHighLim=iY0+iR;
if (xLowLim<0) xLowLim=0; if (xLowLim<0) xLowLim=0;
// decimation apply below // decimation apply below
if (xHighLim>=width) xHighLim=width-1; if (xHighLim>=width) xHighLim=width-1;
if (yLowLim<0) yLowLim=0; if (yLowLim<0) yLowLim=0;
if (yHighLim>=height)yHighLim=height-1; if (yHighLim>=height)yHighLim=height-1;
...@@ -3429,5 +3625,5 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -3429,5 +3625,5 @@ import org.apache.commons.configuration.XMLConfiguration;
return result; return result;
} }
} }
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