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Commit 59172c80 authored by Andrey Filippov's avatar Andrey Filippov
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added strategy comments, strategy list

parent 5aad0ee7
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Showing with 292 additions and 141 deletions
src/main/java/Aberration_Calibration.java
View file @ 59172c80
...@@ -718,6 +718,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi ...@@ -718,6 +718,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
addButton("Edit Strategy",panelFitDistortions,color_configure); addButton("Edit Strategy",panelFitDistortions,color_configure);
addButton("Save Strategy",panelFitDistortions,color_bundle); addButton("Save Strategy",panelFitDistortions,color_bundle);
addButton("Restore Strategy",panelFitDistortions,color_restore); addButton("Restore Strategy",panelFitDistortions,color_restore);
addButton("List Strategy",panelFitDistortions,color_report);
addButton("Run LMA",panelFitDistortions,color_bundle); addButton("Run LMA",panelFitDistortions,color_bundle);
addButton("Bad Nodes",panelFitDistortions,color_bundle); addButton("Bad Nodes",panelFitDistortions,color_bundle);
addButton("Debug deriv",panelFitDistortions,color_debug); addButton("Debug deriv",panelFitDistortions,color_debug);
...@@ -2311,18 +2312,8 @@ if (MORE_BUTTONS) { ...@@ -2311,18 +2312,8 @@ if (MORE_BUTTONS) {
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("List Eyesis4pi") || label.equals("List X-cam")) { if (label.equals("List Eyesis4pi") || label.equals("List X-cam")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
System.out.println("DISTORTION_CALIBRATION_DATA="+((DISTORTION_CALIBRATION_DATA==null)?"null":" NOT null"));
System.out.println("+++++++++++ EYESIS_CAMERA_PARAMETERS.numStations="+EYESIS_CAMERA_PARAMETERS.numStations+
" +EYESIS_CAMERA_PARAMETERS.goniometerHorizontal.length="+EYESIS_CAMERA_PARAMETERS.goniometerHorizontal.length);
if (DISTORTION_CALIBRATION_DATA!=null) {
if (DEBUG_LEVEL>1) System.out.println("+++++++++++ DISTORTION_CALIBRATION_DATA.eyesisCameraParameters.numStations="+DISTORTION_CALIBRATION_DATA.eyesisCameraParameters.numStations+
" +DISTORTION_CALIBRATION_DATA.eyesisCameraParameters.goniometerHorizontal.length="+DISTORTION_CALIBRATION_DATA.eyesisCameraParameters.goniometerHorizontal.length);
}
DistortionCalibrationData dcd=(DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA: DistortionCalibrationData dcd=(DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA:
new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS); new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS);
if (DEBUG_LEVEL>1) System.out.println("+++++++++++ dcd.eyesisCameraParameters.numStations="+dcd.eyesisCameraParameters.numStations+
" +dcd.eyesisCameraParameters.goniometerHorizontal.length="+dcd.eyesisCameraParameters.goniometerHorizontal.length);
dcd.listCameraParameters(label.equals("List X-cam")); dcd.listCameraParameters(label.equals("List X-cam"));
return; return;
} }
...@@ -2486,8 +2477,7 @@ if (MORE_BUTTONS) { ...@@ -2486,8 +2477,7 @@ if (MORE_BUTTONS) {
return; return;
} }
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("Edit Strategy") || label.equals("List Strategy")) {
if (label.equals("Edit Strategy")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
if (LENS_DISTORTIONS==null) { if (LENS_DISTORTIONS==null) {
if (LENS_DISTORTION_PARAMETERS==null){ if (LENS_DISTORTION_PARAMETERS==null){
...@@ -2506,7 +2496,11 @@ if (MORE_BUTTONS) { ...@@ -2506,7 +2496,11 @@ if (MORE_BUTTONS) {
LENS_DISTORTIONS.fittingStrategy=new FittingStrategy(DISTORTION_CALIBRATION_DATA); LENS_DISTORTIONS.fittingStrategy=new FittingStrategy(DISTORTION_CALIBRATION_DATA);
} }
LENS_DISTORTIONS.fittingStrategy.debugLevel=DEBUG_LEVEL; LENS_DISTORTIONS.fittingStrategy.debugLevel=DEBUG_LEVEL;
LENS_DISTORTIONS.fittingStrategy.selectStrategy(LENS_DISTORTIONS.seriesNumber); if (label.equals("Edit Strategy")) {
LENS_DISTORTIONS.fittingStrategy.selectStrategy(LENS_DISTORTIONS.seriesNumber);
} else {
LENS_DISTORTIONS.fittingStrategy.listStrategies();
}
return; return;
} }
/* ======================================================================== */ /* ======================================================================== */
...@@ -2558,6 +2552,7 @@ if (MORE_BUTTONS) { ...@@ -2558,6 +2552,7 @@ if (MORE_BUTTONS) {
return; return;
} }
/* ======================================================================== */ /* ======================================================================== */
if (label.equals("Run LMA")) { if (label.equals("Run LMA")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL; DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
src/main/java/FittingStrategy.java
View file @ 59172c80
...@@ -5,7 +5,7 @@ ...@@ -5,7 +5,7 @@
** Copyright (C) 2011-2014 Elphel, Inc. ** Copyright (C) 2011-2014 Elphel, Inc.
** **
** -----------------------------------------------------------------------------** ** -----------------------------------------------------------------------------**
** **
** FittingStrategy.java is free software: you can redistribute it and/or modify ** FittingStrategy.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
...@@ -21,10 +21,6 @@ ...@@ -21,10 +21,6 @@
** -----------------------------------------------------------------------------** ** -----------------------------------------------------------------------------**
** **
*/ */
import ij.IJ;
import ij.gui.GenericDialog;
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;
...@@ -40,10 +36,14 @@ import java.util.Set; ...@@ -40,10 +36,14 @@ import java.util.Set;
import org.apache.commons.configuration.ConfigurationException; import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLConfiguration; import org.apache.commons.configuration.XMLConfiguration;
import ij.IJ;
import ij.gui.GenericDialog;
import ij.text.TextWindow;
/** /**
* *
* Specifies images to process and parameters to adjust * Specifies images to process and parameters to adjust
* Each parameter cab be: * Each parameter cab be:
* 0 - "fixed" - use individual, per-image parameters, do not modify them * 0 - "fixed" - use individual, per-image parameters, do not modify them
...@@ -57,7 +57,7 @@ import org.apache.commons.configuration.XMLConfiguration; ...@@ -57,7 +57,7 @@ import org.apache.commons.configuration.XMLConfiguration;
* 6 - "per-station" save to all (super) * 6 - "per-station" save to all (super)
* 7 - "weak common" - like common, but enable small individual variations (for a price) - not yet implemented, will have separate weight fixed/floating * 7 - "weak common" - like common, but enable small individual variations (for a price) - not yet implemented, will have separate weight fixed/floating
* 8 - "weak station" - like per-station, but enable individual (for a price) * 8 - "weak station" - like per-station, but enable individual (for a price)
* *
+====================+===========+===========+ +====================+===========+===========+
| | Same TS | Diff TS | | | Same TS | Diff TS |
| +-----+-----+-----+-----+ | +-----+-----+-----+-----+
...@@ -121,7 +121,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -121,7 +121,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
public int [][] parameterMode=null; // per series, per-parameter public int [][] parameterMode=null; // per series, per-parameter
public int [][][] parameterGroups=null; // per series, per-parameter - null or array of group numbers (1 element per image) public int [][][] parameterGroups=null; // per series, per-parameter - null or array of group numbers (1 element per image)
public int [][] zGroups=null; public int [][] zGroups=null;
public boolean saveUnusedGroups=false; // purge groups for parameters when saving to XML, preserve if true public boolean saveUnusedGroups=false; // purge groups for parameters when saving to XML, preserve if true
public double [] lambdas=null; // LMA initial lambda for each step public double [] lambdas=null; // LMA initial lambda for each step
public double defaultLambda=0.001; public double defaultLambda=0.001;
public int [][] parameterList=null; // list of all parameters in the system, each has subcamera number and parameters index public int [][] parameterList=null; // list of all parameters in the system, each has subcamera number and parameters index
...@@ -141,21 +141,21 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -141,21 +141,21 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
"same weight", "same weight",
"variable weight", "variable weight",
}; };
// next arrays will be initialized at buildVariancesMaps only if at least some parameters use variances, otherwise they will be null // next arrays will be initialized at buildVariancesMaps only if at least some parameters use variances, otherwise they will be null
public double [] variationsAverages=null; // holds per extrinsic parameter or per parameter/per station average values public double [] variationsAverages=null; // holds per extrinsic parameter or per parameter/per station average values
public int [] averageCellIndex= null; // for each element in the parameters vector holds index in variationsAverages array public int [] averageCellIndex= null; // for each element in the parameters vector holds index in variationsAverages array
public double [] weightOnAverage= null; // how variation of this parameter influences average (for all or for currenrt station public double [] weightOnAverage= null; // how variation of this parameter influences average (for all or for currenrt station
public double [] weightVariance= null; // weight for LMA over variance of parameters from average public double [] weightVariance= null; // weight for LMA over variance of parameters from average
public double [] varianceErrorsSquared= null; // weighted squared errors public double [] varianceErrorsSquared= null; // weighted squared errors
public String [] strategyComment = null;
public FittingStrategy( public FittingStrategy(
DistortionCalibrationData distortionCalibrationData// per-image parameters DistortionCalibrationData distortionCalibrationData// per-image parameters
) { ) {
this.distortionCalibrationData=distortionCalibrationData; this.distortionCalibrationData=distortionCalibrationData;
setDflt(0); setDflt(0);
} }
public FittingStrategy( public FittingStrategy(
DistortionCalibrationData distortionCalibrationData,// per-image parameters DistortionCalibrationData distortionCalibrationData,// per-image parameters
...@@ -164,10 +164,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -164,10 +164,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.distortionCalibrationData=distortionCalibrationData; this.distortionCalibrationData=distortionCalibrationData;
this.selectedImages=new boolean[numSeries][this.distortionCalibrationData.getNumImages()]; this.selectedImages=new boolean[numSeries][this.distortionCalibrationData.getNumImages()];
this.selectedValidImages=new boolean[numSeries][this.distortionCalibrationData.getNumImages()]; this.selectedValidImages=new boolean[numSeries][this.distortionCalibrationData.getNumImages()];
setDflt(numSeries); setDflt(numSeries);
} }
public FittingStrategy( public FittingStrategy(
boolean smart, boolean smart,
String defaultPath, String defaultPath,
...@@ -188,8 +188,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -188,8 +188,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
pathname); pathname);
System.out.println("Restored fitting strategy from "+pathname); System.out.println("Restored fitting strategy from "+pathname);
} }
/** /**
* Reads FittingStrategy from an XML file * Reads FittingStrategy from an XML file
* @param distortionCalibrationData should be defined before this class! * @param distortionCalibrationData should be defined before this class!
...@@ -243,8 +243,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -243,8 +243,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.parameterGroups=new int[nSer][len][]; this.parameterGroups=new int[nSer][len][];
this.lambdas=new double [nSer]; this.lambdas=new double [nSer];
this.stepDone=new double [nSer]; this.stepDone=new double [nSer];
this.strategyComment=new String[nSer];
for (int i=0;i<nSer;i++){ // iterate through series for (int i=0;i<nSer;i++){ // iterate through series
//this.stopAfterThis //this.stopAfterThis
// read selected images (no check here that it matches to the distortionCalibrationData! // read selected images (no check here that it matches to the distortionCalibrationData!
String sSeries="series.series_"+i; String sSeries="series.series_"+i;
String fs=hConfig.getString(sSeries+".selectedImages"); String fs=hConfig.getString(sSeries+".selectedImages");
...@@ -257,7 +258,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -257,7 +258,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} else { } else {
this.varianceModes[i]=varianceModeDisabled; this.varianceModes[i]=varianceModeDisabled;
} }
for (int j=0;j<this.parameterList.length;j++){ for (int j=0;j<this.parameterList.length;j++){
int nPar=this.parameterList[j][1]; int nPar=this.parameterList[j][1];
int nSub=this.parameterList[j][0]; int nSub=this.parameterList[j][0];
...@@ -299,26 +300,32 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -299,26 +300,32 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} else { } else {
this.zGroups[i]=null; this.zGroups[i]=null;
} }
if (hConfig.getString(sSeries+".strategyComment")!=null) {
this.strategyComment[i]=hConfig.getString(sSeries+".strategyComment");
}
} }
// if (hConfig.getString("variances")!=null){ // if (hConfig.getString("variances")!=null){
// if (!hConfig.configurationAt("variances").isEmpty()){ // if (!hConfig.configurationAt("variances").isEmpty()){
if (hConfig.configurationsAt("variances").size()>0){ if (hConfig.configurationsAt("variances").size()>0){
// System.out.println("hConfig.configurationAt(\"variances\").isEmpty()=false"); // System.out.println("hConfig.configurationAt(\"variances\").isEmpty()=false");
this.distortionCalibrationData.eyesisCameraParameters.getCostsPropertiesXML("variances.",hConfig); this.distortionCalibrationData.eyesisCameraParameters.getCostsPropertiesXML("variances.",hConfig);
} }
this.pathName=pathname; this.pathName=pathname;
// distortionCalibrationData.readAllGrids(); // distortionCalibrationData.readAllGrids();
} }
/** /**
* Adjust selectedImages and parameterGroups after number of images may change, old number of images should be >0 * Adjust selectedImages and parameterGroups after number of images may change, old number of images should be >0
* If the new number is larger, the first images attributes will be copied, the extra ones - use those of the last of the old ones * If the new number is larger, the first images attributes will be copied, the extra ones - use those of the last of the old ones
* @param newNumberOfImages new number of images used by this series * @param newNumberOfImages new number of images used by this series
*/ */
public void adjustNumberOfImages(int newNumberOfImages){ public void adjustNumberOfImages(int newNumberOfImages){
if ((this.selectedImages == null) ||(this.selectedImages[0].length==0)) { if ((this.selectedImages == null) ||(this.selectedImages[0].length==0)) {
String msg="selectedImages array is "+((this.selectedImages == null)?"null":"empty"); String msg="selectedImages array is "+((this.selectedImages == null)?"null":"empty");
IJ.showMessage("Error",msg); IJ.showMessage("Error",msg);
throw new IllegalArgumentException (msg); throw new IllegalArgumentException (msg);
} }
if (this.selectedImages[0].length==newNumberOfImages) return; if (this.selectedImages[0].length==newNumberOfImages) return;
...@@ -334,10 +341,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -334,10 +341,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
for (int i=0;i<newNumberOfImages;i++) this.parameterGroups[nSer][nPar][i]=(i<tmpGroup.length)?tmpGroup[i]:tmpGroup[tmpGroup.length-1]; for (int i=0;i<newNumberOfImages;i++) this.parameterGroups[nSer][nPar][i]=(i<tmpGroup.length)?tmpGroup[i]:tmpGroup[tmpGroup.length-1];
} }
} }
} }
} }
public String selectAndSaveToXML( public String selectAndSaveToXML(
boolean smart, boolean smart,
String defaultPath){ String defaultPath){
...@@ -357,7 +364,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -357,7 +364,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
return pathname; return pathname;
} }
//http://commons.apache.org/configuration/userguide/howto_xml.html //http://commons.apache.org/configuration/userguide/howto_xml.html
public boolean saveToXML(String pathname) { public boolean saveToXML(String pathname) {
if (pathname==null) return false; if (pathname==null) return false;
XMLConfiguration hConfig=new XMLConfiguration(); XMLConfiguration hConfig=new XMLConfiguration();
...@@ -371,10 +378,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -371,10 +378,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
hConfig.addProperty("parameterMap.par_"+i+".index",this.parameterList[i][1]); hConfig.addProperty("parameterMap.par_"+i+".index",this.parameterList[i][1]);
hConfig.addProperty("parameterMap.par_"+i+".visible",this.parameterEnable[i]?"1":"0"); hConfig.addProperty("parameterMap.par_"+i+".visible",this.parameterEnable[i]?"1":"0");
} }
hConfig.addProperty("series",""); hConfig.addProperty("series","");
hConfig.addProperty("series.number",this.selectedImages.length); hConfig.addProperty("series.number",this.selectedImages.length);
for (int i=0;i<this.selectedImages.length;i++){ // iterate through series for (int i=0;i<this.selectedImages.length;i++){ // iterate through series
String sSeries="series.series_"+i; String sSeries="series.series_"+i;
hConfig.addProperty(sSeries,""); hConfig.addProperty(sSeries,"");
...@@ -410,6 +417,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -410,6 +417,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
hConfig.addProperty(sSeries+".lambdas",lambdas[i]); hConfig.addProperty(sSeries+".lambdas",lambdas[i]);
hConfig.addProperty(sSeries+".stepDone",stepDone[i]); hConfig.addProperty(sSeries+".stepDone",stepDone[i]);
hConfig.addProperty(sSeries+".stopAfterThis",this.stopAfterThis[i]); hConfig.addProperty(sSeries+".stopAfterThis",this.stopAfterThis[i]);
hConfig.addProperty(sSeries+".strategyComment",this.strategyComment[i]);
} }
hConfig.addProperty("variances",""); hConfig.addProperty("variances","");
this.distortionCalibrationData.eyesisCameraParameters.setCostsPropertiesXML("variances.",hConfig); this.distortionCalibrationData.eyesisCameraParameters.setCostsPropertiesXML("variances.",hConfig);
...@@ -448,20 +456,21 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -448,20 +456,21 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.stopAfterThis[numSeries]=this.stopAfterThis[sourceSeries]; this.stopAfterThis[numSeries]=this.stopAfterThis[sourceSeries];
this.varianceModes[numSeries]=this.varianceModes[sourceSeries]; this.varianceModes[numSeries]=this.varianceModes[sourceSeries];
this.zGroups[numSeries]=(this.zGroups[sourceSeries]!=null)?this.zGroups[sourceSeries].clone():null; this.zGroups[numSeries]=(this.zGroups[sourceSeries]!=null)?this.zGroups[sourceSeries].clone():null;
this.strategyComment[numSeries] = this.strategyComment[sourceSeries]+" (copy)";
return true; return true;
} else { } else {
return false; return false;
} }
} }
/** /**
* Verifies that series exists and is not empty (valid for LMA) * Verifies that series exists and is not empty (valid for LMA)
* @param num - series to verify * @param num - series to verify
* @return true if series is valid * @return true if series is valid
*/ */
public boolean isSeriesValid(int num){ public boolean isSeriesValidVerbose(int num){
if ((num<0) || (num>=this.selectedImages.length)) return false; if ((num<0) || (num>=this.selectedImages.length)) return false;
boolean someImagesSelected=false; boolean someImagesSelected=false;
for (int i=0;i<this.selectedImages[num].length;i++) if (this.selectedImages[num][i]){ for (int i=0;i<this.selectedImages[num].length;i++) if (this.selectedImages[num][i]){
...@@ -483,6 +492,27 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -483,6 +492,27 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
return true; return true;
} }
public boolean isSeriesValid(int num){
if ((num<0) || (num>=this.selectedImages.length)) return false;
boolean someImagesSelected=false;
for (int i=0;i<this.selectedImages[num].length;i++) if (this.selectedImages[num][i]){
someImagesSelected=true;
break;
}
if (!someImagesSelected) {
return false;
}
boolean someParametersSelected=false;
for (int i=0;i<this.parameterMode[num].length;i++) if (this.parameterMode[num][i]>0){
someParametersSelected=true;
break;
}
if (!someParametersSelected) {
return false;
}
return true;
}
/** /**
* Determins if LMA should stop after this series (either flag is set or next is invalid) * Determins if LMA should stop after this series (either flag is set or next is invalid)
* @param num number of series to test * @param num number of series to test
...@@ -495,7 +525,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -495,7 +525,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
/** /**
* *
* Specifies images to process and parameters to adjust * Specifies images to process and parameters to adjust
* Each parameter cab be: * Each parameter cab be:
* 0 - "fixed" - use individual, per-image parameters, do not modify them * 0 - "fixed" - use individual, per-image parameters, do not modify them
...@@ -521,7 +551,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -521,7 +551,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
* *
*/ */
// public int [][] reverseParameterMap=null; // reversed map - for each [imageNumber][parameterNumber] -> vector index (-1 fixed)\ // public int [][] reverseParameterMap=null; // reversed map - for each [imageNumber][parameterNumber] -> vector index (-1 fixed)\
// selects all enabled images in the specified series (modifies strategy series!) // selects all enabled images in the specified series (modifies strategy series!)
/** /**
...@@ -577,7 +607,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -577,7 +607,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
public void invalidateSelectedImage(int ser,int nImg){ public void invalidateSelectedImage(int ser,int nImg){
this.selectedValidImages[ser][nImg]=false; this.selectedValidImages[ser][nImg]=false;
} }
//this.selectedValidImages //this.selectedValidImages
public boolean [] selectedImages(int ser) { public boolean [] selectedImages(int ser) {
return selectedImages(ser,false); return selectedImages(ser,false);
...@@ -603,11 +633,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -603,11 +633,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
public int getNumSeries(){ public int getNumSeries(){
return this.selectedImages.length; return this.selectedImages.length;
} }
/** /**
* Creates map from the parameter vector index to the {grid image number, parameter number} * Creates map from the parameter vector index to the {grid image number, parameter number}
* When the parameter is shared by several images, the map points to the one which value will be used * When the parameter is shared by several images, the map points to the one which value will be used
* (they might be different). Timestamp of the masterImages[] is used to determine which image to use. * (they might be different). Timestamp of the masterImages[] is used to determine which image to use.
* Simultaneously creates this.reverseParameterMap that maps each of the image/parameter to the parameter vector * Simultaneously creates this.reverseParameterMap that maps each of the image/parameter to the parameter vector
* Needs to be run for each new strategy series * Needs to be run for each new strategy series
* @param numSeries number of fitting strategy series * @param numSeries number of fitting strategy series
...@@ -621,14 +651,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -621,14 +651,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.reverseParameterMap=new int [numImg][numPars]; this.reverseParameterMap=new int [numImg][numPars];
// boolean [] selectedEnabledImagesAll=selectedImages(numSeries,true); // strictly as in series, including no valid points ones // boolean [] selectedEnabledImagesAll=selectedImages(numSeries,true); // strictly as in series, including no valid points ones
boolean [] selectedEnabledImages=selectedImages(numSeries); boolean [] selectedEnabledImages=selectedImages(numSeries);
// set defaults - -1 - "fixed", use individual parameter from this image // set defaults - -1 - "fixed", use individual parameter from this image
for (int i=0;i<numImg;i++) for (int j=0;j<numPars;j++) this.reverseParameterMap[i][j]=-1; for (int i=0;i<numImg;i++) for (int j=0;j<numPars;j++) this.reverseParameterMap[i][j]=-1;
int vectorIndex=0; int vectorIndex=0;
// int [][] tmpMap=new int[numTPars][3]; // temporary array parameterMap[][] (will be truncated) // int [][] tmpMap=new int[numTPars][3]; // temporary array parameterMap[][] (will be truncated)
int [][] tmpMap=new int[numPars*numImg][3]; // temporary array parameterMap[][] (will be truncated) int [][] tmpMap=new int[numPars*numImg][3]; // temporary array parameterMap[][] (will be truncated)
double masterTS=this.distortionCalibrationData.getImageTimestamp(this.masterImages[numSeries]); // timestamp of the master image double masterTS=this.distortionCalibrationData.getImageTimestamp(this.masterImages[numSeries]); // timestamp of the master image
int [] masterVectorIndices = new int [numTPars]; int [] masterVectorIndices = new int [numTPars];
// iterate through all global/subcamera parameters // iterate through all global/subcamera parameters
for (int numTPar=0;numTPar<numTPars;numTPar++) if (this.parameterMode[numSeries][numTPar]!=this.modeFixed){ // skip "fixed" for (int numTPar=0;numTPar<numTPars;numTPar++) if (this.parameterMode[numSeries][numTPar]!=this.modeFixed){ // skip "fixed"
boolean isCommon= boolean isCommon=
(this.parameterMode[numSeries][numTPar]==this.modeCommon) || (this.parameterMode[numSeries][numTPar]==this.modeCommon) ||
...@@ -657,7 +687,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -657,7 +687,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
vectorIndexMaster = masterVectorIndices[numTParMaster]; // use as vectorIndex for slaves vectorIndexMaster = masterVectorIndices[numTParMaster]; // use as vectorIndex for slaves
} }
if (this.debugLevel>2) System.out.println("numTPar="+numTPar+" numSub="+numSub+" numPar="+numPar+" numTParMaster="+numTParMaster); if (this.debugLevel>2) System.out.println("numTPar="+numTPar+" numSub="+numSub+" numPar="+numPar+" numTParMaster="+numTParMaster);
// iterate through available images // iterate through available images
for (int numThisImg=0;numThisImg<numImg;numThisImg++) { for (int numThisImg=0;numThisImg<numImg;numThisImg++) {
...@@ -670,20 +700,20 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -670,20 +700,20 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
// is it "same as" ? // is it "same as" ?
if (vectorIndexMaster >= 0){ if (vectorIndexMaster >= 0){
this.reverseParameterMap[numThisImg][numPar] = vectorIndexMaster; this.reverseParameterMap[numThisImg][numPar] = vectorIndexMaster;
// does not look for same parameter in later images - leave it for the master? // does not look for same parameter in later images - leave it for the master?
} else { } else {
// assign it a new parameter // assign it a new parameter
this.reverseParameterMap[numThisImg][numPar]=vectorIndex; this.reverseParameterMap[numThisImg][numPar]=vectorIndex;
masterVectorIndices[numTPar] = vectorIndex; masterVectorIndices[numTPar] = vectorIndex;
double thisTS=this.distortionCalibrationData.getImageTimestamp(numThisImg); double thisTS=this.distortionCalibrationData.getImageTimestamp(numThisImg);
int thisStation=this.distortionCalibrationData.gIP[numThisImg].getStationNumber(); int thisStation=this.distortionCalibrationData.gIP[numThisImg].getStationNumber();
// set pointer to this first image // set pointer to this first image
tmpMap[vectorIndex][0]=numThisImg; // vectorindex==22 > tmpMap.length? tmpMap[vectorIndex][0]=numThisImg; // vectorindex==22 > tmpMap.length?
tmpMap[vectorIndex][1]=numPar; tmpMap[vectorIndex][1]=numPar;
tmpMap[vectorIndex][2]=this.parameterMode[numSeries][numTPar]; tmpMap[vectorIndex][2]=this.parameterMode[numSeries][numTPar];
double minDist=Math.abs(this.distortionCalibrationData.getImageTimestamp(numThisImg)-masterTS); double minDist=Math.abs(this.distortionCalibrationData.getImageTimestamp(numThisImg)-masterTS);
if (this.debugLevel>2) System.out.println("vectorIndex="+vectorIndex+" numThisImg="+numThisImg); if (this.debugLevel>2) System.out.println("vectorIndex="+vectorIndex+" numThisImg="+numThisImg);
// see if same parameter in some other (later) image(s) is shared // see if same parameter in some other (later) image(s) is shared
for (int numOtherImg=numThisImg + 1; numOtherImg < numImg; numOtherImg++) for (int numOtherImg=numThisImg + 1; numOtherImg < numImg; numOtherImg++)
if ((selectedEnabledImages[numOtherImg]) && // OOB 1 if ((selectedEnabledImages[numOtherImg]) && // OOB 1
(!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numOtherImg))) && (!isSubCamera || (numSub==this.distortionCalibrationData.getImageSubcamera(numOtherImg))) &&
...@@ -693,7 +723,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -693,7 +723,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
isCommon || isCommon ||
(isGroup && (this.parameterGroups[numSeries][numTPar][numThisImg]== (isGroup && (this.parameterGroups[numSeries][numTPar][numThisImg]==
this.parameterGroups[numSeries][numTPar][numOtherImg]))){ this.parameterGroups[numSeries][numTPar][numOtherImg]))){
// assign it a the same parameter // assign it a the same parameter
this.reverseParameterMap[numOtherImg][numPar]=vectorIndex; this.reverseParameterMap[numOtherImg][numPar]=vectorIndex;
double thisDist=Math.abs(this.distortionCalibrationData.getImageTimestamp(numThisImg)-masterTS); double thisDist=Math.abs(this.distortionCalibrationData.getImageTimestamp(numThisImg)-masterTS);
if (thisDist<minDist) { if (thisDist<minDist) {
...@@ -706,17 +736,17 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -706,17 +736,17 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
} }
} }
} }
// reverseParameterMap built, vectorIndex equals to the total number of parameters needed for fitting // reverseParameterMap built, vectorIndex equals to the total number of parameters needed for fitting
//truncate tmpMap into this.parameterMap[][] //truncate tmpMap into this.parameterMap[][]
this.parameterMap=new int[vectorIndex][]; this.parameterMap=new int[vectorIndex][];
for (int i=0;i<vectorIndex;i++) this.parameterMap[i] =tmpMap[i]; for (int i=0;i<vectorIndex;i++) this.parameterMap[i] =tmpMap[i];
this.currentSeriesNumber=numSeries; this.currentSeriesNumber=numSeries;
if (this.debugLevel>2) System.out.println("this.parameterMap.length="+this.parameterMap.length); if (this.debugLevel>2) System.out.println("this.parameterMap.length="+this.parameterMap.length);
return this.parameterMap.length; return this.parameterMap.length;
} }
/** /**
* Prepare data for calculating additional LMA terms for parameter variances * Prepare data for calculating additional LMA terms for parameter variances
* @param numSeries fitting series to use * @param numSeries fitting series to use
...@@ -764,10 +794,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -764,10 +794,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
continue; continue;
} }
int tiltMotor=this.distortionCalibrationData.gIS[setNumber].motors[tiltMotorIndex];// null pointer for triclops after adding variances for tilt int tiltMotor=this.distortionCalibrationData.gIS[setNumber].motors[tiltMotorIndex];// null pointer for triclops after adding variances for tilt
iStationTilt=station+numStations*tiltMotor; iStationTilt=station+numStations*tiltMotor;
if (!tiltList.contains(iStationTilt)) tiltList.add(iStationTilt); if (!tiltList.contains(iStationTilt)) tiltList.add(iStationTilt);
} }
...@@ -859,7 +889,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -859,7 +889,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
System.out.println("buildVariancesMaps() numStationTilts="+numStationTilts+" numSeriesPars="+numSeriesPars+ " useSetWeights="+useSetWeights+ System.out.println("buildVariancesMaps() numStationTilts="+numStationTilts+" numSeriesPars="+numSeriesPars+ " useSetWeights="+useSetWeights+
" number of averages="+startIndex); " number of averages="+startIndex);
} }
this.variationsAverages=new double [startIndex]; // total number of different averages this.variationsAverages=new double [startIndex]; // total number of different averages
int [] numContributors=new int [startIndex]; int [] numContributors=new int [startIndex];
for (int i=0;i<this.variationsAverages.length;i++) { for (int i=0;i<this.variationsAverages.length;i++) {
...@@ -1011,15 +1041,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1011,15 +1041,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
public double [] getVarianceError2(){ return (this.averageCellIndex==null)?null:this.varianceErrorsSquared;} public double [] getVarianceError2(){ return (this.averageCellIndex==null)?null:this.varianceErrorsSquared;}
public double [] getWeights(){ return (this.averageCellIndex==null)?null:this.weightVariance;} public double [] getWeights(){ return (this.averageCellIndex==null)?null:this.weightVariance;}
/** /**
* *
* @return number of the current fitting strategy series * @return number of the current fitting strategy series
*/ */
public int getCurrentSeries(){ public int getCurrentSeries(){
return this.currentSeriesNumber; return this.currentSeriesNumber;
} }
/** /**
* Calculate vector of the parameters used in LMA algorithm, extracted from the * Calculate vector of the parameters used in LMA algorithm, extracted from the
* individual data, using parameter map (calculated once after changing series) * individual data, using parameter map (calculated once after changing series)
...@@ -1038,9 +1068,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1038,9 +1068,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
return vector; return vector;
} }
/** /**
* Saves data from the parameter vector to that of the images * Saves data from the parameter vector to that of the images
* @param vector vector of parameters (after LMA fitting) * @param vector vector of parameters (after LMA fitting)
*/ */
// TODO: Update the temporarily disabled images also, when possible (modify buildParameterMap also? // TODO: Update the temporarily disabled images also, when possible (modify buildParameterMap also?
...@@ -1056,7 +1086,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1056,7 +1086,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
for (int nPar=0;nPar<this.reverseParameterMap[numImg].length;nPar++) if (this.reverseParameterMap[numImg][nPar]>=0){ for (int nPar=0;nPar<this.reverseParameterMap[numImg].length;nPar++) if (this.reverseParameterMap[numImg][nPar]>=0){
// this.distortionCalibrationData.pars[numImg][nPar]=vector[this.reverseParameterMap[numImg][nPar]]; // this.distortionCalibrationData.pars[numImg][nPar]=vector[this.reverseParameterMap[numImg][nPar]];
this.distortionCalibrationData.setParameterValue(numImg,nPar,vector[this.reverseParameterMap[numImg][nPar]],true); this.distortionCalibrationData.setParameterValue(numImg,nPar,vector[this.reverseParameterMap[numImg][nPar]],true);
if (this.debugLevel>2){ if (this.debugLevel>2){
System.out.println(" Updated image "+numImg+" "+distortionCalibrationData.getParameterName(nPar)+" = "+ System.out.println(" Updated image "+numImg+" "+distortionCalibrationData.getParameterName(nPar)+" = "+
// this.distortionCalibrationData.pars[numImg][nPar]) ; //vector[this.reverseParameterMap[numImg][nPar]]); // this.distortionCalibrationData.pars[numImg][nPar]) ; //vector[this.reverseParameterMap[numImg][nPar]]);
...@@ -1094,7 +1124,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1094,7 +1124,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
} }
} }
/** /**
* Calculates current values of all parameters for the particular sensor - some ("fixed") * Calculates current values of all parameters for the particular sensor - some ("fixed")
* are taken from the data stored for this individual image, others - from the parameter * are taken from the data stored for this individual image, others - from the parameter
...@@ -1118,7 +1148,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1118,7 +1148,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
* Calculates which of all parameters for the particular sensor are to be adjusted (to reduce calcualtions) * Calculates which of all parameters for the particular sensor are to be adjusted (to reduce calcualtions)
* @param numImg number of image * @param numImg number of image
* @param vector parameters vector * @param vector parameters vector
* @return mask vector to be used with the results of getImageParametersVector() * @return mask vector to be used with the results of getImageParametersVector()
*/ */
public boolean [] getImageParametersVectorMask (int numImg){ public boolean [] getImageParametersVectorMask (int numImg){
if ((this.reverseParameterMap==null) || (this.reverseParameterMap[numImg]==null)) return null; if ((this.reverseParameterMap==null) || (this.reverseParameterMap[numImg]==null)) return null;
...@@ -1133,7 +1163,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1133,7 +1163,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
* Calculates index in the parameter vector corresponding to each image parameter vector element * Calculates index in the parameter vector corresponding to each image parameter vector element
* @param numImg number of image * @param numImg number of image
* @param vector parameters vector * @param vector parameters vector
* @return mask vector to be used with the results of getImageParametersVector() * @return mask vector to be used with the results of getImageParametersVector()
*/ */
public int [] getImageParametersVectorReverseMap (int numImg){ public int [] getImageParametersVectorReverseMap (int numImg){
if ((this.reverseParameterMap==null) || (this.reverseParameterMap[numImg]==null)) return null; if ((this.reverseParameterMap==null) || (this.reverseParameterMap[numImg]==null)) return null;
...@@ -1185,7 +1215,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1185,7 +1215,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
sb.append("\t"+this.distortionCalibrationData.getImageSubcamera(i)); sb.append("\t"+this.distortionCalibrationData.getImageSubcamera(i));
} }
sb.append("\n"); sb.append("\n");
for (int k=0;k<this.reverseParameterMap[0].length;k++){ for (int k=0;k<this.reverseParameterMap[0].length;k++){
// boolean isSubCamera=this.distortionCalibrationData.isSubcameraParameter(k); // boolean isSubCamera=this.distortionCalibrationData.isSubcameraParameter(k);
// sb.append(this.distortionCalibrationData.getParameterName(this.parameterMap[k][1])); // name of parameter // sb.append(this.distortionCalibrationData.getParameterName(this.parameterMap[k][1])); // name of parameter
...@@ -1193,14 +1223,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1193,14 +1223,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
for (int i=0; i<this.reverseParameterMap.length;i++) if (selectedEnabledImages[i]){ for (int i=0; i<this.reverseParameterMap.length;i++) if (selectedEnabledImages[i]){
int mode =this.reverseParameterMap[i][k]; int mode =this.reverseParameterMap[i][k];
sb.append("\t"+((mode>=0)?mode:"-")); sb.append("\t"+((mode>=0)?mode:"-"));
} }
sb.append("\n"); sb.append("\n");
} }
new TextWindow(title, header, sb.toString(), 800,600); new TextWindow(title, header, sb.toString(), 800,600);
} }
/** /**
* Add/reduce number of series in this fitting strategy * Add/reduce number of series in this fitting strategy
* @param numSeries new number of series * @param numSeries new number of series
...@@ -1221,6 +1251,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1221,6 +1251,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
int [] oldMasterImages=null; int [] oldMasterImages=null;
double [] oldStepDone=null; double [] oldStepDone=null;
boolean [] oldStopAfterThis=null; boolean [] oldStopAfterThis=null;
String [] oldStrategyComment=null;
int oldNumSeries=(this.selectedImages==null)?0:this.selectedImages.length; int oldNumSeries=(this.selectedImages==null)?0:this.selectedImages.length;
int oldLength=0; int oldLength=0;
if (this.selectedImages!=null){ if (this.selectedImages!=null){
...@@ -1229,6 +1260,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1229,6 +1260,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
oldParameterMode=new int[oldNumSeries][]; oldParameterMode=new int[oldNumSeries][];
oldParameterGroups=new int[oldNumSeries][][]; oldParameterGroups=new int[oldNumSeries][][];
oldZGroups=new int[oldNumSeries][]; oldZGroups=new int[oldNumSeries][];
oldStrategyComment = new String [oldNumSeries];
for (int i=0;i<oldNumSeries;i++){ for (int i=0;i<oldNumSeries;i++){
oldSelectedImages[i]=this.selectedImages[i].clone(); oldSelectedImages[i]=this.selectedImages[i].clone();
oldParameterMode[i]= this.parameterMode[i].clone(); // out of bound - 2 oldParameterMode[i]= this.parameterMode[i].clone(); // out of bound - 2
...@@ -1237,6 +1269,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1237,6 +1269,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
oldParameterGroups[i][j]=(parameterGroups[i][j]==null)?null:parameterGroups[i][j].clone(); oldParameterGroups[i][j]=(parameterGroups[i][j]==null)?null:parameterGroups[i][j].clone();
if (this.zGroups[i]!=null) oldZGroups[i]=this.zGroups[i].clone(); if (this.zGroups[i]!=null) oldZGroups[i]=this.zGroups[i].clone();
else this.zGroups[i]=oldZGroups[i]; else this.zGroups[i]=oldZGroups[i];
oldStrategyComment[i]=this.strategyComment[i];
} }
oldVarianceModes=(this.varianceModes==null)?null:this.varianceModes.clone(); oldVarianceModes=(this.varianceModes==null)?null:this.varianceModes.clone();
oldLambdas=this.lambdas.clone(); oldLambdas=this.lambdas.clone();
...@@ -1256,9 +1289,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1256,9 +1289,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.stopAfterThis[i]=oldStopAfterThis[i]; this.stopAfterThis[i]=oldStopAfterThis[i];
this.varianceModes[i]=oldVarianceModes[i]; this.varianceModes[i]=oldVarianceModes[i];
this.zGroups[i]=(oldZGroups[i]!=null)?oldZGroups[i].clone():null; this.zGroups[i]=(oldZGroups[i]!=null)?oldZGroups[i].clone():null;
this.strategyComment[i] = oldStrategyComment[i];
} }
} }
public void updateNumberOfSubcameras(){ // can break "same as"? public void updateNumberOfSubcameras(){ // can break "same as"?
int numPars= this.distortionCalibrationData.getNumParameters(); int numPars= this.distortionCalibrationData.getNumParameters();
int numSubCams=this.distortionCalibrationData.getNumSubCameras(); int numSubCams=this.distortionCalibrationData.getNumSubCameras();
...@@ -1275,7 +1309,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1275,7 +1309,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
for (int i=0;i<numSubPars;i++)subParIndex[i]=(oldTotalPars-numSubPars)+i; for (int i=0;i<numSubPars;i++)subParIndex[i]=(oldTotalPars-numSubPars)+i;
} }
// public boolean isSubcameraParameter(int num){ // public boolean isSubcameraParameter(int num){
int numSeries=this.parameterMode.length; int numSeries=this.parameterMode.length;
if (oldTotalPars<totalNumPars){ // grow, repeat last subcamera if (oldTotalPars<totalNumPars){ // grow, repeat last subcamera
if (this.debugLevel>1) System.out.println("Increasing total number of parameters in fitting strategy: "+oldTotalPars+" -> "+totalNumPars); if (this.debugLevel>1) System.out.println("Increasing total number of parameters in fitting strategy: "+oldTotalPars+" -> "+totalNumPars);
...@@ -1322,7 +1356,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1322,7 +1356,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
} }
} }
private void setDflt(int numSeries){ private void setDflt(int numSeries){
if (numSeries==0) { if (numSeries==0) {
this.selectedImages=null; this.selectedImages=null;
...@@ -1332,6 +1366,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1332,6 +1366,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.parameterGroups=null; this.parameterGroups=null;
this.varianceModes=null; this.varianceModes=null;
this.zGroups=null; this.zGroups=null;
this.strategyComment=null;
return; return;
} }
this.stopAfterThis=new boolean[numSeries]; this.stopAfterThis=new boolean[numSeries];
...@@ -1357,6 +1392,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1357,6 +1392,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.parameterGroups=new int[numSeries][totalNumPars][]; this.parameterGroups=new int[numSeries][totalNumPars][];
this.parameterEnable= new boolean [totalNumPars]; this.parameterEnable= new boolean [totalNumPars];
this.zGroups=new int[numSeries][]; this.zGroups=new int[numSeries][];
this.strategyComment = new String [numSeries];
for (int i=0;i<this.selectedImages.length;i++){ for (int i=0;i<this.selectedImages.length;i++){
invalidateSelectedImages(i); invalidateSelectedImages(i);
for (int j=0;j<this.selectedImages[i].length;j++){ for (int j=0;j<this.selectedImages[i].length;j++){
...@@ -1371,9 +1407,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1371,9 +1407,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.masterImages[i]=0; // first image, supposingly the earliest timestamp this.masterImages[i]=0; // first image, supposingly the earliest timestamp
this.varianceModes[i]=varianceModeDisabled; this.varianceModes[i]=varianceModeDisabled;
this.zGroups[i]=null; this.zGroups[i]=null;
this.strategyComment[i] = "";
} }
initParameterList(); initParameterList();
for (int i=0;i<numPars;i++){ for (int i=0;i<numPars;i++){
this.parameterEnable[i]=true; // initially enable all parameters for the first camera this.parameterEnable[i]=true; // initially enable all parameters for the first camera
...@@ -1387,7 +1424,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1387,7 +1424,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
} }
} }
private void initParameterList(){ private void initParameterList(){
int numPars= this.distortionCalibrationData.getNumParameters(); int numPars= this.distortionCalibrationData.getNumParameters();
int numSubCams=this.distortionCalibrationData.getNumSubCameras(); int numSubCams=this.distortionCalibrationData.getNumSubCameras();
...@@ -1403,7 +1440,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1403,7 +1440,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.parameterList[i][1]=i; this.parameterList[i][1]=i;
// this.parameterEnable[i]=true; // initially enable all parameters for the first camera // this.parameterEnable[i]=true; // initially enable all parameters for the first camera
} }
for (int i=1;i<numSubCams;i++){ for (int i=1;i<numSubCams;i++){
int i1=numPars+numSubPars*(i-1); int i1=numPars+numSubPars*(i-1);
int j1=0; int j1=0;
...@@ -1414,7 +1451,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1414,7 +1451,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
j1++; j1++;
} }
} }
} }
/** /**
* Find parameter number from subcamera and index * Find parameter number from subcamera and index
...@@ -1435,7 +1472,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1435,7 +1472,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
Arrays.sort(array); Arrays.sort(array);
return array; return array;
} }
public boolean selectIndividualImages( public boolean selectIndividualImages(
boolean [] selection, boolean [] selection,
boolean allImages, boolean allImages,
...@@ -1497,11 +1534,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1497,11 +1534,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
enabledSets[i]=false; enabledSets[i]=false;
selectedSets[i]=false; selectedSets[i]=false;
if (imageSets[i]!=null) for (int j=0;j<imageSets[i].length;j++){ if (imageSets[i]!=null) for (int j=0;j<imageSets[i].length;j++){
enabledSets[i] |= enabled[imageSets[i][j]]; enabledSets[i] |= enabled[imageSets[i][j]];
selectedSets[i] |= selection[imageSets[i][j]]; selectedSets[i] |= selection[imageSets[i][j]];
} }
} }
int endIndex=startIndex; int endIndex=startIndex;
int numSet=0; int numSet=0;
for (endIndex=startIndex; (endIndex<enabledSets.length) && (numSet<perPage);endIndex++) if (enabledSets[endIndex]) numSet++; for (endIndex=startIndex; (endIndex<enabledSets.length) && (numSet<perPage);endIndex++) if (enabledSets[endIndex]) numSet++;
...@@ -1540,8 +1577,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1540,8 +1577,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
endIndex, endIndex,
perPage); perPage);
} }
/** /**
* Manage image selection for the current series * Manage image selection for the current series
* @param numSeries series number to manage * @param numSeries series number to manage
...@@ -1567,7 +1604,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1567,7 +1604,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
"Individual images, start from current selection",// 4 "Individual images, start from current selection",// 4
"Image sets, start from empty selection", // 5 "Image sets, start from empty selection", // 5
"Image sets, start from current selection" // 6 "Image sets, start from current selection" // 6
}; };
int numStations=this.distortionCalibrationData.eyesisCameraParameters.getNumStations(); int numStations=this.distortionCalibrationData.eyesisCameraParameters.getNumStations();
int numChannels=this.distortionCalibrationData.eyesisCameraParameters.getNumChannels(0); // for station 0 int numChannels=this.distortionCalibrationData.eyesisCameraParameters.getNumChannels(0); // for station 0
boolean [] selected= this.selectedImages[numSeries]; boolean [] selected= this.selectedImages[numSeries];
...@@ -1593,14 +1630,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1593,14 +1630,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
Arrays.fill(totalPerStation, 0); Arrays.fill(totalPerStation, 0);
int [] imageStations=this.distortionCalibrationData.getStations(); int [] imageStations=this.distortionCalibrationData.getStations();
int [] imageChannels=this.distortionCalibrationData.getChannels(); int [] imageChannels=this.distortionCalibrationData.getChannels();
int numNewEnabled=0; int numNewEnabled=0;
int [] numNewEnabledPerStation=new int [numStations]; int [] numNewEnabledPerStation=new int [numStations];
Arrays.fill(numNewEnabledPerStation, 0); Arrays.fill(numNewEnabledPerStation, 0);
int numNewEnabledSelected=0; int numNewEnabledSelected=0;
int [] numNewEnabledSelectedPerStation=new int [numStations]; int [] numNewEnabledSelectedPerStation=new int [numStations];
Arrays.fill(numNewEnabledSelectedPerStation, 0); Arrays.fill(numNewEnabledSelectedPerStation, 0);
int numEstimatedSelected=0; int numEstimatedSelected=0;
int [] numEstimatedSelectedPerStation=new int [numStations]; int [] numEstimatedSelectedPerStation=new int [numStations];
Arrays.fill(numEstimatedSelectedPerStation, 0); Arrays.fill(numEstimatedSelectedPerStation, 0);
...@@ -1608,7 +1645,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1608,7 +1645,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
int numEstimated=0; int numEstimated=0;
int [] numEstimatedPerStation=new int [numStations]; int [] numEstimatedPerStation=new int [numStations];
Arrays.fill(numEstimatedPerStation, 0); Arrays.fill(numEstimatedPerStation, 0);
int numEstimatedAll=0; int numEstimatedAll=0;
int [] numEstimatedAllPerStation=new int [numStations]; int [] numEstimatedAllPerStation=new int [numStations];
Arrays.fill(numEstimatedAllPerStation, 0); Arrays.fill(numEstimatedAllPerStation, 0);
...@@ -1621,7 +1658,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1621,7 +1658,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
Map <Integer,Integer> mapHM=new HashMap<Integer,Integer>(); Map <Integer,Integer> mapHM=new HashMap<Integer,Integer>();
for (Integer index=0;index<matchedPointersIndex.length;index++) mapMP.put(new Integer(matchedPointersIndex[index]),index); for (Integer index=0;index<matchedPointersIndex.length;index++) mapMP.put(new Integer(matchedPointersIndex[index]),index);
for (Integer index=0;index<hintedMatchIndex.length;index++) mapHM.put(new Integer(hintedMatchIndex[index]),index); for (Integer index=0;index<hintedMatchIndex.length;index++) mapHM.put(new Integer(hintedMatchIndex[index]),index);
int [] numMatchedPointers= new int [matchedPointersIndex.length]; int [] numMatchedPointers= new int [matchedPointersIndex.length];
int [] numMatchedPointersSelected=new int [matchedPointersIndex.length]; int [] numMatchedPointersSelected=new int [matchedPointersIndex.length];
int [] numMatchedPointersEnabled= new int [matchedPointersIndex.length]; int [] numMatchedPointersEnabled= new int [matchedPointersIndex.length];
...@@ -1658,7 +1695,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1658,7 +1695,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
Arrays.fill(numHintedMatchEnabledPerStation[n], 0); Arrays.fill(numHintedMatchEnabledPerStation[n], 0);
} }
for (int i=0;i<selected.length;i++) if (imageStations[i]>=0){ for (int i=0;i<selected.length;i++) if (imageStations[i]>=0){
int mpi=mapMP.get(new Integer(matchedPointers[i])); int mpi=mapMP.get(new Integer(matchedPointers[i]));
int hmi=mapHM.get(new Integer(hintedMatch[i])); int hmi=mapHM.get(new Integer(hintedMatch[i]));
...@@ -1693,11 +1730,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1693,11 +1730,11 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
numMatchedPointersEnabledPerStation[mpi][imageStations[i]]++; numMatchedPointersEnabledPerStation[mpi][imageStations[i]]++;
numMatchedPointersEnabled[mpi]++; numMatchedPointersEnabled[mpi]++;
numHintedMatchEnabledPerStation[hmi][imageStations[i]]++; numHintedMatchEnabledPerStation[hmi][imageStations[i]]++;
numHintedMatchEnabled[hmi]++; numHintedMatchEnabled[hmi]++;
} }
if (estimatedAll[i]){ if (estimatedAll[i]){
numEstimatedAllPerStation[imageStations[i]]++; numEstimatedAllPerStation[imageStations[i]]++;
...@@ -1708,7 +1745,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1708,7 +1745,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
numHintedMatchPerStation[hmi][imageStations[i]]++; numHintedMatchPerStation[hmi][imageStations[i]]++;
numHintedMatch[hmi]++; numHintedMatch[hmi]++;
totalPerStation[imageStations[i]]++; totalPerStation[imageStations[i]]++;
} }
...@@ -1735,7 +1772,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1735,7 +1772,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
sHintedMatch[n]+=" station_"+(i+1)+": ["+numHintedMatchSelectedPerStation[n][i]+" / "+ sHintedMatch[n]+=" station_"+(i+1)+": ["+numHintedMatchSelectedPerStation[n][i]+" / "+
numHintedMatchEnabledPerStation[n][i]+" / "+numHintedMatchPerStation[n][i]+"]"; numHintedMatchEnabledPerStation[n][i]+" / "+numHintedMatchPerStation[n][i]+"]";
} }
} }
int operIndex=0,selectionTypeIndex=0; int operIndex=0,selectionTypeIndex=0;
...@@ -1806,7 +1843,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1806,7 +1843,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
boolean [] selection=new boolean [enabled.length]; boolean [] selection=new boolean [enabled.length];
Arrays.fill(selection,false); Arrays.fill(selection,false);
switch (selectionTypeIndex){ switch (selectionTypeIndex){
case 0: case 0:
selection=enabled.clone(); selection=enabled.clone();
break; break;
case 1: case 1:
...@@ -1834,15 +1871,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1834,15 +1871,15 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
500)) return -1; //perPage)) 500)) return -1; //perPage))
break; break;
} }
for (int i=0;i<selection.length;i++) selection[i] &= requiredMatchedPointers[mapMP.get(new Integer(matchedPointers[i]))]; for (int i=0;i<selection.length;i++) selection[i] &= requiredMatchedPointers[mapMP.get(new Integer(matchedPointers[i]))];
for (int i=0;i<selection.length;i++) selection[i] &= requiredHintedMatch[mapHM.get(new Integer(hintedMatch[i]))]; for (int i=0;i<selection.length;i++) selection[i] &= requiredHintedMatch[mapHM.get(new Integer(hintedMatch[i]))];
for (int i=0;i<selection.length;i++) if (imageStations[i]>=0) selection[i] &= requiredStations[imageStations[i]]; for (int i=0;i<selection.length;i++) if (imageStations[i]>=0) selection[i] &= requiredStations[imageStations[i]];
else selection[i] = false; else selection[i] = false;
for (int i=0;i<selection.length;i++) if (imageChannels[i]>=0) selection[i] &= requiredChannels[imageChannels[i]]; for (int i=0;i<selection.length;i++) if (imageChannels[i]>=0) selection[i] &= requiredChannels[imageChannels[i]];
else selection[i] = false; else selection[i] = false;
// now combine new/old selections // now combine new/old selections
switch (operIndex){ switch (operIndex){
case 0: // keep new selection case 0: // keep new selection
...@@ -1869,10 +1906,126 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1869,10 +1906,126 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.selectedImages[numSeries]=selection; this.selectedImages[numSeries]=selection;
return more?0:1; return more?0:1;
} }
/**
*
* @param numSeries Number of series to edit
* @param useImages Select images for this series
* @param fromToImages - limit number of checkboxes, otherwise window does not show the bottom ones
* @param useParameters Select parameters for this series
* @param askNextSeries Ask for next series number
* @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
* @return -2 - cancel, -1, done, otherwise - number of step to edit
public int selectStrategyStep(
int numSeries,
boolean useImages,
int [] fromToImages,
boolean allImages,
boolean useParameters,
boolean askLambdas,
boolean askNextSeries,
boolean zeroAndOther
){
GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration, step "+numSeries+
" number of enabled images="+this.distortionCalibrationData.getNumEnabled());
gd.addStringField ("Comment", this.strategyComment[numSeries],80);
*/
public void listStrategies() {
if (this.selectedImages == null) {
String msg="No strategies defined";
IJ.showMessage("Error",msg);
return;
}
int fromSer = 0;
int toSer = this.selectedImages.length;
boolean zeroAndOther= true;
GenericDialog gd = new GenericDialog("List Fitting Strategies");
gd.addNumericField("First number of series to list", fromSer, 0);
gd.addNumericField("Last number of series to list", toSer - 1, 0);
gd.addCheckbox ("Use only channel 0 and \"all other channels\"",zeroAndOther);
gd.showDialog();
if (gd.wasCanceled()) return;
fromSer= (int) gd.getNextNumber();
toSer= (int) gd.getNextNumber();
zeroAndOther= gd.getNextBoolean();
listStrategies(fromSer, toSer, zeroAndOther);
}
public void listStrategies(
int fromSer,
int toSer,
boolean zeroAndOther
) {
if (this.selectedImages == null) {
String msg="No strategies defined";
IJ.showMessage("Error",msg);
return;
}
int [] choice_offsets = new int [this.parameterEnable.length];
//
String header="Strategy Number\t";
StringBuffer sb = new StringBuffer();
for (int i=fromSer;i<toSer;i++) if (isSeriesValid(i)) header+="\t"+i;
sb.append("Comment\t");
for (int i=fromSer;i<toSer;i++) if (isSeriesValid(i)) sb.append("\t"+this.strategyComment[i]);sb.append("\n");
sb.append("Number of selected images\t");
for (int i=fromSer;i<toSer;i++) if (isSeriesValid(i)) {
int ns = 0;
for (int j=0; j<this.selectedImages[i].length;j++) if (this.selectedImages[i][j]) ns++;
sb.append("\t"+ns);
}
sb.append("\n");
// parameters
for (int ipar =0; ipar<this.parameterEnable.length;ipar++) if (this.parameterEnable[ipar] &&
(!zeroAndOther || (this.parameterList[ipar][0] <= 1) || (this.parameterList[ipar][0] ==24))){ // in "zeroAndOther" mode do not show other subcameras
int parIndex=this.parameterList[ipar][1];
int subCam=this.parameterList[ipar][0];
boolean isSub=this.distortionCalibrationData.isSubcameraParameter(parIndex);
String sChn=(zeroAndOther && (subCam>=1)&& (subCam<24))?"-head-other":
((zeroAndOther && (subCam>=24))?"-bottom":("-"+subCam));
boolean noWeak=!this.distortionCalibrationData.eyesisCameraParameters.isExtrinsic(parIndex);
boolean isTilt=this.distortionCalibrationData.eyesisCameraParameters.isTilt(parIndex);
// for non-subcamera or subcam 0 - no extra choices. For "zeroAndOther" - only "0". For other subCam - all less than this
int subMaxNum = (this.distortionCalibrationData.isSubcameraParameter(parIndex) && (subCam > 0)) ? (zeroAndOther? 0 : (subCam-1)):-1;
String [] commonChoices = (isTilt?this.definedModesTiltEq:(noWeak?this.definedModesNoWeak:this.definedModes));
String [] theseChoices;
String thisChoice = "";
choice_offsets[ipar] = 0;
sb.append(this.distortionCalibrationData.getParameterName(parIndex)+"\t"+(isSub?(" sub"+sChn):"com "));
for (int numSeries=fromSer;numSeries<toSer;numSeries++) if (isSeriesValid(numSeries)) {
if (subMaxNum < 0){
// theseChoices = commonChoices;
thisChoice = this.definedModesAll[this.parameterMode[numSeries][ipar]];
} else { // only can happen if (!isTilt) && (noWeak)
choice_offsets[ipar] = commonChoices.length;
theseChoices = new String [commonChoices.length + subMaxNum + 1];
for (int ch = 0; ch < commonChoices.length; ch++) theseChoices[ch] = commonChoices[ch];
for (int ch = 0; ch <= subMaxNum; ch++) theseChoices[ch + commonChoices.length] = "same as "+ch;
// choice index for "same as ..." starts with this.definedModesAll.length, but in the listbox index is lower
int indx = this.parameterMode[numSeries][ipar];
if (indx >= this.definedModesAll.length) {
indx -= (this.definedModesAll.length - choice_offsets[ipar]);
}
thisChoice = theseChoices[indx];
// System.out.println("selectStrategyStep(): this.parameterMode["+numSeries+"]["+ipar+"]=" + this.parameterMode[numSeries][ipar]+" indx = "+indx);
}
if (thisChoice.equals("fixed")) thisChoice = "-";
sb.append("\t"+thisChoice);
}
sb.append("\n");
}
new TextWindow("Strategies_List", header, sb.toString(), 800,1000);
System.out.println("** Do not save as .csv - it will replace tabs with commas! ***");
}
/** /**
* *
* @param numSeries Number of series to edit * @param numSeries Number of series to edit
* @param useImages Select images for this series * @param useImages Select images for this series
* @param fromToImages - limit number of checkboxes, otherwise window does not show the bottom ones * @param fromToImages - limit number of checkboxes, otherwise window does not show the bottom ones
...@@ -1916,8 +2069,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1916,8 +2069,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
int sourceSeries= findLastValidSeries(numSeries); int sourceSeries= findLastValidSeries(numSeries);
if (sourceSeries>=0) copySeries(sourceSeries, numSeries); if (sourceSeries>=0) copySeries(sourceSeries, numSeries);
} }
GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration, step "+numSeries+" number of enabled images="+this.distortionCalibrationData.getNumEnabled()); GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration, step "+numSeries+
" number of enabled images="+this.distortionCalibrationData.getNumEnabled());
gd.addStringField ("Comment", this.strategyComment[numSeries],80);
gd.addCheckbox("Advanced image selection (disregard other fields)", showAdvancedImageSelection); gd.addCheckbox("Advanced image selection (disregard other fields)", showAdvancedImageSelection);
gd.addCheckbox("Copy all from the series below, ignore all other fields", false); gd.addCheckbox("Copy all from the series below, ignore all other fields", false);
gd.addNumericField("Source series to copy from", (numSeries>0)?(numSeries-1):(numSeries+1), 0, 3, ""); gd.addNumericField("Source series to copy from", (numSeries>0)?(numSeries-1):(numSeries+1), 0, 3, "");
...@@ -1941,9 +2096,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1941,9 +2096,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
if (this.distortionCalibrationData.eyesisCameraParameters.numStations>1){ if (this.distortionCalibrationData.eyesisCameraParameters.numStations>1){
gd.addMessage("Constrain by stations"); gd.addMessage("Constrain by stations");
// gd.addCheckbox("Remove images of unselected stations below", true); // gd.addCheckbox("Remove images of unselected stations below", true);
for (int i=0;i<this.distortionCalibrationData.eyesisCameraParameters.numStations;i++) gd.addCheckbox("Station "+i, constrainByStation[i]); for (int i=0;i<this.distortionCalibrationData.eyesisCameraParameters.numStations;i++) gd.addCheckbox("Station "+i, constrainByStation[i]);
} }
if (useImages) { if (useImages) {
gd.addNumericField("Image selection range, from", fromToImages[0], 0); gd.addNumericField("Image selection range, from", fromToImages[0], 0);
gd.addNumericField("Image selection range, up to (including)", fromToImages[1], 0); gd.addNumericField("Image selection range, up to (including)", fromToImages[1], 0);
...@@ -1959,7 +2114,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -1959,7 +2114,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
this.selectedImages[numSeries][i]); this.selectedImages[numSeries][i]);
} }
if (allImages) gd.addCheckbox("Enable selected, disable deselected images", false); if (allImages) gd.addCheckbox("Enable selected, disable deselected images", false);
gd.addNumericField("The 'master' (used for common parameters)", this.masterImages[numSeries], 0); gd.addNumericField("The 'master' (used for common parameters)", this.masterImages[numSeries], 0);
} }
...@@ -2065,13 +2220,13 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2065,13 +2220,13 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
"Same target group for station " +i, "Same target group for station " +i,
zGroupsChoices, zGroupsChoices,
zGroupsChoices[zG]); // definedModesAll - includes all others zGroupsChoices[zG]); // definedModesAll - includes all others
} }
} else { } else {
this.zGroups[numSeries]=new int [1]; this.zGroups[numSeries]=new int [1];
this.zGroups[numSeries][0]=0; this.zGroups[numSeries][0]=0;
} }
if (askNextSeries) { if (askNextSeries) {
gd.addCheckbox("Rebuild/Show parameter Map", showDirectMap); gd.addCheckbox("Rebuild/Show parameter Map", showDirectMap);
gd.addCheckbox("Rebuild/Show reverse parameter Map", showReverseMap); gd.addCheckbox("Rebuild/Show reverse parameter Map", showReverseMap);
...@@ -2082,6 +2237,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2082,6 +2237,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return -2; if (gd.wasCanceled()) return -2;
this.strategyComment[numSeries]= gd.getNextString();
showAdvancedImageSelection=gd.getNextBoolean(); showAdvancedImageSelection=gd.getNextBoolean();
if (showAdvancedImageSelection){ if (showAdvancedImageSelection){
int rslt=0; int rslt=0;
...@@ -2116,7 +2272,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2116,7 +2272,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
return numSeries; // caller will repeat with the same series return numSeries; // caller will repeat with the same series
} }
if (copyFromPrevious){ if (copyFromPrevious){
int sourceSeries= findLastValidSeries(sourceStrategy); int sourceSeries= findLastValidSeries(sourceStrategy);
if (sourceSeries>=0) { if (sourceSeries>=0) {
...@@ -2130,7 +2286,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2130,7 +2286,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
return numSeries; // caller will repeat with the same series return numSeries; // caller will repeat with the same series
} }
if (removeAllImages || selectAllImages) { if (removeAllImages || selectAllImages) {
// //
for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){ for (int i =0; i<this.distortionCalibrationData.getNumImages();i++){
// this.selectedImages[numSeries][i]=false; // invalidate - all, regardless of .enabled // this.selectedImages[numSeries][i]=false; // invalidate - all, regardless of .enabled
this.selectedImages[numSeries][i]=selectAllImages || ((i==0) && removeAllImages); // invalidate - all, regardless of .enabled this.selectedImages[numSeries][i]=selectAllImages || ((i==0) && removeAllImages); // invalidate - all, regardless of .enabled
...@@ -2157,14 +2313,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2157,14 +2313,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
(!zeroAndOther || (this.parameterList[i][0] <=1) || (this.parameterList[i][0]==24))){ // in "zeroAndOther" mode do not show other subcameras (!zeroAndOther || (this.parameterList[i][0] <=1) || (this.parameterList[i][0]==24))){ // in "zeroAndOther" mode do not show other subcameras
// for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i]){ // for (int i =0; i<this.parameterEnable.length;i++) if (this.parameterEnable[i]){
this.parameterMode[numSeries][i]=gd.getNextChoiceIndex(); this.parameterMode[numSeries][i]=gd.getNextChoiceIndex();
// make adjustment for "same as (other lower numbered subcamera)" // make adjustment for "same as (other lower numbered subcamera)"
if ((choice_offsets[i] > 0) && (this.parameterMode[numSeries][i] >= choice_offsets[i])){ if ((choice_offsets[i] > 0) && (this.parameterMode[numSeries][i] >= choice_offsets[i])){
System.out.print("selectStrategyStep(): choice_offsets["+i+"]="+choice_offsets[i]+ " this.parameterMode["+numSeries+"]["+i+"]=" + this.parameterMode[numSeries][i]); System.out.print("selectStrategyStep(): choice_offsets["+i+"]="+choice_offsets[i]+ " this.parameterMode["+numSeries+"]["+i+"]=" + this.parameterMode[numSeries][i]);
this.parameterMode[numSeries][i] += (this.definedModesAll.length - choice_offsets[i]); this.parameterMode[numSeries][i] += (this.definedModesAll.length - choice_offsets[i]);
System.out.println(", corrected=" + this.parameterMode[numSeries][i]); System.out.println(", corrected=" + this.parameterMode[numSeries][i]);
} }
if (this.parameterMode[numSeries][i]==this.modeGroup) { if (this.parameterMode[numSeries][i]==this.modeGroup) {
if (this.parameterGroups[numSeries][i]!=null) lastGroups=this.parameterGroups[numSeries][i]; // default groups if (this.parameterGroups[numSeries][i]!=null) lastGroups=this.parameterGroups[numSeries][i]; // default groups
else if (lastGroups!=null) this.parameterGroups[numSeries][i]=lastGroups.clone(); // may be null else if (lastGroups!=null) this.parameterGroups[numSeries][i]=lastGroups.clone(); // may be null
...@@ -2196,9 +2352,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2196,9 +2352,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
if (enableDisableSelected) { if (enableDisableSelected) {
this.distortionCalibrationData.enableSelected(this.selectedImages[numSeries]); this.distortionCalibrationData.enableSelected(this.selectedImages[numSeries]);
} }
if (this.varianceModes!=null) this.varianceModes[numSeries]=gd.getNextChoiceIndex(); if (this.varianceModes!=null) this.varianceModes[numSeries]=gd.getNextChoiceIndex();
boolean editVariancesCosts=gd.getNextBoolean(); boolean editVariancesCosts=gd.getNextBoolean();
if (editVariancesCosts){ if (editVariancesCosts){
for (int i =0; i<this.parameterList.length;i++) { for (int i =0; i<this.parameterList.length;i++) {
...@@ -2220,13 +2376,13 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2220,13 +2376,13 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
} }
} }
} }
if (numStations>1){ if (numStations>1){
for (int i=0;i<numStations;i++){ for (int i=0;i<numStations;i++){
this.zGroups[numSeries][i]=gd.getNextChoiceIndex()-1; this.zGroups[numSeries][i]=gd.getNextChoiceIndex()-1;
} }
} }
if (!gd.wasOKed()) return -1; // pressed Done (no need to ask for the next number) if (!gd.wasOKed()) return -1; // pressed Done (no need to ask for the next number)
if (askNextSeries) { if (askNextSeries) {
...@@ -2252,14 +2408,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2252,14 +2408,14 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
// System.out.println("selectGroups("+numSeries+", "+numPar+")"); // System.out.println("selectGroups("+numSeries+", "+numPar+")");
// } // }
int parIndex=this.parameterList[numPar][1]; int parIndex=this.parameterList[numPar][1];
int subCam=this.parameterList[numPar][0]; int subCam=this.parameterList[numPar][0];
String name=this.distortionCalibrationData.getParameterName(parIndex)+ String name=this.distortionCalibrationData.getParameterName(parIndex)+
(this.distortionCalibrationData.isSubcameraParameter(parIndex)?(" s"+subCam):"com "); (this.distortionCalibrationData.isSubcameraParameter(parIndex)?(" s"+subCam):"com ");
GenericDialog gd = new GenericDialog("Select image groups for "+name); GenericDialog gd = new GenericDialog("Select image groups for "+name);
gd.addMessage("Select which images share the same value of "+name); gd.addMessage("Select which images share the same value of "+name);
if (this.parameterGroups[numSeries][numPar]==null) { if (this.parameterGroups[numSeries][numPar]==null) {
this.parameterGroups[numSeries][numPar]=new int [this.distortionCalibrationData.getNumImages()]; this.parameterGroups[numSeries][numPar]=new int [this.distortionCalibrationData.getNumImages()];
for (int i=0;i<this.parameterGroups[numSeries][numPar].length;i++)this.parameterGroups[numSeries][numPar][i]=0; for (int i=0;i<this.parameterGroups[numSeries][numPar].length;i++)this.parameterGroups[numSeries][numPar][i]=0;
...@@ -2273,18 +2429,18 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2273,18 +2429,18 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
); );
} }
WindowTools.addScrollBars(gd); WindowTools.addScrollBars(gd);
gd.showDialog(); gd.showDialog();
if (gd.wasCanceled()) return false; if (gd.wasCanceled()) return false;
for (int i =0; i<this.distortionCalibrationData.getNumImages();i++) if (this.selectedImages[numSeries][i]){ for (int i =0; i<this.distortionCalibrationData.getNumImages();i++) if (this.selectedImages[numSeries][i]){
this.parameterGroups[numSeries][numPar][i]=gd.getNextChoiceIndex(); this.parameterGroups[numSeries][numPar][i]=gd.getNextChoiceIndex();
} }
return true; return true;
} }
/** /**
* Organizes list of groups and creates a list of selection choices. If all members fit in the range * Organizes list of groups and creates a list of selection choices. If all members fit in the range
* of 0 (length-1) and (force==false), group numbers are preserved, otherwise they are renumbered * of 0 (length-1) and (force==false), group numbers are preserved, otherwise they are renumbered
* @param groups array of integers - group numbers * @param groups array of integers - group numbers
* @param force force renumbering groups * @param force force renumbering groups
* @return list of selection choices * @return list of selection choices
...@@ -2332,7 +2488,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit ...@@ -2332,7 +2488,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
int numSeries=startSerNumber; int numSeries=startSerNumber;
int oldLength=(this.selectedImages==null)?0:this.selectedImages.length; int oldLength=(this.selectedImages==null)?0:this.selectedImages.length;
GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration"); GenericDialog gd = new GenericDialog("Fitting Strategy Step Configuration");
if (oldLength<=0) gd.addNumericField("Number of series in this strategy", defaultLength, 0); if (oldLength<=0) gd.addNumericField("Number of series in this strategy", defaultLength, 0);
gd.addNumericField("Number of series to edit (<0 - none)", numSeries, 0); gd.addNumericField("Number of series to edit (<0 - none)", numSeries, 0);
......
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