added strategy comments, strategy list (59172c80) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+8 −13

Original line number	Diff line number	Diff line
		@@ -718,6 +718,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
		addButton("Edit Strategy",panelFitDistortions,color_configure);
		addButton("Save Strategy",panelFitDistortions,color_bundle);
		addButton("Restore Strategy",panelFitDistortions,color_restore);
		addButton("List Strategy",panelFitDistortions,color_report);
		addButton("Run LMA",panelFitDistortions,color_bundle);
		addButton("Bad Nodes",panelFitDistortions,color_bundle);
		addButton("Debug deriv",panelFitDistortions,color_debug);
		@@ -2311,18 +2312,8 @@ if (MORE_BUTTONS) {
		/* ======================================================================== */
		if (label.equals("List Eyesis4pi") \|\| label.equals("List X-cam")) {
		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:
		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"));
		return;
		}
		@@ -2486,8 +2477,7 @@ if (MORE_BUTTONS) {
		return;
		}
		/* ======================================================================== */

		if (label.equals("Edit Strategy")) {
		if (label.equals("Edit Strategy") \|\| label.equals("List Strategy")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		if (LENS_DISTORTIONS==null) {
		if (LENS_DISTORTION_PARAMETERS==null){
		@@ -2506,7 +2496,11 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS.fittingStrategy=new FittingStrategy(DISTORTION_CALIBRATION_DATA);
		}
		LENS_DISTORTIONS.fittingStrategy.debugLevel=DEBUG_LEVEL;
		if (label.equals("Edit Strategy")) {
		LENS_DISTORTIONS.fittingStrategy.selectStrategy(LENS_DISTORTIONS.seriesNumber);
		} else {
		LENS_DISTORTIONS.fittingStrategy.listStrategies();
		}
		return;
		}
		/* ======================================================================== */
		@@ -2558,6 +2552,7 @@ if (MORE_BUTTONS) {

		return;
		}

		/* ======================================================================== */
		if (label.equals("Run LMA")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;

src/main/java/FittingStrategy.java

+284 −128

Original line number	Diff line number	Diff line
		@@ -21,10 +21,6 @@
		-----------------------------------------------------------------------------
		**
		*/
		import ij.IJ;
		import ij.gui.GenericDialog;
		import ij.text.TextWindow;

		import java.io.BufferedWriter;
		import java.io.File;
		import java.io.FileWriter;
		@@ -40,6 +36,10 @@ import java.util.Set;
		import org.apache.commons.configuration.ConfigurationException;
		import org.apache.commons.configuration.XMLConfiguration;

		import ij.IJ;
		import ij.gui.GenericDialog;
		import ij.text.TextWindow;



		/**
		@@ -149,7 +149,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		public double [] weightVariance= null; // weight for LMA over variance of parameters from average
		public double [] varianceErrorsSquared= null; // weighted squared errors


		public String [] strategyComment = null;

		public FittingStrategy(
		DistortionCalibrationData distortionCalibrationData// per-image parameters
		@@ -243,6 +243,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		this.parameterGroups=new int[nSer][len][];
		this.lambdas=new double [nSer];
		this.stepDone=new double [nSer];
		this.strategyComment=new String[nSer];
		for (int i=0;i<nSer;i++){ // iterate through series
		//this.stopAfterThis
		// read selected images (no check here that it matches to the distortionCalibrationData!
		@@ -299,6 +300,12 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		} else {
		this.zGroups[i]=null;
		}

		if (hConfig.getString(sSeries+".strategyComment")!=null) {
		this.strategyComment[i]=hConfig.getString(sSeries+".strategyComment");
		}


		}
		// if (hConfig.getString("variances")!=null){
		// if (!hConfig.configurationAt("variances").isEmpty()){
		@@ -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+".stepDone",stepDone[i]);
		hConfig.addProperty(sSeries+".stopAfterThis",this.stopAfterThis[i]);
		hConfig.addProperty(sSeries+".strategyComment",this.strategyComment[i]);
		}
		hConfig.addProperty("variances","");
		this.distortionCalibrationData.eyesisCameraParameters.setCostsPropertiesXML("variances.",hConfig);
		@@ -448,6 +456,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		this.stopAfterThis[numSeries]=this.stopAfterThis[sourceSeries];
		this.varianceModes[numSeries]=this.varianceModes[sourceSeries];
		this.zGroups[numSeries]=(this.zGroups[sourceSeries]!=null)?this.zGroups[sourceSeries].clone():null;
		this.strategyComment[numSeries] = this.strategyComment[sourceSeries]+" (copy)";
		return true;
		} else {
		return false;
		@@ -461,7 +470,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		* @param num - series to verify
		* @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;
		boolean someImagesSelected=false;
		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
		}
		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)
		* @param num number of series to test
		@@ -1221,6 +1251,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		int [] oldMasterImages=null;
		double [] oldStepDone=null;
		boolean [] oldStopAfterThis=null;
		String [] oldStrategyComment=null;
		int oldNumSeries=(this.selectedImages==null)?0:this.selectedImages.length;
		int oldLength=0;
		if (this.selectedImages!=null){
		@@ -1229,6 +1260,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		oldParameterMode=new int[oldNumSeries][];
		oldParameterGroups=new int[oldNumSeries][][];
		oldZGroups=new int[oldNumSeries][];
		oldStrategyComment = new String [oldNumSeries];
		for (int i=0;i<oldNumSeries;i++){
		oldSelectedImages[i]=this.selectedImages[i].clone();
		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
		oldParameterGroups[i][j]=(parameterGroups[i][j]==null)?null:parameterGroups[i][j].clone();
		if (this.zGroups[i]!=null) oldZGroups[i]=this.zGroups[i].clone();
		else this.zGroups[i]=oldZGroups[i];
		oldStrategyComment[i]=this.strategyComment[i];
		}
		oldVarianceModes=(this.varianceModes==null)?null:this.varianceModes.clone();
		oldLambdas=this.lambdas.clone();
		@@ -1256,6 +1289,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		this.stopAfterThis[i]=oldStopAfterThis[i];
		this.varianceModes[i]=oldVarianceModes[i];
		this.zGroups[i]=(oldZGroups[i]!=null)?oldZGroups[i].clone():null;
		this.strategyComment[i] = oldStrategyComment[i];
		}
		}

		@@ -1332,6 +1366,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		this.parameterGroups=null;
		this.varianceModes=null;
		this.zGroups=null;
		this.strategyComment=null;
		return;
		}
		this.stopAfterThis=new boolean[numSeries];
		@@ -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.parameterEnable= new boolean [totalNumPars];
		this.zGroups=new int[numSeries][];
		this.strategyComment = new String [numSeries];
		for (int i=0;i<this.selectedImages.length;i++){
		invalidateSelectedImages(i);
		for (int j=0;j<this.selectedImages[i].length;j++){
		@@ -1371,6 +1407,7 @@ 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.varianceModes[i]=varianceModeDisabled;
		this.zGroups[i]=null;
		this.strategyComment[i] = "";
		}

		initParameterList();
		@@ -1869,6 +1906,122 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		this.selectedImages[numSeries]=selection;
		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! *");
		}


		/**
		@@ -1917,7 +2070,9 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		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("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, "");
		@@ -2082,6 +2237,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		WindowTools.addScrollBars(gd);
		gd.showDialog();
		if (gd.wasCanceled()) return -2;
		this.strategyComment[numSeries]= gd.getNextString();
		showAdvancedImageSelection=gd.getNextBoolean();
		if (showAdvancedImageSelection){
		int rslt=0;

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