Added option to "Calculate grids" to skip re-calculation of existing (825895a1) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+22 −3

Original line number	Original line	Diff line number	Diff line
	@@ -2027,7 +2027,7 @@ if (MORE_BUTTONS) {
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel, //distortions, // image to process		imp_sel, //distortions, // image to process
	THREADS_MAX);		THREADS_MAX);
	ImagePlus imp_calibrated0=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,numAbsolutePoints);		ImagePlus imp_calibrated0=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,"grid-",numAbsolutePoints);
	imp_calibrated0.show();		imp_calibrated0.show();
	// }		// }
	// } else {		// } else {
	@@ -2683,12 +2683,14 @@ if (MORE_BUTTONS) {
	}		}
	long startTime=System.nanoTime();		long startTime=System.nanoTime();
	boolean noMessageBoxes=true;		boolean noMessageBoxes=true;
			String prefix="grid-";
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	DISTORTION_PROCESS_CONFIGURATION.debugLevel=MASTER_DEBUG_LEVEL;		DISTORTION_PROCESS_CONFIGURATION.debugLevel=MASTER_DEBUG_LEVEL;
	if (matchSimulatedPattern==null) matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize);		if (matchSimulatedPattern==null) matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize);
	matchSimulatedPattern.debugLevel=MASTER_DEBUG_LEVEL;		matchSimulatedPattern.debugLevel=MASTER_DEBUG_LEVEL;
	String [] sourceFilesList=DISTORTION_PROCESS_CONFIGURATION.selectSourceFiles(); // select files - with/without dialog		String [] sourceFilesList=DISTORTION_PROCESS_CONFIGURATION.selectSourceFiles(); // select files - with/without dialog
	boolean saveGrids=DISTORTION_PROCESS_CONFIGURATION.saveGridImages;		boolean saveGrids=DISTORTION_PROCESS_CONFIGURATION.saveGridImages;
			boolean overwriteGrids=DISTORTION_PROCESS_CONFIGURATION.overwriteResultFiles;
	if (sourceFilesList==null) return;		if (sourceFilesList==null) return;
	showPatternMinMaxPeriodDialog(PATTERN_DETECT);		showPatternMinMaxPeriodDialog(PATTERN_DETECT);
	for (int numFile=0;numFile<sourceFilesList.length;numFile++){		for (int numFile=0;numFile<sourceFilesList.length;numFile++){
	@@ -2696,6 +2698,23 @@ if (MORE_BUTTONS) {
	if (DEBUG_LEVEL>0){		if (DEBUG_LEVEL>0){
	System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing file # "+(numFile+1)+ " (of "+ sourceFilesList.length+"): "+sourceFilesList[numFile]);		System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing file # "+(numFile+1)+ " (of "+ sourceFilesList.length+"): "+sourceFilesList[numFile]);
	}		}
			if (saveGrids && !overwriteGrids){ // check if result already exists
			int i = sourceFilesList[numFile].lastIndexOf('/');
			if (i>0){
			String path=prefix+sourceFilesList[numFile].substring(i+1);
			String srcDir=DISTORTION_PROCESS_CONFIGURATION.selectGridFileDirectory(true,DISTORTION_PROCESS_CONFIGURATION.gridDirectory,true);
			if (srcDir==null){
			saveGrids=false; // do not ask about the next ones too
			} else {
			path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+path;
			File rsltFile=new File(path);
			if ((new File(path)).exists()){
			if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+path+" (as requested in \"Configure Process Distortions\")");
			continue;
			}
			}
			}
			}
	imp_sel=new ImagePlus(sourceFilesList[numFile]); // read source file		imp_sel=new ImagePlus(sourceFilesList[numFile]); // read source file
	JP4_INSTANCE.decodeProperiesFromInfo(imp_sel);		JP4_INSTANCE.decodeProperiesFromInfo(imp_sel);
	matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize); // TODO: is it needed each time?		matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize); // TODO: is it needed each time?
	@@ -2743,7 +2762,7 @@ if (MORE_BUTTONS) {
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel, // image to process		imp_sel, // image to process
	THREADS_MAX);		THREADS_MAX);
	ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,numAbsolutePoints);		ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);
	if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();		if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
	if (saveGrids){		if (saveGrids){
	FileSaver fs=new FileSaver(imp_calibrated);		FileSaver fs=new FileSaver(imp_calibrated);
	@@ -3695,7 +3714,7 @@ if (MORE_BUTTONS) {
	return;		return;
	}		}
	if (DEBUG_LEVEL>0) System.out.println("Matched "+numAbsolutePoints+" laser pointers, grid generated at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));		if (DEBUG_LEVEL>0) System.out.println("Matched "+numAbsolutePoints+" laser pointers, grid generated at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
	ImagePlus [] imp_calibrated={matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,numAbsolutePoints)};		ImagePlus [] imp_calibrated={matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,"grid-",numAbsolutePoints)};
	if (FOCUS_MEASUREMENT_PARAMETERS.showAcquiredImages) imp_calibrated[0].show(); // DISTORTION_PROCESS_CONFIGURATION.showGridImages		if (FOCUS_MEASUREMENT_PARAMETERS.showAcquiredImages) imp_calibrated[0].show(); // DISTORTION_PROCESS_CONFIGURATION.showGridImages
	if (findCenter){		if (findCenter){
	// Read required calibration files		// Read required calibration files

src/main/java/Distortions.java

+9 −0

src/main/java/Goniometer.java

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -848,7 +848,7 @@ horizontal axis:
	// TODO - here - multiple images possible, not just one!		// TODO - here - multiple images possible, not just one!
	// First - create sparse, then remove nulls		// First - create sparse, then remove nulls

	imp_calibrated[numSensor] = this.matchSimulatedPatterns[numSensor].getCalibratedPatternAsImage(images[numSensor],numAbsolutePoints);		imp_calibrated[numSensor] = this.matchSimulatedPatterns[numSensor].getCalibratedPatternAsImage(images[numSensor],"grid-",numAbsolutePoints);
	if (this.goniometerParameters.showAcquiredImages)		if (this.goniometerParameters.showAcquiredImages)
	imp_calibrated[numSensor].show(); // DISTORTION_PROCESS_CONFIGURATION.showGridImages		imp_calibrated[numSensor].show(); // DISTORTION_PROCESS_CONFIGURATION.showGridImages
	} // for (int numSensor=0;numSensor<images.length;numSensor++) if		} // for (int numSensor=0;numSensor<images.length;numSensor++) if

src/main/java/MatchSimulatedPattern.java

+5 −2

Original line number	Original line	Diff line number	Diff line
	@@ -7168,8 +7168,11 @@ y=xy0[1] + dUdeltaUV[0](xy1[1]-xy0[1])+dVdeltaUV[1](xy2[1]-xy0[1])
	ImagePlus imp = new ImagePlus(title, stack);		ImagePlus imp = new ImagePlus(title, stack);
	return imp;		return imp;
	}		}
	public ImagePlus getCalibratedPatternAsImage(ImagePlus imp_src, int numUsedPointers){		public ImagePlus getCalibratedPatternAsImage(
	ImagePlus imp_result=getCalibratedPatternAsImage("grid-"+imp_src.getTitle(), numUsedPointers);		ImagePlus imp_src,
			String prefix, int numUsedPointers){
			// ImagePlus imp_result=getCalibratedPatternAsImage("grid-"+imp_src.getTitle(), numUsedPointers);
			ImagePlus imp_result=getCalibratedPatternAsImage(prefix+imp_src.getTitle(), numUsedPointers);
	// copy all the properties to the new image		// copy all the properties to the new image
	JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);		JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
	jp4_instance.copyProperties (imp_src,imp_result);		jp4_instance.copyProperties (imp_src,imp_result);

Original line number	Original line	Diff line number	Diff line
	@@ -20272,6 +20272,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	public boolean removeOutOfGridPointers=true;		public boolean removeOutOfGridPointers=true;
	public boolean showGridImages=false;		public boolean showGridImages=false;
	public boolean saveGridImages=true;		public boolean saveGridImages=true;
			public boolean overwriteResultFiles=false;
	public int debugLevel=1;		public int debugLevel=1;

	public String selectSourceDirectory(boolean smart, String defaultPath, boolean newAllowed) {		public String selectSourceDirectory(boolean smart, String defaultPath, boolean newAllowed) {
	@@ -20308,6 +20309,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	properties.setProperty(prefix+"removeOutOfGridPointers",this.removeOutOfGridPointers+"");		properties.setProperty(prefix+"removeOutOfGridPointers",this.removeOutOfGridPointers+"");
	properties.setProperty(prefix+"showGridImages", this.showGridImages+"");		properties.setProperty(prefix+"showGridImages", this.showGridImages+"");
	properties.setProperty(prefix+"saveGridImages", this.saveGridImages+"");		properties.setProperty(prefix+"saveGridImages", this.saveGridImages+"");
			properties.setProperty(prefix+"overwriteResultFiles", this.overwriteResultFiles+"");
	properties.setProperty(prefix+"debugLevel", this.debugLevel+"");		properties.setProperty(prefix+"debugLevel", this.debugLevel+"");
	}		}
	public void getProperties(String prefix,Properties properties){		public void getProperties(String prefix,Properties properties){
	@@ -20331,6 +20333,8 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	this.showGridImages=Boolean.parseBoolean(properties.getProperty(prefix+"showGridImages"));		this.showGridImages=Boolean.parseBoolean(properties.getProperty(prefix+"showGridImages"));
	if (properties.getProperty(prefix+"saveGridImages")!=null)		if (properties.getProperty(prefix+"saveGridImages")!=null)
	this.saveGridImages=Boolean.parseBoolean(properties.getProperty(prefix+"saveGridImages"));		this.saveGridImages=Boolean.parseBoolean(properties.getProperty(prefix+"saveGridImages"));
			if (properties.getProperty(prefix+"overwriteResultFiles")!=null)
			this.overwriteResultFiles=Boolean.parseBoolean(properties.getProperty(prefix+"overwriteResultFiles"));
	if (properties.getProperty(prefix+"debugLevel")!=null)		if (properties.getProperty(prefix+"debugLevel")!=null)
	this.debugLevel=Integer.parseInt(properties.getProperty(prefix+"debugLevel"));		this.debugLevel=Integer.parseInt(properties.getProperty(prefix+"debugLevel"));
	}		}
	@@ -20346,6 +20350,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	gd.addCheckbox ("Remove detected laser pointers if they are outside of the grid", this.removeOutOfGridPointers);		gd.addCheckbox ("Remove detected laser pointers if they are outside of the grid", this.removeOutOfGridPointers);
	gd.addCheckbox ("Show grid files as images", this.showGridImages);		gd.addCheckbox ("Show grid files as images", this.showGridImages);
	gd.addCheckbox ("Save grid files", this.saveGridImages);		gd.addCheckbox ("Save grid files", this.saveGridImages);
			gd.addCheckbox ("Overwrite existing result files", this.overwriteResultFiles);



	gd.addNumericField("Debug level", this.debugLevel,0);		gd.addNumericField("Debug level", this.debugLevel,0);
	WindowTools.addScrollBars(gd);		WindowTools.addScrollBars(gd);
	gd.showDialog();		gd.showDialog();
	@@ -20360,6 +20368,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
	this.removeOutOfGridPointers=gd.getNextBoolean();		this.removeOutOfGridPointers=gd.getNextBoolean();
	this.showGridImages= gd.getNextBoolean();		this.showGridImages= gd.getNextBoolean();
	this.saveGridImages= gd.getNextBoolean();		this.saveGridImages= gd.getNextBoolean();

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