Saving subset of parameters (3fa095d3) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+166 −37

Original line number	Diff line number	Diff line
		@@ -48,6 +48,8 @@ import java.util.regex.Pattern;





		//import FocusingField.FocusingFieldMeasurement;
		//import FocusingField.MeasuredSample;
		import Jama.Matrix; // Download here: http://math.nist.gov/javanumerics/jama/
		@@ -579,6 +581,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
		panelRun.setLayout(new GridLayout(1, 0, 5, 5));
		addButton("Process Calibration Files",panelRun);
		addButton("Save",panelRun);
		addButton("Save Selected",panelRun);
		addButton("Restore",panelRun,color_restore);
		addButton("Restore no autoload",panelRun);
		addButton("Restore SFE Latest",panelRun,color_restore);
		@@ -1051,6 +1054,13 @@ if (MORE_BUTTONS) {
		} else if (label.equals("Save")) {
		saveProperties(null,PROCESS_PARAMETERS.kernelsDirectory,PROCESS_PARAMETERS.useXML, PROPERTIES);
		return;
		/* ======================================================================== */
		} else if (label.equals("Save Selected")) {
		Properties selectedProperties=new Properties();
		selectedProperties.setProperty("selected", "true");
		saveProperties(null,PROCESS_PARAMETERS.kernelsDirectory, PROCESS_PARAMETERS.useXML, selectedProperties);
		return;

		/* ======================================================================== */

		} else if (label.equals("Restore") \|\| label.equals("Restore no autoload")) {
		@@ -13010,6 +13020,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
		} else path+=patterns[0];
		if (path==null) return;
		setAllProperties(properties);

		OutputStream os;
		try {
		os = new FileOutputStream(path);
		@@ -13050,6 +13061,7 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
		String directory,
		boolean useXML,
		Properties properties){
		setAllProperties(properties); // NEW. Setting properties from current parameters so missing (in the file) parameters will not cause an error
		String [] XMLPatterns= {".conf-xml",".xml"};
		String [] confPatterns={".conf"};
		String [] patterns=useXML?XMLPatterns:confPatterns;
		@@ -13101,42 +13113,159 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
		}
		/* ======================================================================== */
		public void setAllProperties(Properties properties){
		properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL+"");
		properties.setProperty("SHOW_AS_STACKS", SHOW_AS_STACKS+"");// Show debug images as stacks (false - individual)
		properties.setProperty("FFT_SIZE", FFT_SIZE+"");
		properties.setProperty("MAP_FFT_SIZE", MAP_FFT_SIZE+"");// used to find where grid covers the image
		properties.setProperty("GAUSS_WIDTH", GAUSS_WIDTH+""); // 0.4 (0 - use Hamming window)
		properties.setProperty("FFT_OVERLAP", FFT_OVERLAP+""); // createPSFMap()
		properties.setProperty("PSF_SUBPIXEL", PSF_SUBPIXEL+""); // sub-pixel decimation
		properties.setProperty("PSF_SAVE_FILE", PSF_SAVE_FILE+"");// save PSF array to a multi-slice TIFF file
		properties.setProperty("THREADS_MAX", THREADS_MAX+""); // 100, testing multi-threading, limit maximal number of threads
		properties.setProperty("UPDATE_STATUS", UPDATE_STATUS+""); // update ImageJ status info

		SIMUL.setProperties( "SIMUL.", properties);
		INTERPOLATE.setProperties( "INTERPOLATE.", properties);
		INVERSE.setProperties( "INVERSE.", properties);
		PSF_PARS.setProperties( "PSF_PARS.", properties);
		OTF_FILTER.setProperties( "OTF_FILTER.", properties);
		PATTERN_DETECT.setProperties( "PATTERN_DETECT.", properties);
		COMPONENTS.setProperties( "COMPONENTS.", properties);
		SHOW_RESULTS.setProperties( "SHOW_RESULTS.", properties);
		MULTIFILE_PSF.setProperties( "MULTIFILE_PSF.", properties);
		PROCESS_PARAMETERS.setProperties("PROCESS_PARAMETERS.", properties);
		DISTORTION.setProperties( "DISTORTION.", properties);
		LASER_POINTERS.setProperties("LASER.", properties);
		FLATFIELD_PARAMETERS.setProperties("FLATFIELD_PARAMETERS.", properties);
		PATTERN_PARAMETERS.setProperties ("PATTERN_PARAMETERS.", properties);
		LENS_DISTORTION_PARAMETERS.setProperties("LENS_DISTORTION_PARAMETERS.", properties);
		EYESIS_CAMERA_PARAMETERS.setProperties("EYESIS_CAMERA_PARAMETERS.", properties);
		LASERS.setProperties("LASERS.", properties);
		CAMERAS.setProperties("CAMERAS.", properties);
		DISTORTION_PROCESS_CONFIGURATION.setProperties("DISTORTION_PROCESS_CONFIGURATION.", properties);
		REFINE_PARAMETERS.setProperties("REFINE_PARAMETERS.", properties);
		FOCUS_MEASUREMENT_PARAMETERS.setProperties("FOCUS_MEASUREMENT_PARAMETERS.", properties);
		MOTORS.focusingHistory.setProperties("FOCUSING_HISTORY.", properties);
		GONIOMETER_PARAMETERS.setProperties("GONIOMETER_PARAMETERS.", properties);
		ABERRATIONS_PARAMETERS.setProperties("ABERRATIONS_PARAMETERS.", properties);
		if (FOCUSING_FIELD!=null) FOCUSING_FIELD.setProperties("FOCUSING_FIELD.", properties);
		boolean select= (properties.getProperty("selected")!=null);
		boolean select_MASTER_DEBUG_LEVEL=!select;
		boolean select_SHOW_AS_STACKS=!select;
		boolean select_FFT_SIZE=!select;
		boolean select_MAP_FFT_SIZE=!select;
		boolean select_GAUSS_WIDTH=!select;
		boolean select_FFT_OVERLAP=!select;
		boolean select_PSF_SUBPIXEL=!select;
		boolean select_PSF_SAVE_FILE=!select;
		boolean select_THREADS_MAX=!select;
		boolean select_UPDATE_STATUS=!select;
		boolean select_SIMUL=!select;
		boolean select_INTERPOLATE=!select;
		boolean select_INVERSE=!select;
		boolean select_PSF_PARS=!select;
		boolean select_OTF_FILTER=!select;
		boolean select_PATTERN_DETECT=!select;
		boolean select_COMPONENTS=!select;
		boolean select_SHOW_RESULTS=!select;
		boolean select_MULTIFILE_PSF=!select;
		boolean select_PROCESS_PARAMETERS=!select;
		boolean select_DISTORTION=!select;
		boolean select_LASER_POINTERS=!select;
		boolean select_FLATFIELD_PARAMETERS=!select;
		boolean select_PATTERN_PARAMETERS=!select;
		boolean select_LENS_DISTORTION_PARAMETERS=!select;
		boolean select_EYESIS_CAMERA_PARAMETERS=!select;
		boolean select_LASERS=!select;
		boolean select_CAMERAS=!select;
		boolean select_DISTORTION_PROCESS_CONFIGURATION=!select;
		boolean select_REFINE_PARAMETERS=!select;
		boolean select_FOCUS_MEASUREMENT_PARAMETERS=!select;
		boolean select_MOTORS_focusingHistory=!select;
		boolean select_GONIOMETER_PARAMETERS=!select;
		boolean select_ABERRATIONS_PARAMETERS=!select;
		boolean select_FOCUSING_FIELD=!select;
		if (select) {
		GenericDialog gd = new GenericDialog("Select parameters to save");
		gd.addMessage("===== Individual parameters ======");
		gd.addCheckbox("MASTER_DEBUG_LEVEL", select_MASTER_DEBUG_LEVEL);
		gd.addCheckbox("SHOW_AS_STACKS", select_SHOW_AS_STACKS);
		gd.addCheckbox("FFT_SIZE",select_FFT_SIZE);
		gd.addCheckbox("MAP_FFT_SIZE",select_MAP_FFT_SIZE);
		gd.addCheckbox("GAUSS_WIDTH",select_GAUSS_WIDTH);
		gd.addCheckbox("FFT_OVERLAP",select_FFT_OVERLAP);
		gd.addCheckbox("PSF_SUBPIXEL",select_PSF_SUBPIXEL);
		gd.addCheckbox("PSF_SAVE_FILE",select_PSF_SAVE_FILE);
		gd.addCheckbox("THREADS_MAX",select_THREADS_MAX);
		gd.addCheckbox("UPDATE_STATUS",select_UPDATE_STATUS);
		gd.addMessage("===== Parameter classes ======");
		gd.addCheckbox("SIMUL",select_SIMUL);
		gd.addCheckbox("INTERPOLATE",select_INTERPOLATE);
		gd.addCheckbox("INVERSE",select_INVERSE);
		gd.addCheckbox("PSF_PARS",select_PSF_PARS);
		gd.addCheckbox("OTF_FILTER",select_OTF_FILTER);
		gd.addCheckbox("PATTERN_DETECT",select_PATTERN_DETECT);
		gd.addCheckbox("COMPONENTS",select_COMPONENTS);
		gd.addCheckbox("SHOW_RESULTS",select_SHOW_RESULTS);
		gd.addCheckbox("MULTIFILE_PSF",select_MULTIFILE_PSF);
		gd.addCheckbox("PROCESS_PARAMETERS",select_PROCESS_PARAMETERS);
		gd.addCheckbox("DISTORTION",select_DISTORTION);
		gd.addCheckbox("LASER_POINTERS",select_LASER_POINTERS);
		gd.addCheckbox("FLATFIELD_PARAMETERS",select_FLATFIELD_PARAMETERS);
		gd.addCheckbox("PATTERN_PARAMETERS",select_PATTERN_PARAMETERS);
		gd.addCheckbox("LENS_DISTORTION_PARAMETERS",select_LENS_DISTORTION_PARAMETERS);
		gd.addCheckbox("EYESIS_CAMERA_PARAMETERS",select_EYESIS_CAMERA_PARAMETERS);
		gd.addCheckbox("LASERS",select_LASERS);
		gd.addCheckbox("CAMERAS",select_CAMERAS);
		gd.addCheckbox("DISTORTION_PROCESS_CONFIGURATION",select_DISTORTION_PROCESS_CONFIGURATION);
		gd.addCheckbox("REFINE_PARAMETERS",select_REFINE_PARAMETERS);
		gd.addCheckbox("FOCUS_MEASUREMENT_PARAMETERS",select_FOCUS_MEASUREMENT_PARAMETERS);
		gd.addCheckbox("MOTORS_focusingHistory",select_MOTORS_focusingHistory);
		gd.addCheckbox("GONIOMETER_PARAMETERS",select_GONIOMETER_PARAMETERS);
		gd.addCheckbox("ABERRATIONS_PARAMETERS",select_ABERRATIONS_PARAMETERS);
		gd.addCheckbox("FOCUSING_FIELD",select_FOCUSING_FIELD);
		WindowTools.addScrollBars(gd);
		gd.showDialog();
		if (gd.wasCanceled()) return;
		select_MASTER_DEBUG_LEVEL=gd.getNextBoolean();
		select_SHOW_AS_STACKS=gd.getNextBoolean();
		select_FFT_SIZE=gd.getNextBoolean();
		select_MAP_FFT_SIZE=gd.getNextBoolean();
		select_GAUSS_WIDTH=gd.getNextBoolean();
		select_FFT_OVERLAP=gd.getNextBoolean();
		select_PSF_SUBPIXEL=gd.getNextBoolean();
		select_PSF_SAVE_FILE=gd.getNextBoolean();
		select_THREADS_MAX=gd.getNextBoolean();
		select_UPDATE_STATUS=gd.getNextBoolean();

		select_SIMUL=gd.getNextBoolean();
		select_INTERPOLATE=gd.getNextBoolean();
		select_INVERSE=gd.getNextBoolean();
		select_PSF_PARS=gd.getNextBoolean();
		select_OTF_FILTER=gd.getNextBoolean();
		select_PATTERN_DETECT=gd.getNextBoolean();
		select_COMPONENTS=gd.getNextBoolean();
		select_SHOW_RESULTS=gd.getNextBoolean();
		select_MULTIFILE_PSF=gd.getNextBoolean();
		select_PROCESS_PARAMETERS=gd.getNextBoolean();
		select_DISTORTION=gd.getNextBoolean();
		select_LASER_POINTERS=gd.getNextBoolean();
		select_FLATFIELD_PARAMETERS=gd.getNextBoolean();
		select_PATTERN_PARAMETERS=gd.getNextBoolean();
		select_LENS_DISTORTION_PARAMETERS=gd.getNextBoolean();
		select_EYESIS_CAMERA_PARAMETERS=gd.getNextBoolean();
		select_LASERS=gd.getNextBoolean();
		select_CAMERAS=gd.getNextBoolean();
		select_DISTORTION_PROCESS_CONFIGURATION=gd.getNextBoolean();
		select_REFINE_PARAMETERS=gd.getNextBoolean();
		select_FOCUS_MEASUREMENT_PARAMETERS=gd.getNextBoolean();
		select_MOTORS_focusingHistory=gd.getNextBoolean();
		select_GONIOMETER_PARAMETERS=gd.getNextBoolean();
		select_ABERRATIONS_PARAMETERS=gd.getNextBoolean();
		select_FOCUSING_FIELD=gd.getNextBoolean();
		}

		if (select_MASTER_DEBUG_LEVEL) properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL+"");
		if (select_SHOW_AS_STACKS) properties.setProperty("SHOW_AS_STACKS", SHOW_AS_STACKS+"");// Show debug images as stacks (false - individual)
		if (select_FFT_SIZE) properties.setProperty("FFT_SIZE", FFT_SIZE+"");
		if (select_MAP_FFT_SIZE) properties.setProperty("MAP_FFT_SIZE", MAP_FFT_SIZE+"");// used to find where grid covers the image
		if (select_GAUSS_WIDTH) properties.setProperty("GAUSS_WIDTH", GAUSS_WIDTH+""); // 0.4 (0 - use Hamming window)
		if (select_FFT_OVERLAP) properties.setProperty("FFT_OVERLAP", FFT_OVERLAP+""); // createPSFMap()
		if (select_PSF_SUBPIXEL) properties.setProperty("PSF_SUBPIXEL", PSF_SUBPIXEL+""); // sub-pixel decimation
		if (select_PSF_SAVE_FILE) properties.setProperty("PSF_SAVE_FILE", PSF_SAVE_FILE+"");// save PSF array to a multi-slice TIFF file
		if (select_THREADS_MAX) properties.setProperty("THREADS_MAX", THREADS_MAX+""); // 100, testing multi-threading, limit maximal number of threads
		if (select_UPDATE_STATUS) properties.setProperty("UPDATE_STATUS", UPDATE_STATUS+""); // update ImageJ status info

		if (select_SIMUL) SIMUL.setProperties( "SIMUL.", properties);
		if (select_INTERPOLATE) INTERPOLATE.setProperties( "INTERPOLATE.", properties);
		if (select_INVERSE) INVERSE.setProperties( "INVERSE.", properties);
		if (select_PSF_PARS) PSF_PARS.setProperties( "PSF_PARS.", properties);
		if (select_OTF_FILTER) OTF_FILTER.setProperties( "OTF_FILTER.", properties);
		if (select_PATTERN_DETECT) PATTERN_DETECT.setProperties( "PATTERN_DETECT.", properties);
		if (select_COMPONENTS) COMPONENTS.setProperties( "COMPONENTS.", properties);
		if (select_SHOW_RESULTS) SHOW_RESULTS.setProperties( "SHOW_RESULTS.", properties);
		if (select_MULTIFILE_PSF) MULTIFILE_PSF.setProperties( "MULTIFILE_PSF.", properties);
		if (select_PROCESS_PARAMETERS) PROCESS_PARAMETERS.setProperties("PROCESS_PARAMETERS.", properties);
		if (select_DISTORTION) DISTORTION.setProperties( "DISTORTION.", properties);
		if (select_LASER_POINTERS) LASER_POINTERS.setProperties("LASER.", properties);
		if (select_FLATFIELD_PARAMETERS) FLATFIELD_PARAMETERS.setProperties("FLATFIELD_PARAMETERS.", properties);
		if (select_PATTERN_PARAMETERS) PATTERN_PARAMETERS.setProperties ("PATTERN_PARAMETERS.", properties);
		if (select_LENS_DISTORTION_PARAMETERS) LENS_DISTORTION_PARAMETERS.setProperties("LENS_DISTORTION_PARAMETERS.", properties);
		if (select_EYESIS_CAMERA_PARAMETERS) EYESIS_CAMERA_PARAMETERS.setProperties("EYESIS_CAMERA_PARAMETERS.", properties);
		if (select_LASERS) LASERS.setProperties("LASERS.", properties);
		if (select_CAMERAS) CAMERAS.setProperties("CAMERAS.", properties);
		if (select_DISTORTION_PROCESS_CONFIGURATION) DISTORTION_PROCESS_CONFIGURATION.setProperties("DISTORTION_PROCESS_CONFIGURATION.", properties);
		if (select_REFINE_PARAMETERS) REFINE_PARAMETERS.setProperties("REFINE_PARAMETERS.", properties);
		if (select_FOCUS_MEASUREMENT_PARAMETERS) FOCUS_MEASUREMENT_PARAMETERS.setProperties("FOCUS_MEASUREMENT_PARAMETERS.", properties);
		if (select_MOTORS_focusingHistory) MOTORS.focusingHistory.setProperties("FOCUSING_HISTORY.", properties);
		if (select_GONIOMETER_PARAMETERS) GONIOMETER_PARAMETERS.setProperties("GONIOMETER_PARAMETERS.", properties);
		if (select_ABERRATIONS_PARAMETERS) ABERRATIONS_PARAMETERS.setProperties("ABERRATIONS_PARAMETERS.", properties);
		if ((select_FOCUSING_FIELD) && (FOCUSING_FIELD!=null)) FOCUSING_FIELD.setProperties("FOCUSING_FIELD.", properties);
		if (select) properties.remove("selected");
		}
		/* ======================================================================== */
		public void getAllProperties(Properties properties){

src/main/java/FocusingField.java

+170 −133

Original line number	Diff line number	Diff line
		@@ -340,8 +340,20 @@ public class FocusingField {
		System.out.println("fieldFitting is not initialized, nothing to save");
		return;
		}

		fieldFitting.setProperties(prefix+"fieldFitting.",properties);
		boolean select= (properties.getProperty("selected")!=null);
		boolean select_fieldFitting=!select;
		boolean select_FOCUSING_FIELD=!select;
		if (select) {
		GenericDialog gd = new GenericDialog("Select FocusingField parameters to save");
		gd.addCheckbox("FieldFitting parameter class", select_fieldFitting);
		gd.addCheckbox("FocusingField local parameters", select_FOCUSING_FIELD);
		gd.showDialog();
		if (gd.wasCanceled()) return;
		select_fieldFitting=gd.getNextBoolean();
		select_FOCUSING_FIELD=gd.getNextBoolean();
		}
		if (select_fieldFitting) fieldFitting.setProperties(prefix+"fieldFitting.",properties);
		if (select_FOCUSING_FIELD){
		properties.setProperty(prefix+"pX0_distortions",pX0_distortions+"");
		properties.setProperty(prefix+"pY0_distortions",pY0_distortions+"");
		properties.setProperty(prefix+"currentPX0",currentPX0+"");
		@@ -419,6 +431,7 @@ public class FocusingField {
		}
		}
		}
		}

		public void getProperties(String prefix,Properties properties){
		savedProperties=properties;
		@@ -4574,13 +4587,36 @@ public boolean LevenbergMarquardt(
		if (debugLevel>1) System.out.println ("Mechanical properties not yet initialized, will save properties later");
		return;
		}
		properties.setProperty(prefix+"numberOfLocations",numberOfLocations+"");
		properties.setProperty(prefix+"centerSelect_X",centerSelect[0]+"");
		properties.setProperty(prefix+"centerSelect_Y",centerSelect[1]+"");
		mechanicalFocusingModel.setProperties(prefix+"mechanicalFocusingModel.",properties);
		boolean select= (properties.getProperty("selected")!=null);
		boolean select_mechanicalFocusingModel=!select;
		boolean select_curvatureModel=!select;
		boolean select_fieldStrategies=!select;
		boolean select_FieldFitting=!select;
		if (select) {
		GenericDialog gd = new GenericDialog("Select FieldFitting parameters to save");
		gd.addCheckbox("MechanicalFocusingModel parameter class", select_mechanicalFocusingModel);
		gd.addCheckbox("CurvatureModel parameter classes", select_curvatureModel);
		gd.addCheckbox("FieldStrategies parameter classes", select_fieldStrategies);
		gd.addCheckbox("FieldFitting local parameters", select_FieldFitting);
		gd.showDialog();
		if (gd.wasCanceled()) return;
		select_mechanicalFocusingModel=gd.getNextBoolean();
		select_curvatureModel=gd.getNextBoolean();
		select_fieldStrategies=gd.getNextBoolean();
		select_FieldFitting=gd.getNextBoolean();
		}

		if (select_mechanicalFocusingModel) mechanicalFocusingModel.setProperties(prefix+"mechanicalFocusingModel.",properties);
		if (select_curvatureModel) {
		for (int i=0;i<curvatureModel.length;i++){
		if (curvatureModel[i]!=null) curvatureModel[i].setProperties(prefix+"curvatureModel_"+i+".",properties);
		}
		}
		if (select_FieldFitting) {
		properties.setProperty(prefix+"numberOfLocations",numberOfLocations+"");
		properties.setProperty(prefix+"centerSelect_X",centerSelect[0]+"");
		properties.setProperty(prefix+"centerSelect_Y",centerSelect[1]+"");

		if (channelSelect!=null) for (int i=0;i<channelSelect.length;i++){
		properties.setProperty(prefix+"channelSelect_"+i,channelSelect[i]+"");
		}
		@@ -4613,7 +4649,8 @@ public boolean LevenbergMarquardt(
		}
		}
		}
		fieldStrategies.setProperties(prefix+"fieldStrategies.",properties);
		}
		if (select_fieldStrategies) fieldStrategies.setProperties(prefix+"fieldStrategies.",properties);
		}
		public void getProperties(String prefix,Properties properties){
		if (properties.getProperty(prefix+"numberOfLocations")!=null)

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