fixing bugs for variable images per set (e.g. eo only) (3fd21c81) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

+141 −24

Original line number	Diff line number	Diff line
		@@ -615,6 +615,12 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
		public static double [][][][] PSF_KERNEL_MAP=null; // remove?
		public static String [] COMPONENT_COLOR_NAMES={"green1","red","blue","green2", "greens (diagonal)", "greens (checker)"};
		public static String [] STACK_COLOR_NAMES={"red","green","blue"};

		// last used values for dialogs to suggest next time
		public int LASTUSED_RECALIB_SET = -1;
		public int LASTUSED_RECALIB_CHN = -1;
		public int LASTUSED_MAN_HINT = -1;

		/**
		* DIST_ARRAY:
		* [v][u][0][0] - pixel x of the grid node u,v
		@@ -9379,12 +9385,12 @@ if (MORE_BUTTONS) {
		}
		LENS_DISTORTIONS.debugLevel=DEBUG_LEVEL;
		GenericDialog gd=new GenericDialog("Select grid image to add manual hint");
		gd.addNumericField("Grid Image index", 0,0);
		gd.addNumericField("Grid Image index", LASTUSED_MAN_HINT,0);

		gd.showDialog();
		if (gd.wasCanceled()) return;
		int numGridImage= (int) gd.getNextNumber();

		LASTUSED_MAN_HINT = numGridImage;
		LENS_DISTORTIONS.manualGridHint(numGridImage);
		return;
		}
		@@ -9552,13 +9558,32 @@ if (MORE_BUTTONS) {


		public boolean recalibrateSet() {
		int imageSetNumber = LASTUSED_RECALIB_SET;
		int sel_chn = LASTUSED_RECALIB_CHN;
		boolean reEstimate= true;
		boolean use_eo = true;
		boolean use_lwir = true;
		// double grid_mismatch = 0.1;
		GenericDialog gd=new GenericDialog ("Select image set to re-calibrate");
		gd.addNumericField("Image set number", 0, 0);
		gd.addCheckbox ("Set image set parameters from closest, (re-)estimate orientation", true);
		gd.addNumericField("Image set number", imageSetNumber, 0);
		gd.addCheckbox ("Set image set parameters from closest, (re-)estimate orientation", reEstimate);
		gd.addCheckbox ("Use RGB grids for matching", use_eo);
		gd.addCheckbox ("Use LWIR grids for matching", use_lwir);
		gd.addNumericField("Use single channel (<0 - use all unfiltered)", sel_chn, 0);
		// TODO: distribute results to unselected images
		// gd.addNumericField("Remove outlier channels if relative grid mismatch is above ", grid_mismatch, 2,6,"");
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		int imageSetNumber=(int) gd.getNextNumber();
		boolean reEstimate=gd.getNextBoolean();
		imageSetNumber=(int) gd.getNextNumber();
		reEstimate=gd.getNextBoolean();
		use_eo = gd.getNextBoolean();
		use_lwir = gd.getNextBoolean();
		sel_chn =(int) gd.getNextNumber();

		LASTUSED_RECALIB_SET = imageSetNumber;
		LASTUSED_RECALIB_CHN = sel_chn;

		// grid_mismatch = gd.getNextNumber();
		if (imageSetNumber<0) return false;
		if (reEstimate){
		// boolean OK=
		@@ -9617,12 +9642,25 @@ if (MORE_BUTTONS) {
		useSetsData= gd.getNextBoolean();
		processAllImages= gd.getNextBoolean();

		// Find channel with most weight
		// Find channel with most weight ???
		LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerTilt=tiltCenter;
		LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerAxial=axialCenter;
		LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].interAxisAngle=interCenter;
		// Run once with center position or Goniometer angles to determine average derivatives
		int [][] imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(!processAllImages);
		int tmask = (use_eo ? 1 : 0) + (use_lwir ? 2 : 0);
		int [] type_map = LWIR_PARAMETERS.getTypeMap(); // 0 - eo, 1 -0 lwir
		boolean [] chn_sel = new boolean [type_map.length];
		if (sel_chn >= 0) {
		chn_sel[sel_chn] = true;
		} else {
		for (int chn = 0; chn < chn_sel.length; chn++) {
		chn_sel[chn] = (tmask & ( 1 << type_map[chn])) != 0;
		}
		}
		int [][] imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(
		!processAllImages,
		chn_sel
		);
		int [] imageSet=imageSets[imageSetNumber];
		if (imageSet==null){
		IJ.showMessage("Image set #"+imageSetNumber+" is empty");
		@@ -9727,7 +9765,9 @@ if (MORE_BUTTONS) {
		" Initial tilt=" + tilt0+
		" Initial axial=" + axial0+
		" Initial inter=" + interCenter);
		imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(!processAllImages);
		imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(
		!processAllImages,
		chn_sel);
		imageSet=imageSets[imageSetNumber];
		if (imageSet==null){
		IJ.showMessage("Image set #"+imageSetNumber+" is empty");
		@@ -9806,7 +9846,9 @@ if (MORE_BUTTONS) {
		" Initial axial="+best_axial+
		" Initial inter="+best_inter
		);
		imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(!processAllImages);
		imageSets=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.listImages(
		!processAllImages,
		chn_sel);
		imageSet=imageSets[imageSetNumber];
		if (imageSet==null){
		IJ.showMessage("Image set #"+imageSetNumber+" is empty");
		@@ -10172,21 +10214,34 @@ if (MORE_BUTTONS) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
		// Maybe wrong ! Use folders that have at least all EO channels?
		int min_files = lwirReaderParameters.getNumChannels();// 8; // use folders that have all 8 files
		// int min_files = lwirReaderParameters.getNumChannels();// 8; // use folders that have all 8 files
		int [] type_map = lwirReaderParameters.getTypeMap(); // 0 - eo, 1 -0 lwir

		int lwir_chn0 = lwirReaderParameters.getLwirChn0();
		int eo_chn0 = lwirReaderParameters.getEoChn0();
		int numStations = 3;
		boolean allornone_all = false;
		boolean allornone_eo = true;
		boolean allornone_lwir = true;
		GenericDialog gd = new GenericDialog("Setup Goniometer/Camera Stations");
		gd.addMessage ("Setting up calibration that includes multiple camera tripod or goniometer positions.");
		gd.addMessage ("File selection dialog will open for each station separateley.");
		gd.addNumericField("Number of goniometer/camera stations", numStations,0);
		gd.addMessage ("lwir_chn0 = "+lwir_chn0);
		gd.addMessage ("eo_chn0 = "+eo_chn0);
		gd.addMessage("min_files = "+min_files);
		// gd.addMessage ("min_files = "+min_files);
		gd.addCheckbox ("Process only sets with all channels present", allornone_all);
		gd.addCheckbox ("Process eo channels in a set only if all eo channels are present", allornone_eo);
		gd.addCheckbox ("Process lwir channels in a set only if all lwir channels are present", allornone_lwir);


		gd.showDialog();
		if (gd.wasCanceled()) return false;
		numStations= (int) gd.getNextNumber();
		allornone_all = gd.getNextBoolean();
		allornone_eo = gd.getNextBoolean();
		allornone_lwir = gd.getNextBoolean();

		// String [] grid_extensions={".tif",".tiff"};
		// String [] src_extensions={".tif",".tiff"};
		String [] grid_extensions={".tiff"};
		@@ -10200,12 +10255,14 @@ if (MORE_BUTTONS) {
		// new CalibrationFileManagement.DirectoryContentsFilter (gridFilter, min_files, 0, null);

		String [][] gridFileDirs= new String [numStations][];
		// int [][] gridUseTypes = new int [numStations][]; // +1 - use eo channels,+2 - use lwir channels (in pointed set)
		boolean [][][] gridUseChn = new boolean [numStations][][]; // channels to use in each scene
		String [] sourceStationDirs = new String [numStations]; // directories of the source files per station

		for (int numStation=0;numStation<numStations;numStation++){
		DirectoryChoser dc = new DirectoryChoser(
		gridFilter,
		min_files, // not actually used
		type_map.length, // min_files, // not actually used
		0,
		null);
		dc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
		@@ -10219,11 +10276,56 @@ if (MORE_BUTTONS) {
		dc.setCurrentDirectory(cur_dir);
		int returnVal = dc.showOpenDialog(IJ.getInstance());
		if (returnVal!=JFileChooser.APPROVE_OPTION) return false;
		File [] files = dc.getSelectedFiles();
		File [] files = dc.getSelectedFiles(); // set directory nome
		if (files.length<1) return false;
		// Can not make it work correctly with multiple selection, giving up for now
		ArrayList<File> filelist = new ArrayList<File>();
		for (int nFile=0;nFile<files.length;nFile++) {
		class ScenePathChnFilter{
		File file;
		boolean [] channels;
		ScenePathChnFilter(File file, boolean [] channels){
		this.file=file;
		this.channels = channels; // clone?
		}

		}
		// ArrayList<File> setlist = new ArrayList<File>();
		// ArrayList<Integer> settypes = new ArrayList<Integer>();
		ArrayList<ScenePathChnFilter> setlist = new ArrayList<ScenePathChnFilter>();

		for (int nSet=0;nSet<files.length;nSet++) { // nfile - scene number
		String [] sfiles = files[nSet].list(gridFilter);
		boolean [] avail_chn = new boolean[type_map.length];
		for (String sfile: sfiles) {
		avail_chn[DistortionCalibrationData.pathToChannel(sfile)] = true;
		}
		boolean [] all_type = {true, true};
		boolean [] some_type = {false, false};
		for (int i = 0; i < avail_chn.length; i++) {
		if (avail_chn[i]) {
		some_type[type_map[i]] = true;
		} else {
		all_type[type_map[i]] = false;
		}
		}
		if (allornone_all && !(all_type[0] && all_type[1])) {
		some_type[0] = false;
		some_type[1] = false;
		}
		if (allornone_eo) some_type[0] = all_type[0];
		if (allornone_lwir) some_type[1] = all_type[1];

		if (some_type[0] \|\| some_type[1]) {
		for (int i = 0; i < avail_chn.length; i++) {
		avail_chn[i] &= some_type[type_map[i]];
		}
		setlist.add(new ScenePathChnFilter(files[nSet], avail_chn));
		// setlist.add(files[nSet]);
		// settypes.add((some_type[0]?1:0)+(some_type[1]?2:0));
		}
		/*

		// for (int nFile=0;nFile<files.length;nFile++) {

		int num_match = files[nFile].list(gridFilter).length;
		if (num_match >= min_files) {
		filelist.add(files[nFile]);
		@@ -10235,11 +10337,20 @@ if (MORE_BUTTONS) {
		// }
		// System.out.println("");
		}
		*/
		}
		/*
		int chn = pathToChannel(path);

		gridFileDirs[numStation]=new String[filelist.size()];
		for (int nFile=0;nFile<gridFileDirs[numStation].length;nFile++) {
		gridFileDirs[numStation][nFile]= filelist.get(nFile).getPath();
		*/
		gridFileDirs[numStation]=new String[setlist.size()];
		gridUseChn[numStation]=new boolean [gridFileDirs[numStation].length][];
		for (int nSet=0;nSet<gridFileDirs[numStation].length;nSet++) {
		ScenePathChnFilter scene = setlist.get(nSet);
		gridFileDirs[numStation][nSet]= scene.file.getPath();
		gridUseChn[numStation][nSet] = scene.channels;
		// gridFileDirs[numStation][nSet]= setlist.get(nSet).getPath();
		// gridUseTypes[numStation][nSet]=settypes.get(nSet);
		}
		if ((gridFileDirs[numStation]==null) \|\| (gridFileDirs[numStation].length==0)) {
		if (!IJ.showMessageWithCancel("No files selected","Retry? (Cancel will abort the command)")) return false;
		@@ -10279,6 +10390,8 @@ if (MORE_BUTTONS) {

		DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // new way for LWIR - initialize from dirs
		gridFileDirs,
		gridUseChn, //
		// gridUseTypes, //int [][] gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)
		sourceStationDirs,
		gridFilter,
		sourceFilter,
		@@ -10482,6 +10595,10 @@ if (MORE_BUTTONS) {
		}
		saved_file++;
		}
		if (this.SYNC_COMMAND.stopRequested.get() > 0) {
		System.out.println("User requested stop2");
		break;
		}
		}
		if (DEBUG_LEVEL>0) System.out.println(((this.SYNC_COMMAND.stopRequested.get()>0)?"Partial (interrupted by user) set of grids":"All")+ " grids calculation done at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		return;

src/main/java/com/elphel/imagej/calibration/DistortionCalibrationData.java

+74 −24

Original line number	Diff line number	Diff line
		@@ -92,6 +92,18 @@ import ij.text.TextWindow;
		public boolean updateStatus=true;
		public int debugLevel=2;
		private ShowDoubleFloatArrays SDFA_INSTANCE=null; // just for debugging

		public static int pathToChannel(String path) {
		int last_dash = path.lastIndexOf('-');
		int last = path.lastIndexOf('_');
		if (last_dash >last) last = last_dash;
		int last_dot = path.lastIndexOf('.');
		if (last_dot < 0) {
		last_dot = path.length();
		}
		return Integer.parseInt(path.substring(last+1, last_dot));
		}

		public int getNumStations(){
		return (eyesisCameraParameters==null)?0:eyesisCameraParameters.getNumStations();
		}
		@@ -839,6 +851,8 @@ import ij.text.TextWindow;

		public DistortionCalibrationData (
		String [][] stationFilenames,
		boolean [][][] gridUseChn, // per station, per set - a bmask of permitted channels
		// int [][] gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)
		String [] source_dirs, // directories of the source files per station
		MultipleExtensionsFileFilter gridFilter,
		MultipleExtensionsFileFilter sourceFilter,
		@@ -852,6 +866,8 @@ import ij.text.TextWindow;
		this.debugLevel=debugLevel;
		setupDirDistortionCalibrationData(
		stationFilenames,
		gridUseChn, // per station, per set - a bmask of permitted channels
		// gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)
		source_dirs, // directories of the source files per station
		gridFilter,
		sourceFilter,
		@@ -933,6 +949,7 @@ import ij.text.TextWindow;
		// from data organized as image sets
		public static int getChannelFromPath(String path) {
		// int indexSuffix=path.length()-suffix.length();
		if (path == null) return -1;
		int indexSuffix = path.lastIndexOf(".");
		int indexLastDash=indexSuffix-1;
		while ((indexLastDash>0) &&
		@@ -951,6 +968,8 @@ import ij.text.TextWindow;

		public void setupDirDistortionCalibrationData (
		String [][] stationFilenames, // per-station List of image set directories
		boolean [][][] gridUseChn, // per station, per set - a bmask of permitted channels
		// int [][] gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)
		String [] source_dirs, // directories of the source files per station
		MultipleExtensionsFileFilter gridFilter,
		MultipleExtensionsFileFilter sourceFilter,
		@@ -971,6 +990,7 @@ import ij.text.TextWindow;
		String [] getSourcePaths() {return spaths;} // may not be null
		DirTs(int station,
		String dir, // grid image set directory that contains channel files (may be different timestamps)
		boolean [] permitted_channels, // bitmask of permitted channels (lwir/eo), or null - use nay
		String sdir, // source super directory that contains image set directories with files
		int num_chn,
		MultipleExtensionsFileFilter gridFilter,
		@@ -993,6 +1013,7 @@ import ij.text.TextWindow;
		String [] files = (new File(dir)).list(gridFilter); // are these full files?
		paths = new String[num_chn];
		for (String path:files) {
		/*
		int last_dash = path.lastIndexOf('-');
		int last = path.lastIndexOf('_');
		if (last_dash >last) last = last_dash;
		@@ -1001,7 +1022,11 @@ import ij.text.TextWindow;
		last_dot = path.length();
		}
		int chn = Integer.parseInt(path.substring(last+1, last_dot));
		*/
		int chn = pathToChannel(path);
		if ((permitted_channels == null) \|\| (permitted_channels[chn])) {
		paths[chn] = (new File(dir,path)).getPath();
		}
		//grid-elphelimg_1559195695_507621_4.tiff
		}
		spaths = new String[num_chn];
		@@ -1014,6 +1039,7 @@ import ij.text.TextWindow;
		System.out.println("sfiles == null");
		}
		for (String spath:sfiles) {
		/*
		int last_dash = spath.lastIndexOf('-');
		int last = spath.lastIndexOf('_');
		if (last_dash >last) last = last_dash;
		@@ -1022,6 +1048,8 @@ import ij.text.TextWindow;
		last_dot = spath.length();
		}
		int chn = Integer.parseInt(spath.substring(last+1, last_dot));
		*/
		int chn = pathToChannel(spath);
		spaths[chn] = (new File(set_dir,spath)).getPath();
		}
		}
		@@ -1040,6 +1068,7 @@ import ij.text.TextWindow;
		dirTsList.add(new DirTs(
		numStation,
		stationFilenames[numStation][is], // String dir,
		gridUseChn[numStation][is], //
		source_dirs[numStation],
		numSubCameras, // int num_chn,
		gridFilter,
		@@ -1297,7 +1326,8 @@ import ij.text.TextWindow;
		// boolean invert_color = ((base_channel ^ nc) & 4) != 0;
		boolean invert_color = invertColor(base_channel) ^ invertColor(nc); // eyesisCameraParameters.isLWIR(main_channel);

		if ((this.gIS[nis].imageSet[nc].matchedPointers <= 0) && (nc != base_channel)) { // Later add non-laser conditions
		if ( (this.gIS[nis].imageSet[nc] != null) &&
		(this.gIS[nis].imageSet[nc].matchedPointers <= 0) && (nc != base_channel)) { // Later add non-laser conditions
		int imgNum = this.gIS[nis].imageSet[nc].imgNumber; // with_pointers - base_channel + nc;
		if (this.updateStatus) IJ.showStatus("Re-reading grid file "+(imgNum+1)+" (of "+(numFiles)+"): "+this.gIP[imgNum].path);
		if (this.debugLevel>-1) System.out.print(imgNum+"*("+this.gIP[imgNum].getStationNumber()+
		@@ -2442,16 +2472,36 @@ import ij.text.TextWindow;
		* create list of image indices per image set
		* @return array of image indices for each image set
		*/
		public int [][] listImages(boolean enabledOnly){
		public int [][] listImages(
		boolean enabledOnly,
		//int type_mask // 0 - all, otherwise +1 - eo, +2 - lwir
		boolean [] chn_sel // selected channels or null
		){
		int [][] imageSets = new int [this.gIS.length][];
		for (int i=0;i<this.gIS.length;i++){
		int setSize=0;
		for (int n=0;n<this.gIS[i].imageSet.length;n++) if ((this.gIS[i].imageSet[n]!=null) && (this.gIS[i].imageSet[n].imgNumber>=0) && (!enabledOnly \|\| this.gIS[i].imageSet[n].enabled)) setSize++;
		for (int n=0;n<this.gIS[i].imageSet.length;n++) {
		if ( (this.gIS[i].imageSet[n]!=null) &&
		(this.gIS[i].imageSet[n].imgNumber>=0) &&
		(!enabledOnly \|\| this.gIS[i].imageSet[n].enabled)) {
		if ((chn_sel == null) \|\| (chn_sel[this.gIS[i].imageSet[n].getChannel()])){
		setSize++;
		}
		}
		}
		imageSets[i]=new int [setSize];
		}
		for (int i=0;i<this.gIS.length;i++){
		int index=0;
		for (int n=0;n<this.gIS[i].imageSet.length;n++) if ((this.gIS[i].imageSet[n]!=null) && (this.gIS[i].imageSet[n].imgNumber>=0) && (!enabledOnly \|\| this.gIS[i].imageSet[n].enabled)) imageSets[i][index++]=this.gIS[i].imageSet[n].imgNumber;
		for (int n=0;n<this.gIS[i].imageSet.length;n++) {
		if ( (this.gIS[i].imageSet[n]!=null) &&
		(this.gIS[i].imageSet[n].imgNumber>=0) &&
		(!enabledOnly \|\| this.gIS[i].imageSet[n].enabled)) {
		if ((chn_sel == null) \|\| (chn_sel[this.gIS[i].imageSet[n].getChannel()])){
		imageSets[i][index++]=this.gIS[i].imageSet[n].imgNumber;
		}
		}
		}
		}
		return imageSets;
		}
		@@ -4466,7 +4516,7 @@ import ij.text.TextWindow;
		}
		return small_sensors;
		}
		public boolean isSmallSensor(int numImg) {
		public boolean isSmallSensor(int numImg) { // number of image, not a channel!!!
		boolean [] ss = getSmallSensors();
		if ((this.gIP != null) && (numImg >= 0) && (numImg < this.gIP.length)){
		return ss[this.gIP[numImg].getChannel()];

Admin message