Improved ML output, testing batch execution

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

@@ -201,7 +201,10 @@ public class EyesisCorrectionParameters {
     	public String x3dModelVersion="v01";
     	public String jp4SubDir="jp4"; // FIXME:
 
+    	public String linkedModels="";   // linked models with reference scenes
     	public String x3dDirectory="";
+    	public String videoDirectory=""; // combined (with MPEG) from multiple scene sequences video files
+
 
     	public String mlDirectory="ml";
 
@@ -308,6 +311,8 @@ public class EyesisCorrectionParameters {
   			cp.referenceExposure=    	this.referenceExposure;
   			cp.relativeExposure=    	this.relativeExposure;
   			cp.swapSubchannels01=    	this.swapSubchannels01;
+  			cp.linkedModels=    		this.linkedModels;
+  			cp.videoDirectory=    		this.videoDirectory;
   			cp.x3dDirectory=    		this.x3dDirectory;
   			cp.mlDirectory=    	     	this.mlDirectory;
   			cp.use_x3d_subdirs=    		this.use_x3d_subdirs;
@@ -514,6 +519,8 @@ public class EyesisCorrectionParameters {
     		properties.setProperty(prefix+"cltKernelPrefix",       this.cltKernelPrefix);
     		properties.setProperty(prefix+"cltSuffix",             this.cltSuffix);
 
+    		properties.setProperty(prefix+"linkedModels",          this.linkedModels);
+    		properties.setProperty(prefix+"videoDirectory",        this.videoDirectory);
     		properties.setProperty(prefix+"x3dDirectory",          this.x3dDirectory);
     		properties.setProperty(prefix+"use_x3d_subdirs",       this.use_x3d_subdirs+"");
 
@@ -701,6 +708,8 @@ public class EyesisCorrectionParameters {
 			if (properties.getProperty(prefix+"cltKernelPrefix")!=      null) this.cltKernelPrefix=properties.getProperty(prefix+"cltKernelPrefix");
 			if (properties.getProperty(prefix+"cltSuffix")!=            null) this.cltSuffix=properties.getProperty(prefix+"cltSuffix");
 
+			if (properties.getProperty(prefix+"linkedModels")!=         null) this.linkedModels=properties.getProperty(prefix+"linkedModels");
+			if (properties.getProperty(prefix+"videoDirectory")!=       null) this.videoDirectory=properties.getProperty(prefix+"videoDirectory");
 			if (properties.getProperty(prefix+"x3dDirectory")!=         null) this.x3dDirectory=properties.getProperty(prefix+"x3dDirectory");
 
 			if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean(properties.getProperty(prefix+"use_x3d_subdirs"));
@@ -870,8 +879,18 @@ public class EyesisCorrectionParameters {
 
     		gd.addStringField ("x3d model version",                                this.x3dModelVersion, 20);    // 10a
     		gd.addStringField ("JP4 source image copy model subdirectory",         this.jp4SubDir, 20);    // 10b
+    		
+    		gd.addStringField ("Linked reference models",                          this.linkedModels, 60,
+    				"Directory where links to reference models directories will be created.");
+    		gd.addCheckbox    ("Select linked reference models directory",         false);
+    		
+    		gd.addStringField ("Video directory",                                  this.videoDirectory, 60,
+    				"Directory to store combined video files.");
+    		gd.addCheckbox    ("Select video directory",                           false);
+    		
     		gd.addStringField ("x3d output directory",                             this.x3dDirectory, 60);
     		gd.addCheckbox    ("Select x3d output directory",                      false);
+    		
     		gd.addCheckbox    ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs);
 
     		gd.addStringField ("x3d subdirectory prefix",                          this.x3dSubdirPrefix, 10,
@@ -994,6 +1013,8 @@ public class EyesisCorrectionParameters {
     		this.cltKernelDirectory=     gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true);
     		this.x3dModelVersion=        gd.getNextString(); // 10a
     		this.jp4SubDir=              gd.getNextString(); // 10b
+    		this.linkedModels=           gd.getNextString(); if (gd.getNextBoolean()) selectLinkedModelsDirectory(false, true);
+    		this.videoDirectory=         gd.getNextString(); if (gd.getNextBoolean()) selectVideoDirectory(false, true);
     		this.x3dDirectory=           gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);
     		this.use_x3d_subdirs=        gd.getNextBoolean();
 
@@ -1065,6 +1086,15 @@ public class EyesisCorrectionParameters {
     		
     		gd.addStringField ("x3d model version",                                this.x3dModelVersion, 60);    // 10a
     		gd.addStringField ("jp4 source copy subdirectory",                     this.jp4SubDir, 60);          // 10b
+    		
+    		gd.addStringField ("Linked reference models",                          this.linkedModels, 60,
+    				"Directory where links to reference models directories will be created.");
+    		gd.addCheckbox    ("Select linked reference models directory",         false);
+    		
+    		gd.addStringField ("Video directory",                                  this.videoDirectory, 60,
+    				"Directory to store combined video files.");
+    		gd.addCheckbox    ("Select video directory",                           false);
+    		
     		gd.addStringField ("x3d output directory",                             this.x3dDirectory, 60);       // 8
     		gd.addCheckbox    ("Select x3d output (top model) directory",          false);                       // 9
 
@@ -1230,6 +1260,8 @@ public class EyesisCorrectionParameters {
     		
     		this.x3dModelVersion=        gd.getNextString(); //  10a
     		this.jp4SubDir=              gd.getNextString(); //  10b
+    		this.linkedModels=           gd.getNextString(); if (gd.getNextBoolean()) selectLinkedModelsDirectory(false, true);
+    		this.videoDirectory=         gd.getNextString(); if (gd.getNextBoolean()) selectVideoDirectory(false, true);
     		this.x3dDirectory=           gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);       // 9
     		this.use_x3d_subdirs=        gd.getNextBoolean(); // 10
 //    		this.sourcePrefix=           gd.getNextString();  // 13
@@ -2192,6 +2224,31 @@ public class EyesisCorrectionParameters {
     		return dir;
     	}
 
+    	public String selectLinkedModelsDirectory(boolean smart, boolean newAllowed) {
+    		String dir= CalibrationFileManagement.selectDirectory(
+    				smart,
+    				newAllowed, // save
+    				"linked models directory", // title
+    				"Select linked models directory", // button
+    				null, // filter
+    				this.linkedModels); //this.sourceDirectory);
+    		if (dir!=null) this.linkedModels=dir;
+    		return dir;
+    	}
+
+    	public String selectVideoDirectory(boolean smart, boolean newAllowed) {
+    		String dir= CalibrationFileManagement.selectDirectory(
+    				smart,
+    				newAllowed, // save
+    				"video directory", // title
+    				"Select video directory", // button
+    				null, // filter
+    				this.videoDirectory); //this.sourceDirectory);
+    		if (dir!=null) this.videoDirectory=dir;
+    		return dir;
+    	}
+    	
+    	
     	public String selectMlDirectory(String name, boolean smart, boolean newAllowed) {
     		if ((name != null) && (this.mlDirectory.length()>0) && (!this.mlDirectory.contains(Prefs.getFileSeparator()))) {
     			// relative to the X3D model version
@@ -2218,7 +2275,6 @@ public class EyesisCorrectionParameters {
     	// select qualified (by 'name' - quad timestamp) x3d subdirectory
 
     	public String selectX3dDirectory(String name, String version, boolean smart, boolean newAllowed) {
-
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,
     				newAllowed, // save

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -1118,14 +1118,17 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			default:
 				LOG_LEVEL = "OFF";
 			}
-
+			LOG_LEVEL = "ERROR"; // setting it here to shut up?
 			boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
 			if (!LOG_LEVEL_SET) { // only first time true
 				loci.common.DebugTools.setRootLevel(LOG_LEVEL);
 			}
 			System.out.println("DEBUG_LEVEL = " + DEBUG_LEVEL + ", CLT_PARAMETERS.lwir.getDebugLevel() = "
-					+ CLT_PARAMETERS.lwir.getDebugLevel() + " LOG_LEVEL=" + LOG_LEVEL + "LOG_LEVEL_SET="
+					+ CLT_PARAMETERS.lwir.getDebugLevel() + " LOG_LEVEL=" + LOG_LEVEL + " LOG_LEVEL_SET="
 					+ LOG_LEVEL_SET);
+			//https://www.javadoc.io/doc/org.openmicroscopy/ome-common/6.0.5/loci/common/DebugTools.html#enableLogging(java.lang.String)
+			// Temporary overwrite with public static boolean enableIJLogging​(boolean debug)
+			loci.common.DebugTools.enableIJLogging(false);
 		}
 
 		/* ======================================================================== */

src/main/java/com/elphel/imagej/readers/ElphelJp4Reader.java

@@ -107,7 +107,7 @@ public class ElphelJp4Reader  extends ImageIOReader{
 		// or these readers are combined with all other readers in readers.txt
 		suffixNecessary = true; // false
 		suffixSufficient = true; // false;
-		LOGGER.debug("ElphelTiffReader(), after super()");
+		LOGGER.info("ElphelTiffReader(), after super()");
 		if (REPLACEMENT_TAG_MAP == null) {
 			REPLACEMENT_TAG_MAP = new HashMap<String,String>();
 			for (String [] line: REPLACEMENT_TAGS) {
@@ -156,15 +156,15 @@ public class ElphelJp4Reader  extends ImageIOReader{
 	public void setId(String id) throws FormatException, IOException { // same as for tiff?
 		image_bytes = null;
 //		buffered_data = null;
-		LOGGER.debug("setId("+id+"). before super" );
+		LOGGER.info("setId("+id+"). before super" );
 		file_initialized = false;
 		mapped_externally = false;
 
 		if (Location.getIdMap().containsKey(id)) {
-			LOGGER.debug("id '"+id+"' is already mapped" );
+			LOGGER.info("id '"+id+"' is already mapped" );
 			content_fileName = id; // id; // maybe set to null to handle externally?
 			mapped_externally = true;
-			LOGGER.debug("Starting initFile() method, read file directly");
+			LOGGER.info("Starting initFile() method, read file directly");
 			super.setId(id);
 		} else {
 			// If URL, then read to memory, if normal file - use direct access
@@ -177,7 +177,7 @@ public class ElphelJp4Reader  extends ImageIOReader{
 //				LOGGER.warn("Bad URL1: " + id); // will try direct file, not an error
 			}
 			if (url != null) {
-				LOGGER.debug("Starting initFile() method, read "+ id +" to memory first");
+				LOGGER.info("Starting initFile() method, read "+ id +" to memory first");
 				//https://www.rgagnon.com/javadetails/java-0487.html
 				URLConnection connection = url.openConnection();
 
@@ -194,44 +194,44 @@ public class ElphelJp4Reader  extends ImageIOReader{
 					content_fileName = "unknown." + suffix;
 				}
 				//	 			currentId = fileName; //???
-				//	 			LOGGER.debug("Mime type = "+mime);
+				//	 			LOGGER.info("Mime type = "+mime);
 				// https://stackoverflow.com/questions/2793150/how-to-use-java-net-urlconnection-to-fire-and-handle-http-requests
 
 				//https://stackoverflow.com/questions/2295221/java-net-url-read-stream-to-byte
 				InputStream is =    url.openStream (); //
 				byte[] inBytes = IOUtils.toByteArray(is);
 				if (is != null) is.close();
-				LOGGER.debug("Bytes read: "+ inBytes.length);
+				LOGGER.info("Bytes read: "+ inBytes.length);
 				Location.mapFile(content_fileName, new ByteArrayHandle(inBytes));
 //				HashMap<String,Object> dbg_loc = Location.getIdMap();
 				super.setId(content_fileName);
 			} else { // read file normally
 				content_fileName = id;
-				LOGGER.debug("read file directly");
+				LOGGER.info("read file directly");
 				super.setId(id);
 			}
 		}
 
 		//getReader
 		//	    super.setId(id);
-		LOGGER.debug("setId("+id+"). after super" );
+		LOGGER.info("setId("+id+"). after super" );
 		file_initialized = true;
 	}
 
 	/* @see loci.formats.FormatReader#initFile(String) */
 	@Override
 	protected void initFile(String id) throws FormatException, IOException {
-		LOGGER.debug("initFile("+id+"), currentId="+currentId+",  before super" );
+		LOGGER.info("initFile("+id+"), currentId="+currentId+",  before super" );
 		try {
 			super.initFile(id); // fails class_not_found
 		}
 		catch (IllegalArgumentException e) {
 			throw new FormatException(e);
 		}
-		LOGGER.debug("initFile("+id+"), currentId="+currentId+",  after super" );
+		LOGGER.info("initFile("+id+"), currentId="+currentId+",  after super" );
 		// Below needs to be modified - EXIFService does not work with mapFile
 		MetadataStore store = makeFilterMetadata();
-		LOGGER.debug("Parsing JPEG EXIF data");
+		LOGGER.info("Parsing JPEG EXIF data");
 		HashMap<String, String> tags = null;
 		try {
 			// Reimplementing ExifServiceImpl as original does not have ExifIFD0Directory
@@ -295,7 +295,7 @@ public class ElphelJp4Reader  extends ImageIOReader{
 
 		}
 		catch (ServiceException e) {
-			LOGGER.debug("Could not parse EXIF data", e);
+			LOGGER.info("Could not parse EXIF data", e);
 		}
 		long [] maker_note = null;
 		double exposure = Double.NaN;
@@ -324,14 +324,14 @@ public class ElphelJp4Reader  extends ImageIOReader{
 		int bytes_per_pixel =  1;
 		Hashtable<String, String> property_table = ElphelMeta.getMeta(
 				null, maker_note, exposure, date_time, bytes_per_pixel, true );
-		LOGGER.debug("Created elphelMeta table, size="+property_table.size());
+		LOGGER.info("Created elphelMeta table, size="+property_table.size());
 		for (String key:property_table.keySet()) {
 			addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
 		}
 		MetadataLevel level = getMetadataOptions().getMetadataLevel();
 		if (level != MetadataLevel.MINIMUM) {
 			//			Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
-			//			LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
+			//			LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
 		}
 		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
 	}
@@ -343,9 +343,9 @@ public class ElphelJp4Reader  extends ImageIOReader{
 //		HashMap<String,Object> dbg_loc = Location.getIdMap();
 		String saveCurrentId = currentId;
 		currentId = null;
-		LOGGER.debug("close("+fileOnly+") before super");
+		LOGGER.info("close("+fileOnly+") before super");
 		super.close(fileOnly); // curerent_id == null only during actual close?
-		LOGGER.debug("close("+fileOnly+") after super");
+		LOGGER.info("close("+fileOnly+") after super");
 		currentId = saveCurrentId;
 //		if ((content_fileName != null) && file_initialized){
 		if (!mapped_externally && file_initialized){ // will try to unmap non-mapped file, OK
@@ -385,7 +385,7 @@ public class ElphelJp4Reader  extends ImageIOReader{
 	public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
 			throws FormatException, IOException
 	{
-		LOGGER.debug("openBytes() - before super()");
+		LOGGER.info("openBytes() - before super()");
 		FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
 		if (image_bytes == null) {
 			jp4Decode(no);
@@ -401,7 +401,7 @@ public class ElphelJp4Reader  extends ImageIOReader{
 					         w);
 			dest += w;
 		}
-		LOGGER.debug("openBytes() - after super()");
+		LOGGER.info("openBytes() - after super()");
 		return buf;
 	}
 	public void jp4Decode(int no) throws FormatException, IOException {
@@ -436,7 +436,7 @@ public class ElphelJp4Reader  extends ImageIOReader{
 		} else {
 			image_bytes = ib; // temporary
 		}
-		LOGGER.debug("jp4Decode()");
+		LOGGER.info("jp4Decode()");
 	}
 
 }

src/main/java/com/elphel/imagej/readers/ElphelTiffReader.java

@@ -40,6 +40,8 @@ import org.apache.commons.compress.utils.IOUtils;
 import org.joda.time.DateTime;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+///import ch.qos.logback.classic.Level;
+///import ch.qos.logback.classic.Logger;
 
 import com.drew.imaging.ImageMetadataReader;
 import com.drew.metadata.Metadata;
@@ -162,10 +164,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		//		mergeSubIFDs = true; // false;
 		// TODO: See if the selection is just between 2 readers (jp4 and tiff - just Elphel cameras),
 		// or these readers are combined with all other readers in readers.txt
+		//https://stackoverflow.com/questions/3837801/how-to-change-root-logging-level-programmatically-for-logback
+//		LOGGER.setLevel(Level.ERROR);
+//		Logger root = (Logger)LoggerFactory.getLogger(org.slf4j.Logger.ROOT_LOGGER_NAME);		
+//		root.setLevel(Level.ERROR);
 		suffixNecessary = true; // false
 		suffixSufficient = true; // false;
 ///		mergeSubIFDs = true; // false;
-		LOGGER.debug("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
+		LOGGER.info("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
 		if (REPLACEMENT_TAG_MAP == null) {
 			REPLACEMENT_TAG_MAP = new HashMap<String,String>();
 			for (String [] line: REPLACEMENT_TAGS) {
@@ -211,14 +217,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 
 	  @Override
 	  public void setId(String id) throws FormatException, IOException {
-		  LOGGER.debug("setId("+id+"). before super" );
+		  LOGGER.info("setId("+id+"). before super" );
 		  file_initialized = false;
 		  mapped_externally = false;
 		  if (Location.getIdMap().containsKey(id)) {
-			  LOGGER.debug("id '"+id+"' is already mapped" );
+			  LOGGER.info("id '"+id+"' is already mapped" );
 			  content_fileName = id; // id; // maybe set to null to handle externally?
 			  mapped_externally = true;
-			  LOGGER.debug("Starting setId() method, read file directly");
+			  LOGGER.info("Starting setId() method, read file directly");
 			  super.setId(id);
 		  } else {
 			  // If URL, then read to memory, if normal file - use direct access
@@ -244,7 +250,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 			  }
 
 			  if (url != null) {
-				  LOGGER.debug("Starting initFile() method, read "+ id +" to memory first");
+				  LOGGER.info("Starting initFile() method, read "+ id +" to memory first");
 				  //https://www.rgagnon.com/javadetails/java-0487.html
 				  URLConnection connection = url.openConnection();
 
@@ -261,27 +267,27 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 					  content_fileName = "unknown." + suffix;
 				  }
 				  //	 			currentId = fileName; //???
-				  //	 			LOGGER.debug("Mime type = "+mime);
+				  //	 			LOGGER.info("Mime type = "+mime);
 				  // https://stackoverflow.com/questions/2793150/how-to-use-java-net-urlconnection-to-fire-and-handle-http-requests
 
 				  //https://stackoverflow.com/questions/2295221/java-net-url-read-stream-to-byte
 				  InputStream is =    url.openStream (); //
 				  byte[] inBytes = IOUtils.toByteArray(is);
 				  if (is != null) is.close();
-				  LOGGER.debug("Bytes read: "+ inBytes.length);
+				  LOGGER.info("Bytes read: "+ inBytes.length);
 				  Location.mapFile(content_fileName, new ByteArrayHandle(inBytes));
 //				  HashMap<String,Object> dbg_loc = Location.getIdMap();
 				  super.setId(content_fileName);
 			  } else { // read file normally
 				  content_fileName = id;
-				  LOGGER.debug("read file directly");
+				  LOGGER.info("read file directly");
 				  super.setId(id);
 			  }
 		  }
 
 		  //getReader
 		  //	    super.setId(id);
-		  LOGGER.debug("setId("+id+"). after super" );
+		  LOGGER.info("setId("+id+"). after super" );
 		  file_initialized = true;
 	  }
 
@@ -292,26 +298,26 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
     {
 		// Trying ServiceFactory before it is going to be initialized, so static defaultFactory will be initialized
 		// with small set of services - only needed for Elphel
-		LOGGER.debug("Starting initFile() method");
+		LOGGER.info("Starting initFile() method");
 		super.initFile(id);
-		LOGGER.debug("Ending initFile() method");
+		LOGGER.info("Ending initFile() method");
     }
 
 	/* @see loci.formats.FormatReader#initFile(String) */
 	// copied from ElphelJp4Reader
 	@Override
 	protected void initFile(String id) throws FormatException, IOException {
-		LOGGER.debug("initFile("+id+"), currentId="+currentId+",  before super" );
+		LOGGER.info("initFile("+id+"), currentId="+currentId+",  before super" );
 		try {
 			super.initFile(id); // fails class_not_found
 		}
 		catch (IllegalArgumentException e) {
 			throw new FormatException(e);
 		}
-		LOGGER.debug("initFile("+id+"), currentId="+currentId+",  after super" );
+		LOGGER.info("initFile("+id+"), currentId="+currentId+",  after super" );
 		// Below needs to be modified - EXIFService does not work with mapFile
 		MetadataStore store = makeFilterMetadata();
-		LOGGER.debug("Parsing TIFF EXIF data");
+		LOGGER.info("Parsing TIFF EXIF data");
 		HashMap<String, String> tags = null;
 		try {
 			// Reimplementing ExifServiceImpl as original does not have ExifIFD0Directory
@@ -378,7 +384,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 
 		}
 		catch (ServiceException e) {
-			LOGGER.debug("Could not parse EXIF data", e);
+			LOGGER.info("Could not parse EXIF data", e);
 		}
 		long [] maker_note = null;
 		double exposure = Double.NaN;
@@ -409,14 +415,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		int bytes_per_pixel =  (bpp + 7) / 9;
 		Hashtable<String, String> property_table = ElphelMeta.getMeta(
 				null, maker_note, exposure, date_time, bytes_per_pixel, true );
-		LOGGER.debug("Created elphelMeta table, size="+property_table.size());
+		LOGGER.info("Created elphelMeta table, size="+property_table.size());
 		for (String key:property_table.keySet()) {
 			addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
 		}
 		MetadataLevel level = getMetadataOptions().getMetadataLevel();
 		if (level != MetadataLevel.MINIMUM) {
 			//			Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
-			//			LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
+			//			LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
 		}
 		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
 	}
@@ -436,9 +442,9 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	/* @see loci.formats.IFormatReader#close(boolean) */
 	@Override
 	public void close(boolean fileOnly) throws IOException {
-		LOGGER.debug("close("+fileOnly+") before super");
+		LOGGER.info("close("+fileOnly+") before super");
 		super.close(fileOnly); // curerent_id == null only during actual close?
-		LOGGER.debug("close("+fileOnly+") after super");
+		LOGGER.info("close("+fileOnly+") after super");
 //		if ((content_fileName != null) && file_initialized){
 		if (!mapped_externally && file_initialized){ // will try to unmap non-mapped file, OK
 			Location.mapFile(content_fileName, null);
@@ -463,10 +469,10 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	/* Removed 08/03/2021 to match IP4
 	@Override
 	protected void initStandardMetadata() throws FormatException, IOException {
-		LOGGER.debug("initStandardMetadata() - before super()");
+		LOGGER.info("initStandardMetadata() - before super()");
 		super.initStandardMetadata();
 		String comment = ifds.get(0).getComment(); // IMAGE_DESCRIPTION
-		LOGGER.debug("initStandardMetadata() - after super()");
+		LOGGER.info("initStandardMetadata() - after super()");
 		long[] maker_note = null;
 		double exposure = Double.NaN;
 		String date_time = null;
@@ -505,14 +511,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 				null, maker_note, exposure, date_time, bytes_per_pixel, true );
 
 
-		LOGGER.debug("Created elphelMeta table, size="+property_table.size());
+		LOGGER.info("Created elphelMeta table, size="+property_table.size());
 		for (String key:property_table.keySet()) {
 			addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
 		}
 		MetadataLevel level = getMetadataOptions().getMetadataLevel();
 		if (level != MetadataLevel.MINIMUM) {
 			Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
-			LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
+			LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
 	    }
 		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
 		// convert MAKER_NOTE to the same text format as in com.drew.metadata
@@ -549,9 +555,9 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
 	    throws FormatException, IOException
 	  {
-		LOGGER.debug("openBytes() - before super()");
+		LOGGER.info("openBytes() - before super()");
 	    super.openBytes(no, buf, x, y, w, h);
-		LOGGER.debug("openBytes() - after super()");
+		LOGGER.info("openBytes() - after super()");
 	    return buf;
 	  }
 

src/main/java/com/elphel/imagej/readers/ImagejJp4Tiff.java

@@ -645,17 +645,17 @@ public class ImagejJp4Tiff {
 		}
 
 		if (num_diff == 0) {
-			System.out.println ("No discontinuities remain");
+///			System.out.println ("No discontinuities remain");
 			return center;
 		}
-		System.out.println ("Discontinuities remain, will fix by clusters");
+///		System.out.println ("Discontinuities remain, will fix by clusters");
 		boolean OK = fixByClusters(
 				width,
 				height,
 				FIXCH6_BIT,         // int    bad_bit,
 				idata,              // int [] data)
 				(dbg_img != null)); // boolean debug)
-		System.out.println ("FixByClusters -> "+OK);
+///		System.out.println ("FixByClusters -> "+OK);
 		for (int i = 0; i < idata.length; i++) {
 			pixels[i+640] = idata[i];
 		}

src/main/java/com/elphel/imagej/tileprocessor/GeometryCorrection.java

@@ -801,7 +801,7 @@ public class GeometryCorrection {
 		int    [] full_par_index;
 
 		public RigOffset () {
-			System.out.println("created RigOffset");
+///			System.out.println("created RigOffset");
 			par_scales = new double [VECTOR_LENGTH];
 			par_scales[AUX_AZIMUTH_INDEX] =  1000.0*focalLength/pixelSize;
 			par_scales[AUX_TILT_INDEX] =     1000.0*focalLength/pixelSize;

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

@@ -2025,16 +2025,16 @@ public class QuadCLT extends QuadCLTCPU {
 					false,                     // final boolean                                   updateStatus,
 					debugLevel);               // final int                                       debugLevel);
 			if (debugLevel >-1) System.out.println("Processing set "+(nSet+1)+" (of "+set_channels.length+") finished at "+
-					IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+					IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory1="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
 			if (eyesisCorrections.stopRequested.get()>0) {
 				System.out.println("User requested stop");
 				System.out.println("Processing "+(nSet + 1)+" file sets (of "+set_channels.length+") finished at "+
-						IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+						IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory2="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
 				return;
 			}
 		}
 		System.out.println("processCLTQuadCorrs(): processing "+getTotalFiles(set_channels)+" files ("+set_channels.length+" file sets) finished at "+
-				IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
+				IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory3="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
 	}
 	
 	public static ImagePlus renderGPUFromDSI(

src/main/java/com/elphel/imagej/tileprocessor/TileProcessor.java

@@ -37,7 +37,7 @@ import com.elphel.imagej.common.PolynomialApproximation;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 
 public class TileProcessor {
-	
+	public boolean run_garbage_collection=false;
 	public static String [] SCAN_TITLES4 = {
 			"tile_op",       //  0
 			"final",         //  1 - calculated, filtered, combined disparity
@@ -251,10 +251,11 @@ public class TileProcessor {
 		rig_pre_poles_sel =      null;
 		rig_post_poles_sel =     null;
 		clt_3d_passes_rig_size = 0;
-
-		Runtime runtime = Runtime.getRuntime();
-	    runtime.gc();
-		System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
+		if (run_garbage_collection) {
+			Runtime runtime = Runtime.getRuntime();
+			runtime.gc();
+			System.out.println("--- Free memory30="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
+		}
 	}
 
 	public void saveCLTPasses(boolean rig){
@@ -309,7 +310,7 @@ public class TileProcessor {
 		}
 		Runtime runtime = Runtime.getRuntime();
 	    runtime.gc();
-		System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
+		System.out.println("--- Free memory31="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
 	}
 
 	public void removeNonMeasurement(){ // executed during expansion (CLT 3D)