Merge branch 'lwir' of git.elphel.com:Elphel/imagej-elphel into lwir

pom.xml

@@ -90,6 +90,12 @@
 			<artifactId>loci_tools</artifactId>
 			<version>6.0.1</version>
 		</dependency>
+	<dependency>
+		  <groupId>com.drewnoakes</groupId>
+		  <artifactId>metadata-extractor</artifactId>
+		  <version>2.11.0</version>
+		  <type>java-source</type>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/Eyesis_Correction.java

@@ -70,6 +70,8 @@ import java.util.concurrent.atomic.AtomicInteger;
 import javax.swing.JFileChooser;
 import javax.swing.filechooser.FileFilter;
 
+import com.elphel.imagej.lwir.LwirReader;
+
 import ij.CompositeImage;
 import ij.IJ;
 import ij.ImageJ;
@@ -118,7 +120,8 @@ private Panel panel1,
          panelClt3,
          panelClt4,
          panelClt5,
-         panelClt_GPU
+         panelClt_GPU,
+         panelLWIR
          ;
    JP46_Reader_camera JP4_INSTANCE=null;
 
@@ -384,6 +387,7 @@ private Panel panel1,
    public static boolean DCT_MODE=false; //true; // show all buttons
    public static boolean MODE_3D=false; // 3D-related commands
    public static boolean GPU_MODE=false; // 3D-related commands
+   public static boolean LWIR_MODE = false; // LWIR-related commands
    public PixelMapping.InterSensor.DisparityTiles DISPARITY_TILES=null;
    public ImagePlus DBG_IMP = null;
    public ImagePlus CORRELATE_IMP = null;
@@ -420,7 +424,7 @@ private Panel panel1,
 
 		instance = this;
 		addKeyListener(IJ.getInstance());
-		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?6:0) + (GPU_MODE?1:0);
+		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?6:0) + (GPU_MODE?1:0) +(LWIR_MODE?1:0);
 		setLayout(new GridLayout(menuRows, 1));
 
 		panel6 = new Panel();
@@ -645,7 +649,13 @@ private Panel panel1,
 			addButton("ShowGPU",                    panelClt_GPU, color_conf_process);
 			add(panelClt_GPU);
 		}
-
+		if (LWIR_MODE) {
+			panelLWIR = new Panel();
+			panelLWIR.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
+			addButton("LWIR_ACQUIRE",                   panelLWIR, color_conf_process);
+			add(panelLWIR);
+		}
+//
 		pack();
 
 		GUI.center(this);
@@ -740,6 +750,15 @@ private Panel panel1,
 			IJ.showMessage("Error",msg);
 			throw new IOException (msg);
 		}
+		sValue=	this.prefsProperties.getProperty("LWIR_MODE");
+		if (sValue!=null) {
+			LWIR_MODE=Boolean.parseBoolean(sValue);
+			System.out.println("Read LWIR_MODE="+LWIR_MODE);
+		} else {
+			String msg="LWIR_MODE is undefined in "+this.prefsPath;
+			IJ.showMessage("Error",msg);
+			throw new IOException (msg);
+		}
     }
 
 	public static String stack2string(Exception e) {
@@ -4783,6 +4802,29 @@ private Panel panel1,
     	}
     	TENSORFLOW_INFER_MODEL.test_tensorflow(keep_empty);
     	return;
+/* ======================================================================== */
+    } else if (label.equals("LWIR_ACQUIRE")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+		loci.common.DebugTools.enableLogging("ERROR"); // INFO"); // ERROR");
+        LwirReader lwirReader = new LwirReader();
+        ImagePlus [][] imps = lwirReader.readAllMultiple(
+    			10, // final int     num_frames,
+    			true, // final boolean show,
+    			false); // true); // final boolean scale)
+		for (ImagePlus imp: imps[0]) {
+			imp.show();
+		}
+
+		System.out.println("LWIR_ACQUIRE: got "+imps.length+" image sets");
+		ImagePlus [][] imps_sync =  lwirReader.matchSets(imps, 0.001, 3); // double max_mismatch)
+		if (imps_sync != null) {
+			ImagePlus [] imps_avg = lwirReader.averageMultiFrames(imps_sync);
+			for (ImagePlus imp: imps_avg) {
+				imp.show();
+			}
+		}
+
+
 //JTabbedTest
 // End of buttons code
     }

src/main/java/JP46_Reader_camera.java

@@ -1133,34 +1133,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 			fi.fileFormat = isTiff?FileInfo.TIFF: FileInfo.GIF_OR_JPG; // even if set originally, it is lost after convertToGray32
 			imp.setFileInfo(fi);
 
-			FileInfo ofi = imp.getOriginalFileInfo();
-			fi = imp.getFileInfo();
-
-// testing
-/*
-			if ((ofi!=null) && (ofi.directory!=null) &&  (ofi.fileFormat == FileInfo.TIFF)) {
-				String path = ofi.directory + ofi.fileName;
-				EyesisTiff ET = new EyesisTiff();
-				ImagePlus imptiff = ET.readTiff(path);
-				if (imptiff!=null) {
-					imptiff.show();
-				}
-
-//				IJ.error("TIFF Dumper", "File path not available or not TIFF file");
-				IJ.log("\\Clear");
-				IJ.log("PATH = "+path);
-				try {
-					dumpIFDs(path);
-				} catch(IOException e) {
-					IJ.error("Tiff Dumper", ""+e);
-				}
-				Frame log = WindowManager.getFrame("Log");
-				if (log!=null) log.toFront();
-			}
-*/
 		}
-
-
 		return imp;
 	}
 
@@ -1421,16 +1394,11 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		timestamp=imp.getProperty("timestamp");
 		if (timestamp!=null);
 
-/*
-		System.out.println("FLIPV="+FLIPGV+" FLIPH="+FLIPGH);
-		for (i=0;i<3;i++) System.out.println("FLIPV["+i+"]=  "+FLIPV[i]+" FLIPH["+i+"]=  "+FLIPH[i]);
-		for (i=0;i<3;i++) System.out.println("HEIGHTS["+i+"]="+HEIGHTS[i]);
-		for (i=0;i<2;i++) System.out.println("BLANKS["+i+"]= "+BLANKS[i]);
-*/
 		Rectangle [] r = new Rectangle[3];
 		r[0]=new Rectangle(0, 0,                                        width,HEIGHTS[0]);
 		r[1]=new Rectangle(0, HEIGHTS[0]+BLANKS[0],                     width,HEIGHTS[1]);
 		r[2]=new Rectangle(0, HEIGHTS[0]+BLANKS[0]+HEIGHTS[1]+BLANKS[1],width,HEIGHTS[2]);
+
 // assuming that 		(HEIGHTS[1]==0) && (HEIGHTS[2]!=0) == false
 		if (FLIPGV!=0){
 			if (HEIGHTS[1]>0) {
@@ -1448,13 +1416,10 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		if (FLIPGV>0) for (i=0;i<3;i++) FLIPV[i]=1-FLIPV[i];
 		if (FLIPGH>0) for (i=0;i<3;i++) FLIPH[i]=1-FLIPH[i];
 
-//		for (i=0;i<3;i++) System.out.println("Final: FLIPV["+i+"]=  "+FLIPV[i]+" FLIPH["+i+"]=  "+FLIPH[i]);
 
 // if needed, we'll cut one pixel line. later can modify to add one extra, but then we need to duplicate the pre-last one (same Bayer),
 // not just add zeros - later before sliding FHT the two border lines are repeated for 16 times to reduce border effects.
 		for (i=0;i<3;i++) {
-//			System.out.println("before r["+i+"].x=  "+r[i].x+" r["+i+"].width=  "+r[i].width);
-//			System.out.println("before r["+i+"].y=  "+r[i].y+" r["+i+"].height=  "+r[i].height);
 			if (((r[i].height & 1)==0 ) & (((r[i].y+FLIPV[i])&1)!=0)) r[i].height-=2;
 			r[i].height &=~1;
 			if (((r[i].y+FLIPV[i])&1)!=0) r[i].y+=1;
@@ -1462,16 +1427,8 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 			if (((r[i].width & 1)==0 ) & (((r[i].x+FLIPH[i])&1)!=0)) r[i].width-=2;
 			r[i].width &=~1;
 			if (((r[i].x+FLIPH[i])&1)!=0) r[i].x+=1;
-
-
-
-//			System.out.println("after r["+i+"].x=  "+r[i].x+" r["+i+"].width=  "+r[i].width);
-//			System.out.println("after r["+i+"].y=  "+r[i].y+" r["+i+"].height=  "+r[i].height);
 		}
 		if (r[numImg].height<=0) return null;
-//		ImageProcessor ip=imp.getProcessor();
-//		ip.setRoi(r[numImg]);
-//		ImageProcessor ip_individual=ip.crop().duplicate(); //java.lang.NegativeArraySizeException
 /*
  * When using in multithreaded with (probably) the same composite image
 Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970912

src/main/java/com/elphel/imagej/lwir/LwirReader.java

+/**
+ ** -----------------------------------------------------------------------------**
+ ** LwirReader.java
+ **
+ ** Multithreaded reading cameras - visible and LWIR
+ **
+ **
+ ** Copyright (C) 2019 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  LwirReader.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+package com.elphel.imagej.lwir;
+
+import java.io.IOException;
+import java.util.Properties;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.elphel.imagej.readers.ElphelTiffReader;
+import com.elphel.imagej.readers.ImagejJp4TiffMulti;
+
+import ij.ImagePlus;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
+import loci.formats.FormatException;
+
+public class LwirReader {
+	public static String [] BASE_URLS= {
+			"http://192.168.0.36:2323/bchn0",
+			"http://192.168.0.36:2324/bchn0",
+			"http://192.168.0.36:2325/bchn0",
+			"http://192.168.0.36:2326/bchn0",
+			"http://192.168.0.38:2323/bchn4",
+			"http://192.168.0.38:2324/bchn4",
+			"http://192.168.0.38:2325/bchn4",
+			"http://192.168.0.38:2326/bchn4",
+			};
+//	public static String IMAGE_URL_FIRST="/towp/wait/img/next/save";
+//	public static String IMAGE_URL_NEXT= "/torp/wait/img/next/save";
+//	public static String IMAGE_URL_FIRST="/towp/wait/img/save"; // next image name, same image number/time
+//	public static String IMAGE_URL_NEXT= "/torp/wait/img/save"; // same image name, same image number/time
+
+	public static String IMAGE_URL_FIRST="/towp/wait/img/save";     // next image name, same image number/time
+	public static String IMAGE_URL_NEXT= "/torp/next/wait/img/save"; // same image name, same image number/time
+
+//	public static String IMAGE_URL_FIRST="/towp/wait/bimg/save";     // next image name, same image number/time
+//	public static String IMAGE_URL_NEXT= "/torp/next/wait/bimg/save"; // same image name, same image number/time
+
+	/** Logger for this class. */
+	private static final Logger LOGGER =
+			LoggerFactory.getLogger(ElphelTiffReader.class);
+
+	private ImagejJp4TiffMulti imagejJp4TiffMulti;
+
+	public LwirReader() {
+		imagejJp4TiffMulti = null;
+	}
+
+
+	public ImagePlus[][] readAllMultiple(
+			final int     num_frames,
+			final boolean show,
+			final boolean scale) {
+		return readAllMultiple(num_frames, show, scale, "STD_");
+	}
+
+	public ImagePlus[][] readAllMultiple(
+			final int     num_frames,
+			final boolean show,
+			final boolean scale,
+			final String  std)
+	{
+		String [] urls0 = new String[BASE_URLS.length];
+		String [] urls1 = new String[BASE_URLS.length];
+		ImagePlus [][] imps = new ImagePlus[num_frames][BASE_URLS.length];
+		for (int i = 0; i < BASE_URLS.length; i++) {
+			urls0[i] = BASE_URLS[i] + IMAGE_URL_FIRST;
+			urls1[i] = BASE_URLS[i] + IMAGE_URL_NEXT;
+		}
+		if (imagejJp4TiffMulti == null) {
+			imagejJp4TiffMulti = new ImagejJp4TiffMulti();
+			for (int i = 0; i < 2; i++) {
+				try {
+					imagejJp4TiffMulti.getMultiImages(urls0, imps[0],  scale,  std);
+				} catch (IOException e) {
+					LOGGER.error("readAllMultiple0: IOException, priming" );
+				} catch (FormatException e) {
+					LOGGER.error("readAllMultiple0:FormatException, priming");
+				}
+				LOGGER.error("priming..."+(i+1));
+				try {
+					Thread.sleep(1000);
+				} catch (InterruptedException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+		}
+		for (int n = 0; n < num_frames; n++) {
+			LOGGER.error("---- Acquiring frame set "+n);
+			try {
+				imagejJp4TiffMulti.getMultiImages( (n==0)? urls0:urls1, imps[n],  scale,  std);
+			} catch (IOException e) {
+				LOGGER.error("readAllMultiple0: IOException, n = " + n);
+			} catch (FormatException e) {
+				LOGGER.error("readAllMultiple0:FormatException, n = " + n);
+			}
+		}
+		double [][] img_seconds = new double [num_frames][BASE_URLS.length];
+		int [][]    img_numbers = new int [num_frames][BASE_URLS.length];
+		String [][] img_names = new String [num_frames][BASE_URLS.length];
+		for (int n = 0; n < num_frames; n++) {
+			for (int i = 0; i < imps[n].length; i++) {
+				String dt = null;
+				try {
+					dt = (String) imps[n][i].getProperty("DATE_TIME");
+				} catch (Exception e) {
+					LOGGER.error("Something is wrong!");
+				}
+
+				img_seconds[n][i] = Double.parseDouble(dt.substring(dt.lastIndexOf(":")+1));
+				try {
+					img_numbers[n][i] = Integer.parseInt((String) imps[n][i].getProperty("STD_Image_Number"));
+				} catch (Exception e) {
+					img_numbers[n][i] = -1;
+				}
+				img_names[n][i] = (String) imps[n][i].getProperty("CONTENT_FILENAME");
+				LOGGER.error("Seconds for" + n+":"+i+" - "+img_seconds[n][i]+", number"+img_numbers[n][i]+", name "+img_names[n][i]);
+			}
+		}
+
+
+		for (ImagePlus [] imp_sets :imps) {
+			for (ImagePlus imp: imp_sets) {
+//				imp.show();
+			}
+		}
+		return imps;
+	}
+
+	public ImagePlus [] averageMultiFrames(ImagePlus [][] sets) {
+		int num_frames = sets.length;
+		int num_channels = sets[0].length;
+		ImagePlus [] imps_avg = new ImagePlus [num_channels];
+
+		for (int chn = 0; chn < num_channels; chn++) {
+			int width =  sets[0][chn].getWidth();
+			int height = sets[0][chn].getHeight();
+			String title = sets[0][chn].getTitle()+"_average"+num_frames;
+			float [] pixels_avg = (float []) sets[0][chn].getProcessor().getPixels(); //null pointer
+			for (int n = 1; n < num_frames; n++) {
+				float [] pixels = (float []) sets[n][chn].getProcessor().getPixels();
+				for (int i = 0; i < pixels_avg.length; i++) {
+					pixels_avg[i] += pixels[i];
+				}
+			}
+			double scale = 1.0/num_frames;
+			for (int i = 0; i < pixels_avg.length; i++) {
+				pixels_avg[i] *= scale;
+			}
+			ImageProcessor ip=new FloatProcessor(width,height);
+			ip.setPixels(pixels_avg);
+			ip.resetMinAndMax();
+			imps_avg[chn]=  new ImagePlus(title, ip);
+			Properties properties0 = sets[0][chn].getProperties();
+			for (String key:properties0.stringPropertyNames()) {
+				imps_avg[chn].setProperty(key, properties0.getProperty(key));
+			}
+			// TODO: Overwrite some properties?
+		}
+
+		return imps_avg;
+	}
+
+
+	public ImagePlus [][] matchSets(ImagePlus [][] sets, double max_mismatch, int max_frame_diff){
+		int num_frames = sets.length;
+		int num_channels = sets[0].length;
+		double [][] img_seconds = new double [num_frames][num_channels];
+		int [] frame_offsets = new int[num_channels];
+		double [] time_offsets = new double [num_channels];
+		boolean some_notsynced = false;
+		int fr_min = 0, fr_max = 0;
+		for (int n = 0; n < num_frames; n++) {
+			for (int i = 0; i < num_channels; i++) {
+				String dt = (String) sets[n][i].getProperty("DATE_TIME");
+				img_seconds[n][i] = Double.parseDouble(dt.substring(dt.lastIndexOf(":")+1));
+
+			}
+		}
+		for (int i = 1; i < num_channels; i++) { // compare all to the first channel
+			frame_offsets[i] = 0;
+			time_offsets[i] = secOffs(img_seconds[0][0], img_seconds[0][i]);
+			if (num_frames > max_frame_diff) {
+				if (time_offsets[i] > max_mismatch) {
+					for (int fr_diff = 1; fr_diff < max_frame_diff; fr_diff++) {
+						double aoff = secOffs(img_seconds[fr_diff][0], img_seconds[0][i]);
+						if (aoff < time_offsets[i]) {
+							time_offsets[i] = aoff;
+							frame_offsets[i] = fr_diff; // second channel starts later, than [0]
+						}
+						if (time_offsets[i] <=max_mismatch) break;
+						aoff = secOffs(img_seconds[0][0], img_seconds[fr_diff][i]);
+						if (aoff < time_offsets[i]) {
+							time_offsets[i] = aoff;
+							frame_offsets[i] = -fr_diff; // second channel starts earlier, than [0]
+						}
+						if (time_offsets[i] <=max_mismatch) break;
+					}
+				}
+			}
+			if (time_offsets[i] > max_mismatch) {
+				some_notsynced = true;
+			}
+			if (frame_offsets[i] > 0) {
+				fr_max = frame_offsets[i];
+			}
+			if (frame_offsets[i] < 0) {
+				fr_min = frame_offsets[i];
+			}
+		}
+		if (some_notsynced) {
+			LOGGER.error("*** Some channels are not synchronized, reboot or sensors re-start is needed ***");
+			for (int i = 0; i < num_channels; i++) {
+				LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
+			}
+			return null;
+		}
+		if (((fr_max - fr_min) > max_frame_diff) || ((fr_max - fr_min) > (num_frames - 1))) {
+			LOGGER.error("*** Earliest/latest channels differ by more than 1 frame, that should not happen! ***");
+			for (int i = 0; i < num_channels; i++) {
+				LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
+			}
+			return null;
+		}
+		for (int i = 0; i < num_channels; i++) {
+			// change to info later:
+			LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
+		}
+		ImagePlus [][] imps_synced = new ImagePlus [num_frames - fr_max + fr_min][num_channels];
+		for (int n = 0; n < imps_synced.length; n++) {
+			imps_synced[n][0]= sets[n+fr_max][0];
+			for (int i = 1; i < num_channels; i++) {
+				imps_synced[n][i]= sets[n - fr_min][i];
+			}
+		}
+		return imps_synced;
+	}
+
+	private double secOffs(double sec1, double sec2) {
+		double aoff = Math.abs(sec2 - sec1);
+		if (aoff > 30) {
+			aoff = Math.abs(aoff - 30);
+		}
+		return aoff;
+	}
+
+}

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

@@ -38,6 +38,7 @@ public class ElphelMeta {
 			long[] maker_note,
 			double exposure,
 			String date_time,
+			int bytesPerPixel,
 			boolean scale) throws FormatException, IOException {
 		if (property_table == null) {
 			property_table = new Hashtable<String, String> ();
@@ -45,7 +46,7 @@ public class ElphelMeta {
 		if (!Double.isNaN(exposure)) {
 			property_table.put("EXPOSURE",  String.format("%f",exposure));
 		}
-		if (date_time == null) {
+		if (date_time != null) {
 			property_table.put("DATE_TIME",  date_time);
 		}
 		if (maker_note != null) {
@@ -138,7 +139,7 @@ public class ElphelMeta {
 				property_table.put("FLIPH",     String.format("%d",FLIPH));
 				property_table.put("FLIPV",     String.format("%d",FLIPV));
 				property_table.put("BAYER_MODE",String.format("%d",BAYER_MODE));
-				property_table.put("COLOR_MODE",((COLOR_MODE==2)?"JP46":((COLOR_MODE==5)?"JP4":((COLOR_MODE==0)?"MONO":"OTHER"))));
+				property_table.put("COLOR_MODE",((COLOR_MODE==2)?"JP46":((COLOR_MODE==5)?"JP4":((COLOR_MODE==0)?"MONO":((COLOR_MODE==15)?"RAW":"OTHER")))));
 				property_table.put("DCM_HOR",   String.format("%d",DCM_HOR));
 				property_table.put("DCM_VERT",  String.format("%d",DCM_VERT));
 				property_table.put("BIN_HOR",   String.format("%d",BIN_HOR));
@@ -203,7 +204,12 @@ public class ElphelMeta {
 			/**adjusting gains to have the result picture in the range 0..256 */
 			min_gain=2.0*gains[0];
 			for (i=0;i<4;i++) {
-				if (min_gain > gains[i]*(1.0-blacks[i])) min_gain = gains[i]*(1.0-blacks[i]);
+				if (bytesPerPixel == 1) {
+					if (min_gain > gains[i]*(1.0-blacks[i])) min_gain = gains[i]*(1.0-blacks[i]);
+				} else {
+					if (min_gain > gains[i]) min_gain = gains[i];
+
+				}
 			}
 			property_table.put("GAIN",String.format("%f",min_gain)); // common gain
 

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

@@ -39,7 +39,9 @@ import org.slf4j.LoggerFactory;
 
 import loci.common.ByteArrayHandle;
 import loci.common.Location;
+import loci.common.RandomAccessInputStream;
 import loci.formats.FormatException;
+import loci.formats.FormatTools;
 import loci.formats.in.MetadataLevel;
 import loci.formats.in.TiffReader;
 import loci.formats.meta.MetadataStore;
@@ -85,6 +87,10 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 
 	public static final String ELPHEL_PROPERTY_PREFIX = "ELPHEL_";
 	public static final String CONTENT_FILENAME = "CONTENT_FILENAME";
+    public static final int    TAG_IMAGE_NUMBER          = 0x9211; //com.drew.metadata.exif.ExifDirectoryBase
+    public static final int    TAG_SERIAL_NUMBER         = 0xc62f;
+    public static final int    TAG_IMAGE_DESCRIPTION     = 0x010e;
+
 
 	  /** Merge SubIFDs into the main IFD list. */
 //	  protected transient boolean mergeSubIFDs = true; // false;
@@ -104,6 +110,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 //	private String inId = null; // to close Location.mapFile
 	private URL url = null; // save here actual URL when reading file to memory
 	private String content_fileName = null; // from Content-disposition
+	private boolean mapped_externally = false; // file is read/mapped externally, do not close it here
 	private boolean file_initialized = false;
 	//	  private String companionFile;
 	//	  private String description;
@@ -117,20 +124,60 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	/** Constructs a new Tiff reader. */
 	public ElphelTiffReader() {
 		super(); // "Tagged Image File Format", ELPHEL_TIFF_SUFFIXES); // See if we can use TiffReader without its parent
+		//		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
+		suffixNecessary = true; // false
+		suffixSufficient = true; // false;
 ///		mergeSubIFDs = true; // false;
 		LOGGER.info("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
 	}
 
 	// -- IFormatReader API methods --
 
+	/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
+	@Override
+	public boolean isThisType(String name, boolean open) {
+		if (open) {
+			return super.isThisType(name, open);
+		}
+		return checkSuffix(name, getSuffixes());
+	}
+
+	/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
+	/*
+	 * Check the first few bytes of a file to determine if the file can be read
+	 * by this reader. You can assume that index 0 in the stream corresponds to
+	 * the index 0 in the file. Return true if the file can be read; false if not
+	 * (or if there is no way of checking).
+	 */
+	@Override
+	public boolean isThisType(RandomAccessInputStream stream) throws IOException
+	{
+		final int blockLen = 4;
+		if (!FormatTools.validStream(stream, blockLen, false)) return false;
+
+		byte[] signature = new byte[blockLen];
+		stream.read(signature);
+
+		if (signature[0] != (byte) 0xff || signature[1] != (byte) 0xd8 ||
+				signature[2] != (byte) 0xff || (signature[3] & 0xf0) == 0)
+		{
+			return false;
+		}
+		return true;
+	}
+
 	  @Override
 	  public void setId(String id) throws FormatException, IOException {
 		  LOGGER.debug("setId("+id+"). before super" );
 		  file_initialized = false;
+		  mapped_externally = false;
 		  if (Location.getIdMap().containsKey(id)) {
 			  LOGGER.debug("id '"+id+"' is already mapped" );
-			  content_fileName = null; // id; // maybe set to null to handle externally?
-			  LOGGER.info("Starting initFile() method, read file directly");
+			  content_fileName = id; // id; // maybe set to null to handle externally?
+			  mapped_externally = true;
+			  LOGGER.info("Starting setId() method, read file directly");
 			  super.setId(id);
 		  } else {
 			  // If URL, then read to memory, if normal file - use direct access
@@ -192,6 +239,8 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
             throws FormatException,
                    java.io.IOException
     {
+		// 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.info("Starting initFile() method");
 		super.initFile(id);
 		LOGGER.info("Ending initFile() method");
@@ -216,7 +265,8 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		LOGGER.info("close("+fileOnly+") before super");
 		super.close(fileOnly); // curerent_id == null only during actual close?
 		LOGGER.info("close("+fileOnly+") after super");
-		if ((content_fileName != null) && file_initialized){
+//		if ((content_fileName != null) && file_initialized){
+		if (!mapped_externally && file_initialized){ // will try to unmap non-mapped file, OK
 			Location.mapFile(content_fileName, null);
 			file_initialized = false;
 		}
@@ -246,6 +296,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		double exposure = Double.NaN;
 		String date_time = null;
 		IFDList exifIFDs = tiffParser.getExifIFDs();
+		//ifds.get(0) has 37393=297894 (ImageNumbder), but not exifIFD
+		IFD ifd0 = ifds.get(0);
+		if (ifd0.containsKey(TAG_IMAGE_NUMBER))  addGlobalMeta("Image_Number",          ifd0.get(TAG_IMAGE_NUMBER));
+		if (ifd0.containsKey(TAG_SERIAL_NUMBER)) addGlobalMeta("Serial_Number",         ifd0.get(TAG_SERIAL_NUMBER));
+		if (ifd0.containsKey(TAG_IMAGE_DESCRIPTION)) addGlobalMeta("Image_Description", ifd0.get(TAG_IMAGE_DESCRIPTION));
+
+		//TAG_SERIAL_NUMBER
+
 		if (exifIFDs.size() > 0) {
 			IFD exifIFD = exifIFDs.get(0);
 			tiffParser.fillInIFD(exifIFD);
@@ -266,9 +324,10 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 				}
 			}
 		}
-
+		int bpp =   getBitsPerPixel();
+		int bytes_per_pixel =  (bpp + 7) / 9;
 		Hashtable<String, String> property_table = ElphelMeta.getMeta(
-				null, maker_note, exposure, date_time, true );
+				null, maker_note, exposure, date_time, bytes_per_pixel, true );
 
 
 		LOGGER.info("Created elphelMeta table, size="+property_table.size());
@@ -281,6 +340,16 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 			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
+		if (maker_note != null) {
+			StringBuffer sb_maker_note = new StringBuffer();
+			for (int i = 0; i < maker_note.length; i++) {
+				if (i > 0) sb_maker_note.append(" ");
+				sb_maker_note.append(maker_note[i]);
+			}
+			addGlobalMeta("MAKER_NOTE", sb_maker_note.toString());
+		}
+
 		// check for ImageJ-style TIFF comment
 		boolean ij = checkCommentImageJ(comment);
 //		if (ij) parseCommentImageJ(comment);

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

@@ -64,7 +64,8 @@ public class ImagejJp4Tiff {
 	// -- Constants --
 
 	private static final Logger LOGGER = LoggerFactory.getLogger(ClassList.class);
-	private static final boolean BYPASS_SERVICES = true;
+	private static final boolean BYPASS_SERVICES = false; //  true;
+	private static final String SERVICES_PATH = "services.properties.forelphel";
 
 	// -- Fields --
 
@@ -81,17 +82,29 @@ public class ImagejJp4Tiff {
 //		classList.addClass(com.elphel.imagej.readers.ElphelTiffJp4Reader.class);
 		classList.addClass(com.elphel.imagej.readers.ElphelJp4Reader.class);
 		classList.addClass(com.elphel.imagej.readers.ElphelTiffReader.class);
+		// Trying ServiceFactory before it is going to be initialized, so static defaultFactory will be initialized
+		// with small set of services - only needed for Elphel
+		//URL u = this.getClass().getResource(SERVICES_PATH);
+//		URL u = this.getClass().getResource("/"+SERVICES_PATH);
+
+//		loci.common.DebugTools.enableLogging("ERROR");
 
 		if (!BYPASS_SERVICES) {
 			ServiceFactory factory = null;
 
 			try {
-				factory = new ServiceFactory();
+//				factory = new ServiceFactory();
+				// Still does not work - during initFile->populatePixels it loads all
+				// services, including buggy ones
+
+			factory = new ServiceFactory(); // "/"+SERVICES_PATH);
+
 			} catch (DependencyException e) {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
 			}
 
+
 			OMEXMLService service = null;
 			try {
 				service = factory.getInstance(OMEXMLService.class);
@@ -117,10 +130,13 @@ public class ImagejJp4Tiff {
 	// -- API methods --
 
 	public ImagePlus readTiffJp4(String path) throws IOException, FormatException {
-		return readTiffJp4(path, 	"STD_"); // null);
+		return readTiffJp4(path, true); // null);
+	}
+	public ImagePlus readTiffJp4(String path, boolean scale) throws IOException, FormatException {
+		return readTiffJp4(path, scale,	"STD_"); // null);
 	}
 
-	public ImagePlus readTiffJp4(String path_url, String std ) throws IOException, FormatException { // std - include non-elphel properties with prefix std
+	public ImagePlus readTiffJp4(String path_url, boolean scale, String std ) throws IOException, FormatException { // std - include non-elphel properties with prefix std
 		// determine if it is a file or URL and read url to memory
 		// If URL, then read to memory, if normal file - use direct access
 		url = null;
@@ -131,11 +147,12 @@ public class ImagejJp4Tiff {
 		} catch (MalformedURLException e) {
 			LOGGER.warn("Bad URL: " + path_url);
 		}
+		//https://stackoverflow.com/questions/39086500/read-http-response-header-and-body-from-one-http-request-in-java
 		if (url != null) {
-			LOGGER.info("Read "+ path_url +" to memory first");
+			LOGGER.error("Read "+ path_url +" to memory first");
 			URLConnection connection = url.openConnection();
 
-			String content_disposition = connection.getHeaderField("Content-Disposition");
+			String content_disposition = connection.getHeaderField("Content-Disposition"); // reads file
 			// raw = "attachment; filename=abc.jpg"
 			if(content_disposition != null && content_disposition.indexOf("=") != -1) {
 				content_fileName = content_disposition.split("=")[1]; //getting value after '='
@@ -147,7 +164,8 @@ public class ImagejJp4Tiff {
 				String suffix = slash < 0 ? "" : mime.substring(slash+1);
 				content_fileName = "unknown." + suffix;
 			}
-			InputStream is =    url.openStream (); //
+//			InputStream is =    url.openStream (); // reads file for the second time
+			InputStream is =    connection.getInputStream ();
 			byte[] inBytes = IOUtils.toByteArray(is);
 			if (is != null) is.close();
 			LOGGER.info("Bytes read: "+ inBytes.length);
@@ -182,11 +200,17 @@ public class ImagejJp4Tiff {
 				pixels[i] = ((bb.getShort())) & 0xffff;
 			}
 		}
+		Hashtable<String, Object> meta_hash = reader.getGlobalMetadata();
+
+		boolean degamma = bytes_per_pixel < 2; // both JP4 and 8-bit tiff
+		if (deGammaScale(pixels, reader.getSizeX(), meta_hash, degamma, scale ) == null) {
+			LOGGER.error("Problem degamma/scaling of "+content_fileName);
+
+		}
 
 		ImageProcessor ip=new FloatProcessor(reader.getSizeX(), reader.getSizeY());
 		ip.setPixels(pixels);
 		ip.resetMinAndMax();
-		Hashtable<String, Object> meta_hash = reader.getGlobalMetadata();
 		String prefix = ElphelTiffReader.ELPHEL_PROPERTY_PREFIX;
 		String imageName = content_fileName; // path;
 		String imageNameKey = prefix+ElphelTiffReader.CONTENT_FILENAME;
@@ -208,6 +232,7 @@ public class ImagejJp4Tiff {
 		return imp;
 	}
 
+
 	// -- Helper methods --
 
 	public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
@@ -231,5 +256,100 @@ public class ImagejJp4Tiff {
 		return imp;
 	}
 
+	public float [] deGammaScale(float [] pixels, int width, Hashtable<String, Object> meta_hash, boolean degamma, boolean scale) {
+		int height = pixels.length/width;
+		String prefix = ElphelTiffReader.ELPHEL_PROPERTY_PREFIX;
+		double [] rgains =        {1.0, 1.0, 1.0, 1.0};
+		double [] blacks =        new double[4];
+		double[] blacks256=       new double[4];
+		double [] gammas =        new double[4];
+		long [] gamma_scales =    new long[4];
+		double [][] rgammas =     new double[4][];
+		double min_gain = 1.0;
+		boolean flipv, fliph;
+		if (meta_hash.get(prefix+"FLIPV")!=null) flipv=   Integer.valueOf((String) meta_hash.get(prefix+"FLIPV")).intValue() > 0;  else return null;
+		if (meta_hash.get(prefix+"FLIPH")!=null) fliph=    Integer.valueOf((String) meta_hash.get(prefix+"FLIPV")).intValue() > 0; else return null;
+		if (meta_hash.get(prefix+"GAIN")!=null) min_gain=  Double.valueOf((String) meta_hash.get(prefix+"GAIN")).doubleValue();    else return null;
+		for (int i=0;i<4;i++) { /* r,g,gb,b */
+			if (scale) {
+				if (meta_hash.get(prefix+"gains_"+i)!=null)        rgains[i]=      min_gain/Double.valueOf((String) meta_hash.get(prefix+"gains_"+i)).doubleValue();        else return null;
+			}
+			if (degamma) {
+				if (meta_hash.get(prefix+"blacks_"+i)!=null)       blacks[i]=        Double.valueOf((String) meta_hash.get(prefix+"blacks_"+i)).doubleValue();       else return null;
+				if (meta_hash.get(prefix+"gammas_"+i)!=null)       gammas[i]=        Double.valueOf((String) meta_hash.get(prefix+"gammas_"+i)).doubleValue();       else return null;
+				if (meta_hash.get(prefix+"gamma_scales_"+i)!=null) gamma_scales[i]=  Integer.valueOf((String) meta_hash.get(prefix+"gamma_scales_"+i)).intValue();   else return null;
+			}
+		}
+		if (flipv) {
+			if (scale) {
+				ElphelMeta.swapArrayElements (rgains,       1, 3);
+				ElphelMeta.swapArrayElements (rgains,       0, 2);
+			}
+			if (degamma) {
+				ElphelMeta.swapArrayElements (blacks,      1, 3);
+				ElphelMeta.swapArrayElements (blacks,      0, 2);
+				ElphelMeta.swapArrayElements (gammas,      1, 3);
+				ElphelMeta.swapArrayElements (gammas,      0, 2);
+				ElphelMeta.swapArrayElements (gamma_scales,1, 3);
+				ElphelMeta.swapArrayElements (gamma_scales,0, 2);
+			}
+		}
+		if (fliph) {
+			if (scale) {
+				ElphelMeta.swapArrayElements (rgains,       1, 0);
+				ElphelMeta.swapArrayElements (rgains,       3, 2);
+			}
+			if (degamma) {
+				ElphelMeta.swapArrayElements (blacks,      1, 0);
+				ElphelMeta.swapArrayElements (blacks,      3, 2);
+				ElphelMeta.swapArrayElements (gammas,      1, 0);
+				ElphelMeta.swapArrayElements (gammas,      3, 2);
+				ElphelMeta.swapArrayElements (gamma_scales,1, 0);
+				ElphelMeta.swapArrayElements (gamma_scales,3, 2);
+			}
+		}
+		if (degamma) {
+			for (int i=0;i<4;i++) {
+				rgammas[i]=ElphelMeta.elphel_gamma_calc (gammas[i], blacks[i], gamma_scales[i]);
+				blacks256[i]=256.0*blacks[i];
+				for (int j = 0; j < rgammas[i].length; j++) {
+					rgammas[i][j] -= blacks256[i];
+					if (scale) {
+						rgammas[i][j] *= rgains[i];
+					}
+				}
+			}
+		}
+		if (degamma) {
+			for (int y = 0; y < height; y+=2) {
+				for (int dy = 0; dy < 2; dy++) {
+					int base = (y + dy)*width;
+					for (int x = 0; x < width; x+=2) {
+						for (int dx = 0; dx<2; dx++) {
+							int indx = base + x + dx;
+							int iv = (int) pixels[indx];
+							if (iv < 0) iv = 0;
+							else if (iv > 255) iv = 255;
+							pixels[indx] = (float) rgammas[(dy << 1) + 1 - dx][iv];
+						}
+					}
+				}
+			}
+		} else if (scale) {
+			for (int y = 0; y < height; y+=2) {
+				for (int dy = 0; dy < 2; dy++) {
+					int base = (y + dy)*width;
+					for (int x = 0; x < width; x+=2) {
+						for (int dx = 0; dx<2; dx++) {
+							int indx = base + x + dx;
+							pixels[indx] *= rgains[(dy << 1) + 1 - dx];
+						}
+					}
+				}
+			}
+		}
+		//TODO: Add flips here!
+		return pixels;
+	}
 
 }

src/main/java/com/elphel/imagej/readers/ImagejJp4TiffMulti.java

+/**
+ ** -----------------------------------------------------------------------------**
+ ** ImagejJp4TiffMulti.java
+ **
+ ** Uses loci.format compatible readers for Elphel 8/16 bpp monochrome Tiff and
+ ** JP4 files to read/parse camera files in a single url read operation by
+ ** buffering camera data with Location.mapFile()
+ **
+ **
+ ** Copyright (C) 2019 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  ImagejJp4TiffMulti.java is free software: you can redistribute it and/or modify
+ **  it under the terms of the GNU General Public License as published by
+ **  the Free Software Foundation, either version 3 of the License, or
+ **  (at your option) any later version.
+ **
+ **  This program is distributed in the hope that it will be useful,
+ **  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ **  GNU General Public License for more details.
+ **
+ **  You should have received a copy of the GNU General Public License
+ **  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+package com.elphel.imagej.readers;
+
+import java.io.IOException;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import ij.ImagePlus;
+import loci.formats.ClassList;
+import loci.formats.FormatException;
+
+public class ImagejJp4TiffMulti {
+	private static final int MAX_THREADS =   100;
+	private static final Logger LOGGER =     LoggerFactory.getLogger(ClassList.class);
+	private final ImagejJp4Tiff [] imagejJp4Tiff = new ImagejJp4Tiff [MAX_THREADS];
+
+
+	public ImagePlus [] getMultiImages(
+			final String [] urls,
+			final ImagePlus [] imps,
+			final boolean scale,
+			final String std) throws IOException, FormatException  // std - include non-elphel properties with prefix std
+	{
+//		final ImagePlus [] imps = new ImagePlus [urls.length];
+   		final Thread[] threads = newThreadArray(MAX_THREADS);
+   		final AtomicInteger indxAtomic = new AtomicInteger(0);
+   		final AtomicInteger threadAtomic = new AtomicInteger(0);
+   		for (int ithread = 0; ithread < threads.length; ithread++) {
+   			threads[ithread] = new Thread() {
+   				@Override
+				public void run() {
+   					int threadIndx = threadAtomic.getAndIncrement();
+   					if (imagejJp4Tiff[threadIndx] == null ) {
+   						imagejJp4Tiff[threadIndx] = new ImagejJp4Tiff();
+   					}
+   					for (int indx = indxAtomic.getAndIncrement(); indx < urls.length; indx = indxAtomic.getAndIncrement())
+   					{
+   						try {
+							imps[indx] = imagejJp4Tiff[threadIndx].readTiffJp4(urls[indx], scale, std);
+						} catch (IOException e) {
+							LOGGER.error("getMultiImages IOException " + urls[indx]);
+						} catch (FormatException e) {
+							LOGGER.error("getMultiImages FormatException " + urls[indx]);
+						}
+   					}
+   				}
+   			};
+   		}
+   		startAndJoin(threads);
+		return imps;
+	}
+
+
+
+
+	/* Create a Thread[] array as large as the number of processors available.
+	 * From Stephan Preibisch's Multithreading.java class. See:
+	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
+	 */
+	private Thread[] newThreadArray(int maxCPUs) {
+		int n_cpus = Runtime.getRuntime().availableProcessors();
+		if (n_cpus>maxCPUs)n_cpus=maxCPUs;
+		return new Thread[n_cpus];
+	}
+/* Start all given threads and wait on each of them until all are done.
+	 * From Stephan Preibisch's Multithreading.java class. See:
+	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
+	 */
+	private static void startAndJoin(Thread[] threads)
+	{
+		for (int ithread = 0; ithread < threads.length; ++ithread)
+		{
+			threads[ithread].setPriority(Thread.NORM_PRIORITY);
+			threads[ithread].start();
+		}
+
+		try
+		{
+			for (int ithread = 0; ithread < threads.length; ++ithread)
+				threads[ithread].join();
+		} catch (InterruptedException ie)
+		{
+			throw new RuntimeException(ie);
+		}
+	}
+
+
+}