More on JP4+Tiff reading with bioformatrs.

.gitignore

@@ -8,4 +8,5 @@ attic
 *.log
 FOCUS-PSF*
 src/main/resources/trained_model
-bioformats
+bioformats*.*
\ No newline at end of file
+metadata*.*

pom.xml

@@ -88,7 +88,8 @@
 		<dependency>
 			<groupId>ome</groupId>
 			<artifactId>loci_tools</artifactId>
-			<version>5.9.0</version>
+			<version>6.1.0-SNAPSHOT</version>
+			<type>java-source</type>
 		</dependency>
 	</dependencies>
 

src/main/java/EyesisTiff.java

@@ -31,21 +31,32 @@ import java.awt.image.ColorModel;
 import java.awt.image.DataBufferInt;
 import java.awt.image.Raster;
 import java.awt.image.WritableRaster;
-import java.io.DataInputStream;
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.StringReader;
 import java.io.UnsupportedEncodingException;
 import java.lang.reflect.Array;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Properties;
+import java.util.Set;
 
 import javax.imageio.ImageIO;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import com.elphel.imagej.readers.ElphelTiffReader;
 
 //import org.apache.log4j.Logger;
 
@@ -55,20 +66,15 @@ import ij.WindowManager;
 import ij.io.FileInfo;
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
-import loci.common.ByteArrayHandle;
-import loci.common.Location;
 import loci.common.RandomAccessInputStream;
 import loci.common.services.DependencyException;
 import loci.common.services.ServiceException;
 import loci.common.services.ServiceFactory;
 import loci.formats.ClassList;
-import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
-//import loci.formats.in.TiffReader;
 import loci.formats.meta.IMetadata;
-import loci.formats.meta.MetadataStore;
 import loci.formats.services.OMEXMLService;
 import loci.formats.tiff.IFD;
 import loci.formats.tiff.IFDList;
@@ -86,6 +92,7 @@ public class EyesisTiff {
 		        defaultClasses =
 		          new ClassList<IFormatReader>(
 		        		  EyesisTiff.class.getClassLoader().getResource("readers.txt").getFile(), // @param file Configuration file containing the list of classes.
+//		        		  EyesisTiff.class.getClassLoader().getResource("readers1.txt").getFile(), // @param file Configuration file containing the list of classes.
 		        		  IFormatReader.class, // @param base Base class to which all classes are assignable.
 		        		  null); // @param location Class indicating which package to search for the file.
 		      }
@@ -109,43 +116,14 @@ public class EyesisTiff {
 
 	}
 	public ImagePlus readTiff(String path) {
-//		TiffReader tiffReader = new TiffReader();
-//		tiffReader.initFile(path);
-		   // read in entire file
-		// TODO: add option to get URL
-		//https://docs.openmicroscopy.org/bio-formats/5.9.2/developers/in-memory.html
-	    System.out.println("Reading file into memory from disk: "+path);
-	    File inputFile = new File(path);
-	    int fileSize = (int) inputFile.length();
-	    DataInputStream in = null;
-		try {
-			in = new DataInputStream(new FileInputStream(inputFile));
-		} catch (FileNotFoundException e) {
-		    System.out.println("File not found: "+path);
+		return readTiff(path, 	"STD_"); // null);
 	}
-	    byte[] inBytes = new byte[fileSize];
-	    try {
-			in.readFully(inBytes);
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-	    System.out.println(fileSize + " bytes read.");
 
-	    // determine input file suffix
-	    String fileName = inputFile.getName();
-	    int dot = fileName.lastIndexOf(".");
-	    String suffix = dot < 0 ? "" : fileName.substring(dot);
+	public ImagePlus readTiff(String path, String std ) { // std - include non-elphel properties with prefix std
 
+		String inId = null;
+		inId = path;
 
-	    // map input id string to input byte array
-	    String inId = "inBytes" + suffix;
-	    Location.mapFile(inId, new ByteArrayHandle(inBytes));
-
-	 // read data from byte array using ImageReader
-	    System.out.println();
-	    System.out.println("Reading image data from memory...");
-	    //
 	    ServiceFactory factory = null;
 		try {
 			factory = new ServiceFactory();
@@ -153,6 +131,7 @@ public class EyesisTiff {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
+
 		OMEXMLService service = null;
 		try {
 			service = factory.getInstance(OMEXMLService.class);
@@ -160,6 +139,7 @@ public class EyesisTiff {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
+
 	    IMetadata omeMeta = null;
 		try {
 			omeMeta = service.createOMEXMLMetadata();
@@ -174,8 +154,13 @@ public class EyesisTiff {
 //https://www.javatips.net/api/libbio-formats-java-master/components/scifio/src/loci/formats/in/BaseTiffReader.java
 //https://docs.openmicroscopy.org/bio-formats/5.7.2/developers/reader-guide.html
 		//https://docs.openmicroscopy.org/bio-formats/5.9.2/developers/java-library.html#file-reading-and-performance
+
+		//defaultClasses = new ClassList<IFormatReader>(IFormatReader.class);
+//		ClassList<IFormatReader> cl0 = getCustomReaderClasses(); // new ClassList<IFormatReader>(IFormatReader.class);
+		ClassList<IFormatReader> classList =  new ClassList<IFormatReader>(IFormatReader.class);
+		classList.addClass(com.elphel.imagej.readers.ElphelTiffReader.class);
 	    ImageReader reader = new ImageReader(getCustomReaderClasses());
-//		BaseTiffReader reader = new BaseTiffReader("Base_tiff_reader","tiff");
+//	    ImageReader reader = new ImageReader(classList);
 	    reader.setMetadataStore(omeMeta);
 	    try {
 			reader.setId(inId);
@@ -187,32 +172,10 @@ public class EyesisTiff {
 			//e.printStackTrace();
 		}
 	    /* read-end */
-	    int seriesCount = reader.getSeriesCount();
-	    int imageCount = reader.getImageCount();
-	    int sizeX = reader.getSizeX();
-	    int sizeY = reader.getSizeY();
-	    int sizeZ = reader.getSizeZ();
-	    int sizeC = reader.getSizeC();
-	    int sizeT = reader.getSizeT();
+
+
+
 	    int bpp =   reader.getBitsPerPixel();
-	    int pixelType = reader.getPixelType();
-	    java.util.List<CoreMetadata> cmd = reader.getCoreMetadataList();
-	    java.util.Hashtable<java.lang.String,java.lang.Object> 	gmd = reader.getGlobalMetadata();
-	    MetadataStore mtds = reader.getMetadataStore();
-	    IFormatReader ifr = reader.getReader();
-	    IFormatReader[] ifrs = reader.getReaders(); // all available readers?
-	    // output some details
-	    System.out.println("Series count: " + seriesCount);
-	    System.out.println("First series:");
-	    System.out.println("\tImage count = " + imageCount);
-	    System.out.println("\tSizeX = " + sizeX);
-	    System.out.println("\tSizeY = " + sizeY);
-	    System.out.println("\tSizeZ = " + sizeZ);
-	    System.out.println("\tSizeC = " + sizeC);
-	    System.out.println("\tSizeT = " + sizeT);
-	    System.out.println("\tbppT = " +  bpp);
-	    System.out.println("\treader = " +  ifr.toString());
-	    System.out.println("\tpixelType = " +  pixelType); // 3
 	    byte [] bytes = null;
 	    ImagePlus imp=  null;
 	    try {
@@ -245,11 +208,26 @@ public class EyesisTiff {
 		    ImageProcessor ip=new FloatProcessor(reader.getSizeX(), reader.getSizeY());
 			ip.setPixels(pixels);
 			ip.resetMinAndMax();
-//			imp =  new ImagePlus(fileName, ip); // original jp46 reader had full path as title
-			imp =  new ImagePlus(path, ip); // original jp46 reader had full path as title
+		    Hashtable<String, Object> meta_hash = reader.getGlobalMetadata();
+		    String prefix = ElphelTiffReader.ELPHEL_PROPERTY_PREFIX;
+		    String imageName = path;
+		    String imageNameKey = prefix+ElphelTiffReader.CONTENT_FILENAME;
+		    if (meta_hash.containsKey(imageNameKey)) {
+		    	imageName = meta_hash.get(imageNameKey).toString();
+		    }
+			imp =  new ImagePlus(imageName, ip); // original jp46 reader had full path as title
+
+		    // first - save all as properties, later - only ELPHEL_*
+			for (String key:meta_hash.keySet()) {
+				if (key.startsWith(prefix)) {
+					imp.setProperty(key.substring(prefix.length()), meta_hash.get(key).toString());
+				} else if (std != null) {
+					imp.setProperty(std+(key.replace(" ","_")), meta_hash.get(key).toString());
+				}
+			}
+			encodeProperiesToInfo(imp);
 	    }
 
-//	    ImagePlus imp= makeArrays(pixels, width, height, title);
 	    try {
 			reader.close();
 		} catch (IOException e) {
@@ -662,4 +640,58 @@ the type of pixel data in this file 	getPixelType()
 		return sb.toString();
 	}
 
+// copied from JP46_Reader_camera.java
+	public ImagePlus encodeProperiesToInfo(ImagePlus imp){
+		String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
+		Set<Object> jp4_set;
+		Properties jp4_prop;
+		Iterator<Object> itr;
+		String str;
+		jp4_prop=imp.getProperties();
+		if (jp4_prop!=null) {
+			jp4_set=jp4_prop.keySet();
+			itr=jp4_set.iterator();
+			while(itr.hasNext()) {
+				str = (String) itr.next();
+				//				if (!str.equals("Info")) info+="<"+str+">\""+jp4_prop.getProperty(str)+"\"</"+str+">";
+				if (!str.equals("Info")) info+="<"+str+">"+jp4_prop.getProperty(str)+"</"+str+">";
+			}
+		}
+		info+="</properties>\n";
+		imp.setProperty("Info", info);
+		return imp;
+	}
+
+	public boolean decodeProperiesFromInfo(ImagePlus imp){
+		if (imp.getProperty("Info")==null) return false;
+		String xml= (String) imp.getProperty("Info");
+
+	    DocumentBuilder db=null;
+		try {
+			db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+		} catch (ParserConfigurationException e) {
+			return false;
+		}
+	    InputSource is = new InputSource();
+	    is.setCharacterStream(new StringReader(xml));
+    	Document doc = null;
+	    try {
+	    	doc = db.parse(is);
+	    } catch (SAXException e) {
+	    	return false;
+	    } catch (IOException e) {
+	    	return false;
+	    }
+	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
+	    for (int i=0;i<allNodes.getLength();i++) {
+	        String name= allNodes.item(i).getNodeName();
+            String value=allNodes.item(i).getFirstChild().getNodeValue();
+    		imp.setProperty(name, value);
+
+	    }
+
+		return true;
+	}
+
+
 }

src/main/java/JP46_Reader_camera.java

@@ -59,6 +59,8 @@ import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
+import com.elphel.imagej.readers.ImagejJp4Tiff;
+
 import ij.IJ;
 import ij.ImageJ;
 import ij.ImagePlus;
@@ -75,6 +77,7 @@ import ij.process.ImageConverter;
 import ij.process.ImageProcessor;
 import ij.text.TextWindow;
 import loci.common.RandomAccessInputStream;
+import loci.formats.FormatException;
 import loci.formats.tiff.IFD;
 import loci.formats.tiff.IFDList;
 import loci.formats.tiff.TiffParser;
@@ -96,7 +99,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 
 	static File dir;
 
-	public String camera_url = "http://192.168.0.236:8081/";
+	public String camera_url = "http://192.168.0.36:2323/";
 	public String camera_img = "bimg";
 	public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
 	public String camera_jp46settings = "";
@@ -322,6 +325,10 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		if (demux) showImage=false;
 		double [] xtraExif=new double[1]; // ExposureTime
 		double [] lla = null;
+
+		imp = openJpegOrGif(directory, fileName);
+		imp.show();
+		if (imp != null) return imp;
 		try {
 			imp = openJpegOrGif(directory, fileName);
 			if (imp == null) {
@@ -390,7 +397,35 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 			String arg,
 			boolean scale,
 			ImagePlus imp_src,
-			boolean showImage) {
+			boolean showImage)
+	{
+//		ImagePlus imptiff = (new EyesisTiff()).readTiff(url);
+		ImagePlus imptiff = null;
+		try {
+			imptiff = (new ImagejJp4Tiff()).readTiffJp4(url);
+		} catch (IOException e1) {
+			// TODO Auto-generated catch block
+			e1.printStackTrace();
+		} catch (FormatException e1) {
+			// TODO Auto-generated catch block
+			e1.printStackTrace();
+		}
+		if (imptiff!=null) {
+			imptiff.show();
+			if (imptiff.getType()==ImagePlus.COLOR_RGB) {
+				checkGrayJpegTo32Bits(imptiff);
+			}
+
+			IJ.showStatus("Converting to 32-bits");
+			new ImageConverter(imptiff).convertToGray32();
+			FileInfo fi = imptiff.getFileInfo();
+			//			fi.fileName = name;
+			//			fi.directory = dir;
+			fi.fileFormat = FileInfo.TIFF;
+			imptiff.setFileInfo(fi);
+			return imptiff;
+		}
+
 		long[] ElphelMakerNote=null;
 		ImagePlus imp = null;
 		boolean reuse_imp=false;
@@ -399,14 +434,14 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		double [] xtraExif=new double[1]; // ExposureTime
 
 
-//		System.out.println("imp_src is "+((imp_src!=null)?"not ":"")+"null");
+		//		System.out.println("imp_src is "+((imp_src!=null)?"not ":"")+"null");
 		try {
 			imp = openJpegOrGifUsingURL(url);
 			if (imp == null) {
 				IJ.showMessage("JP46 Reader Error", "Could not open the URL: " + url + " as JPEG/JP46");
 			} else {
 				if ((imp_src==null) && showImage) {
-//					System.out.println("show() 1");
+					//					System.out.println("show() 1");
 					imp.show(); /* Shows before re-ordering*/
 				}
 				/// get rid of the "/towp/wait" if any - there is a chance to re-read the same image
@@ -429,7 +464,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 			if (reuse_imp) {
 				imp=imp_src;
 			} else if ((imp_src!=null) && showImage) { /* tried to reuse, but wrong size */
-//				System.out.println("show() 2");
+				//				System.out.println("show() 2");
 				imp.show(); /* never did that before */
 			}
 			if ((xtraExif!=null) && !Double.isNaN(xtraExif[0])){
@@ -1042,6 +1077,35 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 
 	/* Modified from Opener.java */
 	ImagePlus openJpegOrGif(String dir, String name) {
+		// Testing new readers
+		ImagePlus imptiff = null;
+//		imptiff = (new EyesisTiff()).readTiff(dir+name);
+		try {
+			imptiff = (new ImagejJp4Tiff()).readTiffJp4(dir+name);
+		} catch (IOException e1) {
+			// TODO Auto-generated catch block
+			e1.printStackTrace();
+		} catch (FormatException e1) {
+			// TODO Auto-generated catch block
+			e1.printStackTrace();
+		}
+
+		if (imptiff!=null) {
+			imptiff.show();
+			if (imptiff.getType()==ImagePlus.COLOR_RGB) {
+				checkGrayJpegTo32Bits(imptiff);
+			}
+
+			IJ.showStatus("Converting to 32-bits");
+			new ImageConverter(imptiff).convertToGray32();
+			FileInfo fi = imptiff.getFileInfo();
+			fi.fileName = name;
+			fi.directory = dir;
+			fi.fileFormat = FileInfo.TIFF;
+			imptiff.setFileInfo(fi);
+			return imptiff;
+		}
+
 		ImagePlus imp = null;
 		boolean isTiff = false;
 		Image img = Toolkit.getDefaultToolkit().createImage(dir+name);
@@ -1073,8 +1137,8 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 			fi = imp.getFileInfo();
 
 // testing
-
-			if ((ofi!=null) && (ofi.directory!=null) &&  (ofi.fileFormat ==FileInfo.TIFF)) {
+/*
+			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);
@@ -1093,6 +1157,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 				Frame log = WindowManager.getFrame("Log");
 				if (log!=null) log.toFront();
 			}
+*/
 		}
 
 

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

@@ -29,40 +29,26 @@ import java.util.Hashtable;
 
 //import ij.IJ;
 import loci.formats.FormatException;
-import loci.formats.tiff.IFD;
-import loci.formats.tiff.IFDList;
-import loci.formats.tiff.TiffParser;
-import loci.formats.tiff.TiffRational;
 
 
 public class ElphelMeta {
-	private Hashtable<String, String> property_table = null;
-	public ElphelMeta (TiffParser tiffParser, boolean scale) throws FormatException, IOException {
-		IFDList exifIFDs = tiffParser.getExifIFDs();
+//	private Hashtable<String, String> property_table = null;
+
+	public static Hashtable<String, String> getMeta (Hashtable<String, String> property_table,
+			long[] maker_note,
+			double exposure,
+			String date_time,
+			boolean scale) throws FormatException, IOException {
+		if (property_table == null) {
 			property_table = new Hashtable<String, String> ();
-		long[] maker_note = null;
-		if (exifIFDs.size() > 0) {
-			IFD exifIFD = exifIFDs.get(0);
-	    	tiffParser.fillInIFD(exifIFD);
-			if (exifIFD.containsKey(IFD.MAKER_NOTE)) {
-				maker_note = (long[]) exifIFD.get(IFD.MAKER_NOTE);
-			}
-			if (exifIFD.containsKey(IFD.EXPOSURE_TIME)) {
-				Object exp = exifIFD.get(IFD.EXPOSURE_TIME);
-				if (exp instanceof TiffRational) {
-					TiffRational texp = (TiffRational) exp;
-					double d = 1.0*texp.getNumerator()/texp.getDenominator();
-					property_table.put("EXPOSURE",  String.format("%f",d));
-				}
 		}
-			if (exifIFD.containsKey(IFD.DATE_TIME_ORIGINAL)) {
-				String dt = exifIFD.get(IFD.DATE_TIME_ORIGINAL).toString();
-				if (exifIFD.containsKey(IFD.SUB_SEC_TIME_ORIGINAL)) {
-					dt += "."+exifIFD.get(IFD.SUB_SEC_TIME_ORIGINAL).toString();
-				}
-				property_table.put("DATE_TIME",  dt);
+		if (!Double.isNaN(exposure)) {
+			property_table.put("EXPOSURE",  String.format("%f",exposure));
 		}
+		if (date_time == null) {
+			property_table.put("DATE_TIME",  date_time);
 		}
+		if (maker_note != null) {
 			// copied from JP4_Reader_cam
 			// Add GPS tags when there will be images to experiment (or while reimplementing JP4 reader)
 			double[] gains= new double[4];
@@ -96,7 +82,6 @@ public class ElphelMeta {
 			long     CORING_INDEX_Y=0;
 			long     CORING_INDEX_C=0;
 			double []   satValue={255.0, 255.0, 255.0, 255.0};
-		if  (maker_note !=null) {
 			for (i=0;i<4;i++) { /* r,g,gb,b */
 				gains[i]= maker_note[i]/65536.0;
 				blacks[i]=(maker_note[i+4]>>24)/256.0;
@@ -193,7 +178,7 @@ public class ElphelMeta {
 				property_table.put("FLIPV2",FLIPV2?"1":"0");
 				property_table.put("FLIPV3",FLIPV3?"1":"0");
 			}
-// If there are FLIPH, FLIPV - swap gains, gammas, blacks accordingly. later the images will be also flipped
+			// If there are FLIPH, FLIPV - swap gains, gammas, blacks accordingly. later the images will be also flipped
 			if (FLIPV!=0) {
 				swapArrayElements (gains,       1, 3);
 				swapArrayElements (gains,       0, 2);
@@ -215,9 +200,6 @@ public class ElphelMeta {
 				swapArrayElements (gamma_scales,3, 2);
 			}
 			for (i=0;i<4;i++) rgammas[i]=elphel_gamma_calc (gammas[i], blacks[i], gamma_scales[i]);
-		} else {
-			return; // No MakerNote, return with nothing done
-		}
 			/**adjusting gains to have the result picture in the range 0..256 */
 			min_gain=2.0*gains[0];
 			for (i=0;i<4;i++) {
@@ -237,7 +219,7 @@ public class ElphelMeta {
 				property_table.put("saturation_"+i,String.format("%f",satValue[i]));
 
 			}
-// swap satValue to match FLIPH,FLIPV again
+			// swap satValue to match FLIPH,FLIPV again
 			if (FLIPV!=0) {
 				swapArrayElements (satValue,       1, 3);
 				swapArrayElements (satValue,       0, 2);
@@ -250,19 +232,25 @@ public class ElphelMeta {
 				property_table.put("saturation_"+i,String.format("%f",satValue[i]));
 			}
 		}
-
-	public Hashtable<String, String> getPropertyTable(){
 		return property_table;
 	}
 
+
+
+
+
+	//	public Hashtable<String, String> getPropertyTable(){
+	//		return property_table;
+	//	}
+
 	// -- Helper methods --
 
-	void swapArrayElements (double[]arr,int i, int j) {
+	static void swapArrayElements (double[]arr,int i, int j) {
 		double tmp=arr[i];
 		arr[i]=arr[j];
 		arr[j]=tmp;
 	}
-	void swapArrayElements (long[]arr,int i, int j) {
+	static void swapArrayElements (long[]arr,int i, int j) {
 		long tmp=arr[i];
 		arr[i]=arr[j];
 		arr[j]=tmp;
@@ -270,7 +258,7 @@ public class ElphelMeta {
 	/* reverses gamma calculations in the camera
     returns double[] table , in the range 0.0..255.996
 	 */
-	double [] elphel_gamma_calc (double gamma, double black, long gamma_scale) {
+	static double [] elphel_gamma_calc (double gamma, double black, long gamma_scale) {
 		int i;
 		double x, black256 ,k;
 		int[] gtable = new int[257];

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

@@ -27,15 +27,25 @@
  */
 package com.elphel.imagej.readers;
 import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
 import java.util.Hashtable;
 
+import org.apache.commons.compress.utils.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import loci.common.ByteArrayHandle;
+import loci.common.Location;
 import loci.formats.FormatException;
 import loci.formats.in.MetadataLevel;
 import loci.formats.in.TiffReader;
 import loci.formats.meta.MetadataStore;
+import loci.formats.tiff.IFD;
+import loci.formats.tiff.IFDList;
+import loci.formats.tiff.TiffRational;
 
 /*
   // non-IFD tags (for internal use)
@@ -72,7 +82,9 @@ IFD.java  public static final int MAKER_NOTE = 37500;
 public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 
 	// -- Constants --
+
 	public static final String ELPHEL_PROPERTY_PREFIX = "ELPHEL_";
+	public static final String CONTENT_FILENAME = "CONTENT_FILENAME";
 
 	  /** Merge SubIFDs into the main IFD list. */
 //	  protected transient boolean mergeSubIFDs = true; // false;
@@ -89,7 +101,10 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	//	  public static final int IMAGEJ_TAG = 50839;
 
 	// -- Fields --
-
+//	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 file_initialized = false;
 	//	  private String companionFile;
 	//	  private String description;
 	//	  private String calibrationUnit;
@@ -102,12 +117,75 @@ 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;
+///		mergeSubIFDs = true; // false;
 		LOGGER.info("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
 	}
 
 	// -- IFormatReader API methods --
 
+	  @Override
+	  public void setId(String id) throws FormatException, IOException {
+		  LOGGER.debug("setId("+id+"). before super" );
+		  file_initialized = 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");
+			  super.setId(id);
+		  } else {
+			  // If URL, then read to memory, if normal file - use direct access
+			  //	 		String cameraURL = "http://192.168.0.36:2323/img"; // for testing
+			  // just testing - ignore file name and use camera URL
+			  //	 		id = cameraURL;
+			  url = null;
+			  //	 		String mime = null; // use to select jp4/tiff later? Or to check it is correct
+			  content_fileName = null;
+			  try {
+				  url = new URL(id);
+			  } catch (MalformedURLException e) {
+				  LOGGER.warn("Bad URL: " + id);
+			  }
+			  if (url != null) {
+				  LOGGER.info("Starting initFile() method, read "+ id +" to memory first");
+				  //https://www.rgagnon.com/javadetails/java-0487.html
+				  URLConnection connection = url.openConnection();
+
+				  String content_disposition = connection.getHeaderField("Content-Disposition");
+				  // raw = "attachment; filename=abc.jpg"
+				  if(content_disposition != null && content_disposition.indexOf("=") != -1) {
+					  content_fileName = content_disposition.split("=")[1]; //getting value after '='
+					  // trim quotes
+					  content_fileName= content_fileName.substring(1, content_fileName.length()-1);
+				  } else {
+					  String mime =  connection.getContentType();
+					  int slash = mime.lastIndexOf("/");
+					  String suffix = slash < 0 ? "" : mime.substring(slash+1);
+					  content_fileName = "unknown." + suffix;
+				  }
+				  //	 			currentId = fileName; //???
+				  //	 			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.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.info("read file directly");
+				  super.setId(id);
+			  }
+		  }
+
+		  //getReader
+		  //	    super.setId(id);
+		  LOGGER.debug("setId("+id+"). after super" );
+		  file_initialized = true;
+	  }
 
 	@Override
 	protected void initFile(java.lang.String id)
@@ -117,6 +195,8 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		LOGGER.info("Starting initFile() method");
 		super.initFile(id);
 		LOGGER.info("Ending initFile() method");
+
+
     }
 
 	/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@@ -134,8 +214,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	@Override
 	public void close(boolean fileOnly) throws IOException {
 		LOGGER.info("close("+fileOnly+") before super");
-		super.close(fileOnly);
+		super.close(fileOnly); // curerent_id == null only during actual close?
 		LOGGER.info("close("+fileOnly+") after super");
+		if ((content_fileName != null) && file_initialized){
+			Location.mapFile(content_fileName, null);
+			file_initialized = false;
+		}
+//	    HashMap<String,Object> dbg_loc = Location.getIdMap();
+
 		if (!fileOnly) {
 			//	      companionFile = null;
 			//	      description = null;
@@ -156,8 +242,35 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 		super.initStandardMetadata();
 		String comment = ifds.get(0).getComment(); // IMAGE_DESCRIPTION
 		LOGGER.info("initStandardMetadata() - after super()");
-		ElphelMeta elphelMeta = new ElphelMeta(tiffParser, true);
-		Hashtable<String, String> property_table = elphelMeta.getPropertyTable();
+		long[] maker_note = null;
+		double exposure = Double.NaN;
+		String date_time = null;
+		IFDList exifIFDs = tiffParser.getExifIFDs();
+		if (exifIFDs.size() > 0) {
+			IFD exifIFD = exifIFDs.get(0);
+			tiffParser.fillInIFD(exifIFD);
+			if (exifIFD.containsKey(IFD.MAKER_NOTE)) {
+				maker_note = (long[]) exifIFD.get(IFD.MAKER_NOTE);
+			}
+			if (exifIFD.containsKey(IFD.EXPOSURE_TIME)) {
+				Object exp = exifIFD.get(IFD.EXPOSURE_TIME);
+				if (exp instanceof TiffRational) {
+					TiffRational texp = (TiffRational) exp;
+					exposure = 1.0*texp.getNumerator()/texp.getDenominator();
+				}
+			}
+			if (exifIFD.containsKey(IFD.DATE_TIME_ORIGINAL)) {
+				date_time = exifIFD.get(IFD.DATE_TIME_ORIGINAL).toString();
+				if (exifIFD.containsKey(IFD.SUB_SEC_TIME_ORIGINAL)) {
+					date_time += "."+exifIFD.get(IFD.SUB_SEC_TIME_ORIGINAL).toString();
+				}
+			}
+		}
+
+		Hashtable<String, String> property_table = ElphelMeta.getMeta(
+				null, maker_note, exposure, date_time, true );
+
+
 		LOGGER.info("Created elphelMeta table, size="+property_table.size());
 		for (String key:property_table.keySet()) {
 			addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
@@ -167,6 +280,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 			Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
 			LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
 	    }
+		addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
 		// check for ImageJ-style TIFF comment
 		boolean ij = checkCommentImageJ(comment);
 //		if (ij) parseCommentImageJ(comment);
@@ -220,6 +334,22 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
 	    populateMetadataStoreImageJ(store);
 	  }
 
+	  /**
+	   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
+	   */
+	  @Override
+	  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
+	    throws FormatException, IOException
+	  {
+		LOGGER.info("openBytes() - before super()");
+	    super.openBytes(no, buf, x, y, w, h);
+		LOGGER.info("openBytes() - after super()");
+	    return buf;
+	  }
+
+
+
+
 	  // -- Helper methods --
 
 	  // Convert to Elphel-specific parameters

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

+/**
+ ** -----------------------------------------------------------------------------**
+ ** ImagejJp4Tiff.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.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  ImagejJp4Tiff.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.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Properties;
+import java.util.Set;
+
+import org.apache.commons.compress.utils.IOUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import ij.ImagePlus;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
+import loci.common.ByteArrayHandle;
+import loci.common.Location;
+import loci.common.services.DependencyException;
+import loci.common.services.ServiceException;
+import loci.common.services.ServiceFactory;
+import loci.formats.ClassList;
+import loci.formats.FormatException;
+import loci.formats.IFormatReader;
+import loci.formats.ImageReader;
+import loci.formats.meta.IMetadata;
+import loci.formats.services.OMEXMLService;
+
+public class ImagejJp4Tiff {
+
+	// -- Constants --
+
+	private static final Logger LOGGER = LoggerFactory.getLogger(ClassList.class);
+	private static final boolean BYPASS_SERVICES = true;
+
+	// -- Fields --
+
+	private ImageReader reader = null;
+	private String content_fileName = "undefined"; // from Content-disposition
+	private URL url = null; // save here actual URL when reading file to memory
+	IMetadata omeMeta = null;
+
+	// -- Constructor --
+
+	public ImagejJp4Tiff() {
+		// Bypass readers.txt
+		ClassList<IFormatReader> classList =  new ClassList<IFormatReader>(IFormatReader.class);
+//		classList.addClass(com.elphel.imagej.readers.ElphelTiffJp4Reader.class);
+		classList.addClass(com.elphel.imagej.readers.ElphelJp4Reader.class);
+		classList.addClass(com.elphel.imagej.readers.ElphelTiffReader.class);
+
+		if (!BYPASS_SERVICES) {
+			ServiceFactory factory = null;
+
+			try {
+				factory = new ServiceFactory();
+			} catch (DependencyException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+
+			OMEXMLService service = null;
+			try {
+				service = factory.getInstance(OMEXMLService.class);
+			} catch (DependencyException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+
+			try {
+				omeMeta = service.createOMEXMLMetadata();
+			} catch (ServiceException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+
+		}
+	    reader = new ImageReader(classList);
+	    if (!BYPASS_SERVICES) {
+	    	reader.setMetadataStore(omeMeta);
+	    }
+	}
+
+	// -- API methods --
+
+	public ImagePlus readTiffJp4(String path) throws IOException, FormatException {
+		return readTiffJp4(path, 	"STD_"); // null);
+	}
+
+	public ImagePlus readTiffJp4(String path_url, 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;
+		//	 		String mime = null; // use to select jp4/tiff later? Or to check it is correct
+		content_fileName = null;
+		try {
+			url = new URL(path_url);
+		} catch (MalformedURLException e) {
+			LOGGER.warn("Bad URL: " + path_url);
+		}
+		if (url != null) {
+			LOGGER.info("Read "+ path_url +" to memory first");
+			URLConnection connection = url.openConnection();
+
+			String content_disposition = connection.getHeaderField("Content-Disposition");
+			// raw = "attachment; filename=abc.jpg"
+			if(content_disposition != null && content_disposition.indexOf("=") != -1) {
+				content_fileName = content_disposition.split("=")[1]; //getting value after '='
+				// trim quotes
+				content_fileName= content_fileName.substring(1, content_fileName.length()-1);
+			} else {
+				String mime =  connection.getContentType();
+				int slash = mime.lastIndexOf("/");
+				String suffix = slash < 0 ? "" : mime.substring(slash+1);
+				content_fileName = "unknown." + suffix;
+			}
+			InputStream is =    url.openStream (); //
+			byte[] inBytes = IOUtils.toByteArray(is);
+			if (is != null) is.close();
+			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 = path_url;
+			LOGGER.info("read '"+path_url+"' file directly");
+		}
+		reader.setId(content_fileName);
+		byte [] bytes = null;
+		ImagePlus imp=  null;
+		bytes = reader.openBytes(0);
+		int bpp =   reader.getBitsPerPixel();
+
+		boolean is_le = reader.isLittleEndian();
+		int bytes_per_pixel =  (bpp + 7) / 9;
+		float [] pixels = new float [bytes.length/bytes_per_pixel];
+		if (bytes_per_pixel == 1) {
+			for (int i = 0; i < pixels.length; i++) {
+				pixels[i] = ((bytes[i])) & 0xff;
+			}
+		} else {
+			ByteBuffer bb = ByteBuffer.wrap(bytes);
+			if (is_le) {
+				bb.order( ByteOrder.LITTLE_ENDIAN);
+			} else {
+				bb.order( ByteOrder.BIG_ENDIAN);
+			}
+			for (int i = 0; i < pixels.length; i++) {
+				pixels[i] = ((bb.getShort())) & 0xffff;
+			}
+		}
+
+		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;
+		if (meta_hash.containsKey(imageNameKey)) {
+			imageName = meta_hash.get(imageNameKey).toString();
+		}
+		imp =  new ImagePlus(imageName, ip); // original jp46 reader had full path as title
+
+		// first - save all as properties, later - only ELPHEL_*
+		for (String key:meta_hash.keySet()) {
+			if (key.startsWith(prefix)) {
+				imp.setProperty(key.substring(prefix.length()), meta_hash.get(key).toString());
+			} else if (std != null) {
+				imp.setProperty(std+(key.replace(" ","_").replace("/","_")), meta_hash.get(key).toString());
+			}
+		}
+		encodeProperiesToInfo(imp);
+		Location.mapFile(content_fileName, null);
+		return imp;
+	}
+
+	// -- Helper methods --
+
+	public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
+		String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
+		Set<Object> jp4_set;
+		Properties jp4_prop;
+		Iterator<Object> itr;
+		String str;
+		jp4_prop=imp.getProperties();
+		if (jp4_prop!=null) {
+			jp4_set=jp4_prop.keySet();
+			itr=jp4_set.iterator();
+			while(itr.hasNext()) {
+				str = (String) itr.next();
+				//				if (!str.equals("Info")) info+="<"+str+">\""+jp4_prop.getProperty(str)+"\"</"+str+">";
+				if (!str.equals("Info")) info+="<"+str+">"+jp4_prop.getProperty(str)+"</"+str+">";
+			}
+		}
+		info+="</properties>\n";
+		imp.setProperty("Info", info);
+		return imp;
+	}
+
+
+}

src/main/resources/readers1.txt

+# This document is a configuration file identifying all file format readers
+# available to Bio-Formats, and the order in which they should be used.
+# Please do not edit unless you know what you are doing, see
+# https://docs.openmicroscopy.org/latest/bio-formats/developers/reader-guide.html
+
+#Elphel readers
+com.elphel.imagej.readers.ElphelTiffJp4Reader # tiff,jp4