Working on loci-compatible reader for camera files to use single-read

pass

.gitignore

@@ -7,4 +7,5 @@ NC393I
 attic
 *.log
 FOCUS-PSF*
-src/main/resources/trained_model
+src/main/resources/trained_model
\ No newline at end of file
+bioformats
\ No newline at end of file

pom.xml

@@ -88,7 +88,7 @@
 		<dependency>
 			<groupId>ome</groupId>
 			<artifactId>loci_tools</artifactId>
-			<version>5.0.0</version>
+			<version>5.9.0</version>
 		</dependency>
 	</dependencies>
 

src/main/java/JP46_Reader_camera.java

@@ -39,9 +39,12 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.RandomAccessFile;
 import java.io.StringReader;
+import java.io.UnsupportedEncodingException;
+import java.lang.reflect.Array;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLConnection;
+import java.util.Arrays;
 import java.util.Iterator;
 import java.util.Properties;
 import java.util.Set;
@@ -66,10 +69,15 @@ import ij.gui.GUI;
 import ij.gui.GenericDialog;
 import ij.io.FileInfo;
 import ij.io.OpenDialog;
+import ij.io.Opener;
 import ij.plugin.frame.PlugInFrame;
 import ij.process.ImageConverter;
 import ij.process.ImageProcessor;
 import ij.text.TextWindow;
+import loci.common.RandomAccessInputStream;
+import loci.formats.tiff.IFD;
+import loci.formats.tiff.IFDList;
+import loci.formats.tiff.TiffParser;
 
 
 
@@ -1035,12 +1043,18 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 	/* Modified from Opener.java */
 	ImagePlus openJpegOrGif(String dir, String name) {
 		ImagePlus imp = null;
+		boolean isTiff = false;
 		Image img = Toolkit.getDefaultToolkit().createImage(dir+name);
 		if (img!=null) {
 			try {
 				imp = new ImagePlus(name, img);
 			} catch (IllegalStateException e) {
-				return null; // error loading image
+				//java.lang.IllegalStateException: Error loading image
+				// Try TIFF
+				Opener opener=new Opener(); // Reads Tiff images
+				imp=opener.openImage("", dir+name);
+				if (imp == null) return null; // error loading image
+				isTiff = true;
 			}
 
 			if (imp.getType()==ImagePlus.COLOR_RGB) {
@@ -1049,15 +1063,100 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 
 			IJ.showStatus("Converting to 32-bits");
 			new ImageConverter(imp).convertToGray32();
-
-			FileInfo fi = new FileInfo();
-			fi.fileFormat = FileInfo.GIF_OR_JPG;
+			FileInfo fi = imp.getFileInfo();
 			fi.fileName = name;
 			fi.directory = dir;
+			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;
 	}
+
+	public static void dumpIFDs(String path) throws IOException {
+		IJ.showStatus("Parsing IFDs");
+		RandomAccessInputStream in = new RandomAccessInputStream(path);
+
+		//TiffParser parser = new TiffParser(in);
+		TiffParser parser = new TiffParser(in);
+		IFDList ifdList = parser.getIFDs();
+		IJ.showStatus("");
+		for (IFD ifd : ifdList) {
+			for (Integer key : ifd.keySet()) {
+				int k = key.intValue();
+				String name = IFD.getIFDTagName(k)+String.format("(%d [0x%x])", k,k);
+				String value = prettyValue(ifd.getIFDValue(k), 0);
+				IJ.log(name + " = " + value);
+			}
+		}
+		in.close();
+	}
+
+	private static String prettyValue(Object value, int indent) {
+		if (!value.getClass().isArray()) return value.toString()+" ("+value.getClass().toString()+")";
+		char[] spaceChars = new char[indent];
+		Arrays.fill(spaceChars, ' ');
+		String spaces = new String(spaceChars);
+		StringBuilder sb = new StringBuilder();
+		sb.append("{\n");
+		for (int i=0; i<Array.getLength(value); i++) {
+			sb.append(spaces);
+			sb.append(" ");
+			Object component = Array.get(value, i);
+			sb.append(prettyValue(component, indent + 2));
+			sb.append("\n");
+		}
+		sb.append(spaces);
+		sb.append("}");
+		byte [] bstring=new byte [Array.getLength(value)];
+		for (int i=0;i<bstring.length;i++) {
+			try {
+				bstring[i]= (byte) Integer.parseInt(Array.get(value, i).toString());
+			} catch (NumberFormatException e) {
+				bstring[i] = 0;
+			}
+		}
+		//   String astring=new String((byte []) value);
+		String astring="";
+		try {
+			astring = new String(bstring,"UTF-16");
+		} catch (UnsupportedEncodingException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		sb.append("\n\""+astring+"\"");
+		return sb.toString();
+	}
+
+
+
+
 	@Override
 	public void setTitle (String title) {
 		imageTitle=title;

src/main/java/LwirCamera.java

+/**
+ **
+ ** LwirCamera.java - Control/image acquisition for LWIR cameras
+ ** (initially for Lepton 3.5 sensors, 103992 sesnor boards)
+ **
+ ** Copyright (C) 2019 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  LwirCamera.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/>.
+ ** -----------------------------------------------------------------------------**
+ **
+ */
+
+public class LwirCamera {
+
+}

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

+/**
+ ** -----------------------------------------------------------------------------**
+ ** ElphelTiffReader.java
+ **
+ ** loci.format compatible reader for Elphel 8/16 bpp monochrome Tiff files with
+ ** MakerNote
+ **
+ **
+ ** Copyright (C) 2019 Elphel, Inc.
+ **
+ ** -----------------------------------------------------------------------------**
+ **
+ **  ElphelTiffReader.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.Hashtable;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import loci.formats.FormatException;
+import loci.formats.in.MetadataLevel;
+import loci.formats.in.TiffReader;
+import loci.formats.meta.MetadataStore;
+
+/*
+  // non-IFD tags (for internal use)
+  public static final int LITTLE_ENDIAN = 0;
+  public static final int BIG_TIFF = 1;
+  public static final int REUSE = 3;
+   <MakerNote          tag="0x927c" format="LONG" count="16"  seq="26" dlen="64"/> 37500
+package loci.formats.tiff;
+IFD.java  public static final int MAKER_NOTE = 37500;
+
+ * IFD data
+{       0=false, LITTLE_ENDIAN
+        1=false, BIG_TIFF
+0x0100 256=160,                                     ImageWidth
+0x0101 257=120,                                     ImageLength
+0x0102 258= 16,                                     BitsPerSample
+0x0106 262=  1,                                     PhotometricInterpretation
+0x0129 297=  [I@3d136141,                           PageNumber
+0x8769 34665=242,                                   ExifTag (A pointer to the Exif IFD.)
+0x010e 270=[Ljava.lang.String;@640a5e9d,            ImageDescription
+0x010f 271=Elphel,                                  Make
+0xc62f 50735=00:0E:64:10:8F:15,                     CameraSerialNumber
+0x0110 272=LEPTON35_15,                             Model
+0x0111 273=557,                                     StripOffsets
+0x0131 305=https://git.elphel.com/Elphel/elphel393, Software
+0x9211 37393=122,                                   ImageNumber
+0x0112 274=1,                                       Orientation
+0x0132 306=2019:05:06 14:41:51,                     DateTime
+0x0115 277=1,                                       SamplesPerPixel
+0x0116 278=120,                                     RowsPerStrip
+0x0117 279=38400,                                   StripByteCounts
+0x00fe 254=0                                        NewSubfileType }
+  */
+public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
+
+	// -- Constants --
+	public static final String ELPHEL_PROPERTY_PREFIX = "ELPHEL_";
+
+	  /** Merge SubIFDs into the main IFD list. */
+//	  protected transient boolean mergeSubIFDs = true; // false;
+
+	/** Logger for this class. */
+	private static final Logger LOGGER =
+			LoggerFactory.getLogger(ElphelTiffReader.class);
+
+	//	  public static final String[] ELPHEL_TIFF_SUFFIXES =
+	//	    {"tif", "tiff"}; // , "tf2", "tf8", "btf"};
+
+	//	  public static final String[] COMPANION_SUFFIXES = {"xml", "txt"};
+
+	//	  public static final int IMAGEJ_TAG = 50839;
+
+	// -- Fields --
+
+	//	  private String companionFile;
+	//	  private String description;
+	//	  private String calibrationUnit;
+	//	  private Double physicalSizeZ;
+	//	  private Double timeIncrement;
+	//	  private Integer xOrigin, yOrigin;
+
+	// -- Constructor --
+
+	/** 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;
+		LOGGER.info("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
+	}
+
+	// -- IFormatReader API methods --
+
+
+	@Override
+	protected void initFile(java.lang.String id)
+            throws FormatException,
+                   java.io.IOException
+    {
+		LOGGER.info("Starting initFile() method");
+		super.initFile(id);
+		LOGGER.info("Ending initFile() method");
+    }
+
+	/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
+	@Override
+	public String[] getSeriesUsedFiles(boolean noPixels) {
+		return super.getSeriesUsedFiles(noPixels);
+		//	    if (noPixels) {
+		//	      return companionFile == null ? null : new String[] {companionFile};
+		//	    }
+		//	    if (companionFile != null) return new String[] {companionFile, currentId};
+		//	    return new String[] {currentId};
+	}
+
+	/* @see loci.formats.IFormatReader#close(boolean) */
+	@Override
+	public void close(boolean fileOnly) throws IOException {
+		LOGGER.info("close("+fileOnly+") before super");
+		super.close(fileOnly);
+		LOGGER.info("close("+fileOnly+") after super");
+		if (!fileOnly) {
+			//	      companionFile = null;
+			//	      description = null;
+			//	      calibrationUnit = null;
+			//	      physicalSizeZ = null;
+			//	      timeIncrement = null;
+			//	      xOrigin = null;
+			//	      yOrigin = null;
+		}
+	}
+
+	// -- Internal BaseTiffReader API methods --
+
+	/* @see BaseTiffReader#initStandardMetadata() */
+	@Override
+	protected void initStandardMetadata() throws FormatException, IOException {
+		LOGGER.info("initStandardMetadata() - before super()");
+		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();
+		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.info("initStandardMetadata() - got "+tags.length+" tags");
+	    }
+		// check for ImageJ-style TIFF comment
+		boolean ij = checkCommentImageJ(comment);
+//		if (ij) parseCommentImageJ(comment);
+		/*
+		// check for MetaMorph-style TIFF comment
+		boolean metamorph = checkCommentMetamorph(comment);
+		if (metamorph && level != MetadataLevel.MINIMUM) {
+			parseCommentMetamorph(comment);
+		}
+		put("MetaMorph", metamorph ? "yes" : "no");
+
+		// check for other INI-style comment
+		if (!ij && !metamorph && level != MetadataLevel.MINIMUM) {
+			parseCommentGeneric(comment);
+		}
+		 */
+		// check for another file with the same name
+		/*
+		if (isGroupFiles()) {
+			Location currentFile = new Location(currentId).getAbsoluteFile();
+			String currentName = currentFile.getName();
+			Location directory = currentFile.getParentFile();
+			String[] files = directory.list(true);
+			if (files != null) {
+				for (String file : files) {
+					String name = file;
+					if (name.indexOf(".") != -1) {
+						name = name.substring(0, name.indexOf("."));
+					}
+
+					if (currentName.startsWith(name) &&
+							checkSuffix(name, COMPANION_SUFFIXES))
+					{
+						companionFile = new Location(directory, file).getAbsolutePath();
+						break;
+					}
+				}
+			}
+		}
+		*/
+	}
+
+	  /* @see BaseTiffReader#initMetadataStore() */
+	  @Override
+	protected void initMetadataStore() throws FormatException {
+	    super.initMetadataStore();
+	    MetadataStore store = makeFilterMetadata();
+//	    if (description != null) {
+//	      store.setImageDescription(description, 0);
+//	    }
+	    populateMetadataStoreImageJ(store);
+	  }
+
+	  // -- Helper methods --
+
+	  // Convert to Elphel-specific parameters
+	  /**
+	   * Checks the original metadata table for ImageJ-specific information
+	   * to propagate into the metadata store.
+	   */
+	  private void populateMetadataStoreImageJ(MetadataStore store) {
+	    // TODO: Perhaps we should only populate the physical Z size if the unit is
+	    //       a known, physical quantity such as "micron" rather than "pixel".
+	    //       e.g.: if (calibrationUnit.equals("micron"))
+		/*
+	    if (physicalSizeZ != null) {
+	      double zDepth = physicalSizeZ.doubleValue();
+	      if (zDepth < 0) zDepth = -zDepth;
+	      store.setPixelsPhysicalSizeZ(new PositiveFloat(zDepth), 0);
+	    }
+	    if (timeIncrement != null) {
+	      store.setPixelsTimeIncrement(timeIncrement, 0);
+	    }
+	    */
+	  }
+	//
+	private boolean checkCommentImageJ(String comment) {
+		return comment != null && comment.startsWith("ImageJ=");
+	}
+
+}

src/main/resources/readers.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
+
+# Could not find loci.formats.in.URLReader
+# Could not find loci.formats.in.SlideBook6Reader
+# "loci.formats.in.MicroCTReader" is not valid.
+# Could not find loci.formats.in.CV7000Reader
+# Could not find loci.formats.in.KLBReader
+# java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader
+# at java.net.URLClassLoader.findClass(URLClassLoader.java:382) ~[na:1.8.0_201]
+
+#Elphel readers
+com.elphel.imagej.readers.ElphelTiffReader # extensions same as TiffReader
+
+loci.formats.in.FilePatternReader     # pattern
+##loci.formats.in.URLReader[type=external] # urlreader # Could not find loci.formats.in.URLReader
+
+# readers for compressed/archive files
+loci.formats.in.ZipReader             # zip
+
+# javax.imageio readers
+loci.formats.in.APNGReader            # png [javax.imageio]
+loci.formats.in.JPEGReader            # jpg, jpeg [javax.imageio]
+
+# external readers with unique file extensions
+##loci.formats.in.SlideBook6Reader[type=external]      # sld # Could not find loci.formats.in.SlideBook6Reader
+loci.formats.in.ScreenReader[type=external]         # .screen
+
+# standalone readers with unique file extensions
+loci.formats.in.PGMReader             # pgm
+loci.formats.in.FitsReader            # fits
+loci.formats.in.PCXReader             # pcx
+loci.formats.in.GIFReader             # gif
+loci.formats.in.BMPReader             # bmp
+loci.formats.in.IPLabReader           # ipl
+loci.formats.in.IvisionReader         # ipm
+loci.formats.in.DeltavisionReader     # dv, r3d
+loci.formats.in.MRCReader             # mrc, st, ali
+loci.formats.in.GatanReader           # dm3
+loci.formats.in.GatanDM2Reader        # dm2
+loci.formats.in.ImarisReader          # ims
+loci.formats.in.OpenlabRawReader      # raw
+loci.formats.in.OMEXMLReader          # ome
+loci.formats.in.LIFReader             # lif
+loci.formats.in.AVIReader             # avi
+loci.formats.in.PictReader            # pict, pct
+loci.formats.in.SDTReader             # sdt
+loci.formats.in.SPCReader             # spc
+loci.formats.in.EPSReader             # eps, epsi
+loci.formats.in.SlidebookReader       # sld
+loci.formats.in.AliconaReader         # al3d
+loci.formats.in.MNGReader             # mng
+loci.formats.in.KhorosReader          # xv
+loci.formats.in.VisitechReader        # html, xys
+loci.formats.in.LIMReader             # lim
+loci.formats.in.PSDReader             # psd
+loci.formats.in.InCellReader          # xdce
+loci.formats.in.L2DReader             # l2d
+loci.formats.in.FEIReader             # img
+loci.formats.in.NAFReader             # naf
+loci.formats.in.MINCReader            # mnc
+loci.formats.in.QTReader              # mov
+loci.formats.in.MRWReader             # mrw
+loci.formats.in.TillVisionReader      # vws
+loci.formats.in.ARFReader             # arf
+loci.formats.in.CellomicsReader       # c01
+loci.formats.in.LiFlimReader          # fli
+loci.formats.in.TargaReader           # tga
+loci.formats.in.OxfordInstrumentsReader # top
+loci.formats.in.VGSAMReader           # dti
+loci.formats.in.HISReader             # his
+loci.formats.in.WATOPReader           # wat
+loci.formats.in.SeikoReader           # xqd, xqf
+loci.formats.in.TopometrixReader      # tfr, ffr, zfr, zfp, 2fl
+loci.formats.in.UBMReader             # pr3
+loci.formats.in.QuesantReader         # afm
+loci.formats.in.BioRadGelReader       # 1sc
+loci.formats.in.RHKReader             # sm2, sm3
+loci.formats.in.MolecularImagingReader # stp
+loci.formats.in.CellWorxReader        # pnl, htd
+loci.formats.in.Ecat7Reader           # v
+loci.formats.in.VarianFDFReader       # fdf
+loci.formats.in.AIMReader             # aim
+loci.formats.in.InCell3000Reader      # frm
+loci.formats.in.SpiderReader          # spi
+loci.formats.in.VolocityReader        # mvd2
+loci.formats.in.ImagicReader          # hed
+loci.formats.in.HamamatsuVMSReader    # vms
+loci.formats.in.CellSensReader        # vsi
+loci.formats.in.INRReader             # inr
+loci.formats.in.KodakReader           # bip
+loci.formats.in.VolocityClippingReader # acff
+loci.formats.in.ZeissCZIReader        # czi
+loci.formats.in.SIFReader             # sif
+loci.formats.in.NDPISReader           # ndpis
+loci.formats.in.PovrayReader          # df3
+loci.formats.in.IMODReader            # mod
+loci.formats.in.FakeReader            # fake
+loci.formats.in.AFIReader             # afi
+loci.formats.in.ImspectorReader       # msr
+loci.formats.in.BioRadSCNReader       # scn
+loci.formats.in.ZeissLMSReader        # lms
+loci.formats.in.PQBinReader           # bin
+loci.formats.in.FlowSightReader       # cif
+loci.formats.in.IM3Reader             # im3
+loci.formats.in.I2IReader             # i2i
+loci.formats.in.SPEReader             # spe
+loci.formats.in.OIRReader             # oir
+##loci.formats.in.KLBReader             # klb  # Could not find loci.formats.in.KLBReader
+##loci.formats.in.MicroCTReader         # vff # "loci.formats.in.MicroCTReader" is not valid.
+
+# multi-extension messes
+loci.formats.in.JEOLReader            # dat, img, par
+loci.formats.in.NiftiReader           # hdr, img, nii, nii.gz
+loci.formats.in.AnalyzeReader         # hdr, img
+loci.formats.in.APLReader             # apl, mtb, tnb
+loci.formats.in.NRRDReader            # nrrd, nhdr, pic
+loci.formats.in.ICSReader             # ics, ids
+loci.formats.in.PerkinElmerReader     # rec, ano, csv, htm, tim, zpo, 2, 3, ...
+loci.formats.in.AmiraReader           # am, amiramesh, grey, hx, labels, ...
+loci.formats.in.ScanrReader           # dat, xml, tif
+loci.formats.in.BDReader              # exp, tif
+loci.formats.in.UnisokuReader         # dat, hdr
+loci.formats.in.PDSReader             # hdr, img
+loci.formats.in.FujiReader            # inf, img
+loci.formats.in.OperettaReader        # xml, tif, tiff
+loci.formats.in.InveonReader          # hdr, ct.img, cat, ...
+loci.formats.in.CellVoyagerReader     # xml, tif
+loci.formats.in.ColumbusReader        # xml, tif
+##loci.formats.in.CV7000Reader          # wpi # Could not find loci.formats.in.CV7000Reader
+
+# standard PIC reader must go last (it accepts any PIC)
+loci.formats.in.BioRadReader          # pic
+
+# readers requiring third-party libraries
+loci.formats.in.FV1000Reader          # oib, oif, various [POI]
+loci.formats.in.ZeissZVIReader        # zvi [POI]
+loci.formats.in.IPWReader             # ipw [POI]
+loci.formats.in.JPEG2000Reader        # jp2, j2k [JAI-ImageIO]
+loci.formats.in.JPXReader             # jpx [JAI-ImageIO]
+loci.formats.in.ND2Reader             # nd2, jp2 [JAI-ImageIO]
+loci.formats.in.PCIReader             # cxd [POI]
+loci.formats.in.ImarisHDFReader       # ims [NetCDF]
+loci.formats.in.CellH5Reader          # ch5 [JHDF]
+loci.formats.in.WlzReader	      # wlz [JWlz]
+loci.formats.in.VeecoReader           # hdf [NetCDF]
+
+# TIFF-based readers with unique file extensions
+loci.formats.in.ZeissLSMReader        # lsm, mdb [MDB Tools]
+loci.formats.in.SEQReader             # seq
+loci.formats.in.GelReader             # gel
+loci.formats.in.ImarisTiffReader      # ims
+loci.formats.in.FlexReader            # flex [LuraWave]
+loci.formats.in.SVSReader             # svs
+loci.formats.in.ImaconReader          # fff
+loci.formats.in.LEOReader             # sxm
+loci.formats.in.JPKReader             # jpk
+loci.formats.in.NDPIReader            # ndpi
+loci.formats.in.PCORAWReader          # pcoraw
+
+# TIFF-based readers with slow isThisType
+loci.formats.in.OMETiffReader         # tif
+loci.formats.in.PyramidTiffReader     # tif, tiff
+loci.formats.in.MIASReader            # tif
+loci.formats.in.TCSReader             # xml, tif
+loci.formats.in.LeicaReader           # lei, tif
+loci.formats.in.NikonReader           # nef, tif
+loci.formats.in.FluoviewReader        # tif
+loci.formats.in.PrairieReader         # xml, cfg, tif
+loci.formats.in.MetamorphReader       # stk, tif, nd, scan
+loci.formats.in.MicromanagerReader    # txt, tif
+loci.formats.in.ImprovisionTiffReader # tif
+loci.formats.in.MetamorphTiffReader   # tif
+loci.formats.in.NikonTiffReader       # tif
+loci.formats.in.PhotoshopTiffReader   # tif
+loci.formats.in.FEITiffReader         # tif
+loci.formats.in.SimplePCITiffReader   # tif
+loci.formats.in.NikonElementsTiffReader # tif
+loci.formats.in.TrestleReader         # tif
+loci.formats.in.SISReader             # tif
+loci.formats.in.DNGReader             # cr2, crw, jpg, thm, wav, tif?
+loci.formats.in.ZeissTIFFReader # tif
+loci.formats.in.LeicaSCNReader        # scn
+loci.formats.in.VectraReader          # tif, tiff, qptiff
+loci.formats.in.SlidebookTiffReader   # tiff
+loci.formats.in.IonpathMIBITiffReader   # tif, tiff
+
+# standard TIFF reader must go last (it accepts any TIFF)
+loci.formats.in.TiffDelegateReader    # tif, tiff
+
+# standard text reader must go last (it accepts any plaintext)
+loci.formats.in.TextReader            # txt, csv
+
+# non-TIFF readers with slow isThisType
+loci.formats.in.BurleighReader        # img
+loci.formats.in.OpenlabReader         # liff
+loci.formats.in.DicomReader           # dcm, dicom
+loci.formats.in.SMCameraReader        # (no extension)
+loci.formats.in.SBIGReader            # (no extension)
+loci.formats.in.HRDGDFReader          # (no extension)
+loci.formats.in.HitachiReader         # txt, tif, jpg, bmp
+loci.formats.in.BrukerReader          # fid, acqp
+loci.formats.in.CanonRawReader        # cr2, crw, jpg, thm, wav
+loci.formats.in.OBFReader             # obf, msr