Changeset 2922

Timestamp:

06/29/07 13:03:59 (13 years ago)

Author:

melissa

Message:

• Don't automatically populate OriginalMetadata nodes in OMEXMLMetadataStore. Instead, call populateOriginalMetadata(Hashtable).
• Tweaked/fixed many readers
• Fixed how test framework config files are parsed

Location:

trunk/loci/formats

Files:

• in/AliconaReader.java (modified) (4 diffs)
• in/BMPReader.java (modified) (4 diffs)
• in/BaseTiffReader.java (modified) (3 diffs)
• in/BioRadReader.java (modified) (3 diffs)
• in/DeltavisionReader.java (modified) (6 diffs)
• in/DicomReader.java (modified) (10 diffs)
• in/EPSReader.java (modified) (1 diff)
• in/FitsReader.java (modified) (2 diffs)
• in/FluoviewReader.java (modified) (8 diffs)
• in/GIFReader.java (modified) (17 diffs)
• in/GatanReader.java (modified) (18 diffs)
• in/ICSReader.java (modified) (2 diffs)
• in/IPLabReader.java (modified) (15 diffs)
• in/IPWReader.java (modified) (6 diffs)
• in/ImarisReader.java (modified) (4 diffs)
• in/ImarisTiffReader.java (modified) (1 diff)
• in/KhorosReader.java (modified) (2 diffs)
• in/LIFReader.java (modified) (9 diffs)
• in/LegacyPictReader.java (modified) (1 diff)
• in/LegacyZVIReader.java (modified) (6 diffs)
• in/MNGReader.java (modified) (7 diffs)
• in/MRCReader.java (modified) (7 diffs)
• in/ND2Reader.java (modified) (11 diffs)
• in/NRRDReader.java (modified) (1 diff)
• in/OIBReader.java (modified) (5 diffs)
• in/OIFReader.java (modified) (4 diffs)
• in/OMEXMLReader.java (modified) (2 diffs)
• in/OpenlabRawReader.java (modified) (3 diffs)
• in/OpenlabReader.java (modified) (19 diffs)
• in/PGMReader.java (modified) (2 diffs)
• in/PNGReader.java (modified) (1 diff)
• in/PerkinElmerReader.java (modified) (4 diffs)
• in/PictReader.java (modified) (27 diffs)
• in/QTReader.java (modified) (5 diffs)
• in/SlidebookReader.java (modified) (2 diffs)
• in/ZeissLSMReader.java (modified) (8 diffs)
• ome/OMEXMLMetadataStore.java (modified) (2 diffs)
• test/ConfigurationFiles.java (modified) (1 diff)

trunk/loci/formats/in/AliconaReader.java

@@ -75 +75 @@
     }
 
-    long offset = textureOffset;
-
     for (int i=0; i<numBytes; i++) {
-      in.seek(offset + (no * (core.sizeX[0] + pad)*core.sizeY[0]*(i+1)));
+      in.seek(textureOffset + (no * (core.sizeX[0] + pad)*core.sizeY[0]*(i+1)));
       for (int j=0; j<core.sizeX[0] * core.sizeY[0]; j++) {
-        buf[j*numBytes + i] = (byte) in.read();
+        buf[j*numBytes + i] = (byte) (in.read() & 0xff);
         if (j % core.sizeX[0] == core.sizeX[0] - 1) in.skipBytes(pad);
       }
@@ -105 +103 @@
     // check that this is a valid AL3D file
     status("Verifying Alicona format");
-    byte[] check = new byte[17];
-    in.read(check);
-    String magicString = new String(check);
+    String magicString = in.readString(17);
     if (!magicString.trim().equals("AliconaImaging")) {
       throw new FormatException("Invalid magic string : " +
@@ -118 +114 @@
     status("Reading tags");
 
-    byte[] keyBytes = new byte[20];
-    byte[] valueBytes = new byte[30];
-
     int count = 2;
 
@@ -128 +121 @@
 
     for (int i=0; i<count; i++) {
-      in.read(keyBytes);
-      in.read(valueBytes);
-      in.skipBytes(2);
-
-      String key = new String(keyBytes);
-      String value = new String(valueBytes);
+      String key = in.readString(20);
+      String value = in.readString(30);
       key = key.trim();
       value = value.trim();
 
       addMeta(key, value);
+      in.skipBytes(2);
 
       if (key.equals("TagCount")) count += Integer.parseInt(value);

trunk/loci/formats/in/BMPReader.java

@@ -121 +121 @@
         for (int y=core.sizeY[0]-1; y>=0; y--) {
           for (int x=0; x<core.sizeX[0]; x++) {
-            buf[y*core.sizeX[0] + x] = (byte) in.read();
+            buf[y*core.sizeX[0] + x] = (byte) (in.read() & 0xff);
           }
         }
@@ -129 +129 @@
           for (int x=0; x<core.sizeX[0]; x++) {
             int off = y*core.sizeX[0] + x; 
-            buf[2*core.sizeX[0]*core.sizeY[0] + off] = (byte) in.read();
-            buf[core.sizeX[0]*core.sizeY[0] + off] = (byte) in.read();
-            buf[off] = (byte) in.read();
+            buf[2*core.sizeX[0]*core.sizeY[0] + off] = (byte)(in.read() & 0xff);
+            buf[core.sizeX[0]*core.sizeY[0] + off] = (byte) (in.read() & 0xff);
+            buf[off] = (byte) (in.read() & 0xff);
           }
-          in.skipBytes(2); 
         }
       }
@@ -161 +160 @@
     // read the first header - 14 bytes
 
-    byte[] two = new byte[2];
-    in.read(two);
-    addMeta("Magic identifier", new String(two));
+    addMeta("Magic identifier", in.readString(2));
 
     addMeta("File size (in bytes)", "" + in.readInt());
@@ -226 +223 @@
       for (int i=0; i<nColors; i++) {
         for (int j=palette.length; j>0; j--) {
-          palette[j][i] = (byte) in.read();
+          palette[j][i] = (byte) (in.read() & 0xff);
         }
         in.read();

trunk/loci/formats/in/BaseTiffReader.java

@@ -492 +492 @@
     core.rgb[0] = samples > 1 || p == TiffTools.RGB_PALETTE ||
       p == TiffTools.CFA_ARRAY || p == TiffTools.RGB;
-    //core.interleaved[0] = TiffTools.getSamplesPerPixel(ifds[0]) > 1;
     core.interleaved[0] = true;
     core.littleEndian[0] = TiffTools.isLittleEndian(ifds[0]);
@@ -513 +512 @@
     else if (bitFormat == 2) {
       switch (bps) {
-        case 8:
-          core.pixelType[0] = FormatTools.UINT8;
-          break;
         case 16:
           core.pixelType[0] = FormatTools.INT16;
@@ -528 +524 @@
     else {
       switch (bps) {
-        case 8:
-          core.pixelType[0] = FormatTools.UINT8;
-          break;
         case 16:
           core.pixelType[0] = FormatTools.UINT16;

trunk/loci/formats/in/BioRadReader.java

@@ -146 +146 @@
     byteFormat = in.readShort() != 0;
     int imageNumber = in.readShort();
-    byte[] s = new byte[32];
-    in.read(s);
-    String name = new String(s);
+    String name = in.readString(32);
     int merged = in.readShort();
     int color1 = in.readShort();
@@ -220 +218 @@
       int x = in.readShort();
       int y = in.readShort();
-      s = new byte[80];
-      in.read(s);
-      String text = new String(s);
+      String text = in.readString(80); 
 
       // be sure to remove binary data from the note text
@@ -765 +761 @@
     for (int i=0; i<core.sizeC[0]; i++) {
       store.setLogicalChannel(i, null, null, null, null, null, null, null);
-
-      double white = ramp1max;
-      double black = ramp1min;
-
-      store.setDisplayChannel(new Integer(i),  new Double(black),
-        new Double(white), null, null);
+      store.setDisplayChannel(new Integer(i), new Double(ramp1max),
+        new Double(ramp1min), null, null);
     }
     store.setDisplayOptions(zoom == null ? null : new Float(zoom),

trunk/loci/formats/in/DeltavisionReader.java

@@ -51 +51 @@
   private int bytesPerPixel;
 
-  /** Offset where the ExtHdr starts. */
-  protected int initExtHdrOffset = 1024;
-
   /** Size of one wave in the extended header. */
   protected int wSize;
@@ -64 +61 @@
 
   /**
-   * the Number of ints in each extended header section. These fields appear
+   * The number of ints in each extended header section. These fields appear
    * to be all blank but need to be skipped to get to the floats afterwards
    */
@@ -84 +81 @@
   /* @see loci.formats.IFormatReader#isThisType(byte[]) */
   public boolean isThisType(byte[] block) {
-    return (DataTools.bytesToShort(block, 0, 2, core.littleEndian[0]) ==
-      LITTLE_ENDIAN);
+    return false; 
   }
 
@@ -347 +343 @@
       new DVExtHdrFields[core.sizeZ[0]][core.sizeC[0]][core.sizeT[0]];
 
+    hstream.close();
+
     store.setPixels(new Integer(core.sizeX[0]), new Integer(core.sizeY[0]),
       new Integer(core.sizeZ[0]), new Integer(core.sizeC[0]),
@@ -361 +359 @@
     // Run through every timeslice, for each wavelength, for each z section
     // and fill in the Extended Header information array for that image
-    for (int z = 0; z < core.sizeZ[0]; z++) {
-      for (int t = 0; t < core.sizeT[0]; t++) {
-        for (int w = 0; w < core.sizeC[0]; w++) {
+    for (int z=0; z<core.sizeZ[0]; z++) {
+      for (int t=0; t<core.sizeT[0]; t++) {
+        for (int w=0; w<core.sizeC[0]; w++) {
           extHdrFields[z][w][t] = new DVExtHdrFields(getTotalOffset(z, w, t),
             numIntsPerSection, extHeader, core.littleEndian[0]);
@@ -572 +570 @@
       byte[] extHeader, boolean little)
     {
-      // skip over the int values that have nothing in them
-      offsetWithInts = startingOffset + (numIntsPerSection * 4);
-
-      // DV files store the ND (neuatral density) Filter (normally expressed as
-      // a %T (transmittance)) as an OD (optical density) rating.
-      // To convert from one to the other the formula is %T = 10^(-OD) X 100.
-      oDFilter = Float.intBitsToFloat(
-        DataTools.bytesToInt(extHeader, offsetWithInts + 36, 4, little));
-
-      // fill in the extended header information for the floats
-      photosensorReading =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts, 4, little));
-      timeStampSeconds =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 4, 4, little));
-      stageXCoord =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 8, 4, little));
-      stageYCoord =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 12, 4, little));
-      stageZCoord =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 16, 4, little));
-      minInten =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 20, 4, little));
-      maxInten =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 24, 4, little));
-      meanInten =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 28, 4, little));
-      expTime =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 32, 4, little));
-      ndFilter = (float) Math.pow(10.0, -oDFilter);
-      exFilter =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 40, 4, little));
-      emFilter =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 44, 4, little));
-      exWavelen =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 48, 4, little));
-      emWavelen =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 52, 4, little));
-      intenScaling =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 56, 4, little));
-      energyConvFactor =
-        Float.intBitsToFloat(
-          DataTools.bytesToInt(extHeader, offsetWithInts + 60, 4, little));
+      try { 
+        RandomAccessStream ext = new RandomAccessStream(extHeader); 
+        ext.order(little); 
+
+        // skip over the int values that have nothing in them
+        offsetWithInts = startingOffset + (numIntsPerSection * 4);
+
+        // DV files store the ND (neuatral density) Filter 
+        // (normally expressed as a %T (transmittance)) as an OD 
+        // (optical density) rating.
+        // To convert from one to the other the formula is %T = 10^(-OD) X 100.
+        ext.seek(offsetWithInts + 36);
+        oDFilter = ext.readFloat();
+
+        // fill in the extended header information for the floats
+        ext.seek(offsetWithInts); 
+        photosensorReading = ext.readFloat(); 
+        timeStampSeconds = ext.readFloat(); 
+        stageXCoord = ext.readFloat(); 
+        stageYCoord = ext.readFloat();
+        stageZCoord = ext.readFloat();
+        minInten = ext.readFloat(); 
+        maxInten = ext.readFloat(); 
+        meanInten = ext.readFloat();
+        expTime = ext.readFloat(); 
+        ndFilter = (float) Math.pow(10.0, -oDFilter);
+        ext.skipBytes(4); 
+     
+        exFilter = ext.readFloat();
+        emFilter = ext.readFloat();
+        exWavelen = ext.readFloat();  
+        emWavelen = ext.readFloat();
+        intenScaling = ext.readFloat();
+        energyConvFactor = ext.readFloat(); 
+      }
+      catch (IOException e) {
+        LogTools.trace(e);
+      }
     }
 

trunk/loci/formats/in/DicomReader.java

@@ -93 +93 @@
   // "Digital Imaging and Communications in Medicine" is nasty long.
   public DicomReader() {
-    super("Digital Img. & Comm. in Med.",
-      new String[] {"dcm", "dicom"});
+    super("Digital Img. & Comm. in Med.", new String[] {"dcm", "dicom"});
   }
 
@@ -154 +153 @@
     status("Verifying DICOM format");
 
-    byte[] four = new byte[4];
-    long pos = 0;
     in.seek(128);
-    in.read(four);
-    if ((new String(four)).equals("DICM")) {
+    if (in.readString(4).equals("DICM")) {
       // header exists, so we'll read it
-      in.seek(pos);
-      byte[] header = new byte[128];
-      in.read(header);
-      addMeta("Header information", new String(header));
+      in.seek(0);
+      addMeta("Header information", in.readString(128));
       in.readInt();
       location = 128;
     }
-    else in.seek(pos);
+    else in.seek(0);
 
     status("Reading tags");
@@ -188 +182 @@
       switch (tag) {
         case TRANSFER_SYNTAX_UID:
-          byte[] st = new byte[elementLength];
-          in.read(st);
-          s = new String(st);
+          s = in.readString(elementLength); 
           addInfo(tag, s);
           if (s.indexOf("1.2.4") > -1 || s.indexOf("1.2.5") > -1) {
@@ -201 +193 @@
           break;
         case NUMBER_OF_FRAMES:
-          st = new byte[elementLength];
-          in.read(st);
-          s = new String(st);
+          s = in.readString(elementLength);
           addInfo(tag, s);
           double frames = Double.parseDouble(s);
@@ -213 +203 @@
           break;
         case PHOTOMETRIC_INTERPRETATION:
-          st = new byte[elementLength];
-          in.read(st);
-          String photoInterpretation = new String(st);
-          addInfo(tag, photoInterpretation);
+          addInfo(tag, in.readString(elementLength));
           break;
         case PLANAR_CONFIGURATION:
-          int planarConfiguration = in.readShort();
-          addInfo(tag, planarConfiguration);
+          addInfo(tag, in.readShort());
           break;
         case ROWS:
@@ -231 +217 @@
           break;
         case PIXEL_SPACING:
-          st = new byte[elementLength];
-          in.read(st);
-          String scale = new String(st);
-          addInfo(tag, scale);
+          addInfo(tag, in.readString(elementLength));
           break;
         case SLICE_SPACING:
-          st = new byte[elementLength];
-          in.read(st);
-          String spacing = new String(st);
-          addInfo(tag, spacing);
+          addInfo(tag, in.readString(elementLength));
           break;
         case BITS_ALLOCATED:
@@ -247 +227 @@
           break;
         case PIXEL_REPRESENTATION:
-          int pixelRepresentation = in.readShort();
-          addInfo(tag, pixelRepresentation);
+          addInfo(tag, in.readShort());
           break;
         case WINDOW_CENTER:
@@ -254 +233 @@
         case RESCALE_INTERCEPT:
         case RESCALE_SLOPE:
-          st = new byte[elementLength];
-          in.read(st);
-          String c = new String(st);
-          addInfo(tag, c);
+          addInfo(tag, in.readString(elementLength));
           break;
         case PIXEL_DATA:
@@ -403 +379 @@
       case TM:
       case UI:
-        byte[] s = new byte[elementLength];
-        in.read(s);
-        value = new String(s);
+        value = in.readString(elementLength);
         break;
       case US:
@@ -418 +392 @@
         break;
       case IMPLICIT_VR:
-        s = new byte[elementLength];
-        in.read(s);
-        value = new String(s);
+        value = in.readString(elementLength);
         if (elementLength <= 4 || elementLength > 44) value = null;
         break;

trunk/loci/formats/in/EPSReader.java

@@ -83 +83 @@
       throw new FormatException("Invalid image number: " + no);
     }
-    if (buf.length < core.sizeX[0] * core.sizeY[0] * core.sizeC[0] * (bps / 8)) {
+    if (buf.length < core.sizeX[0] * core.sizeY[0] * core.sizeC[0] * (bps / 8))
+    {
       throw new FormatException("Buffer too small.");
     }

trunk/loci/formats/in/FitsReader.java

@@ -99 +99 @@
     count = 1;
 
-    byte[] b = new byte[80];
-    in.read(b);
-    String line = new String(b);
+    String line = in.readString(80);
     if (!line.startsWith("SIMPLE")) {
       throw new FormatException("Unsupported FITS file.");
@@ -108 +106 @@
     while (true) {
       count++;
-      in.read(b);
-      line = new String(b);
-    
+      line = in.readString(80); 
+
       // parse key/value pair 
       int ndx = line.indexOf("=");

trunk/loci/formats/in/FluoviewReader.java

@@ -25 +25 @@
 package loci.formats.in;
 
+import java.awt.image.BufferedImage;
 import java.io.*;
 import java.util.*;
@@ -59 +60 @@
   private float voxelX = 0f, voxelY = 0f, voxelZ = 0f, voxelC = 0f, voxelT = 0f;
 
+  /** First image. */
+  private BufferedImage zeroImage = null;
+
   // -- Constructor --
 
   /** Constructs a new Fluoview TIFF reader. */
   public FluoviewReader() {
-    super("Olympus Fluoview/Andor Bio-imaging TIFF",
-      new String[] {"tif", "tiff"});
+    super("Olympus Fluoview/ABD TIFF", new String[] {"tif", "tiff"});
   }
 
@@ -98 +101 @@
   }
 
+  /* @see loci.formats.IFormatReader#openBytes(int) */
+  public byte[] openBytes(int no) throws FormatException, IOException {
+    if (core.sizeY[0] == TiffTools.getImageLength(ifds[0])) {
+      return super.openBytes(no);
+    } 
+    return openBytes(no, new byte[core.sizeX[0] * 
+      FormatTools.getBytesPerPixel(core.pixelType[0])]); 
+  }
+
+  /* @see loci.formats.IFormatReader#openBytes(int, byte[]) */
+  public byte[] openBytes(int no, byte[] buf)
+    throws FormatException, IOException
+  {
+    if (core.sizeY[0] == TiffTools.getImageLength(ifds[0])) {
+      return super.openBytes(no, buf);
+    } 
+    FormatTools.assertId(currentId, false, 1);
+    if (no < 0 || no >= core.imageCount[0]) {
+      throw new FormatException("Invalid image number: " + no);
+    } 
+    if (buf.length < core.sizeX[0] * 
+      FormatTools.getBytesPerPixel(core.pixelType[0])) 
+    {
+      throw new FormatException("Buffer too small.");
+    }
+  
+    byte[] b = super.openBytes(0);
+    System.arraycopy(b, 0, buf, 0, buf.length);
+    return buf;
+  }
+
+  /* @see loci.formats.IFormatReader#openImage(int) */
+  public BufferedImage openImage(int no) throws FormatException, IOException {
+    if (core.sizeY[0] == TiffTools.getImageLength(ifds[0])) {
+      return super.openImage(no);
+    } 
+    
+    if (zeroImage == null) zeroImage = super.openImage(0);
+    return zeroImage.getSubimage(0, no, core.sizeX[0], 1); 
+  }
+
+  /* @see loci.formats.IFormatReader#close() */
+  public void close() throws IOException {
+    super.close();
+    zeroImage = null;
+  }
+
   // -- IFormatHandler API methods --
 
@@ -138 +188 @@
     put("Image Type", (char) ras.read());
 
-    byte[] nameBytes = new byte[257];
-    ras.read(nameBytes);
-    put("Image name", new String(nameBytes));
+    put("Image name", ras.readString(257));
 
     ras.skipBytes(4); // skip pointer to data field
@@ -152 +200 @@
 
     // read dimension information
-    byte[] dimNameBytes = new byte[16];
-    byte[] dimCalibrationUnits = new byte[64];
     String[] names = new String[10];
     int[] sizes = new int[10];
     double[] resolutions = new double[10];
     for (int i=0; i<10; i++) {
-      ras.read(dimNameBytes);
-      names[i] = new String(dimNameBytes);
+      names[i] = ras.readString(16);
       sizes[i] = ras.readInt();
       double origin = ras.readDouble();
       resolutions[i] = ras.readDouble();
-      ras.read(dimCalibrationUnits);
 
       put("Dimension " + (i+1) + " Name", names[i]);
@@ -169 +213 @@
       put("Dimension " + (i+1) + " Origin", origin);
       put("Dimension " + (i+1) + " Resolution", resolutions[i]);
-      put("Dimension " + (i+1) + " Units", new String(dimCalibrationUnits));
+      put("Dimension " + (i+1) + " Units", ras.readString(64));
     }
 
@@ -186 +230 @@
 
     // read gray channel data
-    ras.read(dimNameBytes);
-    put("Gray Channel Name", new String(dimNameBytes));
+    put("Gray Channel Name", ras.readString(16));
     put("Gray Channel Size", ras.readInt());
     put("Gray Channel Origin", ras.readDouble());
     put("Gray Channel Resolution", ras.readDouble());
-    ras.read(dimCalibrationUnits);
-    put("Gray Channel Units", new String(dimCalibrationUnits));
+    put("Gray Channel Units", ras.readString(64));
 
     ras.skipBytes(4); // skip pointer to thumbnail data
@@ -267 +309 @@
     core.imageCount[0] = ifds.length;
 
+    if (core.imageCount[0] == 1 && (core.sizeT[0] == core.sizeY[0] || 
+      core.sizeZ[0] == core.sizeY[0]) && (core.sizeT[0] > core.imageCount[0] ||
+      core.sizeZ[0] > core.imageCount[0])) 
+    {
+      core.sizeY[0] = 1;
+      core.imageCount[0] = core.sizeZ[0] * core.sizeT[0] * core.sizeC[0];
+    } 
+    
     // cut up the comment, if necessary
     String comment = (String) getMeta("Comment");

trunk/loci/formats/in/GIFReader.java

@@ -25 +25 @@
 package loci.formats.in;
 
-import java.awt.Rectangle;
 import java.awt.image.BufferedImage;
 import java.io.*;
@@ -40 +39 @@
   // -- Constants --
 
-  /** Status codes. */
-  private static final int STATUS_OK = 0;
-  private static final int STATUS_FORMAT_ERROR = 1;
-  private static final int STATUS_OPEN_ERROR = 2;
-
   /** Maximum buffer size. */
   private static final int MAX_STACK_SIZE = 4096;
@@ -50 +44 @@
   // -- Fields --
 
-  private int status;
-
   /** Global color table used. */
   private boolean gctFlag;
@@ -58 +50 @@
   private int gctSize;
 
-  /** Iterations; 0 = repeat forever. */
-  private int loopCount;
-
   /** Global color table. */
   private int[] gct;
@@ -76 +65 @@
   private int bgColor;
 
-  /** Previous bg color. */
-  private int lastBgColor;
-
-  /** Pixel aspect ratio. */
-  private int pixelAspect;
-
   /** Local color table flag. */
   private boolean lctFlag;
@@ -94 +77 @@
   private int ix, iy, iw, ih;
 
-  /** Last image rectangle. */
-  private Rectangle lastRect;
-
   /** Current data block. */
   private byte[] dBlock = new byte[256];
@@ -108 +88 @@
   /** Use transparent color. */
   private boolean transparency = false;
-
-  /** Delay in ms. */
-  private int delay = 0;
 
   /** Transparent color index. */
@@ -127 +104 @@
   /** Constructs a new GIF reader. */
   public GIFReader() {
-    super("Graphics Interchange Format (GIF)", "gif");
+    super("Graphics Interchange Format", "gif");
   }
 
@@ -155 +132 @@
 
     int[] ints = (int[]) images.get(no);
+    if (no > 0) {
+      int[] prev = (int[]) images.get(no - 1); 
+      for (int i=0; i<ints.length; i++) {
+        if ((ints[i] & 0x00ffffff) == 0) {
+          ints[i] = prev[i];
+        }
+      }
+      images.setElementAt(ints, no); 
+    }
 
     for (int i=0; i<ints.length; i++) {
@@ -183 +169 @@
     status("Verifying GIF format");
 
-    status = STATUS_OK;
     in = new RandomAccessStream(id);
+    in.order(true);
     images = new Vector();
 
-    byte[] buf = new byte[6];
-    in.read(buf);
-    String ident = new String(buf);
+    String ident = in.readString(6);
 
     if (!ident.startsWith("GIF")) {
@@ -197 +181 @@
     status("Reading dimensions");
 
-    core.sizeX[0] = DataTools.read2UnsignedBytes(in, true);
-    core.sizeY[0] = DataTools.read2UnsignedBytes(in, true);
-
-    int packed = DataTools.readUnsignedByte(in);
+    core.sizeX[0] = in.readShort();
+    core.sizeY[0] = in.readShort();
+
+    int packed = in.read() & 0xff;
     gctFlag = (packed & 0x80) != 0;
     gctSize = 2 << (packed & 7);
-    bgIndex = DataTools.readUnsignedByte(in);
-    pixelAspect = DataTools.readUnsignedByte(in);
+    bgIndex = in.read() & 0xff;
+    in.skipBytes(1); 
 
     if (gctFlag) {
       int nbytes = 3 * gctSize;
       byte[] c = new byte[nbytes];
-      int n = in.read(c);
+      in.read(c);
 
       gct = new int[256];
@@ -229 +213 @@
     boolean done = false;
     while (!done) {
-      int code = DataTools.readUnsignedByte(in);
+      int code = in.read() & 0xff;
       switch (code) {
         case 0x2c: // image separator:
-          ix = DataTools.read2UnsignedBytes(in, true);
-          iy = DataTools.read2UnsignedBytes(in, true);
-          iw = DataTools.read2UnsignedBytes(in, true);
-          ih = DataTools.read2UnsignedBytes(in, true);
-
-          packed = DataTools.readUnsignedByte(in);
+          ix = in.readShort();
+          iy = in.readShort();
+          iw = in.readShort();
+          ih = in.readShort();
+          
+          packed = in.read();
           lctFlag = (packed & 0x80) != 0;
           interlace = (packed & 0x40) != 0;
@@ -290 +274 @@
 
           lastDispose = dispose;
-          lastRect = new Rectangle(ix, iy, iw, ih);
-          lastBgColor = bgColor;
           lct = null;
 
           break;
         case 0x21: // extension
-          code = DataTools.readUnsignedByte(in);
+          code = in.read() & 0xff;
           switch (code) {
             case 0xf9: // graphics control extension
-              in.read();
-              packed = DataTools.readUnsignedByte(in);
+              in.skipBytes(1); 
+              packed = in.read() & 0xff;
               dispose = (packed & 0x1c) >> 1;
               transparency = (packed & 1) != 0;
-              delay = DataTools.read2UnsignedBytes(in, true) * 10;
-              transIndex = DataTools.readUnsignedByte(in);
-              in.read();
+              in.skipBytes(2); 
+              transIndex = in.read() & 0xff;
+              in.skipBytes(1); 
               break;
             case 0xff:  // application extension
@@ -320 +302 @@
                     int b1 = ((int) dBlock[1]) & 0xff;
                     int b2 = ((int) dBlock[2]) & 0xff;
-                    loopCount = (b2 << 8) | b1;
                   }
                 }
@@ -381 +362 @@
   private int readBlock() throws IOException {
     if (in.getFilePointer() == in.length()) return -1;
-    blockSize = DataTools.readUnsignedByte(in);
+    blockSize = in.read() & 0xff;
     int n = 0;
     int count;
@@ -413 +394 @@
 
     // initialize GIF data stream decoder
-
-    dataSize = DataTools.readUnsignedByte(in);
+    
+    dataSize = in.read() & 0xff;
 
     clear = 1 << dataSize;
@@ -422 +403 @@
     codeSize = dataSize + 1;
     codeMask = (1 << codeSize) - 1;
-    for (code=0; code < clear; code++) {
+    for (code=0; code<clear; code++) {
       prefix[code] = 0;
       suffix[code] = (byte) code;

trunk/loci/formats/in/GatanReader.java

@@ -37 +37 @@
 public class GatanReader extends FormatReader {
 
-  // -- Constants --
-
-  private static final byte[] GATAN_MAGIC_BLOCK_1 = {0, 0, 0, 3};
-
   // -- Fields --
 
@@ -63 +59 @@
   /* @see loci.formats.IFormatReader#isThisType(byte[]) */
   public boolean isThisType(byte[] block) {
-    if (block == null) return false;
-    if (block.length != GATAN_MAGIC_BLOCK_1.length) return false;
-    for (int i=0; i<block.length; i++) {
-      if (block[i] != GATAN_MAGIC_BLOCK_1[i]) return false;
-    }
-    return true;
+    if (block == null || block.length < 4) return false;
+    return DataTools.bytesToInt(block, false) == 3; 
   }
 
@@ -97 +89 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
-    if (no < 0 || no >= getImageCount()) {
-      throw new FormatException("Invalid image number: " + no);
-    }
-
     return ImageTools.makeImage(openBytes(no), core.sizeX[0], core.sizeY[0],
       1, false, bytesPerPixel, core.littleEndian[0]);
@@ -120 +107 @@
     pixelSizes = new Vector();
 
-    byte[] tmp = new byte[4];
-    in.read(tmp);
+    in.order(false);
+
     // only support version 3
-    if (!isThisType(tmp)) {
+    if (in.readInt() != 3) {
       throw new FormatException("invalid header");
     }
@@ -130 +117 @@
 
     in.skipBytes(4);
-    in.read(tmp);
-    core.littleEndian[0] = DataTools.bytesToInt(tmp, core.littleEndian[0]) == 1;
+    core.littleEndian[0] = in.readInt() == 1;
 
     // TagGroup instance
 
     in.skipBytes(2);
-    in.read(tmp);
-    parseTags(DataTools.bytesToInt(tmp, !core.littleEndian[0]), "initFile");
+    in.order(!core.littleEndian[0]);
+    parseTags(in.readInt(), "initFile");
 
     status("Populating metadata");
@@ -143 +129 @@
     switch (datatype) {
       case 1:
+      case 10:
         core.pixelType[0] = FormatTools.UINT16;
         break;
       case 2:
-        core.pixelType[0] = FormatTools.FLOAT;
-        break;
       case 3:
-        core.pixelType[0] = FormatTools.FLOAT;
-        break;
-      // there is no case 4
       case 5:
-        core.pixelType[0] = FormatTools.FLOAT;
-        break;
-      case 6:
-        core.pixelType[0] = FormatTools.UINT8;
-        break;
-      case 7:
-        core.pixelType[0] = FormatTools.INT32;
-        break;
-      case 8:
-        core.pixelType[0] = FormatTools.UINT32;
-        break;
-      case 9:
-        core.pixelType[0] = FormatTools.INT8;
-        break;
-      case 10:
-        core.pixelType[0] = FormatTools.UINT16;
-        break;
-      case 11:
-        core.pixelType[0] = FormatTools.UINT32;
-        break;
       case 12:
-        core.pixelType[0] = FormatTools.FLOAT;
-        break;
       case 13:
         core.pixelType[0] = FormatTools.FLOAT;
         break;
-      case 14:
-        core.pixelType[0] = FormatTools.UINT8;
-        break;
+      case 7:
+      case 8:
+      case 11:
       case 23:
-        core.pixelType[0] = FormatTools.INT32;
+        core.pixelType[0] = FormatTools.UINT32;
         break;
       default:
-        core.pixelType[0] = FormatTools.INT8;
+        core.pixelType[0] = FormatTools.UINT8;
     }
 
@@ -212 +172 @@
       null); // Use pixels index 0
 
-    Float pixX = null;
-    Float pixY = null;
-    Float pixZ = null;
+    Float pixX = new Float(1);
+    Float pixY = new Float(1);
+    Float pixZ = new Float(1);
 
     if (pixelSizes.size() > 0) {
       pixX = new Float((String) pixelSizes.get(0));
     }
-    else pixX = new Float(1);
 
     if (pixelSizes.size() > 1) {
       pixY = new Float((String) pixelSizes.get(1));
     }
-    else pixY = new Float(1);
 
     if (pixelSizes.size() > 2) {
       pixZ = new Float((String) pixelSizes.get(2));
     }
-    else pixZ = new Float(1);
 
     store.setDimensions(pixX, pixY, pixZ, null, null, null);
@@ -254 +211 @@
    */
   private void parseTags(int numTags, String parent) throws IOException {
-    byte[] temp = new byte[4];
     for (int i=0; i<numTags; i++) {
       byte type = in.readByte();  // can be 21 (data) or 20 (tag group)
-      byte[] twobytes = new byte[2];
-      in.read(twobytes);
-      int length = DataTools.bytesToInt(twobytes, !core.littleEndian[0]);
-      byte[] label = new byte[length];
-      in.read(label);
-      String labelString = new String(label);
+      int length = in.readShort(); 
+      String labelString = in.readString(length);
 
       // image data is in tag with type 21 and label 'Data'
@@ -270 +222 @@
       if (type == 21) {
         in.skipBytes(4);  // equal to '%%%%'
-        in.read(temp);
-        int n = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+        int n = in.readInt(); 
         int dataType = 0;
         if (n == 1) {
-          in.read(temp);
-          dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+          dataType = in.readInt(); 
           String data;
+          in.order(core.littleEndian[0]); 
           switch (dataType) {
             case 2:
-              data = "" + DataTools.read2SignedBytes(in, core.littleEndian[0]);
+            case 4: 
+              data = "" + in.readShort();
               break;
             case 3:
-              data = "" + DataTools.read4SignedBytes(in, core.littleEndian[0]);
-              break;
-            case 4:
-              data =
-                "" + DataTools.read2UnsignedBytes(in, core.littleEndian[0]);
-              break;
-            case 5:
-              data =
-                "" + DataTools.read4UnsignedBytes(in, core.littleEndian[0]);
+            case 5:  
+              data = "" + in.readInt();
               break;
             case 6:
-              data = "" + DataTools.readFloat(in, core.littleEndian[0]);
+              data = "" + in.readFloat();
               break;
             case 7:
-              data = "" + DataTools.readFloat(in, core.littleEndian[0]);
+              data = "" + in.readFloat();
               in.skipBytes(4);
               break;
             case 8:
-              data = "" + DataTools.readSignedByte(in);
-              break;
             case 9:
-              data = "" + DataTools.readSignedByte(in);
-              break;
             case 10:
-              data = "" + DataTools.readSignedByte(in);
+              data = "" + in.read();
               break;
             default:
@@ -325 +266 @@
           addMeta(labelString, data);
           if (labelString.equals("DataType")) datatype = Integer.parseInt(data);
+          in.order(!core.littleEndian[0]); 
         }
         else if (n == 2) {
-          in.read(temp);
-          dataType = DataTools.bytesToInt(temp, core.littleEndian[0]);
+          in.order(core.littleEndian[0]);
+          dataType = in.readInt();
           if (dataType == 18) { // this should always be true
-            in.read(temp);
-            length = DataTools.bytesToInt(temp, core.littleEndian[0]);
-          }
-          byte[] data = new byte[length];
-          in.read(data);
-          addMeta(labelString, new String(label));
+            length = in.readInt(); 
+          }
+          addMeta(labelString, in.readString(length));
+          in.order(!core.littleEndian[0]); 
         }
         else if (n == 3) {
-          in.read(temp);
-          dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+          dataType = in.readInt();
           if (dataType == 20) { // this should always be true
-            in.read(temp);
-            dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
-            in.read(temp);
-            length = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+            dataType = in.readInt(); 
+            length = in.readInt(); 
 
             if ("Data".equals(labelString)) pixelDataNum++;
@@ -365 +302 @@
                 check = in.readByte();
               }
-              in.seek((int) (pos + bpp * length));
+              in.seek((long) (pos + bpp * length));
             }
             else {
@@ -371 +308 @@
               for (int j=0; j<length; j++) {
                 if (dataType == 2 || dataType == 4) {
-                  byte[] two = new byte[2];
-                  in.read(two);
-                  data[j] = (int) DataTools.bytesToShort(two,
-                    !core.littleEndian[0]);
+                  data[j] = in.readShort();
                 }
                 else if (dataType == 7) in.skipBytes(8);
                 else if (dataType == 8 || dataType == 9) in.skipBytes(1);
                 else {
-                  in.read(temp);
-                  data[j] = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+                  data[j] = in.readInt();
                 }
               }
@@ -387 +320 @@
         }
         else {
-          in.read(temp);
-          dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+          dataType = in.readInt();
           // this is a normal struct of simple types
           if (dataType == 15) {
-            int skip = 0;
-            in.read(temp);
-            skip += DataTools.bytesToInt(temp, !core.littleEndian[0]);
-            in.read(temp);
-            int numFields = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+            int skip = in.readInt();
+            int numFields = in.readInt(); 
             for (int j=0; j<numFields; j++) {
-              in.read(temp);
-              skip += DataTools.bytesToInt(temp, !core.littleEndian[0]);
-              in.read(temp);
-              dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+              skip += in.readInt(); 
+              dataType = in.readInt(); 
 
               switch (dataType) {
                 case 2:
+                case 4:
                   skip += 2;
                   break;
                 case 3:
-                  skip += 4;
-                  break;
-                case 4:
-                  skip += 2;
-                  break;
                 case 5:
-                  skip += 4;
-                  break;
                 case 6:
                   skip += 4;
@@ -422 +343 @@
                   break;
                 case 8:
-                  skip += 1;
-                  break;
                 case 9:
                   skip += 1;
@@ -434 +353 @@
             // this is an array of structs
             int skip = 0;
-            in.read(temp);
-            dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+            dataType = in.readInt();
             if (dataType == 15) { // should always be true
-              in.read(temp);
-              skip += DataTools.bytesToInt(temp, !core.littleEndian[0]);
-              in.read(temp);
-              int numFields = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+              skip += in.readInt(); 
+              int numFields = in.readInt(); 
               for (int j=0; j<numFields; j++) {
-                in.read(temp);
-                skip += DataTools.bytesToInt(temp, !core.littleEndian[0]);
-                in.read(temp);
-                dataType = DataTools.bytesToInt(temp, !core.littleEndian[0]);
+                skip += in.readInt(); 
+                dataType = in.readInt(); 
 
                 switch (dataType) {
                   case 2:
+                  case 4:  
                     skip += 2;
                     break;
                   case 3:
-                    skip += 4;
-                    break;
-                  case 4:
-                    skip += 2;
-                    break;
                   case 5:
-                    skip += 4;
-                    break;
                   case 6:
                     skip += 4;
@@ -467 +375 @@
                     break;
                   case 8:
-                    skip += 1;
-                    break;
                   case 9:
                     skip += 1;
@@ -475 +381 @@
               }
             }
-            in.read(temp);
-            skip *= DataTools.bytesToInt(temp, !core.littleEndian[0]);
+            skip *= in.readInt();
             in.skipBytes(skip);
           }
@@ -483 +388 @@
       else if (type == 20) {
         in.skipBytes(2);
-        in.read(temp);
-        parseTags(DataTools.bytesToInt(temp, !core.littleEndian[0]),
-          labelString);
+        parseTags(in.readInt(), labelString); 
       }
     }

trunk/loci/formats/in/ICSReader.java

@@ -159 +159 @@
     if (bytes == 4) {
       float[] f = new float[core.sizeX[0] * core.sizeY[0] * channels];
-      int pt = 0;
       for (int i=0; i<f.length; i++) {
         int p = DataTools.bytesToInt(plane, i*4, 4, core.littleEndian[0]);
@@ -256 +255 @@
     StringTokenizer t;
     String token;
-    b = new byte[(int) reader.length()];
-    reader.read(b);
+    String s = reader.readString((int) reader.length());
     reader.close();
-    String s = new String(b);
     StringTokenizer st = new StringTokenizer(s, "\n");
     String line = st.nextToken();

trunk/loci/formats/in/IPLabReader.java

@@ -68 +68 @@
   /* @see loci.formats.IFormatReader#openBytes(int) */
   public byte[] openBytes(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     byte[] buf = new byte[core.sizeX[0] * core.sizeY[0] * bps * core.sizeC[0]];
     return openBytes(no, buf);
@@ -94 +93 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.makeImage(openBytes(no), core.sizeX[0], core.sizeY[0],
       core.rgb[0] ? core.sizeC[0] : 1, false, bps, core.littleEndian[0]);
@@ -109 +107 @@
     status("Populating metadata");
 
-    byte[] fourBytes = new byte[4];
-    in.read(fourBytes);
-    core.littleEndian[0] = new String(fourBytes).equals("iiii");
+    core.littleEndian[0] = in.readString(4).equals("iiii");
 
     in.order(core.littleEndian[0]);
@@ -144 +140 @@
       case 1:
         ptype = "16 bit signed short";
-        core.pixelType[0] = FormatTools.INT16;
+        core.pixelType[0] = FormatTools.UINT16;
         bps = 2;
         break;
@@ -154 +150 @@
       case 3:
         ptype = "32 bit signed long";
-        core.pixelType[0] = FormatTools.INT32;
+        core.pixelType[0] = FormatTools.UINT32;
         bps = 4;
         break;
@@ -164 +160 @@
       case 5:
         ptype = "Color24";
-        core.pixelType[0] = FormatTools.INT32;
+        core.pixelType[0] = FormatTools.UINT32;
         bps = 1;
         break;
       case 6:
         ptype = "Color48";
-        core.pixelType[0] = FormatTools.INT32;
+        core.pixelType[0] = FormatTools.UINT32;
         bps = 2;
         break;
@@ -212 +208 @@
     status("Reading tags");
 
-    in.read(fourBytes);
-    String tag = new String(fourBytes);
+    String tag = in.readString(4);
     while (!tag.equals("fini") && in.getFilePointer() < in.length() - 4) {
       if (tag.equals("clut")) {
@@ -220 +215 @@
         if (size == 8) {
           // indexed lookup table
-          in.readInt();
+          in.skipBytes(4); 
           int type = in.readInt();
 
-          String clutType = "unknown";
-          switch ((int) type) {
-            case 0:
-              clutType = "monochrome";
-              break;
-            case 1:
-              clutType = "reverse monochrome";
-              break;
-            case 2:
-              clutType = "BGR";
-              break;
-            case 3:
-              clutType = "classify";
-              break;
-            case 4:
-              clutType = "rainbow";
-              break;
-            case 5:
-              clutType = "red";
-              break;
-            case 6:
-              clutType = "green";
-              break;
-            case 7:
-              clutType = "blue";
-              break;
-            case 8:
-              clutType = "cyan";
-              break;
-            case 9:
-              clutType = "magenta";
-              break;
-            case 10:
-              clutType = "yellow";
-              break;
-            case 11:
-              clutType = "saturated pixels";
-              break;
-          }
+          String[] types = new String[] {
+            "monochrome", "reverse monochrome", "BGR", "classify", "rainbow",
+            "red", "green", "blue", "cyan", "magenta", "yellow", 
+            "saturated pixels"
+          };
+          String clutType = (type >= 0 && type < types.length) ? types[type] :
+            "unknown";
           addMeta("LUT type", clutType);
         }
@@ -267 +230 @@
           // explicitly defined lookup table
           // length is 772
-          in.readInt();
-          byte[] colorTable = new byte[256*3];
-          in.read(colorTable);
+          in.skipBytes(4 + 256 * 3);
         }
       }
@@ -283 +244 @@
 
         for (int i=0; i<core.sizeC[0]; i++) {
-          long source = in.readInt();
-
-          String sourceType;
-          switch ((int) source) {
-            case 0:
-              sourceType = "user";
-              break;
-            case 1:
-              sourceType = "plane";
-              break;
-            case 2:
-              sourceType = "sequence";
-              break;
-            case 3:
-              sourceType = "saturated plane";
-              break;
-            case 4:
-              sourceType = "saturated sequence";
-              break;
-            case 5:
-              sourceType = "ROI";
-              break;
-            default:
-              sourceType = "user";
-          }
+          int source = in.readInt();
+          String[] types = new String[] {
+            "user", "plane", "sequence", "saturated plane", 
+            "saturated sequence", "ROI"
+          };
+
+          String sourceType = (source >= 0 && source < types.length) ? 
+            types[source] : "user";
           addMeta("NormalizationSource" + i, sourceType);
 
@@ -335 +279 @@
         int size = in.readInt();
 
-        byte[] headerString = new byte[20];
-        for (int i=0; i<size / (headerString.length + 2); i++) {
+        for (int i=0; i<size / 22; i++) {
           int num = in.readShort();
-          in.read(headerString);
-          String name = new String(fourBytes);
+          String name = in.readString(20);
           addMeta("Header" + num, name);
         }
@@ -356 +298 @@
         int numRoiPts = in.readInt();
 
-        Integer x0 = new Integer((int) roiLeft);
-        Integer x1 = new Integer((int) roiRight);
-        Integer y0 = new Integer((int) roiBottom);
-        Integer y1 = new Integer((int) roiTop);
+        Integer x0 = new Integer(roiLeft);
+        Integer x1 = new Integer(roiRight);
+        Integer y0 = new Integer(roiBottom);
+        Integer y1 = new Integer(roiTop);
         store.setDisplayROI(
           x0, y0, null, x1, y1, null, null, null, null, null);
@@ -367 +309 @@
       else if (tag.equals("mask")) {
         // read in Segmentation Mask
-        int size = in.readInt();
-        in.skipBytes(size);
+        in.skipBytes(in.readInt());
       }
       else if (tag.equals("unit")) {
         // read in units
-        in.readInt(); // size is 48
+        in.skipBytes(4); 
 
         for (int i=0; i<4; i++) {
@@ -402 +343 @@
         // read in notes (image info)
         in.readInt(); // size is 576
-        byte[] temp = new byte[64];
-        in.read(temp);
-        String descriptor = new String(temp);
-        temp = new byte[512];
-        in.read(temp);
-        String notes = new String(temp);
+        String descriptor = in.readString(64);
+        String notes = in.readString(512);
         addMeta("Descriptor", descriptor);
         addMeta("Notes", notes);
@@ -415 +352 @@
 
       if (in.getFilePointer() + 4 <= in.length()) {
-        in.read(fourBytes);
-        tag = new String(fourBytes);
+        tag = in.readString(4);
       }
       else {

trunk/loci/formats/in/IPWReader.java

@@ -144 +144 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
-    if (no < 0 || no >= getImageCount()) {
-      throw new FormatException("Invalid image number: " + no);
-    }
-
     byte[] b = openBytes(no);
     int bytes = b.length / (core.sizeX[0] * core.sizeY[0]);
@@ -291 +286 @@
     }
 
-    // TODO : look into removing this logic, as it appears to be copied directly
-    // from BaseTiffReader
-
     int bitsPerSample = TiffTools.getIFDIntValue(ifds[0],
       TiffTools.BITS_PER_SAMPLE);
@@ -374 +366 @@
       if (debug) trace(t);
     }
+  
+    core.interleaved[0] = true; 
   }
 
@@ -408 +402 @@
         r.exec("dis.read(data)");
 
+        RandomAccessStream ds = new RandomAccessStream(data);
+        ds.order(true);
+
         String entryName = (String) r.getVar("entryName");
         String dirName = (String) r.getVar("dirName");
@@ -420 +417 @@
           // should always be exactly 4 bytes
           // only exists if the file has more than one image
-          addMeta("Frame Rate", new Long(DataTools.bytesToInt(data, true)));
+          addMeta("Frame Rate", new Long(ds.readInt()));
         }
         else if (entryName.equals("FrameInfo")) {
           // should always be 16 bytes (if present)
           for(int i=0; i<data.length/2; i++) {
-            addMeta("FrameInfo "+i,
-              new Short(DataTools.bytesToShort(data, i*2, true)));
+            addMeta("FrameInfo "+i, new Short(ds.readShort()));
           }
         }
@@ -449 +445 @@
           core.imageCount[0]++;
         }
+        ds.close(); 
         r.exec("dis.close()");
         if (debug) {
-          print(depth + 1, ((byte[])
-            r.getVar("data")).length + " bytes read.");
+          print(depth + 1, data.length + " bytes read.");
         }
       }

trunk/loci/formats/in/ImarisReader.java

@@ -93 +93 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.makeImage(openBytes(no), core.sizeX[0],
       core.sizeY[0], 1, false);
@@ -137 +136 @@
     in.readInt();
 
-    byte[] name = new byte[128];
-    in.read(name);
-    String iName = new String(name);
-    addMeta("Image name", iName);
+    addMeta("Image name", in.readString(128));
 
     core.sizeX[0] = in.readShort();
@@ -151 +147 @@
     in.skipBytes(2);
 
-    byte[] date = new byte[32];
-    in.read(date);
-    String origDate = new String(date);
-    addMeta("Original date", origDate);
+    addMeta("Original date", in.readString(32));
 
     float dx = in.readFloat();
@@ -161 +154 @@
     int mag = in.readShort();
 
-    byte[] com = new byte[128];
-    in.read(com);
-    String comment = new String(com);
-    addMeta("Image comment", comment);
+    addMeta("Image comment", in.readString(128));
     int isSurvey = in.readInt();
     addMeta("Survey performed", isSurvey == 0 ? "true" : "false");

trunk/loci/formats/in/ImarisTiffReader.java

@@ -145 +145 @@
     int bitFormat = TiffTools.getIFDIntValue(ifds[0], TiffTools.SAMPLE_FORMAT);
 
-    // TODO : look into removing this logic, since it's copied directly from
-    // BaseTiffReader
-
     while (bitsPerSample % 8 != 0) bitsPerSample++;
     if (bitsPerSample == 24 || bitsPerSample == 48) bitsPerSample /= 3;

trunk/loci/formats/in/KhorosReader.java

@@ -127 +127 @@
     int dependency = in.readInt();
 
-    byte[] comment = new byte[512];
-    in.read(comment);
-    addMeta("Comment", new String(comment));
+    addMeta("Comment", in.readString(512));
 
     in.order(dependency == 4 || dependency == 8);
@@ -144 +142 @@
     switch (type) {
       case 0: 
-        core.pixelType[0] = FormatTools.UINT8; 
-        break;
       case 1: 
         core.pixelType[0] = FormatTools.UINT8; 

trunk/loci/formats/in/LIFReader.java

@@ -58 +58 @@
   private int[] extraDimensions;
 
-  /** Number of valid bits per pixel */
-  private int[][] validBits;
-
   private int bpp;
   private Vector xcal;
@@ -66 +63 @@
   private Vector zcal;
   private Vector seriesNames;
-
-  private Vector channelMins;
-  private Vector channelMaxs;
 
   // -- Constructor --
@@ -119 +113 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.makeImage(openBytes(no), core.sizeX[series],
-      core.sizeY[series], isRGB() ? core.sizeC[series] : 1, false, bpp / 8,
-      core.littleEndian[series], validBits[series]);
+      core.sizeY[series], getRGBChannelCount(), false, bpp / 8,
+      core.littleEndian[series]);
   }
 
@@ -135 +128 @@
 
     core.littleEndian[0] = true;
+    in.order(core.littleEndian[0]);
 
     xcal = new Vector();
     ycal = new Vector();
     zcal = new Vector();
-    channelMins = new Vector();
-    channelMaxs = new Vector();
 
     // read the header
@@ -163 +155 @@
     // number of Unicode characters in the XML block
 
-    int nc = DataTools.read4SignedBytes(in, core.littleEndian[0]);
-    byte[] s = new byte[nc * 2];
-    in.read(s);
-    String xml = DataTools.stripString(new String(s));
+    int nc = in.readInt();
+    String xml = DataTools.stripString(in.readString(nc * 2));
 
     status("Finding image offsets");
 
     while (in.getFilePointer() < in.length()) {
-      if (DataTools.read4SignedBytes(in, core.littleEndian[0]) != 0x70) {
+      if (in.readInt() != 0x70) {
         throw new FormatException("Invalid Memory Block");
       }
@@ -180 +170 @@
       }
 
-      int blockLength = DataTools.read4SignedBytes(in, core.littleEndian[0]);
+      int blockLength = in.readInt();
       if (in.read() != 0x2a) {
         throw new FormatException("Invalid Memory Description");
       }
 
-      int descrLength = DataTools.read4SignedBytes(in, core.littleEndian[0]);
-      byte[] memDescr = new byte[2*descrLength];
-      in.read(memDescr);
+      int descrLength = in.readInt();
+      in.skipBytes(descrLength * 2); 
 
       if (blockLength > 0) {
@@ -359 +348 @@
               if (numChannels == 1) {
                 bps.add(new Integer((String) tmp.get("Resolution")));
-                String sMin = (String) tmp.get("Min");
-                String sMax = (String) tmp.get("Max");
-                if (sMin != null && sMax != null) {
-                  double min = Double.parseDouble(sMin);
-                  double max = Double.parseDouble(sMax);
-                  channelMins.add(new Integer((int) min));
-                  channelMaxs.add(new Integer((int) max));
-                }
               }
             }
@@ -433 +414 @@
     core = new CoreMetadata(numDatasets);
     Arrays.fill(core.orderCertain, true);
-    validBits = new int[numDatasets][];
 
     for (int i=0; i<numDatasets; i++) {
@@ -458 +438 @@
       core.imageCount[i] = core.sizeZ[i] * core.sizeT[i];
       if (!core.rgb[i]) core.imageCount[i] *= core.sizeC[i];
-
-      validBits[i] = new int[core.sizeC[i] != 2 ? core.sizeC[i] : 3];
-      for (int j=0; j<validBits[i].length; j++) {
-        validBits[i][j] = bitsPerPixel[i];
-      }
 
       while (bitsPerPixel[i] % 8 != 0) bitsPerPixel[i]++;

trunk/loci/formats/in/LegacyPictReader.java

@@ -54 +54 @@
   /* @see loci.formats.IFormatReader#openBytes(int) */
   public byte[] openBytes(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.getBytes(openImage(no), false, 3);
   }

trunk/loci/formats/in/LegacyZVIReader.java

@@ -135 +135 @@
     super.initFile(id);
     in = new RandomAccessStream(id);
+    in.order(true);
 
     // Highly questionable decoding strategy:
@@ -226 +227 @@
 
       // read potential header information
-      int theZ = (int) DataTools.read4UnsignedBytes(in, true);
-      int theC = (int) DataTools.read4UnsignedBytes(in, true);
-      int theT = (int) DataTools.read4UnsignedBytes(in, true);
+      int theZ = in.readInt();
+      int theC = in.readInt();
+      int theT = in.readInt();
       pos += 12;
 
@@ -287 +288 @@
 
       // read more header information
-      core.sizeX[0] = (int) DataTools.read4UnsignedBytes(in, true);
-      core.sizeY[0] = (int) DataTools.read4UnsignedBytes(in, true);
+      core.sizeX[0] = in.readInt();
+      core.sizeY[0] = in.readInt();
       // don't know what this is for
-      int alwaysOne = (int) DataTools.read4UnsignedBytes(in, true);
-      bytesPerPixel = (int) DataTools.read4UnsignedBytes(in, true);
+      int alwaysOne = in.readInt();
+      bytesPerPixel = in.readInt();
       // not clear what this value signifies
-      int pixType = (int) DataTools.read4UnsignedBytes(in, true);
+      int pixType = in.readInt(); 
       // doesn't always equal bytesPerPixel * 8
-      int bitDepth = (int) DataTools.read4UnsignedBytes(in, true);
+      int bitDepth = in.readInt(); 
       pos += 24;
 
@@ -302 +303 @@
         case 1:
           type = "8 bit rgb tuple, 24 bpp";
-          core.pixelType[0] = FormatTools.INT8;
+          core.pixelType[0] = FormatTools.UINT8;
           break;
         case 2:
           type = "8 bit rgb quad, 32 bpp";
-          core.pixelType[0] = FormatTools.INT8;
+          core.pixelType[0] = FormatTools.UINT8;
           break;
         case 3:
           type = "8 bit grayscale";
-          core.pixelType[0] = FormatTools.INT8;
+          core.pixelType[0] = FormatTools.UINT8;
           break;
         case 4:
           type = "16 bit signed int, 16 bpp";
-          core.pixelType[0] = FormatTools.INT16;
+          core.pixelType[0] = FormatTools.UINT16;
           break;
         case 5:
           type = "32 bit int, 32 bpp";
-          core.pixelType[0] = FormatTools.INT32;
+          core.pixelType[0] = FormatTools.UINT32;
           break;
         case 6:
@@ -330 +331 @@
         case 8:
           type = "16 bit unsigned short triple, 48 bpp";
-          core.pixelType[0] = FormatTools.INT16;
+          core.pixelType[0] = FormatTools.UINT16;
           break;
         case 9:
           type = "32 bit int triple, 96 bpp";
-          core.pixelType[0] = FormatTools.INT32;
+          core.pixelType[0] = FormatTools.UINT32;
           break;
         default:
@@ -357 +358 @@
       // sorry not a very clever way to find dimension order
 
-      if ((numI == 2) && (cSet.size() == 2))  cFlag = 1;
-      if ((numI == 2) && (zSet.size() == 2))  zFlag = 1;
-      if ((numI == 2) && (tSet.size() == 2))  tFlag = 1;
+      if ((numI == 2) && (cSet.size() == 2)) cFlag = 1;
+      if ((numI == 2) && (zSet.size() == 2)) zFlag = 1;
+      if ((numI == 2) && (tSet.size() == 2)) tFlag = 1;
 
       if ((numI % 3 == 0) && (zSet.size() > 1) && (cFlag == 1)) {

trunk/loci/formats/in/MNGReader.java

@@ -48 +48 @@
 
   /** Constructs a new MNG reader. */
-  public MNGReader() { super("Multiple Network Graphics (MNG)", "mng"); }
+  public MNGReader() { super("Multiple Network Graphics", "mng"); }
 
   // -- IFormatReader API methods --
@@ -62 +62 @@
   /* @see loci.formats.IFormatReader#openBytes(int) */
   public byte[] openBytes(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.getBytes(openImage(no), true, core.sizeC[0]);
   }
@@ -97 +96 @@
     super.initFile(id);
     in = new RandomAccessStream(id);
+    in.order(false);
 
     status("Verifying MNG format");
@@ -114 +114 @@
     status("Reading dimensions");
 
-    core.sizeX[0] = (int) DataTools.read4UnsignedBytes(in, false);
-    core.sizeY[0] = (int) DataTools.read4UnsignedBytes(in, false);
-    long fps = DataTools.read4UnsignedBytes(in, false);
-    long layerCounter = DataTools.read4UnsignedBytes(in, false);
+    core.sizeX[0] = in.readInt();
+    core.sizeY[0] = in.readInt();
+    int fps = in.readInt();
+    int layerCounter = in.readInt();
     in.skipBytes(4);
 
-    long playTime = DataTools.read4UnsignedBytes(in, false);
-    long profile = DataTools.read4UnsignedBytes(in, false);
+    int playTime = in.readInt();
+    int profile = in.readInt();
 
     in.skipBytes(4); // skip the CRC
@@ -132 +132 @@
 
     while (in.getFilePointer() < in.length()) {
-      long len = DataTools.read4UnsignedBytes(in, false);
+      int len = in.readInt();
       in.read(b);
       String code = new String(b);
@@ -148 +148 @@
         stack.add(new Long(in.getFilePointer() + len + 4));
         in.skipBytes(1);
-        maxIterations = DataTools.read4SignedBytes(in, false);
+        maxIterations = in.readInt();
       }
       else if (code.equals("ENDL")) {
@@ -163 +163 @@
       }
 
-      in.seek(fp + (int) len + 4);
+      in.seek(fp + len + 4);
     }
 

trunk/loci/formats/in/MRCReader.java

@@ -63 +63 @@
   /* @see loci.formats.IFormatReader#openBytes(int) */
   public byte[] openBytes(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     byte[] buf = new byte[core.sizeX[0] * core.sizeY[0] * bpp];
     return openBytes(no, buf);
@@ -86 +85 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.makeImage(openBytes(no), core.sizeX[0],
       core.sizeY[0], 1, true, bpp, core.littleEndian[0]);
@@ -124 +122 @@
         break;
       case 1:
+      case 6:
         bpp = 2;
         core.pixelType[0] = FormatTools.UINT16;
@@ -141 +140 @@
         core.pixelType[0] = FormatTools.DOUBLE;
         break;
-      case 6:
-        bpp = 2;
-        core.pixelType[0] = FormatTools.UINT16;
-        break;
       case 16:
         bpp = 2;
@@ -170 +165 @@
     addMeta("Pixel size (Z)", "" + (zlen / mz));
 
-    float alpha = in.readFloat();
-    float beta = in.readFloat();
-    float gamma = in.readFloat();
-
-    addMeta("Alpha angle", "" + alpha);
-    addMeta("Beta angle", "" + beta);
-    addMeta("Gamma angle", "" + gamma);
+    addMeta("Alpha angle", "" + in.readFloat());
+    addMeta("Beta angle", "" + in.readFloat());
+    addMeta("Gamma angle", "" + in.readFloat());
 
     in.skipBytes(12);
@@ -182 +173 @@
     // min, max and mean pixel values
 
-    float min = in.readFloat();
-    float max = in.readFloat();
-    float mean = in.readFloat();
-
-    addMeta("Minimum pixel value", "" + min);
-    addMeta("Maximum pixel value", "" + max);
-    addMeta("Mean pixel value", "" + mean);
+    addMeta("Minimum pixel value", "" + in.readFloat());
+    addMeta("Maximum pixel value", "" + in.readFloat());
+    addMeta("Mean pixel value", "" + in.readFloat());
 
     in.skipBytes(4);
 
     extHeaderSize = in.readInt();
-    int creator = in.readShort();
-
-    in.skipBytes(30);
-
-    int nint = in.readShort();
-    int nreal = in.readShort();
-
-    in.skipBytes(28);
+     
+    in.skipBytes(64);
 
     int idtype = in.readShort();
-    int lens = in.readShort();
-    int nd1 = in.readShort();
-    int nd2 = in.readShort();
-    int vd1 = in.readShort();
-    int vd2 = in.readShort();
-
-    String type = "";
-    switch (idtype) {
-      case 0:
-        type = "mono";
-        break;
-      case 1:
-        type = "tilt";
-        break;
-      case 2:
-        type = "tilts";
-        break;
-      case 3:
-        type = "lina";
-        break;
-      case 4:
-        type = "lins";
-        break;
-      default:
-        type = "unknown";
-    }
+
+    String[] types = new String[] {"mono", "tilt", "tilts", "lina", "lins"};
+    String type = (idtype >= 0 && idtype < types.length) ? types[idtype] :
+      "unknown";
 
     addMeta("Series type", type);
-    addMeta("Lens", "" + lens);
-    addMeta("ND1", "" + nd1);
-    addMeta("ND2", "" + nd2);
-    addMeta("VD1", "" + vd1);
-    addMeta("VD2", "" + vd2);
+    addMeta("Lens", "" + in.readShort());
+    addMeta("ND1", "" + in.readShort());
+    addMeta("ND2", "" + in.readShort());
+    addMeta("VD1", "" + in.readShort());
+    addMeta("VD2", "" + in.readShort());
 
     float[] angles = new float[6];
@@ -248 +207 @@
     addMeta("Number of useful labels", "" + nUsefulLabels);
 
-    byte[] b = new byte[80];
     for (int i=0; i<10; i++) {
-      in.read(b);
-      addMeta("Label " + (i+1), new String(b));
+      addMeta("Label " + (i+1), in.readString(80));
     }
 

trunk/loci/formats/in/ND2Reader.java

@@ -122 +122 @@
   /** Array of image offsets. */
   private long[] offsets;
-
-  /** Number of valid bits per pixel */
-  private int[] validBits;
 
   /** Whether or not the pixel data is compressed using JPEG 2000. */
@@ -176 +173 @@
           pixels[i].length);
       }
+      pixels = null; 
     }
     else {
@@ -328 +326 @@
       pos = in.getFilePointer();
       length = in.readInt();
-      if (pos + length >= in.length()) lastBoxFound = true;
+      if (pos + length >= in.length() || length == 0) lastBoxFound = true;
       box = in.readInt();
       pos = in.getFilePointer();
@@ -343 +341 @@
       offsets[i] = ((Long) vs.get(i)).longValue();
     }
+    vs.clear();
+    vs = null;
 
     status("Finding XML metadata");
@@ -377 +377 @@
       }
     }
+
+    buf = null;
 
     status("Parsing XML");
@@ -476 +478 @@
         }
       }
+      b = null; 
+      xml = null; 
+      st = null; 
     }
 
@@ -483 +488 @@
     core.sizeX[0] = img.getWidth();
     core.sizeY[0] = img.getHeight();
+    core.sizeC[0] = img.getRaster().getNumBands();
+    core.rgb[0] = core.sizeC[0] > 1;
 
     int numInvalid = 0;
@@ -527 +534 @@
     }
 
-    if (core.sizeC[0] == 0) {
-      core.sizeC[0] = openImage(0).getRaster().getNumBands();
-    }
     if (core.sizeC[0] == 2) core.sizeC[0] = 1;
 
@@ -543 +547 @@
     // we calculate this directly (instead of calling getEffectiveSizeC) because
     // sizeZ and sizeT have not been accurately set yet
-    int effectiveC = (core.sizeC[0] / 3) + 1;
+    int effectiveC = ((core.sizeC[0] - 1) / 3) + 1;
 
     if (core.imageCount[0] < core.sizeZ[0] * core.sizeT[0]) {
@@ -593 +597 @@
     }
 
-    if (bits != 0) {
-      validBits = new int[core.sizeC[0] == 2 ? 3 : core.sizeC[0]];
-      for (int i=0; i<validBits.length; i++) validBits[i] = bits;
-    }
-    else validBits = null;
-
-    if (validBits == null) core.pixelType[0] = FormatTools.UINT8;
+    if (bits == 0) core.pixelType[0] = FormatTools.UINT8;
     else {
-      int bpp = validBits[0];
+      int bpp = bits; 
       while (bpp % 8 != 0) bpp++;
       switch (bpp) {
@@ -628 +626 @@
 
     if (core.sizeZ[0] * core.sizeT[0] * core.sizeC[0] < core.imageCount[0]) {
-      core.sizeC[0] = 1;
       core.sizeT[0] = 1;
       core.sizeZ[0] = core.imageCount[0];

trunk/loci/formats/in/NRRDReader.java

@@ -60 +60 @@
   public boolean isThisType(byte[] block) {
     if (block.length < 4) return false;
-    return block[0] == 'N' && block[1] == 'R' && block[2] == 'R' &&
-      block[3] == 'D';
+    return new String(block).startsWith("NRRD"); 
   }
 

trunk/loci/formats/in/OIBReader.java

@@ -112 +112 @@
   private Vector[] tIndices;
 
-  /** Number of valid bits per pixel. */
-  private int[][] validBits;
-
   private Vector rgb;
 
@@ -148 +145 @@
 
     return ImageTools.makeImage(b, core.sizeX[series], core.sizeY[series],
-      getRGBChannelCount(), false, bytes, core.littleEndian[series],
-      validBits[series]);
+      getRGBChannelCount(), false, bytes, core.littleEndian[series]);
   }
 
@@ -318 +314 @@
       core = new CoreMetadata(numSeries);
 
-      validBits = new int[numSeries][];
-
       for (int i=0; i<numSeries; i++) {
         core.sizeX[i] = ((Integer) width.get(i)).intValue();
@@ -393 +387 @@
         nImages.setElementAt(new Integer(core.imageCount[i]), i);
         setSeries(oldSeries);
-
-        validBits[i] = new int[core.sizeC[i] == 2 ? 3 : core.sizeC[i]];
-        int vb = 0;
-        Enumeration k = metadata.keys();
-        while (k.hasMoreElements()) {
-          String key = k.nextElement().toString();
-          if (key.indexOf("ValidBitCounts") != -1) {
-            vb = Integer.parseInt((String) getMeta(key));
-          }
-        }
-        if (vb > 0) {
-          for (int j=0; j<validBits[i].length; j++) validBits[i][j] = vb;
-        }
-        else validBits[i] = null;
 
         core.rgb[i] = ((Boolean) rgb.get(i)).booleanValue();
@@ -457 +437 @@
     for (int i=0; i<width.size(); i++) {
       switch (((Integer) bpp.get(0)).intValue() % 3) {
-        case 0:
-        case 1:
-          core.pixelType[i] = FormatTools.UINT8;
-          break;
         case 2:
           core.pixelType[i] = FormatTools.UINT16;
           break;
-        case 4:
-          core.pixelType[i] = FormatTools.UINT32;
-          break;
-        default:
-          throw new RuntimeException(
-            "Unknown matching for pixel byte width of: " + bpp);
+        default: core.pixelType[i] = FormatTools.UINT8; 
       }
 

trunk/loci/formats/in/OIFReader.java

@@ -48 +48 @@
   /** Helper reader to open the thumbnail. */
   protected BMPReader thumbReader;
-
-  /** Number of valid bits per pixel. */
-  protected int[] validBits;
 
   /** List of files in the current OIF dataset. */
@@ -109 +106 @@
     BufferedImage b = tiffReader[no].openImage(0);
     ColorModel cm = ImageTools.makeColorModel(b.getRaster().getNumBands(),
-      b.getRaster().getTransferType(), validBits);
+      b.getRaster().getTransferType(), null);
     b = ImageTools.makeBuffered(b, cm);
     tiffReader[no].close();
@@ -334 +331 @@
 
     for (int i=0; i<9; i++) {
-      if (code[i].equals("\"X\"")) core.sizeX[0] = Integer.parseInt(size[i]);
-      else if (code[i].equals("\"Y\"")) {
-        core.sizeY[0] = Integer.parseInt(size[i]);
-      }
-      else if (code[i].equals("\"C\"")) {
-        core.sizeC[0] = Integer.parseInt(size[i]);
-      }
-      else if (code[i].equals("\"T\"")) {
-        core.sizeT[0] = Integer.parseInt(size[i]);
-      }
-      else if (code[i].equals("\"Z\"")) {
-        core.sizeZ[0] = Integer.parseInt(size[i]);
-      }
+      int ss = Integer.parseInt(size[i]); 
+      if (code[i].equals("\"X\"")) core.sizeX[0] = ss;
+      else if (code[i].equals("\"Y\"")) core.sizeY[0] = ss; 
+      else if (code[i].equals("\"C\"")) core.sizeC[0] = ss; 
+      else if (code[i].equals("\"T\"")) core.sizeT[0] = ss; 
+      else if (code[i].equals("\"Z\"")) core.sizeZ[0] = ss; 
     }
 
@@ -396 +386 @@
     }
 
-    validBits = new int[core.sizeC[0]];
-    if (validBits.length == 2) validBits = new int[3];
-    for (int i=0; i<validBits.length; i++) {
-      s = (String) getMeta("[Reference Image Parameter] - ValidBitCounts");
-      if (s != null) {
-        validBits[i] = Integer.parseInt(s);
-      }
-      else {
-        i = validBits.length;
-      }
-    }
-
-    int len = validBits.length;
-    for (int i=0; i<len; i++) {
-      if (validBits[i] == 0) {
-        validBits = null;
-        break;
-      }
-    }
-
     core.rgb[0] = tiffReader[0].isRGB();
     core.littleEndian[0] = true;

trunk/loci/formats/in/OMEXMLReader.java

@@ -114 +114 @@
     data = null;
 
-    //byte[] pixels = Compression.base64Decode(pix);
     Base64Codec e = new Base64Codec();
     byte[] pixels = e.base64Decode(pix);
@@ -198 +197 @@
           if (ndx != -1) {
             found = true;
-            String endian = test.substring(ndx + 11);
+            String endian = test.substring(ndx + 11).trim();
+            if (endian.startsWith("\"")) endian = endian.substring(1);
             endianness.add(new Boolean(!endian.toLowerCase().startsWith("t")));
             bigEndianPos.add(new Long(in.getFilePointer() - read - 9 + ndx));

trunk/loci/formats/in/OpenlabRawReader.java

@@ -95 +95 @@
   /* @see loci.formats.IFormatReader#openImage(int) */
   public BufferedImage openImage(int no) throws FormatException, IOException {
-    FormatTools.assertId(currentId, true, 1);
     return ImageTools.makeImage(openBytes(no), core.sizeX[0],
       core.sizeY[0], core.sizeC[0], false, bytesPerPixel, false);
@@ -150 +149 @@
     addMeta("Bytes per pixel", new Integer(bytesPerPixel));
 
+    int plane = core.sizeX[0] * core.sizeY[0] * bytesPerPixel;
     for (int i=1; i<core.imageCount[0]; i++) {
-      offsets[i] =
-        offsets[i-1] + 288 + core.sizeX[0] * core.sizeY[0] * bytesPerPixel;
+      offsets[i] = offsets[i - 1] + 288 + plane;
     }
 
@@ -167 +166 @@
     switch (bytesPerPixel) {
       case 1:
+      case 3:  
         core.pixelType[0] = FormatTools.UINT8;
         break;
       case 2:
         core.pixelType[0] = FormatTools.UINT16;
-        break;
-      case 3:
-        core.pixelType[0] = FormatTools.INT8;
         break;
       default:

trunk/loci/formats/in/OpenlabReader.java

@@ -103 +103 @@
 
     in.skipBytes(24);
-    int volumeType = DataTools.read2SignedBytes(in, false);
+    int volumeType = in.readShort();
     in.skipBytes(272);
 
@@ -110 +110 @@
     if (version == 2) {
       in.skipBytes(2);
-      top = DataTools.read2SignedBytes(in, false);
-      left = DataTools.read2SignedBytes(in, false);
-      bottom = DataTools.read2SignedBytes(in, false);
-      right = DataTools.read2SignedBytes(in, false);
+      top = in.readShort();
+      left = in.readShort();
+      bottom = in.readShort();
+      right = in.readShort();
 
       if (core.sizeX[series] == 0) core.sizeX[series] = right - left;
@@ -119 +119 @@
     }
     else {
-      core.sizeX[series] = DataTools.read4SignedBytes(in, false);
-      core.sizeY[series] = DataTools.read4SignedBytes(in, false);
+      core.sizeX[series] = in.readInt();
+      core.sizeY[series] = in.readInt();
     }
 
@@ -226 +226 @@
 
       in.skipBytes(24);
-      volumeType = DataTools.read2SignedBytes(in, false);
+      volumeType = in.readShort(); 
 
       in.skipBytes(280);
-      int size = DataTools.read4SignedBytes(in, false);
-      int compressedSize = DataTools.read4SignedBytes(in, false);
+      int size = in.readInt();
+      int compressedSize = in.readInt();
       b = new byte[size];
       byte[] c = new byte[compressedSize];
@@ -352 +352 @@
     status("Verifying Openlab LIFF format");
 
+    in.order(false);
     in.skipBytes(4);
-    byte[] b = new byte[4];
-    in.read(b);
-    String s = new String(b);
-    if (!s.equals("impr")) throw new FormatException("Invalid LIFF file.");
-
-    version = DataTools.read4SignedBytes(in, false);
+    if (!in.readString(4).equals("impr")) {
+      throw new FormatException("Invalid LIFF file.");
+    }
+
+    version = in.readInt();
 
     if (version != 2 && version != 5) {
@@ -368 +368 @@
 
     // read offset to first plane
-    int offset = DataTools.read4SignedBytes(in, false);
+    int offset = in.readInt();
     in.seek(offset);
 
@@ -404 +404 @@
 
           in.skipBytes(24);
-          int volumeType = DataTools.read2SignedBytes(in, false);
+          int volumeType = in.readShort();
 
           if (volumeType == MAC_1_BIT || volumeType == MAC_256_GREYS ||
@@ -411 +411 @@
           {
             in.skipBytes(16);
-            b = new byte[128];
-            in.read(b);
-            info.layerName = new String(b);
+            info.layerName = in.readString(128);
 
             if (!info.layerName.trim().equals("Original Image")) {
-              info.timestamp = DataTools.read8SignedBytes(in, false);
+              info.timestamp = in.readLong();
               layerInfoList[0].add(info);
             }
@@ -424 +422 @@
         else if (tag == 69) {
           in.skipBytes(4);
-          int units = DataTools.read2SignedBytes(in, false);
+          int units = in.readShort();
           in.skipBytes(12);
 
-          xCal = Float.intBitsToFloat(DataTools.read4SignedBytes(in, false));
-          yCal = Float.intBitsToFloat(DataTools.read4SignedBytes(in, false));
+          xCal = in.readFloat();
+          yCal = in.readFloat();
         }
         else if (tag == 72 || fmt.equals("USER")) {
@@ -444 +442 @@
 
             if (aChar == 1) {
-              int numVars = DataTools.read2SignedBytes(in, false);
+              int numVars = in.readShort();
               while (numVars > 0) {
                 aChar = (char) in.read();
@@ -466 +464 @@
 
                 if (className.equals("CStringVariable")) {
-                  int strSize = DataTools.read4SignedBytes(in, false);
-                  b = new byte[strSize];
-                  in.read(b);
-                  varStringValue = new String(b);
+                  int strSize = in.readInt();
+                  varStringValue = in.readString(strSize);
                   varNumValue = Float.parseFloat(varStringValue);
 
@@ -475 +471 @@
                 }
                 else if (className.equals("CFloatVariable")) {
-                  varNumValue = Double.longBitsToDouble(
-                    DataTools.read8SignedBytes(in, false));
+                  varNumValue = in.readDouble();
                   varStringValue = "" + varNumValue;
                 }
@@ -482 +477 @@
                 int baseClassVersion = in.read();
                 if (baseClassVersion == 1 || baseClassVersion == 2) {
-                  int strSize = DataTools.read4SignedBytes(in, false);
-                  b = new byte[strSize];
-                  in.read(b);
-                  varName = new String(b);
+                  int strSize = in.readInt();
+                  varName = in.readString(strSize);
                   in.skipBytes(baseClassVersion == 1 ? 3 : 2);
                 }
@@ -532 +525 @@
       if (fmt.equals("PICT")) {
         in.skipBytes(24);
-        int volumeType = DataTools.read2SignedBytes(in, false);
+        int volumeType = in.readShort();
         in.skipBytes(272);
 
@@ -539 +532 @@
         if (version == 2) {
           in.skipBytes(2);
-          top = DataTools.read2SignedBytes(in, false);
-          left = DataTools.read2SignedBytes(in, false);
-          bottom = DataTools.read2SignedBytes(in, false);
-          right = DataTools.read2SignedBytes(in, false);
+          top = in.readShort();
+          left = in.readShort();
+          bottom = in.readShort();
+          right = in.readShort();
 
           if (core.sizeX[series] == 0) core.sizeX[series] = right - left;
@@ -548 +541 @@
         }
         else {
-          core.sizeX[series] = DataTools.read4SignedBytes(in, false);
-          core.sizeY[series] = DataTools.read4SignedBytes(in, false);
+          core.sizeX[series] = in.readInt();
+          core.sizeY[series] = in.readInt();
         }
 
         in.seek(layer.layerStart);
-
-        b = new byte[0];
 
         if (version == 2) {
@@ -566 +557 @@
           // open image using pict reader
           try {
-            b = new byte[(int) (nextTag - in.getFilePointer())];
+            byte[] b = new byte[(int) (nextTag - in.getFilePointer())];
             in.read(b);
             BufferedImage img = pict.open(b);
@@ -672 +663 @@
       switch (bpp[i]) {
         case 1:
-          core.pixelType[i] = FormatTools.INT8;
-          break;
-        case 2:
-          core.pixelType[i] = FormatTools.UINT16;
-          break;
         case 3:
           core.pixelType[i] = FormatTools.UINT8;
           break;
+        case 2:
+        case 6: 
+          core.pixelType[i] = FormatTools.UINT16;
+          break;
         case 4:
-          core.pixelType[i] = FormatTools.INT32;
-          break;
-        case 6:
-          core.pixelType[i] = FormatTools.INT16;
+          core.pixelType[i] = FormatTools.UINT32;
           break;
       }
@@ -715 +702 @@
     throws IOException
   {
-    tag = DataTools.read2SignedBytes(in, false);
-    subTag = DataTools.read2SignedBytes(in, false);
-
-    long nextTag = (version == 2 ? DataTools.read4SignedBytes(in, false) :
-      DataTools.read8SignedBytes(in, false));
+    tag = in.readShort();
+    subTag = in.readShort();
+
+    long nextTag = (version == 2 ? in.readInt() : in.readLong());
 
     byte[] b = new byte[4];

trunk/loci/formats/in/PGMReader.java

@@ -31 +31 @@
 
 /**
- * PGMReader is the file format reader for
- * Portable Gray Map (PGM) images.
+ * PGMReader is the file format reader for Portable Gray Map (PGM) images.
  *
  * Much of this code was adapted from ImageJ (http://rsb.info.nih.gov/ij). 
@@ -124 +123 @@
     boolean isBlackAndWhite = false;
 
-    if (magic.equals("P1") || magic.equals("P2")) {
-      rawBits = false; 
-      core.sizeC[0] = 1; 
-      isBlackAndWhite = magic.equals("P1"); 
-    } 
-    else if (magic.equals("P3")) {
-      rawBits = false;
-      core.sizeC[0] = 3;
-    }
-    else if (magic.equals("P4") || magic.equals("P5")) {
-      rawBits = true;
-      core.sizeC[0] = 1;
-      isBlackAndWhite = magic.equals("P4"); 
-    }
-    else if (magic.equals("P6")) {
-      rawBits = true;
-      core.sizeC[0] = 3;
-    }
-    else throw new FormatException("Unsupported magic number: " + magic); 
- 
+    rawBits = magic.equals("P4") || magic.equals("P5") || magic.equals("P6");
+    core.sizeC[0] = (magic.equals("P3") || magic.equals("P6")) ? 3 : 1;
+    isBlackAndWhite = magic.equals("P1") || magic.equals("P4");
+
     String line = in.readLine().trim();
     while (line.startsWith("#") || line.length() == 0) line = in.readLine();

trunk/loci/formats/in/PNGReader.java

@@ -36 +36 @@
 
   /** Constructs a new PNGReader. */
-  public PNGReader() { super("Portable Network Graphics", new String[] {"png", "pnm"}); }
-
+  public PNGReader() { 
+    super("Portable Network Graphics", new String[] {"png", "pnm"});
+  }
 }

trunk/loci/formats/in/PerkinElmerReader.java

@@ -213 +213 @@
         ((prefix != null) && (s.startsWith(prefix))))
       {
-        if (cfgPos == -1) {
-          if (filename.endsWith(".cfg")) {
-            cfgPos = i;
-            prefix = ls[i].substring(0, d);
-          }
-        }
-
-        if (anoPos == -1) {
-          if (filename.endsWith(".ano")) {
-            anoPos = i;
-            prefix = ls[i].substring(0, d);
-          }
-        }
-
-        if (recPos == -1) {
-          if (filename.endsWith(".rec")) {
-            recPos = i;
-            prefix = ls[i].substring(0, d);
-          }
-        }
-
-        if (timPos == -1) {
-          if (filename.endsWith(".tim")) {
-            timPos = i;
-            prefix = ls[i].substring(0, d);
-          }
-        }
-        if (csvPos == -1) {
-          if (filename.endsWith(".csv")) {
-            csvPos = i;
-            prefix = ls[i].substring(0, d);
-          }
-        }
-        if (zpoPos == -1) {
-          if (filename.endsWith(".zpo")) {
-            zpoPos = i;
-            prefix = ls[i].substring(0, d);
-          }
-        }
-        if (htmPos == -1) {
-          if (filename.endsWith(".htm")) {
-            htmPos = i;
-            prefix = ls[i].substring(0, d);
-          }
+        if (cfgPos == -1 && filename.endsWith(".cfg")) {
+          cfgPos = i;
+          prefix = ls[i].substring(0, d);
+        }
+        if (anoPos == -1 && filename.endsWith(".ano")) {
+          anoPos = i;
+          prefix = ls[i].substring(0, d);
+        }
+        if (recPos == -1 && filename.endsWith(".rec")) {
+          recPos = i;
+          prefix = ls[i].substring(0, d);
+        }
+        if (timPos == -1 && filename.endsWith(".tim")) {
+          timPos = i;
+          prefix = ls[i].substring(0, d);
+        }
+        if (csvPos == -1 && filename.endsWith(".csv")) {
+          csvPos = i;
+          prefix = ls[i].substring(0, d);
+        }
+        if (zpoPos == -1 && filename.endsWith(".zpo")) {
+          zpoPos = i;
+          prefix = ls[i].substring(0, d);
+        }
+        if (htmPos == -1 && filename.endsWith(".htm")) {
+          htmPos = i;
+          prefix = ls[i].substring(0, d);
         }
 
@@ -345 +328 @@
       tiff[i] = new TiffReader();
       if (i > 0) tiff[i].setMetadataCollected(false);
-      //tiff[i].setId(files[i]);
-    }
-
-    // highly questionable metadata parsing
+    }
 
     // we always parse the .tim and .htm files if they exist, along with
@@ -562 +542 @@
       switch (bpp) {
         case 1:
-          core.pixelType[0] = FormatTools.INT8;
+        case 3: 
+          core.pixelType[0] = FormatTools.UINT8;
           break;
         case 2:
           core.pixelType[0] = FormatTools.UINT16;
           break;
-        case 3:
-          core.pixelType[0] = FormatTools.INT8;
-          break;
         case 4:
-          core.pixelType[0] = FormatTools.INT32;
+          core.pixelType[0] = FormatTools.UINT32;
           break;
       }
@@ -631 +609 @@
       new Integer(core.sizeT[0]), // SizeT
       new Integer(core.pixelType[0]), // PixelType
-      new Boolean(!isLittleEndian()), // BigEndian
+      new Boolean(!core.littleEndian[0]), // BigEndian
       core.currentOrder[0], // DimensionOrder
       null, // Use image index 0

trunk/loci/formats/in/PictReader.java

@@ -65 +65 @@
   static {
     int index = 0;
-    for (int i = 0; i < 256; i++) {
+    for (int i=0; i<256; i++) {
       EXPANSION_TABLE[index++] = (i & 128) == 0 ? (byte) 0 : (byte) 1;
       EXPANSION_TABLE[index++] = (i & 64) == 0 ? (byte) 0 : (byte) 1;
@@ -79 +79 @@
   // -- Fields --
 
+  /** Stream for reading pixel data. */
+  protected RandomAccessStream ras;
+
   /** Pixel bytes. */
   protected byte[] bytes;
@@ -90 +93 @@
   /** Image state. */
   protected int pictState;
-
-  /** Pointer into the array of bytes representing the file. */
-  protected int pt;
 
   /** Vector of byte arrays representing individual rows. */
@@ -125 +125 @@
 
   /** Open a PICT image from an array of bytes (used by OpenlabReader). */
-  public BufferedImage open(byte[] pix) throws FormatException {
+  public BufferedImage open(byte[] pix) throws FormatException, IOException {
     // handles case when we call this method directly, instead of
     // through initFile(String)
@@ -137 +137 @@
     pictState = INITIAL;
     bytes = pix;
-    pt = 0;
+    ras = new RandomAccessStream(bytes);
+    ras.order(false);
 
     try {
@@ -340 +341 @@
 
   /** Loop through the remainder of the file and find relevant opcodes. */
-  private boolean driveDecoder() throws FormatException {
+  private boolean driveDecoder() throws FormatException, IOException {
     if (debug) debug("driveDecoder");
     int opcode;
@@ -346 +347 @@
     switch (pictState) {
       case INITIAL:
-        pt += 2;
-        // skip over frame
-        pt += 8;
-        int verOpcode =
-          DataTools.bytesToInt(bytes, pt, 1, core.littleEndian[0]);
-        pt++;
-        int verNumber =
-          DataTools.bytesToInt(bytes, pt, 1, core.littleEndian[0]);
-        pt++;
+        ras.skipBytes(10); 
+        int verOpcode = ras.read(); 
+        int verNumber = ras.read(); 
 
         if (verOpcode == 0x11 && verNumber == 0x01) versionOne = true;
         else if (verOpcode == 0x00 && verNumber == 0x11) {
           versionOne = false;
-          int verNumber2 =
-            DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-          pt += 2;
+          int verNumber2 = ras.readShort(); 
 
           if (verNumber2 != 0x02ff) {
@@ -368 +361 @@
 
           // skip over v2 header -- don't need it here
-          pt += 26;
+          ras.skipBytes(26); 
         }
         else throw new FormatException("Invalid PICT file");
@@ -377 +370 @@
 
       case STATE2:
-        if (versionOne) {
-          opcode = DataTools.bytesToInt(bytes, pt, 1, core.littleEndian[0]);
-          pt++;
-        }
+        if (versionOne) opcode = ras.read(); 
         else {
           // if at odd boundary skip a byte for opcode in PICT v2
 
-          if ((pt & 0x1L) != 0) {
-            pt++;
+          if ((ras.getFilePointer() & 0x1L) != 0) {
+            ras.skipBytes(1); 
           }
-          opcode = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-          pt += 2;
+          opcode = ras.readShort(); 
         }
         return drivePictDecoder(opcode);
@@ -396 +385 @@
 
   /** Handles the opcodes in the PICT file. */
-  private boolean drivePictDecoder(int opcode) throws FormatException {
+  private boolean drivePictDecoder(int opcode) 
+    throws FormatException, IOException
+  {
     if (debug) debug("drivePictDecoder");
 
@@ -408 +399 @@
         break;
       case PICT_CLIP_RGN:
-        int x = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-        pt += x;
+        int x = ras.readShort(); 
+        ras.skipBytes(x - 2); 
         break;
       case PICT_LONGCOMMENT:
-        pt += 2;
-        x = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-        pt += x + 2;
+        ras.skipBytes(2); 
+        x = ras.readShort();
+        ras.skipBytes(x);
         break;
       case PICT_END: // end of PICT
@@ -421 +412 @@
     }
 
-    return (pt < bytes.length);
+    return ras.getFilePointer() < ras.length();
   }
 
   /** Handles bitmap and pixmap opcodes of PICT format. */
-  private void handlePackBits(int opcode) throws FormatException {
+  private void handlePackBits(int opcode) 
+    throws FormatException, IOException 
+  {
     if (debug) debug("handlePackBits(" + opcode + ")");
     if (opcode == PICT_9A) {
@@ -432 +425 @@
     }
     else {
-      rowBytes = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
+      rowBytes = ras.readShort();
       if (versionOne || (rowBytes & 0x8000) == 0) handleBitmap(opcode);
       else handlePixmap(opcode);
@@ -440 +432 @@
 
   /** Extract the image data in a PICT bitmap structure. */
-  private void handleBitmap(int opcode) throws FormatException {
+  private void handleBitmap(int opcode) 
+    throws FormatException, IOException 
+  {
     if (debug) debug("handleBitmap(" + opcode + ")");
     int row;
@@ -451 +445 @@
     // read the bitmap data -- 3 rectangles + mode
 
-    int tlY = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-    pt += 2;
-    int tlX = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-    pt += 2;
-    int brY = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-    pt += 2;
-    int brX = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-    pt += 2;
+    int tlY = ras.readShort();
+    int tlX = ras.readShort(); 
+    int brY = ras.readShort(); 
+    int brX = ras.readShort(); 
 
     // skip next two rectangles
-    pt += 18;
+    ras.skipBytes(18); 
 
     core.sizeX[0] = brX - tlX;
@@ -479 +469 @@
     for (row=0; row < core.sizeY[0]; ++row) {
       if (rowBytes < 8) {  // data is not compressed
-        System.arraycopy(bytes, pt, buf, 0, rowBytes);
+        ras.read(buf, 0, rowBytes); 
 
         for (int j=buf.length; --j >= 0;) {
@@ -488 +478 @@
       else {
         int rawLen;
-        if (rowBytes > 250) {
-          rawLen = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-          pt += 2;
-        }
-        else {
-          rawLen = DataTools.bytesToInt(bytes, pt, 1, core.littleEndian[0]);
-          pt++;
-        }
+        if (rowBytes > 250) rawLen = ras.readShort(); 
+        else rawLen = ras.read(); 
 
         try {
-          System.arraycopy(bytes, pt, buf, 0, rawLen);
-          pt += rawLen;
+          ras.read(buf, 0, rawLen);
         }
         catch (ArrayIndexOutOfBoundsException e) {
@@ -519 +502 @@
 
   /** Extracts the image data in a PICT pixmap structure. */
-  private void handlePixmap(int opcode) throws FormatException {
+  private void handlePixmap(int opcode) 
+    throws FormatException, IOException
+  {
     if (debug) debug("handlePixmap(" + opcode + ")");
     int pixelSize;
@@ -530 +515 @@
       // read the pixmap (9A)
 
-      pt += 4; // skip fake length and fake EOF
-
-      pt += 2;
+      ras.skipBytes(6);
 
       // read the bounding box
-      int tlY = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int tlX = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int brY = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int brX = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-
-      pt += 2; // undocumented extra short in the data structure
-
-      pt += 16;
-
-      pixelSize = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      compCount = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 16; // reserved
+      int tlY = ras.readShort(); 
+      int tlX = ras.readShort(); 
+      int brY = ras.readShort(); 
+      int brX = ras.readShort(); 
+
+      ras.skipBytes(18);
+
+      pixelSize = ras.readShort();
+      compCount = ras.readShort(); 
+      ras.skipBytes(14); 
 
       core.sizeX[0] = brX - tlX;
@@ -570 +546 @@
     else {
       rowBytes &= 0x3fff;  // mask off flags
-
-      int tlY = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int tlX = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int brY = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int brX = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-
-      // unnecessary data
-      pt += 18;
-
-      pixelSize = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      compCount = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-
-      // unnecessary data
-      pt += 14;
+      
+      int tlY = ras.readShort();
+      int tlX = ras.readShort(); 
+      int brY = ras.readShort(); 
+      int brX = ras.readShort(); 
+
+      ras.skipBytes(18);
+
+      pixelSize = ras.readShort();
+      compCount = ras.readShort(); 
+
+      ras.skipBytes(14);
 
       // read the lookup table
 
-      pt += 4;
-      int flags = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
-      int count = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-      pt += 2;
+      ras.skipBytes(4);
+      int flags = ras.readShort(); 
+      int count = ras.readShort(); 
 
       count++;
@@ -603 +569 @@
 
       for (int i=0; i<count; i++) {
-        int index = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-        pt += 2;
+        int index = ras.readShort(); 
         if ((flags & 0x8000) != 0) index = i;
-        lookup[0][index] =
-          DataTools.bytesToShort(bytes, pt, 2, core.littleEndian[0]);
-        pt += 2;
-        lookup[1][index] =
-          DataTools.bytesToShort(bytes, pt, 2, core.littleEndian[0]);
-        pt += 2;
-        lookup[2][index] =
-          DataTools.bytesToShort(bytes, pt, 2, core.littleEndian[0]);
-        pt += 2;
+        lookup[0][index] = ras.readShort();
+        lookup[1][index] = ras.readShort();
+        lookup[2][index] = ras.readShort();
       }
 
@@ -622 +581 @@
 
     // skip over two rectangles
-    pt += 18;
-
-    if (opcode == PICT_BITSRGN || opcode == PICT_PACKBITSRGN) pt += 2;
+    ras.skipBytes(18);
+
+    if (opcode == PICT_BITSRGN || opcode == PICT_PACKBITSRGN) ras.skipBytes(2);
 
     handlePixmap(rowBytes, pixelSize, compCount);
@@ -631 +590 @@
   /** Handles the unpacking of the image data. */
   private void handlePixmap(int rBytes, int pixelSize, int compCount)
-    throws FormatException
+    throws FormatException, IOException
   {
     if (debug) {
@@ -676 +635 @@
       buf = new byte[bufSize];
       for (int row=0; row<core.sizeY[0]; row++) {
-        System.arraycopy(bytes, pt, buf, 0, rBytes);
+        ras.read(buf, 0, rBytes);
 
         switch (pixelSize) {
@@ -701 +660 @@
       buf = new byte[bufSize + 1 + bufSize / 128];
       for (int row=0; row<core.sizeY[0]; row++) {
-        if (rBytes > 250) {
-          rawLen = DataTools.bytesToInt(bytes, pt, 2, core.littleEndian[0]);
-          pt += 2;
-        }
-        else {
-          rawLen = DataTools.bytesToInt(bytes, pt, 1, core.littleEndian[0]);
-          pt++;
-        }
+        if (rBytes > 250) rawLen = ras.readShort(); 
+        else rawLen = ras.read(); 
 
         if (rawLen > buf.length) rawLen = buf.length;
 
-        if ((bytes.length - pt) <= rawLen) {
-          rawLen = bytes.length - pt - 1;
+        if ((ras.length() - ras.getFilePointer()) <= rawLen) {
+          rawLen = (int) (ras.length() - ras.getFilePointer() - 1); 
         }
 
         if (rawLen < 0) {
           rawLen = 0;
-          pt = bytes.length - 1;
-        }
-
-        System.arraycopy(bytes, pt, buf, 0, rawLen);
-        pt += rawLen;
+          ras.seek(ras.length() - 1);
+        }
+
+        ras.read(buf, 0, rawLen);
 
         if (pixelSize == 16) {
@@ -806 +758 @@
     int t;
     byte v;
-    int count = 0; // number of pixels in a byte
-    int maskshift = 1; // num bits to shift mask
-    int pixelshift = 0; // num bits to shift pixel
+    int count = 8 / bitSize; // number of pixels in a byte
+    int maskshift = bitSize; // num bits to shift mask
+    int pixelshift = 8 - bitSize; // num bits to shift pixel
     int tpixelshift = 0;
-    int pixelshiftdelta = 0;
+    int pixelshiftdelta = bitSize;
     int mask = 0;
     int tmask; // temp mask
@@ -821 +773 @@
       case 1:
         mask = 0x80;
-        maskshift = 1;
-        count = 8;
-        pixelshift = 7;
-        pixelshiftdelta = 1;
         break;
       case 2:
         mask = 0xC0;
-        maskshift = 2;
-        count = 4;
-        pixelshift = 6;
-        pixelshiftdelta = 2;
         break;
       case 4:
         mask = 0xF0;
-        maskshift = 4;
-        count = 2;
-        pixelshift = 4;
-        pixelshiftdelta = 4;
         break;
     }

trunk/loci/formats/in/QTReader.java

@@ -331 +331 @@
       case 0:
       case 1:
+      case 3:  
         core.pixelType[0] = FormatTools.UINT8;
         break;
       case 2:
-        core.pixelType[0] = FormatTools.INT16;
+        core.pixelType[0] = FormatTools.UINT16;
         break;
-      case 3:
-        core.pixelType[0] = FormatTools.UINT8;
-        break;
-    }
-
-    /*
-    if (flip) {
-      int tmp = core.sizeX[0];
-      core.sizeX[0] = core.sizeY[0];
-      core.sizeY[0] = tmp;
-    }
-    */
+    }
 
     core.rgb[0] = bitsPerPixel < 40;
@@ -484 +474 @@
 
       // read the atom type
-      byte[] four = new byte[4];
-      in.read(four);
-      String atomType = new String(four);
+      String atomType = in.readString(4);
 
       // if atomSize is 1, then there is an 8 byte extended size
@@ -609 +597 @@
 
           for (int i=0; i<numEntries; i++) {
-            byte[] b = new byte[4];
-            in.read(b);
             if (i == 0) {
-              codec = new String(b);
+              codec = in.readString(4); 
               in.skipBytes(74);
 
@@ -627 +613 @@
             }
             else {
-              altCodec = new String(b);
+              altCodec = in.readString(4); 
               addMeta("Second codec", altCodec);
             }
@@ -738 +724 @@
     String test = null;
     boolean found = false;
-    byte[] b = new byte[4];
     while (!found && in.getFilePointer() < (in.length() - 4)) {
-      in.read(b);
-      test = new String(b);
+      test = in.readString(4);
       if (test.equals("moov")) {
         found = true;

trunk/loci/formats/in/SlidebookReader.java

@@ -102 +102 @@
     super.initFile(id);
     in = new RandomAccessStream(id);
+    in.order(true);
 
     status("Finding offsets to pixel data");
@@ -216 +217 @@
       if (n == 'i') {
         in.skipBytes(79); 
-        core.sizeX[0] = DataTools.read2UnsignedBytes(in, true); 
-        core.sizeY[0] = DataTools.read2UnsignedBytes(in, true); 
+        core.sizeX[0] = in.readShort(); 
+        core.sizeY[0] = in.readShort(); 
         iCount++; 
       }

trunk/loci/formats/in/ZeissLSMReader.java

@@ -159 +159 @@
 
       RandomAccessStream ras = new RandomAccessStream(cz);
-
-      put("MagicNumber", DataTools.read4UnsignedBytes(ras, little));
-      put("StructureSize", DataTools.read4SignedBytes(ras, little));
-      put("DimensionX", DataTools.read4SignedBytes(ras, little));
-      put("DimensionY", DataTools.read4SignedBytes(ras, little));
-
-      core.sizeZ[0] = DataTools.read4SignedBytes(ras, little);
-      int c = DataTools.read4SignedBytes(ras, little);
-      core.sizeT[0] = DataTools.read4SignedBytes(ras, little);
+      ras.order(little);
+
+      put("MagicNumber", ras.readInt());
+      put("StructureSize", ras.readInt());
+      put("DimensionX", ras.readInt());
+      put("DimensionY", ras.readInt());
+
+      core.sizeZ[0] = ras.readInt();
+      int c = ras.readInt();
+      core.sizeT[0] = ras.readInt();
 
       if (c > core.sizeC[0] || c != 1) core.sizeC[0] = c;
@@ -188 +189 @@
       put("DimensionTime", core.sizeT[0]);
 
-      int dataType = DataTools.read4SignedBytes(ras, little);
+      int dataType = ras.readInt();
       switch (dataType) {
         case 1:
@@ -214 +215 @@
         int[] bps = TiffTools.getBitsPerSample(ifd);
         switch (bps[0]) {
-          case 8:
-            core.pixelType[0] = FormatTools.UINT8;
-            break;
           case 16:
             core.pixelType[0] = FormatTools.UINT16;
@@ -228 +226 @@
       }
 
-      put("ThumbnailX", DataTools.read4SignedBytes(ras, little));
-      put("ThumbnailY", DataTools.read4SignedBytes(ras, little));
-
-      put("VoxelSizeX", DataTools.readDouble(ras, little));
-      put("VoxelSizeY", DataTools.readDouble(ras, little));
-      put("VoxelSizeZ", DataTools.readDouble(ras, little));
-
-      put("OriginX", DataTools.readDouble(ras, little));
-      put("OriginY", DataTools.readDouble(ras, little));
-      put("OriginZ", DataTools.readDouble(ras, little));
-
-      int scanType = DataTools.read2UnsignedBytes(ras, little);
+      put("ThumbnailX", ras.readInt());
+      put("ThumbnailY", ras.readInt());
+
+      put("VoxelSizeX", ras.readDouble());
+      put("VoxelSizeY", ras.readDouble());
+      put("VoxelSizeZ", ras.readDouble());
+
+      put("OriginX", ras.readDouble());
+      put("OriginY", ras.readDouble());
+      put("OriginZ", ras.readDouble());
+
+      int scanType = ras.readShort();
       switch (scanType) {
         case 0:
@@ -307 +305 @@
       }
 
-      int spectralScan = DataTools.read2UnsignedBytes(ras, little);
+      int spectralScan = ras.readShort();
       switch (spectralScan) {
         case 0:
@@ -319 +317 @@
       }
 
-      long type = DataTools.read4UnsignedBytes(ras, little);
+      long type = ras.readInt();
       switch ((int) type) {
         case 0:
@@ -334 +332 @@
       }
 
-      long overlayOffset = DataTools.read4UnsignedBytes(ras, little);
-      long inputLUTOffset = DataTools.read4UnsignedBytes(ras, little);
-      long outputLUTOffset = DataTools.read4UnsignedBytes(ras, little);
-      long channelColorsOffset = DataTools.read4UnsignedBytes(ras, little);
-
-      put("TimeInterval", DataTools.readDouble(ras, little));
-
-      long channelDataTypesOffset = DataTools.read4UnsignedBytes(ras, little);
-      long scanInformationOffset = DataTools.read4UnsignedBytes(ras, little);
-      long ksDataOffset = DataTools.read4UnsignedBytes(ras, little);
-      long timeStampOffset = DataTools.read4UnsignedBytes(ras, little);
-      long eventListOffset = DataTools.read4UnsignedBytes(ras, little);
-      long roiOffset = DataTools.read4UnsignedBytes(ras, little);
-      long bleachRoiOffset = DataTools.read4UnsignedBytes(ras, little);
-      long nextRecordingOffset = DataTools.read4UnsignedBytes(ras, little);
-
-      put("DisplayAspectX", DataTools.readDouble(ras, little));
-      put("DisplayAspectY", DataTools.readDouble(ras, little));
-      put("DisplayAspectZ", DataTools.readDouble(ras, little));
-      put("DisplayAspectTime", DataTools.readDouble(ras, little));
-
-      long meanOfRoisOverlayOffset = DataTools.read4UnsignedBytes(ras, little);
-      long topoIsolineOverlayOffset = DataTools.read4UnsignedBytes(ras, little);
-      long topoProfileOverlayOffset = DataTools.read4UnsignedBytes(ras, little);
-      long linescanOverlayOffset = DataTools.read4UnsignedBytes(ras, little);
-
-      put("ToolbarFlags", DataTools.read4UnsignedBytes(ras, little));
-      long channelWavelengthOffset = DataTools.read4UnsignedBytes(ras, little);
-      long channelFactorsOffset = DataTools.read4UnsignedBytes(ras, little);
-
-      double objectiveSphereCorrection = DataTools.readDouble(ras, little);
-      long unmixParamsOffset = DataTools.read4UnsignedBytes(ras, little);
+      long overlayOffset = ras.readInt();
+      long inputLUTOffset = ras.readInt();
+      long outputLUTOffset = ras.readInt();
+      long channelColorsOffset = ras.readInt();
+
+      put("TimeInterval", ras.readDouble());
+
+      long channelDataTypesOffset = ras.readInt();
+      long scanInformationOffset = ras.readInt();
+      long ksDataOffset = ras.readInt();
+      long timeStampOffset = ras.readInt();
+      long eventListOffset = ras.readInt();
+      long roiOffset = ras.readInt();
+      long bleachRoiOffset = ras.readInt();
+      long nextRecordingOffset = ras.readInt();
+
+      put("DisplayAspectX", ras.readDouble());
+      put("DisplayAspectY", ras.readDouble());
+      put("DisplayAspectZ", ras.readDouble());
+      put("DisplayAspectTime", ras.readDouble());
+
+      long meanOfRoisOverlayOffset = ras.readInt();
+      long topoIsolineOverlayOffset = ras.readInt();
+      long topoProfileOverlayOffset = ras.readInt();
+      long linescanOverlayOffset = ras.readInt();
+
+      put("ToolbarFlags", ras.readInt());
+      long channelWavelengthOffset = ras.readInt();
+      long channelFactorsOffset = ras.readInt();
+
+      double objectiveSphereCorrection = ras.readDouble();
+      long unmixParamsOffset = ras.readInt();
 
       // read referenced structures
@@ -420 +418 @@
       if (timeStampOffset != 0) {
         in.seek(timeStampOffset);
-        int blockSize = DataTools.read4SignedBytes(in, little);
-        int numberOfStamps = DataTools.read4SignedBytes(in, little);
+        int blockSize = in.readInt();
+        int numberOfStamps = in.readInt();
         for (int i=0; i<numberOfStamps; i++) {
-          put("TimeStamp" + i, DataTools.readDouble(in, little));
+          put("TimeStamp" + i, in.readDouble());
         }
       }

trunk/loci/formats/ome/OMEXMLMetadataStore.java

@@ -29 +29 @@
 import java.io.IOException;
 import java.lang.reflect.Constructor;
-import java.util.Arrays;
-import java.util.Vector;
+import java.util.*;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
@@ -96 +95 @@
   }
 
-  /** Creates a new key/value pair. */
-  public void setOriginalMetadata(String key, String value) {
-    if (firstImageCA == null) { 
-      ImageNode image = (ImageNode) getChild(root, "Image", 0);
-      CustomAttributesNode ca = 
-        (CustomAttributesNode) getChild(image, "CustomAttributes", 0);
-      firstImageCA = ca.getDOMElement();
-
-      Vector original = DOMUtil.getChildElements("OriginalMetadata", 
-        ca.getDOMElement());
-      if (original.size() == 0) {
-        Element el = DOMUtil.createChild(root.getDOMElement(),
-          "SemanticTypeDefinitions");
-        OMEXMLNode node = OMEXMLNode.createNode(el);
-        node.setAttribute("xmlns",
-          "http://www.openmicroscopy.org/XMLschemas/STD/RC2/STD.xsd");
-        el = DOMUtil.createChild(el, "SemanticType");
-        node = OMEXMLNode.createNode(el);
-        node.setAttribute("Name", "OriginalMetadata");
-        node.setAttribute("AppliesTo", "I");
-
-        Element nameElement = DOMUtil.createChild(el, "Element");
-        OMEXMLNode nameNode = OMEXMLNode.createNode(nameElement);
-        nameNode.setAttribute("Name", "name");
-        nameNode.setAttribute("DBLocation", "ORIGINAL_METADATA.NAME");
-        nameNode.setAttribute("DataType", "string");
-
-        Element valueElement = DOMUtil.createChild(el, "Element");
-        OMEXMLNode valueNode = OMEXMLNode.createNode(valueElement);
-        valueElement.setAttribute("Name", "value");
-        valueElement.setAttribute("DBLocation", "ORIGINAL_METADATA.VALUE");
-        valueElement.setAttribute("DataType", "string");
-      }
-    }
-
-    Element el = DOMUtil.createChild(firstImageCA, "OriginalMetadata");
-    OMEXMLNode node = new AttributeNode(el);
-    node.setAttribute("name", key);
-    node.setAttribute("value", value);
+  /** 
+   * Add each of the key/value pairs in the hashtable as a new
+   * OriginalMetadata node.
+   */
+  public void populateOriginalMetadata(Hashtable h) {
+    ImageNode image = (ImageNode) getChild(root, "Image", 0);
+    CustomAttributesNode ca = 
+      (CustomAttributesNode) getChild(image, "CustomAttributes", 0);
+    firstImageCA = ca.getDOMElement();
+
+    Vector original = DOMUtil.getChildElements("OriginalMetadata", 
+      ca.getDOMElement());
+    if (original.size() == 0) {
+      Element el = DOMUtil.createChild(root.getDOMElement(),
+        "SemanticTypeDefinitions");
+      OMEXMLNode node = OMEXMLNode.createNode(el);
+      node.setAttribute("xmlns",
+        "http://www.openmicroscopy.org/XMLschemas/STD/RC2/STD.xsd");
+      el = DOMUtil.createChild(el, "SemanticType");
+      node = OMEXMLNode.createNode(el);
+      node.setAttribute("Name", "OriginalMetadata");
+      node.setAttribute("AppliesTo", "I");
+
+      Element nameElement = DOMUtil.createChild(el, "Element");
+      OMEXMLNode nameNode = OMEXMLNode.createNode(nameElement);
+      nameNode.setAttribute("Name", "name");
+      nameNode.setAttribute("DBLocation", "ORIGINAL_METADATA.NAME");
+      nameNode.setAttribute("DataType", "string");
+
+      Element valueElement = DOMUtil.createChild(el, "Element");
+      OMEXMLNode valueNode = OMEXMLNode.createNode(valueElement);
+      valueElement.setAttribute("Name", "value");
+      valueElement.setAttribute("DBLocation", "ORIGINAL_METADATA.VALUE");
+      valueElement.setAttribute("DataType", "string");
+    }
+
+    Object[] keys = h.keySet().toArray();
+    for (int i=0; i<h.size(); i++) {
+      Element el = DOMUtil.createChild(firstImageCA, "OriginalMetadata");
+      OMEXMLNode node = new AttributeNode(el);
+      node.setAttribute("name", keys[i].toString());
+      node.setAttribute("value", h.get(keys[i]).toString());
+    } 
   }
 

trunk/loci/formats/test/ConfigurationFiles.java

@@ -141 +141 @@
               s.substring(ndx, s.indexOf(" ", ndx)));
             ndx = s.indexOf("little") + 7;
-            entry.littleEndian[i] = s.substring(ndx).equals("true");
+            entry.littleEndian[i] = 
+              s.substring(ndx, s.indexOf(" ", ndx)).equals("true");
             ndx = s.indexOf("md5") + 4;
-            entry.md5[i] = s.substring(ndx, s.indexOf(" ", ndx));
+            entry.md5[i] = s.substring(ndx);
           }