Merge pull request #1245 from imunro/develop-PQBin

Add reader for PicoQuant .bin files.

components/formats-api/src/loci/formats/readers.txt

@@ -87,6 +87,7 @@ loci.formats.in.FakeReader            # fake
 loci.formats.in.AFIReader             # afi
 loci.formats.in.ImspectorReader       # msr
 loci.formats.in.BioRadSCNReader       # scn
+loci.formats.in.PQBinReader           # bin
 
 # multi-extension messes
 loci.formats.in.JEOLReader            # dat, img, par

components/formats-gpl/src/loci/formats/in/PQBinReader.java

@@ -0,0 +1,270 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2014 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 2 of the 
+ * License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-2.0.html>.
+ * #L%
+ */
+
+package loci.formats.in;
+
+import java.io.IOException;
+
+import loci.common.RandomAccessInputStream;
+import loci.formats.CoreMetadata;
+import loci.formats.FormatException;
+import loci.formats.FormatReader;
+import loci.formats.FormatTools;
+import loci.formats.MetadataTools;
+import loci.formats.meta.MetadataStore;
+import ome.xml.model.primitives.PositiveFloat;
+
+/**
+ * PQBinReader is the file format reader for PicoQuant .bin files.
+ *
+ * <dl><dt><b>Source code:</b></dt>
+ * <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/PQBinReader.java">Trac</a>,
+ * <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/PQBinReader.java;hb=HEAD">Gitweb</a></dd></dl>
+ *
+ * Please Note: This format holds FLIM data arranged so that each decay is stored contiguously. 
+ * Therefore, as in other FLIM format readers e.g. SDTReader.java, on the first call to openBytes
+ * the whole data cube ( x,y,t) (NB actually t not real-time T) is loaded from the file to  a buffer.
+ * On further calls to openBytes the appropriate 2D (x,y)plane (timebin) is returned from this buffer.
+ * This is in the interest of significantly improved  performance when all the planes are requested one after another.
+ * There will be a performance cost if a single plane is requested but this is highly unlikely for FLIM data.
+ *
+ */
+public class PQBinReader extends FormatReader {
+
+  // -- Constants --
+
+  public static final int HEADER_SIZE = 20;
+
+  // -- Fields --
+  /*
+   * Number of time bins in lifetime histogram. 
+   */
+  protected int timeBins;
+
+  /*
+   * Array to hold re-ordered data for all the timeBins
+   */
+  protected byte[] dataStore = null;
+
+  /**
+   * Whether to pre-load all lifetime bins for faster loading.
+   */
+  protected boolean preLoad = true;
+
+  // -- Constructor --
+  /**
+   * Constructs a new PQBin reader.
+   */
+  public PQBinReader() {
+    super("PicoQuant Bin", "bin");
+    domains = new String[]{FormatTools.FLIM_DOMAIN};
+    suffixSufficient = false;
+  }
+
+  // -- IFormatReader API methods --
+
+  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
+  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
+
+    long fileLength = stream.length();
+    int bpp = FormatTools.getBytesPerPixel(FormatTools.UINT32);
+    stream.order(true);
+    // Header
+    int sizeX = stream.readInt();
+    int sizeY = stream.readInt();
+    float pixResol = stream.readFloat();  // resolution of time axis of every Decay (in ns)
+    int sizeT = stream.readInt();     
+    if (( sizeX * sizeY * sizeT * bpp) + HEADER_SIZE  == fileLength)  {
+      return true;
+    }
+    else  {
+      return false;
+    } 
+  }
+
+  /**
+   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
+   */
+  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
+    throws FormatException, IOException
+  {
+    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
+
+
+    int sizeX = getSizeX();
+    int sizeY = getSizeY();
+    int bpp = FormatTools.getBytesPerPixel(getPixelType());
+    boolean little = isLittleEndian();
+
+    int planeSize = sizeX * sizeY * timeBins * bpp;
+    int timeBin = no;
+
+    int binSize = sizeX * sizeY  * bpp;  // size in Bytes of a single 2D timebin.
+
+    // if data is of a manageable size then pre-load for performance
+    if (preLoad)  {
+      if (dataStore == null)
+      {
+        // The whole plane (all timebins) is  copied into storage
+        // to allow different sub-plane sizes to be used for different timebins
+        dataStore = new byte[planeSize];
+        byte[] rowBuf = new byte[bpp * timeBins * sizeX];
+        in.seek(HEADER_SIZE);
+
+        for (int row = 0; row < sizeY; row++) {
+          in.read(rowBuf);
+
+          int input = 0;
+          for (int col = 0; col < sizeX; col++) {
+            // set output to first pixel of this row in 2D plane
+            // corresponding to zeroth timeBin
+            int output = (row * sizeX + col) * bpp;
+
+            for (int t = 0; t < timeBins; t++) {
+              for (int bb = 0; bb < bpp; bb++) {
+                dataStore[output + bb] = rowBuf[input + bb];
+              }
+              output += binSize;
+              input += bpp;
+            }
+          }
+        }
+      }
+        // chanStore loaded
+
+        // copy 2D plane  from chanStore  into buf
+      int iLineSize = sizeX * bpp;
+      int oLineSize = w * bpp;
+      // offset to correct timebin yth line and xth pixel
+      int input = (binSize * timeBin) + (y * iLineSize) + (x * bpp);
+      int output = 0;
+
+      for (int row = 0; row < h; row++) {
+        System.arraycopy(dataStore, input, buf, output, oLineSize);
+        input += iLineSize;
+        output += oLineSize;
+      }
+    }    // endif preLoad
+    else  {   // load each plane individually for large data
+
+      byte[] rowBuf = new byte[bpp * timeBins * w];
+
+      in.seek(HEADER_SIZE +  (y * sizeX * bpp * timeBins));
+
+      for (int row = 0; row < h; row++) {
+        in.skipBytes(x * bpp * timeBins);
+        in.read(rowBuf);
+
+        for (int col = 0; col < w; col++) {
+          int output = (row * w + col) * bpp;
+          int input = (col * timeBins + timeBin) * bpp;
+          for (int bb = 0; bb < bpp; bb++) {
+            buf[output + bb] = rowBuf[input + bb];
+          }
+        }
+
+        in.skipBytes(bpp * timeBins * (sizeX - x - w));
+      }
+    }  // end else
+
+    return buf;
+  }
+
+  /* @see loci.formats.IFormatReader#close(boolean) */
+  public void close(boolean fileOnly) throws IOException {
+    super.close(fileOnly);
+    if (!fileOnly) {
+      // init preLoading
+      dataStore = null;
+      timeBins = 0;
+      preLoad = true;
+    }
+  }
+
+  // -- Internal FormatReader API methods --
+
+  /* @see loci.formats.FormatReader#initFile(String) */
+  protected void initFile(String id) throws FormatException, IOException {
+    super.initFile(id);
+    in = new RandomAccessInputStream(id);
+
+    CoreMetadata m = core.get(0);
+
+    m.littleEndian = true;
+    in.order(isLittleEndian());
+
+    LOGGER.info("Reading header PQBin");
+
+    // Header
+    m.sizeX = in.readInt();
+    m.sizeY = in.readInt();
+    float pixResol = in.readFloat();    // Resolution of every Pixel in Image (in µm)
+    m.sizeT = in.readInt();             // Number of DataPoints per Decay
+
+    float timeResol = in.readFloat();   // resolution of time axis of every Decay (in ns)
+
+    timeBins = m.sizeT;
+
+    m.sizeZ = 1;
+    m.sizeC = 1;
+    m.dimensionOrder = "XYZCT";
+
+    m.pixelType = FormatTools.UINT32;
+    m.rgb = false;
+    m.imageCount = m.sizeT;
+    m.indexed = false;
+    m.falseColor = false;
+    m.metadataComplete = true;
+
+    m.moduloT.type = FormatTools.LIFETIME;
+    m.moduloT.parentType = FormatTools.SPECTRA;
+    m.moduloT.typeDescription = "TCSPC";
+    m.moduloT.start = 0;
+
+    float timeBase = timeResol * 1000;  // Convert to ps
+
+    m.moduloT.step = timeBase / timeBins;
+    m.moduloT.end = m.moduloT.step * (m.sizeT - 1);
+    m.moduloT.unit = "ps";
+
+    // disable pre-load mode for very large files
+    // threshold is set to smaller than the  size of the largest test file currently available
+    if ( m.sizeX * m.sizeY * m.sizeT  >  (900 * 200 * 200))  {
+      preLoad = false;
+    }
+    else  {
+      preLoad = true;
+    }
+
+    MetadataStore store = makeFilterMetadata();
+    MetadataTools.populatePixels(store, this);
+
+    PositiveFloat pRpf = new PositiveFloat((double)pixResol);
+    store.setPixelsPhysicalSizeX(pRpf, 0);
+    store.setPixelsPhysicalSizeY(pRpf, 0);
+
+  }
+
+}

components/formats-gpl/src/loci/formats/in/SDTReader.java

@@ -2,7 +2,7 @@
  * #%L
  * OME Bio-Formats package for reading and converting biological file formats.
  * %%
- * Copyright (C) 2005 - 2013 Open Microscopy Environment:
+ * Copyright (C) 2005 - 2014 Open Microscopy Environment:
  *   - Board of Regents of the University of Wisconsin-Madison
  *   - Glencoe Software, Inc.
  *   - University of Dundee
@@ -340,6 +340,15 @@ protected void initFile(String id) throws FormatException, IOException {
     m.indexed = false;
     m.falseColor = false;
     m.metadataComplete = true;
+
+    // disable pre-load mode for very large files
+    // threshold is set to the size of the largest test file currently available
+    if ( m.sizeX * m.sizeY * m.sizeT  >  (512 * 512 * 512))  {
+      preLoad = false;
+    }
+    else  {
+      preLoad = true;
+    }
 
     if (intensity) {
       m.moduloT.parentType = FormatTools.SPECTRA;