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Add reader for PicoQuant .bin files. #1245
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/* | ||
* #%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% | ||
*/ | ||
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package loci.formats.in; | ||
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import java.io.IOException; | ||
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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; | ||
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/** | ||
* 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 { | ||
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// -- Constants -- | ||
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public static final int HEADER_SIZE = 20; | ||
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// -- Fields -- | ||
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/* | ||
* Number of time bins in lifetime histogram. | ||
*/ | ||
protected int timeBins; | ||
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/* | ||
* Array to hold re-ordered data for all the timeBins in one channel | ||
*/ | ||
protected byte[] dataStore = null; | ||
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// -- Constructor -- | ||
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/** Constructs a new UBM reader. */ | ||
public PQBinReader() { | ||
super("PicoQuant Bin", "bin"); | ||
domains = new String[] {FormatTools.FLIM_DOMAIN}; | ||
suffixSufficient = false; | ||
} | ||
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// -- IFormatReader API methods -- | ||
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/* @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; | ||
} | ||
} | ||
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/** | ||
* @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); | ||
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int sizeX = getSizeX(); | ||
int sizeY = getSizeY(); | ||
int bpp = FormatTools.getBytesPerPixel(getPixelType()); | ||
boolean little = isLittleEndian(); | ||
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int planeSize = sizeX * sizeY * timeBins * bpp; | ||
int timeBin = no; | ||
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byte[] rowBuf = new byte[bpp * timeBins * sizeX]; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Maybe move this array allocation to the |
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int binSize = sizeX * sizeY * bpp; // size in Bytes of a single 2D timebin. | ||
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if (dataStore == null) | ||
{ | ||
// The whole plane (all timebins) is copied into storage | ||
// to allow different sub-plane sizes to be used for different timebins | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I'm a little concerned about the memory usage here. For now, it's probably fine, as the largest file we have is 197MB, but going forward it may be worth trying to limit the number of timebins that are cached (e.g. read at most 128 at a time). |
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dataStore = new byte[planeSize]; | ||
in.seek(HEADER_SIZE); | ||
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for (int row = 0; row < sizeY; row++) { | ||
in.read(rowBuf); | ||
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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; | ||
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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 | ||
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// 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; | ||
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for (int row = 0; row < h; row++) { | ||
System.arraycopy(dataStore, input, buf, output, oLineSize); | ||
input += iLineSize; | ||
output += oLineSize; | ||
} | ||
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return buf; | ||
} | ||
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/* @see loci.formats.IFormatReader#close(boolean) */ | ||
public void close(boolean fileOnly) throws IOException { | ||
super.close(fileOnly); | ||
if (!fileOnly) { | ||
// init preLoading | ||
dataStore = null; | ||
timeBins = 0; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
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} | ||
} | ||
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// -- Internal FormatReader API methods -- | ||
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/* @see loci.formats.FormatReader#initFile(String) */ | ||
protected void initFile(String id) throws FormatException, IOException { | ||
super.initFile(id); | ||
in = new RandomAccessInputStream(id); | ||
in.order(true); | ||
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CoreMetadata m = core.get(0); | ||
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m.littleEndian = true; | ||
in.order(isLittleEndian()); | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. No need to have multiple calls to |
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LOGGER.info("Reading header PQBin"); | ||
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// Header | ||
m.sizeX = in.readInt(); | ||
m.sizeY = in.readInt(); | ||
float pixResol = in.readFloat(); // resolution of time axis of every Decay (in ns) | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Is this the physical pixel width and height? The time resolution appears to be read later. There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. It is! |
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m.sizeT = in.readInt(); // Number of DataPoints per Decay | ||
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float timeResol = in.readFloat(); // resolution of time axis of every Decay (in ns) | ||
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timeBins = m.sizeT; | ||
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m.sizeZ = 1; | ||
m.sizeC = 1; | ||
m.dimensionOrder = "XYZCT"; | ||
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m.pixelType = FormatTools.UINT32; | ||
m.rgb = false; | ||
m.littleEndian = true; | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. No need to set |
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m.imageCount = m.sizeT; | ||
m.indexed = false; | ||
m.falseColor = false; | ||
m.metadataComplete = true; | ||
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m.moduloT.type = FormatTools.LIFETIME; | ||
m.moduloT.parentType = FormatTools.SPECTRA; | ||
m.moduloT.typeDescription = "TCSPC"; | ||
m.moduloT.start = 0; | ||
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float timeBase = timeResol * 1000; // Convert to ps | ||
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m.moduloT.step = timeBase / timeBins; | ||
m.moduloT.end = m.moduloT.step * (m.sizeT - 1); | ||
m.moduloT.unit = "ps"; | ||
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MetadataStore store = makeFilterMetadata(); | ||
MetadataTools.populatePixels(store, this); | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Can At a minimum, it would be useful to have both values in the original metadata table. |
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} | ||
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} |
There was a problem hiding this comment.
Choose a reason for hiding this comment
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This comment should probably reference the correct reader.