/* * #%L * OME Bio-Formats package for reading and converting biological file formats. * %% * Copyright (C) 2005 - 2015 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% */ import java.io.*; import loci.formats.in.SDTReader; /** * Reads SDT files and creates text files containing histogram data. */ public class ExtractSDTData { public static void main(String[] args) throws Exception { if (args.length < 1) { System.out.println("Usage: java ExtractSDTData file.sdt"); System.exit(1); } String id = args[0]; String tid = id.substring(0, id.indexOf(".")); SDTReader r = new SDTReader(); r.setId(id); int bins = r.getTimeBinCount(); int chan = r.getChannelCount(); int w = r.getSizeX(); int h = r.getSizeY(); System.out.println("Data is " + w + " x " + h + ", bins=" + bins + ", channels=" + chan); byte[][] data = new byte[chan][h * w * bins * 2]; for (int c=0; c<chan; c++) { System.out.println("Reading channel #" + c + "..."); r.openBytes(c, data[c]); int i = 0; for (int y=0; y<h; y++) { for (int x=0; x<w; x++) { String oid = tid + "-c" + c + "-row" + y + "-col" + x; System.out.println(oid); PrintWriter out = new PrintWriter(new FileWriter(oid)); for (int b=0; b<bins; b++) { i += 2; int v0 = data[c][i]; int v1 = data[c][i + 1]; int v = (v0 << 8) & v1; out.println(b + " " + v); } out.close(); } } } } }