Java tutorial
/* * #%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% */ package loci.formats.in; import java.io.File; import java.io.IOException; import java.text.DecimalFormatSymbols; import java.util.Arrays; import java.util.ArrayList; import java.util.HashSet; import java.util.Set; import java.util.Vector; import org.joda.time.DateTime; import org.joda.time.DateTimeZone; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import loci.common.DataTools; import loci.common.DateTools; import loci.common.Location; import loci.common.RandomAccessInputStream; import loci.common.xml.XMLTools; import loci.formats.CoreMetadata; import loci.formats.FormatException; import loci.formats.FormatTools; import loci.formats.MetadataTools; import loci.formats.meta.MetadataStore; import loci.formats.tiff.IFD; import loci.formats.tiff.IFDList; import loci.formats.tiff.PhotoInterp; import loci.formats.tiff.TiffIFDEntry; import loci.formats.tiff.TiffParser; import loci.formats.tiff.TiffRational; import ome.xml.model.primitives.PositiveFloat; import ome.xml.model.primitives.PositiveInteger; import ome.xml.model.primitives.Timestamp; import ome.units.quantity.Frequency; import ome.units.quantity.Length; import ome.units.quantity.Temperature; import ome.units.quantity.Time; import ome.units.UNITS; /** * Reader is the file format reader for Metamorph STK files. * * @author Eric Kjellman egkjellman at wisc.edu * @author Melissa Linkert melissa at glencoesoftware.com * @author Curtis Rueden ctrueden at wisc.edu * @author Sebastien Huart Sebastien dot Huart at curie.fr */ public class MetamorphReader extends BaseTiffReader { // -- Constants -- /** Logger for this class. */ private static final Logger LOGGER = LoggerFactory.getLogger(MetamorphReader.class); public static final String SHORT_DATE_FORMAT = "yyyyMMdd HH:mm:ss"; public static final String LONG_DATE_FORMAT = "dd/MM/yyyy HH:mm:ss"; public static final String[] ND_SUFFIX = { "nd" }; public static final String[] STK_SUFFIX = { "stk", "tif", "tiff" }; // IFD tag numbers of important fields private static final int METAMORPH_ID = 33628; private static final int UIC1TAG = METAMORPH_ID; private static final int UIC2TAG = 33629; private static final int UIC3TAG = 33630; private static final int UIC4TAG = 33631; // -- Fields -- /** The TIFF's name */ private String imageName; /** The TIFF's creation date */ private String imageCreationDate; /** The TIFF's emWavelength */ private long[] emWavelength; private double[] wave; private String binning; private double zoom, stepSize; private Double exposureTime; private Vector<String> waveNames; private Vector<String> stageNames; private long[] internalStamps; private double[] zDistances; private Length[] stageX, stageY; private double zStart; private Double sizeX = null, sizeY = null; private double tempZ; private boolean validZ; private Double gain; private int mmPlanes; //number of metamorph planes private MetamorphReader[][] stkReaders; /** List of STK files in the dataset. */ private String[][] stks; private String ndFilename; private boolean canLookForND = true; private boolean[] firstSeriesChannels; private boolean bizarreMultichannelAcquisition = false; private int openFiles = 0; private boolean hasStagePositions = false; private boolean hasChipOffsets = false; private boolean hasAbsoluteZ = false; private boolean hasAbsoluteZValid = false; // -- Constructor -- /** Constructs a new Metamorph reader. */ public MetamorphReader() { super("Metamorph STK", new String[] { "stk", "nd", "tif", "tiff" }); domains = new String[] { FormatTools.LM_DOMAIN }; hasCompanionFiles = true; suffixSufficient = false; datasetDescription = "One or more .stk or .tif/.tiff files plus an " + "optional .nd file"; } // -- IFormatReader API methods -- /* @see loci.formats.IFormatReader#isThisType(String, boolean) */ @Override public boolean isThisType(String name, boolean open) { Location location = new Location(name); if (!location.exists()) { return false; } if (checkSuffix(name, "nd")) return true; if (open) { location = location.getAbsoluteFile(); Location parent = location.getParentFile(); String baseName = location.getName(); while (baseName.indexOf("_") >= 0) { baseName = baseName.substring(0, baseName.lastIndexOf("_")); if (checkSuffix(name, suffixes) && (new Location(parent, baseName + ".nd").exists() || new Location(parent, baseName + ".ND").exists())) { return true; } if (checkSuffix(name, suffixes) && (new Location(parent, baseName + ".htd").exists() || new Location(parent, baseName + ".HTD").exists())) { return false; } } } return super.isThisType(name, open); } /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */ @Override public boolean isThisType(RandomAccessInputStream stream) throws IOException { TiffParser tp = new TiffParser(stream); IFD ifd = tp.getFirstIFD(); if (ifd == null) return false; String software = ifd.getIFDTextValue(IFD.SOFTWARE); boolean validSoftware = software != null && software.trim().toLowerCase().startsWith("metamorph"); return validSoftware || (ifd.containsKey(UIC1TAG) && ifd.containsKey(UIC3TAG) && ifd.containsKey(UIC4TAG)); } /* @see loci.formats.IFormatReader#isSingleFile(String) */ @Override public boolean isSingleFile(String id) throws FormatException, IOException { return !checkSuffix(id, ND_SUFFIX); } /* @see loci.formats.IFormatReader#fileGroupOption(String) */ @Override public int fileGroupOption(String id) throws FormatException, IOException { if (checkSuffix(id, ND_SUFFIX)) return FormatTools.MUST_GROUP; Location l = new Location(id).getAbsoluteFile(); String[] files = l.getParentFile().list(); for (String file : files) { if (checkSuffix(file, ND_SUFFIX) && l.getName().startsWith(file.substring(0, file.lastIndexOf(".")))) { return FormatTools.MUST_GROUP; } } return FormatTools.CANNOT_GROUP; } /* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */ @Override public String[] getSeriesUsedFiles(boolean noPixels) { FormatTools.assertId(currentId, true, 1); if (!noPixels && stks == null) return new String[] { currentId }; else if (stks == null) return new String[0]; Vector<String> v = new Vector<String>(); if (ndFilename != null) v.add(ndFilename); if (!noPixels) { for (String stk : stks[getSeries()]) { if (stk != null && new Location(stk).exists()) { v.add(stk); } } } return v.toArray(new String[v.size()]); } /** * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */ @Override public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException { FormatTools.assertId(currentId, true, 1); if (stks == null) { return super.openBytes(no, buf, x, y, w, h); } int[] coords = FormatTools.getZCTCoords(this, no % getSizeZ()); int ndx = no / getSizeZ(); if (bizarreMultichannelAcquisition) { int[] pos = getZCTCoords(no); ndx = getIndex(pos[0], 0, pos[2]) / getSizeZ(); } if (stks[getSeries()].length == 1) ndx = 0; String file = stks[getSeries()][ndx]; if (file == null) return buf; // the original file is a .nd file, so we need to construct a new reader // for the constituent STK files stkReaders[getSeries()][ndx].setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM)); int plane = stks[getSeries()].length == 1 ? no : coords[0]; try { if (!file.equals(stkReaders[getSeries()][ndx].getCurrentFile())) { openFiles++; } stkReaders[getSeries()][ndx].setId(file); if (bizarreMultichannelAcquisition) { int realX = getZCTCoords(no)[1] == 0 ? x : x + getSizeX(); stkReaders[getSeries()][ndx].openBytes(plane, buf, realX, y, w, h); } else { stkReaders[getSeries()][ndx].openBytes(plane, buf, x, y, w, h); } } finally { int count = stkReaders[getSeries()][ndx].getImageCount(); if (plane == count - 1 || openFiles > 128) { stkReaders[getSeries()][ndx].close(); openFiles--; } } return buf; } /* @see loci.formats.IFormatReader#close(boolean) */ @Override public void close(boolean fileOnly) throws IOException { super.close(fileOnly); if (stkReaders != null) { for (MetamorphReader[] s : stkReaders) { if (s != null) { for (MetamorphReader reader : s) { if (reader != null) reader.close(fileOnly); } } } } if (!fileOnly) { imageName = imageCreationDate = null; emWavelength = null; stks = null; mmPlanes = 0; ndFilename = null; wave = null; binning = null; zoom = stepSize = 0; exposureTime = null; waveNames = stageNames = null; internalStamps = null; zDistances = null; stageX = stageY = null; firstSeriesChannels = null; sizeX = sizeY = null; tempZ = 0d; validZ = false; stkReaders = null; gain = null; bizarreMultichannelAcquisition = false; openFiles = 0; hasStagePositions = false; hasChipOffsets = false; hasAbsoluteZ = false; hasAbsoluteZValid = false; } } // -- Internal FormatReader API methods -- /* @see loci.formats.FormatReader#initFile(String) */ @Override protected void initFile(String id) throws FormatException, IOException { if (checkSuffix(id, ND_SUFFIX)) { LOGGER.info("Initializing " + id); // find an associated STK file String stkFile = id.substring(0, id.lastIndexOf(".")); if (stkFile.indexOf(File.separator) != -1) { stkFile = stkFile.substring(stkFile.lastIndexOf(File.separator) + 1); } Location parent = new Location(id).getAbsoluteFile().getParentFile(); LOGGER.info("Looking for STK file in {}", parent.getAbsolutePath()); String[] dirList = parent.list(true); for (String f : dirList) { int underscore = f.indexOf("_"); if (underscore < 0) underscore = f.indexOf("."); if (underscore < 0) underscore = f.length(); String prefix = f.substring(0, underscore); if ((f.equals(stkFile) || stkFile.startsWith(prefix)) && checkSuffix(f, STK_SUFFIX)) { stkFile = new Location(parent.getAbsolutePath(), f).getAbsolutePath(); break; } } if (!checkSuffix(stkFile, STK_SUFFIX)) { throw new FormatException("STK file not found in " + parent.getAbsolutePath() + "."); } super.initFile(stkFile); } else super.initFile(id); Location ndfile = null; if (checkSuffix(id, ND_SUFFIX)) ndfile = new Location(id); else if (canLookForND && isGroupFiles()) { // an STK file was passed to initFile // let's check the parent directory for an .nd file Location stk = new Location(id).getAbsoluteFile(); String stkName = stk.getName(); String stkPrefix = stkName; if (stkPrefix.indexOf("_") >= 0) { stkPrefix = stkPrefix.substring(0, stkPrefix.indexOf("_") + 1); } Location parent = stk.getParentFile(); String[] list = parent.list(true); int matchingChars = 0; for (String f : list) { if (checkSuffix(f, ND_SUFFIX)) { String prefix = f.substring(0, f.lastIndexOf(".")); if (prefix.indexOf("_") >= 0) { prefix = prefix.substring(0, prefix.indexOf("_") + 1); } if (stkName.startsWith(prefix) || prefix.equals(stkPrefix)) { int charCount = 0; for (int i = 0; i < f.length(); i++) { if (i >= stkName.length()) { break; } if (f.charAt(i) == stkName.charAt(i)) { charCount++; } else { break; } } if (charCount > matchingChars || (charCount == matchingChars && f.charAt(charCount) == '.')) { ndfile = new Location(parent, f).getAbsoluteFile(); matchingChars = charCount; } } } } } String creationTime = null; if (ndfile != null && ndfile.exists() && (fileGroupOption(id) == FormatTools.MUST_GROUP || isGroupFiles())) { // parse key/value pairs from .nd file int zc = getSizeZ(), cc = getSizeC(), tc = getSizeT(); int nstages = 0; String z = null, c = null, t = null; Vector<Boolean> hasZ = new Vector<Boolean>(); waveNames = new Vector<String>(); stageNames = new Vector<String>(); boolean useWaveNames = true; ndFilename = ndfile.getAbsolutePath(); String[] lines = DataTools.readFile(ndFilename).split("\n"); boolean globalDoZ = true; boolean doTimelapse = false; StringBuilder currentValue = new StringBuilder(); String key = ""; for (String line : lines) { int comma = line.indexOf(","); if (comma <= 0) { currentValue.append("\n"); currentValue.append(line); continue; } String value = currentValue.toString(); addGlobalMeta(key, value); if (key.equals("NZSteps")) z = value; else if (key.equals("DoTimelapse")) { doTimelapse = Boolean.parseBoolean(value); } else if (key.equals("NWavelengths")) c = value; else if (key.equals("NTimePoints")) t = value; else if (key.startsWith("WaveDoZ")) { hasZ.add(new Boolean(value.toLowerCase())); } else if (key.startsWith("WaveName")) { String waveName = value.substring(1, value.length() - 1); if (waveName.equals("Both lasers") || waveName.startsWith("DUAL")) { bizarreMultichannelAcquisition = true; } waveNames.add(waveName); } else if (key.startsWith("Stage")) { stageNames.add(value); } else if (key.startsWith("StartTime")) { creationTime = value; } else if (key.equals("ZStepSize")) { value = value.replace(',', '.'); stepSize = Double.parseDouble(value); } else if (key.equals("NStagePositions")) { nstages = Integer.parseInt(value); } else if (key.equals("WaveInFileName")) { useWaveNames = Boolean.parseBoolean(value); } else if (key.equals("DoZSeries")) { globalDoZ = new Boolean(value.toLowerCase()); } key = line.substring(1, comma - 1).trim(); currentValue.delete(0, currentValue.length()); currentValue.append(line.substring(comma + 1).trim()); } if (!globalDoZ) { for (int i = 0; i < hasZ.size(); i++) { hasZ.set(i, false); } } // figure out how many files we need if (z != null) zc = Integer.parseInt(z); if (c != null) cc = Integer.parseInt(c); if (t != null) tc = Integer.parseInt(t); else if (!doTimelapse) { tc = 1; } if (cc == 0) cc = 1; if (cc == 1 && bizarreMultichannelAcquisition) { cc = 2; } if (tc == 0) { tc = 1; } int numFiles = cc * tc; if (nstages > 0) numFiles *= nstages; // determine series count int stagesCount = nstages == 0 ? 1 : nstages; int seriesCount = stagesCount; firstSeriesChannels = new boolean[cc]; Arrays.fill(firstSeriesChannels, true); boolean differentZs = false; for (int i = 0; i < cc; i++) { boolean hasZ1 = i < hasZ.size() && hasZ.get(i).booleanValue(); boolean hasZ2 = i != 0 && (i - 1 < hasZ.size()) && hasZ.get(i - 1).booleanValue(); if (i > 0 && hasZ1 != hasZ2 && globalDoZ) { if (!differentZs) seriesCount *= 2; differentZs = true; } } int channelsInFirstSeries = cc; if (differentZs) { channelsInFirstSeries = 0; for (int i = 0; i < cc; i++) { if ((!hasZ.get(0) && i == 0) || (hasZ.get(0) && hasZ.get(i).booleanValue())) { channelsInFirstSeries++; } else firstSeriesChannels[i] = false; } } stks = new String[seriesCount][]; if (seriesCount == 1) stks[0] = new String[numFiles]; else if (differentZs) { for (int i = 0; i < stagesCount; i++) { stks[i * 2] = new String[channelsInFirstSeries * tc]; stks[i * 2 + 1] = new String[(cc - channelsInFirstSeries) * tc]; } } else { for (int i = 0; i < stks.length; i++) { stks[i] = new String[numFiles / stks.length]; } } String prefix = ndfile.getPath(); prefix = prefix.substring(prefix.lastIndexOf(File.separator) + 1, prefix.lastIndexOf(".")); // build list of STK files boolean anyZ = hasZ.contains(Boolean.TRUE); int[] pt = new int[seriesCount]; for (int i = 0; i < tc; i++) { for (int s = 0; s < stagesCount; s++) { for (int j = 0; j < cc; j++) { boolean validZ = j >= hasZ.size() || hasZ.get(j).booleanValue(); int seriesNdx = s * (seriesCount / stagesCount); if ((seriesCount != 1 && (!validZ || (hasZ.size() > 0 && !hasZ.get(0)))) || (nstages == 0 && ((!validZ && cc > 1) || seriesCount > 1))) { if (anyZ && j > 0 && seriesNdx < seriesCount - 1 && (!validZ || !hasZ.get(0))) { seriesNdx++; } } if (seriesNdx >= stks.length || seriesNdx >= pt.length || pt[seriesNdx] >= stks[seriesNdx].length) { continue; } stks[seriesNdx][pt[seriesNdx]] = prefix; if (j < waveNames.size() && waveNames.get(j) != null) { stks[seriesNdx][pt[seriesNdx]] += "_w" + (j + 1); if (useWaveNames) { String waveName = waveNames.get(j); // If there are underscores in the wavelength name, translate // them to hyphens. (See #558) waveName = waveName.replace('_', '-'); // If there are slashes (forward or backward) in the wavelength // name, translate them to hyphens. (See #5922) waveName = waveName.replace('/', '-'); waveName = waveName.replace('\\', '-'); waveName = waveName.replace('(', '-'); waveName = waveName.replace(')', '-'); stks[seriesNdx][pt[seriesNdx]] += waveName; } } if (nstages > 0) { stks[seriesNdx][pt[seriesNdx]] += "_s" + (s + 1); } if (tc > 1 || doTimelapse) { stks[seriesNdx][pt[seriesNdx]] += "_t" + (i + 1) + ".STK"; } else stks[seriesNdx][pt[seriesNdx]] += ".STK"; pt[seriesNdx]++; } } } ndfile = ndfile.getAbsoluteFile(); // check that each STK file exists for (int s = 0; s < stks.length; s++) { for (int f = 0; f < stks[s].length; f++) { Location l = new Location(ndfile.getParent(), stks[s][f]); stks[s][f] = getRealSTKFile(l); } } String file = locateFirstValidFile(); if (file == null) { throw new FormatException("Unable to locate at least one valid STK file!"); } RandomAccessInputStream s = new RandomAccessInputStream(file, 16); TiffParser tp = new TiffParser(s); IFD ifd = tp.getFirstIFD(); CoreMetadata ms0 = core.get(0); s.close(); ms0.sizeX = (int) ifd.getImageWidth(); ms0.sizeY = (int) ifd.getImageLength(); if (bizarreMultichannelAcquisition) { ms0.sizeX /= 2; } ms0.sizeZ = hasZ.size() > 0 && !hasZ.get(0) ? 1 : zc; ms0.sizeC = cc; ms0.sizeT = tc; ms0.imageCount = getSizeZ() * getSizeC() * getSizeT(); ms0.dimensionOrder = "XYZCT"; if (stks != null && stks.length > 1) { // Note that core can't be replaced with newCore until the end of this block. ArrayList<CoreMetadata> newCore = new ArrayList<CoreMetadata>(); for (int i = 0; i < stks.length; i++) { CoreMetadata ms = new CoreMetadata(); newCore.add(ms); ms.sizeX = getSizeX(); ms.sizeY = getSizeY(); ms.sizeZ = getSizeZ(); ms.sizeC = getSizeC(); ms.sizeT = getSizeT(); ms.pixelType = getPixelType(); ms.imageCount = getImageCount(); ms.dimensionOrder = getDimensionOrder(); ms.rgb = isRGB(); ms.littleEndian = isLittleEndian(); ms.interleaved = isInterleaved(); ms.orderCertain = true; } if (stks.length > nstages) { for (int j = 0; j < stagesCount; j++) { int idx = j * 2 + 1; CoreMetadata midx = newCore.get(idx); CoreMetadata pmidx = newCore.get(j * 2); pmidx.sizeC = stks[j * 2].length / getSizeT(); midx.sizeC = stks[idx].length / midx.sizeT; midx.sizeZ = hasZ.size() > 1 && hasZ.get(1) && core.get(0).sizeZ == 1 ? zc : 1; pmidx.imageCount = pmidx.sizeC * pmidx.sizeT * pmidx.sizeZ; midx.imageCount = midx.sizeC * midx.sizeT * midx.sizeZ; } } core = newCore; } } if (stks == null) { stkReaders = new MetamorphReader[1][1]; stkReaders[0][0] = new MetamorphReader(); stkReaders[0][0].setCanLookForND(false); } else { stkReaders = new MetamorphReader[stks.length][]; for (int i = 0; i < stks.length; i++) { stkReaders[i] = new MetamorphReader[stks[i].length]; for (int j = 0; j < stkReaders[i].length; j++) { stkReaders[i][j] = new MetamorphReader(); stkReaders[i][j].setCanLookForND(false); if (j > 0) { stkReaders[i][j].setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM)); } } } } Vector<String> timestamps = null; MetamorphHandler handler = null; MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this, true); String detectorID = MetadataTools.createLSID("Detector", 0, 0); for (int i = 0; i < getSeriesCount(); i++) { setSeries(i); handler = new MetamorphHandler(getSeriesMetadata()); String instrumentID = MetadataTools.createLSID("Instrument", i); store.setInstrumentID(instrumentID, i); store.setImageInstrumentRef(instrumentID, i); if (i == 0) { store.setDetectorID(detectorID, 0, 0); store.setDetectorType(getDetectorType("Other"), 0, 0); } String comment = getFirstComment(i); if (comment != null && comment.startsWith("<MetaData>")) { try { XMLTools.parseXML(XMLTools.sanitizeXML(comment), handler); } catch (IOException e) { } } if (creationTime != null) { String date = DateTools.formatDate(creationTime, SHORT_DATE_FORMAT, "."); if (date != null) { store.setImageAcquisitionDate(new Timestamp(date), 0); } } store.setImageName(makeImageName(i).trim(), i); if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) { continue; } store.setImageDescription("", i); store.setImagingEnvironmentTemperature(new Temperature(handler.getTemperature(), UNITS.DEGREEC), i); if (sizeX == null) sizeX = handler.getPixelSizeX(); if (sizeY == null) sizeY = handler.getPixelSizeY(); Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX); Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY); if (physicalSizeX != null) { store.setPixelsPhysicalSizeX(physicalSizeX, i); } if (physicalSizeY != null) { store.setPixelsPhysicalSizeY(physicalSizeY, i); } if (zDistances != null) { stepSize = zDistances[0]; } Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize); if (physicalSizeZ != null) { store.setPixelsPhysicalSizeZ(physicalSizeZ, i); } String objectiveID = MetadataTools.createLSID("Objective", i, 0); store.setObjectiveID(objectiveID, i, 0); if (handler.getLensNA() != 0) { store.setObjectiveLensNA(handler.getLensNA(), i, 0); } store.setObjectiveSettingsID(objectiveID, i); int waveIndex = 0; for (int c = 0; c < getEffectiveSizeC(); c++) { if (firstSeriesChannels == null || (stageNames != null && stageNames.size() == getSeriesCount())) { waveIndex = c; } else if (firstSeriesChannels != null) { int s = i % 2; while (firstSeriesChannels[waveIndex] == (s == 1) && waveIndex < firstSeriesChannels.length) { waveIndex++; } } if (waveNames != null && waveIndex < waveNames.size()) { store.setChannelName(waveNames.get(waveIndex).trim(), i, c); } if (handler.getBinning() != null) binning = handler.getBinning(); if (binning != null) { store.setDetectorSettingsBinning(getBinning(binning), i, c); } if (handler.getReadOutRate() != 0) { store.setDetectorSettingsReadOutRate(new Frequency(handler.getReadOutRate(), UNITS.HZ), i, c); } if (gain == null) { gain = handler.getGain(); } if (gain != null) { store.setDetectorSettingsGain(gain, i, c); } store.setDetectorSettingsID(detectorID, i, c); if (wave != null && waveIndex < wave.length) { Length wavelength = FormatTools.getWavelength(wave[waveIndex]); if ((int) wave[waveIndex] >= 1) { // link LightSource to Image String lightSourceID = MetadataTools.createLSID("LightSource", i, c); store.setLaserID(lightSourceID, i, c); store.setChannelLightSourceSettingsID(lightSourceID, i, c); store.setLaserType(getLaserType("Other"), i, c); store.setLaserLaserMedium(getLaserMedium("Other"), i, c); if (wavelength != null) { store.setChannelLightSourceSettingsWavelength(wavelength, i, c); } } } waveIndex++; } timestamps = handler.getTimestamps(); for (int t = 0; t < timestamps.size(); t++) { String date = DateTools.convertDate(DateTools.getTime(timestamps.get(t), SHORT_DATE_FORMAT, "."), DateTools.UNIX, SHORT_DATE_FORMAT + ".SSS"); addSeriesMetaList("timestamp", date); } long startDate = 0; if (timestamps.size() > 0) { startDate = DateTools.getTime(timestamps.get(0), SHORT_DATE_FORMAT, "."); } final Length positionX = handler.getStagePositionX(); final Length positionY = handler.getStagePositionY(); Vector<Double> exposureTimes = handler.getExposures(); if (exposureTimes.size() == 0) { for (int p = 0; p < getImageCount(); p++) { exposureTimes.add(exposureTime); } } else if (exposureTimes.size() == 1 && exposureTimes.size() < getSizeC()) { for (int c = 1; c < getSizeC(); c++) { MetamorphHandler channelHandler = new MetamorphHandler(); String channelComment = getComment(i, c); if (channelComment != null && channelComment.startsWith("<MetaData>")) { try { XMLTools.parseXML(XMLTools.sanitizeXML(channelComment), channelHandler); } catch (IOException e) { } } Vector<Double> channelExpTime = channelHandler.getExposures(); exposureTimes.add(channelExpTime.get(0)); } } int lastFile = -1; IFDList lastIFDs = null; IFD lastIFD = null; long[] lastOffsets = null; double distance = zStart; TiffParser tp = null; RandomAccessInputStream stream = null; for (int p = 0; p < getImageCount(); p++) { int[] coords = getZCTCoords(p); Double deltaT = Double.valueOf(0); Double expTime = exposureTime; Double xmlZPosition = null; int fileIndex = getIndex(0, 0, coords[2]) / getSizeZ(); if (fileIndex >= 0) { String file = stks == null ? currentId : stks[i][fileIndex]; if (file != null) { if (fileIndex != lastFile) { if (stream != null) { stream.close(); } stream = new RandomAccessInputStream(file, 16); tp = new TiffParser(stream); tp.checkHeader(); IFDList f = tp.getIFDs(); if (f.size() > 0) { lastFile = fileIndex; lastIFDs = f; } else { file = null; stks[i][fileIndex] = null; } } } if (file != null) { lastIFD = lastIFDs.get(p % lastIFDs.size()); Object commentEntry = lastIFD.get(IFD.IMAGE_DESCRIPTION); if (commentEntry != null) { if (commentEntry instanceof String) { comment = (String) commentEntry; } else if (commentEntry instanceof TiffIFDEntry) { comment = tp.getIFDValue((TiffIFDEntry) commentEntry).toString(); } } if (comment != null) comment = comment.trim(); if (comment != null && comment.startsWith("<MetaData>")) { String[] lines = comment.split("\n"); timestamps = new Vector<String>(); for (String line : lines) { line = line.trim(); if (line.startsWith("<prop")) { int firstQuote = line.indexOf("\"") + 1; int lastQuote = line.lastIndexOf("\""); String key = line.substring(firstQuote, line.indexOf("\"", firstQuote)); String value = line.substring(line.lastIndexOf("\"", lastQuote - 1) + 1, lastQuote); if (key.equals("z-position")) { xmlZPosition = new Double(value); } else if (key.equals("acquisition-time-local")) { timestamps.add(value); } } } } } } int index = 0; if (timestamps.size() > 0) { if (coords[2] < timestamps.size()) index = coords[2]; String stamp = timestamps.get(index); long ms = DateTools.getTime(stamp, SHORT_DATE_FORMAT, "."); deltaT = new Double((ms - startDate) / 1000.0); } else if (internalStamps != null && p < internalStamps.length) { long delta = internalStamps[p] - internalStamps[0]; deltaT = new Double(delta / 1000.0); if (coords[2] < exposureTimes.size()) index = coords[2]; } if (index == 0 && p > 0 && exposureTimes.size() > 0) { index = coords[1] % exposureTimes.size(); } if (index < exposureTimes.size()) { expTime = exposureTimes.get(index); } if (deltaT != null) { store.setPlaneDeltaT(new Time(deltaT, UNITS.S), i, p); } if (expTime != null) { store.setPlaneExposureTime(new Time(expTime, UNITS.S), i, p); } if (stageX != null && p < stageX.length) { store.setPlanePositionX(stageX[p], i, p); } else if (positionX != null) { store.setPlanePositionX(positionX, i, p); } if (stageY != null && p < stageY.length) { store.setPlanePositionY(stageY[p], i, p); } else if (positionY != null) { store.setPlanePositionY(positionY, i, p); } if (zDistances != null && p < zDistances.length) { if (p > 0) { if (zDistances[p] != 0d) distance += zDistances[p]; else distance += zDistances[0]; } final Length zPos = new Length(distance, UNITS.REFERENCEFRAME); store.setPlanePositionZ(zPos, i, p); } else if (xmlZPosition != null) { final Length zPos = new Length(xmlZPosition, UNITS.REFERENCEFRAME); store.setPlanePositionZ(zPos, i, p); } } if (stream != null) { stream.close(); } } setSeries(0); } // -- Internal BaseTiffReader API methods -- /* @see BaseTiffReader#initStandardMetadata() */ @Override protected void initStandardMetadata() throws FormatException, IOException { super.initStandardMetadata(); CoreMetadata ms0 = core.get(0); ms0.sizeZ = 1; ms0.sizeT = 0; int rgbChannels = getSizeC(); // Now that the base TIFF standard metadata has been parsed, we need to // parse out the STK metadata from the UIC4TAG. TiffIFDEntry uic1tagEntry = null; TiffIFDEntry uic2tagEntry = null; TiffIFDEntry uic4tagEntry = null; try { uic1tagEntry = tiffParser.getFirstIFDEntry(UIC1TAG); uic2tagEntry = tiffParser.getFirstIFDEntry(UIC2TAG); uic4tagEntry = tiffParser.getFirstIFDEntry(UIC4TAG); } catch (IllegalArgumentException exc) { LOGGER.debug("Unknown tag", exc); } try { if (uic4tagEntry != null) { mmPlanes = uic4tagEntry.getValueCount(); } if (mmPlanes == 0) { mmPlanes = ifds.size(); } if (uic2tagEntry != null) { parseUIC2Tags(uic2tagEntry.getValueOffset()); } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { if (uic4tagEntry != null) { parseUIC4Tags(uic4tagEntry.getValueOffset()); } if (uic1tagEntry != null) { parseUIC1Tags(uic1tagEntry.getValueOffset(), uic1tagEntry.getValueCount()); } } in.seek(uic4tagEntry.getValueOffset()); } catch (NullPointerException exc) { LOGGER.debug("", exc); } catch (IOException exc) { LOGGER.debug("Failed to parse proprietary tags", exc); } try { // copy ifds into a new array of Hashtables that will accommodate the // additional image planes IFD firstIFD = ifds.get(0); long[] uic2 = firstIFD.getIFDLongArray(UIC2TAG); if (uic2 == null) { throw new FormatException("Invalid Metamorph file. Tag " + UIC2TAG + " not found."); } ms0.imageCount = uic2.length; Object entry = firstIFD.getIFDValue(UIC3TAG); TiffRational[] uic3 = entry instanceof TiffRational[] ? (TiffRational[]) entry : new TiffRational[] { (TiffRational) entry }; wave = new double[uic3.length]; Vector<Double> uniqueWavelengths = new Vector<Double>(); for (int i = 0; i < uic3.length; i++) { wave[i] = uic3[i].doubleValue(); addSeriesMeta("Wavelength [" + intFormatMax(i, mmPlanes) + "]", wave[i]); Double v = new Double(wave[i]); if (!uniqueWavelengths.contains(v)) uniqueWavelengths.add(v); } if (getSizeC() == 1) { ms0.sizeC = uniqueWavelengths.size(); if (getSizeC() < getImageCount() && getSizeC() > (getImageCount() - getSizeC()) && (getImageCount() % getSizeC()) != 0) { ms0.sizeC = getImageCount(); } } IFDList tempIFDs = new IFDList(); long[] oldOffsets = firstIFD.getStripOffsets(); long[] stripByteCounts = firstIFD.getStripByteCounts(); int rowsPerStrip = (int) firstIFD.getRowsPerStrip()[0]; int stripsPerImage = getSizeY() / rowsPerStrip; if (stripsPerImage * rowsPerStrip != getSizeY()) stripsPerImage++; PhotoInterp check = firstIFD.getPhotometricInterpretation(); if (check == PhotoInterp.RGB_PALETTE) { firstIFD.putIFDValue(IFD.PHOTOMETRIC_INTERPRETATION, PhotoInterp.BLACK_IS_ZERO); } emWavelength = firstIFD.getIFDLongArray(UIC3TAG); // for each image plane, construct an IFD hashtable IFD temp; for (int i = 0; i < getImageCount(); i++) { // copy data from the first IFD temp = new IFD(firstIFD); // now we need a StripOffsets entry - the original IFD doesn't have this long[] newOffsets = new long[stripsPerImage]; if (stripsPerImage * (i + 1) <= oldOffsets.length) { System.arraycopy(oldOffsets, stripsPerImage * i, newOffsets, 0, stripsPerImage); } else { System.arraycopy(oldOffsets, 0, newOffsets, 0, stripsPerImage); long image = (stripByteCounts[0] / rowsPerStrip) * getSizeY(); for (int q = 0; q < stripsPerImage; q++) { newOffsets[q] += i * image; } } temp.putIFDValue(IFD.STRIP_OFFSETS, newOffsets); long[] newByteCounts = new long[stripsPerImage]; if (stripsPerImage * i < stripByteCounts.length) { System.arraycopy(stripByteCounts, stripsPerImage * i, newByteCounts, 0, stripsPerImage); } else { Arrays.fill(newByteCounts, stripByteCounts[0]); } temp.putIFDValue(IFD.STRIP_BYTE_COUNTS, newByteCounts); tempIFDs.add(temp); } ifds = tempIFDs; } catch (IllegalArgumentException exc) { LOGGER.debug("Unknown tag", exc); } catch (NullPointerException exc) { LOGGER.debug("", exc); } catch (FormatException exc) { LOGGER.debug("Failed to build list of IFDs", exc); } // parse (mangle) TIFF comment String descr = ifds.get(0).getComment(); if (descr != null) { String[] lines = descr.split("\n"); StringBuffer sb = new StringBuffer(); for (int i = 0; i < lines.length; i++) { String line = lines[i].trim(); if (line.startsWith("<") && line.endsWith(">")) { // XML comment; this will have already been parsed so can be ignored break; } int colon = line.indexOf(":"); if (colon < 0) { // normal line (not a key/value pair) if (line.length() > 0) { // not a blank line sb.append(line); sb.append(" "); } } else { String descrValue = null; if (i == 0) { // first line could be mangled; make a reasonable guess int dot = line.lastIndexOf(".", colon); if (dot >= 0) { descrValue = line.substring(0, dot + 1); } line = line.substring(dot + 1); colon -= dot + 1; } // append value to description if (descrValue != null) { sb.append(descrValue); if (!descrValue.endsWith(".")) sb.append("."); sb.append(" "); } // add key/value pair embedded in comment as separate metadata String key = line.substring(0, colon); String value = line.substring(colon + 1).trim(); addSeriesMeta(key, value); if (key.equals("Exposure")) { if (value.indexOf("=") != -1) { value = value.substring(value.indexOf("=") + 1).trim(); } if (value.indexOf(" ") != -1) { value = value.substring(0, value.indexOf(" ")); } try { value = value.replace(',', '.'); double exposure = Double.parseDouble(value); exposureTime = new Double(exposure / 1000); } catch (NumberFormatException e) { } } else if (key.equals("Bit Depth")) { if (value.indexOf("-") != -1) { value = value.substring(0, value.indexOf("-")); } try { ms0.bitsPerPixel = Integer.parseInt(value); } catch (NumberFormatException e) { } } else if (key.equals("Gain")) { int space = value.indexOf(" "); if (space != -1) { int nextSpace = value.indexOf(" ", space + 1); if (nextSpace < 0) { nextSpace = value.length(); } try { gain = new Double(value.substring(space, nextSpace)); } catch (NumberFormatException e) { } } } } } // replace comment with trimmed version descr = sb.toString().trim(); if (descr.equals("")) metadata.remove("Comment"); else addSeriesMeta("Comment", descr); } ms0.sizeT = getImageCount() / (getSizeZ() * (getSizeC() / rgbChannels)); if (getSizeT() * getSizeZ() * (getSizeC() / rgbChannels) != getImageCount()) { ms0.sizeT = 1; ms0.sizeZ = getImageCount() / (getSizeC() / rgbChannels); } // if '_t' is present in the file name, swap Z and T sizes // this file was probably part of a larger dataset, but the .nd file is // missing String filename = currentId.substring(currentId.lastIndexOf(File.separator) + 1); if (filename.indexOf("_t") != -1 && getSizeT() > 1) { int z = getSizeZ(); ms0.sizeZ = getSizeT(); ms0.sizeT = z; } if (getSizeZ() == 0) ms0.sizeZ = 1; if (getSizeT() == 0) ms0.sizeT = 1; if (getSizeZ() * getSizeT() * (isRGB() ? 1 : getSizeC()) != getImageCount()) { ms0.sizeZ = getImageCount(); ms0.sizeT = 1; if (!isRGB()) ms0.sizeC = 1; } } // -- Helper methods -- /** * Check that the given STK file exists. If it does, then return the * absolute path. If it does not, then apply various formatting rules until * an existing file is found. * * @return the absolute path of an STK file, or null if no STK file is found. */ private String getRealSTKFile(Location l) { if (l.exists()) return l.getAbsolutePath(); String name = l.getName(); String parent = l.getParent(); if (name.indexOf("_") > 0) { String prefix = name.substring(0, name.indexOf("_")); String suffix = name.substring(name.indexOf("_")); String basePrefix = new Location(currentId).getName(); int end = basePrefix.indexOf("_"); if (end < 0) end = basePrefix.indexOf("."); basePrefix = basePrefix.substring(0, end); if (!basePrefix.equals(prefix)) { name = basePrefix + suffix; Location p = new Location(parent, name); if (p.exists()) return p.getAbsolutePath(); } } // '%' can be converted to '-' if (name.indexOf("%") != -1) { name = name.replaceAll("%", "-"); l = new Location(parent, name); if (!l.exists()) { // try replacing extension name = name.substring(0, name.lastIndexOf(".")) + ".TIF"; l = new Location(parent, name); if (!l.exists()) { name = name.substring(0, name.lastIndexOf(".")) + ".tif"; l = new Location(parent, name); return l.exists() ? l.getAbsolutePath() : null; } } } if (!l.exists()) { // try replacing extension int index = name.lastIndexOf("."); if (index < 0) index = name.length(); name = name.substring(0, index) + ".TIF"; l = new Location(parent, name); if (!l.exists()) { name = name.substring(0, name.lastIndexOf(".")) + ".tif"; l = new Location(parent, name); if (!l.exists()) { name = name.substring(0, name.lastIndexOf(".")) + ".stk"; l = new Location(parent, name); return l.exists() ? l.getAbsolutePath() : null; } } } return l.getAbsolutePath(); } /** * Returns the TIFF comment from the first IFD of the first STK file in the * given series. */ private String getFirstComment(int i) throws IOException { return getComment(i, 0); } private String getComment(int i, int no) throws IOException { if (stks != null && stks[i][no] != null) { RandomAccessInputStream stream = new RandomAccessInputStream(stks[i][no], 16); TiffParser tp = new TiffParser(stream); String comment = tp.getComment(); stream.close(); return comment; } return ifds.get(0).getComment(); } /** Create an appropriate name for the given series. */ private String makeImageName(int i) { String name = ""; if (stageNames != null && stageNames.size() > 0) { int stagePosition = i / (getSeriesCount() / stageNames.size()); name += "Stage" + (stagePosition + 1) + " " + stageNames.get(stagePosition); } if (firstSeriesChannels != null && (stageNames == null || stageNames.size() == 0 || stageNames.size() != getSeriesCount())) { if (name.length() > 0) { name += "; "; } for (int c = 0; c < firstSeriesChannels.length; c++) { if (firstSeriesChannels[c] == ((i % 2) == 0) && c < waveNames.size()) { name += waveNames.get(c) + "/"; } } if (name.length() > 0) { name = name.substring(0, name.length() - 1); } } return name; } /** * Populates metadata fields with some contained in MetaMorph UIC2 Tag. * (for each plane: 6 integers: * zdistance numerator, zdistance denominator, * creation date, creation time, modif date, modif time) * @param uic2offset offset to UIC2 (33629) tag entries * * not a regular tiff tag (6*N entries, N being the tagCount) * @throws IOException */ void parseUIC2Tags(long uic2offset) throws IOException { long saveLoc = in.getFilePointer(); in.seek(uic2offset); /*number of days since the 1st of January 4713 B.C*/ String cDate; /*milliseconds since 0:00*/ String cTime; /*z step, distance separating previous slice from current one*/ String iAsString; zDistances = new double[mmPlanes]; internalStamps = new long[mmPlanes]; for (int i = 0; i < mmPlanes; i++) { iAsString = intFormatMax(i, mmPlanes); if (in.getFilePointer() + 8 > in.length()) break; zDistances[i] = readRational(in).doubleValue(); addSeriesMeta("zDistance[" + iAsString + "]", zDistances[i]); if (zDistances[i] != 0.0) core.get(0).sizeZ++; cDate = decodeDate(in.readInt()); cTime = decodeTime(in.readInt()); internalStamps[i] = DateTools.getTime(cDate + " " + cTime, LONG_DATE_FORMAT, ":"); addSeriesMeta("creationDate[" + iAsString + "]", cDate); addSeriesMeta("creationTime[" + iAsString + "]", cTime); // modification date and time are skipped as they all seem equal to 0...? in.skip(8); } if (getSizeZ() == 0) core.get(0).sizeZ = 1; in.seek(saveLoc); } /** * UIC4 metadata parser * * UIC4 Table contains per-plane blocks of metadata * stage X/Y positions, * camera chip offsets, * stage labels... * @param uic4offset offset of UIC4 table (not tiff-compliant) * @throws IOException */ private void parseUIC4Tags(long uic4offset) throws IOException { long saveLoc = in.getFilePointer(); in.seek(uic4offset); if (in.getFilePointer() + 2 >= in.length()) return; tempZ = 0d; validZ = false; short id = in.readShort(); while (id != 0) { switch (id) { case 28: readStagePositions(); hasStagePositions = true; break; case 29: readRationals(new String[] { "cameraXChipOffset", "cameraYChipOffset" }); hasChipOffsets = true; break; case 37: readStageLabels(); break; case 40: readRationals(new String[] { "UIC4 absoluteZ" }); hasAbsoluteZ = true; break; case 41: readAbsoluteZValid(); hasAbsoluteZValid = true; break; case 46: in.skipBytes(mmPlanes * 8); // TODO break; default: in.skipBytes(4); } id = in.readShort(); } in.seek(saveLoc); if (validZ) zStart = tempZ; } private void readStagePositions() throws IOException { stageX = new Length[mmPlanes]; stageY = new Length[mmPlanes]; String pos; for (int i = 0; i < mmPlanes; i++) { pos = intFormatMax(i, mmPlanes); final Double posX = Double.valueOf(readRational(in).doubleValue()); final Double posY = Double.valueOf(readRational(in).doubleValue()); stageX[i] = new Length(posX, UNITS.REFERENCEFRAME); stageY[i] = new Length(posY, UNITS.REFERENCEFRAME); addSeriesMeta("stageX[" + pos + "]", posX); addSeriesMeta("stageY[" + pos + "]", posY); addGlobalMeta("X position for position #" + (getSeries() + 1), posX); addGlobalMeta("Y position for position #" + (getSeries() + 1), posY); } } private void readRationals(String[] labels) throws IOException { String pos; Set<Double> uniqueZ = new HashSet<Double>(); for (int i = 0; i < mmPlanes; i++) { pos = intFormatMax(i, mmPlanes); for (int q = 0; q < labels.length; q++) { double v = readRational(in).doubleValue(); if (labels[q].endsWith("absoluteZ")) { if (i == 0) { tempZ = v; } uniqueZ.add(v); } addSeriesMeta(labels[q] + "[" + pos + "]", v); } } if (uniqueZ.size() == mmPlanes) { core.get(0).sizeZ = mmPlanes; } } void readStageLabels() throws IOException { int strlen; String iAsString; for (int i = 0; i < mmPlanes; i++) { iAsString = intFormatMax(i, mmPlanes); strlen = in.readInt(); addSeriesMeta("stageLabel[" + iAsString + "]", in.readString(strlen)); } } void readAbsoluteZValid() throws IOException { for (int i = 0; i < mmPlanes; i++) { int valid = in.readInt(); addSeriesMeta("absoluteZValid[" + intFormatMax(i, mmPlanes) + "]", valid); if (i == 0) { validZ = valid == 1; } } } /** * UIC1 entry parser * @throws IOException * @param uic1offset offset as found in the tiff tag 33628 (UIC1Tag) * @param uic1count number of entries in UIC1 table (not tiff-compliant) */ private void parseUIC1Tags(long uic1offset, int uic1count) throws IOException { // Loop through and parse out each field. A field whose // code is "0" represents the end of the fields so we'll stop // when we reach that; much like a NULL terminated C string. long saveLoc = in.getFilePointer(); in.seek(uic1offset); int currentID; long valOrOffset; // variable declarations, because switch is dumb int num, denom; String thedate, thetime; long lastOffset; tempZ = 0d; validZ = false; for (int i = 0; i < uic1count; i++) { if (in.getFilePointer() >= in.length()) break; currentID = in.readInt(); valOrOffset = in.readInt() & 0xffffffffL; lastOffset = in.getFilePointer(); String key = getKey(currentID); Object value = String.valueOf(valOrOffset); boolean skipKey = false; switch (currentID) { case 3: value = valOrOffset != 0 ? "on" : "off"; break; case 4: case 5: case 21: case 22: case 23: case 24: case 38: case 39: value = readRational(in, valOrOffset); break; case 6: case 25: if (valOrOffset < in.length()) { in.seek(valOrOffset); num = in.readInt(); if (num + in.getFilePointer() >= in.length()) { num = (int) (in.length() - in.getFilePointer() - 1); } if (num >= 0) { value = in.readString(num); } } break; case 7: if (valOrOffset < in.length()) { in.seek(valOrOffset); num = in.readInt(); if (num >= 0) { imageName = in.readString(num); value = imageName; } } break; case 8: if (valOrOffset == 1) value = "inside"; else if (valOrOffset == 2) value = "outside"; else value = "off"; break; case 17: // oh how we hate you Julian format... if (valOrOffset < in.length()) { in.seek(valOrOffset); thedate = decodeDate(in.readInt()); thetime = decodeTime(in.readInt()); imageCreationDate = thedate + " " + thetime; value = imageCreationDate; } break; case 16: if (valOrOffset < in.length()) { in.seek(valOrOffset); thedate = decodeDate(in.readInt()); thetime = decodeTime(in.readInt()); value = thedate + " " + thetime; } break; case 26: if (valOrOffset < in.length()) { in.seek(valOrOffset); int standardLUT = in.readInt(); switch (standardLUT) { case 0: value = "monochrome"; break; case 1: value = "pseudocolor"; break; case 2: value = "Red"; break; case 3: value = "Green"; break; case 4: value = "Blue"; break; case 5: value = "user-defined"; break; default: value = "monochrome"; } } break; case 28: if (valOrOffset < in.length()) { if (!hasStagePositions) { in.seek(valOrOffset); readStagePositions(); } skipKey = true; } break; case 29: if (valOrOffset < in.length()) { if (!hasChipOffsets) { in.seek(valOrOffset); readRationals(new String[] { "cameraXChipOffset", "cameraYChipOffset" }); } skipKey = true; } break; case 34: value = String.valueOf(in.readInt()); break; case 42: if (valOrOffset < in.length()) { in.seek(valOrOffset); value = String.valueOf(in.readInt()); } break; case 46: if (valOrOffset < in.length()) { in.seek(valOrOffset); int xBin = in.readInt(); int yBin = in.readInt(); binning = xBin + "x" + yBin; value = binning; } break; case 40: if (valOrOffset != 0 && valOrOffset < in.length()) { if (!hasAbsoluteZ) { in.seek(valOrOffset); readRationals(new String[] { "UIC1 absoluteZ" }); } skipKey = true; } break; case 41: if (valOrOffset != 0 && valOrOffset < in.length()) { if (!hasAbsoluteZValid) { in.seek(valOrOffset); readAbsoluteZValid(); } skipKey = true; } else if (valOrOffset == 0 && getSizeZ() < mmPlanes) { core.get(0).sizeZ = 1; } break; case 49: if (valOrOffset < in.length()) { in.seek(valOrOffset); readPlaneData(); skipKey = true; } break; } if (!skipKey) { addSeriesMeta(key, value); } in.seek(lastOffset); if ("Zoom".equals(key) && value != null) { zoom = Double.parseDouble(value.toString()); } if ("XCalibration".equals(key) && value != null) { if (value instanceof TiffRational) { sizeX = ((TiffRational) value).doubleValue(); } else sizeX = new Double(value.toString()); } if ("YCalibration".equals(key) && value != null) { if (value instanceof TiffRational) { sizeY = ((TiffRational) value).doubleValue(); } else sizeY = new Double(value.toString()); } } in.seek(saveLoc); if (validZ) zStart = tempZ; } // -- Utility methods -- /** Converts a Julian date value into a human-readable string. */ public static String decodeDate(int julian) { long a, b, c, d, e, alpha, z; short day, month, year; // code reused from the Metamorph data specification z = julian + 1; if (z < 2299161L) a = z; else { alpha = (long) ((z - 1867216.25) / 36524.25); a = z + 1 + alpha - alpha / 4; } b = (a > 1721423L ? a + 1524 : a + 1158); c = (long) ((b - 122.1) / 365.25); d = (long) (365.25 * c); e = (long) ((b - d) / 30.6001); day = (short) (b - d - (long) (30.6001 * e)); month = (short) ((e < 13.5) ? e - 1 : e - 13); year = (short) ((month > 2.5) ? (c - 4716) : c - 4715); return intFormat(day, 2) + "/" + intFormat(month, 2) + "/" + year; } /** Converts a time value in milliseconds into a human-readable string. */ public static String decodeTime(int millis) { DateTime tm = new DateTime(millis, DateTimeZone.UTC); String hours = intFormat(tm.getHourOfDay(), 2); String minutes = intFormat(tm.getMinuteOfHour(), 2); String seconds = intFormat(tm.getSecondOfMinute(), 2); String ms = intFormat(tm.getMillisOfSecond(), 3); return hours + ":" + minutes + ":" + seconds + ":" + ms; } /** Formats an integer value with leading 0s if needed. */ public static String intFormat(int myint, int digits) { return String.format("%0" + digits + "d", myint); } /** * Formats an integer with leading 0 using maximum sequence number. * * @param myint integer to format * @param maxint max of "myint" * @return String */ public static String intFormatMax(int myint, int maxint) { return intFormat(myint, String.valueOf(maxint).length()); } /** * Locates the first valid file in the STK arrays. * @return Path to the first valid file. */ private String locateFirstValidFile() { for (int q = 0; q < stks.length; q++) { for (int f = 0; f < stks.length; f++) { if (stks[q][f] != null) { return stks[q][f]; } } } return null; } private TiffRational readRational(RandomAccessInputStream s) throws IOException { return readRational(s, s.getFilePointer()); } private TiffRational readRational(RandomAccessInputStream s, long offset) throws IOException { if (offset >= s.length() - 8) { return null; } s.seek(offset); int num = s.readInt(); int denom = s.readInt(); return new TiffRational(num, denom); } private void setCanLookForND(boolean v) { FormatTools.assertId(currentId, false, 1); canLookForND = v; } private void readPlaneData() throws IOException { in.skipBytes(4); int keyLength = in.read(); String key = in.readString(keyLength); in.skipBytes(4); int type = in.read(); int index = 0; switch (type) { case 1: while (getGlobalMeta("Channel #" + index + " " + key) != null) { index++; } addGlobalMeta("Channel #" + index + " " + key, readRational(in).doubleValue()); break; case 2: int valueLength = in.read(); String value = in.readString(valueLength); if (valueLength == 0) { in.skipBytes(4); valueLength = in.read(); value = in.readString(valueLength); } while (getGlobalMeta("Channel #" + index + " " + key) != null) { index++; } addGlobalMeta("Channel #" + index + " " + key, value); if (key.equals("_IllumSetting_")) { if (waveNames == null) waveNames = new Vector<String>(); waveNames.add(value); } break; } } private String getKey(int id) { switch (id) { case 0: return "AutoScale"; case 1: return "MinScale"; case 2: return "MaxScale"; case 3: return "Spatial Calibration"; case 4: return "XCalibration"; case 5: return "YCalibration"; case 6: return "CalibrationUnits"; case 7: return "Name"; case 8: return "ThreshState"; case 9: return "ThreshStateRed"; // there is no 10 case 11: return "ThreshStateGreen"; case 12: return "ThreshStateBlue"; case 13: return "ThreshStateLo"; case 14: return "ThreshStateHi"; case 15: return "Zoom"; case 16: return "DateTime"; case 17: return "LastSavedTime"; case 18: return "currentBuffer"; case 19: return "grayFit"; case 20: return "grayPointCount"; case 21: return "grayX"; case 22: return "grayY"; case 23: return "grayMin"; case 24: return "grayMax"; case 25: return "grayUnitName"; case 26: return "StandardLUT"; case 27: return "Wavelength"; case 28: return "StagePosition"; case 29: return "CameraChipOffset"; case 30: return "OverlayMask"; case 31: return "OverlayCompress"; case 32: return "Overlay"; case 33: return "SpecialOverlayMask"; case 34: return "SpecialOverlayCompress"; case 35: return "SpecialOverlay"; case 36: return "ImageProperty"; case 38: return "AutoScaleLoInfo"; case 39: return "AutoScaleHiInfo"; case 40: return "AbsoluteZ"; case 41: return "AbsoluteZValid"; case 42: return "Gamma"; case 43: return "GammaRed"; case 44: return "GammaGreen"; case 45: return "GammaBlue"; case 46: return "CameraBin"; case 47: return "NewLUT"; case 48: return "ImagePropertyEx"; case 49: return "PlaneProperty"; case 50: return "UserLutTable"; case 51: return "RedAutoScaleInfo"; case 52: return "RedAutoScaleLoInfo"; case 53: return "RedAutoScaleHiInfo"; case 54: return "RedMinScaleInfo"; case 55: return "RedMaxScaleInfo"; case 56: return "GreenAutoScaleInfo"; case 57: return "GreenAutoScaleLoInfo"; case 58: return "GreenAutoScaleHiInfo"; case 59: return "GreenMinScaleInfo"; case 60: return "GreenMaxScaleInfo"; case 61: return "BlueAutoScaleInfo"; case 62: return "BlueAutoScaleLoInfo"; case 63: return "BlueAutoScaleHiInfo"; case 64: return "BlueMinScaleInfo"; case 65: return "BlueMaxScaleInfo"; case 66: return "OverlayPlaneColor"; } return null; } }