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MetamorphReader.java
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MetamorphReader.java
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/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2017 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.math.BigDecimal;
import java.math.MathContext;
import java.math.RoundingMode;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.Map;
import java.util.HashMap;
import java.util.AbstractMap;
import java.util.Collections;
import java.util.Vector;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
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.Constants;
import loci.common.RandomAccessInputStream;
import loci.common.services.DependencyException;
import loci.common.services.ServiceFactory;
import loci.common.xml.XMLTools;
import loci.formats.CoreMetadata;
import loci.formats.CoreMetadataList;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.MissingLibraryException;
import loci.formats.meta.MetadataStore;
import loci.formats.services.OMEXMLService;
import loci.formats.services.OMEXMLServiceImpl;
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.enums.NamingConvention;
import ome.xml.model.primitives.NonNegativeInteger;
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;
import org.apache.commons.lang.ArrayUtils;
/**
* 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", "scan"};
public static final String[] STK_SUFFIX = {"stk", "tif", "tiff"};
public static final Pattern WELL_COORDS = Pattern.compile(
"\\b([a-z])(\\d+)", Pattern.CASE_INSENSITIVE
);
// 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;
// NDInfoFile Version Strings
private static final String NDINFOFILE_VER1 = "Version 1.0";
private static final String NDINFOFILE_VER2 = "Version 2.0";
// -- Fields --
/** The TIFF's name */
private String imageName;
/** The TIFF's creation date */
private String imageCreationDate;
/** The TIFF's emWavelength */
private long[] emWavelength;
private boolean isHCS;
private String[] stageLabels;
private double[] wave;
private String binning;
private double zoom, stepSize;
private Double exposureTime;
private List<String> waveNames;
private List<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", "scan", "tif", "tiff"});
domains = new String[] {FormatTools.LM_DOMAIN, FormatTools.HCS_DOMAIN};
hasCompanionFiles = true;
suffixSufficient = false;
datasetDescription = "One or more .stk or .tif/.tiff files plus an " +
"optional .nd or .scan file";
canSeparateSeries = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#getDomains() */
@Override
public String[] getDomains() {
FormatTools.assertId(currentId, true, 1);
return isHCS ? new String[] {FormatTools.HCS_DOMAIN} :
new String[] {FormatTools.LM_DOMAIN};
}
/* @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_SUFFIX)) 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)) {
for (String ext : ND_SUFFIX) {
if (new Location(parent, baseName + "." + ext).exists() ||
new Location(parent, baseName + "." + ext.toUpperCase()).exists()) {
return true;
}
}
if (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 ArrayUtils.EMPTY_STRING_ARRAY;
final List<String> v = new ArrayList<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;
stageLabels = null;
isHCS = false;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
Location ndfile = null;
if (checkSuffix(id, ND_SUFFIX)) {
ndfile = new Location(id);
LOGGER.info("Initializing " + id);
// find an associated STK file
String stkFile = id.substring(0, id.lastIndexOf("."));
if (stkFile.indexOf(File.separatorChar) != -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);
Arrays.sort(dirList);
String suffix = getNDVersionSuffix(ndfile);
for (String f : dirList) {
if (!checkSuffix(f, suffix)) {
continue;
}
if (!f.startsWith(stkFile)) {
continue;
}
String s = f.substring(stkFile.length(), f.lastIndexOf("."));
if (s.isEmpty() || s.startsWith("_w") || s.startsWith("_s") || s.startsWith("_t") )
{
stkFile = new Location(parent.getAbsolutePath(), f).getAbsolutePath();
break;
}
}
if (!checkSuffix(stkFile, STK_SUFFIX)) {
throw new FormatException(suffix + " file not found in " +
parent.getAbsolutePath() + ".");
}
super.initFile(stkFile);
}
else super.initFile(id);
if (!checkSuffix(id, ND_SUFFIX) && 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;
final List<Boolean> hasZ = new ArrayList<Boolean>();
waveNames = new ArrayList<String>();
stageNames = new ArrayList<String>();
boolean useWaveNames = true;
ndFilename = ndfile.getAbsolutePath();
String[] lines = DataTools.readFile(ndFilename).split("\n");
boolean globalDoZ = true;
boolean doTimelapse = false;
boolean doWavelength = false;
String version = NDINFOFILE_VER1;
StringBuilder currentValue = new StringBuilder();
String key = "";
for (String line : lines) {
int comma = line.indexOf(',');
if (comma <= 0 && line.indexOf("EndFile") < 0) {
currentValue.append("\n");
currentValue.append(line);
continue;
}
String value = currentValue.toString();
addGlobalMeta(key, value);
if (key.equals("NDInfoFile")) version = 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(Boolean.parseBoolean(value));
}
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 = Boolean.parseBoolean(value);
}
else if (key.equals("DoWave")) {
doWavelength = Boolean.parseBoolean(value);
}
if (comma >= 1) {
key = line.substring(1, comma - 1).trim();
}
else {
key = "";
}
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);
boolean hasZ2 = i != 0 && (i - 1 < hasZ.size()) &&
hasZ.get(i - 1);
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)))
{
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);
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;
String formatSuffix = ".STK";
if (version.equals(NDINFOFILE_VER1)) {
formatSuffix = ".TIF";
if ((anyZ && j < hasZ.size() && hasZ.get(j)) || globalDoZ) {
formatSuffix = ".STK";
}
}
else if (version.equals(NDINFOFILE_VER2)) {
formatSuffix = ".TIF";
}
if (j < waveNames.size() && waveNames.get(j) != null) {
if (doWavelength) {
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) + formatSuffix;
}
else stks[seriesNdx][pt[seriesNdx]] += formatSuffix;
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!");
}
IFD ifd = null;
try (RandomAccessInputStream s = new RandomAccessInputStream(file, 16)) {
TiffParser tp = new TiffParser(s);
ifd = tp.getFirstIFD();
}
CoreMetadata ms0 = core.get(0, 0);
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();
if (isRGB()) {
ms0.sizeC *= 3;
}
ms0.dimensionOrder = "XYZCT";
if (stks != null && stks.length > 1) {
// Note that core can't be replaced with newCore until the end of this block.
CoreMetadataList newCore = new CoreMetadataList();
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, 0);
CoreMetadata pmidx = newCore.get(j * 2, 0);
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, 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));
}
}
}
}
// check stage labels for plate data
int rows = 0;
int cols = 0;
Map<String, Integer> rowMap = null;
Map<String, Integer> colMap = null;
isHCS = true;
if (stageLabels == null && stageNames != null) {
stageLabels = stageNames.toArray(new String[stageNames.size()]);
}
if (null == stageLabels) {
isHCS = false;
} else if (stks == null ||
(stks != null && stageLabels.length == stks.length))
{
Set<Map.Entry<Integer, Integer>> uniqueWells =
new HashSet<Map.Entry<Integer, Integer>>();
rowMap = new HashMap<String, Integer>();
colMap = new HashMap<String, Integer>();
for (String label : stageLabels) {
if (null == label) {
isHCS = false;
break;
}
Map.Entry<Integer, Integer> wellCoords = getWellCoords(label);
if (null == wellCoords) {
isHCS = false;
break;
}
uniqueWells.add(wellCoords);
rowMap.put(label, wellCoords.getKey());
colMap.put(label, wellCoords.getValue());
}
if (uniqueWells.size() != stageLabels.length ||
rowMap.size() == 0)
{
isHCS = false;
} else {
rows = Collections.max(rowMap.values()) + 1;
cols = Collections.max(colMap.values()) + 1;
if (rows > 0 && cols > 0) {
CoreMetadata c = core.get(0, 0);
core.clear();
c.sizeZ = 1;
c.sizeT = 1;
c.imageCount = 1;
for (int s = 0; s < uniqueWells.size(); s++) {
CoreMetadata toAdd = new CoreMetadata(c);
if (s > 0) {
toAdd.seriesMetadata.clear();
}
core.add(toAdd);
}
seriesToIFD = true;
}
}
}
if (rows <= 0 || cols <= 0) {
isHCS = false;
}
List<String> timestamps = null;
MetamorphHandler handler = null;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (isHCS) {
store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
store.setPlateRows(new PositiveInteger(rows), 0);
store.setPlateColumns(new PositiveInteger(cols), 0);
store.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
store.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);
}
int nextObjective = 0;
String instrumentID = MetadataTools.createLSID("Instrument", 0);
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setInstrumentID(instrumentID, 0);
store.setDetectorID(detectorID, 0, 0);
store.setDetectorType(MetadataTools.getDetectorType("Other"), 0, 0);
for (int i=0; i<getSeriesCount(); i++) {
setSeries(i);
// do not reparse the same XML for every well
if (i == 0 || !isHCS) {
handler = new MetamorphHandler(getSeriesMetadata());
}
if (isHCS) {
String label = stageLabels[i];
String wellID = MetadataTools.createLSID("Well", 0, i);
store.setWellID(wellID, 0, i);
store.setWellColumn(new NonNegativeInteger(colMap.get(label)), 0, i);
store.setWellRow(new NonNegativeInteger(rowMap.get(label)), 0, i);
store.setWellSampleID(MetadataTools.createLSID("WellSample", 0, i, 0), 0, i, 0);
store.setWellSampleImageRef(MetadataTools.createLSID("Image", i), 0, i, 0);
store.setWellSampleIndex(new NonNegativeInteger(i), 0, i, 0);
}
store.setImageInstrumentRef(instrumentID, i);
String comment = getFirstComment(i);
if (i == 0 || !isHCS) {
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.CELSIUS), 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];
}
else {
List<Double> zPositions = new ArrayList<Double>();
final List<Double> uniqueZ = new ArrayList<Double>();
for (IFD ifd : ifds) {
MetamorphHandler zPlaneHandler = new MetamorphHandler();
String zComment = ifd.getComment();
if (zComment != null &&
zComment.startsWith("<MetaData>"))
{
try {
XMLTools.parseXML(XMLTools.sanitizeXML(zComment),
zPlaneHandler);
}
catch (IOException e) { }
}
zPositions = zPlaneHandler.getZPositions();
for (Double z : zPositions) {
if (!uniqueZ.contains(z)) uniqueZ.add(z);
}
}
if (uniqueZ.size() > 1 && uniqueZ.size() == getSizeZ()) {
BigDecimal lastZ = BigDecimal.valueOf(uniqueZ.get(uniqueZ.size() - 1));
BigDecimal firstZ = BigDecimal.valueOf(uniqueZ.get(0));
BigDecimal zRange = (lastZ.subtract(firstZ)).abs();
BigDecimal zSize = BigDecimal.valueOf((double)(getSizeZ() - 1));
MathContext mc = new MathContext(10, RoundingMode.HALF_UP);
stepSize = zRange.divide(zSize, mc).doubleValue();
}
}
Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize);
if (physicalSizeZ != null) {
store.setPixelsPhysicalSizeZ(physicalSizeZ, i);
}
if (handler.getLensNA() != 0 || handler.getLensRI() != 0) {
String objectiveID = MetadataTools.createLSID("Objective", 0, nextObjective);
store.setObjectiveID(objectiveID, 0, nextObjective);
if (handler.getLensNA() != 0) {
store.setObjectiveLensNA(handler.getLensNA(), 0, nextObjective);
}
store.setObjectiveSettingsID(objectiveID, i);
if (handler.getLensRI() != 0) {
store.setObjectiveSettingsRefractiveIndex(handler.getLensRI(), i);
}
nextObjective++;
}
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)
{