//
// TCSReader.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.io.IOException;
import java.math.BigInteger;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Vector;
import loci.common.DataTools;
import loci.common.DateTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.common.xml.XMLTools;
import loci.formats.AxisGuesser;
import loci.formats.CoreMetadata;
import loci.formats.FilePattern;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.xml.model.primitives.PositiveFloat;
import loci.formats.tiff.IFD;
import loci.formats.tiff.IFDList;
import loci.formats.tiff.TiffParser;
/**
* TCSReader is the file format reader for Leica TCS TIFF files and their
* companion XML file.
*
* <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/TCSReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/TCSReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class TCSReader extends FormatReader {
// -- Constants --
public static final String DATE_FORMAT = "yyyy:MM:dd HH:mm:ss.SSS";
public static final String PREFIX =
"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><LEICA>";
public static final String SUFFIX = "</LEICA>";
public static final String[] XML_SUFFIX = {"xml"};
// -- Fields --
/** List of TIFF files. */
private Vector<String> tiffs;
/** Helper readers. */
private TiffReader[] tiffReaders;
private TiffParser tiffParser;
private int lastPlane = 0;
private long datestamp;
private String xmlFile;
private double voxelX, voxelY, voxelZ;
// -- Constructor --
public TCSReader() {
super("Leica TCS TIFF", new String[] {"tif", "tiff", "xml"});
domains = new String[] {FormatTools.LM_DOMAIN};
hasCompanionFiles = true;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isSingleFile(String) */
public boolean isSingleFile(String id) throws FormatException, IOException {
if (checkSuffix(id, "xml")) return false;
Location file = new Location(id);
String[] list = file.getParentFile().list();
for (String f : list) {
if (checkSuffix(f, "xml") && DataTools.samePrefix(file.getName(), f)) {
return false;
}
}
return true;
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
if (!open) return false; // not allowed to touch the file system
// check that there is no LEI file
String prefix = name;
if (prefix.indexOf(".") != -1) {
prefix = prefix.substring(0, prefix.lastIndexOf("."));
}
Location lei = new Location(prefix + ".lei");
if (!lei.exists()) {
lei = new Location(prefix + ".LEI");
while (!lei.exists() && prefix.indexOf("_") != -1) {
prefix = prefix.substring(0, prefix.lastIndexOf("_"));
lei = new Location(prefix + ".lei");
if (!lei.exists()) lei = new Location(prefix + ".LEI");
}
}
if (lei.exists()) return false;
try {
RandomAccessInputStream s = new RandomAccessInputStream(name);
boolean isThisType = isThisType(s);
s.close();
return isThisType;
}
catch (IOException e) {
LOGGER.debug("", e);
return false;
}
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
public int fileGroupOption(String id) throws FormatException, IOException {
return MUST_GROUP;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
// check for Leica TCS IFD directory entries
TiffParser tp = new TiffParser(stream);
IFD ifd = tp.getFirstIFD();
if (ifd == null) {
stream.seek(0);
return stream.readString(6).equals("<Data>");
}
String document = ifd.getIFDTextValue(IFD.DOCUMENT_NAME);
if (document == null) document = "";
String software = ifd.getIFDTextValue(IFD.SOFTWARE);
if (software == null) software = "";
software = software.trim();
return document.startsWith("CHANNEL") || software.startsWith("TCS");
}
/* @see loci.formats.IFormatReader#get8BitLookupTable() */
public byte[][] get8BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
return tiffReaders[lastPlane].get8BitLookupTable();
}
/* @see loci.formats.IFormatReader#get16BitLookupTable() */
public short[][] get16BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
return tiffReaders[lastPlane].get16BitLookupTable();
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int n = no;
for (int i=0; i<series; i++) {
n += core[i].imageCount;
}
if (tiffReaders.length == 1) {
return tiffReaders[0].openBytes(n, buf, x, y, w, h);
}
int plane = 0;
if (tiffReaders[0].getImageCount() > 1) {
n /= tiffReaders.length;
plane = n % tiffReaders.length;
}
if (lastPlane != 0) {
tiffReaders[lastPlane].close();
}
lastPlane = n;
tiffReaders[n].setId(tiffs.get(n));
return tiffReaders[n].openBytes(plane, buf, x, y, w, h);
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return xmlFile == null ? null : new String[] {xmlFile};
}
Vector<String> v = new Vector<String>();
v.addAll(tiffs);
if (xmlFile != null) v.add(xmlFile);
return v.toArray(new String[v.size()]);
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
tiffs = null;
if (tiffReaders != null) {
for (TiffReader r : tiffReaders) {
if (r != null) r.close();
}
}
tiffReaders = null;
tiffParser = null;
datestamp = 0;
xmlFile = null;
lastPlane = 0;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
Location l = new Location(id).getAbsoluteFile();
Location parent = l.getParentFile();
String[] list = parent.list();
boolean isXML = checkSuffix(id, XML_SUFFIX);
if (list != null) {
for (String file : list) {
if (checkSuffix(file, XML_SUFFIX) && !isXML && isGroupFiles()) {
xmlFile = new Location(parent, file).getAbsolutePath();
break;
}
else if (checkSuffix(file, TiffReader.TIFF_SUFFIXES) && isXML) {
initFile(new Location(parent, file).getAbsolutePath());
return;
}
}
}
if (isXML) xmlFile = l.getAbsolutePath();
super.initFile(id);
MetadataStore store = makeFilterMetadata();
in = new RandomAccessInputStream(id);
tiffParser = new TiffParser(in);
tiffs = new Vector<String>();
IFDList ifds = tiffParser.getIFDs();
String date = ifds.get(0).getIFDStringValue(IFD.DATE_TIME);
if (date != null) {
datestamp = DateTools.getTime(date, "yyyy:MM:dd HH:mm:ss");
}
groupFiles();
addGlobalMeta("Number of image files", tiffs.size());
tiffReaders = new TiffReader[tiffs.size()];
for (int i=0; i<tiffReaders.length; i++) {
tiffReaders[i] = new TiffReader();
}
tiffReaders[0].setId(tiffs.get(0));
int[] ch = new int[ifds.size()];
int[] idx = new int[ifds.size()];
long[] stamp = new long[ifds.size()];
int channelCount = 0;
core[0].sizeZ = 1;
core[0].sizeC = tiffReaders[0].getSizeC();
core[0].dimensionOrder = isRGB() ? "XYC" : "XY";
if (isGroupFiles()) {
try {
FilePattern fp =
new FilePattern(new Location(currentId).getAbsoluteFile());
AxisGuesser guesser =
new AxisGuesser(fp, "XYTZC", 1, ifds.size(), 1, true);
int[] axisTypes = guesser.getAxisTypes();
int[] count = fp.getCount();
for (int i=axisTypes.length-1; i>=0; i--) {
if (axisTypes[i] == AxisGuesser.Z_AXIS) {
if (getDimensionOrder().indexOf("Z") == -1) {
core[0].dimensionOrder += "Z";
}
core[0].sizeZ *= count[i];
}
else if (axisTypes[i] == AxisGuesser.C_AXIS) {
if (getDimensionOrder().indexOf("C") == -1) {
core[0].dimensionOrder += "C";
}
core[0].sizeC *= count[i];
}
}
}
catch (NullPointerException e) { }
}
for (int i=0; i<ifds.size(); i++) {
String document = ifds.get(i).getIFDStringValue(IFD.DOCUMENT_NAME);
if (document == null) continue;
int index = document.indexOf("INDEX");
String s = document.substring(8, index).trim();
ch[i] = Integer.parseInt(s);
if (ch[i] > channelCount) channelCount = ch[i];
int space = document.indexOf(" ", index + 6);
if (space < 0) continue;
String n = document.substring(index + 6, space).trim();
idx[i] = Integer.parseInt(n);
date = document.substring(space, document.indexOf("FORMAT")).trim();
stamp[i] = DateTools.getTime(date, DATE_FORMAT);
addGlobalMeta("Timestamp for plane #" + i, stamp[i]);
}
core[0].sizeT = 0;
// determine the axis sizes and ordering
boolean unique = true;
for (int i=0; i<stamp.length; i++) {
for (int j=i+1; j<stamp.length; j++) {
if (stamp[j] == stamp[i]) {
unique = false;
break;
}
}
if (unique) {
core[0].sizeT++;
if (getDimensionOrder().indexOf("T") < 0) {
core[0].dimensionOrder += "T";
}
}
else if (i > 0) {
if ((ch[i] != ch[i - 1]) && getDimensionOrder().indexOf("C") < 0) {
core[0].dimensionOrder += "C";
}
else if (getDimensionOrder().indexOf("Z") < 0) {
core[0].dimensionOrder += "Z";
}
}
unique = true;
}
if (getDimensionOrder().indexOf("Z") < 0) core[0].dimensionOrder += "Z";
if (getDimensionOrder().indexOf("C") < 0) core[0].dimensionOrder += "C";
if (getDimensionOrder().indexOf("T") < 0) core[0].dimensionOrder += "T";
if (getSizeC() == 0) core[0].sizeC = 1;
if (getSizeT() == 0) core[0].sizeT = 1;
if (channelCount == 0) channelCount = 1;
if (getSizeZ() <= 1) {
core[0].sizeZ = ifds.size() / (getSizeT() * channelCount);
}
core[0].sizeC *= channelCount;
core[0].imageCount = getSizeZ() * getSizeT() * getSizeC();
// cut up comment
String comment = ifds.get(0).getComment();
if (comment != null && comment.startsWith("[") &&
getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM)
{
String[] lines = comment.split("\n");
for (String line : lines) {
if (!line.startsWith("[")) {
int eq = line.indexOf("=");
if (eq < 0) continue;
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1).trim();
if (key.equals("VoxelSizeX")) {
try {
voxelX = Double.parseDouble(value);
}
catch (NumberFormatException e) { }
}
else if (key.equals("VoxelSizeY")) {
try {
voxelY = Double.parseDouble(value);
}
catch (NumberFormatException e) { }
}
else if (key.equals("VoxelSizeZ")) {
try {
voxelZ = Double.parseDouble(value);
}
catch (NumberFormatException e) { }
}
addGlobalMeta(key, value);
}
}
metadata.remove("Comment");
}
core[0].sizeX = tiffReaders[0].getSizeX();
core[0].sizeY = tiffReaders[0].getSizeY();
core[0].rgb = tiffReaders[0].isRGB();
core[0].pixelType = tiffReaders[0].getPixelType();
core[0].littleEndian = tiffReaders[0].isLittleEndian();
core[0].interleaved = tiffReaders[0].isInterleaved();
core[0].falseColor = true;
core[0].indexed = tiffReaders[0].isIndexed();
if (isRGB()) core[0].imageCount /= (getSizeC() / channelCount);
if (getSizeZ() * getSizeT() * getEffectiveSizeC() !=
(ifds.size() * tiffReaders.length))
{
core[0].sizeZ = 1;
int c = getEffectiveSizeC();
if (c == 0) c = 1;
core[0].sizeT = (ifds.size() * tiffReaders.length) / c;
core[0].imageCount = getSizeT() * c;
if (getSizeT() == 0) {
core[0].sizeT = 1;
core[0].imageCount = ifds.size() * tiffReaders.length;
}
}
if (getImageCount() == ifds.size() * getSizeZ() * getSizeT() &&
ifds.size() > 1)
{
if (getSizeZ() == 1) {
core[0].sizeZ = ifds.size();
}
else if (getSizeT() == 1) {
core[0].sizeT = ifds.size();
}
else core[0].sizeZ *= ifds.size();
}
if (xmlFile != null) {
// parse XML metadata
String xml = DataTools.readFile(xmlFile);
xml = XMLTools.sanitizeXML(PREFIX + xml + SUFFIX);
LeicaHandler handler =
new LeicaHandler(store, getMetadataOptions().getMetadataLevel());
XMLTools.parseXML(xml, handler);
metadata = handler.getGlobalMetadata();
MetadataTools.merge(handler.getGlobalMetadata(), metadata, "");
core = handler.getCoreMetadata().toArray(new CoreMetadata[0]);
for (int i=0; i<getSeriesCount(); i++) {
if (tiffs.size() < core[i].imageCount) {
int div = core[i].imageCount / core[i].sizeC;
core[i].imageCount = tiffs.size();
if (div >= core[i].sizeZ) core[i].sizeZ /= div;
else if (div >= core[i].sizeT) core[i].sizeT /= div;
}
core[i].dimensionOrder = getSizeZ() > getSizeT() ? "XYCZT" : "XYCTZ";
core[i].rgb = false;
core[i].interleaved = false;
core[i].indexed = tiffReaders[0].isIndexed();
}
}
MetadataTools.populatePixels(store, this, true);
for (int i=0; i<getSeriesCount(); i++) {
MetadataTools.setDefaultCreationDate(store, id, i);
}
if (voxelX > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(voxelX), 0);
}
if (voxelY > 0) {
store.setPixelsPhysicalSizeY(new PositiveFloat(voxelY), 0);
}
if (voxelZ > 0) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(voxelZ), 0);
}
}
// -- Helper methods --
private void groupFiles() throws FormatException, IOException {
// look for associated TIFF files
// we assume that two files are grouped if all of the following are true:
//
// * the files are in the same directory
// * the file names are the same length
// * the time stamps are less than 60 seconds apart
// * the files have the same number of bytes
Location current = new Location(currentId).getAbsoluteFile();
if (!checkSuffix(currentId, XML_SUFFIX)) {
tiffs.add(current.getAbsolutePath());
}
if (!isGroupFiles()) return;
Location parent = current.getParentFile();
String[] list = parent.list();
Arrays.sort(list);
HashMap<String, Long> timestamps = new HashMap<String, Long>();
for (String file : list) {
file = new Location(parent, file).getAbsolutePath();
if (file.length() != current.getAbsolutePath().length()) continue;
RandomAccessInputStream rais = new RandomAccessInputStream(file);
if (Math.abs(rais.length() - in.length()) > 16) {
rais.close();
continue;
}
TiffParser tp = new TiffParser(rais);
if (!tp.isValidHeader()) {
continue;
}
IFD ifd = tp.getIFDs().get(0);
String date = ifd.getIFDStringValue(IFD.DATE_TIME);
if (date != null) {
long stamp = DateTools.getTime(date, "yyyy:MM:dd HH:mm:ss");
String software = ifd.getIFDStringValue(IFD.SOFTWARE);
if (software != null && software.trim().startsWith("TCS")) {
timestamps.put(file, new Long(stamp));
}
}
rais.close();
}
String[] files = timestamps.keySet().toArray(new String[timestamps.size()]);
Arrays.sort(files);
for (String file : files) {
long thisStamp = timestamps.get(file).longValue();
boolean match = false;
for (String tiff : tiffs) {
RandomAccessInputStream s = new RandomAccessInputStream(tiff);
TiffParser parser = new TiffParser(s);
IFD ifd = parser.getIFDs().get(0);
s.close();
String date = ifd.getIFDStringValue(IFD.DATE_TIME);
long nextStamp = DateTools.getTime(date, "yyyy:MM:dd HH:mm:ss");
if (Math.abs(thisStamp - nextStamp) < 600000) {
match = true;
break;
}
}
if (match && !tiffs.contains(file)) tiffs.add(file);
}
}
}