/** @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 {
if (getSeriesCount() == 1) return super.openBytes(no, buf, x, y, w, h);
int[] lengths =
new int[] {
getSizeZ(), getEffectiveSizeC(), fieldColumnCount, fieldRowCount, wellCount, getSizeT()
};
int[] zct = getZCTCoords(no);
Well well = getWell(getSeries());
int[] position = new int[] {zct[0], zct[1], well.fieldCol, well.fieldRow, well.well, zct[2]};
int fileIndex = FormatTools.positionToRaster(lengths, position);
RandomAccessInputStream s = null;
if (fileIndex < files.length) {
s = new RandomAccessInputStream(files[fileIndex]);
} else {
s = new RandomAccessInputStream(files[0]);
}
TiffParser parser = new TiffParser(s);
IFD ifd =
files.length == 1 ? ifds.get(getSeries() * getImageCount() + no) : parser.getFirstIFD();
parser.getSamples(ifd, buf, x, y, w, h);
s.close();
return buf;
}
private void parseFile(String tiff, MetamorphHandler handler) throws IOException {
RandomAccessInputStream s = new RandomAccessInputStream(tiff);
TiffParser parser = new TiffParser(s);
IFD firstIFD = parser.getFirstIFD();
String xml = XMLTools.sanitizeXML(firstIFD.getComment());
XMLTools.parseXML(xml, handler);
s.close();
}
private long getTimestamp(String file) throws FormatException, IOException {
RandomAccessInputStream s = new RandomAccessInputStream(file);
TiffParser parser = new TiffParser(s);
parser.setDoCaching(false);
IFD firstIFD = parser.getFirstIFD();
if (firstIFD != null) {
TiffIFDEntry timestamp = (TiffIFDEntry) firstIFD.get(IFD.DATE_TIME);
if (timestamp != null) {
String stamp = parser.getIFDValue(timestamp).toString();
s.close();
stamp = DateTools.formatDate(stamp, BaseTiffReader.DATE_FORMATS);
return DateTools.getTime(stamp, DateTools.ISO8601_FORMAT);
}
}
s.close();
return new Location(file).lastModified();
}
/**
* Constructor RawDataBlockList
*
* @param stream the InputStream from which the data will be read
* @exception IOException on I/O errors, and if an incomplete block is read
*/
public RawDataBlockList(final RandomAccessInputStream stream, int size) throws IOException {
List blocks = new ArrayList();
bigBlockSize = size;
while (true) {
RawDataBlock block = new RawDataBlock(stream, size);
if (block.eof()) {
break;
}
blocks.add(block);
if (size + stream.getFilePointer() > stream.length()) {
break;
}
stream.skipBytes(size);
}
setBlocks((RawDataBlock[]) blocks.toArray(new RawDataBlock[0]));
}
/* @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
if (name.equals(METADATA)
|| name.endsWith(File.separator + METADATA)
|| name.equals(XML)
|| name.endsWith(File.separator + XML)) {
final int blockSize = 1048576;
try {
RandomAccessInputStream stream = new RandomAccessInputStream(name);
long length = stream.length();
String data = stream.readString((int) Math.min(blockSize, length));
stream.close();
return length > 0
&& (data.indexOf("Micro-Manager") >= 0 || data.indexOf("micromanager") >= 0);
} catch (IOException e) {
return false;
}
}
try {
Location parent = new Location(name).getAbsoluteFile().getParentFile();
Location metaFile = new Location(parent, METADATA);
RandomAccessInputStream s = new RandomAccessInputStream(name);
boolean validTIFF = isThisType(s);
s.close();
return validTIFF && isThisType(metaFile.getAbsolutePath(), open);
} catch (NullPointerException e) {
} catch (IOException e) {
}
return false;
}
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
FormatTools.checkPlaneNumber(this, no);
FormatTools.checkBufferSize(this, buf.length, w, h);
final int[] zct = FormatTools.getZCTCoords(this, no);
final byte[] plane;
try {
plane = store.getPlane(zct[0], zct[1], zct[2]);
} catch (ServerError e) {
throw new FormatException(e);
}
RandomAccessInputStream s = new RandomAccessInputStream(plane);
readPlane(s, x, y, w, h, buf);
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
byte[] signature = new byte[blockLen];
stream.read(signature);
if (signature[0] != (byte) 0xff
|| signature[1] != (byte) 0xd8
|| signature[2] != (byte) 0xff
|| ((int) signature[3] & 0xf0) == 0) {
return false;
}
return true;
}
private long readUnsignedLong(RandomAccessInputStream in) throws IOException {
return in.readInt() & 0xffffffffL;
}
private void readTags(RandomAccessInputStream vsi) throws IOException {
// read the VSI header
long fp = vsi.getFilePointer();
if (fp + 24 >= vsi.length()) {
return;
}
int headerSize = vsi.readShort(); // should always be 24
int version = vsi.readShort(); // always 21321
int volumeVersion = vsi.readInt();
long dataFieldOffset = vsi.readLong();
int flags = vsi.readInt();
vsi.skipBytes(4);
int tagCount = flags & 0xfffffff;
if (fp + dataFieldOffset < 0) {
return;
}
vsi.seek(fp + dataFieldOffset);
if (vsi.getFilePointer() >= vsi.length()) {
return;
}
for (int i = 0; i < tagCount; i++) {
if (vsi.getFilePointer() + 16 >= vsi.length()) {
break;
}
// read the data field
int fieldType = vsi.readInt();
int tag = vsi.readInt();
long nextField = vsi.readInt() & 0xffffffffL;
int dataSize = vsi.readInt();
boolean extraTag = ((fieldType & 0x8000000) >> 27) == 1;
boolean extendedField = ((fieldType & 0x10000000) >> 28) == 1;
boolean inlineData = ((fieldType & 0x40000000) >> 30) == 1;
boolean array = (!inlineData && !extendedField) && ((fieldType & 0x20000000) >> 29) == 1;
boolean newVolume = ((fieldType & 0x80000000) >> 31) == 1;
int realType = fieldType & 0xffffff;
int secondTag = -1;
if (extraTag) {
secondTag = vsi.readInt();
}
if (extendedField && realType == NEW_VOLUME_HEADER) {
if (tag == 2007) {
dimensionTag = secondTag;
inDimensionProperties = true;
}
long endPointer = vsi.getFilePointer() + dataSize;
while (vsi.getFilePointer() < endPointer && vsi.getFilePointer() < vsi.length()) {
long start = vsi.getFilePointer();
readTags(vsi);
long end = vsi.getFilePointer();
if (start == end) {
break;
}
}
if (tag == 2007) {
inDimensionProperties = false;
foundChannelTag = false;
}
}
if (inDimensionProperties) {
if (tag == 2012 && !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("Z", dimensionTag);
} else if ((tag == 2100 || tag == 2027) && !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("T", dimensionTag);
} else if (tag == 2039 && !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("L", dimensionTag);
} else if (tag == 2008
&& foundChannelTag
&& !dimensionOrdering.containsValue(dimensionTag)) {
dimensionOrdering.put("C", dimensionTag);
} else if (tag == 2008) {
foundChannelTag = true;
}
}
if (nextField == 0) {
return;
}
if (fp + nextField < vsi.length() && fp + nextField >= 0) {
vsi.seek(fp + nextField);
} else break;
}
}
/**
* Constructs a new SDT header by reading values from the given input source, populating the given
* metadata table.
*/
public SDTInfo(RandomAccessInputStream in, Hashtable meta) throws IOException {
// read bhfileHeader
revision = in.readShort();
infoOffs = in.readInt();
infoLength = in.readShort();
setupOffs = in.readInt();
setupLength = in.readShort();
dataBlockOffs = in.readInt();
noOfDataBlocks = in.readShort();
dataBlockLength = in.readInt();
measDescBlockOffs = in.readInt();
noOfMeasDescBlocks = in.readShort();
measDescBlockLength = in.readShort();
headerValid = in.readUnsignedShort();
reserved1 = (0xffffffffL & in.readInt()); // unsigned
reserved2 = in.readUnsignedShort();
chksum = in.readUnsignedShort();
// save bhfileHeader to metadata table
if (meta != null) {
final String bhfileHeader = "bhfileHeader.";
meta.put(bhfileHeader + "revision", new Short(revision));
meta.put(bhfileHeader + "infoOffs", new Integer(infoOffs));
meta.put(bhfileHeader + "infoLength", new Short(infoLength));
meta.put(bhfileHeader + "setupOffs", new Integer(setupOffs));
meta.put(bhfileHeader + "dataBlockOffs", new Integer(dataBlockOffs));
meta.put(bhfileHeader + "noOfDataBlocks", new Short(noOfDataBlocks));
meta.put(bhfileHeader + "dataBlockLength", new Integer(dataBlockLength));
meta.put(bhfileHeader + "measDescBlockOffs", new Integer(measDescBlockOffs));
meta.put(bhfileHeader + "noOfMeasDescBlocks", new Short(noOfMeasDescBlocks));
meta.put(bhfileHeader + "measDescBlockLength", new Integer(measDescBlockLength));
meta.put(bhfileHeader + "headerValid", new Integer(headerValid));
meta.put(bhfileHeader + "reserved1", new Long(reserved1));
meta.put(bhfileHeader + "reserved2", new Integer(reserved2));
meta.put(bhfileHeader + "chksum", new Integer(chksum));
}
// read file info
in.seek(infoOffs);
byte[] infoBytes = new byte[infoLength];
in.readFully(infoBytes);
info = new String(infoBytes, Constants.ENCODING);
StringTokenizer st = new StringTokenizer(info, "\n");
int count = st.countTokens();
st.nextToken();
String key = null, value = null;
for (int i = 1; i < count - 1; i++) {
String token = st.nextToken().trim();
if (token.indexOf(":") == -1) continue;
key = token.substring(0, token.indexOf(":")).trim();
value = token.substring(token.indexOf(":") + 1).trim();
meta.put(key, value);
}
// read setup
in.seek(setupOffs);
byte[] setupBytes = new byte[setupLength];
in.readFully(setupBytes);
setup = new String(setupBytes, Constants.ENCODING);
int textEnd = setup.indexOf(BINARY_SETUP);
if (textEnd > 0) {
setup = setup.substring(0, textEnd);
textEnd += BINARY_SETUP.length();
in.seek(setupOffs + textEnd);
}
// variables to hold height & width read from header string for measMode 13
int mode13width = 0;
int mode13height = 0;
st = new StringTokenizer(setup, "\n");
while (st.hasMoreTokens()) {
String token = st.nextToken().trim();
if (token.startsWith("#SP")
|| token.startsWith("#DI")
|| token.startsWith("#PR")
|| token.startsWith("#MP")) {
int open = token.indexOf("[");
key = token.substring(open + 1, token.indexOf(",", open));
value = token.substring(token.lastIndexOf(",") + 1, token.length() - 1);
} else if (token.startsWith("#TR") || token.startsWith("#WI")) {
key = token.substring(0, token.indexOf("[")).trim();
value = token.substring(token.indexOf("[") + 1, token.indexOf("]"));
}
if (key != null && value != null) meta.put(key, value);
if (token.indexOf(X_STRING) != -1) {
int ndx = token.indexOf(X_STRING) + X_STRING.length();
int end = token.indexOf("]", ndx);
width = Integer.parseInt(token.substring(ndx, end));
} else if (token.indexOf(Y_STRING) != -1) {
int ndx = token.indexOf(Y_STRING) + Y_STRING.length();
int end = token.indexOf("]", ndx);
height = Integer.parseInt(token.substring(ndx, end));
} else if (token.indexOf(T_STRING) != -1) {
int ndx = token.indexOf(T_STRING) + T_STRING.length();
int end = token.indexOf("]", ndx);
timeBins = Integer.parseInt(token.substring(ndx, end));
} else if (token.indexOf(C_STRING) != -1) {
int ndx = token.indexOf(C_STRING) + C_STRING.length();
int end = token.indexOf("]", ndx);
channels = Integer.parseInt(token.substring(ndx, end));
} else if (token.indexOf(X_IMG_STRING) != -1) {
int ndx = token.indexOf(X_IMG_STRING) + X_IMG_STRING.length();
int end = token.indexOf("]", ndx);
mode13width = Integer.parseInt(token.substring(ndx, end));
} else if (token.indexOf(Y_IMG_STRING) != -1) {
int ndx = token.indexOf(Y_IMG_STRING) + Y_IMG_STRING.length();
int end = token.indexOf("]", ndx);
mode13height = Integer.parseInt(token.substring(ndx, end));
}
}
if (in.getFilePointer() < setupOffs + setupLength) {
// BHBinHdr
in.skipBytes(4);
long baseOffset = in.getFilePointer();
long softwareRevision = readUnsignedLong(in);
long paramLength = readUnsignedLong(in);
long reserved1 = readUnsignedLong(in);
int reserved2 = in.readShort() & 0xffff;
// SPCBinHdr
long fcsOldOffset = readUnsignedLong(in);
long fcsOldSize = readUnsignedLong(in);
long gr1Offset = readUnsignedLong(in);
long gr1Size = readUnsignedLong(in);
long fcsOffset = readUnsignedLong(in);
long fcsSize = readUnsignedLong(in);
long fidaOffset = readUnsignedLong(in);
long fidaSize = readUnsignedLong(in);
long fildaOffset = readUnsignedLong(in);
long fildaSize = readUnsignedLong(in);
long gr2Offset = readUnsignedLong(in);
int grNo = in.readShort() & 0xffff;
int hstNo = in.readShort() & 0xffff;
long hstOffset = readUnsignedLong(in);
long gvdOffset = readUnsignedLong(in);
int gvdSize = in.readShort() & 0xffff;
int fitOffset = in.readShort() & 0xffff;
int fitSize = in.readShort() & 0xffff;
int extdevOffset = in.readShort() & 0xffff;
int extdevSize = in.readShort() & 0xffff;
long binhdrextOffset = readUnsignedLong(in);
int binhdrextSize = in.readShort() & 0xffff;
if (binhdrextOffset != 0) {
in.seek(baseOffset + binhdrextOffset);
long mcsImgOffset = readUnsignedLong(in);
long mcsImgSize = readUnsignedLong(in);
int momNo = in.readShort() & 0xffff;
int momSize = in.readShort() & 0xffff;
long momOffset = readUnsignedLong(in);
long sysparExtOffset = readUnsignedLong(in);
long sysparExtSize = readUnsignedLong(in);
long mosaicOffset = readUnsignedLong(in);
long mosaicSize = readUnsignedLong(in);
// 52 longs reserved
if (mcsImgOffset != 0) {
in.seek(baseOffset + mcsImgOffset);
int mcsActive = in.readInt();
in.skipBytes(4); // Window
mcstaPoints = in.readShort() & 0xffff;
int mcstaFlags = in.readShort() & 0xffff;
int mcstaTimePerPoint = in.readShort() & 0xffff;
float mcsOffset = in.readFloat();
float mcsTpp = in.readFloat();
if (meta != null) {
meta.put("MCS_TA.active", mcsActive);
meta.put("MCS_TA.points", mcstaPoints);
meta.put("MCS_TA.flags", mcstaFlags);
meta.put("MCS_TA.time per point", mcstaTimePerPoint);
}
}
}
}
// read measurement data
if (noOfMeasDescBlocks > 0) {
in.seek(measDescBlockOffs);
hasMeasureInfo = measDescBlockLength >= 211;
hasMeasStopInfo = measDescBlockLength >= 211 + 60;
hasMeasFCSInfo = measDescBlockLength >= 211 + 60 + 38;
hasExtendedMeasureInfo = measDescBlockLength >= 211 + 60 + 38 + 26;
hasMeasHISTInfo = measDescBlockLength >= 211 + 60 + 38 + 26 + 24;
if (hasMeasureInfo) {
time = in.readString(9).trim();
date = in.readString(11).trim();
modSerNo = in.readString(16).trim();
measMode = in.readShort();
cfdLL = in.readFloat();
cfdLH = in.readFloat();
cfdZC = in.readFloat();
cfdHF = in.readFloat();
synZC = in.readFloat();
synFD = in.readShort();
synHF = in.readFloat();
tacR = in.readFloat();
tacG = in.readShort();
tacOF = in.readFloat();
tacLL = in.readFloat();
tacLH = in.readFloat();
adcRE = in.readShort();
ealDE = in.readShort();
ncx = in.readShort();
ncy = in.readShort();
page = in.readUnsignedShort();
colT = in.readFloat();
repT = in.readFloat();
stopt = in.readShort();
overfl = in.readUnsignedByte();
useMotor = in.readShort();
steps = in.readUnsignedShort();
offset = in.readFloat();
dither = in.readShort();
incr = in.readShort();
memBank = in.readShort();
modType = in.readString(16).trim();
synTH = in.readFloat();
deadTimeComp = in.readShort();
polarityL = in.readShort();
polarityF = in.readShort();
polarityP = in.readShort();
linediv = in.readShort();
accumulate = in.readShort();
flbckY = in.readInt();
flbckX = in.readInt();
bordU = in.readInt();
bordL = in.readInt();
pixTime = in.readFloat();
pixClk = in.readShort();
trigger = in.readShort();
scanX = in.readInt();
scanY = in.readInt();
scanRX = in.readInt();
scanRY = in.readInt();
fifoTyp = in.readShort();
epxDiv = in.readInt();
modTypeCode = in.readUnsignedShort();
modFpgaVer = in.readUnsignedShort();
overflowCorrFactor = in.readFloat();
adcZoom = in.readInt();
cycles = in.readInt();
timepoints = stopt;
// save MeasureInfo to metadata table
if (meta != null) {
final String measureInfo = "MeasureInfo.";
meta.put(measureInfo + "time", time);
meta.put(measureInfo + "date", date);
meta.put(measureInfo + "modSerNo", modSerNo);
meta.put(measureInfo + "measMode", new Short(measMode));
meta.put(measureInfo + "cfdLL", new Float(cfdLL));
meta.put(measureInfo + "cfdLH", new Float(cfdLH));
meta.put(measureInfo + "cfdZC", new Float(cfdZC));
meta.put(measureInfo + "cfdHF", new Float(cfdHF));
meta.put(measureInfo + "synZC", new Float(synZC));
meta.put(measureInfo + "synFD", new Short(synFD));
meta.put(measureInfo + "synHF", new Float(synHF));
meta.put(measureInfo + "tacR", new Float(tacR));
meta.put(measureInfo + "tacG", new Short(tacG));
meta.put(measureInfo + "tacOF", new Float(tacOF));
meta.put(measureInfo + "tacLL", new Float(tacLL));
meta.put(measureInfo + "tacLH", new Float(tacLH));
meta.put(measureInfo + "adcRE", new Short(adcRE));
meta.put(measureInfo + "ealDE", new Short(ealDE));
meta.put(measureInfo + "ncx", new Short(ncx));
meta.put(measureInfo + "ncy", new Short(ncy));
meta.put(measureInfo + "page", new Integer(page));
meta.put(measureInfo + "colT", new Float(colT));
meta.put(measureInfo + "repT", new Float(repT));
meta.put(measureInfo + "stopt", new Short(stopt));
meta.put(measureInfo + "overfl", new Integer(overfl));
meta.put(measureInfo + "useMotor", new Short(useMotor));
meta.put(measureInfo + "steps", new Integer(steps));
meta.put(measureInfo + "offset", new Float(offset));
meta.put(measureInfo + "dither", new Short(dither));
meta.put(measureInfo + "incr", new Short(incr));
meta.put(measureInfo + "memBank", new Short(memBank));
meta.put(measureInfo + "modType", modType);
meta.put(measureInfo + "synTH", new Float(synTH));
meta.put(measureInfo + "deadTimeComp", new Short(deadTimeComp));
meta.put(measureInfo + "polarityL", new Short(polarityL));
meta.put(measureInfo + "polarityF", new Short(polarityF));
meta.put(measureInfo + "polarityP", new Short(polarityP));
meta.put(measureInfo + "linediv", new Short(linediv));
meta.put(measureInfo + "accumulate", new Short(accumulate));
meta.put(measureInfo + "flbckY", new Integer(flbckY));
meta.put(measureInfo + "flbckX", new Integer(flbckX));
meta.put(measureInfo + "bordU", new Integer(bordU));
meta.put(measureInfo + "bordL", new Integer(bordL));
meta.put(measureInfo + "pixTime", new Float(pixTime));
meta.put(measureInfo + "pixClk", new Short(pixClk));
meta.put(measureInfo + "trigger", new Short(trigger));
meta.put(measureInfo + "scanX", new Integer(scanX));
meta.put(measureInfo + "scanY", new Integer(scanY));
meta.put(measureInfo + "scanRX", new Integer(scanRX));
meta.put(measureInfo + "scanRY", new Integer(scanRY));
meta.put(measureInfo + "fifoTyp", new Short(fifoTyp));
meta.put(measureInfo + "epxDiv", new Integer(epxDiv));
meta.put(measureInfo + "modTypeCode", new Integer(modTypeCode));
meta.put(measureInfo + "modFpgaVer", new Integer(modFpgaVer));
meta.put(measureInfo + "overflowCorrFactor", new Float(overflowCorrFactor));
meta.put(measureInfo + "adcZoom", new Integer(adcZoom));
meta.put(measureInfo + "cycles", new Integer(cycles));
}
// extract dimensional parameters from measure info
if (scanX > 0) width = scanX;
if (scanY > 0) height = scanY;
if (adcRE > 0) timeBins = adcRE;
if (scanRX > 0) channels = scanRX;
// measurement mode 0 and 1 are both single-point data
if (measMode == 0 || measMode == 1) {
width = 1;
height = 1;
}
// for measurement_mode 13 one channel is stored in each block
// & width & height are not in scanX & scanY
if (measMode == 13) {
width = mode13width;
height = mode13height;
channels = noOfMeasDescBlocks;
}
}
if (hasMeasStopInfo) {
// MeasStopInfo - information collected when measurement is finished
status = in.readUnsignedShort();
flags = in.readUnsignedShort();
stopTime = in.readFloat();
curStep = in.readInt();
curCycle = in.readInt();
curPage = in.readInt();
minSyncRate = in.readFloat();
minCfdRate = in.readFloat();
minTacRate = in.readFloat();
minAdcRate = in.readFloat();
maxSyncRate = in.readFloat();
maxCfdRate = in.readFloat();
maxTacRate = in.readFloat();
maxAdcRate = in.readFloat();
mReserved1 = in.readInt();
mReserved2 = in.readFloat();
// save MeasStopInfo to metadata table
if (meta != null) {
final String measStopInfo = "MeasStopInfo.";
meta.put(measStopInfo + "status", new Integer(status));
meta.put(measStopInfo + "flags", new Integer(flags));
meta.put(measStopInfo + "stopTime", new Float(stopTime));
meta.put(measStopInfo + "curStep", new Integer(curStep));
meta.put(measStopInfo + "curCycle", new Integer(curCycle));
meta.put(measStopInfo + "curPage", new Integer(curPage));
meta.put(measStopInfo + "minSyncRate", new Float(minSyncRate));
meta.put(measStopInfo + "minCfdRate", new Float(minCfdRate));
meta.put(measStopInfo + "minTacRate", new Float(minTacRate));
meta.put(measStopInfo + "minAdcRate", new Float(minAdcRate));
meta.put(measStopInfo + "maxSyncRate", new Float(maxSyncRate));
meta.put(measStopInfo + "maxCfdRate", new Float(maxCfdRate));
meta.put(measStopInfo + "maxTacRate", new Float(maxTacRate));
meta.put(measStopInfo + "maxAdcRate", new Float(maxAdcRate));
meta.put(measStopInfo + "reserved1", new Integer(mReserved1));
meta.put(measStopInfo + "reserved2", new Float(mReserved2));
}
}
if (hasMeasFCSInfo) {
// MeasFCSInfo - information collected when FIFO measurement is finished
chan = in.readUnsignedShort();
fcsDecayCalc = in.readUnsignedShort();
mtResol = (0xffffffffL & in.readInt()); // unsigned
cortime = in.readFloat();
calcPhotons = (0xffffffffL & in.readInt()); // unsigned
fcsPoints = in.readInt();
endTime = in.readFloat();
overruns = in.readUnsignedShort();
fcsType = in.readUnsignedShort();
crossChan = in.readUnsignedShort();
mod = in.readUnsignedShort();
crossMod = in.readUnsignedShort();
crossMtResol = (0xffffffffL & in.readInt()); // unsigned
// save MeasFCSInfo to metadata table
if (meta != null) {
final String measFCSInfo = "MeasFCSInfo.";
meta.put(measFCSInfo + "chan", new Integer(chan));
meta.put(measFCSInfo + "fcsDecayCalc", new Integer(fcsDecayCalc));
meta.put(measFCSInfo + "mtResol", new Long(mtResol));
meta.put(measFCSInfo + "cortime", new Float(cortime));
meta.put(measFCSInfo + "calcPhotons", new Long(calcPhotons));
meta.put(measFCSInfo + "fcsPoints", new Integer(fcsPoints));
meta.put(measFCSInfo + "endTime", new Float(endTime));
meta.put(measFCSInfo + "overruns", new Integer(overruns));
meta.put(measFCSInfo + "fcsType", new Integer(fcsType));
meta.put(measFCSInfo + "crossChan", new Integer(crossChan));
meta.put(measFCSInfo + "mod", new Integer(mod));
meta.put(measFCSInfo + "crossMod", new Integer(crossMod));
meta.put(measFCSInfo + "crossMtResol", new Float(crossMtResol));
}
}
if (hasExtendedMeasureInfo) {
imageX = in.readInt();
imageY = in.readInt();
imageRX = in.readInt();
imageRY = in.readInt();
xyGain = in.readShort();
masterClock = in.readShort();
adcDE = in.readShort();
detType = in.readShort();
xAxis = in.readShort();
// save extra MeasureInfo to metadata table
if (meta != null) {
final String measureInfo = "MeasureInfo.";
meta.put(measureInfo + "imageX", new Integer(imageX));
meta.put(measureInfo + "imageY", new Integer(imageY));
meta.put(measureInfo + "imageRX", new Integer(imageRX));
meta.put(measureInfo + "imageRY", new Integer(imageRY));
meta.put(measureInfo + "xyGain", new Short(xyGain));
meta.put(measureInfo + "masterClock", new Short(masterClock));
meta.put(measureInfo + "adcDE", new Short(adcDE));
meta.put(measureInfo + "detType", new Short(detType));
meta.put(measureInfo + "xAxis", new Short(xAxis));
}
}
if (hasMeasHISTInfo) {
// MeasHISTInfo - extension of FCSInfo, valid only for FIFO meas
// extension of MeasFCSInfo for other histograms (FIDA, FILDA, MCS)
fidaTime = in.readFloat();
fildaTime = in.readFloat();
fidaPoints = in.readInt();
fildaPoints = in.readInt();
mcsTime = in.readFloat();
mcsPoints = in.readInt();
// save MeasHISTInfo to metadata table
if (meta != null) {
final String measHISTInfo = "MeasHISTInfo.";
meta.put(measHISTInfo + "fidaTime", new Float(fidaTime));
meta.put(measHISTInfo + "fildaTime", new Float(fildaTime));
meta.put(measHISTInfo + "fidaPoints", new Integer(fidaPoints));
meta.put(measHISTInfo + "fildaPoints", new Integer(fildaPoints));
meta.put(measHISTInfo + "mcsTime", new Float(mcsTime));
meta.put(measHISTInfo + "mcsPoints", new Integer(mcsPoints));
}
}
}
in.seek(dataBlockOffs);
allBlockOffsets = new long[noOfDataBlocks];
allBlockLengths = new long[noOfDataBlocks];
for (int i = 0; i < noOfDataBlocks; i++) {
// read BHFileBlockHeader
blockNo = in.readShort();
dataOffs = in.readInt();
nextBlockOffs = in.readInt();
blockType = in.readUnsignedShort();
measDescBlockNo = in.readShort();
lblockNo = (0xffffffffL & in.readInt()); // unsigned
int len = in.readInt();
blockLength = (0xffffffffL & len); // unsigned
allBlockOffsets[i] = in.getFilePointer();
allBlockLengths[i] = blockLength;
// save BHFileBlockHeader to metadata table
if (meta != null) {
final String bhFileBlockHeader = "BHFileBlockHeader.";
meta.put(bhFileBlockHeader + "blockNo", new Short(blockNo));
meta.put(bhFileBlockHeader + "dataOffs", new Integer(dataOffs));
meta.put(bhFileBlockHeader + "nextBlockOffs", new Integer(nextBlockOffs));
meta.put(bhFileBlockHeader + "blockType", new Integer(blockType));
meta.put(bhFileBlockHeader + "measDescBlockNo", new Short(measDescBlockNo));
meta.put(bhFileBlockHeader + "lblockNo", new Long(lblockNo));
meta.put(bhFileBlockHeader + "blockLength", new Long(blockLength));
}
in.skipBytes(len);
}
}
private byte[] decodeTile(int no, int row, int col) throws FormatException, IOException {
if (tileMap[getCoreIndex()] == null) {
return new byte[getTileSize()];
}
int[] zct = getZCTCoords(no);
TileCoordinate t = new TileCoordinate(nDimensions[getCoreIndex()]);
t.coordinate[0] = col;
t.coordinate[1] = row;
for (String dim : dimensionOrdering.keySet()) {
int index = dimensionOrdering.get(dim) + 2;
if (dim.equals("Z")) {
t.coordinate[index] = zct[0];
} else if (dim.equals("C")) {
t.coordinate[index] = zct[1];
} else if (dim.equals("T")) {
t.coordinate[index] = zct[2];
}
}
Integer index = (Integer) tileMap[getCoreIndex()].get(t);
if (index == null) {
return new byte[getTileSize()];
}
Long offset = tileOffsets[getCoreIndex()][index];
RandomAccessInputStream ets = new RandomAccessInputStream(usedFiles[getCoreIndex()]);
ets.seek(offset);
CodecOptions options = new CodecOptions();
options.interleaved = isInterleaved();
options.littleEndian = isLittleEndian();
int tileSize = getTileSize();
if (tileSize == 0) {
tileSize = tileX[getCoreIndex()] * tileY[getCoreIndex()] * 10;
}
options.maxBytes = (int) (offset + tileSize);
byte[] buf = null;
long end =
index < tileOffsets[getCoreIndex()].length - 1
? tileOffsets[getCoreIndex()][index + 1]
: ets.length();
IFormatReader reader = null;
String file = null;
switch (compressionType[getCoreIndex()]) {
case RAW:
buf = new byte[tileSize];
ets.read(buf);
break;
case JPEG:
Codec codec = new JPEGCodec();
buf = codec.decompress(ets, options);
break;
case JPEG_2000:
codec = new JPEG2000Codec();
buf = codec.decompress(ets, options);
break;
case PNG:
file = "tile.png";
reader = new APNGReader();
case BMP:
if (reader == null) {
file = "tile.bmp";
reader = new BMPReader();
}
byte[] b = new byte[(int) (end - offset)];
ets.read(b);
Location.mapFile(file, new ByteArrayHandle(b));
reader.setId(file);
buf = reader.openBytes(0);
Location.mapFile(file, null);
break;
}
if (reader != null) {
reader.close();
}
ets.close();
return buf;
}
private void parseETSFile(String file, int s) throws FormatException, IOException {
RandomAccessInputStream etsFile = new RandomAccessInputStream(file);
etsFile.order(true);
// read the volume header
String magic = etsFile.readString(4).trim();
if (!magic.equals("SIS")) {
throw new FormatException("Unknown magic bytes: " + magic);
}
int headerSize = etsFile.readInt();
int version = etsFile.readInt();
nDimensions[s] = etsFile.readInt();
long additionalHeaderOffset = etsFile.readLong();
int additionalHeaderSize = etsFile.readInt();
etsFile.skipBytes(4); // reserved
long usedChunkOffset = etsFile.readLong();
int nUsedChunks = etsFile.readInt();
etsFile.skipBytes(4); // reserved
// read the additional header
etsFile.seek(additionalHeaderOffset);
String moreMagic = etsFile.readString(4).trim();
if (!moreMagic.equals("ETS")) {
throw new FormatException("Unknown magic bytes: " + moreMagic);
}
etsFile.skipBytes(4); // extra version number
int pixelType = etsFile.readInt();
core[s].sizeC = etsFile.readInt();
int colorspace = etsFile.readInt();
compressionType[s] = etsFile.readInt();
int compressionQuality = etsFile.readInt();
tileX[s] = etsFile.readInt();
tileY[s] = etsFile.readInt();
int tileZ = etsFile.readInt();
core[s].rgb = core[s].sizeC > 1;
// read the used chunks
etsFile.seek(usedChunkOffset);
tileOffsets[s] = new Long[nUsedChunks];
ArrayList<TileCoordinate> tmpTiles = new ArrayList<TileCoordinate>();
for (int chunk = 0; chunk < nUsedChunks; chunk++) {
etsFile.skipBytes(4);
TileCoordinate t = new TileCoordinate(nDimensions[s]);
for (int i = 0; i < nDimensions[s]; i++) {
t.coordinate[i] = etsFile.readInt();
}
tileOffsets[s][chunk] = etsFile.readLong();
int nBytes = etsFile.readInt();
etsFile.skipBytes(4);
tmpTiles.add(t);
}
int maxX = 0;
int maxY = 0;
int maxZ = 0;
int maxC = 0;
int maxT = 0;
for (TileCoordinate t : tmpTiles) {
Integer tv = dimensionOrdering.get("T");
Integer zv = dimensionOrdering.get("Z");
Integer cv = dimensionOrdering.get("C");
int tIndex = tv == null ? -1 : tv + 2;
int zIndex = zv == null ? -1 : zv + 2;
int cIndex = cv == null ? -1 : cv + 2;
if (tv == null && zv == null) {
if (t.coordinate.length > 4 && cv == null) {
cIndex = 2;
dimensionOrdering.put("C", cIndex - 2);
}
if (t.coordinate.length > 4) {
if (cv == null) {
tIndex = 3;
} else {
tIndex = cIndex + 2;
}
if (tIndex < t.coordinate.length) {
dimensionOrdering.put("T", tIndex - 2);
} else {
tIndex = -1;
}
}
if (t.coordinate.length > 5) {
if (cv == null) {
zIndex = 4;
} else {
zIndex = cIndex + 1;
}
if (zIndex < t.coordinate.length) {
dimensionOrdering.put("Z", zIndex - 2);
} else {
zIndex = -1;
}
}
}
if (t.coordinate[0] > maxX) {
maxX = t.coordinate[0];
}
if (t.coordinate[1] > maxY) {
maxY = t.coordinate[1];
}
if (tIndex >= 0 && t.coordinate[tIndex] > maxT) {
maxT = t.coordinate[tIndex];
}
if (zIndex >= 0 && t.coordinate[zIndex] > maxZ) {
maxZ = t.coordinate[zIndex];
}
if (cIndex >= 0 && t.coordinate[cIndex] > maxC) {
maxC = t.coordinate[cIndex];
}
}
if (maxX > 1) {
core[s].sizeX = tileX[s] * (maxX + 1);
} else {
core[s].sizeX = tileX[s];
}
if (maxY > 1) {
core[s].sizeY = tileY[s] * (maxY + 1);
} else {
core[s].sizeY = tileY[s];
}
core[s].sizeZ = maxZ + 1;
if (maxC > 0) {
core[s].sizeC *= (maxC + 1);
}
core[s].sizeT = maxT + 1;
if (core[s].sizeZ == 0) {
core[s].sizeZ = 1;
}
core[s].imageCount = core[s].sizeZ * core[s].sizeT;
if (maxC > 0) {
core[s].imageCount *= (maxC + 1);
}
if (maxY > 1) {
rows[s] = maxY + 1;
} else {
rows[s] = 1;
}
if (maxX > 1) {
cols[s] = maxX + 1;
} else {
cols[s] = 1;
}
for (int i = 0; i < tmpTiles.size(); i++) {
tileMap[s].put(tmpTiles.get(i), i);
}
core[s].pixelType = convertPixelType(pixelType);
etsFile.close();
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 64;
String xml = stream.readString(blockLen);
return xml.startsWith("<?xml") && xml.indexOf("<OME") >= 0;
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
if (!checkSuffix(id, "vsi")) {
Location current = new Location(id).getAbsoluteFile();
Location parent = current.getParentFile();
parent = parent.getParentFile();
Location grandparent = parent.getParentFile();
String vsi = parent.getName();
vsi = vsi.substring(1, vsi.length() - 1) + ".vsi";
Location vsiFile = new Location(grandparent, vsi);
if (!vsiFile.exists()) {
throw new FormatException("Could not find .vsi file.");
} else {
id = vsiFile.getAbsolutePath();
}
}
parser = new TiffParser(id);
ifds = parser.getIFDs();
RandomAccessInputStream vsi = new RandomAccessInputStream(id);
vsi.order(parser.getStream().isLittleEndian());
vsi.seek(8);
readTags(vsi);
vsi.seek(parser.getStream().getFilePointer());
vsi.skipBytes(273);
ArrayList<String> files = new ArrayList<String>();
Location file = new Location(id).getAbsoluteFile();
Location dir = file.getParentFile();
String name = file.getName();
name = name.substring(0, name.lastIndexOf("."));
Location pixelsDir = new Location(dir, "_" + name + "_");
String[] stackDirs = pixelsDir.list(true);
if (stackDirs != null) {
for (String f : stackDirs) {
Location stackDir = new Location(pixelsDir, f);
String[] pixelsFiles = stackDir.list(true);
if (pixelsFiles != null) {
for (String pixelsFile : pixelsFiles) {
if (checkSuffix(pixelsFile, "ets")) {
files.add(new Location(stackDir, pixelsFile).getAbsolutePath());
}
}
}
}
}
files.add(file.getAbsolutePath());
usedFiles = files.toArray(new String[files.size()]);
core = new CoreMetadata[files.size() - 1 + ifds.size()];
tileOffsets = new Long[files.size() - 1][];
rows = new int[files.size() - 1];
cols = new int[files.size() - 1];
nDimensions = new int[core.length];
IFDList exifs = parser.getExifIFDs();
compressionType = new int[core.length];
tileX = new int[core.length];
tileY = new int[core.length];
tileMap = new HashMap[core.length];
for (int s = 0; s < core.length; s++) {
core[s] = new CoreMetadata();
}
for (int s = 0; s < core.length; s++) {
tileMap[s] = new HashMap<TileCoordinate, Integer>();
if (s == 0 && !hasFlattenedResolutions()) {
core[s].resolutionCount = ifds.size() + (files.size() == 1 ? 0 : 1);
}
if (s < files.size() - 1) {
setSeries(s);
parseETSFile(files.get(s), s);
core[s].littleEndian = compressionType[s] == RAW;
core[s].interleaved = core[s].rgb;
if (s == 0 && exifs.size() > 0) {
IFD exif = exifs.get(0);
int newX = exif.getIFDIntValue(IFD.PIXEL_X_DIMENSION);
int newY = exif.getIFDIntValue(IFD.PIXEL_Y_DIMENSION);
if (getSizeX() > newX || getSizeY() > newY) {
core[s].sizeX = newX;
core[s].sizeY = newY;
}
}
setSeries(0);
} else {
IFD ifd = ifds.get(s - files.size() + 1);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
core[s].sizeX = (int) ifd.getImageWidth();
core[s].sizeY = (int) ifd.getImageLength();
core[s].sizeZ = 1;
core[s].sizeT = 1;
core[s].sizeC = core[s].rgb ? samples : 1;
core[s].littleEndian = ifd.isLittleEndian();
core[s].indexed =
p == PhotoInterp.RGB_PALETTE
&& (get8BitLookupTable() != null || get16BitLookupTable() != null);
core[s].imageCount = 1;
core[s].pixelType = ifd.getPixelType();
core[s].interleaved = false;
core[s].falseColor = false;
core[s].thumbnail = s != 0;
}
core[s].metadataComplete = true;
core[s].dimensionOrder = "XYCZT";
}
vsi.close();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
/* @see Codec#decompress(RandomAccessInputStream, CodecOptions) */
public byte[] decompress(RandomAccessInputStream in, CodecOptions options)
throws FormatException, IOException {
if (in == null) throw new IllegalArgumentException("No data to decompress.");
// Adapted from LZO for Java, available at
// http://www.oberhumer.com/opensource/lzo/
ByteVector dst = new ByteVector();
int t = in.read() & 0xff;
int mPos;
if (t > 17) {
t -= 17;
// do dst[op++] = src[ip++]; while (--t > 0);
byte[] b = new byte[t];
in.read(b);
dst.add(b);
t = in.read() & 0xff;
// if (t < 16) return;
if (t < 16) {
return dst.toByteArray();
}
}
loop:
for (; ; t = in.read() & 0xff) {
if (t < 16) {
if (t == 0) {
byte f = in.readByte();
while (f == 0) {
t += 255;
f = in.readByte();
}
t += 15 + (f & 0xff);
}
t += 3;
// do dst[op++] = src[ip++]; while (--t > 0);
byte[] b = new byte[t];
in.read(b);
dst.add(b);
t = in.read() & 0xff;
if (t < 16) {
mPos = dst.size() - 0x801 - (t >> 2) - ((in.read() & 0xff) << 2);
if (mPos < 0) {
t = LZO_OVERRUN;
break loop;
}
t = 3;
do {
dst.add(dst.get(mPos++));
} while (--t > 0);
// do dst[op++] = dst[mPos++]; while (--t > 0);
in.seek(in.getFilePointer() - 2);
t = in.read() & 3;
in.skipBytes(1);
if (t == 0) continue;
// do dst[op++] = src[ip++]; while (--t > 0);
b = new byte[t];
in.read(b);
dst.add(b);
t = in.read() & 0xff;
}
}
for (; ; t = in.read() & 0xff) {
if (t >= 64) {
mPos = dst.size() - 1 - ((t >> 2) & 7) - ((in.read() & 0xff) << 3);
t = (t >> 5) - 1;
} else if (t >= 32) {
t &= 31;
if (t == 0) {
byte f = in.readByte();
while (f == 0) {
t += 255;
f = in.readByte();
}
t += 31 + (f & 0xff);
}
mPos = dst.size() - 1 - ((in.read() & 0xff) >> 2);
mPos -= ((in.read() & 0xff) << 6);
} else if (t >= 16) {
mPos = dst.size() - ((t & 8) << 11);
t &= 7;
if (t == 0) {
byte f = in.readByte();
while (f == 0) {
t += 255;
f = in.readByte();
}
t += 7 + (f & 0xff);
}
mPos -= ((in.read() & 0xff) >> 2);
mPos -= ((in.read() & 0xff) << 6);
if (mPos == dst.size()) break loop;
mPos -= 0x4000;
} else {
mPos = dst.size() - 1 - (t >> 2) - ((in.read() & 0xff) << 2);
t = 0;
}
if (mPos < 0) {
t = LZO_OVERRUN;
break loop;
}
t += 2;
// do dst[op++] = dst[mPos++]; while (--t > 0);
do {
dst.add(dst.get(mPos++));
} while (--t > 0);
in.seek(in.getFilePointer() - 2);
t = in.read() & 3;
in.skipBytes(1);
if (t == 0) break;
// do dst[op++] = src[ip++]; while (--t > 0);
byte[] b = new byte[t];
in.read(b);
dst.add(b);
t = 0;
}
}
return dst.toByteArray();
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (noOME) {
throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG);
}
super.initFile(id);
in = new RandomAccessInputStream(id);
binData = new Vector<BinData>();
binDataOffsets = new Vector<Long>();
compression = new Vector<String>();
DefaultHandler handler = new OMEXMLHandler();
try {
RandomAccessInputStream s = new RandomAccessInputStream(id);
XMLTools.parseXML(s, handler);
s.close();
} catch (IOException e) {
throw new FormatException("Malformed OME-XML", e);
}
int lineNumber = 1;
for (BinData bin : binData) {
int line = bin.getRow();
int col = bin.getColumn();
while (lineNumber < line) {
in.readLine();
lineNumber++;
}
binDataOffsets.add(in.getFilePointer() + col - 1);
}
if (binDataOffsets.size() == 0) {
throw new FormatException("Pixel data not found");
}
LOGGER.info("Populating metadata");
OMEXMLMetadata omexmlMeta;
OMEXMLService service;
try {
ServiceFactory factory = new ServiceFactory();
service = factory.getInstance(OMEXMLService.class);
omexmlMeta = service.createOMEXMLMetadata(omexml);
} catch (DependencyException de) {
throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
} catch (ServiceException se) {
throw new FormatException(se);
}
hasSPW = omexmlMeta.getPlateCount() > 0;
addGlobalMeta("Is SPW file", hasSPW);
// TODO
// Hashtable originalMetadata = omexmlMeta.getOriginalMetadata();
// if (originalMetadata != null) metadata = originalMetadata;
int numDatasets = omexmlMeta.getImageCount();
core = new CoreMetadata[numDatasets];
int oldSeries = getSeries();
for (int i = 0; i < numDatasets; i++) {
setSeries(i);
core[i] = new CoreMetadata();
Integer w = omexmlMeta.getPixelsSizeX(i).getValue();
Integer h = omexmlMeta.getPixelsSizeY(i).getValue();
Integer t = omexmlMeta.getPixelsSizeT(i).getValue();
Integer z = omexmlMeta.getPixelsSizeZ(i).getValue();
Integer c = omexmlMeta.getPixelsSizeC(i).getValue();
if (w == null || h == null || t == null || z == null | c == null) {
throw new FormatException("Image dimensions not found");
}
Boolean endian = omexmlMeta.getPixelsBinDataBigEndian(i, 0);
String pixType = omexmlMeta.getPixelsType(i).toString();
core[i].dimensionOrder = omexmlMeta.getPixelsDimensionOrder(i).toString();
core[i].sizeX = w.intValue();
core[i].sizeY = h.intValue();
core[i].sizeT = t.intValue();
core[i].sizeZ = z.intValue();
core[i].sizeC = c.intValue();
core[i].imageCount = getSizeZ() * getSizeC() * getSizeT();
core[i].littleEndian = endian == null ? false : !endian.booleanValue();
core[i].rgb = false;
core[i].interleaved = false;
core[i].indexed = false;
core[i].falseColor = true;
core[i].pixelType = FormatTools.pixelTypeFromString(pixType);
core[i].orderCertain = true;
}
setSeries(oldSeries);
// populate assigned metadata store with the
// contents of the internal OME-XML metadata object
MetadataStore store = getMetadataStore();
MetadataTools.populatePixels(store, this);
service.convertMetadata(omexmlMeta, store);
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 25;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(blockLen).equals(WAT_MAGIC_STRING);
}
private IniList readMetaData(String id) throws IOException {
IniParser parser = new IniParser();
IniList exp =
parser.parseINI(
new BufferedReader(new InputStreamReader(new FileInputStream(id), Constants.ENCODING)));
IniList plate = null;
// Read Plate File
for (String filename : metadataFiles) {
if (checkSuffix(filename, "plt")) {
plate =
parser.parseINI(
new BufferedReader(
new InputStreamReader(new FileInputStream(filename), Constants.ENCODING)));
} else if (filename.endsWith("RoiSummary.txt")) {
roiFile = filename;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
RandomAccessInputStream s = new RandomAccessInputStream(filename);
String line = s.readLine().trim();
while (!line.endsWith(".adf\"")) {
line = s.readLine().trim();
}
plateName = line.substring(line.indexOf(":")).trim();
plateName = plateName.replace('/', File.separatorChar);
plateName = plateName.replace('\\', File.separatorChar);
for (int i = 0; i < 3; i++) {
plateName = plateName.substring(0, plateName.lastIndexOf(File.separator));
}
plateName = plateName.substring(plateName.lastIndexOf(File.separator) + 1);
s.close();
}
}
}
if (plate == null) throw new IOException("No Plate File");
IniTable plateType = plate.getTable("PlateType");
if (plateName == null) {
plateName = plateType.get("Brand");
}
plateDescription = plateType.get("Brand") + " " + plateType.get("Description");
int nWells = Integer.parseInt(plateType.get("Wells"));
if (nWells == 96) {
wellRows = 8;
wellCols = 12;
} else if (nWells == 384) {
wellRows = 16;
wellCols = 24;
}
Location dir = new Location(id).getAbsoluteFile().getParentFile();
String[] wellList = dir.list();
Arrays.sort(wellList);
for (String filename : wellList) {
if (filename.startsWith("Well ")) {
wellLabels.add(filename.split("\\s|\\.")[1]);
}
}
IniTable imageTable = exp.getTable("Image");
boolean montage = imageTable.get("Montaged").equals("1");
if (montage) {
fieldRows = Integer.parseInt(imageTable.get("TilesY"));
fieldCols = Integer.parseInt(imageTable.get("TilesX"));
} else {
fieldRows = 1;
fieldCols = 1;
}
core = new CoreMetadata[wellLabels.size() * fieldRows * fieldCols];
core[0] = new CoreMetadata();
// Hack for current testing/development purposes
// Not all channels have the same Z!!! How to handle???
// FIXME FIXME FIXME
core[0].sizeZ = 1;
// FIXME FIXME FIXME
// END OF HACK
core[0].sizeC = Integer.parseInt(exp.getTable("General").get("Dyes"));
core[0].bitsPerPixel = Integer.parseInt(exp.getTable("Camera").get("BitdepthUsed"));
IniTable dyeTable = exp.getTable("Dyes");
for (int i = 1; i <= getSizeC(); i++) {
channelNames.add(dyeTable.get(Integer.toString(i)));
}
// Count Images
core[0].sizeT = 0;
Location well = new Location(dir.getAbsolutePath(), "Well " + wellLabels.get(1));
for (String channelName : channelNames) {
int timepoints = 0;
for (String filename : well.list()) {
if (filename.startsWith(channelName) && filename.endsWith(".tif")) {
timepoints++;
}
}
if (timepoints > getSizeT()) {
core[0].sizeT = timepoints;
}
}
return exp;
}
/**
* The CodecOptions parameter should have the following fields set: {@link CodecOptions#width
* width} {@link CodecOptions#height height}
*
* @see Codec#decompress(RandomAccessInputStream, CodecOptions)
*/
public byte[] decompress(RandomAccessInputStream in, CodecOptions options)
throws FormatException, IOException {
if (in == null) throw new IllegalArgumentException("No data to decompress.");
if (options == null) options = CodecOptions.getDefaultOptions();
in.skipBytes(8);
int plane = options.width * options.height;
stride = options.width;
int rowInc = stride - 4;
short opcode;
int nBlocks;
int colorA = 0, colorB;
int[] color4 = new int[4];
int index, idx;
int ta, tb;
int blockPtr = 0;
rowPtr = pixelPtr = 0;
int pixelX, pixelY;
int[] pixels = new int[plane];
byte[] rtn = new byte[plane * 3];
while (in.read() != (byte) 0xe1) ;
in.skipBytes(3);
totalBlocks = ((options.width + 3) / 4) * ((options.height + 3) / 4);
while (in.getFilePointer() + 2 < in.length()) {
opcode = in.readByte();
nBlocks = (opcode & 0x1f) + 1;
if ((opcode & 0x80) == 0) {
if (in.getFilePointer() >= in.length()) break;
colorA = (opcode << 8) | in.read();
opcode = 0;
if (in.getFilePointer() >= in.length()) break;
if ((in.read() & 0x80) != 0) {
opcode = 0x20;
nBlocks = 1;
}
in.seek(in.getFilePointer() - 1);
}
switch (opcode & 0xe0) {
case 0x80:
while (nBlocks-- > 0) {
updateBlock(options.width);
}
break;
case 0xa0:
if (in.getFilePointer() + 2 >= in.length()) break;
colorA = in.readShort();
while (nBlocks-- > 0) {
blockPtr = rowPtr + pixelPtr;
for (pixelY = 0; pixelY < 4; pixelY++) {
for (pixelX = 0; pixelX < 4; pixelX++) {
if (blockPtr >= pixels.length) break;
pixels[blockPtr] = colorA;
short s = (short) (pixels[blockPtr] & 0x7fff);
unpack(s, rtn, blockPtr, pixels.length);
blockPtr++;
}
blockPtr += rowInc;
}
updateBlock(options.width);
}
break;
case 0xc0:
case 0x20:
if (in.getFilePointer() + 2 >= in.length()) break;
if ((opcode & 0xe0) == 0xc0) {
colorA = in.readShort();
}
colorB = in.readShort();
color4[0] = colorB;
color4[1] = 0;
color4[2] = 0;
color4[3] = colorA;
ta = (colorA >> 10) & 0x1f;
tb = (colorB >> 10) & 0x1f;
color4[1] |= ((11 * ta + 21 * tb) >> 5) << 10;
color4[2] |= ((21 * ta + 11 * tb) >> 5) << 10;
ta = (colorA >> 5) & 0x1f;
tb = (colorB >> 5) & 0x1f;
color4[1] |= ((11 * ta + 21 * tb) >> 5) << 5;
color4[2] |= ((21 * ta + 11 * tb) >> 5) << 5;
ta = colorA & 0x1f;
tb = colorB & 0x1f;
color4[1] |= (11 * ta + 21 * tb) >> 5;
color4[2] |= (21 * ta + 11 * tb) >> 5;
while (nBlocks-- > 0) {
blockPtr = rowPtr + pixelPtr;
for (pixelY = 0; pixelY < 4; pixelY++) {
if (in.getFilePointer() >= in.length()) break;
index = in.read();
for (pixelX = 0; pixelX < 4; pixelX++) {
idx = (index >> (2 * (3 - pixelX))) & 3;
if (blockPtr >= pixels.length) break;
pixels[blockPtr] = color4[idx];
short s = (short) (pixels[blockPtr] & 0x7fff);
unpack(s, rtn, blockPtr, pixels.length);
blockPtr++;
}
blockPtr += rowInc;
}
updateBlock(options.width);
}
break;
case 0x00:
blockPtr = rowPtr + pixelPtr;
for (pixelY = 0; pixelY < 4; pixelY++) {
for (pixelX = 0; pixelX < 4; pixelX++) {
if ((pixelY != 0) || (pixelX != 0)) {
if (in.getFilePointer() + 2 >= in.length()) break;
colorA = in.readShort();
}
if (blockPtr >= pixels.length) break;
pixels[blockPtr] = colorA;
short s = (short) (pixels[blockPtr] & 0x7fff);
unpack(s, rtn, blockPtr, pixels.length);
blockPtr++;
}
blockPtr += rowInc;
}
updateBlock(options.width);
break;
}
}
return rtn;
}