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 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();
}