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;
}
}
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();
}
