protected void put(String key, IFD ifd, int tag) {
put(key, ifd.getIFDValue(tag));
}
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
CoreMetadata m = core.get(0);
m.sizeZ = 0;
m.sizeT = 0;
MetadataLevel level = getMetadataOptions().getMetadataLevel();
for (IFD ifd : ifds) {
if (level != MetadataLevel.MINIMUM) {
short[] tag1 = (short[]) ifd.getIFDValue(IMAGE_PRO_TAG_1);
if (tag1 != null) {
String seqId = "";
for (int i = 0; i < tag1.length; i++) seqId = seqId + tag1[i];
addGlobalMeta("Image-Pro SEQ ID", seqId);
}
}
int tag2 = ifds.get(0).getIFDIntValue(IMAGE_PRO_TAG_2);
if (tag2 != -1) {
// should be one of these for every image plane
m.sizeZ++;
addGlobalMeta("Frame Rate", tag2);
}
addGlobalMeta("Number of images", getSizeZ());
}
if (getSizeZ() == 0) m.sizeZ = 1;
if (getSizeT() == 0) m.sizeT = 1;
if (getSizeZ() == 1 && getSizeT() == 1) {
m.sizeZ = ifds.size();
}
// default values
addGlobalMeta("frames", getSizeZ());
addGlobalMeta("channels", super.getSizeC());
addGlobalMeta("slices", getSizeT());
// parse the description to get channels, slices and times where applicable
String descr = ifds.get(0).getComment();
metadata.remove("Comment");
if (descr != null) {
String[] lines = descr.split("\n");
for (String token : lines) {
token = token.trim();
int eq = token.indexOf("=");
if (eq == -1) eq = token.indexOf(":");
if (eq != -1) {
String label = token.substring(0, eq);
String data = token.substring(eq + 1);
addGlobalMeta(label, data);
if (label.equals("channels")) m.sizeC = Integer.parseInt(data);
else if (label.equals("frames")) {
m.sizeT = Integer.parseInt(data);
} else if (label.equals("slices")) {
m.sizeZ = Integer.parseInt(data);
}
}
}
}
if (isRGB() && getSizeC() != 3) m.sizeC *= 3;
m.dimensionOrder = "XY";
int maxNdx = 0, max = 0;
int[] dims = {getSizeZ(), getSizeC(), getSizeT()};
String[] axes = {"Z", "C", "T"};
for (int i = 0; i < dims.length; i++) {
if (dims[i] > max) {
max = dims[i];
maxNdx = i;
}
}
m.dimensionOrder += axes[maxNdx];
if (maxNdx != 1) {
if (getSizeC() > 1) {
m.dimensionOrder += "C";
m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]);
} else m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]) + "C";
} else {
if (getSizeZ() > getSizeT()) m.dimensionOrder += "ZT";
else m.dimensionOrder += "TZ";
}
}