// analogous to getConvertedWBS4OME_JPEG in OMEimage.js
// and boundary conditions modifier in updatePic in OMEimage.js
public ChannelBlackScaleData getNormalizedScale(int t) {
if (t < 0 || t >= getDimT()) {
return null;
}
Integer tObj = new Integer(t);
if (cbsMap.containsKey(tObj)) {
return (ChannelBlackScaleData) cbsMap.get(tObj);
}
ChannelBlackScaleData convertedData = new ChannelBlackScaleData();
ChannelBlackScaleData.CBSChunk[] dataChunks = {
CBS.getCBSChunk(ChannelBlackScaleData.RED_CHUNK),
CBS.getCBSChunk(ChannelBlackScaleData.GREEN_CHUNK),
CBS.getCBSChunk(ChannelBlackScaleData.BLUE_CHUNK),
CBS.getCBSChunk(ChannelBlackScaleData.GRAY_CHUNK)
};
ChannelBlackScaleData.CBSChunk[] newChunks =
new ChannelBlackScaleData.CBSChunk[dataChunks.length];
for (int i = 0; i < dataChunks.length; i++) {
ChannelBlackScaleData.CBSChunk chunk = dataChunks[i];
int channel = chunk.getChannel();
int blackLevel = chunk.getBlackLevel();
float scale = chunk.getScale();
float newBlack = getStackGeoMean(channel, t) + getStackGeoSigma(channel, t) * blackLevel;
float scaleMod = scale == 0f ? 0.00001f : scale;
float newScale = 255f / (getStackGeoSigma(channel, t) * scaleMod);
int newB = Math.round(newBlack);
float newS = Math.round(newScale * 100000f) / 100000f;
// black-level overcorrection adjustment
if (newB < getStackMin(channel, t)) {
newB = Math.round((float) Math.ceil(getStackMin(channel, t)));
}
if (newB > getStackMax(channel, t)) {
newB = Math.round((float) Math.floor(getStackMax(channel, t)));
}
// end black-level overcorrection adjustment
// white-level overcorrection adjustment
float whiteLevel =
getStackGeoMean(channel, t) + dataChunks[i].getScale() * getStackGeoSigma(channel, t);
boolean recalculate = false;
if (whiteLevel < getStackMin(channel, t)) {
whiteLevel = getStackMin(channel, t);
recalculate = true;
}
if (whiteLevel > getStackMax(channel, t)) {
whiteLevel = getStackMax(channel, t);
recalculate = true;
}
if (recalculate) {
if (whiteLevel - getStackGeoMean(channel, t) == 0f) {
whiteLevel += 0.00001f;
}
newS = 255f / (whiteLevel - getStackGeoMean(channel, t));
}
// end white-level correction adjustment
newChunks[i] = new ChannelBlackScaleData.CBSChunk(channel, newB, newS);
}
convertedData.setCBSChunk(ChannelBlackScaleData.RED_CHUNK, newChunks[0]);
convertedData.setCBSChunk(ChannelBlackScaleData.GREEN_CHUNK, newChunks[1]);
convertedData.setCBSChunk(ChannelBlackScaleData.BLUE_CHUNK, newChunks[2]);
convertedData.setCBSChunk(ChannelBlackScaleData.RED_CHUNK, newChunks[3]);
cbsMap.put(tObj, convertedData);
return convertedData;
}
