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More .nd2 fixes #420

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merged 2 commits into from
Mar 20, 2013
Merged

More .nd2 fixes #420

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d24d633
ND2: populate the channel color
melissalinkert Mar 19, 2013
55980db
ND2: fix T size adjustment
melissalinkert Mar 19, 2013
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11 changes: 10 additions & 1 deletion components/bio-formats/src/loci/formats/in/NativeND2Reader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -527,7 +527,7 @@ else if (blockType.startsWith("ImageText")) {

// only accept the Z and T sizes from the text annotations
// if both values were set
if (core[0].sizeZ == 0) {
if (core[0].sizeZ == 0 && getSizeT() != imageOffsets.size()) {
core[0].sizeT = 0;
}

Expand Down Expand Up @@ -1640,6 +1640,15 @@ else if (channelNames.size() < getEffectiveSizeC()) {
for (int i=0; i<getSeriesCount(); i++) {
// link Instrument and Image
store.setImageInstrumentRef(instrumentID, i);

// set the channel color
for (int c=0; c<getEffectiveSizeC(); c++) {
int red = colors[c] & 0xff;
int green = (colors[c] & 0xff00) >> 8;
int blue = (colors[c] & 0xff0000) >> 16;
int alpha = (colors[c] & 0xff000000) >> 24;
store.setChannelColor(new Color(red, green, blue, alpha), i, c);
}
}

// populate Dimensions data
Expand Down