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Zeiss CZI: fix series count for fused images #1725

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Apr 21, 2015
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Zeiss CZI: fix series count for fused images #1725

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23 changes: 20 additions & 3 deletions components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -645,9 +645,26 @@ protected void initFile(String id) throws FormatException, IOException {
seriesCount == (planes.size() / getImageCount()) &&
prestitched != null && prestitched)
{
prestitched = false;
ms0.sizeX = planes.get(planes.size() - 1).x;
ms0.sizeY = planes.get(planes.size() - 1).y;
boolean equalTiles = true;
for (SubBlock plane : planes) {
if (plane.x != planes.get(0).x || plane.y != planes.get(0).y) {
equalTiles = false;
break;
}
}
if (getSizeX() > planes.get(0).x && !equalTiles) {
// image was fused; treat the mosaics as a single image
seriesCount = 1;
positions = 1;
acquisitions = 1;
mosaics = 1;
angles = 1;
}
else {
prestitched = false;
ms0.sizeX = planes.get(planes.size() - 1).x;
ms0.sizeY = planes.get(planes.size() - 1).y;
}
}

if (ms0.imageCount * seriesCount > planes.size() * scanDim &&
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