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Incorrect VoxelSize in MetaMorph Reader #1966

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merged 4 commits into from
Sep 30, 2015
Merged

Incorrect VoxelSize in MetaMorph Reader #1966

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0fddc2f
VoxelSize reading in MetaMorph
dgault Sep 7, 2015
82f8339
Merge test fix
dgault Sep 9, 2015
597b688
Z step size only calculated for unique ranges
dgault Sep 10, 2015
d8f1f6e
Updating Physical Z Size calculations to use BigDecimal
dgault Sep 14, 2015
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26 changes: 26 additions & 0 deletions components/formats-gpl/src/loci/formats/in/MetamorphReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -778,6 +778,32 @@ else if (differentZs) {
if (zDistances != null) {
stepSize = zDistances[0];
}
else {
Vector<Double> zPositions = new Vector<Double>();
Vector<Double> uniqueZ = new Vector<Double>();
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An ArrayList would suffice unless you need thread synchronization.


for (IFD ifd : ifds) {
String xml = XMLTools.sanitizeXML(ifd.getComment());
XMLTools.parseXML(xml, handler);

zPositions = handler.getZPositions();
for (Double z : zPositions) {
if (!uniqueZ.contains(z)) uniqueZ.add(z);
}
}

if (uniqueZ.size() > 0) {
CoreMetadata ms0 = core.get(0);
if (getSizeZ() == 0) ms0.sizeZ = 1;

Double zRange = zPositions.get(zPositions.size() - 1) - zPositions.get(0);
stepSize = Math.abs(zRange);
if (ms0.sizeZ > 1) {
stepSize /= (ms0.sizeZ - 1);
}
}
}

Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize);
if (physicalSizeZ != null) {
store.setPixelsPhysicalSizeZ(physicalSizeZ, i);
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