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Don't set _ARRAY_DIMENSIONS attribute
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melissalinkert committed Feb 8, 2022
1 parent fa6dd05 commit 8f430e2
Showing 1 changed file with 1 addition and 24 deletions.
25 changes: 1 addition & 24 deletions src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
Original file line number Diff line number Diff line change
Expand Up @@ -1220,8 +1220,7 @@ public void saveResolutions(int series)
.nested(nested)
.compressor(CompressorFactory.create(
compressionType.toString(), compressionProperties));
ZarrArray.create(getRootPath().resolve(resolutionString),
arrayParams, getArrayAttributes());
ZarrArray.create(getRootPath().resolve(resolutionString), arrayParams);

nTile = new AtomicInteger(0);
tileCount = (int) Math.ceil((double) scaledWidth / tileWidth)
Expand Down Expand Up @@ -1794,28 +1793,6 @@ private Class<?> getBaseReaderClass() throws FormatException, IOException {
}
}

private Map<String, Object> getArrayAttributes() throws InterruptedException {
Map<String, Object> attrs = new HashMap<String, Object>();
String order = null;
if (dimensionOrder != null) {
order = dimensionOrder.toString();
}
else {
IFormatReader reader = readers.take();
try {
order = reader.getDimensionOrder();
}
finally {
readers.put(reader);
}
}

String[] axes =
new StringBuilder(order.toLowerCase()).reverse().toString().split("");
attrs.put("_ARRAY_DIMENSIONS", axes);
return attrs;
}

/**
* Check if the given metadata object contains at least one plate
* with at least one well that links to an image.
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