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Issues 4150 + 4110: Consider ZSTD with pyramid levels and fix integer arithmetic scale problem #4138

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merged 3 commits into from
Feb 8, 2024
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Issues 4150 + 4110: Consider ZSTD with pyramid levels and fix integer arithmetic scale problem #4138

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8f0174e
Issue 4110: Consider ZSTD_0 and ZSTD_1 compressed datasets to also be…
swg08 Jan 7, 2024
ea3862b
Merge branch 'ome:develop' into 4110_czi_zstd_pyramid_levels
swg08 Feb 5, 2024
f3b162f
Update ZeissCZIReader.java
swg08 Feb 5, 2024
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13 changes: 7 additions & 6 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 @@ -734,7 +734,6 @@ protected void initFile(String id) throws FormatException, IOException {
convertPixelType(planes.get(0).directoryEntry.pixelType);

// remove any invalid SubBlocks

int bpp = FormatTools.getBytesPerPixel(getPixelType());
if (isRGB()) {
bpp *= (getSizeC() / originalC);
Expand All @@ -743,16 +742,18 @@ protected void initFile(String id) throws FormatException, IOException {
for (int i=0; i<planes.size(); i++) {
long planeSize = (long) planes.get(i).x * planes.get(i).y * bpp;
int compression = planes.get(i).directoryEntry.compression;
if (compression == UNCOMPRESSED || compression == JPEGXR) {
boolean isCompressed = compression == JPEGXR || compression == ZSTD_0 || compression == ZSTD_1;
if (compression == UNCOMPRESSED || isCompressed) {
long size = planes.get(i).dataSize;
if (size < planeSize || planeSize >= Integer.MAX_VALUE || size < 0) {
// check for reduced resolution in the pyramid
DimensionEntry[] entries = planes.get(i).directoryEntry.dimensionEntries;
int pyramidType = planes.get(i).directoryEntry.pyramidType;
if ((pyramidType == 1 || pyramidType == 2 || compression == JPEGXR) &&
(compression == JPEGXR || size == entries[0].storedSize * entries[1].storedSize * bpp))
if (isCompressed ||
((pyramidType == 1 || pyramidType == 2 ) && (size == entries[0].storedSize * entries[1].storedSize * bpp)))
{
int scale = planes.get(i).x / entries[0].storedSize;
// circumvent integer arithmetic rounding issue by using floating point precision calculation (see issue #4102)
int scale = (int)((double)planes.get(i).x / (double)entries[0].storedSize + 0.5);
if (scale == 1 || (((scale % 2) == 0 || (scale % 3) == 0) && allowAutostitching())) {
if (scale > 1 && scaleFactor == 0) {
scaleFactor = scale % 2 == 0 ? 2 : 3;
Expand Down Expand Up @@ -4186,7 +4187,7 @@ public byte[] readPixelData(RandomAccessInputStream s, Region tile, byte[] buf)
}
}
else {
LOGGER.warn("ZSTD-1 compression used, but no high/low byte unpacking");
LOGGER.debug("ZSTD-1 compression used, but no high/low byte unpacking");
data = decoded;
}

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