From 8f0174e2efd3838e16760e6b33d2940835f6b085 Mon Sep 17 00:00:00 2001
From: swg08 <stephan.wagner-conrad@zeiss.com>
Date: Sun, 7 Jan 2024 21:57:24 +0100
Subject: [PATCH 1/2] Issue 4110: Consider ZSTD_0 and ZSTD_1 compressed
 datasets to also be considered for pyramid level evaluation. Issue 4102: Fix
 an integer arithmetic issue by using floating point arithmetic. -> divide
 with floating point precision and make sure to round to up or down to the
 next integer value - not truncation rounding.

---
 .../src/loci/formats/in/ZeissCZIReader.java           | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
index 1e71c08557b..3acd92c2568 100644
--- a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -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);
@@ -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;

From f3b162f94d93f9d9c9c181bad851970f79cb1a43 Mon Sep 17 00:00:00 2001
From: swg08 <46338941+swg08@users.noreply.github.com>
Date: Mon, 5 Feb 2024 23:27:12 +0100
Subject: [PATCH 2/2] Update ZeissCZIReader.java

Change log level of ZSTD1 without hi/lo flag from warning to debug.
Rationale: The image data is still usable and valid in that case. Changing to debug information.
---
 components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
index 4cb9a62b184..c05d47da625 100644
--- a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
+++ b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -4187,7 +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;
           }