Fix truncation issue in downsampling calculation

Adds toString method to directory entry change maxResolution calculation location (it was wrongly initialised before)
BIOP · Dec 18, 2023 · b3ebfa2 · b3ebfa2
1 parent ffd16f3
commit b3ebfa2
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Showing 2 changed files with 18 additions and 6 deletions.
diff --git a/src/main/java/ch/epfl/biop/formats/in/ZeissQuickStartCZIReader.java b/src/main/java/ch/epfl/biop/formats/in/ZeissQuickStartCZIReader.java
@@ -1161,8 +1161,6 @@ protected void initFile(String id) throws FormatException, IOException {
 
         nPhases = maxValuePerDimension.containsKey("H")? maxValuePerDimension.get("H")+1:1;
 
-        maxResolution = maxValuePerDimension.containsKey(RESOLUTION_LEVEL_DIMENSION)? maxValuePerDimension.get(RESOLUTION_LEVEL_DIMENSION):0; // Used only for auto-determination of the fill color
-
         int nChannels = maxValuePerDimension.containsKey("C")? maxValuePerDimension.get("C")+1:1;
 
         int nSlices = maxValuePerDimension.containsKey("Z")? maxValuePerDimension.get("Z")+1:1;
@@ -1198,7 +1196,7 @@ protected void initFile(String id) throws FormatException, IOException {
         cziPartToSegments.forEach((part, cziSegments) -> { // For each part
             Arrays.asList(cziSegments.subBlockDirectory.data.entries).forEach( // and each entry
                     entry -> {
-                        int downscalingFactor = entry.getDimension("X").size/entry.getDimension("X").storedSize;
+                        int downscalingFactor = (int) Math.round((double)(entry.getDimension("X").size)/(double)(entry.getDimension("X").storedSize));
                         if ((downscalingFactor==1)||(allowAutostitching())) {
                             // Split by resolution level if flattenedResolutions is true
                             ModuloDimensionEntries moduloEntry = new ModuloDimensionEntries(entry,
@@ -1219,9 +1217,11 @@ protected void initFile(String id) throws FormatException, IOException {
                     });
         });
 
+        maxResolution = maxValuePerDimension.containsKey(RESOLUTION_LEVEL_DIMENSION)? maxValuePerDimension.get(RESOLUTION_LEVEL_DIMENSION):0; // Used only for auto-determination of the fill color
+
         // Sort them
         List<CoreSignature> orderedCoreSignatureList = coreSignatureToBlocks.keySet().stream().sorted().collect(Collectors.toList());
-
+        // orderedCoreSignatureList.forEach(System.out::println);
         // We now know how many core index are present in the image... except for extra images!
 
         core = new ArrayList<>();
@@ -1871,7 +1871,6 @@ static class ModuloDimensionEntries {
          ms0.moduloT.type = FormatTools.PHASE;
          ms0.sizeT *= phases;
          */
-
         final List<ModuloDimensionEntry> entryList = new ArrayList<>();
         final int nRotations, nIlluminations, nPhases, filePart;
 
@@ -1883,8 +1882,9 @@ public ModuloDimensionEntries(LibCZI.SubBlockDirectorySegment.SubBlockDirectoryS
             this.nPhases = nPhases;
             this.pixelType = entry.getPixelType();
             this.compression = entry.getCompression();
-            this.downSampling = entry.getDimension("X").size/entry.getDimension("X").storedSize;
+            this.downSampling = (int) Math.round((double)(entry.getDimension("X").size)/(double)(entry.getDimension("X").storedSize));
             this.filePosition = entry.getFilePosition();
+            //System.out.println(entry);
 
             int iRotation = 0;
             int iIllumination = 0;

diff --git a/src/main/java/ch/epfl/biop/formats/in/libczi/LibCZI.java b/src/main/java/ch/epfl/biop/formats/in/libczi/LibCZI.java
@@ -560,6 +560,18 @@ public static class SubBlockDirectorySegmentData {
             public SubBlockDirectoryEntry[] entries;
 
             public static class SubBlockDirectoryEntry {
+                @Override
+                public String toString() {
+                    if (entryDV!=null) {
+                        StringBuilder sb = new StringBuilder();
+                        sb.append("pixelType "+this.getPixelType()+" compression = "+getCompression()+"\n");
+                        for (SubBlockSegment.SubBlockSegmentData.SubBlockDirectoryEntryDV.DimensionEntry entry: getDimensionEntries()) {
+                            sb.append(entry+"\n");
+                        }
+                        return sb.toString();
+                    } else return "entryDE not supported";
+                }
+
                 public SubBlockSegment.SubBlockSegmentData.SubBlockDirectoryEntryDV entryDV;
                 public SubBlockSegment.SubBlockSegmentData.SubBlockDirectoryEntryDE entryDE;