Revert "revert getUsedFiles behaviour to remove skipPixels"

This reverts commit 8aee5d8. # Conflicts: # src/loci/formats/in/ZarrReader.java
dgault · Oct 4, 2023 · b20ef9c · b20ef9c
1 parent 82ac198
commit b20ef9c
Showing 1 changed file with 10 additions and 3 deletions.
diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java
@@ -1089,10 +1089,17 @@ public String[] getUsedFiles(boolean noPixels) {
     FormatTools.assertId(currentId, true, 1);
     String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
     ArrayList<String> usedFiles = new ArrayList<String>();
-    try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath), FileVisitOption.FOLLOW_LINKS)) {
-      paths.filter(Files::isRegularFile)
-      .forEach(path -> usedFiles.add(path.toFile().getAbsolutePath()));
 
+    boolean skipPixels = noPixels || !listPixels();
+    LOGGER.error("ZarrReader getUsed files, skipPixels: {}", skipPixels);
+    LOGGER.error("ZarrReader fetching list of used files: {}", zarrRootPath);
+    try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath), FileVisitOption.FOLLOW_LINKS)) {
+      paths.filter(Files::isRegularFile) 
+      .forEach(path -> {if (!skipPixels || 
+          (skipPixels && (path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))))
+        usedFiles.add(path.toFile().getAbsolutePath());
+        LOGGER.error("Adding to the used files list: {}", path.toFile().getAbsolutePath());
+      });
     } catch (IOException e) {
       e.printStackTrace();
     }