diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java index 14d74a2..e675bba 100644 --- a/src/loci/formats/in/ZarrReader.java +++ b/src/loci/formats/in/ZarrReader.java @@ -166,6 +166,7 @@ public int getOptimalTileWidth() { @Override protected void initFile(String id) throws FormatException, IOException { super.initFile(id); + LOGGER.info("ZarrReader attempting to initialize file: {}", id); final MetadataStore store = makeFilterMetadata(); Location zarrFolder = new Location(id); String zarrPath = zarrFolder.getAbsolutePath(); @@ -174,14 +175,17 @@ protected void initFile(String id) throws FormatException, IOException { Location omeMetaFile = new Location( zarrRootPath + File.separator + "OME", "METADATA.ome.xml" ); String canonicalPath = new Location(zarrRootPath).getCanonicalPath(); + LOGGER.info("ZarrReader initializing ZarrService: {}", canonicalPath); initializeZarrService(canonicalPath); if(omeMetaFile.exists()) { + LOGGER.info("ZarrReader parsing existing OME-XML"); parseOMEXML(omeMetaFile, store); } // Parse base level attributes Map attr = zarrService.getGroupAttr(canonicalPath); int attrIndex = 0; + LOGGER.info("ZarrReader parsing top level group attributes: {}", canonicalPath); if (attr != null && !attr.isEmpty()) { parseResolutionCount(zarrRootPath, "", attr); parseOmeroMetadata(zarrRootPath, attr); @@ -196,13 +200,15 @@ protected void initFile(String id) throws FormatException, IOException { e.printStackTrace(); } } - + LOGGER.info("ZarrReader generating group keys"); generateGroupKeys(attr); // Parse group attributes if (groupKeys.isEmpty()) { + LOGGER.info("ZarrReader adding hroup keys from ZarrService"); groupKeys.addAll(zarrService.getGroupKeys(canonicalPath)); } + LOGGER.info("ZarrReader parsing group Keys"); for (String key: groupKeys) { Map attributes = zarrService.getGroupAttr(canonicalPath+File.separator+key); if (attributes != null && !attributes.isEmpty()) { @@ -226,10 +232,13 @@ protected void initFile(String id) throws FormatException, IOException { } // Parse array attributes + LOGGER.info("ZarrReader attempting to generate Array Keys"); generateArrayKeys(attr); if (arrayPaths.isEmpty()) { + LOGGER.info("ZarrReader adding Array Keys from ZarrService"); arrayPaths.addAll(zarrService.getArrayKeys(canonicalPath)); } + LOGGER.info("ZarrReader ordering Array Paths"); orderArrayPaths(zarrRootPath); if (saveAnnotations()) { @@ -258,6 +267,7 @@ protected void initFile(String id) throws FormatException, IOException { int pixelType = -1; for (int i=0; i