From 290d7678c05d7687f493f8a2e94620539958461f Mon Sep 17 00:00:00 2001 From: David Gault Date: Thu, 26 Oct 2023 15:35:22 +0100 Subject: [PATCH] Add support for environment variable OME_ZARR_LIST_PIXELS --- src/loci/formats/in/ZarrReader.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/loci/formats/in/ZarrReader.java b/src/loci/formats/in/ZarrReader.java index 4ae5b87..675bfe3 100644 --- a/src/loci/formats/in/ZarrReader.java +++ b/src/loci/formats/in/ZarrReader.java @@ -94,6 +94,7 @@ public class ZarrReader extends FormatReader { public static final boolean SAVE_ANNOTATIONS_DEFAULT = false; public static final String LIST_PIXELS_KEY = "omezarr.list_pixels"; public static final boolean LIST_PIXELS_DEFAULT = false; + public static final String LIST_PIXELS_ENV_KEY = "OME_ZARR_LIST_PIXELS"; public static final String INCLUDE_LABELS_KEY = "omezarr.include_labels"; public static final boolean INCLUDE_LABELS_DEFAULT = false; protected transient ZarrService zarrService; @@ -1094,8 +1095,7 @@ public String[] getUsedFiles(boolean noPixels) { String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5); ArrayList usedFiles = new ArrayList(); - - boolean skipPixels = noPixels || !listPixels(); + boolean skipPixels = noPixels || !listPixels() || !systemEnvListPixels(); boolean includeLabels = includeLabels(); LOGGER.error("ZarrReader getUsed files, skipPixels: {}", skipPixels); LOGGER.error("ZarrReader fetching list of used files: {}", zarrRootPath); @@ -1171,4 +1171,10 @@ public boolean includeLabels() { return INCLUDE_LABELS_DEFAULT; } + private boolean systemEnvListPixels() { + String value = System.getenv(LIST_PIXELS_ENV_KEY); + if (value != null && value.equalsIgnoreCase("true")) return true; + if (value != null && value.toLowerCase().equals("false")) return false; + return LIST_PIXELS_DEFAULT; + } }