From 388fd6a380016e60cd0fb0b6ab2bdb5d7a89d451 Mon Sep 17 00:00:00 2001 From: Chris Allan Date: Mon, 12 Apr 2021 10:45:52 +0100 Subject: [PATCH 1/2] Update to jzarr version that supports nested --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 14cea2f..ac0933c 100644 --- a/build.gradle +++ b/build.gradle @@ -32,7 +32,7 @@ repositories { } dependencies { - implementation 'com.bc.zarr:jzarr:0.3.2' + implementation 'com.bc.zarr:jzarr:0.3.3-gs-SNAPSHOT' implementation 'info.picocli:picocli:4.2.0' implementation 'me.tongfei:progressbar:0.9.0' implementation 'ome:formats-bsd:6.4.0' From 6971a02fa6fa4b6af99a94e878f55bd0e4c10d93 Mon Sep 17 00:00:00 2001 From: Chris Allan Date: Mon, 12 Apr 2021 10:48:12 +0100 Subject: [PATCH 2/2] Add test case for nested --- .../raw2ometiff/test/ConversionTest.java | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java b/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java index 9a6b604..b7ec03a 100644 --- a/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java +++ b/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java @@ -20,6 +20,10 @@ import java.util.List; import java.util.Map; +import com.bc.zarr.ZarrArray; +import com.bc.zarr.ZarrGroup; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; import com.glencoesoftware.bioformats2raw.Converter; import com.glencoesoftware.pyramid.PyramidFromDirectoryWriter; @@ -240,6 +244,13 @@ public void testDefaults() throws Exception { input = fake(); assertBioFormats2Raw(); assertTool(); + ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0"); + Assert.assertTrue(series0.getNested()); + // Also ensure we're using the latest .zarray metadata + ObjectMapper objectMapper = new ObjectMapper(); + JsonNode root = objectMapper.readTree( + output.resolve("0/0/.zarray").toFile()); + Assert.assertEquals("/", root.path("dimension_separator").asText()); try (ImageReader reader = new ImageReader()) { reader.setFlattenedResolutions(false); reader.setId(outputOmeTiff.toString());