add temporary omezarrreader command

ome · Aug 29, 2023 · 4dc9e26 · 4dc9e26
1 parent 58a8ef7
commit 4dc9e26
Showing 1 changed file with 59 additions and 0 deletions.
diff --git a/5_Cloud_Bash.ipynb b/5_Cloud_Bash.ipynb
@@ -1387,6 +1387,65 @@
     "Now run: `napari https://play.minio.io/gbi2022/trans_norm.ome.zarr`"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Time permitting"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "SLF4J: Class path contains multiple SLF4J bindings.\n",
+      "SLF4J: Found binding in [jar:file:/Users/jamoore/micromamba/envs/embo/share/bftools-7.0.0-0/bioformats_package.jar!/org/slf4j/impl/StaticLoggerBinder.class]\n",
+      "SLF4J: Found binding in [jar:file:/System/Volumes/Data/scratch/bioimagecourse2023/session1/OMEZarrReader-0.3.1-jar-with-dependencies.jar!/org/slf4j/impl/StaticLoggerBinder.class]\n",
+      "SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.\n",
+      "SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]\n",
+      "Checking file format [Zarr]\n",
+      "Initializing reader\n",
+      "ZarrReader initializing mri.ome.zarr/.zattrs\n",
+      "Exception in thread \"main\" java.lang.IllegalArgumentException: Compressor id:'gzip' not supported.\n",
+      "\tat com.bc.zarr.CompressorFactory.create(CompressorFactory.java:123)\n",
+      "\tat com.bc.zarr.CompressorFactory.create(CompressorFactory.java:87)\n",
+      "\tat com.bc.zarr.ZarrHeader$ZarrHeaderDeSerializer.deserialize(ZarrHeader.java:197)\n",
+      "\tat com.bc.zarr.ZarrHeader$ZarrHeaderDeSerializer.deserialize(ZarrHeader.java:169)\n",
+      "\tat com.fasterxml.jackson.databind.deser.DefaultDeserializationContext.readRootValue(DefaultDeserializationContext.java:323)\n",
+      "\tat com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4730)\n",
+      "\tat com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3690)\n",
+      "\tat com.bc.zarr.ZarrUtils.fromJson(ZarrUtils.java:113)\n",
+      "\tat com.bc.zarr.ZarrArray.open(ZarrArray.java:109)\n",
+      "\tat com.bc.zarr.ZarrArray.open(ZarrArray.java:99)\n",
+      "\tat com.bc.zarr.ZarrArray.open(ZarrArray.java:95)\n",
+      "\tat com.bc.zarr.ZarrArray.open(ZarrArray.java:91)\n",
+      "\tat loci.formats.services.JZarrServiceImpl.getArrayAttr(JZarrServiceImpl.java:116)\n",
+      "\tat loci.formats.in.ZarrReader.initFile(ZarrReader.java:206)\n",
+      "\tat loci.formats.FormatReader.setId(FormatReader.java:1466)\n",
+      "\tat loci.formats.ImageReader.setId(ImageReader.java:863)\n",
+      "\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:660)\n",
+      "\tat loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1043)\n",
+      "\tat loci.formats.tools.ImageInfo.main(ImageInfo.java:1129)\n"
+     ]
+    },
+    {
+     "ename": "",
+     "evalue": "1",
+     "output_type": "error",
+     "traceback": []
+    }
+   ],
+   "source": [
+    "cd /scratch/bioimagecourse2023/session1/EMBO-Practical-Course-2023\n",
+    "export BF_CP=/scratch/bioimagecourse2023/session1/OMEZarrReader-0.3.1-jar-with-dependencies.jar\n",
+    "showinf -nopix mri.ome.zarr/.zattrs"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},