Fix issue with nested zarr chunks

constantinpape · Mar 16, 2022 · a2df2f6 · a2df2f6
1 parent d314948
commit a2df2f6
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Showing 2 changed files with 24 additions and 2 deletions.
diff --git a/include/z5/metadata.hxx b/include/z5/metadata.hxx
@@ -147,6 +147,13 @@ namespace z5 {
                 fillValue = static_cast<double>(fillValJson);
             }
 
+            auto jIt = j.find("dimension_separator");
+            if(jIt != j.end()) {
+                zarrDelimiter = *jIt;
+            } else {
+                zarrDelimiter = ".";
+            }
+
             const auto & compressionOpts = j["compressor"];
 
             std::string zarrCompressorId = compressionOpts.is_null() ? "raw" : compressionOpts["id"];
@@ -156,8 +163,7 @@ namespace z5 {
                 throw std::runtime_error("z5.DatasetMetadata.fromJsonZarr: wrong compressor for zarr format: " + zarrCompressorId);
             }
 
-            types::readZarrCompressionOptionsFromJson(compressor, compressionOpts,
-                                                      compressionOptions);
+            types::readZarrCompressionOptionsFromJson(compressor, compressionOpts, compressionOptions);
         }
 
 

diff --git a/src/python/test/test_dataset.py b/src/python/test/test_dataset.py
@@ -477,6 +477,22 @@ def test_nested(self):
         res = g['data'][:]
         self.assertTrue(np.allclose(data, res))
 
+    def test_nested2(self):
+        f = z5py.ZarrFile(self.path, mode='w', dimension_separator='/')
+        chunks = (10, 10, 10)
+        f.create_dataset('data', shape=self.shape, chunks=chunks, dtype='float64')
+
+        g = z5py.ZarrFile(self.path, mode='a')
+        ds = f['data']
+        data = np.random.rand(*self.shape)
+        ds[:] = data
+        self.assertTrue(os.path.exists(
+            os.path.join(self.path, 'data/0/0/0')
+        ))
+
+        res = ds[:]
+        self.assertTrue(np.allclose(data, res))
+
 
 class TestN5Dataset(DatasetTestMixin, unittest.TestCase):
     data_format = 'n5'