Merge pull request #226 from mulimoen/bugfix/issue_223

Allow chunking on zero-sized extents

Author: aldanor

CHANGELOG.md

@@ -26,6 +26,7 @@
 - Fixed a memory leak when opening datasets.
 - Avoid creating unaligned references in `H5Type` derive macro.
 - Applying filters without chunking will now produce an explicit error.
+- Fixed a bug where chunking could not be enabled for zero-sized extents.
 
 ## 0.8.1
 

hdf5/src/hl/dataset.rs

@@ -414,6 +414,8 @@ impl DatasetBuilderInner {
             chunk.clone()
         } else if chunking_required && chunking_allowed {
             Chunk::MinKB(DEFAULT_CHUNK_SIZE_KB)
+        } else if extents.size() == 0 {
+            Chunk::Exact(vec![1; extents.ndim()])
         } else {
             Chunk::None
         };
@@ -437,7 +439,13 @@ impl DatasetBuilderInner {
             let chunk_size = chunk.iter().product::<usize>();
             ensure!(chunk_size > 0, "All chunk dimensions must be positive, got {:?}", chunk);
             let dims_ok = extents.iter().zip(chunk).all(|(e, c)| e.max.is_none() || *c <= e.dim);
-            ensure!(dims_ok, "Chunk dimensions ({:?}) exceed data shape ({:?})", chunk, extents);
+            let no_extent = extents.size() == 0;
+            ensure!(
+                dims_ok || no_extent,
+                "Chunk dimensions ({:?}) exceed data shape ({:?})",
+                chunk,
+                extents
+            );
         }
         Ok(chunk_shape)
     }

tests/test_dataset.rs

@@ -351,6 +351,17 @@ fn test_create_on_databuilder() {
     let _ds = file.new_dataset::<i32>().shape(2).create("ds4").unwrap();
 }
 
+#[test]
+fn test_issue_223() {
+    let file = new_in_memory_file().unwrap();
+
+    let data: &[u16] = &[];
+    let _ds = file.new_dataset_builder().deflate(3).with_data(data).create("ds2").unwrap();
+
+    let data: Array2<u16> = Array2::from_shape_fn((0, 0), |(_i, _j)| unreachable!());
+    let _ds = file.new_dataset_builder().deflate(3).with_data(&data).create("ds3").unwrap();
+}
+
 #[test]
 fn test_read_write_rename_fields() -> hdf5::Result<()> {
     test_read_write::<RenameStruct>()?;