pub struct Node { /* private fields */ }Expand description
A Zarr hierarchy node.
See https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html#hierarchy.
Implementations§
Source§impl Node
impl Node
Sourcepub fn open<TStorage: ?Sized + ReadableStorageTraits + ListableStorageTraits>(
storage: &Arc<TStorage>,
path: &str,
) -> Result<Self, NodeCreateError>
pub fn open<TStorage: ?Sized + ReadableStorageTraits + ListableStorageTraits>( storage: &Arc<TStorage>, path: &str, ) -> Result<Self, NodeCreateError>
Open a node at path and read metadata and children from storage with default MetadataRetrieveVersion.
§Errors
Returns NodeCreateError if metadata is invalid or there is a failure to list child nodes.
Examples found in repository?
examples/rectilinear_array_write_read.rs (line 142)
10fn rectilinear_array_write_read() -> Result<(), Box<dyn std::error::Error>> {
11 use rayon::prelude::{IntoParallelIterator, ParallelIterator};
12 use zarrs::array::{ArraySubset, ZARR_NAN_F32, codec, data_type};
13 use zarrs::node::Node;
14 use zarrs::storage::store;
15
16 // Create a store
17 // let path = tempfile::TempDir::new()?;
18 // let mut store: ReadableWritableListableStorage =
19 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
20 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
21 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
22 && arg1 == "--usage-log"
23 {
24 let log_writer = Arc::new(std::sync::Mutex::new(
25 // std::io::BufWriter::new(
26 std::io::stdout(),
27 // )
28 ));
29 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
30 chrono::Utc::now().format("[%T%.3f] ").to_string()
31 }));
32 }
33
34 // Create the root group
35 zarrs::group::GroupBuilder::new()
36 .build(store.clone(), "/")?
37 .store_metadata()?;
38
39 // Create a group with attributes
40 let group_path = "/group";
41 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
42 group
43 .attributes_mut()
44 .insert("foo".into(), serde_json::Value::String("bar".into()));
45 group.store_metadata()?;
46
47 println!(
48 "The group metadata is:\n{}\n",
49 group.metadata().to_string_pretty()
50 );
51
52 // Create an array
53 let array_path = "/group/array";
54 let array = zarrs::array::ArrayBuilder::new(
55 vec![8, 8], // array shape
56 MetadataV3::new_with_configuration(
57 "rectilinear",
58 RectilinearChunkGridConfiguration::Inline {
59 chunk_shapes: vec![
60 // Varying: chunk sizes [1, 1, 1, 3, 2] (run-length encoded as [[1,3], 3, 2])
61 ChunkEdgeLengths::Varying(serde_json::from_str("[[1,3], 3, 2]").unwrap()),
62 // Scalar: regular 4-element chunks
63 ChunkEdgeLengths::Scalar(NonZeroU64::new(4).unwrap()),
64 ],
65 },
66 ),
67 data_type::float32(),
68 ZARR_NAN_F32,
69 )
70 .bytes_to_bytes_codecs(vec![
71 #[cfg(feature = "gzip")]
72 Arc::new(codec::GzipCodec::new(5)?),
73 ])
74 .dimension_names(["y", "x"].into())
75 // .storage_transformers(vec![].into())
76 .build(store.clone(), array_path)?;
77
78 // Write array metadata to store
79 array.store_metadata()?;
80
81 // Write some chunks (in parallel)
82 (0..4).into_par_iter().try_for_each(|i| {
83 let chunk_grid = array.chunk_grid();
84 let chunk_indices = vec![i, 0];
85 if let Some(chunk_shape) = chunk_grid.chunk_shape(&chunk_indices)? {
86 let chunk_array = ndarray::ArrayD::<f32>::from_elem(
87 chunk_shape
88 .iter()
89 .map(|u| u.get() as usize)
90 .collect::<Vec<_>>(),
91 i as f32,
92 );
93 array.store_chunk(&chunk_indices, chunk_array)
94 } else {
95 Err(zarrs::array::ArrayError::InvalidChunkGridIndicesError(
96 chunk_indices.to_vec(),
97 ))
98 }
99 })?;
100
101 println!(
102 "The array metadata is:\n{}\n",
103 array.metadata().to_string_pretty()
104 );
105
106 // Write a subset spanning multiple chunks, including updating chunks already written
107 array.store_array_subset(
108 &[3..6, 3..6], // start
109 ndarray::ArrayD::<f32>::from_shape_vec(
110 vec![3, 3],
111 vec![0.1f32, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
112 )?,
113 )?;
114
115 // Store elements directly, in this case set the 7th column to 123.0
116 array.store_array_subset(&[0..8, 6..7], &[123.0f32; 8])?;
117
118 // Store elements directly in a chunk, in this case set the last row of the bottom right chunk
119 array.store_chunk_subset(
120 // chunk indices
121 &[3, 1],
122 // subset within chunk
123 &[1..2, 0..4],
124 &[-4.0f32; 4],
125 )?;
126
127 // Read the whole array
128 let data_all: ndarray::ArrayD<f32> = array.retrieve_array_subset(&array.subset_all())?;
129 println!("The whole array is:\n{data_all}\n");
130
131 // Read a chunk back from the store
132 let chunk_indices = vec![1, 0];
133 let data_chunk: ndarray::ArrayD<f32> = array.retrieve_chunk(&chunk_indices)?;
134 println!("Chunk [1,0] is:\n{data_chunk}\n");
135
136 // Read the central 4x2 subset of the array
137 let subset_4x2 = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
138 let data_4x2: ndarray::ArrayD<f32> = array.retrieve_array_subset(&subset_4x2)?;
139 println!("The middle 4x2 subset is:\n{data_4x2}\n");
140
141 // Show the hierarchy
142 let node = Node::open(&store, "/").unwrap();
143 let tree = node.hierarchy_tree();
144 println!("The Zarr hierarchy tree is:\n{tree}");
145
146 Ok(())
147}More examples
examples/array_write_read.rs (line 152)
8fn array_write_read() -> Result<(), Box<dyn std::error::Error>> {
9 use std::sync::Arc;
10
11 use zarrs::array::{ArraySubset, ZARR_NAN_F32, data_type};
12 use zarrs::node::Node;
13 use zarrs::storage::store;
14
15 // Create a store
16 // let path = tempfile::TempDir::new()?;
17 // let mut store: ReadableWritableListableStorage =
18 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
19 // let mut store: ReadableWritableListableStorage = Arc::new(
20 // zarrs::filesystem::FilesystemStore::new("zarrs/tests/data/array_write_read.zarr")?,
21 // );
22 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
23 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
24 && arg1 == "--usage-log"
25 {
26 let log_writer = Arc::new(std::sync::Mutex::new(
27 // std::io::BufWriter::new(
28 std::io::stdout(),
29 // )
30 ));
31 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
32 chrono::Utc::now().format("[%T%.3f] ").to_string()
33 }));
34 }
35
36 // Create the root group
37 zarrs::group::GroupBuilder::new()
38 .build(store.clone(), "/")?
39 .store_metadata()?;
40
41 // Create a group with attributes
42 let group_path = "/group";
43 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
44 group
45 .attributes_mut()
46 .insert("foo".into(), serde_json::Value::String("bar".into()));
47 group.store_metadata()?;
48
49 println!(
50 "The group metadata is:\n{}\n",
51 group.metadata().to_string_pretty()
52 );
53
54 // Create an array
55 let array_path = "/group/array";
56 let array = zarrs::array::ArrayBuilder::new(
57 vec![8, 8], // array shape
58 vec![4, 4], // regular chunk shape
59 data_type::float32(),
60 ZARR_NAN_F32,
61 )
62 // .bytes_to_bytes_codecs(vec![]) // uncompressed
63 .dimension_names(["y", "x"].into())
64 // .storage_transformers(vec![].into())
65 .build(store.clone(), array_path)?;
66
67 // Write array metadata to store
68 array.store_metadata()?;
69
70 println!(
71 "The array metadata is:\n{}\n",
72 array.metadata().to_string_pretty()
73 );
74
75 // Write some chunks
76 (0..2).into_par_iter().try_for_each(|i| {
77 let chunk_indices: Vec<u64> = vec![0, i];
78 let chunk_subset = array.chunk_grid().subset(&chunk_indices)?.ok_or_else(|| {
79 zarrs::array::ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec())
80 })?;
81 array.store_chunk(
82 &chunk_indices,
83 vec![i as f32 * 0.1; chunk_subset.num_elements() as usize],
84 )
85 })?;
86
87 let subset_all = array.subset_all();
88 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
89 println!("store_chunk [0, 0] and [0, 1]:\n{data_all:+4.1}\n");
90
91 // Store multiple chunks
92 array.store_chunks(
93 &[1..2, 0..2],
94 &[
95 //
96 1.0f32, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
97 //
98 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
99 ],
100 )?;
101 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
102 println!("store_chunks [1..2, 0..2]:\n{data_all:+4.1}\n");
103
104 // Write a subset spanning multiple chunks, including updating chunks already written
105 array.store_array_subset(
106 &[3..6, 3..6],
107 &[-3.3f32, -3.4, -3.5, -4.3, -4.4, -4.5, -5.3, -5.4, -5.5],
108 )?;
109 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
110 println!("store_array_subset [3..6, 3..6]:\n{data_all:+4.1}\n");
111
112 // Store array subset
113 array.store_array_subset(
114 &[0..8, 6..7],
115 &[-0.6f32, -1.6, -2.6, -3.6, -4.6, -5.6, -6.6, -7.6],
116 )?;
117 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
118 println!("store_array_subset [0..8, 6..7]:\n{data_all:+4.1}\n");
119
120 // Store chunk subset
121 array.store_chunk_subset(
122 // chunk indices
123 &[1, 1],
124 // subset within chunk
125 &[3..4, 0..4],
126 &[-7.4f32, -7.5, -7.6, -7.7],
127 )?;
128 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
129 println!("store_chunk_subset [3..4, 0..4] of chunk [1, 1]:\n{data_all:+4.1}\n");
130
131 // Erase a chunk
132 array.erase_chunk(&[0, 0])?;
133 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
134 println!("erase_chunk [0, 0]:\n{data_all:+4.1}\n");
135
136 // Read a chunk
137 let chunk_indices = vec![0, 1];
138 let data_chunk: ArrayD<f32> = array.retrieve_chunk(&chunk_indices)?;
139 println!("retrieve_chunk [0, 1]:\n{data_chunk:+4.1}\n");
140
141 // Read chunks
142 let chunks = ArraySubset::new_with_ranges(&[0..2, 1..2]);
143 let data_chunks: ArrayD<f32> = array.retrieve_chunks(&chunks)?;
144 println!("retrieve_chunks [0..2, 1..2]:\n{data_chunks:+4.1}\n");
145
146 // Retrieve an array subset
147 let subset = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
148 let data_subset: ArrayD<f32> = array.retrieve_array_subset(&subset)?;
149 println!("retrieve_array_subset [2..6, 3..5]:\n{data_subset:+4.1}\n");
150
151 // Show the hierarchy
152 let node = Node::open(&store, "/").unwrap();
153 let tree = node.hierarchy_tree();
154 println!("hierarchy_tree:\n{}", tree);
155
156 Ok(())
157}examples/sharded_array_write_read.rs (line 144)
10fn sharded_array_write_read() -> Result<(), Box<dyn std::error::Error>> {
11 use std::sync::Arc;
12
13 use rayon::prelude::{IntoParallelIterator, ParallelIterator};
14 use zarrs::array::{ArraySubset, codec, data_type};
15 use zarrs::node::Node;
16 use zarrs::storage::store;
17
18 // Create a store
19 // let path = tempfile::TempDir::new()?;
20 // let mut store: ReadableWritableListableStorage =
21 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
22 // let mut store: ReadableWritableListableStorage = Arc::new(
23 // zarrs::filesystem::FilesystemStore::new("zarrs/tests/data/sharded_array_write_read.zarr")?,
24 // );
25 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
26 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
27 && arg1 == "--usage-log"
28 {
29 let log_writer = Arc::new(std::sync::Mutex::new(
30 // std::io::BufWriter::new(
31 std::io::stdout(),
32 // )
33 ));
34 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
35 chrono::Utc::now().format("[%T%.3f] ").to_string()
36 }));
37 }
38
39 // Create the root group
40 zarrs::group::GroupBuilder::new()
41 .build(store.clone(), "/")?
42 .store_metadata()?;
43
44 // Create a group with attributes
45 let group_path = "/group";
46 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
47 group
48 .attributes_mut()
49 .insert("foo".into(), serde_json::Value::String("bar".into()));
50 group.store_metadata()?;
51
52 // Create an array
53 let array_path = "/group/array";
54 let subchunk_shape = vec![4, 4];
55 let array = zarrs::array::ArrayBuilder::new(
56 vec![8, 8], // array shape
57 vec![4, 8], // chunk (shard) shape
58 data_type::uint16(),
59 0u16,
60 )
61 .subchunk_shape(subchunk_shape.clone())
62 .bytes_to_bytes_codecs(vec![
63 #[cfg(feature = "gzip")]
64 Arc::new(codec::GzipCodec::new(5)?),
65 ])
66 .dimension_names(["y", "x"].into())
67 // .storage_transformers(vec![].into())
68 .build(store.clone(), array_path)?;
69
70 // Write array metadata to store
71 array.store_metadata()?;
72
73 // The array metadata is
74 println!(
75 "The array metadata is:\n{}\n",
76 array.metadata().to_string_pretty()
77 );
78
79 // Use default codec options (concurrency etc)
80 let options = CodecOptions::default();
81
82 // Write some shards (in parallel)
83 (0..2).into_par_iter().try_for_each(|s| {
84 let chunk_grid = array.chunk_grid();
85 let chunk_indices = vec![s, 0];
86 if let Some(chunk_shape) = chunk_grid.chunk_shape(&chunk_indices)? {
87 let chunk_array = ndarray::ArrayD::<u16>::from_shape_fn(
88 chunk_shape
89 .iter()
90 .map(|u| u.get() as usize)
91 .collect::<Vec<_>>(),
92 |ij| {
93 (s * chunk_shape[0].get() * chunk_shape[1].get()
94 + ij[0] as u64 * chunk_shape[1].get()
95 + ij[1] as u64) as u16
96 },
97 );
98 array.store_chunk(&chunk_indices, chunk_array)
99 } else {
100 Err(zarrs::array::ArrayError::InvalidChunkGridIndicesError(
101 chunk_indices.to_vec(),
102 ))
103 }
104 })?;
105
106 // Read the whole array
107 let data_all: ArrayD<u16> = array.retrieve_array_subset(&array.subset_all())?;
108 println!("The whole array is:\n{data_all}\n");
109
110 // Read a shard back from the store
111 let shard_indices = vec![1, 0];
112 let data_shard: ArrayD<u16> = array.retrieve_chunk(&shard_indices)?;
113 println!("Shard [1,0] is:\n{data_shard}\n");
114
115 // Read a subchunk from the store
116 let subset_chunk_1_0 = ArraySubset::new_with_ranges(&[4..8, 0..4]);
117 let data_chunk: ArrayD<u16> = array.retrieve_array_subset(&subset_chunk_1_0)?;
118 println!("Chunk [1,0] is:\n{data_chunk}\n");
119
120 // Read the central 4x2 subset of the array
121 let subset_4x2 = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
122 let data_4x2: ArrayD<u16> = array.retrieve_array_subset(&subset_4x2)?;
123 println!("The middle 4x2 subset is:\n{data_4x2}\n");
124
125 // Decode subchunks
126 // In some cases, it might be preferable to decode subchunks in a shard directly.
127 // If using the partial decoder, then the shard index will only be read once from the store.
128 let partial_decoder = array.partial_decoder(&[0, 0])?;
129 println!("Decoded subchunks:");
130 for subchunk_subset in [
131 ArraySubset::new_with_start_shape(vec![0, 0], subchunk_shape.clone())?,
132 ArraySubset::new_with_start_shape(vec![0, 4], subchunk_shape.clone())?,
133 ] {
134 println!("{subchunk_subset}");
135 let decoded_subchunk_bytes = partial_decoder.partial_decode(&subchunk_subset, &options)?;
136 let ndarray = bytes_to_ndarray::<u16>(
137 &subchunk_shape,
138 decoded_subchunk_bytes.into_fixed()?.into_owned(),
139 )?;
140 println!("{ndarray}\n");
141 }
142
143 // Show the hierarchy
144 let node = Node::open(&store, "/").unwrap();
145 let tree = node.hierarchy_tree();
146 println!("The Zarr hierarchy tree is:\n{}", tree);
147
148 println!(
149 "The keys in the store are:\n[{}]",
150 store.list().unwrap_or_default().iter().format(", ")
151 );
152
153 Ok(())
154}examples/array_write_read_ndarray.rs (line 161)
8fn array_write_read() -> Result<(), Box<dyn std::error::Error>> {
9 use std::sync::Arc;
10
11 use zarrs::array::{ArraySubset, ZARR_NAN_F32, data_type};
12 use zarrs::node::Node;
13 use zarrs::storage::store;
14
15 // Create a store
16 // let path = tempfile::TempDir::new()?;
17 // let mut store: ReadableWritableListableStorage =
18 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
19 // let mut store: ReadableWritableListableStorage = Arc::new(
20 // zarrs::filesystem::FilesystemStore::new("zarrs/tests/data/array_write_read.zarr")?,
21 // );
22 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
23 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
24 && arg1 == "--usage-log"
25 {
26 let log_writer = Arc::new(std::sync::Mutex::new(
27 // std::io::BufWriter::new(
28 std::io::stdout(),
29 // )
30 ));
31 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
32 chrono::Utc::now().format("[%T%.3f] ").to_string()
33 }));
34 }
35
36 // Create the root group
37 zarrs::group::GroupBuilder::new()
38 .build(store.clone(), "/")?
39 .store_metadata()?;
40
41 // Create a group with attributes
42 let group_path = "/group";
43 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
44 group
45 .attributes_mut()
46 .insert("foo".into(), serde_json::Value::String("bar".into()));
47 group.store_metadata()?;
48
49 println!(
50 "The group metadata is:\n{}\n",
51 group.metadata().to_string_pretty()
52 );
53
54 // Create an array
55 let array_path = "/group/array";
56 let array = zarrs::array::ArrayBuilder::new(
57 vec![8, 8], // array shape
58 vec![4, 4], // regular chunk shape
59 data_type::float32(),
60 ZARR_NAN_F32,
61 )
62 // .bytes_to_bytes_codecs(vec![]) // uncompressed
63 .dimension_names(["y", "x"].into())
64 // .storage_transformers(vec![].into())
65 .build(store.clone(), array_path)?;
66
67 // Write array metadata to store
68 array.store_metadata()?;
69
70 println!(
71 "The array metadata is:\n{}\n",
72 array.metadata().to_string_pretty()
73 );
74
75 // Write some chunks
76 (0..2).into_par_iter().try_for_each(|i| {
77 let chunk_indices: Vec<u64> = vec![0, i];
78 let chunk_subset = array.chunk_grid().subset(&chunk_indices)?.ok_or_else(|| {
79 zarrs::array::ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec())
80 })?;
81 array.store_chunk(
82 &chunk_indices,
83 ArrayD::<f32>::from_shape_vec(
84 chunk_subset.shape_usize(),
85 vec![i as f32 * 0.1; chunk_subset.num_elements() as usize],
86 )
87 .unwrap(),
88 )
89 })?;
90
91 let subset_all = array.subset_all();
92 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
93 println!("store_chunk [0, 0] and [0, 1]:\n{data_all:+4.1}\n");
94
95 // Store multiple chunks
96 let ndarray_chunks: Array2<f32> = array![
97 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
98 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
99 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
100 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
101 ];
102 array.store_chunks(&[1..2, 0..2], ndarray_chunks)?;
103 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
104 println!("store_chunks [1..2, 0..2]:\n{data_all:+4.1}\n");
105
106 // Write a subset spanning multiple chunks, including updating chunks already written
107 let ndarray_subset: Array2<f32> =
108 array![[-3.3, -3.4, -3.5,], [-4.3, -4.4, -4.5,], [-5.3, -5.4, -5.5],];
109 array.store_array_subset(&[3..6, 3..6], ndarray_subset)?;
110 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
111 println!("store_array_subset [3..6, 3..6]:\n{data_all:+4.1}\n");
112
113 // Store array subset
114 let ndarray_subset: Array2<f32> = array![
115 [-0.6],
116 [-1.6],
117 [-2.6],
118 [-3.6],
119 [-4.6],
120 [-5.6],
121 [-6.6],
122 [-7.6],
123 ];
124 array.store_array_subset(&[0..8, 6..7], ndarray_subset)?;
125 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
126 println!("store_array_subset [0..8, 6..7]:\n{data_all:+4.1}\n");
127
128 // Store chunk subset
129 let ndarray_chunk_subset: Array2<f32> = array![[-7.4, -7.5, -7.6, -7.7],];
130 array.store_chunk_subset(
131 // chunk indices
132 &[1, 1],
133 // subset within chunk
134 &[3..4, 0..4],
135 ndarray_chunk_subset,
136 )?;
137 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
138 println!("store_chunk_subset [3..4, 0..4] of chunk [1, 1]:\n{data_all:+4.1}\n");
139
140 // Erase a chunk
141 array.erase_chunk(&[0, 0])?;
142 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
143 println!("erase_chunk [0, 0]:\n{data_all:+4.1}\n");
144
145 // Read a chunk
146 let chunk_indices = vec![0, 1];
147 let data_chunk: ArrayD<f32> = array.retrieve_chunk(&chunk_indices)?;
148 println!("retrieve_chunk [0, 1]:\n{data_chunk:+4.1}\n");
149
150 // Read chunks
151 let chunks = ArraySubset::new_with_ranges(&[0..2, 1..2]);
152 let data_chunks: ArrayD<f32> = array.retrieve_chunks(&chunks)?;
153 println!("retrieve_chunks [0..2, 1..2]:\n{data_chunks:+4.1}\n");
154
155 // Retrieve an array subset
156 let subset = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
157 let data_subset: ArrayD<f32> = array.retrieve_array_subset(&subset)?;
158 println!("retrieve_array_subset [2..6, 3..5]:\n{data_subset:+4.1}\n");
159
160 // Show the hierarchy
161 let node = Node::open(&store, "/").unwrap();
162 let tree = node.hierarchy_tree();
163 println!("hierarchy_tree:\n{}", tree);
164
165 Ok(())
166}Sourcepub fn open_opt<TStorage: ?Sized + ReadableStorageTraits + ListableStorageTraits>(
storage: &Arc<TStorage>,
path: &str,
version: &MetadataRetrieveVersion,
) -> Result<Self, NodeCreateError>
pub fn open_opt<TStorage: ?Sized + ReadableStorageTraits + ListableStorageTraits>( storage: &Arc<TStorage>, path: &str, version: &MetadataRetrieveVersion, ) -> Result<Self, NodeCreateError>
Open a node at path and read metadata and children from storage with non-default MetadataRetrieveVersion.
§Errors
Returns NodeCreateError if metadata is invalid or there is a failure to list child nodes.
Sourcepub async fn async_open<TStorage: ?Sized + AsyncReadableStorageTraits + AsyncListableStorageTraits>(
storage: Arc<TStorage>,
path: &str,
) -> Result<Self, NodeCreateError>
Available on crate feature async only.
pub async fn async_open<TStorage: ?Sized + AsyncReadableStorageTraits + AsyncListableStorageTraits>( storage: Arc<TStorage>, path: &str, ) -> Result<Self, NodeCreateError>
async only.Asynchronously open a node at path and read metadata and children from storage with default MetadataRetrieveVersion.
§Errors
Returns NodeCreateError if metadata is invalid or there is a failure to list child nodes.
Examples found in repository?
examples/async_array_write_read.rs (line 166)
8async fn async_array_write_read() -> Result<(), Box<dyn std::error::Error>> {
9 use std::sync::Arc;
10
11 use futures::StreamExt;
12 use zarrs::array::{ArraySubset, ZARR_NAN_F32, data_type};
13 use zarrs::node::Node;
14
15 // Create a store
16 let mut store: AsyncReadableWritableListableStorage = Arc::new(
17 zarrs_object_store::AsyncObjectStore::new(object_store::memory::InMemory::new()),
18 );
19 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
20 && arg1 == "--usage-log"
21 {
22 let log_writer = Arc::new(std::sync::Mutex::new(
23 // std::io::BufWriter::new(
24 std::io::stdout(),
25 // )
26 ));
27 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
28 chrono::Utc::now().format("[%T%.3f] ").to_string()
29 }));
30 }
31
32 // Create the root group
33 zarrs::group::GroupBuilder::new()
34 .build(store.clone(), "/")?
35 .async_store_metadata()
36 .await?;
37
38 // Create a group with attributes
39 let group_path = "/group";
40 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
41 group
42 .attributes_mut()
43 .insert("foo".into(), serde_json::Value::String("bar".into()));
44 group.async_store_metadata().await?;
45
46 println!(
47 "The group metadata is:\n{}\n",
48 group.metadata().to_string_pretty()
49 );
50
51 // Create an array
52 let array_path = "/group/array";
53 let array = zarrs::array::ArrayBuilder::new(
54 vec![8, 8], // array shape
55 vec![4, 4], // regular chunk shape
56 data_type::float32(),
57 ZARR_NAN_F32,
58 )
59 // .bytes_to_bytes_codecs(vec![]) // uncompressed
60 .dimension_names(["y", "x"].into())
61 // .storage_transformers(vec![].into())
62 .build_arc(store.clone(), array_path)?;
63
64 // Write array metadata to store
65 array.async_store_metadata().await?;
66
67 println!(
68 "The array metadata is:\n{}\n",
69 array.metadata().to_string_pretty()
70 );
71
72 // Write some chunks
73 let store_chunk = |i: u64| {
74 let array = array.clone();
75 async move {
76 let chunk_indices: Vec<u64> = vec![0, i];
77 let chunk_subset = array.chunk_grid().subset(&chunk_indices)?.ok_or_else(|| {
78 zarrs::array::ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec())
79 })?;
80 array
81 .async_store_chunk(
82 &chunk_indices,
83 vec![i as f32 * 0.1; chunk_subset.num_elements() as usize],
84 )
85 .await
86 }
87 };
88 futures::stream::iter(0..2)
89 .map(Ok)
90 .try_for_each_concurrent(None, store_chunk)
91 .await?;
92
93 let subset_all = array.subset_all();
94 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
95 println!("async_store_chunk [0, 0] and [0, 1]:\n{data_all:+4.1}\n");
96
97 // Store multiple chunks
98 array
99 .async_store_chunks(
100 &[1..2, 0..2],
101 &[
102 //
103 1.0f32, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
104 //
105 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
106 ],
107 )
108 .await?;
109 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
110 println!("async_store_chunks [1..2, 0..2]:\n{data_all:+4.1}\n");
111
112 // Write a subset spanning multiple chunks, including updating chunks already written
113 array
114 .async_store_array_subset(
115 &[3..6, 3..6],
116 &[-3.3, -3.4, -3.5, -4.3, -4.4, -4.5, -5.3, -5.4, -5.5],
117 )
118 .await?;
119 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
120 println!("async_store_array_subset [3..6, 3..6]:\n{data_all:+4.1}\n");
121
122 // Store array subset
123 array
124 .async_store_array_subset(
125 &[0..8, 6..7],
126 &[-0.6f32, -1.6, -2.6, -3.6, -4.6, -5.6, -6.6, -7.6],
127 )
128 .await?;
129 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
130 println!("async_store_array_subset [0..8, 6..7]:\n{data_all:+4.1}\n");
131
132 // Store chunk subset
133 array
134 .async_store_chunk_subset(
135 // chunk indices
136 &[1, 1],
137 // subset within chunk
138 &[3..4, 0..4],
139 &[-7.4f32, -7.5, -7.6, -7.7],
140 )
141 .await?;
142 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
143 println!("async_store_chunk_subset [3..4, 0..4] of chunk [1, 1]:\n{data_all:+4.1}\n");
144
145 // Erase a chunk
146 array.async_erase_chunk(&[0, 0]).await?;
147 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
148 println!("async_erase_chunk [0, 0]:\n{data_all:+4.1}\n");
149
150 // Read a chunk
151 let chunk_indices = vec![0, 1];
152 let data_chunk: ArrayD<f32> = array.async_retrieve_chunk(&chunk_indices).await?;
153 println!("async_retrieve_chunk [0, 1]:\n{data_chunk:+4.1}\n");
154
155 // Read chunks
156 let chunks = ArraySubset::new_with_ranges(&[0..2, 1..2]);
157 let data_chunks: ArrayD<f32> = array.async_retrieve_chunks(&chunks).await?;
158 println!("async_retrieve_chunks [0..2, 1..2]:\n{data_chunks:+4.1}\n");
159
160 // Retrieve an array subset
161 let subset = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
162 let data_subset: ArrayD<f32> = array.async_retrieve_array_subset(&subset).await?;
163 println!("async_retrieve_array_subset [2..6, 3..5]:\n{data_subset:+4.1}\n");
164
165 // Show the hierarchy
166 let node = Node::async_open(store, "/").await.unwrap();
167 let tree = node.hierarchy_tree();
168 println!("hierarchy_tree:\n{}", tree);
169
170 Ok(())
171}Sourcepub async fn async_open_opt<TStorage: ?Sized + AsyncReadableStorageTraits + AsyncListableStorageTraits>(
storage: Arc<TStorage>,
path: &str,
version: &MetadataRetrieveVersion,
) -> Result<Self, NodeCreateError>
Available on crate feature async only.
pub async fn async_open_opt<TStorage: ?Sized + AsyncReadableStorageTraits + AsyncListableStorageTraits>( storage: Arc<TStorage>, path: &str, version: &MetadataRetrieveVersion, ) -> Result<Self, NodeCreateError>
async only.Asynchronously open a node at path and read metadata and children from storage with non-default MetadataRetrieveVersion.
§Errors
Returns NodeCreateError if metadata is invalid or there is a failure to list child nodes.
Sourcepub fn new_with_metadata(
path: NodePath,
metadata: NodeMetadata,
children: Vec<Self>,
) -> Self
pub fn new_with_metadata( path: NodePath, metadata: NodeMetadata, children: Vec<Self>, ) -> Self
Create a new node at path with metadata and children.
Sourcepub fn metadata(&self) -> &NodeMetadata
pub fn metadata(&self) -> &NodeMetadata
Returns a reference to the metadata of the node.
Sourcepub fn hierarchy_tree(&self) -> String
pub fn hierarchy_tree(&self) -> String
Return a tree representation of a hierarchy as a string.
Arrays are annotated with their shape and data type. For example:
a
baz [10000, 1000] float64
foo [10000, 1000] float64
bExamples found in repository?
examples/rectilinear_array_write_read.rs (line 143)
10fn rectilinear_array_write_read() -> Result<(), Box<dyn std::error::Error>> {
11 use rayon::prelude::{IntoParallelIterator, ParallelIterator};
12 use zarrs::array::{ArraySubset, ZARR_NAN_F32, codec, data_type};
13 use zarrs::node::Node;
14 use zarrs::storage::store;
15
16 // Create a store
17 // let path = tempfile::TempDir::new()?;
18 // let mut store: ReadableWritableListableStorage =
19 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
20 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
21 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
22 && arg1 == "--usage-log"
23 {
24 let log_writer = Arc::new(std::sync::Mutex::new(
25 // std::io::BufWriter::new(
26 std::io::stdout(),
27 // )
28 ));
29 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
30 chrono::Utc::now().format("[%T%.3f] ").to_string()
31 }));
32 }
33
34 // Create the root group
35 zarrs::group::GroupBuilder::new()
36 .build(store.clone(), "/")?
37 .store_metadata()?;
38
39 // Create a group with attributes
40 let group_path = "/group";
41 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
42 group
43 .attributes_mut()
44 .insert("foo".into(), serde_json::Value::String("bar".into()));
45 group.store_metadata()?;
46
47 println!(
48 "The group metadata is:\n{}\n",
49 group.metadata().to_string_pretty()
50 );
51
52 // Create an array
53 let array_path = "/group/array";
54 let array = zarrs::array::ArrayBuilder::new(
55 vec![8, 8], // array shape
56 MetadataV3::new_with_configuration(
57 "rectilinear",
58 RectilinearChunkGridConfiguration::Inline {
59 chunk_shapes: vec![
60 // Varying: chunk sizes [1, 1, 1, 3, 2] (run-length encoded as [[1,3], 3, 2])
61 ChunkEdgeLengths::Varying(serde_json::from_str("[[1,3], 3, 2]").unwrap()),
62 // Scalar: regular 4-element chunks
63 ChunkEdgeLengths::Scalar(NonZeroU64::new(4).unwrap()),
64 ],
65 },
66 ),
67 data_type::float32(),
68 ZARR_NAN_F32,
69 )
70 .bytes_to_bytes_codecs(vec![
71 #[cfg(feature = "gzip")]
72 Arc::new(codec::GzipCodec::new(5)?),
73 ])
74 .dimension_names(["y", "x"].into())
75 // .storage_transformers(vec![].into())
76 .build(store.clone(), array_path)?;
77
78 // Write array metadata to store
79 array.store_metadata()?;
80
81 // Write some chunks (in parallel)
82 (0..4).into_par_iter().try_for_each(|i| {
83 let chunk_grid = array.chunk_grid();
84 let chunk_indices = vec![i, 0];
85 if let Some(chunk_shape) = chunk_grid.chunk_shape(&chunk_indices)? {
86 let chunk_array = ndarray::ArrayD::<f32>::from_elem(
87 chunk_shape
88 .iter()
89 .map(|u| u.get() as usize)
90 .collect::<Vec<_>>(),
91 i as f32,
92 );
93 array.store_chunk(&chunk_indices, chunk_array)
94 } else {
95 Err(zarrs::array::ArrayError::InvalidChunkGridIndicesError(
96 chunk_indices.to_vec(),
97 ))
98 }
99 })?;
100
101 println!(
102 "The array metadata is:\n{}\n",
103 array.metadata().to_string_pretty()
104 );
105
106 // Write a subset spanning multiple chunks, including updating chunks already written
107 array.store_array_subset(
108 &[3..6, 3..6], // start
109 ndarray::ArrayD::<f32>::from_shape_vec(
110 vec![3, 3],
111 vec![0.1f32, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
112 )?,
113 )?;
114
115 // Store elements directly, in this case set the 7th column to 123.0
116 array.store_array_subset(&[0..8, 6..7], &[123.0f32; 8])?;
117
118 // Store elements directly in a chunk, in this case set the last row of the bottom right chunk
119 array.store_chunk_subset(
120 // chunk indices
121 &[3, 1],
122 // subset within chunk
123 &[1..2, 0..4],
124 &[-4.0f32; 4],
125 )?;
126
127 // Read the whole array
128 let data_all: ndarray::ArrayD<f32> = array.retrieve_array_subset(&array.subset_all())?;
129 println!("The whole array is:\n{data_all}\n");
130
131 // Read a chunk back from the store
132 let chunk_indices = vec![1, 0];
133 let data_chunk: ndarray::ArrayD<f32> = array.retrieve_chunk(&chunk_indices)?;
134 println!("Chunk [1,0] is:\n{data_chunk}\n");
135
136 // Read the central 4x2 subset of the array
137 let subset_4x2 = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
138 let data_4x2: ndarray::ArrayD<f32> = array.retrieve_array_subset(&subset_4x2)?;
139 println!("The middle 4x2 subset is:\n{data_4x2}\n");
140
141 // Show the hierarchy
142 let node = Node::open(&store, "/").unwrap();
143 let tree = node.hierarchy_tree();
144 println!("The Zarr hierarchy tree is:\n{tree}");
145
146 Ok(())
147}More examples
examples/array_write_read.rs (line 153)
8fn array_write_read() -> Result<(), Box<dyn std::error::Error>> {
9 use std::sync::Arc;
10
11 use zarrs::array::{ArraySubset, ZARR_NAN_F32, data_type};
12 use zarrs::node::Node;
13 use zarrs::storage::store;
14
15 // Create a store
16 // let path = tempfile::TempDir::new()?;
17 // let mut store: ReadableWritableListableStorage =
18 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
19 // let mut store: ReadableWritableListableStorage = Arc::new(
20 // zarrs::filesystem::FilesystemStore::new("zarrs/tests/data/array_write_read.zarr")?,
21 // );
22 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
23 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
24 && arg1 == "--usage-log"
25 {
26 let log_writer = Arc::new(std::sync::Mutex::new(
27 // std::io::BufWriter::new(
28 std::io::stdout(),
29 // )
30 ));
31 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
32 chrono::Utc::now().format("[%T%.3f] ").to_string()
33 }));
34 }
35
36 // Create the root group
37 zarrs::group::GroupBuilder::new()
38 .build(store.clone(), "/")?
39 .store_metadata()?;
40
41 // Create a group with attributes
42 let group_path = "/group";
43 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
44 group
45 .attributes_mut()
46 .insert("foo".into(), serde_json::Value::String("bar".into()));
47 group.store_metadata()?;
48
49 println!(
50 "The group metadata is:\n{}\n",
51 group.metadata().to_string_pretty()
52 );
53
54 // Create an array
55 let array_path = "/group/array";
56 let array = zarrs::array::ArrayBuilder::new(
57 vec![8, 8], // array shape
58 vec![4, 4], // regular chunk shape
59 data_type::float32(),
60 ZARR_NAN_F32,
61 )
62 // .bytes_to_bytes_codecs(vec![]) // uncompressed
63 .dimension_names(["y", "x"].into())
64 // .storage_transformers(vec![].into())
65 .build(store.clone(), array_path)?;
66
67 // Write array metadata to store
68 array.store_metadata()?;
69
70 println!(
71 "The array metadata is:\n{}\n",
72 array.metadata().to_string_pretty()
73 );
74
75 // Write some chunks
76 (0..2).into_par_iter().try_for_each(|i| {
77 let chunk_indices: Vec<u64> = vec![0, i];
78 let chunk_subset = array.chunk_grid().subset(&chunk_indices)?.ok_or_else(|| {
79 zarrs::array::ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec())
80 })?;
81 array.store_chunk(
82 &chunk_indices,
83 vec![i as f32 * 0.1; chunk_subset.num_elements() as usize],
84 )
85 })?;
86
87 let subset_all = array.subset_all();
88 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
89 println!("store_chunk [0, 0] and [0, 1]:\n{data_all:+4.1}\n");
90
91 // Store multiple chunks
92 array.store_chunks(
93 &[1..2, 0..2],
94 &[
95 //
96 1.0f32, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
97 //
98 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
99 ],
100 )?;
101 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
102 println!("store_chunks [1..2, 0..2]:\n{data_all:+4.1}\n");
103
104 // Write a subset spanning multiple chunks, including updating chunks already written
105 array.store_array_subset(
106 &[3..6, 3..6],
107 &[-3.3f32, -3.4, -3.5, -4.3, -4.4, -4.5, -5.3, -5.4, -5.5],
108 )?;
109 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
110 println!("store_array_subset [3..6, 3..6]:\n{data_all:+4.1}\n");
111
112 // Store array subset
113 array.store_array_subset(
114 &[0..8, 6..7],
115 &[-0.6f32, -1.6, -2.6, -3.6, -4.6, -5.6, -6.6, -7.6],
116 )?;
117 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
118 println!("store_array_subset [0..8, 6..7]:\n{data_all:+4.1}\n");
119
120 // Store chunk subset
121 array.store_chunk_subset(
122 // chunk indices
123 &[1, 1],
124 // subset within chunk
125 &[3..4, 0..4],
126 &[-7.4f32, -7.5, -7.6, -7.7],
127 )?;
128 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
129 println!("store_chunk_subset [3..4, 0..4] of chunk [1, 1]:\n{data_all:+4.1}\n");
130
131 // Erase a chunk
132 array.erase_chunk(&[0, 0])?;
133 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
134 println!("erase_chunk [0, 0]:\n{data_all:+4.1}\n");
135
136 // Read a chunk
137 let chunk_indices = vec![0, 1];
138 let data_chunk: ArrayD<f32> = array.retrieve_chunk(&chunk_indices)?;
139 println!("retrieve_chunk [0, 1]:\n{data_chunk:+4.1}\n");
140
141 // Read chunks
142 let chunks = ArraySubset::new_with_ranges(&[0..2, 1..2]);
143 let data_chunks: ArrayD<f32> = array.retrieve_chunks(&chunks)?;
144 println!("retrieve_chunks [0..2, 1..2]:\n{data_chunks:+4.1}\n");
145
146 // Retrieve an array subset
147 let subset = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
148 let data_subset: ArrayD<f32> = array.retrieve_array_subset(&subset)?;
149 println!("retrieve_array_subset [2..6, 3..5]:\n{data_subset:+4.1}\n");
150
151 // Show the hierarchy
152 let node = Node::open(&store, "/").unwrap();
153 let tree = node.hierarchy_tree();
154 println!("hierarchy_tree:\n{}", tree);
155
156 Ok(())
157}examples/sharded_array_write_read.rs (line 145)
10fn sharded_array_write_read() -> Result<(), Box<dyn std::error::Error>> {
11 use std::sync::Arc;
12
13 use rayon::prelude::{IntoParallelIterator, ParallelIterator};
14 use zarrs::array::{ArraySubset, codec, data_type};
15 use zarrs::node::Node;
16 use zarrs::storage::store;
17
18 // Create a store
19 // let path = tempfile::TempDir::new()?;
20 // let mut store: ReadableWritableListableStorage =
21 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
22 // let mut store: ReadableWritableListableStorage = Arc::new(
23 // zarrs::filesystem::FilesystemStore::new("zarrs/tests/data/sharded_array_write_read.zarr")?,
24 // );
25 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
26 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
27 && arg1 == "--usage-log"
28 {
29 let log_writer = Arc::new(std::sync::Mutex::new(
30 // std::io::BufWriter::new(
31 std::io::stdout(),
32 // )
33 ));
34 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
35 chrono::Utc::now().format("[%T%.3f] ").to_string()
36 }));
37 }
38
39 // Create the root group
40 zarrs::group::GroupBuilder::new()
41 .build(store.clone(), "/")?
42 .store_metadata()?;
43
44 // Create a group with attributes
45 let group_path = "/group";
46 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
47 group
48 .attributes_mut()
49 .insert("foo".into(), serde_json::Value::String("bar".into()));
50 group.store_metadata()?;
51
52 // Create an array
53 let array_path = "/group/array";
54 let subchunk_shape = vec![4, 4];
55 let array = zarrs::array::ArrayBuilder::new(
56 vec![8, 8], // array shape
57 vec![4, 8], // chunk (shard) shape
58 data_type::uint16(),
59 0u16,
60 )
61 .subchunk_shape(subchunk_shape.clone())
62 .bytes_to_bytes_codecs(vec![
63 #[cfg(feature = "gzip")]
64 Arc::new(codec::GzipCodec::new(5)?),
65 ])
66 .dimension_names(["y", "x"].into())
67 // .storage_transformers(vec![].into())
68 .build(store.clone(), array_path)?;
69
70 // Write array metadata to store
71 array.store_metadata()?;
72
73 // The array metadata is
74 println!(
75 "The array metadata is:\n{}\n",
76 array.metadata().to_string_pretty()
77 );
78
79 // Use default codec options (concurrency etc)
80 let options = CodecOptions::default();
81
82 // Write some shards (in parallel)
83 (0..2).into_par_iter().try_for_each(|s| {
84 let chunk_grid = array.chunk_grid();
85 let chunk_indices = vec![s, 0];
86 if let Some(chunk_shape) = chunk_grid.chunk_shape(&chunk_indices)? {
87 let chunk_array = ndarray::ArrayD::<u16>::from_shape_fn(
88 chunk_shape
89 .iter()
90 .map(|u| u.get() as usize)
91 .collect::<Vec<_>>(),
92 |ij| {
93 (s * chunk_shape[0].get() * chunk_shape[1].get()
94 + ij[0] as u64 * chunk_shape[1].get()
95 + ij[1] as u64) as u16
96 },
97 );
98 array.store_chunk(&chunk_indices, chunk_array)
99 } else {
100 Err(zarrs::array::ArrayError::InvalidChunkGridIndicesError(
101 chunk_indices.to_vec(),
102 ))
103 }
104 })?;
105
106 // Read the whole array
107 let data_all: ArrayD<u16> = array.retrieve_array_subset(&array.subset_all())?;
108 println!("The whole array is:\n{data_all}\n");
109
110 // Read a shard back from the store
111 let shard_indices = vec![1, 0];
112 let data_shard: ArrayD<u16> = array.retrieve_chunk(&shard_indices)?;
113 println!("Shard [1,0] is:\n{data_shard}\n");
114
115 // Read a subchunk from the store
116 let subset_chunk_1_0 = ArraySubset::new_with_ranges(&[4..8, 0..4]);
117 let data_chunk: ArrayD<u16> = array.retrieve_array_subset(&subset_chunk_1_0)?;
118 println!("Chunk [1,0] is:\n{data_chunk}\n");
119
120 // Read the central 4x2 subset of the array
121 let subset_4x2 = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
122 let data_4x2: ArrayD<u16> = array.retrieve_array_subset(&subset_4x2)?;
123 println!("The middle 4x2 subset is:\n{data_4x2}\n");
124
125 // Decode subchunks
126 // In some cases, it might be preferable to decode subchunks in a shard directly.
127 // If using the partial decoder, then the shard index will only be read once from the store.
128 let partial_decoder = array.partial_decoder(&[0, 0])?;
129 println!("Decoded subchunks:");
130 for subchunk_subset in [
131 ArraySubset::new_with_start_shape(vec![0, 0], subchunk_shape.clone())?,
132 ArraySubset::new_with_start_shape(vec![0, 4], subchunk_shape.clone())?,
133 ] {
134 println!("{subchunk_subset}");
135 let decoded_subchunk_bytes = partial_decoder.partial_decode(&subchunk_subset, &options)?;
136 let ndarray = bytes_to_ndarray::<u16>(
137 &subchunk_shape,
138 decoded_subchunk_bytes.into_fixed()?.into_owned(),
139 )?;
140 println!("{ndarray}\n");
141 }
142
143 // Show the hierarchy
144 let node = Node::open(&store, "/").unwrap();
145 let tree = node.hierarchy_tree();
146 println!("The Zarr hierarchy tree is:\n{}", tree);
147
148 println!(
149 "The keys in the store are:\n[{}]",
150 store.list().unwrap_or_default().iter().format(", ")
151 );
152
153 Ok(())
154}examples/array_write_read_ndarray.rs (line 162)
8fn array_write_read() -> Result<(), Box<dyn std::error::Error>> {
9 use std::sync::Arc;
10
11 use zarrs::array::{ArraySubset, ZARR_NAN_F32, data_type};
12 use zarrs::node::Node;
13 use zarrs::storage::store;
14
15 // Create a store
16 // let path = tempfile::TempDir::new()?;
17 // let mut store: ReadableWritableListableStorage =
18 // Arc::new(zarrs::filesystem::FilesystemStore::new(path.path())?);
19 // let mut store: ReadableWritableListableStorage = Arc::new(
20 // zarrs::filesystem::FilesystemStore::new("zarrs/tests/data/array_write_read.zarr")?,
21 // );
22 let mut store: ReadableWritableListableStorage = Arc::new(store::MemoryStore::new());
23 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
24 && arg1 == "--usage-log"
25 {
26 let log_writer = Arc::new(std::sync::Mutex::new(
27 // std::io::BufWriter::new(
28 std::io::stdout(),
29 // )
30 ));
31 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
32 chrono::Utc::now().format("[%T%.3f] ").to_string()
33 }));
34 }
35
36 // Create the root group
37 zarrs::group::GroupBuilder::new()
38 .build(store.clone(), "/")?
39 .store_metadata()?;
40
41 // Create a group with attributes
42 let group_path = "/group";
43 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
44 group
45 .attributes_mut()
46 .insert("foo".into(), serde_json::Value::String("bar".into()));
47 group.store_metadata()?;
48
49 println!(
50 "The group metadata is:\n{}\n",
51 group.metadata().to_string_pretty()
52 );
53
54 // Create an array
55 let array_path = "/group/array";
56 let array = zarrs::array::ArrayBuilder::new(
57 vec![8, 8], // array shape
58 vec![4, 4], // regular chunk shape
59 data_type::float32(),
60 ZARR_NAN_F32,
61 )
62 // .bytes_to_bytes_codecs(vec![]) // uncompressed
63 .dimension_names(["y", "x"].into())
64 // .storage_transformers(vec![].into())
65 .build(store.clone(), array_path)?;
66
67 // Write array metadata to store
68 array.store_metadata()?;
69
70 println!(
71 "The array metadata is:\n{}\n",
72 array.metadata().to_string_pretty()
73 );
74
75 // Write some chunks
76 (0..2).into_par_iter().try_for_each(|i| {
77 let chunk_indices: Vec<u64> = vec![0, i];
78 let chunk_subset = array.chunk_grid().subset(&chunk_indices)?.ok_or_else(|| {
79 zarrs::array::ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec())
80 })?;
81 array.store_chunk(
82 &chunk_indices,
83 ArrayD::<f32>::from_shape_vec(
84 chunk_subset.shape_usize(),
85 vec![i as f32 * 0.1; chunk_subset.num_elements() as usize],
86 )
87 .unwrap(),
88 )
89 })?;
90
91 let subset_all = array.subset_all();
92 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
93 println!("store_chunk [0, 0] and [0, 1]:\n{data_all:+4.1}\n");
94
95 // Store multiple chunks
96 let ndarray_chunks: Array2<f32> = array![
97 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
98 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
99 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
100 [1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,],
101 ];
102 array.store_chunks(&[1..2, 0..2], ndarray_chunks)?;
103 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
104 println!("store_chunks [1..2, 0..2]:\n{data_all:+4.1}\n");
105
106 // Write a subset spanning multiple chunks, including updating chunks already written
107 let ndarray_subset: Array2<f32> =
108 array![[-3.3, -3.4, -3.5,], [-4.3, -4.4, -4.5,], [-5.3, -5.4, -5.5],];
109 array.store_array_subset(&[3..6, 3..6], ndarray_subset)?;
110 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
111 println!("store_array_subset [3..6, 3..6]:\n{data_all:+4.1}\n");
112
113 // Store array subset
114 let ndarray_subset: Array2<f32> = array![
115 [-0.6],
116 [-1.6],
117 [-2.6],
118 [-3.6],
119 [-4.6],
120 [-5.6],
121 [-6.6],
122 [-7.6],
123 ];
124 array.store_array_subset(&[0..8, 6..7], ndarray_subset)?;
125 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
126 println!("store_array_subset [0..8, 6..7]:\n{data_all:+4.1}\n");
127
128 // Store chunk subset
129 let ndarray_chunk_subset: Array2<f32> = array![[-7.4, -7.5, -7.6, -7.7],];
130 array.store_chunk_subset(
131 // chunk indices
132 &[1, 1],
133 // subset within chunk
134 &[3..4, 0..4],
135 ndarray_chunk_subset,
136 )?;
137 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
138 println!("store_chunk_subset [3..4, 0..4] of chunk [1, 1]:\n{data_all:+4.1}\n");
139
140 // Erase a chunk
141 array.erase_chunk(&[0, 0])?;
142 let data_all: ArrayD<f32> = array.retrieve_array_subset(&subset_all)?;
143 println!("erase_chunk [0, 0]:\n{data_all:+4.1}\n");
144
145 // Read a chunk
146 let chunk_indices = vec![0, 1];
147 let data_chunk: ArrayD<f32> = array.retrieve_chunk(&chunk_indices)?;
148 println!("retrieve_chunk [0, 1]:\n{data_chunk:+4.1}\n");
149
150 // Read chunks
151 let chunks = ArraySubset::new_with_ranges(&[0..2, 1..2]);
152 let data_chunks: ArrayD<f32> = array.retrieve_chunks(&chunks)?;
153 println!("retrieve_chunks [0..2, 1..2]:\n{data_chunks:+4.1}\n");
154
155 // Retrieve an array subset
156 let subset = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
157 let data_subset: ArrayD<f32> = array.retrieve_array_subset(&subset)?;
158 println!("retrieve_array_subset [2..6, 3..5]:\n{data_subset:+4.1}\n");
159
160 // Show the hierarchy
161 let node = Node::open(&store, "/").unwrap();
162 let tree = node.hierarchy_tree();
163 println!("hierarchy_tree:\n{}", tree);
164
165 Ok(())
166}examples/async_array_write_read.rs (line 167)
8async fn async_array_write_read() -> Result<(), Box<dyn std::error::Error>> {
9 use std::sync::Arc;
10
11 use futures::StreamExt;
12 use zarrs::array::{ArraySubset, ZARR_NAN_F32, data_type};
13 use zarrs::node::Node;
14
15 // Create a store
16 let mut store: AsyncReadableWritableListableStorage = Arc::new(
17 zarrs_object_store::AsyncObjectStore::new(object_store::memory::InMemory::new()),
18 );
19 if let Some(arg1) = std::env::args().collect::<Vec<_>>().get(1)
20 && arg1 == "--usage-log"
21 {
22 let log_writer = Arc::new(std::sync::Mutex::new(
23 // std::io::BufWriter::new(
24 std::io::stdout(),
25 // )
26 ));
27 store = Arc::new(UsageLogStorageAdapter::new(store, log_writer, || {
28 chrono::Utc::now().format("[%T%.3f] ").to_string()
29 }));
30 }
31
32 // Create the root group
33 zarrs::group::GroupBuilder::new()
34 .build(store.clone(), "/")?
35 .async_store_metadata()
36 .await?;
37
38 // Create a group with attributes
39 let group_path = "/group";
40 let mut group = zarrs::group::GroupBuilder::new().build(store.clone(), group_path)?;
41 group
42 .attributes_mut()
43 .insert("foo".into(), serde_json::Value::String("bar".into()));
44 group.async_store_metadata().await?;
45
46 println!(
47 "The group metadata is:\n{}\n",
48 group.metadata().to_string_pretty()
49 );
50
51 // Create an array
52 let array_path = "/group/array";
53 let array = zarrs::array::ArrayBuilder::new(
54 vec![8, 8], // array shape
55 vec![4, 4], // regular chunk shape
56 data_type::float32(),
57 ZARR_NAN_F32,
58 )
59 // .bytes_to_bytes_codecs(vec![]) // uncompressed
60 .dimension_names(["y", "x"].into())
61 // .storage_transformers(vec![].into())
62 .build_arc(store.clone(), array_path)?;
63
64 // Write array metadata to store
65 array.async_store_metadata().await?;
66
67 println!(
68 "The array metadata is:\n{}\n",
69 array.metadata().to_string_pretty()
70 );
71
72 // Write some chunks
73 let store_chunk = |i: u64| {
74 let array = array.clone();
75 async move {
76 let chunk_indices: Vec<u64> = vec![0, i];
77 let chunk_subset = array.chunk_grid().subset(&chunk_indices)?.ok_or_else(|| {
78 zarrs::array::ArrayError::InvalidChunkGridIndicesError(chunk_indices.to_vec())
79 })?;
80 array
81 .async_store_chunk(
82 &chunk_indices,
83 vec![i as f32 * 0.1; chunk_subset.num_elements() as usize],
84 )
85 .await
86 }
87 };
88 futures::stream::iter(0..2)
89 .map(Ok)
90 .try_for_each_concurrent(None, store_chunk)
91 .await?;
92
93 let subset_all = array.subset_all();
94 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
95 println!("async_store_chunk [0, 0] and [0, 1]:\n{data_all:+4.1}\n");
96
97 // Store multiple chunks
98 array
99 .async_store_chunks(
100 &[1..2, 0..2],
101 &[
102 //
103 1.0f32, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
104 //
105 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1, 1.0, 1.0, 1.0, 1.0, 1.1, 1.1, 1.1, 1.1,
106 ],
107 )
108 .await?;
109 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
110 println!("async_store_chunks [1..2, 0..2]:\n{data_all:+4.1}\n");
111
112 // Write a subset spanning multiple chunks, including updating chunks already written
113 array
114 .async_store_array_subset(
115 &[3..6, 3..6],
116 &[-3.3, -3.4, -3.5, -4.3, -4.4, -4.5, -5.3, -5.4, -5.5],
117 )
118 .await?;
119 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
120 println!("async_store_array_subset [3..6, 3..6]:\n{data_all:+4.1}\n");
121
122 // Store array subset
123 array
124 .async_store_array_subset(
125 &[0..8, 6..7],
126 &[-0.6f32, -1.6, -2.6, -3.6, -4.6, -5.6, -6.6, -7.6],
127 )
128 .await?;
129 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
130 println!("async_store_array_subset [0..8, 6..7]:\n{data_all:+4.1}\n");
131
132 // Store chunk subset
133 array
134 .async_store_chunk_subset(
135 // chunk indices
136 &[1, 1],
137 // subset within chunk
138 &[3..4, 0..4],
139 &[-7.4f32, -7.5, -7.6, -7.7],
140 )
141 .await?;
142 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
143 println!("async_store_chunk_subset [3..4, 0..4] of chunk [1, 1]:\n{data_all:+4.1}\n");
144
145 // Erase a chunk
146 array.async_erase_chunk(&[0, 0]).await?;
147 let data_all: ArrayD<f32> = array.async_retrieve_array_subset(&subset_all).await?;
148 println!("async_erase_chunk [0, 0]:\n{data_all:+4.1}\n");
149
150 // Read a chunk
151 let chunk_indices = vec![0, 1];
152 let data_chunk: ArrayD<f32> = array.async_retrieve_chunk(&chunk_indices).await?;
153 println!("async_retrieve_chunk [0, 1]:\n{data_chunk:+4.1}\n");
154
155 // Read chunks
156 let chunks = ArraySubset::new_with_ranges(&[0..2, 1..2]);
157 let data_chunks: ArrayD<f32> = array.async_retrieve_chunks(&chunks).await?;
158 println!("async_retrieve_chunks [0..2, 1..2]:\n{data_chunks:+4.1}\n");
159
160 // Retrieve an array subset
161 let subset = ArraySubset::new_with_ranges(&[2..6, 3..5]); // the center 4x2 region
162 let data_subset: ArrayD<f32> = array.async_retrieve_array_subset(&subset).await?;
163 println!("async_retrieve_array_subset [2..6, 3..5]:\n{data_subset:+4.1}\n");
164
165 // Show the hierarchy
166 let node = Node::async_open(store, "/").await.unwrap();
167 let tree = node.hierarchy_tree();
168 println!("hierarchy_tree:\n{}", tree);
169
170 Ok(())
171}Sourcepub fn consolidate_metadata(&self) -> Option<ConsolidatedMetadataMetadata>
pub fn consolidate_metadata(&self) -> Option<ConsolidatedMetadataMetadata>
Consolidate metadata. Returns None for an array.
ConsolidatedMetadataMetadata can be converted into ConsolidatedMetadata in GroupMetadataV3.
Trait Implementations§
Auto Trait Implementations§
impl Freeze for Node
impl Send for Node
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impl Unpin for Node
impl UnsafeUnpin for Node
impl UnwindSafe for Node
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