zarr-python

Zarr Python

Overview

Zarr is a Python library for storing large N-dimensional arrays with chunking and compression. Apply this skill for efficient parallel I/O, cloud-native workflows, and seamless integration with NumPy, Dask, and Xarray.

Quick Start

Installation

uv pip install zarr

Requires Python 3.11+. For cloud storage support, install additional packages:

uv pip install s3fs  # For S3
uv pip install gcsfs  # For Google Cloud Storage

Basic Array Creation

import zarr
import numpy as np

# Create a 2D array with chunking and compression
z = zarr.create_array(
    store="data/my_array.zarr",
    shape=(10000, 10000),
    chunks=(1000, 1000),
    dtype="f4"
)

# Write data using NumPy-style indexing
z[:, :] = np.random.random((10000, 10000))

# Read data
data = z[0:100, 0:100]  # Returns NumPy array

Core Operations

Creating Arrays

Zarr provides multiple convenience functions for array creation:

# Create empty array
z = zarr.zeros(shape=(10000, 10000), chunks=(1000, 1000), dtype='f4',
               store='data.zarr')

# Create filled arrays
z = zarr.ones((5000, 5000), chunks=(500, 500))
z = zarr.full((1000, 1000), fill_value=42, chunks=(100, 100))

# Create from existing data
data = np.arange(10000).reshape(100, 100)
z = zarr.array(data, chunks=(10, 10), store='data.zarr')

# Create like another array
z2 = zarr.zeros_like(z)  # Matches shape, chunks, dtype of z

Opening Existing Arrays

# Open array (read/write mode by default)
z = zarr.open_array('data.zarr', mode='r+')

# Read-only mode
z = zarr.open_array('data.zarr', mode='r')

# The open() function auto-detects arrays vs groups
z = zarr.open('data.zarr')  # Returns Array or Group

Reading and Writing Data

Zarr arrays support NumPy-like indexing:

# Write entire array
z[:] = 42

# Write slices
z[0, :] = np.arange(100)
z[10:20, 50:60] = np.random.random((10, 10))

# Read data (returns NumPy array)
data = z[0:100, 0:100]
row = z[5, :]

# Advanced indexing
z.vindex[[0, 5, 10], [2, 8, 15]]  # Coordinate indexing
z.oindex[0:10, [5, 10, 15]]       # Orthogonal indexing
z.blocks[0, 0]                     # Block/chunk indexing

Resizing and Appending

# Resize array
z.resize(15000, 15000)  # Expands or shrinks dimensions

# Append data along an axis
z.append(np.random.random((1000, 10000)), axis=0)  # Adds rows

Chunking Strategies

Chunking is critical for performance. Choose chunk sizes and shapes based on access patterns.

Chunk Size Guidelines

• Minimum chunk size: 1 MB recommended for optimal performance
• Balance: Larger chunks = fewer metadata operations; smaller chunks = better parallel access
• Memory consideration: Entire chunks must fit in memory during compression

# Configure chunk size (aim for ~1MB per chunk)
# For float32 data: 1MB = 262,144 elements = 512×512 array
z = zarr.zeros(
    shape=(10000, 10000),
    chunks=(512, 512),  # ~1MB chunks
    dtype='f4'
)

Aligning Chunks with Access Patterns

Critical: Chunk shape dramatically affects performance based on how data is accessed.

# If accessing rows frequently (first dimension)
z = zarr.zeros((10000, 10000), chunks=(10, 10000))  # Chunk spans columns

# If accessing columns frequently (second dimension)
z = zarr.zeros((10000, 10000), chunks=(10000, 10))  # Chunk spans rows

# For mixed access patterns (balanced approach)
z = zarr.zeros((10000, 10000), chunks=(1000, 1000))  # Square chunks

Performance example: For a (200, 200, 200) array, reading along the first dimension:

• Using chunks (1, 200, 200): ~107ms
• Using chunks (200, 200, 1): ~1.65ms (65× faster!)

Sharding for Large-Scale Storage

When arrays have millions of small chunks, use sharding to group chunks into larger storage objects:

from zarr.codecs import ShardingCodec, BytesCodec
from zarr.codecs.blosc import BloscCodec

# Create array with sharding
z = zarr.create_array(
    store='data.zarr',
    shape=(100000, 100000),
    chunks=(100, 100),  # Small chunks for access
    shards=(1000, 1000),  # Groups 100 chunks per shard
    dtype='f4'
)

Benefits:

• Reduces file system overhead from millions of small files
• Improves cloud storage performance (fewer object requests)
• Prevents filesystem block size waste

Important: Entire shards must fit in memory before writing.

Compression

Zarr applies compression per chunk to reduce storage while maintaining fast access.

Configuring Compression

from zarr.codecs.blosc import BloscCodec
from zarr.codecs import GzipCodec, ZstdCodec

# Default: Blosc with Zstandard
z = zarr.zeros((1000, 1000), chunks=(100, 100))  # Uses default compression

# Configure Blosc codec
z = zarr.create_array(
    store='data.zarr',
    shape=(1000, 1000),
    chunks=(100, 100),
    dtype='f4',
    codecs=[BloscCodec(cname='zstd', clevel=5, shuffle='shuffle')]
)

# Available Blosc compressors: 'blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib', 'zstd'

# Use Gzip compression
z = zarr.create_array(
    store='data.zarr',
    shape=(1000, 1000),
    chunks=(100, 100),
    dtype='f4',
    codecs=[GzipCodec(level=6)]
)

# Disable compression
z = zarr.create_array(
    store='data.zarr',
    shape=(1000, 1000),
    chunks=(100, 100),
    dtype='f4',
    codecs=[BytesCodec()]  # No compression
)

Compression Performance Tips

• Blosc (default): Fast compression/decompression, good for interactive workloads
• Zstandard: Better compression ratios, slightly slower than LZ4
• Gzip: Maximum compression, slower performance
• LZ4: Fastest compression, lower ratios
• Shuffle: Enable shuffle filter for better compression on numeric data

# Optimal for numeric scientific data
codecs=[BloscCodec(cname='zstd', clevel=5, shuffle='shuffle')]

# Optimal for speed
codecs=[BloscCodec(cname='lz4', clevel=1)]

# Optimal for compression ratio
codecs=[GzipCodec(level=9)]

Storage Backends

Zarr supports multiple storage backends through a flexible storage interface.

Local Filesystem (Default)

from zarr.storage import LocalStore

# Explicit store creation
store = LocalStore('data/my_array.zarr')
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))

# Or use string path (creates LocalStore automatically)
z = zarr.open_array('data/my_array.zarr', mode='w', shape=(1000, 1000),
                    chunks=(100, 100))

In-Memory Storage

from zarr.storage import MemoryStore

# Create in-memory store
store = MemoryStore()
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))

# Data exists only in memory, not persisted

ZIP File Storage

from zarr.storage import ZipStore

# Write to ZIP file
store = ZipStore('data.zip', mode='w')
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))
z[:] = np.random.random((1000, 1000))
store.close()  # IMPORTANT: Must close ZipStore

# Read from ZIP file
store = ZipStore('data.zip', mode='r')
z = zarr.open_array(store=store)
data = z[:]
store.close()

Cloud Storage (S3, GCS)

import s3fs
import zarr

# S3 storage
s3 = s3fs.S3FileSystem(anon=False)  # Use credentials
store = s3fs.S3Map(root='my-bucket/path/to/array.zarr', s3=s3)
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))
z[:] = data

# Google Cloud Storage
import gcsfs
gcs = gcsfs.GCSFileSystem(project='my-project')
store = gcsfs.GCSMap(root='my-bucket/path/to/array.zarr', gcs=gcs)
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))

Cloud Storage Best Practices:

• Use consolidated metadata to reduce latency: zarr.consolidate_metadata(store)
• Align chunk sizes with cloud object sizing (typically 5-100 MB optimal)
• Enable parallel writes using Dask for large-scale data
• Consider shardin