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9ee6be8..ea772f0 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -9,5 +9,6 @@ crate-type = ["cdylib"] [dependencies] pyo3 = { version = "0.7", features = ["extension-module"] } -n5 = { version = "0.4", default-features = false, features = ["filesystem", "gzip", "use_ndarray"]} +n5 = { version = "0.4", default-features = false, features = ["filesystem", "bzip", "gzip", "lz", "xz", "use_ndarray"]} numpy = "0.6" +serde_json = "1.0.39" diff --git a/src/lib.rs b/src/lib.rs index c815a4c..193e455 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -19,6 +19,7 @@ fn create_dataset( dimensions: Vec, block_size: Vec, dtype: &str, + compression: Option<&str>, ) -> PyResult<()> { let dtype = match dtype { "UINT8" => DataType::UINT8, @@ -45,11 +46,23 @@ fn create_dataset( let n = N5Filesystem::open_or_create(root_path)?; if !n.exists(path_name) { + let compression_type: CompressionType = match compression { + None => CompressionType::new::(), + Some(s) => { + match serde_json::from_str(s) { + Ok(c) => c, + Err(_e) => return Err( + exceptions::ValueError::py_err("Could not deserialize compression") + ) + } + } + }; + let data_attrs = DatasetAttributes::new( dimensions.into(), block_size.into(), dtype, - CompressionType::new::(), + compression_type, ); n.create_dataset(path_name, &data_attrs)?; Ok(()) diff --git a/tests/conftest.py b/tests/conftest.py index 16bbfe6..056fd3f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -19,3 +19,13 @@ def ds_dtype(request, tmp_path): pyn5.create_dataset(n5_path, ds_name, DS_SIZE, BLOCKSIZE, dtype) yield pyn5.open(n5_path, ds_name, dtype, False), np.dtype(dtype.lower()) + +@pytest.fixture(params=[ + {"type": "raw"}, + {"type": "bzip2", "blockSize": 5}, + {"type": "gzip", "level": 5}, + {"type": "lz4", "blockSize": 32768}, + {"type": "xz", "preset": 3}, +], ids=lambda d: d.get("type", "raw")) +def compression_dict(request): + yield request.param diff --git a/tests/test_pyn5.py b/tests/test_pyn5.py index f85a32f..3ccc81d 100644 --- a/tests/test_pyn5.py +++ b/tests/test_pyn5.py @@ -7,6 +7,8 @@ import unittest from pathlib import Path import shutil +import json + import numpy as np import pytest @@ -94,6 +96,43 @@ def test_read_write_wrong_dtype(ds_dtype): np.testing.assert_equal(ds.read_ndarray([4, 4, 4], BLOCKSIZE), np.zeros(BLOCKSIZE)) +def test_compression(tmp_path, compression_dict): + root = tmp_path / "test.n5" + + data = np.arange(100, dtype=np.uint8).reshape((10, 10)) + + pyn5.create_dataset( + str(root), "ds", data.shape, (5, 5), data.dtype.name.upper(), + json.dumps(compression_dict) + ) + + with open(root / "ds" / "attributes.json") as f: + attrs = json.load(f) + + assert attrs["compression"] == compression_dict + + ds = pyn5.DatasetUINT8(str(root), "ds", True) + ds.write_ndarray((0, 0), data, 0) + + +def test_default_compression(tmp_path): + root = tmp_path / "test.n5" + + data = np.arange(100, dtype=np.uint8).reshape((10, 10)) + + pyn5.create_dataset( + str(root), "ds", data.shape, (5, 5), data.dtype.name.upper(), + ) + + with open(root / "ds" / "attributes.json") as f: + attrs = json.load(f) + + assert attrs["compression"] == {"type": "gzip", "level": -1} + + ds = pyn5.DatasetUINT8(str(root), "ds", True) + ds.write_ndarray((0, 0), data, 0) + + class TestPythonReadWrite(unittest.TestCase): def setUp(self): self.root = "test.n5"