diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index cc80ce8..678d74b 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -28,7 +28,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python: ["3.9", "3.10", "3.11"] + python: ["3.10", "3.11", "3.12", "3.13"] include: - os: "macos-latest" python: "3.10" diff --git a/README.md b/README.md index cf91bf5..35d6410 100644 --- a/README.md +++ b/README.md @@ -34,19 +34,19 @@ ds.close() # avoid a ResourceWarning (unclosed file) ``` ``` - -Dimensions: (time: 17, node: 648, plan: 21) + Size: 5MB +Dimensions: (time: 17, plan: 21, node: 648) Coordinates: - x (node) float32 ... - y (node) float32 ... - * time (time) datetime64[ns] 1900-01-01 ... 1900-01-02T20:26:40 -Dimensions without coordinates: node, plan + x (node) float32 3kB ... + y (node) float32 3kB ... + * time (time) datetime64[ns] 136B 1900-01-01 ... 1900-01-02T20:26:40 +Dimensions without coordinates: plan, node Data variables: - Z (time, node, plan) ... - U (time, node, plan) ... - V (time, node, plan) ... - W (time, node, plan) ... - MUD (time, node, plan) ... + Z (time, plan, node) float32 925kB ... + U (time, plan, node) float32 925kB ... + V (time, plan, node) float32 925kB ... + W (time, plan, node) float32 925kB ... + MUD (time, plan, node) float32 925kB ... Attributes: title: Sloped flume Rouse profile test language: en @@ -74,6 +74,12 @@ ds = ds.assign(UTIMES100=lambda x: x.U * 100) # Add a new variable ds.drop_vars(["W"]) # Remove variable `VELOCITY W` ``` +## Extracting a specific layer from a 3D DataSet + +```python +ds_bottom = ds.selafin.get_dataset_as_2d(plan=0) # bottom layer +``` + ## Write Selafin ```python @@ -83,9 +89,14 @@ ds.selafin.write("output_file.slf") ## DataSet content ### Dimensions -* time -* node -* plan (only in 3D) +In 2D: +1. time +2. node + +in 3D: +1. time +2. plan +3. node ### Coordinates @@ -99,14 +110,14 @@ ds.selafin.write("output_file.slf") All attributes are optional except `ikle2`: -| Attribute | Description | Default value | -|------------|-------------------------------------------------------------------------|--------------------------| -| title | Serafin title | "" (empty string) | -| language | Language for variable detection | "en" | -| float_size | Float size | 4 (single precision) | -| endian | File endianness | ">" | -| params | Table of integer parameters | (can be rebuilt) | -| ikle2 | Connectivity table in 2D (1-indexed) | - | -| ikle3 | Connectivity table in 3D (1-indexed, only in 3D, optional) | (can be rebuilt from 2D) | -| variables | Dictionary with variable names and units (key is variable abbreviation) | - | -| date_start | Starting date with integers (year to seconds) | (from first time serie) | +| Attribute | Description | Default value | +|------------|-------------------------------------------------------------------------|--------------------------------| +| title | Serafin title | "Converted with array-serafin" | +| language | Language for variable detection | "en" | +| float_size | Float size | 4 (single precision) | +| endian | File endianness | ">" | +| params | Table of integer parameters | (can be rebuilt) | +| ikle2 | Connectivity table in 2D (1-indexed) | - | +| ikle3 | Connectivity table in 3D (1-indexed, only in 3D, optional) | (can be rebuilt from 2D) | +| variables | Dictionary with variable names and units (key is variable abbreviation) | - | +| date_start | Starting date with integers (year to seconds) | (from first time serie) | diff --git a/poetry.lock b/poetry.lock index b472517..ff665f1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. 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--hash=sha256:e8467b6fbf8dbfe0be8c04d61180765fdd3b9ab0fe51313a0bbf87e63634a3d8 \ - --hash=sha256:ee70074df4bae0d9ee98f201cf5f11fd302791cf1cdeb73c34f685d6b632e17d \ - --hash=sha256:f92f2e405eeda47b30ab6231d8b7d136a55f21034d394f93ade322d356948654 \ - --hash=sha256:f9acc272df1022f24fe7dbe9de43fa5d8271985161df14549e4d8d28c90dc9ea -charset-normalizer==3.3.2 ; python_version >= "3.9" \ - --hash=sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027 \ - --hash=sha256:06a81e93cd441c56a9b65d8e1d043daeb97a3d0856d177d5c90ba85acb3db087 \ - --hash=sha256:0a55554a2fa0d408816b3b5cedf0045f4b8e1a6065aec45849de2d6f3f8e9786 \ - --hash=sha256:0b2b64d2bb6d3fb9112bafa732def486049e63de9618b5843bcdd081d8144cd8 \ - --hash=sha256:10955842570876604d404661fbccbc9c7e684caf432c09c715ec38fbae45ae09 \ - --hash=sha256:122c7fa62b130ed55f8f285bfd56d5f4b4a5b503609d181f9ad85e55c89f4185 \ - --hash=sha256:1ceae2f17a9c33cb48e3263960dc5fc8005351ee19db217e9b1bb15d28c02574 \ - 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--hash=sha256:e59e304978767a54663af13c07b3d1af22ddee3bb2fb0618ca1593e4f593a106 \ + --hash=sha256:e85e99945e688e32d5a35c1ff38ed0b3f41f43fad8df0bdf79f72b2ba7bc5272 \ + --hash=sha256:ece47d672db52ac607a3d9599a9d48dcb2f2f735c6c2d1f34130085bb12b112a \ + --hash=sha256:f4039b9cbc3048b2416cc57ab3bda989a6fcf9b36cf8937f01a6e731b64f80d7 +toolz==1.0.0 ; python_version >= "3.10" \ + --hash=sha256:292c8f1c4e7516bf9086f8850935c799a874039c8bcf959d47b600e4c44a6236 \ + --hash=sha256:2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02 +typing-extensions==4.15.0 ; python_version < "3.11" and python_version >= "3.10" \ + --hash=sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466 \ + --hash=sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548 +tzdata==2025.2 ; python_version >= "3.10" \ + --hash=sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8 \ + --hash=sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9 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--hash=sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166 diff --git a/requirements/requirements.txt b/requirements/requirements.txt index a7a4cc2..7ab1329 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,91 +1,130 @@ -numpy==2.0.0 ; python_version >= "3.9" \ - --hash=sha256:04494f6ec467ccb5369d1808570ae55f6ed9b5809d7f035059000a37b8d7e86f \ - --hash=sha256:0a43f0974d501842866cc83471bdb0116ba0dffdbaac33ec05e6afed5b615238 \ - --hash=sha256:0e50842b2295ba8414c8c1d9d957083d5dfe9e16828b37de883f51fc53c4016f \ - --hash=sha256:0ec84b9ba0654f3b962802edc91424331f423dcf5d5f926676e0150789cb3d95 \ - --hash=sha256:17067d097ed036636fa79f6a869ac26df7db1ba22039d962422506640314933a \ - --hash=sha256:1cde1753efe513705a0c6d28f5884e22bdc30438bf0085c5c486cdaff40cd67a \ - --hash=sha256:1e72728e7501a450288fc8e1f9ebc73d90cfd4671ebbd631f3e7857c39bd16f2 \ - --hash=sha256:2635dbd200c2d6faf2ef9a0d04f0ecc6b13b3cad54f7c67c61155138835515d2 \ - 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--hash=sha256:f8bfc0e12dc78f777f323f55c58649591b2cd0c43534e8355c51d3fede5f4dee +python-dateutil==2.9.0.post0 ; python_version >= "3.10" \ --hash=sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3 \ --hash=sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427 -pytz==2024.1 ; python_version >= "3.9" \ - --hash=sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812 \ - --hash=sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319 -six==1.16.0 ; python_version >= "3.9" \ - --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \ - --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254 -tzdata==2024.1 ; python_version >= "3.9" \ - --hash=sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd \ - --hash=sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252 -xarray==2024.6.0 ; python_version >= "3.9" \ - 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--git a/tests/data/r3d_bump_extracted_bottom_layer.slf b/tests/data/r3d_bump_extracted_bottom_layer.slf new file mode 100644 index 0000000..8929bb3 Binary files /dev/null and b/tests/data/r3d_bump_extracted_bottom_layer.slf differ diff --git a/tests/data/r3d_bump_extracted_top_layer.slf b/tests/data/r3d_bump_extracted_top_layer.slf new file mode 100644 index 0000000..a541f17 Binary files /dev/null and b/tests/data/r3d_bump_extracted_top_layer.slf differ diff --git a/tests/io_test.py b/tests/io_test.py index 126326b..8b5f67e 100644 --- a/tests/io_test.py +++ b/tests/io_test.py @@ -1,5 +1,6 @@ import numpy as np import pandas as pd +from pathlib import Path import pytest import xarray as xr from scipy.spatial import Delaunay @@ -28,6 +29,14 @@ ], ) +NODE_TIME = pytest.mark.parametrize( + "dim_test", + [ + pytest.param("node", id="node"), + pytest.param("time", id="time"), + ], +) + def write_netcdf(ds, nc_out): # Remove dict and multi-dimensional arrays not supported in netCDF @@ -47,6 +56,11 @@ def equals_dataset_vs_netcdf_export(ds, nc_out): return ds_nc.equals(ds) +def equals_two_binary_files(slf_in, slf_out): + with open(slf_in, "rb") as in_slf1, open(slf_out, "rb") as in_slf2: + return in_slf1.read() == in_slf2.read() + + @TIDAL_FLATS def test_open_dataset(slf_in): with xr.open_dataset(slf_in, engine="selafin") as ds: @@ -96,9 +110,7 @@ def test_to_selafin(tmp_path, slf_in): with xr.open_dataset(slf_out, engine="selafin") as ds_slf2: assert ds_slf2.equals(ds_slf) - # Compare binary files - with open(slf_in, "rb") as in_slf1, open(slf_out, "rb") as in_slf2: - assert in_slf1.read() == in_slf2.read() + assert equals_two_binary_files(slf_in, slf_out) @TIDAL_FLATS @@ -113,9 +125,7 @@ def test_to_selafin_eager_mode(tmp_path, slf_in): with xr.open_dataset(slf_out, engine="selafin") as ds_slf2: assert ds_slf2.equals(ds_slf) - # Compare binary files - with open(slf_in, "rb") as in_slf1, open(slf_out, "rb") as in_slf2: - assert in_slf1.read() == in_slf2.read() + assert equals_two_binary_files(slf_in, slf_out) @TIDAL_FLATS @@ -174,12 +184,68 @@ def test_dim(slf_in): repr(ds) +@DIMS +@NODE_TIME +def test_dask_mean_consistency(slf_in, dim_test): # requires dask + def analyze_block(ds_block: xr.Dataset) -> xr.Dataset: + return ds_block.mean(dim=dim_test) + + # --- Reference computation without Dask --- + ds_ref = xr.open_dataset(slf_in, engine="selafin", chunks=None) + ref = ds_ref.mean(dim=dim_test) + + # --- Dask-based computation --- + with xr.open_dataset(slf_in, engine="selafin") as ds: + ds = ds.chunk({"time": -1, "node": 50}) + result = xr.map_blocks(analyze_block, ds) + computed = result.compute() + + # --- Structural checks --- + assert set(computed.data_vars) == set(ref.data_vars) + for var in ref.data_vars: + da_ref = ref[var] + da_comp = computed[var] + # shapes should match (node dim gone) + assert da_ref.shape == da_comp.shape, f"Shape mismatch for {var}" + # coordinate consistency + assert all(c in da_comp.coords for c in da_ref.coords), f"Missing coords in {var}" + + # # This check won't work because local mean != global mean >> find another type of assertion + # np.testing.assert_allclose( + # da_ref.values, + # da_comp.values, + # rtol=1e-6, + # atol=1e-8, + # err_msg=f"Mismatch in mean(node) for {var}" + # ) + + @BUMP def test_eager_vs_lazy(slf_in): - with xr.load_dataset(slf_in, engine="selafin") as ds_eager: + with xr.load_dataset(slf_in, lazy_loading=False, engine="selafin") as ds_eager: z_levels_eager = ds_eager.Z.isel(time=0).drop_vars("time") dz_eager = z_levels_eager.diff(dim="plan") - with xr.open_dataset(slf_in, engine="selafin") as ds_lazy: + with xr.open_dataset(slf_in, lazy_loading=True, engine="selafin") as ds_lazy: z_levels_lazy = ds_lazy.Z.isel(time=0).drop_vars("time") dz_lazy = z_levels_lazy.diff(dim="plan") xr.testing.assert_allclose(dz_eager, dz_lazy, rtol=1e-3) + + +@BUMP +def test_get_dataset_as_2d(tmp_path, slf_in): + with xr.load_dataset(slf_in, engine="selafin") as ds: + # Bottom layer + FILENAME = "r3d_bump_extracted_bottom_layer.slf" + ref_path = Path('tests') / 'data' / FILENAME + out_path = tmp_path / FILENAME + ds_bottom_layer = ds.selafin.get_dataset_as_2d(plan=0) + ds_bottom_layer.selafin.write(out_path) + assert equals_two_binary_files(ref_path, out_path) + + # Top layer + FILENAME = "r3d_bump_extracted_top_layer.slf" + ref_path = Path('tests') / 'data' / FILENAME + out_path = tmp_path / FILENAME + ds_top_layer = ds.selafin.get_dataset_as_2d(plan=4) + ds_top_layer.selafin.write(out_path) + assert equals_two_binary_files(ref_path, out_path) diff --git a/xarray_selafin/Serafin.py b/xarray_selafin/Serafin.py index b6dd26b..b812fcf 100644 --- a/xarray_selafin/Serafin.py +++ b/xarray_selafin/Serafin.py @@ -1100,9 +1100,13 @@ def read_var_in_frame(self, time_index, var_ID): pos_var = self._get_var_index(var_ID) self._seek_to_frame(time_index, pos_var) self.file.read(4) - return self.unpack_array( + array = self.unpack_array( self.header.float_size * self.header.nb_nodes, self.header.np_type ) + if len(array) != self.header.nb_nodes: + raise SerafinRequestError("CRITICAL ERROR: buffer was truncated (%i vs %i values) while reading" + % (len(array), self.header.nb_nodes)) + return array def read_vars_in_frame(self, time_index, var_IDs=None): """! diff --git a/xarray_selafin/xarray_backend.py b/xarray_selafin/xarray_backend.py index dd50323..d669014 100644 --- a/xarray_selafin/xarray_backend.py +++ b/xarray_selafin/xarray_backend.py @@ -1,187 +1,61 @@ +""" +Documentation on how to implement a new backend in xarray +* https://docs.xarray.dev/en/latest/internals/how-to-add-new-backend.html +* https://tutorial.xarray.dev/advanced/backends/2.Backend_with_Lazy_Loading.html +""" import os from datetime import datetime from datetime import timedelta -from operator import attrgetter - import numpy as np +from operator import attrgetter +import threading import xarray as xr -from xarray.backends import BackendArray -from xarray.backends import BackendEntrypoint +from xarray.backends import BackendArray, BackendEntrypoint from xarray.core import indexing from xarray_selafin import Serafin +try: + import dask + DASK_AVAILABLE = True +except ImportError: + DASK_AVAILABLE = False + + DEFAULT_DATE_START = (1900, 1, 1, 0, 0, 0) +def range_from_key(k, n): + if isinstance(k, slice): + return range(*k.indices(n)) + elif isinstance(k, int): + return range(k, k + 1) + else: + raise ValueError("index must be int or slice") + + def compute_duration_between_datetime(t0, time_serie): return (time_serie - t0).astype("timedelta64[s]").astype(float) -def read_serafin(f, lang): - resin = Serafin.Read(f, lang) +def read_serafin(filepath, lang): + resin = Serafin.Read(filepath, lang) resin.__enter__() resin.read_header() resin.get_time() return resin -def write_serafin(fout, ds): - # Title - try: - title = ds.attrs["title"] - except KeyError: - title = "Converted with array-serafin" - - slf_header = Serafin.SerafinHeader(title) - - # File precision - try: - float_size = ds.attrs["float_size"] - except KeyError: - float_size = 4 # Default: single precision - if float_size == 4: - slf_header.to_single_precision() - elif float_size == 8: - slf_header.to_double_precision() - else: - raise NotImplementedError - - try: - slf_header.endian = ds.attrs["endian"] - except KeyError: - pass # Default: ">" - - try: - slf_header.nb_frames = ds.time.size - except AttributeError: - slf_header.nb_frames = 0 - - try: - slf_header.date = ds.attrs["date_start"] - except KeyError: - # Retrieve starting date from first time - if slf_header.nb_frames == 0: - first_time = ds.time - else: - first_time = ds.time[0] - first_date_str = first_time.values.astype(str) # "1900-01-01T00:00:00.000000000" - first_date_str = first_date_str.rstrip("0") + "0" # "1900-01-01T00:00:00.0" - try: - date = datetime.strptime(first_date_str, "%Y-%m-%dT%H:%M:%S.%f") - slf_header.date = attrgetter("year", "month", "day", "hour", "minute", "second")(date) - except ValueError: - slf_header.date = DEFAULT_DATE_START - - # Variables - try: - slf_header.language = ds.attrs["language"] - except KeyError: - slf_header.language = Serafin.LANG - for var in ds.data_vars: - try: - name, unit = ds.attrs["variables"][var] - slf_header.add_variable_str(var, name, unit) - except KeyError: - try: - slf_header.add_variable_from_ID(var) - except Serafin.SerafinRequestError: - slf_header.add_variable_str(var, var, "?") - slf_header.nb_var = len(slf_header.var_IDs) - - if "plan" in ds.dims: # 3D - is_2d = False - nplan = len(ds.plan) - slf_header.nb_nodes_per_elem = 6 - slf_header.nb_elements = len(ds.attrs["ikle2"]) * (nplan - 1) - else: # 2D - is_2d = True - nplan = 1 # just to do a multiplication - slf_header.nb_nodes_per_elem = ds.attrs["ikle2"].shape[1] - slf_header.nb_elements = len(ds.attrs["ikle2"]) - - slf_header.nb_nodes = ds.sizes["node"] * nplan - slf_header.nb_nodes_2d = ds.sizes["node"] - - x = ds.coords["x"].values - y = ds.coords["y"].values - if not is_2d: - x = np.tile(x, nplan) - y = np.tile(y, nplan) - slf_header.x = x - slf_header.y = y - slf_header.mesh_origin = (0, 0) # Should be integers - slf_header.x_stored = x - slf_header.mesh_origin[0] - slf_header.y_stored = y - slf_header.mesh_origin[1] - slf_header.ikle_2d = ds.attrs["ikle2"] - if is_2d: - slf_header.ikle = slf_header.ikle_2d.flatten() - else: - try: - slf_header.ikle = ds.attrs["ikle3"] - except KeyError: - # Rebuild IKLE from 2D - slf_header.ikle = slf_header.compute_ikle(len(ds.plan), slf_header.nb_nodes_per_elem) - - try: - slf_header.ipobo = ds.attrs["ipobo"] - except KeyError: - # Rebuild IPOBO - slf_header.build_ipobo() - - if "plan" in ds.dims: # 3D - slf_header.nb_planes = len(ds.plan) - slf_header.is_2d = False - shape = (slf_header.nb_var, slf_header.nb_planes, slf_header.nb_nodes_2d) - else: # 2D (converted if required) - # if ds.attrs["type"] == "3D": - # slf_header.is_2d = False # to enable conversion from 3D - # slf_header = slf_header.copy_as_2d() - slf_header.is_2d = True - shape = (slf_header.nb_var, slf_header.nb_nodes_2d) - - try: - slf_header.params = ds.attrs["params"] - except KeyError: - slf_header.build_params() - - with Serafin.Write(fout, slf_header.language, overwrite=True) as resout: - resout.write_header(slf_header) - - t0 = np.datetime64(datetime(*slf_header.date)) - - try: - time_serie = compute_duration_between_datetime(t0, ds.time.values) - except AttributeError: - return # no time (header only is written) - if isinstance(time_serie, float): - time_serie = [time_serie] - for it, t_ in enumerate(time_serie): - temp = np.empty(shape, dtype=slf_header.np_float_type) - for iv, var in enumerate(slf_header.var_IDs): - if slf_header.nb_frames == 1: - temp[iv] = ds[var].values - else: - temp[iv] = ds.isel(time=it)[var].values - if slf_header.nb_planes > 1: - temp[iv] = np.reshape( - np.ravel(temp[iv]), (slf_header.nb_planes, slf_header.nb_nodes_2d) - ) - resout.write_entire_frame( - slf_header, - t_, - np.reshape(temp, (slf_header.nb_var, slf_header.nb_nodes)), - ) - - class SelafinLazyArray(BackendArray): - # not implemented yet: too slow - def __init__(self, slf_reader, var, dtype, shape): - self.slf_reader = slf_reader - self.var = var - self.dtype = dtype + + def __init__(self, filename_or_obj, shape, dtype, lock, var): + self.filename_or_obj = filename_or_obj self.shape = shape + self.dtype = dtype + self.lock = lock + # Below are other backend specific keyword arguments + self.var = var def __getitem__(self, key): return indexing.explicit_indexing_adapter( @@ -191,70 +65,76 @@ def __getitem__(self, key): self._raw_indexing_method, ) - def _raw_indexing_method(self, key): - ndim = len(self.shape) + def _raw_indexing_method_unlocked(self, key): + ndim = self.ndim # = len(self.shape) if ndim not in (2, 3): - raise NotImplementedError(f"Unsupported SELAFIN shape {self.shape}") + raise NotImplementedError(f"Unsupported SELAFIN shape {ndim}") + assert len(key) == len(self.shape) if not isinstance(key, tuple): raise NotImplementedError("SELAFIN access must use tuple indexing") - # --- Parse keys - if ndim == 3: - # 3D file - if len(key) == 3: - time_key, plan_key, node_key = key - elif len(key) == 2: - time_key, node_key = key - plan_key = slice(None) - else: - raise NotImplementedError("Only (time, plan, node) or (time, node) supported for 3D files") - else: - # 2D file - if len(key) == 2: - time_key, node_key = key - elif len(key) == 1: - time_key = key[0] - node_key = slice(None) - else: - raise NotImplementedError("Only (time, node) supported for 2D files") - - # --- helper - def _range_from_key(k, n): - if isinstance(k, slice): - return range(*k.indices(n)) - elif isinstance(k, int): - return [k] + nb_nodes_2d = self.shape[-1] # last dimension + + # Parse keys + if ndim == 3: # (3D) + time_key, plan_key, node_key = key + else: # ndim = 2 (2D) + time_key, node_key = key + plan_key = None + + # Build indices + time_range = range_from_key(time_key, self.shape[0]) + if ndim == 3: # (3D) + nb_planes = self.shape[1] + plan_range = range_from_key(plan_key, nb_planes) + node_range = range_from_key(node_key, nb_nodes_2d) + ds_shape = (len(time_range), len(plan_range), len(node_range)) + else: # ndim = 2 (2D) + nb_planes = 1 + node_range = range_from_key(node_key, nb_nodes_2d) + ds_shape = (len(time_range), len(node_range)) + plan_range = None + + res_array = np.empty(ds_shape, dtype=self.dtype) + + for ds_index_time, time_index in enumerate(time_range): + flatten_values = self.filename_or_obj.read_var_in_frame(time_index, self.var) # flatten np.ndarray + if ndim == 3: + all_values = flatten_values.reshape((nb_planes, nb_nodes_2d)) + if plan_range == slice(None, None, None) and node_key == slice(None, None, None): # avoid a subset to speedup + res_array[ds_index_time, :, :] = all_values + else: + res_array[ds_index_time, :, :] = all_values[np.ix_(plan_range, node_range)] else: - raise ValueError("index must be int or slice") - - time_indices = _range_from_key(time_key, self.shape[0]) - - if ndim == 3: - plan_indices = _range_from_key(plan_key, self.shape[1]) - node_indices = _range_from_key(node_key, self.shape[2]) - data_shape = (len(time_indices), len(plan_indices), len(node_indices)) - else: - node_indices = _range_from_key(node_key, self.shape[1]) - data_shape = (len(time_indices), len(node_indices)) + if node_key == slice(None, None, None): # avoid a subset to speedup + res_array[ds_index_time, :] = flatten_values + else: + res_array[ds_index_time, :] = flatten_values[node_range] - data = np.empty(data_shape, dtype=self.dtype) + # Remove some dimensions if it was selected by integer + squeeze_dims = [] + if isinstance(time_key, int): + squeeze_dims.append(0) + if isinstance(plan_key, int): + squeeze_dims.append(1) + if isinstance(node_key, int): + squeeze_dims.append(-1) + if squeeze_dims: + res_array = np.squeeze(res_array, axis=tuple(squeeze_dims)) - for it, t in enumerate(time_indices): - temp = self.slf_reader.read_var_in_frame(t, self.var) - if ndim == 3: - temp = np.reshape(temp, (self.shape[1], self.shape[2])) # (nplan, nnode) - values = temp[np.ix_(plan_indices, node_indices)] - data[it, :, :] = values - else: - temp = np.asarray(temp) # (nnode,) - values = temp[node_indices] - data[it, :] = values + return res_array - return data.squeeze() + def _raw_indexing_method(self, key): + if self.lock is None: + return self._raw_indexing_method_unlocked(key) + else: + with self.lock: + return self._raw_indexing_method_unlocked(key) class SelafinBackendEntrypoint(BackendEntrypoint): + def open_dataset( self, filename_or_obj, @@ -262,8 +142,10 @@ def open_dataset( drop_variables=None, decode_times=True, # Below are custom arguments + disable_lock=False, lazy_loading=True, lang=Serafin.LANG, + # `chunks` and `cache` DO NOT go here, they are handled by xarray ): # Initialize SELAFIN reader slf = read_serafin(filename_or_obj, lang) @@ -291,14 +173,28 @@ def open_dataset( shape = (len(times), nplan, npoin2) dims = ["time", "plan", "node"] + if disable_lock: + file_lock = None + else: + if DASK_AVAILABLE: + file_lock = dask.utils.SerializableLock() + else: + file_lock = threading.Lock() + for var in vars: if lazy_loading: - lazy_array = SelafinLazyArray(slf, var, dtype, shape) + lazy_array = SelafinLazyArray( + filename_or_obj=slf, + shape=shape, + dtype=dtype, + lock=file_lock, + var=var, + ) data = indexing.LazilyIndexedArray(lazy_array) data_vars[var] = xr.Variable(dims=dims, data=data) else: data = np.empty(shape, dtype=dtype) - for time_index, t in enumerate(times): + for time_index, _ in enumerate(times): values = slf.read_var_in_frame(time_index, var) if is_2d: data[time_index, :] = values @@ -348,19 +244,174 @@ def guess_can_open(filename_or_obj): return ext.lower() in {".slf"} description = "A SELAFIN file format backend for Xarray" - url = "https://www.example.com/selafin_backend_documentation" + url = "https://github.com/oceanmodeling/xarray-selafin/" @xr.register_dataset_accessor("selafin") class SelafinAccessor: + def __init__(self, xarray_obj): - self._obj = xarray_obj + self._ds = xarray_obj + self._header = None + + def get_dataset_as_2d(self, plan): + """Generate a copy of the current DataSet in a 2D format""" + # Check input DataSet + if "plan" not in self._ds.dims: + raise RuntimeError("get_dataset_as_2d requires a 3D DataSet") + assert 0 <= plan <= self._ds.sizes.get("plan") - 1 + + # Generate a shallow copy + ds_out = self._ds.copy(deep=False).isel(plan=plan) + + nb_nodes_2d = self._ds.sizes.get("node") + + # Remove or adapt some attributes (if present) + if "ipobo" in self._ds.attrs: + ds_out.attrs["ipobo"] = self._ds.attrs["ipobo"][:nb_nodes_2d] + ds_out.attrs.pop("ikle3", None) + + return ds_out + + def _build_header(self): + """Build a SerafinHeader corresponding to DataSet""" + ds = self._ds + + # Title + title = ds.attrs.get("title", "Converted with array-serafin") + header = Serafin.SerafinHeader(title) + + # File precision + float_size = ds.attrs.get("float_size", 4) # Default: single precision + if float_size == 4: + header.to_single_precision() + elif float_size == 8: + header.to_double_precision() + else: + raise NotImplementedError + + header.endian = ds.attrs.get("endian", ">") # Default: ">" + + header.nb_frames = ds.sizes.get("time", 0) + + try: + header.date = ds.attrs["date_start"] + except KeyError: + # Retrieve starting date from first time + if header.nb_frames == 0: + first_time = ds.time + else: + first_time = ds.time[0] + first_date_str = first_time.values.astype(str) # "1900-01-01T00:00:00.000000000" + first_date_str = first_date_str.rstrip("0") + "0" # "1900-01-01T00:00:00.0" + try: + date = datetime.strptime(first_date_str, "%Y-%m-%dT%H:%M:%S.%f") + header.date = attrgetter("year", "month", "day", "hour", "minute", "second")(date) + except ValueError: + header.date = DEFAULT_DATE_START + + # Variables + header.language = ds.attrs.get("language", Serafin.LANG) + for var in ds.data_vars: + try: + name, unit = ds.attrs["variables"][var] + header.add_variable_str(var, name, unit) + except KeyError: + try: + header.add_variable_from_ID(var) + except Serafin.SerafinRequestError: + header.add_variable_str(var, var, "?") + header.nb_var = len(header.var_IDs) + + if "plan" in ds.dims: # 3D + header.is_2d = False + nplan = len(ds.plan) + header.nb_nodes_per_elem = 6 + header.nb_elements = len(ds.attrs["ikle2"]) * (nplan - 1) + header.nb_planes = nplan + else: # 2D + header.is_2d = True + nplan = 1 # just to do a multiplication below + header.nb_nodes_per_elem = ds.attrs["ikle2"].shape[1] + header.nb_elements = len(ds.attrs["ikle2"]) + header.nb_planes = 0 # convention in Selafin for 2D files + + header.nb_nodes_2d = ds.sizes["node"] + header.nb_nodes = header.nb_nodes_2d * nplan + + x = ds.coords["x"].values + y = ds.coords["y"].values + if not header.is_2d: + x = np.tile(x, nplan) + y = np.tile(y, nplan) + header.x = x + header.y = y + header.mesh_origin = (0, 0) # Should be integers + header.x_stored = x - header.mesh_origin[0] + header.y_stored = y - header.mesh_origin[1] + header.ikle_2d = ds.attrs["ikle2"] + if header.is_2d: + header.ikle = header.ikle_2d.flatten() + else: + try: + header.ikle = ds.attrs["ikle3"] + except KeyError: + # Rebuild IKLE from 2D + header.ikle = header.compute_ikle(nplan, header.nb_nodes_per_elem) + + try: + header.ipobo = ds.attrs["ipobo"] + except KeyError: + # Rebuild IPOBO + header.build_ipobo() + + try: + header.params = ds.attrs["params"] + except KeyError: + header.build_params() + + self._header = header + + def _write_all(self, filepath): + """Writes header and all data frames into output file""" + header = self._header + + with Serafin.Write(filepath, header.language, overwrite=True) as resout: + resout.write_header(header) + + t0 = np.datetime64(datetime(*header.date)) + + try: + time_serie = compute_duration_between_datetime(t0, self._ds.time.values) + except AttributeError: + return # no time (header only is written) + if isinstance(time_serie, float): + time_serie = [time_serie] + + shape = (header.nb_var, header.nb_nodes) + values = np.empty(shape, dtype=header.np_float_type) + for time_index, time in enumerate(time_serie): + for var_index, var in enumerate(header.var_IDs): + if header.nb_frames in (0, 1): + array = self._ds[var].values + else: + array = self._ds.isel(time=time_index)[var].values + if header.is_2d: + values[var_index, :] = array + else: + values[var_index, :] = array.ravel() + + resout.write_entire_frame( + header, + time, + values, + ) def write(self, filepath, **kwargs): """ Write data from an Xarray dataset to a SELAFIN file. Parameters: - - filename: String with the path to the output SELAFIN file. + - filepath: String with the path to the output SELAFIN file. """ - ds = self._obj - write_serafin(filepath, ds) + self._build_header() + self._write_all(filepath)