From fe178c67ac9428477ca146dd6ac453bf1cccfc78 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Mon, 11 Sep 2023 10:37:00 +0200 Subject: [PATCH] Apply suggestions and avoid using chmod on windows --- src/spikeinterface/core/waveform_extractor.py | 111 +++++++++--------- .../tests/common_extension_tests.py | 28 +++-- 2 files changed, 73 insertions(+), 66 deletions(-) diff --git a/src/spikeinterface/core/waveform_extractor.py b/src/spikeinterface/core/waveform_extractor.py index 431440c846..3647e915bf 100644 --- a/src/spikeinterface/core/waveform_extractor.py +++ b/src/spikeinterface/core/waveform_extractor.py @@ -1751,9 +1751,7 @@ def __init__(self, waveform_extractor): if self.format == "binary": self.extension_folder = self.folder / self.extension_name if not self.extension_folder.is_dir(): - if not self.waveform_extractor.is_read_only(): - self.extension_folder.mkdir() - else: + if self.waveform_extractor.is_read_only(): warn( "WaveformExtractor: cannot save extension in read-only mode. " "Extension will be saved in memory." @@ -1761,15 +1759,16 @@ def __init__(self, waveform_extractor): self.format = "memory" self.extension_folder = None self.folder = None + else: + self.extension_folder.mkdir() + else: import zarr mode = "r+" if not self.waveform_extractor.is_read_only() else "r" zarr_root = zarr.open(self.folder, mode=mode) if self.extension_name not in zarr_root.keys(): - if not self.waveform_extractor.is_read_only(): - self.extension_group = zarr_root.create_group(self.extension_name) - else: + if self.waveform_extractor.is_read_only(): warn( "WaveformExtractor: cannot save extension in read-only mode. " "Extension will be saved in memory." @@ -1777,6 +1776,8 @@ def __init__(self, waveform_extractor): self.format = "memory" self.extension_folder = None self.folder = None + else: + self.extension_group = zarr_root.create_group(self.extension_name) else: self.extension_group = zarr_root[self.extension_name] else: @@ -1893,56 +1894,58 @@ def save(self, **kwargs): self._save(**kwargs) def _save(self, **kwargs): - if not self.waveform_extractor.is_read_only(): - if self.format == "binary": - import pandas as pd - - for ext_data_name, ext_data in self._extension_data.items(): - if isinstance(ext_data, dict): - with (self.extension_folder / f"{ext_data_name}.json").open("w") as f: - json.dump(ext_data, f) - elif isinstance(ext_data, np.ndarray): - np.save(self.extension_folder / f"{ext_data_name}.npy", ext_data) - elif isinstance(ext_data, pd.DataFrame): - ext_data.to_csv(self.extension_folder / f"{ext_data_name}.csv", index=True) - else: - try: - with (self.extension_folder / f"{ext_data_name}.pkl").open("wb") as f: - pickle.dump(ext_data, f) - except: - raise Exception(f"Could not save {ext_data_name} as extension data") - elif self.format == "zarr": - from .zarrrecordingextractor import get_default_zarr_compressor - import pandas as pd - import numcodecs - - compressor = kwargs.get("compressor", None) - if compressor is None: - compressor = get_default_zarr_compressor() - for ext_data_name, ext_data in self._extension_data.items(): - if ext_data_name in self.extension_group: - del self.extension_group[ext_data_name] - if isinstance(ext_data, dict): + # Only save if not read only + if self.waveform_extractor.is_read_only(): + return + if self.format == "binary": + import pandas as pd + + for ext_data_name, ext_data in self._extension_data.items(): + if isinstance(ext_data, dict): + with (self.extension_folder / f"{ext_data_name}.json").open("w") as f: + json.dump(ext_data, f) + elif isinstance(ext_data, np.ndarray): + np.save(self.extension_folder / f"{ext_data_name}.npy", ext_data) + elif isinstance(ext_data, pd.DataFrame): + ext_data.to_csv(self.extension_folder / f"{ext_data_name}.csv", index=True) + else: + try: + with (self.extension_folder / f"{ext_data_name}.pkl").open("wb") as f: + pickle.dump(ext_data, f) + except: + raise Exception(f"Could not save {ext_data_name} as extension data") + elif self.format == "zarr": + from .zarrrecordingextractor import get_default_zarr_compressor + import pandas as pd + import numcodecs + + compressor = kwargs.get("compressor", None) + if compressor is None: + compressor = get_default_zarr_compressor() + for ext_data_name, ext_data in self._extension_data.items(): + if ext_data_name in self.extension_group: + del self.extension_group[ext_data_name] + if isinstance(ext_data, dict): + self.extension_group.create_dataset( + name=ext_data_name, data=[ext_data], object_codec=numcodecs.JSON() + ) + self.extension_group[ext_data_name].attrs["dict"] = True + elif isinstance(ext_data, np.ndarray): + self.extension_group.create_dataset(name=ext_data_name, data=ext_data, compressor=compressor) + elif isinstance(ext_data, pd.DataFrame): + ext_data.to_xarray().to_zarr( + store=self.extension_group.store, + group=f"{self.extension_group.name}/{ext_data_name}", + mode="a", + ) + self.extension_group[ext_data_name].attrs["dataframe"] = True + else: + try: self.extension_group.create_dataset( - name=ext_data_name, data=[ext_data], object_codec=numcodecs.JSON() - ) - self.extension_group[ext_data_name].attrs["dict"] = True - elif isinstance(ext_data, np.ndarray): - self.extension_group.create_dataset(name=ext_data_name, data=ext_data, compressor=compressor) - elif isinstance(ext_data, pd.DataFrame): - ext_data.to_xarray().to_zarr( - store=self.extension_group.store, - group=f"{self.extension_group.name}/{ext_data_name}", - mode="a", + name=ext_data_name, data=ext_data, object_codec=numcodecs.Pickle() ) - self.extension_group[ext_data_name].attrs["dataframe"] = True - else: - try: - self.extension_group.create_dataset( - name=ext_data_name, data=ext_data, object_codec=numcodecs.Pickle() - ) - except: - raise Exception(f"Could not save {ext_data_name} as extension data") + except: + raise Exception(f"Could not save {ext_data_name} as extension data") def reset(self): """ diff --git a/src/spikeinterface/postprocessing/tests/common_extension_tests.py b/src/spikeinterface/postprocessing/tests/common_extension_tests.py index f44d58470c..f7272ddefe 100644 --- a/src/spikeinterface/postprocessing/tests/common_extension_tests.py +++ b/src/spikeinterface/postprocessing/tests/common_extension_tests.py @@ -2,6 +2,7 @@ import numpy as np import pandas as pd import shutil +import platform from pathlib import Path from spikeinterface import extract_waveforms, load_extractor, load_waveforms, compute_sparsity @@ -78,12 +79,13 @@ def setUp(self): self.we2 = we2 # make we read-only - we_ro_folder = cache_folder / "toy_waveforms_2seg_readonly" - if not we_ro_folder.is_dir(): - shutil.copytree(we2.folder, we_ro_folder) + if platform.system() != "Windows": + we_ro_folder = cache_folder / "toy_waveforms_2seg_readonly" + if not we_ro_folder.is_dir(): + shutil.copytree(we2.folder, we_ro_folder) # change permissions (R+X) - we_ro_folder.chmod(0o555) - self.we_ro = load_waveforms(we_ro_folder) + we_ro_folder.chmod(0o555) + self.we_ro = load_waveforms(we_ro_folder) self.sparsity2 = compute_sparsity(we2, method="radius", radius_um=30) we_memory = extract_waveforms( @@ -108,8 +110,9 @@ def setUp(self): def tearDown(self): # allow pytest to delete RO folder - we_ro_folder = cache_folder / "toy_waveforms_2seg_readonly" - we_ro_folder.chmod(0o777) + if platform.system() != "Windows": + we_ro_folder = cache_folder / "toy_waveforms_2seg_readonly" + we_ro_folder.chmod(0o777) def _test_extension_folder(self, we, in_memory=False): if self.extension_function_kwargs_list is None: @@ -193,8 +196,9 @@ def test_extension(self): print(f"{ext_data_name} of type {type(ext_data_mem)} not tested.") # read-only - Extension is memory only - _ = self.extension_class.get_extension_function()(self.we_ro, load_if_exists=False) - assert self.extension_class.extension_name in self.we_ro.get_available_extension_names() - ext_ro = self.we_ro.load_extension(self.extension_class.extension_name) - assert ext_ro.format == "memory" - assert ext_ro.extension_folder is None + if platform.system() != "Windows": + _ = self.extension_class.get_extension_function()(self.we_ro, load_if_exists=False) + assert self.extension_class.extension_name in self.we_ro.get_available_extension_names() + ext_ro = self.we_ro.load_extension(self.extension_class.extension_name) + assert ext_ro.format == "memory" + assert ext_ro.extension_folder is None