from __future__ import absolute_import, division, print_function import warnings from distutils.version import LooseVersion from io import BytesIO import numpy as np from .. import Variable from ..core.indexing import NumpyIndexingAdapter from ..core.pycompat import OrderedDict, basestring, iteritems from ..core.utils import Frozen, FrozenOrderedDict from .common import BackendArray, WritableCFDataStore from .file_manager import CachingFileManager, DummyFileManager from .locks import ensure_lock, get_write_lock from .netcdf3 import ( encode_nc3_attr_value, encode_nc3_variable, is_valid_nc3_name) def _decode_string(s): if isinstance(s, bytes): return s.decode('utf-8', 'replace') return s def _decode_attrs(d): # don't decode _FillValue from bytes -> unicode, because we want to ensure # that its type matches the data exactly return OrderedDict((k, v if k == '_FillValue' else _decode_string(v)) for (k, v) in iteritems(d)) class ScipyArrayWrapper(BackendArray): def __init__(self, variable_name, datastore): self.datastore = datastore self.variable_name = variable_name array = self.get_variable().data self.shape = array.shape self.dtype = np.dtype(array.dtype.kind + str(array.dtype.itemsize)) def get_variable(self, needs_lock=True): ds = self.datastore._manager.acquire(needs_lock) return ds.variables[self.variable_name] def __getitem__(self, key): data = NumpyIndexingAdapter(self.get_variable().data)[key] # Copy data if the source file is mmapped. This makes things consistent # with the netCDF4 library by ensuring we can safely read arrays even # after closing associated files. copy = self.datastore.ds.use_mmap return np.array(data, dtype=self.dtype, copy=copy) def __setitem__(self, key, value): with self.datastore.lock: data = self.get_variable(needs_lock=False) try: data[key] = value except TypeError: if key is Ellipsis: # workaround for GH: scipy/scipy#6880 data[:] = value else: raise def _open_scipy_netcdf(filename, mode, mmap, version): import scipy.io import gzip # if the string ends with .gz, then gunzip and open as netcdf file if isinstance(filename, basestring) and filename.endswith('.gz'): try: return scipy.io.netcdf_file(gzip.open(filename), mode=mode, mmap=mmap, version=version) except TypeError as e: # TODO: gzipped loading only works with NetCDF3 files. if 'is not a valid NetCDF 3 file' in e.message: raise ValueError('gzipped file loading only supports ' 'NetCDF 3 files.') else: raise if isinstance(filename, bytes) and filename.startswith(b'CDF'): # it's a NetCDF3 bytestring filename = BytesIO(filename) try: return scipy.io.netcdf_file(filename, mode=mode, mmap=mmap, version=version) except TypeError as e: # netcdf3 message is obscure in this case errmsg = e.args[0] if 'is not a valid NetCDF 3 file' in errmsg: msg = """ If this is a NetCDF4 file, you may need to install the netcdf4 library, e.g., $ pip install netcdf4 """ errmsg += msg raise TypeError(errmsg) else: raise class ScipyDataStore(WritableCFDataStore): """Store for reading and writing data via scipy.io.netcdf. This store has the advantage of being able to be initialized with a StringIO object, allow for serialization without writing to disk. It only supports the NetCDF3 file-format. """ def __init__(self, filename_or_obj, mode='r', format=None, group=None, mmap=None, lock=None): import scipy import scipy.io if (mode != 'r' and scipy.__version__ < LooseVersion('0.13')): # pragma: no cover warnings.warn('scipy %s detected; ' 'the minimal recommended version is 0.13. ' 'Older version of this library do not reliably ' 'read and write files.' % scipy.__version__, ImportWarning) if group is not None: raise ValueError('cannot save to a group with the ' 'scipy.io.netcdf backend') if format is None or format == 'NETCDF3_64BIT': version = 2 elif format == 'NETCDF3_CLASSIC': version = 1 else: raise ValueError('invalid format for scipy.io.netcdf backend: %r' % format) if (lock is None and mode != 'r' and isinstance(filename_or_obj, basestring)): lock = get_write_lock(filename_or_obj) self.lock = ensure_lock(lock) if isinstance(filename_or_obj, basestring): manager = CachingFileManager( _open_scipy_netcdf, filename_or_obj, mode=mode, lock=lock, kwargs=dict(mmap=mmap, version=version)) else: scipy_dataset = _open_scipy_netcdf( filename_or_obj, mode=mode, mmap=mmap, version=version) manager = DummyFileManager(scipy_dataset) self._manager = manager @property def ds(self): return self._manager.acquire() def open_store_variable(self, name, var): return Variable(var.dimensions, ScipyArrayWrapper(name, self), _decode_attrs(var._attributes)) def get_variables(self): return FrozenOrderedDict((k, self.open_store_variable(k, v)) for k, v in iteritems(self.ds.variables)) def get_attrs(self): return Frozen(_decode_attrs(self.ds._attributes)) def get_dimensions(self): return Frozen(self.ds.dimensions) def get_encoding(self): encoding = {} encoding['unlimited_dims'] = { k for k, v in self.ds.dimensions.items() if v is None} return encoding def set_dimension(self, name, length, is_unlimited=False): if name in self.ds.dimensions: raise ValueError('%s does not support modifying dimensions' % type(self).__name__) dim_length = length if not is_unlimited else None self.ds.createDimension(name, dim_length) def _validate_attr_key(self, key): if not is_valid_nc3_name(key): raise ValueError("Not a valid attribute name") def set_attribute(self, key, value): self._validate_attr_key(key) value = encode_nc3_attr_value(value) setattr(self.ds, key, value) def encode_variable(self, variable): variable = encode_nc3_variable(variable) return variable def prepare_variable(self, name, variable, check_encoding=False, unlimited_dims=None): if check_encoding and variable.encoding: if variable.encoding != {'_FillValue': None}: raise ValueError('unexpected encoding for scipy backend: %r' % list(variable.encoding)) data = variable.data # nb. this still creates a numpy array in all memory, even though we # don't write the data yet; scipy.io.netcdf does not not support # incremental writes. if name not in self.ds.variables: self.ds.createVariable(name, data.dtype, variable.dims) scipy_var = self.ds.variables[name] for k, v in iteritems(variable.attrs): self._validate_attr_key(k) setattr(scipy_var, k, v) target = ScipyArrayWrapper(name, self) return target, data def sync(self): self.ds.sync() def close(self): self._manager.close()