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2548 lines
98 KiB
2548 lines
98 KiB
import os
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import re
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import functools
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import itertools
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import warnings
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import weakref
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import contextlib
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import operator
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from operator import itemgetter, index as opindex, methodcaller
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from collections.abc import Mapping
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import numpy as np
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from . import format
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from ._datasource import DataSource
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from numpy.core import overrides
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from numpy.core.multiarray import packbits, unpackbits
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from numpy.core._multiarray_umath import _load_from_filelike
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from numpy.core.overrides import set_array_function_like_doc, set_module
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from ._iotools import (
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LineSplitter, NameValidator, StringConverter, ConverterError,
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ConverterLockError, ConversionWarning, _is_string_like,
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has_nested_fields, flatten_dtype, easy_dtype, _decode_line
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)
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from numpy.compat import (
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asbytes, asstr, asunicode, os_fspath, os_PathLike,
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pickle
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)
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__all__ = [
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'savetxt', 'loadtxt', 'genfromtxt',
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'recfromtxt', 'recfromcsv', 'load', 'save', 'savez',
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'savez_compressed', 'packbits', 'unpackbits', 'fromregex', 'DataSource'
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]
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array_function_dispatch = functools.partial(
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overrides.array_function_dispatch, module='numpy')
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class BagObj:
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"""
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BagObj(obj)
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Convert attribute look-ups to getitems on the object passed in.
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Parameters
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----------
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obj : class instance
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Object on which attribute look-up is performed.
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Examples
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--------
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>>> from numpy.lib.npyio import BagObj as BO
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>>> class BagDemo:
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... def __getitem__(self, key): # An instance of BagObj(BagDemo)
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... # will call this method when any
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... # attribute look-up is required
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... result = "Doesn't matter what you want, "
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... return result + "you're gonna get this"
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...
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>>> demo_obj = BagDemo()
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>>> bagobj = BO(demo_obj)
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>>> bagobj.hello_there
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"Doesn't matter what you want, you're gonna get this"
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>>> bagobj.I_can_be_anything
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"Doesn't matter what you want, you're gonna get this"
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"""
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def __init__(self, obj):
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# Use weakref to make NpzFile objects collectable by refcount
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self._obj = weakref.proxy(obj)
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def __getattribute__(self, key):
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try:
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return object.__getattribute__(self, '_obj')[key]
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except KeyError:
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raise AttributeError(key) from None
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def __dir__(self):
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"""
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Enables dir(bagobj) to list the files in an NpzFile.
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This also enables tab-completion in an interpreter or IPython.
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"""
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return list(object.__getattribute__(self, '_obj').keys())
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def zipfile_factory(file, *args, **kwargs):
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"""
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Create a ZipFile.
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Allows for Zip64, and the `file` argument can accept file, str, or
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pathlib.Path objects. `args` and `kwargs` are passed to the zipfile.ZipFile
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constructor.
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"""
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if not hasattr(file, 'read'):
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file = os_fspath(file)
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import zipfile
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kwargs['allowZip64'] = True
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return zipfile.ZipFile(file, *args, **kwargs)
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class NpzFile(Mapping):
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"""
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NpzFile(fid)
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A dictionary-like object with lazy-loading of files in the zipped
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archive provided on construction.
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`NpzFile` is used to load files in the NumPy ``.npz`` data archive
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format. It assumes that files in the archive have a ``.npy`` extension,
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other files are ignored.
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The arrays and file strings are lazily loaded on either
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getitem access using ``obj['key']`` or attribute lookup using
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``obj.f.key``. A list of all files (without ``.npy`` extensions) can
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be obtained with ``obj.files`` and the ZipFile object itself using
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``obj.zip``.
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Attributes
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----------
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files : list of str
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List of all files in the archive with a ``.npy`` extension.
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zip : ZipFile instance
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The ZipFile object initialized with the zipped archive.
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f : BagObj instance
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An object on which attribute can be performed as an alternative
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to getitem access on the `NpzFile` instance itself.
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allow_pickle : bool, optional
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Allow loading pickled data. Default: False
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.. versionchanged:: 1.16.3
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Made default False in response to CVE-2019-6446.
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pickle_kwargs : dict, optional
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Additional keyword arguments to pass on to pickle.load.
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These are only useful when loading object arrays saved on
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Python 2 when using Python 3.
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max_header_size : int, optional
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Maximum allowed size of the header. Large headers may not be safe
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to load securely and thus require explicitly passing a larger value.
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See :py:func:`ast.literal_eval()` for details.
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This option is ignored when `allow_pickle` is passed. In that case
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the file is by definition trusted and the limit is unnecessary.
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Parameters
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----------
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fid : file or str
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The zipped archive to open. This is either a file-like object
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or a string containing the path to the archive.
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own_fid : bool, optional
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Whether NpzFile should close the file handle.
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Requires that `fid` is a file-like object.
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Examples
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--------
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>>> from tempfile import TemporaryFile
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>>> outfile = TemporaryFile()
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>>> x = np.arange(10)
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>>> y = np.sin(x)
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>>> np.savez(outfile, x=x, y=y)
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>>> _ = outfile.seek(0)
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>>> npz = np.load(outfile)
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>>> isinstance(npz, np.lib.npyio.NpzFile)
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True
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>>> npz
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NpzFile 'object' with keys x, y
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>>> sorted(npz.files)
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['x', 'y']
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>>> npz['x'] # getitem access
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array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
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>>> npz.f.x # attribute lookup
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array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
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"""
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# Make __exit__ safe if zipfile_factory raises an exception
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zip = None
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fid = None
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_MAX_REPR_ARRAY_COUNT = 5
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def __init__(self, fid, own_fid=False, allow_pickle=False,
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pickle_kwargs=None, *,
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max_header_size=format._MAX_HEADER_SIZE):
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# Import is postponed to here since zipfile depends on gzip, an
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# optional component of the so-called standard library.
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_zip = zipfile_factory(fid)
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self._files = _zip.namelist()
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self.files = []
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self.allow_pickle = allow_pickle
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self.max_header_size = max_header_size
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self.pickle_kwargs = pickle_kwargs
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for x in self._files:
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if x.endswith('.npy'):
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self.files.append(x[:-4])
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else:
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self.files.append(x)
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self.zip = _zip
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self.f = BagObj(self)
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if own_fid:
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self.fid = fid
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def __enter__(self):
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return self
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def __exit__(self, exc_type, exc_value, traceback):
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self.close()
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def close(self):
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"""
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Close the file.
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"""
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if self.zip is not None:
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self.zip.close()
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self.zip = None
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if self.fid is not None:
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self.fid.close()
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self.fid = None
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self.f = None # break reference cycle
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def __del__(self):
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self.close()
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# Implement the Mapping ABC
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def __iter__(self):
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return iter(self.files)
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def __len__(self):
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return len(self.files)
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def __getitem__(self, key):
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# FIXME: This seems like it will copy strings around
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# more than is strictly necessary. The zipfile
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# will read the string and then
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# the format.read_array will copy the string
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# to another place in memory.
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# It would be better if the zipfile could read
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# (or at least uncompress) the data
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# directly into the array memory.
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member = False
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if key in self._files:
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member = True
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elif key in self.files:
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member = True
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key += '.npy'
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if member:
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bytes = self.zip.open(key)
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magic = bytes.read(len(format.MAGIC_PREFIX))
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bytes.close()
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if magic == format.MAGIC_PREFIX:
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bytes = self.zip.open(key)
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return format.read_array(bytes,
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allow_pickle=self.allow_pickle,
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pickle_kwargs=self.pickle_kwargs,
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max_header_size=self.max_header_size)
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else:
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return self.zip.read(key)
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else:
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raise KeyError(f"{key} is not a file in the archive")
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def __contains__(self, key):
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return (key in self._files or key in self.files)
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def __repr__(self):
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# Get filename or default to `object`
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if isinstance(self.fid, str):
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filename = self.fid
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else:
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filename = getattr(self.fid, "name", "object")
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# Get the name of arrays
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array_names = ', '.join(self.files[:self._MAX_REPR_ARRAY_COUNT])
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if len(self.files) > self._MAX_REPR_ARRAY_COUNT:
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array_names += "..."
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return f"NpzFile {filename!r} with keys: {array_names}"
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@set_module('numpy')
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def load(file, mmap_mode=None, allow_pickle=False, fix_imports=True,
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encoding='ASCII', *, max_header_size=format._MAX_HEADER_SIZE):
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"""
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Load arrays or pickled objects from ``.npy``, ``.npz`` or pickled files.
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.. warning:: Loading files that contain object arrays uses the ``pickle``
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module, which is not secure against erroneous or maliciously
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constructed data. Consider passing ``allow_pickle=False`` to
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load data that is known not to contain object arrays for the
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safer handling of untrusted sources.
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Parameters
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----------
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file : file-like object, string, or pathlib.Path
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The file to read. File-like objects must support the
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``seek()`` and ``read()`` methods and must always
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be opened in binary mode. Pickled files require that the
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file-like object support the ``readline()`` method as well.
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mmap_mode : {None, 'r+', 'r', 'w+', 'c'}, optional
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If not None, then memory-map the file, using the given mode (see
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`numpy.memmap` for a detailed description of the modes). A
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memory-mapped array is kept on disk. However, it can be accessed
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and sliced like any ndarray. Memory mapping is especially useful
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for accessing small fragments of large files without reading the
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entire file into memory.
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allow_pickle : bool, optional
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Allow loading pickled object arrays stored in npy files. Reasons for
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disallowing pickles include security, as loading pickled data can
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execute arbitrary code. If pickles are disallowed, loading object
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arrays will fail. Default: False
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.. versionchanged:: 1.16.3
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Made default False in response to CVE-2019-6446.
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fix_imports : bool, optional
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Only useful when loading Python 2 generated pickled files on Python 3,
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which includes npy/npz files containing object arrays. If `fix_imports`
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is True, pickle will try to map the old Python 2 names to the new names
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used in Python 3.
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encoding : str, optional
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What encoding to use when reading Python 2 strings. Only useful when
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loading Python 2 generated pickled files in Python 3, which includes
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npy/npz files containing object arrays. Values other than 'latin1',
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'ASCII', and 'bytes' are not allowed, as they can corrupt numerical
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data. Default: 'ASCII'
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max_header_size : int, optional
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Maximum allowed size of the header. Large headers may not be safe
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to load securely and thus require explicitly passing a larger value.
|
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See :py:func:`ast.literal_eval()` for details.
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This option is ignored when `allow_pickle` is passed. In that case
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the file is by definition trusted and the limit is unnecessary.
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Returns
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-------
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result : array, tuple, dict, etc.
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Data stored in the file. For ``.npz`` files, the returned instance
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of NpzFile class must be closed to avoid leaking file descriptors.
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Raises
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------
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OSError
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If the input file does not exist or cannot be read.
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UnpicklingError
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If ``allow_pickle=True``, but the file cannot be loaded as a pickle.
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ValueError
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The file contains an object array, but ``allow_pickle=False`` given.
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EOFError
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When calling ``np.load`` multiple times on the same file handle,
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if all data has already been read
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See Also
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--------
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save, savez, savez_compressed, loadtxt
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memmap : Create a memory-map to an array stored in a file on disk.
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lib.format.open_memmap : Create or load a memory-mapped ``.npy`` file.
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Notes
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-----
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- If the file contains pickle data, then whatever object is stored
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in the pickle is returned.
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- If the file is a ``.npy`` file, then a single array is returned.
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- If the file is a ``.npz`` file, then a dictionary-like object is
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returned, containing ``{filename: array}`` key-value pairs, one for
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each file in the archive.
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- If the file is a ``.npz`` file, the returned value supports the
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context manager protocol in a similar fashion to the open function::
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with load('foo.npz') as data:
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a = data['a']
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The underlying file descriptor is closed when exiting the 'with'
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block.
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Examples
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--------
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Store data to disk, and load it again:
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>>> np.save('/tmp/123', np.array([[1, 2, 3], [4, 5, 6]]))
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>>> np.load('/tmp/123.npy')
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array([[1, 2, 3],
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[4, 5, 6]])
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Store compressed data to disk, and load it again:
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>>> a=np.array([[1, 2, 3], [4, 5, 6]])
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>>> b=np.array([1, 2])
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>>> np.savez('/tmp/123.npz', a=a, b=b)
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>>> data = np.load('/tmp/123.npz')
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>>> data['a']
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array([[1, 2, 3],
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[4, 5, 6]])
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>>> data['b']
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array([1, 2])
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>>> data.close()
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Mem-map the stored array, and then access the second row
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directly from disk:
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>>> X = np.load('/tmp/123.npy', mmap_mode='r')
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>>> X[1, :]
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memmap([4, 5, 6])
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"""
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if encoding not in ('ASCII', 'latin1', 'bytes'):
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# The 'encoding' value for pickle also affects what encoding
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# the serialized binary data of NumPy arrays is loaded
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# in. Pickle does not pass on the encoding information to
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# NumPy. The unpickling code in numpy.core.multiarray is
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# written to assume that unicode data appearing where binary
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# should be is in 'latin1'. 'bytes' is also safe, as is 'ASCII'.
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#
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# Other encoding values can corrupt binary data, and we
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# purposefully disallow them. For the same reason, the errors=
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# argument is not exposed, as values other than 'strict'
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|
# result can similarly silently corrupt numerical data.
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raise ValueError("encoding must be 'ASCII', 'latin1', or 'bytes'")
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|
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pickle_kwargs = dict(encoding=encoding, fix_imports=fix_imports)
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|
|
with contextlib.ExitStack() as stack:
|
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if hasattr(file, 'read'):
|
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fid = file
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own_fid = False
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else:
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fid = stack.enter_context(open(os_fspath(file), "rb"))
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own_fid = True
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|
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# Code to distinguish from NumPy binary files and pickles.
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_ZIP_PREFIX = b'PK\x03\x04'
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_ZIP_SUFFIX = b'PK\x05\x06' # empty zip files start with this
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N = len(format.MAGIC_PREFIX)
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magic = fid.read(N)
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|
if not magic:
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raise EOFError("No data left in file")
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|
# If the file size is less than N, we need to make sure not
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# to seek past the beginning of the file
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fid.seek(-min(N, len(magic)), 1) # back-up
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if magic.startswith(_ZIP_PREFIX) or magic.startswith(_ZIP_SUFFIX):
|
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# zip-file (assume .npz)
|
|
# Potentially transfer file ownership to NpzFile
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|
stack.pop_all()
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ret = NpzFile(fid, own_fid=own_fid, allow_pickle=allow_pickle,
|
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pickle_kwargs=pickle_kwargs,
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max_header_size=max_header_size)
|
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return ret
|
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elif magic == format.MAGIC_PREFIX:
|
|
# .npy file
|
|
if mmap_mode:
|
|
if allow_pickle:
|
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max_header_size = 2**64
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return format.open_memmap(file, mode=mmap_mode,
|
|
max_header_size=max_header_size)
|
|
else:
|
|
return format.read_array(fid, allow_pickle=allow_pickle,
|
|
pickle_kwargs=pickle_kwargs,
|
|
max_header_size=max_header_size)
|
|
else:
|
|
# Try a pickle
|
|
if not allow_pickle:
|
|
raise ValueError("Cannot load file containing pickled data "
|
|
"when allow_pickle=False")
|
|
try:
|
|
return pickle.load(fid, **pickle_kwargs)
|
|
except Exception as e:
|
|
raise pickle.UnpicklingError(
|
|
f"Failed to interpret file {file!r} as a pickle") from e
|
|
|
|
|
|
def _save_dispatcher(file, arr, allow_pickle=None, fix_imports=None):
|
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return (arr,)
|
|
|
|
|
|
@array_function_dispatch(_save_dispatcher)
|
|
def save(file, arr, allow_pickle=True, fix_imports=True):
|
|
"""
|
|
Save an array to a binary file in NumPy ``.npy`` format.
|
|
|
|
Parameters
|
|
----------
|
|
file : file, str, or pathlib.Path
|
|
File or filename to which the data is saved. If file is a file-object,
|
|
then the filename is unchanged. If file is a string or Path, a ``.npy``
|
|
extension will be appended to the filename if it does not already
|
|
have one.
|
|
arr : array_like
|
|
Array data to be saved.
|
|
allow_pickle : bool, optional
|
|
Allow saving object arrays using Python pickles. Reasons for disallowing
|
|
pickles include security (loading pickled data can execute arbitrary
|
|
code) and portability (pickled objects may not be loadable on different
|
|
Python installations, for example if the stored objects require libraries
|
|
that are not available, and not all pickled data is compatible between
|
|
Python 2 and Python 3).
|
|
Default: True
|
|
fix_imports : bool, optional
|
|
Only useful in forcing objects in object arrays on Python 3 to be
|
|
pickled in a Python 2 compatible way. If `fix_imports` is True, pickle
|
|
will try to map the new Python 3 names to the old module names used in
|
|
Python 2, so that the pickle data stream is readable with Python 2.
|
|
|
|
See Also
|
|
--------
|
|
savez : Save several arrays into a ``.npz`` archive
|
|
savetxt, load
|
|
|
|
Notes
|
|
-----
|
|
For a description of the ``.npy`` format, see :py:mod:`numpy.lib.format`.
|
|
|
|
Any data saved to the file is appended to the end of the file.
|
|
|
|
Examples
|
|
--------
|
|
>>> from tempfile import TemporaryFile
|
|
>>> outfile = TemporaryFile()
|
|
|
|
>>> x = np.arange(10)
|
|
>>> np.save(outfile, x)
|
|
|
|
>>> _ = outfile.seek(0) # Only needed here to simulate closing & reopening file
|
|
>>> np.load(outfile)
|
|
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
|
|
|
|
|
|
>>> with open('test.npy', 'wb') as f:
|
|
... np.save(f, np.array([1, 2]))
|
|
... np.save(f, np.array([1, 3]))
|
|
>>> with open('test.npy', 'rb') as f:
|
|
... a = np.load(f)
|
|
... b = np.load(f)
|
|
>>> print(a, b)
|
|
# [1 2] [1 3]
|
|
"""
|
|
if hasattr(file, 'write'):
|
|
file_ctx = contextlib.nullcontext(file)
|
|
else:
|
|
file = os_fspath(file)
|
|
if not file.endswith('.npy'):
|
|
file = file + '.npy'
|
|
file_ctx = open(file, "wb")
|
|
|
|
with file_ctx as fid:
|
|
arr = np.asanyarray(arr)
|
|
format.write_array(fid, arr, allow_pickle=allow_pickle,
|
|
pickle_kwargs=dict(fix_imports=fix_imports))
|
|
|
|
|
|
def _savez_dispatcher(file, *args, **kwds):
|
|
yield from args
|
|
yield from kwds.values()
|
|
|
|
|
|
@array_function_dispatch(_savez_dispatcher)
|
|
def savez(file, *args, **kwds):
|
|
"""Save several arrays into a single file in uncompressed ``.npz`` format.
|
|
|
|
Provide arrays as keyword arguments to store them under the
|
|
corresponding name in the output file: ``savez(fn, x=x, y=y)``.
|
|
|
|
If arrays are specified as positional arguments, i.e., ``savez(fn,
|
|
x, y)``, their names will be `arr_0`, `arr_1`, etc.
|
|
|
|
Parameters
|
|
----------
|
|
file : str or file
|
|
Either the filename (string) or an open file (file-like object)
|
|
where the data will be saved. If file is a string or a Path, the
|
|
``.npz`` extension will be appended to the filename if it is not
|
|
already there.
|
|
args : Arguments, optional
|
|
Arrays to save to the file. Please use keyword arguments (see
|
|
`kwds` below) to assign names to arrays. Arrays specified as
|
|
args will be named "arr_0", "arr_1", and so on.
|
|
kwds : Keyword arguments, optional
|
|
Arrays to save to the file. Each array will be saved to the
|
|
output file with its corresponding keyword name.
|
|
|
|
Returns
|
|
-------
|
|
None
|
|
|
|
See Also
|
|
--------
|
|
save : Save a single array to a binary file in NumPy format.
|
|
savetxt : Save an array to a file as plain text.
|
|
savez_compressed : Save several arrays into a compressed ``.npz`` archive
|
|
|
|
Notes
|
|
-----
|
|
The ``.npz`` file format is a zipped archive of files named after the
|
|
variables they contain. The archive is not compressed and each file
|
|
in the archive contains one variable in ``.npy`` format. For a
|
|
description of the ``.npy`` format, see :py:mod:`numpy.lib.format`.
|
|
|
|
When opening the saved ``.npz`` file with `load` a `NpzFile` object is
|
|
returned. This is a dictionary-like object which can be queried for
|
|
its list of arrays (with the ``.files`` attribute), and for the arrays
|
|
themselves.
|
|
|
|
Keys passed in `kwds` are used as filenames inside the ZIP archive.
|
|
Therefore, keys should be valid filenames; e.g., avoid keys that begin with
|
|
``/`` or contain ``.``.
|
|
|
|
When naming variables with keyword arguments, it is not possible to name a
|
|
variable ``file``, as this would cause the ``file`` argument to be defined
|
|
twice in the call to ``savez``.
|
|
|
|
Examples
|
|
--------
|
|
>>> from tempfile import TemporaryFile
|
|
>>> outfile = TemporaryFile()
|
|
>>> x = np.arange(10)
|
|
>>> y = np.sin(x)
|
|
|
|
Using `savez` with \\*args, the arrays are saved with default names.
|
|
|
|
>>> np.savez(outfile, x, y)
|
|
>>> _ = outfile.seek(0) # Only needed here to simulate closing & reopening file
|
|
>>> npzfile = np.load(outfile)
|
|
>>> npzfile.files
|
|
['arr_0', 'arr_1']
|
|
>>> npzfile['arr_0']
|
|
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
|
|
|
|
Using `savez` with \\**kwds, the arrays are saved with the keyword names.
|
|
|
|
>>> outfile = TemporaryFile()
|
|
>>> np.savez(outfile, x=x, y=y)
|
|
>>> _ = outfile.seek(0)
|
|
>>> npzfile = np.load(outfile)
|
|
>>> sorted(npzfile.files)
|
|
['x', 'y']
|
|
>>> npzfile['x']
|
|
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
|
|
|
|
"""
|
|
_savez(file, args, kwds, False)
|
|
|
|
|
|
def _savez_compressed_dispatcher(file, *args, **kwds):
|
|
yield from args
|
|
yield from kwds.values()
|
|
|
|
|
|
@array_function_dispatch(_savez_compressed_dispatcher)
|
|
def savez_compressed(file, *args, **kwds):
|
|
"""
|
|
Save several arrays into a single file in compressed ``.npz`` format.
|
|
|
|
Provide arrays as keyword arguments to store them under the
|
|
corresponding name in the output file: ``savez(fn, x=x, y=y)``.
|
|
|
|
If arrays are specified as positional arguments, i.e., ``savez(fn,
|
|
x, y)``, their names will be `arr_0`, `arr_1`, etc.
|
|
|
|
Parameters
|
|
----------
|
|
file : str or file
|
|
Either the filename (string) or an open file (file-like object)
|
|
where the data will be saved. If file is a string or a Path, the
|
|
``.npz`` extension will be appended to the filename if it is not
|
|
already there.
|
|
args : Arguments, optional
|
|
Arrays to save to the file. Please use keyword arguments (see
|
|
`kwds` below) to assign names to arrays. Arrays specified as
|
|
args will be named "arr_0", "arr_1", and so on.
|
|
kwds : Keyword arguments, optional
|
|
Arrays to save to the file. Each array will be saved to the
|
|
output file with its corresponding keyword name.
|
|
|
|
Returns
|
|
-------
|
|
None
|
|
|
|
See Also
|
|
--------
|
|
numpy.save : Save a single array to a binary file in NumPy format.
|
|
numpy.savetxt : Save an array to a file as plain text.
|
|
numpy.savez : Save several arrays into an uncompressed ``.npz`` file format
|
|
numpy.load : Load the files created by savez_compressed.
|
|
|
|
Notes
|
|
-----
|
|
The ``.npz`` file format is a zipped archive of files named after the
|
|
variables they contain. The archive is compressed with
|
|
``zipfile.ZIP_DEFLATED`` and each file in the archive contains one variable
|
|
in ``.npy`` format. For a description of the ``.npy`` format, see
|
|
:py:mod:`numpy.lib.format`.
|
|
|
|
|
|
When opening the saved ``.npz`` file with `load` a `NpzFile` object is
|
|
returned. This is a dictionary-like object which can be queried for
|
|
its list of arrays (with the ``.files`` attribute), and for the arrays
|
|
themselves.
|
|
|
|
Examples
|
|
--------
|
|
>>> test_array = np.random.rand(3, 2)
|
|
>>> test_vector = np.random.rand(4)
|
|
>>> np.savez_compressed('/tmp/123', a=test_array, b=test_vector)
|
|
>>> loaded = np.load('/tmp/123.npz')
|
|
>>> print(np.array_equal(test_array, loaded['a']))
|
|
True
|
|
>>> print(np.array_equal(test_vector, loaded['b']))
|
|
True
|
|
|
|
"""
|
|
_savez(file, args, kwds, True)
|
|
|
|
|
|
def _savez(file, args, kwds, compress, allow_pickle=True, pickle_kwargs=None):
|
|
# Import is postponed to here since zipfile depends on gzip, an optional
|
|
# component of the so-called standard library.
|
|
import zipfile
|
|
|
|
if not hasattr(file, 'write'):
|
|
file = os_fspath(file)
|
|
if not file.endswith('.npz'):
|
|
file = file + '.npz'
|
|
|
|
namedict = kwds
|
|
for i, val in enumerate(args):
|
|
key = 'arr_%d' % i
|
|
if key in namedict.keys():
|
|
raise ValueError(
|
|
"Cannot use un-named variables and keyword %s" % key)
|
|
namedict[key] = val
|
|
|
|
if compress:
|
|
compression = zipfile.ZIP_DEFLATED
|
|
else:
|
|
compression = zipfile.ZIP_STORED
|
|
|
|
zipf = zipfile_factory(file, mode="w", compression=compression)
|
|
|
|
for key, val in namedict.items():
|
|
fname = key + '.npy'
|
|
val = np.asanyarray(val)
|
|
# always force zip64, gh-10776
|
|
with zipf.open(fname, 'w', force_zip64=True) as fid:
|
|
format.write_array(fid, val,
|
|
allow_pickle=allow_pickle,
|
|
pickle_kwargs=pickle_kwargs)
|
|
|
|
zipf.close()
|
|
|
|
|
|
def _ensure_ndmin_ndarray_check_param(ndmin):
|
|
"""Just checks if the param ndmin is supported on
|
|
_ensure_ndmin_ndarray. It is intended to be used as
|
|
verification before running anything expensive.
|
|
e.g. loadtxt, genfromtxt
|
|
"""
|
|
# Check correctness of the values of `ndmin`
|
|
if ndmin not in [0, 1, 2]:
|
|
raise ValueError(f"Illegal value of ndmin keyword: {ndmin}")
|
|
|
|
def _ensure_ndmin_ndarray(a, *, ndmin: int):
|
|
"""This is a helper function of loadtxt and genfromtxt to ensure
|
|
proper minimum dimension as requested
|
|
|
|
ndim : int. Supported values 1, 2, 3
|
|
^^ whenever this changes, keep in sync with
|
|
_ensure_ndmin_ndarray_check_param
|
|
"""
|
|
# Verify that the array has at least dimensions `ndmin`.
|
|
# Tweak the size and shape of the arrays - remove extraneous dimensions
|
|
if a.ndim > ndmin:
|
|
a = np.squeeze(a)
|
|
# and ensure we have the minimum number of dimensions asked for
|
|
# - has to be in this order for the odd case ndmin=1, a.squeeze().ndim=0
|
|
if a.ndim < ndmin:
|
|
if ndmin == 1:
|
|
a = np.atleast_1d(a)
|
|
elif ndmin == 2:
|
|
a = np.atleast_2d(a).T
|
|
|
|
return a
|
|
|
|
|
|
# amount of lines loadtxt reads in one chunk, can be overridden for testing
|
|
_loadtxt_chunksize = 50000
|
|
|
|
|
|
def _check_nonneg_int(value, name="argument"):
|
|
try:
|
|
operator.index(value)
|
|
except TypeError:
|
|
raise TypeError(f"{name} must be an integer") from None
|
|
if value < 0:
|
|
raise ValueError(f"{name} must be nonnegative")
|
|
|
|
|
|
def _preprocess_comments(iterable, comments, encoding):
|
|
"""
|
|
Generator that consumes a line iterated iterable and strips out the
|
|
multiple (or multi-character) comments from lines.
|
|
This is a pre-processing step to achieve feature parity with loadtxt
|
|
(we assume that this feature is a nieche feature).
|
|
"""
|
|
for line in iterable:
|
|
if isinstance(line, bytes):
|
|
# Need to handle conversion here, or the splitting would fail
|
|
line = line.decode(encoding)
|
|
|
|
for c in comments:
|
|
line = line.split(c, 1)[0]
|
|
|
|
yield line
|
|
|
|
|
|
# The number of rows we read in one go if confronted with a parametric dtype
|
|
_loadtxt_chunksize = 50000
|
|
|
|
|
|
def _read(fname, *, delimiter=',', comment='#', quote='"',
|
|
imaginary_unit='j', usecols=None, skiplines=0,
|
|
max_rows=None, converters=None, ndmin=None, unpack=False,
|
|
dtype=np.float64, encoding="bytes"):
|
|
r"""
|
|
Read a NumPy array from a text file.
|
|
|
|
Parameters
|
|
----------
|
|
fname : str or file object
|
|
The filename or the file to be read.
|
|
delimiter : str, optional
|
|
Field delimiter of the fields in line of the file.
|
|
Default is a comma, ','. If None any sequence of whitespace is
|
|
considered a delimiter.
|
|
comment : str or sequence of str or None, optional
|
|
Character that begins a comment. All text from the comment
|
|
character to the end of the line is ignored.
|
|
Multiple comments or multiple-character comment strings are supported,
|
|
but may be slower and `quote` must be empty if used.
|
|
Use None to disable all use of comments.
|
|
quote : str or None, optional
|
|
Character that is used to quote string fields. Default is '"'
|
|
(a double quote). Use None to disable quote support.
|
|
imaginary_unit : str, optional
|
|
Character that represent the imaginay unit `sqrt(-1)`.
|
|
Default is 'j'.
|
|
usecols : array_like, optional
|
|
A one-dimensional array of integer column numbers. These are the
|
|
columns from the file to be included in the array. If this value
|
|
is not given, all the columns are used.
|
|
skiplines : int, optional
|
|
Number of lines to skip before interpreting the data in the file.
|
|
max_rows : int, optional
|
|
Maximum number of rows of data to read. Default is to read the
|
|
entire file.
|
|
converters : dict or callable, optional
|
|
A function to parse all columns strings into the desired value, or
|
|
a dictionary mapping column number to a parser function.
|
|
E.g. if column 0 is a date string: ``converters = {0: datestr2num}``.
|
|
Converters can also be used to provide a default value for missing
|
|
data, e.g. ``converters = lambda s: float(s.strip() or 0)`` will
|
|
convert empty fields to 0.
|
|
Default: None
|
|
ndmin : int, optional
|
|
Minimum dimension of the array returned.
|
|
Allowed values are 0, 1 or 2. Default is 0.
|
|
unpack : bool, optional
|
|
If True, the returned array is transposed, so that arguments may be
|
|
unpacked using ``x, y, z = read(...)``. When used with a structured
|
|
data-type, arrays are returned for each field. Default is False.
|
|
dtype : numpy data type
|
|
A NumPy dtype instance, can be a structured dtype to map to the
|
|
columns of the file.
|
|
encoding : str, optional
|
|
Encoding used to decode the inputfile. The special value 'bytes'
|
|
(the default) enables backwards-compatible behavior for `converters`,
|
|
ensuring that inputs to the converter functions are encoded
|
|
bytes objects. The special value 'bytes' has no additional effect if
|
|
``converters=None``. If encoding is ``'bytes'`` or ``None``, the
|
|
default system encoding is used.
|
|
|
|
Returns
|
|
-------
|
|
ndarray
|
|
NumPy array.
|
|
|
|
Examples
|
|
--------
|
|
First we create a file for the example.
|
|
|
|
>>> s1 = '1.0,2.0,3.0\n4.0,5.0,6.0\n'
|
|
>>> with open('example1.csv', 'w') as f:
|
|
... f.write(s1)
|
|
>>> a1 = read_from_filename('example1.csv')
|
|
>>> a1
|
|
array([[1., 2., 3.],
|
|
[4., 5., 6.]])
|
|
|
|
The second example has columns with different data types, so a
|
|
one-dimensional array with a structured data type is returned.
|
|
The tab character is used as the field delimiter.
|
|
|
|
>>> s2 = '1.0\t10\talpha\n2.3\t25\tbeta\n4.5\t16\tgamma\n'
|
|
>>> with open('example2.tsv', 'w') as f:
|
|
... f.write(s2)
|
|
>>> a2 = read_from_filename('example2.tsv', delimiter='\t')
|
|
>>> a2
|
|
array([(1. , 10, b'alpha'), (2.3, 25, b'beta'), (4.5, 16, b'gamma')],
|
|
dtype=[('f0', '<f8'), ('f1', 'u1'), ('f2', 'S5')])
|
|
"""
|
|
# Handle special 'bytes' keyword for encoding
|
|
byte_converters = False
|
|
if encoding == 'bytes':
|
|
encoding = None
|
|
byte_converters = True
|
|
|
|
if dtype is None:
|
|
raise TypeError("a dtype must be provided.")
|
|
dtype = np.dtype(dtype)
|
|
|
|
read_dtype_via_object_chunks = None
|
|
if dtype.kind in 'SUM' and (
|
|
dtype == "S0" or dtype == "U0" or dtype == "M8" or dtype == 'm8'):
|
|
# This is a legacy "flexible" dtype. We do not truly support
|
|
# parametric dtypes currently (no dtype discovery step in the core),
|
|
# but have to support these for backward compatibility.
|
|
read_dtype_via_object_chunks = dtype
|
|
dtype = np.dtype(object)
|
|
|
|
if usecols is not None:
|
|
# Allow usecols to be a single int or a sequence of ints, the C-code
|
|
# handles the rest
|
|
try:
|
|
usecols = list(usecols)
|
|
except TypeError:
|
|
usecols = [usecols]
|
|
|
|
_ensure_ndmin_ndarray_check_param(ndmin)
|
|
|
|
if comment is None:
|
|
comments = None
|
|
else:
|
|
# assume comments are a sequence of strings
|
|
if "" in comment:
|
|
raise ValueError(
|
|
"comments cannot be an empty string. Use comments=None to "
|
|
"disable comments."
|
|
)
|
|
comments = tuple(comment)
|
|
comment = None
|
|
if len(comments) == 0:
|
|
comments = None # No comments at all
|
|
elif len(comments) == 1:
|
|
# If there is only one comment, and that comment has one character,
|
|
# the normal parsing can deal with it just fine.
|
|
if isinstance(comments[0], str) and len(comments[0]) == 1:
|
|
comment = comments[0]
|
|
comments = None
|
|
else:
|
|
# Input validation if there are multiple comment characters
|
|
if delimiter in comments:
|
|
raise TypeError(
|
|
f"Comment characters '{comments}' cannot include the "
|
|
f"delimiter '{delimiter}'"
|
|
)
|
|
|
|
# comment is now either a 1 or 0 character string or a tuple:
|
|
if comments is not None:
|
|
# Note: An earlier version support two character comments (and could
|
|
# have been extended to multiple characters, we assume this is
|
|
# rare enough to not optimize for.
|
|
if quote is not None:
|
|
raise ValueError(
|
|
"when multiple comments or a multi-character comment is "
|
|
"given, quotes are not supported. In this case quotechar "
|
|
"must be set to None.")
|
|
|
|
if len(imaginary_unit) != 1:
|
|
raise ValueError('len(imaginary_unit) must be 1.')
|
|
|
|
_check_nonneg_int(skiplines)
|
|
if max_rows is not None:
|
|
_check_nonneg_int(max_rows)
|
|
else:
|
|
# Passing -1 to the C code means "read the entire file".
|
|
max_rows = -1
|
|
|
|
fh_closing_ctx = contextlib.nullcontext()
|
|
filelike = False
|
|
try:
|
|
if isinstance(fname, os.PathLike):
|
|
fname = os.fspath(fname)
|
|
if isinstance(fname, str):
|
|
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
|
|
if encoding is None:
|
|
encoding = getattr(fh, 'encoding', 'latin1')
|
|
|
|
fh_closing_ctx = contextlib.closing(fh)
|
|
data = fh
|
|
filelike = True
|
|
else:
|
|
if encoding is None:
|
|
encoding = getattr(fname, 'encoding', 'latin1')
|
|
data = iter(fname)
|
|
except TypeError as e:
|
|
raise ValueError(
|
|
f"fname must be a string, filehandle, list of strings,\n"
|
|
f"or generator. Got {type(fname)} instead.") from e
|
|
|
|
with fh_closing_ctx:
|
|
if comments is not None:
|
|
if filelike:
|
|
data = iter(data)
|
|
filelike = False
|
|
data = _preprocess_comments(data, comments, encoding)
|
|
|
|
if read_dtype_via_object_chunks is None:
|
|
arr = _load_from_filelike(
|
|
data, delimiter=delimiter, comment=comment, quote=quote,
|
|
imaginary_unit=imaginary_unit,
|
|
usecols=usecols, skiplines=skiplines, max_rows=max_rows,
|
|
converters=converters, dtype=dtype,
|
|
encoding=encoding, filelike=filelike,
|
|
byte_converters=byte_converters)
|
|
|
|
else:
|
|
# This branch reads the file into chunks of object arrays and then
|
|
# casts them to the desired actual dtype. This ensures correct
|
|
# string-length and datetime-unit discovery (like `arr.astype()`).
|
|
# Due to chunking, certain error reports are less clear, currently.
|
|
if filelike:
|
|
data = iter(data) # cannot chunk when reading from file
|
|
|
|
c_byte_converters = False
|
|
if read_dtype_via_object_chunks == "S":
|
|
c_byte_converters = True # Use latin1 rather than ascii
|
|
|
|
chunks = []
|
|
while max_rows != 0:
|
|
if max_rows < 0:
|
|
chunk_size = _loadtxt_chunksize
|
|
else:
|
|
chunk_size = min(_loadtxt_chunksize, max_rows)
|
|
|
|
next_arr = _load_from_filelike(
|
|
data, delimiter=delimiter, comment=comment, quote=quote,
|
|
imaginary_unit=imaginary_unit,
|
|
usecols=usecols, skiplines=skiplines, max_rows=max_rows,
|
|
converters=converters, dtype=dtype,
|
|
encoding=encoding, filelike=filelike,
|
|
byte_converters=byte_converters,
|
|
c_byte_converters=c_byte_converters)
|
|
# Cast here already. We hope that this is better even for
|
|
# large files because the storage is more compact. It could
|
|
# be adapted (in principle the concatenate could cast).
|
|
chunks.append(next_arr.astype(read_dtype_via_object_chunks))
|
|
|
|
skiprows = 0 # Only have to skip for first chunk
|
|
if max_rows >= 0:
|
|
max_rows -= chunk_size
|
|
if len(next_arr) < chunk_size:
|
|
# There was less data than requested, so we are done.
|
|
break
|
|
|
|
# Need at least one chunk, but if empty, the last one may have
|
|
# the wrong shape.
|
|
if len(chunks) > 1 and len(chunks[-1]) == 0:
|
|
del chunks[-1]
|
|
if len(chunks) == 1:
|
|
arr = chunks[0]
|
|
else:
|
|
arr = np.concatenate(chunks, axis=0)
|
|
|
|
# NOTE: ndmin works as advertised for structured dtypes, but normally
|
|
# these would return a 1D result plus the structured dimension,
|
|
# so ndmin=2 adds a third dimension even when no squeezing occurs.
|
|
# A `squeeze=False` could be a better solution (pandas uses squeeze).
|
|
arr = _ensure_ndmin_ndarray(arr, ndmin=ndmin)
|
|
|
|
if arr.shape:
|
|
if arr.shape[0] == 0:
|
|
warnings.warn(
|
|
f'loadtxt: input contained no data: "{fname}"',
|
|
category=UserWarning,
|
|
stacklevel=3
|
|
)
|
|
|
|
if unpack:
|
|
# Unpack structured dtypes if requested:
|
|
dt = arr.dtype
|
|
if dt.names is not None:
|
|
# For structured arrays, return an array for each field.
|
|
return [arr[field] for field in dt.names]
|
|
else:
|
|
return arr.T
|
|
else:
|
|
return arr
|
|
|
|
|
|
@set_array_function_like_doc
|
|
@set_module('numpy')
|
|
def loadtxt(fname, dtype=float, comments='#', delimiter=None,
|
|
converters=None, skiprows=0, usecols=None, unpack=False,
|
|
ndmin=0, encoding='bytes', max_rows=None, *, quotechar=None,
|
|
like=None):
|
|
r"""
|
|
Load data from a text file.
|
|
|
|
Parameters
|
|
----------
|
|
fname : file, str, pathlib.Path, list of str, generator
|
|
File, filename, list, or generator to read. If the filename
|
|
extension is ``.gz`` or ``.bz2``, the file is first decompressed. Note
|
|
that generators must return bytes or strings. The strings
|
|
in a list or produced by a generator are treated as lines.
|
|
dtype : data-type, optional
|
|
Data-type of the resulting array; default: float. If this is a
|
|
structured data-type, the resulting array will be 1-dimensional, and
|
|
each row will be interpreted as an element of the array. In this
|
|
case, the number of columns used must match the number of fields in
|
|
the data-type.
|
|
comments : str or sequence of str or None, optional
|
|
The characters or list of characters used to indicate the start of a
|
|
comment. None implies no comments. For backwards compatibility, byte
|
|
strings will be decoded as 'latin1'. The default is '#'.
|
|
delimiter : str, optional
|
|
The character used to separate the values. For backwards compatibility,
|
|
byte strings will be decoded as 'latin1'. The default is whitespace.
|
|
|
|
.. versionchanged:: 1.23.0
|
|
Only single character delimiters are supported. Newline characters
|
|
cannot be used as the delimiter.
|
|
|
|
converters : dict or callable, optional
|
|
Converter functions to customize value parsing. If `converters` is
|
|
callable, the function is applied to all columns, else it must be a
|
|
dict that maps column number to a parser function.
|
|
See examples for further details.
|
|
Default: None.
|
|
|
|
.. versionchanged:: 1.23.0
|
|
The ability to pass a single callable to be applied to all columns
|
|
was added.
|
|
|
|
skiprows : int, optional
|
|
Skip the first `skiprows` lines, including comments; default: 0.
|
|
usecols : int or sequence, optional
|
|
Which columns to read, with 0 being the first. For example,
|
|
``usecols = (1,4,5)`` will extract the 2nd, 5th and 6th columns.
|
|
The default, None, results in all columns being read.
|
|
|
|
.. versionchanged:: 1.11.0
|
|
When a single column has to be read it is possible to use
|
|
an integer instead of a tuple. E.g ``usecols = 3`` reads the
|
|
fourth column the same way as ``usecols = (3,)`` would.
|
|
unpack : bool, optional
|
|
If True, the returned array is transposed, so that arguments may be
|
|
unpacked using ``x, y, z = loadtxt(...)``. When used with a
|
|
structured data-type, arrays are returned for each field.
|
|
Default is False.
|
|
ndmin : int, optional
|
|
The returned array will have at least `ndmin` dimensions.
|
|
Otherwise mono-dimensional axes will be squeezed.
|
|
Legal values: 0 (default), 1 or 2.
|
|
|
|
.. versionadded:: 1.6.0
|
|
encoding : str, optional
|
|
Encoding used to decode the inputfile. Does not apply to input streams.
|
|
The special value 'bytes' enables backward compatibility workarounds
|
|
that ensures you receive byte arrays as results if possible and passes
|
|
'latin1' encoded strings to converters. Override this value to receive
|
|
unicode arrays and pass strings as input to converters. If set to None
|
|
the system default is used. The default value is 'bytes'.
|
|
|
|
.. versionadded:: 1.14.0
|
|
max_rows : int, optional
|
|
Read `max_rows` rows of content after `skiprows` lines. The default is
|
|
to read all the rows. Note that empty rows containing no data such as
|
|
empty lines and comment lines are not counted towards `max_rows`,
|
|
while such lines are counted in `skiprows`.
|
|
|
|
.. versionadded:: 1.16.0
|
|
|
|
.. versionchanged:: 1.23.0
|
|
Lines containing no data, including comment lines (e.g., lines
|
|
starting with '#' or as specified via `comments`) are not counted
|
|
towards `max_rows`.
|
|
quotechar : unicode character or None, optional
|
|
The character used to denote the start and end of a quoted item.
|
|
Occurrences of the delimiter or comment characters are ignored within
|
|
a quoted item. The default value is ``quotechar=None``, which means
|
|
quoting support is disabled.
|
|
|
|
If two consecutive instances of `quotechar` are found within a quoted
|
|
field, the first is treated as an escape character. See examples.
|
|
|
|
.. versionadded:: 1.23.0
|
|
${ARRAY_FUNCTION_LIKE}
|
|
|
|
.. versionadded:: 1.20.0
|
|
|
|
Returns
|
|
-------
|
|
out : ndarray
|
|
Data read from the text file.
|
|
|
|
See Also
|
|
--------
|
|
load, fromstring, fromregex
|
|
genfromtxt : Load data with missing values handled as specified.
|
|
scipy.io.loadmat : reads MATLAB data files
|
|
|
|
Notes
|
|
-----
|
|
This function aims to be a fast reader for simply formatted files. The
|
|
`genfromtxt` function provides more sophisticated handling of, e.g.,
|
|
lines with missing values.
|
|
|
|
Each row in the input text file must have the same number of values to be
|
|
able to read all values. If all rows do not have same number of values, a
|
|
subset of up to n columns (where n is the least number of values present
|
|
in all rows) can be read by specifying the columns via `usecols`.
|
|
|
|
.. versionadded:: 1.10.0
|
|
|
|
The strings produced by the Python float.hex method can be used as
|
|
input for floats.
|
|
|
|
Examples
|
|
--------
|
|
>>> from io import StringIO # StringIO behaves like a file object
|
|
>>> c = StringIO("0 1\n2 3")
|
|
>>> np.loadtxt(c)
|
|
array([[0., 1.],
|
|
[2., 3.]])
|
|
|
|
>>> d = StringIO("M 21 72\nF 35 58")
|
|
>>> np.loadtxt(d, dtype={'names': ('gender', 'age', 'weight'),
|
|
... 'formats': ('S1', 'i4', 'f4')})
|
|
array([(b'M', 21, 72.), (b'F', 35, 58.)],
|
|
dtype=[('gender', 'S1'), ('age', '<i4'), ('weight', '<f4')])
|
|
|
|
>>> c = StringIO("1,0,2\n3,0,4")
|
|
>>> x, y = np.loadtxt(c, delimiter=',', usecols=(0, 2), unpack=True)
|
|
>>> x
|
|
array([1., 3.])
|
|
>>> y
|
|
array([2., 4.])
|
|
|
|
The `converters` argument is used to specify functions to preprocess the
|
|
text prior to parsing. `converters` can be a dictionary that maps
|
|
preprocessing functions to each column:
|
|
|
|
>>> s = StringIO("1.618, 2.296\n3.141, 4.669\n")
|
|
>>> conv = {
|
|
... 0: lambda x: np.floor(float(x)), # conversion fn for column 0
|
|
... 1: lambda x: np.ceil(float(x)), # conversion fn for column 1
|
|
... }
|
|
>>> np.loadtxt(s, delimiter=",", converters=conv)
|
|
array([[1., 3.],
|
|
[3., 5.]])
|
|
|
|
`converters` can be a callable instead of a dictionary, in which case it
|
|
is applied to all columns:
|
|
|
|
>>> s = StringIO("0xDE 0xAD\n0xC0 0xDE")
|
|
>>> import functools
|
|
>>> conv = functools.partial(int, base=16)
|
|
>>> np.loadtxt(s, converters=conv)
|
|
array([[222., 173.],
|
|
[192., 222.]])
|
|
|
|
This example shows how `converters` can be used to convert a field
|
|
with a trailing minus sign into a negative number.
|
|
|
|
>>> s = StringIO('10.01 31.25-\n19.22 64.31\n17.57- 63.94')
|
|
>>> def conv(fld):
|
|
... return -float(fld[:-1]) if fld.endswith(b'-') else float(fld)
|
|
...
|
|
>>> np.loadtxt(s, converters=conv)
|
|
array([[ 10.01, -31.25],
|
|
[ 19.22, 64.31],
|
|
[-17.57, 63.94]])
|
|
|
|
Using a callable as the converter can be particularly useful for handling
|
|
values with different formatting, e.g. floats with underscores:
|
|
|
|
>>> s = StringIO("1 2.7 100_000")
|
|
>>> np.loadtxt(s, converters=float)
|
|
array([1.e+00, 2.7e+00, 1.e+05])
|
|
|
|
This idea can be extended to automatically handle values specified in
|
|
many different formats:
|
|
|
|
>>> def conv(val):
|
|
... try:
|
|
... return float(val)
|
|
... except ValueError:
|
|
... return float.fromhex(val)
|
|
>>> s = StringIO("1, 2.5, 3_000, 0b4, 0x1.4000000000000p+2")
|
|
>>> np.loadtxt(s, delimiter=",", converters=conv, encoding=None)
|
|
array([1.0e+00, 2.5e+00, 3.0e+03, 1.8e+02, 5.0e+00])
|
|
|
|
Note that with the default ``encoding="bytes"``, the inputs to the
|
|
converter function are latin-1 encoded byte strings. To deactivate the
|
|
implicit encoding prior to conversion, use ``encoding=None``
|
|
|
|
>>> s = StringIO('10.01 31.25-\n19.22 64.31\n17.57- 63.94')
|
|
>>> conv = lambda x: -float(x[:-1]) if x.endswith('-') else float(x)
|
|
>>> np.loadtxt(s, converters=conv, encoding=None)
|
|
array([[ 10.01, -31.25],
|
|
[ 19.22, 64.31],
|
|
[-17.57, 63.94]])
|
|
|
|
Support for quoted fields is enabled with the `quotechar` parameter.
|
|
Comment and delimiter characters are ignored when they appear within a
|
|
quoted item delineated by `quotechar`:
|
|
|
|
>>> s = StringIO('"alpha, #42", 10.0\n"beta, #64", 2.0\n')
|
|
>>> dtype = np.dtype([("label", "U12"), ("value", float)])
|
|
>>> np.loadtxt(s, dtype=dtype, delimiter=",", quotechar='"')
|
|
array([('alpha, #42', 10.), ('beta, #64', 2.)],
|
|
dtype=[('label', '<U12'), ('value', '<f8')])
|
|
|
|
Quoted fields can be separated by multiple whitespace characters:
|
|
|
|
>>> s = StringIO('"alpha, #42" 10.0\n"beta, #64" 2.0\n')
|
|
>>> dtype = np.dtype([("label", "U12"), ("value", float)])
|
|
>>> np.loadtxt(s, dtype=dtype, delimiter=None, quotechar='"')
|
|
array([('alpha, #42', 10.), ('beta, #64', 2.)],
|
|
dtype=[('label', '<U12'), ('value', '<f8')])
|
|
|
|
Two consecutive quote characters within a quoted field are treated as a
|
|
single escaped character:
|
|
|
|
>>> s = StringIO('"Hello, my name is ""Monty""!"')
|
|
>>> np.loadtxt(s, dtype="U", delimiter=",", quotechar='"')
|
|
array('Hello, my name is "Monty"!', dtype='<U26')
|
|
|
|
Read subset of columns when all rows do not contain equal number of values:
|
|
|
|
>>> d = StringIO("1 2\n2 4\n3 9 12\n4 16 20")
|
|
>>> np.loadtxt(d, usecols=(0, 1))
|
|
array([[ 1., 2.],
|
|
[ 2., 4.],
|
|
[ 3., 9.],
|
|
[ 4., 16.]])
|
|
|
|
"""
|
|
|
|
if like is not None:
|
|
return _loadtxt_with_like(
|
|
like, fname, dtype=dtype, comments=comments, delimiter=delimiter,
|
|
converters=converters, skiprows=skiprows, usecols=usecols,
|
|
unpack=unpack, ndmin=ndmin, encoding=encoding,
|
|
max_rows=max_rows
|
|
)
|
|
|
|
if isinstance(delimiter, bytes):
|
|
delimiter.decode("latin1")
|
|
|
|
if dtype is None:
|
|
dtype = np.float64
|
|
|
|
comment = comments
|
|
# Control character type conversions for Py3 convenience
|
|
if comment is not None:
|
|
if isinstance(comment, (str, bytes)):
|
|
comment = [comment]
|
|
comment = [
|
|
x.decode('latin1') if isinstance(x, bytes) else x for x in comment]
|
|
if isinstance(delimiter, bytes):
|
|
delimiter = delimiter.decode('latin1')
|
|
|
|
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
|
|
converters=converters, skiplines=skiprows, usecols=usecols,
|
|
unpack=unpack, ndmin=ndmin, encoding=encoding,
|
|
max_rows=max_rows, quote=quotechar)
|
|
|
|
return arr
|
|
|
|
|
|
_loadtxt_with_like = array_function_dispatch()(loadtxt)
|
|
|
|
|
|
def _savetxt_dispatcher(fname, X, fmt=None, delimiter=None, newline=None,
|
|
header=None, footer=None, comments=None,
|
|
encoding=None):
|
|
return (X,)
|
|
|
|
|
|
@array_function_dispatch(_savetxt_dispatcher)
|
|
def savetxt(fname, X, fmt='%.18e', delimiter=' ', newline='\n', header='',
|
|
footer='', comments='# ', encoding=None):
|
|
"""
|
|
Save an array to a text file.
|
|
|
|
Parameters
|
|
----------
|
|
fname : filename or file handle
|
|
If the filename ends in ``.gz``, the file is automatically saved in
|
|
compressed gzip format. `loadtxt` understands gzipped files
|
|
transparently.
|
|
X : 1D or 2D array_like
|
|
Data to be saved to a text file.
|
|
fmt : str or sequence of strs, optional
|
|
A single format (%10.5f), a sequence of formats, or a
|
|
multi-format string, e.g. 'Iteration %d -- %10.5f', in which
|
|
case `delimiter` is ignored. For complex `X`, the legal options
|
|
for `fmt` are:
|
|
|
|
* a single specifier, `fmt='%.4e'`, resulting in numbers formatted
|
|
like `' (%s+%sj)' % (fmt, fmt)`
|
|
* a full string specifying every real and imaginary part, e.g.
|
|
`' %.4e %+.4ej %.4e %+.4ej %.4e %+.4ej'` for 3 columns
|
|
* a list of specifiers, one per column - in this case, the real
|
|
and imaginary part must have separate specifiers,
|
|
e.g. `['%.3e + %.3ej', '(%.15e%+.15ej)']` for 2 columns
|
|
delimiter : str, optional
|
|
String or character separating columns.
|
|
newline : str, optional
|
|
String or character separating lines.
|
|
|
|
.. versionadded:: 1.5.0
|
|
header : str, optional
|
|
String that will be written at the beginning of the file.
|
|
|
|
.. versionadded:: 1.7.0
|
|
footer : str, optional
|
|
String that will be written at the end of the file.
|
|
|
|
.. versionadded:: 1.7.0
|
|
comments : str, optional
|
|
String that will be prepended to the ``header`` and ``footer`` strings,
|
|
to mark them as comments. Default: '# ', as expected by e.g.
|
|
``numpy.loadtxt``.
|
|
|
|
.. versionadded:: 1.7.0
|
|
encoding : {None, str}, optional
|
|
Encoding used to encode the outputfile. Does not apply to output
|
|
streams. If the encoding is something other than 'bytes' or 'latin1'
|
|
you will not be able to load the file in NumPy versions < 1.14. Default
|
|
is 'latin1'.
|
|
|
|
.. versionadded:: 1.14.0
|
|
|
|
|
|
See Also
|
|
--------
|
|
save : Save an array to a binary file in NumPy ``.npy`` format
|
|
savez : Save several arrays into an uncompressed ``.npz`` archive
|
|
savez_compressed : Save several arrays into a compressed ``.npz`` archive
|
|
|
|
Notes
|
|
-----
|
|
Further explanation of the `fmt` parameter
|
|
(``%[flag]width[.precision]specifier``):
|
|
|
|
flags:
|
|
``-`` : left justify
|
|
|
|
``+`` : Forces to precede result with + or -.
|
|
|
|
``0`` : Left pad the number with zeros instead of space (see width).
|
|
|
|
width:
|
|
Minimum number of characters to be printed. The value is not truncated
|
|
if it has more characters.
|
|
|
|
precision:
|
|
- For integer specifiers (eg. ``d,i,o,x``), the minimum number of
|
|
digits.
|
|
- For ``e, E`` and ``f`` specifiers, the number of digits to print
|
|
after the decimal point.
|
|
- For ``g`` and ``G``, the maximum number of significant digits.
|
|
- For ``s``, the maximum number of characters.
|
|
|
|
specifiers:
|
|
``c`` : character
|
|
|
|
``d`` or ``i`` : signed decimal integer
|
|
|
|
``e`` or ``E`` : scientific notation with ``e`` or ``E``.
|
|
|
|
``f`` : decimal floating point
|
|
|
|
``g,G`` : use the shorter of ``e,E`` or ``f``
|
|
|
|
``o`` : signed octal
|
|
|
|
``s`` : string of characters
|
|
|
|
``u`` : unsigned decimal integer
|
|
|
|
``x,X`` : unsigned hexadecimal integer
|
|
|
|
This explanation of ``fmt`` is not complete, for an exhaustive
|
|
specification see [1]_.
|
|
|
|
References
|
|
----------
|
|
.. [1] `Format Specification Mini-Language
|
|
<https://docs.python.org/library/string.html#format-specification-mini-language>`_,
|
|
Python Documentation.
|
|
|
|
Examples
|
|
--------
|
|
>>> x = y = z = np.arange(0.0,5.0,1.0)
|
|
>>> np.savetxt('test.out', x, delimiter=',') # X is an array
|
|
>>> np.savetxt('test.out', (x,y,z)) # x,y,z equal sized 1D arrays
|
|
>>> np.savetxt('test.out', x, fmt='%1.4e') # use exponential notation
|
|
|
|
"""
|
|
|
|
# Py3 conversions first
|
|
if isinstance(fmt, bytes):
|
|
fmt = asstr(fmt)
|
|
delimiter = asstr(delimiter)
|
|
|
|
class WriteWrap:
|
|
"""Convert to bytes on bytestream inputs.
|
|
|
|
"""
|
|
def __init__(self, fh, encoding):
|
|
self.fh = fh
|
|
self.encoding = encoding
|
|
self.do_write = self.first_write
|
|
|
|
def close(self):
|
|
self.fh.close()
|
|
|
|
def write(self, v):
|
|
self.do_write(v)
|
|
|
|
def write_bytes(self, v):
|
|
if isinstance(v, bytes):
|
|
self.fh.write(v)
|
|
else:
|
|
self.fh.write(v.encode(self.encoding))
|
|
|
|
def write_normal(self, v):
|
|
self.fh.write(asunicode(v))
|
|
|
|
def first_write(self, v):
|
|
try:
|
|
self.write_normal(v)
|
|
self.write = self.write_normal
|
|
except TypeError:
|
|
# input is probably a bytestream
|
|
self.write_bytes(v)
|
|
self.write = self.write_bytes
|
|
|
|
own_fh = False
|
|
if isinstance(fname, os_PathLike):
|
|
fname = os_fspath(fname)
|
|
if _is_string_like(fname):
|
|
# datasource doesn't support creating a new file ...
|
|
open(fname, 'wt').close()
|
|
fh = np.lib._datasource.open(fname, 'wt', encoding=encoding)
|
|
own_fh = True
|
|
elif hasattr(fname, 'write'):
|
|
# wrap to handle byte output streams
|
|
fh = WriteWrap(fname, encoding or 'latin1')
|
|
else:
|
|
raise ValueError('fname must be a string or file handle')
|
|
|
|
try:
|
|
X = np.asarray(X)
|
|
|
|
# Handle 1-dimensional arrays
|
|
if X.ndim == 0 or X.ndim > 2:
|
|
raise ValueError(
|
|
"Expected 1D or 2D array, got %dD array instead" % X.ndim)
|
|
elif X.ndim == 1:
|
|
# Common case -- 1d array of numbers
|
|
if X.dtype.names is None:
|
|
X = np.atleast_2d(X).T
|
|
ncol = 1
|
|
|
|
# Complex dtype -- each field indicates a separate column
|
|
else:
|
|
ncol = len(X.dtype.names)
|
|
else:
|
|
ncol = X.shape[1]
|
|
|
|
iscomplex_X = np.iscomplexobj(X)
|
|
# `fmt` can be a string with multiple insertion points or a
|
|
# list of formats. E.g. '%10.5f\t%10d' or ('%10.5f', '$10d')
|
|
if type(fmt) in (list, tuple):
|
|
if len(fmt) != ncol:
|
|
raise AttributeError('fmt has wrong shape. %s' % str(fmt))
|
|
format = asstr(delimiter).join(map(asstr, fmt))
|
|
elif isinstance(fmt, str):
|
|
n_fmt_chars = fmt.count('%')
|
|
error = ValueError('fmt has wrong number of %% formats: %s' % fmt)
|
|
if n_fmt_chars == 1:
|
|
if iscomplex_X:
|
|
fmt = [' (%s+%sj)' % (fmt, fmt), ] * ncol
|
|
else:
|
|
fmt = [fmt, ] * ncol
|
|
format = delimiter.join(fmt)
|
|
elif iscomplex_X and n_fmt_chars != (2 * ncol):
|
|
raise error
|
|
elif ((not iscomplex_X) and n_fmt_chars != ncol):
|
|
raise error
|
|
else:
|
|
format = fmt
|
|
else:
|
|
raise ValueError('invalid fmt: %r' % (fmt,))
|
|
|
|
if len(header) > 0:
|
|
header = header.replace('\n', '\n' + comments)
|
|
fh.write(comments + header + newline)
|
|
if iscomplex_X:
|
|
for row in X:
|
|
row2 = []
|
|
for number in row:
|
|
row2.append(number.real)
|
|
row2.append(number.imag)
|
|
s = format % tuple(row2) + newline
|
|
fh.write(s.replace('+-', '-'))
|
|
else:
|
|
for row in X:
|
|
try:
|
|
v = format % tuple(row) + newline
|
|
except TypeError as e:
|
|
raise TypeError("Mismatch between array dtype ('%s') and "
|
|
"format specifier ('%s')"
|
|
% (str(X.dtype), format)) from e
|
|
fh.write(v)
|
|
|
|
if len(footer) > 0:
|
|
footer = footer.replace('\n', '\n' + comments)
|
|
fh.write(comments + footer + newline)
|
|
finally:
|
|
if own_fh:
|
|
fh.close()
|
|
|
|
|
|
@set_module('numpy')
|
|
def fromregex(file, regexp, dtype, encoding=None):
|
|
r"""
|
|
Construct an array from a text file, using regular expression parsing.
|
|
|
|
The returned array is always a structured array, and is constructed from
|
|
all matches of the regular expression in the file. Groups in the regular
|
|
expression are converted to fields of the structured array.
|
|
|
|
Parameters
|
|
----------
|
|
file : path or file
|
|
Filename or file object to read.
|
|
|
|
.. versionchanged:: 1.22.0
|
|
Now accepts `os.PathLike` implementations.
|
|
regexp : str or regexp
|
|
Regular expression used to parse the file.
|
|
Groups in the regular expression correspond to fields in the dtype.
|
|
dtype : dtype or list of dtypes
|
|
Dtype for the structured array; must be a structured datatype.
|
|
encoding : str, optional
|
|
Encoding used to decode the inputfile. Does not apply to input streams.
|
|
|
|
.. versionadded:: 1.14.0
|
|
|
|
Returns
|
|
-------
|
|
output : ndarray
|
|
The output array, containing the part of the content of `file` that
|
|
was matched by `regexp`. `output` is always a structured array.
|
|
|
|
Raises
|
|
------
|
|
TypeError
|
|
When `dtype` is not a valid dtype for a structured array.
|
|
|
|
See Also
|
|
--------
|
|
fromstring, loadtxt
|
|
|
|
Notes
|
|
-----
|
|
Dtypes for structured arrays can be specified in several forms, but all
|
|
forms specify at least the data type and field name. For details see
|
|
`basics.rec`.
|
|
|
|
Examples
|
|
--------
|
|
>>> from io import StringIO
|
|
>>> text = StringIO("1312 foo\n1534 bar\n444 qux")
|
|
|
|
>>> regexp = r"(\d+)\s+(...)" # match [digits, whitespace, anything]
|
|
>>> output = np.fromregex(text, regexp,
|
|
... [('num', np.int64), ('key', 'S3')])
|
|
>>> output
|
|
array([(1312, b'foo'), (1534, b'bar'), ( 444, b'qux')],
|
|
dtype=[('num', '<i8'), ('key', 'S3')])
|
|
>>> output['num']
|
|
array([1312, 1534, 444])
|
|
|
|
"""
|
|
own_fh = False
|
|
if not hasattr(file, "read"):
|
|
file = os.fspath(file)
|
|
file = np.lib._datasource.open(file, 'rt', encoding=encoding)
|
|
own_fh = True
|
|
|
|
try:
|
|
if not isinstance(dtype, np.dtype):
|
|
dtype = np.dtype(dtype)
|
|
if dtype.names is None:
|
|
raise TypeError('dtype must be a structured datatype.')
|
|
|
|
content = file.read()
|
|
if isinstance(content, bytes) and isinstance(regexp, str):
|
|
regexp = asbytes(regexp)
|
|
elif isinstance(content, str) and isinstance(regexp, bytes):
|
|
regexp = asstr(regexp)
|
|
|
|
if not hasattr(regexp, 'match'):
|
|
regexp = re.compile(regexp)
|
|
seq = regexp.findall(content)
|
|
if seq and not isinstance(seq[0], tuple):
|
|
# Only one group is in the regexp.
|
|
# Create the new array as a single data-type and then
|
|
# re-interpret as a single-field structured array.
|
|
newdtype = np.dtype(dtype[dtype.names[0]])
|
|
output = np.array(seq, dtype=newdtype)
|
|
output.dtype = dtype
|
|
else:
|
|
output = np.array(seq, dtype=dtype)
|
|
|
|
return output
|
|
finally:
|
|
if own_fh:
|
|
file.close()
|
|
|
|
|
|
#####--------------------------------------------------------------------------
|
|
#---- --- ASCII functions ---
|
|
#####--------------------------------------------------------------------------
|
|
|
|
|
|
@set_array_function_like_doc
|
|
@set_module('numpy')
|
|
def genfromtxt(fname, dtype=float, comments='#', delimiter=None,
|
|
skip_header=0, skip_footer=0, converters=None,
|
|
missing_values=None, filling_values=None, usecols=None,
|
|
names=None, excludelist=None,
|
|
deletechars=''.join(sorted(NameValidator.defaultdeletechars)),
|
|
replace_space='_', autostrip=False, case_sensitive=True,
|
|
defaultfmt="f%i", unpack=None, usemask=False, loose=True,
|
|
invalid_raise=True, max_rows=None, encoding='bytes',
|
|
*, ndmin=0, like=None):
|
|
"""
|
|
Load data from a text file, with missing values handled as specified.
|
|
|
|
Each line past the first `skip_header` lines is split at the `delimiter`
|
|
character, and characters following the `comments` character are discarded.
|
|
|
|
Parameters
|
|
----------
|
|
fname : file, str, pathlib.Path, list of str, generator
|
|
File, filename, list, or generator to read. If the filename
|
|
extension is ``.gz`` or ``.bz2``, the file is first decompressed. Note
|
|
that generators must return bytes or strings. The strings
|
|
in a list or produced by a generator are treated as lines.
|
|
dtype : dtype, optional
|
|
Data type of the resulting array.
|
|
If None, the dtypes will be determined by the contents of each
|
|
column, individually.
|
|
comments : str, optional
|
|
The character used to indicate the start of a comment.
|
|
All the characters occurring on a line after a comment are discarded.
|
|
delimiter : str, int, or sequence, optional
|
|
The string used to separate values. By default, any consecutive
|
|
whitespaces act as delimiter. An integer or sequence of integers
|
|
can also be provided as width(s) of each field.
|
|
skiprows : int, optional
|
|
`skiprows` was removed in numpy 1.10. Please use `skip_header` instead.
|
|
skip_header : int, optional
|
|
The number of lines to skip at the beginning of the file.
|
|
skip_footer : int, optional
|
|
The number of lines to skip at the end of the file.
|
|
converters : variable, optional
|
|
The set of functions that convert the data of a column to a value.
|
|
The converters can also be used to provide a default value
|
|
for missing data: ``converters = {3: lambda s: float(s or 0)}``.
|
|
missing : variable, optional
|
|
`missing` was removed in numpy 1.10. Please use `missing_values`
|
|
instead.
|
|
missing_values : variable, optional
|
|
The set of strings corresponding to missing data.
|
|
filling_values : variable, optional
|
|
The set of values to be used as default when the data are missing.
|
|
usecols : sequence, optional
|
|
Which columns to read, with 0 being the first. For example,
|
|
``usecols = (1, 4, 5)`` will extract the 2nd, 5th and 6th columns.
|
|
names : {None, True, str, sequence}, optional
|
|
If `names` is True, the field names are read from the first line after
|
|
the first `skip_header` lines. This line can optionally be preceded
|
|
by a comment delimiter. If `names` is a sequence or a single-string of
|
|
comma-separated names, the names will be used to define the field names
|
|
in a structured dtype. If `names` is None, the names of the dtype
|
|
fields will be used, if any.
|
|
excludelist : sequence, optional
|
|
A list of names to exclude. This list is appended to the default list
|
|
['return','file','print']. Excluded names are appended with an
|
|
underscore: for example, `file` would become `file_`.
|
|
deletechars : str, optional
|
|
A string combining invalid characters that must be deleted from the
|
|
names.
|
|
defaultfmt : str, optional
|
|
A format used to define default field names, such as "f%i" or "f_%02i".
|
|
autostrip : bool, optional
|
|
Whether to automatically strip white spaces from the variables.
|
|
replace_space : char, optional
|
|
Character(s) used in replacement of white spaces in the variable
|
|
names. By default, use a '_'.
|
|
case_sensitive : {True, False, 'upper', 'lower'}, optional
|
|
If True, field names are case sensitive.
|
|
If False or 'upper', field names are converted to upper case.
|
|
If 'lower', field names are converted to lower case.
|
|
unpack : bool, optional
|
|
If True, the returned array is transposed, so that arguments may be
|
|
unpacked using ``x, y, z = genfromtxt(...)``. When used with a
|
|
structured data-type, arrays are returned for each field.
|
|
Default is False.
|
|
usemask : bool, optional
|
|
If True, return a masked array.
|
|
If False, return a regular array.
|
|
loose : bool, optional
|
|
If True, do not raise errors for invalid values.
|
|
invalid_raise : bool, optional
|
|
If True, an exception is raised if an inconsistency is detected in the
|
|
number of columns.
|
|
If False, a warning is emitted and the offending lines are skipped.
|
|
max_rows : int, optional
|
|
The maximum number of rows to read. Must not be used with skip_footer
|
|
at the same time. If given, the value must be at least 1. Default is
|
|
to read the entire file.
|
|
|
|
.. versionadded:: 1.10.0
|
|
encoding : str, optional
|
|
Encoding used to decode the inputfile. Does not apply when `fname` is
|
|
a file object. The special value 'bytes' enables backward compatibility
|
|
workarounds that ensure that you receive byte arrays when possible
|
|
and passes latin1 encoded strings to converters. Override this value to
|
|
receive unicode arrays and pass strings as input to converters. If set
|
|
to None the system default is used. The default value is 'bytes'.
|
|
|
|
.. versionadded:: 1.14.0
|
|
ndmin : int, optional
|
|
Same parameter as `loadtxt`
|
|
|
|
.. versionadded:: 1.23.0
|
|
${ARRAY_FUNCTION_LIKE}
|
|
|
|
.. versionadded:: 1.20.0
|
|
|
|
Returns
|
|
-------
|
|
out : ndarray
|
|
Data read from the text file. If `usemask` is True, this is a
|
|
masked array.
|
|
|
|
See Also
|
|
--------
|
|
numpy.loadtxt : equivalent function when no data is missing.
|
|
|
|
Notes
|
|
-----
|
|
* When spaces are used as delimiters, or when no delimiter has been given
|
|
as input, there should not be any missing data between two fields.
|
|
* When the variables are named (either by a flexible dtype or with `names`),
|
|
there must not be any header in the file (else a ValueError
|
|
exception is raised).
|
|
* Individual values are not stripped of spaces by default.
|
|
When using a custom converter, make sure the function does remove spaces.
|
|
|
|
References
|
|
----------
|
|
.. [1] NumPy User Guide, section `I/O with NumPy
|
|
<https://docs.scipy.org/doc/numpy/user/basics.io.genfromtxt.html>`_.
|
|
|
|
Examples
|
|
--------
|
|
>>> from io import StringIO
|
|
>>> import numpy as np
|
|
|
|
Comma delimited file with mixed dtype
|
|
|
|
>>> s = StringIO(u"1,1.3,abcde")
|
|
>>> data = np.genfromtxt(s, dtype=[('myint','i8'),('myfloat','f8'),
|
|
... ('mystring','S5')], delimiter=",")
|
|
>>> data
|
|
array((1, 1.3, b'abcde'),
|
|
dtype=[('myint', '<i8'), ('myfloat', '<f8'), ('mystring', 'S5')])
|
|
|
|
Using dtype = None
|
|
|
|
>>> _ = s.seek(0) # needed for StringIO example only
|
|
>>> data = np.genfromtxt(s, dtype=None,
|
|
... names = ['myint','myfloat','mystring'], delimiter=",")
|
|
>>> data
|
|
array((1, 1.3, b'abcde'),
|
|
dtype=[('myint', '<i8'), ('myfloat', '<f8'), ('mystring', 'S5')])
|
|
|
|
Specifying dtype and names
|
|
|
|
>>> _ = s.seek(0)
|
|
>>> data = np.genfromtxt(s, dtype="i8,f8,S5",
|
|
... names=['myint','myfloat','mystring'], delimiter=",")
|
|
>>> data
|
|
array((1, 1.3, b'abcde'),
|
|
dtype=[('myint', '<i8'), ('myfloat', '<f8'), ('mystring', 'S5')])
|
|
|
|
An example with fixed-width columns
|
|
|
|
>>> s = StringIO(u"11.3abcde")
|
|
>>> data = np.genfromtxt(s, dtype=None, names=['intvar','fltvar','strvar'],
|
|
... delimiter=[1,3,5])
|
|
>>> data
|
|
array((1, 1.3, b'abcde'),
|
|
dtype=[('intvar', '<i8'), ('fltvar', '<f8'), ('strvar', 'S5')])
|
|
|
|
An example to show comments
|
|
|
|
>>> f = StringIO('''
|
|
... text,# of chars
|
|
... hello world,11
|
|
... numpy,5''')
|
|
>>> np.genfromtxt(f, dtype='S12,S12', delimiter=',')
|
|
array([(b'text', b''), (b'hello world', b'11'), (b'numpy', b'5')],
|
|
dtype=[('f0', 'S12'), ('f1', 'S12')])
|
|
|
|
"""
|
|
|
|
if like is not None:
|
|
return _genfromtxt_with_like(
|
|
like, fname, dtype=dtype, comments=comments, delimiter=delimiter,
|
|
skip_header=skip_header, skip_footer=skip_footer,
|
|
converters=converters, missing_values=missing_values,
|
|
filling_values=filling_values, usecols=usecols, names=names,
|
|
excludelist=excludelist, deletechars=deletechars,
|
|
replace_space=replace_space, autostrip=autostrip,
|
|
case_sensitive=case_sensitive, defaultfmt=defaultfmt,
|
|
unpack=unpack, usemask=usemask, loose=loose,
|
|
invalid_raise=invalid_raise, max_rows=max_rows, encoding=encoding,
|
|
ndmin=ndmin,
|
|
)
|
|
|
|
_ensure_ndmin_ndarray_check_param(ndmin)
|
|
|
|
if max_rows is not None:
|
|
if skip_footer:
|
|
raise ValueError(
|
|
"The keywords 'skip_footer' and 'max_rows' can not be "
|
|
"specified at the same time.")
|
|
if max_rows < 1:
|
|
raise ValueError("'max_rows' must be at least 1.")
|
|
|
|
if usemask:
|
|
from numpy.ma import MaskedArray, make_mask_descr
|
|
# Check the input dictionary of converters
|
|
user_converters = converters or {}
|
|
if not isinstance(user_converters, dict):
|
|
raise TypeError(
|
|
"The input argument 'converter' should be a valid dictionary "
|
|
"(got '%s' instead)" % type(user_converters))
|
|
|
|
if encoding == 'bytes':
|
|
encoding = None
|
|
byte_converters = True
|
|
else:
|
|
byte_converters = False
|
|
|
|
# Initialize the filehandle, the LineSplitter and the NameValidator
|
|
if isinstance(fname, os_PathLike):
|
|
fname = os_fspath(fname)
|
|
if isinstance(fname, str):
|
|
fid = np.lib._datasource.open(fname, 'rt', encoding=encoding)
|
|
fid_ctx = contextlib.closing(fid)
|
|
else:
|
|
fid = fname
|
|
fid_ctx = contextlib.nullcontext(fid)
|
|
try:
|
|
fhd = iter(fid)
|
|
except TypeError as e:
|
|
raise TypeError(
|
|
"fname must be a string, a filehandle, a sequence of strings,\n"
|
|
f"or an iterator of strings. Got {type(fname)} instead."
|
|
) from e
|
|
with fid_ctx:
|
|
split_line = LineSplitter(delimiter=delimiter, comments=comments,
|
|
autostrip=autostrip, encoding=encoding)
|
|
validate_names = NameValidator(excludelist=excludelist,
|
|
deletechars=deletechars,
|
|
case_sensitive=case_sensitive,
|
|
replace_space=replace_space)
|
|
|
|
# Skip the first `skip_header` rows
|
|
try:
|
|
for i in range(skip_header):
|
|
next(fhd)
|
|
|
|
# Keep on until we find the first valid values
|
|
first_values = None
|
|
|
|
while not first_values:
|
|
first_line = _decode_line(next(fhd), encoding)
|
|
if (names is True) and (comments is not None):
|
|
if comments in first_line:
|
|
first_line = (
|
|
''.join(first_line.split(comments)[1:]))
|
|
first_values = split_line(first_line)
|
|
except StopIteration:
|
|
# return an empty array if the datafile is empty
|
|
first_line = ''
|
|
first_values = []
|
|
warnings.warn('genfromtxt: Empty input file: "%s"' % fname, stacklevel=2)
|
|
|
|
# Should we take the first values as names ?
|
|
if names is True:
|
|
fval = first_values[0].strip()
|
|
if comments is not None:
|
|
if fval in comments:
|
|
del first_values[0]
|
|
|
|
# Check the columns to use: make sure `usecols` is a list
|
|
if usecols is not None:
|
|
try:
|
|
usecols = [_.strip() for _ in usecols.split(",")]
|
|
except AttributeError:
|
|
try:
|
|
usecols = list(usecols)
|
|
except TypeError:
|
|
usecols = [usecols, ]
|
|
nbcols = len(usecols or first_values)
|
|
|
|
# Check the names and overwrite the dtype.names if needed
|
|
if names is True:
|
|
names = validate_names([str(_.strip()) for _ in first_values])
|
|
first_line = ''
|
|
elif _is_string_like(names):
|
|
names = validate_names([_.strip() for _ in names.split(',')])
|
|
elif names:
|
|
names = validate_names(names)
|
|
# Get the dtype
|
|
if dtype is not None:
|
|
dtype = easy_dtype(dtype, defaultfmt=defaultfmt, names=names,
|
|
excludelist=excludelist,
|
|
deletechars=deletechars,
|
|
case_sensitive=case_sensitive,
|
|
replace_space=replace_space)
|
|
# Make sure the names is a list (for 2.5)
|
|
if names is not None:
|
|
names = list(names)
|
|
|
|
if usecols:
|
|
for (i, current) in enumerate(usecols):
|
|
# if usecols is a list of names, convert to a list of indices
|
|
if _is_string_like(current):
|
|
usecols[i] = names.index(current)
|
|
elif current < 0:
|
|
usecols[i] = current + len(first_values)
|
|
# If the dtype is not None, make sure we update it
|
|
if (dtype is not None) and (len(dtype) > nbcols):
|
|
descr = dtype.descr
|
|
dtype = np.dtype([descr[_] for _ in usecols])
|
|
names = list(dtype.names)
|
|
# If `names` is not None, update the names
|
|
elif (names is not None) and (len(names) > nbcols):
|
|
names = [names[_] for _ in usecols]
|
|
elif (names is not None) and (dtype is not None):
|
|
names = list(dtype.names)
|
|
|
|
# Process the missing values ...............................
|
|
# Rename missing_values for convenience
|
|
user_missing_values = missing_values or ()
|
|
if isinstance(user_missing_values, bytes):
|
|
user_missing_values = user_missing_values.decode('latin1')
|
|
|
|
# Define the list of missing_values (one column: one list)
|
|
missing_values = [list(['']) for _ in range(nbcols)]
|
|
|
|
# We have a dictionary: process it field by field
|
|
if isinstance(user_missing_values, dict):
|
|
# Loop on the items
|
|
for (key, val) in user_missing_values.items():
|
|
# Is the key a string ?
|
|
if _is_string_like(key):
|
|
try:
|
|
# Transform it into an integer
|
|
key = names.index(key)
|
|
except ValueError:
|
|
# We couldn't find it: the name must have been dropped
|
|
continue
|
|
# Redefine the key as needed if it's a column number
|
|
if usecols:
|
|
try:
|
|
key = usecols.index(key)
|
|
except ValueError:
|
|
pass
|
|
# Transform the value as a list of string
|
|
if isinstance(val, (list, tuple)):
|
|
val = [str(_) for _ in val]
|
|
else:
|
|
val = [str(val), ]
|
|
# Add the value(s) to the current list of missing
|
|
if key is None:
|
|
# None acts as default
|
|
for miss in missing_values:
|
|
miss.extend(val)
|
|
else:
|
|
missing_values[key].extend(val)
|
|
# We have a sequence : each item matches a column
|
|
elif isinstance(user_missing_values, (list, tuple)):
|
|
for (value, entry) in zip(user_missing_values, missing_values):
|
|
value = str(value)
|
|
if value not in entry:
|
|
entry.append(value)
|
|
# We have a string : apply it to all entries
|
|
elif isinstance(user_missing_values, str):
|
|
user_value = user_missing_values.split(",")
|
|
for entry in missing_values:
|
|
entry.extend(user_value)
|
|
# We have something else: apply it to all entries
|
|
else:
|
|
for entry in missing_values:
|
|
entry.extend([str(user_missing_values)])
|
|
|
|
# Process the filling_values ...............................
|
|
# Rename the input for convenience
|
|
user_filling_values = filling_values
|
|
if user_filling_values is None:
|
|
user_filling_values = []
|
|
# Define the default
|
|
filling_values = [None] * nbcols
|
|
# We have a dictionary : update each entry individually
|
|
if isinstance(user_filling_values, dict):
|
|
for (key, val) in user_filling_values.items():
|
|
if _is_string_like(key):
|
|
try:
|
|
# Transform it into an integer
|
|
key = names.index(key)
|
|
except ValueError:
|
|
# We couldn't find it: the name must have been dropped,
|
|
continue
|
|
# Redefine the key if it's a column number and usecols is defined
|
|
if usecols:
|
|
try:
|
|
key = usecols.index(key)
|
|
except ValueError:
|
|
pass
|
|
# Add the value to the list
|
|
filling_values[key] = val
|
|
# We have a sequence : update on a one-to-one basis
|
|
elif isinstance(user_filling_values, (list, tuple)):
|
|
n = len(user_filling_values)
|
|
if (n <= nbcols):
|
|
filling_values[:n] = user_filling_values
|
|
else:
|
|
filling_values = user_filling_values[:nbcols]
|
|
# We have something else : use it for all entries
|
|
else:
|
|
filling_values = [user_filling_values] * nbcols
|
|
|
|
# Initialize the converters ................................
|
|
if dtype is None:
|
|
# Note: we can't use a [...]*nbcols, as we would have 3 times the same
|
|
# ... converter, instead of 3 different converters.
|
|
converters = [StringConverter(None, missing_values=miss, default=fill)
|
|
for (miss, fill) in zip(missing_values, filling_values)]
|
|
else:
|
|
dtype_flat = flatten_dtype(dtype, flatten_base=True)
|
|
# Initialize the converters
|
|
if len(dtype_flat) > 1:
|
|
# Flexible type : get a converter from each dtype
|
|
zipit = zip(dtype_flat, missing_values, filling_values)
|
|
converters = [StringConverter(dt, locked=True,
|
|
missing_values=miss, default=fill)
|
|
for (dt, miss, fill) in zipit]
|
|
else:
|
|
# Set to a default converter (but w/ different missing values)
|
|
zipit = zip(missing_values, filling_values)
|
|
converters = [StringConverter(dtype, locked=True,
|
|
missing_values=miss, default=fill)
|
|
for (miss, fill) in zipit]
|
|
# Update the converters to use the user-defined ones
|
|
uc_update = []
|
|
for (j, conv) in user_converters.items():
|
|
# If the converter is specified by column names, use the index instead
|
|
if _is_string_like(j):
|
|
try:
|
|
j = names.index(j)
|
|
i = j
|
|
except ValueError:
|
|
continue
|
|
elif usecols:
|
|
try:
|
|
i = usecols.index(j)
|
|
except ValueError:
|
|
# Unused converter specified
|
|
continue
|
|
else:
|
|
i = j
|
|
# Find the value to test - first_line is not filtered by usecols:
|
|
if len(first_line):
|
|
testing_value = first_values[j]
|
|
else:
|
|
testing_value = None
|
|
if conv is bytes:
|
|
user_conv = asbytes
|
|
elif byte_converters:
|
|
# converters may use decode to workaround numpy's old behaviour,
|
|
# so encode the string again before passing to the user converter
|
|
def tobytes_first(x, conv):
|
|
if type(x) is bytes:
|
|
return conv(x)
|
|
return conv(x.encode("latin1"))
|
|
user_conv = functools.partial(tobytes_first, conv=conv)
|
|
else:
|
|
user_conv = conv
|
|
converters[i].update(user_conv, locked=True,
|
|
testing_value=testing_value,
|
|
default=filling_values[i],
|
|
missing_values=missing_values[i],)
|
|
uc_update.append((i, user_conv))
|
|
# Make sure we have the corrected keys in user_converters...
|
|
user_converters.update(uc_update)
|
|
|
|
# Fixme: possible error as following variable never used.
|
|
# miss_chars = [_.missing_values for _ in converters]
|
|
|
|
# Initialize the output lists ...
|
|
# ... rows
|
|
rows = []
|
|
append_to_rows = rows.append
|
|
# ... masks
|
|
if usemask:
|
|
masks = []
|
|
append_to_masks = masks.append
|
|
# ... invalid
|
|
invalid = []
|
|
append_to_invalid = invalid.append
|
|
|
|
# Parse each line
|
|
for (i, line) in enumerate(itertools.chain([first_line, ], fhd)):
|
|
values = split_line(line)
|
|
nbvalues = len(values)
|
|
# Skip an empty line
|
|
if nbvalues == 0:
|
|
continue
|
|
if usecols:
|
|
# Select only the columns we need
|
|
try:
|
|
values = [values[_] for _ in usecols]
|
|
except IndexError:
|
|
append_to_invalid((i + skip_header + 1, nbvalues))
|
|
continue
|
|
elif nbvalues != nbcols:
|
|
append_to_invalid((i + skip_header + 1, nbvalues))
|
|
continue
|
|
# Store the values
|
|
append_to_rows(tuple(values))
|
|
if usemask:
|
|
append_to_masks(tuple([v.strip() in m
|
|
for (v, m) in zip(values,
|
|
missing_values)]))
|
|
if len(rows) == max_rows:
|
|
break
|
|
|
|
# Upgrade the converters (if needed)
|
|
if dtype is None:
|
|
for (i, converter) in enumerate(converters):
|
|
current_column = [itemgetter(i)(_m) for _m in rows]
|
|
try:
|
|
converter.iterupgrade(current_column)
|
|
except ConverterLockError:
|
|
errmsg = "Converter #%i is locked and cannot be upgraded: " % i
|
|
current_column = map(itemgetter(i), rows)
|
|
for (j, value) in enumerate(current_column):
|
|
try:
|
|
converter.upgrade(value)
|
|
except (ConverterError, ValueError):
|
|
errmsg += "(occurred line #%i for value '%s')"
|
|
errmsg %= (j + 1 + skip_header, value)
|
|
raise ConverterError(errmsg)
|
|
|
|
# Check that we don't have invalid values
|
|
nbinvalid = len(invalid)
|
|
if nbinvalid > 0:
|
|
nbrows = len(rows) + nbinvalid - skip_footer
|
|
# Construct the error message
|
|
template = " Line #%%i (got %%i columns instead of %i)" % nbcols
|
|
if skip_footer > 0:
|
|
nbinvalid_skipped = len([_ for _ in invalid
|
|
if _[0] > nbrows + skip_header])
|
|
invalid = invalid[:nbinvalid - nbinvalid_skipped]
|
|
skip_footer -= nbinvalid_skipped
|
|
#
|
|
# nbrows -= skip_footer
|
|
# errmsg = [template % (i, nb)
|
|
# for (i, nb) in invalid if i < nbrows]
|
|
# else:
|
|
errmsg = [template % (i, nb)
|
|
for (i, nb) in invalid]
|
|
if len(errmsg):
|
|
errmsg.insert(0, "Some errors were detected !")
|
|
errmsg = "\n".join(errmsg)
|
|
# Raise an exception ?
|
|
if invalid_raise:
|
|
raise ValueError(errmsg)
|
|
# Issue a warning ?
|
|
else:
|
|
warnings.warn(errmsg, ConversionWarning, stacklevel=2)
|
|
|
|
# Strip the last skip_footer data
|
|
if skip_footer > 0:
|
|
rows = rows[:-skip_footer]
|
|
if usemask:
|
|
masks = masks[:-skip_footer]
|
|
|
|
# Convert each value according to the converter:
|
|
# We want to modify the list in place to avoid creating a new one...
|
|
if loose:
|
|
rows = list(
|
|
zip(*[[conv._loose_call(_r) for _r in map(itemgetter(i), rows)]
|
|
for (i, conv) in enumerate(converters)]))
|
|
else:
|
|
rows = list(
|
|
zip(*[[conv._strict_call(_r) for _r in map(itemgetter(i), rows)]
|
|
for (i, conv) in enumerate(converters)]))
|
|
|
|
# Reset the dtype
|
|
data = rows
|
|
if dtype is None:
|
|
# Get the dtypes from the types of the converters
|
|
column_types = [conv.type for conv in converters]
|
|
# Find the columns with strings...
|
|
strcolidx = [i for (i, v) in enumerate(column_types)
|
|
if v == np.str_]
|
|
|
|
if byte_converters and strcolidx:
|
|
# convert strings back to bytes for backward compatibility
|
|
warnings.warn(
|
|
"Reading unicode strings without specifying the encoding "
|
|
"argument is deprecated. Set the encoding, use None for the "
|
|
"system default.",
|
|
np.VisibleDeprecationWarning, stacklevel=2)
|
|
def encode_unicode_cols(row_tup):
|
|
row = list(row_tup)
|
|
for i in strcolidx:
|
|
row[i] = row[i].encode('latin1')
|
|
return tuple(row)
|
|
|
|
try:
|
|
data = [encode_unicode_cols(r) for r in data]
|
|
except UnicodeEncodeError:
|
|
pass
|
|
else:
|
|
for i in strcolidx:
|
|
column_types[i] = np.bytes_
|
|
|
|
# Update string types to be the right length
|
|
sized_column_types = column_types[:]
|
|
for i, col_type in enumerate(column_types):
|
|
if np.issubdtype(col_type, np.character):
|
|
n_chars = max(len(row[i]) for row in data)
|
|
sized_column_types[i] = (col_type, n_chars)
|
|
|
|
if names is None:
|
|
# If the dtype is uniform (before sizing strings)
|
|
base = {
|
|
c_type
|
|
for c, c_type in zip(converters, column_types)
|
|
if c._checked}
|
|
if len(base) == 1:
|
|
uniform_type, = base
|
|
(ddtype, mdtype) = (uniform_type, bool)
|
|
else:
|
|
ddtype = [(defaultfmt % i, dt)
|
|
for (i, dt) in enumerate(sized_column_types)]
|
|
if usemask:
|
|
mdtype = [(defaultfmt % i, bool)
|
|
for (i, dt) in enumerate(sized_column_types)]
|
|
else:
|
|
ddtype = list(zip(names, sized_column_types))
|
|
mdtype = list(zip(names, [bool] * len(sized_column_types)))
|
|
output = np.array(data, dtype=ddtype)
|
|
if usemask:
|
|
outputmask = np.array(masks, dtype=mdtype)
|
|
else:
|
|
# Overwrite the initial dtype names if needed
|
|
if names and dtype.names is not None:
|
|
dtype.names = names
|
|
# Case 1. We have a structured type
|
|
if len(dtype_flat) > 1:
|
|
# Nested dtype, eg [('a', int), ('b', [('b0', int), ('b1', 'f4')])]
|
|
# First, create the array using a flattened dtype:
|
|
# [('a', int), ('b1', int), ('b2', float)]
|
|
# Then, view the array using the specified dtype.
|
|
if 'O' in (_.char for _ in dtype_flat):
|
|
if has_nested_fields(dtype):
|
|
raise NotImplementedError(
|
|
"Nested fields involving objects are not supported...")
|
|
else:
|
|
output = np.array(data, dtype=dtype)
|
|
else:
|
|
rows = np.array(data, dtype=[('', _) for _ in dtype_flat])
|
|
output = rows.view(dtype)
|
|
# Now, process the rowmasks the same way
|
|
if usemask:
|
|
rowmasks = np.array(
|
|
masks, dtype=np.dtype([('', bool) for t in dtype_flat]))
|
|
# Construct the new dtype
|
|
mdtype = make_mask_descr(dtype)
|
|
outputmask = rowmasks.view(mdtype)
|
|
# Case #2. We have a basic dtype
|
|
else:
|
|
# We used some user-defined converters
|
|
if user_converters:
|
|
ishomogeneous = True
|
|
descr = []
|
|
for i, ttype in enumerate([conv.type for conv in converters]):
|
|
# Keep the dtype of the current converter
|
|
if i in user_converters:
|
|
ishomogeneous &= (ttype == dtype.type)
|
|
if np.issubdtype(ttype, np.character):
|
|
ttype = (ttype, max(len(row[i]) for row in data))
|
|
descr.append(('', ttype))
|
|
else:
|
|
descr.append(('', dtype))
|
|
# So we changed the dtype ?
|
|
if not ishomogeneous:
|
|
# We have more than one field
|
|
if len(descr) > 1:
|
|
dtype = np.dtype(descr)
|
|
# We have only one field: drop the name if not needed.
|
|
else:
|
|
dtype = np.dtype(ttype)
|
|
#
|
|
output = np.array(data, dtype)
|
|
if usemask:
|
|
if dtype.names is not None:
|
|
mdtype = [(_, bool) for _ in dtype.names]
|
|
else:
|
|
mdtype = bool
|
|
outputmask = np.array(masks, dtype=mdtype)
|
|
# Try to take care of the missing data we missed
|
|
names = output.dtype.names
|
|
if usemask and names:
|
|
for (name, conv) in zip(names, converters):
|
|
missing_values = [conv(_) for _ in conv.missing_values
|
|
if _ != '']
|
|
for mval in missing_values:
|
|
outputmask[name] |= (output[name] == mval)
|
|
# Construct the final array
|
|
if usemask:
|
|
output = output.view(MaskedArray)
|
|
output._mask = outputmask
|
|
|
|
output = _ensure_ndmin_ndarray(output, ndmin=ndmin)
|
|
|
|
if unpack:
|
|
if names is None:
|
|
return output.T
|
|
elif len(names) == 1:
|
|
# squeeze single-name dtypes too
|
|
return output[names[0]]
|
|
else:
|
|
# For structured arrays with multiple fields,
|
|
# return an array for each field.
|
|
return [output[field] for field in names]
|
|
return output
|
|
|
|
|
|
_genfromtxt_with_like = array_function_dispatch()(genfromtxt)
|
|
|
|
|
|
def recfromtxt(fname, **kwargs):
|
|
"""
|
|
Load ASCII data from a file and return it in a record array.
|
|
|
|
If ``usemask=False`` a standard `recarray` is returned,
|
|
if ``usemask=True`` a MaskedRecords array is returned.
|
|
|
|
Parameters
|
|
----------
|
|
fname, kwargs : For a description of input parameters, see `genfromtxt`.
|
|
|
|
See Also
|
|
--------
|
|
numpy.genfromtxt : generic function
|
|
|
|
Notes
|
|
-----
|
|
By default, `dtype` is None, which means that the data-type of the output
|
|
array will be determined from the data.
|
|
|
|
"""
|
|
kwargs.setdefault("dtype", None)
|
|
usemask = kwargs.get('usemask', False)
|
|
output = genfromtxt(fname, **kwargs)
|
|
if usemask:
|
|
from numpy.ma.mrecords import MaskedRecords
|
|
output = output.view(MaskedRecords)
|
|
else:
|
|
output = output.view(np.recarray)
|
|
return output
|
|
|
|
|
|
def recfromcsv(fname, **kwargs):
|
|
"""
|
|
Load ASCII data stored in a comma-separated file.
|
|
|
|
The returned array is a record array (if ``usemask=False``, see
|
|
`recarray`) or a masked record array (if ``usemask=True``,
|
|
see `ma.mrecords.MaskedRecords`).
|
|
|
|
Parameters
|
|
----------
|
|
fname, kwargs : For a description of input parameters, see `genfromtxt`.
|
|
|
|
See Also
|
|
--------
|
|
numpy.genfromtxt : generic function to load ASCII data.
|
|
|
|
Notes
|
|
-----
|
|
By default, `dtype` is None, which means that the data-type of the output
|
|
array will be determined from the data.
|
|
|
|
"""
|
|
# Set default kwargs for genfromtxt as relevant to csv import.
|
|
kwargs.setdefault("case_sensitive", "lower")
|
|
kwargs.setdefault("names", True)
|
|
kwargs.setdefault("delimiter", ",")
|
|
kwargs.setdefault("dtype", None)
|
|
output = genfromtxt(fname, **kwargs)
|
|
|
|
usemask = kwargs.get("usemask", False)
|
|
if usemask:
|
|
from numpy.ma.mrecords import MaskedRecords
|
|
output = output.view(MaskedRecords)
|
|
else:
|
|
output = output.view(np.recarray)
|
|
return output
|