parent
c94fb86e2d
commit
cc6477015a
2 changed files with 1 additions and 211 deletions
@ -1,210 +0,0 @@ |
||||
import os |
||||
import numpy as np |
||||
import collections |
||||
from contextlib import closing |
||||
|
||||
from common.file_helpers import mkdirs_exists_ok |
||||
|
||||
class ColumnStoreReader(): |
||||
def __init__(self, path, mmap=False, allow_pickle=False, direct_io=False, prefix="", np_data=None): |
||||
if not (path and os.path.isdir(path)): |
||||
raise ValueError("Not a column store: {}".format(path)) |
||||
|
||||
self._path = os.path.realpath(path) |
||||
self._keys = os.listdir(self._path) |
||||
self._mmap = mmap |
||||
self._allow_pickle = allow_pickle |
||||
self._direct_io = direct_io |
||||
self._is_dict = 'columnstore' in self._keys |
||||
self._prefix = prefix |
||||
self._np_data = np_data |
||||
|
||||
@property |
||||
def path(self): |
||||
return self._path |
||||
|
||||
def close(self): |
||||
pass |
||||
|
||||
def get(self, key): |
||||
try: |
||||
return self[key] |
||||
except KeyError: |
||||
return None |
||||
|
||||
def keys(self): |
||||
if self._is_dict: |
||||
if not self._np_data: |
||||
self._np_data = self._load(os.path.join(self._path, 'columnstore')) |
||||
# return top level keys by matching on prefix and splitting on '/' |
||||
return { |
||||
k[len(self._prefix):].split('/')[0] |
||||
for k in self._np_data.keys() |
||||
if k.startswith(self._prefix) |
||||
} |
||||
|
||||
return list(self._keys) |
||||
|
||||
def iteritems(self): |
||||
for k in self: |
||||
yield (k, self[k]) |
||||
|
||||
def itervalues(self): |
||||
for k in self: |
||||
yield self[k] |
||||
|
||||
def get_npy_path(self, key): |
||||
"""Gets a filesystem path for an npy file containing the specified array, |
||||
or none if the column store does not contain key. |
||||
""" |
||||
if key in self: |
||||
return os.path.join(self._path, key) |
||||
else: |
||||
return None |
||||
|
||||
def _load(self, path): |
||||
if self._mmap: |
||||
# note that direct i/o does nothing for mmap since file read/write interface is not used |
||||
return np.load(path, mmap_mode='r', allow_pickle=self._allow_pickle, fix_imports=False) |
||||
|
||||
if self._direct_io: |
||||
opener = lambda path, flags: os.open(path, os.O_RDONLY | os.O_DIRECT) |
||||
with open(path, 'rb', buffering=0, opener=opener) as f: |
||||
return np.load(f, allow_pickle=self._allow_pickle, fix_imports=False) |
||||
|
||||
return np.load(path, allow_pickle=self._allow_pickle, fix_imports=False) |
||||
|
||||
def __getitem__(self, key): |
||||
try: |
||||
if self._is_dict: |
||||
path = os.path.join(self._path, 'columnstore') |
||||
else: |
||||
path = os.path.join(self._path, key) |
||||
|
||||
# TODO(mgraczyk): This implementation will need to change for zip. |
||||
if not self._is_dict and os.path.isdir(path): |
||||
return ColumnStoreReader(path) |
||||
else: |
||||
if self._is_dict and self._np_data: |
||||
ret = self._np_data |
||||
else: |
||||
ret = self._load(path) |
||||
|
||||
if type(ret) == np.lib.npyio.NpzFile: |
||||
if self._is_dict: |
||||
if self._prefix+key in ret.keys(): |
||||
return ret[self._prefix+key] |
||||
if any(k.startswith(self._prefix+key+"/") for k in ret.keys()): |
||||
return ColumnStoreReader(self._path, mmap=self._mmap, allow_pickle=self._allow_pickle, direct_io=self._direct_io, prefix=self._prefix+key+"/", np_data=ret) |
||||
raise KeyError(self._prefix+key) |
||||
|
||||
# if it's saved as compressed, it has arr_0 only in the file. deref this |
||||
return ret['arr_0'] |
||||
else: |
||||
return ret |
||||
except IOError: |
||||
raise KeyError(key) |
||||
|
||||
def __contains__(self, item): |
||||
try: |
||||
self[item] |
||||
return True |
||||
except KeyError: |
||||
return False |
||||
|
||||
def __len__(self): |
||||
return len(self._keys) |
||||
|
||||
def __bool__(self): |
||||
return bool(self._keys) |
||||
|
||||
def __iter__(self): |
||||
return iter(self._keys) |
||||
|
||||
def __str__(self): |
||||
return "ColumnStoreReader({})".format(str({k: "..." for k in self._keys})) |
||||
|
||||
def __enter__(self): return self |
||||
def __exit__(self, type, value, traceback): self.close() |
||||
|
||||
class ColumnStoreWriter(): |
||||
def __init__(self, path, allow_pickle=False): |
||||
self._path = path |
||||
self._allow_pickle = allow_pickle |
||||
mkdirs_exists_ok(self._path) |
||||
|
||||
def map_column(self, path, dtype, shape): |
||||
npy_path = os.path.join(self._path, path) |
||||
mkdirs_exists_ok(os.path.dirname(npy_path)) |
||||
return np.lib.format.open_memmap(npy_path, mode='w+', dtype=dtype, shape=shape) |
||||
|
||||
def add_column(self, path, data, dtype=None, compression=False, overwrite=False): |
||||
npy_path = os.path.join(self._path, path) |
||||
mkdirs_exists_ok(os.path.dirname(npy_path)) |
||||
|
||||
if overwrite: |
||||
f = open(npy_path, "wb") |
||||
else: |
||||
f = os.fdopen(os.open(npy_path, os.O_WRONLY | os.O_CREAT | os.O_EXCL), "wb") |
||||
|
||||
with closing(f) as f: |
||||
data2 = np.array(data, copy=False, dtype=dtype) |
||||
if compression: |
||||
np.savez_compressed(f, data2) |
||||
else: |
||||
np.save(f, data2, allow_pickle=self._allow_pickle, fix_imports=False) |
||||
|
||||
def add_group(self, group_name): |
||||
# TODO(mgraczyk): This implementation will need to change if we add zip or compression. |
||||
return ColumnStoreWriter(os.path.join(self._path, group_name)) |
||||
|
||||
def add_dict(self, data, dtypes=None, compression=False, overwrite=False): |
||||
# default name exists to have backward compatibility with equivalent directory structure |
||||
npy_path = os.path.join(self._path, "columnstore") |
||||
mkdirs_exists_ok(os.path.dirname(npy_path)) |
||||
|
||||
flat_dict = dict() |
||||
_flatten_dict(flat_dict, "", data) |
||||
for k, v in flat_dict.items(): |
||||
dtype = dtypes[k] if dtypes is not None and k in dtypes else None |
||||
flat_dict[k] = np.array(v, copy=False, dtype=dtype) |
||||
|
||||
if overwrite: |
||||
f = open(npy_path, "wb") |
||||
else: |
||||
f = os.fdopen(os.open(npy_path, os.O_WRONLY | os.O_CREAT | os.O_EXCL), "wb") |
||||
|
||||
with closing(f) as f: |
||||
if compression: |
||||
np.savez_compressed(f, **flat_dict) |
||||
else: |
||||
np.savez(f, **flat_dict) |
||||
|
||||
def close(self): |
||||
pass |
||||
|
||||
def __enter__(self): return self |
||||
def __exit__(self, type, value, traceback): self.close() |
||||
|
||||
|
||||
def _flatten_dict(flat, ns, d): |
||||
for k, v in d.items(): |
||||
p = (ns + "/" if len(ns) else "") + k |
||||
if isinstance(v, collections.Mapping): |
||||
_flatten_dict(flat, p, v) |
||||
else: |
||||
flat[p] = v |
||||
|
||||
|
||||
def _save_dict_as_column_store(values, writer, compression): |
||||
for k, v in values.items(): |
||||
if isinstance(v, collections.Mapping): |
||||
_save_dict_as_column_store(v, writer.add_group(k), compression) |
||||
else: |
||||
writer.add_column(k, v, compression=compression) |
||||
|
||||
|
||||
def save_dict_as_column_store(values, output_path, compression=False): |
||||
with ColumnStoreWriter(output_path) as writer: |
||||
_save_dict_as_column_store(values, writer, compression) |
||||
|
Loading…
Reference in new issue