h5config/storage/hdf5.py

   1 # Copyright (C) 2011 W. Trevor King <wking@drexel.edu>
   2 #
   3 # This file is part of h5config.
   4 #
   5 # h5config is free software; you can redistribute it and/or modify it
   6 # under the terms of the GNU General Public License as published by the
   7 # Free Software Foundation, either version 3 of the License, or (at your
   8 # option) any later version.
   9 #
  10 # h5config is distributed in the hope that it will be useful, but
  11 # WITHOUT ANY WARRANTY; without even the implied warranty of
  12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  13 # General Public License for more details.
  14 #
  15 # You should have received a copy of the GNU General Public License
  16 # along with h5config.  If not, see <http://www.gnu.org/licenses/>.
  17
  18 """HDF5 backend implementation
  19 """
  20
  21 import os.path as _os_path
  22 import types as _types
  23
  24 import h5py as _h5py
  25 import numpy as _numpy
  26
  27 from .. import LOG as _LOG
  28 from .. import config as _config
  29 from . import FileStorage as _FileStorage
  30
  31
  32 def pprint_HDF5(*args, **kwargs):
  33     print(pformat_HDF5(*args, **kwargs))
  34
  35 def pformat_HDF5(filename, group='/'):
  36     try:
  37         with _h5py.File(filename, 'r') as f:
  38             cwg = f[group]
  39             ret = '\n'.join(_pformat_hdf5(cwg))
  40     except IOError as e:
  41         if 'unable to open' in e.message:
  42             if _os_path.getsize(filename) == 0:
  43                 return 'EMPTY'
  44             return None
  45         raise
  46     return ret
  47
  48 def _pformat_hdf5(cwg, depth=0):
  49     lines = []
  50     lines.append('  '*depth + cwg.name)
  51     depth += 1
  52     for key,value in cwg.iteritems():
  53         if isinstance(value, _h5py.Group):
  54             lines.extend(_pformat_hdf5(value, depth))
  55         elif isinstance(value, _h5py.Dataset):
  56             lines.append('  '*depth + str(value))
  57             lines.append('  '*(depth+1) + str(value[...]))
  58         else:
  59             lines.append('  '*depth + str(value))
  60     return lines
  61
  62 def h5_create_group(cwg, path, force=False):
  63     "Create the group where the settings are stored (if necessary)."
  64     if path == '/':
  65         return cwg
  66     gpath = ['']
  67     for group in path.strip('/').split('/'):
  68         gpath.append(group)
  69         if group not in cwg.keys():
  70             _LOG.debug('creating group {} in {}'.format(
  71                     '/'.join(gpath), cwg.file))
  72             cwg.create_group(group)
  73         _cwg = cwg[group]
  74         if isinstance(_cwg, _h5py.Dataset):
  75             if force:
  76                 _LOG.info('overwrite {} in {} ({}) with a group'.format(
  77                         '/'.join(gpath), _cwg.file, _cwg))
  78                 del cwg[group]
  79                 _cwg = cwg.create_group(group)
  80             else:
  81                 raise ValueError(_cwg)
  82         cwg = _cwg
  83     return cwg
  84
  85
  86 class HDF5_Storage (_FileStorage):
  87     """Back a `Config` class with an HDF5 file.
  88
  89     The `.save` and `.load` methods have an optional `group` argument
  90     that allows you to save and load settings from an externally
  91     opened HDF5 file.  This can make it easier to stash several
  92     related `Config` classes in a single file.  For example
  93
  94     >>> import os
  95     >>> import tempfile
  96     >>> from ..test import TestConfig
  97     >>> fd,filename = tempfile.mkstemp(
  98     ...     suffix='.'+HDF5_Storage.extension, prefix='pypiezo-')
  99     >>> os.close(fd)
 100
 101     >>> f = _h5py.File(filename, 'a')
 102     >>> c = TestConfig(storage=HDF5_Storage(
 103     ...     filename='untouched_file.h5', group='/untouched/group'))
 104     >>> c['alive'] = True
 105     >>> group = f.create_group('base')
 106     >>> c.save(group=group)
 107     >>> pprint_HDF5(filename)  # doctest: +REPORT_UDIFF, +ELLIPSIS
 108     /
 109       /base
 110         <HDF5 dataset "age": shape (), type "<f8">
 111           1.3
 112         <HDF5 dataset "alive": shape (), type "|b1">
 113           True
 114         <HDF5 dataset "bids": shape (3,), type "<f8">
 115           [ 5.4  3.2  1. ]
 116         <HDF5 dataset "children": shape (), type "|S1">
 117     <BLANKLINE>
 118         <HDF5 dataset "claws": shape (2,), type "<i8">
 119           [1 2]
 120         <HDF5 dataset "daisies": shape (), type "<i...">
 121           13
 122         <HDF5 dataset "name": shape (), type "|S1">
 123     <BLANKLINE>
 124         <HDF5 dataset "species": shape (), type "|S14">
 125           Norwegian Blue
 126         <HDF5 dataset "spouse": shape (), type "|S1">
 127     <BLANKLINE>
 128         <HDF5 dataset "words": shape (2,), type "|S7">
 129           ['cracker' 'wants']
 130     >>> c.clear()
 131     >>> c['alive']
 132     False
 133     >>> c.load(group=group)
 134     >>> c['alive']
 135     True
 136
 137     >>> f.close()
 138     >>> os.remove(filename)
 139     """
 140     extension = 'h5'
 141
 142     def __init__(self, group='/', **kwargs):
 143         super(HDF5_Storage, self).__init__(**kwargs)
 144         if isinstance(group, _h5py.Group):
 145             self._file_checked = True
 146         else:
 147             assert group.startswith('/'), group
 148             if not group.endswith('/'):
 149                 group += '/'
 150             self._file_checked = False
 151         self.group = group
 152
 153     def _check_file(self):
 154         if self._file_checked:
 155             return
 156         self._setup_file()
 157         self._file_checked = True
 158
 159     def _setup_file(self):
 160         self._create_basedir(filename=self._filename)
 161         with _h5py.File(self._filename, 'a') as f:
 162             cwg = f  # current working group
 163             h5_create_group(cwg, self.group)
 164
 165     def _load(self, config, group=None):
 166         f = None
 167         try:
 168             if group is None:
 169                 if isinstance(self.group, _h5py.Group):
 170                     group = self.group
 171                 else:
 172                     self._check_file()
 173                     f = _h5py.File(self._filename, 'r')
 174                     group = f[self.group]
 175             for s in config.settings:
 176                 if s.name not in group.keys():
 177                     continue
 178                 if isinstance(s, _config.ConfigListSetting):
 179                     try:
 180                         cwg = h5_create_group(group, s.name)
 181                     except ValueError:
 182                         pass
 183                     else:
 184                         value = []
 185                         for i in sorted(int(x) for x in cwg.keys()):
 186                             instance = s.config_class()
 187                             try:
 188                                 _cwg = h5_create_group(cwg, str(i))
 189                             except ValueError:
 190                                 pass
 191                             else:
 192                                 self._load(config=instance, group=_cwg)
 193                                 value.append(instance)
 194                         config[s.name] = value
 195                 elif isinstance(s, _config.ConfigSetting):
 196                     try:
 197                         cwg = h5_create_group(group, s.name)
 198                     except ValueError:
 199                         pass
 200                     else:
 201                         if not config[s.name]:
 202                             config[s.name] = s.config_class()
 203                         self._load(config=config[s.name], group=cwg)
 204                 else:
 205                     try:
 206                         v = group[s.name][...]
 207                     except Exception as e:
 208                         _LOG.error('Could not access {}/{}: {}'.format(
 209                                 group.name, s.name, e))
 210                         raise
 211                     if isinstance(v, _numpy.ndarray):
 212                         if isinstance(s, _config.BooleanSetting):
 213                             v = bool(v)  # array(True, dtype=bool) -> True
 214                         elif v.dtype.type == _numpy.string_:
 215                             if isinstance(s, _config.ListSetting):
 216                                 try:
 217                                     v = list(v)
 218                                 except TypeError:
 219                                     v = []
 220                             else:
 221                                 v = str(v) # array('abc', dtype='|S3') -> 'abc'
 222                         elif isinstance(s, _config.IntegerSetting):
 223                             v = int(v)  # array(3, dtpe='int32') -> 3
 224                         elif isinstance(s, _config.FloatSetting):
 225                             v = float(v)  # array(1.2, dtype='float64') -> 1.2
 226                         elif isinstance(s, _config.NumericSetting):
 227                             raise NotImplementedError(type(s))
 228                         elif isinstance(s, _config.ListSetting):
 229                             v = list(v)  # convert from numpy array
 230                     if isinstance(v, _types.StringTypes):
 231                         # convert back from None, etc.
 232                         v = s.convert_from_text(v)
 233                     config[s.name] = v
 234         finally:
 235             if f:
 236                 f.close()
 237
 238     def _save(self, config, group=None):
 239         f = None
 240         try:
 241             if group is None:
 242                 if isinstance(self.group, _h5py.Group):
 243                     group = self.group
 244                 else:
 245                     self._check_file()
 246                     f = _h5py.File(self._filename, 'a')
 247                     group = f[self.group]
 248             for s in config.settings:
 249                 value = None
 250                 if isinstance(s, (_config.BooleanSetting,
 251                                   _config.NumericSetting,
 252                                   _config.ListSetting)):
 253                     value = config[s.name]
 254                     if value in [None, []]:
 255                         value = s.convert_to_text(value)
 256                 elif isinstance(s, _config.ConfigListSetting):
 257                     configs = config[s.name]
 258                     if configs:
 259                         cwg = h5_create_group(group, s.name, force=True)
 260                         for i,cfg in enumerate(configs):
 261                             _cwg = h5_create_group(cwg, str(i), force=True)
 262                             self._save(config=cfg, group=_cwg)
 263                         continue
 264                 elif isinstance(s, _config.ConfigSetting):
 265                     cfg = config[s.name]
 266                     if cfg:
 267                         cwg = h5_create_group(group, s.name, force=True)
 268                         self._save(config=cfg, group=cwg)
 269                         continue
 270                 if value is None:  # not set yet, or invalid
 271                     value = s.convert_to_text(config[s.name])
 272                 try:
 273                     del group[s.name]
 274                 except KeyError:
 275                     pass
 276                 group[s.name] = value
 277         finally:
 278             if f:
 279                 f.close()