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First implemenation of a json I/O
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Simon Kuberski
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443e4eb74e
commit
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2 changed files with 301 additions and 0 deletions
265
pyerrors/input/json.py
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265
pyerrors/input/json.py
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import json
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import gzip
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from ..obs import Obs
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import getpass
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import socket
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import datetime
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from .. import version as pyerrorsversion
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import platform
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import numpy as np
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def dump_to_json(ol, fname, description='', indent=4):
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"""Export a list of Obs or structures containing Obs to a .json.gz file
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Parameters
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-----------------
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ol : list
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List of objects that will be exported. At the moments, these objects can be
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either of: Obs, list, np.ndarray
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All Obs inside a structure have to be defined on the same set of configurations.
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fname : str
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Filename of the output file
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description : str
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Optional string that describes the contents of the json file
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indent : int
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Specify the indentation level of the json file. None or 0 is permissible and
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saves disk space.
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"""
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def _default(self, obj):
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return str(obj)
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my_encoder = json.JSONEncoder
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_default.default = json.JSONEncoder().default
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my_encoder.default = _default
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class deltalist:
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def __init__(self, li):
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self.cnfg = li[0]
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self.deltas = li[1:]
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def __repr__(self):
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s = '[%d' % (self.cnfg)
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for d in self.deltas:
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s += ', %1.15e' % (d)
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s += ']'
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return s
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def __str__(self):
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return self.__repr__()
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def _gen_data_d_from_list(ol):
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dl = []
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for name in ol[0].e_names:
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ed = {}
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ed['id'] = name
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ed['replica'] = []
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for r_name in ol[0].e_content[name]:
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rd = {}
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rd['name'] = r_name
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if ol[0].is_merged.get(r_name, False):
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rd['is_merged'] = True
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rd['deltas'] = []
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for i in range(len(ol[0].idl[r_name])):
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rd['deltas'].append([ol[0].idl[r_name][i]])
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for o in ol:
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rd['deltas'][-1].append(o.deltas[r_name][i])
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rd['deltas'][-1] = deltalist(rd['deltas'][-1])
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ed['replica'].append(rd)
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dl.append(ed)
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return dl
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def _assert_equal_properties(ol, otype=Obs):
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for o in ol:
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if not isinstance(o, otype):
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raise Exception('Wrong data type in list!')
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for o in ol[1:]:
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if not ol[0].is_merged == o.is_merged:
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raise Exception('All Obs in list have to be defined on the same set of configs!')
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if not ol[0].reweighted == o.reweighted:
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raise Exception('All Obs in list have to have the same property .reweighted!')
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if not ol[0].e_content == o.e_content:
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raise Exception('All Obs in list have to be defined on the same set of configs!')
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# more stringend tests --> compare idl?
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def write_Obs_to_dict(o):
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d = {}
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d['type'] = 'Obs'
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d['layout'] = '1'
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d['tag'] = o.tag
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if o.reweighted:
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d['reweighted'] = o.reweighted
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d['value'] = [o.value]
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d['data'] = _gen_data_d_from_list([o])
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return d
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def write_List_to_dict(ol):
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_assert_equal_properties(ol)
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d = {}
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d['type'] = 'List'
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d['layout'] = '%d' % len(ol)
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if len(set([o.tag for o in ol])) > 1:
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d['tag'] = ''
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for o in ol:
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d['tag'] += '%s\n' % (o.tag)
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else:
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d['tag'] = ol[0].tag
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if ol[0].reweighted:
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d['reweighted'] = ol[0].reweighted
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d['value'] = [o.value for o in ol]
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d['data'] = _gen_data_d_from_list(ol)
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return d
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def write_Array_to_dict(oa):
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ol = np.ravel(oa)
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_assert_equal_properties(ol)
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d = {}
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d['type'] = 'Array'
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d['layout'] = str(oa.shape).lstrip('(').rstrip(')')
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if len(set([o.tag for o in ol])) > 1:
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d['tag'] = ''
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for o in ol:
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d['tag'] += '%s\n' % (o.tag)
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else:
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d['tag'] = ol[0].tag
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if ol[0].reweighted:
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d['reweighted'] = ol[0].reweighted
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d['value'] = [o.value for o in ol]
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d['data'] = _gen_data_d_from_list(ol)
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return d
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if not isinstance(ol, list):
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ol = [ol]
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d = {}
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d['program'] = 'pyerrors %s' % (pyerrorsversion.__version__)
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d['version'] = '0.1'
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d['who'] = getpass.getuser()
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d['date'] = str(datetime.datetime.now())[:-7]
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d['host'] = socket.gethostname() + ', ' + platform.platform()
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if description:
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d['description'] = description
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d['obsdata'] = []
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for io in ol:
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if isinstance(io, Obs):
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d['obsdata'].append(write_Obs_to_dict(io))
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elif isinstance(io, list):
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d['obsdata'].append(write_List_to_dict(io))
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elif isinstance(io, np.ndarray):
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d['obsdata'].append(write_Array_to_dict(io))
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if not fname.endswith('.json') and not fname.endswith('.gz'):
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fname += '.json'
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if not fname.endswith('.gz'):
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fname += '.gz'
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jsonstring = json.dumps(d, indent=indent, cls=my_encoder)
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# workaround for un-indentation of delta lists
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jsonstring = jsonstring.replace('"[', '[').replace(']"', ']')
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fp = gzip.open(fname, 'wb')
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fp.write(jsonstring.encode('utf-8'))
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fp.close()
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# this would be nicer, since it does not need a string
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# with gzip.open(fname, 'wt', encoding='UTF-8') as zipfile:
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# json.dump(d, zipfile, indent=indent)
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def load_json(fname, verbose=True):
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"""Import a list of Obs or structures containing Obs to a .json.gz file.
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The following structures are supported: Obs, list, np.ndarray
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Parameters
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-----------------
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fname : str
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Filename of the input file
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verbose : bool
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Print additional information that was written to the file.
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"""
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def _gen_obsd_from_datad(d):
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retd = {}
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retd['names'] = []
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retd['idl'] = []
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retd['deltas'] = []
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retd['is_merged'] = {}
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for ens in d:
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for rep in ens['replica']:
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retd['names'].append(rep['name'])
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retd['idl'].append([di[0] for di in rep['deltas']])
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retd['deltas'].append([di[1:] for di in rep['deltas']])
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retd['is_merged'][rep['name']] = rep.get('is_merged', False)
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retd['deltas'] = np.array(retd['deltas'])
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return retd
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def get_Obs_from_dict(o):
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layouts = o.get('layout', '1').strip()
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if layouts != '1':
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raise Exception("layout is %s has to be 1 for type Obs." % (layouts), RuntimeWarning)
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values = o['value']
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od = _gen_obsd_from_datad(o['data'])
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ret = Obs([[ddi[0] + values[0] for ddi in di] for di in od['deltas']], od['names'], idl=od['idl'])
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ret.reweighted = o.get('reweighted', False)
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ret.is_merged = od['is_merged']
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ret.tag = o.get('tag', '')
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return ret
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def get_List_from_dict(o):
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layouts = o.get('layout', '1').strip()
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layout = int(layouts)
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values = o['value']
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od = _gen_obsd_from_datad(o['data'])
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ret = []
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for i in range(layout):
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ret.append(Obs([list(di[:, i] + values[i]) for di in od['deltas']], od['names'], idl=od['idl']))
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ret[-1].reweighted = o.get('reweighted', False)
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ret[-1].is_merged = od['is_merged']
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ret[-1].tag = o.get('tag', '')
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return ret
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def get_Array_from_dict(o):
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layouts = o.get('layout', '1').strip()
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layout = [int(ls.strip()) for ls in layouts.split(',')]
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values = o['value']
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od = _gen_obsd_from_datad(o['data'])
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ret = []
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for i in range(np.prod(layout)):
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ret.append(Obs([di[:, i] + values[i] for di in od['deltas']], od['names'], idl=od['idl']))
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ret[-1].reweighted = o.get('reweighted', False)
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ret[-1].is_merged = od['is_merged']
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ret[-1].tag = o.get('tag', '')
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return np.reshape(ret, layout)
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if not fname.endswith('.json') and not fname.endswith('.gz'):
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fname += '.json'
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if not fname.endswith('.gz'):
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fname += '.gz'
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with gzip.open(fname, 'r') as fin:
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d = json.loads(fin.read().decode('utf-8'))
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prog = d.get('program', '')
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version = d.get('version', '')
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who = d.get('who', '')
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date = d.get('date', '')
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host = d.get('host', '')
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if prog and verbose:
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print('Data has been written using %s.' % (prog))
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if version and verbose:
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print('Format version %s' % (version))
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if np.any([who, date, host] and verbose):
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print('Written by %s on %s on host %s' % (who, date, host))
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description = d.get('description', '')
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if description and verbose:
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print()
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print(description)
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obsdata = d['obsdata']
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ol = []
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for io in obsdata:
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if io['type'] == 'Obs':
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ol.append(get_Obs_from_dict(io))
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elif io['type'] == 'List':
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ol.append(get_List_from_dict(io))
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elif io['type'] == 'Array':
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ol.append(get_Array_from_dict(io))
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return ol
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36
tests/io_test.py
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36
tests/io_test.py
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@ -0,0 +1,36 @@
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import pyerrors.obs as pe
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import pyerrors.input.json as jsonio
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import numpy as np
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import os
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def test_jsonio():
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o = pe.pseudo_Obs(1.0, .2, 'one')
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o2 = pe.pseudo_Obs(0.5, .1, 'two|r1')
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o3 = pe.pseudo_Obs(0.5, .1, 'two|r2')
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o4 = pe.merge_obs([o2, o3])
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do = o - .2 * o4
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o5 = pe.pseudo_Obs(0.8, .1, 'two|r2')
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testl = [o3, o5]
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mat = np.array([[pe.pseudo_Obs(1.0, .1, 'mat'), pe.pseudo_Obs(0.3, .1, 'mat')], [pe.pseudo_Obs(0.2, .1, 'mat'), pe.pseudo_Obs(2.0, .4, 'mat')]])
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ol = [do, testl, mat]
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fname = 'test_rw'
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jsonio.dump_to_json(ol, fname, indent=1)
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rl = jsonio.load_json(fname)
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os.remove(fname + '.json.gz')
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for i in range(len(rl)):
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if isinstance(ol[i], pe.Obs):
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o = ol[i] - rl[i]
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assert(o.is_zero())
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or1 = np.ravel(ol[i])
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or2 = np.ravel(rl[i])
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for j in range(len(or1)):
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o = or1[i] - or2[i]
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assert(o.is_zero())
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