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Merge pull request #53 from s-kuberski/feature/json_io
Introduced JSON I/O for dictionaries
This commit is contained in:
Fabian Joswig
GitHub
commit
eab2ba45ff
2 changed files with 322 additions and 3 deletions
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@ -6,6 +6,7 @@ import socket
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import datetime
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import platform
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import warnings
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import re
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from ..obs import Obs
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from ..covobs import Covobs
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from ..correlators import Corr
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@ -20,7 +21,7 @@ def create_json_string(ol, description='', indent=1):
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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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List of objects that will be exported. At the moment, these objects can be
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either of: Obs, list, numpy.ndarray, Corr.
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All Obs inside a structure have to be defined on the same set of configurations.
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description : str
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@ -246,7 +247,7 @@ def dump_to_json(ol, fname, description='', indent=1, gz=True):
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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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List of objects that will be exported. At the moment, these objects can be
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either of: Obs, list, numpy.ndarray, Corr.
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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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@ -476,7 +477,7 @@ def import_json_string(json_string, verbose=True, full_output=False):
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def load_json(fname, verbose=True, gz=True, full_output=False):
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"""Import a list of Obs or structures containing Obs from a .json.gz file.
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"""Import a list of Obs or structures containing Obs from a .json(.gz) file.
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The following structures are supported: Obs, list, numpy.ndarray, Corr
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If the list contains only one element, it is unpacked from the list.
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@ -507,3 +508,215 @@ def load_json(fname, verbose=True, gz=True, full_output=False):
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d = fin.read()
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return import_json_string(d, verbose, full_output)
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def _ol_from_dict(ind, reps='DICTOBS'):
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"""Convert a dictionary of Obs objects to a list and a dictionary that contains
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placeholders instead of the Obs objects.
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Parameters
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----------
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ind : dict
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Dict of JSON valid structures and objects that will be exported.
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At the moment, these object can be either of: Obs, list, numpy.ndarray, Corr.
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All Obs inside a structure have to be defined on the same set of configurations.
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reps : str
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Specify the structure of the placeholder in exported dict to be reps[0-9]+.
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"""
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obstypes = (Obs, Corr, np.ndarray)
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if not reps.isalnum():
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raise Exception('Placeholder string has to be alphanumeric!')
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ol = []
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counter = 0
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def dict_replace_obs(d):
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nonlocal ol
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nonlocal counter
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x = {}
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for k, v in d.items():
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if isinstance(v, dict):
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v = dict_replace_obs(v)
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elif isinstance(v, list) and all([isinstance(o, Obs) for o in v]):
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v = obslist_replace_obs(v)
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elif isinstance(v, list):
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v = list_replace_obs(v)
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elif isinstance(v, obstypes):
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ol.append(v)
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v = reps + '%d' % (counter)
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counter += 1
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elif isinstance(v, str):
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if bool(re.match(r'%s[0-9]+' % (reps), v)):
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raise Exception('Dict contains string %s that matches the placeholder! %s Cannot be savely exported.' % (v, reps))
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x[k] = v
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return x
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def list_replace_obs(li):
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nonlocal ol
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nonlocal counter
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x = []
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for e in li:
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if isinstance(e, list):
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e = list_replace_obs(e)
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elif isinstance(e, list) and all([isinstance(o, Obs) for o in e]):
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e = obslist_replace_obs(e)
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elif isinstance(e, dict):
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e = dict_replace_obs(e)
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elif isinstance(e, obstypes):
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ol.append(e)
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e = reps + '%d' % (counter)
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counter += 1
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elif isinstance(e, str):
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if bool(re.match(r'%s[0-9]+' % (reps), e)):
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raise Exception('Dict contains string %s that matches the placeholder! %s Cannot be savely exported.' % (e, reps))
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x.append(e)
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return x
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def obslist_replace_obs(li):
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nonlocal ol
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nonlocal counter
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il = []
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for e in li:
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il.append(e)
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ol.append(il)
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x = reps + '%d' % (counter)
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counter += 1
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return x
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nd = dict_replace_obs(ind)
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return ol, nd
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def dump_dict_to_json(od, fname, description='', indent=1, reps='DICTOBS', gz=True):
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"""Export a dict of Obs or structures containing Obs to a .json(.gz) file
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Parameters
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----------
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od : dict
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Dict of JSON valid structures and objects that will be exported.
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At the moment, these objects can be either of: Obs, list, numpy.ndarray, Corr.
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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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reps : str
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Specify the structure of the placeholder in exported dict to be reps[0-9]+.
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gz : bool
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If True, the output is a gzipped json. If False, the output is a json file.
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"""
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if not isinstance(od, dict):
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raise Exception('od has to be a dictionary. Did you want to use dump_to_json?')
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infostring = ('This JSON file contains a python dictionary that has been parsed to a list of structures. '
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'OBSDICT contains the dictionary, where Obs or other structures have been replaced by '
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'' + reps + '[0-9]+. The field description contains the additional description of this JSON file. '
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'This file may be parsed to a dict with the pyerrors routine load_json_dict.')
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desc_dict = {'INFO': infostring, 'OBSDICT': {}, 'description': description}
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ol, desc_dict['OBSDICT'] = _ol_from_dict(od, reps=reps)
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dump_to_json(ol, fname, description=desc_dict, indent=indent, gz=gz)
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def _od_from_list_and_dict(ol, ind, reps='DICTOBS'):
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"""Parse a list of Obs or structures containing Obs and an accompanying
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dict, where the structures have been replaced by placeholders to a
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dict that contains the structures.
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The following structures are supported: Obs, list, numpy.ndarray, Corr
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Parameters
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----------
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ol : list
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List of objects -
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At the moment, these objects can be either of: Obs, list, numpy.ndarray, Corr.
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All Obs inside a structure have to be defined on the same set of configurations.
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ind : dict
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Dict that defines the structure of the resulting dict and contains placeholders
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reps : str
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Specify the structure of the placeholder in imported dict to be reps[0-9]+.
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"""
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if not reps.isalnum():
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raise Exception('Placeholder string has to be alphanumeric!')
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counter = 0
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def dict_replace_string(d):
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nonlocal counter
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nonlocal ol
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x = {}
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for k, v in d.items():
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if isinstance(v, dict):
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v = dict_replace_string(v)
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elif isinstance(v, list):
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v = list_replace_string(v)
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elif isinstance(v, str) and bool(re.match(r'%s[0-9]+' % (reps), v)):
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index = int(v[len(reps):])
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v = ol[index]
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counter += 1
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x[k] = v
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return x
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def list_replace_string(li):
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nonlocal counter
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nonlocal ol
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x = []
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for e in li:
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if isinstance(e, list):
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e = list_replace_string(e)
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elif isinstance(e, dict):
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e = dict_replace_string(e)
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elif isinstance(e, str) and bool(re.match(r'%s[0-9]+' % (reps), e)):
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index = int(e[len(reps):])
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e = ol[index]
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counter += 1
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x.append(e)
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return x
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nd = dict_replace_string(ind)
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if counter == 0:
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raise Exception('No placeholder has been replaced! Check if reps is set correctly.')
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return nd
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def load_json_dict(fname, verbose=True, gz=True, full_output=False, reps='DICTOBS'):
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"""Import a dict of Obs or structures containing Obs from a .json(.gz) file.
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The following structures are supported: Obs, list, numpy.ndarray, Corr
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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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gz : bool
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If True, assumes that data is gzipped. If False, assumes JSON file.
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full_output : bool
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If True, a dict containing auxiliary information and the data is returned.
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If False, only the data is returned.
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reps : str
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Specify the structure of the placeholder in imported dict to be reps[0-9]+.
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"""
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indata = load_json(fname, verbose=verbose, gz=gz, full_output=True)
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description = indata['description']['description']
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indict = indata['description']['OBSDICT']
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ol = indata['obsdata']
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od = _od_from_list_and_dict(ol, indict, reps=reps)
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if full_output:
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indata['description'] = description
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indata['obsdata'] = od
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return indata
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else:
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return od
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106
tests/io_test.py
106
tests/io_test.py
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@ -3,6 +3,7 @@ import gzip
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import numpy as np
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import pyerrors as pe
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import pyerrors.input.json as jsonio
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import pytest
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def test_jsonio():
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@ -136,3 +137,108 @@ def test_json_corr_2d_io():
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assert recover[index] is None
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assert my_corr.tag == recover.tag
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assert my_corr.prange == recover.prange
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def test_json_dict_io():
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def check_dict_equality(d1, d2):
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def dict_check_obs(d1, d2):
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for k, v in d1.items():
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if isinstance(v, dict):
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v = dict_check_obs(v, d2[k])
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elif isinstance(v, list) and all([isinstance(o, pe.Obs) for o in v]):
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for i in range(len(v)):
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assert((v[i] - d2[k][i]).is_zero())
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elif isinstance(v, list):
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v = list_check_obs(v, d2[k])
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elif isinstance(v, pe.Obs):
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assert((v - d2[k]).is_zero())
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elif isinstance(v, pe.Corr):
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for i in range(v.T):
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assert((v[i] - d2[k][i]).is_zero())
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elif isinstance(v, np.ndarray):
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a1 = np.ravel(v)
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a2 = np.ravel(d2[k])
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for i in range(len(a1)):
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assert((a1[i] - a2[i]).is_zero())
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def list_check_obs(l1, l2):
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for ei in range(len(l1)):
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e = l1[ei]
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if isinstance(e, list):
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e = list_check_obs(e, l2[ei])
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elif isinstance(e, list) and all([isinstance(o, pe.Obs) for o in e]):
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for i in range(len(e)):
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assert((e[i] - l2[ei][i]).is_zero())
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elif isinstance(e, dict):
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e = dict_check_obs(e, l2[ei])
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elif isinstance(e, pe.Obs):
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assert((e - l2[ei]).is_zero())
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elif isinstance(e, pe.Corr):
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for i in range(e.T):
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assert((e[i] - l2[ei][i]).is_zero())
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elif isinstance(e, np.ndarray):
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a1 = np.ravel(e)
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a2 = np.ravel(l2[ei])
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for i in range(len(a1)):
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assert((a1[i] - a2[i]).is_zero())
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dict_check_obs(d1, d2)
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return True
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od = {
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'l':
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{
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'a': pe.pseudo_Obs(1, .2, 'testa', samples=10),
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'b': [pe.pseudo_Obs(1.1, .1, 'test', samples=10), pe.pseudo_Obs(1.2, .1, 'test', samples=10), pe.pseudo_Obs(1.3, .1, 'test', samples=10)],
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'c': {
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'd': 1,
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'e': pe.pseudo_Obs(.2, .01, 'teste', samples=10),
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'f': pe.Corr([pe.pseudo_Obs(.1, .01, 'a', samples=10), pe.pseudo_Obs(.1, .01, 'a', samples=10), pe.pseudo_Obs(.1, .01, 'a', samples=10), pe.pseudo_Obs(.1, .01, 'a', samples=10)]),
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'g': np.reshape(np.asarray([pe.pseudo_Obs(.1, .01, 'a', samples=10), pe.pseudo_Obs(.1, .01, 'a', samples=10), pe.pseudo_Obs(.1, .01, 'a', samples=10), pe.pseudo_Obs(.1, .01, 'a', samples=10)]), (2, 2)),
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}
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},
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's':
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{
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'a': 'Infor123',
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'b': ['Some', 'list'],
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'd': pe.pseudo_Obs(.01, .001, 'testd', samples=10) * pe.cov_Obs(1, .01, 'cov1'),
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'se': None,
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'sf': 1.2,
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}
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}
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fname = 'test_rw'
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desc = 'This is a random description'
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with pytest.raises(Exception):
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jsonio.dump_dict_to_json(od, fname, description=desc, reps='|Test')
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jsonio.dump_dict_to_json(od, fname, description=desc, reps='TEST')
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nd = jsonio.load_json_dict(fname, full_output=True, reps='TEST')
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with pytest.raises(Exception):
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nd = jsonio.load_json_dict(fname, full_output=True)
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jsonio.dump_dict_to_json(od, fname, description=desc)
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nd = jsonio.load_json_dict(fname, full_output=True)
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assert (desc == nd['description'])
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assert(check_dict_equality(od, nd['obsdata']))
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nd = jsonio.load_json_dict(fname, full_output=False)
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assert(check_dict_equality(od, nd))
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nl = jsonio.load_json(fname, full_output=True)
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nl = jsonio.load_json(fname, full_output=False)
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with pytest.raises(Exception):
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jsonio.dump_dict_to_json(nl, fname, description=desc)
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od['k'] = 'DICTOBS2'
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with pytest.raises(Exception):
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jsonio.dump_dict_to_json(od, fname, description=desc)
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od['k'] = ['DICTOBS2']
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with pytest.raises(Exception):
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jsonio.dump_dict_to_json(od, fname, description=desc)
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os.remove(fname + '.json.gz')
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