mirror of
https://github.com/fjosw/pyerrors.git
synced 2025-05-14 19:43:41 +02:00
Fabian Joswig
GitHub
commit
d4c913ab88
3 changed files with 970 additions and 1 deletions
873
pyerrors/input/dobs.py
Normal file
873
pyerrors/input/dobs.py
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@ -0,0 +1,873 @@
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from collections import defaultdict
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import gzip
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import lxml.etree as et
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import getpass
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import socket
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import datetime
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import json
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import warnings
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import numpy as np
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from ..obs import Obs
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from ..obs import _merge_idx
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from ..covobs import Covobs
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from .. import version as pyerrorsversion
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# Based on https://stackoverflow.com/a/10076823
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def _etree_to_dict(t):
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""" Convert the content of an XML file to a python dict"""
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d = {t.tag: {} if t.attrib else None}
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children = list(t)
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if children:
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dd = defaultdict(list)
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for dc in map(_etree_to_dict, children):
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for k, v in dc.items():
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dd[k].append(v)
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d = {t.tag: {k: v[0] if len(v) == 1 else v
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for k, v in dd.items()}}
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if t.attrib:
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d[t.tag].update(('@' + k, v)
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for k, v in t.attrib.items())
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if t.text:
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text = t.text.strip()
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if children or t.attrib:
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if text:
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d[t.tag]['#data'] = [text]
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else:
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d[t.tag] = text
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return d
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def _dict_to_xmlstring(d):
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if isinstance(d, dict):
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iters = ''
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for k in d:
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if k.startswith('#'):
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for la in d[k]:
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iters += la
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iters = '<array>\n' + iters + '<%sarray>\n' % ('/')
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return iters
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if isinstance(d[k], dict):
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iters += '<%s>\n' % (k) + _dict_to_xmlstring(d[k]) + '<%s%s>\n' % ('/', k)
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elif isinstance(d[k], str):
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if len(d[k]) > 100:
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iters += '<%s>\n ' % (k) + d[k] + ' \n<%s%s>\n' % ('/', k)
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else:
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iters += '<%s> ' % (k) + d[k] + ' <%s%s>\n' % ('/', k)
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elif isinstance(d[k], list):
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for i in range(len(d[k])):
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iters += _dict_to_xmlstring(d[k][i])
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elif not d[k]:
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return '\n'
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else:
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raise Exception('Type', type(d[k]), 'not supported in export!')
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else:
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raise Exception('Type', type(d), 'not supported in export!')
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return iters
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def _dict_to_xmlstring_spaces(d, space=' '):
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s = _dict_to_xmlstring(d)
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o = ''
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c = 0
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cm = False
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for li in s.split('\n'):
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if li.startswith('<%s' % ('/')):
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c -= 1
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cm = True
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for i in range(c):
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o += space
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o += li + '\n'
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if li.startswith('<') and not cm:
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if not '<%s' % ('/') in li:
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c += 1
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cm = False
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return o
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def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
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"""Export a list of Obs or structures containing Obs to an xml string
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according to the Zeuthen pobs format.
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Tags are not written or recovered automatically. The separator | is removed from the replica names.
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Parameters
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----------
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obsl : list
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List of Obs that will be exported.
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The Obs inside a structure have to be defined on the same ensemble.
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name : str
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The name of the observable.
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spec : str
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Optional string that describes the contents of the file.
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origin : str
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Specify where the data has its origin.
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symbol : list
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A list of symbols that describe the observables to be written. May be empty.
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enstag : str
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Enstag that is written to pobs. If None, the ensemble name is used.
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"""
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od = {}
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ename = obsl[0].e_names[0]
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names = list(obsl[0].deltas.keys())
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nr = len(names)
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onames = [name.replace('|', '') for name in names]
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for o in obsl:
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if len(o.e_names) != 1:
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raise Exception('You try to export dobs to obs!')
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if o.e_names[0] != ename:
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raise Exception('You try to export dobs to obs!')
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if len(o.deltas.keys()) != nr:
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raise Exception('Incompatible obses in list')
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od['observables'] = {}
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od['observables']['schema'] = {'name': 'lattobs', 'version': '1.0'}
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od['observables']['origin'] = {
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'who': getpass.getuser(),
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'date': str(datetime.datetime.now())[:-7],
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'host': socket.gethostname(),
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'tool': {'name': 'pyerrors', 'version': pyerrorsversion.__version__}}
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od['observables']['pobs'] = {}
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pd = od['observables']['pobs']
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pd['spec'] = spec
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pd['origin'] = origin
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pd['name'] = name
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if enstag:
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if not isinstance(enstag, str):
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raise Exception('enstag has to be a string!')
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pd['enstag'] = enstag
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else:
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pd['enstag'] = ename
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pd['nr'] = '%d' % (nr)
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pd['array'] = []
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osymbol = 'cfg'
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if not isinstance(symbol, list):
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raise Exception('Symbol has to be a list!')
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if not (len(symbol) == 0 or len(symbol) == len(obsl)):
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raise Exception('Symbol has to be a list of lenght 0 or %d!' % (len(obsl)))
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for s in symbol:
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osymbol += ' %s' % s
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for r in range(nr):
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ad = {}
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ad['id'] = onames[r]
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Nconf = len(obsl[0].deltas[names[r]])
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layout = '%d i f%d' % (Nconf, len(obsl))
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ad['layout'] = layout
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ad['symbol'] = osymbol
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data = ''
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for c in range(Nconf):
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data += '%d ' % obsl[0].idl[names[r]][c]
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for o in obsl:
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num = o.deltas[names[r]][c] + o.r_values[names[r]]
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if num == 0:
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data += '0 '
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else:
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data += '%1.16e ' % (num)
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data += '\n'
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ad['#data'] = data
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pd['array'].append(ad)
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rs = '<?xml version="1.0" encoding="utf-8"?>\n' + _dict_to_xmlstring_spaces(od)
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return rs
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def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], enstag=None, gz=True):
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"""Export a list of Obs or structures containing Obs to a .xml.gz file
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according to the Zeuthen pobs format.
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Tags are not written or recovered automatically. The separator | is removed from the replica names.
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Parameters
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----------
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obsl : list
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List of Obs that will be exported.
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The Obs inside a structure have to be defined on the same ensemble.
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fname : str
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Filename of the output file.
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name : str
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The name of the observable.
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spec : str
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Optional string that describes the contents of the file.
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origin : str
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Specify where the data has its origin.
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symbol : list
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A list of symbols that describe the observables to be written. May be empty.
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enstag : str
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Enstag that is written to pobs. If None, the ensemble name is used.
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gz : bool
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If True, the output is a gzipped xml. If False, the output is an xml file.
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"""
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pobsstring = create_pobs_string(obsl, name, spec, origin, symbol, enstag)
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if not fname.endswith('.xml') and not fname.endswith('.gz'):
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fname += '.xml'
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if gz:
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if not fname.endswith('.gz'):
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fname += '.gz'
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fp = gzip.open(fname, 'wb')
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fp.write(pobsstring.encode('utf-8'))
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else:
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fp = open(fname, 'w', encoding='utf-8')
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fp.write(pobsstring)
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fp.close()
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def _import_data(string):
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return json.loads("[" + ",".join(string.replace(' +', ' ').split()) + "]")
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def _check(condition):
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if not condition:
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raise Exception("XML file format not supported")
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class _NoTagInDataError(Exception):
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"""Raised when tag is not in data"""
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def __init__(self, tag):
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self.tag = tag
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super().__init__('Tag %s not in data!' % (self.tag))
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def _find_tag(dat, tag):
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for i in range(len(dat)):
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if dat[i].tag == tag:
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return i
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raise _NoTagInDataError(tag)
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def _import_array(arr):
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name = arr[_find_tag(arr, 'id')].text.strip()
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index = _find_tag(arr, 'layout')
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try:
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sindex = _find_tag(arr, 'symbol')
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except _NoTagInDataError:
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sindex = 0
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if sindex > index:
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tmp = _import_data(arr[sindex].tail)
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else:
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tmp = _import_data(arr[index].tail)
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li = arr[index].text.strip()
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m = li.split()
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if m[1] == "i" and m[2][0] == "f":
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nc = int(m[0])
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na = int(m[2].lstrip('f'))
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_dat = []
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mask = []
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for a in range(na):
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mask += [a]
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_dat += [np.array(tmp[1 + a:: na + 1])]
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_check(len(tmp[0:: na + 1]) == nc)
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return [name, tmp[0:: na + 1], mask, _dat]
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elif m[1][0] == 'f' and len(m) < 3:
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sh = (int(m[0]), int(m[1].lstrip('f')))
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return np.reshape(tmp, sh)
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elif any(['f' in s for s in m]):
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for si in range(len(m)):
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if m[si] == 'f':
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break
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sh = [int(m[i]) for i in range(si)]
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return np.reshape(tmp, sh)
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else:
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print(name, m)
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_check(False)
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def _import_rdata(rd):
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name, idx, mask, deltas = _import_array(rd)
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return deltas, name, idx
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def _import_cdata(cd):
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_check(cd[0].tag == "id")
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_check(cd[1][0].text.strip() == "cov")
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cov = _import_array(cd[1])
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grad = _import_array(cd[2])
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return cd[0].text.strip(), cov, grad
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def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
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"""Import a list of Obs from an xml.gz file in the Zeuthen pobs format.
|
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Tags are not written or recovered automatically.
|
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|
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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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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 as list.
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separatior_insertion: str or int
|
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|
str: replace all occurences of "separator_insertion" within the replica names
|
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|
by "|%s" % (separator_insertion) when constructing the names of the replica.
|
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|
int: Insert the separator "|" at the position given by separator_insertion.
|
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|
None (default): Replica names remain unchanged.
|
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|
"""
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if not fname.endswith('.xml') and not fname.endswith('.gz'):
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|
fname += '.xml'
|
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|
if gz:
|
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|
if not fname.endswith('.gz'):
|
||||||
|
fname += '.gz'
|
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|
with gzip.open(fname, 'r') as fin:
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|
content = fin.read()
|
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|
else:
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||||||
|
if fname.endswith('.gz'):
|
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|
warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
|
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|
with open(fname, 'r') as fin:
|
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|
content = fin.read()
|
||||||
|
|
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|
# parse xml file content
|
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|
root = et.fromstring(content)
|
||||||
|
|
||||||
|
_check(root[2].tag == 'pobs')
|
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|
pobs = root[2]
|
||||||
|
|
||||||
|
version = root[0][1].text.strip()
|
||||||
|
|
||||||
|
_check(root[1].tag == 'origin')
|
||||||
|
file_origin = _etree_to_dict(root[1])['origin']
|
||||||
|
|
||||||
|
deltas = []
|
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|
names = []
|
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|
idl = []
|
||||||
|
for i in range(5, len(pobs)):
|
||||||
|
delta, name, idx = _import_rdata(pobs[i])
|
||||||
|
deltas.append(delta)
|
||||||
|
if separator_insertion is None:
|
||||||
|
pass
|
||||||
|
elif isinstance(separator_insertion, int):
|
||||||
|
name = name[:separator_insertion] + '|' + name[separator_insertion:]
|
||||||
|
elif isinstance(separator_insertion, str):
|
||||||
|
name = name.replace(separator_insertion, "|%s" % (separator_insertion))
|
||||||
|
else:
|
||||||
|
raise Exception("separator_insertion has to be string or int, is ", type(separator_insertion))
|
||||||
|
names.append(name)
|
||||||
|
idl.append(idx)
|
||||||
|
res = [Obs([d[i] for d in deltas], names, idl=idl) for i in range(len(deltas[0]))]
|
||||||
|
|
||||||
|
descriptiond = {}
|
||||||
|
for i in range(4):
|
||||||
|
descriptiond[pobs[i].tag] = pobs[i].text.strip()
|
||||||
|
|
||||||
|
_check(pobs[4].tag == "nr")
|
||||||
|
|
||||||
|
_check(pobs[5].tag == 'array')
|
||||||
|
if pobs[5][1].tag == 'symbol':
|
||||||
|
symbol = pobs[5][1].text.strip()
|
||||||
|
descriptiond['symbol'] = symbol
|
||||||
|
|
||||||
|
if full_output:
|
||||||
|
retd = {}
|
||||||
|
tool = file_origin.get('tool', None)
|
||||||
|
if tool:
|
||||||
|
program = tool['name'] + ' ' + tool['version']
|
||||||
|
else:
|
||||||
|
program = ''
|
||||||
|
retd['program'] = program
|
||||||
|
retd['version'] = version
|
||||||
|
retd['who'] = file_origin['who']
|
||||||
|
retd['date'] = file_origin['date']
|
||||||
|
retd['host'] = file_origin['host']
|
||||||
|
retd['description'] = descriptiond
|
||||||
|
retd['obsdata'] = res
|
||||||
|
return retd
|
||||||
|
else:
|
||||||
|
return res
|
||||||
|
|
||||||
|
|
||||||
|
# Reading (and writing) dobs is not yet working properly:
|
||||||
|
# we have to loop over root[2:] because each entry is a dobs
|
||||||
|
# But maybe this is just a problem with Ben's implementation
|
||||||
|
|
||||||
|
# this is based on Mattia Bruno's implementation at https://github.com/mbruno46/pyobs/blob/master/pyobs/IO/xml.py
|
||||||
|
def import_dobs_string(content, noempty=False, full_output=False, separator_insertion=True):
|
||||||
|
"""Import a list of Obs from a string in the Zeuthen dobs format.
|
||||||
|
|
||||||
|
Tags are not written or recovered automatically.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
content : str
|
||||||
|
XML string containing the data
|
||||||
|
noemtpy : bool
|
||||||
|
If True, ensembles with no contribution to the Obs are not included.
|
||||||
|
If False, ensembles are included as written in the file, possibly with vanishing entries.
|
||||||
|
full_output : bool
|
||||||
|
If True, a dict containing auxiliary information and the data is returned.
|
||||||
|
If False, only the data is returned as list.
|
||||||
|
separatior_insertion: str, int or bool
|
||||||
|
str: replace all occurences of "separator_insertion" within the replica names
|
||||||
|
by "|%s" % (separator_insertion) when constructing the names of the replica.
|
||||||
|
int: Insert the separator "|" at the position given by separator_insertion.
|
||||||
|
True (default): separator "|" is inserted after len(ensname), assuming that the
|
||||||
|
ensemble name is a prefix to the replica name.
|
||||||
|
None or False: No separator is inserted.
|
||||||
|
"""
|
||||||
|
|
||||||
|
root = et.fromstring(content)
|
||||||
|
|
||||||
|
_check(root.tag == 'OBSERVABLES')
|
||||||
|
_check(root[0].tag == 'SCHEMA')
|
||||||
|
version = root[0][1].text.strip()
|
||||||
|
|
||||||
|
_check(root[1].tag == 'origin')
|
||||||
|
file_origin = _etree_to_dict(root[1])['origin']
|
||||||
|
|
||||||
|
_check(root[2].tag == 'dobs')
|
||||||
|
|
||||||
|
dobs = root[2]
|
||||||
|
|
||||||
|
descriptiond = {}
|
||||||
|
for i in range(3):
|
||||||
|
descriptiond[dobs[i].tag] = dobs[i].text.strip()
|
||||||
|
|
||||||
|
_check(dobs[3].tag == 'array')
|
||||||
|
|
||||||
|
symbol = []
|
||||||
|
if dobs[3][1].tag == 'symbol':
|
||||||
|
symbol = dobs[3][1].text.strip()
|
||||||
|
descriptiond['symbol'] = symbol
|
||||||
|
mean = _import_array(dobs[3])[0]
|
||||||
|
|
||||||
|
_check(dobs[4].tag == "ne")
|
||||||
|
ne = int(dobs[4].text.strip())
|
||||||
|
_check(dobs[5].tag == "nc")
|
||||||
|
nc = int(dobs[5].text.strip())
|
||||||
|
|
||||||
|
idld = {}
|
||||||
|
deltad = {}
|
||||||
|
covd = {}
|
||||||
|
gradd = {}
|
||||||
|
names = []
|
||||||
|
e_names = []
|
||||||
|
enstags = {}
|
||||||
|
for k in range(6, len(list(dobs))):
|
||||||
|
if dobs[k].tag == "edata":
|
||||||
|
_check(dobs[k][0].tag == "enstag")
|
||||||
|
ename = dobs[k][0].text.strip()
|
||||||
|
e_names.append(ename)
|
||||||
|
_check(dobs[k][1].tag == "nr")
|
||||||
|
R = int(dobs[k][1].text.strip())
|
||||||
|
for i in range(2, 2 + R):
|
||||||
|
deltas, rname, idx = _import_rdata(dobs[k][i])
|
||||||
|
if separator_insertion is None or False:
|
||||||
|
pass
|
||||||
|
elif separator_insertion is True:
|
||||||
|
if rname.startswith(ename):
|
||||||
|
rname = rname[:len(ename)] + '|' + rname[len(ename):]
|
||||||
|
elif isinstance(separator_insertion, int):
|
||||||
|
rname = rname[:separator_insertion] + '|' + rname[separator_insertion:]
|
||||||
|
elif isinstance(separator_insertion, str):
|
||||||
|
rname = rname.replace(separator_insertion, "|%s" % (separator_insertion))
|
||||||
|
else:
|
||||||
|
raise Exception("separator_insertion has to be string or int, is ", type(separator_insertion))
|
||||||
|
if '|' in rname:
|
||||||
|
new_ename = rname[:rname.index('|')]
|
||||||
|
else:
|
||||||
|
new_ename = ename
|
||||||
|
enstags[new_ename] = ename
|
||||||
|
idld[rname] = idx
|
||||||
|
deltad[rname] = deltas
|
||||||
|
names.append(rname)
|
||||||
|
elif dobs[k].tag == "cdata":
|
||||||
|
cname, cov, grad = _import_cdata(dobs[k])
|
||||||
|
covd[cname] = cov
|
||||||
|
if grad.shape[1] == 1:
|
||||||
|
gradd[cname] = [grad for i in range(len(mean))]
|
||||||
|
else:
|
||||||
|
gradd[cname] = grad.T
|
||||||
|
else:
|
||||||
|
_check(False)
|
||||||
|
names = list(set(names))
|
||||||
|
|
||||||
|
for name in names:
|
||||||
|
for i in range(len(deltad[name])):
|
||||||
|
deltad[name][i] = np.array(deltad[name][i]) + mean[i]
|
||||||
|
|
||||||
|
res = []
|
||||||
|
for i in range(len(mean)):
|
||||||
|
deltas = []
|
||||||
|
idl = []
|
||||||
|
obs_names = []
|
||||||
|
for name in names:
|
||||||
|
h = np.unique(deltad[name][i])
|
||||||
|
if len(h) == 1 and np.all(h == mean[i]) and noempty:
|
||||||
|
continue
|
||||||
|
deltas.append(deltad[name][i])
|
||||||
|
obs_names.append(name)
|
||||||
|
idl.append(idld[name])
|
||||||
|
res.append(Obs(deltas, obs_names, idl=idl))
|
||||||
|
print(mean, 'vs', res)
|
||||||
|
_check(len(e_names) == ne)
|
||||||
|
|
||||||
|
cnames = list(covd.keys())
|
||||||
|
for i in range(len(res)):
|
||||||
|
new_covobs = {name: Covobs(0, covd[name], name, grad=gradd[name][i]) for name in cnames}
|
||||||
|
if noempty:
|
||||||
|
for name in cnames:
|
||||||
|
if np.all(new_covobs[name].grad == 0):
|
||||||
|
del new_covobs[name]
|
||||||
|
cnames_loc = list(new_covobs.keys())
|
||||||
|
else:
|
||||||
|
cnames_loc = cnames
|
||||||
|
for name in cnames_loc:
|
||||||
|
res[i].names.append(name)
|
||||||
|
res[i].shape[name] = 1
|
||||||
|
res[i].idl[name] = []
|
||||||
|
res[i]._covobs = new_covobs
|
||||||
|
|
||||||
|
if symbol:
|
||||||
|
for i in range(len(res)):
|
||||||
|
res[i].tag = symbol[i]
|
||||||
|
if res[i].tag == 'None':
|
||||||
|
res[i].tag = None
|
||||||
|
if not noempty:
|
||||||
|
_check(len(res[0].covobs.keys()) == nc)
|
||||||
|
if full_output:
|
||||||
|
retd = {}
|
||||||
|
tool = file_origin.get('tool', None)
|
||||||
|
if tool:
|
||||||
|
program = tool['name'] + ' ' + tool['version']
|
||||||
|
else:
|
||||||
|
program = ''
|
||||||
|
retd['program'] = program
|
||||||
|
retd['version'] = version
|
||||||
|
retd['who'] = file_origin['who']
|
||||||
|
retd['date'] = file_origin['date']
|
||||||
|
retd['host'] = file_origin['host']
|
||||||
|
retd['description'] = descriptiond
|
||||||
|
retd['enstags'] = enstags
|
||||||
|
retd['obsdata'] = res
|
||||||
|
return retd
|
||||||
|
else:
|
||||||
|
return res
|
||||||
|
|
||||||
|
|
||||||
|
def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insertion=True):
|
||||||
|
"""Import a list of Obs from an xml.gz file in the Zeuthen dobs format.
|
||||||
|
|
||||||
|
Tags are not written or recovered automatically.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
fname : str
|
||||||
|
Filename of the input file.
|
||||||
|
noemtpy : bool
|
||||||
|
If True, ensembles with no contribution to the Obs are not included.
|
||||||
|
If False, ensembles are included as written in the file.
|
||||||
|
full_output : bool
|
||||||
|
If True, a dict containing auxiliary information and the data is returned.
|
||||||
|
If False, only the data is returned as list.
|
||||||
|
gz : bool
|
||||||
|
If True, assumes that data is gzipped. If False, assumes XML file.
|
||||||
|
separatior_insertion: str, int or bool
|
||||||
|
str: replace all occurences of "separator_insertion" within the replica names
|
||||||
|
by "|%s" % (separator_insertion) when constructing the names of the replica.
|
||||||
|
int: Insert the separator "|" at the position given by separator_insertion.
|
||||||
|
True (default): separator "|" is inserted after len(ensname), assuming that the
|
||||||
|
ensemble name is a prefix to the replica name.
|
||||||
|
None or False: No separator is inserted.
|
||||||
|
"""
|
||||||
|
|
||||||
|
if not fname.endswith('.xml') and not fname.endswith('.gz'):
|
||||||
|
fname += '.xml'
|
||||||
|
if gz:
|
||||||
|
if not fname.endswith('.gz'):
|
||||||
|
fname += '.gz'
|
||||||
|
with gzip.open(fname, 'r') as fin:
|
||||||
|
content = fin.read().decode('utf-8')
|
||||||
|
else:
|
||||||
|
if fname.endswith('.gz'):
|
||||||
|
warnings.warn("Trying to read from %s without unzipping!" % fname, UserWarning)
|
||||||
|
with open(fname, 'r', encoding='utf-8') as fin:
|
||||||
|
content = fin.read()
|
||||||
|
|
||||||
|
# open and read gzipped xml file
|
||||||
|
infile = gzip.open(fname)
|
||||||
|
content = infile.read()
|
||||||
|
|
||||||
|
return import_dobs_string(content, noempty, full_output, separator_insertion=separator_insertion)
|
||||||
|
|
||||||
|
|
||||||
|
def _dobsdict_to_xmlstring(d):
|
||||||
|
if isinstance(d, dict):
|
||||||
|
iters = ''
|
||||||
|
for k in d:
|
||||||
|
if k.startswith('#value'):
|
||||||
|
for li in d[k]:
|
||||||
|
iters += li
|
||||||
|
return iters + '\n'
|
||||||
|
elif k.startswith('#'):
|
||||||
|
for li in d[k]:
|
||||||
|
iters += li
|
||||||
|
iters = '<array>\n' + iters + '<%sarray>\n' % ('/')
|
||||||
|
return iters
|
||||||
|
if isinstance(d[k], dict):
|
||||||
|
iters += '<%s>\n' % (k) + _dobsdict_to_xmlstring(d[k]) + '<%s%s>\n' % ('/', k)
|
||||||
|
elif isinstance(d[k], str):
|
||||||
|
if len(d[k]) > 100:
|
||||||
|
iters += '<%s>\n ' % (k) + d[k] + ' \n<%s%s>\n' % ('/', k)
|
||||||
|
else:
|
||||||
|
iters += '<%s> ' % (k) + d[k] + ' <%s%s>\n' % ('/', k)
|
||||||
|
elif isinstance(d[k], list):
|
||||||
|
tmps = ''
|
||||||
|
if k in ['edata', 'cdata']:
|
||||||
|
for i in range(len(d[k])):
|
||||||
|
tmps += '<%s>\n' % (k) + _dobsdict_to_xmlstring(d[k][i]) + '</%s>\n' % (k)
|
||||||
|
else:
|
||||||
|
for i in range(len(d[k])):
|
||||||
|
tmps += _dobsdict_to_xmlstring(d[k][i])
|
||||||
|
iters += tmps
|
||||||
|
elif isinstance(d[k], (int, float)):
|
||||||
|
iters += '<%s> ' % (k) + str(d[k]) + ' <%s%s>\n' % ('/', k)
|
||||||
|
elif not d[k]:
|
||||||
|
return '\n'
|
||||||
|
else:
|
||||||
|
raise Exception('Type', type(d[k]), 'not supported in export!')
|
||||||
|
else:
|
||||||
|
raise Exception('Type', type(d), 'not supported in export!')
|
||||||
|
return iters
|
||||||
|
|
||||||
|
|
||||||
|
def _dobsdict_to_xmlstring_spaces(d, space=' '):
|
||||||
|
s = _dobsdict_to_xmlstring(d)
|
||||||
|
o = ''
|
||||||
|
c = 0
|
||||||
|
cm = False
|
||||||
|
for li in s.split('\n'):
|
||||||
|
if li.startswith('<%s' % ('/')):
|
||||||
|
c -= 1
|
||||||
|
cm = True
|
||||||
|
for i in range(c):
|
||||||
|
o += space
|
||||||
|
o += li + '\n'
|
||||||
|
if li.startswith('<') and not cm:
|
||||||
|
if not '<%s' % ('/') in li:
|
||||||
|
c += 1
|
||||||
|
cm = False
|
||||||
|
return o
|
||||||
|
|
||||||
|
|
||||||
|
def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=None, enstags={}):
|
||||||
|
"""Generate the string for the export of a list of Obs or structures containing Obs
|
||||||
|
to a .xml.gz file according to the Zeuthen dobs format.
|
||||||
|
|
||||||
|
Tags are not written or recovered automatically. The separator |is removed from the replica names.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
obsl : list
|
||||||
|
List of Obs that will be exported.
|
||||||
|
The Obs inside a structure do not have to be defined on the same set of configurations,
|
||||||
|
but the storage requirement is increased, if this is not the case.
|
||||||
|
name : str
|
||||||
|
The name of the observable.
|
||||||
|
spec : str
|
||||||
|
Optional string that describes the contents of the file.
|
||||||
|
origin : str
|
||||||
|
Specify where the data has its origin.
|
||||||
|
symbol : list
|
||||||
|
A list of symbols that describe the observables to be written. May be empty.
|
||||||
|
who : str
|
||||||
|
Provide the name of the person that exports the data.
|
||||||
|
enstags : dict
|
||||||
|
Provide alternative enstag for ensembles in the form enstags = {ename: enstag}
|
||||||
|
Otherwise, the ensemble name is used.
|
||||||
|
"""
|
||||||
|
od = {}
|
||||||
|
r_names = []
|
||||||
|
for o in obsl:
|
||||||
|
r_names += [name for name in o.names if name.split('|')[0] in o.mc_names]
|
||||||
|
r_names = sorted(set(r_names))
|
||||||
|
mc_names = sorted(set([n.split('|')[0] for n in r_names]))
|
||||||
|
for tmpname in mc_names:
|
||||||
|
if tmpname not in enstags:
|
||||||
|
enstags[tmpname] = tmpname
|
||||||
|
ne = len(set(mc_names))
|
||||||
|
cov_names = []
|
||||||
|
for o in obsl:
|
||||||
|
cov_names += list(o.cov_names)
|
||||||
|
cov_names = sorted(set(cov_names))
|
||||||
|
nc = len(set(cov_names))
|
||||||
|
od['OBSERVABLES'] = {}
|
||||||
|
od['OBSERVABLES']['SCHEMA'] = {'NAME': 'lattobs', 'VERSION': '1.0'}
|
||||||
|
if who is None:
|
||||||
|
who = getpass.getuser()
|
||||||
|
od['OBSERVABLES']['origin'] = {
|
||||||
|
'who': who,
|
||||||
|
'date': str(datetime.datetime.now())[:-7],
|
||||||
|
'host': socket.gethostname(),
|
||||||
|
'tool': {'name': 'pyerrors', 'version': pyerrorsversion.__version__}}
|
||||||
|
od['OBSERVABLES']['dobs'] = {}
|
||||||
|
pd = od['OBSERVABLES']['dobs']
|
||||||
|
pd['spec'] = spec
|
||||||
|
pd['origin'] = origin
|
||||||
|
pd['name'] = name
|
||||||
|
pd['array'] = {}
|
||||||
|
pd['array']['id'] = 'val'
|
||||||
|
pd['array']['layout'] = '1 f%d' % (len(obsl))
|
||||||
|
osymbol = ''
|
||||||
|
if symbol:
|
||||||
|
if not isinstance(symbol, list):
|
||||||
|
raise Exception('Symbol has to be a list!')
|
||||||
|
if not (len(symbol) == 0 or len(symbol) == len(obsl)):
|
||||||
|
raise Exception('Symbol has to be a list of lenght 0 or %d!' % (len(obsl)))
|
||||||
|
osymbol = symbol[0]
|
||||||
|
for s in symbol[1:]:
|
||||||
|
osymbol += ' %s' % s
|
||||||
|
pd['array']['symbol'] = osymbol
|
||||||
|
|
||||||
|
pd['array']['#values'] = [' '.join(['%1.16e' % o.value for o in obsl])]
|
||||||
|
pd['ne'] = '%d' % (ne)
|
||||||
|
pd['nc'] = '%d' % (nc)
|
||||||
|
pd['edata'] = []
|
||||||
|
for name in mc_names:
|
||||||
|
ed = {}
|
||||||
|
ed['enstag'] = enstags[name]
|
||||||
|
onames = sorted([n for n in r_names if (n.startswith(name + '|') or n == name)])
|
||||||
|
nr = len(onames)
|
||||||
|
ed['nr'] = nr
|
||||||
|
ed[''] = []
|
||||||
|
|
||||||
|
for r in range(nr):
|
||||||
|
ad = {}
|
||||||
|
repname = onames[r]
|
||||||
|
ad['id'] = repname.replace('|', '')
|
||||||
|
idx = _merge_idx([o.idl.get(repname, []) for o in obsl])
|
||||||
|
Nconf = len(idx)
|
||||||
|
layout = '%d i f%d' % (Nconf, len(obsl))
|
||||||
|
ad['layout'] = layout
|
||||||
|
data = ''
|
||||||
|
counters = [0 for o in obsl]
|
||||||
|
for ci in idx:
|
||||||
|
data += '%d ' % ci
|
||||||
|
for oi in range(len(obsl)):
|
||||||
|
o = obsl[oi]
|
||||||
|
if repname in o.idl:
|
||||||
|
if counters[oi] < 0:
|
||||||
|
data += '0 '
|
||||||
|
continue
|
||||||
|
if o.idl[repname][counters[oi]] == ci:
|
||||||
|
num = o.deltas[repname][counters[oi]]
|
||||||
|
if num == 0:
|
||||||
|
data += '0 '
|
||||||
|
else:
|
||||||
|
data += '%1.16e ' % (num)
|
||||||
|
counters[oi] += 1
|
||||||
|
if counters[oi] >= len(o.idl[repname]):
|
||||||
|
counters[oi] = -1
|
||||||
|
else:
|
||||||
|
data += '0 '
|
||||||
|
else:
|
||||||
|
data += '0 '
|
||||||
|
data += '\n'
|
||||||
|
ad['#data'] = data
|
||||||
|
ed[''].append(ad)
|
||||||
|
pd['edata'].append(ed)
|
||||||
|
|
||||||
|
allcov = {}
|
||||||
|
for o in obsl:
|
||||||
|
for name in o.cov_names:
|
||||||
|
if name in allcov:
|
||||||
|
if not np.array_equal(allcov[name], o.covobs[name].cov):
|
||||||
|
raise Exception('Inconsistent covariance matrices for %s!' % (name))
|
||||||
|
else:
|
||||||
|
allcov[name] = o.covobs[name].cov
|
||||||
|
pd['cdata'] = []
|
||||||
|
for name in cov_names:
|
||||||
|
cd = {}
|
||||||
|
cd['id'] = name
|
||||||
|
|
||||||
|
covd = {'id': 'cov'}
|
||||||
|
if allcov[name].shape == ():
|
||||||
|
ncov = 1
|
||||||
|
covd['layout'] = '1 1 f'
|
||||||
|
covd['#data'] = '%1.14e' % (allcov[name])
|
||||||
|
else:
|
||||||
|
shape = allcov[name].shape
|
||||||
|
assert (shape[0] == shape[1])
|
||||||
|
ncov = shape[0]
|
||||||
|
covd['layout'] = '%d %d f' % (ncov, ncov)
|
||||||
|
ds = ''
|
||||||
|
for i in range(ncov):
|
||||||
|
for j in range(ncov):
|
||||||
|
val = allcov[name][i][j]
|
||||||
|
if val == 0:
|
||||||
|
ds += '0 '
|
||||||
|
else:
|
||||||
|
ds += '%1.14e ' % (val)
|
||||||
|
ds += '\n'
|
||||||
|
covd['#data'] = ds
|
||||||
|
|
||||||
|
gradd = {'id': 'grad'}
|
||||||
|
gradd['layout'] = '%d f%d' % (ncov, len(obsl))
|
||||||
|
ds = ''
|
||||||
|
for i in range(ncov):
|
||||||
|
for o in obsl:
|
||||||
|
if name in o.covobs:
|
||||||
|
val = o.covobs[name].grad[i]
|
||||||
|
if val != 0:
|
||||||
|
ds += '%1.14e ' % (val)
|
||||||
|
else:
|
||||||
|
ds += '0 '
|
||||||
|
else:
|
||||||
|
ds += '0 '
|
||||||
|
gradd['#data'] = ds
|
||||||
|
cd['array'] = [covd, gradd]
|
||||||
|
pd['cdata'].append(cd)
|
||||||
|
|
||||||
|
rs = '<?xml version="1.0" encoding="utf-8"?>\n' + _dobsdict_to_xmlstring_spaces(od)
|
||||||
|
|
||||||
|
return rs
|
||||||
|
|
||||||
|
|
||||||
|
def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=None, enstags={}, gz=True):
|
||||||
|
"""Export a list of Obs or structures containing Obs to a .xml.gz file
|
||||||
|
according to the Zeuthen dobs format.
|
||||||
|
|
||||||
|
Tags are not written or recovered automatically. The separator | is removed from the replica names.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
obsl : list
|
||||||
|
List of Obs that will be exported.
|
||||||
|
The Obs inside a structure do not have to be defined on the same set of configurations,
|
||||||
|
but the storage requirement is increased, if this is not the case.
|
||||||
|
fname : str
|
||||||
|
Filename of the output file.
|
||||||
|
name : str
|
||||||
|
The name of the observable.
|
||||||
|
spec : str
|
||||||
|
Optional string that describes the contents of the file.
|
||||||
|
origin : str
|
||||||
|
Specify where the data has its origin.
|
||||||
|
symbol : list
|
||||||
|
A list of symbols that describe the observables to be written. May be empty.
|
||||||
|
who : str
|
||||||
|
Provide the name of the person that exports the data.
|
||||||
|
enstags : dict
|
||||||
|
Provide alternative enstag for ensembles in the form enstags = {ename: enstag}
|
||||||
|
Otherwise, the ensemble name is used.
|
||||||
|
gz : bool
|
||||||
|
If True, the output is a gzipped XML. If False, the output is a XML file.
|
||||||
|
"""
|
||||||
|
|
||||||
|
dobsstring = create_dobs_string(obsl, name, spec, origin, symbol, who, enstags=enstags)
|
||||||
|
|
||||||
|
if not fname.endswith('.xml') and not fname.endswith('.gz'):
|
||||||
|
fname += '.xml'
|
||||||
|
|
||||||
|
if gz:
|
||||||
|
if not fname.endswith('.gz'):
|
||||||
|
fname += '.gz'
|
||||||
|
|
||||||
|
fp = gzip.open(fname, 'wb')
|
||||||
|
fp.write(dobsstring.encode('utf-8'))
|
||||||
|
else:
|
||||||
|
fp = open(fname, 'w', encoding='utf-8')
|
||||||
|
fp.write(dobsstring)
|
||||||
|
fp.close()
|
||||||
2
setup.py
2
setup.py
|
|
@ -9,5 +9,5 @@ setup(name='pyerrors',
|
||||||
author_email='fabian.joswig@ed.ac.uk',
|
author_email='fabian.joswig@ed.ac.uk',
|
||||||
packages=find_packages(),
|
packages=find_packages(),
|
||||||
python_requires='>=3.6.0',
|
python_requires='>=3.6.0',
|
||||||
install_requires=['numpy>=1.16', 'autograd @ git+https://github.com/HIPS/autograd.git', 'numdifftools', 'matplotlib>=3.3', 'scipy', 'iminuit>=2', 'h5py']
|
install_requires=['numpy>=1.16', 'autograd @ git+https://github.com/HIPS/autograd.git', 'numdifftools', 'matplotlib>=3.3', 'scipy', 'iminuit>=2', 'h5py', 'lxml']
|
||||||
)
|
)
|
||||||
|
|
|
||||||
|
|
@ -3,6 +3,7 @@ import gzip
|
||||||
import numpy as np
|
import numpy as np
|
||||||
import pyerrors as pe
|
import pyerrors as pe
|
||||||
import pyerrors.input.json as jsonio
|
import pyerrors.input.json as jsonio
|
||||||
|
import pyerrors.input.dobs as dobsio
|
||||||
import pytest
|
import pytest
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -251,3 +252,98 @@ def test_renorm_deriv_of_corr(tmp_path):
|
||||||
pe.input.json.dump_to_json(c, (tmp_path / 'test').as_posix())
|
pe.input.json.dump_to_json(c, (tmp_path / 'test').as_posix())
|
||||||
recover = pe.input.json.load_json((tmp_path / 'test').as_posix())
|
recover = pe.input.json.load_json((tmp_path / 'test').as_posix())
|
||||||
assert np.all([o == 0 for o in (c - recover)[1:-1]])
|
assert np.all([o == 0 for o in (c - recover)[1:-1]])
|
||||||
|
|
||||||
|
|
||||||
|
def test_dobsio():
|
||||||
|
o = pe.pseudo_Obs(1.0, .2, 'one|r1')
|
||||||
|
o1 = pe.pseudo_Obs(1.5, .2, 'one|r1')
|
||||||
|
|
||||||
|
ol = [o, o1]
|
||||||
|
fname = 'test_rw'
|
||||||
|
dobsio.write_pobs(ol, fname, 'Testobs')
|
||||||
|
rl = dobsio.read_pobs(fname)
|
||||||
|
|
||||||
|
for i in range(len(ol)):
|
||||||
|
assert (ol[i] - rl[i].is_zero())
|
||||||
|
|
||||||
|
od = {
|
||||||
|
'obsdata': ol,
|
||||||
|
'name': 'testn',
|
||||||
|
'spec': 'tests',
|
||||||
|
'origin': 'testo',
|
||||||
|
'symbol': ['A', 'B']
|
||||||
|
}
|
||||||
|
dobsio.write_pobs(ol, fname, od['name'], od['spec'], od['origin'], od['symbol'])
|
||||||
|
rd = dobsio.read_pobs(fname, full_output=True)
|
||||||
|
|
||||||
|
for i in range(len(od['obsdata'])):
|
||||||
|
assert (od['obsdata'][i] - rd['obsdata'][i].is_zero())
|
||||||
|
|
||||||
|
assert(od['spec'] == rd['description']['spec'])
|
||||||
|
assert(od['origin'] == rd['description']['origin'])
|
||||||
|
assert(od['name'] == rd['description']['name'])
|
||||||
|
assert(rd['description']['enstag'] == ol[0].e_names[0])
|
||||||
|
|
||||||
|
dobsio.write_dobs(ol, fname, 'Testobs')
|
||||||
|
rl = dobsio.read_dobs(fname)
|
||||||
|
|
||||||
|
for i in range(len(ol)):
|
||||||
|
assert (ol[i] - rl[i].is_zero())
|
||||||
|
|
||||||
|
dobsio.write_dobs(ol, fname, od['name'], od['spec'], od['origin'], od['symbol'])
|
||||||
|
rd = dobsio.read_dobs(fname, full_output=True)
|
||||||
|
os.remove(fname + '.xml.gz')
|
||||||
|
|
||||||
|
for i in range(len(od['obsdata'])):
|
||||||
|
assert (od['obsdata'][i] - rd['obsdata'][i].is_zero())
|
||||||
|
|
||||||
|
assert(od['spec'] == rd['description']['spec'])
|
||||||
|
assert(od['origin'] == rd['description']['origin'])
|
||||||
|
assert(od['name'] == rd['description']['name'])
|
||||||
|
|
||||||
|
o2 = pe.pseudo_Obs(0.5, .1, 'two|r1')
|
||||||
|
o3 = pe.pseudo_Obs(0.5, .1, 'two|r2')
|
||||||
|
o4 = pe.merge_obs([o2, o3])
|
||||||
|
otag = 'This has been merged!'
|
||||||
|
o4.tag = otag
|
||||||
|
do = o - .2 * o4
|
||||||
|
co1 = pe.cov_Obs(1., .123, 'cov1')
|
||||||
|
co3 = pe.cov_Obs(4., .1 ** 2, 'cov3')
|
||||||
|
do *= co1 / co3
|
||||||
|
do.tag = {'A': 2}
|
||||||
|
|
||||||
|
o5 = pe.pseudo_Obs(0.8, .1, 'two|r2')
|
||||||
|
co2 = pe.cov_Obs([1, 2], [[.12, .004], [.004, .02]], 'cov2')
|
||||||
|
o5 /= co2[0]
|
||||||
|
o5.tag = 2 * otag
|
||||||
|
|
||||||
|
tt1 = pe.Obs([np.random.rand(100)], ['t|r1'], idl=[range(2, 202, 2)])
|
||||||
|
tt2 = pe.Obs([np.random.rand(100)], ['t|r2'], idl=[range(2, 202, 2)])
|
||||||
|
tt3 = pe.Obs([np.random.rand(102)], ['qe|r1'])
|
||||||
|
|
||||||
|
tt = tt1 + tt2 + tt3
|
||||||
|
|
||||||
|
tt.tag = 'Test Obs: Ä'
|
||||||
|
|
||||||
|
ol = [o2, o3, o4, do, o5, tt]
|
||||||
|
print(ol)
|
||||||
|
fname = 'test_rw'
|
||||||
|
|
||||||
|
dobsio.write_dobs(ol, fname, 'TEST')
|
||||||
|
|
||||||
|
rl = dobsio.read_dobs(fname, noempty=True)
|
||||||
|
os.remove(fname + '.xml.gz')
|
||||||
|
[o.gamma_method() for o in rl]
|
||||||
|
|
||||||
|
for i in range(len(ol)):
|
||||||
|
assert (ol[i] - rl[i].is_zero())
|
||||||
|
|
||||||
|
for i in range(len(ol)):
|
||||||
|
if isinstance(ol[i], pe.Obs):
|
||||||
|
o = ol[i] - rl[i]
|
||||||
|
assert(o.is_zero())
|
||||||
|
or1 = np.ravel(ol[i])
|
||||||
|
or2 = np.ravel(rl[i])
|
||||||
|
for j in range(len(or1)):
|
||||||
|
o = or1[j] - or2[j]
|
||||||
|
assert(o.is_zero())
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue