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Merge pull request #30 from s-kuberski/feature/json_io

Browse source 
covobs in json I/O
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Fabian Joswig 2021-12-14 15:54:20 +00:00 • committed by GitHub
commit d2911afa31
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2 changed files with 128 additions and 27 deletions
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143
pyerrors/input/json.py
View file

@ -7,6 +7,7 @@ import datetime
import platform
import warnings
from ..obs import Obs
from ..covobs import Covobs
from .. import version as pyerrorsversion
@ -48,9 +49,25 @@ def create_json_string(ol, description='', indent=1):
def __str__(self):
return self.__repr__()
class Floatlist:
def __init__(self, li):
self.li = list(li)
def __repr__(self):
s = '['
for i in range(len(self.li)):
if i > 0:
s += ', '
s += '%1.15e' % (self.li[i])
s += ']'
return s
def __str__(self):
return self.__repr__()
def _gen_data_d_from_list(ol):
dl = []
for name in ol[0].e_names:
for name in ol[0].mc_names:
ed = {}
ed['id'] = name
ed['replica'] = []
@ -69,6 +86,23 @@ def create_json_string(ol, description='', indent=1):
dl.append(ed)
return dl
def _gen_cdata_d_from_list(ol):
dl = []
for name in ol[0].cov_names:
ed = {}
ed['id'] = name
ed['layout'] = str(ol[0].covobs[name].cov.shape).lstrip('(').rstrip(')').rstrip(',')
ed['cov'] = Floatlist(np.ravel(ol[0].covobs[name].cov))
ncov = ol[0].covobs[name].cov.shape[0]
ed['grad'] = []
for i in range(ncov):
ed['grad'].append([])
for o in ol:
ed['grad'][-1].append(o.covobs[name].grad[i][0])
ed['grad'][-1] = Floatlist(ed['grad'][-1])
dl.append(ed)
return dl
def _assert_equal_properties(ol, otype=Obs):
for o in ol:
if not isinstance(o, otype):
@ -92,7 +126,12 @@ def create_json_string(ol, description='', indent=1):
if o.reweighted:
d['reweighted'] = o.reweighted
d['value'] = [o.value]
d['data'] = _gen_data_d_from_list([o])
data = _gen_data_d_from_list([o])
if len(data) > 0:
d['data'] = data
cdata = _gen_cdata_d_from_list([o])
if len(cdata) > 0:
d['cdata'] = cdata
return d
def write_List_to_dict(ol):
@ -106,7 +145,12 @@ def create_json_string(ol, description='', indent=1):
if ol[0].reweighted:
d['reweighted'] = ol[0].reweighted
d['value'] = [o.value for o in ol]
d['data'] = _gen_data_d_from_list(ol)
data = _gen_data_d_from_list(ol)
if len(data) > 0:
d['data'] = data
cdata = _gen_cdata_d_from_list(ol)
if len(cdata) > 0:
d['cdata'] = cdata
return d
def write_Array_to_dict(oa):
@ -121,7 +165,12 @@ def create_json_string(ol, description='', indent=1):
if ol[0].reweighted:
d['reweighted'] = ol[0].reweighted
d['value'] = [o.value for o in ol]
d['data'] = _gen_data_d_from_list(ol)
data = _gen_data_d_from_list(ol)
if len(data) > 0:
d['data'] = data
cdata = _gen_cdata_d_from_list(ol)
if len(cdata) > 0:
d['cdata'] = cdata
return d
if not isinstance(ol, list):
@ -154,9 +203,9 @@ def create_json_string(ol, description='', indent=1):
deltas = False
split = s.split('\n')
for i in range(len(split)):
if '"deltas":' in split[i]:
if '"deltas":' in split[i] or '"cov":' in split[i] or '"grad":' in split[i]:
deltas = True
elif deltas:
if deltas:
split[i] = split[i].replace('"[', '[').replace(']"', ']')
if split[i][-1] == ']':
deltas = False
@ -222,16 +271,32 @@ def import_json_string(json_string, verbose=True, full_output=False):
def _gen_obsd_from_datad(d):
retd = {}
retd['names'] = []
retd['idl'] = []
retd['deltas'] = []
retd['is_merged'] = {}
if d:
retd['names'] = []
retd['idl'] = []
retd['deltas'] = []
retd['is_merged'] = {}
for ens in d:
for rep in ens['replica']:
retd['names'].append(rep['name'])
retd['idl'].append([di[0] for di in rep['deltas']])
retd['deltas'].append(np.array([di[1:] for di in rep['deltas']]))
retd['is_merged'][rep['name']] = rep.get('is_merged', False)
return retd
def _gen_covobsd_from_cdatad(d):
retd = {}
for ens in d:
for rep in ens['replica']:
retd['names'].append(rep['name'])
retd['idl'].append([di[0] for di in rep['deltas']])
retd['deltas'].append(np.array([di[1:] for di in rep['deltas']]))
retd['is_merged'][rep['name']] = rep.get('is_merged', False)
retl = []
name = ens['id']
layouts = ens.get('layout', '1').strip()
layout = [int(ls.strip()) for ls in layouts.split(',') if len(ls) > 0]
cov = np.reshape(ens['cov'], layout)
grad = ens['grad']
nobs = len(grad[0])
for i in range(nobs):
retl.append({'name': name, 'cov': cov, 'grad': [g[i] for g in grad]})
retd[name] = retl
return retd
def get_Obs_from_dict(o):
@ -240,11 +305,21 @@ def import_json_string(json_string, verbose=True, full_output=False):
raise Exception("layout is %s has to be 1 for type Obs." % (layouts), RuntimeWarning)
values = o['value']
od = _gen_obsd_from_datad(o['data'])
od = _gen_obsd_from_datad(o.get('data', {}))
cd = _gen_covobsd_from_cdatad(o.get('cdata', {}))
if od:
ret = Obs([[ddi[0] + values[0] for ddi in di] for di in od['deltas']], od['names'], idl=od['idl'])
ret.is_merged = od['is_merged']
else:
ret = Obs([], [])
ret._value = values[0]
for name in cd:
co = cd[name][0]
ret._covobs[name] = Covobs(None, co['cov'], co['name'], grad=co['grad'])
ret.names.append(co['name'])
ret = Obs([[ddi[0] + values[0] for ddi in di] for di in od['deltas']], od['names'], idl=od['idl'])
ret.reweighted = o.get('reweighted', False)
ret.is_merged = od['is_merged']
ret.tag = o.get('tag', [None])[0]
return ret
@ -252,14 +327,25 @@ def import_json_string(json_string, verbose=True, full_output=False):
layouts = o.get('layout', '1').strip()
layout = int(layouts)
values = o['value']
od = _gen_obsd_from_datad(o['data'])
od = _gen_obsd_from_datad(o.get('data', {}))
cd = _gen_covobsd_from_cdatad(o.get('cdata', {}))
ret = []
taglist = o.get('tag', layout * [None])
for i in range(layout):
ret.append(Obs([list(di[:, i] + values[i]) for di in od['deltas']], od['names'], idl=od['idl']))
if od:
ret.append(Obs([list(di[:, i] + values[i]) for di in od['deltas']], od['names'], idl=od['idl']))
ret[-1].is_merged = od['is_merged']
else:
ret.append(Obs([], []))
ret[-1]._value = values[i]
print('Created Obs with means= ', values[i])
for name in cd:
co = cd[name][i]
ret[-1]._covobs[name] = Covobs(None, co['cov'], co['name'], grad=co['grad'])
ret[-1].names.append(co['name'])
ret[-1].reweighted = o.get('reweighted', False)
ret[-1].is_merged = od['is_merged']
ret[-1].tag = taglist[i]
return ret
@ -268,14 +354,23 @@ def import_json_string(json_string, verbose=True, full_output=False):
layout = [int(ls.strip()) for ls in layouts.split(',') if len(ls) > 0]
N = np.prod(layout)
values = o['value']
od = _gen_obsd_from_datad(o['data'])
od = _gen_obsd_from_datad(o.get('data', {}))
cd = _gen_covobsd_from_cdatad(o.get('cdata', {}))
ret = []
taglist = o.get('tag', N * [None])
for i in range(N):
ret.append(Obs([di[:, i] + values[i] for di in od['deltas']], od['names'], idl=od['idl']))
if od:
ret.append(Obs([di[:, i] + values[i] for di in od['deltas']], od['names'], idl=od['idl']))
ret[-1].is_merged = od['is_merged']
else:
ret.append(Obs([], []))
ret[-1]._value = values[i]
for name in cd:
co = cd[name][i]
ret[-1]._covobs[name] = Covobs(None, co['cov'], co['name'], grad=co['grad'])
ret[-1].names.append(co['name'])
ret[-1].reweighted = o.get('reweighted', False)
ret[-1].is_merged = od['is_merged']
ret[-1].tag = taglist[i]
return np.reshape(ret, layout)

12
tests/io_test.py
View file

@ -13,10 +13,16 @@ def test_jsonio():
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')
o5.tag = 2*otag
co2 = pe.cov_Obs([1, 2], [[.12, .004], [.004, .02]], 'cov2')
o5 /= co2[0]
o3 /= co2[1]
o5.tag = 2 * otag
testl = [o3, o5]
arr = np.array([o3, o5])
@ -33,7 +39,7 @@ def test_jsonio():
tt.tag = 'Test Obs: Ä'
ol = [o4, do, testl, mat, arr, np.array([o]), np.array([tt, tt]), [tt, tt]]
ol = [o4, do, testl, mat, arr, np.array([o]), np.array([tt, tt]), [tt, tt], co1, co2, np.array(co2), co1 / co2[0]]
fname = 'test_rw'
jsonio.dump_to_json(ol, fname, indent=1, description='[I am a tricky description]')
@ -45,7 +51,7 @@ def test_jsonio():
for o, r in zip(ol, rl):
assert np.all(o == r)
for i in range(len(rl)):
for i in range(len(ol)):
if isinstance(ol[i], pe.Obs):
o = ol[i] - rl[i]
assert(o.is_zero())