From 8674dff110c3410f029b41eab511b46d43a71c67 Mon Sep 17 00:00:00 2001 From: fjosw Date: Tue, 14 Dec 2021 15:55:20 +0000 Subject: [PATCH] Documentation updated --- docs/pyerrors/input/json.html | 285 ++++++++++++++++++++++++++++------ 1 file changed, 237 insertions(+), 48 deletions(-) diff --git a/docs/pyerrors/input/json.html b/docs/pyerrors/input/json.html index c974e296..0e5ed556 100644 --- a/docs/pyerrors/input/json.html +++ b/docs/pyerrors/input/json.html @@ -87,6 +87,7 @@ import platform import warnings from ..obs import Obs +from ..covobs import Covobs from .. import version as pyerrorsversion @@ -128,9 +129,25 @@ 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'] = [] @@ -149,6 +166,23 @@ 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): @@ -172,7 +206,12 @@ 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): @@ -186,7 +225,12 @@ 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): @@ -201,7 +245,12 @@ 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): @@ -234,9 +283,9 @@ 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 @@ -302,16 +351,32 @@ 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): @@ -320,11 +385,21 @@ 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 @@ -332,14 +407,25 @@ 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 @@ -348,14 +434,23 @@ 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) @@ -489,9 +584,25 @@ 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'] = [] @@ -510,6 +621,23 @@ 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): @@ -533,7 +661,12 @@ 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): @@ -547,7 +680,12 @@ 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): @@ -562,7 +700,12 @@ 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): @@ -595,9 +738,9 @@ 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 @@ -730,16 +873,32 @@ If True, the output is a gzipped json. If False, the output is a json file. 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): @@ -748,11 +907,21 @@ If True, the output is a gzipped json. If False, the output is a json file. 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 @@ -760,14 +929,25 @@ If True, the output is a gzipped json. If False, the output is a json file. 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 @@ -776,14 +956,23 @@ If True, the output is a gzipped json. If False, the output is a json file. 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)