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dobs: Zeros are written if config is not part of the Obs, these are ignored on input
This commit is contained in:
Simon Kuberski
parent
e34d49d88d
commit
dc5116aa2f
2 changed files with 27 additions and 26 deletions
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@ -397,7 +397,7 @@ def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
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# this is based on Mattia Bruno's implementation at https://github.com/mbruno46/pyobs/blob/master/pyobs/IO/xml.py
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def import_dobs_string(content, noempty=False, full_output=False, separator_insertion=True):
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def import_dobs_string(content, full_output=False, separator_insertion=True):
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"""Import a list of Obs from a string in the Zeuthen dobs format.
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Tags are not written or recovered automatically.
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@ -406,9 +406,6 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
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----------
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content : str
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XML string containing the data
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noemtpy : bool
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If True, ensembles with no contribution to the Obs are not included.
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If False, ensembles are included as written in the file, possibly with vanishing entries.
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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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@ -507,7 +504,11 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
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for name in names:
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for i in range(len(deltad[name])):
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deltad[name][i] = np.array(deltad[name][i]) + mean[i]
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tmp = np.zeros_like(deltad[name][i])
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for j in range(len(deltad[name][i])):
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if deltad[name][i][j] != 0.:
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tmp[j] = deltad[name][i][j] + mean[i]
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deltad[name][i] = tmp
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res = []
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for i in range(len(mean)):
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@ -516,11 +517,19 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
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obs_names = []
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for name in names:
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h = np.unique(deltad[name][i])
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if len(h) == 1 and np.all(h == mean[i]) and noempty:
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if len(h) == 1 and np.all(h == mean[i]):
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continue
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deltas.append(deltad[name][i])
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obs_names.append(name)
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idl.append(idld[name])
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repdeltas = []
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repidl = []
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for j in range(len(deltad[name][i])):
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if deltad[name][i][j] != 0.:
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repdeltas.append(deltad[name][i][j])
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repidl.append(idld[name][j])
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if len(repdeltas) > 0:
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obs_names.append(name)
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deltas.append(repdeltas)
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idl.append(repidl)
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res.append(Obs(deltas, obs_names, idl=idl))
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res[-1]._value = mean[i]
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_check(len(e_names) == ne)
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@ -528,13 +537,10 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
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cnames = list(covd.keys())
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for i in range(len(res)):
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new_covobs = {name: Covobs(0, covd[name], name, grad=gradd[name][i]) for name in cnames}
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if noempty:
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for name in cnames:
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if np.all(new_covobs[name].grad == 0):
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del new_covobs[name]
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cnames_loc = list(new_covobs.keys())
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else:
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cnames_loc = cnames
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for name in cnames:
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if np.all(new_covobs[name].grad == 0):
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del new_covobs[name]
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cnames_loc = list(new_covobs.keys())
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for name in cnames_loc:
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res[i].names.append(name)
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res[i].shape[name] = 1
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@ -546,8 +552,6 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
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res[i].tag = symbol[i]
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if res[i].tag == 'None':
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res[i].tag = None
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if not noempty:
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_check(len(res[0].covobs.keys()) == nc)
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if full_output:
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retd = {}
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tool = file_origin.get('tool', None)
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@ -568,7 +572,7 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
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return res
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def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insertion=True):
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def read_dobs(fname, full_output=False, gz=True, separator_insertion=True):
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"""Import a list of Obs from an xml.gz file in the Zeuthen dobs format.
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Tags are not written or recovered automatically.
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@ -577,9 +581,6 @@ def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insert
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----------
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fname : str
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Filename of the input file.
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noemtpy : bool
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If True, ensembles with no contribution to the Obs are not included.
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If False, ensembles are included as written in the 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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@ -615,7 +616,7 @@ def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insert
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with open(fname, 'r') as fin:
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content = fin.read()
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return import_dobs_string(content, noempty, full_output, separator_insertion=separator_insertion)
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return import_dobs_string(content, full_output, separator_insertion=separator_insertion)
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def _dobsdict_to_xmlstring(d):
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@ -782,7 +783,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
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o = obsl[oi]
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if repname in o.idl:
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if counters[oi] < 0:
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num = offsets[oi]
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num = 0
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if num == 0:
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data += '0 '
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else:
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@ -798,7 +799,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
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if counters[oi] >= len(o.idl[repname]):
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counters[oi] = -1
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else:
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num = offsets[oi]
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num = 0
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if num == 0:
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data += '0 '
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else:
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@ -339,7 +339,7 @@ def test_dobsio():
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dobsio.write_dobs(ol, fname, 'TEST')
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rl = dobsio.read_dobs(fname, noempty=True)
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rl = dobsio.read_dobs(fname)
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os.remove(fname + '.xml.gz')
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[o.gamma_method() for o in rl]
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