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dobs: Zeros are written if config is not part of the Obs, these are ignored on input

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This commit is contained in:
Simon Kuberski 2023-02-02 15:31:46 +01:00
parent e34d49d88d
commit dc5116aa2f
2 changed files with 27 additions and 26 deletions
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51
pyerrors/input/dobs.py
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@ -397,7 +397,7 @@ def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
# this is based on Mattia Bruno's implementation at https://github.com/mbruno46/pyobs/blob/master/pyobs/IO/xml.py # 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): def import_dobs_string(content, full_output=False, separator_insertion=True):
"""Import a list of Obs from a string in the Zeuthen dobs format. """Import a list of Obs from a string in the Zeuthen dobs format.
Tags are not written or recovered automatically. Tags are not written or recovered automatically.
@ -406,9 +406,6 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
---------- ----------
content : str content : str
XML string containing the data 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 full_output : bool
If True, a dict containing auxiliary information and the data is returned. If True, a dict containing auxiliary information and the data is returned.
If False, only the data is returned as list. If False, only the data is returned as list.
@ -507,7 +504,11 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
for name in names: for name in names:
for i in range(len(deltad[name])): for i in range(len(deltad[name])):
deltad[name][i] = np.array(deltad[name][i]) + mean[i] tmp = np.zeros_like(deltad[name][i])
for j in range(len(deltad[name][i])):
if deltad[name][i][j] != 0.:
tmp[j] = deltad[name][i][j] + mean[i]
deltad[name][i] = tmp
res = [] res = []
for i in range(len(mean)): for i in range(len(mean)):
@ -516,11 +517,19 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
obs_names = [] obs_names = []
for name in names: for name in names:
h = np.unique(deltad[name][i]) h = np.unique(deltad[name][i])
if len(h) == 1 and np.all(h == mean[i]) and noempty: if len(h) == 1 and np.all(h == mean[i]):
continue continue
deltas.append(deltad[name][i]) repdeltas = []
obs_names.append(name) repidl = []
idl.append(idld[name]) for j in range(len(deltad[name][i])):
if deltad[name][i][j] != 0.:
repdeltas.append(deltad[name][i][j])
repidl.append(idld[name][j])
if len(repdeltas) > 0:
obs_names.append(name)
deltas.append(repdeltas)
idl.append(repidl)
res.append(Obs(deltas, obs_names, idl=idl)) res.append(Obs(deltas, obs_names, idl=idl))
res[-1]._value = mean[i] res[-1]._value = mean[i]
_check(len(e_names) == ne) _check(len(e_names) == ne)
@ -528,13 +537,10 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
cnames = list(covd.keys()) cnames = list(covd.keys())
for i in range(len(res)): for i in range(len(res)):
new_covobs = {name: Covobs(0, covd[name], name, grad=gradd[name][i]) for name in cnames} new_covobs = {name: Covobs(0, covd[name], name, grad=gradd[name][i]) for name in cnames}
if noempty: for name in cnames:
for name in cnames: if np.all(new_covobs[name].grad == 0):
if np.all(new_covobs[name].grad == 0): del new_covobs[name]
del new_covobs[name] cnames_loc = list(new_covobs.keys())
cnames_loc = list(new_covobs.keys())
else:
cnames_loc = cnames
for name in cnames_loc: for name in cnames_loc:
res[i].names.append(name) res[i].names.append(name)
res[i].shape[name] = 1 res[i].shape[name] = 1
@ -546,8 +552,6 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
res[i].tag = symbol[i] res[i].tag = symbol[i]
if res[i].tag == 'None': if res[i].tag == 'None':
res[i].tag = None res[i].tag = None
if not noempty:
_check(len(res[0].covobs.keys()) == nc)
if full_output: if full_output:
retd = {} retd = {}
tool = file_origin.get('tool', None) tool = file_origin.get('tool', None)
@ -568,7 +572,7 @@ def import_dobs_string(content, noempty=False, full_output=False, separator_inse
return res return res
def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insertion=True): def read_dobs(fname, full_output=False, gz=True, separator_insertion=True):
"""Import a list of Obs from an xml.gz file in the Zeuthen dobs format. """Import a list of Obs from an xml.gz file in the Zeuthen dobs format.
Tags are not written or recovered automatically. Tags are not written or recovered automatically.
@ -577,9 +581,6 @@ def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insert
---------- ----------
fname : str fname : str
Filename of the input file. 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 full_output : bool
If True, a dict containing auxiliary information and the data is returned. If True, a dict containing auxiliary information and the data is returned.
If False, only the data is returned as list. If False, only the data is returned as list.
@ -615,7 +616,7 @@ def read_dobs(fname, noempty=False, full_output=False, gz=True, separator_insert
with open(fname, 'r') as fin: with open(fname, 'r') as fin:
content = fin.read() content = fin.read()
return import_dobs_string(content, noempty, full_output, separator_insertion=separator_insertion) return import_dobs_string(content, full_output, separator_insertion=separator_insertion)
def _dobsdict_to_xmlstring(d): def _dobsdict_to_xmlstring(d):
@ -782,7 +783,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
o = obsl[oi] o = obsl[oi]
if repname in o.idl: if repname in o.idl:
if counters[oi] < 0: if counters[oi] < 0:
num = offsets[oi] num = 0
if num == 0: if num == 0:
data += '0 ' data += '0 '
else: else:
@ -798,7 +799,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
if counters[oi] >= len(o.idl[repname]): if counters[oi] >= len(o.idl[repname]):
counters[oi] = -1 counters[oi] = -1
else: else:
num = offsets[oi] num = 0
if num == 0: if num == 0:
data += '0 ' data += '0 '
else: else:

2
tests/json_io_test.py
View file

@ -339,7 +339,7 @@ def test_dobsio():
dobsio.write_dobs(ol, fname, 'TEST') dobsio.write_dobs(ol, fname, 'TEST')
rl = dobsio.read_dobs(fname, noempty=True) rl = dobsio.read_dobs(fname)
os.remove(fname + '.xml.gz') os.remove(fname + '.xml.gz')
[o.gamma_method() for o in rl] [o.gamma_method() for o in rl]