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https://github.com/fjosw/pyerrors.git
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Some changes on dobs
This commit is contained in:
Simon Kuberski
parent
be1eeccd8e
commit
0f735c0d2d
2 changed files with 192 additions and 297 deletions
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@ -13,9 +13,9 @@ from ..covobs import Covobs
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from .. import version as pyerrorsversion
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# standard pobs
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# https://stackoverflow.com/a/10076823
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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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@ -38,164 +38,6 @@ def _etree_to_dict(t):
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return d
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def _get_data_from_root(d, root):
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tree = et.ElementTree(root)
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nl = []
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pl = []
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for node in root.findall('.//array'):
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nl.append(node)
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pl.append(tree.getpath(node))
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for nd in range(len(nl)):
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s = pl[nd].split('/')
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ad = d
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for i in range(len(s) - 1):
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if len(s[i]) > 0:
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ad = ad[s[i]]
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nr = int(ad['nr'])
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ad = ad['array']
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if '[' in s[-1]:
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ai = int(s[-1].lstrip('array[').rstrip(']')) - 1
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ad = ad[ai]
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if nr == 1:
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dats = [t for t in nl[nd].itertext()][0]
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else:
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dats = [t for t in nl[nd].itertext()][-1]
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dats = [o.strip() for o in dats.split('\n')]
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layout = ad['layout']
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sl = layout.split()
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datl = []
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idx = []
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for di in dats:
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if len(di) > 0:
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ds = di.split()
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if sl[1] == 'i':
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i = int(ds[0])
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idx.append(i)
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df = np.asarray(ds[1:], dtype=np.float64)
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else:
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df = np.asarray(ds, dtype=np.float64)
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nfloat = int(sl[-1].lstrip('f'))
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assert len(df) == nfloat
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datl.append(df)
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ad['idx'] = idx
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ad['#data'] = np.transpose(np.array(datl))
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return d
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# https://stackoverflow.com/a/9808122
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def _find(key, value):
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for k, v in (value.items() if isinstance(value, dict) else enumerate(value) if isinstance(value, list) else []):
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if k == key:
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yield v
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elif isinstance(v, (dict, list)):
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for result in _find(key, v):
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yield result
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# generate obs from all 'array' entries inside a dict
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def _gen_obs_from_dict(d):
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pobs_list = [a for a in _find('array', d)]
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ol = []
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for po in pobs_list:
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if isinstance(po, list):
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names = []
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idl = [poi['idx'] for poi in po]
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names = [poi['id'] for poi in po]
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for i in range(len(po[0])):
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tag = po[0]['symbol'].split()[-8 + i]
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data = [poi['#data'][i] for poi in po]
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ol.append(Obs(data, names, idl=idl))
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ol[-1].tag = tag
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print(tag)
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return ol
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# generate obs from entries inside a 'pobs'-dict
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def _gen_obs_from_pobs_dict(d):
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po = d['array']
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if isinstance(po, dict):
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po = [po]
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enstag = d['enstag']
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nr = int(d['nr'])
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assert len(po) == nr, 'Lenght of array %d does not match nr=%d' % (len(po), nr)
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ol = []
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names = []
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idl = [poi['idx'] for poi in po]
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names = [poi['id'] for poi in po]
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names = [name.replace(enstag, enstag + '|') for name in names]
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if len(po[0]['symbol'].split()) >= len(po[0]):
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gettag = True
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else:
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gettag = False
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nobs = np.shape(po[0]['#data'])[0]
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print(nobs, 'observables')
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for i in range(nobs):
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if gettag:
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tag = po[0]['symbol'].split()[i + 1]
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else:
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tag = po[0]['symbol']
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data = [poi['#data'][i] for poi in po]
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ol.append(Obs(data, names, idl=idl))
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ol[-1].tag = tag
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return ol
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def _read_pobs_traditional(fname, full_output=False):
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"""Import a list of Obs from an xml.gz file in the Zeuthen pobs format,
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this does not include pobs that are written using the dobs package.
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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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"""
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# open and read gzipped xml file
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infile = gzip.open(fname)
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content = infile.read()
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# parse xml file content
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root = et.fromstring(content)
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# parse to dict
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d = _etree_to_dict(root)
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# get the actual data from the xml file
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d = _get_data_from_root(d, root)
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# pobs dict:
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pod = d[list(d.keys())[0]]['pobs']
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# convert data to Obs
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ol = _gen_obs_from_pobs_dict(pod)
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if full_output:
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retd = {}
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retd['obsdata'] = ol
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for k in pod.keys():
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if k == 'spec' and isinstance(pod[k], dict):
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retd[k] = ''
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if '#data' in pod[k]:
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if isinstance(pod[k]['#data'], list):
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for el in pod[k]['#data']:
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retd[k] += el
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else:
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retd[k] = pod[k]['#data']
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for li in pod[k]:
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if not li == '#data':
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retd[k] += '\n<%s>\n ' % (li) + pod[k][li] + '\n<%s%s>' % ('/', li)
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elif not k == 'array':
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retd[k] = pod[k]
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return retd
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else:
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return ol
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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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@ -243,7 +85,7 @@ def _dict_to_xmlstring_spaces(d, space=' '):
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return o
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def create_pobs_string(obsl, name, spec='', origin='', symbol=[]):
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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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@ -262,6 +104,8 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[]):
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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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@ -288,7 +132,12 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[]):
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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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pd['enstag'] = ename
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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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@ -322,7 +171,7 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[]):
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return rs
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def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], gz=True):
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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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@ -343,10 +192,12 @@ def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], gz=True):
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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 json. If False, the output is a json file.
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"""
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pobsstring = create_pobs_string(obsl, name, spec, origin, symbol)
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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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@ -372,11 +223,18 @@ def _check(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 Exception('Tag %s not in data!' % (tag))
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raise _NoTagInDataError(tag)
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def _import_array(arr):
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@ -384,7 +242,7 @@ def _import_array(arr):
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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:
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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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@ -430,7 +288,7 @@ def _import_cdata(cd):
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return cd[0].text.strip(), cov, grad
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def read_pobs(fname, full_output=False, gz=True):
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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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@ -442,6 +300,10 @@ def read_pobs(fname, full_output=False, gz=True):
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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 position separator_insertion
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"""
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if not fname.endswith('.xml') and not fname.endswith('.gz'):
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@ -463,32 +325,28 @@ def read_pobs(fname, full_output=False, gz=True):
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_check(root[2].tag == 'pobs')
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pobs = root[2]
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if root.tag == 'observables' and False:
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_check(root[0].tag in ['schema'])
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version = root[0][1].text.strip()
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version = root[0][1].text.strip()
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_check(root[1].tag == 'origin')
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file_origin = _etree_to_dict(root[1])['origin']
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_check(root[1].tag == 'origin')
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file_origin = _etree_to_dict(root[1])['origin']
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res = _read_pobs_traditional(fname)
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else:
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# _check(root.tag in ['OBSERVABLES'])
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# _check(root[0].tag in ['SCHEMA'])
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version = root[0][1].text.strip()
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_check(root[1].tag == 'origin')
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file_origin = _etree_to_dict(root[1])['origin']
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deltas = []
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names = []
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idl = []
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for i in range(5, len(pobs)):
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delta, name, idx = _import_rdata(pobs[i])
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deltas.append(delta)
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names.append(name)
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idl.append(idx)
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res = [Obs([d[i] for d in deltas], names, idl=idl) for i in range(len(deltas[0]))]
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deltas = []
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names = []
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idl = []
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for i in range(5, len(pobs)):
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delta, name, idx = _import_rdata(pobs[i])
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deltas.append(delta)
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if separator_insertion is None:
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pass
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elif isinstance(separator_insertion, int):
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name = name[:separator_insertion] + '|' + name[separator_insertion:]
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elif isinstance(separator_insertion, str):
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name = name.replace(separator_insertion, "|%s" % (separator_insertion))
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else:
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raise Exception("separator_insertion has to be string or int, is ", type(separator_insertion))
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names.append(name)
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idl.append(idx)
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res = [Obs([d[i] for d in deltas], names, idl=idl) for i in range(len(deltas[0]))]
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descriptiond = {}
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for i in range(4):
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@ -520,9 +378,13 @@ def read_pobs(fname, full_output=False, gz=True):
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return res
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# Reading (and writing) dobs is not yet working properly:
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# we have to loop over root[2:] because each entry is a dobs
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# But maybe this is just a problem with Ben's implementation
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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):
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"""Import a list of Obs from an xml.gz file in the Zeuthen dobs format.
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def import_dobs_string(content, noempty=False, full_output=False, separator_insertion=None):
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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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@ -536,6 +398,10 @@ def import_dobs_string(content, noempty=False, full_output=False):
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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 position separator_insertion
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"""
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root = et.fromstring(content)
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@ -574,6 +440,7 @@ def import_dobs_string(content, noempty=False, full_output=False):
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gradd = {}
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names = []
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e_names = []
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enstags = {}
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for k in range(6, len(list(dobs))):
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if dobs[k].tag == "edata":
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_check(dobs[k][0].tag == "enstag")
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@ -583,8 +450,20 @@ def import_dobs_string(content, noempty=False, full_output=False):
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R = int(dobs[k][1].text.strip())
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for i in range(2, 2 + R):
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deltas, rname, idx = _import_rdata(dobs[k][i])
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if rname != ename:
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rname = rname[:len(ename)] + '|' + rname[len(ename):]
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if separator_insertion is None:
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if rname.startswith(ename):
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rname = rname[:len(ename)] + '|' + rname[len(ename):]
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elif isinstance(separator_insertion, int):
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rname = rname[:separator_insertion] + '|' + rname[separator_insertion:]
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elif isinstance(separator_insertion, str):
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rname = rname.replace(separator_insertion, "|%s" % (separator_insertion))
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else:
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raise Exception("separator_insertion has to be string or int, is ", type(separator_insertion))
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if '|' in rname:
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new_ename = rname[:rname.index('|')]
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else:
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new_ename = ename
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enstags[new_ename] = ename
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idld[rname] = idx
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deltad[rname] = deltas
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names.append(rname)
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@ -602,6 +481,7 @@ def import_dobs_string(content, noempty=False, full_output=False):
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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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res = []
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for i in range(len(mean)):
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deltas = []
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@ -615,7 +495,7 @@ def import_dobs_string(content, noempty=False, full_output=False):
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obs_names.append(name)
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idl.append(idld[name])
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res.append(Obs(deltas, obs_names, idl=idl))
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print(mean, 'vs', res)
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_check(len(e_names) == ne)
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cnames = list(covd.keys())
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@ -654,13 +534,14 @@ def import_dobs_string(content, noempty=False, full_output=False):
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retd['date'] = file_origin['date']
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retd['host'] = file_origin['host']
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retd['description'] = descriptiond
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retd['enstags'] = enstags
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retd['obsdata'] = res
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return retd
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else:
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return res
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def read_dobs(fname, noempty=False, full_output=False, gz=True):
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def read_dobs(fname, noempty=False, 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 dobs format.
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Tags are not written or recovered automatically.
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|
|
@ -677,6 +558,10 @@ def read_dobs(fname, noempty=False, full_output=False, gz=True):
|
|||
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 or int
|
||||
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 position separator_insertion
|
||||
"""
|
||||
|
||||
if not fname.endswith('.xml') and not fname.endswith('.gz'):
|
||||
|
|
@ -696,7 +581,7 @@ def read_dobs(fname, noempty=False, full_output=False, gz=True):
|
|||
infile = gzip.open(fname)
|
||||
content = infile.read()
|
||||
|
||||
return import_dobs_string(content, noempty, full_output)
|
||||
return import_dobs_string(content, noempty, full_output, separator_insertion=separator_insertion)
|
||||
|
||||
|
||||
def _dobsdict_to_xmlstring(d):
|
||||
|
|
@ -758,7 +643,7 @@ def _dobsdict_to_xmlstring_spaces(d, space=' '):
|
|||
return o
|
||||
|
||||
|
||||
def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=None):
|
||||
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.
|
||||
|
||||
|
|
@ -780,6 +665,9 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
|
|||
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 = []
|
||||
|
|
@ -787,6 +675,9 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
|
|||
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:
|
||||
|
|
@ -827,7 +718,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
|
|||
pd['edata'] = []
|
||||
for name in mc_names:
|
||||
ed = {}
|
||||
ed['enstag'] = name
|
||||
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
|
||||
|
|
@ -852,7 +743,6 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
|
|||
data += '0 '
|
||||
continue
|
||||
if o.idl[repname][counters[oi]] == ci:
|
||||
# c = o.idl[repname][counters[oi]]
|
||||
num = o.deltas[repname][counters[oi]]
|
||||
if num == 0:
|
||||
data += '0 '
|
||||
|
|
@ -926,7 +816,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
|
|||
return rs
|
||||
|
||||
|
||||
def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=None, gz=True):
|
||||
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.
|
||||
|
||||
|
|
@ -950,11 +840,14 @@ def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=No
|
|||
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 json. If False, the output is a json file.
|
||||
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)
|
||||
dobsstring = create_dobs_string(obsl, name, spec, origin, symbol, who, enstags=enstags)
|
||||
|
||||
if not fname.endswith('.xml') and not fname.endswith('.gz'):
|
||||
fname += '.xml'
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import pyerrors.input.json as jsonio
|
|||
import pyerrors.input.dobs as dobsio
|
||||
import pytest
|
||||
|
||||
|
||||
def test_jsonio():
|
||||
o = pe.pseudo_Obs(1.0, .2, 'one')
|
||||
o2 = pe.pseudo_Obs(0.5, .1, 'two|r1')
|
||||
|
|
@ -139,99 +140,6 @@ def test_json_corr_2d_io():
|
|||
assert my_corr.prange == recover.prange
|
||||
|
||||
|
||||
def test_dobsio():
|
||||
o = pe.pseudo_Obs(1.0, .2, 'one')
|
||||
o1 = pe.pseudo_Obs(1.5, .2, 'one')
|
||||
|
||||
ol = [o, o1]
|
||||
fname = 'test_rw'
|
||||
dobsio.write_pobs(ol, fname, 'Testobs')
|
||||
rl = dobsio.read_pobs(fname)
|
||||
|
||||
for o, r in zip(ol, rl):
|
||||
assert np.all(o == r)
|
||||
|
||||
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 o, r in zip(od['obsdata'], rd['obsdata']):
|
||||
assert np.all(o == r)
|
||||
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 o, r in zip(ol, rl):
|
||||
assert np.all(o == r)
|
||||
|
||||
dobsio.write_dobs(ol, fname, od['name'], od['spec'], od['origin'], od['symbol'])
|
||||
rd = dobsio.read_dobs(fname, full_output=True)
|
||||
|
||||
for o, r in zip(od['obsdata'], rd['obsdata']):
|
||||
assert np.all(o == r)
|
||||
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]
|
||||
#o3 /= co2[1]
|
||||
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'])
|
||||
|
||||
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)
|
||||
[o.gamma_method() for o in rl]
|
||||
|
||||
#os.remove(fname + '.xml.gz')
|
||||
|
||||
for o, r in zip(ol, rl):
|
||||
assert np.all(o == r)
|
||||
|
||||
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())
|
||||
|
||||
def test_json_dict_io():
|
||||
def check_dict_equality(d1, d2):
|
||||
def dict_check_obs(d1, d2):
|
||||
|
|
@ -344,3 +252,97 @@ def test_renorm_deriv_of_corr(tmp_path):
|
|||
pe.input.json.dump_to_json(c, (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]])
|
||||
|
||||
|
||||
def test_dobsio():
|
||||
o = pe.pseudo_Obs(1.0, .2, 'one')
|
||||
o1 = pe.pseudo_Obs(1.5, .2, 'one')
|
||||
|
||||
ol = [o, o1]
|
||||
fname = 'test_rw'
|
||||
dobsio.write_pobs(ol, fname, 'Testobs')
|
||||
rl = dobsio.read_pobs(fname)
|
||||
|
||||
for o, r in zip(ol, rl):
|
||||
assert np.all(o == r)
|
||||
|
||||
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 o, r in zip(od['obsdata'], rd['obsdata']):
|
||||
assert np.all(o == r)
|
||||
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 o, r in zip(ol, rl):
|
||||
assert np.all(o == r)
|
||||
|
||||
dobsio.write_dobs(ol, fname, od['name'], od['spec'], od['origin'], od['symbol'])
|
||||
rd = dobsio.read_dobs(fname, full_output=True)
|
||||
|
||||
for o, r in zip(od['obsdata'], rd['obsdata']):
|
||||
assert np.all(o == r)
|
||||
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]
|
||||
#o3 /= co2[1]
|
||||
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'])
|
||||
|
||||
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)
|
||||
[o.gamma_method() for o in rl]
|
||||
|
||||
#os.remove(fname + '.xml.gz')
|
||||
|
||||
for o, r in zip(ol, rl):
|
||||
assert np.all(o == r)
|
||||
|
||||
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
Reference in a new issue