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flake8 compliance
This commit is contained in:
jkuhl-uni
parent
53f727092d
commit
302a7ae439
1 changed files with 168 additions and 109 deletions
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@ -8,39 +8,55 @@ import numpy as np # Thinly-wrapped numpy
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from ..obs import Obs
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from . import utils
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def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version = "1.0c", **kwargs):
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def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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version="1.0c", **kwargs):
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"""Read sfcf c format from given folder structure.
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Parameters
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----------
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quarks: str
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Label of the quarks used in the sfcf input file. e.g. "quark quark"
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for version 0.0 this does NOT need to be given with the typical " - " that is present in the output file,
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for version 0.0 this does NOT need to be given with the typical " - "
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that is present in the output file,
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this is done automatically for this version
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noffset: int
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Offset of the source (only relevant when wavefunctions are used)
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wf: int
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ID of wave function
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wf2: int
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ID of the second wavefunction (only relevant for boundary-to-boundary correlation functions)
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ID of the second wavefunction
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(only relevant for boundary-to-boundary correlation functions)
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im: bool
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if True, read imaginary instead of real part of the correlation function.
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if True, read imaginary instead of real part
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of the correlation function.
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b2b: bool
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if True, read a time-dependent boundary-to-boundary correlation function
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if True, read a time-dependent boundary-to-boundary
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correlation function
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single: bool
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if True, read time independent boundary to boundary correlation function
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if True, read time independent boundary to boundary
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correlation function
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names: list
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Alternative labeling for replicas/ensembles. Has to have the appropriate length
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Alternative labeling for replicas/ensembles.
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Has to have the appropriate length
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ens_name : str
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replaces the name of the ensemble
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version: str
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version of SFCF, with which the measurement was done. if the compact output option (-c) was spectified, append a c to the version (e.g. "1.0c")
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version of SFCF, with which the measurement was done.
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if the compact output option (-c) was spectified,
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append a "c" to the version (e.g. "1.0c")
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if the append output option (-a) was specified,
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append an "a" to the version
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replica: list
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list of replica to be read, default is all
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files: list
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list of files to be read per replica, default is all. for non-conpact ouztput format, hand the folders to be read here.
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list of files to be read per replica, default is all.
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for non-conpact ouztput format, hand the folders to be read here.
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check_configs:
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list of list of supposed configs, eg. [range(1,1000)] for one replicum with 1000 configs
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list of list of supposed configs, eg. [range(1,1000)]
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for one replicum with 1000 configs
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TODO:
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- whats going on with files here?
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"""
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if kwargs.get('im'):
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im = 1
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@ -63,15 +79,17 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
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if "files" in kwargs:
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files = kwargs.get("files")
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#due to higher usage in current projects, compact file format is default
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# due to higher usage in current projects,
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# compact file format is default
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compact = True
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appended = False
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#get version string
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known_versions = ["0.0","1.0","2.0","1.0c","2.0c","1.0a","2.0a"]
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# get version string
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known_versions = ["0.0", "1.0", "2.0", "1.0c", "2.0c", "1.0a", "2.0a"]
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if not version in known_versions:
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if version not in known_versions:
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raise Exception("This version is not known!")
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#if the letter c is appended to the version, the compact fileformat is used (former read_sfcf_c)
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# if the letter c is appended to the version,
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# the compact fileformat is used (former read_sfcf_c)
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if(version[-1] == "c"):
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appended = False
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compact = True
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@ -103,15 +121,19 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
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if not fnmatch.fnmatch(exc, prefix + '*'):
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ls = list(set(ls) - set([exc]))
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if len(ls) > 1:
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ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0])) # New version, to cope with ids, etc.
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# New version, to cope with ids, etc.
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ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
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if not appended:
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replica = len(ls)
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else:
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replica = len([l.split(".")[-1] for l in ls])//len(set([l.split(".")[-1] for l in ls]))
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print('Read', part, 'part of', name, 'from', prefix[:-1], ',', replica, 'replica')
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replica = len([file.split(".")[-1] for file in ls])\
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// len(set([file.split(".")[-1] for file in ls]))
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print('Read', part, 'part of', name, 'from', prefix[:-1],
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',', replica, 'replica')
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if 'names' in kwargs:
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new_names = kwargs.get('names')
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if len(new_names)!=len(set(new_names)):
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if len(new_names) != len(set(new_names)):
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raise Exception("names are not unique!")
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if len(new_names) != replica:
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raise Exception('Names does not have the required length', replica)
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@ -123,32 +145,36 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
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for entry in ls:
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try:
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idx = entry.index('r')
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except:
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raise Exception("Automatic recognition of replicum failed, please enter the key word 'names'.")
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except Exception:
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raise Exception("Automatic recognition of replicum failed, \
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please enter the key word 'names'.")
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if 'ens_name' in kwargs:
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new_names.append(kwargs.get('ens_name') + '|' + entry[idx:])
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new_names.append(kwargs.get('ens_name') + '|' +
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entry[idx:])
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else:
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new_names.append(entry[:idx] + '|' + entry[idx:])
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else:
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for exc in ls:
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if not fnmatch.fnmatch(exc, prefix + '*.'+name):
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ls = list(set(ls) - set([exc]))
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ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
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for entry in ls:
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myentry = entry[:-len(name)-1]
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print(myentry)
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# print(myentry)
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try:
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idx = myentry.index('r')
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except:
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raise Exception("Automatic recognition of replicum failed, please enter the key word 'names'.")
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except Exception:
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raise Exception("Automatic recognition of replicum failed, \
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please enter the key word 'names'.")
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if 'ens_name' in kwargs:
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new_names.append(kwargs.get('ens_name') + '|' + myentry[idx:])
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new_names.append(kwargs.get('ens_name') + '|' +
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myentry[idx:])
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else:
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new_names.append(myentry[:idx] + '|' + myentry[idx:])
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#print(new_names)
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# print(new_names)
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idl = []
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if not appended:
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for i, item in enumerate(ls):
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@ -157,24 +183,26 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
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sub_ls = kwargs.get("files")
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sub_ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
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else:
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for (dirpath, dirnames, filenames) in os.walk(path + '/' + item):
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for (dirpath, dirnames, filenames) in \
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os.walk(path + '/' + item):
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if compact:
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sub_ls.extend(filenames)
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else:
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sub_ls.extend(dirnames)
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break
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#print(sub_ls)
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for exc in sub_ls:
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# print(sub_ls)
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for exc in sub_ls:
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if compact:
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if not fnmatch.fnmatch(exc, prefix + '*'):
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sub_ls = list(set(sub_ls) - set([exc]))
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sub_ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
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sub_ls.sort(key=lambda x:
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int(re.findall(r'\d+', x)[-1]))
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else:
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if not fnmatch.fnmatch(exc, 'cfg*'):
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sub_ls = list(set(sub_ls) - set([exc]))
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sub_ls.sort(key=lambda x: int(x[3:]))
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#print(sub_ls)
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# print(sub_ls)
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rep_idl = []
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no_cfg = len(sub_ls)
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for cfg in sub_ls:
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@ -183,54 +211,73 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
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rep_idl.append(int(cfg.split("n")[-1]))
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else:
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rep_idl.append(int(cfg[3:]))
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except:
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raise Exception("Couldn't parse idl from directroy, problem with file "+cfg)
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except Exception:
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raise Exception("Couldn't parse idl from directroy, \
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problem with file "+cfg)
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rep_idl.sort()
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#maybe there is a better way to print the idls
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# maybe there is a better way to print the idls
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print(item, ':', no_cfg, ' configurations')
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idl.append(rep_idl)
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#here we have found all the files we need to look into.
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# here we have found all the files we need to look into.
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if i == 0:
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#here, we want to find the place within the file, where the correlator we need is stored.
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# here, we want to find the place within the file,
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# where the correlator we need is stored.
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if compact:
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#to do so, the pattern needed is put together from the input values
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pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf)
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# to do so, the pattern needed is put together
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# from the input values
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pattern = 'name ' + name + '\nquarks '\
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+ quarks + '\noffset '\
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+ str(noffset) + '\nwf '\
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+ str(wf)
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if b2b:
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pattern += '\nwf_2 ' + str(wf2)
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#and the file is parsed through to find the pattern
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with open(path + '/' + item + '/' + sub_ls[0], 'r') as file:
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# and the file is parsed through to find the pattern
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with open(path + '/' + item + '/' + sub_ls[0], 'r') \
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as file:
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content = file.read()
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match = re.search(pattern, content)
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if match:
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#the start and end point of the correlator in quaetion is extracted for later use in the other files
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start_read = content.count('\n', 0, match.start()) + 5 + b2b
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end_match = re.search(r'\n\s*\n', content[match.start():])
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T = content[match.start():].count('\n', 0, end_match.start()) - 4 - b2b
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# the start and end point of the correlator
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# in quaetion is extracted for later use in
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# the other files
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start_read = content.count('\n', 0, match.start())\
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+ 5 + b2b
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end_match = re.search(r'\n\s*\n',
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content[match.start():])
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T = content[match.start():]\
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.count('\n', 0, end_match.start()) - 4 - b2b
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assert T > 0
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print(T, 'entries, starting to read in line', start_read)
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print(T, 'entries, starting to read in line',
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start_read)
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else:
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raise Exception('Correlator with pattern\n' + pattern + '\nnot found.')
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raise Exception('Correlator with pattern\n'
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+ pattern + '\nnot found.')
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else:
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#this part does the same as above, but for non-compactified versions of the files
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with open(path + '/' + item + '/' + sub_ls[0] + '/' + name) as fp:
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# this part does the same as above,
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# but for non-compactified versions of the files
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with open(path + '/' + item + '/' + sub_ls[0] + '/'
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+ name) as fp:
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for k, line in enumerate(fp):
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if version == "0.0":
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#check if this is really the right file by matchin pattern similar to above
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pattern = "# "+name+" : offset "+str(noffset)+", wf "+str(wf)
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#if b2b, a second wf is needed
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# check if this is really the right file
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# by matching pattern similar to above
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pattern = "# "+name+" : offset "+str(noffset)\
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+ ", wf "+str(wf)
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# if b2b, a second wf is needed
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if b2b:
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pattern+=", wf_2 "+str(wf2)
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pattern += ", wf_2 "+str(wf2)
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qs = quarks.split(" ")
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pattern+=" : "+qs[0]+" - "+qs[1]
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#print(pattern)
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if read == 1 and not line.strip() and k > start + 1:
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pattern += " : " + qs[0]+" - " + qs[1]
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# print(pattern)
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if read == 1 and not line.strip() \
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and k > start + 1:
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break
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if read == 1 and k >= start:
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T += 1
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if version == "0.0":
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if pattern in line:
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#print(line)
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# print(line)
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read = 1
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start = k+1
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else:
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@ -239,121 +286,133 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
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start = k + 7 + b2b
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T -= b2b
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print(str(T)+" entries found.")
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#we found where the correlator that is to be read is in the files
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#after preparing the datastructure the correlators get parsed into...
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# we found where the correlator
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# that is to be read is in the files
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# after preparing the datastructure
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# the correlators get parsed into...
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deltas = []
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for j in range(T):
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deltas.append([])
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for t in range(T):
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deltas[t].append(np.zeros(no_cfg))
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#... the actual parsing can start. we iterate through all measurement files in the path given...
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# ...the actual parsing can start.
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# we iterate through all measurement files in the path given...
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if compact:
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for cfg in range(no_cfg):
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with open(path + '/' + item + '/' + sub_ls[cfg]) as fp:
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lines = fp.readlines()
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#check, if the correlator is in fact printed completely
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if(start_read + T>len(lines)):
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raise Exception("EOF before end of correlator data! Maybe "+path + '/' + item + '/' + sub_ls[cfg]+" is corrupted?")
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#and start to read the correlator.
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#the range here is chosen like this, since this allows for implementing a security check for every read correlator later...
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for k in range(start_read - 6,start_read + T):
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# check, if the correlator is in fact
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# printed completely
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if(start_read + T > len(lines)):
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raise Exception("EOF before end of correlator data! \
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Maybe "+path + '/' + item + '/' + sub_ls[cfg]+" \
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is corrupted?")
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# and start to read the correlator.
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# the range here is chosen like this,
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# since this allows for implementing
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# a security check for every read correlator later...
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for k in range(start_read - 6, start_read + T):
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if k == start_read - 5 - b2b:
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if lines[k].strip() != 'name ' + name:
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raise Exception('Wrong format', sub_ls[cfg])
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raise Exception('Wrong format',
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sub_ls[cfg])
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if(k >= start_read and k < start_read + T):
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floats = list(map(float, lines[k].split()))
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deltas[k - start_read][i][cfg] = floats[-2:][im]
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deltas[k - start_read][i][cfg] = \
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floats[-2:][im]
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else:
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for cnfg, subitem in enumerate(sub_ls):
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with open(path + '/' + item + '/' + subitem + '/' + name) as fp:
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#since the non-compatified files are typically not so long, we can iterate over the whole file.
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#here one can also implement the chekc from above.
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with open(path + '/' + item + '/' + subitem
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+ '/' + name) as fp:
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# since the non-compatified files
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# are typically not so long,
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# we can iterate over the whole file.
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# here one can also implement the chekc from above.
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for k, line in enumerate(fp):
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if(k >= start and k < start + T):
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floats = list(map(float, line.split()))
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if version == "0.0":
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deltas[k-start][i][cnfg] = floats[im]
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else:
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deltas[k - start][i][cnfg] = floats[1 + im - single]
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deltas[k - start][i][cnfg] = \
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floats[1 + im - single]
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else:
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for exc in ls:
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if not fnmatch.fnmatch(exc, prefix + '*.'+name):
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ls = list(set(ls) - set([exc]))
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ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
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#print(ls)
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pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf)
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# print(ls)
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pattern = 'name ' + name + '\nquarks '\
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+ quarks + '\noffset ' + str(noffset)\
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+ '\nwf ' + str(wf)
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if b2b:
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pattern += '\nwf_2 ' + str(wf2)
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for rep,file in enumerate(ls):
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for rep, file in enumerate(ls):
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rep_idl = []
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with open(path + '/' + file, 'r') as fp:
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content = fp.readlines()
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data_starts = []
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for l,line in enumerate(content):
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for linenumber, line in enumerate(content):
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if "[run]" in line:
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data_starts.append(l)
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if len(set([data_starts[i]-data_starts[i-1] for i in range(1,len(data_starts))])) > 1:
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raise Exception ("Irregularities in file structure found, not all runs have the same output length")
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#print(data_starts)
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#first chunk of data
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data_starts.append(linenumber)
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if len(set([data_starts[i]-data_starts[i-1] for i in
|
||||
range(1, len(data_starts))])) > 1:
|
||||
raise Exception("Irregularities in file structure found,\
|
||||
not all runs have the same output length")
|
||||
# first chunk of data
|
||||
chunk = content[:data_starts[1]]
|
||||
for l,line in enumerate(chunk):
|
||||
for linenumber, line in enumerate(chunk):
|
||||
if line.startswith("gauge_name"):
|
||||
gauge_line = l
|
||||
#meta_data["gauge_name"] = (line.strip()).split("/")[-1]
|
||||
gauge_line = linenumber
|
||||
elif line.startswith("[correlator]"):
|
||||
corr_line = l
|
||||
corr_line = linenumber
|
||||
found_pat = ""
|
||||
for li in chunk[corr_line+1:corr_line+6+b2b]:
|
||||
found_pat += li
|
||||
if re.search(pattern,found_pat):
|
||||
if re.search(pattern, found_pat):
|
||||
start_read = corr_line+7+b2b
|
||||
T=len(chunk)-1-start_read
|
||||
T = len(chunk)-1-start_read
|
||||
if rep == 0:
|
||||
deltas = []
|
||||
for t in range(T):
|
||||
deltas.append([])
|
||||
for t in range(T):
|
||||
deltas[t].append(np.zeros(len(data_starts)))
|
||||
#all other chunks should follow the same structure
|
||||
# all other chunks should follow the same structure
|
||||
for cnfg in range(len(data_starts)):
|
||||
start = data_starts[cnfg]
|
||||
stop = start+data_starts[1]
|
||||
chunk = content[start:stop]
|
||||
#meta_data = {}
|
||||
|
||||
# meta_data = {}
|
||||
try:
|
||||
rep_idl.append(int(chunk[gauge_line].split("n")[-1]))
|
||||
except:
|
||||
raise Exception("Couldn't parse idl from directroy, problem with chunk around line "+gauge_line)
|
||||
|
||||
except Exception:
|
||||
raise Exception("Couldn't parse idl from directroy, \
|
||||
problem with chunk around line "+gauge_line)
|
||||
|
||||
found_pat = ""
|
||||
for li in chunk[corr_line+1:corr_line+6+b2b]:
|
||||
found_pat += li
|
||||
if re.search(pattern,found_pat):
|
||||
#print("found pattern")
|
||||
for t,line in enumerate(chunk[start_read:start_read+T]):
|
||||
if re.search(pattern, found_pat):
|
||||
for t, line in \
|
||||
enumerate(chunk[start_read:start_read+T]):
|
||||
floats = list(map(float, line.split()))
|
||||
deltas[t][rep][cnfg] = floats[-2:][im]
|
||||
idl.append(rep_idl)
|
||||
|
||||
#print(new_names)
|
||||
#print(deltas)
|
||||
#print(idl)
|
||||
if "check_configs" in kwargs:
|
||||
print("Checking for missing configs...")
|
||||
che = kwargs.get("check_configs")
|
||||
if not (len(che) == len(idl)):
|
||||
raise Exception("check_configs has to be the same length as replica!")
|
||||
raise Exception("check_configs has to be the same length\
|
||||
as replica!")
|
||||
for r in range(len(idl)):
|
||||
print("checking "+new_names[r])
|
||||
utils.check_idl(idl[r], che[r])
|
||||
print("Done")
|
||||
result = []
|
||||
for t in range(T):
|
||||
result.append(Obs(deltas[t], new_names, idl = idl))
|
||||
result.append(Obs(deltas[t], new_names, idl=idl))
|
||||
return result
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue