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implemented read_sfcf for append-mode output, bug fixes

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jkuhl-uni 2022-01-03 21:34:04 +01:00
parent 31c2ada963
commit ebdc17aa66
1 changed files with 249 additions and 152 deletions
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121
pyerrors/input/sfcf.py
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@ -8,7 +8,7 @@ import numpy as np # Thinly-wrapped numpy
from ..obs import Obs from ..obs import Obs
from . import utils from . import utils
def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version = "1.0", **kwargs): def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version = "1.0c", **kwargs):
"""Read sfcf c format from given folder structure. """Read sfcf c format from given folder structure.
Parameters Parameters
@ -65,48 +65,61 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
#due to higher usage in current projects, compact file format is default #due to higher usage in current projects, compact file format is default
compact = True compact = True
appended = False
#get version string #get version string
known_versions = ["0.0","1.0","2.0","1.0c","2.0c","1.0a","2.0a"] known_versions = ["0.0","1.0","2.0","1.0c","2.0c","1.0a","2.0a"]
if "version" in kwargs:
version = kwargs.get("version")
if not version in known_versions: if not version in known_versions:
raise Exception("This version is not known!") raise Exception("This version is not known!")
#if the letter c is appended to the version, the compact fileformat is used (former read_sfcf_c) #if the letter c is appended to the version, the compact fileformat is used (former read_sfcf_c)
if(version[-1] == "c"): if(version[-1] == "c"):
appended = False
compact = True compact = True
version = version[:-1] version = version[:-1]
elif(version[-1] == "a"):
appended = True
compact = False
version = version[:-1]
else: else:
compact = False compact = False
appended = False
read = 0 read = 0
T = 0 T = 0
start = 0 start = 0
ls = [] ls = []
if "replica" in kwargs:
ls = reps
else:
for (dirpath, dirnames, filenames) in os.walk(path): for (dirpath, dirnames, filenames) in os.walk(path):
if not appended:
ls.extend(dirnames) ls.extend(dirnames)
else:
ls.extend(filenames)
break break
if not ls: if not ls:
raise Exception('Error, directory not found') raise Exception('Error, directory not found')
# Exclude folders with different names # Exclude folders with different names
if "replica" in kwargs:
ls = reps
else:
for exc in ls: for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*'): if not fnmatch.fnmatch(exc, prefix + '*'):
ls = list(set(ls) - set([exc])) ls = list(set(ls) - set([exc]))
if len(ls) > 1: if len(ls) > 1:
ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0])) # New version, to cope with ids, etc. ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0])) # New version, to cope with ids, etc.
if not appended:
replica = len(ls) replica = len(ls)
else:
replica = len([l.split(".")[-1] for l in ls])//len(set([l.split(".")[-1] for l in ls]))
print('Read', part, 'part of', name, 'from', prefix[:-1], ',', replica, 'replica') print('Read', part, 'part of', name, 'from', prefix[:-1], ',', replica, 'replica')
idl = []
if 'names' in kwargs: if 'names' in kwargs:
new_names = kwargs.get('names') new_names = kwargs.get('names')
if len(new_names)!=len(set(new_names)): if len(new_names)!=len(set(new_names)):
raise Exception("names are nor unique!") raise Exception("names are not unique!")
if len(new_names) != replica: if len(new_names) != replica:
raise Exception('Names does not have the required length', replica) raise Exception('Names does not have the required length', replica)
else: else:
# Adjust replica names to new bookmarking system # Adjust replica names to new bookmarking system
new_names = [] new_names = []
if not appended:
for entry in ls: for entry in ls:
try: try:
idx = entry.index('r') idx = entry.index('r')
@ -117,6 +130,26 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
new_names.append(kwargs.get('ens_name') + '|' + entry[idx:]) new_names.append(kwargs.get('ens_name') + '|' + entry[idx:])
else: else:
new_names.append(entry[:idx] + '|' + entry[idx:]) new_names.append(entry[:idx] + '|' + entry[idx:])
else:
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*.'+name):
ls = list(set(ls) - set([exc]))
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
for entry in ls:
myentry = entry.removesuffix("."+name)
try:
idx = myentry.index('r')
except:
raise Exception("Automatic recognition of replicum failed, please enter the key word 'names'.")
if 'ens_name' in kwargs:
new_names.append(kwargs.get('ens_name') + '|' + myentry[idx:])
else:
new_names.append(myentry[:idx] + '|' + myentry[idx:])
#print(new_names)
idl = []
if not appended:
for i, item in enumerate(ls): for i, item in enumerate(ls):
sub_ls = [] sub_ls = []
if "files" in kwargs: if "files" in kwargs:
@ -158,7 +191,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
#here we have found all the files we need to look into. #here we have found all the files we need to look into.
if i == 0: if i == 0:
#here, we want to find the place within the file, where the correlator we need is stored. #here, we want to find the place within the file, where the correlator we need is stored.
if compact: if compact:
#to do so, the pattern needed is put together from the input values #to do so, the pattern needed is put together from the input values
pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf) pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf)
@ -212,9 +244,9 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
for j in range(T): for j in range(T):
deltas.append([]) deltas.append([])
sublength = no_cfg
for j in range(T): for t in range(T):
deltas[j].append(np.zeros(sublength)) deltas[t].append(np.zeros(no_cfg))
#... the actual parsing can start. we iterate through all measurement files in the path given... #... the actual parsing can start. we iterate through all measurement files in the path given...
if compact: if compact:
for cfg in range(no_cfg): for cfg in range(no_cfg):
@ -245,6 +277,71 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, version =
else: else:
deltas[k - start][i][cnfg] = floats[1 + im - single] deltas[k - start][i][cnfg] = floats[1 + im - single]
else:
for exc in ls:
if not fnmatch.fnmatch(exc, prefix + '*.'+name):
ls = list(set(ls) - set([exc]))
ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
#print(ls)
pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + str(wf)
if b2b:
pattern += '\nwf_2 ' + str(wf2)
for rep,file in enumerate(ls):
rep_idl = []
with open(path + '/' + file, 'r') as fp:
content = fp.readlines()
data_starts = []
for l,line in enumerate(content):
if "[run]" in line:
data_starts.append(l)
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")
#print(data_starts)
#first chunk of data
chunk = content[:data_starts[1]]
for l,line in enumerate(chunk):
if line.startswith("gauge_name"):
gauge_line = l
#meta_data["gauge_name"] = (line.strip()).split("/")[-1]
elif line.startswith("[correlator]"):
corr_line = l
found_pat = ""
for li in chunk[corr_line+1:corr_line+6+b2b]:
found_pat += li
if re.search(pattern,found_pat):
start_read = corr_line+7+b2b
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
for cnfg in range(len(data_starts)):
start = data_starts[cnfg]
stop = start+data_starts[1]
chunk = content[start:stop]
#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)
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]):
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: if "check_configs" in kwargs:
print("Checking for missing configs...") print("Checking for missing configs...")
che = kwargs.get("check_configs") che = kwargs.get("check_configs")