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https://github.com/fjosw/pyerrors.git
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minor bug fixes, big bug fix in append mode read in
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jkuhl-uni
parent
b36d559ac3
commit
ecfaa8ed67
1 changed files with 45 additions and 63 deletions
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@ -118,11 +118,11 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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for exc in ls:
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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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# 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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if len(ls) > 1:
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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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replica = len(ls)
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else:
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replica = len([file.split(".")[-1] for file in ls]) // len(set([file.split(".")[-1] for file in ls]))
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@ -213,58 +213,39 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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if i == 0:
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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
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# from the input values
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pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + 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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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
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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()) + 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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assert T > 0
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print(T, 'entries, starting to read in line', start_read)
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else:
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raise Exception('Correlator with pattern\n' + pattern + '\nnot found.')
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else:
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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] + '/' + 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
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# by matching 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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if b2b:
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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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# to do so, the pattern needed is put together
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# from the input values
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if version == "0.0":
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for k, line in enumerate(file):
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if read == 1 and not line.strip() 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 pattern in line:
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read = 1
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start = k + 1
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print(str(T) + " entries found.")
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else:
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pattern = 'name ' + name + '\nquarks ' + quarks + '\noffset ' + str(noffset) + '\nwf ' + 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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if compact:
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file = open(path + '/' + item + '/' + sub_ls[0], "r")
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else:
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# for non-compactified versions of the files
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file = open(path + '/' + item + '/' + sub_ls[0] + '/' + name, "r")
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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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read = 1
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start = k + 1
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else:
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if '[correlator]' in line:
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read = 1
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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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content = file.read()
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match = re.search(pattern, content)
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if match:
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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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assert T > 0
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print(T, 'entries, starting to read in line', start_read)
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else:
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raise Exception('Correlator with pattern\n' + pattern + '\nnot found.')
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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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@ -292,8 +273,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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',
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sub_ls[cfg])
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raise Exception('Wrong format', 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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@ -305,12 +285,12 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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if(k >= start_read and k < start_read + 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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deltas[k - start][i][cnfg] = floats[im - single]
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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_read][i][cnfg] = floats[1 + im - single]
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else:
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if "files" in kwargs:
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@ -320,7 +300,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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if b2b:
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pattern += '\nwf_2 ' + str(wf2)
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@ -332,8 +311,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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(linenumber)
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if len(set([data_starts[i] - data_starts[i - 1] for i in
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range(1, len(data_starts))])) > 1:
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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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# first chunk of data
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chunk = content[:data_starts[1]]
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@ -343,11 +321,15 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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elif line.startswith("[correlator]"):
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corr_line = linenumber
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found_pat = ""
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for li in chunk[corr_line + 1:corr_line + 6 + b2b]:
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for li in chunk[corr_line + 1: corr_line + 6 + b2b]:
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found_pat += li
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if re.search(pattern, found_pat):
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start_read = corr_line + 7 + b2b
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T = len(chunk) - 1 - start_read
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break
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endline = corr_line + 6 + b2b
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while not chunk[endline] == "\n":
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endline += 1
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T = endline - start_read
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if rep == 0:
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deltas = []
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for t in range(T):
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@ -363,7 +345,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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try:
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rep_idl.append(int(chunk[gauge_line].split("n")[-1]))
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except Exception:
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raise Exception("Couldn't parse idl from directroy, problem with chunk around line " + gauge_line)
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raise Exception("Couldn't parse idl from directory, problem with chunk around line ", gauge_line)
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found_pat = ""
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for li in chunk[corr_line + 1:corr_line + 6 + b2b]:
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@ -371,7 +353,7 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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if re.search(pattern, found_pat):
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for t, line in enumerate(chunk[start_read:start_read + T]):
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floats = list(map(float, line.split()))
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deltas[t][rep][cnfg] = floats[-2:][im]
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deltas[t][rep][cnfg] = floats[im + 1 - single]
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idl.append(rep_idl)
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if "check_configs" in kwargs:
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