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Impr/fix refactor sfcf read (#164)

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* refactor read_sfcf

* adding tests for find_corr and read_compact_file

* add necessary broken data for tests

* fixed appended mode reading

* factored out sort_names and find_files

* now also using sort_files in sfcf.py

* edited tests to fit with new structure

* added find_files function

* shifted helpfunctions to bottom of file

* removed some debug lines

* linting

* Fixed requested changes, added silent mode

* added Exception if correlator is not found by read_append_rep

* use tmp_path fixture

* linting silent keyword

* try to fix testing for a_bb

* tests: Exception testing in test_find_corr made more explicit.

---------

Co-authored-by: Fabian Joswig <fabian.joswig@ed.ac.uk>
This commit is contained in:
Justus Kuhlmann 2023-03-15 18:46:12 +01:00 • committed by GitHub
parent 991199a680
commit 41fec09816
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7 changed files with 880 additions and 315 deletions
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115
pyerrors/input/openQCD.py
View file

@ -1,6 +1,5 @@
import os
import fnmatch
import re
import struct
import warnings
import numpy as np # Thinly-wrapped numpy
@ -10,75 +9,7 @@ from ..obs import Obs
from ..fits import fit_lin
from ..obs import CObs
from ..correlators import Corr
def _find_files(path, prefix, postfix, ext, known_files=[]):
found = []
files = []
if postfix != "":
if postfix[-1] != ".":
postfix = postfix + "."
if postfix[0] != ".":
postfix = "." + postfix
if ext[0] == ".":
ext = ext[1:]
pattern = prefix + "*" + postfix + ext
for (dirpath, dirnames, filenames) in os.walk(path + "/"):
found.extend(filenames)
break
if known_files != []:
for kf in known_files:
if kf not in found:
raise FileNotFoundError("Given file " + kf + " does not exist!")
return known_files
if not found:
raise FileNotFoundError(f"Error, directory '{path}' not found")
for f in found:
if fnmatch.fnmatch(f, pattern):
files.append(f)
if files == []:
raise Exception("No files found after pattern filter!")
files = _sort_names(files)
return files
def _sort_names(ll):
r_pattern = r'r(\d+)'
id_pattern = r'id(\d+)'
# sort list by id first
if all([re.search(id_pattern, entry) for entry in ll]):
ll.sort(key=lambda x: int(re.findall(id_pattern, x)[0]))
# then by replikum
if all([re.search(r_pattern, entry) for entry in ll]):
ll.sort(key=lambda x: int(re.findall(r_pattern, x)[0]))
# as the rearrangements by one key let the other key untouched, the list is sorted now
else:
# fallback
sames = ''
if len(ll) > 1:
for i in range(len(ll[0])):
checking = ll[0][i]
for rn in ll[1:]:
is_same = (rn[i] == checking)
if is_same:
sames += checking
else:
break
print(ll[0][len(sames):])
ll.sort(key=lambda x: int(re.findall(r'\d+', x[len(sames):])[0]))
return ll
from .utils import sort_names
def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
@ -171,7 +102,7 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
else:
rep_names = names
rep_names = _sort_names(rep_names)
rep_names = sort_names(rep_names)
print_err = 0
if 'print_err' in kwargs:
@ -561,6 +492,46 @@ def _parse_array_openQCD2(d, n, size, wa, quadrupel=False):
return arr
def _find_files(path, prefix, postfix, ext, known_files=[]):
found = []
files = []
if postfix != "":
if postfix[-1] != ".":
postfix = postfix + "."
if postfix[0] != ".":
postfix = "." + postfix
if ext[0] == ".":
ext = ext[1:]
pattern = prefix + "*" + postfix + ext
for (dirpath, dirnames, filenames) in os.walk(path + "/"):
found.extend(filenames)
break
if known_files != []:
for kf in known_files:
if kf not in found:
raise FileNotFoundError("Given file " + kf + " does not exist!")
return known_files
if not found:
raise FileNotFoundError(f"Error, directory '{path}' not found")
for f in found:
if fnmatch.fnmatch(f, pattern):
files.append(f)
if files == []:
raise Exception("No files found after pattern filter!")
files = sort_names(files)
return files
def _read_array_openQCD2(fp):
t = fp.read(4)
d = struct.unpack('i', t)[0]
@ -974,7 +945,7 @@ def _read_flow_obs(path, prefix, c, dtr_cnfg=1, version="openQCD", obspos=0, sum
deltas.append(Q_top)
rep_names = _sort_names(rep_names)
rep_names = sort_names(rep_names)
idl = [range(int(configlist[rep][r_start_index[rep]]), int(configlist[rep][r_stop_index[rep]]) + 1, 1) for rep in range(len(deltas))]
deltas = [deltas[nrep][r_start_index[nrep]:r_stop_index[nrep] + 1] for nrep in range(len(deltas))]