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Merge branch 'develop' into documentation
This commit is contained in:
fjosw
commit
399547a957
2 changed files with 6 additions and 75 deletions
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@ -1,6 +1,3 @@
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#!/usr/bin/env python
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# coding: utf-8
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import os
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import fnmatch
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import re
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@ -42,7 +39,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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if 'files' in kwargs:
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ls = kwargs.get('files')
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else:
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# Exclude files with different names
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for exc in ls:
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if not fnmatch.fnmatch(exc, prefix + '*' + postfix + '.dat'):
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ls = list(set(ls) - set([exc]))
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@ -69,7 +65,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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print('Read reweighting factors from', prefix[:-1], ',',
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replica, 'replica', end='')
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# Adjust replica names to new bookmarking system
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if names is None:
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rep_names = []
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for entry in ls:
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@ -88,7 +83,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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tmp_array = []
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with open(path + '/' + ls[rep], 'rb') as fp:
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# header
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t = fp.read(4) # number of reweighting factors
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if rep == 0:
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nrw = struct.unpack('i', t)[0]
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@ -97,7 +91,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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for k in range(nrw):
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deltas.append([])
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else:
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# little weird if-clause due to the /2 operation needed.
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if ((nrw != struct.unpack('i', t)[0] and (not version == '2.0')) or (nrw != struct.unpack('i', t)[0] / 2 and version == '2.0')):
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raise Exception('Error: different number of reweighting factors for replicum', rep)
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@ -110,8 +103,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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for i in range(nrw):
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t = fp.read(4)
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nfct.append(struct.unpack('i', t)[0])
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# print('nfct: ', nfct) # Hasenbusch factor,
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# 1 for rat reweighting
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else:
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for i in range(nrw):
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nfct.append(1)
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@ -124,7 +115,6 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
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if not struct.unpack('i', fp.read(4))[0] == 0:
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print('something is wrong!')
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# body
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while 0 < 1:
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t = fp.read(4)
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if len(t) < 4:
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@ -220,7 +210,6 @@ def extract_t0(path, prefix, dtr_read, xmin,
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if not ls:
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raise Exception('Error, directory not found')
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# Exclude files with different names
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for exc in ls:
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if not fnmatch.fnmatch(exc, prefix + '*.ms.dat'):
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ls = list(set(ls) - set([exc]))
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@ -232,7 +221,6 @@ def extract_t0(path, prefix, dtr_read, xmin,
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r_start = kwargs.get('r_start')
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if len(r_start) != replica:
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raise Exception('r_start does not match number of replicas')
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# Adjust Configuration numbering to python index
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r_start = [o - 1 if o else None for o in r_start]
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else:
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r_start = [None] * replica
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@ -251,7 +239,6 @@ def extract_t0(path, prefix, dtr_read, xmin,
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for rep in range(replica):
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with open(path + '/' + ls[rep], 'rb') as fp:
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# Read header
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t = fp.read(12)
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header = struct.unpack('iii', t)
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if rep == 0:
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@ -270,7 +257,6 @@ def extract_t0(path, prefix, dtr_read, xmin,
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Ysl = []
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# Read body
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while 0 < 1:
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t = fp.read(4)
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if(len(t) < 4):
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@ -334,12 +320,6 @@ def _parse_array_openQCD2(d, n, size, wa, quadrupel=False):
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return arr
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# mimic the read_array routine of openQCD-2.0.
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# fp is the opened file handle
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# returns the dict array
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# at this point we only parse a 2d array
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# d = 2
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# n = [nfct[irw], 2*nsrc[irw]]
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def _read_array_openQCD2(fp):
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t = fp.read(4)
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d = struct.unpack('i', t)[0]
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@ -400,13 +380,11 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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last configurations that need to be read (per replicum)
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files: list
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specify the exact files that need to be read
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from path, pratical if e.g. only one replicum is needed
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from path, practical if e.g. only one replicum is needed
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names: list
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Alternative labeling for replicas/ensembles.
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Has to have the appropriate length
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"""
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# one could read L from the header in case of sfQCD
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# c = 0.35
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known_versions = ["1.0", "1.2", "1.4", "1.6", "2.0", "sfqcd"]
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if version not in known_versions:
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@ -426,11 +404,9 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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r_start = kwargs.get("r_start")
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if "r_stop" in kwargs:
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r_stop = kwargs.get("r_stop")
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# if one wants to read specific files with this method...
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if "files" in kwargs:
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files = kwargs.get("files")
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else:
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# find files in path
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found = []
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files = []
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for (dirpath, dirnames, filenames) in os.walk(path + "/"):
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@ -441,14 +417,12 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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if fnmatch.fnmatch(f, prefix + "*" + ".ms.dat"):
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files.append(f)
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print(files)
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# now that we found our files, we dechiffer them...
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rep_names = []
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deltas = []
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idl = []
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for rep, file in enumerate(files):
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with open(path + "/" + file, "rb") as fp:
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# header
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t = fp.read(12)
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header = struct.unpack('<iii', t)
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# step size in integration steps "dnms"
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@ -477,7 +451,6 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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Q = []
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ncs = []
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while 0 < 1:
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# int nt
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t = fp.read(4)
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if(len(t) < 4):
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break
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@ -524,8 +497,6 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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if len(Q_round) != len(ncs) // dtr_cnfg:
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raise Exception("qtops and ncs dont have the same length")
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# replica = len(files)
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truncated_file = file[:-7]
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print(truncated_file)
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idl_start = 1
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@ -553,7 +524,6 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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rep_names = names
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deltas.append(np.array(Q_round))
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idl.append(range(idl_start, idl_stop))
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# print(idl)
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result = Obs(deltas, rep_names, idl=idl)
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return result
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@ -594,7 +564,6 @@ def read_qtop_sector(target=0, **kwargs):
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dtr_cnfg = 1
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qtop = read_qtop(path, prefix, c, dtr_cnfg=dtr_cnfg,
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version=version, **kwargs)
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# unpack to original values, project onto target sector
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names = qtop.names
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print(names)
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print(qtop.deltas.keys())
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@ -43,15 +43,16 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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.
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if the compact output option (-c) was spectified,
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if the compact output option (-c) was specified,
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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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append an "a" to the version. Currently supported versions
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are "0.0", "1.0", "2.0", "1.0c", "2.0c", "1.0a" and "2.0a".
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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.
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for non-conpact ouztput format, hand the folders to be read here.
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for non-compact output 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)]
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for one replicum with 1000 configs
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@ -77,17 +78,12 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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if "replica" in kwargs:
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reps = kwargs.get("replica")
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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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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,
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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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@ -119,7 +115,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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@ -135,8 +130,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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else:
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# Adjust replica names to new bookmarking system
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new_names = []
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if not appended:
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for entry in ls:
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@ -157,7 +150,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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try:
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idx = myentry.index('r')
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except Exception:
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@ -167,7 +159,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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new_names.append(kwargs.get('ens_name') + '|' + 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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idl = []
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if not appended:
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for i, item in enumerate(ls):
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@ -183,7 +174,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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if compact:
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if not fnmatch.fnmatch(exc, prefix + '*'):
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@ -194,7 +184,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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rep_idl = []
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no_cfg = len(sub_ls)
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for cfg in sub_ls:
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@ -206,26 +195,19 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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except Exception:
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raise Exception("Couldn't parse idl from directroy, 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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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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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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# in question 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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@ -248,7 +230,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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break
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if read == 1 and k >= start:
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@ -265,30 +246,19 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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
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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.
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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
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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! 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,
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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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@ -300,10 +270,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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
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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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|
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@ -320,7 +286,6 @@ 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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@ -335,7 +300,6 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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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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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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for linenumber, line in enumerate(chunk):
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if line.startswith("gauge_name"):
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@ -354,12 +318,10 @@ def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0,
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deltas.append([])
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for t in range(T):
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deltas[t].append(np.zeros(len(data_starts)))
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# all other chunks should follow the same structure
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for cnfg in range(len(data_starts)):
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start = data_starts[cnfg]
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stop = start + data_starts[1]
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chunk = content[start:stop]
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# meta_data = {}
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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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||||
|
|
|
|||
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