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Merge branch 'develop' into documentation
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fjosw
commit
6d3a4164f9
3 changed files with 3 additions and 26 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 ctypes
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import hashlib
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import autograd.numpy as np # Thinly-wrapped numpy
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@ -573,7 +573,6 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
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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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# print(filenames)
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found.extend(filenames)
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break
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for f in found:
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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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@ -39,7 +36,7 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=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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@ -47,7 +44,7 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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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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@ -69,17 +66,12 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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else:
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b2b = False
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single = False
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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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@ -127,8 +119,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=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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@ -149,7 +139,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=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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@ -159,7 +148,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=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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@ -174,8 +162,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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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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if compact:
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for exc in sub_ls:
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if not fnmatch.fnmatch(exc, prefix + '*'):
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@ -186,7 +172,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=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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@ -201,7 +186,7 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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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,
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# where the correlator we need is stored.
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@ -255,8 +240,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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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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@ -312,7 +295,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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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:
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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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@ -340,7 +322,6 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type='bi', noffset=0, wf=0,
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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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