mirror of
https://github.com/fjosw/pyerrors.git
synced 2025-03-15 14:50:25 +01:00
first ver. of just one SFCF read method
This commit is contained in:
jkuhl-uni
parent
089cbc0783
commit
66cdd46a92
1 changed files with 165 additions and 73 deletions
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@ -8,11 +8,11 @@ import numpy as np # Thinly-wrapped numpy
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from ..obs import Obs
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def read_sfcf(path, prefix, name, **kwargs):
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"""Read sfcf C format from given folder structure.
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def read_sfcf_old(path, prefix, name, quarks, noffset = 0, wf=0, wf2=0, **kwargs):
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"""Read sfcf format (from around 2012) from given folder structure.
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Parameters
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----------
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Keyword arguments
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-----------------
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im -- if True, read imaginary instead of real part of the correlation function.
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single -- if True, read a boundary-to-boundary correlation function with a single value
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b2b -- if True, read a time-dependent boundary-to-boundary correlation function
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@ -24,17 +24,13 @@ def read_sfcf(path, prefix, name, **kwargs):
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else:
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im = 0
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part = 'real'
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if kwargs.get('single'):
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b2b = 1
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single = 1
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else:
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b2b = 0
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single = 0
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b2b = 0
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if kwargs.get('b2b'):
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b2b = 1
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quarks = quarks.split(" ")
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read = 0
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T = 0
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start = 0
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@ -43,7 +39,8 @@ def read_sfcf(path, prefix, name, **kwargs):
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ls.extend(dirnames)
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break
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if not ls:
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raise Exception('Error, directory not found')
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print('Error, directory not found')
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#sys.exit()
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for exc in ls:
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if fnmatch.fnmatch(exc, prefix + '*'):
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ls = list(set(ls) - set(exc))
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@ -56,17 +53,12 @@ def read_sfcf(path, prefix, name, **kwargs):
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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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for entry in ls:
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idx = entry.index('r')
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new_names.append(entry[:idx] + '|' + entry[idx:])
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new_names = ls
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print(replica, 'replica')
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for i, item in enumerate(ls):
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print(item)
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sub_ls = []
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for (dirpath, dirnames, filenames) in os.walk(path + '/' + item):
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for (dirpath, dirnames, filenames) in os.walk(path+'/'+item):
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sub_ls.extend(dirnames)
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break
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for exc in sub_ls:
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@ -75,18 +67,25 @@ def read_sfcf(path, prefix, name, **kwargs):
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sub_ls.sort(key=lambda x: int(x[3:]))
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no_cfg = len(sub_ls)
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print(no_cfg, 'configurations')
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if i == 0:
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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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#check if this is really the right file
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pattern = "# "+name+" : offset "+str(noffset)+", wf "+"0"
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#if b2b, a second wf is needed
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if b2b:
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pattern+=", wf_2 "+"0"
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pattern+=" : "+quarks[0]+" - "+quarks[1]
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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 '[correlator]' in line:
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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 + 7 + b2b
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T -= b2b
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start = k+1
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print(str(T)+" entries found.")
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deltas = []
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for j in range(T):
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@ -97,11 +96,12 @@ def read_sfcf(path, prefix, name, **kwargs):
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deltas[j].append(np.zeros(sublength))
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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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with open(path + '/' + item + '/' + subitem + '/'+name) as fp:
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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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deltas[k - start][i][cnfg] = floats[1 + im - single]
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deltas[k-start][i][cnfg] = floats[im]
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result = []
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for t in range(T):
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@ -110,7 +110,7 @@ def read_sfcf(path, prefix, name, **kwargs):
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return result
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def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwargs):
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def read_sfcf(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwargs):
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"""Read sfcf c format from given folder structure.
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Parameters
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@ -121,11 +121,11 @@ def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwarg
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wf2 -- ID of the second wavefunction (only relevant for boundary-to-boundary correlation functions)
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im -- if True, read imaginary instead of real part of the correlation function.
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b2b -- if True, read a time-dependent boundary-to-boundary correlation function
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single -- if True, read time independent boundary to boundary correlation function
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names -- Alternative labeling for replicas/ensembles. Has to have the appropriate length
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ens_name : str
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replaces the name of the ensemble
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"""
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if kwargs.get('im'):
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im = 1
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part = 'imaginary'
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@ -133,12 +133,38 @@ def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwarg
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im = 0
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part = 'real'
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if kwargs.get('b2b'):
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if kwargs.get('single'):
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b2b = 1
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single = 1
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else:
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b2b = 0
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if kwargs.get('b2b'):
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b2b = 1
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else:
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b2b = 0
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single = 0
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files = []
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if "files" in kwargs:
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files = kwargs.get("files")
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#due to higher usage in current projects, compact file format is default
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compact = True
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#get version string
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version = "1.0"
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known_versions = ["0.0","1.0","2.0","1.0c","2.0c"]
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if "version" in kwargs:
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version = kwargs.get("version")
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if not version 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, the compact fileformat is used (former read_sfcf_c)
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if(version[-1] == "c"):
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compact = True
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version = version[:-1]
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else:
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compact = False
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read = 0
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T = 0
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start = 0
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ls = []
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for (dirpath, dirnames, filenames) in os.walk(path):
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ls.extend(dirnames)
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@ -146,12 +172,17 @@ def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwarg
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if not ls:
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raise Exception('Error, directory not found')
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# Exclude folders with different names
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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(files) != 0:
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ls = files
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else:
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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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ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0])) # New version, to cope with ids, etc.
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replica = len(ls)
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print('Read', part, 'part of', name, 'from', prefix[:-1], ',', replica, 'replica')
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if 'names' in kwargs:
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new_names = kwargs.get('names')
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if len(new_names) != replica:
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@ -160,52 +191,99 @@ def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwarg
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# Adjust replica names to new bookmarking system
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new_names = []
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for entry in ls:
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idx = entry.index('r')
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try:
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idx = entry.index('r')
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except:
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idx = len(entry)-2
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if 'ens_name' in kwargs:
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new_names.append(kwargs.get('ens_name') + '|' + entry[idx:])
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else:
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new_names.append(entry[:idx] + '|' + entry[idx:])
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print('Read', part, 'part of', name, 'from', prefix[:-1], ',', replica, 'replica')
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for i, item in enumerate(ls):
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sub_ls = []
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for (dirpath, dirnames, filenames) in os.walk(path + '/' + item):
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sub_ls.extend(filenames)
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if compact:
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sub_ls.extend(filenames)
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else:
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sub_ls.extend(dirnames)
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break
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for exc in sub_ls:
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if not fnmatch.fnmatch(exc, prefix + '*'):
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sub_ls = list(set(sub_ls) - set([exc]))
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sub_ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
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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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sub_ls = list(set(sub_ls) - set([exc]))
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sub_ls.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
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else:
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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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if compact:
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first_cfg = int(re.findall(r'\d+', sub_ls[0])[-1])
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first_cfg = int(re.findall(r'\d+', sub_ls[0])[-1])
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last_cfg = len(sub_ls) + first_cfg - 1
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last_cfg = len(sub_ls) + first_cfg - 1
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for cfg in range(1, len(sub_ls)):
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if int(re.findall(r'\d+', sub_ls[cfg])[-1]) != first_cfg + cfg:
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last_cfg = cfg + first_cfg - 1
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break
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for cfg in range(1, len(sub_ls)):
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if int(re.findall(r'\d+', sub_ls[cfg])[-1]) != first_cfg + cfg:
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last_cfg = cfg + first_cfg - 1
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break
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no_cfg = last_cfg - first_cfg + 1
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print(item, ':', no_cfg, 'evenly spaced configurations (', first_cfg, '-', last_cfg, ') ,', len(sub_ls) - no_cfg, 'configs omitted\n')
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no_cfg = last_cfg - first_cfg + 1
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print(item, ':', no_cfg, 'evenly spaced configurations (', first_cfg, '-', last_cfg, ') ,', len(sub_ls) - no_cfg, 'configs omitted\n')
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else:
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no_cfg = len(sub_ls)
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print(no_cfg, 'configurations')
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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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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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if compact:
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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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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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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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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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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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#print(path + '/' + item + '/')# + sub_ls[0] + '/' + name)
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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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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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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 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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#we found where the correlator that is to be read is in the files
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deltas = []
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for j in range(T):
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deltas.append([])
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@ -213,16 +291,30 @@ def read_sfcf_c(path, prefix, name, quarks='.*', noffset=0, wf=0, wf2=0, **kwarg
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sublength = no_cfg
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for j in range(T):
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deltas[j].append(np.zeros(sublength))
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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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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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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', 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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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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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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if version == "0.0":
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deltas[k-start][i][cnfg] = floats[im]
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else:
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deltas[k - start][i][cnfg] = floats[1 + im - single]
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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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for k, line in enumerate(fp):
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if k == start_read - 5 - b2b:
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if line.strip() != 'name ' + name:
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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, line.split()))
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deltas[k - start_read][i][cfg] = floats[-2:][im]
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result = []
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for t in range(T):
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