# pyerrors.input.misc API documentation

# pyerrors.input.misc

View Source

    #!/usr/bin/env python
    # coding: utf-8

    import os
    import fnmatch
    import re
    import struct
    import numpy as np  # Thinly-wrapped numpy
    from ..obs import Obs

    def read_pbp(path, prefix, **kwargs):
        """Read pbp format from given folder structure. Returns a list of length nrw

        Keyword arguments
        -----------------
        r_start -- list which contains the first config to be read for each replicum
        r_stop -- list which contains the last config to be read for each replicum

        """

        extract_nfct = 1

        ls = []
        for (dirpath, dirnames, filenames) in os.walk(path):
            ls.extend(filenames)
            break

        if not ls:
            raise Exception('Error, directory not found')

        # Exclude files with different names
        for exc in ls:
            if not fnmatch.fnmatch(exc, prefix + '*.dat'):
                ls = list(set(ls) - set([exc]))
        if len(ls) > 1:
            ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
        replica = len(ls)

        if 'r_start' in kwargs:
            r_start = kwargs.get('r_start')
            if len(r_start) != replica:
                raise Exception('r_start does not match number of replicas')
            # Adjust Configuration numbering to python index
            r_start = [o - 1 if o else None for o in r_start]
        else:
            r_start = [None] * replica

        if 'r_stop' in kwargs:
            r_stop = kwargs.get('r_stop')
            if len(r_stop) != replica:
                raise Exception('r_stop does not match number of replicas')
        else:
            r_stop = [None] * replica

        print(r'Read <bar{psi}\psi> from', prefix[:-1], ',', replica, 'replica', end='')

        print_err = 0
        if 'print_err' in kwargs:
            print_err = 1
            print()

        deltas = []

        for rep in range(replica):
            tmp_array = []
            with open(path + '/' + ls[rep], 'rb') as fp:

                # header
                t = fp.read(4)  # number of reweighting factors
                if rep == 0:
                    nrw = struct.unpack('i', t)[0]
                    for k in range(nrw):
                        deltas.append([])
                else:
                    if nrw != struct.unpack('i', t)[0]:
                        raise Exception('Error: different number of reweighting factors for replicum', rep)

                for k in range(nrw):
                    tmp_array.append([])

                # This block is necessary for openQCD1.6 ms1 files
                nfct = []
                if extract_nfct == 1:
                    for i in range(nrw):
                        t = fp.read(4)
                        nfct.append(struct.unpack('i', t)[0])
                    print('nfct: ', nfct)  # Hasenbusch factor, 1 for rat reweighting
                else:
                    for i in range(nrw):
                        nfct.append(1)

                nsrc = []
                for i in range(nrw):
                    t = fp.read(4)
                    nsrc.append(struct.unpack('i', t)[0])

                # body
                while 0 < 1:
                    t = fp.read(4)
                    if len(t) < 4:
                        break
                    if print_err:
                        config_no = struct.unpack('i', t)
                    for i in range(nrw):
                        tmp_nfct = 1.0
                        for j in range(nfct[i]):
                            t = fp.read(8 * nsrc[i])
                            t = fp.read(8 * nsrc[i])
                            tmp_rw = struct.unpack('d' * nsrc[i], t)
                            tmp_nfct *= np.mean(np.asarray(tmp_rw))
                            if print_err:
                                print(config_no, i, j, np.mean(np.asarray(tmp_rw)), np.std(np.asarray(tmp_rw)))
                                print('Sources:', np.asarray(tmp_rw))
                                print('Partial factor:', tmp_nfct)
                        tmp_array[i].append(tmp_nfct)

                for k in range(nrw):
                    deltas[k].append(tmp_array[k][r_start[rep]:r_stop[rep]])

        rep_names = []
        for entry in ls:
            truncated_entry = entry.split('.')[0]
            idx = truncated_entry.index('r')
            rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
        print(',', nrw, r'<bar{psi}\psi> with', nsrc, 'sources')
        result = []
        for t in range(nrw):
            result.append(Obs(deltas[t], rep_names))

        return result

def read_pbp(path, prefix, **kwargs):
View Source

    def read_pbp(path, prefix, **kwargs):
        """Read pbp format from given folder structure. Returns a list of length nrw

        Keyword arguments
        -----------------
        r_start -- list which contains the first config to be read for each replicum
        r_stop -- list which contains the last config to be read for each replicum

        """

        extract_nfct = 1

        ls = []
        for (dirpath, dirnames, filenames) in os.walk(path):
            ls.extend(filenames)
            break

        if not ls:
            raise Exception('Error, directory not found')

        # Exclude files with different names
        for exc in ls:
            if not fnmatch.fnmatch(exc, prefix + '*.dat'):
                ls = list(set(ls) - set([exc]))
        if len(ls) > 1:
            ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0]))
        replica = len(ls)

        if 'r_start' in kwargs:
            r_start = kwargs.get('r_start')
            if len(r_start) != replica:
                raise Exception('r_start does not match number of replicas')
            # Adjust Configuration numbering to python index
            r_start = [o - 1 if o else None for o in r_start]
        else:
            r_start = [None] * replica

        if 'r_stop' in kwargs:
            r_stop = kwargs.get('r_stop')
            if len(r_stop) != replica:
                raise Exception('r_stop does not match number of replicas')
        else:
            r_stop = [None] * replica

        print(r'Read <bar{psi}\psi> from', prefix[:-1], ',', replica, 'replica', end='')

        print_err = 0
        if 'print_err' in kwargs:
            print_err = 1
            print()

        deltas = []

        for rep in range(replica):
            tmp_array = []
            with open(path + '/' + ls[rep], 'rb') as fp:

                # header
                t = fp.read(4)  # number of reweighting factors
                if rep == 0:
                    nrw = struct.unpack('i', t)[0]
                    for k in range(nrw):
                        deltas.append([])
                else:
                    if nrw != struct.unpack('i', t)[0]:
                        raise Exception('Error: different number of reweighting factors for replicum', rep)

                for k in range(nrw):
                    tmp_array.append([])

                # This block is necessary for openQCD1.6 ms1 files
                nfct = []
                if extract_nfct == 1:
                    for i in range(nrw):
                        t = fp.read(4)
                        nfct.append(struct.unpack('i', t)[0])
                    print('nfct: ', nfct)  # Hasenbusch factor, 1 for rat reweighting
                else:
                    for i in range(nrw):
                        nfct.append(1)

                nsrc = []
                for i in range(nrw):
                    t = fp.read(4)
                    nsrc.append(struct.unpack('i', t)[0])

                # body
                while 0 < 1:
                    t = fp.read(4)
                    if len(t) < 4:
                        break
                    if print_err:
                        config_no = struct.unpack('i', t)
                    for i in range(nrw):
                        tmp_nfct = 1.0
                        for j in range(nfct[i]):
                            t = fp.read(8 * nsrc[i])
                            t = fp.read(8 * nsrc[i])
                            tmp_rw = struct.unpack('d' * nsrc[i], t)
                            tmp_nfct *= np.mean(np.asarray(tmp_rw))
                            if print_err:
                                print(config_no, i, j, np.mean(np.asarray(tmp_rw)), np.std(np.asarray(tmp_rw)))
                                print('Sources:', np.asarray(tmp_rw))
                                print('Partial factor:', tmp_nfct)
                        tmp_array[i].append(tmp_nfct)

                for k in range(nrw):
                    deltas[k].append(tmp_array[k][r_start[rep]:r_stop[rep]])

        rep_names = []
        for entry in ls:
            truncated_entry = entry.split('.')[0]
            idx = truncated_entry.index('r')
            rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:])
        print(',', nrw, r'<bar{psi}\psi> with', nsrc, 'sources')
        result = []
        for t in range(nrw):
            result.append(Obs(deltas[t], rep_names))

        return result

Read pbp format from given folder structure. Returns a list of length nrw

###### Keyword arguments

r_start -- list which contains the first config to be read for each replicum r_stop -- list which contains the last config to be read for each replicum