pyerrors.input.misc
1import os 2import fnmatch 3import re 4import struct 5import numpy as np # Thinly-wrapped numpy 6import matplotlib.pyplot as plt 7from matplotlib import gridspec 8from ..obs import Obs 9from ..fits import fit_lin 10 11 12def fit_t0(t2E_dict, fit_range, plot_fit=False): 13 zero_crossing = np.argmax(np.array( 14 [o.value for o in t2E_dict.values()]) > 0.0) 15 16 x = list(t2E_dict.keys())[zero_crossing - fit_range: 17 zero_crossing + fit_range] 18 y = list(t2E_dict.values())[zero_crossing - fit_range: 19 zero_crossing + fit_range] 20 [o.gamma_method() for o in y] 21 22 fit_result = fit_lin(x, y) 23 24 if plot_fit is True: 25 plt.figure() 26 gs = gridspec.GridSpec(2, 1, height_ratios=[3, 1], wspace=0.0, hspace=0.0) 27 ax0 = plt.subplot(gs[0]) 28 xmore = list(t2E_dict.keys())[zero_crossing - fit_range - 2: zero_crossing + fit_range + 2] 29 ymore = list(t2E_dict.values())[zero_crossing - fit_range - 2: zero_crossing + fit_range + 2] 30 [o.gamma_method() for o in ymore] 31 ax0.errorbar(xmore, [yi.value for yi in ymore], yerr=[yi.dvalue for yi in ymore], fmt='x') 32 xplot = np.linspace(np.min(x), np.max(x)) 33 yplot = [fit_result[0] + fit_result[1] * xi for xi in xplot] 34 [yi.gamma_method() for yi in yplot] 35 ax0.fill_between(xplot, y1=[yi.value - yi.dvalue for yi in yplot], y2=[yi.value + yi.dvalue for yi in yplot]) 36 retval = (-fit_result[0] / fit_result[1]) 37 retval.gamma_method() 38 ylim = ax0.get_ylim() 39 ax0.fill_betweenx(ylim, x1=retval.value - retval.dvalue, x2=retval.value + retval.dvalue, color='gray', alpha=0.4) 40 ax0.set_ylim(ylim) 41 ax0.set_ylabel(r'$t^2 \langle E(t) \rangle - 0.3 $') 42 xlim = ax0.get_xlim() 43 44 fit_res = [fit_result[0] + fit_result[1] * xi for xi in x] 45 residuals = (np.asarray([o.value for o in y]) - [o.value for o in fit_res]) / np.asarray([o.dvalue for o in y]) 46 ax1 = plt.subplot(gs[1]) 47 ax1.plot(x, residuals, 'ko', ls='none', markersize=5) 48 ax1.tick_params(direction='out') 49 ax1.tick_params(axis="x", bottom=True, top=True, labelbottom=True) 50 ax1.axhline(y=0.0, ls='--', color='k') 51 ax1.fill_between(xlim, -1.0, 1.0, alpha=0.1, facecolor='k') 52 ax1.set_xlim(xlim) 53 ax1.set_ylabel('Residuals') 54 ax1.set_xlabel(r'$t/a^2$') 55 56 plt.draw() 57 return -fit_result[0] / fit_result[1] 58 59 60def read_pbp(path, prefix, **kwargs): 61 """Read pbp format from given folder structure. 62 63 Parameters 64 ---------- 65 r_start : list 66 list which contains the first config to be read for each replicum 67 r_stop : list 68 list which contains the last config to be read for each replicum 69 70 Returns 71 ------- 72 result : list[Obs] 73 list of observables read 74 """ 75 76 ls = [] 77 for (dirpath, dirnames, filenames) in os.walk(path): 78 ls.extend(filenames) 79 break 80 81 if not ls: 82 raise Exception('Error, directory not found') 83 84 # Exclude files with different names 85 for exc in ls: 86 if not fnmatch.fnmatch(exc, prefix + '*.dat'): 87 ls = list(set(ls) - set([exc])) 88 if len(ls) > 1: 89 ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0])) 90 replica = len(ls) 91 92 if 'r_start' in kwargs: 93 r_start = kwargs.get('r_start') 94 if len(r_start) != replica: 95 raise Exception('r_start does not match number of replicas') 96 # Adjust Configuration numbering to python index 97 r_start = [o - 1 if o else None for o in r_start] 98 else: 99 r_start = [None] * replica 100 101 if 'r_stop' in kwargs: 102 r_stop = kwargs.get('r_stop') 103 if len(r_stop) != replica: 104 raise Exception('r_stop does not match number of replicas') 105 else: 106 r_stop = [None] * replica 107 108 print(r'Read <bar{psi}\psi> from', prefix[:-1], ',', replica, 'replica', end='') 109 110 print_err = 0 111 if 'print_err' in kwargs: 112 print_err = 1 113 print() 114 115 deltas = [] 116 117 for rep in range(replica): 118 tmp_array = [] 119 with open(path + '/' + ls[rep], 'rb') as fp: 120 121 t = fp.read(4) # number of reweighting factors 122 if rep == 0: 123 nrw = struct.unpack('i', t)[0] 124 for k in range(nrw): 125 deltas.append([]) 126 else: 127 if nrw != struct.unpack('i', t)[0]: 128 raise Exception('Error: different number of factors for replicum', rep) 129 130 for k in range(nrw): 131 tmp_array.append([]) 132 133 # This block is necessary for openQCD1.6 ms1 files 134 nfct = [] 135 for i in range(nrw): 136 t = fp.read(4) 137 nfct.append(struct.unpack('i', t)[0]) 138 print('nfct: ', nfct) # Hasenbusch factor, 1 for rat reweighting 139 140 nsrc = [] 141 for i in range(nrw): 142 t = fp.read(4) 143 nsrc.append(struct.unpack('i', t)[0]) 144 145 # body 146 while True: 147 t = fp.read(4) 148 if len(t) < 4: 149 break 150 if print_err: 151 config_no = struct.unpack('i', t) 152 for i in range(nrw): 153 tmp_nfct = 1.0 154 for j in range(nfct[i]): 155 t = fp.read(8 * nsrc[i]) 156 t = fp.read(8 * nsrc[i]) 157 tmp_rw = struct.unpack('d' * nsrc[i], t) 158 tmp_nfct *= np.mean(np.asarray(tmp_rw)) 159 if print_err: 160 print(config_no, i, j, np.mean(np.asarray(tmp_rw)), np.std(np.asarray(tmp_rw))) 161 print('Sources:', np.asarray(tmp_rw)) 162 print('Partial factor:', tmp_nfct) 163 tmp_array[i].append(tmp_nfct) 164 165 for k in range(nrw): 166 deltas[k].append(tmp_array[k][r_start[rep]:r_stop[rep]]) 167 168 rep_names = [] 169 for entry in ls: 170 truncated_entry = entry.split('.')[0] 171 idx = truncated_entry.index('r') 172 rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:]) 173 print(',', nrw, r'<bar{psi}\psi> with', nsrc, 'sources') 174 result = [] 175 for t in range(nrw): 176 result.append(Obs(deltas[t], rep_names)) 177 178 return result
def
fit_t0(t2E_dict, fit_range, plot_fit=False):
13def fit_t0(t2E_dict, fit_range, plot_fit=False): 14 zero_crossing = np.argmax(np.array( 15 [o.value for o in t2E_dict.values()]) > 0.0) 16 17 x = list(t2E_dict.keys())[zero_crossing - fit_range: 18 zero_crossing + fit_range] 19 y = list(t2E_dict.values())[zero_crossing - fit_range: 20 zero_crossing + fit_range] 21 [o.gamma_method() for o in y] 22 23 fit_result = fit_lin(x, y) 24 25 if plot_fit is True: 26 plt.figure() 27 gs = gridspec.GridSpec(2, 1, height_ratios=[3, 1], wspace=0.0, hspace=0.0) 28 ax0 = plt.subplot(gs[0]) 29 xmore = list(t2E_dict.keys())[zero_crossing - fit_range - 2: zero_crossing + fit_range + 2] 30 ymore = list(t2E_dict.values())[zero_crossing - fit_range - 2: zero_crossing + fit_range + 2] 31 [o.gamma_method() for o in ymore] 32 ax0.errorbar(xmore, [yi.value for yi in ymore], yerr=[yi.dvalue for yi in ymore], fmt='x') 33 xplot = np.linspace(np.min(x), np.max(x)) 34 yplot = [fit_result[0] + fit_result[1] * xi for xi in xplot] 35 [yi.gamma_method() for yi in yplot] 36 ax0.fill_between(xplot, y1=[yi.value - yi.dvalue for yi in yplot], y2=[yi.value + yi.dvalue for yi in yplot]) 37 retval = (-fit_result[0] / fit_result[1]) 38 retval.gamma_method() 39 ylim = ax0.get_ylim() 40 ax0.fill_betweenx(ylim, x1=retval.value - retval.dvalue, x2=retval.value + retval.dvalue, color='gray', alpha=0.4) 41 ax0.set_ylim(ylim) 42 ax0.set_ylabel(r'$t^2 \langle E(t) \rangle - 0.3 $') 43 xlim = ax0.get_xlim() 44 45 fit_res = [fit_result[0] + fit_result[1] * xi for xi in x] 46 residuals = (np.asarray([o.value for o in y]) - [o.value for o in fit_res]) / np.asarray([o.dvalue for o in y]) 47 ax1 = plt.subplot(gs[1]) 48 ax1.plot(x, residuals, 'ko', ls='none', markersize=5) 49 ax1.tick_params(direction='out') 50 ax1.tick_params(axis="x", bottom=True, top=True, labelbottom=True) 51 ax1.axhline(y=0.0, ls='--', color='k') 52 ax1.fill_between(xlim, -1.0, 1.0, alpha=0.1, facecolor='k') 53 ax1.set_xlim(xlim) 54 ax1.set_ylabel('Residuals') 55 ax1.set_xlabel(r'$t/a^2$') 56 57 plt.draw() 58 return -fit_result[0] / fit_result[1]
def
read_pbp(path, prefix, **kwargs):
61def read_pbp(path, prefix, **kwargs): 62 """Read pbp format from given folder structure. 63 64 Parameters 65 ---------- 66 r_start : list 67 list which contains the first config to be read for each replicum 68 r_stop : list 69 list which contains the last config to be read for each replicum 70 71 Returns 72 ------- 73 result : list[Obs] 74 list of observables read 75 """ 76 77 ls = [] 78 for (dirpath, dirnames, filenames) in os.walk(path): 79 ls.extend(filenames) 80 break 81 82 if not ls: 83 raise Exception('Error, directory not found') 84 85 # Exclude files with different names 86 for exc in ls: 87 if not fnmatch.fnmatch(exc, prefix + '*.dat'): 88 ls = list(set(ls) - set([exc])) 89 if len(ls) > 1: 90 ls.sort(key=lambda x: int(re.findall(r'\d+', x[len(prefix):])[0])) 91 replica = len(ls) 92 93 if 'r_start' in kwargs: 94 r_start = kwargs.get('r_start') 95 if len(r_start) != replica: 96 raise Exception('r_start does not match number of replicas') 97 # Adjust Configuration numbering to python index 98 r_start = [o - 1 if o else None for o in r_start] 99 else: 100 r_start = [None] * replica 101 102 if 'r_stop' in kwargs: 103 r_stop = kwargs.get('r_stop') 104 if len(r_stop) != replica: 105 raise Exception('r_stop does not match number of replicas') 106 else: 107 r_stop = [None] * replica 108 109 print(r'Read <bar{psi}\psi> from', prefix[:-1], ',', replica, 'replica', end='') 110 111 print_err = 0 112 if 'print_err' in kwargs: 113 print_err = 1 114 print() 115 116 deltas = [] 117 118 for rep in range(replica): 119 tmp_array = [] 120 with open(path + '/' + ls[rep], 'rb') as fp: 121 122 t = fp.read(4) # number of reweighting factors 123 if rep == 0: 124 nrw = struct.unpack('i', t)[0] 125 for k in range(nrw): 126 deltas.append([]) 127 else: 128 if nrw != struct.unpack('i', t)[0]: 129 raise Exception('Error: different number of factors for replicum', rep) 130 131 for k in range(nrw): 132 tmp_array.append([]) 133 134 # This block is necessary for openQCD1.6 ms1 files 135 nfct = [] 136 for i in range(nrw): 137 t = fp.read(4) 138 nfct.append(struct.unpack('i', t)[0]) 139 print('nfct: ', nfct) # Hasenbusch factor, 1 for rat reweighting 140 141 nsrc = [] 142 for i in range(nrw): 143 t = fp.read(4) 144 nsrc.append(struct.unpack('i', t)[0]) 145 146 # body 147 while True: 148 t = fp.read(4) 149 if len(t) < 4: 150 break 151 if print_err: 152 config_no = struct.unpack('i', t) 153 for i in range(nrw): 154 tmp_nfct = 1.0 155 for j in range(nfct[i]): 156 t = fp.read(8 * nsrc[i]) 157 t = fp.read(8 * nsrc[i]) 158 tmp_rw = struct.unpack('d' * nsrc[i], t) 159 tmp_nfct *= np.mean(np.asarray(tmp_rw)) 160 if print_err: 161 print(config_no, i, j, np.mean(np.asarray(tmp_rw)), np.std(np.asarray(tmp_rw))) 162 print('Sources:', np.asarray(tmp_rw)) 163 print('Partial factor:', tmp_nfct) 164 tmp_array[i].append(tmp_nfct) 165 166 for k in range(nrw): 167 deltas[k].append(tmp_array[k][r_start[rep]:r_stop[rep]]) 168 169 rep_names = [] 170 for entry in ls: 171 truncated_entry = entry.split('.')[0] 172 idx = truncated_entry.index('r') 173 rep_names.append(truncated_entry[:idx] + '|' + truncated_entry[idx:]) 174 print(',', nrw, r'<bar{psi}\psi> with', nsrc, 'sources') 175 result = [] 176 for t in range(nrw): 177 result.append(Obs(deltas[t], rep_names)) 178 179 return result
Read pbp format from given folder structure.
Parameters
- r_start (list): list which contains the first config to be read for each replicum
- r_stop (list): list which contains the last config to be read for each replicum
Returns
- result (list[Obs]): list of observables read