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Merge branch 'develop' into fix/covariance_idl

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Fabian Joswig 2022-04-19 17:29:55 +01:00 • committed by GitHub
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3 changed files with 105 additions and 25 deletions
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6
pyerrors/correlators.py
View file

@ -621,7 +621,7 @@ class Corr:
raise Exception('Unknown variant.')
def fit(self, function, fitrange=None, silent=False, **kwargs):
"""Fits function to the data
r'''Fits function to the data
Parameters
----------
@ -629,10 +629,12 @@ class Corr:
function to fit to the data. See fits.least_squares for details.
fitrange : list
Two element list containing the timeslices on which the fit is supposed to start and stop.
Caution: This range is inclusive as opposed to standard python indexing.
`fitrange=[4, 6]` corresponds to the three entries 4, 5 and 6.
If not specified, self.prange or all timeslices are used.
silent : bool
Decides whether output is printed to the standard output.
"""
'''
if self.N != 1:
raise Exception("Correlator must be projected before fitting")

102
pyerrors/input/bdio.py
View file

@ -302,11 +302,24 @@ def read_mesons(file_path, bdio_path='./libbdio.so', **kwargs):
Parameters
----------
file_path -- path to the bdio file
bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)
stop -- stops reading at given configuration number (default None)
alternative_ensemble_name -- Manually overwrite ensemble name
file_path : str
path to the bdio file
bdio_path : str
path to the shared bdio library libbdio.so (default ./libbdio.so)
start : int
The first configuration to be read (default 1)
stop : int
The last configuration to be read (default None)
step : int
Fixed step size between two measurements (default 1)
alternative_ensemble_name : str
Manually overwrite ensemble name
"""
start = kwargs.get('start', 1)
stop = kwargs.get('stop', None)
step = kwargs.get('step', 1)
bdio = ctypes.cdll.LoadLibrary(bdio_path)
bdio_open = bdio.bdio_open
@ -353,9 +366,9 @@ def read_mesons(file_path, bdio_path='./libbdio.so', **kwargs):
prop_kappa = [] # Contains propagator kappas (Component of corr_kappa)
prop_source = [] # Contains propagator source positions
# Check noise type for multiple replica?
cnfg_no = -1
corr_no = -1
data = []
idl = []
fbdio = bdio_open(ctypes.c_char_p(b_path), ctypes.c_char_p(b_read), ctypes.c_char_p(b_form))
@ -418,18 +431,20 @@ def read_mesons(file_path, bdio_path='./libbdio.so', **kwargs):
prop_kappa.append(_get_kwd(tmp_string, 'KAPPA='))
prop_source.append(_get_kwd(tmp_string, 'x0='))
if ruinfo == 4:
if 'stop' in kwargs:
if cnfg_no >= kwargs.get('stop') - 1:
cnfg_no = int(_get_kwd(tmp_string, 'CNFG_ID='))
if stop:
if cnfg_no > kwargs.get('stop'):
break
cnfg_no += 1
print('\r%s %i' % ('Reading configuration', cnfg_no + 1), end='\r')
if cnfg_no == 0:
idl.append(cnfg_no)
print('\r%s %i' % ('Reading configuration', cnfg_no), end='\r')
if len(idl) == 1:
no_corrs = len(corr_name)
data = []
for c in range(no_corrs):
data.append([])
corr_no = 0
bdio_close(fbdio)
print('\nEnsemble: ', ensemble_name)
@ -441,7 +456,7 @@ def read_mesons(file_path, bdio_path='./libbdio.so', **kwargs):
print('Number of time values: ', d0)
print('Number of random sources: ', d1)
print('Number of corrs: ', len(corr_name))
print('Number of configurations: ', cnfg_no + 1)
print('Number of configurations: ', len(idl))
corr_kappa = [] # Contains kappa values for both propagators of given correlation function
corr_source = []
@ -452,12 +467,29 @@ def read_mesons(file_path, bdio_path='./libbdio.so', **kwargs):
else:
corr_source.append(int(prop_source[int(item[0])]))
if stop is None:
stop = idl[-1]
idl_target = range(start, stop + 1, step)
if set(idl) != set(idl_target):
try:
indices = [idl.index(i) for i in idl_target]
except ValueError as err:
raise Exception('Configurations in file do no match target list!', err)
else:
indices = None
result = {}
for c in range(no_corrs):
tmp_corr = []
tmp_data = np.asarray(data[c])
for t in range(d0 - 2):
tmp_corr.append(Obs([np.asarray(data[c])[:, t]], [ensemble_name]))
result[(corr_name[c], corr_source[c]) + tuple(sorted(corr_kappa[c]))] = tmp_corr
if indices:
deltas = [tmp_data[:, t][index] for index in indices]
else:
deltas = tmp_data[:, t]
tmp_corr.append(Obs([deltas], [ensemble_name], idl=[idl_target]))
result[(corr_name[c], corr_source[c]) + tuple(corr_kappa[c])] = tmp_corr
# Check that all data entries have the same number of configurations
if len(set([o[0].N for o in list(result.values())])) != 1:
@ -480,10 +512,24 @@ def read_dSdm(file_path, bdio_path='./libbdio.so', **kwargs):
Parameters
----------
file_path -- path to the bdio file
bdio_path -- path to the shared bdio library libbdio.so (default ./libbdio.so)
stop -- stops reading at given configuration number (default None)
file_path : str
path to the bdio file
bdio_path : str
path to the shared bdio library libbdio.so (default ./libbdio.so)
start : int
The first configuration to be read (default 1)
stop : int
The last configuration to be read (default None)
step : int
Fixed step size between two measurements (default 1)
alternative_ensemble_name : str
Manually overwrite ensemble name
"""
start = kwargs.get('start', 1)
stop = kwargs.get('stop', None)
step = kwargs.get('step', 1)
bdio = ctypes.cdll.LoadLibrary(bdio_path)
bdio_open = bdio.bdio_open
@ -529,9 +575,9 @@ def read_dSdm(file_path, bdio_path='./libbdio.so', **kwargs):
# d1 = 0 # nnoise
prop_kappa = [] # Contains propagator kappas (Component of corr_kappa)
# Check noise type for multiple replica?
cnfg_no = -1
corr_no = -1
data = []
idl = []
fbdio = bdio_open(ctypes.c_char_p(b_path), ctypes.c_char_p(b_read), ctypes.c_char_p(b_form))
@ -586,12 +632,13 @@ def read_dSdm(file_path, bdio_path='./libbdio.so', **kwargs):
if ruinfo == 2:
prop_kappa.append(_get_kwd(tmp_string, 'KAPPA='))
if ruinfo == 4:
if 'stop' in kwargs:
if cnfg_no >= kwargs.get('stop') - 1:
cnfg_no = int(_get_kwd(tmp_string, 'CNFG_ID='))
if stop:
if cnfg_no > kwargs.get('stop'):
break
cnfg_no += 1
print('\r%s %i' % ('Reading configuration', cnfg_no + 1), end='\r')
if cnfg_no == 0:
idl.append(cnfg_no)
print('\r%s %i' % ('Reading configuration', cnfg_no), end='\r')
if len(idl) == 1:
no_corrs = len(corr_name)
data = []
for c in range(no_corrs):
@ -612,9 +659,18 @@ def read_dSdm(file_path, bdio_path='./libbdio.so', **kwargs):
for item in corr_props:
corr_kappa.append(float(prop_kappa[int(item)]))
if stop is None:
stop = idl[-1]
idl_target = range(start, stop + 1, step)
try:
indices = [idl.index(i) for i in idl_target]
except ValueError as err:
raise Exception('Configurations in file do no match target list!', err)
result = {}
for c in range(no_corrs):
result[(corr_name[c], str(corr_kappa[c]))] = Obs([np.asarray(data[c])], [ensemble_name])
deltas = [np.asarray(data[c])[index] for index in indices]
result[(corr_name[c], str(corr_kappa[c]))] = Obs([deltas], [ensemble_name], idl=[idl_target])
# Check that all data entries have the same number of configurations
if len(set([o.N for o in list(result.values())])) != 1:

22
tests/fits_test.py
View file

@ -157,6 +157,28 @@ def test_correlated_fit():
assert(diff.is_zero_within_error(sigma=5))
def test_fit_corr_independent():
dim = 50
x = np.arange(dim)
y = 0.84 * np.exp(-0.12 * x) + np.random.normal(0.0, 0.1, dim)
yerr = [0.1] * dim
oy = []
for i, item in enumerate(x):
oy.append(pe.pseudo_Obs(y[i], yerr[i], str(i)))
def func(a, x):
y = a[0] * anp.exp(-a[1] * x)
return y
out = pe.least_squares(x, oy, func)
out_corr = pe.least_squares(x, oy, func, correlated_fit=True)
assert np.isclose(out.chisquare, out_corr.chisquare)
assert (out[0] - out_corr[0]).is_zero(atol=1e-5)
assert (out[1] - out_corr[1]).is_zero(atol=1e-5)
def test_total_least_squares():
dim = 10 + int(30 * np.random.rand())
x = np.arange(dim) + np.random.normal(0.0, 0.15, dim)