pyerrors 2.9.0__tar.gz → 2.11.0__tar.gz

{pyerrors-2.9.0 → pyerrors-2.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyerrors
-Version: 2.9.0
+Version: 2.11.0
 Summary: Error propagation and statistical analysis for Monte Carlo simulations
 Home-page: https://github.com/fjosw/pyerrors
 Author: Fabian Joswig
@@ -17,11 +17,28 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.8.0
 Description-Content-Type: text/markdown
-Provides-Extra: test
 License-File: LICENSE
+Requires-Dist: numpy<2,>=1.24
+Requires-Dist: autograd>=1.6.2
+Requires-Dist: numdifftools>=0.9.41
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: scipy>=1.10
+Requires-Dist: iminuit>=2.21
+Requires-Dist: h5py>=3.8
+Requires-Dist: lxml>=4.9
+Requires-Dist: python-rapidjson>=1.10
+Requires-Dist: pandas>=2.0
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-benchmark; extra == "test"
+Requires-Dist: hypothesis; extra == "test"
+Requires-Dist: nbmake; extra == "test"
+Requires-Dist: flake8; extra == "test"
 
 [![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
 # pyerrors

{pyerrors-2.9.0 → pyerrors-2.11.0}/pyerrors/__init__.py

@@ -487,5 +487,6 @@ from . import linalg
 from . import mpm
 from . import roots
 from . import integrate
+from . import special
 
 from .version import __version__

{pyerrors-2.9.0 → pyerrors-2.11.0}/pyerrors/correlators.py

@@ -8,6 +8,7 @@ from .obs import Obs, reweight, correlate, CObs
 from .misc import dump_object, _assert_equal_properties
 from .fits import least_squares
 from .roots import find_root
+from . import linalg
 
 
 class Corr:
@@ -298,7 +299,7 @@ class Corr:
             transposed = [None if _check_for_none(self, G) else G.T for G in self.content]
             return 0.5 * (Corr(transposed) + self)
 
-    def GEVP(self, t0, ts=None, sort="Eigenvalue", **kwargs):
+    def GEVP(self, t0, ts=None, sort="Eigenvalue", vector_obs=False, **kwargs):
         r'''Solve the generalized eigenvalue problem on the correlator matrix and returns the corresponding eigenvectors.
 
         The eigenvectors are sorted according to the descending eigenvalues, the zeroth eigenvector(s) correspond to the
@@ -317,14 +318,21 @@ class Corr:
             If sort="Eigenvector" it gives a reference point for the sorting method.
         sort : string
             If this argument is set, a list of self.T vectors per state is returned. If it is set to None, only one vector is returned.
-            - "Eigenvalue": The eigenvector is chosen according to which eigenvalue it belongs individually on every timeslice.
+            - "Eigenvalue": The eigenvector is chosen according to which eigenvalue it belongs individually on every timeslice. (default)
             - "Eigenvector": Use the method described in arXiv:2004.10472 to find the set of v(t) belonging to the state.
               The reference state is identified by its eigenvalue at $t=t_s$.
+            - None: The GEVP is solved only at ts, no sorting is necessary
+        vector_obs : bool
+            If True, uncertainties are propagated in the eigenvector computation (default False).
 
         Other Parameters
         ----------------
         state : int
            Returns only the vector(s) for a specified state. The lowest state is zero.
+        method : str
+           Method used to solve the GEVP.
+           - "eigh": Use scipy.linalg.eigh to solve the GEVP. (default for vector_obs=False)
+           - "cholesky": Use manually implemented solution via the Cholesky decomposition. Automatically chosen if vector_obs==True.
         '''
 
         if self.N == 1:
@@ -342,16 +350,34 @@ class Corr:
         else:
             symmetric_corr = self.matrix_symmetric()
 
-        G0 = np.vectorize(lambda x: x.value)(symmetric_corr[t0])
-        np.linalg.cholesky(G0)  # Check if matrix G0 is positive-semidefinite.
+        def _get_mat_at_t(t, vector_obs=vector_obs):
+            if vector_obs:
+                return symmetric_corr[t]
+            else:
+                return np.vectorize(lambda x: x.value)(symmetric_corr[t])
+        G0 = _get_mat_at_t(t0)
+
+        method = kwargs.get('method', 'eigh')
+        if vector_obs:
+            chol = linalg.cholesky(G0)
+            chol_inv = linalg.inv(chol)
+            method = 'cholesky'
+        else:
+            chol = np.linalg.cholesky(_get_mat_at_t(t0, vector_obs=False))  # Check if matrix G0 is positive-semidefinite.
+            if method == 'cholesky':
+                chol_inv = np.linalg.inv(chol)
+            else:
+                chol_inv = None
 
         if sort is None:
             if (ts is None):
                 raise Exception("ts is required if sort=None.")
             if (self.content[t0] is None) or (self.content[ts] is None):
                 raise Exception("Corr not defined at t0/ts.")
-            Gt = np.vectorize(lambda x: x.value)(symmetric_corr[ts])
-            reordered_vecs = _GEVP_solver(Gt, G0)
+            Gt = _get_mat_at_t(ts)
+            reordered_vecs = _GEVP_solver(Gt, G0, method=method, chol_inv=chol_inv)
+            if kwargs.get('auto_gamma', False) and vector_obs:
+                [[o.gm() for o in ev if isinstance(o, Obs)] for ev in reordered_vecs]
 
         elif sort in ["Eigenvalue", "Eigenvector"]:
             if sort == "Eigenvalue" and ts is not None:
@@ -359,8 +385,8 @@ class Corr:
             all_vecs = [None] * (t0 + 1)
             for t in range(t0 + 1, self.T):
                 try:
-                    Gt = np.vectorize(lambda x: x.value)(symmetric_corr[t])
-                    all_vecs.append(_GEVP_solver(Gt, G0))
+                    Gt = _get_mat_at_t(t)
+                    all_vecs.append(_GEVP_solver(Gt, G0, method=method, chol_inv=chol_inv))
                 except Exception:
                     all_vecs.append(None)
             if sort == "Eigenvector":
@@ -369,15 +395,17 @@ class Corr:
                 all_vecs = _sort_vectors(all_vecs, ts)
 
             reordered_vecs = [[v[s] if v is not None else None for v in all_vecs] for s in range(self.N)]
+            if kwargs.get('auto_gamma', False) and vector_obs:
+                [[[o.gm() for o in evn] for evn in ev if evn is not None] for ev in reordered_vecs]
         else:
-            raise Exception("Unkown value for 'sort'.")
+            raise Exception("Unknown value for 'sort'. Choose 'Eigenvalue', 'Eigenvector' or None.")
 
         if "state" in kwargs:
             return reordered_vecs[kwargs.get("state")]
         else:
             return reordered_vecs
 
-    def Eigenvalue(self, t0, ts=None, state=0, sort="Eigenvalue"):
+    def Eigenvalue(self, t0, ts=None, state=0, sort="Eigenvalue", **kwargs):
         """Determines the eigenvalue of the GEVP by solving and projecting the correlator
 
         Parameters
@@ -387,7 +415,7 @@ class Corr:
 
         All other parameters are identical to the ones of Corr.GEVP.
         """
-        vec = self.GEVP(t0, ts=ts, sort=sort)[state]
+        vec = self.GEVP(t0, ts=ts, sort=sort, **kwargs)[state]
         return self.projected(vec)
 
     def Hankel(self, N, periodic=False):
@@ -1075,7 +1103,7 @@ class Corr:
                     newcontent.append(self.content[t] + y.content[t])
             return Corr(newcontent)
 
-        elif isinstance(y, (Obs, int, float, CObs)):
+        elif isinstance(y, (Obs, int, float, CObs, complex)):
             newcontent = []
             for t in range(self.T):
                 if _check_for_none(self, self.content[t]):
@@ -1103,7 +1131,7 @@ class Corr:
                     newcontent.append(self.content[t] * y.content[t])
             return Corr(newcontent)
 
-        elif isinstance(y, (Obs, int, float, CObs)):
+        elif isinstance(y, (Obs, int, float, CObs, complex)):
             newcontent = []
             for t in range(self.T):
                 if _check_for_none(self, self.content[t]):
@@ -1386,8 +1414,13 @@ class Corr:
         return Corr(newcontent)
 
 
-def _sort_vectors(vec_set, ts):
+def _sort_vectors(vec_set_in, ts):
     """Helper function used to find a set of Eigenvectors consistent over all timeslices"""
+
+    if isinstance(vec_set_in[ts][0][0], Obs):
+        vec_set = [anp.vectorize(lambda x: float(x))(vi) if vi is not None else vi for vi in vec_set_in]
+    else:
+        vec_set = vec_set_in
     reference_sorting = np.array(vec_set[ts])
     N = reference_sorting.shape[0]
     sorted_vec_set = []
@@ -1406,9 +1439,9 @@ def _sort_vectors(vec_set, ts):
                 if current_score > best_score:
                     best_score = current_score
                     best_perm = perm
-            sorted_vec_set.append([vec_set[t][k] for k in best_perm])
+            sorted_vec_set.append([vec_set_in[t][k] for k in best_perm])
         else:
-            sorted_vec_set.append(vec_set[t])
+            sorted_vec_set.append(vec_set_in[t])
 
     return sorted_vec_set
 
@@ -1418,10 +1451,63 @@ def _check_for_none(corr, entry):
     return len(list(filter(None, np.asarray(entry).flatten()))) < corr.N ** 2
 
 
-def _GEVP_solver(Gt, G0):
-    """Helper function for solving the GEVP and sorting the eigenvectors.
+def _GEVP_solver(Gt, G0, method='eigh', chol_inv=None):
+    r"""Helper function for solving the GEVP and sorting the eigenvectors.
+
+    Solves $G(t)v_i=\lambda_i G(t_0)v_i$ and returns the eigenvectors v_i
 
     The helper function assumes that both provided matrices are symmetric and
     only processes the lower triangular part of both matrices. In case the matrices
-    are not symmetric the upper triangular parts are effectively discarded."""
-    return scipy.linalg.eigh(Gt, G0, lower=True)[1].T[::-1]
+    are not symmetric the upper triangular parts are effectively discarded.
+
+    Parameters
+    ----------
+    Gt : array
+        The correlator at time t for the left hand side of the GEVP
+    G0 : array
+        The correlator at time t0 for the right hand side of the GEVP
+    Method used to solve the GEVP.
+       - "eigh": Use scipy.linalg.eigh to solve the GEVP.
+       - "cholesky": Use manually implemented solution via the Cholesky decomposition.
+    chol_inv : array, optional
+        Inverse of the Cholesky decomposition of G0. May be provided to
+        speed up the computation in the case of method=='cholesky'
+
+    """
+    if isinstance(G0[0][0], Obs):
+        vector_obs = True
+    else:
+        vector_obs = False
+
+    if method == 'cholesky':
+        if vector_obs:
+            cholesky = linalg.cholesky
+            inv = linalg.inv
+            eigv = linalg.eigv
+            matmul = linalg.matmul
+        else:
+            cholesky = np.linalg.cholesky
+            inv = np.linalg.inv
+
+            def eigv(x, **kwargs):
+                return np.linalg.eigh(x)[1]
+
+            def matmul(*operands):
+                return np.linalg.multi_dot(operands)
+        N = Gt.shape[0]
+        output = [[] for j in range(N)]
+        if chol_inv is None:
+            chol = cholesky(G0)  # This will automatically report if the matrix is not pos-def
+            chol_inv = inv(chol)
+
+        try:
+            new_matrix = matmul(chol_inv, Gt, chol_inv.T)
+            ev = eigv(new_matrix)
+            ev = matmul(chol_inv.T, ev)
+            output = np.flip(ev, axis=1).T
+        except (np.linalg.LinAlgError, TypeError, ValueError):  # The above code can fail because of linalg-errors or because the entry of the corr is None
+            for s in range(N):
+                output[s] = None
+        return output
+    elif method == 'eigh':
+        return scipy.linalg.eigh(Gt, G0, lower=True)[1].T[::-1]

{pyerrors-2.9.0 → pyerrors-2.11.0}/pyerrors/fits.py

@@ -168,12 +168,12 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
     '''
     output = Fit_result()
 
-    if (type(x) == dict and type(y) == dict and type(func) == dict):
+    if (isinstance(x, dict) and isinstance(y, dict) and isinstance(func, dict)):
         xd = {key: anp.asarray(x[key]) for key in x}
         yd = y
         funcd = func
         output.fit_function = func
-    elif (type(x) == dict or type(y) == dict or type(func) == dict):
+    elif (isinstance(x, dict) or isinstance(y, dict) or isinstance(func, dict)):
         raise TypeError("All arguments have to be dictionaries in order to perform a combined fit.")
     else:
         x = np.asarray(x)
@@ -365,7 +365,7 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
         raise Exception('The minimization procedure did not converge.')
 
     output.chisquare = chisquare
-    output.dof = x_all.shape[-1] - n_parms + len(loc_priors)
+    output.dof = y_all.shape[-1] - n_parms + len(loc_priors)
     output.p_value = 1 - scipy.stats.chi2.cdf(output.chisquare, output.dof)
     if output.dof > 0:
         output.chisquare_by_dof = output.chisquare / output.dof
@@ -393,7 +393,7 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
             hat_vector = prepare_hat_matrix()
             A = W @ hat_vector
             P_phi = A @ np.linalg.pinv(A.T @ A) @ A.T
-            expected_chisquare = np.trace((np.identity(x_all.shape[-1]) - P_phi) @ W @ cov @ W)
+            expected_chisquare = np.trace((np.identity(y_all.shape[-1]) - P_phi) @ W @ cov @ W)
             output.chisquare_by_expected_chisquare = output.chisquare / expected_chisquare
             if not silent:
                 print('chisquare/expected_chisquare:', output.chisquare_by_expected_chisquare)

{pyerrors-2.9.0 → pyerrors-2.11.0}/pyerrors/input/hadrons.py

@@ -88,7 +88,7 @@ def read_hd5(filestem, ens_id, group, attrs=None, idl=None, part="real"):
 
     path_obj = Path(filestem)
     path = path_obj.parent.as_posix()
-    filestem = path_obj.stem
+    filestem = path_obj.name
 
     files, idx = _get_files(path, filestem, idl)
 

{pyerrors-2.9.0 → pyerrors-2.11.0}/pyerrors/input/openQCD.py

@@ -1286,7 +1286,9 @@ def read_ms5_xsf(path, prefix, qc, corr, sep="r", **kwargs):
                         imagsamples[repnum][t].append(corrres[1][t])
             if 'idl' in kwargs:
                 left_idl = list(left_idl)
-                if len(left_idl) > 0:
+                if expected_idl[repnum] == left_idl:
+                    raise ValueError("None of the idls searched for were found in replikum of file " + file)
+                elif len(left_idl) > 0:
                     warnings.warn('Could not find idls ' + str(left_idl) + ' in replikum of file ' + file, UserWarning)
         repnum += 1
     s = "Read correlator " + corr + " from " + str(repnum) + " replika with idls" + str(realsamples[0][t])