From 1a7fcaffafbc80e64c2b266303e6fe1152946d6a Mon Sep 17 00:00:00 2001
From: Hu Zhao <zhao@mbd.rwth-aachen.de>
Date: Thu, 27 Oct 2022 16:52:15 +0200
Subject: [PATCH] refactor: use check_bounds
---
src/psimpy/inference/bayes_inference.py | 11 ++++-------
src/psimpy/sampler/latin.py | 6 +++++-
src/psimpy/sampler/metropolis_hastings.py | 15 +++++++++------
src/psimpy/sampler/saltelli.py | 3 +++
4 files changed, 21 insertions(+), 14 deletions(-)
diff --git a/src/psimpy/inference/bayes_inference.py b/src/psimpy/inference/bayes_inference.py
index 31a3fc5..9980154 100644
--- a/src/psimpy/inference/bayes_inference.py
+++ b/src/psimpy/inference/bayes_inference.py
@@ -3,6 +3,7 @@ import sys
from abc import ABC
from abc import abstractmethod
from psimpy.sampler.metropolis_hastings import MetropolisHastings
+from psimpy.utility.util_funcs import check_bounds
from typing import Union
from beartype.typing import Callable
from beartype import beartype
@@ -75,13 +76,7 @@ class BayesInferenceBase(ABC):
kwgs_ln_pxl : dict, optional
Keyword arguments for `ln_pxl`.
"""
- self.ndim = ndim
-
- if bounds is not None:
- if bounds.ndim != 2:
- raise ValueError("bounds must be a 2d numpy array")
- elif bounds.shape[0] != ndim or bounds.shape[1] != 2:
- raise ValueError("bounds must be of shape (ndim, 2)")
+ self.ndim = ndim
self.bounds = bounds
self.args_prior = () if args_prior is None else args_prior
@@ -175,6 +170,8 @@ class GridEstimation(BayesInferenceBase):
if self.bounds is None:
raise ValueError("bounds must be provided for grid estimation")
+ else:
+ check_bounds(self.ndim, self.bounds)
steps = (self.bounds[:,1] - self.bounds[:,0]) / np.array(nbins)
starts = steps/2 + self.bounds[:,0]
diff --git a/src/psimpy/sampler/latin.py b/src/psimpy/sampler/latin.py
index 821f1c3..3804d80 100644
--- a/src/psimpy/sampler/latin.py
+++ b/src/psimpy/sampler/latin.py
@@ -1,6 +1,6 @@
import numpy as np
from scipy.spatial.distance import pdist
-from psimpy.utility.util_funcs import scale_samples
+from psimpy.utility.util_funcs import check_bounds, scale_samples
from typing import Union
from beartype import beartype
@@ -31,7 +31,11 @@ class LHS:
Number of iterations if `criterion='maxmin'`.
"""
self.ndim = ndim
+
+ if bounds is not None:
+ check_bounds(ndim, bounds)
self.bounds = bounds
+
self.rng = np.random.default_rng(seed)
self.seed = seed
diff --git a/src/psimpy/sampler/metropolis_hastings.py b/src/psimpy/sampler/metropolis_hastings.py
index 5298c4e..dfb2d23 100644
--- a/src/psimpy/sampler/metropolis_hastings.py
+++ b/src/psimpy/sampler/metropolis_hastings.py
@@ -1,5 +1,6 @@
import numpy as np
import sys
+from psimpy.utility.util_funcs import check_bounds
from typing import Union
from beartype.typing import Callable
from beartype import beartype
@@ -10,12 +11,17 @@ class MetropolisHastings:
@beartype
def __init__(
- self, ndim: int, init_state: np.ndarray, f_sample: Callable,
+ self,
+ ndim: int,
+ init_state: np.ndarray,
+ f_sample: Callable,
target: Union[Callable, None] = None,
ln_target: Union[Callable, None] = None,
bounds: Union[np.ndarray, None] = None,
f_density: Union[Callable, None] = None,
- symmetric: bool = True, nburn: int = 0, nthin: int = 1,
+ symmetric: bool = True,
+ nburn: int = 0,
+ nthin: int = 1,
seed: Union[int, None] = None,
args_target: Union[list, None] = None,
kwgs_target: Union[dict, None] = None,
@@ -83,10 +89,7 @@ class MetropolisHastings:
raise ValueError(f"init_state must contain ndim={ndim} elements")
if bounds is not None:
- if bounds.ndim != 2:
- raise ValueError("bounds must be a 2d numpy array")
- elif bounds.shape[0] != ndim or bounds.shape[1] != 2:
- raise ValueError("bounds must be of shape (ndim, 2)")
+ check_bounds(ndim, bounds)
if not all([
init_state[i] >= bounds[i,0] and
diff --git a/src/psimpy/sampler/saltelli.py b/src/psimpy/sampler/saltelli.py
index afb9f08..f7e1de7 100644
--- a/src/psimpy/sampler/saltelli.py
+++ b/src/psimpy/sampler/saltelli.py
@@ -1,5 +1,6 @@
from SALib.sample import saltelli
import numpy as np
+from psimpy.utility.util_funcs import check_bounds
from typing import Union
from beartype import beartype
@@ -31,6 +32,8 @@ class Saltelli:
"""
if bounds is None:
bounds = np.array([[0, 1] for i in range(ndim)])
+ else:
+ check_bounds(ndim, bounds)
self.problem = {
'num_vars': ndim,
--
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