CUQIpy 1.1.0__tar.gz → 1.1.0.post0.dev17__tar.gz

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/CUQIpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CUQIpy
-Version: 1.1.0
+Version: 1.1.0.post0.dev17
 Summary: Computational Uncertainty Quantification for Inverse problems in Python
 Maintainer-email: "Nicolai A. B. Riis" <nabr@dtu.dk>, "Jakob S. Jørgensen" <jakj@dtu.dk>, "Amal M. Alghamdi" <amaal@dtu.dk>, Chao Zhang <chaz@dtu.dk>
 License:                                  Apache License

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CUQIpy
-Version: 1.1.0
+Version: 1.1.0.post0.dev17
 Summary: Computational Uncertainty Quantification for Inverse problems in Python
 Maintainer-email: "Nicolai A. B. Riis" <nabr@dtu.dk>, "Jakob S. Jørgensen" <jakj@dtu.dk>, "Amal M. Alghamdi" <amaal@dtu.dk>, Chao Zhang <chaz@dtu.dk>
 License:                                  Apache License

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-07-05T13:16:30+0200",
+ "date": "2024-08-26T08:07:58+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "e1833beaad21264a01eea69959efffa942db3f34",
- "version": "1.1.0"
+ "full-revisionid": "9d87eb837ab12ccedf61101e396df2ab1cb37764",
+ "version": "1.1.0.post0.dev17"
 }
 '''  # END VERSION_JSON
 

cuqipy-1.1.0.post0.dev17/cuqi/experimental/mcmc/__init__.py

@@ -0,0 +1,15 @@
+""" Re-implementation of sampler module in a more object oriented way. """
+
+from ._sampler import Sampler, ProposalBasedSampler
+from ._langevin_algorithm import ULA, MALA
+from ._mh import MH
+from ._pcn import PCN
+from ._rto import LinearRTO, RegularizedLinearRTO
+from ._cwmh import CWMH
+from ._laplace_approximation import UGLA
+from ._hmc import NUTS
+from ._gibbs import HybridGibbs
+from ._conjugate import Conjugate
+from ._conjugate_approx import ConjugateApprox
+from ._direct import Direct
+from ._utilities import find_valid_samplers

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_conjugate.py

@@ -1,12 +1,12 @@
 import numpy as np
 from abc import ABC, abstractmethod
 import math
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 from cuqi.distribution import Posterior, Gaussian, Gamma, GMRF
 from cuqi.implicitprior import RegularizedGaussian, RegularizedGMRF
 from cuqi.utilities import get_non_default_args
 
-class ConjugateNew(SamplerNew):
+class Conjugate(Sampler):
     """ Conjugate sampler
 
     Sampler for sampling a posterior distribution which is a so-called "conjugate" distribution, i.e., where the likelihood and prior are conjugate to each other - denoted as a conjugate pair.   
@@ -34,7 +34,7 @@ class ConjugateNew(SamplerNew):
     def _initialize(self):
         pass
 
-    @SamplerNew.target.setter # Overwrite the target setter to set the conjugate pair
+    @Sampler.target.setter # Overwrite the target setter to set the conjugate pair
     def target(self, value):
         """ Set the target density. Runs validation of the target. """
         self._target = value

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_conjugate_approx.py

@@ -1,10 +1,10 @@
 import numpy as np
-from cuqi.experimental.mcmc import ConjugateNew
+from cuqi.experimental.mcmc import Conjugate
 from cuqi.experimental.mcmc._conjugate import _ConjugatePair, _get_conjugate_parameter, _check_conjugate_parameter_is_scalar_reciprocal
 from cuqi.distribution import LMRF, Gamma
 import scipy as sp
 
-class ConjugateApproxNew(ConjugateNew):
+class ConjugateApprox(Conjugate):
     """ Approximate Conjugate sampler
 
     Sampler for sampling a posterior distribution where the likelihood and prior can be approximated
@@ -17,7 +17,7 @@ class ConjugateApproxNew(ConjugateNew):
 
     LMRF likelihood must have zero mean.
 
-    For more details on conjugacy see :class:`ConjugateNew`.
+    For more details on conjugacy see :class:`Conjugate`.
 
     """
 

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_cwmh.py

@@ -1,10 +1,10 @@
 import numpy as np
 import cuqi
-from cuqi.experimental.mcmc import ProposalBasedSamplerNew
+from cuqi.experimental.mcmc import ProposalBasedSampler
 from cuqi.array import CUQIarray
 from numbers import Number
 
-class CWMHNew(ProposalBasedSamplerNew):
+class CWMH(ProposalBasedSampler):
     """Component-wise Metropolis Hastings sampler.
 
     Allows sampling of a target distribution by a component-wise random-walk
@@ -40,7 +40,7 @@ class CWMHNew(ProposalBasedSamplerNew):
 
     kwargs : dict
         Additional keyword arguments to be passed to the base class 
-        :class:`ProposalBasedSamplerNew`.
+        :class:`ProposalBasedSampler`.
 
     Example
     -------
@@ -61,14 +61,14 @@ class CWMHNew(ProposalBasedSamplerNew):
             dim=dim, logpdf_func=logpdf_func)
 
         # Set up sampler
-        sampler = cuqi.experimental.mcmc.CWMHNew(target, scale=1)
+        sampler = cuqi.experimental.mcmc.CWMH(target, scale=1)
 
         # Sample
         samples = sampler.sample(2000).get_samples()
 
     """
 
-    _STATE_KEYS = ProposalBasedSamplerNew._STATE_KEYS.union(['_scale_temp'])
+    _STATE_KEYS = ProposalBasedSampler._STATE_KEYS.union(['_scale_temp'])
 
     def __init__(self, target:cuqi.density.Density=None, proposal=None, scale=1,
                  initial_point=None, **kwargs):
@@ -78,7 +78,7 @@ class CWMHNew(ProposalBasedSamplerNew):
     def _initialize(self):
         if isinstance(self.scale, Number):
             self.scale = np.ones(self.dim)*self.scale
-        self._acc = [np.ones((self.dim))] # Overwrite acc from ProposalBasedSamplerNew with list of arrays
+        self._acc = [np.ones((self.dim))] # Overwrite acc from ProposalBasedSampler with list of arrays
 
         # Handling of temporary scale parameter due to possible bug in old CWMH
         self._scale_temp = self.scale.copy()

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_direct.py

@@ -1,6 +1,6 @@
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 
-class DirectNew(SamplerNew):
+class Direct(Sampler):
     """ Direct sampler
 
     This sampler is used to sample from a target distribution directly. It simply calls the sample method of the target object to generate a sample.

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_gibbs.py

@@ -1,5 +1,5 @@
 from cuqi.distribution import JointDistribution
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 from cuqi.samples import Samples
 from typing import Dict
 import numpy as np
@@ -12,9 +12,9 @@ except ImportError:
         warnings.warn("Module mcmc: Progressbar not found. Install progressbar2 to get sampling progress.")
         return iterable
 
-# Not subclassed from SamplerNew as Gibbs handles multiple samplers and samples multiple parameters
+# Not subclassed from Sampler as Gibbs handles multiple samplers and samples multiple parameters
 # Similar approach as for JointDistribution
-class HybridGibbsNew: 
+class HybridGibbs: 
     """
     Hybrid Gibbs sampler for sampling a joint distribution.
 
@@ -80,13 +80,13 @@ class HybridGibbsNew:
 
         # Define sampling strategy
         sampling_strategy = {
-            'x': cuqi.experimental.mcmc.LinearRTONew(maxit=15),
-            'd': cuqi.experimental.mcmc.ConjugateNew(),
-            'l': cuqi.experimental.mcmc.ConjugateNew(),
+            'x': cuqi.experimental.mcmc.LinearRTO(maxit=15),
+            'd': cuqi.experimental.mcmc.Conjugate(),
+            'l': cuqi.experimental.mcmc.Conjugate(),
         }
 
         # Define Gibbs sampler
-        sampler = cuqi.experimental.mcmc.HybridGibbsNew(posterior, sampling_strategy)
+        sampler = cuqi.experimental.mcmc.HybridGibbs(posterior, sampling_strategy)
 
         # Run sampler
         samples = sampler.sample(Ns=1000, Nb=200)
@@ -98,7 +98,7 @@ class HybridGibbsNew:
             
     """
 
-    def __init__(self, target: JointDistribution, sampling_strategy: Dict[str, SamplerNew], num_sampling_steps: Dict[str, int] = None):
+    def __init__(self, target: JointDistribution, sampling_strategy: Dict[str, Sampler], num_sampling_steps: Dict[str, int] = None):
 
         # Store target and allow conditioning to reduce to a single density
         self.target = target() # Create a copy of target distribution (to avoid modifying the original)
@@ -150,13 +150,13 @@ class HybridGibbsNew:
         for sampler in self.samplers.values():
             sampler.validate_target()
 
-    def sample(self, Ns) -> 'HybridGibbsNew':
+    def sample(self, Ns) -> 'HybridGibbs':
         """ Sample from the joint distribution using Gibbs sampling """
         for _ in progressbar(range(Ns)):
             self.step()
             self._store_samples()
 
-    def warmup(self, Nb) -> 'HybridGibbsNew':
+    def warmup(self, Nb) -> 'HybridGibbs':
         """ Warmup (tune) the Gibbs sampler """
         for idx in progressbar(range(Nb)):
             self.step()

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_hmc.py

@@ -1,10 +1,10 @@
 import numpy as np
 import numpy as np
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 from cuqi.array import CUQIarray
 from numbers import Number
 
-class NUTSNew(SamplerNew):
+class NUTS(Sampler):
     """No-U-Turn Sampler (Hoffman and Gelman, 2014).
 
     Samples a distribution given its logpdf and gradient using a Hamiltonian
@@ -58,7 +58,7 @@ class NUTSNew(SamplerNew):
         target = tp.posterior
 
         # Set up sampler
-        sampler = cuqi.experimental.mcmc.NUTSNew(target)
+        sampler = cuqi.experimental.mcmc.NUTS(target)
 
         # Sample
         sampler.warmup(5000)
@@ -87,11 +87,11 @@ class NUTSNew(SamplerNew):
 
     """
 
-    _STATE_KEYS = SamplerNew._STATE_KEYS.union({'_epsilon', '_epsilon_bar',
+    _STATE_KEYS = Sampler._STATE_KEYS.union({'_epsilon', '_epsilon_bar',
                                                 '_H_bar', '_mu',
                                                 '_alpha', '_n_alpha'})
 
-    _HISTORY_KEYS = SamplerNew._HISTORY_KEYS.union({'num_tree_node_list',
+    _HISTORY_KEYS = Sampler._HISTORY_KEYS.union({'num_tree_node_list',
                                                     'epsilon_list',
                                                     'epsilon_bar_list'})
 
@@ -120,7 +120,7 @@ class NUTSNew(SamplerNew):
     def _initialize(self):
 
         # Arrays to store acceptance rate
-        self._acc = [None] # Overwrites acc from SamplerNew. TODO. Check if this is necessary
+        self._acc = [None] # Overwrites acc from Sampler. TODO. Check if this is necessary
 
         self._alpha = 0 # check if meaningful value
         self._n_alpha = 0 # check if meaningful value
@@ -188,7 +188,7 @@ class NUTSNew(SamplerNew):
         self._opt_acc_rate = value
 
     #=========================================================================
-    #================== Implement methods required by SamplerNew =============
+    #================== Implement methods required by Sampler =============
     #=========================================================================
     def validate_target(self):
         # Check if the target has logd and gradient methods

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_langevin_algorithm.py

@@ -1,9 +1,9 @@
 import numpy as np
 import cuqi
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 from cuqi.array import CUQIarray
 
-class ULANew(SamplerNew): # Refactor to Proposal-based sampler?
+class ULA(Sampler): # Refactor to Proposal-based sampler?
     """Unadjusted Langevin algorithm (ULA) (Roberts and Tweedie, 1996)
 
     Samples a distribution given its logpdf and gradient (up to a constant) based on
@@ -52,7 +52,7 @@ class ULANew(SamplerNew): # Refactor to Proposal-based sampler?
             gradient_func=gradient_func)
 
         # Set up sampler
-        sampler = cuqi.experimental.mcmc.ULANew(target, scale=1/dim**2)
+        sampler = cuqi.experimental.mcmc.ULA(target, scale=1/dim**2)
 
         # Sample
         sampler.sample(2000)
@@ -61,7 +61,7 @@ class ULANew(SamplerNew): # Refactor to Proposal-based sampler?
     # TODO: update demo once sampler merged
     """
 
-    _STATE_KEYS = SamplerNew._STATE_KEYS.union({'current_target_logd', 'scale', 'current_target_grad'})
+    _STATE_KEYS = Sampler._STATE_KEYS.union({'current_target_logd', 'scale', 'current_target_grad'})
 
     def __init__(self, target=None, scale=1.0, **kwargs):
 
@@ -125,7 +125,7 @@ class ULANew(SamplerNew): # Refactor to Proposal-based sampler?
         pass
 
 
-class MALANew(ULANew): # Refactor to Proposal-based sampler?
+class MALA(ULA): # Refactor to Proposal-based sampler?
     """  Metropolis-adjusted Langevin algorithm (MALA) (Roberts and Tweedie, 1996)
 
     Samples a distribution given its logd and gradient (up to a constant) based on
@@ -174,7 +174,7 @@ class MALANew(ULANew): # Refactor to Proposal-based sampler?
             gradient_func=gradient_func)
 
         # Set up sampler
-        sampler = cuqi.experimental.mcmc.MALANew(target, scale=1/5**2)
+        sampler = cuqi.experimental.mcmc.MALA(target, scale=1/5**2)
 
         # Sample
         sampler.sample(2000)

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_laplace_approximation.py

@@ -2,9 +2,9 @@ import scipy as sp
 import numpy as np
 import cuqi
 from cuqi.solver import CGLS
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 
-class UGLANew(SamplerNew):
+class UGLA(Sampler):
     """ Unadjusted (Gaussian) Laplace Approximation sampler
     
     Samples an approximate posterior where the prior is approximated

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_mh.py

@@ -1,9 +1,9 @@
 import numpy as np
 import cuqi
-from cuqi.experimental.mcmc import ProposalBasedSamplerNew
+from cuqi.experimental.mcmc import ProposalBasedSampler
 
 
-class MHNew(ProposalBasedSamplerNew):
+class MH(ProposalBasedSampler):
     """ Metropolis-Hastings (MH) sampler.
 
     Parameters
@@ -18,11 +18,11 @@ class MHNew(ProposalBasedSamplerNew):
         Scaling parameter for the proposal distribution.
 
     kwargs : dict
-        Additional keyword arguments to be passed to the base class :class:`ProposalBasedSamplerNew`.
+        Additional keyword arguments to be passed to the base class :class:`ProposalBasedSampler`.
 
     """
 
-    _STATE_KEYS = ProposalBasedSamplerNew._STATE_KEYS.union({'scale', '_scale_temp'})
+    _STATE_KEYS = ProposalBasedSampler._STATE_KEYS.union({'scale', '_scale_temp'})
 
     def __init__(self, target=None, proposal=None, scale=1, **kwargs):
         super().__init__(target, proposal=proposal, scale=scale, **kwargs)

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_pcn.py

@@ -1,11 +1,11 @@
 import numpy as np
 import cuqi
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 from cuqi.array import CUQIarray
 
-class PCNNew(SamplerNew):  # Refactor to Proposal-based sampler?
+class PCN(Sampler):  # Refactor to Proposal-based sampler?
 
-    _STATE_KEYS = SamplerNew._STATE_KEYS.union({'scale', 'current_likelihood_logd', 'lambd'})
+    _STATE_KEYS = Sampler._STATE_KEYS.union({'scale', 'current_likelihood_logd', 'lambd'})
 
     def __init__(self, target=None, scale=1.0, **kwargs):
 

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_rto.py

@@ -4,10 +4,10 @@ from scipy.sparse.linalg import LinearOperator as scipyLinearOperator
 import numpy as np
 import cuqi
 from cuqi.solver import CGLS, FISTA
-from cuqi.experimental.mcmc import SamplerNew
+from cuqi.experimental.mcmc import Sampler
 
 
-class LinearRTONew(SamplerNew):
+class LinearRTO(Sampler):
     """
     Linear RTO (Randomize-Then-Optimize) sampler.
 
@@ -155,7 +155,7 @@ class LinearRTONew(SamplerNew):
         """ Get the default initial point for the sampler. Defaults to an array of zeros. """
         return np.zeros(self.dim)
 
-class RegularizedLinearRTONew(LinearRTONew):
+class RegularizedLinearRTO(LinearRTO):
     """
     Regularized Linear RTO (Randomize-Then-Optimize) sampler.
 

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_sampler.py

@@ -13,7 +13,7 @@ except ImportError:
         warnings.warn("Module mcmc: Progressbar not found. Install progressbar2 to get sampling progress.")
         return iterable
 
-class SamplerNew(ABC):
+class Sampler(ABC):
     """ Abstract base class for all samplers.
     
     Provides a common interface for all samplers. The interface includes methods for sampling, warmup and getting the samples in an object oriented way.
@@ -194,7 +194,7 @@ class SamplerNew(ABC):
 
         self.set_state(state)
 
-    def sample(self, Ns, batch_size=0, sample_path='./CUQI_samples/') -> 'SamplerNew':
+    def sample(self, Ns, batch_size=0, sample_path='./CUQI_samples/') -> 'Sampler':
         """ Sample Ns samples from the target density.
 
         Parameters
@@ -239,7 +239,7 @@ class SamplerNew(ABC):
         return self
     
 
-    def warmup(self, Nb, tune_freq=0.1) -> 'SamplerNew':
+    def warmup(self, Nb, tune_freq=0.1) -> 'Sampler':
         """ Warmup the sampler by drawing Nb samples.
 
         Parameters
@@ -407,10 +407,10 @@ class SamplerNew(ABC):
             msg += f"\t {key}: {value} \n"
         return msg
 
-class ProposalBasedSamplerNew(SamplerNew, ABC):
+class ProposalBasedSampler(Sampler, ABC):
     """ Abstract base class for samplers that use a proposal distribution. """
 
-    _STATE_KEYS = SamplerNew._STATE_KEYS.union({'current_target_logd', 'scale'})
+    _STATE_KEYS = Sampler._STATE_KEYS.union({'current_target_logd', 'scale'})
 
     def __init__(self, target=None, proposal=None, scale=1, **kwargs):
         """ Initializer for abstract base class for samplers that use a proposal distribution.
@@ -419,7 +419,7 @@ class ProposalBasedSamplerNew(SamplerNew, ABC):
 
         Initialization of the sampler should be done in the _initialize method.
 
-        See :class:`SamplerNew` for additional details.
+        See :class:`Sampler` for additional details.
 
         Parameters
         ----------
@@ -433,7 +433,7 @@ class ProposalBasedSamplerNew(SamplerNew, ABC):
             The scale parameter for the proposal distribution.
 
         **kwargs : dict
-            Additional keyword arguments passed to the :class:`SamplerNew` initializer.
+            Additional keyword arguments passed to the :class:`Sampler` initializer.
 
         """
 

{cuqipy-1.1.0 → cuqipy-1.1.0.post0.dev17}/cuqi/experimental/mcmc/_utilities.py

@@ -4,7 +4,7 @@ import inspect
 def find_valid_samplers(target):
     """ Finds all samplers in the cuqi.experimental.mcmc module that accept the provided target. """
 
-    all_samplers = [(name, cls) for name, cls in inspect.getmembers(cuqi.experimental.mcmc, inspect.isclass) if issubclass(cls, cuqi.experimental.mcmc.SamplerNew)]
+    all_samplers = [(name, cls) for name, cls in inspect.getmembers(cuqi.experimental.mcmc, inspect.isclass) if issubclass(cls, cuqi.experimental.mcmc.Sampler)]
     valid_samplers = []
 
     for name, sampler in all_samplers:

cuqipy-1.1.0/cuqi/experimental/mcmc/__init__.py

@@ -1,15 +0,0 @@
-""" Re-implementation of sampler module in a more object oriented way. """
-
-from ._sampler import SamplerNew, ProposalBasedSamplerNew
-from ._langevin_algorithm import ULANew, MALANew
-from ._mh import MHNew
-from ._pcn import PCNNew
-from ._rto import LinearRTONew, RegularizedLinearRTONew
-from ._cwmh import CWMHNew
-from ._laplace_approximation import UGLANew
-from ._hmc import NUTSNew
-from ._gibbs import HybridGibbsNew
-from ._conjugate import ConjugateNew
-from ._conjugate_approx import ConjugateApproxNew
-from ._direct import DirectNew
-from ._utilities import find_valid_samplers