CUQIpy 1.3.0.post0.dev86__py3-none-any.whl → 1.3.0.post0.dev104__py3-none-any.whl

cuqi/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-04-10T10:50:04+0200",
+ "date": "2025-04-28T12:59:25+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "fe056d15f6ff918511cf7ee579dc8e7689c1dbc4",
- "version": "1.3.0.post0.dev86"
+ "full-revisionid": "c62aed4105837bc321e7e325f1b1a2286c659b2f",
+ "version": "1.3.0.post0.dev104"
 }
 '''  # END VERSION_JSON
 

cuqi/experimental/mcmc/_rto.py

@@ -3,7 +3,7 @@ from scipy.linalg.interpolative import estimate_spectral_norm
 from scipy.sparse.linalg import LinearOperator as scipyLinearOperator
 import numpy as np
 import cuqi
-from cuqi.solver import CGLS, FISTA, ADMM, ScipyLinearLSQ
+from cuqi.solver import CGLS, FISTA, ADMM, ScipyLinearLSQ, ScipyMinimizer
 from cuqi.experimental.mcmc import Sampler
 
 
@@ -167,6 +167,7 @@ class RegularizedLinearRTO(LinearRTO):
     ADMM:  [2] Boyd et al. "Distributed optimization and statistical learning via the alternating direction method of multipliers."Foundations and Trends® in Machine learning, 2011.
            Used when prior.proximal is a list of penalty terms.
     ScipyLinearLSQ: Wrapper for Scipy's lsq_linear for the Trust Region Reflective algorithm. Optionally used when the constraint is either "nonnegativity" or "box".
+    ScipyMinimizer: Wrapper for Scipy's minimize. Optionally used when the constraint is either "nonnegativity" or "box".
 
     Parameters
     ------------
@@ -177,7 +178,7 @@ class RegularizedLinearRTO(LinearRTO):
         Initial point for the sampler. *Optional*.
 
     maxit : int
-        Maximum number of iterations of the FISTA/ADMM/ScipyLinearLSQ solver. *Optional*.
+        Maximum number of iterations of the FISTA/ADMM/ScipyLinearLSQ/ScipyMinimizer solver. *Optional*.
 
     inner_max_it : int
         Maximum number of iterations of the CGLS solver used within the ADMM solver. *Optional*.
@@ -191,7 +192,7 @@ class RegularizedLinearRTO(LinearRTO):
         See [2] or `cuqi.solver.ADMM`
 
     abstol : float
-        Absolute tolerance of the FISTA/ScipyLinearLSQ solver. *Optional*.
+        Absolute tolerance of the FISTA/ScipyLinearLSQ/ScipyMinimizer solver. *Optional*.
     
     inner_abstol : float
         Tolerance parameter for ScipyLinearLSQ's inner solve of the unbounded least-squares problem. *Optional*.
@@ -200,7 +201,7 @@ class RegularizedLinearRTO(LinearRTO):
         If True, FISTA is used as solver, otherwise ISTA is used. *Optional*.
     
     solver : string
-        If set to "ScipyLinearLSQ", solver is set to cuqi.solver.ScipyLinearLSQ, otherwise FISTA/ISTA or ADMM is used. Note "ScipyLinearLSQ" can only be used with `RegularizedGaussian` of `box` or `nonnegativity` constraint. *Optional*.
+        Options are "FISTA" (default for a single constraint or regularization), "ADMM" (default and the only option for multiple constraints or regularizations), "ScipyLinearLSQ" and "ScipyMinimizer". Note "ScipyLinearLSQ" and "ScipyMinimizer" can only be used with `RegularizedGaussian` of a single `box` or `nonnegativity` constraint. *Optional*.
 
     callback : callable, optional
         A function that will be called after each sampling step. It can be useful for monitoring the sampler during sampling.
@@ -234,11 +235,11 @@ class RegularizedLinearRTO(LinearRTO):
 
     @solver.setter
     def solver(self, value):
-        if value == "ScipyLinearLSQ":
+        if value == "ScipyLinearLSQ" or value == "ScipyMinimizer":
             if (self.target.prior.preset["constraint"] == "nonnegativity" or self.target.prior.preset["constraint"] == "box"):
                 self._solver = value
             else:
-                raise ValueError("ScipyLinearLSQ only supports RegularizedGaussian with box or nonnegativity constraint.")
+                raise ValueError("ScipyLinearLSQ and ScipyMinimizer only support RegularizedGaussian with box or nonnegativity constraint.")
         else:
             self._solver = value
 
@@ -281,15 +282,22 @@ class RegularizedLinearRTO(LinearRTO):
             sim = ADMM(self.M, y, self.proximal,
                         self.current_point, self.penalty_parameter, maxit = self.maxit, inner_max_it = self.inner_max_it, adaptive = self.adaptive)
         elif self.solver == "ScipyLinearLSQ":
-                A_op = sp.sparse.linalg.LinearOperator((sum([llh.dim for llh in self.likelihoods])+self.target.prior.dim, self.target.prior.dim),
-                                        matvec=lambda x: self.M(x, 1),
-                                        rmatvec=lambda x: self.M(x, 2)
-                                        )
-                sim = ScipyLinearLSQ(A_op, y, self.target.prior._box_bounds, 
-                                     max_iter = self.maxit,
-                                     lsmr_maxiter = self.inner_max_it, 
-                                     tol = self.abstol,
-                                     lsmr_tol = self.inner_abstol)
+            A_op = sp.sparse.linalg.LinearOperator((sum([llh.distribution.dim for llh in self.likelihoods])+self.target.prior.dim, self.target.prior.dim),
+                                    matvec=lambda x: self.M(x, 1),
+                                    rmatvec=lambda x: self.M(x, 2)
+                                    )
+            sim = ScipyLinearLSQ(A_op, y, self.target.prior._box_bounds, 
+                                    max_iter = self.maxit,
+                                    lsmr_maxiter = self.inner_max_it, 
+                                    tol = self.abstol,
+                                    lsmr_tol = self.inner_abstol)
+        elif self.solver == "ScipyMinimizer":
+            # Adapt bounds format, as scipy.minimize requires a bounds format 
+            # different than that in scipy.lsq_linear.
+            bounds = [(self.target.prior._box_bounds[0][i], self.target.prior._box_bounds[1][i]) for i in range(self.target.prior.dim)]
+            # Note that the objective function is defined as 0.5*||Mx-y||^2, 
+            # and the corresponding gradient (gradfunc) is given by M^T(Mx-y).
+            sim = ScipyMinimizer(lambda x: 0.5*np.sum((self.M(x, 1)-y)**2), self.current_point, gradfunc=lambda x: self.M(self.M(x, 1) - y, 2), bounds=bounds, tol=self.abstol, options={"maxiter": self.maxit})
         else:
             raise ValueError("Choice of solver not supported.")
 

cuqi/solver/_solver.py

@@ -196,8 +196,11 @@ class ScipyLSQ(object):
         'trf', Trust Region Reflective algorithm: for large sparse problems with bounds.
         'dogbox', dogleg algorithm with rectangular trust regions, for small problems with bounds.
         'lm', Levenberg-Marquardt algorithm as implemented in MINPACK. Doesn't handle bounds and sparse Jacobians.
+    tol : The numerical tolerance for convergence checks.
+    maxit : The maximum number of iterations.
+    kwargs : Additional keyword arguments passed to scipy's least_squares. Empty by default. See documentation for scipy.optimize.least_squares
     """
-    def __init__(self, func, x0, jacfun='2-point', method='trf', loss='linear', tol=1e-6, maxit=1e4):
+    def __init__(self, func, x0, jacfun='2-point', method='trf', loss='linear', tol=1e-6, maxit=1e4, **kwargs):
         self.func = func
         self.x0 = x0
         self.jacfun = jacfun
@@ -205,6 +208,7 @@ class ScipyLSQ(object):
         self.loss = loss
         self.tol = tol
         self.maxit = int(maxit)
+        self.kwargs = kwargs
     
     def solve(self):
         """Runs optimization algorithm and returns solution and info.
@@ -215,7 +219,7 @@ class ScipyLSQ(object):
             Solution found (array_like) and optimization information (dictionary).
         """
         solution = least_squares(self.func, self.x0, jac=self.jacfun, \
-                                method=self.method, loss=self.loss, xtol=self.tol, max_nfev=self.maxit)
+                                method=self.method, loss=self.loss, xtol=self.tol, max_nfev=self.maxit, **self.kwargs)
         info = {"success": solution['success'],
                 "message": solution['message'],
                 "func": solution['fun'],

{cuqipy-1.3.0.post0.dev86.dist-info → cuqipy-1.3.0.post0.dev104.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CUQIpy
-Version: 1.3.0.post0.dev86
+Version: 1.3.0.post0.dev104
 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-1.3.0.post0.dev86.dist-info → cuqipy-1.3.0.post0.dev104.dist-info}/RECORD

@@ -1,6 +1,6 @@
 cuqi/__init__.py,sha256=LsGilhl-hBLEn6Glt8S_l0OJzAA1sKit_rui8h-D-p0,488
 cuqi/_messages.py,sha256=fzEBrZT2kbmfecBBPm7spVu7yHdxGARQB4QzXhJbCJ0,415
-cuqi/_version.py,sha256=5BoF7RelweJtRYABv01YoLMQTIvAp9dGHYbyo9mk5u4,509
+cuqi/_version.py,sha256=guMao82iJ7XuaWXVsBLkNDaBLZLETh0C0JtSWy0RCeA,510
 cuqi/config.py,sha256=wcYvz19wkeKW2EKCGIKJiTpWt5kdaxyt4imyRkvtTRA,526
 cuqi/diagnostics.py,sha256=5OrbJeqpynqRXOe5MtOKKhe7EAVdOEpHIqHnlMW9G_c,3029
 cuqi/array/__init__.py,sha256=-EeiaiWGNsE3twRS4dD814BIlfxEsNkTCZUc5gjOXb0,30
@@ -52,7 +52,7 @@ cuqi/experimental/mcmc/_langevin_algorithm.py,sha256=1UunuocpzG1h6GiYefEHFOMykEM
 cuqi/experimental/mcmc/_laplace_approximation.py,sha256=I5ZLtU0lA34YflRbqxKi5UgJBhhHzxqUyVW5JE5-l2w,5916
 cuqi/experimental/mcmc/_mh.py,sha256=MXo0ahXP4KGFkaY4HtvcBE-TMQzsMlTmLKzSvpz7drU,2941
 cuqi/experimental/mcmc/_pcn.py,sha256=wqJBZLuRFSwxihaI53tumAg6AWVuceLMOmXssTetd1A,3374
-cuqi/experimental/mcmc/_rto.py,sha256=2RJm1NMIvmCbTBn0M8S8vNLaRjaS1_7S9gVOdG9I8Bo,14159
+cuqi/experimental/mcmc/_rto.py,sha256=BY55Njw3-dcmjd-V1vQ58CisEDllQ8zaEj92pWB6LCM,15158
 cuqi/experimental/mcmc/_sampler.py,sha256=VK-VsPRaYET43C5quhu2f1OstEX5DKYKVyjKABTRHZE,20288
 cuqi/experimental/mcmc/_utilities.py,sha256=kUzHbhIS3HYZRbneNBK41IogUYX5dS_bJxqEGm7TQBI,525
 cuqi/geometry/__init__.py,sha256=Tz1WGzZBY-QGH3c0GiyKm9XHN8MGGcnU6TUHLZkzB3o,842
@@ -87,14 +87,14 @@ cuqi/sampler/_sampler.py,sha256=TkZ_WAS-5Q43oICa-Elc2gftsRTBd7PEDUMDZ9tTGmU,5712
 cuqi/samples/__init__.py,sha256=vCs6lVk-pi8RBqa6cIN5wyn6u-K9oEf1Na4k1ZMrYv8,44
 cuqi/samples/_samples.py,sha256=hUc8OnCF9CTCuDTrGHwwzv3wp8mG_6vsJAFvuQ-x0uA,35832
 cuqi/solver/__init__.py,sha256=KYgAi_8VoAwljTB3S2I87YnJkRtedskLee7hQp_-zp8,220
-cuqi/solver/_solver.py,sha256=_Q47Atv8Ze6eMJzA22s0OzdW4lcDigRhbotnCzmrQWE,30662
+cuqi/solver/_solver.py,sha256=X3EWD-26o9UOBsWRuy0ktYsJiUXwpCGm0lvTdQM6dRI,30964
 cuqi/testproblem/__init__.py,sha256=DWTOcyuNHMbhEuuWlY5CkYkNDSAqhvsKmJXBLivyblU,202
 cuqi/testproblem/_testproblem.py,sha256=x769LwwRdJdzIiZkcQUGb_5-vynNTNALXWKato7sS0Q,52540
 cuqi/utilities/__init__.py,sha256=d5QXRzmI6EchS9T4b7eTezSisPWuWklO8ey4YBx9kI0,569
 cuqi/utilities/_get_python_variable_name.py,sha256=wxpCaj9f3ZtBNqlGmmuGiITgBaTsY-r94lUIlK6UAU4,2043
 cuqi/utilities/_utilities.py,sha256=as8cFswoxROS0Z7WUKzLIE-ZtEKCXes5M3Gdmmb47No,18414
-cuqipy-1.3.0.post0.dev86.dist-info/licenses/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
-cuqipy-1.3.0.post0.dev86.dist-info/METADATA,sha256=lG1Acs-TjKb60yfRHgywc3q1EQY1HuI9bjLQA5CAQNE,18623
-cuqipy-1.3.0.post0.dev86.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-cuqipy-1.3.0.post0.dev86.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
-cuqipy-1.3.0.post0.dev86.dist-info/RECORD,,
+cuqipy-1.3.0.post0.dev104.dist-info/licenses/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
+cuqipy-1.3.0.post0.dev104.dist-info/METADATA,sha256=ocRbxXFZqKPsVVnPjFNgacaxLE8zeXDD71iHGk6q6j8,18624
+cuqipy-1.3.0.post0.dev104.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
+cuqipy-1.3.0.post0.dev104.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
+cuqipy-1.3.0.post0.dev104.dist-info/RECORD,,

{cuqipy-1.3.0.post0.dev86.dist-info → cuqipy-1.3.0.post0.dev104.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any