CUQIpy 1.1.0.post0.dev39__py3-none-any.whl → 1.1.1.post0.dev5__py3-none-any.whl

{CUQIpy-1.1.0.post0.dev39.dist-info → CUQIpy-1.1.1.post0.dev5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CUQIpy
-Version: 1.1.0.post0.dev39
+Version: 1.1.1.post0.dev5
 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.post0.dev39.dist-info → CUQIpy-1.1.1.post0.dev5.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=SFVwuROZ7PjMxlopbxtd_O7tlfLQi9nwgd9r4SLXD7o,509
+cuqi/_version.py,sha256=GBlEQB0vnqLdJQ4FNiN2Ih7mYmB2x4_rO95Eva1C9oI,508
 cuqi/config.py,sha256=wcYvz19wkeKW2EKCGIKJiTpWt5kdaxyt4imyRkvtTRA,526
 cuqi/diagnostics.py,sha256=5OrbJeqpynqRXOe5MtOKKhe7EAVdOEpHIqHnlMW9G_c,3029
 cuqi/array/__init__.py,sha256=-EeiaiWGNsE3twRS4dD814BIlfxEsNkTCZUc5gjOXb0,30
@@ -24,7 +24,7 @@ cuqi/distribution/_gamma.py,sha256=9vljt5iaBDCHRhrVCMLc2RWDuBchZRQcv9buJMDYPlM,3
 cuqi/distribution/_gaussian.py,sha256=DmmgVxKp4iEiEYWDdDcRoh35y14Oepn-zDHex0WVaYo,33316
 cuqi/distribution/_gmrf.py,sha256=OwId8qQWEtmC2fxVhL4iBHZnc8ZCrZzfV6yGXDE3k30,9522
 cuqi/distribution/_inverse_gamma.py,sha256=XRcNGW_jzORL08V7VvtsuMUoQioBAGbN12qe8hCXJvg,3309
-cuqi/distribution/_joint_distribution.py,sha256=jRsV1Dt-pW6sG_xNqF0TugeVKDJY4Kh5aBLsIWfv394,15043
+cuqi/distribution/_joint_distribution.py,sha256=7TxDaZ7y362LfxEpD4I5Z0icdtsBmOBJGnpIkz_bYXA,15900
 cuqi/distribution/_laplace.py,sha256=5exLvlzJm2AgfvZ3KUSkjfwlGwwbsktBxP8z0iLMik8,1401
 cuqi/distribution/_lmrf.py,sha256=rdGoQ-fPe1oW6Z29P-l3woq0NX3_RxUQ2rzm1VzemNM,3290
 cuqi/distribution/_lognormal.py,sha256=st1Uhf67qy2Seo65hA88JQ7lkEjQkW6KxznXahF_0SU,2844
@@ -57,7 +57,7 @@ cuqi/implicitprior/_regularizedUnboundedUniform.py,sha256=H2fTOSqYTlDiLxQ7Ya6wnp
 cuqi/likelihood/__init__.py,sha256=QXif382iwZ5bT3ZUqmMs_n70JVbbjxbqMrlQYbMn4Zo,1776
 cuqi/likelihood/_likelihood.py,sha256=z3AXAbIrv_DjOYh4jy3iDHemuIFUUJu6wdvJ5e2dgW0,6913
 cuqi/model/__init__.py,sha256=IcN4aZCnyp9o-8TNIoZ8vew99QQgi0EmZvnsIuR6qYI,49
-cuqi/model/_model.py,sha256=bmS5X-FxhY1n5I0ahBlIPbUFynw-2Vw2s9N-exMX-BU,26627
+cuqi/model/_model.py,sha256=2MtQaahSGOVm45tvxh_xbke9vo_Aq0tpyNvLg9TK9dA,27791
 cuqi/operator/__init__.py,sha256=0pc9p-KPyl7KtPV0noB0ddI0CP2iYEHw5rbw49D8Njk,136
 cuqi/operator/_operator.py,sha256=yNwPTh7jR07AiKMbMQQ5_54EgirlKFsbq9JN1EODaQI,8856
 cuqi/pde/__init__.py,sha256=NyS_ZYruCvy-Yg24qKlwm3ZIX058kLNQX9bqs-xg4ZM,99
@@ -85,8 +85,8 @@ cuqi/testproblem/_testproblem.py,sha256=x769LwwRdJdzIiZkcQUGb_5-vynNTNALXWKato7s
 cuqi/utilities/__init__.py,sha256=H7xpJe2UinjZftKvE2JuXtTi4DqtkR6uIezStAXwfGg,428
 cuqi/utilities/_get_python_variable_name.py,sha256=QwlBVj2koJRA8s8pWd554p7-ElcI7HUwY32HknaR92E,1827
 cuqi/utilities/_utilities.py,sha256=Jc4knn80vLoA7kgw9FzXwKVFGaNBOXiA9kgvltZU3Ao,11777
-CUQIpy-1.1.0.post0.dev39.dist-info/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
-CUQIpy-1.1.0.post0.dev39.dist-info/METADATA,sha256=tPkKE5LGWKpgvgM1zkAfKPq4tV0kLGVpbdZSz5ZCn3E,18390
-CUQIpy-1.1.0.post0.dev39.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
-CUQIpy-1.1.0.post0.dev39.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
-CUQIpy-1.1.0.post0.dev39.dist-info/RECORD,,
+CUQIpy-1.1.1.post0.dev5.dist-info/LICENSE,sha256=kJWRPrtRoQoZGXyyvu50Uc91X6_0XRaVfT0YZssicys,10799
+CUQIpy-1.1.1.post0.dev5.dist-info/METADATA,sha256=PV1PVHglGQb4105G0vt1Px1jAmsP4PBQ91IvzVMiCFk,18389
+CUQIpy-1.1.1.post0.dev5.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
+CUQIpy-1.1.1.post0.dev5.dist-info/top_level.txt,sha256=AgmgMc6TKfPPqbjV0kvAoCBN334i_Lwwojc7HE3ZwD0,5
+CUQIpy-1.1.1.post0.dev5.dist-info/RECORD,,

cuqi/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-08-29T10:46:43+0300",
+ "date": "2024-08-31T21:02:04+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "9d8920342c73b1bd8e7a47a216eb34056ea2f5d6",
- "version": "1.1.0.post0.dev39"
+ "full-revisionid": "b38281138379969a9a8c4683ba3ecf8a88031939",
+ "version": "1.1.1.post0.dev5"
 }
 '''  # END VERSION_JSON
 

cuqi/distribution/_joint_distribution.py

@@ -175,6 +175,10 @@ class JointDistribution:
                 kwargs[ordered_keys[index]] = arg
         return kwargs
 
+    def _sum_evaluated_densities(self):
+        """ Return the sum of the evaluated densities in the joint distribution """
+        return sum([density.logd() for density in self._evaluated_densities])
+
     def _reduce_to_single_density(self):
         """ Reduce the joint distribution to a single density if possible.
 
@@ -183,7 +187,6 @@ class JointDistribution:
         This method is a hack to allow our current samplers to work with
         the joint distribution. It should be removed in the future.
         """
-
         # Count number of distributions and likelihoods
         n_dist = len(self._distributions)
         n_likelihood = len(self._likelihoods)
@@ -201,16 +204,29 @@ class JointDistribution:
             # Ensure parameter names match, otherwise return the joint distribution
             if set(self._likelihoods[0].get_parameter_names()) != set(self._distributions[0].get_parameter_names()):
                 return self
-            return Posterior(self._likelihoods[0], self._distributions[0])
-        
+            return self._add_constants_to_density(Posterior(self._likelihoods[0], self._distributions[0]))
+
         # If exactly one distribution and no likelihoods its a Distribution
         if n_dist == 1 and n_likelihood == 0:
-            return self._distributions[0]
-
+            return self._add_constants_to_density(self._distributions[0])        
+        
         # If no distributions and exactly one likelihood its a Likelihood
         if n_likelihood == 1 and n_dist == 0:
             return self._likelihoods[0]
 
+        # If only evaluated densities left return joint to ensure logd method is available
+        if n_dist == 0 and n_likelihood == 0:
+            return self
+        
+    def _add_constants_to_density(self, density: Density):
+        """ Add the constants (evaluated densities) to a single density. Used when reducing to single density. """
+
+        if isinstance(density, EvaluatedDensity):
+            raise ValueError("Cannot add the sum of all evaluated densities to an EvaluatedDensity.")
+
+        density._constant += self._sum_evaluated_densities()
+        return density
+
     def _as_stacked(self) -> _StackedJointDistribution:
         """ Return a stacked JointDistribution with the same densities. """
         return _StackedJointDistribution(*self._densities)

cuqi/model/_model.py

@@ -19,10 +19,10 @@ class Model(object):
         Forward operator.
 
     range_geometry : integer or cuqi.geometry.Geometry
-        If integer is given a _DefaultGeometry is created with dimension of the integer.
+        If integer is given, a cuqi.geometry._DefaultGeometry is created with dimension of the integer.
 
     domain_geometry : integer or cuqi.geometry.Geometry
-        If integer is given a _DefaultGeometry is created with dimension of the integer.
+        If integer is given, a cuqi.geometry._DefaultGeometry is created with dimension of the integer.
 
     gradient : callable function, optional
         The direction-Jacobian product of the forward operator Jacobian with 
@@ -35,14 +35,20 @@ class Model(object):
         The Jacobian of the forward operator with respect to the forward operator input,
         evaluated at a point (`wrt`). The signature of the Jacobian function should be (`wrt`).
         The Jacobian function should return a 2D ndarray of shape (range_dim, domain_dim).
-        The Jacobian function is used to specify the gradient function (vector-Jacobian product)
+        The Jacobian function is used to specify the gradient function by computing the vector-Jacobian
+        product (VJP), here we refer to the vector in the VJP as the `direction` since it is the direction at 
+        which the gradient is computed.
         automatically and thus the gradient function should not be specified when the Jacobian
         function is specified.
 
+
+    :ivar range_geometry: The geometry representing the range.
+    :ivar domain_geometry: The geometry representing the domain.
+
     Example
     -------
 
-    Consider a forward model :math:`F: \mathbb{R}^2 \rightarrow \mathbb{R}` defined by the following forward operator:
+    Consider a forward model :math:`F: \mathbb{R}^2 \\rightarrow \mathbb{R}` defined by the following forward operator:
 
     .. math::
 
@@ -141,11 +147,17 @@ class Model(object):
         self._non_default_args = cuqi.utilities.get_non_default_args(self._forward_func)
 
     @property
-    def domain_dim(self): 
+    def domain_dim(self):
+        """
+        The dimension of the domain
+        """
         return self.domain_geometry.par_dim
 
     @property
     def range_dim(self): 
+        """
+        The dimension of the range
+        """
         return self.range_geometry.par_dim
 
     def _2fun(self, x, geometry, is_par):
@@ -466,28 +478,61 @@ class LinearModel(Model):
     forward : 2D ndarray or callable function.
         Forward operator.
 
-    adjoint : 2d ndarray or callable function. (optional if matrix is passed as forward)
+    adjoint : 2D ndarray or callable function. (optional if matrix is passed as forward)
 
     range_geometry : integer or cuqi.geometry.Geometry (optional)
-        If integer is given a _DefaultGeometry is created with dimension of the integer.
+        If integer is given, a cuqi.geometry._DefaultGeometry is created with dimension of the integer.
 
     domain_geometry : integer or cuqi.geometry.Geometry (optional)
-        If integer is given a _DefaultGeometry is created with dimension of the integer.
+        If integer is given, a cuqi.geometry._DefaultGeometry is created with dimension of the integer.
 
-    Attributes
-    -----------
-    range_geometry : cuqi.geometry.Geometry
-        The geometry representing the range.
 
-    domain_geometry : cuqi.geometry.Geometry
-        The geometry representing the domain.
+    :ivar range_geometry: The geometry representing the range.
+    :ivar domain_geometry: The geometry representing the domain.
 
-    Methods
-    -----------
-    :meth:`forward` the forward operator.
-    :meth:`range_dim` the dimension of the range.
-    :meth:`domain_dim` the dimension of the domain.
-    :meth:`get_matrix` returns an ndarray with the matrix representing the forward operator.
+    Example
+    -------
+
+    Consider a linear model represented by a matrix, i.e., :math:`y=Ax` where 
+    :math:`A` is a matrix.
+    
+    We can define such a linear model by passing the matrix :math:`A`:
+
+    .. code-block:: python
+
+        import numpy as np
+        from cuqi.model import LinearModel
+
+        A = np.random.randn(2,3)
+
+        model = LinearModel(A)
+
+    The dimension of the range and domain geometries will be automatically 
+    inferred from the matrix :math:`A`.
+        
+    Meanwhile, such a linear model can also be defined by a forward function 
+    and an adjoint function:
+
+    .. code-block:: python
+
+        import numpy as np
+        from cuqi.model import LinearModel
+
+        A = np.random.randn(2,3)
+
+        def forward(x):
+            return A@x
+
+        def adjoint(y):
+            return A.T@y
+
+        model = LinearModel(forward,
+                            adjoint=adjoint,
+                            range_geometry=2,
+                            domain_geometry=3)
+
+    Note that you would need to specify the range and domain geometries in this
+    case as they cannot be inferred from the forward and adjoint functions.
     """
     # Linear forward model with forward and adjoint (transpose).
     
@@ -552,6 +597,9 @@ class LinearModel(Model):
 
 
     def get_matrix(self):
+        """
+        Returns an ndarray with the matrix representing the forward operator.
+        """
         if self._matrix is not None: #Matrix exists so return it
             return self._matrix
         else:
@@ -594,24 +642,14 @@ class PDEModel(Model):
         Forward operator assembling, solving and observing the pde.
 
     range_geometry : integer or cuqi.geometry.Geometry (optional)
-        If integer is given a _DefaultGeometry is created with dimension of the integer.
+        If integer is given, a cuqi.geometry._DefaultGeometry is created with dimension of the integer.
 
     domain_geometry : integer or cuqi.geometry.Geometry (optional)
-        If integer is given a _DefaultGeometry is created with dimension of the integer.
-
-    Attributes
-    -----------
-    range_geometry : cuqi.geometry.Geometry
-        The geometry representing the range.
+        If integer is given, a cuqi.geometry._DefaultGeometry is created with dimension of the integer.
 
-    domain_geometry : cuqi.geometry.Geometry
-        The geometry representing the domain.
 
-    Methods
-    -----------
-    :meth:`forward` the forward operator.
-    :meth:`range_dim` the dimension of the range.
-    :meth:`domain_dim` the dimension of the domain.
+    :ivar range_geometry: The geometry representing the range.
+    :ivar domain_geometry: The geometry representing the domain.
     """
     def __init__(self, PDE: cuqi.pde.PDE, range_geometry, domain_geometry):