Merge branch 'master' into power_method_symmetric

Signed-off-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>

CHANGELOG.md

@@ -1,3 +1,16 @@
+
+* x.x.x
+  - Fix bug in IndicatorBox proximal_conjugate
+  - Allow CCPi Regulariser functions for non CIL object
+  - Add norm for CompositionOperator
+  - Refactor SIRT algorithm to make it more computationally and memory efficient
+  - Optimisation in L2NormSquared
+  - Added support for partitioner, when partitions have size 1
+  - Fix for show_geometry bug for 2D data
+  - Added warmstart capability to proximal evaluation of the CIL TotalVariation function.
+  - FBP split processing bug fix - now respects panel origin
+
+
 * 23.0.1
   - Fix bug with NikonReader requiring ROI to be set in constructor.
 

NOTICE.txt

@@ -40,6 +40,7 @@ Gemma Fardell (2019 - present) - 1
 Kris Thielemans (2020 - present) - 5
 Laura Murgatroyd (2021 - present) - 1
 Evelina Ametova (2018-2020) - 3, (2020-2021) - 6 
+Margaret Duff (2023 - present) - 1 
 
 CIL Contributors:
 Srikanth Nagella (2017-2018) - 1
@@ -52,6 +53,7 @@ Richard Brown (2020-2021) - 5
 Sam Tygier (2022) - 1
 Andrew Sharits (2022) - 8
 Kyle Pidgeon (2023) - 1
+Letizia Protopapa (2023) - 1
 
 CIL Advisory Board:
 Llion Evans - 9

Wrappers/Python/cil/framework/framework.py

@@ -126,7 +126,6 @@ def _construct_BlockGeometry_from_indices(self, indices):
             ag = self.geometry.copy()
             ag.config.angles.angle_data = numpy.take(self.geometry.angles, mask, axis=0)
             ags.append(ag)
-
         return BlockGeometry(*ags)
 
     def partition(self, num_batches, mode, seed=None):
@@ -200,8 +199,11 @@ def _partition_deterministic(self, num_batches, stagger=False, indices=None):
 
         for i in range(num_batches):
             out[i].fill(
-                numpy.take(self.array, partition_indices[i], axis=axis)
+                numpy.squeeze(
+                    numpy.take(self.array, partition_indices[i], axis=axis)
+                )
             )
+
         return out
 
     def _partition_random_permutation(self, num_batches, seed=None):
@@ -2111,7 +2113,6 @@ def shape(self):
                      AcquisitionGeometry.ANGLE: self.config.angles.num_positions,
                      AcquisitionGeometry.VERTICAL: self.config.panel.num_pixels[1],        
                      AcquisitionGeometry.HORIZONTAL: self.config.panel.num_pixels[0]}
-
         shape = []
         for label in self.dimension_labels:
             shape.append(shape_dict[label])

Wrappers/Python/cil/optimisation/algorithms/SIRT.py

@@ -19,9 +19,9 @@
 
 from cil.optimisation.algorithms import Algorithm
 from cil.optimisation.functions import IndicatorBox
+from cil.framework import BlockDataContainer
 from numpy import inf
 import numpy
-import warnings
 import logging
 
 class SIRT(Algorithm):    
@@ -35,36 +35,38 @@ class SIRT(Algorithm):
 
     The SIRT algorithm is 
 
-    .. math:: x^{k+1} =  \mathrm{proj}_{C}( x^{k} + D ( A^{T} ( M * (b - Ax) ) ) ),
+    .. math:: x^{k+1} =  \mathrm{proj}_{C}( x^{k} + \omega * D ( A^{T} ( M * (b - Ax) ) ) ),
 
-    where :math:`M = \frac{1}{A*\mathbb{1}}`, :math:`D = \frac{1}{A^{T}\mathbb{1}}`, :math:`\mathbb{1}` is a :code:`DataContainer` of ones
-    and :math:`\mathrm{prox}_{C}` is the projection over a set :math:`C`.
+    where,
+    :math:`M = \frac{1}{A*\mathbb{1}}`,
+    :math:`D = \frac{1}{A^{T}\mathbb{1}}`,
+    :math:`\mathbb{1}` is a :code:`DataContainer` of ones,
+    :math:`\mathrm{prox}_{C}` is the projection over a set :math:`C`,
+    and :math:`\omega` is the relaxation parameter.
 
     Parameters
     ----------
 
     initial : DataContainer, default = None
-              Starting point of the algorithm, default value = Zero DataContainer 
+        Starting point of the algorithm, default value = Zero DataContainer 
     operator : LinearOperator
-              The operator A.
+        The operator A.
     data : DataContainer
-           The data b.
+        The data b.
     lower : :obj:`float`, default = None
-            Lower bound constraint, default value = :code:`-inf`.
+        Lower bound constraint 
     upper : :obj:`float`, default = None
-            Upper bound constraint, default value = :code:`-inf`.
+        Upper bound constraint
     constraint : Function, default = None
-                A function with :code:`proximal` method, e.g., :class:`.IndicatorBox` function and :meth:`.IndicatorBox.proximal`,
-                or :class:`.TotalVariation` function and :meth:`.TotalVariation.proximal`.
+        A function with :code:`proximal` method, e.g., :class:`.IndicatorBox` function and :meth:`.IndicatorBox.proximal`, 
+        or :class:`.TotalVariation` function and :meth:`.TotalVariation.proximal`.
 
     kwargs:
         Keyword arguments used from the base class :class:`.Algorithm`.    
 
     Note 
     ----
-    
-    If :code:`constraint` is not passed, then :code:`lower` and :code:`upper` are looked at and an :class:`.IndicatorBox`
-    function is created.
+    If :code:`constraint` is not passed, :code:`lower` and :code:`upper` are used to create an :class:`.IndicatorBox` and apply its :code:`proximal`.
 
     If :code:`constraint` is passed, :code:`proximal` method is required to be implemented.
 
@@ -77,9 +79,6 @@ class SIRT(Algorithm):
 
     .. math:: D = \frac{1}{A*\mathbb{1}} = \frac{1}{\sum_{i}a_{i,j}}
 
-    In case of division errors above, :meth:`.fix_weights` can be used, where :code:`np.nan`, :code:`+np.inf` and :code:`-np.inf` values
-    are replaced with 1.0.
-
 
     Examples
     --------
@@ -105,57 +104,104 @@ def set_up(self, initial, operator, data, lower=None, upper=None, constraint=Non
         logging.info("{} setting up".format(self.__class__.__name__, ))
 
         self.x = initial.copy()
+        self.tmp_x = self.x * 0.0
         self.operator = operator
         self.data = data
 
         self.r = data.copy()
 
-        self.relax_par = 1.0
-
         self.constraint = constraint
         if constraint is None:
             if lower is not None or upper is not None:
-                if lower is None:
-                    lower=-inf
-                if upper is None:
-                    upper=inf
+                # IndicatorBox accepts None for lower and/or upper
                 self.constraint=IndicatorBox(lower=lower,upper=upper)
-
+
+        self._relaxation_parameter = 1
+
         # Set up scaling matrices D and M.
-        self.M = 1./self.operator.direct(self.operator.domain_geometry().allocate(value=1.0))                
-        self.D = 1./self.operator.adjoint(self.operator.range_geometry().allocate(value=1.0))
+        self._set_up_weights()
 
         self.configured = True
         logging.info("{} configured".format(self.__class__.__name__, ))
 
-    def fix_weights(self):
 
-        r""" In case of division error when the preconditioning arrays :code:`M` and :code:`D`
-        are defined, the :code:`np.nan`, :code:`+np.inf` and :code:`-np.inf` values are replaced with one.
+    @property
+    def relaxation_parameter(self):
+        return self._relaxation_parameter
+
+    @property
+    def D(self):
+        return self._Dscaled / self._relaxation_parameter
+
+    def set_relaxation_parameter(self, value=1.0):
+        """Set the relaxation parameter :math:`\omega`
+       
+        Parameters
+        ----------
+        value : float
+            The relaxation parameter to be applied to the update. Must be between 0 and 2 to guarantee asymptotic convergence.
+
         """
+        if value <= 0 or value >= 2:
+            raise ValueError("Expected relaxation parameter to be in range 0-2. Got {}".format(value))
+
+        self._relaxation_parameter = value
+        self._set_up_weights()
+        self._Dscaled *= self._relaxation_parameter
+
+
+    def _set_up_weights(self):
+        self.M = 1./self.operator.direct(self.operator.domain_geometry().allocate(value=1.0))                
+        self._Dscaled = 1./self.operator.adjoint(self.operator.range_geometry().allocate(value=1.0))
 
-        # fix for possible +inf, -inf, nan values 
-        for arr in [self.M, self.D]:  
-
-            tmp = arr.as_array()
-            arr_replace = numpy.isfinite(tmp)
-            tmp[~arr_replace] = 1.0     
-            arr.fill(tmp)                     
+        for arr in [self.M, self._Dscaled]:  
+            self._remove_nan_or_inf(arr, replace_with=1.0)
+
+
+    def _remove_nan_or_inf(self, datacontainer, replace_with=1.0):
+        """Replace nan and inf in datacontainer with a given value.
+        
+        Parameters:
+        -------------
+        
+        datacontainer: DataContainer, BlockDataContainer
+        
+        replace_with: float, default 1.0
+            Value to replace elements that evaluate to NaN or inf
+            
+            
+        In case the input datacontainer is a :code:`BlockDataContainer` the substitution is executed for each container in the :code:`BlockDataContainer`.
+        """
+        if isinstance(datacontainer, BlockDataContainer):
+            for block in datacontainer.containers:
+                self._remove_nan_or_inf(block, replace_with=replace_with)
+            return
+        tmp = datacontainer.as_array()
+        numpy.nan_to_num(tmp, copy=False, nan=replace_with, posinf=replace_with, neginf=replace_with)
+        datacontainer.fill(tmp)
+
 
     def update(self):
 
         r""" Performs a single iteration of the SIRT algorithm
 
-        .. math:: x^{k+1} =  \mathrm{proj}_{C}( x^{k} + D ( A^{T} ( M * (b - Ax) ) ) )
+        .. math:: x^{k+1} =  \mathrm{proj}_{C}( x^{k} + \omega * D ( A^{T} ( M * (b - Ax) ) ) )
 
         """
 
-        self.r = self.data - self.operator.direct(self.x)
-
-        self.x += self.relax_par * (self.D*self.operator.adjoint(self.M*self.r))
+        # self.r = self.data - self.operator.direct(self.x)
+        self.operator.direct(self.x, out=self.r)
+        self.r.sapyb(-1, self.data, 1.0, out=self.r)
 
+        # self.D is prescaled by _relaxation_parameter (default 1)
+        self.r *= self.M
+        self.operator.adjoint(self.r, out=self.tmp_x)
+        self.x.sapyb(1.0, self.tmp_x, self._Dscaled, out=self.x)
+
+
         if self.constraint is not None:
-            self.x = self.constraint.proximal(self.x, tau=1)
+            # IndicatorBox allows inplace operation for proximal
+            self.constraint.proximal(self.x, tau=1, out=self.x)
 
     def update_objective(self):
         r"""Returns the objective 
@@ -164,8 +210,3 @@ def update_objective(self):
 
         """
         self.loss.append(self.r.squared_norm())
-
-
-
-
-

Wrappers/Python/cil/optimisation/functions/IndicatorBox.py

@@ -142,36 +142,6 @@ def __call__(self, x):
             return self.evaluate(x)
         return 0.0
 
-    def proximal_conjugate(self, x, tau, out=None):
-        r'''Proximal operator of the convex conjugate of IndicatorBox at x:
-
-          .. math:: prox_{\tau * f^{*}}(x)
-
-          Parameters
-          ----------
-          x : DataContainer
-              Input to the proximal operator
-          tau : float
-              Step size. Notice it is ignored in IndicatorBox, see ``proximal`` for details
-          out : DataContainer, optional
-              Output of the proximal operator. If not provided, a new DataContainer is created.
-
-        '''
-
-        # x - tau * self.proximal(x/tau, tau)
-        should_return = False
-
-        if out is None:
-            out = self.proximal(x, tau)
-            should_return = True
-        else:
-            self.proximal(x, tau, out=out)
-
-        out.sapyb(-1., x, 1., out=out)
-
-        if should_return:
-            return out
-
     def proximal(self, x, tau, out=None):
         r'''Proximal operator of IndicatorBox at x
 

Wrappers/Python/cil/optimisation/functions/L2NormSquared.py

@@ -88,21 +88,15 @@ def gradient(self, x, out=None):
             b) :math:`F'(x) = 2(x-b)`
                 
         """
-
-        if out is not None:
-
-            out.fill(x)
-            if self.b is not None:
-                out -= self.b
-            out *= 2
-
+
+        if self.b is None:
+            ret = x.multiply(2, out=out)
         else:
-
-            y = x
-            if self.b is not None:
-                y = x - self.b
-            return 2*y
-
+            ret = x.sapyb(2, self.b, -2, out=out)
+
+        if out is None:
+            return ret
+
 
     def convex_conjugate(self, x):
 
@@ -119,7 +113,7 @@ def convex_conjugate(self, x):
         if self.b is not None:
             tmp = x.dot(self.b) 
 
-        return (1./4.) * x.squared_norm() + tmp
+        return 0.25 * x.squared_norm() + tmp
 
 
     def proximal(self, x, tau, out = None):
@@ -134,23 +128,16 @@ def proximal(self, x, tau, out = None):
                         
         """            
 
-        if out is None:
-
-            if self.b is None:
-                return x/(1+2*tau)
-            else:
-                tmp = x.subtract(self.b)
-                tmp /= (1+2*tau)
-                tmp += self.b
-                return tmp
+        mult = 1/(1+2*tau)
 
+        if self.b is None:
+            ret = x.multiply(mult, out=out)
         else:
-            if self.b is not None:
-                x.subtract(self.b, out=out)
-                out /= (1+2*tau)
-                out += self.b
-            else:
-                x.divide((1+2*tau), out=out)
+            ret = x.sapyb(mult, self.b, (1-mult), out=out)
+
+        if out is None:
+            return ret
+
 
 
 class WeightedL2NormSquared(Function):