Merge branch 'master' into binner_padder_patch

Signed-off-by: Gemma Fardell <47746591+gfardell@users.noreply.github.com>

CHANGELOG.md

@@ -5,9 +5,12 @@
   - 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
   - FBP split processing bug fix - now respects panel origin set in geometry
   - Binner/Padder/Slicer bug fix - now respects panel origin set in geometry
+  - Added warmstart capability to proximal evaluation of the CIL TotalVariation function.
+  - Tidied up documentation in the framework folder
 
 * 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

Wrappers/Python/cil/framework/BlockDataContainer.py

@@ -33,7 +33,7 @@ class BlockDataContainer(object):
        will fail 
     2) algebra between `BlockDataContainer`s and `list` or `numpy array` will 
        work as long as the number of `rows` and element of the arrays match,
-       indipendently on the fact that the `BlockDataContainer` could be nested
+       independently on the fact that the `BlockDataContainer` could be nested
     3) algebra between `BlockDataContainer` and one `DataContainer` is possible.
        It will require all the `DataContainers` in the block to be
        compatible with the `DataContainer` we want to operate with. 
@@ -147,7 +147,7 @@ def subtract(self, other, *args, **kwargs):
         '''Algebra: subtract method of BlockDataContainer with number/DataContainer or BlockDataContainer
         
         :param: other (number, DataContainer or subclasses or BlockDataContainer
-        :param: out (optional): provides a placehold for the resul.
+        :param: out (optional): provides a placeholder for the result.
         '''
         out = kwargs.get('out', None)
         if out is not None:
@@ -157,8 +157,8 @@ def subtract(self, other, *args, **kwargs):
     def multiply(self, other, *args, **kwargs):
         '''Algebra: multiply method of BlockDataContainer with number/DataContainer or BlockDataContainer
         
-        :param: other (number, DataContainer or subclasses or BlockDataContainer
-        :param: out (optional): provides a placehold for the resul.
+        :param: other (number, DataContainer or subclasses or BlockDataContainer)
+        :param: out (optional): provides a placeholder for the result.
         '''
         out = kwargs.get('out', None)
         if out is not None:
@@ -168,8 +168,8 @@ def multiply(self, other, *args, **kwargs):
     def divide(self, other, *args, **kwargs):
         '''Algebra: divide method of BlockDataContainer with number/DataContainer or BlockDataContainer
         
-        :param: other (number, DataContainer or subclasses or BlockDataContainer
-        :param: out (optional): provides a placehold for the resul.
+        :param: other (number, DataContainer or subclasses or BlockDataContainer)
+        :param: out (optional): provides a placeholder for the result.
         '''
         out = kwargs.get('out', None)
         if out is not None:
@@ -180,7 +180,7 @@ def power(self, other, *args, **kwargs):
         '''Algebra: power method of BlockDataContainer with number/DataContainer or BlockDataContainer
         
         :param: other (number, DataContainer or subclasses or BlockDataContainer
-        :param: out (optional): provides a placehold for the resul.
+        :param: out (optional): provides a placeholder for the result.
         '''
         out = kwargs.get('out', None)
         if out is not None:
@@ -190,8 +190,8 @@ def power(self, other, *args, **kwargs):
     def maximum(self, other, *args, **kwargs):
         '''Algebra: power method of BlockDataContainer with number/DataContainer or BlockDataContainer
         
-        :param: other (number, DataContainer or subclasses or BlockDataContainer
-        :param: out (optional): provides a placehold for the resul.
+        :param: other (number, DataContainer or subclasses or BlockDataContainer)
+        :param: out (optional): provides a placeholder for the result.
         '''
         out = kwargs.get('out', None)
         if out is not None:
@@ -201,8 +201,8 @@ def maximum(self, other, *args, **kwargs):
     def minimum(self, other, *args, **kwargs):
         '''Algebra: power method of BlockDataContainer with number/DataContainer or BlockDataContainer
         
-        :param: other (number, DataContainer or subclasses or BlockDataContainer
-        :param: out (optional): provides a placehold for the resul.
+        :param: other (number, DataContainer or subclasses or BlockDataContainer)
+        :param: out (optional): provides a placeholder for the result.
         '''
         out = kwargs.get('out', None)
         if out is not None:
@@ -224,14 +224,14 @@ def sapyb(self, a, y, b, out, num_threads = NUM_THREADS):
         Example:
         --------
 
-        a = 2
-        b = 3
-        ig = ImageGeometry(10,11)
-        x = ig.allocate(1)
-        y = ig.allocate(2)
-        bdc1 = BlockDataContainer(2*x, y)
-        bdc2 = BlockDataContainer(x, 2*y)
-        out = bdc1.sapyb(a,bdc2,b)
+        >>> a = 2
+        >>> b = 3
+        >>> ig = ImageGeometry(10,11)
+        >>> x = ig.allocate(1)
+        >>> y = ig.allocate(2)
+        >>> bdc1 = BlockDataContainer(2*x, y)
+        >>> bdc2 = BlockDataContainer(x, 2*y)
+        >>> out = bdc1.sapyb(a,bdc2,b)
         '''
         if out is None:
             raise ValueError("out container cannot be None")
@@ -249,7 +249,7 @@ def binary_operations(self, operation, other, *args, **kwargs):
         '''Algebra: generic method of algebric operation with BlockDataContainer with number/DataContainer or BlockDataContainer
         
         Provides commutativity with DataContainer and subclasses, i.e. this 
-        class's reverse algebric methods take precedence w.r.t. direct algebric
+        class's reverse algebraic methods take precedence w.r.t. direct algebraic
         methods of DataContainer and subclasses.
         
         This method is not to be used directly

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):
@@ -2153,7 +2155,6 @@ 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])
@@ -2992,12 +2993,12 @@ def __str__ (self, representation=False):
     def get_data_axes_order(self,new_order=None):
         '''returns the axes label of self as a list
         
-        if new_order is None returns the labels of the axes as a sorted-by-key list
-        if new_order is a list of length number_of_dimensions, returns a list
+        If new_order is None returns the labels of the axes as a sorted-by-key list.
+        If new_order is a list of length number_of_dimensions, returns a list
         with the indices of the axes in new_order with respect to those in 
         self.dimension_labels: i.e.
-          self.dimension_labels = {0:'horizontal',1:'vertical'}
-          new_order = ['vertical','horizontal']
+          >>> self.dimension_labels = {0:'horizontal',1:'vertical'}
+          >>> new_order = ['vertical','horizontal']
           returns [1,0]
         '''
         if new_order is None:
@@ -3125,19 +3126,18 @@ def sapyb(self, a, y, b, out=None, num_threads=NUM_THREADS):
         out : return DataContainer, if None a new DataContainer is returned, default None. 
             out can be self or y.
         num_threads : number of threads to use during the calculation, using the CIL C library
+            It will try to use the CIL C library and default to numpy operations, in case the C library does not handle the types.
         
-        It will try to use the CIL C library and default to numpy operations, in case the C library does
-        not handle the types.
         
-        Example:
+        Example
         -------
 
-        a = 2
-        b = 3
-        ig = ImageGeometry(10,11)
-        x = ig.allocate(1)
-        y = ig.allocate(2)
-        out = x.sapyb(a,y,b)
+        >>> a = 2
+        >>> b = 3
+        >>> ig = ImageGeometry(10,11)
+        >>> x = ig.allocate(1)
+        >>> y = ig.allocate(2)
+        >>> out = x.sapyb(a,y,b)
         '''
         ret_out = False
 
@@ -3328,11 +3328,8 @@ def norm(self, **kwargs):
         return numpy.sqrt(self.squared_norm(**kwargs))
 
     def dot(self, other, *args, **kwargs):
-        '''return the inner product of 2 DataContainers viewed as vectors
-        
-        applies to real and complex data. In such case the dot method returns
-
-        a.dot(b.conjugate())
+        '''returns the inner product of 2 DataContainers viewed as vectors. Suitable for real and complex data.
+          For complex data,  the dot method returns a.dot(b.conjugate())
         '''
         method = kwargs.get('method', 'numpy')
         if method not in ['numpy','reduce']: