Merge remote-tracking branch 'upstream/master' into DataOrder-rebase

.gitignore

@@ -2,4 +2,6 @@
 __pycache__/
 /Wrappers/Python/build/
 /Wrappers/Python/cil/version.py
+/build*
+*.vscode*
 *.egg*

CHANGELOG.md

@@ -1,12 +1,16 @@
 * 24.x.x
   - New Features:
+    - Added SVRG and LSVRG stochastic functions (#1625)
     - Added SAG and SAGA stochastic functions (#1624)
     - Allow `SumFunction` with 1 item (#1857)
-    - Added `labels` module with `ImageDimensionLabels`, `AcquisitionDimensionLabels`,`AcquisitionDimensions`, `AcquisitionTypes`, `UnitsAngles`, `FillTypes`. (#1692)
+    - Added `labels` module with `ImageDimensionLabels`, `AcquisitionDimensionLabels`,`AcquisitionDimensions`, `AcquisitionTypes`, `UnitsAngles`, `FillTypes` (#1692)
   - Enhancements:
     - Use ravel instead of flat in KullbackLeibler numba backend (#1874)
     - Upgrade Python wrapper (#1873, #1875)
     - Internal refactor: Replaced string-based label checks with enum-based checks for improved type safety and consistency (#1692)
+  - Bug fixes:
+    - `ImageData` removes dimensions of size 1 from the input array. This fixes an issue where single slice reconstructions from 3D data would fail due to shape mismatches (#1885)
+    - Make Binner accept accelerated=False (#1887)
 
 * 24.1.0
   - New Features:
@@ -35,9 +39,6 @@
     - Merged the files `BlockGeometry.py` and `BlockDataContainer.py` in `framework` to one file `block.py`. Please use `from cil.framework import BlockGeometry, BlockDataContainer` as before (#1799)
     - Bug fix in `FGP_TV` function to set the default behaviour not to enforce non-negativity (#1826).
 
-
-
-
 * 24.0.0
   - Update to new CCPi-Regularisation toolkit v24.0.0. This is a backward incompatible release of the toolkit.
   - CIL plugin support for TIGRE version v2.6

Wrappers/Python/cil/framework/acquisition_data.py

@@ -21,6 +21,7 @@
 from .data_container import DataContainer
 from .partitioner import Partitioner
 
+
 class AcquisitionData(DataContainer, Partitioner):
     '''DataContainer for holding 2D or 3D sinogram'''
     __container_priority__ = 1
@@ -62,7 +63,8 @@ def __init__(self,
         elif issubclass(type(array) , DataContainer):
             array = array.as_array()
         elif issubclass(type(array) , numpy.ndarray):
-            pass
+            # remove singleton dimensions
+            array = numpy.squeeze(array)
         else:
             raise TypeError('array must be a CIL type DataContainer or numpy.ndarray got {}'.format(type(array)))
 

Wrappers/Python/cil/framework/acquisition_geometry.py

@@ -344,7 +344,7 @@ class Parallel2D(SystemConfiguration):
     def __init__ (self, ray_direction, detector_pos, detector_direction_x, rotation_axis_pos, units='units'):
         """Constructor method
         """
-        super(Parallel2D, self).__init__(dof=2, geometry = AcquisitionTypes.PARALLEL, units=units)
+        super(Parallel2D, self).__init__(dof=2, geometry=AcquisitionTypes.PARALLEL, units=units)
 
         #source
         self.ray.direction = ray_direction
@@ -518,7 +518,7 @@ class Parallel3D(SystemConfiguration):
     def __init__ (self,  ray_direction, detector_pos, detector_direction_x, detector_direction_y, rotation_axis_pos, rotation_axis_direction, units='units'):
         """Constructor method
         """
-        super(Parallel3D, self).__init__(dof=3, geometry = AcquisitionTypes.PARALLEL, units=units)
+        super(Parallel3D, self).__init__(dof=3, geometry=AcquisitionTypes.PARALLEL, units=units)
 
         #source
         self.ray.direction = ray_direction
@@ -803,7 +803,7 @@ class Cone2D(SystemConfiguration):
     def __init__ (self, source_pos, detector_pos, detector_direction_x, rotation_axis_pos, units='units'):
         """Constructor method
         """
-        super(Cone2D, self).__init__(dof=2, geometry = AcquisitionTypes.CONE, units=units)
+        super(Cone2D, self).__init__(dof=2, geometry=AcquisitionTypes.CONE, units=units)
 
         #source
         self.source.position = source_pos
@@ -982,7 +982,7 @@ class Cone3D(SystemConfiguration):
     def __init__ (self, source_pos, detector_pos, detector_direction_x, detector_direction_y, rotation_axis_pos, rotation_axis_direction, units='units'):
         """Constructor method
         """
-        super(Cone3D, self).__init__(dof=3, geometry = AcquisitionTypes.CONE, units=units)
+        super(Cone3D, self).__init__(dof=3, geometry=AcquisitionTypes.CONE, units=units)
 
         #source
         self.source.position = source_pos

Wrappers/Python/cil/framework/data_container.py

@@ -93,8 +93,6 @@ def size(self):
     __container_priority__ = 1
     def __init__ (self, array, deep_copy=True, dimension_labels=None,
                   **kwargs):
-        '''Holds the data'''
-
         if type(array) == numpy.ndarray:
             if deep_copy:
                 self.array = array.copy()
@@ -192,8 +190,6 @@ def reorder(self, order):
         :param order: ordered list of labels from self.dimension_labels
         :type order: list, sting
         '''
-
-
         try:
             if len(order) != len(self.shape):
                 raise ValueError('The axes list for resorting must have {0} dimensions. Got {1}'.format(len(self.shape), len(order)))
@@ -220,7 +216,6 @@ def reorder(self, order):
         else:
             self.geometry.set_labels(dimension_labels_new)
 
-
     def fill(self, array, **dimension):
         '''fills the internal data array with the DataContainer, numpy array or number provided
 
@@ -243,10 +238,6 @@ def fill(self, array, **dimension):
             return
         if dimension == {}:
             if isinstance(array, numpy.ndarray):
-                if array.shape != self.shape:
-                    raise ValueError('Cannot fill with the provided array.' + \
-                                     'Expecting shape {0} got {1}'.format(
-                                     self.shape,array.shape))
                 numpy.copyto(self.array, array)
             elif isinstance(array, Number):
                 self.array.fill(array)
@@ -543,7 +534,6 @@ def sapyb(self, a, y, b, out=None, num_threads=NUM_THREADS):
         ax = self * a
         y.multiply(b, out=out)
         out.add(ax, out=out)
-
         return out
 
     def _axpby(self, a, b, y, out, dtype=numpy.float32, num_threads=NUM_THREADS):
@@ -629,19 +619,19 @@ def _axpby(self, a, b, y, out, dtype=numpy.float32, num_threads=NUM_THREADS):
                                   ctypes.POINTER(ctypes.c_float),  # pointer to the second array
                                   ctypes.POINTER(ctypes.c_float),  # pointer to the third array
                                   ctypes.POINTER(ctypes.c_float),  # pointer to A
-                                  ctypes.c_int,  # type of type of A selector (int)
+                                  ctypes.c_int,                    # type of type of A selector (int)
                                   ctypes.POINTER(ctypes.c_float),  # pointer to B
-                                  ctypes.c_int,  # type of type of B selector (int)
-                                  ctypes.c_longlong,  # type of size of first array
+                                  ctypes.c_int,                    # type of type of B selector (int)
+                                  ctypes.c_longlong,               # type of size of first array
                                   ctypes.c_int]                    # number of threads
-        cilacc.daxpby.argtypes = [ctypes.POINTER(ctypes.c_double),  # pointer to the first array
-                                  ctypes.POINTER(ctypes.c_double),  # pointer to the second array
-                                  ctypes.POINTER(ctypes.c_double),  # pointer to the third array
-                                  ctypes.POINTER(ctypes.c_double),  # type of A (c_double)
-                                  ctypes.c_int,  # type of type of A selector (int)
-                                  ctypes.POINTER(ctypes.c_double),  # type of B (c_double)
-                                  ctypes.c_int,  # type of type of B selector (int)
-                                  ctypes.c_longlong,  # type of size of first array
+        cilacc.daxpby.argtypes = [ctypes.POINTER(ctypes.c_double), # pointer to the first array
+                                  ctypes.POINTER(ctypes.c_double), # pointer to the second array
+                                  ctypes.POINTER(ctypes.c_double), # pointer to the third array
+                                  ctypes.POINTER(ctypes.c_double), # type of A (c_double)
+                                  ctypes.c_int,                    # type of type of A selector (int)
+                                  ctypes.POINTER(ctypes.c_double), # type of B (c_double)
+                                  ctypes.c_int,                    # type of type of B selector (int)
+                                  ctypes.c_longlong,               # type of size of first array
                                   ctypes.c_int]                    # number of threads
 
         if f(x_p, y_p, out_p, a_p, a_vec, b_p, b_vec, ndx.size, num_threads) != 0:

Wrappers/Python/cil/framework/image_data.py

@@ -63,7 +63,8 @@ def __init__(self,
         elif issubclass(type(array) , DataContainer):
             array = array.as_array()
         elif issubclass(type(array) , numpy.ndarray):
-            pass
+            # remove singleton dimensions
+            array = numpy.squeeze(array)
         else:
             raise TypeError('array must be a CIL type DataContainer or numpy.ndarray got {}'.format(type(array)))
 
@@ -190,7 +191,6 @@ def apply_circular_mask(self, radius=0.99, in_place=True):
 
             return image_data_out
 
-
     def reorder(self, order):
         '''
         Reorders the data in memory as requested. This is an in-place operation.

Wrappers/Python/cil/framework/processors.py

@@ -153,11 +153,11 @@ def __call__(self, x, out=None):
 
         return out
 
-
 class DataProcessor(Processor):
     '''Basically an alias of Processor Class'''
     pass
 
+
 class DataProcessor23D(DataProcessor):
     '''Regularizers DataProcessor
     '''

Wrappers/Python/cil/framework/vector_geometry.py

@@ -23,6 +23,7 @@
 
 from .labels import FillTypes
 
+
 class VectorGeometry:
     '''Geometry describing VectorData to contain 1D array'''
     @property