combine Acquisition{Types,Dimensions}(StrEnum) => AcquisitionType(Flag)

Wrappers/Python/cil/framework/__init__.py

@@ -27,4 +27,4 @@
 from .processors import DataProcessor, Processor, AX, PixelByPixelDataProcessor, CastDataContainer
 from .block import BlockDataContainer, BlockGeometry
 from .partitioner import Partitioner
-from .labels import AcquisitionDimensionLabels, ImageDimensionLabels, FillTypes, UnitsAngles, AcquisitionTypes, AcquisitionDimensions
+from .labels import AcquisitionDimensionLabels, ImageDimensionLabels, FillTypes, UnitsAngles, AcquisitionType

Wrappers/Python/cil/framework/acquisition_geometry.py

@@ -22,7 +22,7 @@
 
 import numpy
 
-from .labels import AcquisitionDimensionLabels, UnitsAngles, AcquisitionTypes, FillTypes, AcquisitionDimensions
+from .labels import AcquisitionDimensionLabels, UnitsAngles, AcquisitionType, FillTypes
 from .acquisition_data import AcquisitionData
 from .image_geometry import ImageGeometry
 
@@ -186,10 +186,7 @@ class SystemConfiguration(object):
 
     @property
     def dimension(self):
-        if self._dimension == 2:
-            return AcquisitionDimensions.DIM2.value
-        else:
-            return AcquisitionDimensions.DIM3.value
+        return AcquisitionType.DIM2 if self._dimension == 2 else AcquisitionType.DIM3
 
     @dimension.setter
     def dimension(self,val):
@@ -203,8 +200,8 @@ def geometry(self):
         return self._geometry
 
     @geometry.setter
-    def geometry(self,val):
-        self._geometry = AcquisitionTypes(val)
+    def geometry(self, val):
+        self._geometry = AcquisitionType(val)
 
     def __init__(self, dof, geometry, units='units'):
         """Initialises the system component attributes for the acquisition type
@@ -213,7 +210,7 @@ def __init__(self, dof, geometry, units='units'):
         self.geometry = geometry
         self.units = units
 
-        if self.geometry == AcquisitionTypes.PARALLEL:
+        if AcquisitionType.PARALLEL & self.geometry:
             self.ray = DirectionVector(dof)
         else:
             self.source = PositionVector(dof)
@@ -344,7 +341,7 @@ 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=AcquisitionType.PARALLEL, units=units)
 
         #source
         self.ray.direction = ray_direction
@@ -518,7 +515,7 @@ 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=AcquisitionType.PARALLEL, units=units)
 
         #source
         self.ray.direction = ray_direction
@@ -803,7 +800,7 @@ 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=AcquisitionType.CONE, units=units)
 
         #source
         self.source.position = source_pos
@@ -982,7 +979,7 @@ 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=AcquisitionType.CONE, units=units)
 
         #source
         self.source.position = source_pos
@@ -1819,7 +1816,7 @@ def get_centre_of_rotation(self, distance_units='default', angle_units='radian')
             offset = offset_distance/ self.config.panel.pixel_size[0]
             offset_units = 'pixels'
 
-            if self.dimension == '3D' and self.config.panel.pixel_size[0] != self.config.panel.pixel_size[1]:
+            if AcquisitionType.DIM3 & self.dimension and self.config.panel.pixel_size[0] != self.config.panel.pixel_size[1]:
                 #if aspect ratio of pixels isn't 1:1 need to convert angle by new ratio
                 y_pix = 1 /self.config.panel.pixel_size[1]
                 x_pix = math.tan(angle_rad)/self.config.panel.pixel_size[0]
@@ -1884,7 +1881,7 @@ def set_centre_of_rotation(self, offset=0.0, distance_units='default', angle=0.0
         else:
             raise ValueError("`distance_units` is not recognised. Must be 'default' or 'pixels'. Got {}".format(distance_units))
 
-        if self.dimension == '2D':
+        if AcquisitionType.DIM2 & self.dimension:
             self.config.system.set_centre_of_rotation(offset_distance)
         else:
             self.config.system.set_centre_of_rotation(offset_distance, angle_rad)
@@ -1921,7 +1918,7 @@ def set_centre_of_rotation_by_slice(self, offset1, slice_index1=None, offset2=No
         if not hasattr(self.config.system, 'set_centre_of_rotation'):
             raise NotImplementedError()
 
-        if self.dimension == '2D':
+        if AcquisitionType.DIM2 & self.dimension:
             if offset2 is not None:
                 warnings.warn("2D so offset2 is ingored", UserWarning, stacklevel=2)
             self.set_centre_of_rotation(offset1)
@@ -2118,7 +2115,7 @@ def copy(self):
     def get_centre_slice(self):
         '''returns a 2D AcquisitionGeometry that corresponds to the centre slice of the input'''
 
-        if self.dimension == '2D':
+        if AcquisitionType.DIM2 & self.dimension:
             return self
 
         AG_2D = copy.deepcopy(self)
@@ -2133,7 +2130,7 @@ def get_ImageGeometry(self, resolution=1.0):
         num_voxel_xy = int(numpy.ceil(self.config.panel.num_pixels[0] * resolution))
         voxel_size_xy = self.config.panel.pixel_size[0] / (resolution * self.magnification)
 
-        if self.dimension == '3D':
+        if AcquisitionType.DIM3 & self.dimension:
             num_voxel_z = int(numpy.ceil(self.config.panel.num_pixels[1] * resolution))
             voxel_size_z = self.config.panel.pixel_size[1] / (resolution * self.magnification)
         else:
@@ -2161,7 +2158,7 @@ def get_slice(self, channel=None, angle=None, vertical=None, horizontal=None):
             geometry_new.config.angles.angle_data = geometry_new.config.angles.angle_data[angle]
 
         if vertical is not None:
-            if geometry_new.geom_type == AcquisitionTypes.PARALLEL or vertical == 'centre' or abs(geometry_new.pixel_num_v/2 - vertical) < 1e-6:
+            if AcquisitionType.PARALLEL & geometry_new.geom_type or vertical == 'centre' or abs(geometry_new.pixel_num_v/2 - vertical) < 1e-6:
                 geometry_new = geometry_new.get_centre_slice()
             else:
                 raise ValueError("Can only subset centre slice geometry on cone-beam data. Expected vertical = 'centre'. Got vertical = {0}".format(vertical))

Wrappers/Python/cil/framework/labels.py

@@ -15,7 +15,7 @@
 #
 # Authors:
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
-from enum import Enum, auto, unique
+from enum import Enum, Flag as _Flag, auto, unique
 try:
     from enum import EnumType
 except ImportError: # Python<3.11
@@ -40,7 +40,6 @@ def _missing_(cls, value: str):
         return cls.__members__.get(value.upper(), None)
 
     def __eq__(self, value: str) -> bool:
-        """Uses value.upper() for case-insensitivity"""
         try:
             value = self.__class__[value.upper()]
         except (KeyError, ValueError, AttributeError):
@@ -60,7 +59,6 @@ def _generate_next_value_(name: str, start, count, last_values) -> str:
         return name.lower()
 
 
-
 class Backends(StrEnum):
     """
     Available backends for CIL.
@@ -228,27 +226,46 @@ class UnitsAngles(StrEnum):
     RADIAN = auto()
 
 
-class AcquisitionTypes(StrEnum):
+class _FlagMeta(EnumType):
+    """Python<3.12 requires this in a metaclass (rather than directly in Flag)"""
+    def __contains__(self, item) -> bool:
+        return item.upper() in self.__members__ if isinstance(item, str) else super().__contains__(item)
+
+
+@unique
+class Flag(_Flag, metaclass=_FlagMeta):
+    """Case-insensitive Flag"""
+    @classmethod
+    def _missing_(cls, value):
+        return cls.__members__.get(value.upper(), None) if isinstance(value, str) else super()._missing_(value)
+
+    def __eq__(self, value: str) -> bool:
+        return super().__eq__(self.__class__[value.upper()] if isinstance(value, str) else value)
+
+
+class AcquisitionType(Flag):
     """
-    Available acquisition types.
+    Available acquisition types & dimensions.
 
     Attributes
     ----------
     PARALLEL: Parallel beam.
     CONE: Cone beam.
+    DIM2: 2D acquisition.
+    DIM3: 3D acquisition.
     """
     PARALLEL = auto()
     CONE = auto()
+    DIM2 = auto()
+    DIM3 = auto()
 
-
-class AcquisitionDimensions(StrEnum):
-    """
-    Available acquisition dimensions.
-
-    Attributes
-    ----------
-    DIM2 ('2D'): 2D acquisition.
-    DIM3 ('3D'): 3D acquisition.
-    """
-    DIM2 = "2D"
-    DIM3 = "3D"
+    @classmethod
+    def _missing_(cls, value):
+        """2D/3D aliases"""
+        if isinstance(value, str):
+            value = {'2D': 'DIM2', '3D': 'DIM3'}.get(value.upper(), value)
+        return super()._missing_(value)
+
+    def __str__(self) -> str:
+        """2D/3D special handling"""
+        return '2D' if self == self.DIM2 else '3D' if self == self.DIM3 else self.name

Wrappers/Python/cil/io/NEXUSDataWriter.py

@@ -18,7 +18,8 @@
 
 import numpy as np
 import os
-from cil.framework import AcquisitionData, AcquisitionGeometry, ImageData, ImageGeometry
+from cil.framework import AcquisitionData, ImageData
+from cil.framework.labels import AcquisitionType
 from cil.version import version
 import datetime
 from cil.io import utilities
@@ -158,7 +159,7 @@ def write(self):
                 f.create_group('entry1/tomo_entry/config/rotation_axis')
 
                 ds_data.attrs['geometry'] = str(self.data.geometry.config.system.geometry)
-                ds_data.attrs['dimension'] = self.data.geometry.config.system.dimension
+                ds_data.attrs['dimension'] = str(self.data.geometry.config.system.dimension)
                 ds_data.attrs['num_channels'] = self.data.geometry.config.channels.num_channels
 
                 f.create_dataset('entry1/tomo_entry/config/detector/direction_x',
@@ -192,7 +193,7 @@ def write(self):
                 ds_data.attrs['pixel_size_h'] = self.data.geometry.config.panel.pixel_size[0]
                 ds_data.attrs['panel_origin'] = self.data.geometry.config.panel.origin
 
-                if self.data.geometry.config.system.dimension == '3D':
+                if AcquisitionType.DIM3 & self.data.geometry.config.system.dimension:
                     f.create_dataset('entry1/tomo_entry/config/detector/direction_y',
                                      (self.data.geometry.config.system.detector.direction_y.shape),
                                      dtype = 'float32',

Wrappers/Python/cil/io/NikonDataReader.py

@@ -16,9 +16,9 @@
 # Authors:
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 
-from cil.framework import AcquisitionData, AcquisitionGeometry
+from cil.framework import AcquisitionGeometry
+from cil.framework.labels import AcquisitionType
 from cil.io.TIFF import TIFFStackReader
-import warnings
 import numpy as np
 import os
 
@@ -334,7 +334,7 @@ def get_geometry(self):
     def get_roi(self):
         '''returns the roi'''
         roi = self._roi_par[:]
-        if self._ag.dimension == '2D':
+        if AcquisitionType.DIM2 & self._ag.dimension:
             roi.pop(1)
 
         roidict = {}

Wrappers/Python/cil/plugins/astra/operators/ProjectionOperator.py

@@ -18,7 +18,7 @@
 
 import logging
 
-from cil.framework import BlockGeometry, AcquisitionDimensionLabels, ImageDimensionLabels
+from cil.framework import BlockGeometry, AcquisitionDimensionLabels, ImageDimensionLabels, AcquisitionType
 from cil.optimisation.operators import BlockOperator, LinearOperator, ChannelwiseOperator
 from cil.plugins.astra.operators import AstraProjector2D, AstraProjector3D
 
@@ -127,7 +127,7 @@ def __init__(self,
         if device == 'gpu':
             operator = AstraProjector3D(volume_geometry_sc,
                                         sinogram_geometry_sc)
-        elif self.sinogram_geometry.dimension == '2D':
+        elif AcquisitionType.DIM2 & self.sinogram_geometry.dimension:
             operator = AstraProjector2D(volume_geometry_sc,
                                         sinogram_geometry_sc,
                                         device=device)

Wrappers/Python/cil/plugins/astra/processors/FBP.py

@@ -15,9 +15,7 @@
 #
 # Authors:
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
-import warnings
-
-from cil.framework import DataProcessor, ImageDimensionLabels, AcquisitionDimensionLabels
+from cil.framework import DataProcessor, ImageDimensionLabels, AcquisitionDimensionLabels, AcquisitionType
 from cil.plugins.astra.processors.FBP_Flexible import FBP_Flexible
 from cil.plugins.astra.processors.FDK_Flexible import FDK_Flexible
 from cil.plugins.astra.processors.FBP_Flexible import FBP_CPU
@@ -81,7 +79,7 @@ def __init__(self, image_geometry=None, acquisition_geometry=None, device='gpu')
             if acquisition_geometry.geom_type == 'cone':
                 raise NotImplementedError("Cannot process cone-beam data without a GPU")
 
-            if acquisition_geometry.dimension == '2D':
+            if AcquisitionType.DIM2 & acquisition_geometry.dimension:
                 processor = FBP_CPU(image_geometry, acquisition_geometry)
             else:
                 raise NotImplementedError("Cannot process 3D data without a GPU")

Wrappers/Python/cil/plugins/astra/processors/FBP_Flexible.py

@@ -17,7 +17,7 @@
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 
 
-from cil.framework import AcquisitionGeometry, Processor, ImageData
+from cil.framework import AcquisitionGeometry, Processor, ImageData, AcquisitionType
 from cil.plugins.astra.processors.FDK_Flexible import FDK_Flexible
 from cil.plugins.astra.utilities import convert_geometry_to_astra_vec_3D, convert_geometry_to_astra
 import logging
@@ -76,7 +76,7 @@ def __init__(self, volume_geometry,
         detector_position = sino_geom_cone.config.system.detector.position
         detector_direction_x = sino_geom_cone.config.system.detector.direction_x
 
-        if sino_geom_cone.dimension == '2D':
+        if AcquisitionType.DIM2 & sino_geom_cone.dimension:
             tmp = AcquisitionGeometry.create_Cone2D(cone_source, detector_position, detector_direction_x)
         else:
             detector_direction_y = sino_geom_cone.config.system.detector.direction_y
@@ -141,7 +141,7 @@ def check_input(self, dataset):
             raise ValueError("Expected input data to be parallel beam geometry , got {0}"\
                  .format(self.sinogram_geometry.geom_type))
 
-        if self.sinogram_geometry.dimension != '2D':
+        if not AcquisitionType.DIM2 & self.sinogram_geometry.dimension:
             raise ValueError("Expected input data to be 2D , got {0}"\
                  .format(self.sinogram_geometry.dimension))
 

Wrappers/Python/cil/plugins/astra/utilities/convert_geometry_to_astra.py

@@ -19,7 +19,7 @@
 
 import astra
 import numpy as np
-from cil.framework import UnitsAngles
+from cil.framework import AcquisitionType, UnitsAngles
 
 def convert_geometry_to_astra(volume_geometry, sinogram_geometry):
     """
@@ -39,13 +39,8 @@ def convert_geometry_to_astra(volume_geometry, sinogram_geometry):
         The ASTRA vol_geom and proj_geom
 
     """
-
     # determine if the geometry is 2D or 3D
-
-    if sinogram_geometry.pixel_num_v > 1:
-        dimension = '3D'
-    else:
-        dimension = '2D'
+    dimension = AcquisitionType.DIM3 if sinogram_geometry.pixel_num_v > 1 else AcquisitionType.DIM2
 
     #get units
 
@@ -54,7 +49,7 @@ def convert_geometry_to_astra(volume_geometry, sinogram_geometry):
     else:
         angles_rad = sinogram_geometry.config.angles.angle_data
 
-    if dimension == '2D':
+    if AcquisitionType.DIM2 & dimension:
         vol_geom = astra.create_vol_geom(volume_geometry.voxel_num_y,
                                          volume_geometry.voxel_num_x,
                                          volume_geometry.get_min_x(),
@@ -77,7 +72,7 @@ def convert_geometry_to_astra(volume_geometry, sinogram_geometry):
         else:
             NotImplemented
 
-    elif dimension == '3D':
+    elif AcquisitionType.DIM3 & dimension:
         vol_geom = astra.create_vol_geom(volume_geometry.voxel_num_y,
                                          volume_geometry.voxel_num_x,
                                          volume_geometry.voxel_num_z,

Wrappers/Python/cil/plugins/astra/utilities/convert_geometry_to_astra_vec_3D.py

@@ -19,7 +19,7 @@
 
 import astra
 import numpy as np
-from cil.framework import UnitsAngles
+from cil.framework import AcquisitionType, UnitsAngles
 
 def convert_geometry_to_astra_vec_3D(volume_geometry, sinogram_geometry_in):
 
@@ -57,7 +57,7 @@ def convert_geometry_to_astra_vec_3D(volume_geometry, sinogram_geometry_in):
     #get units
     degrees = angles.angle_unit == UnitsAngles.DEGREE
 
-    if sinogram_geometry.dimension == '2D':
+    if AcquisitionType.DIM2 & sinogram_geometry.dimension:
         #create a 3D astra geom from 2D CIL geometry
         volume_geometry_temp = volume_geometry.copy()
         volume_geometry_temp.voxel_num_z = 1