Phase contribution (#1737)

Add Paganin phase retrieval methods

Signed-off-by: Hannah Robarts <[email protected]>
Co-authored-by: Jakob Sauer Jørgensen <[email protected]>

CHANGELOG.md

@@ -4,6 +4,7 @@
   - New Features:
     - Added method to plot filter in `GenericFilteredBackProjection` (#1667)
     - Added wavelet operator, wrapping PyWavelets operator as a CIL operator (#1618)
+    - Added PaganinProcessor processor, to perform phase retrieval from phase contrast images (#1737)
     - Added L1Sparsity function, allowing calculations of `|Ax-b|_1` and its proximal, in the case of orthogonal operators, `A` (#1618)
     - Options in algorithms GD, ISTA and FISTA to pass a `cil.optimisation.utilities.StepSizeRule` or a `cil.optimisation.utilities.Preconditioner`(#1768)
     - an implementation of the Armijo Rule as a child class of  `cil.optimisation.utilities.StepSizeRule` (#1768)

Wrappers/Python/cil/framework/framework.py

@@ -967,7 +967,22 @@ def get_centre_slice(self):
         return self
 
     def calculate_magnification(self):
-        return [None, None, 1.0]
+        '''Method to calculate magnification and distance from the sample to 
+        the detector using the detector positions and the rotation axis. 
+        For parallel beam geometry magnification = 1
+        
+        Returns
+        -------
+        list
+            A list containing the [0] distance from the source to the rotate 
+            axis, [1] distance from the rotate axis to the detector, 
+            [2] magnification of the system
+
+        '''
+        ab = (self.rotation_axis.position - self.detector.position)
+        dist_center_detector = float(numpy.sqrt(ab.dot(ab)))
+
+        return [None, dist_center_detector, 1.0]
 
 class Parallel3D(SystemConfiguration):
     r'''This class creates the SystemConfiguration of a parallel beam 3D tomographic system
@@ -1116,7 +1131,22 @@ def __eq__(self, other):
         return False
 
     def calculate_magnification(self):
-        return [None, None, 1.0]
+        '''Method to calculate magnification and distance from the sample to 
+        the detector using the detector positions and the rotation axis. 
+        For parallel beam geometry magnification = 1
+        
+        Returns
+        -------
+        list
+            A list containing the [0] distance from the source to the rotate 
+            axis, [1] distance from the rotate axis to the detector, 
+            [2] magnification of the system
+
+        '''
+        ab = (self.rotation_axis.position - self.detector.position)
+        dist_center_detector = float(numpy.sqrt(ab.dot(ab)))
+
+        return [None, dist_center_detector, 1.0]
 
     def get_centre_slice(self):
         """Returns the 2D system configuration corresponding to the centre slice