folder structure to separate different cases

proxtoolbox/Algorithms/SimpleAlgortihm.py

@@ -129,9 +129,8 @@ class SimpleAlgorithm:
         if hasattr(self, 'truth'):
             Relerrs = change.copy()
 
-        # Different algorithms will have different qualities that one
-        # should monitor.  Since we take a fixed point perspective, the main
-        # thing to monitor is the change in the iterates.
+        # Different algorithms will have different qualities that one should monitor.
+        # Since we take a fixed point perspective, the main thing to monitor is the change in the iterates.
         shadow = self.prox1.work(u)
 
         ##### LOOP
@@ -143,18 +142,15 @@ class SimpleAlgorithm:
             u_new = self.evaluate(u)
 
             if self.diagnostic:
-                # the next prox operation only gets used in the computation of
-                # the size of the gap.  This extra step is not
-                # required in alternating projections, which makes RAAR
+                # the next prox operation only gets used in the computation of the size of the gap.
+                # This extra step is not required in alternating projections, which makes RAAR a bit slower
                 u2 = self.prox2.work(u_new)
                 u1 = self.prox1.work(u2)
 
-            # compute the normalized change in successive iterates: 
-            # change(iter) = sum(sum((feval('P_M',M,u)-tmp).^2))/norm_data;
+            # compute the normalized change in successive iterates
             tmp_change = 0
             tmp_gap = 0
             tmp_shadow = 0
-
             # the simple case, where everything can be calculated in one difference
             if self.product_space_dimension == 1 or (p == 1 and q == 1):
                 tmp_change = phase_offset_compensated_norm(u, u_new, norm_type='fro', norm_factor=norm_data) ** 2
@@ -216,9 +212,8 @@ class SimpleAlgorithm:
             # update iterate
             u = u_new
             if self.diagnostic:
-                # For Douglas-Rachford,in general it is appropriate to monitor the SHADOWS of the iterates, since in
-                # the convex case these converge even for beta=1.
-                # (see Bauschke-Combettes-Luke, J. Approx. Theory, 2004)
+                # For Douglas-Rachford, in general it is appropriate to monitor the SHADOWS of the iterates, since in
+                # the convex case these converge even for beta=1. (see Bauschke-Combettes-Luke, J. Approx. Theory, 2004)
                 shadow = u2
 
         ##### POSTPROCESSING

proxtoolbox/Problems/OrbitalTomog/orbital_tomog_3d_data_processor.py → proxtoolbox/Problems/OrbitalTomog/molecule_3d/orbital_tomog_3d_data_processor.py

-from .orbitaltomog_data_processor import support_from_autocorrelation
-from proxtoolbox.Utilities.OrbitalTomog.array_tools import shifted_fft, shifted_ifft
-from proxtoolbox.Utilities.OrbitalTomog.binning import bin_2d_array, bin_array
+from proxtoolbox.Problems.OrbitalTomog.planar_molecule.orbitaltomog_data_processor import support_from_autocorrelation
+from proxtoolbox.Utilities.OrbitalTomog.array_tools import shifted_fft
+from proxtoolbox.Utilities.OrbitalTomog.binning import bin_array
 import numpy as np
 from skimage.io import imread
-from .Graphics.stack_viewer import XYZStackViewer
+from proxtoolbox.Problems.OrbitalTomog.Graphics.stack_viewer import XYZStackViewer
 
 
 def data_processor(config):

proxtoolbox/Problems/OrbitalTomog/pentacene_3d_config.py → proxtoolbox/Problems/OrbitalTomog/molecule_3d/pentacene_3d_config.py

@@ -103,7 +103,7 @@ new_config = {
     'lambda_switch': 100,
 
     'sparsity_parameter': 100,
-    'use_sparsity_with_support': False,
+    'use_sparsity_with_support': True,
     'symmetry_type': 1,  # -1 for antissymmetric functions, 1 for symmetric ones.
     'symmetry_axis': -1,  # which axis is symmetric. (mirror plane perpendicular to this axis)
 

proxtoolbox/Problems/OrbitalTomog/Coronene_demo.py → proxtoolbox/Problems/OrbitalTomog/planar_molecule/Coronene_demo.py

-from proxtoolbox.Problems.OrbitalTomog import coronene_config  # base config
-from proxtoolbox.Problems.OrbitalTomog import orbitaltomog_data_processor  # extends config
+from proxtoolbox.Problems.OrbitalTomog.planar_molecule import coronene_config, orbitaltomog_data_processor
 from proxtoolbox.Problems.OrbitalTomog.phase import Phase
 # sys.path.append('../proxtoolbox/Problems/Phase')