Added and tested Siemens nonneg. It works.

TestSuite/Phase_Siemens_nonneg_demo.py

+import sys
+sys.path.append('../proxtoolbox/Problems/Phase')
+sys.path.append('..')
+import Siemens_processor
+import Siemens_nonneg_in
+from phase import Phase
+
+Siemens = Phase(Siemens_nonneg_in.new_config)
+Siemens.solve()
+Siemens.compare_to_matlab()
+#Siemens.compare_data_to_matlab()
+#JWST.show()

proxtoolbox/Problems/Phase/Siemens_nonneg_in.py

+#                   Siemens_amplitude_in
+#              written on October 6, 2011 by
+#                        Russell Luke
+#                 University of Goettingen
+#
+# DESCRIPTION:  parameter input file for main_dvr.m
+#
+##########################################################################
+## This is the input file that the user sees/modifies.  It should be simple, 
+## avoid jargon or acronyms, and should be a model for a menu-driven GUI
+
+new_config = {
+
+    ## We start very general.
+    ## What type of problem is being solved?  Classification 
+    ## is according to the geometry:  Affine, Cone, Convex, 
+    ## Phase, Affine-sparsity, Nonlinear-sparsity, Sudoku
+
+    'problem_family' : 'Phase',
+
+    ##==========================================
+    ## Problem parameters
+    ##==========================================
+    ## What is the name of the data file?
+    'data_filename' : 'Siemens_processor',
+
+
+    ## What type of object are we working with?
+    ## Options are: 'phase', 'real', 'nonnegative', 'complex'
+    'object' : 'nonnegative',
+
+    ## What type of constraints do we have?
+    ## Options are: 'support only', 'real and support', 'nonnegative and support',
+    ##              'amplitude only', 'minimum amplitude', 'sparse real', 'sparse complex', and 'hybrid'
+    'constraint' : 'nonnegative and support',
+
+    ## What type of measurements are we working with?
+    ## Options are: 'single diffraction', 'diversity diffraction', 
+    ##              'ptychography', and 'complex'
+    'experiment' : 'single diffraction',
+
+    ## Next we move to things that most of our users will know 
+    ## better than we will.  Some of these may be overwritten in the 
+    ## data processor file which the user will most likely write. 
+    ## Are the measurements in the far field or near field?
+    ## Options are: 'far field' or 'near field', 
+    'distance' : 'far field',
+
+    ## What are the dimensions of the measurements?
+    'Nx' : 512,
+    'Ny' : 512,
+    'Nz':1, # only 2 dimensional arrays
+
+    ## What are the noise characteristics (Poisson or Gaussian or none)?
+    'noise':'Gaussian',
+
+    ##==========================================
+    ##  Algorithm parameters
+    ##==========================================
+    ## Now set some algorithm parameters that the user should be 
+    ## able to control (without too much damage)
+
+    ## Algorithm:
+    'algorithm' : 'RAAR',#'RAAR', 'AP',  
+    'numruns':1, # the only time this parameter will
+    # be different than 1 is when we are
+    # benchmarking...not something a normal user
+    # would be doing.
+
+
+    ## The following are parameters specific to RAAR, HPR, and HAAR that the 
+    ## user should be able to set/modify.  Surely
+    ## there will be other algorithm specific parameters that a user might 
+    ## want to play with.  Don't know how best 
+    ## to do this.  Thinking of a GUI interface, we could hard code all the 
+    ##  parameters the user might encounter and have the menu options change
+    ## depending on the value of the method field. 
+    ## do different things depending on the chosen algorithm:
+        ## maximum number of iterations and tolerances
+        'MAXIT' : 500,
+        'TOL' : 1e-5,
+
+        ## relaxaton parameters in RAAR, HPR and HAAR
+        'beta_0' : 1.0,                # starting relaxation prameter (only used with
+        # HAAR, HPR and RAAR)
+        'beta_max' :0.5,             # maximum relaxation prameter (only used with
+        # HAAR, RAAR, and HPR)
+        'beta_switch' : 50,           # iteration at which beta moves from beta_0 -> beta_max
+
+        ## parameter for the data regularization 
+        ## need to discuss how/whether the user should
+        ## put in information about the noise
+        'data_ball' : 0.1,  
+        # the above is the percentage of the gap
+        # between the measured data and the
+        # initial guess satisfying the
+        # qualitative constraints.  For a number 
+        # very close to one, the gap is not expected 
+        # to improve much.  For a number closer to 0
+        # the gap is expected to improve a lot.  
+        # Ultimately the size of the gap depends
+        # on the inconsistency of the measurement model 
+        # with the qualitative constraints.
+
+    ##==========================================
+    ## parameters for plotting and diagnostics
+    ##==========================================
+    'verbose' : 1, # options are 0 or 1
+    'graphics' : 1, # whether or not to display figures, options are 0 or 1.
+                       # default is 1.
+    'anim' : 1,  # whether or not to disaply ``real time" reconstructions
+                    # options are 0=no, 1=yes, 2=make a movie
+                    # default is 1.
+    'graphics_display' : 'Phase_graphics', # unless specified, a default 
+                                # plotting subroutine will generate 
+                                # the graphics.  Otherwise, the user
+                                # can write their own plotting subroutine
+
+    ##======================================================================
+    ##  Technical/software specific parameters
+    ##======================================================================
+    ## Given the parameter values above, the following technical/algorithmic
+    ## parameters are automatically set.  The user does not need to know 
+    ## about these details, and so probably these parameters should be set in 
+    ## a module one level below this one.  
+    }

proxtoolbox/Problems/Phase/Siemens_processor.py

@@ -48,7 +48,7 @@ def Siemens_processor(config):
         # in Luke.m this is changed to the magnitude.
         config['data']=M**2
         config['norm_rt_data']=norm(S,'fro')
-        config['norm_data']=config['norm_rt_data']^2
+        config['norm_data']=config['norm_rt_data']**2
         config['data_zeros'] = np.where(M==0)
         # below, we make the support too small to increase the inconsistency
         # Stmp=zeros(size(S))
@@ -59,9 +59,9 @@ def Siemens_processor(config):
         # use the abs_illumination field to represent the
         # support constraint.
         config['amplitude'] = config['norm_rt_data']*S/(norm(S,'fro'))
-        config['amplitude'] = config['amplitude']/norm(config['amplitude'],'fro')*config['norm_rt_data'][0]
-        config['supp_phase'] = np.nonzero(ones(m,n))
-        config['illumination_phase'] = np.nonzero(ones(m,n))
+        config['amplitude'] = config['amplitude']/norm(config['amplitude'],'fro')*config['norm_rt_data']
+        config['supp_phase'] = np.nonzero(np.ones((config['Ny'],config['Nx'])))
+        config['illumination_phase'] = np.nonzero(np.ones((config['Ny'],config['Nx'])))
     elif config['object'] == 'complex':
         # put some phase across S
         points = config['Nx']

proxtoolbox/Problems/Phase/phase.py

@@ -254,9 +254,12 @@ class Phase(Problem):
                 f = h5py.File('Phase_test_data/JWST_u1_ap_' + str(self.config['MAXIT']) + '.mat')
 
             u1 = f['u1'].value.view(np.complex)
-        elif self.config['data_filename'] == 'Siemens_processor':
+        elif self.config['data_filename'] == 'Siemens_processor' and self.config['constraint'] == 'amplitude':
             f = h5py.File('Phase_test_data/siemens_amplitude_u1_' + str(self.config['MAXIT']) + '.mat')
             u1 = f['u1'].value.view(np.complex)
+        elif self.config['data_filename'] == 'Siemens_processor' and self.config['constraint'] == 'nonnegative and support':
+            f = h5py.File('Phase_test_data/siemens_nonneg_u1_' + str(self.config['MAXIT']) + '.mat')
+            u1 = f['u1'].value.view(np.float64)
         else:
             if self.config['algorithm'] == 'RAAR':
                 if self.config['beta_0'] == 0.95: