added filters

2 files changed, 334 insertions, 0 deletions

diff --git a/Wrappers/Python/ccpi/filters/Regularizer.py b/Wrappers/Python/ccpi/filters/Regularizer.py
new file mode 100644
index 0000000..8623f41
--- /dev/null
+++ b/Wrappers/Python/ccpi/filters/Regularizer.py
@@ -0,0 +1,334 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Aug  8 14:26:00 2017
+
+@author: ofn77899
+"""
+
+from ccpi.filters import cpu_regularizers
+import numpy as np
+from enum import Enum
+import timeit
+
+class Regularizer():
+    '''Class to handle regularizer algorithms to be used during reconstruction
+    
+    Currently 5 CPU (OMP) regularization algorithms are available:
+        
+    1) SplitBregman_TV
+    2) FGP_TV
+    3) LLT_model
+    4) PatchBased_Regul
+    5) TGV_PD
+    
+    Usage:
+        the regularizer can be invoked as object or as static method
+        Depending on the actual regularizer the input parameter may vary, and 
+        a different default setting is defined.
+        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
+
+        out = reg(input=u0, regularization_parameter=10., number_of_iterations=30,
+          tolerance_constant=1e-4, 
+          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
+
+        out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10.,
+          number_of_iterations=30, tolerance_constant=1e-4, 
+          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
+        
+        A number of optional parameters can be passed or skipped
+        out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10. )
+
+    '''
+    class Algorithm(Enum):
+        SplitBregman_TV = cpu_regularizers.SplitBregman_TV
+        FGP_TV = cpu_regularizers.FGP_TV
+        LLT_model = cpu_regularizers.LLT_model
+        PatchBased_Regul = cpu_regularizers.PatchBased_Regul
+        TGV_PD = cpu_regularizers.TGV_PD
+    # Algorithm
+    
+    class TotalVariationPenalty(Enum):
+        isotropic = 0
+        l1 = 1
+    # TotalVariationPenalty
+        
+    def __init__(self , algorithm, debug = True):
+        self.setAlgorithm ( algorithm )
+        self.debug = debug
+    # __init__
+    
+    def setAlgorithm(self, algorithm):
+        self.algorithm = algorithm
+        self.pars = self.getDefaultParsForAlgorithm(algorithm)
+    # setAlgorithm
+        
+    def getDefaultParsForAlgorithm(self, algorithm):
+        pars = dict()
+        
+        if algorithm == Regularizer.Algorithm.SplitBregman_TV :
+            pars['algorithm'] = algorithm
+            pars['input'] = None
+            pars['regularization_parameter'] = None
+            pars['number_of_iterations'] = 35
+            pars['tolerance_constant'] = 0.0001
+            pars['TV_penalty'] = Regularizer.TotalVariationPenalty.isotropic
+            
+        elif algorithm == Regularizer.Algorithm.FGP_TV :
+            pars['algorithm'] = algorithm
+            pars['input'] = None
+            pars['regularization_parameter'] = None
+            pars['number_of_iterations'] = 50
+            pars['tolerance_constant'] = 0.001
+            pars['TV_penalty'] = Regularizer.TotalVariationPenalty.isotropic
+            
+        elif algorithm == Regularizer.Algorithm.LLT_model:
+            pars['algorithm'] = algorithm
+            pars['input'] = None
+            pars['regularization_parameter'] = None
+            pars['time_step'] = None
+            pars['number_of_iterations'] = None
+            pars['tolerance_constant'] = None
+            pars['restrictive_Z_smoothing'] = 0
+            
+        elif algorithm == Regularizer.Algorithm.PatchBased_Regul:
+            pars['algorithm'] = algorithm
+            pars['input'] = None
+            pars['searching_window_ratio'] = None
+            pars['similarity_window_ratio'] = None
+            pars['PB_filtering_parameter'] = None
+            pars['regularization_parameter'] = None
+            
+        elif algorithm == Regularizer.Algorithm.TGV_PD:
+            pars['algorithm'] = algorithm
+            pars['input'] = None
+            pars['first_order_term'] = None
+            pars['second_order_term'] = None
+            pars['number_of_iterations'] = None
+            pars['regularization_parameter'] = None
+            
+        else:
+            raise Exception('Unknown regularizer algorithm')
+
+        self.acceptedInputKeywords = pars.keys()
+            
+        return pars
+    # parsForAlgorithm
+    
+    def setParameter(self, **kwargs):
+        '''set named parameter for the regularization engine
+        
+        raises Exception if the named parameter is not recognized
+        Typical usage is:
+            
+        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
+        reg.setParameter(input=u0)    
+        reg.setParameter(regularization_parameter=10.)
+        
+        it can be also used as
+        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
+        reg.setParameter(input=u0 , regularization_parameter=10.)
+        '''
+        
+        for key , value in kwargs.items():
+            if key in self.pars.keys():
+                self.pars[key] = value
+            else:
+                raise Exception('Wrong parameter {0} for regularizer algorithm'.format(key))
+    # setParameter
+	
+    def getParameter(self, key):
+        if type(key) is str:
+            if key in self.acceptedInputKeywords:
+                return self.pars[key]
+            else:
+                raise Exception('Unrecongnised parameter: {0} '.format(key) )
+        elif type(key) is list:
+            outpars = []
+            for k in key:
+                outpars.append(self.getParameter(k))
+            return outpars
+        else:
+            raise Exception('Unhandled input {0}' .format(str(type(key))))
+        # getParameter
+	
+        
+    def __call__(self, input = None, regularization_parameter = None,
+                 output_all = False, **kwargs):
+        '''Actual call for the regularizer. 
+        
+        One can either set the regularization parameters first and then call the
+        algorithm or set the regularization parameter during the call (as 
+        is done in the static methods). 
+        '''
+        
+        if kwargs is not None:
+            for key, value in kwargs.items():
+                #print("{0} = {1}".format(key, value))                        
+                self.pars[key] = value
+                    
+        if input is not None: 
+            self.pars['input'] = input
+        if regularization_parameter is not None:
+            self.pars['regularization_parameter'] = regularization_parameter
+            
+        if self.debug:
+            print ("--------------------------------------------------")
+            for key, value in self.pars.items():
+                if key== 'algorithm' :
+                    print("{0} = {1}".format(key, value.__name__))
+                elif key == 'input':
+                    print("{0} = {1}".format(key, np.shape(value)))
+                else:
+                    print("{0} = {1}".format(key, value))
+        
+            
+        if None in self.pars:
+                raise Exception("Not all parameters have been provided")
+        
+        input = self.pars['input']
+        regularization_parameter = self.pars['regularization_parameter']
+        if self.algorithm == Regularizer.Algorithm.SplitBregman_TV :
+            ret = self.algorithm(input, regularization_parameter,
+                              self.pars['number_of_iterations'],
+                              self.pars['tolerance_constant'],
+                              self.pars['TV_penalty'].value )    
+        elif self.algorithm == Regularizer.Algorithm.FGP_TV :
+            ret = self.algorithm(input, regularization_parameter,
+                              self.pars['number_of_iterations'],
+                              self.pars['tolerance_constant'],
+                              self.pars['TV_penalty'].value )
+        elif self.algorithm == Regularizer.Algorithm.LLT_model :
+            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
+            # no default
+            ret = self.algorithm(input, 
+                              regularization_parameter,
+                              self.pars['time_step'] , 
+                              self.pars['number_of_iterations'],
+                              self.pars['tolerance_constant'],
+                              self.pars['restrictive_Z_smoothing'] )
+        elif self.algorithm == Regularizer.Algorithm.PatchBased_Regul :
+            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
+            # no default
+            ret = self.algorithm(input, regularization_parameter,
+                                  self.pars['searching_window_ratio'] , 
+                                  self.pars['similarity_window_ratio'] , 
+                                  self.pars['PB_filtering_parameter'])
+        elif self.algorithm == Regularizer.Algorithm.TGV_PD :
+            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
+            # no default
+            if len(np.shape(input)) == 2:
+                ret = self.algorithm(input, regularization_parameter,
+                                  self.pars['first_order_term'] , 
+                                  self.pars['second_order_term'] , 
+                                  self.pars['number_of_iterations'])
+            elif len(np.shape(input)) == 3:
+                #assuming it's 3D
+                # run independent calls on each slice
+                out3d = input.copy()
+                for i in range(np.shape(input)[0]):
+                    out = self.algorithm(input[i], regularization_parameter,
+                                 self.pars['first_order_term'] , 
+                                 self.pars['second_order_term'] , 
+                                 self.pars['number_of_iterations'])
+                    # copy the result in the 3D image
+                    out3d[i] = out[0].copy()
+                # append the rest of the info that the algorithm returns
+                output = [out3d]
+                for i in range(1,len(out)):
+                    output.append(out[i])
+                ret = output
+                
+                
+            
+        if output_all:
+            return ret
+        else:
+            return ret[0]
+        
+    # __call__
+    
+    @staticmethod
+    def SplitBregman_TV(input, regularization_parameter , **kwargs):
+        start_time = timeit.default_timer()
+        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
+        out = list( reg(input, regularization_parameter, **kwargs) )
+        out.append(reg.pars)
+        txt = reg.printParametersToString()
+        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+        out.append(txt)
+        return out
+        
+    @staticmethod
+    def FGP_TV(input, regularization_parameter , **kwargs):
+        start_time = timeit.default_timer()
+        reg = Regularizer(Regularizer.Algorithm.FGP_TV)
+        out = list( reg(input, regularization_parameter, **kwargs) )
+        out.append(reg.pars)
+        txt = reg.printParametersToString()
+        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+        out.append(txt)
+        return out
+    
+    @staticmethod
+    def LLT_model(input, regularization_parameter , time_step, number_of_iterations,
+                  tolerance_constant, restrictive_Z_smoothing=0):
+        start_time = timeit.default_timer()
+        reg = Regularizer(Regularizer.Algorithm.LLT_model)
+        out = list( reg(input, regularization_parameter, time_step=time_step, 
+                        number_of_iterations=number_of_iterations,
+                        tolerance_constant=tolerance_constant, 
+                        restrictive_Z_smoothing=restrictive_Z_smoothing) )
+        out.append(reg.pars)
+        txt = reg.printParametersToString()
+        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+        out.append(txt)
+        return out
+    
+    @staticmethod
+    def PatchBased_Regul(input, regularization_parameter,
+                        searching_window_ratio, 
+                        similarity_window_ratio,
+                        PB_filtering_parameter):
+        start_time = timeit.default_timer()
+        reg = Regularizer(Regularizer.Algorithm.PatchBased_Regul)   
+        out = list( reg(input, 
+                        regularization_parameter,
+                        searching_window_ratio=searching_window_ratio, 
+                        similarity_window_ratio=similarity_window_ratio,
+                        PB_filtering_parameter=PB_filtering_parameter )
+            )
+        out.append(reg.pars)
+        txt = reg.printParametersToString()
+        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+        out.append(txt)
+        return out
+    
+    @staticmethod
+    def TGV_PD(input, regularization_parameter , first_order_term, 
+               second_order_term, number_of_iterations):
+        start_time = timeit.default_timer()
+        
+        reg = Regularizer(Regularizer.Algorithm.TGV_PD)
+        out = list( reg(input, regularization_parameter, 
+                        first_order_term=first_order_term, 
+                        second_order_term=second_order_term,
+                        number_of_iterations=number_of_iterations) )
+        out.append(reg.pars)
+        txt = reg.printParametersToString()
+        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+        out.append(txt)
+        
+        return out
+    
+    def printParametersToString(self):
+        txt = r''
+        for key, value in self.pars.items():
+            if key== 'algorithm' :
+                txt += "{0} = {1}".format(key, value.__name__)
+            elif key == 'input':
+                txt += "{0} = {1}".format(key, np.shape(value))
+            else:
+                txt += "{0} = {1}".format(key, value)
+            txt += '\n'
+        return txt
+        
diff --git a/Wrappers/Python/ccpi/filters/__init__.py b/Wrappers/Python/ccpi/filters/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/Wrappers/Python/ccpi/filters/__init__.py