pcnn_network.__init__() - Code Metrics - Inspection of "#289: [ccore] pyclustering interface unification." - annoviko/pyclustering - Measure and Improve Code Quality continuously with Scrutinizer

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created 2017-08-08 08:19 UTC
pcnn_network.init() C

↳ Parent: pcnn_network
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How to fix Long Method

"""!

@brief Neural Network: Pulse Coupled Neural Network
@details Based on book description:
         - T.Lindblad, J.M.Kinser. Image Processing Using Pulse-Coupled Neural Networks (2nd edition). 2005.

@authors Andrei Novikov ([email protected])
@date 2014-2017
@copyright GNU Public License

@cond GNU_PUBLIC_LICENSE
    PyClustering is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
    
    PyClustering is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
    
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
@endcond

"""

import matplotlib.pyplot as plt;
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
import matplotlib.animation as animation;
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

import random;
import numpy;
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from PIL import Image;
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from pyclustering.nnet import *;

import pyclustering.core.pcnn_wrapper as wrapper;

from pyclustering.utils import draw_dynamics;


class pcnn_parameters:
    """!
    @brief Parameters for pulse coupled neural network.
    
    """
    
    def __init__(self):
        """!
        @brief    Default constructor of parameters for pulse-coupled neural network.
        @details  Constructor initializes parameters by default non-zero values that can be
                  used for simple simulation.
        """
        
        ## Multiplier for the feeding compartment at the current step.
        self.VF = 1.0;
        
        ## Multiplier for the linking compartment at the current step.  
        self.VL = 1.0;
        
        ## Multiplier for the threshold at the current step.    
        self.VT = 10.0;
        
        
        ## Multiplier for the feeding compartment at the previous step.    
        self.AF = 0.1;
        
        ## Multiplier for the linking compartment at the previous step.
        self.AL = 0.1;
        
        ## Multiplier for the threshold at the previous step.
        self.AT = 0.5;
        
        
        ## Synaptic weight - neighbours influence on linking compartment
        self.W = 1.0;
        
        ## Synaptic weight - neighbours influence on feeding compartment.
        self.M = 1.0;
        
        
        ## Linking strength in the network.
        self.B = 0.1;
        
        ## Enable/disable Fast-Linking mode. Fast linking helps to overcome some of the effects of time quantisation. This process allows the linking wave to progress a lot faster than the feeding wave.
        self.FAST_LINKING = False;
    
    
class pcnn_dynamic:
    """!
    @brief Represents output dynamic of PCNN (pulse-coupled neural network).
    
    """

    @property
    def output(self):
        """!
        @brief (list) Returns oscillato outputs during simulation.
        
        """
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            return wrapper.pcnn_dynamic_get_output(self.__ccore_pcnn_dynamic_pointer);
            
        return self.__dynamic;
    
    
    @property
    def time(self):
        """!
        @brief (list) Returns sampling times when dynamic is measured during simulation.
        
        """
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            return wrapper.pcnn_dynamic_get_time(self.__ccore_pcnn_dynamic_pointer);
        
        return list(range(len(self)));
    
    
    def __init__(self, dynamic, ccore = None):
        """!
        @brief Constructor of PCNN dynamic.
        
        @param[in] dynamic (list): Dynamic of oscillators on each step of simulation. If ccore pointer is specified than it can be ignored.
        @param[in] ccore (ctypes.pointer): Pointer to CCORE pcnn_dynamic instance in memory.
        
        """
        self.__OUTPUT_TRUE = 1;    # fire value for oscillators.
        self.__OUTPUT_FALSE = 0;   # rest value for oscillators.
        
        self.__dynamic = dynamic;
        self.__ccore_pcnn_dynamic_pointer = ccore;
    
    
    def __del__(self):
        """!
        @brief Default destructor of PCNN dynamic.
        
        """
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            wrapper.pcnn_dynamic_destroy(self.__ccore_pcnn_dynamic_pointer);
    
    
    def __len__(self):
        """!
        @brief (uint) Returns number of simulation steps that are stored in dynamic.
        
        """
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            return wrapper.pcnn_dynamic_get_size(self.__ccore_pcnn_dynamic_pointer);

        
        return len(self.__dynamic);
    
    
    def allocate_sync_ensembles(self):
        """!
        @brief Allocate clusters in line with ensembles of synchronous oscillators where each
               synchronous ensemble corresponds to only one cluster.
        
        @return (list) Grours (lists) of indexes of synchronous oscillators. 
                For example, [ [index_osc1, index_osc3], [index_osc2], [index_osc4, index_osc5] ].
                
        """
        
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            return wrapper.pcnn_dynamic_allocate_sync_ensembles(self.__ccore_pcnn_dynamic_pointer);
        
        sync_ensembles = [];
        traverse_oscillators = set();
        
        number_oscillators = len(self.__dynamic[0]);
        
        for t in range(len(self.__dynamic) - 1, 0, -1):
            sync_ensemble = [];
            for i in range(number_oscillators):
                if (self.__dynamic[t][i] == self.__OUTPUT_TRUE):
                    if (i not in traverse_oscillators):
                        sync_ensemble.append(i);
                        traverse_oscillators.add(i);
            
            if (sync_ensemble != []):
                sync_ensembles.append(sync_ensemble);

        
        return sync_ensembles;


    def allocate_spike_ensembles(self):
        """!
        @brief Analyses output dynamic of network and allocates spikes on each iteration as a list of indexes of oscillators.
        @details Each allocated spike ensemble represents list of indexes of oscillators whose output is active.
        
        @return (list) Spike ensembles of oscillators.
        
        """
        
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            return wrapper.pcnn_dynamic_allocate_spike_ensembles(self.__ccore_pcnn_dynamic_pointer);
        
        spike_ensembles = [];
        number_oscillators = len(self.__dynamic[0]);
        
        for t in range(len(self.__dynamic)):
            spike_ensemble = [];
            
            for index in range(number_oscillators):
                if (self.__dynamic[t][index] == self.__OUTPUT_TRUE):
                    spike_ensemble.append(index);
            
            if (len(spike_ensemble) > 0):
                spike_ensembles.append(spike_ensemble);
        
        return spike_ensembles;
    
    
    def allocate_time_signal(self):
        """!
        @brief Analyses output dynamic and calculates time signal (signal vector information) of network output.
           
        @return (list) Time signal of network output.
        
        """
        
        if (self.__ccore_pcnn_dynamic_pointer is not None):
            return wrapper.pcnn_dynamic_allocate_time_signal(self.__ccore_pcnn_dynamic_pointer);
        
        signal_vector_information = [];
        for t in range(0, len(self.__dynamic)):
            signal_vector_information.append(sum(self.__dynamic[t]));
        
        return signal_vector_information;


class pcnn_visualizer:
    """!
    @brief Visualizer of output dynamic of pulse-coupled neural network (PCNN).
    
    """
    
    @staticmethod
    def show_time_signal(pcnn_output_dynamic):
        """!
        @brief Shows time signal (signal vector information) using network dynamic during simulation.
        
        @param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network.
        
        """
        
        time_signal = pcnn_output_dynamic.allocate_time_signal();
        time_axis = range(len(time_signal));
        
        plt.subplot(1, 1, 1);
        plt.plot(time_axis, time_signal, '-');
        plt.ylabel("G (time signal)");
        plt.xlabel("t (iteration)");
        plt.grid(True);
        
        plt.show();
        
    @staticmethod
    def show_output_dynamic(pcnn_output_dynamic, separate_representation = False):
        """!
        @brief Shows output dynamic (output of each oscillator) during simulation.
        
        @param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network.
        @param[in] separate_representation (list): Consists of lists of oscillators where each such list consists of oscillator indexes that will be shown on separated stage.
        
        """
        
        draw_dynamics(pcnn_output_dynamic.time, pcnn_output_dynamic.output, x_title = "t", y_title = "y(t)", separate = separate_representation);
    
    @staticmethod
    def animate_spike_ensembles(pcnn_output_dynamic, image_size):
        """!
        @brief Shows animation of output dynamic (output of each oscillator) during simulation.
        
        @param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network.
        @param[in] image_size (list): Image size represented as [height, width].
        
        """
        
        figure = plt.figure();
        
        time_signal = pcnn_output_dynamic.allocate_time_signal();
        spike_ensembles = pcnn_output_dynamic.allocate_spike_ensembles();
        
        spike_animation = [];
        ensemble_index = 0;
        for t in range(len(time_signal)):
            image_color_segments = [(255, 255, 255)] * (image_size[0] * image_size[1]);
            
            if (time_signal[t] > 0):
                for index_pixel in spike_ensembles[ensemble_index]:
                    image_color_segments[index_pixel] = (0, 0, 0);
                
                ensemble_index += 1;
                
            stage = numpy.array(image_color_segments, numpy.uint8);
            stage = numpy.reshape(stage, image_size + ((3),)); # ((3),) it's size of RGB - third dimension.
            image_cluster = Image.fromarray(stage, 'RGB');
            
            spike_animation.append( [ plt.imshow(image_cluster, interpolation = 'none') ] );
            
        
        im_ani = animation.ArtistAnimation(figure, spike_animation, interval = 75, repeat_delay = 3000, blit = True)

        plt.show();


class pcnn_network(network):
    """!
    @brief Model of oscillatory network that is based on the Eckhorn model.
    
    Example:
    @code
        # Create pulse-coupled neural network:
        # - 9 oscillators.
        # - default parameters.
        # - grid type of connections (each oscillator has connection with four neighbors).
        net = pcnn_network(9, None, conn_type.GRID_FOUR, ccore = ccore_flag);
        
        # Create external stimulus. Number of stimulus should be equal to number of neurons.
        stimulus = [1, 1, 1, 0, 0, 0, 1, 1, 1];
        
        # Simulate dynamic of the network during 40 iterations
        dynamic = net.simulate(40, stimulus);
        
        # Allocate synchronous oscillators
        ensembles = dynamic.allocate_sync_ensembles();
        print(ensembles);
        
        # Show output dynamic of the network
        pcnn_visualizer.show_output_dynamic(dynamic);
        
        # Show time signal vector information
        pcnn_visualizer.show_time_signal(dynamic);
    @endcode
    
    """
    
    __OUTPUT_TRUE = 1;    # fire value for oscillators.
    __OUTPUT_FALSE = 0;   # rest value for oscillators.
    
    def __init__(self, num_osc, parameters = None, type_conn = conn_type.ALL_TO_ALL, type_conn_represent = conn_represent.MATRIX, height = None, width = None, ccore = False):
        """!
        @brief Constructor of oscillatory network is based on Kuramoto model.
        
        @param[in] num_osc (uint): Number of oscillators in the network.
        @param[in] parameters (pcnn_parameters): Parameters of the network.
        @param[in] type_conn (conn_type): Type of connection between oscillators in the network (all-to-all, grid, bidirectional list, etc.).
        @param[in] type_conn_represent (conn_represent): Internal representation of connection in the network: matrix or list.
        @param[in] height (uint): Number of oscillators in column of the network, this argument is used 
                    only for network with grid structure (GRID_FOUR, GRID_EIGHT), for other types this argument is ignored.
        @param[in] width (uint): Number of oscillotors in row of the network, this argument is used only 
                    for network with grid structure (GRID_FOUR, GRID_EIGHT), for other types this argument is ignored.
        @param[in] ccore (bool): If True then all interaction with object will be performed via CCORE library (C++ implementation of pyclustering).
        
        """
        
        self._outputs = None;            # list of outputs of oscillors.
    
        self._feeding = None;            # feeding compartment of each oscillator.    
        self._linking = None;            # linking compartment of each oscillator. 
        self._threshold = None;          # threshold of each oscillator.
        
        self._params = None;
        
        self.__ccore_pcnn_pointer = None;
        
        # set parameters of the network
        if (parameters is not None):
            self._params = parameters;
        else:
            self._params = pcnn_parameters();
        
        if (ccore is True):
            network_height = height;
            network_width = width;
            
            if ( (type_conn == conn_type.GRID_FOUR) or (type_conn == conn_type.GRID_EIGHT) ):
                if ( (network_height is None) or (network_width is None) ):
                    side_size = num_osc ** (0.5);
                    if (side_size - math.floor(side_size) > 0):
                        raise NameError('Invalid number of oscillators in the network in case of grid structure');
                
                    network_height = int(side_size);
                    network_width = int(side_size);
            else:
                network_height = 0;
                network_width = 0;
                
            self.__ccore_pcnn_pointer = wrapper.pcnn_create(num_osc, type_conn, network_height, network_width, self._params);
        else:
            super().__init__(num_osc, type_conn, type_conn_represent, height, width);
            
            self._outputs = [0.0] * self._num_osc;
            
            self._feeding = [0.0] * self._num_osc;
            self._linking = [0.0] * self._num_osc;
            self._threshold = [ random.random() for i in range(self._num_osc) ];
    
    
    def __del__(self):
        """!
        @brief Default destructor of PCNN.
        
        """
        if (self.__ccore_pcnn_pointer is not None):
            wrapper.pcnn_destroy(self.__ccore_pcnn_pointer);
            self.__ccore_pcnn_pointer = None;
    
    
    def __len__(self):
        """!
        @brief (uint) Returns size of oscillatory network.
        
        """
        
        if (self.__ccore_pcnn_pointer is not None):
            return wrapper.pcnn_get_size(self.__ccore_pcnn_pointer);
        
        return self._num_osc;
    
        
    def simulate(self, steps, stimulus):
        """!
        @brief Performs static simulation of pulse coupled neural network using.
        
        @param[in] steps (uint): Number steps of simulations during simulation.
        @param[in] stimulus (list): Stimulus for oscillators, number of stimulus should be equal to number of oscillators.
        
        @return (pcnn_dynamic) Dynamic of oscillatory network - output of each oscillator on each step of simulation.
        
        """
        
        if (len(stimulus) != len(self)):
            raise NameError('Number of stimulus should be equal to number of oscillators. Each stimulus corresponds to only one oscillators.');
        
        if (self.__ccore_pcnn_pointer is not None):
            ccore_instance_dynamic = wrapper.pcnn_simulate(self.__ccore_pcnn_pointer, steps, stimulus);
            return pcnn_dynamic(None, ccore_instance_dynamic);
        
        dynamic = [];
        dynamic.append(self._outputs);
        
        for step in range(1, steps, 1):

            self._outputs = self._calculate_states(stimulus);
            
            dynamic.append(self._outputs);
        
        return pcnn_dynamic(dynamic);
    
    
    def _calculate_states(self, stimulus):
        """!
        @brief Calculates states of oscillators in the network for current step and stored them except outputs of oscillators.
        
        @param[in] stimulus (list): Stimulus for oscillators, number of stimulus should be equal to number of oscillators.
        
        @return (list) New outputs for oscillators (do not stored it).
        
        """
        
        feeding = [0.0] * self._num_osc;
        linking = [0.0] * self._num_osc;
        outputs = [0.0] * self._num_osc;
        threshold = [0.0] * self._num_osc;
        
        # Used by Fast-Linking
        output_change = False;
        
        for index in range(0, self._num_osc, 1):
            neighbors = self.get_neighbors(index);
            
            feeding_influence = 0.0;
            linking_influence = 0.0;
            
            for index_neighbour in neighbors:
                feeding_influence += self._outputs[index_neighbour] * self._params.M;
                linking_influence += self._outputs[index_neighbour] * self._params.W;
            
            feeding_influence *= self._params.VF;
            linking_influence *= self._params.VL;
            
            feeding[index] = self._params.AF * self._feeding[index] + stimulus[index] + feeding_influence;
            linking[index] = self._params.AL * self._linking[index] + linking_influence;
            
            # calculate internal activity
            internal_activity = feeding[index] * (1.0 + self._params.B * linking[index]);
            
            # calculate output of the oscillator
            if (internal_activity > self._threshold[index]):
                outputs[index] = self.__OUTPUT_TRUE;
            else:
                outputs[index] = self.__OUTPUT_FALSE;
            
            # In case of Fast Linking we should calculate threshould until output is changed.
            if (self._params.FAST_LINKING is not True):
                threshold[index] = self._params.AT * self._threshold[index] + self._params.VT * outputs[index];
        
        
        # In case of Fast Linking we need to wait until output is changed.
        if (self._params.FAST_LINKING is True):
            current_output_change = False;
            previous_outputs = outputs[:];
            
            while (output_change is True):               
                for index in range(0, self._num_osc, 1):
                    linking_influence = 0.0;
            
                    for index_neighbour in neighbors:
                        linking_influence += previous_outputs[index_neighbour] * self._params.W;
                    
                    linking_influence *= self._params.VL;
                    linking[index] = linking_influence;
                    
                    internal_activity = feeding[index] * (1.0 + self._params.B * linking[index]);
                    
                    # calculate output of the oscillator
                    if (internal_activity > self._threshold[index]):
                        outputs[index] = self.__OUTPUT_TRUE;
                    else:
                        outputs[index] = self.__OUTPUT_FALSE;
                        
                    if (outputs[index] != previous_outputs[index]):
                        current_output_change = True;
                
                output_change = current_output_change;
                current_output_change = False;
                
                if (output_change is True):
                    previous_outputs = outputs[:];
        
        # In case of Fast Linking threshould should be calculated after fast linking.
        if (self._params.FAST_LINKING is True):
            for index in range(0, self._num_osc, 1):
                threshold[index] = self._params.AT * self._threshold[index] + self._params.VT * outputs[index];
        
        self._feeding = feeding[:];
        self._linking = linking[:];
        self._threshold = threshold[:];
        
        return outputs

        

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pcnn_network.init() C

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How to fix Long Method

Long Method

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2. Missing init.py files

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2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

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2. Missing init.py files

annoviko / pyclustering

Push — master ( 27be37...a60125 )

pcnn_network.__init__() C

Complexity

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Importance

How to fix Long Method

Long Method

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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pcnn_network.init() C

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