"""!

@brief Cluster analysis algorithm: X-Means
@details Based on article description:
		 - D.Pelleg, A.Moore. X-means: Extending K-means with Efficient Estimation of the Number of Clusters. 2000.

@authors Andrei Novikov (pyclustering@yandex.ru)
@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 numpy
import random

from enum import IntEnum
from math import log

from numba import jit
from numba import int32, float32

from modules.clustering.pyc_encoder import type_encoding
from modules.clustering.pyc_utils import euclidean_distance_sqrt, euclidean_distance
from modules.clustering.pyc_utils import list_math_addition_number, list_math_addition, list_math_division_number

@jit(nopython = True)
def minimum_noiseless_description_length(clusters, centers, pointer_data):
	"""!
	@brief Calculates splitting criterion for input clusters using minimum noiseless description length criterion.
		
	@param[in] clusters (list): Clusters for which splitting criterion should be calculated.
	@param[in] centers (list): Centers of the clusters.
		
	@return (double) Returns splitting criterion in line with bayesian information criterion. 
			Low value of splitting cretion means that current structure is much better.
		
	@see __bayesian_information_criterion(clusters, centers)
		
	"""
		
	scores = float('inf')
		
	W = 0.0
	K = len(clusters)
	N = 0.0

	sigma_sqrt = 0.0
		
	alpha = 0.9
	betta = 0.9
		
	for index_cluster in range(0, len(clusters), 1):
		Ni = len(clusters[index_cluster])
		if (Ni == 0): 
			return float('inf')
			
		Wi = 0.0
		for index_object in clusters[index_cluster]:
			# euclidean_distance_sqrt should be used in line with paper, but in this case results are
			# very poor, therefore square root is used to improved.
			Wi += euclidean_distance(pointer_data[index_object], centers[index_cluster])
			
		sigma_sqrt += Wi
		W += Wi / Ni
		N += Ni
		
	if (N - K > 0):
		sigma_sqrt /= (N - K)
		sigma = sigma_sqrt ** 0.5
			
		Kw = (1.0 - K / N) * sigma_sqrt
		Ks = ( 2.0 * alpha * sigma / (N ** 0.5) ) * ( (alpha ** 2.0) * sigma_sqrt / N + W - Kw / 2.0 ) ** 0.5
			
		scores = sigma_sqrt * (2 * K)**0.5 * ((2 * K)**0.5 + betta) / N + W - sigma_sqrt + Ks + 2 * alpha**0.5 * sigma_sqrt / N
		
	return scores

@jit(nopython = False)
def bayesian_information_criterion(clusters, centers, pointer_data):
	"""!
	@brief Calculates splitting criterion for input clusters using bayesian information criterion.
		
	@param[in] clusters (list): Clusters for which splitting criterion should be calculated.
	@param[in] centers (list): Centers of the clusters.
		
	@return (double) Splitting criterion in line with bayesian information criterion.
			High value of splitting criterion means that current structure is much better.
				
	@see __minimum_noiseless_description_length(clusters, centers)
		
	"""
	
	scores = numpy.full(len(clusters), fill_value = 9999999999999999999999.9, dtype = numpy.float32)

	dimension = len(pointer_data[0])
		  
	# estimation of the noise variance in the data set
	sigma_sqrt = 0.0
	K = len(clusters)
	N = 0.0
		  
	for index_cluster in range(0, len(clusters), 1):
		for index_object in clusters[index_cluster]:
			sigma_sqrt += euclidean_distance_sqrt(pointer_data[index_object], centers[index_cluster])

		N += len(clusters[index_cluster])
	  
	if (N - K > 0):
		sigma_sqrt /= (N - K)
		p = (K - 1) + dimension * K + 1
			
		# splitting criterion	
		for index_cluster in range(0, len(clusters), 1):
			n = len(clusters[index_cluster])
				
			L = n * log(n) - n * log(N) - n * 0.5 * log(2.0 * numpy.pi) - n * dimension * 0.5 * log(sigma_sqrt) - (n - K) * 0.5
				
			# BIC calculation
			scores[index_cluster] = L - p * 0.5 * log(N)

	if len(scores) == 1:
		return_item = scores[0]
		
	else:
		return_item = numpy.sum(scores)
	
	return return_item


class splitting_type(IntEnum):
	"""!
	@brief Enumeration of splitting types that can be used as splitting creation of cluster in X-Means algorithm.
	
	"""
	
	## Bayesian information criterion (BIC) to approximate the correct number of clusters.
	## Kass's formula is used to calculate BIC:
	## \f[BIC(\theta) = L(D) - \frac{1}{2}pln(N)\f]
	##
	## The number of free parameters \f$p\f$ is simply the sum of \f$K - 1\f$ class probabilities, \f$MK\f$ centroid coordinates, and one variance estimate:
	## \f[p = (K - 1) + MK + 1\f]
	##
	## The log-likelihood of the data:
	## \f[L(D) = n_jln(n_j) - n_jln(N) - \frac{n_j}{2}ln(2\pi) - \frac{n_jd}{2}ln(\hat{\sigma}^2) - \frac{n_j - K}{2}\f]
	##
	## The maximum likelihood estimate (MLE) for the variance:
	## \f[\hat{\sigma}^2 = \frac{1}{N - K}\sum\limits_{j}\sum\limits_{i}||x_{ij} - \hat{C}_j||^2\f]
	BAYESIAN_INFORMATION_CRITERION = 0
	
	## Minimum noiseless description length (MNDL) to approximate the correct number of clusters.
	## Beheshti's formula is used to calculate upper bound:
	## \f[Z = \frac{\sigma^2 \sqrt{2K} }{N}(\sqrt{2K} + \beta) + W - \sigma^2 + \frac{2\alpha\sigma}{\sqrt{N}}\sqrt{\frac{\alpha^2\sigma^2}{N} + W - \left(1 - \frac{K}{N}\right)\frac{\sigma^2}{2}} + \frac{2\alpha^2\sigma^2}{N}\f]
	##
	## where \f$\alpha\f$ and \f$\beta\f$ represent the parameters for validation probability and confidence probability.
	##
	## To improve clustering results some contradiction is introduced:
	## \f[W = \frac{1}{n_j}\sum\limits_{i}||x_{ij} - \hat{C}_j||\f]
	## \f[\hat{\sigma}^2 = \frac{1}{N - K}\sum\limits_{j}\sum\limits_{i}||x_{ij} - \hat{C}_j||\f]
	MINIMUM_NOISELESS_DESCRIPTION_LENGTH = 1


class xmeans:
	"""!
	@brief Class represents clustering algorithm X-Means.
	@details X-means clustering method starts with the assumption of having a minimum number of clusters, 
			 and then dynamically increases them. X-means uses specified splitting criterion to control 
			 the process of splitting clusters. Method K-Means++ can be used for calculation of initial centers.
			 
	
	Example:
	@code
		# sample for cluster analysis (represented by list)
		sample = read_sample(path_to_sample)
		
		# create object of X-Means algorithm that uses CCORE for processing
		# initial centers - optional parameter, if it is None, then random centers will be used by the algorithm.
		# let's avoid random initial centers and initialize them using K-Means++ method:
		initial_centers = kmeans_plusplus_initializer(sample, 2).initialize()
		xmeans_instance = xmeans(sample, initial_centers, ccore = True)
		
		# run cluster analysis
		xmeans_instance.process()
		
		# obtain results of clustering
		clusters = xmeans_instance.get_clusters()
		
		# display allocated clusters
		draw_clusters(sample, clusters)
	@endcode
	
	@see center_initializer
	
	"""
	
	def __init__(self, data, initial_centers = None, kmax = 20, tolerance = 0.025, criterion = splitting_type.BAYESIAN_INFORMATION_CRITERION, ccore = False):
		"""!
		@brief Constructor of clustering algorithm X-Means.
		
		@param[in] data (list): Input data that is presented as list of points (objects), each point should be represented by list or tuple.
		@param[in] initial_centers (list): Initial coordinates of centers of clusters that are represented by list: [center1, center2, ...], 
					if it is not specified then X-Means starts from the random center.
		@param[in] kmax (uint): Maximum number of clusters that can be allocated.
		@param[in] tolerance (double): Stop condition for each iteration: if maximum value of change of centers of clusters is less than tolerance than algorithm will stop processing.
		@param[in] criterion (splitting_type): Type of splitting creation.
		@param[in] ccore (bool): Defines should be CCORE (C++ pyclustering library) used instead of Python code or not.
		
		"""
		
		self.__pointer_data = data
		self.__clusters = []
		
		if (initial_centers is not None):
			self.__centers = initial_centers[:]
		else:
			self.__centers = [ [random.random() for _ in range(len(data[0])) ] ]
		
		self.__kmax = kmax
		self.__tolerance = tolerance
		self.__criterion = criterion
		 
		self.__ccore = ccore

	def process(self):
		"""!
		@brief Performs cluster analysis in line with rules of X-Means algorithm.
		
		@remark Results of clustering can be obtained using corresponding gets methods.
		
		@see get_clusters()
		@see get_centers()
		
		"""
		
		self.__clusters = []
		while ( len(self.__centers) <= self.__kmax ):
			current_cluster_number = len(self.__centers)
				
			self.__clusters, self.__centers = self.__improve_parameters(self.__centers)
			allocated_centers = self.__improve_structure(self.__clusters, self.__centers)
				
			if (current_cluster_number == len(allocated_centers)):
			#if ( (current_cluster_number == len(allocated_centers)) or (len(allocated_centers) > self.__kmax) ):
				break
			else:
				 self.__centers = allocated_centers
			
		self.__clusters, self.__centers = self.__improve_parameters(self.__centers)


	def get_clusters(self):
		"""!
		@brief Returns list of allocated clusters, each cluster contains indexes of objects in list of data.
		
		@return (list) List of allocated clusters.
		
		@see process()
		@see get_centers()
		
		"""

		return self.__clusters


	def get_centers(self):
		"""!
		@brief Returns list of centers for allocated clusters.
		
		@return (list) List of centers for allocated clusters.
		
		@see process()
		@see get_clusters()
		
		"""
		 
		return self.__centers


	def get_cluster_encoding(self):
		"""!
		@brief Returns clustering result representation type that indicate how clusters are encoded.
		
		@return (type_encoding) Clustering result representation.
		
		@see get_clusters()
		
		"""
		
		return type_encoding.CLUSTER_INDEX_LIST_SEPARATION

	def __improve_parameters(self, centers, available_indexes = None):
		"""!
		@brief Performs k-means clustering in the specified region.
		
		@param[in] centers (list): Centers of clusters.
		@param[in] available_indexes (list): Indexes that defines which points can be used for k-means clustering, if None - then all points are used.
		
		@return (list) List of allocated clusters, each cluster contains indexes of objects in list of data.
		
		"""

		changes = numpy.Inf

		stop_condition = self.__tolerance * self.__tolerance # Fast solution

		clusters = []

		while (changes > stop_condition):
			clusters = self.__update_clusters(centers, available_indexes)
			clusters = [ cluster for cluster in clusters if len(cluster) > 0 ] 
			
			updated_centers = self.__update_centers(clusters)
		  
			changes = max([euclidean_distance_sqrt(centers[index], updated_centers[index]) for index in range(len(updated_centers))])	# Fast solution
			  
			centers = updated_centers
		
		return (clusters, centers)
	 
	def __improve_structure(self, clusters, centers):
		"""!
		@brief Check for best structure: divides each cluster into two and checks for best results using splitting criterion.
		
		@param[in] clusters (list): Clusters that have been allocated (each cluster contains indexes of points from data).
		@param[in] centers (list): Centers of clusters.
		
		@return (list) Allocated centers for clustering.
		
		"""
		 
		difference = 0.001
		  
		allocated_centers = []
		amount_free_centers = self.__kmax - len(centers)

		for index_cluster in range(len(clusters)):
			# split cluster into two child clusters
			parent_child_centers = []
			parent_child_centers.append(list_math_addition_number(centers[index_cluster], -difference))
			parent_child_centers.append(list_math_addition_number(centers[index_cluster], difference))
		  
			# solve k-means problem for children where data of parent are used.
			(parent_child_clusters, parent_child_centers) = self.__improve_parameters(parent_child_centers, clusters[index_cluster])
			  
			# If it's possible to split current data
			if (len(parent_child_clusters) > 1):
				# Calculate splitting criterion
				parent_scores = self.__splitting_criterion([ clusters[index_cluster] ], [ centers[index_cluster] ])
				child_scores = self.__splitting_criterion([ parent_child_clusters[0], parent_child_clusters[1] ], parent_child_centers)
			  
				split_require = False
				
				# Reallocate number of centers (clusters) in line with scores
				if (self.__criterion == splitting_type.BAYESIAN_INFORMATION_CRITERION):
					if (parent_scores < child_scores): split_require = True
					
				elif (self.__criterion == splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH):
					# If its score for the split structure with two children is smaller than that for the parent structure, 
					# then representing the data samples with two clusters is more accurate in comparison to a single parent cluster.
					if (parent_scores > child_scores): split_require = True
				
				if ( (split_require is True) and (amount_free_centers > 0) ):
					allocated_centers.append(parent_child_centers[0])
					allocated_centers.append(parent_child_centers[1])
					
					amount_free_centers -= 1
				else:
					allocated_centers.append(centers[index_cluster])

					
			else:
				allocated_centers.append(centers[index_cluster])
		  
		return allocated_centers
	 
	 
	def __splitting_criterion(self, clusters, centers):
		"""!
		@brief Calculates splitting criterion for input clusters.
		
		@param[in] clusters (list): Clusters for which splitting criterion should be calculated.
		@param[in] centers (list): Centers of the clusters.
		
		@return (double) Returns splitting criterion. High value of splitting cretion means that current structure is much better.
		
		@see __bayesian_information_criterion(clusters, centers)
		@see __minimum_noiseless_description_length(clusters, centers)
		
		"""
		
		if (self.__criterion == splitting_type.BAYESIAN_INFORMATION_CRITERION):
			return bayesian_information_criterion(clusters = clusters, centers = centers, pointer_data = self.__pointer_data)
		
		elif (self.__criterion == splitting_type.MINIMUM_NOISELESS_DESCRIPTION_LENGTH):
			return minimum_noiseless_description_length(clusters = clusters, centers = centers, pointer_data = self.__pointer_data)
		
		else:
			assert 0

	def __update_clusters(self, centers, available_indexes = None):
		"""!
		@brief Calculates Euclidean distance to each point from the each cluster.
			   Nearest points are captured by according clusters and as a result clusters are updated.
			   
		@param[in] centers (list): Coordinates of centers of clusters that are represented by list: [center1, center2, ...].
		@param[in] available_indexes (list): Indexes that defines which points can be used from imput data, if None - then all points are used.
		
		@return (list) Updated clusters.
		
		"""
			
		bypass = None
		if (available_indexes is None):
			bypass = range(len(self.__pointer_data))
		else:
			bypass = available_indexes
		  
		clusters = [[] for _ in range(len(centers))]
		for index_point in bypass:
			index_optim = -1
			dist_optim = 0.0
			  
			for index in range(len(centers)):
				# dist = euclidean_distance(data[index_point], centers[index])		 # Slow solution
				dist = euclidean_distance_sqrt(self.__pointer_data[index_point], centers[index])	  # Fast solution
				  
				if ( (dist < dist_optim) or (index is 0)):
					index_optim = index
					dist_optim = dist
			  
			clusters[index_optim].append(index_point)
			  
		return clusters
			 
	def __update_centers(self, clusters):
		"""!
		@brief Updates centers of clusters in line with contained objects.
		
		@param[in] clusters (list): Clusters that contain indexes of objects from data.
		
		@return (list) Updated centers.
		
		"""
		 
		centers = [[] for _ in range(len(clusters))]
		dimension = len(self.__pointer_data[0])
		  
		for index in range(len(clusters)):
			point_sum = [0.0] * dimension
			  
			for index_point in clusters[index]:
				point_sum = list_math_addition(point_sum, self.__pointer_data[index_point])
			
			centers[index] = list_math_division_number(point_sum, len(clusters[index]))
			  
		return centers