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'''
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Wrapper for CCORE library (part of this project).
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Copyright (C) 2015 Andrei Novikov ([email protected])
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pyclustering is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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pyclustering is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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'''
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from ctypes import *;
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from pyclustering.core.definitions import *;
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# API that is required for interaction with DLL.
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def create_pointer_data(sample):
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"Allocates memory for representing input data for processing that is described by structure 'data_representation' and returns pointer this structure."
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"(in) sample - dataset for processing."
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"Returns pointer to the data for processing."
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input_data = data_representation();
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input_data.number_objects = len(sample);
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input_data.dimension = len(sample[0]);
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pointer_objects = (POINTER(c_double) * input_data.number_objects)();
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for index in range(0, input_data.number_objects):
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point = (c_double * input_data.dimension)();
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for dimension in range(0, input_data.dimension):
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point[dimension] = sample[index][dimension];
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pointer_objects[index] = cast(point, POINTER(c_double));
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input_data.pointer_objects = cast(pointer_objects, POINTER(POINTER(c_double)));
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input_data = pointer(input_data);
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return input_data;
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def extract_clusters(ccore_result):
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"Parse clustering result that is provided by the CCORE. Return Python list of clusters."
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"(in) ccore_result - pointer to clustering result that has been returned by CCORE."
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"Returns Python list of clusters."
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pointer_clustering_result = cast(ccore_result, POINTER(clustering_result)); # clustering_result * clusters
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number_clusters = pointer_clustering_result[0].number_clusters;
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list_of_clusters = [];
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for index_cluster in range(0, number_clusters):
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clusters = cast(pointer_clustering_result[0].pointer_clusters, POINTER(cluster_representation)); # cluster_representation * cluster
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objects = cast(clusters[index_cluster].pointer_objects, POINTER(c_uint)); # cluster->objects (unsigned int *)
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list_of_clusters.append([]);
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pointer_container = list_of_clusters[index_cluster];
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for index_object in range(0, clusters[index_cluster].number_objects):
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pointer_container.append(objects[index_object]);
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return list_of_clusters;
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def extract_dynamics(ccore_result):
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"Parse dynamic result that is provided by the CCORE. Return Python tuple that represent dynamics (times, dynamic)."
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"(in) ccore_result - pointer to dynamic result that has been returned by CCORE."
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"Returns Python tuple dynamic (times, dynamic)."
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pointer_dynamic_result = cast(ccore_result, POINTER(dynamic_result)); # dynamic_result * pointer_dynamic_result
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size_dynamic = pointer_dynamic_result[0].size_dynamic;
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size_network = pointer_dynamic_result[0].size_network;
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pointer_time = cast(pointer_dynamic_result[0].times, POINTER(c_double));
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pointer_pointer_dynamic = cast(pointer_dynamic_result[0].dynamic, POINTER(POINTER(c_double)));
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times = [];
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dynamic = [];
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for index in range(0, size_dynamic):
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times.append(pointer_time[index]);
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dynamic.append([]);
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pointer_dynamic = cast(pointer_pointer_dynamic[index], POINTER(c_double));
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for object_dynamic in range(0, size_network):
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dynamic[index].append(pointer_dynamic[object_dynamic]);
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return (times, dynamic);
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def extract_pyclustering_package(ccore_package_pointer):
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if (ccore_package_pointer == 0):
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return [];
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pointer_package = cast(ccore_package_pointer, POINTER(pyclustering_package));
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size = pointer_package[0].size;
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type_package = pointer_package[0].type;
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result = [];
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pointer_data = None;
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if (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_INT):
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pointer_data = cast(pointer_package[0].data, POINTER(c_int));
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elif (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_UNSIGNED_INT):
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pointer_data = cast(pointer_package[0].data, POINTER(c_uint));
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elif (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_FLOAT):
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pointer_data = cast(pointer_package[0].data, POINTER(c_float));
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elif (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_DOUBLE):
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pointer_data = cast(pointer_package[0].data, POINTER(c_double));
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elif (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_LONG):
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pointer_data = cast(pointer_package[0].data, POINTER(c_long));
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elif (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_UNSIGNED_LONG):
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pointer_data = cast(pointer_package[0].data, POINTER(c_ulong));
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elif (type_package == pyclustering_type_data.PYCLUSTERING_TYPE_LIST):
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# pointer_package[0].data == pyclustering_package **
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pointer_data = cast(pointer_package[0].data, POINTER(POINTER(pyclustering_package)));
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for index in range(0, size):
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pointer_package = cast(pointer_data[index], (POINTER(pyclustering_package)));
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result.append(extract_pyclustering_package(pointer_package));
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else:
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assert(0);
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if (type_package != pyclustering_type_data.PYCLUSTERING_TYPE_LIST):
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for index in range(0, size):
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result.append(pointer_data[index]);
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return result;
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def destroy_object(pointer_object):
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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ccore.destroy_object(pointer_object);
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# Implemented algorithms.
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def dbscan(sample, eps, min_neighbors, return_noise = False):
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"Clustering algorithm DBSCAN returns allocated clusters and noise that are consisted from input data. Calculation is performed via CCORE."
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"(in) data - input data that is presented as list of points (objects), each point should be represented by list or tuple."
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"(in) eps - connectivity radius between points, points may be connected if distance between them less then the radius."
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"(in) min_neighbors - minimum number of shared neighbors that is requied for establish links between points."
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"(in) return_noise - if True than list of points that have been marked as noise will be returned."
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"If return_noise is False: Returns list of allocated clusters, each cluster contains indexes of objects in list of data."
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"If return_noise is True: Returns tuple of list of allicated clusters and list of points that are marked as noise."
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pointer_data = create_pointer_data(sample);
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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result = ccore.dbscan_algorithm(pointer_data, c_double(eps), c_uint(min_neighbors));
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list_of_clusters = extract_clusters(result);
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ccore.free_clustering_result(result);
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noise = list_of_clusters[len(list_of_clusters) - 1];
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list_of_clusters.remove(noise);
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if (return_noise is True):
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return (list_of_clusters, noise);
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else:
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return list_of_clusters;
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def cure(sample, number_clusters, number_represent_points, compression):
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pointer_data = create_pointer_data(sample);
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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result = ccore.cure_algorithm(pointer_data, c_uint(number_clusters), c_uint(number_represent_points), c_double(compression));
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list_of_clusters = extract_clusters(result);
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ccore.free_clustering_result(result);
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return list_of_clusters;
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def hierarchical(sample, number_clusters):
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"Clustering algorithm hierarchical returns allocated clusters and noise that are consisted from input data. Calculation is performed via CCORE."
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"(in) data - input data that is presented as list of points (objects), each point should be represented by list or tuple."
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"(in) number_clusters - number of cluster that should be allocated."
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"Returns list of allocated clusters, each cluster contains indexes of objects in list of data."
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pointer_data = create_pointer_data(sample);
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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result = ccore.hierarchical_algorithm(pointer_data, c_uint(number_clusters));
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list_of_clusters = extract_clusters(result);
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ccore.free_clustering_result(result);
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return list_of_clusters;
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217
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218
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def kmeans(sample, centers, tolerance):
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"Clustering algorithm K-Means returns allocated clusters. Calculation is performed via CCORE."
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"(in) data - input data that is presented as list of points (objects), each point should be represented by list or tuple."
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"(in) centers - initial coordinates of centers of clusters that are represented by list: [center1, center2, ...]."
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223
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"(in) tolerance - stop condition: if maximum value of change of centers of clusters is less than tolerance than algorithm will stop processing."
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"Returns list of allocated clusters, each cluster contains indexes of objects in list of data."
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pointer_data = create_pointer_data(sample);
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pointer_centers = create_pointer_data(centers);
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230
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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result = ccore.kmeans_algorithm(pointer_data, pointer_centers, c_double(tolerance));
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list_of_clusters = extract_clusters(result);
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ccore.free_clustering_result(result);
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return list_of_clusters;
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def kmedians(sample, centers, tolerance):
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pointer_data = create_pointer_data(sample);
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pointer_centers = create_pointer_data(centers);
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243
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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result = ccore.kmedians_algorithm(pointer_data, pointer_centers, c_double(tolerance));
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list_of_clusters = extract_clusters(result);
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ccore.free_clustering_result(result);
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248
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249
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return list_of_clusters;
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251
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252
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def rock(sample, eps, number_clusters, threshold):
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253
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"Clustering algorithm ROCK returns allocated clusters and noise that are consisted from input data. Calculation is performed via CCORE."
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254
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255
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"(in) data - input data - list of points where each point is represented by list of coordinates."
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256
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"(in) eps - connectivity radius (similarity threshold), points are neighbors if distance between them is less than connectivity radius."
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257
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"(in) number_clusters - defines number of clusters that should be allocated from the input data set."
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258
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"(in) threshold - value that defines degree of normalization that influences on choice of clusters for merging during processing."
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259
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260
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"Returns list of allocated clusters, each cluster contains indexes of objects in list of data."
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261
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262
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pointer_data = create_pointer_data(sample);
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263
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264
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ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
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265
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result = ccore.rock_algorithm(pointer_data, c_double(eps), c_uint(number_clusters), c_double(threshold));
|
|
266
|
|
|
|
|
267
|
|
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list_of_clusters = extract_pyclustering_package(result);
|
|
268
|
|
|
ccore.free_pyclustering_package(result);
|
|
269
|
|
|
|
|
270
|
|
|
return list_of_clusters;
|
|
271
|
|
|
|
|
272
|
|
|
|
|
273
|
|
|
def xmeans(sample, centers, kmax, tolerance):
|
|
274
|
|
|
"Clustering algorithm X-Means returns allocated clusters. Calculation is performed via CCORE."
|
|
275
|
|
|
|
|
276
|
|
|
"(in) data - input data that is presented as list of points (objects), each point should be represented by list or tuple."
|
|
|
|
|
|
|
277
|
|
|
"(in) centers - initial coordinates of centers of clusters that are represented by list: [center1, center2, ...]."
|
|
|
|
|
|
|
278
|
|
|
"(in) kmax - maximum number of clusters that can be allocated."
|
|
|
|
|
|
|
279
|
|
|
|
|
280
|
|
|
"Returns list of allocated clusters, each cluster contains indexes of objects in list of data."
|
|
|
|
|
|
|
281
|
|
|
|
|
282
|
|
|
pointer_data = create_pointer_data(sample);
|
|
283
|
|
|
pointer_centers = create_pointer_data(centers);
|
|
284
|
|
|
|
|
285
|
|
|
ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
|
|
286
|
|
|
result = ccore.xmeans_algorithm(pointer_data, pointer_centers, c_uint(kmax), c_double(tolerance));
|
|
287
|
|
|
|
|
288
|
|
|
list_of_clusters = extract_clusters(result);
|
|
289
|
|
|
|
|
290
|
|
|
ccore.free_clustering_result(result);
|
|
291
|
|
|
return list_of_clusters;
|
|
292
|
|
|
|
|
293
|
|
|
|
|
294
|
|
|
"CCORE Interface for HSYNCNET oscillatory network"
|
|
|
|
|
|
|
295
|
|
|
|
|
296
|
|
|
def hsyncnet_create_network(sample, number_clusters, initial_phases):
|
|
297
|
|
|
pointer_data = create_pointer_data(sample);
|
|
298
|
|
|
|
|
299
|
|
|
ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
|
|
300
|
|
|
pointer_network = ccore.hsyncnet_create_network(pointer_data, c_uint(number_clusters), c_uint(initial_phases));
|
|
301
|
|
|
|
|
302
|
|
|
return pointer_network;
|
|
303
|
|
|
|
|
304
|
|
|
|
|
305
|
|
|
def hsyncnet_destroy_network(pointer_network):
|
|
306
|
|
|
ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
|
|
307
|
|
|
ccore.hsyncnet_destroy_network(pointer_network);
|
|
308
|
|
|
|
|
309
|
|
|
|
|
310
|
|
|
def hsyncnet_process(network_pointer, order, solution, collect_dynamic):
|
|
311
|
|
|
ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
|
|
312
|
|
|
return ccore.hsyncnet_process(network_pointer, c_double(order), c_uint(solution), c_bool(collect_dynamic));
|
|
313
|
|
|
|
|
314
|
|
|
|
|
315
|
|
|
def hsyncnet_analyser_destroy(pointer_analyser):
|
|
316
|
|
|
ccore = cdll.LoadLibrary(PATH_DLL_CCORE_64);
|
|
317
|
|
|
ccore.syncnet_analyser_destroy(pointer_analyser);
|
|
318
|
|
|
|
|
319
|
|
|
|
annoviko /
pyclustering
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