Commit 0b307187826ee27ddd5368d2cd2f81671d5fd59a
1 parent
933b2505a1
Exists in
master
normalize the global value of disequilibrium by the number of clusters
Showing 1 changed file with 2 additions and 2 deletions Inline Diff
bin/measures.py
| 1 | ''' | 1 | ''' |
| 2 | This module is a part of my library. | 2 | This module is a part of my library. |
| 3 | It aims to compute some measures for clustering. | 3 | It aims to compute some measures for clustering. |
| 4 | ''' | 4 | ''' |
| 5 | 5 | ||
| 6 | import numpy as np | 6 | import numpy as np |
| 7 | 7 | ||
| 8 | def disequilibrium_(matrix1, matrix2, isGlobal=False, mod=None): | 8 | def disequilibrium_(matrix1, matrix2, isGlobal=False, mod=None): |
| 9 | ''' | 9 | ''' |
| 10 | Compute disequilibrium for all the clusters. | 10 | Compute disequilibrium for all the clusters. |
| 11 | The disequilibrium is compute from the difference | 11 | The disequilibrium is compute from the difference |
| 12 | between two clustering sets. | 12 | between two clustering sets. |
| 13 | isGlobal permet à l'utilisateur de choisir le dénominateur de | 13 | isGlobal permet à l'utilisateur de choisir le dénominateur de |
| 14 | la fonction : | 14 | la fonction : |
| 15 | - True : divise la valeur par le nombre d'élément du cluster | 15 | - True : divise la valeur par le nombre d'élément du cluster |
| 16 | - False : divise la valeur par le nombre d'élément total | 16 | - False : divise la valeur par le nombre d'élément total |
| 17 | 17 | ||
| 18 | withPower permet à l'utilisateur de décider d'appliquer un carré 2 ou | 18 | withPower permet à l'utilisateur de décider d'appliquer un carré 2 ou |
| 19 | une valeur absolue. | 19 | une valeur absolue. |
| 20 | ''' | 20 | ''' |
| 21 | 21 | ||
| 22 | def divide_line(a, divider): | 22 | def divide_line(a, divider): |
| 23 | ''' | 23 | ''' |
| 24 | Sub function used for dividing matrix by a vector line by line. | 24 | Sub function used for dividing matrix by a vector line by line. |
| 25 | ''' | 25 | ''' |
| 26 | return np.divide(a, divider, out=np.zeros_like(a), where=divider!=0) | 26 | return np.divide(a, divider, out=np.zeros_like(a), where=divider!=0) |
| 27 | 27 | ||
| 28 | dividers1 = 0 | 28 | dividers1 = 0 |
| 29 | dividers2 = 0 | 29 | dividers2 = 0 |
| 30 | 30 | ||
| 31 | if isGlobal: | 31 | if isGlobal: |
| 32 | dividers1 = matrix1.sum() | 32 | dividers1 = matrix1.sum() |
| 33 | dividers2 = matrix2.sum() | 33 | dividers2 = matrix2.sum() |
| 34 | else: | 34 | else: |
| 35 | dividers1 = matrix1.sum(axis=1) | 35 | dividers1 = matrix1.sum(axis=1) |
| 36 | dividers2 = matrix2.sum(axis=1) | 36 | dividers2 = matrix2.sum(axis=1) |
| 37 | 37 | ||
| 38 | matrix1_divided = np.apply_along_axis(divide_line, 0, np.asarray(matrix1, dtype=np.float), dividers1) | 38 | matrix1_divided = np.apply_along_axis(divide_line, 0, np.asarray(matrix1, dtype=np.float), dividers1) |
| 39 | 39 | ||
| 40 | matrix2_divided = np.apply_along_axis(divide_line, 0, np.asarray(matrix2, dtype=np.float), dividers2) | 40 | matrix2_divided = np.apply_along_axis(divide_line, 0, np.asarray(matrix2, dtype=np.float), dividers2) |
| 41 | 41 | ||
| 42 | diff = matrix1_divided - matrix2_divided | 42 | diff = matrix1_divided - matrix2_divided |
| 43 | 43 | ||
| 44 | mask = (matrix2==0) & (matrix1==0) | 44 | mask = (matrix2==0) & (matrix1==0) |
| 45 | result = diff | 45 | result = diff |
| 46 | 46 | ||
| 47 | if mod != None or mod == "": | 47 | if mod != None or mod == "": |
| 48 | for word in mod.split(" "): | 48 | for word in mod.split(" "): |
| 49 | if word == "power": | 49 | if word == "power": |
| 50 | result = np.power(result,2) | 50 | result = np.power(result,2) |
| 51 | elif word == "human": | 51 | elif word == "human": |
| 52 | result = result * 100 | 52 | result = result * 100 |
| 53 | elif word == "abs": | 53 | elif word == "abs": |
| 54 | result = np.absolute(result) | 54 | result = np.absolute(result) |
| 55 | else: | 55 | else: |
| 56 | raise Exception("Need to specify an accepted mod of the disequilibrium (\"power\", \"human\" or \"abs\"") | 56 | raise Exception("Need to specify an accepted mod of the disequilibrium (\"power\", \"human\" or \"abs\"") |
| 57 | return (mask, result) | 57 | return (mask, result) |
| 58 | 58 | ||
| 59 | 59 | ||
| 60 | 60 | ||
| 61 | def disequilibrium_mean_by_cluster(mask, matrix): | 61 | def disequilibrium_mean_by_cluster(mask, matrix): |
| 62 | ''' | 62 | ''' |
| 63 | Mean of disequilibrium | 63 | Mean of disequilibrium |
| 64 | matrix is the disequilibrium calculated | 64 | matrix is the disequilibrium calculated |
| 65 | from number of occurences belonging to a class, | 65 | from number of occurences belonging to a class, |
| 66 | for each cluster. | 66 | for each cluster. |
| 67 | ''' | 67 | ''' |
| 68 | nb_k = len(matrix) | 68 | nb_k = len(matrix) |
| 69 | results = np.zeros((nb_k)) | 69 | results = np.zeros((nb_k)) |
| 70 | for i in range(nb_k): | 70 | for i in range(nb_k): |
| 71 | results[i] = matrix[i].sum() / mask[i].sum() | 71 | results[i] = matrix[i].sum() / mask[i].sum() |
| 72 | return results | 72 | return results |
| 73 | 73 | ||
| 74 | 74 | ||
| 75 | def disequilibrium(matrix1, matrix2, isGlobal=False): | 75 | def disequilibrium(matrix1, matrix2, isGlobal=False): |
| 76 | ''' | 76 | ''' |
| 77 | Disequilibrium matrix | 77 | Disequilibrium matrix |
| 78 | And Disequilibrium value | 78 | And Disequilibrium value |
| 79 | ''' | 79 | ''' |
| 80 | mask, result = disequilibrium_(matrix1, matrix2, isGlobal) | 80 | mask, result = disequilibrium_(matrix1, matrix2, isGlobal) |
| 81 | result_human = result * 100 | 81 | result_human = result * 100 |
| 82 | result_power = np.power(result, 2) | 82 | result_power = np.power(result, 2) |
| 83 | 83 | ||
| 84 | return ( | 84 | return ( |
| 85 | mask, | 85 | mask, |
| 86 | result_human, | 86 | result_human, |
| 87 | disequilibrium_mean_by_cluster(mask, result_power).sum() | 87 | disequilibrium_mean_by_cluster(mask, result_power).sum()/matrix1.shape[0] |
| 88 | ) | 88 | ) |
| 89 | 89 | ||
| 90 | 90 | ||
| 91 | def entropy(count_matrix): | 91 | def entropy(count_matrix): |
| 92 | def divide_line(a, divider): | 92 | def divide_line(a, divider): |
| 93 | ''' | 93 | ''' |
| 94 | Sub function used for dividing matrix by a vector line by line. | 94 | Sub function used for dividing matrix by a vector line by line. |
| 95 | ''' | 95 | ''' |
| 96 | return np.divide(a, divider, out=np.zeros_like(a), where=divider!=0) | 96 | return np.divide(a, divider, out=np.zeros_like(a), where=divider!=0) |
| 97 | 97 | ||
| 98 | dividers = count_matrix.sum(axis=1) | 98 | dividers = count_matrix.sum(axis=1) |
| 99 | 99 | ||
| 100 | matrix_divided = np.apply_along_axis(divide_line, 0, np.asarray(count_matrix, dtype=np.float), dividers) | 100 | matrix_divided = np.apply_along_axis(divide_line, 0, np.asarray(count_matrix, dtype=np.float), dividers) |
| 101 | 101 | ||
| 102 | result_matrix = -1 * matrix_divided * np.log2(matrix_divided, where=count_matrix != 0) | 102 | result_matrix = -1 * matrix_divided * np.log2(matrix_divided, where=count_matrix != 0) |
| 103 | result = result_matrix.sum(axis=1) * dividers / dividers.sum() | 103 | result = result_matrix.sum(axis=1) * dividers / dividers.sum() |
| 104 | result = result.sum() | 104 | result = result.sum() |
| 105 | return (result_matrix, result) | 105 | return (result_matrix, result) |
| 106 |