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Last change
on this file since 1182 was
1182,
checked in by Maciej Komosinski, 3 years ago
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More concise code and less redundancy in dissimilarity classes, added support for archive of genotypes, added hard limit on the number of genotype chars
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File size:
935 bytes
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| Rev | Line | |
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| [1113] | 1 | from abc import ABC |
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| 2 | |
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| 3 | import numpy as np |
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| 4 | |
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| 5 | from evolalg.base.frams_step import FramsStep |
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| 6 | from evolalg.dissimilarity.dissimilarity import Dissimilarity |
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| 7 | |
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| 8 | |
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| 9 | class FramsDissimilarity(FramsStep): |
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| 10 | |
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| [1182] | 11 | def __init__(self, frams_lib, reduction="mean", output_field="dissim",knn=None, *args, **kwargs): |
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| [1113] | 12 | super(FramsDissimilarity, self).__init__(frams_lib, *args, **kwargs) |
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| 13 | |
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| 14 | self.output_field = output_field |
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| [1182] | 15 | self.fn_reduce = Dissimilarity.get_reduction_by_name(reduction) |
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| [1145] | 16 | self.knn = knn |
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| [1113] | 17 | |
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| 18 | |
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| 19 | def call(self, population): |
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| [1139] | 20 | super(FramsDissimilarity, self).call(population) |
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| [1113] | 21 | if len(population) == 0: |
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| 22 | return [] |
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| [1182] | 23 | dissim_matrix = self.frams.dissimilarity([_.genotype for _ in population], 1) |
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| 24 | dissim = Dissimilarity.reduce(dissim_matrix, self.fn_reduce, self.knn) |
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| [1113] | 25 | for d,ind in zip(dissim, population): |
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| 26 | setattr(ind, self.output_field, d) |
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| [1145] | 27 | return population |
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