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comparison src/breadcrumbs/src/MLPYDistanceAdaptor.py @ 0:0de566f21448 draft default tip

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v2
author sagun98
date Thu, 03 Jun 2021 18:13:32 +0000
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1 """
2 Author: Timothy Tickle
3 Description: Allows KMedoids on a custom metric space.
4 """
5
6 #####################################################################################
7 #Copyright (C) <2012>
8 #
9 #Permission is hereby granted, free of charge, to any person obtaining a copy of
10 #this software and associated documentation files (the "Software"), to deal in the
11 #Software without restriction, including without limitation the rights to use, copy,
12 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
13 #and to permit persons to whom the Software is furnished to do so, subject to
14 #the following conditions:
15 #
16 #The above copyright notice and this permission notice shall be included in all copies
17 #or substantial portions of the Software.
18 #
19 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
20 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
21 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
22 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
23 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
24 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
25 #####################################################################################
26
27 __author__ = "Timothy Tickle"
28 __copyright__ = "Copyright 2012"
29 __credits__ = ["Timothy Tickle"]
30 __license__ = "MIT"
31 __maintainer__ = "Timothy Tickle"
32 __email__ = "ttickle@sph.harvard.edu"
33 __status__ = "Development"
34
35 #External libraries
36 from scipy.spatial.distance import squareform
37
38 class MLPYDistanceAdaptor:
39 """
40 Allows one to use custom distance metrics with KMedoids in the MLPY package.
41 """
42
43 npaMatrix = None
44 """
45 Distance matrix to reference.
46 """
47
48 def __init__(self, npaDistanceMatrix, fIsCondensedMatrix):
49 """
50 Constructor requires a matrix of distances, could be condensed or square matrices
51
52 :param npaDistanceMatrix: The distance matrix to be used
53 :type Numpy array
54 :param fIsCondensedMatrix: Indicator of the matrix being square (true = condensed; false = square)
55 :type Boolean
56 """
57
58 if fIsCondensedMatrix:
59 self.npaMatrix = squareform(npaDistanceMatrix)
60 else:
61 self.npaMatrix = npaDistanceMatrix
62
63 def compute(self,x,y):
64 """
65 This is the only method required in the interface to MLPY to be a distance metric.
66 Does NOT want values but positions, the positions will be used for accessing the distance matrix already provided.
67
68 :param x: X position as a array of 1 number
69 :type Numpy array
70 :param y: Y position as a array of 1 number
71 :type Boolean
72 """
73
74 if(self.npaMatrix == None):
75 raise Exception("".join(["MLPYDistanceAdaptor. Attempted to compute distance with out a distance matrix passed in during construction."]))
76 return self.npaMatrix[x[0],y[0]]