diff options
| -rw-r--r-- | gn3/computations/slink.py | 48 | ||||
| -rw-r--r-- | tests/unit/computations/test_slink.py | 11 |
2 files changed, 58 insertions, 1 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py index 59d0975..8d51f29 100644 --- a/gn3/computations/slink.py +++ b/gn3/computations/slink.py @@ -123,9 +123,55 @@ def nearest(lists, i, j): def slink(lists): """ + DESCRIPTION: + TODO: Not quite sure what this function does. Work through the code with a + fine tooth comb, once we understand the context of its use, so as to + give a better description + + The name of the function does not clearly establish what the function + does either, meaning, once that is established, the function should be + renamed to give the user an idea of what it does without necessarily + reading through a ton of code. + + We should also look into refactoring the function to reduce/eliminate + the multiple levels of nested-loops and conditionals + + PARAMETERS: + lists (list of lists of numbers): Give this a better name. + Each item of this list is a list of coordinates of the members in the + group. + What 'member' and 'group' in this context means, is not yet established. """ try: - nearest(lists, 1, 2) + size = len(lists) + listindex = range(size) + listindexcopy = list(range(size)) + listscopy = [[item for item in child] for child in lists] + initSize = size + candidate = [] + while initSize >2: + mindist = 1e10 + for i in range(initSize): + for j in range(i+1,initSize): + if listscopy[i][j] < mindist: + mindist = listscopy[i][j] + candidate=[[i,j]] + elif listscopy[i][j] == mindist: + mindist = listscopy[i][j] + candidate.append([i,j]) + else: + pass + newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist) + listindexcopy.pop(candidate[0][1]) + listindexcopy[candidate[0][0]] = newmem + + initSize -= 1 + for i in range(initSize): + for j in range(i+1,initSize): + listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j]) + listscopy[j][i] = listscopy[i][j] + listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1])) + return listindexcopy except Exception as e: # TODO: Look into making the logging log output to the system's # configured logger(s) diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py index da17ac3..5627767 100644 --- a/tests/unit/computations/test_slink.py +++ b/tests/unit/computations/test_slink.py @@ -207,3 +207,14 @@ class TestSlink(TestCase): for data in [1, "test", [], 2.945, nearest, [0]]: with self.subTest(data=data): self.assertEqual(slink(data), []) + + def test_slink_with_data(self): + for data, expected in [ + [[[0,9],[9,0]],[0,1,9]], + [[[0,9,3],[9,0,7],[3,7,0]],[(0,2,3),1,7]], + [[[0,9,3,6],[9,0,7,5],[3,7,0,9],[6,5,9,0]],[(0,2,3),(1,3,5),6]], + [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8], + [11,10,2,8,0]], + [(0,(2,4,2),3),(1,3,5),6]]]: + with self.subTest(data=data): + self.assertEqual(slink(data), expected) |