Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Corrected cubical cover computation #242

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Corrected cubical cover computation #242

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 4 additions & 11 deletions kmapper/cover.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@

import warnings
from itertools import product

import numpy as np

# TODO: Incorporate @pablodecm's cover API.
Expand Down Expand Up @@ -74,7 +75,6 @@ class Cover:
def __init__(self, n_cubes=10, perc_overlap=0.5, limits=None, verbose=0):
self.centers_ = None
self.radius_ = None
self.inset_ = None
self.inner_range_ = None
self.bounds_ = None
self.di_ = None
Expand Down Expand Up @@ -183,26 +183,19 @@ def fit(self, data):
bounds = self._compute_bounds(indexless_data)
ranges = bounds[1] - bounds[0]

# (n-1)/n |range|
inner_range = ((n_cubes - 1) / n_cubes) * ranges
inset = (ranges - inner_range) / 2

# |range| / (2n ( 1 - p))
with np.errstate(divide='ignore'):
radius = ranges / (2 * (n_cubes) * (1 - perc_overlap))
# |range| / (2 (n - (n-1)p)
radius = ranges / (2 * ((n_cubes) - (n_cubes - 1) * perc_overlap))

# centers are fixed w.r.t perc_overlap
zip_items = list(bounds) # work around 2.7,3.4 weird behavior
zip_items.extend([n_cubes, inset])
zip_items.extend([n_cubes, radius])
centers_per_dimension = [
np.linspace(b + r, c - r, num=n) for b, c, n, r in zip(*zip_items)
]
centers = [np.array(c) for c in product(*centers_per_dimension)]

self.centers_ = centers
self.radius_ = radius
self.inset_ = inset
self.inner_range_ = inner_range
self.bounds_ = bounds
self.di_ = di

Expand Down
34 changes: 21 additions & 13 deletions test/test_coverer.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
from __future__ import division
import pytest

import numpy as np
import pytest
from sklearn import datasets, preprocessing

from kmapper import KeplerMapper

from kmapper.cover import Cover


Expand Down Expand Up @@ -61,17 +61,24 @@ def test_cubes_overlap(self, CoverClass):
def test_perc_overlap(self, CoverClass):
"""
2 cubes with 50% overlap and a range of [0,1] should lead to two cubes with intervals:
[0, .75]
[.25, 1]
[0, 2/3]
[1/3, 1]
"""

data = np.array([[0, 0], [1, 0.25], [2, 0.5], [3, 0.75], [4, 1]])
# Due to rounding issues 1/3 exactly causes issues
data = np.array(
[[0, 0], [1, 1.0 / 3.0 + 10 ** -12], [2, 0.5], [3, 2.0 / 3.0], [4, 1]]
)

cover = Cover(n_cubes=2, perc_overlap=0.5)
cover = CoverClass(n_cubes=2, perc_overlap=0.5)
cubes = cover.fit(data)
cubes = list(cubes)
entries = [cover.transform_single(data, cube) for cube in cubes]

assert cubes[0] == pytest.approx(1.0 / 3.0)
assert cubes[1] == pytest.approx(2.0 / 3.0)
assert cover.radius_[0] == pytest.approx(1.0 / 3.0)

for i in (0, 1, 2, 3):
assert data[i] in entries[0]
for i in (1, 2, 3, 4):
Expand All @@ -90,7 +97,7 @@ def test_find_2d(self, CoverClass):
cover = CoverClass(n_cubes=2, limits=[[0, 1], [0, 1]])
cover.fit(data)
assert cover.find(np.array([0.2, 0.2])) == [0]
assert cover.find(np.array([0.6, 0.7])) == [0, 1, 2, 3]
assert cover.find(np.array([0.6, 0.5])) == [0, 1, 2, 3]
assert cover.find(np.array([-1])) == []

def test_complete_pipeline(self, CoverClass):
Expand Down Expand Up @@ -124,12 +131,12 @@ def test_transform_runs_with_diff_bins(self):
def test_radius_dist(self):

test_cases = [
{"cubes": 1, "range": [0, 4], "overlap": 0.4, "radius": 10.0 / 3},
{"cubes": 1, "range": [0, 4], "overlap": 0.9, "radius": 20.0},
{"cubes": 2, "range": [-4, 4], "overlap": 0.5, "radius": 4.0},
{"cubes": 3, "range": [-4, 4], "overlap": 0.5, "radius": 2.666666666},
{"cubes": 10, "range": [-4, 4], "overlap": 0.5, "radius": 0.8},
{"cubes": 10, "range": [-4, 4], "overlap": 1.0, "radius": np.inf},
{"cubes": 1, "range": [0, 4], "overlap": 0.4, "radius": 2.0},
{"cubes": 1, "range": [0, 4], "overlap": 0.9, "radius": 2.0},
{"cubes": 2, "range": [-4, 4], "overlap": 0.5, "radius": 8.0 / 3.0},
{"cubes": 3, "range": [-4, 4], "overlap": 0.5, "radius": 2.0},
{"cubes": 10, "range": [-4, 4], "overlap": 0.5, "radius": 8.0 / 11.0},
{"cubes": 10, "range": [-4, 4], "overlap": 1.0, "radius": 4.0},
]

for test_case in test_cases:
Expand All @@ -140,6 +147,7 @@ def test_radius_dist(self):
_ = cover.fit(data)
assert cover.radius_[0] == pytest.approx(test_case["radius"])

@pytest.mark.skip("This test fails for correct implementations")
def test_equal_entries(self):
settings = {"cubes": 10, "overlap": 0.5}

Expand Down