From 7f323484acdeafca93efdd9bdd20ed428f8fb95b Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sat, 28 Mar 2020 12:45:00 +0100 Subject: Optional sort_results --- src/python/gudhi/point_cloud/dtm.py | 4 +--- src/python/gudhi/point_cloud/knn.py | 19 +++++++++++++------ 2 files changed, 14 insertions(+), 9 deletions(-) (limited to 'src') diff --git a/src/python/gudhi/point_cloud/dtm.py b/src/python/gudhi/point_cloud/dtm.py index ba011eaf..678524f2 100644 --- a/src/python/gudhi/point_cloud/dtm.py +++ b/src/python/gudhi/point_cloud/dtm.py @@ -35,9 +35,7 @@ class DTM: X (numpy.array): coordinates for mass points. """ if self.params.setdefault("metric", "euclidean") != "neighbors": - # KNN gives sorted distances, which is unnecessary here. - # Maybe add a parameter to say we don't need sorting? - self.knn = KNN(self.k, return_index=False, return_distance=True, **self.params) + self.knn = KNN(self.k, return_index=False, return_distance=True, sort_results=False, **self.params) self.knn.fit(X) return self diff --git a/src/python/gudhi/point_cloud/knn.py b/src/python/gudhi/point_cloud/knn.py index bb7757f2..8369f1f8 100644 --- a/src/python/gudhi/point_cloud/knn.py +++ b/src/python/gudhi/point_cloud/knn.py @@ -33,6 +33,9 @@ class KNN: p (float): norm L^p on input points (including numpy.inf) if metric is "minkowski". Defaults to 2. n_jobs (int): number of jobs to schedule for parallel processing of nearest neighbors on the CPU. If -1 is given all processors are used. Default: 1. + sort_results (bool): if True, then distances and indices of each point are + sorted on return, so that the first column contains the closest points. + Otherwise, neighbors are returned in an arbitrary order. Defaults to True. kwargs: additional parameters are forwarded to the backends. """ self.k = k @@ -115,18 +118,22 @@ class KNN: X = numpy.array(X) if self.return_index: neighbors = numpy.argpartition(X, k - 1)[:, 0:k] - distances = numpy.take_along_axis(X, neighbors, axis=-1) - ngb_order = numpy.argsort(distances, axis=-1) - neighbors = numpy.take_along_axis(neighbors, ngb_order, axis=-1) + if self.params.get("sort_results", True): + X = numpy.take_along_axis(X, neighbors, axis=-1) + ngb_order = numpy.argsort(X, axis=-1) + neighbors = numpy.take_along_axis(neighbors, ngb_order, axis=-1) + else: + ngb_order = neighbors if self.return_distance: - distances = numpy.take_along_axis(distances, ngb_order, axis=-1) + distances = numpy.take_along_axis(X, ngb_order, axis=-1) return neighbors, distances else: return neighbors if self.return_distance: distances = numpy.partition(X, k - 1)[:, 0:k] - # partition is not guaranteed to sort the lower half, although it often does - distances.sort(axis=-1) + if self.params.get("sort_results"): + # partition is not guaranteed to sort the lower half, although it often does + distances.sort(axis=-1) return distances return None -- cgit v1.2.3