dccb5015ca3443c490aa4f1100892b0bfb5f957b,geomstats/riemannian_metric.py,RiemannianMetric,mean,#RiemannianMetric#Any#Any#Any#Any#Any#,241

Before Change


        // TODO(nina): profile this code to study performance,
        // i.e. what to do with sq_dists_between_iterates.

        if isinstance(points, list):
            points = gs.vstack(points)

        if point_type == "vector":
            points = gs.to_ndarray(points, to_ndim=2)
        if point_type == "matrix":
            points = gs.to_ndarray(points, to_ndim=3)

After Change



        sq_dists_between_iterates = []
        iteration = 0
        sq_dist = gs.array([[0.]])
        variance = gs.array([[0.]])

        //iteration = gs.constant(0)

        def while_loop_body(iteration, mean, variance, sq_dist):
            tangent_mean = gs.zeros_like(mean)

            logs = self.log(point=points, base_point=mean)
            tangent_mean += gs.einsum("nk,nj->j", weights, logs)

            tangent_mean /= sum_weights

            mean_next = self.exp(
                tangent_vec=tangent_mean,
                base_point=mean)

            sq_dist = self.squared_dist(mean_next, mean)
            sq_dists_between_iterates.append(sq_dist)

            variance = self.variance(points=points,
                                     weights=weights,
                                     base_point=mean_next)

            mean = mean_next
            iteration += 1
            return [iteration, mean, variance, sq_dist]

        def while_loop_cond(iteration, mean, variance, sq_dist):
            result = gs.logical_or(
                gs.isclose(variance, 0.),
                gs.less_equal(sq_dist, epsilon * variance))
            return result[0, 0]

        last_iteration, mean, variance, sq_dist = gs.while_loop(
            lambda i, m, v, sq: while_loop_cond(i, m, v, sq),
            lambda i, m, v, sq: while_loop_body(i, m, v, sq),
            loop_vars=[iteration, mean, variance, sq_dist],
            maximum_iterations=n_max_iterations)
        //while iteration < n_max_iterations:

        //    if gs.isclose(variance, 0.)[0, 0]:
        //        break
Italian Trulli
In pattern: SUPERPATTERN

Frequency: 4

Non-data size: 7

Instances


Project Name: geomstats/geomstats
Commit Name: dccb5015ca3443c490aa4f1100892b0bfb5f957b
Time: 2018-12-31
Author: ninamio78@gmail.com
File Name: geomstats/riemannian_metric.py
Class Name: RiemannianMetric
Method Name: mean


Project Name: geomstats/geomstats
Commit Name: 01673d1a6dcb41a20e19f951ee450c44c07aeafd
Time: 2019-06-16
Author: ninamio78@gmail.com
File Name: geomstats/riemannian_metric.py
Class Name: RiemannianMetric
Method Name: mean


Project Name: prody/ProDy
Commit Name: 223584e2a0b97b006b6ac944253e2573963a7a88
Time: 2018-09-25
Author: jamesmkrieger@gmail.com
File Name: prody/proteins/starfile.py
Class Name:
Method Name: parseImagesFromSTAR


Project Name: matplotlib/matplotlib
Commit Name: 34b8eb46e5de6b760bc131e461755042716e259d
Time: 2018-02-07
Author: story645@gmail.com
File Name: lib/matplotlib/category.py
Class Name: StrCategoryConverter
Method Name: convert