ALL: allow to change number of threads used for kdtree #353
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houndci-bot
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Dec 6, 2021
| @@ -66,6 +66,8 @@ class GITIM(Interface): | |||
| :param bool warnings: Print warnings | |||
| :param bool autoassign: If true (default) detect the interface | |||
| every time a new frame is selected. | |||
| :param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball | |||
| If -1 is given all CPU threads are used (default: -1) | |||
| @@ -66,6 +66,8 @@ class GITIM(Interface): | |||
| :param bool warnings: Print warnings | |||
| :param bool autoassign: If true (default) detect the interface | |||
| every time a new frame is selected. | |||
| :param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball | |||
| >>> print(repr(inter.atoms)) | ||
| <AtomGroup with 855 atoms> | ||
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| >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True,workers=1) |
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| @@ -519,7 +524,11 @@ def _(): | |||
| <AtomGroup with 2025 atoms> | |||
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| >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True) | |||
| >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True,workers=-1) | |||
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| @@ -171,7 +176,7 @@ def _define_cluster_group(self): | |||
| # the smaller clusters of the other phase | |||
| labels, counts, neighbors = utilities.do_cluster_analysis_dbscan( | |||
| self.cluster_group, cluster_cut, | |||
| self.cluster_threshold_density, self.molecular) | |||
| self.cluster_threshold_density, self.molecular,workers=self.workers) | |||
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missing whitespace after ','
| @@ -60,6 +60,8 @@ class SASA(GITIM): | |||
| :param bool warnings: Print warnings | |||
| :param bool autoassign: If true (default) detect the interface | |||
| every time a new frame is selected. | |||
| :param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball | |||
| @@ -56,7 +59,7 @@ def do_cluster_analysis_dbscan(group, | |||
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| neighborhoods = np.array([ | |||
| np.array(neighbors) | |||
| for neighbors in tree.query_ball_point(points, cluster_cut, n_jobs=-1) | |||
| for neighbors in tree.query_ball_point(points, cluster_cut, workers=workers) | |||
| @@ -46,6 +46,9 @@ def do_cluster_analysis_dbscan(group, | |||
| clusters. This is on average O(N log N) thanks to the O(log N) | |||
| scaling of the kdtree. | |||
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| To avoid problems in environments with limited resources, | |||
| @@ -31,7 +31,7 @@ def determine_samples(threshold_density, cluster_cut, n_neighbors): | |||
| def do_cluster_analysis_dbscan(group, | |||
| cluster_cut, | |||
| threshold_density=None, | |||
| molecular=True): | |||
| molecular=True,workers=1): | |||
| :param bool autoassign: If true (default) detect the interface | ||
| every time a new frame is selected. | ||
| :param int workers: Passes the workers option to scipy.spatial.cKDTree.query_ball | ||
| If -1 is given all CPU threads are used (default: -1) |
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fixes #352 |
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