From 33bcbdb4f9f1fb14f6cc96896adc767174076dd5 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Sun, 30 Jun 2019 00:46:02 +0200
Subject: [PATCH] Restrict numpy threads for morphology extraction
---
scripts/extension/attributes/morphology.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/scripts/extension/attributes/morphology.py b/scripts/extension/attributes/morphology.py
index 635a72c..0cb522a 100644
--- a/scripts/extension/attributes/morphology.py
+++ b/scripts/extension/attributes/morphology.py
@@ -4,8 +4,13 @@ import os
import sys
import json
-import luigi
+# this is a task called by multiple processes,
+# so we need to restrict the number of threads used by numpy
+from cluster_tools.utils.numpy_utils import set_numpy_threads
+set_numpy_threads(1)
import numpy as np
+
+import luigi
import pandas as pd
import nifty.tools as nt
from skimage.measure import regionprops, marching_cubes_lewiner, mesh_surface_area
@@ -22,7 +27,6 @@ from cluster_tools.cluster_tasks import SlurmTask, LocalTask
#
-# FIXME something in here uses a lot of threads
class MorphologyBase(luigi.Task):
""" Morphology base class
"""
--
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