From c50f6fd874a9e33bb2865544b1c8661892b6ccc6 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 23 Oct 2017 13:45:52 +0100
Subject: [PATCH] Atlas tests use less memory
---
tests/test_atlases_query.py | 18 ++++++++++++------
1 file changed, 12 insertions(+), 6 deletions(-)
diff --git a/tests/test_atlases_query.py b/tests/test_atlases_query.py
index 7b61bb36a..671e185c0 100644
--- a/tests/test_atlases_query.py
+++ b/tests/test_atlases_query.py
@@ -34,16 +34,17 @@ def _repeat(iterator, n):
yield elem
-# We can't cache all atlases, because CI
-# jobs will take up too much memory and
-# be killed
-_atlases = cache.Cache(3)
+
+_atlases = cache.Cache()
def _get_atlas(atlasID, res, summary=False):
atlas = _atlases.get((atlasID, res, summary), default=None)
if atlas is None:
atlas = fslatlases.loadAtlas(atlasID,
loadSummary=summary,
- resolution=res)
+ resolution=res,
+ loadData=False,
+ calcRange=False,
+ indexed=True)
_atlases.put((atlasID, res, summary), atlas)
return atlas
@@ -75,7 +76,12 @@ def _get_zero_mask(aimg):
if isinstance(aimg, fslatlases.LabelAtlas):
zmask = aimg[:] == 0
elif isinstance(aimg, fslatlases.ProbabilisticAtlas):
- zmask = np.all(aimg[:] == 0, axis=-1)
+
+ # Keep memory usage down
+ zmask = np.ones(aimg.shape[:3], dtype=np.bool)
+ for vol in range(aimg.shape[-1]):
+ zmask = np.logical_and(zmask, aimg[..., vol] == 0)
+
_zero_masks[atlasID, summary, res] = zmask
return zmask
--
GitLab