From b9e06b062f3139646fcccd1afe460fb63c66189a Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 12 Apr 2017 11:01:33 +0100
Subject: [PATCH] Atlas module unit tests
---
tests/test_atlases.py | 83 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 83 insertions(+)
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index 6522e23ce..7a32e0fc1 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -131,6 +131,7 @@ def test_add_remove_atlas():
added = [False]
removed = [False]
reg = atlases.registry
+ reg.rescanAtlases()
def atlas_added(r, topic, val):
assert topic == 'add'
@@ -167,3 +168,85 @@ def test_add_remove_atlas():
finally:
shutil.rmtree(testdir)
+
+
+def test_load_atlas():
+
+ reg = atlases.registry
+ reg.rescanAtlases()
+
+ probatlas = reg.loadAtlas('harvardoxford-cortical')
+ probsumatlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
+ lblatlas = reg.loadAtlas('talairach')
+
+ assert isinstance(probatlas, atlases.ProbabilisticAtlas)
+ assert isinstance(probsumatlas, atlases.LabelAtlas)
+ assert isinstance(lblatlas, atlases.LabelAtlas)
+
+
+def test_label_atlas():
+ reg = atlases.registry
+ reg.rescanAtlases()
+
+ # Label atlas (i.e. not a probabilistic atlas)
+ atlas = reg.loadAtlas('talairach')
+
+ # coordinates are MNI152
+ taltests = [
+ ([ 23, -37, -22], 89),
+ ([-29, -78, -22], 157),
+ ([ 48, 39, -22], 196),
+ ([ 6, 56, 37], 1034),
+ ([ 6, -78, 50], 862)]
+
+ for coords, expected in taltests:
+ assert atlas.label(coords) == expected
+
+ assert atlas.label([ 999, 999, 999]) is None
+ assert atlas.label([-999, -999, -999]) is None
+
+ # Summary atlas (a thresholded probabilistic atlas)
+ atlas = reg.loadAtlas('harvardoxford-cortical', loadSummary=True)
+ hoctests = [
+ ([-23, 58, 20], 0),
+ ([-23, 27, -20], 32),
+ ([-37, -75, 29], 21),
+ ([ -1, 37, 6], 28),
+ ([ 54, -44, -27], 15)]
+
+ for coords, expected in hoctests:
+ assert atlas.label(coords) == expected
+
+ assert atlas.label([ 999, 999, 999]) is None
+ assert atlas.label([-999, -999, -999]) is None
+
+
+def test_prob_atlas():
+ reg = atlases.registry
+ reg.rescanAtlases()
+
+ atlas = reg.loadAtlas('harvardoxford-cortical')
+
+ assert len(atlas.proportions([ 999, 999, 999])) == 0
+ assert len(atlas.proportions([-999, -999, -999])) == 0
+
+ # Coordinates are MNI152
+ # Expected proportions are lists of (volume, proportion) tuples
+ hoctests = [
+ ([ 41, -14, 18], [( 1, 5), (41, 74), (42, 10)]),
+ ([ 41, -72, 34], [(21, 72)]),
+ ([-39, -21, 58], [(6, 39), (16, 19)]),
+ ([-37, -28, 13], [(42, 4), (44, 48), (45, 19)]),
+ ([-29, -42, -11], [(34, 21), (35, 23), (37, 26), (38, 24)])]
+
+ for coords, expected in hoctests:
+
+ result = atlas.proportions(coords)
+ expidxs = [e[0] for e in expected]
+
+ for i in range(len(result)):
+ if i not in expidxs:
+ assert result[i] == 0
+
+ for expidx, expprob in expected:
+ assert result[expidx] == expprob
--
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