From fffeab28d5d2f862a3f1e96a87362d30e135fffa Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 8 May 2019 11:58:58 +0100
Subject: [PATCH] TEST: use new resample module
---
tests/test_atlases.py | 9 +++++----
tests/test_atlases_query.py | 7 +++++--
tests/test_scripts/test_atlasq_query.py | 4 +++-
3 files changed, 13 insertions(+), 7 deletions(-)
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index 80be87c74..c2d257f60 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -17,9 +17,10 @@ import mock
import pytest
import tests
-import fsl.utils.transform as transform
-import fsl.data.atlases as atlases
-import fsl.data.image as fslimage
+import fsl.utils.transform as transform
+import fsl.utils.image.resample as resample
+import fsl.data.atlases as atlases
+import fsl.data.image as fslimage
datadir = op.join(op.dirname(__file__), 'testdata')
@@ -286,7 +287,7 @@ def test_prepareMask():
np.array(np.random.random(ashape), dtype=np.float32),
xform=atlas.voxToWorldMat)
- goodmask2, xf = goodmask1.resample(m2shape)
+ goodmask2, xf = resample.resample(goodmask1, m2shape)
goodmask2 = fslimage.Image(goodmask2, xform=xf)
wrongdims = fslimage.Image(
diff --git a/tests/test_atlases_query.py b/tests/test_atlases_query.py
index f90c8d406..693366a2e 100644
--- a/tests/test_atlases_query.py
+++ b/tests/test_atlases_query.py
@@ -14,6 +14,7 @@ import pytest
import fsl.data.atlases as fslatlases
import fsl.data.image as fslimage
import fsl.utils.transform as transform
+import fsl.utils.image.resample as resample
import fsl.utils.cache as cache
from . import (testdir, make_random_mask)
@@ -256,7 +257,8 @@ def _gen_mask_query(atlas, qtype, qin, maskres):
# aggresively to make sure there
# is no overlap between the different
# resolutions
- mask, xform = mask.resample(a.shape[:3], dtype=np.float32, order=1)
+ mask, xform = resample.resample(
+ mask, a.shape[:3], dtype=np.float32, order=1)
mask[mask < 1.0] = 0
mask[a_zmask == 0] = 0
@@ -279,7 +281,8 @@ def _eval_mask_query(atlas, query, qtype, qin):
if maskres == res:
rmask = mask[:]
else:
- rmask = mask.resample(atlas.shape[:3], dtype=np.float32, order=0)[0]
+ rmask = resample.resample(
+ mask, atlas.shape[:3], dtype=np.float32, order=0)[0]
rmask = np.array(rmask, dtype=np.bool)
diff --git a/tests/test_scripts/test_atlasq_query.py b/tests/test_scripts/test_atlasq_query.py
index 63465d24d..a36e1eb5f 100644
--- a/tests/test_scripts/test_atlasq_query.py
+++ b/tests/test_scripts/test_atlasq_query.py
@@ -16,6 +16,7 @@ import scipy.ndimage as ndi
import pytest
import fsl.utils.transform as transform
+import fsl.utils.image.resample as resample
import fsl.data.atlases as fslatlases
import fsl.data.image as fslimage
import fsl.scripts.atlasq as fslatlasq
@@ -329,7 +330,8 @@ def _gen_mask_query(atlas, use_label, q_type, q_in, res):
# resampled into the atlas resolution,
# it is still either in or out of the
# atlas space
- mask, xform = mask.resample(a.shape[:3], dtype=np.float32, order=1)
+ mask, xform = resample.resample(
+ mask, a.shape[:3], dtype=np.float32, order=1)
thres = np.percentile(mask[mask > 0], 75)
--
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