From 1165eeb90036c845f401abdca58e88a0cab3a7da Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sat, 27 Apr 2019 15:32:24 +0100
Subject: [PATCH] TEST: fsl.utils.transform -> fsl.transform. Re-jigged
transform test modules. Fix to mesh test
---
tests/test_atlases.py | 2 +-
tests/test_atlases_query.py | 8 ++++----
tests/test_fsl_convert_x5.py | 6 +++---
tests/test_image.py | 8 ++++----
tests/test_mesh.py | 19 +++++++++++++------
tests/test_mghimage.py | 8 ++++----
tests/test_scripts/test_atlasq_query.py | 8 ++++----
tests/test_transform/__init__.py | 0
.../test_affine.py} | 5 ++---
.../test_flirt.py} | 10 +++++-----
.../test_nonlinear.py} | 6 +++---
11 files changed, 43 insertions(+), 37 deletions(-)
create mode 100644 tests/test_transform/__init__.py
rename tests/{test_transform.py => test_transform/test_affine.py} (99%)
rename tests/{test_transform_flirt.py => test_transform/test_flirt.py} (92%)
rename tests/{test_transform_nonlinear.py => test_transform/test_nonlinear.py} (93%)
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index b2dfec113..97150cf26 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -17,10 +17,10 @@ import mock
import pytest
import tests
-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
+import fsl.transform as transform
datadir = op.join(op.dirname(__file__), 'testdata')
diff --git a/tests/test_atlases_query.py b/tests/test_atlases_query.py
index 693366a2e..f431130c3 100644
--- a/tests/test_atlases_query.py
+++ b/tests/test_atlases_query.py
@@ -11,11 +11,11 @@ import numpy as np
import pytest
-import fsl.data.atlases as fslatlases
-import fsl.data.image as fslimage
-import fsl.utils.transform as transform
+import fsl.data.atlases as fslatlases
+import fsl.data.image as fslimage
+import fsl.transform as transform
import fsl.utils.image.resample as resample
-import fsl.utils.cache as cache
+import fsl.utils.cache as cache
from . import (testdir, make_random_mask)
diff --git a/tests/test_fsl_convert_x5.py b/tests/test_fsl_convert_x5.py
index aa3854f2c..0dab1ec52 100644
--- a/tests/test_fsl_convert_x5.py
+++ b/tests/test_fsl_convert_x5.py
@@ -3,9 +3,9 @@
import numpy as np
-import fsl.utils.tempdir as tempdir
-import fsl.utils.transform as transform
-import fsl.data.image as fslimage
+import fsl.utils.tempdir as tempdir
+import fsl.transform as transform
+import fsl.data.image as fslimage
import fsl.scripts.fsl_convert_x5 as fsl_convert_x5
diff --git a/tests/test_image.py b/tests/test_image.py
index 4a5ae2e80..605dbbc82 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -19,10 +19,10 @@ import nibabel as nib
from nibabel.spatialimages import ImageFileError
-import fsl.data.constants as constants
-import fsl.data.image as fslimage
-import fsl.utils.path as fslpath
-import fsl.utils.transform as transform
+import fsl.data.constants as constants
+import fsl.data.image as fslimage
+import fsl.utils.path as fslpath
+import fsl.transform as transform
from fsl.utils.tempdir import tempdir
diff --git a/tests/test_mesh.py b/tests/test_mesh.py
index 243944b2e..a7a4ca5d1 100644
--- a/tests/test_mesh.py
+++ b/tests/test_mesh.py
@@ -6,13 +6,13 @@
#
-import os.path as op
-import numpy as np
-import mock
-import pytest
+import os.path as op
+import numpy as np
+from unittest import mock
+import pytest
-import fsl.utils.transform as transform
-import fsl.data.mesh as fslmesh
+import fsl.transform as transform
+import fsl.data.mesh as fslmesh
from . import tempdir
@@ -257,6 +257,13 @@ def test_needsFixing():
def test_trimesh_no_trimesh():
+ # Make sure trimesh and rtree
+ # are imported before messing
+ # with sys.modules, otherwise
+ # weird things can happen.
+ import trimesh
+ import rtree
+
mods = ['trimesh', 'rtree']
for mod in mods:
diff --git a/tests/test_mghimage.py b/tests/test_mghimage.py
index 2496ac4eb..ef53e2fd9 100644
--- a/tests/test_mghimage.py
+++ b/tests/test_mghimage.py
@@ -12,10 +12,10 @@ import shutil
import numpy as np
import nibabel as nib
-import fsl.utils.tempdir as tempdir
-import fsl.utils.transform as transform
-import fsl.data.mghimage as fslmgh
-import fsl.data.image as fslimage
+import fsl.utils.tempdir as tempdir
+import fsl.transform as transform
+import fsl.data.mghimage as fslmgh
+import fsl.data.image as fslimage
datadir = op.join(op.abspath(op.dirname(__file__)), 'testdata')
diff --git a/tests/test_scripts/test_atlasq_query.py b/tests/test_scripts/test_atlasq_query.py
index a36e1eb5f..20c48634a 100644
--- a/tests/test_scripts/test_atlasq_query.py
+++ b/tests/test_scripts/test_atlasq_query.py
@@ -15,11 +15,11 @@ import scipy.ndimage as ndi
import pytest
-import fsl.utils.transform as transform
+import fsl.transform as transform
+import fsl.data.atlases as fslatlases
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
+import fsl.data.image as fslimage
+import fsl.scripts.atlasq as fslatlasq
from .. import (tempdir,
make_random_mask,
diff --git a/tests/test_transform/__init__.py b/tests/test_transform/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/test_transform.py b/tests/test_transform/test_affine.py
similarity index 99%
rename from tests/test_transform.py
rename to tests/test_transform/test_affine.py
index 442ceaa7d..90901c6ba 100644
--- a/tests/test_transform.py
+++ b/tests/test_transform/test_affine.py
@@ -19,11 +19,10 @@ import six
import pytest
-import fsl.utils.transform as transform
-import fsl.data.image as fslimage
+import fsl.transform as transform
-datadir = op.join(op.dirname(__file__), 'testdata')
+datadir = op.join(op.dirname(__file__), '..', 'testdata')
def readlines(filename):
diff --git a/tests/test_transform_flirt.py b/tests/test_transform/test_flirt.py
similarity index 92%
rename from tests/test_transform_flirt.py
rename to tests/test_transform/test_flirt.py
index 2419cbbe2..98ebc08a2 100644
--- a/tests/test_transform_flirt.py
+++ b/tests/test_transform/test_flirt.py
@@ -9,14 +9,14 @@ import os.path as op
import numpy as np
-import fsl.data.image as fslimage
-import fsl.utils.transform as transform
-import fsl.utils.tempdir as tempdir
+import fsl.data.image as fslimage
+import fsl.transform as transform
+import fsl.utils.tempdir as tempdir
-from .test_transform import readlines
+from .test_affine import readlines
-datadir = op.join(op.dirname(__file__), 'testdata')
+datadir = op.join(op.dirname(__file__), '..', 'testdata')
def test_read_write():
diff --git a/tests/test_transform_nonlinear.py b/tests/test_transform/test_nonlinear.py
similarity index 93%
rename from tests/test_transform_nonlinear.py
rename to tests/test_transform/test_nonlinear.py
index 7c24d90da..8a5a051a1 100644
--- a/tests/test_transform_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -4,9 +4,9 @@
import numpy as np
import nibabel as nib
-import fsl.data.image as fslimage
-import fsl.utils.transform as transform
-import fsl.utils.transform.nonlinear as nonlinear
+import fsl.data.image as fslimage
+import fsl.transform as transform
+import fsl.transform.nonlinear as nonlinear
def _random_field():
--
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