From 98e9ddeb328811ca11a69a485b09541e9de8c205 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 1 Jul 2019 15:03:41 +0930
Subject: [PATCH] TEST: Move transform test data, add test for coef->disp field
conversion
---
tests/test_transform/test_affine.py | 2 +-
tests/test_transform/test_flirt.py | 2 +-
tests/test_transform/test_nonlinear.py | 27 +++++++++++++++++++
.../test_transform_test_axisBounds.txt | 0
.../testdata/test_transform_test_compose.txt | 0
.../testdata/test_transform_test_concat.txt | 0
...test_transform_test_flirtMatrixToSform.txt | 0
.../testdata/test_transform_test_invert.txt | 0
.../test_transform_test_scaleoffsetxform.txt | 0
.../test_transform_test_transform_00.txt | 0
.../test_transform_test_transform_01.txt | 0
.../test_transform_test_transform_02.txt | 0
.../test_transform_test_transform_03.txt | 0
.../test_transform_test_transform_04.txt | 0
.../test_transform_test_transform_05.txt | 0
.../test_transform_test_transform_06.txt | 0
.../test_transform_test_transform_07.txt | 0
.../test_transform_test_transform_08.txt | 0
.../test_transform_test_transform_09.txt | 0
.../test_transform_test_transform_10.txt | 0
.../test_transform_test_transform_11.txt | 0
.../test_transform_test_transform_12.txt | 0
.../test_transform_test_transform_13.txt | 0
.../test_transform_test_transform_14.txt | 0
.../test_transform_test_transform_15.txt | 0
.../test_transform_test_transform_16.txt | 0
.../test_transform_test_transform_17.txt | 0
.../test_transform_test_transform_18.txt | 0
.../test_transform_test_transform_19.txt | 0
.../test_transform_test_transform_20.txt | 0
.../test_transform_test_transform_coords.txt | 0
31 files changed, 29 insertions(+), 2 deletions(-)
rename tests/{ => test_transform}/testdata/test_transform_test_axisBounds.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_compose.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_concat.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_flirtMatrixToSform.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_invert.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_scaleoffsetxform.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_00.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_01.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_02.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_03.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_04.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_05.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_06.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_07.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_08.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_09.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_10.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_11.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_12.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_13.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_14.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_15.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_16.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_17.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_18.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_19.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_20.txt (100%)
rename tests/{ => test_transform}/testdata/test_transform_test_transform_coords.txt (100%)
diff --git a/tests/test_transform/test_affine.py b/tests/test_transform/test_affine.py
index 90901c6ba..73ec93c4c 100644
--- a/tests/test_transform/test_affine.py
+++ b/tests/test_transform/test_affine.py
@@ -22,7 +22,7 @@ import pytest
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/test_flirt.py b/tests/test_transform/test_flirt.py
index 98ebc08a2..c301fc75c 100644
--- a/tests/test_transform/test_flirt.py
+++ b/tests/test_transform/test_flirt.py
@@ -16,7 +16,7 @@ import fsl.utils.tempdir as tempdir
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/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index 2017bb55c..59a6d7d63 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python
import itertools as it
+import os.path as op
import numpy as np
import nibabel as nib
@@ -8,6 +9,10 @@ import nibabel as nib
import fsl.data.image as fslimage
import fsl.transform as transform
import fsl.transform.nonlinear as nonlinear
+import fsl.transform.fnirt as fnirt
+
+
+datadir = op.join(op.dirname(__file__), 'testdata')
def _random_image():
@@ -191,3 +196,25 @@ def test_DisplacementField_transform():
got = absfield.transform(rcoords)
assert np.all(np.isnan(got[0, :]))
assert np.all(np.isclose(got[1, :], scoords[1, :]))
+
+def test_coefficientFieldToDisplacementField():
+
+ nldir = op.join(datadir, 'nonlinear')
+ src = op.join(nldir, 'src.nii.gz')
+ ref = op.join(nldir, 'ref.nii.gz')
+ cf = op.join(nldir, 'coefficientfield.nii.gz')
+ df = op.join(nldir, 'displacementfield.nii.gz')
+
+ src = fslimage.Image(src)
+ ref = fslimage.Image(ref)
+ cf = fnirt.readFnirt(cf, src, ref)
+ rdf = fnirt.readFnirt(df, src, ref)
+ adf = nonlinear.convertDisplacementType(rdf)
+
+ tol = dict(atol=1e-5, rtol=1e-5)
+
+ rcnv = nonlinear.coefficientFieldToDisplacementField(cf)
+ acnv = nonlinear.coefficientFieldToDisplacementField(cf, dispType='absolute')
+
+ assert np.all(np.isclose(rcnv.data, rdf.data, **tol))
+ assert np.all(np.isclose(acnv.data, adf.data, **tol))
diff --git a/tests/testdata/test_transform_test_axisBounds.txt b/tests/test_transform/testdata/test_transform_test_axisBounds.txt
similarity index 100%
rename from tests/testdata/test_transform_test_axisBounds.txt
rename to tests/test_transform/testdata/test_transform_test_axisBounds.txt
diff --git a/tests/testdata/test_transform_test_compose.txt b/tests/test_transform/testdata/test_transform_test_compose.txt
similarity index 100%
rename from tests/testdata/test_transform_test_compose.txt
rename to tests/test_transform/testdata/test_transform_test_compose.txt
diff --git a/tests/testdata/test_transform_test_concat.txt b/tests/test_transform/testdata/test_transform_test_concat.txt
similarity index 100%
rename from tests/testdata/test_transform_test_concat.txt
rename to tests/test_transform/testdata/test_transform_test_concat.txt
diff --git a/tests/testdata/test_transform_test_flirtMatrixToSform.txt b/tests/test_transform/testdata/test_transform_test_flirtMatrixToSform.txt
similarity index 100%
rename from tests/testdata/test_transform_test_flirtMatrixToSform.txt
rename to tests/test_transform/testdata/test_transform_test_flirtMatrixToSform.txt
diff --git a/tests/testdata/test_transform_test_invert.txt b/tests/test_transform/testdata/test_transform_test_invert.txt
similarity index 100%
rename from tests/testdata/test_transform_test_invert.txt
rename to tests/test_transform/testdata/test_transform_test_invert.txt
diff --git a/tests/testdata/test_transform_test_scaleoffsetxform.txt b/tests/test_transform/testdata/test_transform_test_scaleoffsetxform.txt
similarity index 100%
rename from tests/testdata/test_transform_test_scaleoffsetxform.txt
rename to tests/test_transform/testdata/test_transform_test_scaleoffsetxform.txt
diff --git a/tests/testdata/test_transform_test_transform_00.txt b/tests/test_transform/testdata/test_transform_test_transform_00.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_00.txt
rename to tests/test_transform/testdata/test_transform_test_transform_00.txt
diff --git a/tests/testdata/test_transform_test_transform_01.txt b/tests/test_transform/testdata/test_transform_test_transform_01.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_01.txt
rename to tests/test_transform/testdata/test_transform_test_transform_01.txt
diff --git a/tests/testdata/test_transform_test_transform_02.txt b/tests/test_transform/testdata/test_transform_test_transform_02.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_02.txt
rename to tests/test_transform/testdata/test_transform_test_transform_02.txt
diff --git a/tests/testdata/test_transform_test_transform_03.txt b/tests/test_transform/testdata/test_transform_test_transform_03.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_03.txt
rename to tests/test_transform/testdata/test_transform_test_transform_03.txt
diff --git a/tests/testdata/test_transform_test_transform_04.txt b/tests/test_transform/testdata/test_transform_test_transform_04.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_04.txt
rename to tests/test_transform/testdata/test_transform_test_transform_04.txt
diff --git a/tests/testdata/test_transform_test_transform_05.txt b/tests/test_transform/testdata/test_transform_test_transform_05.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_05.txt
rename to tests/test_transform/testdata/test_transform_test_transform_05.txt
diff --git a/tests/testdata/test_transform_test_transform_06.txt b/tests/test_transform/testdata/test_transform_test_transform_06.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_06.txt
rename to tests/test_transform/testdata/test_transform_test_transform_06.txt
diff --git a/tests/testdata/test_transform_test_transform_07.txt b/tests/test_transform/testdata/test_transform_test_transform_07.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_07.txt
rename to tests/test_transform/testdata/test_transform_test_transform_07.txt
diff --git a/tests/testdata/test_transform_test_transform_08.txt b/tests/test_transform/testdata/test_transform_test_transform_08.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_08.txt
rename to tests/test_transform/testdata/test_transform_test_transform_08.txt
diff --git a/tests/testdata/test_transform_test_transform_09.txt b/tests/test_transform/testdata/test_transform_test_transform_09.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_09.txt
rename to tests/test_transform/testdata/test_transform_test_transform_09.txt
diff --git a/tests/testdata/test_transform_test_transform_10.txt b/tests/test_transform/testdata/test_transform_test_transform_10.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_10.txt
rename to tests/test_transform/testdata/test_transform_test_transform_10.txt
diff --git a/tests/testdata/test_transform_test_transform_11.txt b/tests/test_transform/testdata/test_transform_test_transform_11.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_11.txt
rename to tests/test_transform/testdata/test_transform_test_transform_11.txt
diff --git a/tests/testdata/test_transform_test_transform_12.txt b/tests/test_transform/testdata/test_transform_test_transform_12.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_12.txt
rename to tests/test_transform/testdata/test_transform_test_transform_12.txt
diff --git a/tests/testdata/test_transform_test_transform_13.txt b/tests/test_transform/testdata/test_transform_test_transform_13.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_13.txt
rename to tests/test_transform/testdata/test_transform_test_transform_13.txt
diff --git a/tests/testdata/test_transform_test_transform_14.txt b/tests/test_transform/testdata/test_transform_test_transform_14.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_14.txt
rename to tests/test_transform/testdata/test_transform_test_transform_14.txt
diff --git a/tests/testdata/test_transform_test_transform_15.txt b/tests/test_transform/testdata/test_transform_test_transform_15.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_15.txt
rename to tests/test_transform/testdata/test_transform_test_transform_15.txt
diff --git a/tests/testdata/test_transform_test_transform_16.txt b/tests/test_transform/testdata/test_transform_test_transform_16.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_16.txt
rename to tests/test_transform/testdata/test_transform_test_transform_16.txt
diff --git a/tests/testdata/test_transform_test_transform_17.txt b/tests/test_transform/testdata/test_transform_test_transform_17.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_17.txt
rename to tests/test_transform/testdata/test_transform_test_transform_17.txt
diff --git a/tests/testdata/test_transform_test_transform_18.txt b/tests/test_transform/testdata/test_transform_test_transform_18.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_18.txt
rename to tests/test_transform/testdata/test_transform_test_transform_18.txt
diff --git a/tests/testdata/test_transform_test_transform_19.txt b/tests/test_transform/testdata/test_transform_test_transform_19.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_19.txt
rename to tests/test_transform/testdata/test_transform_test_transform_19.txt
diff --git a/tests/testdata/test_transform_test_transform_20.txt b/tests/test_transform/testdata/test_transform_test_transform_20.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_20.txt
rename to tests/test_transform/testdata/test_transform_test_transform_20.txt
diff --git a/tests/testdata/test_transform_test_transform_coords.txt b/tests/test_transform/testdata/test_transform_test_transform_coords.txt
similarity index 100%
rename from tests/testdata/test_transform_test_transform_coords.txt
rename to tests/test_transform/testdata/test_transform_test_transform_coords.txt
--
GitLab