diff --git a/tests/test_transform.py b/tests/test_transform.py
index 709337990997080288c8df10797b33c06936280c..6d1991adb4e30617ff217232defba61040a072ee 100644
--- a/tests/test_transform.py
+++ b/tests/test_transform.py
@@ -5,43 +5,116 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+import os.path as op
+
import numpy as np
-import numpy.linalg as npla
import fsl.utils.transform as transform
+
+datadir = op.join(op.dirname(__file__), 'testdata')
+
+
+def readlines(filename):
+ with open(filename, 'rt') as f:
+ lines = f.readlines()
+ lines = [l.strip() for l in lines]
+ lines = [l for l in lines if not l.startswith('#')]
+ lines = [l for l in lines if l != '']
+ return lines
+
+
+def test_invert():
+
+ testfile = op.join(datadir, 'test_transform_test_invert.txt')
+ testdata = np.loadtxt(testfile)
+
+ nmatrices = testdata.shape[0] / 4
+
+ for i in range(nmatrices):
+
+ x = testdata[i * 4:i * 4 + 4, 0:4]
+ invx = testdata[i * 4:i * 4 + 4, 4:8]
+ result = transform.invert(x)
+
+ assert np.all(np.isclose(invx, result))
+
+
+def test_concat():
+
+ testfile = op.join(datadir, 'test_transform_test_concat.txt')
+ lines = readlines(testfile)
+
+
+ ntests = len(lines) / 4
+ tests = []
+
+ for i in range(ntests):
+ ilines = lines[i * 4:i * 4 + 4]
+
+ data = np.genfromtxt(ilines)
+ ninputs = data.shape[1] / 4 - 1
+
+ inputs = []
+
+ for j in range(ninputs):
+ inputs.append(data[:, j * 4:j * 4 + 4])
+
+ output = data[:, -4:]
+
+ tests.append((inputs, output))
+
+ for inputs, expected in tests:
+
+ result = transform.concat(*inputs)
+
+ assert np.all(np.isclose(result, expected))
+
+
def test_scaleOffsetXform():
- scales = [1, 2, 3]
- offsets = [4, 5, 6]
+ testfile = op.join(datadir, 'test_transform_test_scaleoffsetxform.txt')
+ lines = readlines(testfile)
+ ntests = len(lines) / 5
- expected = np.eye(4)
- expected[0, 0] = scales[ 0]
- expected[1, 1] = scales[ 1]
- expected[2, 2] = scales[ 2]
- expected[0, 3] = offsets[0]
- expected[1, 3] = offsets[1]
- expected[2, 3] = offsets[2]
+ for i in range(ntests):
+
+ lineoff = i * 5
+ scales, offsets = lines[lineoff].split(',')
- generated = transform.scaleOffsetXform(scales, offsets)
+ scales = [float(s) for s in scales .split()]
+ offsets = [float(o) for o in offsets.split()]
- assert np.all(np.isclose(expected, generated))
+ expected = lines[lineoff + 1: lineoff + 5]
+ expected = [[float(v) for v in l.split()] for l in expected]
+ expected = np.array(expected)
+ result = transform.scaleOffsetXform(scales, offsets)
- scale = 5
- offset = 3
+ assert np.all(np.isclose(result, expected))
- expected = np.eye(4)
- expected[0, 0] = scale
- expected[1, 1] = 1
- expected[2, 2] = 1
- expected[2, 2] = 1
- expected[0, 3] = offset
- generated = transform.scaleOffsetXform(scale, offset)
- assert np.all(np.isclose(expected, generated))
+def test_compose_and_decompose():
+ testfile = op.join(datadir, 'test_transform_test_compose.txt')
+ lines = readlines(testfile)
+ ntests = len(lines) / 4
-def test_invert():
+ for i in range(ntests):
+
+ xform = lines[i * 4: i * 4 + 4]
+ xform = np.genfromtxt(xform)
+
+ scales, offsets, rotations = transform.decompose(xform)
+ result = transform.compose(scales, offsets, rotations)
+
+ assert np.all(np.isclose(xform, result))
+
+ # The decompose function does not support a
+ # different rotation origin, but we test
+ # explicitly passing the origin for
+ # completeness
+ scales, offsets, rotations = transform.decompose(xform)
+ result = transform.compose(scales, offsets, rotations, [0, 0, 0])
- pass
+ assert np.all(np.isclose(xform, result))
diff --git a/tests/testdata/test_transform_test_compose.txt b/tests/testdata/test_transform_test_compose.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28161a926d99eddb164ed600677c19491075879e
--- /dev/null
+++ b/tests/testdata/test_transform_test_compose.txt
@@ -0,0 +1,66 @@
+# Test data for test_transform:test_compose.
+#
+# Each test is just an affine transformation matrix.
+# The matrix is decomposed into its components,
+# and then recomposed, and the result compared with
+# the input.
+
+1.0 0.0 0.0 0.0
+0.0 1.0 0.0 0.0
+0.0 0.0 1.0 0.0
+0.0 0.0 0.0 1.0
+
+
+-1.0 0.0 0.0 0.0
+0.0 1.0 0.0 0.0
+0.0 0.0 1.0 0.0
+0.0 0.0 0.0 1.0
+
+1.0 0.0 0.0 0.0
+0.0 -1.0 0.0 0.0
+0.0 0.0 1.0 0.0
+0.0 0.0 0.0 1.0
+
+1.0 0.0 0.0 0.0
+0.0 1.0 0.0 0.0
+0.0 0.0 -1.0 0.0
+0.0 0.0 0.0 1.0
+
+0.5 0.0 0.0 0.0
+0.0 2.4 0.0 0.0
+0.0 0.0 1.6 0.0
+0.0 0.0 0.0 1.0
+
+0.5 0.0 0.0 10.0
+0.0 2.4 0.0 -25.0
+0.0 0.0 1.6 53.0
+0.0 0.0 0.0 1.0
+
+0.5 0.0 0.0 10.0
+0.0 0.0 -1.6 -6.7877502441
+0.0 2.4 0.0 29.7931518555
+0.0 0.0 0.0 1.0
+
+0.0 -2.4 -0.0 30.6160888672
+0.0 0.0 -1.6 -6.7877502441
+0.5 0.0 0.0 50.5961608887
+0.0 0.0 0.0 1.0
+
+-0.0 1.3765834472 1.3106432709 0.0736983719
+ 0.0 -1.9659649063 0.9177222982 14.1062102814
+ 0.5 0.0 0.0 50.5961608887
+ 0.0 0.0 0.0 1.0
+
+ 0.453766452 -0.7004337463 0.4832135801 16.789591468
+-0.0159784155 1.6056689296 1.1880787388 -16.2943532298
+-0.2093817023 -1.640493784 0.9565424959 66.1123321137
+ 0.0 0.0 0.0 1.0
+
+-1.1974397443 -0.8580717933 -0.3645386503 -50.0240993667
+-0.7458801726 1.1196201539 -0.5710576979 -106.3700007704
+ 0.7128023509 -0.2699020211 -1.2099478647 -7.4191935569
+ 0.0 0.0 0.0 1.0
+
+
+
+
diff --git a/tests/testdata/test_transform_test_concat.txt b/tests/testdata/test_transform_test_concat.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6218eec65a80fce0c6137aa3b936844b866bcf98
--- /dev/null
+++ b/tests/testdata/test_transform_test_concat.txt
@@ -0,0 +1,55 @@
+# Test data for test_transform:test_concat.
+#
+# Each set of four lines contains a set of 4x4
+# matrices to be concatenated (in order). The
+# last matrix of each set is the expected result.
+
+1 0 0 0 1 0 0 0
+0 1 0 0 0 1 0 0
+0 0 1 0 0 0 1 0
+0 0 0 1 0 0 0 1
+
+1 0 0 0 1 0 0 0 1 0 0 0
+0 1 0 0 0 1 0 0 0 1 0 0
+0 0 1 0 0 0 1 0 0 0 1 0
+0 0 0 1 0 0 0 1 0 0 0 1
+
+1 0 0 0 2 0 0 0 2 0 0 0
+0 1 0 0 0 1 0 0 0 1 0 0
+0 0 1 0 0 0 1 0 0 0 1 0
+0 0 0 1 0 0 0 1 0 0 0 1
+
+1 0 0 0 2 0 0 0 2 0 0 0
+0 2 0 0 0 1 0 0 0 2 0 0
+0 0 1 0 0 0 1 0 0 0 1 0
+0 0 0 1 0 0 0 1 0 0 0 1
+
+1 0 0 0 2 0 0 0 2 0 0 0
+0 2 0 0 0 1 0 0 0 2 0 0
+0 0 0.5 0 0 0 2 0 0 0 1 0
+0 0 0 1 0 0 0 1 0 0 0 1
+
+1 0 0 5 1 0 0 5 1 0 0 10
+0 1 0 0 0 1 0 0 0 1 0 0
+0 0 1 0 0 0 1 0 0 0 1 0
+0 0 0 1 0 0 0 1 0 0 0 1
+
+1 0 0 5 1 0 0 5 1 0 0 10
+0 1 0 10 0 1 0 -11 0 1 0 -1
+0 0 1 0 0 0 1 0 0 0 1 0
+0 0 0 1 0 0 0 1 0 0 0 1
+
+-0.9997461427 -0.0138411649 -0.0177840895 86.2687562744 0.4995293021 -0.0288470406 -0.0208370071 -52.4121894836 -0.4998648078 0.018194362 0.0057373182 141.0497999726
+-0.0129887148 0.9988017675 -0.0471861176 78.2934660214 0.0181582421 0.8188890815 0.0380228758 -79.7248840332 0.0110884427 0.8201107175 -0.0004052935 2.7375548032
+-0.0184158914 0.0469431359 0.9987278995 79.2867553867 0.0118636154 -0.0387438014 0.8191658258 -71.8998947144 0.0035016511 0.00027795 0.8202924096 4.7010056936
+ 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+
+-2.0 0.0 0.0 90.0 0.5 0.0 0.0 0.0 1.099592034 -0.0201869499 -0.0383800223 -13.9469605 3.0 0.0 0.0 0.0 -3.298776102 0.0605608496 0.1343300781 103.9469605
+ 0.0 2.0 0.0 -126.0 0.0 0.5 0.0 0.0 0.0351074645 0.9816051002 0.1625775275 7.338456156 0.0 3.0 0.0 0.0 0.1053223934 2.9448153006 0.5690213463 -118.661543844
+ 0.0 0.0 2.0 -72.0 0.0 0.0 0.5 0.0 0.056531896 -0.1960538631 1.18656088 29.70779308 0.0 0.0 3.5 0.0 0.1695956881 -0.5881615893 4.15296308 -42.29220692
+ 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+
+0.5 0.0 0.0 0.0 -2.0 -0.0 -0.0 180.0 -1.0697441868 0.0 0.0 98.5041786294 1.0 0.0 0.0 0.0 1.0697441868 0.0 0.0 -8.5041786294
+0.0 0.5 0.0 0.0 0.0 2.0 0.0 252.0 0.0 1.0030898154 0.223667641 -133.9357410938 0.0 1.0 0.0 0.0 0.0 1.0030898154 0.223667641 -7.9357410938
+0.0 0.0 0.5 0.0 0.0 0.0 2.0 144.0 0.0 -0.202107448 1.1100963122 -77.9863761881 0.0 0.0 1.0 0.0 0.0 -0.202107448 1.1100963122 -5.9863761881
+0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
diff --git a/tests/testdata/test_transform_test_invert.txt b/tests/testdata/test_transform_test_invert.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21c3251c2bb8d60ac798904d55133a3a4d11f2a6
--- /dev/null
+++ b/tests/testdata/test_transform_test_invert.txt
@@ -0,0 +1,64 @@
+# Test data for test_transform:test_invert.
+#
+# Pairs of 4x4 matrices - columns 0-3 are
+# the matrix, and 4-7 are its inverse
+
+1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0
+0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0
+0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0
+0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+
+2.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0
+0.0 2.0 0.0 0.0 0.0 0.5 0.0 0.0
+0.0 0.0 2.0 0.0 0.0 0.0 0.5 0.0
+0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+
+0.5 0.0 0.0 0.0 2.0 0.0 0.0 0.0
+0.0 0.5 0.0 0.0 0.0 2.0 0.0 0.0
+0.0 0.0 0.5 0.0 0.0 0.0 2.0 0.0
+0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+
+-2.0 0.0 0.0 90.0 -0.5 0.0 0.0 45.0
+ 0.0 2.0 0.0 -126.0 0.0 0.5 0.0 63.0
+ 0.0 0.0 2.0 -72.0 0.0 0.0 0.5 36.0
+ 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
+
+-1.000000 0.000000 0.000000 90.000000 -1.0 -0.0 -0.0 90.0
+ 0.000000 1.000000 0.000000 -126.000000 0.0 1.0 0.0 126.0
+ 0.000000 0.000000 1.000000 -72.000000 0.0 0.0 1.0 72.0
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+-0.500000 0.000000 -0.000000 90.000000 -2.0 -0.0 -0.0 180.0
+ 0.000000 0.500000 -0.000000 -126.000000 0.0 2.0 0.0 252.0
+ 0.000000 0.000000 0.500000 -72.000000 0.0 0.0 2.0 144.0
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+-0.998351 0.172174 -0.001494 88.454048 -0.9983502856 0.0558051012 0.0134829296 94.7258462378
+ 0.055805 2.891963 -0.260024 -92.767029 0.0191304269 0.3213296014 0.0865595511 36.0827985889
+ 0.013483 0.779035 0.965601 -92.031090 -0.001493904 -0.2600239915 0.9656009985 64.8758010985
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+-0.374721 0.013086 0.098275 97.767311 -2.66468674 0.0722679469 0.0731063439 275.2545057881
+ 0.010162 0.351788 -2.071789 -111.735596 0.093050276 2.5016056231 0.9189276383 354.1399342608
+ 0.010280 0.129224 5.630100 -91.104904 0.0027297296 -0.0575496704 0.1563917091 7.5508265955
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+-0.388466 -0.008614 -0.667304 102.035919 -2.5458450588 0.2688093573 -0.0000011573 240.3890243945
+ 0.041017 -0.081580 -6.319922 72.090378 -0.0564513141 -0.5346421283 2.502913283 147.3211514593
+-0.000000 0.381914 -1.365036 -41.159451 -0.0157941235 -0.1495838306 -0.0323085812 11.0653193311
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+ 0.187901 0.567822 -0.807414 301.810486 0.187902 0.515238 0.836195 -331.561887
+ 0.515238 0.376990 0.874776 -291.188751 0.955833 0.634599 -0.605804 204.125469
+ 0.836196 -0.359885 -0.357576 508.114258 -0.522595 0.566194 -0.231439 440.191288
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+-2.000000 0.000000 -0.000000 90.000000 -0.5 -0.0 -0.0 45.0
+ 0.000000 0.000000 -2.000000 90.000000 0.0 0.0 0.5 36.0
+ 0.000000 2.000000 -0.000000 -72.000000 -0.0 -0.5 -0.0 45.0
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
+
+ 1.912642 0.560466 0.166370 -120.273781 0.4781604465 0.0748382388 -0.125546007 48.6068918211
+ 0.299353 -0.449972 -1.925594 92.759918 0.1401164411 -0.1124929472 0.4665968825 34.5763635373
+-0.502184 1.866388 -0.514206 -15.622035 0.0415925106 -0.4813986086 -0.1285515567 47.6487470535
+ 0.000000 0.000000 0.000000 1.000000 0.0 0.0 0.0 1.0
diff --git a/tests/testdata/test_transform_test_scaleoffsetxform.txt b/tests/testdata/test_transform_test_scaleoffsetxform.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5b0944060425167784712df6b9489b1e0380a59
--- /dev/null
+++ b/tests/testdata/test_transform_test_scaleoffsetxform.txt
@@ -0,0 +1,54 @@
+# Test data for test_transform:test_scaleOffsetXform.
+#
+# The first line specifies the scale and
+# offset parameters (separated with a comma).
+# This is followed by the expected
+#
+#
+1, 0
+1 0 0 0
+0 1 0 0
+0 0 1 0
+0 0 0 1
+
+1 1, 0
+1 0 0 0
+0 1 0 0
+0 0 1 0
+0 0 0 1
+
+1 1 1, 0
+1 0 0 0
+0 1 0 0
+0 0 1 0
+0 0 0 1
+
+1, 1
+1 0 0 1
+0 1 0 0
+0 0 1 0
+0 0 0 1
+
+1 1, 1 1
+1 0 0 1
+0 1 0 1
+0 0 1 0
+0 0 0 1
+
+1 1 1, 1 1 1
+1 0 0 1
+0 1 0 1
+0 0 1 1
+0 0 0 1
+
+1 2 3, 4 5 6
+1 0 0 4
+0 2 0 5
+0 0 3 6
+0 0 0 1
+
+1 10, 20 5 5
+1 0 0 20
+0 10 0 5
+0 0 1 5
+0 0 0 1