Transform module testing complete

tests/test_transform.py

@@ -13,6 +13,7 @@ import numpy     as np
 import pytest
 
 import fsl.utils.transform as transform
+import fsl.data.image      as fslimage
 
 
 datadir = op.join(op.dirname(__file__), 'testdata')
@@ -253,3 +254,53 @@ def test_transform():
 
     with pytest.raises(ValueError):
         transform.transform(badcoords[:, (1, 2, 3)], xform, axes=[1, 2])
+
+
+def test_flirtMatrixToSform():
+    
+    testfile = op.join(datadir, 'test_transform_test_flirtMatrixToSform.txt')
+    lines    = readlines(testfile)
+    ntests   = len(lines) / 18
+
+    for i in range(ntests):
+        tlines    = lines[i * 18: i * 18 + 18]
+        srcShape  = [int(  w) for w in tlines[0].split()]
+        srcXform  = np.genfromtxt(tlines[1:5])
+        refShape  = [int(  w) for w in tlines[5].split()]
+        refXform  = np.genfromtxt(tlines[6:10])
+        flirtMat  = np.genfromtxt(tlines[10:14])
+        expected  = np.genfromtxt(tlines[14:18])
+
+        srcImg = fslimage.Image(np.zeros(srcShape), xform=srcXform)
+        refImg = fslimage.Image(np.zeros(refShape), xform=refXform)
+
+        result = transform.flirtMatrixToSform(flirtMat, srcImg, refImg)
+
+        assert np.all(np.isclose(result, expected))
+
+
+def test_sformToFlirtMatrix():
+    testfile = op.join(datadir, 'test_transform_test_flirtMatrixToSform.txt')
+    lines    = readlines(testfile)
+    ntests   = len(lines) / 18
+
+    for i in range(ntests):
+        tlines      = lines[i * 18: i * 18 + 18]
+        srcShape    = [int(  w) for w in tlines[0].split()]
+        srcXform    = np.genfromtxt(tlines[1:5])
+        refShape    = [int(  w) for w in tlines[5].split()]
+        refXform    = np.genfromtxt(tlines[6:10])
+        expected    = np.genfromtxt(tlines[10:14])
+        srcXformOvr = np.genfromtxt(tlines[14:18])
+
+        srcImg1 = fslimage.Image(np.zeros(srcShape), xform=srcXform)
+        srcImg2 = fslimage.Image(np.zeros(srcShape), xform=srcXform)
+        refImg  = fslimage.Image(np.zeros(refShape), xform=refXform)
+
+        srcImg2.voxToWorldMat = srcXformOvr
+
+        result1 = transform.sformToFlirtMatrix(srcImg1, refImg, srcXformOvr)
+        result2 = transform.sformToFlirtMatrix(srcImg2, refImg)
+
+        assert np.all(np.isclose(result1, expected))
+        assert np.all(np.isclose(result2, expected))

tests/testdata/test_transform_test_flirtMatrixToSform.txt

+# Test data for test_trasform:test_flirtMatrixToSform.
+#
+# Source shape
+# Source sform
+# Ref shape
+# Ref sform
+# Flirt mat
+# Expected result
+64 64 51
+-3 0 0 0
+ 0 3 0 0
+ 0 0 3 0
+ 0 0 0 1
+174 192 192
+-1 0 0 0
+ 0 1 0 0
+ 0 0 1 0
+ 0 0 0 1
+0.999902305     -0.01382370227  -0.002076008527 -9.96418133
+0.01387598986    0.9995186947    0.02774033918  -0.9784486659
+0.001691535807  -0.02776642771   0.999613178     34.26763376
+0  0  0  1
+-2.9997069836   0.0414711051   0.0062280255   9.9641809464
+ 0.0416279696   2.9985561371   0.0832210183  -0.978448689 
+ 0.0050746072  -0.0832992867   2.9988396168  34.2676353455
+ 0.0            0.0            0.0            1.0
+
+64 64 51
+-3 0 0 0
+ 0 3 0 0
+ 0 0 3 0
+ 0 0 0 1
+91 109 91
+-2.0  0.0  -0.0   90.0
+ 0.0  2.0  -0.0 -126.0
+ 0.0  0.0   2.0  -72.0
+ 0.0  0.0   0.0    1.0
+1.066596657  0.04185305106  0.0313680447  -21.01545453
+-0.0278838133  1.08492943  0.1200141384  3.254608605
+-0.02264077087  -0.1506102631  1.159656209  14.04435425
+0  0  0  1
+-3.1997900009   -0.1255591512   -0.0941041335  111.0154571533
+-0.0836514384    3.2547883987    0.360042423  -122.7453918457
+-0.067922309    -0.4518307745    3.4789686203  -57.9556465149
+ 0.0             0.0             0.0             1.0
+
+96 96 65
+-2 0 0 0
+ 0 2 0 0
+ 0 0 2 0
+ 0 0 0 1
+182 218 182
+-1.0  0.0  -0.0   90.0
+ 0.0  1.0  -0.0 -126.0
+ 0.0  0.0   1.0  -72.0
+ 0.0  0.0   0.0    1.0
+0.9770925311  0.2282763526  0.08361742115  -31.03359277
+-0.2174139321  1.034970829  0.2368454135  21.28393351
+-0.03214544114  -0.1330475704  1.107802568  23.65687239
+0  0  0  1
+-1.954185009    -0.4565527141   -0.167234838   121.0335922241
+-0.4348278642    2.0699417591    0.4736908376 -104.7160644531
+-0.0642908812   -0.2660951316    2.2156050205  -48.3431282043
+ 0.0             0.0             0.0             1.0
+
+64 64 21
+-4 0 0 0
+ 0 4 0 0
+ 0 0 6 0
+ 0 0 0 1
+256 256 128
+-1.0 0.0 0.0  0.0
+ 0.0 1.0 0.0  0.0
+ 0.0 0.0 1.25 0.0
+ 0.0 0.0 0.0  1.0
+1.04608  -0.0092732  -0.0230782  -3.88992
+0.00607773  1.01145  0.105602  -3.84974
+0.0244433  -0.0793108  1.05191  15.932
+0  0  0  1
+-4.184319973    0.0370928012   0.1384692043   3.8899199963
+ 0.0243109204   4.045800209    0.6336119771  -3.8497400284
+ 0.0977732018  -0.3172431886   6.3114600182  15.9320001602
+ 0.0            0.0            0.0            1.0