TEST: Test convertx5 script

tests/test_scripts/test_fsl_convert_x5.py

 #!/usr/bin/env python
 
 
+import os.path as op
+
 import numpy as np
 
 import fsl.utils.tempdir    as tempdir
 import fsl.transform.affine as affine
 import fsl.transform.flirt  as flirt
+import fsl.transform.fnirt  as fnirt
 import fsl.transform.x5     as x5
 import fsl.data.image       as fslimage
 
 import fsl.scripts.fsl_convert_x5 as fsl_convert_x5
 
 
+
 def random_image():
     vx, vy, vz = np.random.randint(10, 50, 3)
     dx, dy, dz = np.random.randint( 1, 10, 3)
@@ -50,8 +54,70 @@ def test_convert_flirt():
         assert src.sameSpace(gotsrc)
         assert ref.sameSpace(gotref)
 
-        fsl_convert_x5.main('flirt -s src -r ref src2ref.x5 '
-                            'src2ref_copy.mat'.split())
+        fsl_convert_x5.main('flirt src2ref.x5 src2ref_copy.mat'.split())
 
         gotxform = flirt.readFlirt('src2ref_copy.mat')
         assert np.all(np.isclose(gotxform, xform))
+
+
+def test_convert_fnirt_displacement_field():
+
+    datadir = op.join(op.dirname(__file__), '..',
+                      'test_transform', 'testdata', 'nonlinear')
+    srcfile = op.join(datadir, 'src.nii.gz')
+    reffile = op.join(datadir, 'ref.nii.gz')
+    dffile  = op.join(datadir, 'displacementfield.nii.gz')
+
+    with tempdir.tempdir():
+
+        # nii -> x5
+        fsl_convert_x5.main('fnirt -s {} -r {} {} disp.x5'.format(
+            srcfile, reffile, dffile).split())
+
+        # x5 -> nii
+        fsl_convert_x5.main('fnirt disp.x5 disp.nii.gz'.split())
+
+        src   = fslimage.Image(srcfile)
+        ref   = fslimage.Image(reffile)
+        df    = fnirt.readFnirt(dffile, src, ref)
+        dfnii = fnirt.readFnirt('disp.nii.gz', src, ref)
+
+        assert dfnii.src.sameSpace(src)
+        assert dfnii.ref.sameSpace(ref)
+        assert dfnii.srcSpace == df.srcSpace
+        assert dfnii.refSpace == df.refSpace
+        assert dfnii.displacementType == df.displacementType
+        assert np.all(np.isclose(dfnii.data, df.data))
+
+
+def test_convert_fnirt_coefficient_field():
+
+    datadir = op.join(op.dirname(__file__), '..',
+                      'test_transform', 'testdata', 'nonlinear')
+    srcfile = op.join(datadir, 'src.nii.gz')
+    reffile = op.join(datadir, 'ref.nii.gz')
+    cffile  = op.join(datadir, 'coefficientfield.nii.gz')
+
+    with tempdir.tempdir():
+
+        # nii -> x5
+        fsl_convert_x5.main('fnirt -s {} -r {} {} coef.x5'.format(
+            srcfile, reffile, cffile).split())
+
+        # x5 -> nii
+        fsl_convert_x5.main('fnirt coef.x5 coef.nii.gz'.split())
+
+        src   = fslimage.Image(srcfile)
+        ref   = fslimage.Image(reffile)
+        cf    = fnirt.readFnirt(cffile, src, ref)
+        cfnii = fnirt.readFnirt('coef.nii.gz', src, ref)
+
+        assert cfnii.src.sameSpace(src)
+        assert cfnii.ref.sameSpace(ref)
+        assert cfnii.srcSpace    == cf.srcSpace
+        assert cfnii.refSpace    == cf.refSpace
+        assert cfnii.knotSpacing == cf.knotSpacing
+
+        assert np.all(np.isclose(cfnii.fieldToRefMat, cf.fieldToRefMat))
+        assert np.all(np.isclose(cfnii.srcToRefMat,   cf.srcToRefMat))
+        assert np.all(np.isclose(cfnii.data,          cf.data))