TEST: More basic tests for x5 scripts

tests/test_scripts/test_fsl_apply_x5.py

@@ -3,6 +3,8 @@
 
 import numpy as np
 
+import pytest
+
 import fsl.scripts.fsl_apply_x5 as fsl_apply_x5
 import fsl.data.image           as fslimage
 import fsl.utils.image.resample as resample
@@ -31,6 +33,17 @@ def _random_image(aff, shape=None):
     return fslimage.Image(data, xform=aff)
 
 
+def test_help():
+    def run(args):
+        with pytest.raises(SystemExit) as e:
+            fsl_apply_x5.main(args)
+        assert e.value.code == 0
+
+    run([])
+    run(['-h'])
+
+
+
 def test_linear():
     with tempdir.tempdir():
 

tests/test_scripts/test_fsl_convert_x5.py

@@ -2,6 +2,9 @@
 
 
 import os.path as op
+import hashlib
+
+import pytest
 
 import numpy as np
 
@@ -28,6 +31,20 @@ def random_image():
     return fslimage.Image(data, xform=aff)
 
 
+def test_convert_flirt_help():
+
+    def run(args):
+        with pytest.raises(SystemExit) as e:
+            fsl_convert_x5.main(args)
+        assert e.value.code == 0
+
+    run([])
+    run(['-h'])
+    run(['flirt'])
+    run(['fnirt'])
+    run(['flirt', '-h'])
+    run(['fnirt', '-h'])
+
 
 def test_convert_flirt():
     with tempdir.tempdir():
@@ -60,6 +77,42 @@ def test_convert_flirt():
         assert np.all(np.isclose(gotxform, xform))
 
 
+def test_convert_flirt_sameformat():
+    with tempdir.tempdir():
+        src = random_image()
+        ref = random_image()
+        src.save('src')
+        ref.save('ref')
+
+        xform = affine.compose(
+            np.random.randint(1, 10, 3),
+            np.random.randint(-100, 100, 3),
+            (np.random.random(3) - 0.5) * np.pi)
+
+        np.savetxt('src2ref.mat', xform)
+
+        # test both .mat and .x5
+        fsl_convert_x5.main('flirt -s src -r ref '
+                            'src2ref.mat src2ref.x5'.split())
+
+        # mat -> mat
+        fsl_convert_x5.main('flirt -s src -r ref '
+                            'src2ref.mat copy.mat'.split())
+
+        # x5 -> x5
+        fsl_convert_x5.main('flirt -s src -r ref '
+                            'src2ref.x5 copy.x5'.split())
+
+        with open('src2ref.mat', 'rb') as f: origmat = hashlib.md5(f.read()).digest()
+        with open('copy.mat',    'rb') as f: copymat = hashlib.md5(f.read()).digest()
+        with open('src2ref.x5',  'rb') as f: origx5  = hashlib.md5(f.read()).digest()
+        with open('copy.x5',     'rb') as f: copyx5  = hashlib.md5(f.read()).digest()
+
+        assert origmat == copymat
+        assert origx5  == copyx5
+
+
+
 def test_convert_fnirt_deformation_field():
 
     datadir = op.join(op.dirname(__file__), '..',
@@ -124,3 +177,33 @@ def test_convert_fnirt_coefficient_field():
         diff = np.abs(dfnii.data -  df.data)
         tols = {'rtol' : 1e-5, 'atol' : 1e-5}
         assert np.all(np.isclose(dfnii.data, df.data, **tols))
+
+
+def test_convert_fnirt_sameformat():
+
+    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():
+
+        base = list('fnirt -s {} -r {}'.format(srcfile, reffile).split())
+
+        # test both .mat and .x5
+        fsl_convert_x5.main(base + [dffile, 'src2ref.x5'])
+
+        # nii -> nii
+        fsl_convert_x5.main(base + [dffile, 'copy.nii.gz'])
+
+        # x5 -> x5
+        fsl_convert_x5.main(base + [dffile, 'copy.x5'])
+
+        with open(dffile,        'rb') as f: origdef = hashlib.md5(f.read()).digest()
+        with open('copy.nii.gz', 'rb') as f: copydef = hashlib.md5(f.read()).digest()
+        with open('src2ref.x5',  'rb') as f: origx5  = hashlib.md5(f.read()).digest()
+        with open('copy.x5',     'rb') as f: copyx5  = hashlib.md5(f.read()).digest()
+
+        assert origdef == copydef
+        assert origx5  == copyx5