TEST: test fslstats wrapper

tests/test_wrappers/test_fslstats.py

+#!/usr/bin/env python
+
+
+import os
+import os.path as op
+import sys
+import contextlib
+
+import numpy as np
+
+import fsl.utils.run as run
+import fsl.utils.tempdir as tempdir
+import fsl.wrappers  as fw
+
+from .. import mockFSLDIR as mockFSLDIR_base, make_random_image
+
+
+mock_fslstats = """
+#!{}
+
+shape = {{outshape}}
+
+import sys
+import numpy as np
+
+data = np.random.randint(1, 10, shape)
+
+if len(shape) == 1:
+    data = data.reshape(1, -1)
+
+np.savetxt(sys.stdout, data, fmt='%i')
+""".format(sys.executable).strip()
+
+
+@contextlib.contextmanager
+def mockFSLDIR(shape):
+    with mockFSLDIR_base() as fd:
+        fname  = op.join(fd, 'bin', 'fslstats')
+        script = mock_fslstats.format(outshape=shape)
+        with open(fname, 'wt') as f:
+            f.write(script)
+        os.chmod(fname, 0o755)
+        yield fd
+
+
+def test_fslstats_cmdline():
+    with tempdir.tempdir(), run.dryrun(), mockFSLDIR(1) as fsldir:
+
+        make_random_image('image')
+        cmd = op.join(fsldir, 'bin', 'fslstats')
+
+        result   = fw.fslstats('image').m.r.mask('mask').k('mask').r.run(True)
+        expected = cmd + ' image -m -r -k mask -k mask -r'
+        assert result[0] == expected
+
+        result   = fw.fslstats('image', t=True, K='mask').m.R.u(123).s.volume.run(True)
+        expected = cmd + ' -t -K mask image -m -R -u 123 -s -v'
+        assert result[0] == expected
+
+        result   = fw.fslstats('image', K='mask').n.V.p(1).run(True)
+        expected = cmd + ' -K mask image -n -V -p 1'
+        assert result[0] == expected
+
+        result   = fw.fslstats('image', t=True).H(10, 1, 99).d('diff').run(True)
+        expected = cmd + ' -t image -H 10 1 99 -d diff'
+        assert result[0] == expected
+
+
+def test_fslstats_result():
+    with tempdir.tempdir():
+
+        with mockFSLDIR('(1,)') as fsldir:
+            result = fw.fslstats('image').run()
+            assert np.isscalar(result)
+
+        with mockFSLDIR('(2,)') as fsldir:
+            result = fw.fslstats('image').run()
+            assert result.shape == (2,)
+
+        # 3 mask lbls, 2 values
+        with mockFSLDIR('(3, 2)') as fsldir:
+            result = fw.fslstats('image', K='mask').run()
+            assert result.shape == (3, 2)
+
+        # 5 vols, 2 values
+        with mockFSLDIR('(5, 2)') as fsldir:
+            result = fw.fslstats('image', t=True).run()
+            assert result.shape == (5, 2)
+
+        # 5 vols, 3 mask lbls, 2 values
+        with mockFSLDIR('(15, 2)') as fsldir:
+            make_random_image('image', (10, 10, 10, 5))
+            result = fw.fslstats('image', K='mask', t=True).run()
+            assert result.shape == (5, 3, 2)