Merge branch 'enh/pathutils' into 'master'

Enh/pathutils

See merge request fsl/fslpy!247

tests/test_scripts/test_imrm.py

+#!/usr/bin/env python
+#
+# test_imrm.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+
+from fsl.utils.tempdir import tempdir
+import fsl.scripts.imrm as imrm
+
+from tests import touch
+
+def test_imrm_usage():
+    assert imrm.main([]) != 0
+
+
+def test_imrm():
+    # (files present, command, expected)
+    tests = [
+        ('a.nii',       'a',       ''),
+        ('a.nii.gz',    'a',       ''),
+        ('a.img a.hdr', 'a',       ''),
+        ('a.img',       'a',       ''),
+        ('a.hdr',       'a',       ''),
+        ('a.nii b.nii', 'a',       'b.nii'),
+        ('a.nii b.nii', 'a b',     ''),
+        ('a.nii b.nii', 'a b.nii', ''),
+
+        # suffix doesn't have to be correct
+        ('a.nii.gz', 'a.nii',  ''),
+
+        # files don't exist -> no problem
+        ('a.nii', 'b',  'a.nii'),
+    ]
+
+    for files, command, expected in tests:
+        with tempdir():
+
+            for f in files.split():
+                touch(f)
+
+            print('files',    files)
+            print('command',  command)
+            print('expected', expected)
+
+            ret = imrm.main(('imrm ' + command).split())
+
+            assert ret == 0
+            assert sorted(os.listdir()) == sorted(expected.split())

tests/test_scripts/test_imtest.py

+#!/usr/bin/env python
+#
+# test_imtest.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+import os.path as op
+
+import fsl.utils.path     as fslpath
+from   fsl.utils.tempdir  import tempdir
+
+import fsl.scripts.imtest as imtest
+
+from tests import CaptureStdout, touch
+
+
+def test_wrongargs():
+    cap = CaptureStdout()
+    with cap:
+        assert imtest.main([]) == 0
+    assert cap.stdout.strip() == '0'
+
+
+def test_imtest():
+    # (files, input, expected)
+    tests = [
+        ('a.nii', 'a',        '1'),
+        ('a.nii', 'a.nii',    '1'),
+        ('a.nii', 'a.nii.gz', '1'), # imtest is suffix-agnostic
+
+        ('a.img a.hdr', 'a',     '1'),
+        ('a.img a.hdr', 'a.img', '1'),
+        ('a.img a.hdr', 'a.hdr', '1'),
+        ('a.img',       'a',     '0'),
+        ('a.img',       'a.img', '0'),
+        ('a.img',       'a.hdr', '0'),
+        ('a.hdr',       'a',     '0'),
+        ('a.hdr',       'a.img', '0'),
+        ('a.hdr',       'a.hdr', '0'),
+
+        ('dir/a.nii',           'dir/a', '1'),
+        ('dir/a.img dir/a.hdr', 'dir/a', '1'),
+    ]
+
+    for files, input, expected in tests:
+        with tempdir():
+            for f in files.split():
+                dirname = op.dirname(f)
+                if dirname != '':
+                    os.makedirs(dirname, exist_ok=True)
+                touch(f)
+
+            cap = CaptureStdout()
+            with cap:
+                assert imtest.main([input]) == 0
+
+            assert cap.stdout.strip() == expected
+
+    # test that sym-links are
+    # followed correctly
+    with tempdir():
+        touch('image.nii.gz')
+        os.symlink('image.nii.gz', 'link.nii.gz')
+        cap = CaptureStdout()
+        with cap:
+            assert imtest.main(['link']) == 0
+        assert cap.stdout.strip() == '1'
+
+    # sym-links in sub-directories
+    # (old imtest would not work
+    # in this scenario)
+    with tempdir():
+        os.mkdir('subdir')
+        impath = op.join('subdir', 'image.nii.gz')
+        lnpath = op.join('subdir', 'link.nii.gz')
+        touch(impath)
+        os.symlink('image.nii.gz', lnpath)
+        cap = CaptureStdout()
+        with cap:
+            assert imtest.main([lnpath]) == 0
+        assert cap.stdout.strip() == '1'

tests/test_scripts/test_remove_ext.py

+#!/usr/bin/env python
+#
+# test_remove_ext.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import fsl.scripts.remove_ext as remove_ext
+
+from tests import CaptureStdout
+
+def test_usage():
+    assert remove_ext.main([]) != 0
+
+def test_remove_ext():
+    # (input, expected output)
+    tests = [
+        ('a',                 'a'),
+        ('a.nii',             'a'),
+        ('a.nii.gz',          'a'),
+        ('a.txt',             'a.txt'),
+        ('a.nii b.img c.hdr', 'a b c'),
+        ('a.nii b.img b.hdr', 'a b b'),
+        ('a b.img c.txt',     'a b c.txt'),
+        ('a.nii.gz b c.mnc',  'a b c'),
+    ]
+
+    for input, expected in tests:
+
+        cap = CaptureStdout()
+        with cap:
+            ret = remove_ext.main(input.split())
+
+        assert ret == 0
+
+        got = cap.stdout.split()
+        assert sorted(got) == sorted(expected.split())

tests/test_scripts/test_vest2text.py

+#!/usr/bin/env python
+#
+# test_vest2text.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import numpy as np
+
+import fsl.data.vest         as fslvest
+import fsl.scripts.Text2Vest as Text2Vest
+import fsl.scripts.Vest2Text as Vest2Text
+
+from tests import tempdir
+
+
+def test_usage():
+    assert Vest2Text.main([]) == 0
+    assert Text2Vest.main([]) == 0
+
+
+def test_Vest2Text():
+    with tempdir():
+        data = np.random.random((20, 10))
+        vest = fslvest.generateVest(data)
+
+        with open('data.vest', 'wt') as f:
+            f.write(vest)
+
+        assert Vest2Text.main(['data.vest', 'data.txt']) == 0
+
+        got = np.loadtxt('data.txt')
+
+        assert np.all(np.isclose(data, got))
+
+
+def test_Text2Vest():
+    with tempdir():
+        data = np.random.random((20, 10))
+
+        np.savetxt('data.txt', data)
+
+        assert Text2Vest.main(['data.txt', 'data.vest']) == 0
+
+        got = fslvest.loadVestFile('data.vest', ignoreHeader=False)
+
+        assert np.all(np.isclose(data, got))

tests/test_vest.py

@@ -6,16 +6,20 @@
 #
 
 
-import os.path as op
-import            shutil
-import            tempfile
-import            warnings
+import os.path  as op
+import textwrap as tw
+import             io
+import             shutil
+import             tempfile
+import             warnings
 
-import numpy   as np
-import            pytest
+import numpy    as np
+import             pytest
 
 import fsl.data.vest as vest
 
+from tests import tempdir
+
 
 testfile1 = """%!VEST-LUT
 %%BeginInstance
@@ -214,3 +218,75 @@ def test_loadVestLutFile():
 
     finally:
         shutil.rmtree(testdir)
+
+
+def test_generateVest():
+    def readvest(vstr):
+        lines = vstr.split('\n')
+        nrows = [l for l in lines if 'NumPoints' in l][0]
+        ncols = [l for l in lines if 'NumWaves'  in l][0]
+        nrows = int(nrows.split()[1])
+        ncols = int(ncols.split()[1])
+        data  = '\n'.join(lines[3:])
+        data  = np.loadtxt(io.StringIO(data)).reshape((nrows, ncols))
+
+        return ((nrows, ncols), data)
+
+    # shape, expectedshape
+    tests = [
+        ((10,   ), ( 1, 10)),
+        ((10,  1), (10,  1)),
+        (( 1, 10), ( 1, 10)),
+        (( 3,  5), ( 3,  5)),
+        (( 5,  3), ( 5,  3))
+    ]
+
+    for shape, expshape in tests:
+        data = np.random.random(shape)
+        vstr = vest.generateVest(data)
+
+        gotshape, gotdata = readvest(vstr)
+
+        data = data.reshape(expshape)
+
+        assert expshape == gotshape
+        assert np.all(np.isclose(data, gotdata))
+
+
+def test_loadVestFile():
+    def genvest(data, path, shapeOverride=None):
+        if shapeOverride is None:
+            nrows, ncols = data.shape
+        else:
+            nrows, ncols = shapeOverride
+
+        with open(path, 'wt') as f:
+            f.write(f'/NumWaves {ncols}\n')
+            f.write(f'/NumPoints {nrows}\n')
+            f.write( '/Matrix\n')
+
+            if np.issubdtype(data.dtype, np.integer): fmt = '%d'
+            else:                                     fmt = '%0.12f'
+
+            np.savetxt(f, data, fmt=fmt)
+
+    with tempdir():
+        data = np.random.randint(1, 100, (10, 20))
+        genvest(data, 'data.vest')
+        assert np.all(data == vest.loadVestFile('data.vest'))
+
+        data = np.random.random((20, 10))
+        genvest(data, 'data.vest')
+        assert np.all(np.isclose(data, vest.loadVestFile('data.vest')))
+
+        # should pass
+        vest.loadVestFile('data.vest', ignoreHeader=False)
+
+        # invalid VEST header
+        genvest(data, 'data.vest', (10, 20))
+
+        # default behaviour - ignore header
+        assert np.all(np.isclose(data, vest.loadVestFile('data.vest')))
+
+        with pytest.raises(ValueError):
+            vest.loadVestFile('data.vest', ignoreHeader=False)