Unit tests for dicom module

tests/test_dicom.py

+#!/usr/bin/env python
+#
+# test_dicom.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os.path as op
+import            tarfile
+
+import mock
+import pytest
+
+import fsl.data.dicom    as fsldcm
+import fsl.utils.tempdir as tempdir
+
+from . import tempdir
+
+
+datadir = op.join(op.dirname(__file__), 'testdata')
+
+
+def setup_module():
+
+    if not fsldcm.enabled():
+        raise RuntimeError('dcm2niix is not present - tests cannot be run')
+
+
+def test_disabled():
+
+    with mock.patch('fsl.data.dicom.enabled', return_value=False):
+        with pytest.raises(RuntimeError):
+            fsldcm.scanDir('.')
+        with pytest.raises(RuntimeError):
+            fsldcm.loadSeries({})
+
+
+def test_enabled():
+
+    try:
+        fsldcm.enabled.invalidate()
+        assert fsldcm.enabled()
+        fsldcm.enabled.invalidate()
+        # test dcm2niix not present
+        with mock.patch('subprocess.check_output',
+                        side_effect=FileNotFoundError()):
+            assert not fsldcm.enabled()
+
+        # test presence of different versions
+        tests = [(b'version v2.1.20191212', True),
+                 (b'version v1.0.20160930', True),
+                 (b'version v1.0.20160929', False),
+                 (b'version v0.0.00000000', False),
+                 (b'version blurgh',        False)]
+
+        for verstr, expected in tests:
+            fsldcm.enabled.invalidate()
+            with mock.patch('subprocess.check_output', return_value=verstr):
+                assert fsldcm.enabled() == expected
+
+    finally:
+        fsldcm.enabled.invalidate()
+
+
+def test_scanDir():
+
+    with tempdir() as td:
+
+        series = fsldcm.scanDir(td)
+        assert len(series) == 0
+
+        datafile = op.join(datadir, 'example_dicom.tbz2')
+
+        with tarfile.open(datafile) as f:
+            f.extractall()
+
+        series = fsldcm.scanDir(td)
+        assert len(series) == 2
+
+        for s in series:
+            assert s['PatientName'] == 'MCCARTHY_PAUL'
+
+
+def test_loadSeries():
+
+    with tempdir() as td:
+
+        datafile = op.join(datadir, 'example_dicom.tbz2')
+
+        with tarfile.open(datafile) as f:
+            f.extractall()
+
+        series = fsldcm.scanDir(td)
+
+        expShapes = [(512, 512, 25),
+                     (512, 512, 29)]
+
+        for s, expShape in zip(series, expShapes):
+
+            img = fsldcm.loadSeries(s)
+
+            assert len(img) == 1
+
+            img = img[0]
+
+            assert img.shape              == expShape
+            assert img.get('PatientName') == 'MCCARTHY_PAUL'
+            assert 'PatientName'                    in img.keys()
+            assert 'MCCARTHY_PAUL'                  in img.values()
+            assert ('PatientName', 'MCCARTHY_PAUL') in img.items()