Add nifti io unit tests

nigsp/tests/test_graph.py

@@ -8,7 +8,7 @@
 
 # ### Unit tests
 def test_zerocross():
-    """Text zerocross with legendre polynomials."""
+    """Test zerocross with legendre polynomials."""
     def _bonnet(d, x):
         if(d == 0):
             return np.ones_like(x)
@@ -28,7 +28,7 @@ def _bonnet(d, x):
 
 
 def test_nodestrength():
-    """Text nodestrength with random matrix."""
+    """Test nodestrength with random matrix."""
     a = np.random.rand(3, 3)
     a = a - a.mean()
     b = np.abs(a)

nigsp/tests/test_integration.py

@@ -11,6 +11,7 @@
 
 # ### Integration tests
 def test_integration(timeseries, sc_mtx, atlas, mean_fc, sdi, testdir):
+    """Integration test for FULL workflow."""
     testdir = join(testdir, 'testdir')
     mean_fc_mat = np.genfromtxt(mean_fc)
     sdi_mat = np.genfromtxt(sdi)

nigsp/tests/test_io.py

@@ -91,10 +91,17 @@ def test_check_mtx_dim_cases(data, shape):
     assert data_out.ndim == 2
 
 
-def test_load_nifti_get_mask():
+def test_load_nifti_get_mask(atlas):
     """Test load_nifti_get_mask."""
-    # #!#
-    pass
+    img = nibabel.load(atlas)
+    data = img.get_fdata()
+    mask = data.any(axis=-1).squeeze()
+
+    d, m, i = io.load_nifti_get_mask(atlas, ndim=3)
+
+    assert (data == d).all()
+    assert (mask == m).all()
+    assert (img.header['dim'] == i.header['dim']).all()
 
 
 def test_load_txt():
@@ -110,6 +117,7 @@ def test_load_txt():
 
 
 def test_load_mat():
+    """Test load_mat."""
     a = rand(5)
     b = 'likealeaf'
     n = 'inthewind'
@@ -122,11 +130,13 @@ def test_load_mat():
     remove(n)
 
 
-def test_export_nifti():
-    # #!# NEEDS IMAGE
-    # io.export_nifti(rand(3, 4, 5), img, 'book')
-    # assert isfile('book.nii.gz')
-    pass
+def test_export_nifti(atlas):
+    """Test export_nifti."""
+    img = nibabel.load(atlas)
+    shape = img.get_fdata().shape
+    io.export_nifti(empty(shape), img, 'book')
+    assert isfile('book.nii.gz')
+    remove('book.nii.gz')
 
 
 @mark.parametrize('ext_in, ext_out', [
@@ -169,6 +179,7 @@ def test_break_check_nifti_dim(data):
 
 
 def test_break_check_mtx_dim():
+    """Break check_mtx_dim."""
     with raises(ValueError) as errorinfo:
         io.check_mtx_dim('river', empty(0))
     assert 'river is empty' in str(errorinfo.value)
@@ -183,6 +194,7 @@ def test_break_check_mtx_dim():
 
 
 def test_break_load_nifti_get_mask():
+    """Break load_nifti_get_mask."""
     sys.modules['nibabel'] = None
     with raises(ImportError) as errorinfo:
         io.load_nifti_get_mask('reavers')
@@ -191,6 +203,7 @@ def test_break_load_nifti_get_mask():
 
 
 def test_break_load_mat():
+    """Break load_mat."""
     sys.modules['pymatreader'] = None
     with raises(ImportError) as errorinfo:
         io.load_mat('simon')
@@ -208,12 +221,14 @@ def test_break_load_mat():
 
 
 def test_break_load_xls():
+    """Break load_xls."""
     with raises(NotImplementedError) as errorinfo:
         io.load_xls('firefly')
     assert 'loading is not' in str(errorinfo.value)
 
 
 def test_break_export_nifti():
+    """Break export_nifti."""
     sys.modules['nibabel'] = None
     with raises(ImportError) as errorinfo:
         io.export_nifti(rand(3), None, 'reavers')
@@ -222,6 +237,7 @@ def test_break_export_nifti():
 
 
 def test_break_export_mtx():
+    """Break export_mtx."""
     with raises(NotImplementedError) as errorinfo:
         io.export_mtx(rand(3, 4), 'lostinthewoods', ext='.xls')
     assert 'output is not' in str(errorinfo.value)