TEST: Test get/set_norm_zooms

Author: effigies

nibabel/freesurfer/tests/test_mghformat.py

@@ -390,6 +390,54 @@ def check_dtypes(self, expected, actual):
         # MGH requires the actual to be a big endian version of expected
         assert_equal(expected.newbyteorder('>'), actual)
 
+    def test_norm_zooms_edge_cases(self):
+        img_klass = self.image_class
+        aff = np.eye(4)
+        arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
+        img = img_klass(arr, aff)
+
+        assert_array_almost_equal(img.header.get_zooms(),
+                                  (1, 1, 1, 0))
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (1, 1, 1, 0))
+
+        img.header.set_zooms((1, 1, 1, 2000))
+        assert_array_almost_equal(img.header.get_zooms(),
+                                  (1, 1, 1, 2000))
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (1, 1, 1, 2))
+
+        img.header.set_norm_zooms((2, 2, 2, 3))
+        assert_array_almost_equal(img.header.get_zooms(),
+                                  (2, 2, 2, 3000))
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (2, 2, 2, 3))
+
+        # It's legal to set zooms for spatial dimensions only
+        img.header.set_norm_zooms((3, 3, 3))
+        assert_array_almost_equal(img.header.get_zooms(),
+                                  (3, 3, 3, 3000))
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (3, 3, 3, 3))
+
+        arr = np.arange(24, dtype=np.int16).reshape((2, 3, 4))
+        img = img_klass(arr, aff)
+
+        assert_array_almost_equal(img.header.get_zooms(), (1, 1, 1))
+        assert_array_almost_equal(img.header.get_norm_zooms(), (1, 1, 1))
+
+        img.header.set_zooms((2, 2, 2))
+        assert_array_almost_equal(img.header.get_zooms(), (2, 2, 2))
+        assert_array_almost_equal(img.header.get_norm_zooms(), (2, 2, 2))
+
+        img.header.set_norm_zooms((3, 3, 3))
+        assert_array_almost_equal(img.header.get_zooms(), (3, 3, 3))
+        assert_array_almost_equal(img.header.get_norm_zooms(), (3, 3, 3))
+
+        # Cannot set TR as zoom for 3D image
+        assert_raises(HeaderDataError, img.header.set_zooms, (4, 4, 4, 5))
+        assert_raises(HeaderDataError, img.header.set_norm_zooms, (4, 4, 4, 5))
+
 
 class TestMGHHeader(_TestLabeledWrapStruct):
     header_class = MGHHeader

nibabel/tests/test_nifti1.py

@@ -1087,6 +1087,55 @@ def test_write_scaling(self):
             with np.errstate(invalid='ignore'):
                 self._check_write_scaling(slope, inter, e_slope, e_inter)
 
+    def test_norm_zooms_edge_cases(self):
+        img_klass = self.image_class
+        arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
+        aff = np.eye(4)
+        img = img_klass(arr, aff)
+
+        # Unknown units = 2 warnings
+        with warnings.catch_warnings(record=True) as warns:
+            assert_array_almost_equal(img.header.get_norm_zooms(),
+                                      (1, 1, 1, 1))
+            assert_equal(len(warns), 2)
+        assert_raises(ValueError, img.header.get_norm_zooms, True)
+
+        img.header.set_xyzt_units(xyz='meter')
+        with warnings.catch_warnings(record=True) as warns:
+            assert_array_almost_equal(img.header.get_norm_zooms(),
+                                      (1000, 1000, 1000, 1))
+            assert_equal(len(warns), 1)
+        assert_raises(ValueError, img.header.get_norm_zooms, True)
+
+        img.header.set_xyzt_units(xyz='mm', t='sec')
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (1, 1, 1, 1))
+        img.header.set_xyzt_units(xyz='micron', t='sec')
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (0.001, 0.001, 0.001, 1))
+
+        img.header.set_xyzt_units(t='sec')
+        with warnings.catch_warnings(record=True) as warns:
+            assert_array_equal(img.header.get_norm_zooms(), (1, 1, 1, 1))
+            assert_equal(len(warns), 1)
+        assert_raises(ValueError, img.header.get_norm_zooms, True)
+
+        img.header.set_xyzt_units(xyz='mm', t='msec')
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (1, 1, 1, 0.001))
+
+        img.header.set_xyzt_units(xyz='mm', t='usec')
+        assert_array_almost_equal(img.header.get_norm_zooms(),
+                                  (1, 1, 1, 0.000001))
+
+        # Verify `set_norm_zooms` resets units
+        img.header.set_xyzt_units(xyz='meter', t='usec')
+        assert_equal(img.header.get_xyzt_units(), ('meter', 'usec'))
+        img.header.set_norm_zooms((2, 2, 2, 2.5))
+        assert_array_almost_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
+        assert_array_almost_equal(img.header.get_zooms(), (2, 2, 2, 2.5))
+        assert_equal(img.header.get_xyzt_units(), ('mm', 'sec'))
+
 
 class TestNifti1Image(TestNifti1Pair):
     # Run analyze-flavor spatialimage tests

nibabel/tests/test_spatialimages.py

@@ -539,6 +539,28 @@ def test_slicer(self):
                         assert_array_equal(sliced_data, img.dataobj[sliceobj])
                         assert_array_equal(sliced_data, img.get_data()[sliceobj])
 
+    def test_norm_zooms(self):
+        ''' Should be true for all images '''
+        img_klass = self.image_class
+        arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
+        aff = np.eye(4)
+        img = img_klass(arr, aff)
+        img.header.set_norm_zooms((2, 2, 2, 2.5))
+        assert_array_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
+
+    def test_norm_zooms_edge_cases(self):
+        ''' Override for classes where *_norm_zooms != *_zooms '''
+        img_klass = self.image_class
+        arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
+        aff = np.eye(4)
+        img = img_klass(arr, aff)
+        img.header.set_zooms((2, 2, 2, 2.5))
+        assert_array_equal(img.header.get_zooms(), (2, 2, 2, 2.5))
+        assert_array_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
+        img.header.set_norm_zooms((2, 2, 2, 2.5))
+        assert_array_equal(img.header.get_zooms(), (2, 2, 2, 2.5))
+        assert_array_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
+
     def test_api_deprecations(self):
 
         class FakeImage(self.image_class):