expand tests to cover incomplete metadata

Author: pattonw

tests/fixtures/metadatas/empty.json

@@ -0,0 +1 @@
+{}

tests/fixtures/metadatas/incomplete1.json

@@ -0,0 +1,9 @@
+{
+    "axis_names": [
+        "c0^",
+        "c1^",
+        "d0",
+        "d1",
+        "d2"
+    ]
+}

tests/fixtures/metadatas/incomplete2.json

@@ -0,0 +1,7 @@
+{
+    "units": [
+        "",
+        "",
+        ""
+    ]
+}

tests/fixtures/metadatas/incomplete3.json

@@ -0,0 +1,19 @@
+{
+    "offset": [
+        0,
+        0,
+        0
+    ],
+    "voxel_size": [
+        1,
+        1,
+        1
+    ],
+    "axis_names": [
+        "c0^",
+        "c1^",
+        "d0",
+        "d1",
+        "d2"
+    ]
+}

tests/test_array.py

@@ -17,18 +17,20 @@ def test_constructor():
     Array(data, offset, (2, 2, 2))
 
     # dims don't match
-    with pytest.raises(AssertionError):
+    with pytest.raises(ValueError):
         Array(data, offset, (1, 1))
 
     Array(data, offset, (1, 1, 3))
     Array(data, offset, (1, 1, 4))
 
     Array(data, (1, 1, 1), (1, 1, 2))
 
+
 def test_dtype():
     for dtype in [np.float32, np.uint8, np.uint64]:
         assert Array(np.zeros((1,), dtype=dtype), (0,), (1,)).dtype == dtype
 
+
 def test_getitem():
     a = Array(np.arange(0, 10).reshape(2, 5), (0, 0), (1, 1))
 
@@ -62,6 +64,7 @@ def test_getitem():
     b = a[Roi((1, 1), (1, 4))]
     np.testing.assert_array_equal(b, [[6, 7, 8, 9]])
 
+
 def test_setitem():
     # set entirely with numpy array
 
@@ -136,6 +139,7 @@ def test_setitem():
     assert a[Coordinate((1, 1))] == 1
     assert a[Coordinate((1, 2))] == 2
 
+
 def test_to_ndarray():
     a = Array(np.arange(0, 10).reshape(2, 5), (0, 0), (1, 1))
 
@@ -163,8 +167,11 @@ def test_to_ndarray():
     )
     np.testing.assert_array_equal(b, compare)
 
+
 def test_to_ndarray_with_slices():
-    a = Array(np.arange(0, 10*10).reshape(10, 2, 5), (0, 0), (1, 1), adapter=slice(0, 1))
+    a = Array(
+        np.arange(0, 10 * 10).reshape(10, 2, 5), (0, 0), (1, 1), adapter=slice(0, 1)
+    )
 
     b = a.to_ndarray(Roi((0, 0), (1, 5)))
     compare = np.array([[[0, 1, 2, 3, 4]]])
@@ -180,32 +187,43 @@ def test_to_ndarray_with_slices():
 
     b = a.to_ndarray(Roi((0, 0), (5, 5)), fill_value=1)
     compare = np.array(
-        [[
-            [0, 1, 2, 3, 4],
-            [5, 6, 7, 8, 9],
-            [1, 1, 1, 1, 1],
-            [1, 1, 1, 1, 1],
-            [1, 1, 1, 1, 1],
-        ]]
+        [
+            [
+                [0, 1, 2, 3, 4],
+                [5, 6, 7, 8, 9],
+                [1, 1, 1, 1, 1],
+                [1, 1, 1, 1, 1],
+                [1, 1, 1, 1, 1],
+            ]
+        ]
     )
     np.testing.assert_array_equal(b, compare)
 
+
 def test_adapters():
-    a = Array(np.arange(0, 10*10).reshape(10, 2, 5), (0, 0), (1, 1))
+    a = Array(np.arange(0, 10 * 10).reshape(10, 2, 5), (0, 0), (1, 1))
     assert a.dtype == int
 
-    a = Array(np.arange(0, 10*10).reshape(10, 2, 5), (0, 0), (1, 1), adapter=lambda x: x > 2)
+    a = Array(
+        np.arange(0, 10 * 10).reshape(10, 2, 5), (0, 0), (1, 1), adapter=lambda x: x > 2
+    )
     assert a.dtype == bool
 
-    a = Array(np.arange(0, 10*10).reshape(10, 2, 5), (0, 0), (1, 1), adapter=lambda x: x + 0.5)
+    a = Array(
+        np.arange(0, 10 * 10).reshape(10, 2, 5),
+        (0, 0),
+        (1, 1),
+        adapter=lambda x: x + 0.5,
+    )
     assert a.dtype == float
 
+
 def test_slicing():
-    a = Array(np.arange(0, 4*4).reshape(4, 2, 2), (0, 0), (1, 1))
-    
+    a = Array(np.arange(0, 4 * 4).reshape(4, 2, 2), (0, 0), (1, 1))
+
     a.adapt(np.s_[0:3, 1, :])
     assert a.shape == (3, 2)
-    assert a.axis_names == ["c0^", "d1"]
+    assert a.axis_names == ["c0^", "d1"], a.axis_names
     assert a.units == [""]
 
     a.adapt(np.s_[2, :])
@@ -217,11 +235,10 @@ def test_slicing():
 
     assert all([x == 42 for x in a._source_data[2, 1, :]]), a._source_data[2, 1, :]
 
-
     # test with list indexing
-    a = Array(np.arange(0, 4*4).reshape(4, 2, 2), (0, 0), (1, 1))
+    a = Array(np.arange(0, 4 * 4).reshape(4, 2, 2), (0, 0), (1, 1))
 
-    a.adapt(np.s_[[0,1,2], 1, :])
+    a.adapt(np.s_[[0, 1, 2], 1, :])
     assert a.shape == (3, 2)
     assert a.axis_names == ["c0^", "d1"]
     assert a.units == [""]
@@ -235,26 +252,24 @@ def test_slicing():
 
     assert all([x == 42 for x in a._source_data[2, 1, :]]), a._source_data[:]
 
-    
     # test weird case
-    a = Array(np.arange(0, 4*4).reshape(4, 2, 2), (0, 0), (1, 1))
+    a = Array(np.arange(0, 4 * 4).reshape(4, 2, 2), (0, 0), (1, 1))
 
-    a.adapt(np.s_[[2,2,2], 1, :])
+    a.adapt(np.s_[[2, 2, 2], 1, :])
     assert a.shape == (3, 2)
     assert a.axis_names == ["c0^", "d1"]
     assert a.units == [""]
 
     a[:, :] = np.array([42, 43, 44]).reshape(3, 1)
     assert all([x == 44 for x in a._source_data[2, 1, :]]), a._source_data[2, 1, :]
 
-
     # test_bool_indexing
-    a = Array(np.arange(0, 4*4).reshape(4, 2, 2), (0, 0), (1, 1))
+    a = Array(np.arange(0, 4 * 4).reshape(4, 2, 2), (0, 0), (1, 1))
 
     a.adapt(np.s_[np.array([True, True, True, False]), 1, :])
     assert a.shape == (3, 2)
     assert a.axis_names == ["c0^", "d1"]
     assert a.units == [""]
-    
+
     with pytest.raises(RuntimeError):
         a[:, :] = np.array([42, 43, 44]).reshape(3, 1)

tests/test_datasets.py

@@ -20,17 +20,18 @@
 @pytest.mark.parametrize("store", stores.keys())
 @pytest.mark.parametrize("dtype", [np.float32, np.uint8, np.uint64])
 def test_helpers(tmpdir, store, dtype):
+    shape = Coordinate(1, 1, 10, 20, 30)
+    chunk_shape = Coordinate(2, 3, 10, 10, 10)
     store = tmpdir / store
     metadata = MetaDataFormat().parse(
+        shape,
         {
             "offset": [100, 200, 400],
             "voxel_size": [1, 2, 3],
             "axis_names": ["sample^", "channel^", "z", "y", "x"],
             "units": ["nm", "nm", "nm"],
         }
     )
-    shape = Coordinate(1, 1, 10, 20, 30)
-    chunk_shape = Coordinate(2, 3, 10, 10, 10)
 
     # test prepare_ds fails if array does not exist and mode is read
     with pytest.raises(ArrayNotFoundError):

tests/test_metadata.py

@@ -7,6 +7,16 @@
 
 
 fixtures_dir = Path(__file__).parent / "fixtures"
+incomplete_metadatas = {
+    "incomplete1": "metadatas/incomplete1.json",
+    "incomplete2": "metadatas/incomplete2.json",
+    "incomplete3": "metadatas/incomplete3.json",
+}
+incomplete_metadata_formats = {
+    "incomplete1": MetaDataFormat(),
+    "incomplete2": MetaDataFormat(),
+    "incomplete3": MetaDataFormat(),
+}
 metadata_jsons = {
     "default": "metadatas/default.json",
     "simple": "metadatas/simple.json",
@@ -27,10 +37,12 @@
     ),
 }
 
+
 @pytest.fixture(params=metadata_jsons.keys())
 def metadata(request):
     return metadata_formats[request.param].parse(
-        json.loads(open(fixtures_dir / metadata_jsons[request.param]).read())
+        (10, 2, 100, 100, 100),
+        json.loads(open(fixtures_dir / metadata_jsons[request.param]).read()),
     )
 
 
@@ -39,3 +51,26 @@ def test_parse_metadata(metadata):
     assert metadata.voxel_size == Coordinate(1, 2, 3)
     assert metadata.axis_names == ["sample^", "channel^", "z", "y", "x"]
     assert metadata.units == ["nm", "nm", "nm"]
+
+
+@pytest.fixture(params=incomplete_metadatas.keys())
+def incomplete_metadata(request):
+    return incomplete_metadata_formats[request.param].parse(
+        (10, 2, 100, 100, 100),
+        json.loads(open(fixtures_dir / incomplete_metadatas[request.param]).read()),
+    )
+
+
+def test_parse_incomplete_metadata(incomplete_metadata):
+    assert incomplete_metadata.offset == Coordinate(0, 0, 0)
+    assert incomplete_metadata.voxel_size == Coordinate(1, 1, 1)
+    assert incomplete_metadata.axis_names == ["c0^", "c1^", "d0", "d1", "d2"]
+    assert incomplete_metadata.units == ["", "", ""]
+
+
+def test_empty_metadata():
+    metadata = MetaDataFormat().parse((10, 2, 100, 100, 100), {})
+    assert metadata.offset == Coordinate(0, 0, 0, 0, 0)
+    assert metadata.voxel_size == Coordinate(1, 1, 1, 1, 1)
+    assert metadata.axis_names == ["d0", "d1", "d2", "d3", "d4"]
+    assert metadata.units == ["", "", "", "", ""]