Merged tests from broken PR (#59)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: timtreis

tests/conftest.py

@@ -59,7 +59,11 @@ def sdata_blobs() -> SpatialData:
 @pytest.fixture
 def test_sdata_single_image():
     """Creates a simple sdata object."""
-    images = {"data1": sd.models.Image2DModel.parse(np.zeros((1, 10, 10)), dims=("c", "y", "x"))}
+    images = {
+        "data1_image": sd.models.Image2DModel.parse(
+            np.zeros((1, 10, 10)), dims=("c", "y", "x"), transformations={"data1": sd.transformations.Identity()}
+        )
+    }
     sdata = sd.SpatialData(images=images)
     return sdata
 
@@ -77,9 +81,15 @@ def test_sdata_single_image_with_label():
 def test_sdata_multiple_images():
     """Creates an sdata object with multiple images."""
     images = {
-        "data1": sd.models.Image2DModel.parse(np.zeros((1, 10, 10)), dims=("c", "y", "x")),
-        "data2": sd.models.Image2DModel.parse(np.zeros((1, 10, 10)), dims=("c", "y", "x")),
-        "data3": sd.models.Image2DModel.parse(np.zeros((1, 10, 10)), dims=("c", "y", "x")),
+        "data1_image": sd.models.Image2DModel.parse(
+            np.zeros((1, 10, 10)), dims=("c", "y", "x"), transformations={"data1": sd.transformations.Identity()}
+        ),
+        "data2_image": sd.models.Image2DModel.parse(
+            np.zeros((1, 10, 10)), dims=("c", "y", "x"), transformations={"data1": sd.transformations.Identity()}
+        ),
+        "data3_image": sd.models.Image2DModel.parse(
+            np.zeros((1, 10, 10)), dims=("c", "y", "x"), transformations={"data1": sd.transformations.Identity()}
+        ),
     }
     sdata = sd.SpatialData(images=images)
     return sdata

tests/pl/test_render.py

@@ -0,0 +1,36 @@
+import matplotlib.pyplot as plt
+import pytest
+
+
+def test_render_images_can_plot_one_cyx_image(request):
+    sdata = request.getfixturevalue("test_sdata_single_image")
+
+    _, ax = plt.subplots(1, 1)
+
+    sdata.pl.render_images().pl.show(ax=ax)
+
+    assert ax.get_title() == sdata.coordinate_systems[0]
+
+
+@pytest.mark.parametrize(
+    "share_coordinate_system",
+    [
+        "all",
+        "two",
+        "none",
+    ],
+)
+def test_render_images_can_plot_multiple_cyx_images(share_coordinate_system: str, request):
+    fun = request.getfixturevalue("get_sdata_with_multiple_images")
+    sdata = fun(share_coordinate_system)
+    sdata.pl.render_images().pl.show()
+    axs = plt.gcf().get_axes()
+
+    if share_coordinate_system == "all":
+        assert len(axs) == 1
+
+    elif share_coordinate_system == "two":
+        assert len(axs) == 2
+
+    elif share_coordinate_system == "none":
+        assert len(axs) == 3

tests/pp/test_basic.py

@@ -4,16 +4,15 @@
 @pytest.mark.parametrize(
     "sdata, keys ",
     [
-        ("test_sdata_multiple_images", 0),
-        ("test_sdata_multiple_images", {"a": 0}),
-        ("test_sdata_multiple_images", None),
-        ("test_sdata_multiple_images", ["my_key", 0]),
+        ("get_sdata_with_multiple_images", 0),
+        ("get_sdata_with_multiple_images", {"a": 0}),
+        ("get_sdata_with_multiple_images", None),
+        ("get_sdata_with_multiple_images", ["my_key", 0]),
     ],
 )
 def test_typerror_when_key_is_invalid(sdata, keys, request):
     """Tests wether the images inside sdata can be clipped to a bounding box."""
-
-    sdata = request.getfixturevalue(sdata)
+    sdata = request.getfixturevalue(sdata)(share_coordinate_system="all")
 
     with pytest.raises(TypeError):
         sdata.pp.get_elements(keys)
@@ -22,14 +21,12 @@ def test_typerror_when_key_is_invalid(sdata, keys, request):
 @pytest.mark.parametrize(
     "sdata, keys ",
     [
-        ("test_sdata_multiple_images", "data4"),
-        ("test_sdata_multiple_images", ["data1", "data4"]),
+        ("get_sdata_with_multiple_images", "data4"),
+        ("get_sdata_with_multiple_images", ["data1", "data4"]),
     ],
 )
 def test_valuerror_when_key_is_of_correct_type_but_not_in_sdata(sdata, keys, request):
-    """Tests wether the images inside sdata can be clipped to a bounding box."""
-
-    sdata = request.getfixturevalue(sdata)
+    sdata = request.getfixturevalue(sdata)(share_coordinate_system="all")
 
     with pytest.raises(ValueError):
         sdata.pp.get_elements(keys)

tests/test_image.py

@@ -12,87 +12,4 @@
 def test_sdata_fixture(sdata, request):
     """Tests the sdata fixture."""
     sdata = request.getfixturevalue(sdata)
-    assert sdata.images["data1"].shape == (1, 10, 10)
-
-
-# @pytest.mark.parametrize(
-#     "sdata",
-#     [
-#         "test_sdata_single_image",
-#         "test_sdata_multiple_images",
-#         "test_sdata_multiple_images_dims"
-#     ],
-# )
-# def test_image_accessor_correct_image_key_string(sdata, request):
-#     """Tests the image accessor with a correct image key string."""
-#     sdata = request.getfixturevalue(sdata)
-#     sdata.im['data1']
-
-#     assert sdata.im.i == 'data1'
-
-
-# @pytest.mark.parametrize(
-#     "sdata, query",
-#     [
-#         ("test_sdata_single_image", ["data1"]),
-#         ("test_sdata_multiple_images", ["data1"]),
-#         ("test_sdata_multiple_images", ["data1", "data2"]),
-#         ("test_sdata_multiple_images", ["data1", "data3"]),
-#         ("test_sdata_multiple_images_dims", ['data1']),
-#         ("test_sdata_multiple_images_dims", ['data1', 'data2']),
-#     ],
-# )
-# def test_image_accessor_correct_image_key_list(sdata, query, request):
-#     """Tests the image accessor with a correct image key list."""
-#     sdata = request.getfixturevalue(sdata)
-#     sdata.im[query]
-#     assert sdata.im.i == query
-
-
-# @pytest.mark.parametrize(
-#     "sdata",
-#     [
-#         "test_sdata_single_image",
-#         "test_sdata_multiple_images",
-#         "test_sdata_multiple_images_dims"
-#     ],
-# )
-# def test_image_accessor_wrong_correct_image_key_string(sdata, request):
-#     """Tests the image accessor with a wrong image key string."""
-#     sdata = request.getfixturevalue(sdata)
-#     with pytest.raises(AssertionError):
-#         sdata.im['wrong']
-
-
-# @pytest.mark.parametrize(
-#     "sdata",
-#     [
-#         "test_sdata_single_image",
-#         "test_sdata_multiple_images",
-#         "test_sdata_multiple_images_dims"
-#     ],
-# )
-# def test_image_accessor_correct_channel(sdata, request):
-#     """Tests the image accessor with a wrong image key string."""
-#     sdata = request.getfixturevalue(sdata)
-#     sdata.im[0]
-
-#     assert isinstance(sdata.im.i, list)
-#     assert sdata.im.c == 0
-
-
-# @pytest.mark.parametrize(
-#     "sdata",
-#     [
-#         "test_sdata_single_image",
-#         "test_sdata_multiple_images",
-#         "test_sdata_multiple_images_dims"
-#     ],
-# )
-# def test_image_accessor_correct_image_key_and_channel(sdata, request):
-#     """Tests the image accessor with a wrong image key string."""
-#     sdata = request.getfixturevalue(sdata)
-#     sdata.im['data1', 0]
-
-#     assert isinstance(sdata.im.i, str)
-#     assert sdata.im.c == 0
+    assert sdata.images["data1_image"].shape == (1, 10, 10)

tests/test_pp.py

@@ -4,15 +4,15 @@
 @pytest.mark.parametrize(
     "sdata, keys",
     [
-        ("test_sdata_multiple_images", "data1"),
-        ("test_sdata_multiple_images", ["data1"]),
-        ("test_sdata_multiple_images", ["data1", "data2"]),
+        ("get_sdata_with_multiple_images", "data1"),
+        ("get_sdata_with_multiple_images", ["data1"]),
+        ("get_sdata_with_multiple_images", ["data1", "data2"]),
     ],
 )
 def test_can_subset_to_one_or_more_images(sdata, keys, request):
     """Tests whether a subset of images can be selected from the sdata object."""
 
-    sdata = request.getfixturevalue(sdata)
+    sdata = request.getfixturevalue(sdata)(share_coordinate_system="all")
 
     clipped_sdata = sdata.pp.get_elements(keys)