8185 - Refactor test (#8231)

Fixes #8185

### Description

## Reorganize tests

I have looked at the imports in each test file and the test title to
identify which files were being tested. I mirrored the file structure of
MONAI on the `tests` folder and moved the files accordingly. I used some
helper scripts, but the process required substantial manual
intervention. When uncertain, I moved the tests to the `integration`
folder since the confusion always involved many imports, and I could not
find clarity from the test name.

Please review the integration folder carefully, which is the one that I
feel the least confident about.

```

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->
- [x] Non-breaking change (fix or new feature that would not break existing functionality).
- [x] Quick tests passed locally by running `./runtests.sh --quick --unittests  --disttests`.

---------

Signed-off-by: YunLiu <[email protected]>
Signed-off-by: R. Garcia-Dias <[email protected]>
Signed-off-by: Rafael Garcia-Dias <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Rafael Garcia-Dias <[email protected]>
Co-authored-by: YunLiu <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>

monai/transforms/io/array.py

@@ -11,7 +11,6 @@
 """
 A collection of "vanilla" transforms for IO functions.
 """
-
 from __future__ import annotations
 
 import inspect

runtests.sh

@@ -728,7 +728,7 @@ if [ $doDistTests = true ]
 then
     echo "${separator}${blue}run distributed unit test cases${noColor}"
     torch_validate
-    for i in tests/test_*_dist.py
+    for i in  $(find ./tests/ -name "*_dist.py")
     do
         echo "$i"
         ${cmdPrefix}${cmd} "$i"
@@ -740,7 +740,7 @@ if [ $doNetTests = true ]
 then
     set +e  # disable exit on failure so that diagnostics can be given on failure
     echo "${separator}${blue}integration${noColor}"
-    for i in tests/*integration_*.py
+    for i in tests/integration/*.py
     do
         echo "$i"
         ${cmdPrefix}${cmd} "$i"

tests/apps/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/deepedit/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/deepgrow/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/deepgrow/transforms/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/detection/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/detection/metrics/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/detection/networks/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/test_retinanet.py → tests/apps/detection/networks/test_retinanet.py

@@ -101,7 +101,6 @@
 @unittest.skipUnless(has_torchvision, "Requires torchvision")
 @skip_if_quick
 class TestRetinaNet(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES)
     def test_retina_shape(self, model, input_param, input_shape):
         backbone = model(**input_param)

tests/test_retinanet_detector.py → tests/apps/detection/networks/test_retinanet_detector.py

@@ -93,7 +93,6 @@
 
 
 class NaiveNetwork(torch.nn.Module):
-
     def __init__(self, spatial_dims, num_classes, **kwargs):
         super().__init__()
         self.spatial_dims = spatial_dims
@@ -115,7 +114,6 @@ def forward(self, images):
 @unittest.skipUnless(has_torchvision, "Requires torchvision")
 @skip_if_quick
 class TestRetinaNetDetector(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES)
     def test_retina_detector_resnet_backbone_shape(self, input_param, input_shape):
         returned_layers = [1]

tests/test_box_transform.py → tests/apps/detection/test_box_transform.py

@@ -79,7 +79,6 @@
 
 
 class TestBoxTransform(unittest.TestCase):
-
     @parameterized.expand(TESTS_2D_mask)
     def test_value_2d_mask(self, mask, expected_box_label):
         box_label = convert_mask_to_box(mask)

tests/apps/detection/utils/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/test_anchor_box.py → tests/apps/detection/utils/test_anchor_box.py

@@ -42,7 +42,6 @@
 @SkipIfBeforePyTorchVersion((1, 11))
 @unittest.skipUnless(has_torchvision, "Requires torchvision")
 class TestAnchorGenerator(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES_2D)
     def test_anchor_2d(self, input_param, image_shape, feature_maps_shapes):
         torch_anchor_utils, _ = optional_import("torchvision.models.detection.anchor_utils")

tests/test_atss_box_matcher.py → tests/apps/detection/utils/test_atss_box_matcher.py

@@ -33,7 +33,6 @@
 
 
 class TestATSS(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES)
     def test_atss(self, input_param, boxes, anchors, num_anchors_per_level, num_anchors_per_loc, expected_matches):
         matcher = ATSSMatcher(**input_param, debug=True)

tests/test_box_coder.py → tests/apps/detection/utils/test_box_coder.py

@@ -21,7 +21,6 @@
 
 
 class TestBoxTransform(unittest.TestCase):
-
     def test_value(self):
         box_coder = BoxCoder(weights=[1, 1, 1, 1, 1, 1])
         test_dtype = [torch.float32, torch.float16]

tests/test_detector_boxselector.py → tests/apps/detection/utils/test_detector_boxselector.py

@@ -56,7 +56,6 @@
 
 
 class TestBoxSelector(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_box_selector(self, input_param, boxes, logits, image_shape, expected_results):
         box_selector = BoxSelector(**input_param)

tests/test_detector_utils.py → tests/apps/detection/utils/test_detector_utils.py

@@ -79,7 +79,6 @@
 
 
 class TestDetectorUtils(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES)
     def test_detector_utils(self, input_param, input_shape, expected_shape):
         size_divisible = 32 * ensure_tuple(input_param["conv1_t_stride"])[0]

tests/test_hardnegsampler.py → tests/apps/detection/utils/test_hardnegsampler.py

@@ -37,7 +37,6 @@
 
 
 class TestSampleSlices(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, target_label0, target_label1, concat_fg_probs, expected_result_pos, expected_result_neg):
         compute_dtypes = [torch.float16, torch.float32]

tests/apps/maisi/networks/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/test_autoencoderkl_maisi.py → tests/apps/maisi/networks/test_autoencoderkl_maisi.py

@@ -77,7 +77,6 @@
 
 
 class TestAutoencoderKlMaisi(unittest.TestCase):
-
     @parameterized.expand(CASES)
     def test_shape(self, input_param, input_shape, expected_shape, expected_latent_shape):
         net = AutoencoderKlMaisi(**input_param).to(device)

tests/test_controlnet_maisi.py → tests/apps/maisi/networks/test_controlnet_maisi.py

@@ -129,7 +129,6 @@
 
 @SkipIfBeforePyTorchVersion((2, 0))
 class TestControlNet(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES)
     @skipUnless(has_einops, "Requires einops")
     def test_shape_unconditioned_models(self, input_param, expected_num_down_blocks_residuals, expected_shape):

tests/apps/nuclick/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/pathology/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/pathology/handlers/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/test_from_engine_hovernet.py → tests/apps/pathology/handlers/test_from_engine_hovernet.py

@@ -28,7 +28,6 @@
 
 
 class TestFromEngineHovernet(unittest.TestCase):
-
     @parameterized.expand(CASES)
     def test_results(self, input, expected):
         output = from_engine_hovernet(keys=["A", "B"], nested_key="C")(input)

tests/test_prepare_batch_hovernet.py → tests/apps/pathology/test_prepare_batch_hovernet.py

@@ -35,7 +35,6 @@ def forward(self, x: torch.Tensor):
 
 
 class TestPrepareBatchHoVerNet(unittest.TestCase):
-
     @parameterized.expand([TEST_CASE_0])
     def test_content(self, input_args, expected_value):
         device = torch.device("cuda" if torch.cuda.is_available() else "cpu")

tests/test_sliding_window_hovernet_inference.py → tests/apps/pathology/test_sliding_window_hovernet_inference.py

@@ -21,7 +21,7 @@
 from monai.data import MetaTensor
 from monai.inferers import sliding_window_inference
 from monai.utils import optional_import
-from tests.test_sliding_window_inference import TEST_CASES
+from tests.inferers.test_sliding_window_inference import TEST_CASES
 
 _, has_tqdm = optional_import("tqdm")
 
@@ -36,7 +36,6 @@
 
 
 class TestSlidingWindowHoVerNetInference(unittest.TestCase):
-
     @parameterized.expand(TEST_CASES_PADDING)
     def test_sliding_window_with_padding(
         self, key, image_shape, roi_shape, sw_batch_size, overlap, mode, device, extra_input_padding

tests/apps/pathology/transforms/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/apps/pathology/transforms/post/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/test_generate_distance_map.py → tests/apps/pathology/transforms/post/test_generate_distance_map.py

@@ -36,7 +36,6 @@
 
 
 class TestGenerateDistanceMap(unittest.TestCase):
-
     @parameterized.expand(EXCEPTION_TESTS)
     def test_value(self, arguments, mask, probmap, exception_type):
         with self.assertRaises(exception_type):

tests/test_generate_distance_mapd.py → tests/apps/pathology/transforms/post/test_generate_distance_mapd.py

@@ -55,7 +55,6 @@
 
 
 class TestGenerateDistanceMapd(unittest.TestCase):
-
     @parameterized.expand(EXCEPTION_TESTS)
     def test_value(self, arguments, mask, border_map, exception_type):
         with self.assertRaises(exception_type):

tests/test_generate_instance_border.py → tests/apps/pathology/transforms/post/test_generate_instance_border.py

@@ -34,7 +34,6 @@
 
 
 class TestGenerateInstanceBorder(unittest.TestCase):
-
     @parameterized.expand(EXCEPTION_TESTS)
     def test_value(self, arguments, mask, hover_map, exception_type):
         with self.assertRaises(exception_type):

tests/test_generate_instance_borderd.py → tests/apps/pathology/transforms/post/test_generate_instance_borderd.py

@@ -44,7 +44,6 @@
 
 
 class TestGenerateInstanceBorderd(unittest.TestCase):
-
     @parameterized.expand(EXCEPTION_TESTS)
     def test_value(self, arguments, mask, hover_map, exception_type):
         with self.assertRaises(exception_type):

tests/test_generate_instance_centroid.py → tests/apps/pathology/transforms/post/test_generate_instance_centroid.py

@@ -41,7 +41,6 @@
 
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 class TestGenerateInstanceCentroid(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, in_type, test_data, offset, expected):
         inst_bbox = get_bbox(test_data[None])

tests/test_generate_instance_centroidd.py → tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py

@@ -41,7 +41,6 @@
 
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 class TestGenerateInstanceCentroidd(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, in_type, test_data, offset, expected):
         inst_bbox = get_bbox(test_data[None])

tests/test_generate_instance_contour.py → tests/apps/pathology/transforms/post/test_generate_instance_contour.py

@@ -46,7 +46,6 @@
 
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 class TestGenerateInstanceContour(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, in_type, test_data, min_num_points, offset, expected):
         inst_bbox = get_bbox(test_data[None])

tests/test_generate_instance_contourd.py → tests/apps/pathology/transforms/post/test_generate_instance_contourd.py

@@ -46,7 +46,6 @@
 
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 class TestGenerateInstanceContourd(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, in_type, test_data, min_num_points, offset, expected):
         inst_bbox = get_bbox(test_data[None])

tests/test_generate_instance_type.py → tests/apps/pathology/transforms/post/test_generate_instance_type.py

@@ -41,7 +41,6 @@
 
 
 class TestGenerateInstanceType(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, in_type, type_pred, seg_pred, bbox, expected):
         result = GenerateInstanceType()(in_type(type_pred[None]), in_type(seg_pred[None]), bbox, 1)

tests/test_generate_instance_typed.py → tests/apps/pathology/transforms/post/test_generate_instance_typed.py

@@ -41,7 +41,6 @@
 
 
 class TestGenerateInstanceTyped(unittest.TestCase):
-
     @parameterized.expand(TEST_CASE)
     def test_shape(self, in_type, type_pred, seg_pred, bbox, expected):
         test_data = {"type_pred": in_type(type_pred[None]), "seg": in_type(seg_pred[None]), "bbox": bbox, "id": 1}

tests/test_generate_watershed_markers.py → tests/apps/pathology/transforms/post/test_generate_watershed_markers.py

@@ -38,7 +38,6 @@
 @unittest.skipUnless(has_skimage, "Requires scikit-image library.")
 @unittest.skipUnless(has_scipy, "Requires scipy library.")
 class TestGenerateWatershedMarkers(unittest.TestCase):
-
     @parameterized.expand(EXCEPTION_TESTS)
     def test_value(self, arguments, mask, probmap, exception_type):
         with self.assertRaises(exception_type):