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Merged
wyli merged 3 commits into from
Mar 25, 2021
Merged

Support multidimensional labels #1851

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79d3189
Add label dimensions to be compatible with changes in model output
bhashemian Mar 25, 2021
27c22d6
Update test case outputs and add new test case
bhashemian Mar 25, 2021
9962dee
Merge branch 'master' into support_multidimensional_labels
bhashemian Mar 25, 2021
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5 changes: 4 additions & 1 deletion monai/apps/pathology/datasets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,10 @@ def __getitem__(self, index):
grid_shape=self.grid_shape,
patch_size=self.patch_size,
)
labels = np.array(sample["label"], dtype=np.float32)[:, np.newaxis, np.newaxis]
labels = np.array(sample["label"], dtype=np.float32)
# expand dimensions to have 4 dimension as batch, class, height, and width.
for _ in range(4 - labels.ndim):
labels = np.expand_dims(labels, 1)
patches = [{"image": images[i], "label": labels[i]} for i in range(len(sample["label"]))]
if self.transform:
patches = self.transform(patches)
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53 changes: 40 additions & 13 deletions tests/test_patch_wsi_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
"image_reader_name": "cuCIM",
},
[
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[1]])},
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[1]]])},
],
]

Expand All @@ -41,10 +41,10 @@
"image_reader_name": "cuCIM",
},
[
{"image": np.array([[[247]], [[245]], [[248]]], dtype=np.uint8), "label": np.array([[0]])},
{"image": np.array([[[245]], [[247]], [[244]]], dtype=np.uint8), "label": np.array([[0]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[0]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[1]])},
{"image": np.array([[[247]], [[245]], [[248]]], dtype=np.uint8), "label": np.array([[[0]]])},
{"image": np.array([[[245]], [[247]], [[244]]], dtype=np.uint8), "label": np.array([[[0]]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[[0]]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[[1]]])},
],
]

Expand All @@ -60,10 +60,25 @@
"image_reader_name": "cuCIM",
},
[
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[1]])},
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[1]]])},
],
]

TEST_CASE_3 = [
FILE_URL,
{
"data": [
{"image": "./CMU-1.tiff", "location": [0, 0], "label": [[[0, 1], [1, 0]]]},
],
"region_size": 1,
"grid_shape": 1,
"patch_size": 1,
"image_reader_name": "cuCIM",
},
[
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[0, 1], [1, 0]]])},
],
]

TEST_CASE_OPENSLIDE_0 = [
FILE_URL,
Expand All @@ -77,7 +92,7 @@
"image_reader_name": "OpenSlide",
},
[
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[1]])},
{"image": np.array([[[239]], [[239]], [[239]]], dtype=np.uint8), "label": np.array([[[1]]])},
],
]

Expand All @@ -91,16 +106,23 @@
"image_reader_name": "OpenSlide",
},
[
{"image": np.array([[[247]], [[245]], [[248]]], dtype=np.uint8), "label": np.array([[0]])},
{"image": np.array([[[245]], [[247]], [[244]]], dtype=np.uint8), "label": np.array([[0]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[0]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[1]])},
{"image": np.array([[[247]], [[245]], [[248]]], dtype=np.uint8), "label": np.array([[[0]]])},
{"image": np.array([[[245]], [[247]], [[244]]], dtype=np.uint8), "label": np.array([[[0]]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[[0]]])},
{"image": np.array([[[246]], [[246]], [[246]]], dtype=np.uint8), "label": np.array([[[1]]])},
],
]


class TestPatchWSIDataset(unittest.TestCase):
@parameterized.expand([TEST_CASE_0, TEST_CASE_1, TEST_CASE_2])
@parameterized.expand(
[
TEST_CASE_0,
TEST_CASE_1,
TEST_CASE_2,
TEST_CASE_3,
]
)
@skipUnless(has_cim, "Requires CuCIM")
def test_read_patches_cucim(self, file_url, input_parameters, expected):
self.camelyon_data_download(file_url)
Expand All @@ -112,7 +134,12 @@ def test_read_patches_cucim(self, file_url, input_parameters, expected):
self.assertIsNone(assert_array_equal(samples[i]["label"], expected[i]["label"]))
self.assertIsNone(assert_array_equal(samples[i]["image"], expected[i]["image"]))

@parameterized.expand([TEST_CASE_OPENSLIDE_0, TEST_CASE_OPENSLIDE_1])
@parameterized.expand(
[
TEST_CASE_OPENSLIDE_0,
TEST_CASE_OPENSLIDE_1,
]
)
@skipUnless(has_osl, "Requires OpenSlide")
def test_read_patches_openslide(self, file_url, input_parameters, expected):
self.camelyon_data_download(file_url)
Expand Down