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Merged
bhashemian merged 2 commits into from
Mar 31, 2021
Merged

Update pathology unittests #1910

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4d89402
Update pathology unittests
bhashemian Mar 31, 2021
140a388
Merge branch 'master' into ignore_pathology_test_artifacts
wyli Mar 31, 2021
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4 changes: 2 additions & 2 deletions tests/test_cuimage_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
PILImage, has_pil = optional_import("PIL.Image")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", os.path.basename(FILE_URL))
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))

HEIGHT = 32914
WIDTH = 46000
Expand Down Expand Up @@ -105,7 +105,7 @@ def test_read_rgba(self, img_expected):
image = {}
reader = WSIReader("cuCIM")
for mode in ["RGB", "RGBA"]:
file_path = self.create_rgba_image(img_expected, "test_cu_tiff_image", mode=mode)
file_path = self.create_rgba_image(img_expected, "temp_cu_tiff_image", mode=mode)
img_obj = reader.read(file_path)
image[mode], _ = reader.get_data(img_obj)

Expand Down
38 changes: 20 additions & 18 deletions tests/test_masked_inference_wsi_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,13 @@
_, has_osl = optional_import("openslide")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", os.path.basename(FILE_URL))
base_name, extension = os.path.splitext(os.path.basename(FILE_URL))
FILE_NAME = "temp_" + base_name
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", FILE_NAME + extension)

MASK1 = os.path.join(os.path.dirname(__file__), "testing_data", "tissue_mask1.npy")
MASK2 = os.path.join(os.path.dirname(__file__), "testing_data", "tissue_mask2.npy")
MASK4 = os.path.join(os.path.dirname(__file__), "testing_data", "tissue_mask4.npy")
MASK1 = os.path.join(os.path.dirname(__file__), "testing_data", "temp_tissue_mask1.npy")
MASK2 = os.path.join(os.path.dirname(__file__), "testing_data", "temp_tissue_mask2.npy")
MASK4 = os.path.join(os.path.dirname(__file__), "testing_data", "temp_tissue_mask4.npy")

HEIGHT = 32914
WIDTH = 46000
Expand Down Expand Up @@ -47,7 +49,7 @@ def prepare_data():
[
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
],
Expand All @@ -62,12 +64,12 @@ def prepare_data():
[
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [101, 100],
},
],
Expand All @@ -82,22 +84,22 @@ def prepare_data():
[
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 101],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [101, 100],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [101, 101],
},
],
Expand All @@ -121,7 +123,7 @@ def prepare_data():
],
dtype=np.uint8,
),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
],
Expand All @@ -139,17 +141,17 @@ def prepare_data():
[
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [101, 100],
},
],
Expand All @@ -167,7 +169,7 @@ def prepare_data():
[
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
],
Expand All @@ -182,12 +184,12 @@ def prepare_data():
[
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [100, 100],
},
{
"image": np.array([[[243]], [[243]], [[243]]], dtype=np.uint8),
"name": "CMU-1",
"name": FILE_NAME,
"mask_location": [101, 100],
},
],
Expand Down
2 changes: 1 addition & 1 deletion tests/test_openslide_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@


FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", os.path.basename(FILE_URL))
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))

HEIGHT = 32914
WIDTH = 46000
Expand Down
2 changes: 1 addition & 1 deletion tests/test_patch_wsi_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
_, has_osl = optional_import("openslide")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", os.path.basename(FILE_URL))
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))

TEST_CASE_0 = [
{
Expand Down
2 changes: 1 addition & 1 deletion tests/test_smartcache_patch_wsi_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
_, has_cim = optional_import("cucim")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", os.path.basename(FILE_URL))
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))

TEST_CASE_0 = [
{
Expand Down