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Merged
merged 3 commits into from
Apr 1, 2021
Merged

followup of #1878 #1913

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5a621b9
followup of #1878, fixes tests, remove json loading
wyli Apr 1, 2021
a72942a
Update test ordinal numbers
bhashemian Apr 1, 2021
7009f01
Merge branch 'master' into followup-1878
bhashemian Apr 1, 2021
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15 changes: 3 additions & 12 deletions monai/apps/pathology/metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import json
from typing import Dict, List, Tuple, Union
from typing import Dict, List, Tuple

import numpy as np

Expand Down Expand Up @@ -51,7 +50,7 @@ class LesionFROC:

def __init__(
self,
data: Union[List[Dict], str],
data: List[Dict],
grow_distance: int = 75,
itc_diameter: int = 200,
eval_thresholds: Tuple = (0.25, 0.5, 1, 2, 4, 8),
Expand All @@ -61,10 +60,7 @@ def __init__(
image_reader_name: str = "cuCIM",
) -> None:

if isinstance(data, str):
self.data = self._load_data(data)
else:
self.data = data
self.data = data
self.grow_distance = grow_distance
self.itc_diameter = itc_diameter
self.eval_thresholds = eval_thresholds
Expand All @@ -75,11 +71,6 @@ def __init__(
box_size=nms_box_size,
)

def _load_data(self, file_path: str) -> List[Dict]:
with open(file_path, "r") as f:
data: List[Dict] = json.load(f)
return data

def prepare_inference_result(self, sample: Dict):
"""
Prepare the probability map for detection evaluation.
Expand Down
9 changes: 5 additions & 4 deletions tests/test_lesion_froc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,7 +185,7 @@ def prepare_test_data():
]


TEST_CASE_5 = [
TEST_CASE_6 = [
{
"data": [
{
Expand All @@ -207,7 +207,7 @@ def prepare_test_data():
2.0 / 3.0,
]

TEST_CASE_6 = [
TEST_CASE_7 = [
{
"data": [
{
Expand All @@ -229,7 +229,7 @@ def prepare_test_data():
0.4,
]

TEST_CASE_7 = [
TEST_CASE_8 = [
{
"data": [
{
Expand Down Expand Up @@ -257,7 +257,7 @@ def prepare_test_data():
1.0 / 3.0,
]

TEST_CASE_8 = [
TEST_CASE_9 = [
{
"data": [
{
Expand Down Expand Up @@ -305,6 +305,7 @@ def setUp(self):
TEST_CASE_6,
TEST_CASE_7,
TEST_CASE_8,
TEST_CASE_9,
]
)
def test_read_patches_cucim(self, input_parameters, expected):
Expand Down