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4173 Enhance decathlon datalist for test section format #4186

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merged 9 commits into from
Apr 27, 2022
Merged

4173 Enhance decathlon datalist for test section format #4186

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42a45e0
Merge pull request #19 from Project-MONAI/master
Nic-Ma Feb 1, 2021
cd16a13
Merge pull request #32 from Project-MONAI/master
Nic-Ma Feb 24, 2021
6f87afd
Merge pull request #180 from Project-MONAI/dev
Nic-Ma Jul 22, 2021
f398298
Merge pull request #214 from Project-MONAI/dev
Nic-Ma Sep 8, 2021
ec463d6
Merge pull request #397 from Project-MONAI/dev
Nic-Ma Apr 4, 2022
e0f41e3
Merge pull request #408 from Project-MONAI/dev
Nic-Ma Apr 27, 2022
34555f0
[DLMED] enhance test datalist
Nic-Ma Apr 27, 2022
8c72581
[MONAI] python code formatting
monai-bot Apr 27, 2022
122635c
[DLMED] fix flake8
Nic-Ma Apr 27, 2022
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3 changes: 2 additions & 1 deletion monai/data/decathlon_datalist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,8 @@ def load_decathlon_datalist(
if data_list_key not in json_data:
raise ValueError(f'Data list {data_list_key} not specified in "{data_list_file_path}".')
expected_data = json_data[data_list_key]
if data_list_key == "test":
if data_list_key == "test" and not isinstance(expected_data[0], dict):
# decathlon datalist may save the test images in a list directly instead of dict
expected_data = [{"image": i} for i in expected_data]

if base_dir is None:
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4 changes: 3 additions & 1 deletion monai/metrics/confusion_matrix.py
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Expand Up @@ -102,7 +102,9 @@ def _compute_tensor(self, y_pred: torch.Tensor, y: torch.Tensor): # type: ignor

return get_confusion_matrix(y_pred=y_pred, y=y, include_background=self.include_background)

def aggregate(self, compute_sample: bool = False, reduction: Union[MetricReduction, str, None] = None): # type: ignore
def aggregate( # type: ignore
self, compute_sample: bool = False, reduction: Union[MetricReduction, str, None] = None
):
"""
Execute reduction for the confusion matrix values.

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6 changes: 5 additions & 1 deletion tests/test_load_decathlon_datalist.py
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Expand Up @@ -29,7 +29,7 @@ def test_seg_values(self):
{"image": "spleen_19.nii.gz", "label": "spleen_19.nii.gz"},
{"image": "spleen_31.nii.gz", "label": "spleen_31.nii.gz"},
],
"test": ["spleen_15.nii.gz", "spleen_23.nii.gz"],
"test": [{"image": "spleen_15.nii.gz"}, {"image": "spleen_23.nii.gz"}],
}
json_str = json.dumps(test_data)
file_path = os.path.join(tempdir, "test_data.json")
Expand All @@ -38,6 +38,8 @@ def test_seg_values(self):
result = load_decathlon_datalist(file_path, True, "training", tempdir)
self.assertEqual(result[0]["image"], os.path.join(tempdir, "spleen_19.nii.gz"))
self.assertEqual(result[0]["label"], os.path.join(tempdir, "spleen_19.nii.gz"))
result = load_decathlon_datalist(file_path, True, "test", None)
self.assertEqual(result[0]["image"], os.path.join(tempdir, "spleen_15.nii.gz"))

def test_cls_values(self):
with tempfile.TemporaryDirectory() as tempdir:
Expand Down Expand Up @@ -81,6 +83,8 @@ def test_seg_no_basedir(self):
result = load_decathlon_datalist(file_path, True, "training", None)
self.assertEqual(result[0]["image"], os.path.join(tempdir, "spleen_19.nii.gz"))
self.assertEqual(result[0]["label"], os.path.join(tempdir, "spleen_19.nii.gz"))
result = load_decathlon_datalist(file_path, True, "test", None)
self.assertEqual(result[0]["image"], os.path.join(tempdir, "spleen_15.nii.gz"))

def test_seg_no_labels(self):
with tempfile.TemporaryDirectory() as tempdir:
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