add unit test and modify readme

Signed-off-by: Yiheng Wang <[email protected]>
Project-MONAI · Aug 24, 2023 · 7aedfc9 · 7aedfc9
1 parent baf8b25
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diff --git a/ci/unit_tests/test_spleen_deepedit_annotation.py b/ci/unit_tests/test_spleen_deepedit_annotation.py
@@ -120,6 +120,25 @@ def test_infer_config(self, override):
         )
         check_workflow(inferrer, check_properties=True)
 
+    @parameterized.expand([TEST_CASE_2])
+    def test_infer_click_config(self, override):
+        override["dataset_dir"] = self.dataset_dir
+        override["use_click"] = True
+        override[
+            "dataset#data"
+        ] = "$[{'image': i, 'background': [], 'spleen': [[6, 6, 6], [8, 8, 8]]} for i in @datalist]"
+        bundle_root = override["bundle_root"]
+        print(override)
+
+        inferrer = ConfigWorkflow(
+            workflow="infer",
+            config_file=os.path.join(bundle_root, "configs/inference.json"),
+            logging_file=os.path.join(bundle_root, "configs/logging.conf"),
+            meta_file=os.path.join(bundle_root, "configs/metadata.json"),
+            **override,
+        )
+        check_workflow(inferrer, check_properties=True)
+
 
 if __name__ == "__main__":
     loader = unittest.TestLoader()

diff --git a/models/spleen_deepedit_annotation/configs/metadata.json b/models/spleen_deepedit_annotation/configs/metadata.json
@@ -29,7 +29,7 @@
     "pytorch_version": "1.13.1",
     "numpy_version": "1.22.2",
     "optional_packages_version": {
-        "nibabel": "4.0.1",
+        "itk": "5.3.0",
         "pytorch-ignite": "0.4.9",
         "scikit-image": "0.19.3"
     },

diff --git a/models/spleen_deepedit_annotation/docs/README.md b/models/spleen_deepedit_annotation/docs/README.md
@@ -133,12 +133,10 @@ For interactive segmentation mode, in which the user provides clicks, set the **
 python -m monai.bundle run --config_file configs/inference.json --use_click true
 ```
 
-Clicks should be added to the data dictionary that is passed to the preprocessing transforms. Label names are the keys and their values are the clicks coordinates.
-
-Like the following format:
+Clicks should be added to the data dictionary that is passed to the preprocessing transforms. The add keys are defined in `label_names` in `configs/inference.json`, and the corresponding values are the clicks coordinates. The following is an example of a data dictionary:
 
 ```
-data_dict = {'background': [], 'spleen': [[I1, J1, K1], [I2, J2, K2]]}
+{"image": "example.nii.gz", "background": [], "spleen": [[I1, J1, K1], [I2, J2, K2]]}
 ```
 where **[I1,J1,K1]** and **[I2,J2,K2]** are the point coordinates