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Update DeepEdit infer to accept clicks from viewer #491

Merged
merged 11 commits into from
Aug 28, 2023
19 changes: 19 additions & 0 deletions ci/unit_tests/test_spleen_deepedit_annotation.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()
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113 changes: 72 additions & 41 deletions models/spleen_deepedit_annotation/configs/inference.json
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
],
"number_intensity_ch": 1,
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"use_click": false,
"network_def": {
"_target_": "DynUNet",
"spatial_dims": 3,
Expand Down Expand Up @@ -60,49 +61,79 @@
"res_block": true
},
"network": "$@network_def.to(@device)",
"preprocessing_transforms": [
{
"_target_": "LoadImaged",
"keys": "image",
"reader": "ITKReader"
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},
{
"_target_": "EnsureChannelFirstd",
"keys": "image"
},
{
"_target_": "Orientationd",
"keys": "image",
"axcodes": "RAS"
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": -175,
"a_max": 250,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
}
],
"auto_seg_transforms": [
{
"_target_": "Resized",
"keys": "image",
"spatial_size": "@spatial_size",
"mode": "area"
},
{
"_target_": "DiscardAddGuidanced",
"keys": "image",
"label_names": "@label_names",
"number_intensity_ch": "@number_intensity_ch"
}
],
"deepedit_transforms": [
{
"_target_": "AddGuidanceFromPointsDeepEditd",
"ref_image": "image",
"guidance": "guidance",
"label_names": "@label_names"
},
{
"_target_": "Resized",
"keys": "image",
"spatial_size": "@spatial_size",
"mode": "area"
},
{
"_target_": "ResizeGuidanceMultipleLabelDeepEditd",
"guidance": "guidance",
"ref_image": "image"
},
{
"_target_": "AddGuidanceSignalDeepEditd",
"keys": "image",
"guidance": "guidance",
"number_intensity_ch": "@number_intensity_ch"
}
],
"extra_transforms": [
{
"_target_": "EnsureTyped",
"keys": "image"
}
],
"preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": "image",
"reader": "ITKReader"
},
{
"_target_": "EnsureChannelFirstd",
"keys": "image"
},
{
"_target_": "Orientationd",
"keys": "image",
"axcodes": "RAS"
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": -175,
"a_max": 250,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
},
{
"_target_": "Resized",
"keys": "image",
"spatial_size": "@spatial_size",
"mode": "area"
},
{
"_target_": "DiscardAddGuidanced",
"keys": "image",
"label_names": "@label_names",
"number_intensity_ch": "@number_intensity_ch"
},
{
"_target_": "EnsureTyped",
"keys": "image"
}
]
"transforms": "$@preprocessing_transforms + (@deepedit_transforms if @use_click else @auto_seg_transforms) + @extra_transforms"
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},
"dataset": {
"_target_": "Dataset",
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5 changes: 3 additions & 2 deletions models/spleen_deepedit_annotation/configs/metadata.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
{
"schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
"version": "0.4.7",
"version": "0.4.8",
"changelog": {
"0.4.8": "Add infer transforms to manage clicks from viewer",
"0.4.7": "fix the wrong GPU index issue of multi-node",
"0.4.6": "update to use rc7 which solves dynunet issue",
"0.4.5": "remove error dollar symbol in readme",
Expand All @@ -28,7 +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"
},
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18 changes: 18 additions & 0 deletions models/spleen_deepedit_annotation/docs/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -118,10 +118,28 @@ python -m monai.bundle run --config_file "['configs/train.json','configs/evaluat

#### Execute inference:


For automatic inference mode:


```
python -m monai.bundle run --config_file configs/inference.json
```

For interactive segmentation mode, in which the user provides clicks, set the **use_click** flag to true:


```
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. The add keys are defined in `label_names` in `configs/inference.json`, and the corresponding values are the point coordinates. The following is an example of a data dictionary:

```
{"image": "example.nii.gz", "background": [], "spleen": [[I1, J1, K1], [I2, J2, K2]]}
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```
where **[I1,J1,K1]** and **[I2,J2,K2]** are the point coordinates.

#### Export checkpoint to TensorRT based models with fp32 or fp16 precision:

```bash
Expand Down