address changes suggested by mhub dev

MHubAI · Nov 14, 2023 · db1dd3b · db1dd3b
1 parent f3d5674
commit db1dd3b
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Showing 6 changed files with 13 additions and 54 deletions.
diff --git a/models/bamf_nnunet_ct_liver/config/default.yml b/models/bamf_nnunet_ct_liver/config/default.yml
@@ -19,21 +19,17 @@ modules:
     meta: 
       mod: '%Modality'
 
-  NiftiConverter:
-
   NNUnetRunner:
-    in_data: 'nifti:mod=ct'
-    nnunet_task: 'Task773_Liver'
-    nnunet_model: '3d_fullres'
+    in_data: nifti:mod=ct
+    nnunet_task: Task773_Liver
+    nnunet_model: 3d_fullres
     roi: LIVER
 
   BamfProcessorRunner:
-    in_data: 'nifti:mod=ct'
 
   DsegConverter:
-    model_name: 'Bamf NNUnet CT Liver'
+    model_name: Bamf NNUnet CT Liver
     skip_empty_slices: True
-    json_config_path: '/app/models/bamf_nnunet_ct_liver/config/meta.json'
 
   DataOrganizer:
     targets:

diff --git a/models/bamf_nnunet_ct_liver/config/meta.json b/models/bamf_nnunet_ct_liver/config/meta.json
diff --git a/models/bamf_nnunet_ct_liver/config/slicer.yml b/models/bamf_nnunet_ct_liver/config/slicer.yml
@@ -7,6 +7,7 @@ execute:
 - NrrdImporter
 - NiftiConverter
 - NNUnetRunner
+- BamfProcessorRunner
 - JsonSegExporter
 - DataOrganizer
 
@@ -25,6 +26,8 @@ modules:
     nnunet_model: '3d_fullres'
     roi: LIVER
 
+  BamfProcessorRunner:
+
   DataOrganizer:
     targets:
     - nifti:mod=seg-->[basename]

diff --git a/models/bamf_nnunet_ct_liver/dockerfiles/Dockerfile b/models/bamf_nnunet_ct_liver/dockerfiles/Dockerfile
@@ -12,10 +12,8 @@ RUN pip3 install --no-cache-dir \
   nnunet 
 
 # Clone the main branch of MHubAI/models
-RUN git stash \
- && git sparse-checkout set "models/bamf_nnunet_ct_liver" \
- && git fetch https://github.com/MHubAI/models.git main \
- && git merge FETCH_HEAD
+ARG MHUB_MODELS_REPO
+RUN buildutils/import_mhub_model.sh bamf_nnunet_ct_liver ${MHUB_MODELS_REPO}
 
 # Pull weights into the container
 ENV WEIGHTS_DIR=/root/.nnunet/nnUNet_models/nnUNet/
@@ -30,5 +28,5 @@ RUN rm ${WEIGHTS_DIR}${WEIGHTS_FN}
 ENV WEIGHTS_FOLDER=$WEIGHTS_DIR
 
 # Default run script
-ENTRYPOINT ["python3", "-m", "mhubio.run"]
+ENTRYPOINT ["mhub.run"]
 CMD ["--config", "/app/models/bamf_nnunet_ct_liver/config/default.yml"]
diff --git a/models/bamf_nnunet_ct_liver/meta.json b/models/bamf_nnunet_ct_liver/meta.json
@@ -57,6 +57,7 @@
             "weights": "28.08.2023",
             "pub": "23.10.2023"
         },
+        "cite": "Murugesan, Gowtham Krishnan, Diana McCrumb, Mariam Aboian, Tej Verma, Rahul Soni, Fatima Memon, and Jeff Van Oss. The AIMI Initiative: AI-Generated Annotations for Imaging Data Commons Collections. arXiv preprint arXiv:2310.14897 (2023).",
         "licence": {
             "code": "MIT",
             "weights": "CC BY-NC 4.0"

diff --git a/models/bamf_nnunet_ct_liver/utils/BamfProcessorRunner.py b/models/bamf_nnunet_ct_liver/utils/BamfProcessorRunner.py
@@ -17,24 +17,18 @@
 import shutil
 
 
-@IO.ConfigInput('in_data', 'nifti:mod=ct|mr', the="input data to run BamfProcessor on")
+
 class BamfProcessorRunner(Module):
 
     @IO.Instance
-    @IO.Input("in_data", the="input data to run nnunet on")
+    @IO.Input('in_data', 'nifti:mod=ct|mr', the='input data to run nnunet on')
     def task(self, instance: Instance, in_data: InstanceData, out_data: InstanceData) -> None:
 
        # Log bamf runner info
         self.v("Running BamfProcessor on....")
         self.v(f" > input data:  {in_data.abspath}")
         self.v(f" > output data: {out_data.abspath}")
 
-        # data
-        # bring input data in nnunet specific format
-        # NOTE: only for nifti data as we hardcode the nnunet-formatted-filename (and extension) for now.
-        assert in_data.type.ftype == FileType.NIFTI
-        assert in_data.abspath.endswith('.nii.gz')
-
         # read image
         self.v(f"Reading image from {in_data.abspath}")
         img_itk = sitk.ReadImage(in_data.abspath)