Update leaf segmentation container and inference notebook

.github/workflows/publish-segmentation-image.yaml

@@ -10,14 +10,24 @@ on:
 
 env:
   REGISTRY: ghcr.io
-  IMAGE_NAME: als-computing/microct-segmentation
+  IMAGE_NAME: ${{ github.repository }}
 
 jobs:
   build-and-push-image:
     runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: general
+            context: ./segmentation/general_model
+            file: ./segmentation/general_model/Dockerfile
+          - name: leaf
+            context: ./segmentation/leaf_segmentation
+            file: ./segmentation/leaf_segmentation/Dockerfile
 
     steps:
     - name: Checkout repository
@@ -36,16 +46,16 @@ jobs:
       id: meta
       uses: docker/metadata-action@v5
       with:
-        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-${{ matrix.name }}
         tags: |
           type=sha
           type=raw,value=latest
 
     - name: Build and push Docker image
       uses: docker/build-push-action@v6
       with:
-        context: ./segmentation
-        file: ./segmentation/Dockerfile
+        context: ${{ matrix.context }}
+        file: ${{ matrix.file }}
         push: true
         tags: ${{ steps.meta.outputs.tags }}
         labels: ${{ steps.meta.outputs.labels }}

.gitignore

@@ -3,4 +3,6 @@ env/
 .env/
 .venv/
 ENV/
-.ENV/.DS_Store
+.ENV/
+.DS_Store
+*.zip

segmentation/Dockerfile → segmentation/general_model/Dockerfile

@@ -30,15 +30,10 @@ RUN mamba install --yes -c conda-forge -c astra-toolbox -c simpleitk -c pytorch
     opencv matplotlib vtk pytorch torchvision torchaudio pytorch-cuda=12.4 \
     && mamba clean --all -f -y
 
-# Install Detectron2 (requires pytorch)
-RUN python -m pip install --no-build-isolation 'git+https://github.com/facebookresearch/detectron2.git'
+# Install Dependencies
+RUN python -m pip install opencv-python astra-toolbox vtk jupyter ipykernel tifffile ipywidgets
 
 # # install SYRIS
-# COPY syris syris
-# # RUN git clone git@github.com:ufo-kit/syris.git
-# RUN conda install -c conda-forge -y cmake pybind11 -- the NERSC docs say something about not using cmake
-# RUN cd syris && pip install -r requirements.txt && pip install .
-# RUN rm -fR syris
 
 
 # for NERSC jupyterhub environment
@@ -58,5 +53,5 @@ ENV VTK_DEFAULT_EGL_DEVICE=0
 
 # expected by entrypoint script
 RUN mkdir -p /alsuser /alsdata
-
+    
 WORKDIR /alsuser