Support SAM2 (Inference only) as base model for all the apps (#1777)

* Support SAM2 (Inference only) as base model for all the apps Signed-off-by: Sachidanand Alle <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Support SAM2 for python >=3.10 Signed-off-by: Sachidanand Alle <[email protected]> * Update python version dep for docs build Signed-off-by: Sachidanand Alle <[email protected]> * Fix setup.cfg for sam2 Signed-off-by: Sachidanand Alle <[email protected]> * Fix setup.cfg for sam2 Signed-off-by: Sachidanand Alle <[email protected]> * Fix setup.cfg for sam2 Signed-off-by: Sachidanand Alle <[email protected]> * Fix github space error Signed-off-by: Sachidanand Alle <[email protected]> * Fix github dep workflow fix Signed-off-by: Sachidanand Alle <[email protected]> * Final fixes after verifying e2e Signed-off-by: Sachidanand Alle <[email protected]> --------- Signed-off-by: Sachidanand Alle <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Project-MONAI · Nov 7, 2024 · 6cb96f6 · 6cb96f6
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diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -28,26 +28,13 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-      - name: clean up
-        run: |
-          sudo rm -rf /usr/share/dotnet
-          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
       - name: Build
         run: |
           rm -rf /opt/hostedtoolcache
-          ./runtests.sh --clean
           docker system prune -f
           DOCKER_BUILDKIT=1 docker build -t projectmonai/monailabel:${{ github.event.inputs.tag || 'latest'  }} -f Dockerfile .
       - name: Verify
         run: |
-          ./runtests.sh --clean
           docker run --rm -i --ipc=host --net=host -v $(pwd):/workspace projectmonai/monailabel:${{ github.event.inputs.tag || 'latest'  }} /workspace/runtests.sh --net
       - name: Publish
         run: |

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -39,6 +39,10 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - if: runner.os == 'Linux'
+        name: Cleanup (Linux only)
+        run: |
+          rm -rf /opt/hostedtoolcache
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
@@ -59,6 +63,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
+          rm -rf /opt/hostedtoolcache
           sudo apt-get install openslide-tools -y
           python -m pip install --upgrade pip wheel
           pip install -r requirements-dev.txt
@@ -107,9 +112,10 @@ jobs:
           key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
       - name: Install dependencies
         run: |
+          rm -rf /opt/hostedtoolcache
           sudo apt-get install openslide-tools -y
           python -m pip install --user --upgrade pip setuptools wheel
-          python -m pip install torch>=1.7 torchvision
+          python -m pip install torch torchvision
       - name: Build Package
         run: |
           ./runtests.sh --clean
@@ -144,7 +150,7 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -165,6 +171,7 @@ jobs:
           key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
       - name: Install dependencies
         run: |
+          rm -rf /opt/hostedtoolcache
           sudo apt-get install openslide-tools -y
           python -m pip install --upgrade pip wheel
           python -m pip install -r docs/requirements.txt

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -49,12 +49,12 @@ jobs:
           key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
       - name: Install dependencies
         run: |
+          rm -rf /opt/hostedtoolcache
           sudo apt-get install openslide-tools -y
           python -m pip install --user --upgrade pip setuptools wheel
-          python -m pip install torch>=1.7 torchvision
+          python -m pip install torch torchvision
       - name: Build Package
         run: |
-          rm -rf /opt/hostedtoolcache
           ./runtests.sh --clean
           BUILD_OHIF=true python setup.py sdist bdist_wheel --build-number $(date +'%Y%m%d%H%M')
           ls -l dist

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -20,7 +20,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git a/README.md b/README.md
@@ -83,6 +83,7 @@ In addition, you can find a table of the basic supported fields, modalities, vie
       <li>Segmentation</li>
       <li>DeepGrow</li>
       <li>DeepEdit</li>
+      <li>SAM2 (2D/3D)</li>
     </ul>
   </td>
   <td>
@@ -114,6 +115,7 @@ In addition, you can find a table of the basic supported fields, modalities, vie
       <li>NuClick</li>
       <li>Segmentation</li>
       <li>Classification</li>
+      <li>SAM2 (2D)</li>
     </ul>
   </td>
   <td>
@@ -143,6 +145,7 @@ In addition, you can find a table of the basic supported fields, modalities, vie
       <li>DeepEdit</li>
       <li>Tooltracking</li>
       <li>InBody/OutBody</li>
+      <li>SAM2 (2D)</li>
     </ul>
   </td>
   <td>
@@ -164,6 +167,12 @@ In addition, you can find a table of the basic supported fields, modalities, vie
 <tr>
 </table>
 
+> [**SAM2**](https://github.com/facebookresearch/sam2/)
+>
+> By default, SAM2 is included for all the above Apps only when **_python >= 3.10_**
+>  - **sam_2d**: for any organ or tissue and others over a given slice/2D image.
+>  - **sam_3d**: to support SAM2 propagation over multiple slices (Radiology/MONAI-Bundle).
+
 # Getting Started with MONAI Label
 ### MONAI Label requires a few steps to get started:
 - Step 1: [Install MONAI Label](#step-1-installation)

diff --git a/monailabel/sam2/__init__.py b/monailabel/sam2/__init__.py