Merge branch 'main' into ignite-issue

.dockerignore

@@ -12,8 +12,24 @@
 __pycache__
 .idea
 .vscode
-
-Dockerfile
-sample-apps/**/model
-node_modules
 .webpack
+node_modules/
+*.log
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.venv/
+ubuntu_venv/
+
+# apps
+sample-apps/*/logs
+sample-apps/*/train
+sample-apps/*/model
+docs/build
+docs/source/apidocs

.github/workflows/blossom-ci.yml

@@ -47,7 +47,7 @@ jobs:
         github.actor == 'diazandr3s' ||
         github.actor == 'tangy5' ||
         github.actor == 'wyli' ||
-        github.actor == 'YanxuanLiu'
+        github.actor == 'wendell-hom'
       )
     steps:
       - name: Check if comment is issued by authorized person

.github/workflows/docker.yml

@@ -28,26 +28,23 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-      - name: clean up
+      - name: Cleanup
         run: |
-          sudo rm -rf /usr/share/dotnet
+          echo Before Cleanup...
+          df -h
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip wheel
+          rm -rf /opt/hostedtoolcache
+          rm -rf /usr/share/dotnet/
+          cd /opt
+          find . -maxdepth 1 -mindepth 1 '!' -path ./containerd '!' -path ./actionarchivecache '!' -path ./runner '!' -path ./runner-cache -exec rm -rf '{}' ';'
+          cd -
+          echo After Cleanup...
+          df -h
       - name: Build
         run: |
-          rm -rf /opt/hostedtoolcache
-          ./runtests.sh --clean
-          docker system prune -f
-          DOCKER_BUILDKIT=1 docker build -t projectmonai/monailabel:${{ github.event.inputs.tag || 'latest'  }} -f Dockerfile .
+          DOCKER_BUILDKIT=0 docker build -t projectmonai/monailabel:${{ 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: |

.github/workflows/pythonapp.yml

@@ -32,13 +32,17 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         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
@@ -50,7 +54,7 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -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
@@ -72,7 +77,7 @@ jobs:
         run: |
           $(pwd)/runtests.sh --unittests
       - name: Upload coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: false
           file: ./coverage.xml
@@ -83,7 +88,7 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -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

.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
@@ -91,7 +91,7 @@ jobs:
         run: |
           rm dist/monai*.tar.gz
 
-      - name: Publish distribution to Test PyPI
+      - name: Publish distribution to Test
         if: ${{ github.event.inputs.test_py == 'true' }}
         uses: pypa/gh-action-pypi-publish@master
         with:

.gitignore

@@ -120,6 +120,8 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.venv/
+ubuntu_venv/
 
 # Spyder project settings
 .spyderproject
@@ -139,12 +141,6 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# virtualenv
-.venv/
-venv/
-ENV/
-ubuntu_venv/
-
 # IDE
 .idea/
 .vscode/
@@ -166,7 +162,7 @@ junit
 test-output.xml
 studies
 tests/data
-yarn.lock
+
 # Packages
 node_modules
 yarn.lock

.readthedocs.yml

@@ -20,7 +20,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

Dockerfile

@@ -11,29 +11,37 @@
 
 # To build with a different base image
 # please run `./runtests.sh --clean && DOCKER_BUILDKIT=1 docker build -t projectmonai/monailabel:latest .`
-# to use different version of MONAI pass `--build-arg MONAI_IMAGE=...`
-
-ARG MONAI_IMAGE=projectmonai/monai:1.4.0
+# to use different version of MONAI pass `--build-arg FINAL_IMAGE=...`
 
+#ARG FINAL_IMAGE=pytorch/pytorch:2.5.1-cuda12.4-cudnn9-runtime
+ARG FINAL_IMAGE=ubuntu:22.04
+ARG BUILD_IMAGE=python:3.10
 ARG NODE_IMAGE=node:slim
 
-FROM ${NODE_IMAGE} as ohifbuild
-ADD . /opt/monailabel
+# Phase1: Build OHIF Viewer
+FROM ${NODE_IMAGE} AS ohifbuild
+COPY plugins/ohifv3 /opt/ohifv3
 RUN apt update -y && apt install -y git
-RUN cd /opt/monailabel/plugins/ohifv3 && ./build.sh
-
-FROM ${MONAI_IMAGE} as build
-LABEL maintainer="[email protected]"
+RUN cd /opt/ohifv3 && ./build.sh /opt/ohifv3/release
 
+# Phase2: Build MONAI Label Package
+FROM ${BUILD_IMAGE} AS build
+WORKDIR /opt/monailabel
+RUN python -m pip install pip setuptools wheel twine
 ADD . /opt/monailabel/
-COPY --from=ohifbuild /opt/monailabel/monailabel/endpoints/static/ohif /opt/monailabel/monailabel/endpoints/static/ohif
-RUN python -m pip install --upgrade --no-cache-dir pip setuptools wheel twine \
-    && cd /opt/monailabel \
-    && BUILD_OHIF=false python setup.py sdist bdist_wheel --build-number $(date +'%Y%m%d%H%M')
+COPY --from=ohifbuild /opt/ohifv3/release /opt/monailabel/monailabel/endpoints/static/ohif
+RUN BUILD_OHIF=false python setup.py bdist_wheel --build-number $(date +'%Y%m%d%H%M')
 
-FROM ${MONAI_IMAGE}
+# Phase3: Build Final Docker
+FROM ${FINAL_IMAGE}
 LABEL maintainer="[email protected]"
+WORKDIR /opt/monailabel
+COPY requirements.txt /opt/monailabel/requirements.txt
+
+RUN apt update -y && apt install -y git curl openslide-tools python3 python-is-python3 python3-pip
+RUN python -m pip install --no-cache-dir pytest torch torchvision torchaudio
 
 COPY --from=build /opt/monailabel/dist/monailabel* /opt/monailabel/dist/
-RUN python -m pip install --upgrade --no-cache-dir pip \
-    && python -m pip install /opt/monailabel/dist/monailabel*.whl
+RUN python -m pip install -v --no-cache-dir /opt/monailabel/dist/monailabel*.whl
+RUN python -m pip uninstall sam2 -y
+RUN python -m pip install -v --no-cache-dir -r /opt/monailabel/requirements.txt

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>
@@ -210,6 +213,19 @@ To install the _**latest features**_ using one of the following options:
   <pre>docker run --gpus all --rm -ti --ipc=host --net=host projectmonai/monailabel:latest bash</pre>
 </details>
 
+### SAM-2
+
+> By default, [**SAM2**](https://github.com/facebookresearch/sam2/) model is included for all the Apps 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).
+
+If you are using `pip install monailabel` by default it uses [SAM-2](https://huggingface.co/facebook/sam2-hiera-large) models.
+<br/>
+To use [SAM-2.1](https://huggingface.co/facebook/sam2.1-hiera-large) use one of following options.
+ - Use monailabel [Docker](https://hub.docker.com/r/projectmonai/monailabel) instead of pip package
+ - Run monailabel in dev mode (git checkout)
+ - If you have installed monailabel via pip then uninstall **_sam2_** package `pip uninstall sam2` and then run `pip install -r requirements.txt` or install latest **SAM-2** from it's [github](https://github.com/facebookresearch/sam2/tree/main?tab=readme-ov-file#installation).
+
 ## Step 2 MONAI Label Sample Applications
 
 <h3>Radiology</h3>

monailabel/client/client.py

@@ -336,6 +336,7 @@ def infer(self, model, image_id, params, label_in=None, file=None, session_id=No
         fields = {"params": json.dumps(params) if params else "{}"}
         files = {"label": label_in} if label_in else {}
         files.update({"file": file} if file and not session_id else {})
+        logger.info(f"Files: {files}")
 
         status, form, files, _ = MONAILabelUtils.http_multipart(
             "POST", self._server_url, selector, fields, files, headers=self._headers
@@ -584,6 +585,9 @@ def send_response(conn, content_type="application/json"):
 
     @staticmethod
     def save_result(files, tmpdir):
+        if not files:
+            return None
+
         for name in files:
             data = files[name]
             result_file = os.path.join(tmpdir, name)

monailabel/config.py

@@ -8,14 +8,18 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
 import os
+from importlib.metadata import distributions
 from typing import Any, Dict, List, Optional
 
 from pydantic import AnyHttpUrl
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
+def is_package_installed(name):
+    return name in sorted(x.name for x in distributions())
+
+
 class Settings(BaseSettings):
     MONAI_LABEL_API_STR: str = ""
     MONAI_LABEL_PROJECT_NAME: str = "MONAILabel"
@@ -98,6 +102,19 @@ class Settings(BaseSettings):
     MONAI_ZOO_REPO: str = "Project-MONAI/model-zoo/hosting_storage_v1"
     MONAI_ZOO_AUTH_TOKEN: str = ""
 
+    # Refer: https://github.com/facebookresearch/sam2?tab=readme-ov-file#model-description
+    # Refer: https://huggingface.co/facebook/sam2-hiera-large
+    MONAI_SAM_MODEL_PT: str = (
+        "https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_large.pt"
+        if is_package_installed("SAM-2")
+        else "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_large.pt"
+    )
+    MONAI_SAM_MODEL_CFG: str = (
+        "https://huggingface.co/facebook/sam2.1-hiera-large/resolve/main/sam2.1_hiera_l.yaml"
+        if is_package_installed("SAM-2")
+        else "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_l.yaml"
+    )
+
     model_config = SettingsConfigDict(
         env_file=".env",
         case_sensitive=True,

monailabel/endpoints/infer.py

@@ -91,10 +91,8 @@ def send_response(datastore, result, output, background_tasks):
     if output == "json":
         return res_json
 
-    m_type = get_mime_type(res_img)
-
     if output == "image":
-        return FileResponse(res_img, media_type=m_type, filename=os.path.basename(res_img))
+        return FileResponse(res_img, media_type=get_mime_type(res_img), filename=os.path.basename(res_img))
 
     if output == "dicom_seg":
         res_dicom_seg = result.get("dicom_seg")
@@ -106,7 +104,7 @@ def send_response(datastore, result, output, background_tasks):
     res_fields = dict()
     res_fields["params"] = (None, json.dumps(res_json), "application/json")
     if res_img and os.path.exists(res_img):
-        res_fields["image"] = (os.path.basename(res_img), open(res_img, "rb"), m_type)
+        res_fields["image"] = (os.path.basename(res_img), open(res_img, "rb"), get_mime_type(res_img))
     else:
         logger.info(f"Return only Result Json as Result Image is not available: {res_img}")
         return res_json