Fix Release Build/setup.py for SAM2 dependency (#1779)

* SAM-2 as extra dependency for PyPi

Signed-off-by: Sachidanand Alle <[email protected]>

* Disable release test once

Signed-off-by: Sachidanand Alle <[email protected]>

* Fix release build

Signed-off-by: Sachidanand Alle <[email protected]>

* Fix release build

Signed-off-by: Sachidanand Alle <[email protected]>

* Fix github sam2 packaging for PyPI release

Signed-off-by: Sachidanand Alle <[email protected]>

* Fix build error

Signed-off-by: Sachidanand Alle <[email protected]>

* Fix build error

Signed-off-by: Sachidanand Alle <[email protected]>

---------

Signed-off-by: Sachidanand Alle <[email protected]>

.dockerignore

@@ -14,6 +14,7 @@ __pycache__
 .vscode
 .webpack
 node_modules/
+*.log
 
 # Environments
 .env

.github/workflows/release.yml

@@ -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:

Dockerfile

@@ -36,7 +36,12 @@ RUN BUILD_OHIF=false python setup.py bdist_wheel --build-number $(date +'%Y%m%d%
 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 --no-cache-dir /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

@@ -167,12 +167,6 @@ 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)
@@ -219,6 +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/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.util import find_spec
 from typing import Any, Dict, List, Optional
 
 from pydantic import AnyHttpUrl
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
+def is_package_installed(name):
+    return False if find_spec(name) is None else True
+
+
 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/sam2/infer.py

@@ -22,6 +22,8 @@
 import pylab
 import schedule
 import torch
+from hydra import initialize_config_dir
+from hydra.core.global_hydra import GlobalHydra
 from monai.transforms import KeepLargestConnectedComponent, LoadImaged
 from PIL import Image
 from sam2.build_sam import build_sam2, build_sam2_video_predictor
@@ -114,13 +116,21 @@ def __init__(
             self._config.update(config)
 
         # Download PreTrained Model
-        # https://github.com/facebookresearch/sam2?tab=readme-ov-file#model-description
-        pt = "sam2.1_hiera_large.pt"
-        url = f"https://dl.fbaipublicfiles.com/segment_anything_2/092824/{pt}"
-        self.path = os.path.join(model_dir, f"pretrained_{pt}")
-        download_file(url, self.path)
+        pt_url = settings.MONAI_SAM_MODEL_PT
+        conf_url = settings.MONAI_SAM_MODEL_CFG
+        sam_pt = pt_url.split("/")[-1]
+        sam_conf = conf_url.split("/")[-1]
+
+        self.path = os.path.join(model_dir, sam_pt)
+        self.config_path = os.path.join(model_dir, sam_conf)
+
+        GlobalHydra.instance().clear()
+        initialize_config_dir(config_dir=model_dir)
+
+        download_file(pt_url, self.path)
+        download_file(conf_url, self.config_path)
+        self.config_path = sam_conf
 
-        self.config_path = "configs/sam2.1/sam2.1_hiera_l.yaml"
         self.predictors = {}
         self.image_cache = {}
         self.inference_state = None
@@ -393,8 +403,8 @@ def main():
         force=True,
     )
 
-    app_name = "pathology"
-    app_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "..", "sample-apps", app_name))
+    app_name = "radiology"
+    app_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "sample-apps", app_name))
     model_dir = os.path.join(app_dir, "model")
     logger.info(f"Model Dir: {model_dir}")
     if app_name == "pathology":

requirements.txt

@@ -45,7 +45,7 @@ scikit-learn
 scipy
 google-auth==2.29.0
 SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
-
+#sam2>=0.4.1; python_version >= '3.10'
 
 # scipy and scikit-learn latest packages are missing on python 3.8
 # sudo apt-get install openslide-tools -y

sample-apps/endoscopy/main.py

@@ -58,9 +58,9 @@ def __init__(self, app_dir, studies, conf):
             print(f"    all, {', '.join(configs.keys())}")
             print("---------------------------------------------------------------------------------------")
             print("")
-            exit(-1)
+            # exit(-1)
 
-        models = models.split(",")
+        models = models.split(",") if models else []
         models = [m.strip() for m in models]
         invalid = [m for m in models if m != "all" and not configs.get(m)]
         if invalid:
@@ -85,7 +85,7 @@ def __init__(self, app_dir, studies, conf):
 
         logger.info(f"+++ Using Models: {list(self.models.keys())}")
 
-        self.sam = strtobool(conf.get("sam", "true"))
+        self.sam = strtobool(conf.get("sam2", "true"))
         super().__init__(
             app_dir=app_dir,
             studies=studies,

sample-apps/monaibundle/main.py

@@ -46,7 +46,7 @@ def __init__(self, app_dir, studies, conf):
             self.epistemic_simulation_size = int(conf.get("epistemic_simulation_size", "5"))
             self.epistemic_dropout = float(conf.get("epistemic_dropout", "0.2"))
 
-        self.sam = strtobool(conf.get("sam", "true"))
+        self.sam = strtobool(conf.get("sam2", "true"))
         super().__init__(
             app_dir=app_dir,
             studies=studies,

sample-apps/pathology/main.py

@@ -54,7 +54,7 @@ def __init__(self, app_dir, studies, conf):
 
         configs = {k: v for k, v in sorted(configs.items())}
 
-        models = conf.get("models", "all")
+        models = conf.get("models")
         if not models:
             print("")
             print("---------------------------------------------------------------------------------------")
@@ -63,9 +63,9 @@ def __init__(self, app_dir, studies, conf):
             print(f"    all, {', '.join(configs.keys())}")
             print("---------------------------------------------------------------------------------------")
             print("")
-            exit(-1)
+            # exit(-1)
 
-        models = models.split(",")
+        models = models.split(",") if models else []
         models = [m.strip() for m in models]
         invalid = [m for m in models if m != "all" and not configs.get(m)]
         if invalid:
@@ -90,7 +90,7 @@ def __init__(self, app_dir, studies, conf):
 
         logger.info(f"+++ Using Models: {list(self.models.keys())}")
 
-        self.sam = strtobool(conf.get("sam", "true"))
+        self.sam = strtobool(conf.get("sam2", "true"))
         super().__init__(
             app_dir=app_dir,
             studies=studies,

sample-apps/radiology/main.py

@@ -64,7 +64,7 @@ def __init__(self, app_dir, studies, conf):
             print("")
             exit(-1)
 
-        models = models.split(",")
+        models = models.split(",") if models else []
         models = [m.strip() for m in models]
         # Can be configured with --conf scribbles false or true
         self.scribbles = conf.get("scribbles", "true") == "true"
@@ -100,7 +100,7 @@ def __init__(self, app_dir, studies, conf):
         # Load models from bundle config files, local or released in Model-Zoo, e.g., --conf bundles <spleen_ct_segmentation>
         self.bundles = get_bundle_models(app_dir, conf, conf_key="bundles") if conf.get("bundles") else None
 
-        self.sam = strtobool(conf.get("sam", "true"))
+        self.sam = strtobool(conf.get("sam2", "true"))
         super().__init__(
             app_dir=app_dir,
             studies=studies,

setup.cfg

@@ -70,7 +70,8 @@ install_requires =
     scikit-learn
     scipy
     google-auth>=2.29.0
-    SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
+    sam2>=0.4.1; python_version >= '3.10'
+    #SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
 
 [flake8]
 select = B,C,E,F,N,P,T4,W,B9