Merge branch 'main' into main

.github/workflows/blossom-ci.yml

@@ -45,7 +45,6 @@ jobs:
       diazandr3s,\
       tangy5,\
       wyli,\
-      pxLi,\
       YanxuanLiu,\
       ', format('{0},', github.actor)) && github.event.comment.body == '/build'
     steps:

.github/workflows/docker-plugin.yml

@@ -26,10 +26,10 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: clean up
         run: |
           sudo rm -rf /usr/share/dotnet

.github/workflows/docker.yml

@@ -28,10 +28,10 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: clean up
         run: |
           sudo rm -rf /usr/share/dotnet

.github/workflows/pythonapp.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest]
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -50,7 +50,7 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -83,7 +83,7 @@ jobs:
       MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
         with:

docs/source/quickstart.rst

@@ -394,8 +394,6 @@ On the local machine follow the commands listed below to install MONAI Label, an
   monailabel datasets --download --name Task09_Spleen --output .
 
   # start the bundle app in MONAI label server
-  # the MONAI Bundle app requires access to MODEL ZOO, please set the authentication token first.
-  export MONAI_ZOO_AUTH_TOKEN=<Your github auth token>
   # and start annotating the images using bundle with the Swin UNETR bundle
   monailabel start_server --app monaibundle --studies Task09_Spleen/imagesTr --conf models swin_unetr_btcv_segmentation
 
@@ -450,7 +448,6 @@ Prerequisite: Check Model Zoo `Release <https://github.com/Project-MONAI/model-z
 
   # Step 4: start the bundle app in MONAI label server
   # the MONAI Bundle app requires access to MODEL ZOO, please set the authentication token first.
-  export MONAI_ZOO_AUTH_TOKEN=<Your github auth token>
   monailabel start_server --app monaibundle --studies Task09_Spleen/imagesTr --conf models renalStructures_UNEST_segmentation
 
 

monailabel/app.py

@@ -11,6 +11,7 @@
 
 import os
 import pathlib
+from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
 from fastapi.middleware import Middleware
@@ -41,11 +42,24 @@
 origins = [str(origin) for origin in settings.MONAI_LABEL_CORS_ORIGINS] if settings.MONAI_LABEL_CORS_ORIGINS else ["*"]
 print(f"Allow Origins: {origins}")
 
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    print("App Init...")
+    instance = app_instance()
+    instance.server_mode(True)
+    instance.on_init_complete()
+
+    yield
+    print("App Shutdown...")
+
+
 app = FastAPI(
     title=settings.MONAI_LABEL_PROJECT_NAME,
     openapi_url="/openapi.json",
     docs_url=None,
     redoc_url="/docs",
+    lifespan=lifespan,
     middleware=[
         Middleware(
             CORSMiddleware,
@@ -101,10 +115,3 @@ async def favicon():
 def reload():
     clear_cache()
     return {}
-
-
-@app.on_event("startup")
-async def startup_event():
-    instance = app_instance()
-    instance.server_mode(True)
-    instance.on_init_complete()

monailabel/config.py

@@ -12,7 +12,8 @@
 import os
 from typing import Any, Dict, List, Optional
 
-from pydantic import AnyHttpUrl, BaseSettings
+from pydantic import AnyHttpUrl
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class Settings(BaseSettings):
@@ -21,7 +22,7 @@ class Settings(BaseSettings):
 
     MONAI_LABEL_APP_DIR: str = ""
     MONAI_LABEL_STUDIES: str = ""
-    MONAI_LABEL_APP_CONF: Dict[str, str] = {}
+    MONAI_LABEL_APP_CONF: Dict[str, Any] = {}
 
     MONAI_LABEL_AUTH_ENABLE: bool = False
     MONAI_LABEL_AUTH_REALM_URI: str = "http://localhost:8080/realms/monailabel"
@@ -82,7 +83,7 @@ class Settings(BaseSettings):
     MONAI_LABEL_SERVER_PORT: int = 8000
     MONAI_LABEL_CORS_ORIGINS: List[AnyHttpUrl] = []
 
-    MONAI_LABEL_AUTO_UPDATE_SCORING = True
+    MONAI_LABEL_AUTO_UPDATE_SCORING: bool = True
 
     MONAI_LABEL_SESSIONS: bool = True
     MONAI_LABEL_SESSION_PATH: str = ""
@@ -93,13 +94,15 @@ class Settings(BaseSettings):
     MONAI_LABEL_TRACKING_ENABLED: bool = True
     MONAI_LABEL_TRACKING_URI: str = ""
 
-    MONAI_ZOO_SOURCE: str = os.environ.get("BUNDLE_DOWNLOAD_SRC", "github")
+    MONAI_ZOO_SOURCE: str = os.environ.get("BUNDLE_DOWNLOAD_SRC", "monaihosting")
     MONAI_ZOO_REPO: str = "Project-MONAI/model-zoo/hosting_storage_v1"
     MONAI_ZOO_AUTH_TOKEN: str = ""
 
-    class Config:
-        env_file = ".env"
-        case_sensitive = True
+    model_config = SettingsConfigDict(
+        env_file=".env",
+        case_sensitive=True,
+        extra="ignore",
+    )
 
 
 settings = Settings()

monailabel/datastore/local.py

@@ -398,7 +398,7 @@ def get_dataset_archive(self, limit_cases: Optional[int]) -> str:
                         path = d[key]
                         archive.write(path, arcname=os.path.join(key, os.path.basename(path)))
                 # add metadata
-                datastore_metadata: str = self._datastore.json(exclude={"base_path"})
+                datastore_metadata: str = self._datastore.model_dump_json(exclude={"base_path"})
                 archive.writestr("metadata.json", datastore_metadata)
 
             assert archive.filename is not None, "ZIP archive could not be created"
@@ -670,7 +670,8 @@ def _init_from_datastore_file(self, throw_exception=False):
                     ts = os.stat(self._datastore_config_path).st_mtime
                     if self._config_ts != ts:
                         logger.debug(f"Reload Datastore; old ts: {self._config_ts}; new ts: {ts}")
-                        self._datastore = LocalDatastoreModel.parse_file(self._datastore_config_path)
+                        with open(self._datastore_config_path) as fp:
+                            self._datastore = LocalDatastoreModel.model_validate_json(fp.read())
                         self._datastore.base_path = self._datastore_path
                         self._config_ts = ts
             logger.debug("Release the Lock...")
@@ -684,7 +685,7 @@ def _write_to_file():
             logger.debug("+++ Datastore is updated...")
             self._ignore_event_config = True
             with open(self._datastore_config_path, "w") as f:
-                f.write(json.dumps(self._datastore.dict(exclude={"base_path"}), indent=2, default=str))
+                f.write(json.dumps(self._datastore.model_dump(exclude={"base_path"}), indent=2, default=str))
             self._config_ts = os.stat(self._datastore_config_path).st_mtime
 
         if lock:
@@ -716,4 +717,4 @@ def status(self) -> Dict[str, Any]:
         }
 
     def json(self):
-        return self._datastore.dict(exclude={"base_path"})
+        return self._datastore.model_dump(exclude={"base_path"})

monailabel/endpoints/login.py

@@ -61,4 +61,4 @@ async def access_token(form_data: OAuth2PasswordRequestForm = Depends()):
 
 @router.get("/token/valid", summary="Check If current token is Valid")
 async def valid_token(user: User = Depends(get_current_user)):
-    return user.dict()
+    return user.model_dump()

monailabel/endpoints/wsi_infer.py

@@ -96,7 +96,7 @@ def run_wsi_inference(
 
     config = instance.info().get("config", {}).get("infer", {})
     request.update(config)
-    request.update(wsi.dict(exclude={"params"}))
+    request.update(wsi.model_dump(exclude={"params"}))
     if wsi.params:
         request.update(wsi.params)
 
@@ -139,7 +139,7 @@ async def api_run_wsi_v2_inference(
     image: str = "",
     session_id: str = "",
     file: UploadFile = File(None),
-    wsi: str = Form(WSIInput().json()),
+    wsi: str = Form(WSIInput().model_dump_json()),
     output: Optional[ResultType] = None,
     user: User = Depends(RBAC(settings.MONAI_LABEL_AUTH_ROLE_USER)),
 ):

monailabel/interfaces/app.py

@@ -416,7 +416,7 @@ def train(self, request):
         if not task:
             raise MONAILabelException(
                 MONAILabelError.INVALID_INPUT,
-                f"Train Task is not Initialized. There is no model '{model}' available",
+                f"Train Task is not Initialized. There is no model '{model}' available; {request}",
             )
 
         request = copy.deepcopy(request)

monailabel/interfaces/utils/app.py

@@ -88,7 +88,7 @@ def run_main():
     logger.debug("------------------------------------------------------")
     logger.debug("SETTINGS")
     logger.debug("------------------------------------------------------")
-    logger.debug(json.dumps(settings.dict(), indent=2))
+    logger.debug(json.dumps(settings.model_dump(), indent=2))
     logger.debug("")
 
     app_dir = args.app if args.app else settings.MONAI_LABEL_APP_DIR

monailabel/main.py

@@ -62,7 +62,7 @@ def args_start_server(self, parser):
         parser.add_argument("--workers", default=None, type=int, help="Number of worker processes")
         parser.add_argument("--limit_concurrency", default=None, type=int, help="Max concurrent connections")
         parser.add_argument("--access_log", action="store_true", help="Enable access log")
-        parser.add_argument("--root_path", default="/", help="Application root path")
+        parser.add_argument("--root_path", default="", help="Application root path")
         parser.add_argument("--log_level", default="info", help="Log level")
 
         parser.add_argument("-l", "--log_config", default=None, type=str, help="Logging config")
@@ -290,7 +290,7 @@ def start_server_validate_args(self, args):
             "MONAI_LABEL_DATASTORE_PASSWORD",
             "MONAI_LABEL_DATASTORE_API_KEY",
         ]
-        for k, v in settings.dict().items():
+        for k, v in settings.model_dump().items():
             v = f"'{json.dumps(v)}'" if isinstance(v, list) or isinstance(v, dict) else v
             logger.debug(f"ENV SETTINGS:: {k} = {'*' * len(v) if k in sensitive else v}")
         logger.info("")
@@ -316,7 +316,7 @@ def start_server_init_settings(self, args):
         if args.dryrun:
             export_key = "set " if any(platform.win32_ver()) else "export "
             with open("env.bat" if any(platform.win32_ver()) else ".env", "w") as f:
-                for k, v in settings.dict().items():
+                for k, v in settings.model_dump().items():
                     v = f"'{json.dumps(v)}'" if isinstance(v, list) or isinstance(v, dict) else v
                     e = f"{export_key}{k}={v}"
                     f.write(e)
@@ -338,7 +338,7 @@ def start_server_init_settings(self, args):
             logger.debug("**********************************************************")
             logger.debug("                  ENV VARIABLES/SETTINGS                  ")
             logger.debug("**********************************************************")
-            for k, v in settings.dict().items():
+            for k, v in settings.model_dump().items():
                 if isinstance(v, list) or isinstance(v, dict):
                     v = json.dumps(v)
                 elif v is not None:

monailabel/utils/others/generic.py

@@ -255,22 +255,11 @@ def is_openslide_supported(name):
 
 def get_zoo_bundle(model_dir, conf, models, conf_key):
     zoo_repo = conf.get("zoo_repo", settings.MONAI_ZOO_REPO)
-    auth_token = conf.get("auth_token", settings.MONAI_ZOO_AUTH_TOKEN)
-    auth_token = auth_token if auth_token else None
-    try:
-        zoo_info = get_all_bundles_list(auth_token=auth_token)
-    except:
-        print("")
-        print("---------------------------------------------------------------------------------------")
-        print(
-            "Github access rate limit reached, please provide personal auth token by setting env MONAI_ZOO_AUTH_TOKEN"
-        )
-        print("or --conf auth_token <personal auth token>")
-        exit(-1)
+    zoo_info = get_all_bundles_list()
 
     # filter model zoo bundle with MONAI Label supported bundles according to the maintaining list, return all version bundles list
     available = [i[0] for i in zoo_info if i[0] in MAINTAINED_BUNDLES]
-    available_with_version = {b: get_bundle_versions(b, auth_token=auth_token)["all_versions"] for b in available}
+    available_with_version = {b: get_bundle_versions(b)["all_versions"] for b in available}
 
     available_both = available + [k + "_v" + v for k, versions in available_with_version.items() for v in versions]
 
@@ -316,7 +305,7 @@ def get_zoo_bundle(model_dir, conf, models, conf_key):
             if not os.path.exists(p):
                 name = k if k in available else version_to_name.get(k)
                 version = None if k in available else name_to_version.get(k)
-                download(name=name, version=version, bundle_dir=model_dir, source="github", repo=zoo_repo)
+                download(name=name, version=version, bundle_dir=model_dir, source="monaihosting", repo=zoo_repo)
                 if version:
                     shutil.move(os.path.join(model_dir, name), p)
         bundles[k] = p
@@ -350,7 +339,7 @@ def get_bundle_models(app_dir, conf, conf_key="models"):
     models = models.split(",")
     models = [m.strip() for m in models]
 
-    if zoo_source == "github":  # if in github env, access model zoo
+    if zoo_source == "monaihosting":  # if in github env, access model zoo
         bundles = get_zoo_bundle(model_dir, conf, models, conf_key)
     else:  # if not in github env, no "model zoo" access, users either provide bundles locally, or auto download with latest
         bundles: Dict[str, str] = {}

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/MonaiLabelClient.java

@@ -19,6 +19,7 @@
 import java.io.InputStream;
 import java.lang.reflect.Type;
 import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -190,7 +191,7 @@ public static Document infer(String model, String image, String imageFile, Strin
 
 		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
 		DocumentBuilder builder = factory.newDocumentBuilder();
-		InputStream inputStream = new ByteArrayInputStream(response.getBytes());
+		InputStream inputStream = new ByteArrayInputStream(response.getBytes(StandardCharsets.UTF_8));
 		Document dom = builder.parse(inputStream);
 		return dom;
 	}

plugins/slicer/CMakeLists.txt

@@ -15,12 +15,12 @@ project(MONAILabel)
 
 #-----------------------------------------------------------------------------
 # Extension meta-information
-set(EXTENSION_HOMEPAGE "https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/slicer/MONAILabel")
+set(EXTENSION_HOMEPAGE "https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/slicer")
 set(EXTENSION_CATEGORY "Active Learning")
-set(EXTENSION_CONTRIBUTORS "NVIDIA, KCL")
-set(EXTENSION_DESCRIPTION "This is Active Learning solution developed under project MONAILabel")
+set(EXTENSION_CONTRIBUTORS "Sachidanand Alle (NVIDIA), Andres Diaz-Pinto (KCL), Alvin Ihsani (NVIDIA), Fernando Perez-Garcia (UCL/KCL)")
+set(EXTENSION_DESCRIPTION "This extension offers Active Learning solution developed under project MONAILabel (Powered by the NVIDIA, KCL).")
 set(EXTENSION_ICONURL "https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Resources/Icons/MONAILabel.png")
-set(EXTENSION_SCREENSHOTURLS "https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/1.png https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/2.png")
+set(EXTENSION_SCREENSHOTURLS "https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/1.png https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/2.png https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/3.png")
 set(EXTENSION_DEPENDS "NA") # Specified as a list or "NA" if no dependencies
 
 #-----------------------------------------------------------------------------