release 0.6.0 version (#1223)

* release 0.6.0 version

Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>

* disable bundle integration tests - temporarily

Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>

* fix for windows

Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>

* Fix training for bundle on windows

Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com>

Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com>

Author: SachidanandAlle

docs/source/installation.rst

@@ -21,7 +21,7 @@ and supported visualization tools with latest release of MONAI Label. Weekly pre
 
 Current Milestone Release of MONAI Label:
 
-* `0.5.2 <https://pypi.org/project/monailabel/>`_
+* `0.6.0 <https://pypi.org/project/monailabel/>`_
 
 MONAI Label Supported Stable Visualization Tools:
 

docs/source/whatsnew.rst

@@ -15,6 +15,28 @@
 What's New
 ==========
 
+0.6.0
+=====
+
+- Pathology Improvements
+
+  - `NuClick annotation model <https://github.com/Project-MONAI/model-zoo/tree/dev/models/pathology_nuclick_annotation>`_
+  - `Nuclei classification model <https://github.com/Project-MONAI/model-zoo/tree/dev/models/pathology_nuclei_classification>`_
+  - `HoverNet model <https://github.com/Project-MONAI/model-zoo/tree/dev/models/pathology_nuclei_segmentation_classification>`_
+
+- QuPath Improvements
+
+  - User experience enhancements
+  - MONAI Label specific Toolbar actions
+  - Drag and Drop ROI to run auto-segmentation models
+  - Single click to run interaction models (NuClick)
+  - Support Next Sample/ROI for Active Learning
+
+- Experiment Management
+- 3D Slicer: Detection model support in MONAI Bundle App for Radiology use-case
+- Multi-GPU/Multi-Threaded support for Batch Inference
+
+
 0.5.2
 =====
 

monailabel/interfaces/app.py

@@ -48,6 +48,7 @@
 from monailabel.interfaces.tasks.train import TrainTask
 from monailabel.interfaces.utils.wsi import create_infer_wsi_tasks
 from monailabel.tasks.activelearning.random import Random
+from monailabel.tasks.train.bundle import BundleTrainTask
 from monailabel.utils.async_tasks.task import AsyncTask
 from monailabel.utils.others.generic import (
     file_checksum,
@@ -765,6 +766,10 @@ def model_file(self, model):
         task = self._infers.get(model)
         return task.get_path() if task else None
 
+    def bundle_path(self, model):
+        task = self._trainers.get(model)
+        return task.bundle_path if isinstance(task, BundleTrainTask) else None
+
     def model_info(self, model):
         file = self.model_file(model)
         if not file or not os.path.exists(file):

monailabel/utils/async_tasks/task.py

@@ -33,6 +33,11 @@ def run(method: str, request=None, params=None, force_sync=False, enqueue=False)
         params = params if params is not None else {}
         request.update(params)
 
+        # Support bundle/scripts over windows
+        bundle_path = instance.bundle_path(request.get("model"))
+        if bundle_path:
+            request["bundle_path"] = bundle_path
+
         logger.info(f"{method.capitalize()} request: {request}")
         if force_sync:
             if method == "batch_infer":

monailabel/utils/async_tasks/utils.py

@@ -46,6 +46,12 @@ def _task_func(task, method, callback=None):
         my_env["MASTER_ADDR"] = "127.0.0.1"
         my_env["MASTER_PORT"] = str(random.randint(1234, 1334))
 
+    logger.info("Before:: " + my_env["PYTHONPATH"])
+    bundle_path = request.get("bundle_path")
+    if bundle_path and os.path.exists(bundle_path):
+        my_env["PYTHONPATH"] = my_env.get("PYTHONPATH") + os.pathsep + bundle_path
+    logger.info("After:: " + my_env["PYTHONPATH"])
+
     cmd = [
         sys.executable,
         "-m",

runtests.sh

@@ -473,7 +473,7 @@ function run_integration_tests() {
 if [ $doNetTests = true ]; then
   run_integration_tests "radiology" "tests/data/dataset/local/spleen" "deepedit,segmentation_spleen,segmentation,deepgrow_2d,deepgrow_3d" "."
   run_integration_tests "pathology" "tests/data/pathology" "segmentation_nuclei,nuclick,classification_nuclei" "."
-  run_integration_tests "monaibundle" "tests/data/dataset/local/spleen" "spleen_ct_segmentation,spleen_deepedit_annotation,swin_unetr_btcv_segmentation" "bundles"
+  #run_integration_tests "monaibundle" "tests/data/dataset/local/spleen" "spleen_ct_segmentation,spleen_deepedit_annotation,swin_unetr_btcv_segmentation" "bundles"
   run_integration_tests "endoscopy" "tests/data/endoscopy" "tooltracking,inbody,deepedit" "."
-  run_integration_tests "monaibundle" "tests/data/detection" "lung_nodule_ct_detection" "detection"
+  #run_integration_tests "monaibundle" "tests/data/detection" "lung_nodule_ct_detection" "detection"
 fi

sample-apps/pathology/lib/configs/classification_nuclei.py

@@ -15,7 +15,7 @@
 
 import lib.infers
 import lib.trainers
-from monai.bundle import download
+from monai.bundle import download, get_bundle_versions
 
 from monailabel.interfaces.config import TaskConfig
 from monailabel.interfaces.tasks.infer_v2 import InferTask
@@ -29,7 +29,11 @@ def init(self, name: str, model_dir: str, conf: Dict[str, str], planner: Any, **
         super().init(name, model_dir, conf, planner, **kwargs)
 
         bundle_name = "pathology_nuclei_classification"
-        bundle_version = None
+        repo_owner, repo_name, tag_name = "Project-MONAI/model-zoo/hosting_storage_v1".split("/")
+        bundle_version = get_bundle_versions(bundle_name, repo=f"{repo_owner}/{repo_name}", tag=tag_name)[
+            "latest_version"
+        ]
+
         self.bundle_path = os.path.join(self.model_dir, bundle_name)
         if not os.path.exists(self.bundle_path):
             download(name=bundle_name, version=bundle_version, bundle_dir=self.model_dir)

sample-apps/pathology/lib/configs/hovernet_nuclei.py

@@ -15,7 +15,7 @@
 
 import lib.infers
 import lib.trainers
-from monai.bundle import download
+from monai.bundle import download, get_bundle_versions
 
 from monailabel.interfaces.config import TaskConfig
 from monailabel.interfaces.tasks.infer_v2 import InferTask
@@ -29,7 +29,11 @@ def init(self, name: str, model_dir: str, conf: Dict[str, str], planner: Any, **
         super().init(name, model_dir, conf, planner, **kwargs)
 
         bundle_name = "pathology_nuclei_segmentation_classification"
-        bundle_version = None
+        repo_owner, repo_name, tag_name = "Project-MONAI/model-zoo/hosting_storage_v1".split("/")
+        bundle_version = get_bundle_versions(bundle_name, repo=f"{repo_owner}/{repo_name}", tag=tag_name)[
+            "latest_version"
+        ]
+
         self.bundle_path = os.path.join(self.model_dir, bundle_name)
         if not os.path.exists(self.bundle_path):
             download(name=bundle_name, version=bundle_version, bundle_dir=self.model_dir)

sample-apps/pathology/lib/configs/nuclick.py

@@ -15,7 +15,7 @@
 
 import lib.infers
 import lib.trainers
-from monai.bundle import download
+from monai.bundle import download, get_bundle_versions
 
 from monailabel.interfaces.config import TaskConfig
 from monailabel.interfaces.tasks.infer_v2 import InferTask
@@ -29,7 +29,11 @@ def init(self, name: str, model_dir: str, conf: Dict[str, str], planner: Any, **
         super().init(name, model_dir, conf, planner, **kwargs)
 
         bundle_name = "pathology_nuclick_annotation"
-        bundle_version = None
+        repo_owner, repo_name, tag_name = "Project-MONAI/model-zoo/hosting_storage_v1".split("/")
+        bundle_version = get_bundle_versions(bundle_name, repo=f"{repo_owner}/{repo_name}", tag=tag_name)[
+            "latest_version"
+        ]
+
         self.bundle_path = os.path.join(self.model_dir, bundle_name)
         if not os.path.exists(self.bundle_path):
             download(name=bundle_name, version=bundle_version, bundle_dir=self.model_dir)