upgrade monai to 0.8.0 version + fix handler + tag support for docker… (#548)

* upgrade monai to 0.8.0 version + fix handler + tag support for docker build

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

* update install docs for DockerHub install method

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

Author: SachidanandAlle

.github/workflows/docker.yml

@@ -1,5 +1,11 @@
 name: docker
-on: workflow_dispatch
+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag name to publish'
+        required: true
+        default: 'latest'
 
 jobs:
   docker_build:
@@ -22,18 +28,18 @@ jobs:
           sudo apt-get install docker-ce
       - name: Build
         run: |
-          DOCKER_BUILDKIT=1 docker build -t projectmonai/monailabel:latest -f Dockerfile .
+          DOCKER_BUILDKIT=1 docker build -t projectmonai/monailabel:${{ github.event.inputs.tag }} -f Dockerfile .
       - name: Publish
         run: |
           echo "${{ secrets.DOCKER_PW }}" | docker login -u projectmonai --password-stdin
-          docker push projectmonai/monailabel:latest
+          docker push projectmonai/monailabel:${{ github.event.inputs.tag }}
           docker logout
           docker image prune -f
 
   docker_test_dockerhub:
     needs: docker_build
     container:
-      image: docker://projectmonai/monailabel:latest
+      image: docker://projectmonai/monailabel:${{ github.event.inputs.tag }}
       options: "--shm-size=4g --ipc=host"
     runs-on: ubuntu-latest
     steps:

docs/source/installation.rst

@@ -62,6 +62,14 @@ The milestone versions are currently planned and released every few months.  As
 codebase is under active development, you may want to install MONAI from GitHub
 for the latest features
 
+From DockerHub
+**************
+To install latest from `DockerHub <https://hub.docker.com/r/projectmonai/monailabel>`_:
+::
+
+    docker run -it --rm --gpus all --ipc=host --net=host -v ~:/workspace/ projectmonai/monailabel:latest bash
+
+
 MONAI Label CLI
 ---------------
 Simple *monailabel* command will help user to download sample apps, datasets and run server.

monailabel/deepedit/handlers.py

@@ -139,13 +139,13 @@ def __call__(self, engine: Engine) -> None:
                 )
             plot_2d_or_3d_image(
                 # add batch dim and plot the first item
-                show_image[None],
-                step,
-                self._writer,
-                0,
-                self.max_channels,
-                self.max_frames,
-                "step_" + str(step) + "_image_" + filename,
+                data=show_image[None],
+                step=step,
+                writer=self._writer,
+                index=0,
+                max_channels=self.max_channels,
+                max_frames=self.max_frames,
+                tag="step_" + str(step) + "_image_" + filename,
             )
 
         """
@@ -162,13 +162,13 @@ def __call__(self, engine: Engine) -> None:
                 )
             plot_2d_or_3d_image(
                 # add batch dim and plot the first item
-                show_label[None],
-                step,
-                self._writer,
-                0,
-                self.max_channels,
-                self.max_frames,
-                "step_" + str(step) + "_label_" + filename,
+                data=show_label[None],
+                step=step,
+                writer=self._writer,
+                index=0,
+                max_channels=self.max_channels,
+                max_frames=self.max_frames,
+                tag="step_" + str(step) + "_label_" + filename,
             )
 
         """
@@ -187,13 +187,13 @@ def __call__(self, engine: Engine) -> None:
                     )
                 plot_2d_or_3d_image(
                     # add batch dim and plot the first item
-                    show_prediction[None],
-                    step,
-                    self._writer,
-                    0,
-                    self.max_channels,
-                    self.max_frames,
-                    "step_" + str(step) + f"_prediction_for_label_{str(idx)}_" + filename,
+                    data=show_prediction[None],
+                    step=step,
+                    writer=self._writer,
+                    index=0,
+                    max_channels=self.max_channels,
+                    max_frames=self.max_frames,
+                    tag="step_" + str(step) + f"_prediction_for_label_{str(idx)}_" + filename,
                 )
 
         """
@@ -214,13 +214,13 @@ def __call__(self, engine: Engine) -> None:
             show_pos_clicks = show_label * (1 - show_pos_clicks)
             plot_2d_or_3d_image(
                 # add batch dim and plot the first item
-                show_pos_clicks[None],
-                step,
-                self._writer,
-                0,
-                self.max_channels,
-                self.max_frames,
-                "step_" + str(step) + "_all_clicks_" + filename,
+                data=show_pos_clicks[None],
+                step=step,
+                writer=self._writer,
+                index=0,
+                max_channels=self.max_channels,
+                max_frames=self.max_frames,
+                tag="step_" + str(step) + "_all_clicks_" + filename,
             )
 
         self._writer.flush()

requirements.txt

@@ -1,6 +1,6 @@
 aiofiles==0.6.0
 fastapi==0.65.2
-monai[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, openslide]==0.8.0rc3
+monai[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, openslide]==0.8.0
 pyyaml==5.4.1
 python-multipart==0.0.5
 requests-toolbelt==0.9.1

setup.cfg

@@ -26,7 +26,7 @@ setup_requires =
 install_requires =
     aiofiles==0.6.0
     fastapi==0.65.2
-    monai[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, openslide]==0.8.0rc3
+    monai[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, openslide]==0.8.0
     pyyaml==5.4.1
     python-multipart==0.0.5
     requests-toolbelt==0.9.1