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Integrate TM Docker plug-in changes to enable passing UID:GID as argu…
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…ment.

- add new liver tumor 2.0 sample

Signed-off-by: Victor Chang <[email protected]>
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mocsharp committed Nov 1, 2023
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8 changes: 4 additions & 4 deletions deploy/monai-deploy-express/.env
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# Container Images
INFORMATICS_GATEWAY_IMAGE=ghcr.io/project-monai/monai-deploy-informatics-gateway:0.4.1
INFORMATICS_GATEWAY_CONFIG_IMAGE=dwdraju/alpine-curl-jq:latest
WORKFLOW_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-workflow-manager:2023.5.0-beta.185
TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:2023.5.0-beta.185
WORKFLOW_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-workflow-manager:2023.5.0-beta.238
TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:2023.5.0-beta.238

MINIO_IMAGE=minio/minio:latest
MONGODB_IMAGE=mongo:5.0.12
ORTHANC_IMAGE=osimis/orthanc:23.3.4
RABBITMQ_IMAGE=rabbitmq:3.11-management
ORTHANC_IMAGE=osimis/orthanc:23.9.2-full
RABBITMQ_IMAGE=rabbitmq:3.12.7-management

ELK_VERSION=8.7.0
ELASTICSEARCH_IMAGE=docker.elastic.co/elasticsearch/elasticsearch:${ELK_VERSION}
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48 changes: 44 additions & 4 deletions deploy/monai-deploy-express/README.md
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Expand Up @@ -99,7 +99,7 @@ The first time calling `docker compose up` may take longer as it needs to pull a

- The following error indicates that the `docker compose` version may not be up-to-date. If the problem persists, modify the `TASK_MANAGER_DATA` variable defined in the `.env` file and change `$PWD/.md/mdtm` to a fully qualified path. E.g. `/home/monai/some/path/to/.md/mdtm/`.
```
ERROR: Named volume "$PWD/.md/mdtm:/var/lib/monai:rw" is used in service "task-manager" but no declaration was found in the volumes section.
ERROR: Named volume "$PWD/.md/mdtm:/var/lib/mde:rw" is used in service "task-manager" but no declaration was found in the volumes section.
```

*WHY? The value of `TASK_MANAGER_DATA` is exposed to the Task Manager container as an environment variable in order for Task Manager to map the volume from the host to the MAP container correctly.*
Expand All @@ -112,7 +112,7 @@ The first time calling `docker compose up` may take longer as it needs to pull a

- If you start Monai Deploy Express from within a container, you are likely to have problems when starting the system with 'docker compose up', such as:
```
ERROR: Named volume "$PWD/.md/mdtm:/var/lib/monai:rw" is used in service "task-manager" but no declaration was found in the volumes section.
ERROR: Named volume "$PWD/.md/mdtm:/var/lib/mde:rw" is used in service "task-manager" but no declaration was found in the volumes section.
```

- If you start Monai Deploy Express from within a container, you are likely to have problems when starting the system with 'docker compose up', such as:
Expand Down Expand Up @@ -156,6 +156,7 @@ The **sample-workflows** directory includes the following four sample workflow d
- `lung-seg.json`: AI Lung Segmentation MAP
- `liver-seg.json`: AI Liver Segmentation MAP
- `liver-lung-seg.json`: AI Lung & AI Liver Combo
- `liver-tumor.json`: AI Liver Tumor 2.0 MAP (MONAI Deploy 0.6)
*Note: in these examples, we will be using `curl` command to register MONAI Deploy workflow definitions with the Workflow Manager. To learn more about `curl`, visit the [curl Man Page](https://curl.se/docs/manpage.html).*
Expand Down Expand Up @@ -193,7 +194,7 @@ This example uses the `alpine` container image instead of a MAP to print all fil
#### Description
In this section, we will download a DICOM dataset, upload it to Orthanc and then run the [Liver Segmentation MAP](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/examples/apps/ai_livertumor_seg_app) from the
In this section, we will download a DICOM dataset, upload it to Orthanc and then run the [Liver Segmentation MAP](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/0.5.1/examples/apps/ai_livertumor_seg_app) from the
[MONAI Deploy App SDK](https://github.com/Project-MONAI/monai-deploy-app-sdk). Finally, we can expect the AI-generated segmentation result to appear in Orthanc.
Expand Down Expand Up @@ -300,6 +301,45 @@ In the `liver-lung-seg.json` workflow definition, we combined the AI Lung MAP an
In this example, the [Chest CT dataset](https://drive.google.com/file/d/1IGXUgZ7NQCwsix57cdSgr-iYErevqETO/view?usp=sharing) should only launch the AI Lung MAP, while the [Abdomen CT dataset](https://drive.google.com/file/d/1d8Scm3q-kHTqr_-KfnXH0rPnCgKld2Iy/view?usp=sharing) would launch the AI Liver MAP.
### AI Liver Tumor 2.0 MAP
#### Description
In this section, we will download a DICOM dataset, upload it to Orthanc and then run the [Liver Segmentation MAP](https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/0.6.0/examples/apps/ai_livertumor_seg_app) from the
[MONAI Deploy App SDK](https://github.com/Project-MONAI/monai-deploy-app-sdk). Finally, we can expect the AI-generated segmentation result to appear in Orthanc.
#### Steps
1. Download the [Abdomen CT dataset](#running-a-monai-deploy-workflow) dataset
2. Download the AI Liver Tumor 2.0 MAP
```bash
docker pull ghcr.io/mmelqin/monai_ai_livertumor_seg_app_stl-x64-workstation-dgpu-linux-amd64:2.0
```
3. Upload the dataset as described in [Uploading Data](#upload-dicom-datasets)
4. Deploy the workflow definition to MONAI Deploy Workflow Manager:
5.
```bash
curl --request POST --header 'Content-Type: application/json' --data "@sample-workflows/liver-tumor.json" http://localhost:5001/workflows
```
If the `curl` command runs successfully, expect a `workflow_id` to be returned and printed to the terminal:
```
{"workflow_id":"811620da-381f-4daa-854d-600948e67228"}
```
6. Navigate to Orthanc, select any study and then click *Send to DICOM Modality* from the menu on the left.
In the popup dialog, select **MONAI-DEPLOY** to start a C-STORE request to the Informatics Gateway.
7. Wait for the workflow to complete; the entire workflow takes roughly one minute and thirty seconds to complete. To see the AI-generated segmentation object, reload the Orthanc study page.
8. To see the output of the container, run the following commands:
```bash
> docker container list -a | grep monai_ai_livertumor_seg_app_stl
# locate the container ID and run the following
> docker logs {CONTAINER ID}
```
## Using Kibana
A default dataview is imported to Kibana at startup. To load the saved search, navigate to http://localhost:5601/, click on Analytics > Discover from the 🍔 menu. From the top right click *Open* and select *MONAI-Default*.
Expand Down Expand Up @@ -416,7 +456,7 @@ A MONAI Deploy [workflow definition](https://github.com/Project-MONAI/monai-depl
"entrypoint": "/bin/bash,-c", # entrypoint of your container image; separated by commas
"command": "python3 -u /opt/monai/app/app.py", # commands to execute with the container image; separated by commas
"task_timeout_minutes": "5", # how long this task is expected to execute; terminated after the configured value
"temp_storage_container_path": "/var/lib/monai/", # how thd Docker plug-in maps your data from host to container - this is mapped to `$TASK_MANAGER_DATA` in the docker-compose file
"temp_storage_container_path": "/var/lib/mde/", # how thd Docker plug-in maps your data from host to container - this is mapped to `$TASK_MANAGER_DATA` in the docker-compose file
"env_MONAI_INPUTPATH": "/var/monai/input/", # an environment varible provided to the container to read the input data
"env_MONAI_OUTPUTPATH": "/var/monai/output/", # an environment variable provided to the container to write AI-genrated results
"env_MONAI_MODELPATH": "/opt/monai/models/", # an environment variable provided to the container to located AI models
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2 changes: 1 addition & 1 deletion deploy/monai-deploy-express/docker-compose.yml
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Expand Up @@ -209,7 +209,7 @@ services:
container_name: $TASK_MANAGER_CONTAINERNAME
volumes:
- ./configs/task-manager.json:/opt/monai/wm/appsettings.json
- $TASK_MANAGER_DATA:/var/lib/monai/:rw
- $TASK_MANAGER_DATA:/var/lib/mde/:rw
- /var/run/docker.sock:/var/run/docker.sock
# - $MONAI_DEPLOY_PLUGINS:/opt/monai/wm/plug-ins/
environment:
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7 changes: 7 additions & 0 deletions deploy/monai-deploy-express/init.sh
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Expand Up @@ -18,6 +18,13 @@ RUNDIR=$PWD/.md
echo "Initializing directories..."
[ -d $RUNDIR ] && echo "Removing existin $RUNDIR" && sudo rm -r $RUNDIR
mkdir -p $RUNDIR/esdata/ && echo "Created $RUNDIR/"
mkdir -p $RUNDIR/minio/ && echo "Created $RUNDIR/minio/"
mkdir -p $RUNDIR/rabbitmq/ && echo "Created $RUNDIR/rabbitmq/"
mkdir -p $RUNDIR/orthanc/ && echo "Created $RUNDIR/orthanc/"
mkdir -p $RUNDIR/mongodb/ && echo "Created $RUNDIR/mongodb/"
mkdir -p $RUNDIR/mdwm/ && echo "Created $RUNDIR/mdwm/"
mkdir -p $RUNDIR/mdtm/ && echo "Created $RUNDIR/mdtm/"
mkdir -p $RUNDIR/mdig/ && echo "Created $RUNDIR/mdig/"
sudo chown 1000:1000 -R $RUNDIR/esdata && echo "Permission updated"
echo "Directories setup"
echo "Ready to run docker compose up"
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Expand Up @@ -21,7 +21,7 @@
"server_url": "unix:///var/run/docker.sock",
"entrypoint": "/bin/sh,-c",
"command": "/usr/bin/find /var/monai/input -type f",
"temp_storage_container_path": "/var/lib/monai/",
"temp_storage_container_path": "/var/lib/mde/",
"MYINPUT": "/var/monai/input/"
},
"artifacts": {
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Expand Up @@ -37,7 +37,7 @@
"entrypoint": "/bin/bash,-c",
"command": "python3 -u /opt/monai/app/app.py",
"task_timeout_minutes": "5",
"temp_storage_container_path": "/var/lib/monai/",
"temp_storage_container_path": "/var/lib/mde/",
"env_MONAI_INPUTPATH": "/var/monai/input/",
"env_MONAI_OUTPUTPATH": "/var/monai/output/",
"env_MONAI_MODELPATH": "/opt/monai/models/",
Expand Down Expand Up @@ -93,7 +93,7 @@
"entrypoint": "/bin/bash,-c",
"command": "python3 -u /opt/monai/app/app.py",
"task_timeout_minutes": "5",
"temp_storage_container_path": "/var/lib/monai/",
"temp_storage_container_path": "/var/lib/mde/",
"env_MONAI_INPUTPATH": "/var/monai/input/",
"env_MONAI_OUTPUTPATH": "/var/monai/output/",
"env_MONAI_MODELPATH": "/opt/monai/models/",
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Expand Up @@ -33,7 +33,7 @@
"entrypoint": "/bin/bash,-c",
"command": "python3 -u /opt/monai/app/app.py",
"task_timeout_minutes": "5",
"temp_storage_container_path": "/var/lib/monai/",
"temp_storage_container_path": "/var/lib/mde/",
"env_MONAI_INPUTPATH": "/var/monai/input/",
"env_MONAI_OUTPUTPATH": "/var/monai/output/",
"env_MONAI_MODELPATH": "/opt/monai/models/",
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84 changes: 84 additions & 0 deletions deploy/monai-deploy-express/sample-workflows/liver-tumor.json
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{
"name": "ai-liver-seg",
"version": "1.0.0",
"description": "AI Liver Tumor 2.0",
"informatics_gateway": {
"ae_title": "MONAI-DEPLOY",
"data_origins": [
"ORTHANC"
],
"export_destinations": [
"ORTHANC"
]
},
"tasks": [
{
"id": "router",
"description": "Ensure series description contains liver",
"type": "router",
"task_destinations": [
{
"name": "liver",
"conditions": ["{{ context.dicom.series.any('0008','103E')}} == 'CT series for liver tumor from nii 014'"]
}
]
},
{
"id": "liver",
"description": "Execute Liver Segmentation MAP",
"type": "docker",
"args": {
"container_image": "ghcr.io/mmelqin/monai_ai_livertumor_seg_app_stl-x64-workstation-dgpu-linux-amd64:2.0",
"server_url": "unix:///var/run/docker.sock",
"user": "1000:1000",
"entrypoint": "/bin/bash,-c",
"command": "python3 -u /opt/holoscan/app/",
"task_timeout_minutes": "5",
"temp_storage_container_path": "/var/lib/mde/",
"env_HOLOSCAN_INPUT_PATH": "/var/holoscan/input/",
"env_HOLOSCAN_OUTPUT_PATH": "/var/holoscan/output/",
"env_HOLOSCAN_MODEL_PATH": "/opt/holoscan/models/",
"env_HOLOSCAN_WORKDIR": "/var/holoscan/"
},
"artifacts": {
"input": [
{
"name": "env_HOLOSCAN_INPUT_PATH",
"value": "{{ context.input.dicom }}"
}
],
"output": [
{
"name": "env_HOLOSCAN_OUTPUT_PATH",
"mandatory": true
}
]
},
"task_destinations": [
{
"name": "export-liver-seg"
}
]
},
{
"id": "export-liver-seg",
"description": "Export Segmentation Storage Object",
"type": "export",
"export_destinations": [
{
"Name": "ORTHANC"
}
],
"artifacts": {
"input": [
{
"name": "export-dicom",
"value": "{{ context.executions.liver.artifacts.env_HOLOSCAN_OUTPUT_PATH }}",
"mandatory": true
}
],
"output": []
}
}
]
}
2 changes: 1 addition & 1 deletion deploy/monai-deploy-express/sample-workflows/lung-seg.json
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Expand Up @@ -33,7 +33,7 @@
"entrypoint": "/bin/bash,-c",
"command": "python3 -u /opt/monai/app/app.py",
"task_timeout_minutes": "5",
"temp_storage_container_path": "/var/lib/monai/",
"temp_storage_container_path": "/var/lib/mde/",
"env_MONAI_INPUTPATH": "/var/monai/input/",
"env_MONAI_OUTPUTPATH": "/var/monai/output/",
"env_MONAI_MODELPATH": "/opt/monai/models/",
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