slicer_monai.yaml

AWSTemplateFormatVersion: 2010-09-09
Description: Windows Server with NICE DCV (login as administrator)

Metadata:
  License:
    Description: >
      Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
      SPDX-License-Identifier: MIT-0

      Permission is hereby granted, free of charge, to any person obtaining a copy of this
      software and associated documentation files (the "Software"), to deal in the Software
      without restriction, including without limitation the rights to use, copy, modify,
      merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
      permit persons to whom the Software is furnished to do so.

      THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
      INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
      PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
      HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
      OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
      SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  AWS::CloudFormation::Interface:
    ParameterGroups:
      - Label:
          default: Instance type
        Parameters:
          - InstanceType
      - Label:
          default: EC2 configuration
        Parameters:
          - EC2Name
      - Label:
          default: Allowed inbound source IP prefixes to NICE DCV port 8443
        Parameters:
          - IngressIPv4

Mappings:
  AMIRegionMap:
    af-south-1:
      NICEDCVAMI: ami-03d47e4bac006f330
    ap-south-1:
      NICEDCVAMI: ami-0e776ca6a86a5e730
    eu-north-1:
      NICEDCVAMI: ami-01c816b3591d5dd97
    eu-west-3:
      NICEDCVAMI: ami-0625f6a74fb6afe05
    eu-south-1:
      NICEDCVAMI: ami-0ec6afec9aaece072
    eu-west-2:
      NICEDCVAMI: ami-0b1a1b220220beb02
    eu-west-1:
      NICEDCVAMI: ami-022508a67c81e6c28
    ap-northeast-2:
      NICEDCVAMI: ami-0c31940939aa476b1
    ap-northeast-1:
      NICEDCVAMI: ami-0321bbe7ef4a14e68
    me-south-1:
      NICEDCVAMI: ami-0360a805f5ec40544
    ca-central-1:
      NICEDCVAMI: ami-0c01afbe70f4fdf7c
    sa-east-1:
      NICEDCVAMI: ami-0b0c54a4745049317
    ap-east-1:
      NICEDCVAMI: ami-05e4a897ad6341d4b
    ap-southeast-1:
      NICEDCVAMI: ami-0071215a86fc69d89
    ap-southeast-2:
      NICEDCVAMI: ami-0dc354d026444eaca
    eu-central-1:
      NICEDCVAMI: ami-04c15076684cbc808
    us-east-1:
      NICEDCVAMI: ami-0c46f9b9e1760377c
    us-east-2:
      NICEDCVAMI: ami-03ddf915d48800443
    us-west-1:
      NICEDCVAMI: ami-092e5726b56b55e76
    us-west-2:
      NICEDCVAMI: ami-0b3de9114492317cb

Parameters:
  InstanceType:
    Description: Instance type ( https://aws.amazon.com/ec2/instance-types/#Accelerated_Computing )
    Type: String
    Default: g4dn.xlarge
    AllowedValues:
      - g4dn.xlarge
      - g4dn.2xlarge
      - g4dn.4xlarge
      - g5.xlarge
      - g5.2xlarge

  EC2Name:
    Description: Name of EC2 instance
    Type: String
    Default: Windows Server-NICE-DCV
  IngressIPv4:
    Type: String
    Description: Allowed source prefix (IPv4) ( https://checkip.amazonaws.com )
    Default: 0.0.0.0/0

Resources:
  VPC:
    Type: AWS::EC2::VPC
    Properties:
      CidrBlock: 10.192.0.0/16
      EnableDnsSupport: true
      EnableDnsHostnames: true
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}
        - Key: Name
          Value: !Sub ${AWS::StackName} - VPC

  InternetGateway:
    Type: AWS::EC2::InternetGateway
    Properties:
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}
        - Key: Name
          Value: !Sub ${AWS::StackName} - IGW

  InternetGatewayAttachment:
    Type: AWS::EC2::VPCGatewayAttachment
    Properties:
      InternetGatewayId: !Ref InternetGateway
      VpcId: !Ref VPC

  PublicSubnet:
    Type: AWS::EC2::Subnet
    Properties:
      VpcId: !Ref VPC
      AvailabilityZone: !Select [1, !GetAZs ""]
      CidrBlock: 10.192.10.0/24
      MapPublicIpOnLaunch: True
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}
        - Key: Name
          Value: !Sub ${AWS::StackName} - Public Subnet

  PublicRouteTable:
    Type: AWS::EC2::RouteTable
    Properties:
      VpcId: !Ref VPC
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}
        - Key: Name
          Value: !Sub ${AWS::StackName} - Public Routes

  DefaultPublicRoute:
    Type: AWS::EC2::Route
    DependsOn: InternetGatewayAttachment
    Properties:
      RouteTableId: !Ref PublicRouteTable
      DestinationCidrBlock: 0.0.0.0/0
      GatewayId: !Ref InternetGateway

  PublicSubnetRouteTableAssociation:
    Type: AWS::EC2::SubnetRouteTableAssociation
    Properties:
      RouteTableId: !Ref PublicRouteTable
      SubnetId: !Ref PublicSubnet

  S3GatewayEndpoint:
    Type: AWS::EC2::VPCEndpoint
    Properties:
      PolicyDocument:
        Version: 2012-10-17
        Statement:
          - Effect: Allow
            Principal: "*"
            Action:
              - "s3:*"
            Resource:
              - "arn:aws:s3:::*"
      RouteTableIds:
        - !Ref PublicRouteTable
      ServiceName: !Sub "com.amazonaws.${AWS::Region}.s3"
      VpcId: !Ref VPC

  SecurityGroup:
    Type: AWS::EC2::SecurityGroup
    Properties:
      GroupDescription: Allow inbound DCV
      VpcId: !Ref VPC
      SecurityGroupIngress:
        - Description: NICE DCV (IPv4)
          IpProtocol: "tcp"
          FromPort: "8443"
          ToPort: "8443"
          CidrIp: !Ref IngressIPv4
        - Description: NICE DCV QUIC (IPv4)
          IpProtocol: "udp"
          FromPort: "8443"
          ToPort: "8443"
          CidrIp: !Ref IngressIPv4
      SecurityGroupEgress:
        - Description: Allow all outbound traffic (IPv4)
          IpProtocol: "-1"
          CidrIp: 0.0.0.0/0
        - Description: Allow all outbound traffic (IPv6)
          IpProtocol: "-1"
          CidrIpv6: "::/0"
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}
        - Key: Name
          Value: !Sub "[${AWS::StackName}] - ${EC2Name}"

  S3DataBucket:
    Type: AWS::S3::Bucket
    Properties:
      PublicAccessBlockConfiguration:
        BlockPublicAcls: true
        BlockPublicPolicy: true
        IgnorePublicAcls: true
        RestrictPublicBuckets: true
      BucketEncryption:
        ServerSideEncryptionConfiguration:
          - ServerSideEncryptionByDefault:
              SSEAlgorithm: AES256

  InstanceIamRole:
    Type: AWS::IAM::Role
    Properties:
      AssumeRolePolicyDocument:
        Statement:
          - Effect: Allow
            Principal:
              Service: [ec2.amazonaws.com]
            Action: ["sts:AssumeRole"]
      Path: /
      Policies:
        - PolicyName: dcvLicensing
          PolicyDocument:
            Version: "2012-10-17"
            Statement:
              - Effect: Allow
                Action:
                  - s3:GetObject
                Resource: !Sub "arn:${AWS::Partition}:s3:::dcv-license.${AWS::Region}/*"
        - PolicyName: fullAccessToDataBucket
          PolicyDocument:
            Version: "2012-10-17"
            Statement:
              - Effect: Allow
                Action:
                  - s3:ListBucket
                  - s3:GetObject
                  - s3:PutObject
                Resource:
                  - !GetAtt S3DataBucket.Arn
                  - !Sub "${S3DataBucket.Arn}/*"
      ManagedPolicyArns:
        - !Sub "arn:${AWS::Partition}:iam::aws:policy/AmazonSSMManagedInstanceCore"
        - !Sub "arn:${AWS::Partition}:iam::aws:policy/AmazonS3ReadOnlyAccess"
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}

  InstanceProfile:
    Type: AWS::IAM::InstanceProfile
    Properties:
      Path: /
      Roles:
        - !Ref InstanceIamRole

  EC2Instance:
    Type: AWS::EC2::Instance
    CreationPolicy:
      ResourceSignal:
        Timeout: PT90M
    Properties:
      ImageId: !FindInMap [AMIRegionMap, !Ref "AWS::Region", NICEDCVAMI]
      InstanceType: !Ref InstanceType
      IamInstanceProfile: !Ref InstanceProfile
      SubnetId: !Ref PublicSubnet
      Monitoring: true
      SecurityGroupIds:
        - !Ref SecurityGroup
      BlockDeviceMappings:
        - DeviceName: /dev/sda1
          Ebs:
            VolumeSize: 100
            VolumeType: gp3
            DeleteOnTermination: true
            Encrypted: true
      UserData:
        Fn::Base64: !Sub |
          <script>
          @echo off
          cfn-init.exe -v --stack ${AWS::StackId} --resource EC2Instance --region ${AWS::Region} --configsets setup

          cd \windows\temp\

          @echo ** https://docs.aws.amazon.com/systems-manager/latest/userguide/sysman-install-win.html
          powershell -command "(New-Object System.Net.WebClient).DownloadFile('https://amazon-ssm-${AWS::Region}.s3.${AWS::Region}.amazonaws.com/latest/windows_amd64/AmazonSSMAgentSetup.exe', 'AmazonSSMAgentSetup.exe')"
          c:\windows\temp\AmazonSSMAgentSetup.exe /S

          @echo ** install Chocolatey windows package manager
          powershell -comand "Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))"
          SET "PATH=%PATH%;%PROGRAMDATA%\chocolatey\bin\"

          @echo ** install aws cli
          choco install awscli -y

          @echo ** install git
          choco install git.install -y

          @echo ** install python
          choco install python39 -y
          call RefreshEnv.cmd

          @echo ** install firefox
          choco install firefox -y

          @echo ** download and install the latest nvidia graphics driver
          echo $Bucket = 'ec2-windows-nvidia-drivers' > download-nvidia-driver.ps1
          echo $KeyPrefix = 'latest' >> download-nvidia-driver.ps1
          echo $LocalPath = '.\NVIDIA' >> download-nvidia-driver.ps1
          echo $Objects = Get-S3Object -BucketName $Bucket -KeyPrefix $KeyPrefix -Region us-east-1 >> download-nvidia-driver.ps1
          echo foreach ($Object in $Objects) { >> download-nvidia-driver.ps1
          echo     $LocalFileName = $Object.Key >> download-nvidia-driver.ps1
          echo     if ($LocalFileName -ne '' -and $LocalFileName -like '*server2019*' -and $Object.Size -ne 0) { >> download-nvidia-driver.ps1
          echo         $LocalFilePath = Join-Path $LocalPath 'nvidia-latest-driver.exe' >> download-nvidia-driver.ps1
          echo         Copy-S3Object -BucketName $Bucket -Key $Object.Key -LocalFile $LocalFilePath -Region us-east-1 >> download-nvidia-driver.ps1
          echo     } >> download-nvidia-driver.ps1
          echo } >> download-nvidia-driver.ps1
          powershell -file download-nvidia-driver.ps1
          START /WAIT .\NVIDIA\nvidia-latest-driver.exe -s -n

          @echo ** install MONAI label
          python -m pip install --upgrade pip setuptools wheel
          python -m pip install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu117
          python -m pip install monailabel
          mkdir C:\monai-label
          powershell -command "$shortcut=(New-Object -ComObject WScript.Shell).CreateShortcut('C:\Users\Administrator\Desktop\monai-label.lnk');$shortcut.TargetPath='C:\monai-label\';$shortcut.Save()"

          @echo ** install TotalSegmentator
          python -m pip install TotalSegmentator

          @echo ** install lungmask
          python -m pip install lungmask

          @echo ** download 3D Slicer
          mkdir C:\slicer
          cd C:\slicer
          powershell -command "(New-Object System.Net.WebClient).DownloadFile('https://slicer-packages.kitware.com/api/v1/item/637f7a7f517443dc5dc73276/download', 'slicer-setup.exe')"
          powershell -command "$shortcut=(New-Object -ComObject WScript.Shell).CreateShortcut('C:\Users\Administrator\Desktop\slicer.lnk');$shortcut.TargetPath='C:\slicer\';$shortcut.Save()"

          cfn-signal.exe -e %errorlevel% --stack ${AWS::StackId} --resource EC2Instance --region ${AWS::Region}
          shutdown -r
          </script>
      Tags:
        - Key: Name
          Value: !Ref EC2Name
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}
        - Key: GitHub
          Value: https://github.com/aws-samples/amazon-ec2-nice-dcv-samples

  ElasticIP:
    Type: AWS::EC2::EIP
    Properties:
      InstanceId: !Ref EC2Instance
      Tags:
        - Key: StackName
          Value: !Sub ${AWS::StackName}
        - Key: StackId
          Value: !Sub ${AWS::StackId}

Outputs:
  InstanceID:
    Description: EC2 Instance ID
    Value: !Ref EC2Instance

  PublicIP:
    Description: EC2 Public IP
    Value: !GetAtt EC2Instance.PublicIp

  SSMsessionManager:
    Description: SSM Session Manager login ("net user administrator MyStr@ngAdminPassw0rd" to change administrator password)
    Value: !Sub "https://${AWS::Region}.console.aws.amazon.com/systems-manager/session-manager/${EC2Instance}"

  DCVwebConsole:
    Description: DCV web console (login as administrator)
    Value: !Sub "https://${EC2Instance.PublicIp}:8443"

  DCVdownload:
    Description: DCV client download
    Value: https://download.nice-dcv.com

  S3DataBucket:
    Description: S3 bucket for storing data
    Value: !Ref S3DataBucket