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| name: Publish wiki | ||
| on: | ||
| push: | ||
| branches: [main] | ||
| paths: | ||
| - wiki/** | ||
| - .github/workflows/publish-wiki.yaml | ||
| concurrency: | ||
| group: publish-wiki | ||
| cancel-in-progress: true | ||
| permissions: | ||
| contents: write | ||
| jobs: | ||
| publish-wiki: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: Andrew-Chen-Wang/github-wiki-action@v4 |
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| # DICOM Instance Test Info | ||
| - This page about test info of raccoon-dicom | ||
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| ## DICOM Instances' Info | ||
| | Patient ID | Procedure Code | Modality | Series Count | Image Count | | ||
| |--------------|----------------|----------|--------------|---------------| | ||
| | C3L-00277 | 36643-5 | DX | 1 | 1 | | ||
| | C3N-00953 | 42274-1 | CT | 3 | 11 | | ||
| | TCGA-G4-6304 | 42274-1 | CT | 3 | 14 | | ||
| | 123456 | | SM | 1 | 1 (Frame: 15) | | ||
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| ## Test Search For Studies | ||
| ### Query By `StudyDate (0008, 0020)` | ||
| #### Step 100 | ||
| - StudyDate=19990101-19991231 | ||
| - Expect 2 matches | ||
| #### Step 110 | ||
| - StudyDate=20220101-20221231 | ||
| - Expect 0 match | ||
| ### Step 170: Query By `PatientID (0010, 0020)` | ||
| - PatientID=TCGA-G4-6304 | ||
| - Expect 1 match | ||
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| ### Step 120: Query By `PatientName (0010, 0010)` & `StudyDate (0008, 0020)` | ||
| - PatientName=TCGA\*&StudyDate=20100101-20101231 | ||
| - Expect 0 match | ||
| - PatientName=TCGA\*&StudyDate=19990101-19991231 | ||
| - Expect 1 match | ||
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| ### Step 130: Query By `PatientName (0010, 0010)` & `PatientBirthDate (0010, 0030)` | ||
| - PatientName=ChestXR\*&PatientBirthDate=19590101 | ||
| - Expect 0 match | ||
| - PatientName=ChestXR\*&PatientBirthDate=19601218 | ||
| - Expect 1 match | ||
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| ### Step 140: Query By `PatientID (0010, 0020)` & `AccessionNumber (0008, 0050)` | ||
| - PatientID=C3N-00953&AccessionNumber=4444 | ||
| - Expect 0 match | ||
| - PatientID=C3N-00953&AccessionNumber=2794663908550664 | ||
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| ## Test Search For Series | ||
| ### Step 150 | ||
| - Use StudyInstanceUID from [Query By `PatientID (0010, 0020)` & `AccessionNumber (0008, 0050)`](https://github.com/Chinlinlee/raccoon-dicom/wiki/DICOM-Instance-Test-Info#query-by-patientid-0010-0020--accessionnumber-0008-0050) to search | ||
| - Expect 3 series | ||
| ### Step 180 | ||
| - Use StudyInstanceUID from [170](https://github.com/Chinlinlee/raccoon-dicom/wiki/DICOM-Instance-Test-Info#query-by-patientid-0010-0020-170) to search | ||
| - Expect 3 series | ||
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| ## Test Search For Instances | ||
| ### Step 160 | ||
| - Use response's SeriesInstanceUIDs from [150](https://github.com/Chinlinlee/raccoon-dicom/wiki/DICOM-Instance-Test-Info#150) | ||
| - Expect 1 image, 5 images, and 5 images in 3 series, respectively | ||
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| ## Test limit | ||
| - Query limit=1 in study level | ||
| - Expect 1 match |
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| # Step by Step guide to installing - Windows | ||
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| ## Download Raccoon | ||
| ### Use git | ||
| ```bash | ||
| git clone https://github.com/Chinlinlee/raccoon-dicom.git | ||
| ``` | ||
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| ### Alternative, Download ZIP | ||
|  | ||
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| > ⚠️ Please unzip by yourself | ||
| ## Install Environment Requirements | ||
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| ### Environment Requirements | ||
| The following is a list of requirements, we will install each software next. | ||
| - [Node.js](https://nodejs.org/zh-tw/download) >= 16 | ||
| - [Mongodb](https://www.mongodb.com/try/download/community) >= 4 | ||
| - [Imagemagick](https://imagemagick.org/script/download.php) | ||
| - openJDK >= 11 | ||
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| ### Install Node.js 16 | ||
| - [Click here to download Node.js 16 installer](https://nodejs.org/download/release/v16.20.0/node-v16.20.0-x64.msi) | ||
| - Open `node-v16.20.0-x64.msi` that you downloaded | ||
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|  | ||
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| - **Select Install Destination** and click Next | ||
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|  | ||
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| - Click Install | ||
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|  | ||
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| #### Verify Node.js has been installed successfully | ||
| Open cmd and type `node -v`. | ||
| If present v16.20.0, congratulations install successfully. | ||
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|  | ||
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| ### Install MongoDB | ||
| - Enter Home of MongoDB: https://www.mongodb.com/try/download/community | ||
| - Select Version → `4.4.21`，`Platform` → `Windows` -> `Package` → `msi` and click Download | ||
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|  | ||
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| - Open `mongodb-windows-x86_64-4.4.21-signed.msi` that you downloaded | ||
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|  | ||
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| - Select Complete | ||
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|  | ||
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| - Set Data Directory and Log Directory and then click Next | ||
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|  | ||
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| - Install MongoDB Compass | ||
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|  | ||
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| - Click Install | ||
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|  | ||
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| - Installation Completed! | ||
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|  | ||
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| #### Create User in MongoDB | ||
| Since the MongoDB connection with Raccoon-DICOM requires username and password. | ||
| You need to create a user in the MongoDB to use Raccoon-DICOM. | ||
| - Open MongoDB Compass | ||
| - Enter the following connection string in New Connection and click Connect. | ||
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| ```bash | ||
| mongodb://localhost:27017 | ||
| ``` | ||
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|  | ||
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| - Click `>_MONGOSH` below. | ||
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|  | ||
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| - Enter the following command to switch to admin database | ||
| ```bash | ||
| use admin; | ||
| ``` | ||
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|  | ||
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| - Enter the following command to create root user | ||
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| > **Warning** | ||
| > ⚠️Please change the username and password to a secure one by yourself! | ||
| ```js | ||
| db.createUser({ | ||
| user : "root", | ||
| pwd : "root" , | ||
| roles : [{role : "root" , db:"admin"}] | ||
| }); | ||
| ``` | ||
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| > If present { ok: 1 }, it means the creation was successful! | ||
| ### Install ImageMagick | ||
| - Enter Download page of ImageMagick: https://imagemagick.org/script/download.php | ||
| - Click `Windows Binary Release` to redirect to Windows paragraph | ||
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|  | ||
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| - Click `ImageMagick-7.1.0-27-Q16-HDRI-x64-dll.exe` to download | ||
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| - Open `ImageMagick-7.1.0-27-Q16-HDRI-x64-dll` that you downloaded | ||
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| - Select install destination and click Next | ||
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| - Click Install | ||
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| - Click Next, and uncheck `View Index.html`, and click Finish | ||
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| #### Verify installation is complete | ||
| Open cmd (command prompt) and enter "magick -version". If you see the following message, the installation is successful! | ||
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| ### Install JAVA JDK | ||
| - Go to https://adoptium.net/temurin/releases/ | ||
| - Select Operating System: Windows | ||
| - Architecture: x64 | ||
| - Package Type: JDK | ||
| - Version: 11 | ||
| - Click to download | ||
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| - Open `OpenJDK11U-jdk_x64_windows_hotspot_11.0.19_7` that you downloaded one | ||
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| - Select install destination and click Next | ||
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| - Click Install | ||
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| - Completed! | ||
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| > ⚠️Please reboot after installation | ||
| #### Verify JAVA is installed successfully | ||
| - Open the command prompt and enter `javac --version` | ||
| - If present version info on cmd, congrats! | ||
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| ## Raccoon-DICOM Installation | ||
| The required software has been installed, and you can now proceed with setting up Raccoon! | ||
| ⚠️ Note: Before the following steps, please navigate to the Raccoon project directory. | ||
| ### Install Node.js Packages | ||
| Open the command prompt and navigate to the Raccoon project directory, then execute the following command: | ||
| ```bash | ||
| npm i --only=production | ||
| ``` | ||
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| > **Note** | ||
| > --only=production means only install dependencies in the `dependencies` block of package.json file | ||
| ### Configure dotenv `.env` file | ||
| - Copy `.env.template` in the project root and rename it to `.env` | ||
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|  | ||
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| - Modify `.env` | ||
| ```text | ||
| # MongoDB | ||
| MONGODB_NAME="raccoon-dicom" | ||
| MONGODB_HOSTS=["mongodb"] | ||
| MONGODB_PORTS=[27017] | ||
| MONGODB_USER="root" | ||
| MONGODB_PASSWORD="root" | ||
| MONGODB_AUTH_SOURCE="admin" | ||
| MONGODB_OPTIONS="" | ||
| MONGODB_IS_SHARDING_MODE=false | ||
| # Server | ||
| SERVER_PORT=8081 | ||
| SERVER_SESSION_SECRET_KEY="secret-key" | ||
| # DICOM Web | ||
| DICOM_STORE_ROOTPATH="/dicomFiles" | ||
| DICOMWEB_HOST="{host}" | ||
| DICOMWEB_PORT=8081 | ||
| DICOMWEB_API="dicom-web" | ||
| # DICOM DIMSE | ||
| ENABLE_DIMSE=true | ||
| DIMSE_AE_TITLE="RACCOONQRSCP" # default: RACCOONQRSCP | ||
| DIMSE_HOSTNAME="0.0.0.0" # default: 127.0.0.1 | ||
| DIMSE_PORT=11112 # default: 11112 | ||
| DIMSE_MAX_PDULEN_RCV=16378 | ||
| DIMSE_MAX_PDULEN_SND=16378 | ||
| DIMSE_NOT_ASYNC=false | ||
| DIMSE_MAX_OPS_INVOKED=0 | ||
| DIMSE_MAX_OPS_PERFORMED=0 | ||
| DIMSE_NOT_PACK_PDV=false | ||
| DIMSE_CONNECT_TIMEOUT=0 | ||
| DIMSE_REQUEST_TIMEOUT=0 | ||
| DIMSE_ACCEPT_TIMEOUT=0 | ||
| DIMSE_RELEASE_TIMEOUT=0 | ||
| DIMSE_SEND_TIMEOUT=0 | ||
| DIMSE_STORE_TIMEOUT=0 | ||
| DIMSE_RESPONSE_TIMEOUT=0 | ||
| DIMSE_RETRIEVE_TIMEOUT=0 | ||
| DIMSE_RETRIEVE_TIMEOUT_TOTAL=0 | ||
| DIMSE_IDLE_TIMEOUT=0 | ||
| DIMSE_SOCLOSE_DELAY=50 | ||
| DIMSE_SOSND_BUFFER=0 | ||
| DIMSE_SORCV_BUFFER=0 | ||
| DIMSE_TCP_DELAY=false | ||
| # DIMSE TLS | ||
| DIMSE_TLS=false | ||
| DIMSE_TLS_NULL=false | ||
| DIMSE_TLS_3DES=false | ||
| DIMSE_TLS_AES=false | ||
| DIMSE_TLS_CIPHER="" | ||
| DIMSE_TLS13=false | ||
| DIMSE_TLS12=false | ||
| DIMSE_TLS11=false | ||
| DIMSE_TLS1=false | ||
| DIMSE_SSL3=false | ||
| DIMSE_SSL2HELLO=false | ||
| DIMSE_TLS_PROTOCOL="" | ||
| DIMSE_TLS_EIA_HTTPS=false | ||
| DIMSE_TLS_EIA_LDAPS=false | ||
| DIMSE_TLS_NOAUTH=false | ||
| DIMSE_KEY_STORE="./config/certs/key.p12" | ||
| DIMSE_KEY_STORE_TYPE="PKCS12" | ||
| DIMSE_KEY_STORE_PASS="secret" | ||
| DIMSE_KEY_PASS="secret" | ||
| DIMSE_TRUST_STORE="./config/certs/cacerts.p12" | ||
| DIMSE_TRUST_STORE_TYPE="PKCS12" | ||
| DIMSE_TRUST_STORE_PASS="secret" | ||
| # FHIR | ||
| SYCN_TO_FHIR_SERVER=false | ||
| FHIRSERVER_BASE_URL="http://localhost:8088/fhir" | ||
| ``` | ||
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| ## Deploy Raccoon-DICOM | ||
| - Open command prompt and enter Raccoon project directory, then execute following command | ||
| ``` | ||
| node server.js | ||
| ``` | ||
|
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| ## Test Raccoon-DICOM features | ||
| ### Upload DICOM Instance (STOW-RS) | ||
| - The following steps will use the file test/dicomFiles/jpeg2000/example-jpeg-2000.dcm for uploading test | ||
| - Use curl for uploading | ||
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| ```powershell | ||
| curl --location --request POST "http://localhost:8081/dicom-web/studies" ^ | ||
| --header "Accept: application/dicom+json" ^ | ||
| --header "Content-Type: multipart/related; type=\"application/dicom\"" ^ | ||
| --form "file=@example-jpeg-2000.dcm; type=application/dicom" | ||
| ``` | ||
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| - If present message following, congrats upload successful!! | ||
| ```json | ||
| {"00081190":{"vr":"UT","Value":["http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543"]},"00081198":{"vr":"SQ","Value":[]},"00081199":{"vr":"SQ","Value":[{"00081150":{"vr":"UI","Value":["1.2.840.10008.5.1.4.1.1.77.1.6"]},"00081155":{"vr":"UI","Value":["1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0"]},"00081190":{"vr":"UT","Value":["http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543/series/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560606509.3/instances/1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0"]}}]}} | ||
| ``` | ||
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| ### Get Image info (QIDO-RS) | ||
| - Open browser or Postman | ||
| - Access http://localhost:8081/dicom-web/studies and get DICOM Json | ||
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| ### Retrieve Image (WADO-RS) | ||
| - Open browser or Postman | ||
| - Access http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543/series/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560606509.3/instances/1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0/frames/1/rendered | ||
| - Result: | ||
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| - You can also test imagemagick is working normally：Access http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543/series/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560606509.3/instances/1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0/frames/1/rendered?iccprofile=rommrgb | ||
| - Check whether the color changes | ||
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