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Dicoogle Distributed NoSQL plugin - MongoDB

Dicoogle plugin for distributed database of DICOM metadata using MongoDB Sharding. The plugin indexes all metadata as it is configured in Dicoogle (by default, it indexes the DIM required fields) except the PixelData.

Requirements

  • Running:
    • Dicoogle v2.5.0
    • MongoDB
  • Testing:
    • dcmtk

Instructions

  1. Compile and build: mvn install;

  2. Copy the build target/distributed-nosql-2.5.0-jar-with-dependencies.jar to your DicoogleDir/Plugins folder;

  3. Run Dicoogle. Example: sh DicoogleServer.sh.

Configuration

Plugin configuration is available at DicoogleDir/Plugins/settings/dicoogle-distributed-nosql.xml Upon initialization, if no configurations file is supplied, the Dicoogle Platform creates one with the default values. This plugin allows the configuration of the MongoDB host, port, database name and database collection. Example:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<configuration>
    <host>localhost</host>
    <port>27017</port>
    <dbName>DicoogleDatabase</dbName>
    <collectionName>DicoogleObjs</collectionName>
</configuration>

Test the query plugin

  1. Activate the Query Retrieve Service in Dicoogle Management tab available at localhost:8080/#/management running on port 1045

  2. Use one of the following services:

    • HTTP search endpoint:
    http://localhost:8080/searchDIM?query=PatientID:*&keyword=true
    • DCMTK query toolkit:
    findscu -S -k 0008,0052="IMAGE" -k PatientID="*" -aec DICOOGLE-STORAGE localhost 1045

Test the index plugin

  1. Activate the Storage Service in Dicoogle Management tab available at localhost:8080/#/management running on port 6666

  2. Navigate to the folder where the DICOM dataset is contained. Example: cd ~/dicom-dataset

  3. Run the following command to recursively find every file ending with .dcm and using dcmtktoolkit, sending via C-STORE to Dicoogle.

    dcmsend -aec DICOOGLE-STORAGE localhost 6666 $(find . -name '*.dcm' -print)

    Alternatively, you can skip the step 1. and run the following command, replacing <dir> with the directory path to your DICOM dataset folder.

    dcmsend -aec DICOOGLE-STORAGE localhost 6666 $(find <dir> -name '*.dcm' -print)

TODO List

  • Support complex queries (with AND and OR)
  • Support to index all the DICOM TAGS; currently only the DIM are supported
  • Use sync and async MongoDB drivers for different cases; for instance, use async for insert and delete MongoDB documents and use sync for find/query operations where the user should wait for the data retrieval

Acknowledgments

  • Thank you to the contributors of dicoogle-mongo-plugin as the translation of queries to MongoDB queries was adapted from their work