Dicoogle Classification Database

This plugin integrates a database for indexing and querying classification data with Dicoogle.

Building

This is a Maven project.

mvn install

The plugin jar "class-db-1.0.0-plugin.jar" will be in the target folder.

Configuring

A configuration is required for the classification database to work. Specify as many classifier elements as there are classifiers and as many criterion elements as desired. Criteria can also include a variable number of criteria that the specific classification method depends on, often used for conditional classification. The index-path element is optional and is used for specifying the classification index' directory path. These classifiers are expected to be compliant with the Dicoogle Classification API.

Example:

<configuration>
    <index-path>/opt/dicoogle/my-predictions</index-path>
    <classifiers>
        <classifier name="my-classifier">
          <criterion id="liver" />
          <criterion id="lesionType" depends="head-neck" />
        </classifier>
        <classifier name="my-classifier-2">
          <criterion id="head-neck" />
        </classifier>
    </classifiers>
</configuration>

Usage

This plugin will register a new indexer and query provider. When an indexing procedure is issued, this indexer will take all registered classifiers, classify the files and store the results in its own embedded database.

Query Provider API

public Iterable<SearchResult> query(String query);
public Iterable<SearchResult> query(String query, Map<String, Object> options);

The query provider accepts standard Lucene syntax queries. The available fields are "classifier", "criterion", as well as the actual criteria available, or prepended by the classifier's name with a forward slash. Free keyword queries are also supported.

• mammo/microcalcifications:true -- all predictions where the classifier mammo predicted microcalcifications as true.
• liver:true or just liver -- all predictions where liver was predicted true
• bodyPart:torso -- all files where criterion bodyPart was predicted torso
• uri:file:/001.dcm -- all predictions of the given file

Web Services

GET /classification/classify?classifier={}&criterion={}

Request for a classification procedure and return the predictions. The classification database is not involved.

GET /classification/query?query={}

Query for predicted data.

License

Copyright (C) 2017 UA.PT Bioinformatics - http://bioinformatics.ua.pt

dicoogle-class-db is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

dicoogle-class-db is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.