diff --git a/plugins/dicom-web/.gitignore b/plugins/dicom-web/.gitignore new file mode 100644 index 0000000..a6f89c2 --- /dev/null +++ b/plugins/dicom-web/.gitignore @@ -0,0 +1 @@ +/target/ \ No newline at end of file diff --git a/plugins/dicom-web/README.md b/plugins/dicom-web/README.md new file mode 100644 index 0000000..d64f221 --- /dev/null +++ b/plugins/dicom-web/README.md @@ -0,0 +1,100 @@ +Dicoogle Plugin - Sample +======================== + +This is a Dicoogle plugin to serve as an example. Those that are interested in developing a new +plugin may use this one as a template. + +Getting Started +--------------- + +### Installing and running Dicoogle + +1. Make sure that you have Java installed in your system. Versions 8 and 11 are known to work. +1. Go to https://www.dicoogle.com/downloads and get version 3 of Dicoogle +3. Extract your contents to its own directory (e.g. "~/dicoogle" or "C:\dicoogle", depending on the platform). +4. Run Dicoogle with: sh DicoogleClient.sh (OSX / Linux) or DicoogleClient.bat (Windows). +5. You should see your web browser opening the Dicoogle user interface. Is it running? You're ok! + +### Downloading and building the plugin + +Maven is required in order to build the project. An IDE with Maven support such as Netbeans may also help. + +1. Clone the git repository at https://github.com/bioinformatics-ua/dicoogle-plugin-sample.git + +2. Go to the project's base directory in a command line and run `mvn package`. + Alternatively, open the Maven project of the plugin with your IDE, then force it to build your project. + +3. If the building task is successful, you will have a new shaded jar (with the necessary dependencies) + in the `target` folder (e.g. `target/dicoogle-plugin-sample-3.1.0.jar`) + +### Developing your own plugin based on this sample + +The first class to look into is [`RSIPluginSet`][pluginset]. +It is the main entry point for everything else. +Once modified to suit your needs, build the plugin again and re-deploy it to Dicoogle (see below). + +Be sure to consult the [Dicoogle Learning Pack][learningpack] for more information. + +[pluginset]: src/main/java/org/dicoogle/plugins/dicomweb/RSIPluginSet.java +[learningpack]: https://bioinformatics-ua.github.io/dicoogle-learning-pack/docs/developing-plugins/ + +### Using your plugin + +1. Copy your plugin's built jar (`target/dicoogle-plugin-sample-3.1.0.jar`) + to the "Plugins" folder inside the root folder of Dicoogle. + +2. Run Dicoogle. The plugin will be automatically included. + +Available content +----------------- + +- `RSIIndexer` : a sample indexer, only logs the DIM contents of files +- `RSIStorage` : a sample storage service, keeps files in memory buffers +- `RSIQuery` : a sample query provider, returns random data on request +- `RSIJettyPlugin` : a sample plugin for providing web services, holds `RSIWebService` +- `RSIWebService` : a sample web service in the form of a servlet, serves a web page and a few other services +- `RSIRestPlugin` : a sample Restlet server resource, provides dummy data +- Sample HTML5 content and consuming web service: helps you to build a web app + +Web service plugin sample and Web App: +-------------------------------------- + +To test the webservice plugin, you may open your browser and navigate to these URLs: + +- `http://localhost:8080/sample/hello?uid=1111` +- `http://localhost:8080/dashboardSample` +- `http://localhost:8080/ext/dicoogle-test` (restlet) + +You may also use the built-in Dicoogle services for testing other plugins: + +- GET `http://localhost:8080/search?query=test&provider=dicoogle-plugin-sample` to test the query provider + - Note: You will need to record `dicoogle-plugin-sample` + as a DIM provider first. In `confs/server.xml`, + add the query provider in `config/archive/dim-providers` + like this: + ```xml + + + + + + dicoogle-plugin-sample + + + ``` + Then restart Dicoogle. + Remember to remove the provider from the list after testing + if you do not want to keep it. +- POST `http://localhost:8080/management/tasks/index?plugin=dicoogle-plugin-sample&uri=` to test the indexer + +Platforms +---------- + +Dicoogle has been tested in: + +- Windows +- Linux +- Mac OS X + +For more information, please visit https://www.dicoogle.com + diff --git a/plugins/dicom-web/dependency-reduced-pom.xml b/plugins/dicom-web/dependency-reduced-pom.xml new file mode 100644 index 0000000..601cf6a --- /dev/null +++ b/plugins/dicom-web/dependency-reduced-pom.xml @@ -0,0 +1,122 @@ + + + + dicoogle-plugins + pt.ua.ieeta + 3.4.1 + ../../pom.xml + + 4.0.0 + org.dicoogle.plugins + dicomweb + dicomweb + 1.0.0-SNAPSHOT + + + + src/main/resources/html5/ + + + WebPlugins/webplugin-sample + src/main/resources/webplugin-sample/dist + + package.json + module.js + + + + + + maven-compiler-plugin + 3.13.0 + + 1.8 + 1.8 + + + + maven-shade-plugin + 3.6.0 + + + package + + shade + + + + + *:* + + **/*.SF + **/*.DSA + **/*.RSA + **/module-info.class + **/module-info.java + + + + true + + + org.dcm4che3 + org.dcm4che5 + + + + + + + + maven-jar-plugin + 2.3.1 + + C:\Users\bastiao\Projects\Dicoogle\dicoogle\dicoogle\target\Plugins + + + + + + + + mavencentral + https://repo1.maven.org/maven2/ + + + + false + + dicoogle-public + https://dev.bmd-software.com/nexus/content/repositories/dicoogle-public + + + maven-restlet + Public online Restlet repository + https://maven.restlet.talend.com + + + + dcm4che + https://www.dcm4che.org/maven2/ + + + sourceforge-releases + Sourceforge Releases + https://oss.sonatype.org/content/repositories/sourceforge-releases + + + + + pt.ua.ieeta + dicoogle + 3.4.1 + provided + + + + 3.4.1 + UTF-8 + 9.0.3.v20130506 + 5.33.1 + + diff --git a/plugins/dicom-web/pom.xml b/plugins/dicom-web/pom.xml new file mode 100644 index 0000000..5a23a7b --- /dev/null +++ b/plugins/dicom-web/pom.xml @@ -0,0 +1,214 @@ + + + 4.0.0 + org.dicoogle.plugins + dicomweb + dicomweb + 1.0.0-SNAPSHOT + jar + + pt.ua.ieeta + dicoogle-plugins + 3.4.1 + ../../pom.xml + + + + UTF-8 + + + 3.4.1 + 5.33.1 + + + 9.0.3.v20130506 + + + + + + + + src/main/resources/html5/ + + + src/main/resources/webplugin-sample/dist + WebPlugins/webplugin-sample + false + + package.json + module.js + + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 3.13.0 + + 1.8 + 1.8 + + + + org.apache.maven.plugins + maven-shade-plugin + 3.6.0 + + + package + + shade + + + + + *:* + + **/*.SF + **/*.DSA + **/*.RSA + **/module-info.class + **/module-info.java + + + + true + + + + org.dcm4che3 + org.dcm4che5 + + + + + + + + + + + org.apache.maven.plugins + maven-jar-plugin + 2.3.1 + + C:\Users\bastiao\Projects\Dicoogle\dicoogle\dicoogle\target\Plugins + + + + + + + + mavencentral + https://repo1.maven.org/maven2/ + + true + + + + + dicoogle-public + https://dev.bmd-software.com/nexus/content/repositories/dicoogle-public + + false + + + + + maven-restlet + Public online Restlet repository + https://maven.restlet.talend.com + + + + dcm4che + https://www.dcm4che.org/maven2/ + + true + + + + + sourceforge-releases + Sourceforge Releases + https://oss.sonatype.org/content/repositories/sourceforge-releases + + + + + + org.restlet.jse + org.restlet.ext.json + 2.1.2 + + + pt.ua.ieeta + dicoogle-sdk + ${dicoogle.version} + + + pt.ua.ieeta + dicoogle + ${dicoogle.version} + provided + + + org.eclipse.jetty + jetty-webapp + ${jetty.version} + + + + org.dcm4che + dcm4che-core + ${dcm4che.version} + + + + org.dcm4che + dcm4che-image + ${dcm4che.version} + + + org.dcm4che + dcm4che-imageio + ${dcm4che.version} + + + org.dcm4che + dcm4che-imageio-opencv + ${dcm4che.version} + + + org.dcm4che + dcm4che-imageio-rle + ${dcm4che.version} + + + com.fasterxml.jackson.core + jackson-core + 2.9.2 + + + com.fasterxml.jackson.core + jackson-databind + 2.9.2 + + + com.fasterxml.jackson.core + jackson-annotations + 2.9.2 + + + + + + + diff --git a/plugins/dicom-web/short-license.txt b/plugins/dicom-web/short-license.txt new file mode 100644 index 0000000..23158a0 --- /dev/null +++ b/plugins/dicom-web/short-license.txt @@ -0,0 +1,16 @@ +Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + +This file is part of Dicoogle/${project.name}. + +Dicoogle/${project.name} is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +Dicoogle/${project.name} 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 General Public License for more details. + +You should have received a copy of the GNU General Public License +along with Dicoogle. If not, see . diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomJson.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomJson.java new file mode 100644 index 0000000..05ce1ae --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomJson.java @@ -0,0 +1,269 @@ +/** + * Copyright (c) 2015 BMD Software, Lda. + * All Rights Reserved + * + * All information contained herein is, and remains the property of BMD Software, Lda. and its suppliers, if any. + * The intellectual and technical concepts contained herein are proprietary to BMD Software, Lda. and its suppliers, + * being protected by trade secret or copyright law. Dissemination of this information or reproduction of this + * material is strictly forbidden unless prior written permission is obtained from BMD Software, Lda. + * + * This file is part of Dicoogle/dicoogle-plugins. + */ +package org.dicoogle.plugins.dicomweb; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.data.ElementDictionary; +import org.dcm4che3.data.Tag; +import org.dcm4che3.data.VR; +import org.json.JSONArray; +import org.json.JSONException; +import org.json.JSONObject; + +import java.util.Arrays; + +/** + * DICOM JSON Serialization utility module + */ +public final class DicomJson { + private static final org.slf4j.Logger LOG = org.slf4j.LoggerFactory.getLogger(DicomJson.class); + + private DicomJson() {} + + /** + * This method builds a JSON object from the given DICOM attributes, including sequences. + * It is used to create the JSON representation of DICOM metadata. + * + * The attributes are expected to be a root dataset containing a SOP Instance UID. + * + * VRs OB, OW, OD, and OF are not serialized so that other routines may add Bulk data URIs instead. + * + * @param dicomAttributes The DICOM attributes to convert to JSON. + * @return A JSONObject representing the DICOM attributes. + */ + public static JSONObject fromAttributes(Attributes dicomAttributes) { + String sopInstanceUID = dicomAttributes.getString(Tag.SOPInstanceUID); + return fromAttributes(dicomAttributes, sopInstanceUID); + } + + /** + * This method builds a JSON object from the given DICOM attributes, including sequences. + * It is used to create the JSON representation of DICOM metadata. + * + * Nested datasets can also be serialized here. + * + * Values of VR OB, OW, OD, and OF are not serialized + * so that other routines may add Bulk data URIs instead. + * + * @param dicomAttributes The DICOM attributes to convert to JSON. + * @param sopInstanceUID The SOP Instance UID at the root dataset for the DICOM instance. + * @return A JSONObject representing the DICOM attributes. + */ + public static JSONObject fromAttributes(Attributes dicomAttributes, String sopInstanceUID) { + JSONObject instanceObject = new JSONObject(); + + Arrays.stream(dicomAttributes.tags()).forEach(tag -> { + try { + VR vr = dicomAttributes.getVR(tag); + + switch (vr) { + case SQ: { + // Handle DICOM sequences recursively + JSONArray sequenceArray = new JSONArray(); + dicomAttributes.getSequence(tag).forEach(item -> { + sequenceArray.put(fromAttributes(item, sopInstanceUID)); + }); + JSONObject sequenceObj = new JSONObject(); + sequenceObj.put("vr", "SQ"); + if (sequenceArray.length() > 0) { + sequenceObj.put("Value", sequenceArray); + } + instanceObject.put(formatTag(tag), sequenceObj); + break; + } + case OB: + case OW: + case OD: + case OF: + case UN: { + // do not serialize these here + break; + } + // handle numeric values + case US: + case SS: + case UL: + case SL: { + int[] intValues = dicomAttributes.getInts(tag); + JSONArray valueArray = serializeNumberValues(intValues); + JSONObject valueObj = new JSONObject(); + valueObj.put("vr", vr.toString()); + if (valueArray.length() > 0) { + valueObj.put("Value", valueArray); + } + instanceObject.put(formatTag(tag), valueObj); + break; + } + case FL: { + float[] floatValues = dicomAttributes.getFloats(tag); + JSONArray valueArray = serializeNumberValues(floatValues); + JSONObject valueObj = new JSONObject(); + valueObj.put("vr", vr.toString()); + if (valueArray.length() > 0) { + valueObj.put("Value", valueArray); + } + instanceObject.put(formatTag(tag), valueObj); + break; + } + case FD: { + double[] doubleValues = dicomAttributes.getDoubles(tag); + JSONArray valueArray = serializeNumberValues(doubleValues); + JSONObject valueObj = new JSONObject(); + valueObj.put("vr", vr.toString()); + if (valueArray.length() > 0) { + valueObj.put("Value", valueArray); + } + instanceObject.put(formatTag(tag), valueObj); + break; + } + case PN: + // TODO(#697): treat person names correctly as per DICOM F.2.2 + // treat any other as strings + default: { + JSONArray valueArray = serializeStringValues(dicomAttributes.getStrings(tag)); + JSONObject valueObj = new JSONObject(); + valueObj.put("vr", vr.toString()); + if (valueArray.length() > 0) { + valueObj.put("Value", valueArray); + } + instanceObject.put(formatTag(tag), valueObj); + } + } + } catch (JSONException e) { + LOG.error("Error creating JSON object for tag {} in SOPInstanceUID {}", tag, sopInstanceUID, e); + } + }); + + return instanceObject; + } + + /** Serialize a list of textual values as an array of strings. + * + * @param values The list of strings to serialize (may contain null values) + * @return A DICOM JSON array of values to be put in the "Value" field + */ + static JSONArray serializeStringValues(String[] values) { + JSONArray valueArray = new JSONArray(); + if (values != null) { + for (String v : values) { + if (v == null || v.isEmpty()) { + valueArray.put(JSONObject.NULL); + } else { + valueArray.put(v); + } + } + } + return valueArray; + } + + /** Serialize a list of 32-bit integer values as an array of numbers. + * + * @param values The list of integers to serialize + * @return A DICOM JSON array of values to be put in the "Value" field + */ + static JSONArray serializeNumberValues(int[] values) { + JSONArray valueArray = new JSONArray(); + if (values != null) { + for (int v : values) { + valueArray.put(v); + } + } + return valueArray; + } + + /** Serialize a list of 32-bit floating point values as an array of numbers. + * + * @param values The list of numbers to serialize + * @return A DICOM JSON array of values to be put in the "Value" field + */ + static JSONArray serializeNumberValues(float[] values) { + JSONArray valueArray = new JSONArray(); + if (values != null) { + for (float v : values) { + if (Float.isFinite(v)) { + try { + valueArray.put(v); + } catch (JSONException e) { + // we already checked whether the value is finite, + // so this should not happen + throw new RuntimeException("Failed to serialize float value: " + v, e); + } + } else if (Float.isNaN(v)) { + // put "NaN" + valueArray.put("NaN"); + } else { + // infinity or -infinity + valueArray.put(v > 0 ? "inf" : "-inf"); + } + } + } + return valueArray; + } + + /** Serialize a list of 64-bit floating point values as an array of numbers. + * + * @param values The list of numbers to serialize + * @return A DICOM JSON array of values to be put in the "Value" field + */ + static JSONArray serializeNumberValues(double[] values) { + JSONArray valueArray = new JSONArray(); + if (values != null) { + for (double v : values) { + if (Double.isFinite(v)) { + try { + valueArray.put(v); + } catch (JSONException e) { + // we already checked whether the value is finite, + // so this should not happen + throw new RuntimeException("Failed to serialize double value: " + v, e); + } + } else if (Double.isNaN(v)) { + // put "NaN" + valueArray.put("NaN"); + } else { + // infinity or -infinity + valueArray.put(v > 0 ? "inf" : "-inf"); + } + } + } + return valueArray; + } + + /** + * This method converts a DICOM tag keyword into its DICOM JSON form, + * as necessary to return the final JSON response in DICOMWeb. + * + * @param keyword The DICOM tag keyword to convert (e.g. SOPInstanceUID) + */ + public static String convertToDicomTag(String keyword) throws IllegalAccessException { + int tag = tagForKeyword(keyword); + return formatTag(tag); + } + + /** Convert a DICOM keyword to the respective DICOM tag + * by consulting the standard element dictionary. + * @param keyword the DICOM keyword (e.g. SOPInstanceUID) + * @return the corresponding DICOM tag in integer form + */ + public static int tagForKeyword(String keyword) { + return ElementDictionary.getStandardElementDictionary().tagForKeyword(keyword); + } + + /** Convert a DICOM tag to DICOM JSON + * + * @param tag the DICOM tag in integer form + * @return a string in the form GGGGEEEE + */ + public static String formatTag(int tag) { + return String.format("%04X%04X", (tag >> 16) & 0xFFFF, tag & 0xFFFF); + } +} diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomWebJettyPlugin.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomWebJettyPlugin.java new file mode 100644 index 0000000..d946029 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomWebJettyPlugin.java @@ -0,0 +1,140 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ +package org.dicoogle.plugins.dicomweb; + +import java.net.URL; + +import org.dicoogle.plugins.dicomweb.query.InstancesJettyWebService; +import org.dicoogle.plugins.dicomweb.query.MetadataSeriesJettyWebService; +import org.dicoogle.plugins.dicomweb.query.SeriesJettyWebService; +import org.dicoogle.plugins.dicomweb.query.StudiesJettyWebService; +import org.eclipse.jetty.server.handler.HandlerList; +import org.eclipse.jetty.servlet.ServletContextHandler; +import org.eclipse.jetty.servlet.ServletHolder; +import org.eclipse.jetty.webapp.WebAppContext; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import pt.ua.dicoogle.sdk.JettyPluginInterface; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.settings.ConfigurationHolder; + +/** Example of a Jetty Servlet plugin. + * + * @author Luís A. Bastião Silva - + */ +public class DicomWebJettyPlugin implements JettyPluginInterface, PlatformCommunicatorInterface { + private static final Logger logger = LoggerFactory.getLogger(DicomWebJettyPlugin.class); + + private boolean enabled; + private ConfigurationHolder settings; + private DicooglePlatformInterface platform; + private final StudiesJettyWebService studyWebService; + private final SeriesJettyWebService seriesWebService; + private final InstancesJettyWebService instancesWebService; + private final MetadataSeriesJettyWebService metadataWebService; + + public DicomWebJettyPlugin() { + this.studyWebService = new StudiesJettyWebService(); + this.seriesWebService = new SeriesJettyWebService(); + this.instancesWebService = new InstancesJettyWebService(); + this.metadataWebService = new MetadataSeriesJettyWebService(); + this.enabled = true; + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface pi) { + this.platform = pi; + // since web service is not a plugin interface, the platform interface must be provided manually + this.studyWebService.setPlatformProxy(pi); + this.seriesWebService.setPlatformProxy(pi); + this.instancesWebService.setPlatformProxy(pi); + this.metadataWebService.setPlatformProxy(pi); + } + + @Override + public String getName() { + return "RSI"; + } + + @Override + public boolean enable() { + this.enabled = true; + return true; + } + + @Override + public boolean disable() { + this.enabled = false; + return true; + } + + @Override + public boolean isEnabled() { + return this.enabled; + } + + @Override + public void setSettings(ConfigurationHolder settings) { + this.settings = settings; + // use settings here + } + + @Override + public ConfigurationHolder getSettings() { + return settings; + } + + + @Override + public HandlerList getJettyHandlers() { + + ServletContextHandler handler = new ServletContextHandler(); + handler.setContextPath("/dicomweb"); + handler.addServlet(new ServletHolder(this.studyWebService), "/studies"); + handler.addServlet(new ServletHolder(this.studyWebService), "/studies/*"); + + handler.addServlet(new ServletHolder(this.seriesWebService), "/series"); + handler.addServlet(new ServletHolder(this.instancesWebService), "/instances"); + + + /* TODO: Change here if you want + * During the development stage you can point to a directory in your machine, + * such as: file:///Users/bastiao/myHtml5Files + */ + URL url = DicomWebJettyPlugin.class.getResource("/WEBAPP"); + logger.debug("Retrieving web app from \"{}\"", url); + String directoryToServeAssets = url.toString(); + + final WebAppContext webpages = new WebAppContext(directoryToServeAssets, "/dashboardSample"); + webpages.setInitParameter("org.eclipse.jetty.servlet.Default.dirAllowed", "true"); // disables directory listing + webpages.setInitParameter("useFileMappedBuffer", "false"); + webpages.setInitParameter("cacheControl", "max-age=0, public"); + + webpages.setWelcomeFiles(new String[]{"index.html"}); + + HandlerList l = new HandlerList(); + l.addHandler(handler); + l.addHandler(webpages); + + return l; + } + +} diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomWebPluginSet.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomWebPluginSet.java new file mode 100644 index 0000000..80f78c8 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/DicomWebPluginSet.java @@ -0,0 +1,87 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ + +package org.dicoogle.plugins.dicomweb; + +import java.io.IOException; +import java.util.Collection; +import java.util.Collections; +import net.xeoh.plugins.base.annotations.PluginImplementation; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.sdk.JettyPluginInterface; +import pt.ua.dicoogle.sdk.PluginSet; +import pt.ua.dicoogle.sdk.settings.ConfigurationHolder; + + +@PluginImplementation +public class DicomWebPluginSet implements PluginSet { + // use slf4j for logging purposes + private static final Logger logger = LoggerFactory.getLogger(DicomWebPluginSet.class); + + // We will list each of our plugins as an attribute to the plugin set + + private final DicomWebJettyPlugin jettyWeb; + + // Additional resources may be added here. + private ConfigurationHolder settings; + + public DicomWebPluginSet() throws IOException { + logger.info("Initializing RSI Plugin Set"); + + // construct all plugins here + this.jettyWeb = new DicomWebJettyPlugin(); + + + logger.info("RSI Plugin Set is ready"); + } + + + /** This method is used to retrieve a name for identifying the plugin set. Keep it as a constant value. + * + * @return a unique name for the plugin set + */ + @Override + public String getName() { + return "DICOMweb"; + } + + + + @Override + public Collection getJettyPlugins() { + return Collections.singleton((JettyPluginInterface) this.jettyWeb); + } + + @Override + public void shutdown() { + logger.info("Plugin sample will shutdown"); + } + + @Override + public void setSettings(ConfigurationHolder xmlSettings) { + this.settings = xmlSettings; + } + + @Override + public ConfigurationHolder getSettings() { + return this.settings; + } + +} \ No newline at end of file diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/Convert2PNG.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/Convert2PNG.java new file mode 100644 index 0000000..eabfeec --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/Convert2PNG.java @@ -0,0 +1,371 @@ +package org.dicoogle.plugins.dicomweb.query; + +import javax.imageio.ImageIO; +import javax.imageio.ImageReader; +import javax.imageio.ImageWriter; +import javax.imageio.ImageWriteParam; +import javax.imageio.stream.ImageInputStream; +import javax.imageio.stream.ImageOutputStream; + +import org.dcm4che2.imageio.plugins.dcm.DicomImageReadParam; + +import pt.ua.dicoogle.sdk.StorageInputStream; + +import java.awt.Image; +import java.awt.image.BufferedImage; +import java.io.IOException; +import java.io.ByteArrayOutputStream; +import java.io.InputStream; +import java.util.Iterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.server.web.utils.ImageLoader; + +/** + * Handles conversion between the images (formats) found inside a DICOM file + * and the PNG image format, for proper lossless web view. + * + + */ +public class Convert2PNG { + private static final Logger logger = LoggerFactory.getLogger(Convert2PNG.class); + + private synchronized static ImageReader createDICOMImageReader() { + Iterator it = ImageIO.getImageReadersByFormatName("DICOM"); // gets the first registered ImageReader that can read DICOM data + + ImageReader sReader = it.next(); + return sReader; + } + + private synchronized static ImageWriter createPNGImageWriter() { + Iterator it = ImageIO.getImageWritersByFormatName("JPEG"); // gets the first registered ImageWriter that can write PNG data + + ImageWriter sWriter = it.next(); + return sWriter; + } + + // Transformations that can be applied on each conversion. + /** + * No transform applied. + */ + @Deprecated + public static final int TRANSFORM_NONE = 0; + /** + * Scale image based on a width target. + */ + @Deprecated + public static final int TRANSFORM_SCALE_BY_WIDTH = 1; + /** + * Scale image based on a height target. + */ + @Deprecated + public static final int TRANSFORM_SCALE_BY_HEIGHT = 2; + /** + * Scale image based on a percentage value. + */ + @Deprecated + public static final int TRANSFORM_SCALE_BY_PERCENT = 3; + + /** + * Reads an input DICOM file, applies a transformation to it if any, and returns + * the desired frame as a PNG-encoded memory stream. + * + * @param dcmStream The Dicoogle storage input Stream for the DICOM File. + * @param frameIndex the index of the frame wanted (zero based). + * @param transformType the transform to execute. + * @param transformParam1 the param used on width and height based scales. + * @param transformParam2 the param used on percentage based scales. + * @return the frame encoded in a PNG memory stream. + */ + @Deprecated + public static ByteArrayOutputStream DICOM2PNGStream(StorageInputStream dcmStream, int frameIndex, int transformType, + int transformParam1, float transformParam2) { + // setup the DICOM reader + ImageReader reader = createDICOMImageReader(); + if (reader == null) // if no valid reader was found abort + return null; + + DicomImageReadParam readParams = (DicomImageReadParam) reader.getDefaultReadParam(); // and set the default params for it (height, weight, alpha) // FIXME is this even needed? + + // setup the PNG writer + ImageWriter writer = createPNGImageWriter(); // gets the first registered ImageWriter that can save PNG data + if (writer == null) // if no valid writer was found abort + return null; + + ImageWriteParam writeParams = writer.getDefaultWriteParam(); // and set the default params for it (height, weight, alpha) + // writeParams.setCompressionMode(ImageWriteParam.MODE_EXPLICIT); // activate PNG compression to save on bandwidth + // writeParams.setCompressionType("Deflater"); // overall best compressor for black and white pictures + // writeParams.setCompressionQuality(0.0F); // best compression ratio (but longer [de]compression time) + // NOTE the above compression params are not currently needed because ImageIO already automatically compresses PNG by default, it's depicted on + // http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4829970 as a bug but it's more of a "can't set the compression level" problem as it uses the + // Deflater.BEST_COMPRESSION as default (see line 144 of com.sun.imageio.plugins.png.PNGImageWriter), the code remains comment so if in the future + // ImageIO allows for compression level set we can set it to the best compression level again + writeParams.setProgressiveMode(ImageWriteParam.MODE_DEFAULT); // activate progressive mode (adam7), best for low bandwidth connections + + try { + ImageInputStream inStream = ImageIO.createImageInputStream(dcmStream.getInputStream()); + + reader.setInput(inStream); + + // make sure that we will read a frame within bounds + int frameCount = reader.getNumImages(true); // get the number of avalable frame in the DICOM file + if ((frameCount < 1) || (frameIndex < 0) || (frameIndex >= frameCount)) // if teither the file has no frames or the frame wanted is outside of bounds abort + return null; + + // read the specified frame from the file + BufferedImage image = reader.read(frameIndex, readParams); + + inStream.close(); + + + // if no frame was read abort + if (image == null) + return null; + + // if there is a transform to be applied to the image, this is the right place to do it + switch (transformType) { + case TRANSFORM_SCALE_BY_WIDTH: + image = scaleImageByWidth(image, transformParam1); + break; + case TRANSFORM_SCALE_BY_HEIGHT: + image = scaleImageByHeight(image, transformParam1); + break; + case TRANSFORM_SCALE_BY_PERCENT: + image = scaleImageByPercent(image, transformParam2); + break; + } + // mount the resulting memory stream + ByteArrayOutputStream result = new ByteArrayOutputStream(); + + // write the specified frame to the resulting stream + ImageOutputStream outStream = ImageIO.createImageOutputStream(result); + writer.setOutput(outStream); + writer.write(image); + outStream.close(); + + return result; + } catch (IOException e) { + System.out.println("\nError: couldn't read dicom image!" + e.getMessage()); + return null; + } + } + + /** + * Reads an input DICOM file and returns the desired frame as a PNG-encoded memory stream. + * + * @param dcmStream The Dicoogle storage input Stream for the DICOM File. + * @param frameIndex the index of the frame wanted (starting with #0). + * @return the frame encoded in a PNG memory stream. + * @throws IOException if the I/O operations on the images fail + */ + public static ByteArrayOutputStream DICOM2PNGStream(StorageInputStream dcmStream, int frameIndex) + throws IOException { + return DICOM2PNGStream(dcmStream.getInputStream(), frameIndex); + } + + /** + * Reads an input DICOM file and returns the desired frame as a PNG-encoded memory stream. + * + * @param iStream an input stream for the DICOM File. + * @param frameIndex the index of the frame wanted (starting with #0). + * @return the frame encoded in a PNG memory stream. + * @throws IOException if the I/O operations on the images fail + */ + public static ByteArrayOutputStream DICOM2PNGStream(InputStream iStream, int frameIndex) throws IOException { + // setup the PNG writer + ImageWriter writer = createPNGImageWriter(); + + ImageWriteParam writeParams = writer.getDefaultWriteParam(); // and set the default params for it (height, weight, alpha) + writeParams.setProgressiveMode(ImageWriteParam.MODE_DEFAULT); // activate progressive mode (adam7), best for low bandwidth connections + + BufferedImage image = ImageLoader.loadImage(iStream); + + // mount the resulting memory stream + ByteArrayOutputStream result = new ByteArrayOutputStream(); + + // write the specified frame to the resulting stream + try (ImageOutputStream outStream = ImageIO.createImageOutputStream(result)) { + writer.setOutput(outStream); + writer.write(image); + } + + return result; + } + + /** + * Reads an input DICOM file, scales it to fit in the given dimensions and returns the + * desired frame as a PNG-encoded memory stream. + * + * @param inStream The Dicoogle storage input Stream for the DICOM File. + * @param frameIndex the index of the frame wanted (starting with #0). + * @param width the maximum width of the resulting image + * @param height the maximum height of the resulting image + * @return the frame encoded in a PNG memory stream. + * @throws IOException if the I/O operations on the images fail + */ + public static ByteArrayOutputStream DICOM2ScaledPNGStream(InputStream inStream, int frameIndex, int width, + int height) throws IOException { + if (inStream == null) { + throw new NullPointerException("dcmStream"); + } + if (frameIndex < 0) { + throw new IllegalArgumentException("bad frameIndex"); + } + if (width <= 0) { + throw new IllegalArgumentException("bad width"); + } + if (height <= 0) { + throw new IllegalArgumentException("bad height"); + } + + // setup the PNG writer + BufferedImage image = ImageLoader.loadImage(inStream); + + image = scaleImage(image, width, height); + + // mount the resulting memory stream + ByteArrayOutputStream result = new ByteArrayOutputStream(); + + // write the specified frame to the resulting stream + try (ImageOutputStream outStream = ImageIO.createImageOutputStream(result)) { + ImageWriter writer = createPNGImageWriter(); + ImageWriteParam writeParams = writer.getDefaultWriteParam(); // and set the default params for it + writeParams.setProgressiveMode(ImageWriteParam.MODE_DEFAULT); // activate progressive mode (adam7), best for low bandwidth connections + writer.setOutput(outStream); + writer.write(image); + } + + return result; + } + + /** + * Reads an input DICOM file, scales it to fit in the given dimensions and returns the + * desired frame as a PNG-encoded memory stream. + * + * @param dcmStream The Dicoogle storage input Stream for the DICOM File. + * @param frameIndex the index of the frame wanted (starting with #0). + * @param width the maximum width of the resulting image + * @param height the maximum height of the resulting image + * @return the frame encoded in a PNG memory stream. + * @throws IOException if the I/O operations on the images fail + */ + public static ByteArrayOutputStream DICOM2ScaledPNGStream(StorageInputStream dcmStream, int frameIndex, int width, + int height) throws IOException { + return DICOM2ScaledPNGStream(dcmStream.getInputStream(), frameIndex, width, height); + } + + /** + * Retrieve the number of frames from an input DICOM file. + * + * @param dcmFile The Dicoogle storage input Stream for the DICOM File. + * @return an integer representing the number of frames in the image, + * or -1 if the operation fails + */ + public static int getNumberOfFrames(StorageInputStream dcmFile) { + // setup the DICOM reader + ImageReader reader = createDICOMImageReader(); + + try (ImageInputStream inStream = ImageIO.createImageInputStream(dcmFile.getInputStream())) { + + reader.setInput(inStream); + + // make sure that we will read a frame within bounds + int frameCount = reader.getNumImages(true); + + return frameCount; + + } catch (IOException e) { + logger.error("Failed to read DICOM image", e); + } + return -1; + } + + /** + * Resize a BufferedImage to the specified width, preserving the original image aspect ratio. + * + * @param image the original image to scale. + * @param width the target width. + * @return a BufferedImage scaled to the target width. + */ + public static BufferedImage scaleImageByWidth(BufferedImage image, int width) { + if (width <= 0) + return image; + + Image scaledImage = image.getScaledInstance(width, -1, Image.SCALE_SMOOTH); // scale the input, smooth scaled + BufferedImage result = + new BufferedImage(scaledImage.getWidth(null), scaledImage.getHeight(null), BufferedImage.TYPE_INT_RGB); // create the output image + + result.getGraphics().drawImage(scaledImage, 0, 0, null); // draw the scaled image onto the output + + return result; + } + + /** + * Resize a BufferedImage to the specified height, preserving the original image aspect ratio. + * + * @param image the original image to scale. + * @param height the target height. + * @return a BufferedImage scaled to the target height. + */ + public static BufferedImage scaleImageByHeight(BufferedImage image, int height) { + if (height <= 0) + return image; + + Image scaledImage = image.getScaledInstance(-1, height, Image.SCALE_SMOOTH); // scale the input, smooth scaled + BufferedImage result = + new BufferedImage(scaledImage.getWidth(null), scaledImage.getHeight(null), BufferedImage.TYPE_INT_RGB); // create the output image + result.getGraphics().drawImage(scaledImage, 0, 0, null); // draw the scaled image onto the output + + return result; + } + + /** + * Resize a BufferedImage based on the specified percentage, preserving the original image aspect ratio. + * + * @param image the original image to scale. + * @param percent the percentage to scale to, 1.0 is original, 0.5 is half, 2.0 is double, etc. + * @return a BufferedImage scaled to the target percentage. + */ + public static BufferedImage scaleImageByPercent(BufferedImage image, float percent) { + if ((percent <= 0.0F) || (percent == 1.0F)) // if the scale is either null, negative or none at all return the original image + return image; + + Image scaledImage = image.getScaledInstance((int) (percent * image.getWidth()), -1, Image.SCALE_SMOOTH); // scale the input, smooth scaled + BufferedImage result = + new BufferedImage(scaledImage.getWidth(null), scaledImage.getHeight(null), BufferedImage.TYPE_INT_RGB); // create the output image + + result.getGraphics().drawImage(scaledImage, 0, 0, null); // draw the scaled image onto the output + + return result; + } + + /** + * Resize a BufferedImage to fit the specified dimensions, while preserving the original image aspect ratio. + * The image scaling procedure will guarantee that at least one of the dimensions will be equal to + * the maximum target. + * + * @param image the original image to scale. + * @param width the maximum width of the target + * @param height the maximum height of the target + * @return a copy of the image, scaled to fit into the given dimensions + * @throws IllegalArgumentException on bad width and height dimensions + * @throws NullPointerException on null image + */ + public static BufferedImage scaleImage(BufferedImage image, int width, int height) { + if (image == null) { + throw new NullPointerException("image is null"); + } + if (width <= 0) { + throw new IllegalArgumentException("illegal width dimension: " + width); + } + if (height <= 0) { + throw new IllegalArgumentException("illegal height dimension: " + height); + } + + if (width < height) { + return scaleImageByHeight(image, height); + } else { + return scaleImageByWidth(image, width); + } + } +} \ No newline at end of file diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/FrameRetrieval.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/FrameRetrieval.java new file mode 100644 index 0000000..d00a8c7 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/FrameRetrieval.java @@ -0,0 +1,127 @@ +package org.dicoogle.plugins.dicomweb.query; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.io.DicomInputStream; +import org.dicoogle.plugins.dicomweb.DicomJson; +import org.eclipse.jetty.server.Request; +import org.eclipse.jetty.server.Response; + +import org.json.JSONObject; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.datastructs.SearchResult; +import pt.ua.dicoogle.sdk.task.Task; + +import javax.imageio.ImageIO; +import javax.imageio.stream.ImageInputStream; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; +import java.awt.image.BufferedImage; +import java.io.*; +import java.net.URI; +import java.util.HashMap; +import java.util.UUID; +import java.util.concurrent.ExecutionException; + +public class FrameRetrieval implements PlatformCommunicatorInterface { + + public static final String FRAME_RETRIEVAL = "frame_retrieval"; + private DicooglePlatformInterface platform; + + + public void process(HttpServletRequest request, HttpServletResponse resp) throws IOException { + File jpegFile = new File("/path/to/image.jpg"); + + String path = request.getPathInfo(); // e.g., /1.2.3/series/4.5.6/metadata + + String[] parts = path.split("/"); + String studyUID = parts[1]; + String seriesUID = parts[3]; + String sopUID = parts[5]; + String frame = parts[7]; + String boundary = "----Boundary_" + UUID.randomUUID(); + + + resp.setStatus(HttpServletResponse.SC_OK); + resp.setContentType("multipart/related; type=\"image/jpeg\"; boundary=" + boundary); + + int frameIndex = 0; // 0-based index for the frame + frameIndex = Integer.parseInt(frame) - 1; + HashMap extraFields = new HashMap<>(); + + extraFields.put("SOPInstanceUID", "SOPInstanceUID"); + Iterable rr = null; + try { + // Use the UID in the query if necessary. + Task> result = this.platform.query("lucene", "SOPInstanceUID:" + sopUID, extraFields); + rr = result.get(); + } catch (InterruptedException | ExecutionException ex) { + } + URI uri = null; + if (rr != null) { + for (SearchResult sr : rr) { + uri = sr.getURI(); + + } + } + OutputStream out = resp.getOutputStream(); + //DicomFrameExtractor.extract(new File(uri.toURL().getPath())); + InputStream stream = uri.toURL().openStream(); + ByteArrayOutputStream arr = Convert2PNG.DICOM2PNGStream( stream, frameIndex); + // Start multipart body + writeBoundary(out, false, boundary); + writeHeaders(out, "image/jpeg"); + out.write(arr.toByteArray()); + // Write JPEG binary content + out.write("\r\n".getBytes()); + + // End boundary + writeBoundary(out, true, boundary); + + + + /*if (uri != null) { + // Start multipart body + writeBoundary(out, false, boundary); + writeHeaders(out, "image/jpeg"); + + // Write JPEG binary content + copyStream(jpegInput, out); + out.write("\r\n".getBytes()); + + // End boundary + writeBoundary(out, true, boundary); + }*/ + } + + + + + private void writeBoundary(OutputStream out, boolean isFinal, String BOUNDARY) throws IOException { + if (isFinal) { + out.write(("--" + BOUNDARY + "--\r\n").getBytes()); + } else { + out.write(("--" + BOUNDARY + "\r\n").getBytes()); + } + } + + private void writeHeaders(OutputStream out, String contentType) throws IOException, IOException { + out.write(("Content-Type: " + contentType + "\r\n").getBytes()); + out.write("Content-Transfer-Encoding: binary\r\n".getBytes()); + out.write("\r\n".getBytes()); + } + + private void copyStream(InputStream in, OutputStream out) throws IOException { + byte[] buffer = new byte[8192]; + int bytesRead; + while ((bytesRead = in.read(buffer)) != -1) { + out.write(buffer, 0, bytesRead); + } + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface dicooglePlatformInterface) { + this.platform = dicooglePlatformInterface; + } +} + diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/InstancesJettyWebService.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/InstancesJettyWebService.java new file mode 100644 index 0000000..9db8cc3 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/InstancesJettyWebService.java @@ -0,0 +1,144 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ +package org.dicoogle.plugins.dicomweb.query; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.io.DicomInputStream; +import org.dicoogle.plugins.dicomweb.DicomJson; +import org.json.JSONArray; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.datastructs.SearchResult; +import pt.ua.dicoogle.sdk.task.Task; + +import javax.servlet.ServletException; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; +import java.io.IOException; +import java.util.*; +import java.util.concurrent.ExecutionException; + +/** Sample Jetty servlet-based web service. + * + * @author Luís A. Bastião Silva - + */ +public class InstancesJettyWebService extends HttpServlet implements PlatformCommunicatorInterface { + private static final Logger logger = LoggerFactory.getLogger(InstancesJettyWebService.class); + + private DicooglePlatformInterface platform; + public class ResponseObject { + private String action; + + public ResponseObject(String action) { + this.action = action; + } + + public String getAction() { + return action; + } + + public void setAction(String action) { + this.action = action; + } + } + public InstancesJettyWebService() { + } + + @Override + protected void doGet(HttpServletRequest req, HttpServletResponse response) + throws ServletException, IOException { + + + HashMap extraFields = new HashMap<>(); + extraFields.put("PatientName", "PatientName"); + extraFields.put("PatientID", "PatientID"); + extraFields.put("Modality", "Modality"); + extraFields.put("StudyDate", "StudyDate"); + extraFields.put("SeriesInstanceUID", "SeriesInstanceUID"); + extraFields.put("StudyID", "StudyID"); + extraFields.put("StudyInstanceUID", "StudyInstanceUID"); + extraFields.put("Thumbnail", "Thumbnail"); + extraFields.put("SOPInstanceUID", "SOPInstanceUID"); + Iterable rr = null; + try { + // Use the UID in the query if necessary. + Task> result = this.platform.query("lucene", "SeriesInstanceUID:"+req.getParameter("SeriesInstanceUID"), extraFields); + rr = result.get(); + } catch (InterruptedException | ExecutionException ex) { + logger.warn("Operation failed", ex); + } + + // Construct a JSON response by iterating over SearchResult elements. + List> results = new ArrayList<>(); + JSONArray jsonArray = new JSONArray(); + + Set keys = new HashSet<>(); + + // Assuming SearchResult has a method getAttribute for retrieving properties. + if (rr != null) { + for (SearchResult sr : rr) { + Map resultMap = new HashMap<>(); + // Assuming each SearchResult has a method getAttribute for retrieving properties. + resultMap.put("PatientName", sr.get("PatientName")); + resultMap.put("PatientID", sr.get("PatientID")); + resultMap.put("Modality", sr.get("Modality")); + resultMap.put("StudyDate", sr.get("StudyDate")); + resultMap.put("SeriesInstanceUID", sr.get("SeriesInstanceUID")); + resultMap.put("StudyID", sr.get("StudyID")); + resultMap.put("StudyInstanceUID", sr.get("StudyInstanceUID")); + resultMap.put("Thumbnail", sr.get("Thumbnail")); + resultMap.put("SOPInstanceUID", sr.get("SOPInstanceUID")); + results.add(resultMap); + JSONObject json = new JSONObject(); + if (keys.add((String)sr.get("SOPInstanceUID"))) { +// Read Dicom from URI + // Assuming getURI() returns the URI of the DICOM object. + try (DicomInputStream dcm = new DicomInputStream(sr.getURI().toURL().openStream())) { + // Process the DICOM object as needed. + // For example, you can read attributes or perform other operations. + Attributes attributes = dcm.readDataset(-1, -1); + + JSONObject obj = DicomJson.fromAttributes(attributes, (String)sr.get("SOPInstanceUID")); + jsonArray.put(obj); + } catch (IOException e) { + logger.error("Error reading DICOM object", e); + } + + } + + } + } + + response.setContentType("application/json;charset=utf-8"); + response.setContentType("application/json;charset=utf-8"); + + response.getWriter().write(jsonArray.toString()); + + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface core) { + this.platform = core; + } + +} diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/InstancesProcess.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/InstancesProcess.java new file mode 100644 index 0000000..5758f2f --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/InstancesProcess.java @@ -0,0 +1,135 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ +package org.dicoogle.plugins.dicomweb.query; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.io.DicomInputStream; +import org.dicoogle.plugins.dicomweb.DicomJson; +import org.json.JSONArray; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.datastructs.SearchResult; +import pt.ua.dicoogle.sdk.task.Task; + +import javax.servlet.ServletException; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; +import java.io.IOException; +import java.util.*; +import java.util.concurrent.ExecutionException; +// Import file +import java.io.File; +/** Sample Jetty servlet-based web service. + * + * @author Luís A. Bastião Silva - + */ +public class InstancesProcess implements PlatformCommunicatorInterface { + private static final Logger logger = LoggerFactory.getLogger(InstancesProcess.class); + + private DicooglePlatformInterface platform; + + public void process(HttpServletRequest req, HttpServletResponse response) + throws ServletException, IOException { + String path = req.getPathInfo(); // e.g., /1.2.3/series/4.5.6/metadata + + String[] parts = path.split("/"); + + + String studyUID = parts[1]; + String seriesUID = parts[3]; + String sopUID = parts[5]; + + HashMap extraFields = new HashMap<>(); + extraFields.put("PatientName", "PatientName"); + extraFields.put("PatientID", "PatientID"); + extraFields.put("Modality", "Modality"); + extraFields.put("StudyDate", "StudyDate"); + extraFields.put("SeriesInstanceUID", "SeriesInstanceUID"); + extraFields.put("StudyID", "StudyID"); + extraFields.put("StudyInstanceUID", "StudyInstanceUID"); + extraFields.put("Thumbnail", "Thumbnail"); + extraFields.put("SOPInstanceUID", "SOPInstanceUID"); + Iterable rr = null; + try { + // Use the UID in the query if necessary. + Task> result = this.platform.query("lucene", "SOPInstanceUID:"+req.getParameter("SOPInstanceUID"), extraFields); + rr = result.get(); + } catch (InterruptedException | ExecutionException ex) { + logger.warn("Operation failed", ex); + } + + // Construct a JSON response by iterating over SearchResult elements. + List> results = new ArrayList<>(); + JSONArray jsonArray = new JSONArray(); + + Set keys = new HashSet<>(); + + // Assuming SearchResult has a method getAttribute for retrieving properties. + if (rr != null) { + for (SearchResult sr : rr) { + Map resultMap = new HashMap<>(); + // Assuming each SearchResult has a method getAttribute for retrieving properties. + resultMap.put("PatientName", sr.get("PatientName")); + resultMap.put("PatientID", sr.get("PatientID")); + resultMap.put("Modality", sr.get("Modality")); + resultMap.put("StudyDate", sr.get("StudyDate")); + resultMap.put("SeriesInstanceUID", sr.get("SeriesInstanceUID")); + resultMap.put("StudyID", sr.get("StudyID")); + resultMap.put("StudyInstanceUID", sr.get("StudyInstanceUID")); + resultMap.put("Thumbnail", sr.get("Thumbnail")); + resultMap.put("SOPInstanceUID", sr.get("SOPInstanceUID")); + results.add(resultMap); + JSONObject json = new JSONObject(); + if (keys.add((String)sr.get("SOPInstanceUID"))) { +// Read Dicom from URI + // Assuming getURI() returns the URI of the DICOM object. + try (DicomInputStream dcm = new DicomInputStream(sr.getURI().toURL().openStream())) { + // Process the DICOM object as needed. + // For example, you can read attributes or perform other operations. + Attributes attributes = dcm.readDataset(-1, -1); + + + JSONObject obj = DicomJson.fromAttributes(attributes, (String)sr.get("SOPInstanceUID")); + jsonArray.put(obj); + } catch (IOException e) { + logger.error("Error reading DICOM object", e); + } + + } + + } + } + + response.setContentType("application/json;charset=utf-8"); + response.setContentType("application/json;charset=utf-8"); + + response.getWriter().write(jsonArray.toString()); + + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface core) { + this.platform = core; + } + +} diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/MetadataSeriesJettyWebService.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/MetadataSeriesJettyWebService.java new file mode 100644 index 0000000..6c1d125 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/MetadataSeriesJettyWebService.java @@ -0,0 +1,129 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ +package org.dicoogle.plugins.dicomweb.query; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.io.DicomInputStream; +import org.dicoogle.plugins.dicomweb.DicomJson; +import org.json.JSONArray; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.datastructs.SearchResult; +import pt.ua.dicoogle.sdk.task.Task; + +import javax.servlet.ServletException; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; +import java.io.IOException; +import java.util.*; +import java.util.concurrent.ExecutionException; + +/** Sample Jetty servlet-based web service. + * + * @author Luís A. Bastião Silva - + */ +public class MetadataSeriesJettyWebService implements PlatformCommunicatorInterface { + private static final Logger logger = LoggerFactory.getLogger(MetadataSeriesJettyWebService.class); + + private DicooglePlatformInterface platform; + public void process(HttpServletRequest req, HttpServletResponse response) + throws ServletException, IOException { + String path = req.getPathInfo(); // e.g., /1.2.3/series/4.5.6/metadata + + String[] parts = path.split("/"); + String studyUID = parts[1]; + String seriesUID = parts[3]; + + HashMap extraFields = new HashMap<>(); + extraFields.put("PatientName", "PatientName"); + extraFields.put("PatientID", "PatientID"); + extraFields.put("Modality", "Modality"); + extraFields.put("StudyDate", "StudyDate"); + extraFields.put("SeriesInstanceUID", "SeriesInstanceUID"); + extraFields.put("StudyID", "StudyID"); + extraFields.put("StudyInstanceUID", "StudyInstanceUID"); + extraFields.put("Thumbnail", "Thumbnail"); + extraFields.put("SOPInstanceUID", "SOPInstanceUID"); + Iterable rr = null; + try { + // Use the UID in the query if necessary. + Task> result = this.platform.query("lucene", "SeriesInstanceUID:"+seriesUID, extraFields); + rr = result.get(); + } catch (InterruptedException | ExecutionException ex) { + logger.warn("Operation failed", ex); + } + + // Construct a JSON response by iterating over SearchResult elements. + List> results = new ArrayList<>(); + JSONArray jsonArray = new JSONArray(); + + Set keys = new HashSet<>(); + + // Assuming SearchResult has a method getAttribute for retrieving properties. + if (rr != null) { + for (SearchResult sr : rr) { + Map resultMap = new HashMap<>(); + // Assuming each SearchResult has a method getAttribute for retrieving properties. + resultMap.put("PatientName", sr.get("PatientName")); + resultMap.put("PatientID", sr.get("PatientID")); + resultMap.put("Modality", sr.get("Modality")); + resultMap.put("StudyDate", sr.get("StudyDate")); + resultMap.put("SeriesInstanceUID", sr.get("SeriesInstanceUID")); + resultMap.put("StudyID", sr.get("StudyID")); + resultMap.put("StudyInstanceUID", sr.get("StudyInstanceUID")); + resultMap.put("Thumbnail", sr.get("Thumbnail")); + resultMap.put("SOPInstanceUID", sr.get("SOPInstanceUID")); + results.add(resultMap); + JSONObject json = new JSONObject(); + if (keys.add((String)sr.get("SOPInstanceUID"))) { +// Read Dicom from URI + // Assuming getURI() returns the URI of the DICOM object. + try (DicomInputStream dcm = new DicomInputStream(sr.getURI().toURL().openStream())) { + // Process the DICOM object as needed. + // For example, you can read attributes or perform other operations. + Attributes attributes = dcm.readDataset(-1, -1); + + JSONObject obj = DicomJson.fromAttributes(attributes, (String)sr.get("SOPInstanceUID")); + jsonArray.put(obj); + } catch (IOException e) { + logger.error("Error reading DICOM object", e); + } + + } + + } + } + + response.setContentType("application/json;charset=utf-8"); + response.setContentType("application/json;charset=utf-8"); + + response.getWriter().write(jsonArray.toString()); + + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface core) { + this.platform = core; + } + +} diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/SeriesJettyWebService.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/SeriesJettyWebService.java new file mode 100644 index 0000000..ef533c2 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/SeriesJettyWebService.java @@ -0,0 +1,148 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ +package org.dicoogle.plugins.dicomweb.query; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.io.DicomInputStream; +import org.dicoogle.plugins.dicomweb.DicomJson; +import org.json.JSONArray; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.datastructs.SearchResult; +import pt.ua.dicoogle.sdk.task.Task; + +import javax.servlet.ServletException; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; +import java.io.IOException; +import java.util.*; +import java.util.concurrent.ExecutionException; + +/** Sample Jetty servlet-based web service. + * + * @author Luís A. Bastião Silva - + */ +public class SeriesJettyWebService extends HttpServlet implements PlatformCommunicatorInterface { + private static final Logger logger = LoggerFactory.getLogger(SeriesJettyWebService.class); + + private DicooglePlatformInterface platform; + public class ResponseObject { + private String action; + + public ResponseObject(String action) { + this.action = action; + } + + public String getAction() { + return action; + } + + public void setAction(String action) { + this.action = action; + } + } + public SeriesJettyWebService() { + } + + @Override + protected void doGet(HttpServletRequest req, HttpServletResponse response) + throws ServletException, IOException { + + + HashMap extraFields = new HashMap<>(); + extraFields.put("PatientName", "PatientName"); + extraFields.put("PatientID", "PatientID"); + extraFields.put("Modality", "Modality"); + extraFields.put("StudyDate", "StudyDate"); + extraFields.put("SeriesInstanceUID", "SeriesInstanceUID"); + extraFields.put("StudyID", "StudyID"); + extraFields.put("StudyInstanceUID", "StudyInstanceUID"); + extraFields.put("Thumbnail", "Thumbnail"); + extraFields.put("SOPInstanceUID", "SOPInstanceUID"); + Iterable rr = null; + try { + // Use the UID in the query if necessary. + Task> result = this.platform.query("lucene", "StudyInstanceUID:"+req.getParameter("StudyInstanceUID"), extraFields); + rr = result.get(); + } catch (InterruptedException | ExecutionException ex) { + logger.warn("Operation failed", ex); + } + + // Construct a JSON response by iterating over SearchResult elements. + List> results = new ArrayList<>(); + JSONArray jsonArray = new JSONArray(); + + Set keys = new HashSet<>(); + + // Assuming SearchResult has a method getAttribute for retrieving properties. + if (rr != null) { + for (SearchResult sr : rr) { + Map resultMap = new HashMap<>(); + // Assuming each SearchResult has a method getAttribute for retrieving properties. + resultMap.put("PatientName", sr.get("PatientName")); + resultMap.put("PatientID", sr.get("PatientID")); + resultMap.put("Modality", sr.get("Modality")); + resultMap.put("StudyDate", sr.get("StudyDate")); + resultMap.put("SeriesInstanceUID", sr.get("SeriesInstanceUID")); + resultMap.put("StudyID", sr.get("StudyID")); + resultMap.put("StudyInstanceUID", sr.get("StudyInstanceUID")); + resultMap.put("Thumbnail", sr.get("Thumbnail")); + resultMap.put("SOPInstanceUID", sr.get("SOPInstanceUID")); + results.add(resultMap); + JSONObject json = new JSONObject(); + if (keys.add((String)sr.get("SeriesInstanceUID"))) { +// Read Dicom from URI + // Assuming getURI() returns the URI of the DICOM object. + try (DicomInputStream dcm = new DicomInputStream(sr.getURI().toURL().openStream())) { + // Process the DICOM object as needed. + // For example, you can read attributes or perform other operations. + Attributes attributes = dcm.readDataset(-1, -1); + + JSONObject obj = DicomJson.fromAttributes(attributes, (String)sr.get("SOPInstanceUID")); + jsonArray.put(obj); + } catch (IOException e) { + logger.error("Error reading DICOM object", e); + } + + } + + } + } + String modality = req.getParameter("Modality"); + // if modality == ANN, SEG or OT, then return emtpy json array + if (modality != null && (modality.equals("ANN") || modality.equals("SEG") || modality.equals("OT"))) { + jsonArray = new JSONArray(); + } + response.setContentType("application/json;charset=utf-8"); + response.setContentType("application/json;charset=utf-8"); + + response.getWriter().write(jsonArray.toString()); + + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface core) { + this.platform = core; + } + +} diff --git a/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/StudiesJettyWebService.java b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/StudiesJettyWebService.java new file mode 100644 index 0000000..8f3f0e2 --- /dev/null +++ b/plugins/dicom-web/src/main/java/org/dicoogle/plugins/dicomweb/query/StudiesJettyWebService.java @@ -0,0 +1,198 @@ +/** + * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ + * + * This file is part of Dicoogle/dicoogle-plugin-sample. + * + * Dicoogle/dicoogle-plugin-sample is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * Dicoogle/dicoogle-plugin-sample 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 General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Dicoogle. If not, see . + */ +package org.dicoogle.plugins.dicomweb.query; + +import java.io.IOException; +import java.util.*; +import java.util.concurrent.ExecutionException; +import javax.servlet.ServletException; +import javax.servlet.http.HttpServlet; +import javax.servlet.http.HttpServletRequest; +import javax.servlet.http.HttpServletResponse; + +import org.dcm4che3.data.Attributes; +import org.dcm4che3.io.DicomInputStream; +import org.dicoogle.plugins.dicomweb.DicomJson; +import org.json.JSONArray; +import org.json.JSONObject; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import pt.ua.dicoogle.sdk.core.DicooglePlatformInterface; +import pt.ua.dicoogle.sdk.core.PlatformCommunicatorInterface; +import pt.ua.dicoogle.sdk.datastructs.SearchResult; +import pt.ua.dicoogle.sdk.task.Task; + +/** Sample Jetty servlet-based web service. + * + * @author Luís A. Bastião Silva - + */ +public class StudiesJettyWebService extends HttpServlet implements PlatformCommunicatorInterface { + private static final Logger logger = LoggerFactory.getLogger(StudiesJettyWebService.class); + + private DicooglePlatformInterface platform; + public class ResponseObject { + private String action; + + public ResponseObject(String action) { + this.action = action; + } + + public String getAction() { + return action; + } + + public void setAction(String action) { + this.action = action; + } + } + public StudiesJettyWebService() { + } + + @Override + protected void doGet(HttpServletRequest req, HttpServletResponse response) + throws ServletException, IOException { + + + HashMap extraFields = new HashMap<>(); + extraFields.put("PatientName", "PatientName"); + extraFields.put("PatientID", "PatientID"); + extraFields.put("Modality", "Modality"); + extraFields.put("StudyDate", "StudyDate"); + extraFields.put("SeriesInstanceUID", "SeriesInstanceUID"); + extraFields.put("StudyID", "StudyID"); + extraFields.put("StudyInstanceUID", "StudyInstanceUID"); + extraFields.put("Thumbnail", "Thumbnail"); + extraFields.put("SOPInstanceUID", "SOPInstanceUID"); + String path = req.getPathInfo(); // e.g., /1.2.3/series/4.5.6/metadata + + logger.info("Path: " + path); + if (path != null) { + + String[] parts = path.split("/"); + + if (parts.length == 6 && + "series".equals(parts[2]) && + "instances".equals(parts[4])) { + + String studyUID = parts[1]; + String seriesUID = parts[3]; + String sopUID = parts[5]; + + InstancesProcess instancesProcess = new InstancesProcess(); + instancesProcess.setPlatformProxy(platform); + instancesProcess.process(req, response); + return; + + } else if (parts.length == 8 && + "series".equals(parts[2]) && + "instances".equals(parts[4]) && + "frames".equals(parts[6])) { + + // Match: .../instances/{sopUID}/frames/{frame} + String studyUID = parts[1]; + String seriesUID = parts[3]; + String sopUID = parts[5]; + String frame = parts[7]; + FrameRetrieval frameRetrieval = new FrameRetrieval(); + frameRetrieval.setPlatformProxy(platform); + frameRetrieval.process(req, response); + return; + } + } + + if (path != null && path.matches("^/[^/]+/series/[^/]+/metadata$")) { + logger.info("Path matches /series/metadata"); + + MetadataSeriesJettyWebService metadataService = new MetadataSeriesJettyWebService(); + metadataService.setPlatformProxy(platform); + metadataService.process(req, response); + return; + } + + + Iterable rr = null; + try { + // Use the UID in the query if necessary. + Task> result = this.platform.query("lucene", "*:*", extraFields); + rr = result.get(); + } catch (InterruptedException | ExecutionException ex) { + logger.warn("Operation failed", ex); + } + + // Construct a JSON response by iterating over SearchResult elements. + List> results = new ArrayList<>(); + JSONArray jsonArray = new JSONArray(); + + Set studies = new HashSet<>(); + + // Assuming SearchResult has a method getAttribute for retrieving properties. + if (rr != null) { + for (SearchResult sr : rr) { + Map resultMap = new HashMap<>(); + // Assuming each SearchResult has a method getAttribute for retrieving properties. + resultMap.put("PatientName", sr.get("PatientName")); + resultMap.put("PatientID", sr.get("PatientID")); + resultMap.put("Modality", sr.get("Modality")); + resultMap.put("StudyDate", sr.get("StudyDate")); + resultMap.put("SeriesInstanceUID", sr.get("SeriesInstanceUID")); + resultMap.put("StudyID", sr.get("StudyID")); + resultMap.put("StudyInstanceUID", sr.get("StudyInstanceUID")); + resultMap.put("Thumbnail", sr.get("Thumbnail")); + resultMap.put("SOPInstanceUID", sr.get("SOPInstanceUID")); + // Get Modality from query params. If it is present, only allow that modality. + String modality = req.getParameter("modality"); + if (modality != null && !modality.isEmpty()) { + if (!modality.equalsIgnoreCase((String)sr.get("Modality"))) { + continue; // Skip this result if modality does not match. + } + } + results.add(resultMap); + JSONObject json = new JSONObject(); + if (studies.add((String)sr.get("StudyInstanceUID"))) { +// Read Dicom from URI + // Assuming getURI() returns the URI of the DICOM object. + try (DicomInputStream dcm = new DicomInputStream(sr.getURI().toURL().openStream())) { + // Process the DICOM object as needed. + // For example, you can read attributes or perform other operations. + Attributes attributes = dcm.readDataset(-1, -1); + + JSONObject obj = DicomJson.fromAttributes(attributes, (String)sr.get("SOPInstanceUID")); + jsonArray.put(obj); + } catch (IOException e) { + logger.error("Error reading DICOM object", e); + } + + } + + } + } + + response.setContentType("application/json;charset=utf-8"); + response.setContentType("application/json;charset=utf-8"); + + response.getWriter().write(jsonArray.toString()); + + } + + @Override + public void setPlatformProxy(DicooglePlatformInterface core) { + this.platform = core; + } + +} diff --git a/plugins/dicom-web/src/main/resources/html5/WEBAPP/index.html b/plugins/dicom-web/src/main/resources/html5/WEBAPP/index.html new file mode 100644 index 0000000..cfd23f3 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/html5/WEBAPP/index.html @@ -0,0 +1,23 @@ + + + + + Dicoogle Dashboard Plugin + + + + + + + + +
+ Dicoogle Web content - dashboard plugin sample +
+
+ +
+ + diff --git a/plugins/dicom-web/src/main/resources/html5/WEBAPP/webservicesWrapper.js b/plugins/dicom-web/src/main/resources/html5/WEBAPP/webservicesWrapper.js new file mode 100644 index 0000000..ede17a4 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/html5/WEBAPP/webservicesWrapper.js @@ -0,0 +1,12 @@ +$( document ).ready(function() { + console.log( "document loaded" ); + $("#dashboardDicoogleSample").append("This is my Plugin in JS"); + $.get("/sample/hello?uid=111111", function (data) { + console.log(data); + $("#dashboardDicoogleSample").append(". This data now comes from web service: " + data.action); + }); + }); + + $( window ).load(function() { + console.log( "window loaded" ); +}); \ No newline at end of file diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/.gitignore b/plugins/dicom-web/src/main/resources/webplugin-sample/.gitignore new file mode 100644 index 0000000..26ade9b --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/.gitignore @@ -0,0 +1,2 @@ +.parcel-cache/ +node_modules/ diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/README.md b/plugins/dicom-web/src/main/resources/webplugin-sample/README.md new file mode 100644 index 0000000..44c5c59 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/README.md @@ -0,0 +1,16 @@ +# Dicoogle Health Check web UI plugin + +> Checks for issues in the Dicoogle archive. + +This is a web UI menu plugin for Dicoogle. +The development tutorial is available in the [Dicoogle Learning Pack](https://bioinformatics-ua.github.io/dicoogle-learning-pack/docs/webplugins/). + +## Building + +```bash +npm install +``` + +## Deploying + +Place `dist/module.js` and `dist/package.json` in a folder in the `WebPlugins/` directory. diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/build-package-json.js b/plugins/dicom-web/src/main/resources/webplugin-sample/build-package-json.js new file mode 100644 index 0000000..48e6849 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/build-package-json.js @@ -0,0 +1,28 @@ +// This build script updates the output package.json file. +// +// Although using the original package.json file works, +// it is better to provide a simple version to production, +// to reduce size and simplify the plugin. +const fs = require('fs'); +const packageJson = require('./package.json'); + +const { + name, + version, + private, + description, + license, + dicoogle, +} = packageJson; + +const out = { + name, + version, + private, + description, + license, + main: dicoogle['module-file'] || 'module.js', + dicoogle, +}; +fs.mkdirSync('dist', {recursive: true}); +fs.writeFileSync("dist/package.json", JSON.stringify(out, undefined, 2)); diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/dist/module.js b/plugins/dicom-web/src/main/resources/webplugin-sample/dist/module.js new file mode 100644 index 0000000..a36da81 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/dist/module.js @@ -0,0 +1 @@ +var e=require("dicoogle-client");Object.defineProperty(module.exports,"__esModule",{value:!0,configurable:!0}),Object.defineProperty(module.exports,"default",{get:function(){return n},set:void 0,enumerable:!0,configurable:!0});const t=e();class n{constructor(){}render(e,n){let l=document.createElement("h3");l.innerText="Health Check",e.appendChild(l);let r=document.createElement("span");r.innerText="Checking Dicoogle health...",e.appendChild(r),t.getPlugins().then(({plugins:t,dead:n})=>{let l=[];if(0===t.filter(e=>"storage"===e.type).length&&l.push("No storage providers are installed"),0===t.filter(e=>"query"===e.type&&e.dim).length&&l.push("No DICOM data query providers are installed"),0===t.filter(e=>"index"===e.type&&e.dim).length&&l.push("No DICOM data indexers are installed"),n.length>0&&l.push("The following plugins are dead: "+n.map(e=>`${e.name} (${e.cause.message})`).join(", ")),0===l.length)r.innerText="✓ No issues were found!";else{r.innerText=`\u{26A0}\u{FE0F} There are ${l.length} ${1===l.length?"issue":"issues"} in this installation.`;let t=document.createElement("ul");for(let e of l){let n=document.createElement("li");n.innerText=e,t.appendChild(n)}e.appendChild(t)}})}} \ No newline at end of file diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/dist/package.json b/plugins/dicom-web/src/main/resources/webplugin-sample/dist/package.json new file mode 100644 index 0000000..5550989 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/dist/package.json @@ -0,0 +1,13 @@ +{ + "name": "dicoogle-healthcheck", + "version": "1.0.0", + "private": true, + "description": "Example web UI plugin for Dicoogle", + "license": "MIT", + "main": "module.js", + "dicoogle": { + "slot-id": "menu", + "caption": "Health Check", + "module-file": "module.js" + } +} \ No newline at end of file diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/package-lock.json b/plugins/dicom-web/src/main/resources/webplugin-sample/package-lock.json new file mode 100644 index 0000000..c9e08a6 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/package-lock.json @@ -0,0 +1,3927 @@ +{ + "name": "dicoogle-healthcheck", + "version": "1.0.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "dicoogle-healthcheck", + "version": "1.0.0", + "license": "MIT", + "dependencies": { + "dicoogle-client": "~5.2.0" + 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Bastião Silva ", + "Eduardo Pinho " + ], + "license": "MIT", + "repository": { + "type": "git", + "url": "bioinformatics-ua/dicoogle-plugin-sample" + }, + "keywords": [ + "dicoogle", + "dicoogle-plugin" + ], + "dicoogle": { + "slot-id": "menu", + "caption": "Health Check", + "module-file": "module.js" + }, + "engines": { + "node": ">=16", + "npm": ">=7" + }, + "source": "src/index.js", + "main": "dist/module.js", + "files": [ + "dist/module.js" + ], + "scripts": { + "build": "node build-package-json.js && parcel build --no-source-maps", + "build-debug": "node build-package-json.js && parcel build --no-optimize", + "build-watch": "node build-package-json.js && parcel watch --no-optimize", + "prepare": "npm run build" + }, + "targets": { + "main": { + "context": "browser", + "outputFormat": "commonjs", + "isLibrary": false, + "includeNodeModules": { + "@swc/helpers": true, + "react": false, + "react-dom": false, + "dicoogle-client": false, + "dicoogle-webcore": false, + "reflux": false, + "react-bootstrap": false, + "react-bootstrap-table": false, + "react-router": false, + "react-router-bootstrap": false + }, + "optimize": true, + "sourceMap": { + "inline": true + }, + "engines": { + "browsers": "> 1%, last 2 versions, not dead" + } + } + }, + "devDependencies": { + "parcel": "^2.13.3" + }, + "dependencies": { + "dicoogle-client": "~5.2.0" + } +} diff --git a/plugins/dicom-web/src/main/resources/webplugin-sample/src/index.js b/plugins/dicom-web/src/main/resources/webplugin-sample/src/index.js new file mode 100644 index 0000000..c8b3382 --- /dev/null +++ b/plugins/dicom-web/src/main/resources/webplugin-sample/src/index.js @@ -0,0 +1,66 @@ +const Dicoogle = require('dicoogle-client')(); + +export default class MyPlugin { + + constructor() { + // TODO initialize plugin here + } + + /** + * @param {HTMLDivElement} parent dedicated container div for this plugin + * @param {HTMLDivElement} slot the web UI plugin slot + */ + render(parent, slot) { + // create header + const head = document.createElement('h3'); + head.innerText = 'Health Check'; + parent.appendChild(head); + + // create main info span + const baseInfo = document.createElement('span'); + baseInfo.innerText = 'Checking Dicoogle health...'; + parent.appendChild(baseInfo); + + // request for the full list of plugins + Dicoogle.getPlugins().then(({ plugins, dead }) => { + const problems = []; + + // check for no storage + if (plugins.filter(p => p.type === 'storage').length === 0) { + problems.push("No storage providers are installed"); + } + + // check for no DICOM query provider + if (plugins.filter(p => p.type === 'query' && p.dim).length === 0) { + problems.push("No DICOM data query providers are installed"); + } + + // check for no DICOM index provider + if (plugins.filter(p => p.type === 'index' && p.dim).length === 0) { + problems.push("No DICOM data indexers are installed"); + } + + if (dead.length > 0) { + problems.push("The following plugins are dead: " + dead + .map(p => `${p.name} (${p.cause.message})`).join(', ')) + } + + // update DOM with problems + if (problems.length === 0) { + baseInfo.innerText = "✓ No issues were found!"; + } else { + baseInfo.innerText = `⚠️ There are ${problems.length} ${problems.length === 1 ? "issue" : "issues"} in this installation.`; + + // create list of issues found + const ul = document.createElement('ul'); + for (const problem of problems) { + // one list item per problem + let problemItem = document.createElement('li'); + problemItem.innerText = problem; + ul.appendChild(problemItem); + } + parent.appendChild(ul); + } + }); + } +} diff --git a/pom.xml b/pom.xml index 6e9532a..3926b35 100644 --- a/pom.xml +++ b/pom.xml @@ -25,5 +25,7 @@ plugins/filestorage plugins/lucene + plugins/dicom-web +