Machine learning provider interface

dicoogle/pom.xml

@@ -10,7 +10,7 @@
     <parent>
         <groupId>pt.ua.ieeta</groupId>
         <artifactId>dicoogle-all</artifactId>
-        <version>3.4.1-SNAPSHOT</version>
+        <version>3.5.0-1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -376,12 +376,6 @@
             <version>2.9.5</version>
         </dependency>
 
-        <dependency>
-            <groupId>dcm4che</groupId>
-            <artifactId>dcm4che-imageio</artifactId>
-            <version>${dcm4che.version}</version>
-        </dependency>
-
         <dependency>
             <groupId>org.jdom</groupId>
             <artifactId>jdom2</artifactId>
@@ -465,5 +459,20 @@
             <artifactId>raven-log4j2</artifactId>
             <version>5.0.2</version>
         </dependency>
+        <dependency>
+            <groupId>dcm4che</groupId>
+            <artifactId>dcm4che-imageio</artifactId>
+            <version>${dcm4che.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.dcm4che</groupId>
+            <artifactId>dcm4che-imageio</artifactId>
+            <version>3.3.8</version>
+        </dependency>
+        <dependency>
+            <groupId>org.dcm4che</groupId>
+            <artifactId>dcm4che-core</artifactId>
+            <version>3.3.8</version>
+        </dependency>
     </dependencies>
 </project>

dicoogle/src/main/java/pt/ua/dicoogle/Main.java

@@ -19,6 +19,7 @@
 package pt.ua.dicoogle;
 
 import org.dcm4che2.data.TransferSyntax;
+import org.dcm4che3.imageio.plugins.dcm.DicomImageReaderSpi;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.xml.sax.SAXException;
@@ -31,6 +32,8 @@
 import pt.ua.dicoogle.sdk.settings.server.ServerSettings;
 import pt.ua.dicoogle.server.web.auth.Authentication;
 
+import javax.imageio.ImageIO;
+import javax.imageio.spi.IIORegistry;
 import javax.swing.*;
 import java.awt.*;
 import java.io.File;
@@ -172,6 +175,13 @@ private static void LaunchDicoogle() {
         // Start the initial Services of Dicoogle
         pt.ua.dicoogle.server.ControlServices.getInstance();
 
+        // Register Image Reader for DICOM Objects
+        if(settings.getArchiveSettings().isSupportWSI()){
+            IIORegistry.getDefaultInstance().registerServiceProvider(new DicomImageReaderSpi());
+            ImageIO.setUseCache(false);
+            System.setProperty("dcm4che.useImageIOServiceRegistry", "true");
+        }
+
         // Launch Async Index
         // It monitors a folder, and when a file is touched an event
         // triggers and index is updated.

dicoogle/src/main/java/pt/ua/dicoogle/core/mlprovider/DatastoreRequest.java

@@ -0,0 +1,116 @@
+/**
+ * Copyright (C) 2014  Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/
+ *
+ * This file is part of Dicoogle/dicoogle.
+ *
+ * Dicoogle/dicoogle 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 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 <http://www.gnu.org/licenses/>.
+ */
+package pt.ua.dicoogle.core.mlprovider;
+
+import pt.ua.dicoogle.sdk.datastructs.dim.BulkAnnotation;
+import pt.ua.dicoogle.sdk.datastructs.dim.DimLevel;
+import pt.ua.dicoogle.sdk.mlprovider.MLDataType;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Java object to represent datastore requests.
+ * Datastore requests can be for image ROIs or DICOM objects.
+ * In case of DICOM objects, the DIM level and DIM UID must be provided.
+ * @author Rui Jesus
+ */
+public class DatastoreRequest {
+
+    /**
+     * The name of the ML Provider plugin to update the dataset to.
+     */
+    private String provider;
+
+    /**
+     * The type of dataset to upload
+     */
+    private MLDataType dataType;
+
+    private DimLevel dimLevel;
+
+    private ArrayList<String> uids;
+
+    /**
+     * The dataset to upload.
+     * Each key should be a SOPInstanceUID and optionally the value should be a list of annotations.
+     */
+    private Map<String, List<BulkAnnotation>> dataset;
+
+    public String getProvider() {
+        return provider;
+    }
+
+    public void setProvider(String provider) {
+        this.provider = provider;
+    }
+
+    public MLDataType getDataType() {
+        return dataType;
+    }
+
+    public void setDataType(MLDataType dataType) {
+        this.dataType = dataType;
+    }
+
+    public DimLevel getDimLevel() {
+        return dimLevel;
+    }
+
+    public void setDimLevel(DimLevel dimLevel) {
+        this.dimLevel = dimLevel;
+    }
+
+    public ArrayList<String> getUids() {
+        return uids;
+    }
+
+    public void setUids(ArrayList<String> uids) {
+        this.uids = uids;
+    }
+
+    public Map<String, List<BulkAnnotation>> getDataset() {
+        return dataset;
+    }
+
+    public void setDataset(Map<String, List<BulkAnnotation>> dataset) {
+        this.dataset = dataset;
+    }
+
+    /**
+     * Check if this request has enough information to be processed.
+     * For example, if it is of DICOM type, it must specify the dim level and the dim uid.
+     * @return true if the request can processed, false otherwise.
+     */
+    public boolean validate(){
+        if(provider == null || provider.isEmpty())
+            return false;
+
+        switch (dataType){
+            case DICOM:
+                if(this.dimLevel == null || this.uids == null || this.uids.isEmpty())
+                    return false;
+            case IMAGE:
+                return this.dataset != null && !this.dataset.isEmpty();
+            default:
+                return false;
+        }
+    }
+}

dicoogle/src/main/java/pt/ua/dicoogle/core/mlprovider/PrepareDatastoreTask.java

@@ -0,0 +1,163 @@
+/**
+ * Copyright (C) 2014  Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/
+ *
+ * This file is part of Dicoogle/dicoogle.
+ *
+ * Dicoogle/dicoogle 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 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 <http://www.gnu.org/licenses/>.
+ */
+package pt.ua.dicoogle.core.mlprovider;
+
+import org.dcm4che2.data.BasicDicomObject;
+import org.dcm4che2.data.Tag;
+import org.dcm4che2.data.TransferSyntax;
+import org.dcm4che2.data.VR;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import pt.ua.dicoogle.plugins.PluginController;
+import pt.ua.dicoogle.sdk.datastructs.SearchResult;
+import pt.ua.dicoogle.sdk.datastructs.dim.BulkAnnotation;
+import pt.ua.dicoogle.sdk.datastructs.dim.Point2D;
+import pt.ua.dicoogle.sdk.mlprovider.*;
+import pt.ua.dicoogle.server.web.dicom.ROIExtractor;
+import pt.ua.dicoogle.server.web.utils.cache.WSICache;
+
+import javax.imageio.ImageIO;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.*;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+
+/**
+ * This task processes Datastore Requests, and builds the appropriate ML Dataset.
+ */
+public class PrepareDatastoreTask implements Callable<MLDataset> {
+
+    private static final Logger logger = LoggerFactory.getLogger(PrepareDatastoreTask.class);
+    private final DatastoreRequest request;
+    private final PluginController controller;
+    private String dataset;
+
+    private final ROIExtractor roiExtractor;
+
+    private final WSICache wsiCache;
+
+    public PrepareDatastoreTask(PluginController controller, DatastoreRequest request) {
+        this.controller = controller;
+        this.request = request;
+        this.dataset = UUID.randomUUID().toString();
+
+        this.wsiCache = WSICache.getInstance();
+        this.roiExtractor = new ROIExtractor();
+    }
+
+    @Override
+    public MLDataset call() throws Exception {
+
+        if(!request.validate())
+            return null;
+
+        switch (request.getDataType()){
+            case DICOM:
+                return new MLDicomDataset(request.getDimLevel(), request.getUids());
+            case IMAGE:
+                //throw new UnsupportedOperationException("Datastore requests for image objects is not supported");
+
+                HashMap<String, String> extraFields = new HashMap<>();
+
+                String path = this.ensureAndCreatePath();
+
+                extraFields.put("SOPInstanceUID", "SOPInstanceUID");
+                extraFields.put("SharedFunctionalGroupsSequence_PixelMeasuresSequence_PixelSpacing", "SharedFunctionalGroupsSequence_PixelMeasuresSequence_PixelSpacing");
+                extraFields.put("Rows", "Rows");
+                extraFields.put("Columns", "Columns");
+                extraFields.put("NumberOfFrames", "NumberOfFrames");
+                extraFields.put("TotalPixelMatrixColumns", "TotalPixelMatrixColumns");
+                extraFields.put("TotalPixelMatrixRows", "TotalPixelMatrixRows");
+                extraFields.put("ImageType", "ImageType");
+
+                MLImageDataset mlDataset = new MLImageDataset();
+                HashMap<ImageEntry, MLlabel> dataset = new HashMap<>();
+                Set<String> classes = new HashSet<>();
+
+                this.request.getDataset().entrySet().forEach((entry -> {
+                    try {
+
+                        // Query this image using the first available query provider
+                        Iterable<SearchResult> results = controller
+                                .query(controller.getQueryProvidersName(true).get(0), "SOPInstanceUID:" + entry.getKey(), extraFields).get();
+
+                        int c = 0;
+                        for (SearchResult image : results) {
+
+                            BasicDicomObject dcm = new BasicDicomObject();
+                            dcm.putString(Tag.TransferSyntaxUID, VR.CS, "1.2.840.10008.1.2.4.50");
+
+                            for(BulkAnnotation annotation: entry.getValue()){
+                                for(List<Point2D> points: annotation.getAnnotations()){
+                                    BufferedImage roi = roiExtractor.extractROI(image.get("SOPInstanceUID").toString(), annotation.getAnnotationType(), points);
+                                    String roiFileName = annotation.getLabel().getName() + c++;
+                                    classes.add(annotation.getLabel().getName());
+                                    File output = new File(path + File.separator + roiFileName + ".jpeg");
+                                    ImageIO.write(roi, "jpeg", output);
+                                    dataset.put(new ImageEntry(dcm, output.toURI()), annotation.getLabel());
+                                }
+                            }
+                        }
+
+                    } catch (IOException | InterruptedException | ExecutionException e) {
+                        logger.error("Error preparing datastore task", e);
+                    }
+                }));
+
+                mlDataset.setMultiClass(classes.size() > 2);
+                mlDataset.setDataset(dataset);
+
+                return mlDataset;
+            default:
+                return null;
+        }
+    }
+
+    private String ensureAndCreatePath(){
+        Path datasetsFolder = Paths.get("datasets");
+        // Check if the folder exists
+        if (!Files.exists(datasetsFolder)) {
+            try {
+                Files.createDirectories(datasetsFolder);
+                System.out.println("Datasets folder didn't exist, creating one.");
+            } catch (Exception e) {
+                System.err.println("Failed to create datasets folder: " + e.getMessage());
+            }
+        }
+
+        Path datasetFolder = Paths.get("datasets" + File.separator + System.currentTimeMillis());
+
+        if (!Files.exists(datasetFolder)) {
+            try {
+                Files.createDirectories(datasetFolder);
+            } catch (Exception e) {
+                System.err.println("Failed to create dataset folder: " + e.getMessage());
+            }
+        }
+
+        return datasetFolder.toString();
+    }
+
+}