Started implementation of labeled datastore endpoint. Improvements to…

… data models.
bioinformatics-ua · Feb 23, 2024 · 7cbff44 · 7cbff44
1 parent 9ee9d25
commit 7cbff44
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Showing 10 changed files with 216 additions and 43 deletions.
diff --git a/dicoogle/src/main/java/pt/ua/dicoogle/core/mlprovider/PrepareDatastoreTask.java b/dicoogle/src/main/java/pt/ua/dicoogle/core/mlprovider/PrepareDatastoreTask.java
@@ -18,18 +18,28 @@
  */
 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.mlprovider.MLDataset;
-import pt.ua.dicoogle.sdk.mlprovider.MLDicomDataset;
-import pt.ua.dicoogle.sdk.mlprovider.MLImageDataset;
+import pt.ua.dicoogle.sdk.datastructs.dim.BulkAnnotation;
+import pt.ua.dicoogle.sdk.mlprovider.*;
 import pt.ua.dicoogle.server.web.dicom.ROIExtractor;
 import pt.ua.dicoogle.server.web.utils.cache.WSICache;
 
-import java.util.HashMap;
-import java.util.UUID;
+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;
 
@@ -65,10 +75,12 @@ public MLDataset call() throws Exception {
         switch (request.getDataType()){
             case DICOM:
                 return new MLDicomDataset(request.getDimLevel(), request.getUids());
-            case IMAGE: // Not operational
-                throw new UnsupportedOperationException("Datastore requests for image objects is not supported");
-                /*
-                HashMap<String, String> extraFields = new HashMap<String, String>();
+            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");
@@ -80,6 +92,8 @@ public MLDataset call() throws Exception {
                 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 {
@@ -88,18 +102,59 @@ public MLDataset call() throws Exception {
                         Iterable<SearchResult> results = controller
                                 .query(controller.getQueryProvidersName(true).get(0), "SOPInstanceUID:" + entry.getKey(), extraFields).get();
 
+                        int c = 0;
                         for (SearchResult image : results) {
-                            //List<ImageROI> rois = (List<ImageROI>) roiExtractor.extractROI();
+
+                            BasicDicomObject dcm = new BasicDicomObject();
+                            dcm.putString(Tag.TransferSyntaxUID, VR.CS, "1.2.840.10008.1.2.4.50");
+
+                            for(BulkAnnotation annotation: entry.getValue()){
+                                BufferedImage roi = roiExtractor.extractROI(image.get("SOPInstanceUID").toString(), annotation);
+                                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 (InterruptedException | ExecutionException e) {
+                    } 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();
+    }
+
 }
diff --git a/dicoogle/src/main/java/pt/ua/dicoogle/plugins/PluginController.java b/dicoogle/src/main/java/pt/ua/dicoogle/plugins/PluginController.java
@@ -863,16 +863,18 @@ public Task<MLDataset> datastore(final DatastoreRequest datasetRequest) {
         String uuid = UUID.randomUUID().toString();
         Task<MLDataset> prepareTask =
                 new Task<>("MLPrepareDatastoreTask" + uuid, new PrepareDatastoreTask(this, datasetRequest));
+        MLProviderInterface mlInterface = getMachineLearningProviderByName(datasetRequest.getProvider(), true);
+        if (mlInterface == null) {
+            logger.error("MLProvider with name {} not found", datasetRequest.getProvider());
+            prepareTask.cancel(true);
+            return prepareTask;
+        }
+
         prepareTask.onCompletion(() -> {
-            MLProviderInterface mlInterface = getMachineLearningProviderByName(datasetRequest.getProvider(), true);
-            if (mlInterface == null) {
-                logger.error("MLProvider with name {} not found", prepareTask.getName());
-            } else {
-                try {
-                    mlInterface.dataStore(prepareTask.get());
-                } catch (InterruptedException | ExecutionException e) {
-                    logger.error("Task {} failed execution", prepareTask.getName(), e);
-                }
+            try {
+                mlInterface.dataStore(prepareTask.get());
+            } catch (InterruptedException | ExecutionException e) {
+                logger.error("Task {} failed execution", prepareTask.getName(), e);
             }
         });
         logger.debug("Fired prepare dataset task with uuid {}", uuid);

diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/datastructs/dim/BulkAnnotation.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/datastructs/dim/BulkAnnotation.java
@@ -18,6 +18,8 @@
  */
 package pt.ua.dicoogle.sdk.datastructs.dim;
 
+import pt.ua.dicoogle.sdk.mlprovider.MLlabel;
+
 import java.util.Arrays;
 import java.util.List;
 
@@ -69,7 +71,7 @@ public enum CoordinateType {
 
     private AnnotationType annotationType;
 
-    private String label;
+    private MLlabel label;
 
     private List<Point2D> points;
 
@@ -99,11 +101,11 @@ public void setAnnotationType(AnnotationType annotationType) {
         this.annotationType = annotationType;
     }
 
-    public String getLabel() {
+    public MLlabel getLabel() {
         return label;
     }
 
-    public void setLabel(String label) {
+    public void setLabel(MLlabel label) {
         this.label = label;
     }
 

diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/datastructs/dim/ImageROI.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/datastructs/dim/ImageROI.java
@@ -50,9 +50,9 @@ private FileType(String s, String mimeType) {
 
     private double y;
 
-    private int width;
+    private double width;
 
-    private int height;
+    private double height;
 
     private String sopInstanceUID;
 
@@ -67,6 +67,14 @@ public ImageROI(String sopInstanceUID, int x, int y, int width, int height) {
         this.height = height;
     }
 
+    public ImageROI(String sopInstanceUID, double x, double y, double width, double height, URI roi) {
+        this.x = x;
+        this.y = y;
+        this.width = width;
+        this.height = height;
+        this.uriROI = roi;
+    }
+
     public double getX() {
         return x;
     }
@@ -91,15 +99,15 @@ public void setSopInstanceUID(String sopInstanceUID) {
         this.sopInstanceUID = sopInstanceUID;
     }
 
-    public int getWidth() {
+    public double getWidth() {
         return width;
     }
 
     public void setWidth(int width) {
         this.width = width;
     }
 
-    public int getHeight() {
+    public double getHeight() {
         return height;
     }
 

diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/ImageEntry.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/ImageEntry.java
@@ -0,0 +1,68 @@
+/**
+ * Copyright (C) 2014  Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/
+ *
+ * This file is part of Dicoogle/dicoogle-sdk.
+ *
+ * Dicoogle/dicoogle-sdk 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-sdk 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.sdk.mlprovider;
+
+import org.dcm4che2.data.DicomObject;
+
+import java.net.URI;
+import java.util.Objects;
+
+/**
+ * Used to map the metadata of regions of interest.
+ */
+public class ImageEntry {
+
+    private DicomObject object;
+
+    private URI file;
+
+    public ImageEntry(DicomObject object, URI file) {
+        this.object = object;
+        this.file = file;
+    }
+
+    public DicomObject getObject() {
+        return object;
+    }
+
+    public void setObject(DicomObject object) {
+        this.object = object;
+    }
+
+    public URI getFile() {
+        return file;
+    }
+
+    public void setFile(URI file) {
+        this.file = file;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        ImageEntry that = (ImageEntry) o;
+        return object.equals(that.object) && file.equals(that.file);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(file);
+    }
+}
diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLCSVDataset.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLCSVDataset.java
@@ -24,4 +24,7 @@ public class MLCSVDataset extends MLDataset {
 
     private InputStream csvFile;
 
+    public MLCSVDataset(){
+        super("", MLDataType.CSV);
+    }
 }
diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLDataset.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLDataset.java
@@ -22,4 +22,26 @@ public abstract class MLDataset {
 
     protected String name;
 
+    protected MLDataType dataType;
+
+    public MLDataset(String name, MLDataType dataType) {
+        this.name = name;
+        this.dataType = dataType;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public MLDataType getDataType() {
+        return dataType;
+    }
+
+    public void setDataType(MLDataType dataType) {
+        this.dataType = dataType;
+    }
 }
diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLDicomDataset.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLDicomDataset.java
@@ -32,11 +32,13 @@ public class MLDicomDataset extends MLDataset {
     private List<String> dimUIDs;
 
     public MLDicomDataset(DimLevel level){
+        super("", MLDataType.DICOM);
         this.level = level;
         dimUIDs = new ArrayList<>();
     }
 
     public MLDicomDataset(DimLevel level, List<String> dimUIDs){
+        super("", MLDataType.DICOM);
         this.level = level;
         this.dimUIDs = dimUIDs;
     }

diff --git a/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLImageDataset.java b/sdk/src/main/java/pt/ua/dicoogle/sdk/mlprovider/MLImageDataset.java
@@ -18,25 +18,32 @@
  */
 package pt.ua.dicoogle.sdk.mlprovider;
 
-import java.net.URI;
 import java.util.HashMap;
-import java.util.List;
 
 /**
  * An ML dataset of image objects.
  * Optionally an array of labels can be given to create a labelled dataset.
  */
 public class MLImageDataset extends MLDataset {
 
-    private HashMap<URI, List<MLlabel>> dataset;
+    private HashMap<ImageEntry, MLlabel> dataset;
 
     private boolean multiClass;
 
-    public HashMap<URI, List<MLlabel>> getDataset() {
+    public MLImageDataset() {
+        super("name", MLDataType.IMAGE);
+    }
+
+    public MLImageDataset(HashMap<ImageEntry, MLlabel> dataset) {
+        super("", MLDataType.IMAGE);
+        this.dataset = dataset;
+    }
+
+    public HashMap<ImageEntry, MLlabel> getDataset() {
         return dataset;
     }
 
-    public void setDataset(HashMap<URI, List<MLlabel>> dataset) {
+    public void setDataset(HashMap<ImageEntry, MLlabel> dataset) {
         this.dataset = dataset;
     }