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Reworked bulk annotation to be compliant with the standard. Applied c…
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@Rui-Jesus
Rui-Jesus committed Jun 7, 2024
1 parent c0baaec commit ab6a824
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Showing 10 changed files with 143 additions and 134 deletions.
15 changes: 9 additions & 6 deletions dicoogle/src/main/java/pt/ua/dicoogle/core/mlprovider/PrepareDatastoreTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
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;
Expand Down Expand Up @@ -109,12 +110,14 @@ public MLDataset call() throws Exception {
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());
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());
}
}
}

Expand Down
41 changes: 23 additions & 18 deletions dicoogle/src/main/java/pt/ua/dicoogle/server/web/dicom/ROIExtractor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import pt.ua.dicoogle.sdk.datastructs.dim.Point2D;
import pt.ua.dicoogle.sdk.datastructs.wsi.WSIFrame;
import pt.ua.dicoogle.server.web.utils.cache.WSICache;
import sun.reflect.annotation.AnnotationType;

import javax.imageio.ImageIO;
import javax.imageio.ImageReader;
Expand All @@ -37,6 +38,8 @@
import java.util.*;
import java.util.List;

import static pt.ua.dicoogle.sdk.datastructs.dim.BulkAnnotation.AnnotationType.*;

public class ROIExtractor {

private static final Logger logger = LoggerFactory.getLogger(ROIExtractor.class);
Expand All @@ -49,18 +52,18 @@ public ROIExtractor() {
this.wsiCache = WSICache.getInstance();
}

public BufferedImage extractROI(String sopInstanceUID, BulkAnnotation bulkAnnotation) {
public BufferedImage extractROI(String sopInstanceUID, BulkAnnotation.AnnotationType type, List<Point2D> annotation) {
DicomMetaData metaData;
try {
metaData = getDicomMetadata(sopInstanceUID);
} catch (IOException e) {
logger.error("Could not extract metadata", e);
return null;
}
return extractROI(metaData, bulkAnnotation);
return extractROI(metaData, type, annotation);
}

public BufferedImage extractROI(DicomMetaData dicomMetaData, BulkAnnotation bulkAnnotation) {
public BufferedImage extractROI(DicomMetaData dicomMetaData, BulkAnnotation.AnnotationType type, List<Point2D> annotation) {

ImageReader imageReader = getImageReader();

Expand All @@ -84,7 +87,7 @@ public BufferedImage extractROI(DicomMetaData dicomMetaData, BulkAnnotation bulk
descriptor.extractData(dicomMetaData.getAttributes());

try {
return getROIFromAnnotation(bulkAnnotation, descriptor, imageReader, param);
return getROIFromAnnotation(type, annotation, descriptor, imageReader, param);
} catch (IllegalArgumentException e) {
logger.error("Error writing ROI", e);
}
Expand All @@ -105,19 +108,20 @@ private static ImageReader getImageReader() {
/**
* Given an annotation and an image, return the section of the image the annotation intersects.
* It only works with rectangle type annotations.
* @param annotation the annotation to intersect
* @param type the annotation type
* @param annotation a list of points defining the annotation to extract
* @param descriptor descriptor of the WSI pyramid, contains information about the dimensions of the image.
* @param imageReader
* @param param
* @return the intersection of the annotation on the image.
* @throws IllegalArgumentException when the annotation is not one of the supported types.
*/
private BufferedImage getROIFromAnnotation(BulkAnnotation annotation, WSISopDescriptor descriptor, ImageReader imageReader, DicomImageReadParam param) throws IllegalArgumentException {
if(notSupportedTypes.contains(annotation.getAnnotationType())){
private BufferedImage getROIFromAnnotation(BulkAnnotation.AnnotationType type, List<Point2D> annotation, WSISopDescriptor descriptor, ImageReader imageReader, DicomImageReadParam param) throws IllegalArgumentException {
if(notSupportedTypes.contains(type)){
throw new IllegalArgumentException("Trying to build a ROI with an unsupported annotation type");
}

List<Point2D> constructionPoints = annotation.getBoundingBox(); //Points that will be used to construct the ROI.
List<Point2D> constructionPoints = BulkAnnotation.getBoundingBox(type, annotation); //Points that will be used to construct the ROI.

Point2D annotationPoint1 = constructionPoints.get(0);
Point2D annotationPoint2 = constructionPoints.get(3);
Expand All @@ -134,8 +138,8 @@ private BufferedImage getROIFromAnnotation(BulkAnnotation annotation, WSISopDesc

// We need to perform clipping if annotation is not a rectangle
Shape clippingShape = null;
if(annotation.getAnnotationType() != BulkAnnotation.AnnotationType.RECTANGLE){
clippingShape = getClippingShape(annotation, constructionPoints.get(0));
if(type != BulkAnnotation.AnnotationType.RECTANGLE){
clippingShape = getClippingShape(type, annotation, constructionPoints.get(0));
if (clippingShape != null) g.setClip(clippingShape);
}

Expand Down Expand Up @@ -199,25 +203,26 @@ private BufferedImage getROIFromAnnotation(BulkAnnotation annotation, WSISopDesc
* Given an annotation, get it as a Shape to apply as a clipping shape for the ROIs.
* The points of this shape are normalized according to the starting point.
* This is only needed when dealing with non-rectangle annotations.
* @param annotation
* @param type the type of annotation
* @param annotation the list of points of the annotation
* @param startingPoint starting point of the rectangle that contains the annotation
* @return a shape to use to clip the ROI
*/
private Shape getClippingShape(BulkAnnotation annotation, Point2D startingPoint){
switch (annotation.getAnnotationType()){
private Shape getClippingShape(BulkAnnotation.AnnotationType type, List<Point2D> annotation, Point2D startingPoint){
switch (type){
case POLYLINE:
case POLYGON:
Polygon polygon = new Polygon();
for(Point2D p : annotation.getPoints()){
for(Point2D p : annotation){
polygon.addPoint((int) (p.getX() - startingPoint.getX()), (int) (p.getY() - startingPoint.getY()));
}
return polygon;
case ELLIPSE:
double minX = annotation.getPoints().get(0).getX();
double maxX = annotation.getPoints().get(1).getX();
double minX = annotation.get(0).getX();
double maxX = annotation.get(1).getX();

double minY = annotation.getPoints().get(2).getY();
double maxY = annotation.getPoints().get(3).getY();
double minY = annotation.get(2).getY();
double maxY = annotation.get(3).getY();

return new Ellipse2D.Double(minX - startingPoint.getX(), minY - startingPoint.getY(), Math.abs(maxX - minX), Math.abs(maxY - minY));

Expand Down
17 changes: 5 additions & 12 deletions dicoogle/src/main/java/pt/ua/dicoogle/server/web/servlets/ROIServlet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,29 +78,26 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response)
return;
}

BulkAnnotation annotation;
List<Point2D> annotation;
BulkAnnotation.AnnotationType annotationType = BulkAnnotation.AnnotationType.RECTANGLE;
try{
int nX = Integer.parseInt(x);
int nY = Integer.parseInt(y);
int nWidth = Integer.parseInt(width);
int nHeight = Integer.parseInt(height);
annotation = new BulkAnnotation();
Point2D tl = new Point2D(nX, nY);
Point2D tr = new Point2D(nX + nWidth, nY);
Point2D bl = new Point2D(nX, nY + nHeight);
Point2D br = new Point2D(nX + nWidth, nY + nHeight);
List<Point2D> points = new ArrayList<>();
points.add(tl); points.add(tr); points.add(bl); points.add(br);
annotation.setPoints(points);
annotation.setAnnotationType(BulkAnnotation.AnnotationType.RECTANGLE);
annotation = Arrays.asList(tl, tr, bl, br);
} catch (NumberFormatException e){
response.sendError(Status.CLIENT_ERROR_BAD_REQUEST.getCode(), "ROI provided was invalid");
return;
}

DicomMetaData metaData = getDicomMetadata(sopInstanceUID);

BufferedImage bi = roiExtractor.extractROI(metaData, annotation);
BufferedImage bi = roiExtractor.extractROI(metaData, annotationType, annotation);

if(bi != null){
response.setContentType("image/jpeg");
Expand Down Expand Up @@ -136,13 +133,9 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response)
String type = body.get("type").asText();
List<Point2D> points = mapper.readValue(body.get("points").toString(), new TypeReference<List<Point2D>>(){});

BulkAnnotation annotation = new BulkAnnotation();
annotation.setPoints(points);
annotation.setAnnotationType(BulkAnnotation.AnnotationType.valueOf(type));

DicomMetaData dicomMetaData = this.getDicomMetadata(sopInstanceUID);

BufferedImage bi = roiExtractor.extractROI(dicomMetaData, annotation);
BufferedImage bi = roiExtractor.extractROI(dicomMetaData, BulkAnnotation.AnnotationType.valueOf(type), points);

if(bi != null){
response.setContentType("image/jpeg");
Expand Down
81 changes: 39 additions & 42 deletions dicoogle/src/main/java/pt/ua/dicoogle/server/web/servlets/mlprovider/InferServlet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,10 +48,7 @@
import java.awt.image.BufferedImage;
import java.io.*;
import java.nio.file.Files;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import java.util.*;
import java.util.concurrent.ExecutionException;

public class InferServlet extends HttpServlet {
Expand Down Expand Up @@ -150,8 +147,8 @@ private Task<MLInference> sendWSIRequest(String provider, String modelID, String
ObjectMapper mapper = new ObjectMapper();
MLInferenceRequest predictionRequest = new MLInferenceRequest(true, DimLevel.INSTANCE, uid, modelID);
predictionRequest.setParameters(parameters);
BulkAnnotation annotation = new BulkAnnotation();
annotation.setPoints(roi);
BulkAnnotation annotation = new BulkAnnotation(roiType, BulkAnnotation.PixelOrigin.VOLUME);
annotation.setAnnotations(Collections.singletonList(roi));
annotation.setAnnotationType(roiType);

try {
Expand All @@ -171,11 +168,11 @@ private Task<MLInference> sendWSIRequest(String provider, String modelID, String
}

// Verify dimensions of annotation, reject if too big. In the future, adopt a sliding window strategy to process large processing windows.
double area = annotation.getArea();
double area = annotation.getArea(annotation.getAnnotations().get(0));
if(area > 16000000) // This equates to a maximum of 4000x4000 which represents in RGB an image of 48MB
return null;

BufferedImage bi = roiExtractor.extractROI(dicomMetaData, annotation);
BufferedImage bi = roiExtractor.extractROI(dicomMetaData, annotation.getAnnotationType(), annotation.getAnnotations().get(0));
predictionRequest.setRoi(bi);
Task<MLInference> task = PluginController.getInstance().infer(provider, predictionRequest);
if(task != null){
Expand All @@ -191,15 +188,14 @@ private Task<MLInference> sendWSIRequest(String provider, String modelID, String

// Coordinates need to be converted if we're working with WSI
if(!prediction.getAnnotations().isEmpty()){
Point2D tl = annotation.getBoundingBox().get(0);
Point2D tl = annotation.getBoundingBox(annotation.getAnnotations().get(0)).get(0);
convertCoordinates(prediction, tl, scale);
}

response.setContentType("application/json");
PrintWriter out = response.getWriter();
mapper.writeValue(out, prediction);
out.close();
out.flush();
} catch (InterruptedException | ExecutionException e) {
log.error("Could not make prediction", e);
try {
Expand Down Expand Up @@ -247,39 +243,36 @@ private Task<MLInference> sendRequest(String provider, String modelID, DimLevel
String boundary = UUID.randomUUID().toString();
response.setContentType("multipart/form-data; boundary=" + boundary);

ServletOutputStream out = response.getOutputStream();

out.print("--" + boundary);
out.println();
out.print("Content-Disposition: form-data; name=\"params\"");
out.println();
out.print("Content-Type: application/json");
out.println(); out.println();
out.print(mapper.writeValueAsString(prediction));
out.println();
out.print("--" + boundary);
out.println();
out.print("Content-Disposition: form-data; name=\"dicomseg\"; filename=\"dicomseg.dcm\"");
out.println();
out.print("Content-Type: application/dicom");
out.println(); out.println();

try (InputStream fi = Files.newInputStream(prediction.getDicomSEG())) {
IOUtils.copy(fi, out);
out.flush();
try (ServletOutputStream out = response.getOutputStream()){
out.print("--" + boundary);
out.println();
out.print("Content-Disposition: form-data; name=\"params\"");
out.println();
out.print("Content-Type: application/json");
out.println(); out.println();
out.print(mapper.writeValueAsString(prediction));
out.println();
out.print("--" + boundary);
out.println();
out.print("Content-Disposition: form-data; name=\"dicomseg\"; filename=\"dicomseg.dcm\"");
out.println();
out.print("Content-Type: application/dicom");
out.println(); out.println();

try (InputStream fi = Files.newInputStream(prediction.getDicomSEG())) {
IOUtils.copy(fi, out);
out.flush();
}

out.println();
out.print("--" + boundary + "--");
}

out.println();
out.print("--" + boundary + "--");
out.flush();
out.close();

} else {
response.setContentType("application/json");
PrintWriter out = response.getWriter();
mapper.writeValue(out, prediction);
out.close();
out.flush();
}

try{
Expand Down Expand Up @@ -320,9 +313,11 @@ private DicomMetaData getDicomMetadata(String sop) throws IOException{
*/
private void convertCoordinates(MLInference prediction, Point2D tl, double scale){
for(BulkAnnotation ann : prediction.getAnnotations()){
for(Point2D p : ann.getPoints()){
p.setX((p.getX() + tl.getX()) * scale);
p.setY((p.getY() + tl.getY()) * scale);
for(List<Point2D> points : ann.getAnnotations()){
for(Point2D p : points){
p.setX((p.getX() + tl.getX()) * scale);
p.setY((p.getY() + tl.getY()) * scale);
}
}
}
}
Expand All @@ -334,9 +329,11 @@ private void convertCoordinates(MLInference prediction, Point2D tl, double scale
* @return the ml prediction with the converted coordinates.
*/
private void scaleAnnotation(BulkAnnotation annotation, double scale){
for(Point2D p : annotation.getPoints()){
p.setX((p.getX()) * scale);
p.setY((p.getY()) * scale);
for(List<Point2D> ann : annotation.getAnnotations()){
for(Point2D p : ann){
p.setX((p.getX()) * scale);
p.setY((p.getY()) * scale);
}
}
}
}
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