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Added code to import the ROI annotations and store them in the Metada…
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…taStore

Added code to import the ROI annotations and store them in the MetadataStore. tested ok in fiji by me and out slidebook project manager
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@nicolapapp
nicolapapp committed Nov 15, 2023
1 parent 4dce999 commit 0fd31bd
Showing 1 changed file with 112 additions and 2 deletions.
114 changes: 112 additions & 2 deletions components/formats-bsd/src/loci/formats/in/SlideBook7Reader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,18 @@ public class SlideBook7Reader extends FormatReader {
public static Logger LOGGER =
LoggerFactory.getLogger(SlideBook7Reader.class);

enum EGraphicType {
ePoint,
eLine,
eRectangle,
ePolygon,
eVolume,
eObjectPath, // sequence of submask id's
eArrow,
eShape, // for stereology marks
eEllipse
}

static class StrIntPair
{
public String mStr;
Expand Down Expand Up @@ -2800,6 +2812,89 @@ public void close(boolean fileOnly) throws IOException {
mDataLoader = null;
}


protected int addAnnotation(MetadataStore store, CAnnotation70 inAnn, int inCapture, int inRegionIndex, int inRoiManagerRoiIndex)
{
if(inAnn.mGraphicType70 == 4) return inRoiManagerRoiIndex; //EGraphicType.ePoint
if(inAnn.mGraphicType70 == 5) return inRoiManagerRoiIndex; //EGraphicType.ePoint
if(inAnn.mGraphicType70 == 6) return inRoiManagerRoiIndex; //EGraphicType.ePoint
if(inAnn.mGraphicType70 == 7) return inRoiManagerRoiIndex; //EGraphicType.ePoint

String roiID = MetadataTools.createLSID("ROI", inRoiManagerRoiIndex);
store.setROIID(roiID, inRoiManagerRoiIndex);
store.setImageROIRef(roiID, inCapture, inRoiManagerRoiIndex);

store.setROIName("ROI " + inRegionIndex , inRoiManagerRoiIndex);

String shapeID =MetadataTools.createLSID("Shape", inRoiManagerRoiIndex, 0);
if(inAnn.mGraphicType70 == 0) //EGraphicType.ePoint
{
store.setPointID(shapeID, inRoiManagerRoiIndex, 0);
CSBPoint <Integer> thePoint1 = inAnn.mVertexes.get(0);
store.setPointX((double)thePoint1.mX,inRoiManagerRoiIndex, 0);
store.setPointY((double)thePoint1.mY,inRoiManagerRoiIndex, 0);
}
else if(inAnn.mGraphicType70 == 1) //EGraphicType.eLine
{
CSBPoint <Integer> thePoint1 = inAnn.mVertexes.get(0);
CSBPoint <Integer> thePoint2 = inAnn.mVertexes.get(1);
store.setLineID(shapeID, inRoiManagerRoiIndex, 0);
store.setLineX1((double)thePoint1.mX,inRoiManagerRoiIndex, 0);
store.setLineY1((double)thePoint1.mY,inRoiManagerRoiIndex, 0);
store.setLineX2((double)thePoint2.mX,inRoiManagerRoiIndex, 0);
store.setLineY2((double)thePoint2.mY,inRoiManagerRoiIndex, 0);
}
else if(inAnn.mGraphicType70 == 2) //EGraphicType.eRectangle
{
CSBPoint <Integer> thePoint1 = inAnn.mVertexes.get(0);
CSBPoint <Integer> thePoint2 = inAnn.mVertexes.get(1);
int left = thePoint1.mX;
int top = thePoint1.mY;
int width = thePoint2.mX - thePoint1.mX;
int height = thePoint2.mY - thePoint1.mY;
store.setRectangleID(shapeID, inRoiManagerRoiIndex, 0);
store.setRectangleX((double) left, inRoiManagerRoiIndex, 0);
store.setRectangleY((double) top, inRoiManagerRoiIndex, 0);
store.setRectangleWidth((double) width, inRoiManagerRoiIndex, 0);
store.setRectangleHeight((double) height, inRoiManagerRoiIndex, 0);
//store.setRectangleText(cellObjectName, inRoiManagerRoiIndex, 0);
//store.setRectangleTheT(new NonNegativeInteger(roiTime), inRoiManagerRoiIndex, 0);
//store.setRectangleTheC(new NonNegativeInteger(roiChannel), inRoiManagerRoiIndex, 0);
//store.setRectangleTheZ(new NonNegativeInteger(roiZSlice), inRoiManagerRoiIndex, 0);
}
else if(inAnn.mGraphicType70 == 3) //EGraphicType.ePolygon
{
store.setPolygonID(shapeID, inRoiManagerRoiIndex, 0);
int numVertex = inAnn.mVertexes.size();
final StringBuilder p = new StringBuilder();

for (int j=0; j<numVertex; j++) {
CSBPoint <Integer> thePoint = inAnn.mVertexes.get(j);
p.append(thePoint.mX);
p.append(",");
p.append(thePoint.mY);
if (j < numVertex - 1) p.append(" ");
}
store.setPolygonPoints(p.toString(), inRoiManagerRoiIndex, 0);
}
else if(inAnn.mGraphicType70 == 8) //EGraphicType.eEllipse
{
CSBPoint <Integer> thePoint1 = inAnn.mVertexes.get(0);
CSBPoint <Integer> thePoint2 = inAnn.mVertexes.get(1);
int theCenterX = (thePoint2.mX + thePoint1.mX)/2;
int theCenterY = (thePoint2.mY + thePoint1.mY)/2;
int theRadiusX = (thePoint2.mX - thePoint1.mX)/2;
int theRadiusY = (thePoint2.mY - thePoint1.mY)/2;
store.setEllipseID(shapeID, inRoiManagerRoiIndex, 0);
store.setEllipseX((double) theCenterX, inRoiManagerRoiIndex, 0);
store.setEllipseY((double) theCenterY, inRoiManagerRoiIndex, 0);
store.setEllipseRadiusX((double) theRadiusX, inRoiManagerRoiIndex, 0);
store.setEllipseRadiusY((double) theRadiusY, inRoiManagerRoiIndex, 0);
}
inRoiManagerRoiIndex++;
return inRoiManagerRoiIndex;
}

/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
Expand Down Expand Up @@ -2879,15 +2974,30 @@ protected void initFile(String id) throws FormatException, IOException {
MetadataTools.populatePixels(store, this, true);

// add extended meta data
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM)
{

// set instrument information
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);

// set up extended meta data
int roiManagerRoiIndex = 0;
for (int capture=0; capture < numCaptures; capture++) {
CImageGroup theCurrentImageGroup = mDataLoader.GetImageGroup(capture);
CImageGroup theCurrentImageGroup = mDataLoader.GetImageGroup(capture);
// annotation roi's

int theAnnoSize = theCurrentImageGroup.mAnnotationList.size();
for(int theAnnoIndex = 0; theAnnoIndex < theAnnoSize; theAnnoIndex++)
{
CImageGroup.CAnnotations theAnno = theCurrentImageGroup.mAnnotationList.get(theAnnoIndex);
for(int theCubeIndex=0; theCubeIndex < theAnno.mCubeAnnotationList.size(); theCubeIndex++)
{
CCubeAnnotation70 theCubeAnno = theAnno.mCubeAnnotationList.get(theCubeIndex);
roiManagerRoiIndex = addAnnotation(store,theCubeAnno.mAnn,capture,theCubeAnno.mRegionIndex,roiManagerRoiIndex);
}
}

// link Instrument and Image
store.setImageInstrumentRef(instrumentID, capture);

Expand Down

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