BioGTK.QuPath Class Reference

Classes
class	GeoJsonFeature
class	GeoJsonFeatureCollection
class	GeoJsonGeometry
class	GeoJsonLineString
class	GeoJsonPoint
class	GeoJsonPolygon
class	Properties

Static Public Member Functions
static PointD[]	GetPoints (GeoJsonGeometry p, BioImage b)
static void	Save (string file, BioImage b)
static ROI[]	ReadROI (string filePath, BioImage b)

Member Function Documentation

GetPoints()

static PointD[] BioGTK.QuPath.GetPoints ( GeoJsonGeometry  p, BioImage  b  )

inlinestatic

        {
            if (p.type == "Point")
            {
                List<PointD> points = new List<PointD>();
                double[] gs = JsonConvert.DeserializeObject<double[]>(p.coordinates.ToString());
                points.Add(new PointD(gs[0], gs[1]));
                for (int i = 0; i < points.Count; i++)
                {
                    points[i] = new PointD(b.StageSizeX + (points[i].X / b.SizeX) * b.Volume.Width, b.StageSizeY + (points[i].Y / b.SizeY) * b.Volume.Height);
                }
                return points.ToArray();
            }
            else if(p.type == "Polygon")
            {
                List<PointD> points = new List<PointD>();
                double[][][] gs = JsonConvert.DeserializeObject<double[][][]>(p.coordinates.ToString());
                foreach (double[] item in gs[0])
                {
                    points.Add(new PointD(item[0], item[1]));
                }
                for (int i = 0; i < points.Count; i++)
                {
                    points[i] = new PointD(b.StageSizeX + (points[i].X / b.SizeX)*b.Volume.Width, b.StageSizeY + (points[i].Y / b.SizeY) * b.Volume.Height);
                }
                return points.ToArray();
            }
            else
            {
                List<PointD> points = new List<PointD>();
                double[][] gs = JsonConvert.DeserializeObject<double[][]>(p.coordinates.ToString());
                foreach (double[] item in gs)
                {
                    points.Add(new PointD(item[0], item[1]));
                }
                for (int i = 0; i < points.Count; i++)
                {
                    points[i] = new PointD(b.StageSizeX + (points[i].X / b.SizeX) * b.Volume.Width, b.StageSizeY + (points[i].Y / b.SizeY) * b.Volume.Height);
                }
                return points.ToArray();
            }
        }

ReadROI()

static ROI[] BioGTK.QuPath.ReadROI ( string  filePath, BioImage  b  )

inlinestatic

        {
            List<ROI> rois = new List<ROI>();
            string st = File.ReadAllText(filePath);
            GeoJsonFeatureCollection gs = JsonConvert.DeserializeObject<GeoJsonFeatureCollection>(st);
 
            foreach (GeoJsonFeature f in gs.features)
            {
                ROI r = new ROI();
                if(f.geometry.type == "Polygon")
                {
                    r.type = ROI.Type.Polygon;
                    r.closed = true;
                    r.AddPoints(GetPoints(f.geometry,b));
                    if(f.geometry.plane != null)
                        r.coord = f.geometry.GetZCT();
                }
                else if(f.geometry.type == "LineString")
                {
                    r.type = ROI.Type.Line;
                    r.AddPoints(GetPoints(f.geometry, b));
                    if (r.PointsD.Count > 2)
                        r.type = ROI.Type.Polyline;
                    if (f.geometry.plane != null)
                        r.coord = f.geometry.GetZCT();
                }
                else
                {
                    r.type = ROI.Type.Point;
                    r.AddPoints(GetPoints(f.geometry, b));
                    if (f.geometry.plane != null)
                        r.coord = f.geometry.GetZCT();
                }
                rois.Add(r);
            }
            return rois.ToArray();
        }

Save()

static void BioGTK.QuPath.Save ( string  file, BioImage  b  )

inlinestatic

        {
            string j = "{ \"type\":\"FeatureCollection\",\"features\":[";
            int i = 0;
            foreach (ROI roi in b.Annotations)
            {
                if(i==0)
                    j += "{\"type\":\"Feature\",\"geometry\":";
                else
                    j += ",{\"type\":\"Feature\",\"geometry\":";
                if (roi.type == ROI.Type.Point)
                {
                    GeoJsonPoint p = GeoJsonPoint.FromROI(roi,b);
                    j+= JsonConvert.SerializeObject(p);
                }
                else if (roi.type == ROI.Type.Rectangle || (roi.type == ROI.Type.Polygon && roi.closed) || roi.type == ROI.Type.Freeform)
                {
                    GeoJsonPolygon p = GeoJsonPolygon.FromROI(roi, b);
                    j += JsonConvert.SerializeObject(p);
                }
                else if (roi.type == ROI.Type.Polyline || roi.type == ROI.Type.Line || roi.type == ROI.Type.Polygon)
                {
                    GeoJsonLineString p = GeoJsonLineString.FromROI(roi, b);
                    j += JsonConvert.SerializeObject(p);
                }
 
                j += ",\"properties\":{\"object_type\":\"annotation\",\"isLocked\":false}}";
                i++;
            }
            j += "]}";
            File.WriteAllText(file,j);
        }

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The documentation for this class was generated from the following file:

• D:/Kari/repos/BioGTK/Source/QuPath.cs