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| Original file line number | Diff line number | Diff line change |
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@@ -29,3 +29,5 @@ packages | |
| *.v2 | ||
| *.v2 | ||
| *.v2 | ||
| .vs/ProjectEvaluation/biolib.metadata.v7.bin | ||
| *.bin | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,265 @@ | ||
| using System; | ||
| using System.Collections.Generic; | ||
| using System.Linq; | ||
| using System.Text; | ||
| using System.Threading.Tasks; | ||
| using Newtonsoft.Json; | ||
| using System.IO; | ||
| using AForge; | ||
|
|
||
| namespace BioLib | ||
| { | ||
| public class QuPath | ||
| { | ||
| public class GeoJsonFeatureCollection | ||
| { | ||
| public string type { get; set; } | ||
| public List<GeoJsonFeature> features { get; set; } | ||
| } | ||
|
|
||
| public class GeoJsonFeature | ||
| { | ||
| public string type { get; set; } | ||
| public GeoJsonGeometry geometry { get; set; } | ||
| public IDictionary<string, object> properties { get; set; } | ||
| } | ||
|
|
||
| public class GeoJsonGeometry | ||
| { | ||
| public class GeoJsonPlane | ||
| { | ||
| public int c { get; set; } | ||
| public int z { get; set; } | ||
| public int t { get; set; } | ||
| } | ||
| public string type { get; set; } | ||
| public GeoJsonPlane plane { get; set; } | ||
| public object coordinates { get; set; } | ||
|
|
||
| public ZCT GetZCT() | ||
| { | ||
| if (plane.c < 0) | ||
| return new ZCT(plane.z,0,plane.t); | ||
| else | ||
| return new ZCT(plane.z,plane.c,plane.t); | ||
| } | ||
| } | ||
|
|
||
| public class GeoJsonPoint | ||
| { | ||
| public class GeoJsonPlane | ||
| { | ||
| public int c { get; set; } | ||
| public int z { get; set; } | ||
| public int t { get; set; } | ||
| } | ||
| public string type { get; set; } | ||
| public double[] coordinates { get; set; } | ||
| public GeoJsonPlane plane { get; set; } | ||
| public static GeoJsonPoint FromROI(ROI roi, BioImage b) | ||
| { | ||
| GeoJsonPoint g = new GeoJsonPoint(); | ||
| PointD p = b.ToImageSpace(roi.PointsD[0]); | ||
| g.coordinates = new double[2] { p.X, p.Y }; | ||
| g.type = "Point"; | ||
| g.plane = new GeoJsonPlane(); | ||
| g.plane.z = roi.coord.Z; | ||
| g.plane.c = roi.coord.C; | ||
| g.plane.t = roi.coord.T; | ||
| return g; | ||
| } | ||
| } | ||
| public static PointD[] GetPoints(GeoJsonGeometry p,BioImage b) | ||
| { | ||
| 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(); | ||
| } | ||
| } | ||
| public class GeoJsonLineString | ||
| { | ||
| public class GeoJsonPlane | ||
| { | ||
| public int c { get; set; } | ||
| public int z { get; set; } | ||
| public int t { get; set; } | ||
| } | ||
| public string type { get; set; } | ||
| public double[][] coordinates { get; set; } | ||
| public GeoJsonPlane plane { get; set; } | ||
| public static GeoJsonLineString FromROI(ROI roi, BioImage b) | ||
| { | ||
| GeoJsonLineString g = new GeoJsonLineString(); | ||
| double[][] ds = new double[roi.PointsD.Count][]; | ||
| for (int i = 0; i < roi.PointsD.Count; i++) | ||
| { | ||
| PointD po = b.ToImageSpace(roi.PointsD[i]); | ||
| ds[i] = new double[2] { po.X, po.Y }; | ||
| } | ||
| g.coordinates = ds; | ||
| g.type = "LineString"; | ||
| g.plane = new GeoJsonPlane(); | ||
| g.plane.z = roi.coord.Z; | ||
| g.plane.c = roi.coord.C; | ||
| g.plane.t = roi.coord.T; | ||
| return g; | ||
| } | ||
| } | ||
|
|
||
| public class GeoJsonPolygon | ||
| { | ||
| public class GeoJsonPlane | ||
| { | ||
| public int c { get; set; } | ||
| public int z { get; set; } | ||
| public int t { get; set; } | ||
| } | ||
| public string type { get; set; } | ||
| public double[][][] coordinates { get; set; } | ||
| public GeoJsonPlane plane { get; set; } | ||
| public static GeoJsonPolygon FromROI(ROI roi, BioImage b) | ||
| { | ||
| int pc = roi.PointsD.Count; | ||
| if (roi.PointsD.Last() != roi.PointsD.First()) | ||
| pc = roi.PointsD.Count + 1; | ||
| GeoJsonPolygon g = new GeoJsonPolygon(); | ||
| double[][][] dds = new double[1][][]; | ||
| double[][] ds = new double[pc][]; | ||
| for (int i = 0; i < pc; i++) | ||
| { | ||
| if (i >= roi.PointsD.Count) | ||
| { | ||
| PointD po = b.ToImageSpace(roi.PointsD[0]); | ||
| ds[i] = new double[2] { (int)po.X, (int)po.Y }; | ||
| } | ||
| else | ||
| { | ||
| PointD po = b.ToImageSpace(roi.PointsD[i]); | ||
| ds[i] = new double[2] { (int)po.X, (int)po.Y }; | ||
| } | ||
| } | ||
|
|
||
| dds[0] = ds; | ||
| g.coordinates = dds; | ||
| g.type = "Polygon"; | ||
| g.plane = new GeoJsonPlane(); | ||
| g.plane.z = roi.coord.Z; | ||
| g.plane.c = roi.coord.C; | ||
| g.plane.t = roi.coord.T; | ||
| return g; | ||
| } | ||
| } | ||
|
|
||
| public class Properties | ||
| { | ||
| public string ObjectType { get; set; } | ||
| public bool IsLocked { get; set; } | ||
| } | ||
|
|
||
| public static void Save(string file, BioImage b) | ||
| { | ||
| 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); | ||
| } | ||
|
|
||
| public static ROI[] ReadROI(string filePath, BioImage b) | ||
| { | ||
| 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(); | ||
| } | ||
| } | ||
| } |