3.4.1 OMERO Support.

Author: BiologyTools

BioGTK.csproj

@@ -427,6 +427,7 @@
   </ItemGroup>
 
   <ItemGroup>
+    <PackageReference Include="BioLib" Version="3.4.1" />
     <PackageReference Include="Flurl" Version="4.0.0" />
     <PackageReference Include="Flurl.Http" Version="4.0.2" />
     <PackageReference Include="ImageJ.NET" Version="154.0.0.2" />
@@ -439,18 +440,14 @@
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
-    <PackageReference Include="ScottPlot" Version="5.0.47" />
+    <PackageReference Include="ScottPlot" Version="5.0.48" />
     <PackageReference Include="SkiaSharp" Version="3.116.1" />
     <PackageReference Include="SkiaSharp.NativeAssets.Linux" Version="3.116.1" />
     <PackageReference Include="SkiaSharp.NativeAssets.macOS" Version="3.116.1" />
     <PackageReference Include="SkiaSharp.NativeAssets.Win32" Version="3.116.1" />
     <PackageReference Include="SkiaSharp.Views.Gtk3" Version="3.116.1" />
-    <PackageReference Include="TorchSharp-cpu" Version="0.104.0" />
-    <PackageReference Include="YamlDotNet" Version="16.2.1" />  
-  </ItemGroup>
-
-  <ItemGroup>
-    <ProjectReference Include="..\BioLib\BioLib.csproj" />
+    <PackageReference Include="TorchSharp-cpu" Version="0.105.0" />
+    <PackageReference Include="YamlDotNet" Version="16.3.0" />  
   </ItemGroup>
 
   <ItemGroup>

Source/ImageView.cs

@@ -346,36 +346,24 @@ private async void Render(object sender, SkiaSharp.Views.Desktop.SKPaintSurfaceE
                                 canvas.DrawImage(SKImages[i], 0, 0, paint);
                                 if (overviewImage != null)
                                 {
+                                    var ims = BitmapToSKImage(overviewImage.GetImageRGB());
+                                    paint.Style = SKPaintStyle.Fill;
                                     // Draw the overview image at the top-left corner
-                                    canvas.DrawImage(BitmapToSKImage(overviewImage), 0, 0, paint);
+                                    canvas.DrawImage(ims, 0, 0, paint);
                                 }
                                 // Set the paint style to stroke for drawing rectangles
                                 paint.Style = SKPaintStyle.Stroke;
                                 // Draw the gray rectangle representing the overview's entire visible region
                                 paint.Color = SKColors.Gray;
                                 canvas.DrawRect(overview.X, overview.Y, overview.Width, overview.Height, paint);
                                 paint.Color = SKColors.Red;
-                                if (!openSlide)
-                                {
-                                    double dsx = _slideBase.Schema.Resolutions[Level].UnitsPerPixel / Resolution;
-                                    Resolution rs = SelectedImage.Resolutions[Level];
-                                    double dx = ((double)PyramidalOrigin.X / (rs.SizeX * dsx)) * overview.Width;
-                                    double dy = ((double)PyramidalOrigin.Y / (rs.SizeY * dsx)) * overview.Height;
-                                    double dw = ((double)viewStack.AllocatedWidth / (rs.SizeX)) * overview.Width * dsx;
-                                    double dh = ((double)viewStack.AllocatedHeight / (rs.SizeY)) * overview.Height * dsx;
-                                    canvas.DrawRect((int)dx, (int)dy, (int)dw, (int)dh, paint);
-                                }
-                                else
-                                {
-                                    double dsx = _openSlideBase.Schema.Resolutions[Level].UnitsPerPixel / Resolution;
-                                    var rs = _openSlideBase.Schema.Resolutions.Last();
-                                    Resolution rss = SelectedImage.Resolutions[Level];
-                                    double dx = ((double)PyramidalOrigin.X / (rss.SizeX * dsx)) * overview.Width;
-                                    double dy = ((double)PyramidalOrigin.Y / (rss.SizeY * dsx)) * overview.Height;
-                                    double dw = ((double)viewStack.AllocatedWidth / (rss.SizeX * dsx)) * overview.Width;
-                                    double dh = ((double)viewStack.AllocatedHeight / (rss.SizeY * dsx)) * overview.Height;
-                                    canvas.DrawRect((int)dx, (int)dy, (int)dw, (int)dh, paint);
-                                }
+                                double dsx = _slideBase.Schema.Resolutions[Level].UnitsPerPixel / Resolution;
+                                Resolution rs = SelectedImage.Resolutions[Level];
+                                double dx = ((double)PyramidalOrigin.X / (rs.SizeX * dsx)) * overview.Width;
+                                double dy = ((double)PyramidalOrigin.Y / (rs.SizeY * dsx)) * overview.Height;
+                                double dw = ((double)viewStack.AllocatedWidth / (rs.SizeX)) * overview.Width * dsx;
+                                double dh = ((double)viewStack.AllocatedHeight / (rs.SizeY)) * overview.Height * dsx;
+                                canvas.DrawRect((int)dx, (int)dy, (int)dw, (int)dh, paint);
                             }
                         }
                         catch (Exception ex)
@@ -832,7 +820,6 @@ private void InitPreview()
                 Bitmap bm = BioImage.GetTile(SelectedImage, SelectedImage.GetFrameIndex(GetCoordinate().Z, GetCoordinate().C, GetCoordinate().T), MacroResolution.Value - 2, 0, 0, SelectedImage.Resolutions[MacroResolution.Value - 2].SizeX, SelectedImage.Resolutions[MacroResolution.Value - 2].SizeY);
                 ResizeBilinear re = new ResizeBilinear(overview.Width, overview.Height);
                 Bitmap bmp = re.Apply(bm.GetImageRGB());
-                bmp.SwitchRedBlue();
                 overviewImage = bmp;
             }
             else
@@ -851,7 +838,6 @@ private void InitPreview()
                 Bitmap bm = BioImage.GetTile(SelectedImage, SelectedImage.GetFrameIndex(GetCoordinate().Z, GetCoordinate().C, GetCoordinate().T), lev, 0, 0, SelectedImage.Resolutions[lev].SizeX, SelectedImage.Resolutions[lev].SizeY);
                 ResizeBilinear re = new ResizeBilinear(overview.Width, overview.Height);
                 Bitmap bmp = re.Apply(bm.GetImageRGB());
-                bmp.SwitchRedBlue();
                 overviewImage = bmp;
             }
             ShowOverview = true;

Source/OMERO.cs

@@ -68,6 +68,7 @@ protected OMERO(Builder builder, IntPtr handle) : base(handle)
 
         private void View_ItemActivated(object o, ItemActivatedArgs args)
         {
+            BioLib.OMERO.ReConnect();
             TreePath path = args.Path;
             store.GetIter(out TreeIter iter, path);
             string selectedItem;
@@ -154,6 +155,8 @@ private void InitIcons()
                         if (db.getId() == long.Parse(sts[1]))
                             continue;
                         List<long> str = BioLib.OMERO.GetDatasetIds(db.getId());
+                        if (str.Count == 0)
+                            BioLib.OMERO.ReConnect();
                         foreach (var item in str)
                         {
                             Image image = new Image();