5.7.0

BiologyTools · Nov 17, 2024 · 2b8a954 · 2b8a954
1 parent 9795c24
commit 2b8a954
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Showing 11 changed files with 1,783 additions and 142 deletions.
diff --git a/BioGTK.csproj b/BioGTK.csproj
@@ -415,33 +415,37 @@
   </ItemGroup>
 
   <ItemGroup>
+    <PackageReference Include="AForgeBio" Version="1.9.1" />
+    <PackageReference Include="BioLib" Version="2.9.1" />
     <PackageReference Include="Flurl" Version="4.0.0" />
     <PackageReference Include="Flurl.Http" Version="4.0.2" />
     <PackageReference Include="ImageJ.NET" Version="154.0.0.2" />
     <PackageReference Include="ManagedCuda.NETStandard" Version="9.1.300" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="Microsoft.ML.OnnxRuntime" Version="1.19.2" />
-    <PackageReference Include="Microsoft.ML.TorchSharp" Version="0.21.1" />
+    <PackageReference Include="Microsoft.ML.OnnxRuntime" Version="1.20.0" />
+    <PackageReference Include="Microsoft.ML.TorchSharp" Version="0.22.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
-    <PackageReference Include="NuGet.Build.Tasks.Pack" Version="6.11.1">
+    <PackageReference Include="NuGet.Build.Tasks.Pack" Version="6.12.1">
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
-    <PackageReference Include="ScottPlot" Version="5.0.41" />
+    <PackageReference Include="ScottPlot" Version="5.0.46" />
     <PackageReference Include="SkiaSharp" Version="3.0.0-preview.4.1" />
     <PackageReference Include="SkiaSharp.NativeAssets.Linux" Version="3.0.0-preview.4.1" />
     <PackageReference Include="SkiaSharp.NativeAssets.macOS" Version="3.0.0-preview.4.1" />
     <PackageReference Include="SkiaSharp.NativeAssets.Win32" Version="3.0.0-preview.4.1" />
     <PackageReference Include="SkiaSharp.Views.Gtk3" Version="3.0.0-preview.4.1" />
     <PackageReference Include="TorchSharp-cpu" Version="0.103.1" />
-    <PackageReference Include="YamlDotNet" Version="16.1.3" />  
-  </ItemGroup>
-
-  <ItemGroup>
-    <ProjectReference Include="..\BioLib\BioLib.csproj" />
+    <PackageReference Include="YamlDotNet" Version="16.2.0" />  
   </ItemGroup>
 
   <ItemGroup>
+    <None Update="macro-commands.csv">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
+    <None Update="macro-functions.txt">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
     <None Update="README.md">
       <Pack>True</Pack>
       <PackagePath>\</PackagePath>

diff --git a/BioGTK.sln b/BioGTK.sln
@@ -7,12 +7,6 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "BioGTK", "BioGTK.csproj", "
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "BioGTKApp", "..\BioGTKApp\BioGTKApp\BioGTKApp\BioGTKApp.csproj", "{801F7535-D991-4B84-A897-9C21FE1BC53A}"
 EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "BioLib", "..\BioLib\BioLib.csproj", "{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "AForgeBio", "..\..\..\Shared\AForgeBio\AForgeBio\AForgeBio\AForgeBio.csproj", "{F1EB0132-53E8-4C11-862A-841A36FF6B00}"
-EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "OpenSlideGTK", "..\OpenSlideGTK\src\OpenSlideSharp\OpenSlideGTK.csproj", "{1590E60A-FC05-4C6E-A33B-35411596C516}"
-EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -47,42 +41,6 @@ Global
 		{801F7535-D991-4B84-A897-9C21FE1BC53A}.Release|ARM64.Build.0 = Release|ARM64
 		{801F7535-D991-4B84-A897-9C21FE1BC53A}.Release|x64.ActiveCfg = Release|x64
 		{801F7535-D991-4B84-A897-9C21FE1BC53A}.Release|x64.Build.0 = Release|x64
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Debug|ARM64.ActiveCfg = Debug|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Debug|ARM64.Build.0 = Debug|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Debug|x64.ActiveCfg = Debug|x64
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Debug|x64.Build.0 = Debug|x64
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Release|Any CPU.Build.0 = Release|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Release|ARM64.ActiveCfg = Release|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Release|ARM64.Build.0 = Release|Any CPU
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Release|x64.ActiveCfg = Release|x64
-		{CE0A81BF-5815-47B8-9B71-86E2D84AEB24}.Release|x64.Build.0 = Release|x64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Debug|ARM64.ActiveCfg = Debug|ARM64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Debug|ARM64.Build.0 = Debug|ARM64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Debug|x64.ActiveCfg = Debug|x64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Debug|x64.Build.0 = Debug|x64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Release|Any CPU.Build.0 = Release|Any CPU
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Release|ARM64.ActiveCfg = Release|ARM64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Release|ARM64.Build.0 = Release|ARM64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Release|x64.ActiveCfg = Release|x64
-		{F1EB0132-53E8-4C11-862A-841A36FF6B00}.Release|x64.Build.0 = Release|x64
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Debug|ARM64.ActiveCfg = Debug|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Debug|ARM64.Build.0 = Debug|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Debug|x64.ActiveCfg = Debug|x64
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Debug|x64.Build.0 = Debug|x64
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Release|Any CPU.Build.0 = Release|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Release|ARM64.ActiveCfg = Release|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Release|ARM64.Build.0 = Release|Any CPU
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Release|x64.ActiveCfg = Release|x64
-		{1590E60A-FC05-4C6E-A33B-35411596C516}.Release|x64.Build.0 = Release|x64
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

diff --git a/Glade/TabsView.glade b/Glade/TabsView.glade
@@ -142,10 +142,10 @@
                       </object>
                     </child>
                     <child>
-                      <object class="GtkMenuItem">
+                      <object class="GtkMenuItem" id="renameMenu">
                         <property name="visible">True</property>
                         <property name="can-focus">False</property>
-                        <property name="label" translatable="yes">Clear Recent</property>
+                        <property name="label" translatable="yes">Rename</property>
                         <property name="use-underline">True</property>
                       </object>
                     </child>

diff --git a/Glade/TabsView.glade~ b/Glade/TabsView.glade~
@@ -142,10 +142,10 @@
                       </object>
                     </child>
                     <child>
-                      <object class="GtkMenuItem">
+                      <object class="GtkMenuItem" id="renameMenu">
                         <property name="visible">True</property>
                         <property name="can-focus">False</property>
-                        <property name="label" translatable="yes">Clear Recent</property>
+                        <property name="label" translatable="yes">Rename</property>
                         <property name="use-underline">True</property>
                       </object>
                     </child>
@@ -445,13 +445,6 @@
                         <property name="label" translatable="yes">To Short</property>
                       </object>
                     </child>
-                    <child>
-                      <object class="GtkMenuItem" id="toFloatMen">
-                        <property name="visible">True</property>
-                        <property name="can-focus">False</property>
-                        <property name="label" translatable="yes">To Float</property>
-                      </object>
-                    </child>
                   </object>
                 </child>
               </object>

diff --git a/Glade/TextInput.glade b/Glade/TextInput.glade
@@ -2,90 +2,120 @@
 <!-- Generated with glade 3.40.0 -->
 <interface>
   <requires lib="gtk+" version="3.24"/>
-  <object class="GtkWindow" id="textInput">
-    <property name="width-request">379</property>
-    <property name="height-request">92</property>
+  <object class="GtkDialog" id="textInput">
+    <property name="name">textInput</property>
     <property name="can-focus">False</property>
-    <property name="title" translatable="yes">Set ROI Text</property>
-    <property name="resizable">False</property>
-    <property name="modal">True</property>
     <property name="type-hint">dialog</property>
-    <child>
-      <object class="GtkFixed">
-        <property name="visible">True</property>
+    <child internal-child="vbox">
+      <object class="GtkBox">
         <property name="can-focus">False</property>
-        <child>
-          <object class="GtkButton" id="okBut">
-            <property name="label" translatable="yes">OK</property>
-            <property name="visible">True</property>
-            <property name="can-focus">True</property>
-            <property name="receives-default">True</property>
-          </object>
-          <packing>
-            <property name="x">323</property>
-            <property name="y">52</property>
-          </packing>
-        </child>
-        <child>
-          <object class="GtkButton" id="cancelBut">
-            <property name="label" translatable="yes">Cancel</property>
-            <property name="visible">True</property>
-            <property name="can-focus">True</property>
-            <property name="receives-default">True</property>
-          </object>
-          <packing>
-            <property name="x">251</property>
-            <property name="y">52</property>
-          </packing>
-        </child>
-        <child>
-          <object class="GtkEntry" id="textinputBox">
-            <property name="width-request">361</property>
-            <property name="visible">True</property>
-            <property name="can-focus">True</property>
-          </object>
-          <packing>
-            <property name="x">11</property>
-            <property name="y">11</property>
-          </packing>
-        </child>
-        <child>
-          <object class="GtkColorButton" id="colorBut">
-            <property name="width-request">82</property>
-            <property name="visible">True</property>
-            <property name="can-focus">True</property>
-            <property name="receives-default">True</property>
-            <property name="rgba">rgb(255,255,255)</property>
-          </object>
-          <packing>
-            <property name="x">11</property>
-            <property name="y">52</property>
-          </packing>
-        </child>
-        <child>
-          <object class="GtkLabel">
-            <property name="visible">True</property>
+        <property name="orientation">vertical</property>
+        <property name="spacing">2</property>
+        <child internal-child="action_area">
+          <object class="GtkButtonBox">
             <property name="can-focus">False</property>
-            <property name="label" translatable="yes">Set Color</property>
+            <property name="layout-style">end</property>
+            <child>
+              <object class="GtkButton" id="cancelBut">
+                <property name="label" translatable="yes">Cancel</property>
+                <property name="visible">True</property>
+                <property name="can-focus">True</property>
+                <property name="receives-default">True</property>
+              </object>
+              <packing>
+                <property name="expand">True</property>
+                <property name="fill">True</property>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkButton" id="okBut">
+                <property name="label" translatable="yes">OK</property>
+                <property name="visible">True</property>
+                <property name="can-focus">True</property>
+                <property name="receives-default">True</property>
+              </object>
+              <packing>
+                <property name="expand">True</property>
+                <property name="fill">True</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
           </object>
           <packing>
-            <property name="x">29</property>
-            <property name="y">60</property>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">0</property>
           </packing>
         </child>
         <child>
-          <object class="GtkFontButton" id="fontBut">
-            <property name="width-request">100</property>
+          <object class="GtkFixed">
             <property name="visible">True</property>
-            <property name="can-focus">True</property>
-            <property name="receives-default">True</property>
-            <property name="font">Sans 12</property>
-            <property name="language">en-us</property>
-            <property name="preview-text">Choose Font</property>
+            <property name="can-focus">False</property>
+            <child>
+              <object class="GtkFixed">
+                <property name="width-request">100</property>
+                <property name="height-request">80</property>
+                <property name="visible">True</property>
+                <property name="can-focus">False</property>
+                <property name="margin-top">41</property>
+                <child>
+                  <object class="GtkEntry" id="textinputBox">
+                    <property name="width-request">403</property>
+                    <property name="visible">True</property>
+                    <property name="can-focus">True</property>
+                  </object>
+                  <packing>
+                    <property name="x">11</property>
+                    <property name="y">11</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkColorButton" id="colorBut">
+                    <property name="width-request">82</property>
+                    <property name="visible">True</property>
+                    <property name="can-focus">True</property>
+                    <property name="receives-default">True</property>
+                    <property name="rgba">rgb(255,255,255)</property>
+                  </object>
+                  <packing>
+                    <property name="x">11</property>
+                    <property name="y">52</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkLabel">
+                    <property name="visible">True</property>
+                    <property name="can-focus">False</property>
+                    <property name="label" translatable="yes">Set Color</property>
+                  </object>
+                  <packing>
+                    <property name="x">29</property>
+                    <property name="y">60</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFontButton" id="fontBut">
+                    <property name="width-request">100</property>
+                    <property name="visible">True</property>
+                    <property name="can-focus">True</property>
+                    <property name="receives-default">True</property>
+                    <property name="font">Sans 12</property>
+                    <property name="language">en-us</property>
+                    <property name="preview-text">Choose Font</property>
+                  </object>
+                  <packing>
+                    <property name="x">96</property>
+                    <property name="y">52</property>
+                  </packing>
+                </child>
+              </object>
+            </child>
           </object>
           <packing>
-            <property name="x">96</property>
-            <property name="y">52</property>
+            <property name="expand">False</property>
+            <property name="fill">True</property>
+            <property name="position">1</property>
           </packing>
         </child>
       </object>

diff --git a/Glade/TextInput.glade~ b/Glade/TextInput.glade~
@@ -6,6 +6,7 @@
     <property name="width-request">379</property>
     <property name="height-request">92</property>
     <property name="can-focus">False</property>
+    <property name="title" translatable="yes">Set ROI Text</property>
     <property name="resizable">False</property>
     <property name="modal">True</property>
     <property name="type-hint">dialog</property>

diff --git a/Source/App.cs b/Source/App.cs
@@ -81,6 +81,11 @@ private static void UpdateStitching()
             if (RuntimeInformation.IsOSPlatform(OSPlatform.OSX))
             {
                 useGPU = false;
+                OpenSlideBase.useGPU = false;
+                SlideBase.useGPU = false;
+                OpenSlideBase.UseVips = false;
+                SlideBase.UseVips = false;
+                return;
             }
             OpenSlideBase.useGPU = useGPU;
             SlideBase.useGPU = useGPU;
@@ -124,6 +129,7 @@ public static bool UseFiji
         public static bool SetFijiOrImageJPath()
         {
             bool ifb;
+            BioLib.Settings.Load();
             string st = BioLib.Settings.GetSettings("ImageJPath");
             if (st != "")
             {
@@ -187,6 +193,7 @@ public static void Initialize()
             recorder = Recorder.Create();
             //color = ColorTool.Create();
             UpdateStitching();
+            BioLib.Settings.Load();
         }
 
         public static void ApplyStyles(Widget widget)