5.7.0 Mac OS related bug fixes.

BioGTK.csproj

@@ -3,25 +3,25 @@
     <TargetFramework>net8.0</TargetFramework>
     <OutputType>Library</OutputType>
     <RuntimeIdentifiers>osx-x64;linux-x64;win-x64;win-arm64;linux-arm64;osx-arm64;</RuntimeIdentifiers>
-    <AssemblyVersion>5.6.1</AssemblyVersion>
-    <FileVersion>5.6.1</FileVersion>
+    <AssemblyVersion>5.7.0</AssemblyVersion>
+    <FileVersion>5.7.0</FileVersion>
     <GeneratePackageOnBuild>True</GeneratePackageOnBuild>
     <PackageId>BioGTK</PackageId>
     <Title>BioGTK</Title>
     <PackageProjectUrl>https://github.com/BiologyTools/BioGTK</PackageProjectUrl>
     <PackageIcon>banner.jpg</PackageIcon>
     <PackageReadmeFile>README.md</PackageReadmeFile>
-    <PackageVersion>5.6.1</PackageVersion>
+    <PackageVersion>5.7.0</PackageVersion>
     <RepositoryUrl>https://github.com/BiologyTools/BioGTK</RepositoryUrl>
     <PackageTags>Biology; GTK; ImageJ; Bio-Formats; Image-Stacks; Microscopy; Whole-Slide-Image; Segment-Anything; SAM; QuPath;</PackageTags>
     <PackageLicenseExpression> GPL-3.0-only</PackageLicenseExpression>
     <PackageRequireLicenseAcceptance>True</PackageRequireLicenseAcceptance>
     <Description>A .NET application &amp; library for editing &amp; annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters &amp; macro functions. Supports Windows, Linux and Mac.</Description>
-    <Version>5.6.1</Version>
+    <Version>5.7.0</Version>
     <Platforms>AnyCPU</Platforms>
     <AllowUnsafeBlocks>True</AllowUnsafeBlocks>
     <PlatformTarget>AnyCPU</PlatformTarget>
-    <PackageReleaseNotes>CUDA support for Linux as well as MacOS related bug fixes.</PackageReleaseNotes>
+    <PackageReleaseNotes>CUDA support for Linux and Mac related bug fixes.</PackageReleaseNotes>
     <Authors>Erik Repo</Authors>
   </PropertyGroup>
 
@@ -49,13 +49,6 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
     <WarningLevel>7</WarningLevel>
   </PropertyGroup>
-
-  <ItemGroup>
-    <Content Remove="C:\Users\Erikr\.nuget\packages\biolib\2.9.0.1\contentFiles\any\net8.0\tile_copy.cu" />
-    <Content Remove="C:\Users\Erikr\.nuget\packages\biolib\2.9.0.1\contentFiles\any\net8.0\tile_copy.ptx" />
-    <Content Remove="C:\Users\Erikr\.nuget\packages\biolib\2.9.0\contentFiles\any\net8.0\tile_copy.cu" />
-    <Content Remove="C:\Users\Erikr\.nuget\packages\biolib\2.9.0\contentFiles\any\net8.0\tile_copy.ptx" />
-  </ItemGroup>
   <ItemGroup>
     <Content Include="bio.icns">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
@@ -411,16 +404,6 @@
       <Pack>True</Pack>
       <PackageCopyToOutput>true</PackageCopyToOutput>
     </Content>
-    <Content Include="macro-commands.csv">
-      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
-      <Pack>True</Pack>
-      <PackageCopyToOutput>true</PackageCopyToOutput>
-    </Content>
-    <Content Include="macro-functions.txt">
-      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
-      <Pack>True</Pack>
-      <PackageCopyToOutput>true</PackageCopyToOutput>
-    </Content>
     <Content Include="tile_copy.cu">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </Content>
@@ -472,14 +455,16 @@
     <CFBundleName>BioGTK</CFBundleName>
     <CFBundleDisplayName>BioGTK</CFBundleDisplayName>
     <CFBundleIdentifier>com.BioGTK</CFBundleIdentifier>
-    <CFBundleVersion>5.6.1</CFBundleVersion>
+    <CFBundleVersion>5.7.0</CFBundleVersion>
     <CFBundlePackageType>APPL</CFBundlePackageType>
     <CFBundleSignature>????</CFBundleSignature>
     <CFBundleExecutable>BioGTKApp</CFBundleExecutable>
     <CFBundleIconFile>bio.icns</CFBundleIconFile>
-    <CFBundleShortVersionString>5.6.1</CFBundleShortVersionString>
+    <CFBundleShortVersionString>5.7.0</CFBundleShortVersionString>
     <NSPrincipalClass>NSApplication</NSPrincipalClass>
     <NSHighResolutionCapable>true</NSHighResolutionCapable>
     <ImplicitUsings>enable</ImplicitUsings>
+	<CFBundleDocumentTypes>.ome.tif</CFBundleDocumentTypes>
+	<CFBundleTypeName>OME-TIFF</CFBundleTypeName>
   </PropertyGroup>
 </Project>

Source/App.cs

@@ -1,5 +1,6 @@
 using Bio;
 using Gtk;
+using javax.swing.filechooser;
 using OpenSlideGTK;
 using System;
 using System.Collections.Generic;
@@ -87,15 +88,90 @@ private static void UpdateStitching()
             SlideBase.UseVips = useVips;
 
         }
-        public static bool UseFiji = false;
+        public static bool ToConsole
+        {
+            get
+            {
+                return BioLib.Recorder.outputConsole;
+            }
+            set
+            {
+                BioLib.Recorder.outputConsole = value;
+            }
+        }
+        static bool useFiji = true;
+        public static bool UseFiji
+        {
+            get
+            {
+                if (OperatingSystem.IsMacOS())
+                {
+                    return true;
+                }
+                else
+                {
+                    if(Fiji.ImageJPath.Contains("Fiji"))
+                        return true;
+                    else
+                        return false;
+                }
+            }
+        }
+        /// This function creates a file chooser dialog that allows the user to select the location of
+        /// the ImageJ executable
+        /// 
+        /// @return A boolean value.
+        public static bool SetFijiOrImageJPath()
+        {
+            bool ifb;
+            string st = BioLib.Settings.GetSettings("ImageJPath");
+            if (st != "")
+            {
+                if (st.Contains("Fiji"))
+                {
+                    BioLib.Fiji.ImageJPath = st;
+                }
+                else
+                    BioLib.ImageJ.ImageJPath = st;
+                return true;
+            }
+            string title = "Select ImageJ Executable Location";
+            if (OperatingSystem.IsMacOS())
+                title = "Select ImageJ Executable Location (Fiji.app/Contents/MacOS/ImageJ-macosx)";
+            Gtk.FileChooserDialog filechooser =
+            new Gtk.FileChooserDialog(title, Scripting.window,
+            FileChooserAction.Open,
+            "Cancel", ResponseType.Cancel,
+            "Save", ResponseType.Accept);
+            filechooser.SetCurrentFolder(System.IO.Path.GetDirectoryName(Environment.ProcessPath));
+            if (filechooser.Run() != (int)ResponseType.Accept)
+                return false;
+            if(filechooser.Filename.Contains("Fiji"))
+                Fiji.ImageJPath = filechooser.Filename;
+            else
+                ImageJ.ImageJPath = filechooser.Filename;
+            BioLib.Settings.AddSettings("ImageJPath", filechooser.Filename);
+            filechooser.Destroy();
+            BioLib.Settings.Save();
+            return true;
+        }
         /// Initialize() is a function that initializes the BioImage Suite Web
-        public static void Initialize(bool requireImageJ = false)
+        public static void Initialize()
         {
             Console.WriteLine("Initializing components.");
-            BioImage.Initialize();
+            SetFijiOrImageJPath();
+            if (Fiji.ImageJPath == "")
+            {
+                ImageJ.Initialize(ImageJ.ImageJPath);
+                BioImage.Initialize(ImageJ.ImageJPath);
+            }
+            else
+            {
+                Fiji.Initialize(Fiji.ImageJPath);
+                BioImage.Initialize(Fiji.ImageJPath);
+            }
             Console.WriteLine("Loading settings.");
-            Settings.Load();
-            Fiji.Initialize(requireImageJ);
+            BioLib.Settings.Load();
             updater = Updater.Create();
             tools = Tools.Create();
             filters = FiltersView.Create();

Source/BioConsole.cs

@@ -234,7 +234,7 @@ private void ImagejBut_Clicked(object sender, EventArgs e)
         {
             if (ImageView.SelectedImage == null)
                 return;
-            Fiji.RunOnImage(textBox.Buffer.Text, headless, onTab, useBioformats, resultsBox.Active);
+            Fiji.RunOnImage(ImageView.SelectedImage,textBox.Buffer.Text, headless, onTab, useBioformats, resultsBox.Active);
             consoleBox.Buffer.Text += textBox.Buffer.Text + Environment.NewLine;
             textBox.Buffer.Text = "";
         }