4.2.0 ImageJ.NET Implementation.

BiologyTools · Aug 1, 2024 · df7a8dc · df7a8dc
1 parent 5a371b1
commit df7a8dc
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Showing 9 changed files with 2,007 additions and 1,621 deletions.
diff --git a/BioCore.sln b/BioCore.sln
@@ -9,8 +9,6 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "BioCoreApp", "..\BioCoreApp
 EndProject
 Project("{54435603-DBB4-11D2-8724-00A0C9A8B90C}") = "BioCoreSetup", "..\BioCoreSetup\BioCoreSetup\BioCoreSetup.vdproj", "{9F71BCBA-FB42-48F3-8CE2-B492365008A6}"
 EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "BioLib", "..\BioLib\BioLib.csproj", "{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}"
-EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -57,18 +55,6 @@ Global
 		{9F71BCBA-FB42-48F3-8CE2-B492365008A6}.Release|x64.Build.0 = Release
 		{9F71BCBA-FB42-48F3-8CE2-B492365008A6}.Release|x86.ActiveCfg = Release
 		{9F71BCBA-FB42-48F3-8CE2-B492365008A6}.Release|x86.Build.0 = Release
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Debug|x64.ActiveCfg = Debug|x64
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Debug|x64.Build.0 = Debug|x64
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Debug|x86.ActiveCfg = Debug|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Debug|x86.Build.0 = Debug|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Release|Any CPU.Build.0 = Release|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Release|x64.ActiveCfg = Release|x64
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Release|x64.Build.0 = Release|x64
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Release|x86.ActiveCfg = Release|Any CPU
-		{C7A4FE0F-B632-48C8-AFD4-573973CC7E92}.Release|x86.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

diff --git a/BioCore/BioCore.csproj b/BioCore/BioCore.csproj
@@ -63,6 +63,7 @@
   </ItemGroup>
 
   <ItemGroup>
+    <PackageReference Include="BioLib" Version="2.5.0" />
     <PackageReference Include="FlaUI.Core" Version="4.0.0" />
     <PackageReference Include="FlaUI.UIA3" Version="4.0.0" />
     <PackageReference Include="H.InputSimulator" Version="1.4.2" />
@@ -121,9 +122,6 @@
       <PackagePath>\</PackagePath>
     </None>
   </ItemGroup>
-  <ItemGroup>
-    <ProjectReference Include="..\..\BioLib\BioLib.csproj" />
-  </ItemGroup>
   <ItemGroup>
     <Using Include="AForge.Bitmap">
       <Alias>Bitmap</Alias>

diff --git a/BioCore/Source/App.cs b/BioCore/Source/App.cs
@@ -49,7 +49,7 @@ public static void Initialize(bool requireImageJ = false)
         {
             BioImage.Initialize();
             Microscope.Initialize();
-            ImageJ.Initialize();
+            Fiji.Initialize(requireImageJ);
             tabsView = new TabsView();
             viewer = new ImageView();
             stackTools = new StackTools();
@@ -384,8 +384,8 @@ private static void ItemClicked(object sender, EventArgs e)
             }
             else if (ts.Text.EndsWith(".ijm"))
             {
-                string s =  File.ReadAllText(Path.GetDirectoryName(ImageJ.ImageJPath) + "/macros/" + ts.Text);
-                ImageJ.RunOnImage(s, BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.newTab);
+                string s =  File.ReadAllText(Path.GetDirectoryName(Fiji.ImageJPath) + "/macros/" + ts.Text);
+                Fiji.RunOnImage(s, BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.newTab);
             }
             else
             {

diff --git a/BioCore/Source/BioConsole.cs b/BioCore/Source/BioConsole.cs
@@ -43,7 +43,7 @@ private void imagejBut_Click(object sender, EventArgs e)
         {
             if (ImageView.SelectedImage == null)
                 return;
-            ImageJ.RunOnImage(textBox.Text, headlessBox.Checked, tabRadioBut.Checked, biofBox.Checked, newTabBox.Checked);
+            Fiji.RunOnImage(textBox.Text, headlessBox.Checked, tabRadioBut.Checked, biofBox.Checked, newTabBox.Checked);
             consoleBox.Text += textBox.Text + Environment.NewLine;
             textBox.Text = "";
             string filename = "";
@@ -169,12 +169,12 @@ private void textBox_TextChanged(object sender, EventArgs e)
             preds.Clear();
             i = 0;
             ind = -1;
-            foreach (var cs in ImageJ.Macro.Commands)
+            foreach (var cs in Fiji.Macro.Commands)
             {
                 if (cs.Value.Name.StartsWith(pred))
                     preds.Add(cs.Value.Name);
             }
-            foreach (var cs in ImageJ.Macro.Functions)
+            foreach (var cs in Fiji.Macro.Functions)
             {
                 if (cs.Value[0].Name.StartsWith(pred))
                     preds.Add(cs.Value[0].Name);

diff --git a/BioCore/Source/ColorTool.cs b/BioCore/Source/ColorTool.cs
@@ -26,20 +26,20 @@ public ColorS Color
                 colors = value;
             }
         }
-/*
+
         /// It updates the GUI
         public void UpdateGUI()
         {
-            color = new ColorS((ushort)redBox.Value, (ushort)greenBox.Value, (ushort)blueBox.Value);
-            colorPanel.BackColor = System.Drawing.Color.FromArgb(color.R / ushort.MaxValue,color.G / ushort.MaxValue,color.B / ushort.MaxValue);
+            colors = new ColorS((ushort)redBox.Value, (ushort)greenBox.Value, (ushort)blueBox.Value);
+            colorPanel.BackColor = System.Drawing.Color.FromArgb(colors.R / ushort.MaxValue,colors.G / ushort.MaxValue,colors.B / ushort.MaxValue);
             if (rBar.Value != redBox.Value)
                 redBox.Value = rBar.Value;
             if (gBar.Value != greenBox.Value)
                 greenBox.Value = gBar.Value;
             if (bBar.Value != blueBox.Value)
                 blueBox.Value = bBar.Value;
         }
-        */
+
         /* A constructor. */
         public ColorTool()
         {
@@ -50,8 +50,8 @@ public ColorTool()
         public ColorTool(ColorS col, int bitPerPixel)
         {
             InitializeComponent();
-            this.bitsPerPixel = bitPerPixel;
-            if(bitsPerPixel == 8)
+            this.bitsPerPx = bitPerPixel;
+            if(bitsPerPx == 8)
             {
                 rBar.Maximum = 255;
                 gBar.Maximum = 255;