Merge branch 'master' of https://github.com/xieguigang/mzkit

xieguigang · Dec 9, 2024 · b517680 · b517680
2 parents 775d58e + ee94b2c
commit b517680
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diff --git a/Rscript/Library/mzkit_app/src/mzkit/comprehensive/TissueMorphology.vb b/Rscript/Library/mzkit_app/src/mzkit/comprehensive/TissueMorphology.vb
@@ -76,21 +76,18 @@ Imports Microsoft.VisualBasic.Imaging.Drawing2D.Colors
 Imports Microsoft.VisualBasic.Language
 Imports Microsoft.VisualBasic.Linq
 Imports Microsoft.VisualBasic.MIME.Html.CSS
+Imports Microsoft.VisualBasic.MIME.Html.Render
 Imports Microsoft.VisualBasic.Scripting.MetaData
 Imports Microsoft.VisualBasic.Scripting.Runtime
+Imports R_graphics.Common.Runtime
 Imports SMRUCC.Rsharp.Runtime
 Imports SMRUCC.Rsharp.Runtime.Components
-Imports SMRUCC.Rsharp.Runtime.Internal.Invokes
 Imports SMRUCC.Rsharp.Runtime.Internal.Object
 Imports SMRUCC.Rsharp.Runtime.Interop
 Imports SMRUCC.Rsharp.Runtime.Vectorization
 Imports RgraphicsDev = R_graphics.Common.Runtime.graphicsDevice
-Imports std = System.Math
 Imports RInternal = SMRUCC.Rsharp.Runtime.Internal
-Imports R_graphics.Common.Runtime
-Imports Microsoft.VisualBasic.MIME.Html.Render
-
-
+Imports std = System.Math
 
 #If NET48 Then
 Imports Pen = System.Drawing.Pen
@@ -118,6 +115,7 @@ Imports GraphicsPath = Microsoft.VisualBasic.Imaging.GraphicsPath
 Imports FontStyle = Microsoft.VisualBasic.Imaging.FontStyle
 #End If
 
+
 ''' <summary>
 ''' spatial tissue region handler
 ''' 
@@ -135,6 +133,7 @@ Module TissueMorphology
         Call RInternal.generic.add("plot", GetType(TissueRegion()), AddressOf PlotTissueMap)
     End Sub
 
+    <RGenericOverloads("as.data.frame")>
     Private Function createTissueTable(tissues As TissueRegion(), args As list, env As Environment) As dataframe
         Dim labels As String() = tissues _
             .Select(Function(i) i.label.Replicate(n:=i.nsize)) _
@@ -164,14 +163,15 @@ Module TissueMorphology
         }
     End Function
 
+    <RGenericOverloads("as.data.frame")>
     Private Function createUMAPTable(umap As UMAPPoint(), args As list, env As Environment) As dataframe
         Dim px As Integer() = umap.Select(Function(i) i.Pixel.X).ToArray
         Dim py As Integer() = umap.Select(Function(i) i.Pixel.Y).ToArray
         Dim x As Double() = umap.Select(Function(i) i.x).ToArray
         Dim y As Double() = umap.Select(Function(i) i.y).ToArray
         Dim z As Double() = umap.Select(Function(i) i.z).ToArray
-        Dim cluster As Integer() = umap _
-            .Select(Function(i) Integer.Parse(i.class)) _
+        Dim cluster As String() = umap _
+            .Select(Function(i) i.class) _
             .ToArray
 
         Return New dataframe With {
@@ -189,6 +189,7 @@ Module TissueMorphology
         }
     End Function
 
+    <RGenericOverloads("plot")>
     Public Function PlotTissueMap(tissue As TissueRegion(), args As list, env As Environment) As Object
         If args.CheckGraphicsDeviceExists Then
             ' draw on current graphics context

diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology.html
@@ -90,6 +90,24 @@ <h1>TissueMorphology</h1>
       <table class="table-three-line">
         <caption>.NET clr function exports</caption>
         <tbody><tr>
+  <td id="as.data.frame.tissueregion">
+    <a href="./TissueMorphology/as.data.frame.tissueregion.html">as.data.frame.tissueregion</a>
+  </td>
+  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/TissueMorphology/TissueRegion.html">TissueRegion</a>: <p>a tissue polygon region object</p></td>
+</tr>
+<tr>
+  <td id="as.data.frame.umappoint">
+    <a href="./TissueMorphology/as.data.frame.umappoint.html">as.data.frame.umappoint</a>
+  </td>
+  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/TissueMorphology/UMAPPoint.html">UMAPPoint</a>: <p>3d scatter data point, a spatial spot or a single cell data</p></td>
+</tr>
+<tr>
+  <td id="plot.tissueregion">
+    <a href="./TissueMorphology/plot.tissueregion.html">plot.tissueregion</a>
+  </td>
+  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/TissueMorphology/TissueRegion.html">TissueRegion</a>: <p>a tissue polygon region object</p></td>
+</tr>
+<tr>
   <td id="tag_samples">
     <a href="./TissueMorphology/tag_samples.html">tag_samples</a>
   </td>

diff --git a/src/assembly/BrukerDataReader/BrukerDataReader.NET5.vbproj b/src/assembly/BrukerDataReader/BrukerDataReader.NET5.vbproj
@@ -146,6 +146,10 @@
     </None>
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\BinaryData\binarydata-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\SQLite3\SQLite3.vbproj" />

diff --git a/src/assembly/Comprehensive/Comprehensive.NET5.vbproj b/src/assembly/Comprehensive/Comprehensive.NET5.vbproj
@@ -164,5 +164,9 @@
 		<Import Include="System.Data" />
 	</ItemGroup>
 
+	<ItemGroup>
+	  <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+	</ItemGroup>
+
 
 </Project>
diff --git a/src/assembly/LoadR.NET5/LoadR.NET5.vbproj b/src/assembly/LoadR.NET5/LoadR.NET5.vbproj
@@ -62,6 +62,10 @@
     </None>
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\R-sharp\R#\Rsharp-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\R-sharp\studio\RData\RData.NET5.vbproj" />

diff --git a/src/assembly/NMRFidTool/NMRFidTool.vbproj b/src/assembly/NMRFidTool/NMRFidTool.vbproj
@@ -10,6 +10,10 @@
     <GenerateDocumentationFile>True</GenerateDocumentationFile>
   </PropertyGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\BinaryData\binarydata-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Mathematica\Math\DataFittings\linear-netcore5.vbproj" />

diff --git a/src/assembly/SignalReader/SignalReader.vbproj b/src/assembly/SignalReader/SignalReader.vbproj
@@ -32,6 +32,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/assembly/SpectrumTree/spectrumTree.NETCore5.vbproj b/src/assembly/SpectrumTree/spectrumTree.NETCore5.vbproj
@@ -199,6 +199,10 @@
     </None>
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\BinaryData\binarydata-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\HDSPack\HDSPack.vbproj" />

diff --git a/src/assembly/ThermoRawFileReader/MSFileReader.NET5.vbproj b/src/assembly/ThermoRawFileReader/MSFileReader.NET5.vbproj
@@ -102,6 +102,10 @@
     </None>
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Mathematica\Math\Math\Math.NET5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Mathematica\SignalProcessing\SignalProcessing\signalprocessing-netcore5.vbproj" />

diff --git a/src/assembly/assembly/assembly-netcore5.vbproj b/src/assembly/assembly/assembly-netcore5.vbproj
@@ -157,6 +157,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/assembly/mzPack/mzpack.NET5.vbproj b/src/assembly/mzPack/mzpack.NET5.vbproj
@@ -145,6 +145,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/assembly/mzPackExtensions/mzPackExtensions.NET5.vbproj b/src/assembly/mzPackExtensions/mzPackExtensions.NET5.vbproj
@@ -168,4 +168,10 @@
 		</Reference>
 	</ItemGroup>
 
+
+
+	<ItemGroup>
+	  <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+	</ItemGroup>
+
 </Project>
diff --git a/src/metadb/Chemoinformatics/chemoinformatics-netcore5.vbproj b/src/metadb/Chemoinformatics/chemoinformatics-netcore5.vbproj
@@ -486,6 +486,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/metadb/FormulaSearch.Extensions/FormulaSearch.Extensions.NET5.vbproj b/src/metadb/FormulaSearch.Extensions/FormulaSearch.Extensions.NET5.vbproj
@@ -386,6 +386,10 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Graph\graph-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Mathematica\Math\Math.Statistics\stats-netcore5.vbproj" />

diff --git a/src/metadb/Massbank/massbank.NET5.vbproj b/src/metadb/Massbank/massbank.NET5.vbproj
@@ -434,6 +434,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/metadb/MoNA/MoNA.NET5.vbproj b/src/metadb/MoNA/MoNA.NET5.vbproj
@@ -128,4 +128,8 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
 </Project>
diff --git a/src/metadb/SMILES/SMILES.NET5.vbproj b/src/metadb/SMILES/SMILES.NET5.vbproj
@@ -115,4 +115,8 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
 </Project>
diff --git a/src/metadb/XrefEngine/XrefEngine.NET5.vbproj b/src/metadb/XrefEngine/XrefEngine.NET5.vbproj
@@ -129,4 +129,8 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
 </Project>
diff --git a/src/metadna/MetaDNA_visual/metaDNA_visual.NET5.vbproj b/src/metadna/MetaDNA_visual/metaDNA_visual.NET5.vbproj
@@ -84,6 +84,10 @@
     </None>
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\GCModeller\core\Bio.Assembly\biocore-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Graph\graph-netcore5.vbproj" />

diff --git a/src/metadna/metaDNA/metaDNA.NET5.vbproj b/src/metadna/metaDNA/metaDNA.NET5.vbproj
@@ -105,6 +105,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzkit b/src/mzkit
diff --git a/src/mzmath/GCxGC/GCxGC.vbproj b/src/mzmath/GCxGC/GCxGC.vbproj
@@ -8,6 +8,10 @@
     <Configurations>Debug;Release;LipidSearch;mzkit;Rsharp_app_release</Configurations>
   </PropertyGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Mathematica\Math\Math\Math.NET5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data_science\Mathematica\SignalProcessing\SignalProcessing\signalprocessing-netcore5.vbproj" />

diff --git a/src/mzmath/MSEngine/MSEngine.vbproj b/src/mzmath/MSEngine/MSEngine.vbproj
@@ -221,6 +221,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzmath/MSFinder/MSFinder.vbproj b/src/mzmath/MSFinder/MSFinder.vbproj
@@ -184,6 +184,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzmath/MoleculeNetworking/MoleculeNetworking.vbproj b/src/mzmath/MoleculeNetworking/MoleculeNetworking.vbproj
@@ -253,6 +253,10 @@
     <None Remove="NewFolder\**" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\BinaryData\binarydata-netcore5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\BinaryData\HDSPack\HDSPack.vbproj" />

diff --git a/src/mzmath/Mummichog/Mummichog.vbproj b/src/mzmath/Mummichog/Mummichog.vbproj
@@ -96,6 +96,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzmath/SingleCells/SingleCells.vbproj b/src/mzmath/SingleCells/SingleCells.vbproj
@@ -26,6 +26,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzmath/SpatialMath/SpatialMath.vbproj b/src/mzmath/SpatialMath/SpatialMath.vbproj
@@ -13,6 +13,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj b/src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj
@@ -136,4 +136,8 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
 </Project>
diff --git a/src/mzmath/ms2_math-core/mzmath-netcore5.vbproj b/src/mzmath/ms2_math-core/mzmath-netcore5.vbproj
@@ -417,6 +417,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/mzmath/ms2_simulator/ms2_simulator.NET5.vbproj b/src/mzmath/ms2_simulator/ms2_simulator.NET5.vbproj
@@ -138,6 +138,10 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\Trinity\Trinity.NET5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Data\word2vec\word2vec.vbproj" />

diff --git a/src/mzmath/mz_deco/deconv.NET5.vbproj b/src/mzmath/mz_deco/deconv.NET5.vbproj
@@ -355,6 +355,7 @@
 
   <ItemGroup>
     <PackageReference Include="System.Composition" Version="8.0.0" />
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
     <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
   </ItemGroup>
 

diff --git a/src/visualize/ComprehensiveMsPlot/ComprehensiveMsPlot.vbproj b/src/visualize/ComprehensiveMsPlot/ComprehensiveMsPlot.vbproj
@@ -8,6 +8,10 @@
     <Configurations>Debug;Release;LipidSearch;mzkit;Rsharp_app_release</Configurations>
   </PropertyGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\gr\Microsoft.VisualBasic.Imaging\imaging.NET5.vbproj" />
     <ProjectReference Include="..\..\..\..\GCModeller\src\runtime\sciBASIC#\Microsoft.VisualBasic.Core\src\Core.vbproj" />

diff --git a/src/visualize/KCF b/src/visualize/KCF
diff --git a/src/visualize/MsImaging/MsImaging.NET5.vbproj b/src/visualize/MsImaging/MsImaging.NET5.vbproj
@@ -267,6 +267,7 @@
 
     <ItemGroup>
       <PackageReference Include="System.Composition" Version="8.0.0" />
+      <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
       <PackageReference Include="System.Resources.Extensions" Version="8.0.0" />
     </ItemGroup>
 

diff --git a/src/visualize/SDF.Extensions/SDF.Extensions.NET5.vbproj b/src/visualize/SDF.Extensions/SDF.Extensions.NET5.vbproj
@@ -97,4 +97,8 @@
     <Import Include="System.Data" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="System.Numerics.Vectors" Version="4.6.0" />
+  </ItemGroup>
+
 </Project>