Merge https://github.com/xieguigang/mzkit

src/assembly/assembly/MarkupData/imzML/XML/ScanData.vb

@@ -102,6 +102,9 @@ Namespace MarkupData.imzML
 
     End Interface
 
+    ''' <summary>
+    ''' the MSI pixel data spot model of [x,z,intensity]
+    ''' </summary>
     Public Class PixelScanIntensity : Implements IMSIPixel, RasterPixel
 
         ''' <summary>
@@ -112,6 +115,15 @@ Namespace MarkupData.imzML
         Public Property x As Integer Implements IMSIPixel.x, RasterPixel.X
         Public Property y As Integer Implements IMSIPixel.y, RasterPixel.Y
 
+        Sub New()
+        End Sub
+
+        Sub New(x As Integer, y As Integer, intensity As Double)
+            Me.x = x
+            Me.y = y
+            Me.totalIon = intensity
+        End Sub
+
         <MethodImpl(MethodImplOptions.AggressiveInlining)>
         Public Function GetPoint() As Point
             Return New Point(x, y)

src/visualize/TissueMorphology/HEMap/Cell.vb

@@ -1,64 +1,58 @@
 #Region "Microsoft.VisualBasic::021b9dc0adf1db588e2f8a3c06bf29c5, mzkit\src\visualize\TissueMorphology\HEMap\Cell.vb"
 
-    ' Author:
-    ' 
-    '       xieguigang ([email protected], BioNovoGene Co., LTD.)
-    ' 
-    ' Copyright (c) 2018 [email protected], BioNovoGene Co., LTD.
-    ' 
-    ' 
-    ' MIT License
-    ' 
-    ' 
-    ' Permission is hereby granted, free of charge, to any person obtaining a copy
-    ' of this software and associated documentation files (the "Software"), to deal
-    ' in the Software without restriction, including without limitation the rights
-    ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-    ' copies of the Software, and to permit persons to whom the Software is
-    ' furnished to do so, subject to the following conditions:
-    ' 
-    ' The above copyright notice and this permission notice shall be included in all
-    ' copies or substantial portions of the Software.
-    ' 
-    ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-    ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-    ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-    ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-    ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-    ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-    ' SOFTWARE.
-
-
-
-    ' /********************************************************************************/
-
-    ' Summaries:
-
-
-    ' Code Statistics:
-
-    '   Total Lines: 52
-    '    Code Lines: 21
-    ' Comment Lines: 24
-    '   Blank Lines: 7
-    '     File Size: 1.33 KB
-
-
-    ' Class Cell
-    ' 
-    '     Properties: B, Black, G, isBlack, layers
-    '                 R, ScaleX, ScaleY, X, Y
-    ' 
-    ' /********************************************************************************/
+' Author:
+' 
+'       xieguigang ([email protected], BioNovoGene Co., LTD.)
+' 
+' Copyright (c) 2018 [email protected], BioNovoGene Co., LTD.
+' 
+' 
+' MIT License
+' 
+' 
+' Permission is hereby granted, free of charge, to any person obtaining a copy
+' of this software and associated documentation files (the "Software"), to deal
+' in the Software without restriction, including without limitation the rights
+' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+' copies of the Software, and to permit persons to whom the Software is
+' furnished to do so, subject to the following conditions:
+' 
+' The above copyright notice and this permission notice shall be included in all
+' copies or substantial portions of the Software.
+' 
+' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+' SOFTWARE.
+
+
+
+' /********************************************************************************/
+
+' Summaries:
+
+
+' Code Statistics:
+
+'   Total Lines: 52
+'    Code Lines: 21
+' Comment Lines: 24
+'   Blank Lines: 7
+'     File Size: 1.33 KB
+
+
+' Class Cell
+' 
+'     Properties: B, Black, G, isBlack, layers
+'                 R, ScaleX, ScaleY, X, Y
+' 
+' /********************************************************************************/
 
 #End Region
 
-Imports System.Drawing
-Imports Microsoft.VisualBasic.Data.GraphTheory
-Imports Microsoft.VisualBasic.Imaging
-Imports Microsoft.VisualBasic.Linq
-Imports Microsoft.VisualBasic.Math.LinearAlgebra
-
 Public Class Cell
 
     ''' <summary>

src/visualize/TissueMorphology/HEMap/SpatialRegister.vb

@@ -0,0 +1,114 @@
+Imports System.Drawing
+Imports System.IO
+Imports Microsoft.VisualBasic.DataStorage.netCDF
+Imports Microsoft.VisualBasic.DataStorage.netCDF.Components
+Imports Microsoft.VisualBasic.DataStorage.netCDF.Data
+Imports Microsoft.VisualBasic.DataStorage.netCDF.DataVector
+Imports Microsoft.VisualBasic.Imaging.BitmapImage
+Imports Microsoft.VisualBasic.Scripting.Runtime
+Imports any = Microsoft.VisualBasic.Scripting
+
+Public Class SpatialRegister
+
+    Public Property HEstain As Image
+    Public Property mappings As SpotMap()
+    Public Property offset As PointF
+    Public Property rotation As Double
+    Public Property mirror As Boolean
+    Public Property label As String
+    Public Property spotColor As String
+    Public Property viewSize As Size
+    Public Property MSIscale As Size
+    Public Property MSIdims As Size
+
+    Public Sub Save(file As Stream)
+        Using buf As New CDFWriter(file)
+            Call Save(buf)
+        End Using
+    End Sub
+
+    Public Shared Function ParseFile(file As Stream) As SpatialRegister
+        Dim buf As New netCDFReader(file)
+        Dim view_size As String = buf!view_size
+        Dim msi_scale As String = buf!msi_scale
+        Dim spot_color As String = buf!spot_color
+        Dim label As String = buf!label
+        Dim mirror As String = buf!mirror
+        Dim rotation As Single = buf!rotation
+        Dim offset As String = buf!offset
+        Dim spot_number As Integer = buf!spot_number
+        Dim msi_dims As String = buf!msi_dims
+        Dim heatmap As doubles = buf.getDataVariable("heatmap")
+        Dim x As doubles = buf.getDataVariable("x")
+        Dim y As doubles = buf.getDataVariable("y")
+        Dim x0 As integers = buf.getDataVariable("x0")
+        Dim y0 As integers = buf.getDataVariable("y0")
+        Dim img As longs = buf.getDataVariable("img")
+        Dim img_size As Size = CStr(buf!img_size).SizeParser
+        Dim bitmap As Bitmap = New Bitmap(img_size.Width, img_size.Height)
+        Dim image As BitmapBuffer = BitmapBuffer.FromBitmap(bitmap)
+        Dim mappings As SpotMap() = heatmap _
+            .Select(Function(s, i)
+                        Return New SpotMap With {
+                            .heatmap = s,
+                            .STX = x(i),
+                            .STY = y(i),
+                            .spotXY = {x0(i), y0(i)},
+                            .flag = 1,
+                            .physicalXY = .spotXY
+                        }
+                    End Function) _
+            .ToArray
+
+        Call image.WriteARGBStream(img.Select(Function(l) CUInt(l)).ToArray)
+        Call image.Dispose()
+        Call file.Close()
+
+        Return New SpatialRegister With {
+            .label = label,
+            .mirror = mirror.ParseBoolean,
+            .MSIscale = msi_scale.SizeParser,
+            .offset = any.CTypeDynamic(offset, GetType(PointF)),
+            .rotation = rotation,
+            .spotColor = spot_color,
+            .viewSize = view_size.SizeParser,
+            .HEstain = bitmap,
+            .mappings = mappings,
+            .MSIdims = msi_dims.SizeParser
+        }
+    End Function
+
+    Private Sub Save(buf As CDFWriter)
+        Dim view_size As New attribute("view_size", $"{viewSize.Width},{viewSize.Height}")
+        Dim msi_scale As New attribute("msi_scale", $"{MSIscale.Width},{MSIscale.Height}")
+        Dim spot_color As New attribute("spot_color", spotColor)
+        Dim label As New attribute("label", _label)
+        Dim mirror As New attribute("mirror", _mirror.ToString.ToLower)
+        Dim rotation As New attribute("rotation", _rotation.ToString, CDFDataTypes.FLOAT)
+        Dim offset As New attribute("offset", $"{_offset.X},{_offset.Y}")
+        Dim spot_number As New attribute("spot_number", mappings.Length.ToString, CDFDataTypes.INT)
+        Dim img_size As New attribute("img_size", $"{HEstain.Width},{HEstain.Height}")
+        Dim msi_dims As New attribute("msi_dims", $"{MSIdims.Width},{MSIdims.Height}")
+
+        Dim mapping_dims As New Dimension("mapping_size", mappings.Length)
+        Dim img As BitmapBuffer = BitmapBuffer.FromBitmap(HEstain)
+        Dim stream As UInteger() = img.GetARGBStream
+        Dim image_size As New Dimension("HEstain_image", stream.Length)
+
+        Call buf.GlobalAttributes(
+            view_size, msi_scale,
+            spot_color, label,
+            mirror, rotation,
+            offset, spot_number,
+            img_size,
+            msi_dims
+        )
+
+        Call buf.AddVariable("heatmap", New doubles(mappings.Select(Function(si) CDbl(si.heatmap))), mapping_dims)
+        Call buf.AddVariable("x", New doubles(mappings.Select(Function(si) si.STX)), mapping_dims)
+        Call buf.AddVariable("y", New doubles(mappings.Select(Function(si) si.STY)), mapping_dims)
+        Call buf.AddVariable("x0", New integers(mappings.Select(Function(si) si.spotXY(0))), mapping_dims)
+        Call buf.AddVariable("y0", New integers(mappings.Select(Function(si) si.spotXY(1))), mapping_dims)
+        Call buf.AddVariable("img", New longs(stream), image_size)
+    End Sub
+End Class