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| <?xml version="1.0" encoding="utf-8"?> | ||
| <configuration> | ||
| <startup> | ||
| <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6"/> | ||
| </startup> | ||
| </configuration> |
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| #Region "Microsoft.VisualBasic::c0cce5893014d4ddec6d19af3b8b7869, CLI_tools\Cluster\CLI.vb" | ||
|
|
||
| ' Author: | ||
| ' | ||
| ' asuka ([email protected]) | ||
| ' xie ([email protected]) | ||
| ' xieguigang ([email protected]) | ||
| ' | ||
| ' Copyright (c) 2018 GPL3 Licensed | ||
| ' | ||
| ' | ||
| ' GNU GENERAL PUBLIC LICENSE (GPL3) | ||
| ' | ||
| ' | ||
| ' This program is free software: you can redistribute it and/or modify | ||
| ' it under the terms of the GNU General Public License as published by | ||
| ' the Free Software Foundation, either version 3 of the License, or | ||
| ' (at your option) any later version. | ||
| ' | ||
| ' This program is distributed in the hope that it will be useful, | ||
| ' but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ' GNU General Public License for more details. | ||
| ' | ||
| ' You should have received a copy of the GNU General Public License | ||
| ' along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
|
|
||
|
|
||
|
|
||
| ' /********************************************************************************/ | ||
|
|
||
| ' Summaries: | ||
|
|
||
| ' Module CLI | ||
| ' | ||
| ' Function: bTree, bTreeCluster, bTreePartitioning, ClusterDataSet, ClusterNumbers | ||
| ' | ||
| ' /********************************************************************************/ | ||
|
|
||
| #End Region | ||
|
|
||
| Imports Microsoft.VisualBasic | ||
| Imports Microsoft.VisualBasic.CommandLine.Reflection | ||
| Imports Microsoft.VisualBasic.DataMining.Framework.KMeans | ||
| Imports Microsoft.VisualBasic.DataVisualization.Network.FileStream | ||
| Imports Microsoft.VisualBasic.DocumentFormat.Csv | ||
| Imports Microsoft.VisualBasic.Linq | ||
|
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||
| Module CLI | ||
|
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||
| ''' <summary> | ||
| ''' 对一组数字进行聚类操作，其实在这里就是将这组数值生成Entity数据对象，然后将数值本身作为自动生成的Entity对象的一个唯一属性 | ||
| ''' </summary> | ||
| ''' <param name="args"></param> | ||
| ''' <returns></returns> | ||
| <ExportAPI("/n.cluster", | ||
| Info:="Cluserting the numbers.", | ||
| Usage:="/n.cluster /in <txt/values> /n <num_of_cluster> [/out <out.csv>]")> | ||
| Public Function ClusterNumbers(args As CommandLine.CommandLine) As Integer | ||
| Dim [in] As String = args("/in") | ||
| Dim out As String = args("/out") | ||
| Dim nums As Double() | ||
|
|
||
| If [in].FileExists Then | ||
| nums = [in].ReadAllLines.ToArray(Function(s) Val(s)) | ||
| If String.IsNullOrEmpty(out) Then | ||
| out = [in].TrimFileExt & ".cluster.csv" | ||
| End If | ||
| Else | ||
| nums = [in].Split(","c).ToArray(Function(s) Val(s.Trim)) | ||
| If String.IsNullOrEmpty(out) Then | ||
| out = App.CurrentDirectory & "/ClusterNumber.Csv" | ||
| End If | ||
| End If | ||
|
|
||
| Return nums.ValueGroups(args.GetInt32("/n")) > out | ||
| End Function | ||
|
|
||
| <ExportAPI("/kmeans", | ||
| Info:="Performance a kmeans clustering operation.", | ||
| Usage:="/kmeans /MAT <entity_matrix.Csv> /n <num_of_cluster> [/map <Name> /out <cluster.csv>]")> | ||
| Public Function ClusterDataSet(args As CommandLine.CommandLine) As Integer | ||
|
|
||
| Throw New Exception("Hello world!") | ||
|
|
||
| Dim inFile As String = args("/MAT") | ||
| Dim n As Integer = args.GetInt32("/n") | ||
| Dim out As String = args.GetValue("/out", inFile.TrimFileExt & ".Cluster.Csv") | ||
| Dim ds As IEnumerable(Of EntityLDM) = EntityLDM.Load(inFile, args.GetValue("/map", "Name")) | ||
|
|
||
| Return Kmeans(ds, n) > out | ||
| End Function | ||
|
|
||
| <ExportAPI("/bTree.Cluster", | ||
| Info:="Performance a binary tree clustering operations on the input data set.", | ||
| Usage:="/bTree.Cluster /MAT <entity_matrix.csv> [/map <Name> /parallel /out <out.cluster.csv>]")> | ||
| Public Function bTreeCluster(args As CommandLine.CommandLine) As Integer | ||
| Dim inFile As String = args - "/MAT" | ||
| Dim parallel As Boolean = args.GetBoolean("/parallel") | ||
| Dim out As String = args.GetValue("/out", $"{inFile.TrimFileExt}.{NameOf(bTreeCluster)}.csv") | ||
| Dim map As String = args.GetValue("/map", "Name") | ||
| Dim maps As Dictionary(Of String, String) = | ||
| New Dictionary(Of String, String) From {{map, NameOf(EntityLDM.Name)}} | ||
| Dim dataSet As IEnumerable(Of EntityLDM) = | ||
| inFile.LoadCsv(Of EntityLDM)(maps:=maps) | ||
| dataSet = dataSet.TreeCluster | ||
| Return dataSet.SaveTo(out) | ||
| End Function | ||
|
|
||
| ''' <summary> | ||
| ''' Converts the bTree clustering result into the cytoscape network model file. | ||
| ''' </summary> | ||
| ''' <param name="args"></param> | ||
| ''' <returns></returns> | ||
| <ExportAPI("/bTree", | ||
| Info:="Converts the bTree clustering result into the cytoscape network model file.", | ||
| Usage:="/bTree /cluster <tree.cluster.csv> [/out <outDIR>]")> | ||
| Public Function bTree(args As CommandLine.CommandLine) As Integer | ||
| Dim inFile As String = args - "/cluster" | ||
| Dim out As String = ("/out" <= args) ^ $"{inFile.TrimFileExt}-bTree/" | ||
| Dim clusters As IEnumerable(Of EntityLDM) = inFile.LoadCsv(Of EntityLDM) | ||
| Dim tree As Network = clusters.bTreeNET | ||
| Return tree > out | ||
| End Function | ||
|
|
||
| ''' <summary> | ||
| ''' Partitioning the binary tree cluster by using the clustering path. | ||
| ''' </summary> | ||
| ''' <param name="args"></param> | ||
| ''' <returns></returns> | ||
| <ExportAPI("/bTree.Partitioning", | ||
| Info:="Partitioning the binary tree cluster by using the clustering path.", | ||
| Usage:="/bTree.Partitioning /cluster <clusters.csv> [/depth <-1> /out <partions.csv>]")> | ||
| <ParameterInfo("/depth", True, | ||
| Description:="The maximum depth of the clustering path using for the partitioning operations. | ||
| Default or value zero or negative is using the shortest path in the cluster entity.")> | ||
| Public Function bTreePartitioning(args As CommandLine.CommandLine) As Integer | ||
| Dim inFile As String = args - "/cluster" | ||
| Dim depth As Integer = args.GetValue("/depth", -1) | ||
| Dim out As String = args.GetValue("/out", inFile.TrimFileExt & $".{depth}.csv") | ||
| Dim result As List(Of Partition) = inFile.LoadCsv(Of EntityLDM).Partitioning(depth) | ||
| Return result > out | ||
| End Function | ||
| End Module |
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