Fixed bn fusion, started work on integration

MIPT-Oulu · Sep 5, 2018 · 2dbb59a · 2dbb59a
1 parent 96cf1da
commit 2dbb59a
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Showing 19 changed files with 1,702 additions and 307 deletions.
diff --git a/3DHistoGrading/3DHistoGrading.csproj b/3DHistoGrading/3DHistoGrading.csproj
@@ -100,6 +100,7 @@
   <ItemGroup>
     <Compile Include="Components\Functions.cs" />
     <Compile Include="Components\Grading.cs" />
+    <Compile Include="Components\Interaction.cs" />
     <Compile Include="Components\Rendering.cs" />
     <Compile Include="MainForm.cs">
       <SubType>Form</SubType>
@@ -109,6 +110,9 @@
     </Compile>
     <Compile Include="Program.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
+    <EmbeddedResource Include="MainForm.resx">
+      <DependentUpon>MainForm.cs</DependentUpon>
+    </EmbeddedResource>
     <EmbeddedResource Include="Properties\Resources.resx">
       <Generator>ResXFileCodeGenerator</Generator>
       <LastGenOutput>Resources.Designer.cs</LastGenOutput>

diff --git a/3DHistoGrading/Components/Functions.cs b/3DHistoGrading/Components/Functions.cs
@@ -116,6 +116,7 @@ public static vtkImageData volumeSlicer(vtkImageData volume, int[] sliceN, int a
             //slicer.Update();
 
             //Return copy of the slice
+
             return permuter.GetOutput();
         }
 

diff --git a/3DHistoGrading/Components/Interaction.cs b/3DHistoGrading/Components/Interaction.cs
@@ -0,0 +1,52 @@
+using System;
+using System.IO;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+using Kitware.VTK;
+
+namespace HistoGrading.Components
+{
+    class Interaction
+    {
+        //Declarations
+        static vtkRenderWindow renWin;
+
+        //Public methods
+        public void set_renderer(vtkRenderWindow input_renwin)
+        {
+            renWin = input_renwin;
+        }
+        public vtkRenderWindowInteractor coordinate_interactor()
+        {
+            //Declare new interactor style
+            vtkInteractorStyle interactorSyle = vtkInteractorStyle.New();
+
+            //Set new mouse events
+            interactorSyle.LeftButtonPressEvt += null;
+            interactorSyle.LeftButtonReleaseEvt += new vtkObject.vtkObjectEventHandler(get_coordinates);
+
+            //Create new interactor
+            vtkRenderWindowInteractor interactor = vtkRenderWindowInteractor.New();
+            interactor.SetInteractorStyle(interactorSyle);
+
+            return interactor;
+        }
+
+        //Interactors
+        private static void get_coordinates(vtkObject sender, vtkObjectEventArgs e)
+        {
+            int[] cur = renWin.GetPosition();
+            string txt = "";
+            foreach(int num in cur)
+            {
+                txt += System.String.Format("{0}",num);
+                txt += "|";
+            }
+            StreamWriter file = new StreamWriter(@"C:\\users\\jfrondel\\desktop\\GITS\\VTKOUTPUT.txt");
+            file.WriteLine(txt);
+        }
+    }
+}
diff --git a/3DHistoGrading/Components/Rendering.cs b/3DHistoGrading/Components/Rendering.cs
@@ -159,7 +159,7 @@ public void connectMask(vtkImageData mask)
             }
         }
 
-        public class imagePipeLine
+        private class imagePipeLine
         {
             //Image variables
             private vtkImageActor actor = vtkImageActor.New();
@@ -446,5 +446,6 @@ public int[] getDims()
             }
 
         }
+
     }
 }
diff --git a/3DHistoGrading/MainForm.Designer.cs b/3DHistoGrading/MainForm.Designer.cs
diff --git a/3DHistoGrading/MainForm.cs b/3DHistoGrading/MainForm.cs
@@ -426,5 +426,11 @@ private void gminBar_Scroll(object sender, ScrollEventArgs e)
                 gminBar_ValueChanged(this, null);
             }
         }
+
+
+        //New Functions
+        private void voiButton_Click(object sender, EventArgs e)
+        {
+        }
     }
 }
diff --git a/CNTKIntegration/CNTKIntegration.sln b/CNTKIntegration/CNTKIntegration.sln
@@ -0,0 +1,31 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 15
+VisualStudioVersion = 15.0.27428.2015
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "CNTKIntegration", "CNTKIntegration\CNTKIntegration.csproj", "{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Debug|x64 = Debug|x64
+		Release|Any CPU = Release|Any CPU
+		Release|x64 = Release|x64
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Debug|x64.ActiveCfg = Debug|x64
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Debug|x64.Build.0 = Debug|x64
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Release|Any CPU.Build.0 = Release|Any CPU
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Release|x64.ActiveCfg = Release|x64
+		{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}.Release|x64.Build.0 = Release|x64
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {7361E0DF-AC8E-4D38-9310-21114107E1CE}
+	EndGlobalSection
+EndGlobal
diff --git a/CNTKIntegration/CNTKIntegration/App.config b/CNTKIntegration/CNTKIntegration/App.config
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+    <startup> 
+        <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6.1" />
+    </startup>
+</configuration>
diff --git a/CNTKIntegration/CNTKIntegration/CNTKIntegration.csproj b/CNTKIntegration/CNTKIntegration/CNTKIntegration.csproj
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\build\OpenCvSharp3-AnyCPU.props" Condition="Exists('..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\build\OpenCvSharp3-AnyCPU.props')" />
+  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+    <ProjectGuid>{DF287675-FBD0-4E44-AC82-7A5B3DC9F5B5}</ProjectGuid>
+    <OutputType>Exe</OutputType>
+    <RootNamespace>CNTKIntegration</RootNamespace>
+    <AssemblyName>CNTKIntegration</AssemblyName>
+    <TargetFrameworkVersion>v4.6.1</TargetFrameworkVersion>
+    <FileAlignment>512</FileAlignment>
+    <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
+    <NuGetPackageImportStamp>
+    </NuGetPackageImportStamp>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+    <PlatformTarget>AnyCPU</PlatformTarget>
+    <DebugSymbols>true</DebugSymbols>
+    <DebugType>full</DebugType>
+    <Optimize>false</Optimize>
+    <OutputPath>bin\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+    <PlatformTarget>AnyCPU</PlatformTarget>
+    <DebugType>pdbonly</DebugType>
+    <Optimize>true</Optimize>
+    <OutputPath>bin\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|x64'">
+    <DebugSymbols>true</DebugSymbols>
+    <OutputPath>bin\x64\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <DebugType>full</DebugType>
+    <PlatformTarget>x64</PlatformTarget>
+    <ErrorReport>prompt</ErrorReport>
+    <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>true</Prefer32Bit>
+  </PropertyGroup>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Release|x64'">
+    <OutputPath>bin\x64\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <Optimize>true</Optimize>
+    <DebugType>pdbonly</DebugType>
+    <PlatformTarget>x64</PlatformTarget>
+    <ErrorReport>prompt</ErrorReport>
+    <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>true</Prefer32Bit>
+  </PropertyGroup>
+  <ItemGroup>
+    <Reference Include="Cntk.Core.Managed-2.5.1, Version=1.0.0.0, Culture=neutral, PublicKeyToken=21fff2ec8197defe, processorArchitecture=AMD64">
+      <HintPath>..\packages\CNTK.CPUOnly.2.5.1\lib\net45\x64\Cntk.Core.Managed-2.5.1.dll</HintPath>
+    </Reference>
+    <Reference Include="Kitware.mummy.Runtime, Version=1.0.2.599, Culture=neutral, PublicKeyToken=995c7fb9db2c1b44, processorArchitecture=AMD64">
+      <HintPath>..\packages\Activiz.NET.x64.5.8.0\lib\net20\Kitware.mummy.Runtime.dll</HintPath>
+    </Reference>
+    <Reference Include="Kitware.VTK, Version=5.8.0.607, Culture=neutral, PublicKeyToken=995c7fb9db2c1b44, processorArchitecture=AMD64">
+      <HintPath>..\packages\Activiz.NET.x64.5.8.0\lib\net20\Kitware.VTK.dll</HintPath>
+    </Reference>
+    <Reference Include="OpenCvSharp, Version=1.0.0.0, Culture=neutral, PublicKeyToken=6adad1e807fea099, processorArchitecture=MSIL">
+      <HintPath>..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\lib\net46\OpenCvSharp.dll</HintPath>
+    </Reference>
+    <Reference Include="OpenCvSharp.Blob, Version=1.0.0.0, Culture=neutral, PublicKeyToken=6adad1e807fea099, processorArchitecture=MSIL">
+      <HintPath>..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\lib\net46\OpenCvSharp.Blob.dll</HintPath>
+    </Reference>
+    <Reference Include="OpenCvSharp.Extensions, Version=1.0.0.0, Culture=neutral, PublicKeyToken=6adad1e807fea099, processorArchitecture=MSIL">
+      <HintPath>..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\lib\net46\OpenCvSharp.Extensions.dll</HintPath>
+    </Reference>
+    <Reference Include="OpenCvSharp.UserInterface, Version=1.0.0.0, Culture=neutral, PublicKeyToken=6adad1e807fea099, processorArchitecture=MSIL">
+      <HintPath>..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\lib\net46\OpenCvSharp.UserInterface.dll</HintPath>
+    </Reference>
+    <Reference Include="System" />
+    <Reference Include="System.Core" />
+    <Reference Include="System.Drawing" />
+    <Reference Include="System.Xml.Linq" />
+    <Reference Include="System.Data.DataSetExtensions" />
+    <Reference Include="Microsoft.CSharp" />
+    <Reference Include="System.Data" />
+    <Reference Include="System.Net.Http" />
+    <Reference Include="System.Xml" />
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="Components\DataTypes.cs" />
+    <Compile Include="Components\Functions.cs" />
+    <Compile Include="Models\UNet.cs" />
+    <Compile Include="Program.cs" />
+    <Compile Include="Properties\AssemblyInfo.cs" />
+  </ItemGroup>
+  <ItemGroup>
+    <None Include="App.config" />
+    <None Include="packages.config" />
+  </ItemGroup>
+  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <Import Project="..\packages\CNTK.Deps.MKL.2.5.1\build\net45\CNTK.Deps.MKL.targets" Condition="Exists('..\packages\CNTK.Deps.MKL.2.5.1\build\net45\CNTK.Deps.MKL.targets')" />
+  <Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
+    <PropertyGroup>
+      <ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them.  For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
+    </PropertyGroup>
+    <Error Condition="!Exists('..\packages\CNTK.Deps.MKL.2.5.1\build\net45\CNTK.Deps.MKL.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\CNTK.Deps.MKL.2.5.1\build\net45\CNTK.Deps.MKL.targets'))" />
+    <Error Condition="!Exists('..\packages\CNTK.Deps.OpenCV.Zip.2.5.1\build\net45\CNTK.Deps.OpenCV.Zip.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\CNTK.Deps.OpenCV.Zip.2.5.1\build\net45\CNTK.Deps.OpenCV.Zip.targets'))" />
+    <Error Condition="!Exists('..\packages\CNTK.CPUOnly.2.5.1\build\net45\CNTK.CPUOnly.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\CNTK.CPUOnly.2.5.1\build\net45\CNTK.CPUOnly.targets'))" />
+    <Error Condition="!Exists('..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\build\OpenCvSharp3-AnyCPU.props')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\OpenCvSharp3-AnyCPU.3.4.1.20180830\build\OpenCvSharp3-AnyCPU.props'))" />
+  </Target>
+  <Import Project="..\packages\CNTK.Deps.OpenCV.Zip.2.5.1\build\net45\CNTK.Deps.OpenCV.Zip.targets" Condition="Exists('..\packages\CNTK.Deps.OpenCV.Zip.2.5.1\build\net45\CNTK.Deps.OpenCV.Zip.targets')" />
+  <Import Project="..\packages\CNTK.CPUOnly.2.5.1\build\net45\CNTK.CPUOnly.targets" Condition="Exists('..\packages\CNTK.CPUOnly.2.5.1\build\net45\CNTK.CPUOnly.targets')" />
+</Project>
diff --git a/CNTKIntegration/CNTKIntegration/Components/DataTypes.cs b/CNTKIntegration/CNTKIntegration/Components/DataTypes.cs
@@ -0,0 +1,100 @@
+using System;
+using System.IO;
+using System.Drawing;
+using System.Runtime.InteropServices;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Kitware.VTK;
+using OpenCvSharp;
+using OpenCvSharp.Extensions;
+
+namespace CNTKIntegration.Components
+{
+    class DataTypes
+    {
+        //3D byte array to vtkimagedata
+        public static vtkImageData byteToVTK(byte[,,] data)
+        {
+            //Get input dimensions
+            int[] dims = new int[] { data.GetLength(0), data.GetLength(1), data.GetLength(2) };
+            //Create VTK data for putput
+            vtkImageData vtkdata = vtkImageData.New();
+            //Character array for conversion
+            vtkUnsignedCharArray charArray = vtkUnsignedCharArray.New();
+            //Pin byte array
+            GCHandle pinnedArray = GCHandle.Alloc(data, GCHandleType.Pinned);
+            //Set character array input
+            charArray.SetArray(pinnedArray.AddrOfPinnedObject(), dims[0] * dims[1] * dims[2], 1);
+            //Set vtkdata properties and connect array
+            //Data from char array
+            vtkdata.GetPointData().SetScalars(charArray);
+            //Number of scalars/pixel
+            vtkdata.SetNumberOfScalarComponents(1);
+            //Data extent, 1st and last axis are swapped from the char array
+            //Data is converted back to original orientation
+            vtkdata.SetExtent(0, dims[0] - 1, 0, dims[1] - 1, 0, dims[2] - 1);
+            //Scalar type
+            vtkdata.SetScalarTypeToUnsignedChar();
+            vtkdata.Update();
+
+            //Return vtk data
+            return vtkdata;
+        }
+
+        //vtkimagedata to 1d byte array
+        public static byte[] vtkToByte(vtkImageData vtkdata)
+        {
+            //Get vtk data dimensions
+            int[] extent = vtkdata.GetExtent();
+            int[] dims = new int[] { extent[1] - extent[0], extent[3] - extent[2], extent[5] - extent[4] };
+            //New byte array for conversions
+            byte[] bytedata = new byte[dims[0] * dims[1] * dims[2]];
+            //pin bytedata to memory
+            GCHandle pinnedArray = GCHandle.Alloc(bytedata, GCHandleType.Pinned);
+            //Get pointer to pinned array
+            IntPtr ptr = pinnedArray.AddrOfPinnedObject();
+            //VTK exporter
+            vtkImageExport exporter = vtkImageExport.New();
+            //Connect input data to exporter
+            exporter.SetInput(vtkdata);
+            exporter.Update();
+            //Export data to byte array
+            exporter.Export(ptr);
+            //Free pinned array
+            pinnedArray.Free();
+            //Return byte array
+            return bytedata;
+        }
+
+        //byte array to float
+        public static float[] byteToFloat(byte[] bytedata, float mu = (float)0, float sd = (float)0)
+        {
+            //Empty array for putput
+            float[] floatdata = new float[bytedata.Length];
+
+            //Iterate over bytedata
+            Parallel.For(0,bytedata.Length, k =>
+            {
+                //If normalization parameters are not give, return bytedata cast as float data
+                if (mu == 0)
+                {
+                    floatdata[k] = (float)bytedata[k];
+                }
+                //Otherwise normalize data
+                else
+                {
+                    floatdata[k] = (float)bytedata[k]-mu;
+                    if (sd != 0)
+                    {
+                        floatdata[k] /= sd;
+                    }
+                }
+            });
+
+            //return float data
+            return floatdata;
+        }
+    }
+}
-Original file line number
+Diff line change
@@ Expand Up @@
                 //slicer.Update();
                 //Return copy of the slice
                 return permuter.GetOutput();
             }
@@ Expand Down @@