diff --git a/czi-format/inspector/czi-inspector.sln b/czi-format/inspector/czi-inspector.sln
index 55ae1e4dfaedb83e549c65dfa88045bb3f2d0e2c..fa68d0df1f7ad1cdceadb17829c3e18b73426a42 100644
--- a/czi-format/inspector/czi-inspector.sln
+++ b/czi-format/inspector/czi-inspector.sln
@@ -3,7 +3,7 @@ Microsoft Visual Studio Solution File, Format Version 12.00
# Visual Studio 15
VisualStudioVersion = 15.0.28307.168
MinimumVisualStudioVersion = 10.0.40219.1
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "czi-inspector", "czi-inspector\czi-inspector.csproj", "{CC796EBE-77A0-442F-A44F-0863E03B2F54}"
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "czi-inspector", "czi-inspector\czi-inspector.csproj", "{22AC8E5E-5E7C-482E-B600-B1B2E7B93143}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
@@ -11,15 +11,15 @@ Global
Release|Any CPU = Release|Any CPU
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {CC796EBE-77A0-442F-A44F-0863E03B2F54}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
- {CC796EBE-77A0-442F-A44F-0863E03B2F54}.Debug|Any CPU.Build.0 = Debug|Any CPU
- {CC796EBE-77A0-442F-A44F-0863E03B2F54}.Release|Any CPU.ActiveCfg = Release|Any CPU
- {CC796EBE-77A0-442F-A44F-0863E03B2F54}.Release|Any CPU.Build.0 = Release|Any CPU
+ {22AC8E5E-5E7C-482E-B600-B1B2E7B93143}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+ {22AC8E5E-5E7C-482E-B600-B1B2E7B93143}.Debug|Any CPU.Build.0 = Debug|Any CPU
+ {22AC8E5E-5E7C-482E-B600-B1B2E7B93143}.Release|Any CPU.ActiveCfg = Release|Any CPU
+ {22AC8E5E-5E7C-482E-B600-B1B2E7B93143}.Release|Any CPU.Build.0 = Release|Any CPU
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
GlobalSection(ExtensibilityGlobals) = postSolution
- SolutionGuid = {E88F4F44-F469-4F79-B35D-08A631D14253}
+ SolutionGuid = {A64E8A42-D10C-4B53-AF19-A5717B0F97DF}
EndGlobalSection
EndGlobal
diff --git a/czi-format/inspector/czi-inspector/App.config b/czi-format/inspector/czi-inspector/App.config
new file mode 100644
index 0000000000000000000000000000000000000000..56efbc7b5f15b5166cc89dae0406895b57de0b67
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/App.config
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+ <startup>
+ <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.7.2" />
+ </startup>
+</configuration>
\ No newline at end of file
diff --git a/czi-format/inspector/czi-inspector/CziFile.cs b/czi-format/inspector/czi-inspector/CziFile.cs
new file mode 100644
index 0000000000000000000000000000000000000000..21807645950f1addf3ca1dd8791d694cba17d1cb
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/CziFile.cs
@@ -0,0 +1,14 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace czi_inspector
+{
+ class CziFile
+ {
+ public bool IsMasterFile => (Header.FilePart == 0) && (Header.MasterFileGuid == Header.FileGuid);
+ public CziFileHeader Header { get; set; } = new CziFileHeader();
+ }
+}
diff --git a/czi-format/inspector/czi-inspector/CziFileHeader.cs b/czi-format/inspector/czi-inspector/CziFileHeader.cs
new file mode 100644
index 0000000000000000000000000000000000000000..db8a3af21bd0a8f97d49c628f33142a353094552
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/CziFileHeader.cs
@@ -0,0 +1,18 @@
+namespace czi_inspector
+{
+ class CziFileHeader
+ {
+ public SegmentHeader Header { get; set; }
+
+ public int MajorVersion { get; set; }
+ public int MinorVersion { get; set; }
+ public string MasterFileGuid { get; set; }
+ public string FileGuid { get; set; }
+
+ public int FilePart { get; set; }
+ public long DirectoryPosition { get; set; }
+ public long MetadataPosition { get; set; }
+ public bool UpdatePending { get; set; }
+ public long AttachmentDirectoryPosition { get; set; }
+ }
+}
diff --git a/czi-format/inspector/czi-inspector/CziParser.cs b/czi-format/inspector/czi-inspector/CziParser.cs
new file mode 100644
index 0000000000000000000000000000000000000000..97deb37a9f7fefdc91199b67153cd1539d143023
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/CziParser.cs
@@ -0,0 +1,103 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace czi_inspector
+{
+ class CziParser
+ {
+ const int SegmentHeaderSize = 32;
+ const int FileHeaderSegmentSize = SegmentHeaderSize + 80;
+ const int IntSize = 4;
+ const int BoolSize = 4;
+ const int LongSize = 8;
+ const int GuidSize = 16;
+
+ private int _bufferOffset = 0;
+
+
+ public CziParser()
+ {
+
+ }
+
+ public CziFile Parse(string file)
+ {
+ CziFile result = new CziFile();
+
+ byte[] buffer;
+ using (FileStream fileStream = new FileStream(file, FileMode.Open, FileAccess.Read))
+ {
+ using (BinaryReader reader = new BinaryReader(fileStream))
+ {
+ buffer = new byte[FileHeaderSegmentSize];
+ reader.Read(buffer, 0, FileHeaderSegmentSize);
+ result.Header = ParseFileHeader(buffer);
+
+ fileStream.Seek(result.Header.MetadataPosition, SeekOrigin.Begin);
+ buffer = new byte[10000];
+ reader.Read(buffer, 0, 10000);
+ ParseMetadata(buffer);
+ }
+ }
+
+ return result;
+ }
+
+ private void ParseMetadata(byte[] buffer)
+ {
+ SegmentHeader metadataHeader = ParseSegmentHeader(buffer);
+ byte[] metadata = new byte[metadataHeader.UsedSize];
+ Array.Copy(buffer, _bufferOffset, metadata, 0, metadataHeader.UsedSize);
+
+ Console.WriteLine(Encoding.UTF8.GetString(metadata));
+ }
+
+ private CziFileHeader ParseFileHeader(byte[] buffer)
+ {
+ CziFileHeader fileHeader = new CziFileHeader();
+ fileHeader.Header = ParseSegmentHeader(buffer);
+
+ fileHeader.MajorVersion = BitConverter.ToInt32(buffer, _bufferOffset);
+ _bufferOffset += IntSize;
+ fileHeader.MinorVersion = BitConverter.ToInt32(buffer, _bufferOffset);
+ _bufferOffset += IntSize;
+ _bufferOffset += 8; // 8 Bytes are reserved.
+
+ fileHeader.MasterFileGuid = BitConverter.ToString(buffer, _bufferOffset, 16);
+ _bufferOffset += GuidSize;
+ fileHeader.FileGuid = BitConverter.ToString(buffer, _bufferOffset, 16);
+ _bufferOffset += GuidSize;
+ fileHeader.FilePart = BitConverter.ToInt32(buffer, _bufferOffset);
+ _bufferOffset += IntSize;
+ fileHeader.DirectoryPosition = BitConverter.ToInt64(buffer, _bufferOffset);
+ _bufferOffset += LongSize;
+ fileHeader.MetadataPosition = BitConverter.ToInt64(buffer, _bufferOffset);
+ _bufferOffset += LongSize;
+ fileHeader.UpdatePending = BitConverter.ToBoolean(buffer, _bufferOffset);
+ _bufferOffset += BoolSize;
+ fileHeader.AttachmentDirectoryPosition = BitConverter.ToInt32(buffer, _bufferOffset);
+ _bufferOffset += IntSize;
+
+ return fileHeader;
+ }
+
+ private SegmentHeader ParseSegmentHeader(byte[] buffer)
+ {
+ Utils.Assert(buffer.Length >= (16 + 8 + 8));
+
+ SegmentHeader header = new SegmentHeader
+ {
+ Id = Encoding.UTF8.GetString(buffer, 0, 16).RemoveNullCharacters(),
+ AllocatedSize = BitConverter.ToInt64(buffer, 16),
+ UsedSize = BitConverter.ToInt64(buffer, 24)
+ };
+
+ _bufferOffset += SegmentHeaderSize;
+ return header;
+ }
+ }
+}
diff --git a/czi-format/inspector/czi-inspector/Program.cs b/czi-format/inspector/czi-inspector/Program.cs
index 04d40e5d48449e536d26fdb412be152377a2e676..fdb53d0e723ea27982b411f959739ea64896306b 100644
--- a/czi-format/inspector/czi-inspector/Program.cs
+++ b/czi-format/inspector/czi-inspector/Program.cs
@@ -10,45 +10,12 @@ namespace czi_inspector
{
static void Main(string[] args)
{
- string file = args[0];
- string substring = args[1];
- string encoding = args[2];
- Regex regex = new Regex(substring, RegexOptions.IgnoreCase);
- Encoding selectedEncoding = GetEncoding(encoding);
-
- const int bufferSize = 1024;
- byte[] buffer = new byte[bufferSize];
- int count = 0;
- Stopwatch stopwatch = new Stopwatch();
- stopwatch.Start();
-
- //var wholeFileBuffer = File.ReadAllBytes(file);
- //string wholeFileString = selectedEncoding.GetString(wholeFileBuffer);
- //count = regex.Matches(substring).Count;
- using (FileStream reader = new FileStream(file, FileMode.Open, FileAccess.Read))
+ if (args.Length < 1)
{
- while (reader.Read(buffer, 0, bufferSize) > 0)
- {
- string bufferString = selectedEncoding.GetString(buffer);
- var matches = regex.Matches(bufferString).Count;
- count += matches;
- if (matches > 0)
- Console.WriteLine(bufferString);
- }
+ Console.WriteLine("Wrong method or operand...");
+ return;
}
- stopwatch.Stop();
- Console.WriteLine("Found: {0} occurencies of {1} in file {2} in {3} ms.", count, substring, file, stopwatch.Elapsed.TotalMilliseconds);
-
- }
-
- private static Encoding GetEncoding(string encoding)
- {
- encoding = encoding.ToUpper();
- if (encoding == "ASCII") return Encoding.ASCII;
- if (encoding == "UTF8") return Encoding.UTF8;
- if (encoding == "UNICODE") return Encoding.Unicode;
- if (encoding == "UTF32") return Encoding.UTF32;
- throw new Exception("Try different encoding, currently supported: ASCII, UTF8, UTF32, UNICODE.");
+ CziFile parsed = new CziParser().Parse(args[0]);
}
}
}
diff --git a/czi-format/inspector/czi-inspector/Properties/AssemblyInfo.cs b/czi-format/inspector/czi-inspector/Properties/AssemblyInfo.cs
new file mode 100644
index 0000000000000000000000000000000000000000..d2879dc61a2a28ef4827ab6487b3632b0f63300d
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/Properties/AssemblyInfo.cs
@@ -0,0 +1,36 @@
+using System.Reflection;
+using System.Runtime.CompilerServices;
+using System.Runtime.InteropServices;
+
+// General Information about an assembly is controlled through the following
+// set of attributes. Change these attribute values to modify the information
+// associated with an assembly.
+[assembly: AssemblyTitle("czi-inspector")]
+[assembly: AssemblyDescription("")]
+[assembly: AssemblyConfiguration("")]
+[assembly: AssemblyCompany("")]
+[assembly: AssemblyProduct("czi-inspector")]
+[assembly: AssemblyCopyright("Copyright © 2019")]
+[assembly: AssemblyTrademark("")]
+[assembly: AssemblyCulture("")]
+
+// Setting ComVisible to false makes the types in this assembly not visible
+// to COM components. If you need to access a type in this assembly from
+// COM, set the ComVisible attribute to true on that type.
+[assembly: ComVisible(false)]
+
+// The following GUID is for the ID of the typelib if this project is exposed to COM
+[assembly: Guid("22ac8e5e-5e7c-482e-b600-b1b2e7b93143")]
+
+// Version information for an assembly consists of the following four values:
+//
+// Major Version
+// Minor Version
+// Build Number
+// Revision
+//
+// You can specify all the values or you can default the Build and Revision Numbers
+// by using the '*' as shown below:
+// [assembly: AssemblyVersion("1.0.*")]
+[assembly: AssemblyVersion("1.0.0.0")]
+[assembly: AssemblyFileVersion("1.0.0.0")]
diff --git a/czi-format/inspector/czi-inspector/SegmentHeader.cs b/czi-format/inspector/czi-inspector/SegmentHeader.cs
new file mode 100644
index 0000000000000000000000000000000000000000..f9ed30b751b081f8bd5f1f4d0b25d139b56fe314
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/SegmentHeader.cs
@@ -0,0 +1,9 @@
+namespace czi_inspector
+{
+ public class SegmentHeader
+ {
+ public string Id { get; set; }
+ public long AllocatedSize { get; set; }
+ public long UsedSize { get; set; }
+ }
+}
diff --git a/czi-format/inspector/czi-inspector/Utils.cs b/czi-format/inspector/czi-inspector/Utils.cs
new file mode 100644
index 0000000000000000000000000000000000000000..7783156cc856f86eaee71e8a3778406457c589f8
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/Utils.cs
@@ -0,0 +1,16 @@
+using System;
+using System.Collections.Generic;
+using System.Diagnostics;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace czi_inspector
+{
+ internal static class Utils
+ {
+ internal static string RemoveNullCharacters(this string src) => src.Replace("\0", string.Empty);
+
+ internal static void Assert(bool exp) => Trace.Assert(exp);
+ }
+}
diff --git a/czi-format/inspector/czi-inspector/czi-inspector.csproj b/czi-format/inspector/czi-inspector/czi-inspector.csproj
index 68783fa7bd0fbea2c2ab063e839a1b8c9ea23f77..cd7f98ffae80a27530b57346d91abf348733a374 100644
--- a/czi-format/inspector/czi-inspector/czi-inspector.csproj
+++ b/czi-format/inspector/czi-inspector/czi-inspector.csproj
@@ -1,9 +1,58 @@
-<Project Sdk="Microsoft.NET.Sdk">
-
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <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>{22AC8E5E-5E7C-482E-B600-B1B2E7B93143}</ProjectGuid>
<OutputType>Exe</OutputType>
- <TargetFramework>netcoreapp2.1</TargetFramework>
<RootNamespace>czi_inspector</RootNamespace>
+ <AssemblyName>czi-inspector</AssemblyName>
+ <TargetFrameworkVersion>v4.7.2</TargetFrameworkVersion>
+ <FileAlignment>512</FileAlignment>
+ <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
+ <Deterministic>true</Deterministic>
</PropertyGroup>
-
-</Project>
+ <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>
+ <ItemGroup>
+ <Reference Include="System" />
+ <Reference Include="System.Core" />
+ <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="CziFile.cs" />
+ <Compile Include="CziFileHeader.cs" />
+ <Compile Include="CziParser.cs" />
+ <Compile Include="Program.cs" />
+ <Compile Include="Properties\AssemblyInfo.cs" />
+ <Compile Include="SegmentHeader.cs" />
+ <Compile Include="Utils.cs" />
+ </ItemGroup>
+ <ItemGroup>
+ <None Include="App.config" />
+ </ItemGroup>
+ <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+</Project>
\ No newline at end of file
diff --git a/czi-format/inspector/czi-inspector/czi-inspector.csproj.user b/czi-format/inspector/czi-inspector/czi-inspector.csproj.user
new file mode 100644
index 0000000000000000000000000000000000000000..d7496f1176cc96f8f1509cfb62a6de3f9b242e1f
--- /dev/null
+++ b/czi-format/inspector/czi-inspector/czi-inspector.csproj.user
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Release|AnyCPU'">
+ <StartArguments>--dump data\CZT-Stack-Anno.czi cztstackdump.txt</StartArguments>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|AnyCPU'">
+ <StartArguments>data\CZT-Stack-Anno.czi</StartArguments>
+ </PropertyGroup>
+</Project>
\ No newline at end of file