Upgrade libczicompressc to version 0.5.2 (#22)

* Upgrade libczicompressc to 0.5.2

* Adapt tests

* Use LFS for CZIs

Author: m-ringler

.gitattributes

@@ -2,3 +2,4 @@
 *.png filter=lfs diff=lfs merge=lfs -text
 *.nupkg filter=lfs diff=lfs merge=lfs -text
 *.pdf filter=lfs diff=lfs merge=lfs -text
+*.czi filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -431,4 +431,7 @@ FodyWeavers.xsd
 
 ##################################
 ### END VisualStudio.gitignore ###
-##################################
+##################################
+
+# Be able to commit local nupkg
+!czishrink/packages_local/*.nupkg

czishrink/Directory.Build.props

@@ -10,6 +10,6 @@
     <GenerateDocumentationFile>True</GenerateDocumentationFile>
     <TreatWarningsAsErrors>true</TreatWarningsAsErrors>
     <!-- Version -->
-    <VersionPrefix>1.0.1<!--fix/version-stuff--></VersionPrefix>
+    <VersionPrefix>1.0.2<!--feature/upgrade-libczicompressc-0_5_2--></VersionPrefix>
   </PropertyGroup>
-</Project>
+</Project>

czishrink/Directory.Packages.props

@@ -21,7 +21,7 @@
     <PackageVersion Include="DynamicData" Version="8.1.1" />
     <PackageVersion Include="FluentAssertions" Version="6.12.0" />
     <PackageVersion Include="Fody" Version="6.8.0" />
-    <PackageVersion Include="libczicompressc" Version="0.5.1-alpha.0" />
+    <PackageVersion Include="libczicompressc" Version="0.5.2" />
     <PackageVersion Include="MessageBox.Avalonia" Version="3.1.5.1" />
     <PackageVersion Include="Microsoft.NET.Test.Sdk" Version="17.8.0" />
     <PackageVersion Include="Microsoft.Extensions.Logging.Abstractions" Version="7.0.1" />
@@ -37,4 +37,4 @@
     <PackageVersion Include="xunit" Version="2.6.1" />
     <PackageVersion Include="xunit.runner.visualstudio" Version="2.5.3" />
   </ItemGroup>
-</Project>
+</Project>

czishrink/libczicompressc/libczicompressc.nuspec

@@ -2,7 +2,7 @@
 <package xmlns="http://schemas.microsoft.com/packaging/2013/05/nuspec.xsd">
   <metadata>
     <id>libczicompressc</id>
-    <version>0.5.1-alpha.0</version>
+    <version>0.5.2</version>
     <title>Native runtimes for CZI ZStd compression</title>
     <authors>Carl Zeiss Microscopy</authors>
     <owners>Carl Zeiss Microscopy</owners>
@@ -11,6 +11,6 @@
     <license type="expression">MIT</license>
     <projectUrl>https://github.com/zeissmicroscopy/czicompress/</projectUrl>
     <copyright>© Carl Zeiss Microscopy GmbH and others. All rights reserved.</copyright>
-    <repository type="git" url="https://github.com/ZEISS/czicompress" branch="main" commit="029973e80f064bce28b22122213e327037eef782" />
+    <repository type="git" url="https://github.com/ZEISS/czicompress" branch="main" commit="40a2ba8489544626c2481ca95177b3235b5c0de7" />
   </metadata>
 </package>

czishrink/netczicompressTests/Models/PInvokeFileProcessorTests.cs

@@ -5,6 +5,9 @@
 namespace netczicompressTests.Models;
 
 using System.Reactive.Disposables;
+using System.Text;
+using System.Xml.Linq;
+using System.Xml.XPath;
 
 /// <summary>
 /// Tests for <see cref="PInvokeFileProcessor"/>.
@@ -23,7 +26,7 @@ public void Ctr_WhenCalledWithNoOp_Throws()
     [InlineData(CompressionMode.CompressUncompressed)]
     [InlineData(CompressionMode.CompressAll)]
     [InlineData(CompressionMode.CompressUncompressedAndZstd)]
-    public void CompressAndDecompressOneFile_FilesHaveCorrectSize(
+    public void CompressAndDecompressOneFile_FilesHaveCorrectSizeAndMetadata(
         CompressionMode mode)
     {
         // ARRANGE
@@ -43,13 +46,17 @@ public void CompressAndDecompressOneFile_FilesHaveCorrectSize(
         decompressor.ProcessFile(compressed, uncompressed, _ => { }, CancellationToken.None);
 
         var compressedSize = GetLength(compressed);
+
         var decompressedSize = GetLength(uncompressed);
         var originalSize = GetLength(testFile);
 
         // ASSERT
-        compressedSize.Should().Be(58432L);
+        compressedSize.Should().Be(58528L);
         decompressedSize.Should().BeCloseTo(originalSize, 2048);
-        decompressedSize.Should().Be(99552L);
+        decompressedSize.Should().Be(99648L);
+
+        Metadata.FromFile(compressed).CurrentCompressionParameters.Should().Be("Lossless: True");
+        Metadata.FromFile(uncompressed).CurrentCompressionParameters.Should().BeEmpty();
     }
 
     [Theory]
@@ -114,9 +121,9 @@ public void GetLibFullName_WhenCalled_ReturnsExpected()
     }
 
     [Theory]
-    [InlineData(0, 99552L, 57760L)]
-    [InlineData(2, 99552L, 57920L)]
-    [InlineData(4, 99552L, 57472L)]
+    [InlineData(0, 99648L, 57856L)]
+    [InlineData(2, 99648L, 58016L)]
+    [InlineData(4, 99648L, 57568L)]
     public void CompressWithLevel_FilesHaveCorrectSize(
         int compressionLevel, long expectedUncompressedSize, long expectedCompressedSize)
     {
@@ -160,4 +167,50 @@ private static string GetTestFilePath()
         var testFile = Path.Combine(dirname ?? ".", "mandelbrot.czi");
         return testFile;
     }
+
+    private class Metadata
+    {
+        public required XDocument Xml { get; init; }
+
+        public string? CurrentCompressionParameters => this.Xml
+            .XPathSelectElement(
+                "ImageDocument/Metadata/Information/Image/CurrentCompressionParameters")
+            ?.Value;
+
+        public static Metadata FromFile(string path) => new() { Xml = ParseMetadataXml(path) };
+
+        private static XDocument ParseMetadataXml(string filePath)
+        {
+            return XDocument.Parse(ReadMetadataXml(filePath));
+        }
+
+        private static string ReadMetadataXml(string filePath)
+        {
+            // These numbers are from the ZISRAW file specification.
+            const int SegmentHeaderSize = 16 + 8 + 8;
+            const int MetadataPositionInFileHeader = 60;
+            const int MetadataHeaderSize = 256;
+
+            using var stream = File.OpenRead(filePath);
+
+            // BinaryReader uses little-endian as required.
+            using var reader = new BinaryReader(stream);
+
+            // Read metadataPosition from ZISRAW file header
+            stream.Position = SegmentHeaderSize + MetadataPositionInFileHeader;
+            long metadataHeaderPosition = reader.ReadInt64() + SegmentHeaderSize;
+
+            // Read size of XML from ZISRAWMETADATA header
+            stream.Position = metadataHeaderPosition;
+            int metadataSize = reader.ReadInt32();
+
+            // Read XML bytes from ZISRAWMETADATA segment
+            stream.Position = metadataHeaderPosition + MetadataHeaderSize;
+            var xmlBytes = reader.ReadBytes(metadataSize);
+
+            // Decode (always UTF-8 according to the spec)
+            var result = Encoding.UTF8.GetString(xmlBytes);
+            return result;
+        }
+    }
 }

czishrink/netczicompressTests/mandelbrot.czi

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ece5a42ad9d7af0f84d1d8fb14ed47bacb58a3d54c0acc17d06af1c8a278446c
+size 2031800