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Tile Cache Fix.
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@BiologyTools
BiologyTools committed Apr 21, 2024
1 parent b60f463 commit 75dc4c2
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Showing 2 changed files with 50 additions and 35 deletions.
8 changes: 4 additions & 4 deletions BioCore/BioCore.csproj
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<PropertyGroup>
<TargetFramework>net8.0-windows</TargetFramework>
<Nullable>enable</Nullable>
<Version>4.0.0</Version>
<Version>4.0.1</Version>
<UseWindowsForms>true</UseWindowsForms>
<ImplicitUsings>enable</ImplicitUsings>
<AllowUnsafeBlocks>True</AllowUnsafeBlocks>
Expand All @@ -23,9 +23,9 @@
<PackageId>BioCore</PackageId>
<Platforms>AnyCPU;x86;x64</Platforms>
<Description>A .NET library &amp; program for annotating, &amp; editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal &amp; series.</Description>
<AssemblyVersion>4.0.0</AssemblyVersion>
<FileVersion>4.0.0</FileVersion>
<PackageReleaseNotes>.NET8 update.</PackageReleaseNotes>
<AssemblyVersion>4.0.1</AssemblyVersion>
<FileVersion>4.0.1</FileVersion>
<PackageReleaseNotes>Tile Cache Fix.</PackageReleaseNotes>
</PropertyGroup>

<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">
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77 changes: 46 additions & 31 deletions BioCore/Source/Bio/ISlideSource.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,30 +10,38 @@
using AForge;
namespace BioCore
{
public class LruCache<TKey, TValue>
public class LruCache<TileInformation, TValue>
{
public class Info
{
public ZCT Coordinate { get; set; }
public TileIndex Index { get; set; }
}
private readonly int capacity;
private Dictionary<TKey, LinkedListNode<(TKey key, TValue value)>> cacheMap = new Dictionary<TKey, LinkedListNode<(TKey key, TValue value)>>();
private LinkedList<(TKey key, TValue value)> lruList = new LinkedList<(TKey key, TValue value)>();
private Dictionary<Info, LinkedListNode<(Info key, TValue value)>> cacheMap = new Dictionary<Info, LinkedListNode<(Info key, TValue value)>>();
private LinkedList<(Info key, TValue value)> lruList = new LinkedList<(Info key, TValue value)>();

public LruCache(int capacity)
{
this.capacity = capacity;
}

public TValue Get(TKey key)
public TValue Get(Info key)
{
if (cacheMap.TryGetValue(key, out var node))
foreach (LinkedListNode<(Info key, TValue value)> item in cacheMap.Values)
{
lruList.Remove(node);
lruList.AddLast(node);
return node.Value.value;
Info k = item.Value.key;
if(k.Coordinate == key.Coordinate && k.Index == key.Index)
{
lruList.Remove(item);
lruList.AddLast(item);
return item.Value.value;
}
}

return default(TValue);
}

public void Add(TKey key, TValue value)
public void Add(Info key, TValue value)
{
if (cacheMap.Count >= capacity)
{
Expand All @@ -50,41 +58,48 @@ public void Add(TKey key, TValue value)
lruList.Remove(cacheMap[key]);
}

var newNode = new LinkedListNode<(TKey key, TValue value)>((key, value));
var newNode = new LinkedListNode<(Info key, TValue value)>((key, value));
lruList.AddLast(newNode);
cacheMap[key] = newNode;
}
}
public class TileCache
{
private LruCache<TileInfo, byte[]> cache;
private LruCache<TileInformation, byte[]> cache;
private int capacity;
SlideSourceBase source = null;
public TileCache(SlideSourceBase source, int capacity = 10000)
public TileCache(SlideSourceBase source, int capacity = 1000)
{
this.source = source;
this.capacity = capacity;
this.cache = new LruCache<TileInfo, byte[]>(capacity);
this.cache = new LruCache<TileInformation, byte[]>(capacity);
}

public async Task<byte[]> GetTile(TileInfo info)
public async Task<byte[]> GetTile(TileInformation info)
{
byte[] data = cache.Get(info);
LruCache<TileInformation, byte[]>.Info inf = new LruCache<TileInformation, byte[]>.Info();
inf.Coordinate = info.Coordinate;
inf.Index = info.Index;
byte[] data = cache.Get(inf);
if (data != null)
{
return data;
}
byte[] tile = await LoadTile(info);
if(tile!=null)
AddTile(info, tile);
return tile;
}

private void AddTile(TileInfo tileId, byte[] tile)
private void AddTile(TileInformation tileId, byte[] tile)
{
cache.Add(tileId, tile);
LruCache<TileInformation, byte[]>.Info inf = new LruCache<TileInformation, byte[]>.Info();
inf.Coordinate = tileId.Coordinate;
inf.Index = tileId.Index;
cache.Add(inf, tile);
}

private async Task<byte[]> LoadTile(TileInfo tileId)
private async Task<byte[]> LoadTile(TileInformation tileId)
{
try
{
Expand All @@ -97,7 +112,7 @@ private async Task<byte[]> LoadTile(TileInfo tileId)
}
}

public class TileInfo
public class TileInformation
{
public TileIndex Index { get; set; }
public Extent Extent { get; set; }
Expand All @@ -124,7 +139,7 @@ public static void Resister(string extensionUpper, Func<string, bool, ISlideSour

public static ISlideSource Create(BioImage source, SlideImage im, bool enableCache = true)
{

var ext = Path.GetExtension(source.file).ToUpper();
try
{
Expand All @@ -134,12 +149,12 @@ public static ISlideSource Create(BioImage source, SlideImage im, bool enableCac
if (!string.IsNullOrEmpty(SlideBase.DetectVendor(source.file)))
{
SlideBase b = new SlideBase(source, im, enableCache);

}
}
catch (Exception e)
{
Console.WriteLine(e.Message);
catch (Exception e)
{
Console.WriteLine(e.Message);
}
return null;
}
Expand All @@ -161,13 +176,13 @@ public async Task<byte[]> GetSlice(SliceInfo sliceInfo)
List<Tuple<Extent, byte[]>> tiles = new List<Tuple<Extent, byte[]>>();
foreach (BruTile.TileInfo t in tileInfos)
{
TileInfo tf = new TileInfo();
TileInformation tf = new TileInformation();
tf.Extent = t.Extent;
tf.Coordinate = App.viewer.GetCoordinate();
tf.Index = t.Index;
byte[] c = await cache.GetTile(tf);
if (c != null)
tiles.Add(Tuple.Create(t.Extent.WorldToPixelInvertedY(curUnitsPerPixel), c));
if(c!=null)
tiles.Add(Tuple.Create(t.Extent.WorldToPixelInvertedY(curUnitsPerPixel), c));
}
var srcPixelExtent = sliceInfo.Extent.WorldToPixelInvertedY(curUnitsPerPixel);
var dstPixelExtent = sliceInfo.Extent.WorldToPixelInvertedY(sliceInfo.Resolution);
Expand Down Expand Up @@ -264,7 +279,7 @@ public void Dispose()
GC.SuppressFinalize(this);
}

public async Task<byte[]> GetTileAsync(TileInfo tileInfo)
public async Task<byte[]> GetTileAsync(TileInformation tileInfo)
{
if (tileInfo == null)
return null;
Expand All @@ -275,7 +290,7 @@ public async Task<byte[]> GetTileAsync(TileInfo tileInfo)
var curLevelOffsetYPixel = -tileInfo.Extent.MaxY / Schema.Resolutions[tileInfo.Index.Level].UnitsPerPixel;
var curTileWidth = (int)(tileInfo.Extent.MaxX > Schema.Extent.Width ? tileWidth - (tileInfo.Extent.MaxX - Schema.Extent.Width) / r : tileWidth);
var curTileHeight = (int)(-tileInfo.Extent.MinY > Schema.Extent.Height ? tileHeight - (-tileInfo.Extent.MinY - Schema.Extent.Height) / r : tileHeight);
var bgraData = await Image.ReadRegionAsync(tileInfo.Index.Level, (long)curLevelOffsetXPixel, (long)curLevelOffsetYPixel, curTileWidth, curTileHeight, tileInfo.Coordinate);
var bgraData = await Image.ReadRegionAsync(tileInfo.Index.Level, (long)curLevelOffsetXPixel, (long)curLevelOffsetYPixel, curTileWidth, curTileHeight,tileInfo.Coordinate);
//We check to see if the data is valid.
if (bgraData.Length != curTileWidth * curTileHeight * 4)
return null;
Expand Down Expand Up @@ -381,7 +396,7 @@ public SliceInfo() { }
/// <param name="unitsPerPixel">um/pixel</param>
public SliceInfo(double xPixel, double yPixel, double widthPixel, double heightPixel, double unitsPerPixel, ZCT coord)
{
Extent = new Extent(xPixel, yPixel, xPixel + widthPixel, yPixel + heightPixel).PixelToWorldInvertedY(unitsPerPixel);
Extent = new Extent(xPixel, yPixel, xPixel + widthPixel,yPixel + heightPixel).PixelToWorldInvertedY(unitsPerPixel);
Resolution = unitsPerPixel;
}

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