BioLib.SlideBase Class Reference

Inheritance diagram for BioLib.SlideBase:

Public Member Functions
	SlideBase (BioImage source, SlideImage im, bool enableCache=true)
void	RebuildSchemaForWell (BioImage b)
override IReadOnlyDictionary< string, byte[]>	GetExternImages ()
byte[]	GetTile (TileInfo tileInfo, ZCT coord)

Static Public Member Functions
static string	DetectVendor (string source)
static byte[]	ConvertRgbaToRgb (byte[] rgbaArray)

Public Attributes
readonly SlideImage	SlideImage

Protected Member Functions
void	InitResolutions (IDictionary< int, BruTile.Resolution > resolutions, int tileWidth, int tileHeight)
override void	Dispose (bool disposing)

Constructor & Destructor Documentation

SlideBase()

BioLib.SlideBase.SlideBase	(	BioImage	source,
		SlideImage	im,
		bool	enableCache = true )

        {
            Source = source.file;
            SlideImage = im;
            Image = im;
            double baseUnitsPerPixel = source.PhysicalSizeX > 0
                ? source.PhysicalSizeX
                : source.PhysicalSizeY > 0
                    ? source.PhysicalSizeY
                    : 1;
            MinUnitsPerPixel = UseRealResolution ? baseUnitsPerPixel : 1;
            if (MinUnitsPerPixel <= 0) MinUnitsPerPixel = 1;
            var height = SlideImage.Dimensions.Height;
            var width = SlideImage.Dimensions.Width;
            double stageX = 0;
            double stageY = 0;
            if (source.Resolutions != null && source.Resolutions.Count > 0)
            {
                stageX = source.Resolutions[0].StageSizeX;
                stageY = source.Resolutions[0].StageSizeY;
            }
            //ExternInfo = GetInfo();
            Schema = new TileSchema
            {
                YAxis = YAxis.OSM,
                Format = "jpg",
                Extent = new Extent(
                    stageX,
                    -(stageY + (height * MinUnitsPerPixel)),
                    stageX + (width * MinUnitsPerPixel),
                    -stageY),
                OriginX = stageX,
                OriginY = stageY,
            };
            InitResolutions(Schema.Resolutions, 256, 256);
        }

Member Function Documentation

ConvertRgbaToRgb()

static byte[] BioLib.SlideBase.ConvertRgbaToRgb ( byte[] rgbaArray )

static

        {
            // Initialize a new byte array for RGB24 format
            byte[] rgbArray = new byte[(rgbaArray.Length / 4) * 3];
 
            for (int i = 0, j = 0; i < rgbaArray.Length; i += 4, j += 3)
            {
                // Copy the R, G, B values, skip the A value
                rgbArray[j] = rgbaArray[i];     // B
                rgbArray[j + 1] = rgbaArray[i + 1]; // G
                rgbArray[j + 2] = rgbaArray[i + 2]; // R
            }
 
            return rgbArray;
        }

DetectVendor()

static string BioLib.SlideBase.DetectVendor ( string source )

static

        {
            return SlideImage.DetectVendor(source);
        }

Dispose()

override void BioLib.SlideBase.Dispose ( bool disposing )

protected

        {
            if (!disposedValue)
            {
                if (disposing)
                {
                    SlideImage.Dispose();
                }
                disposedValue = true;
            }
            base.Dispose(disposing);
        }

GetExternImages()

override IReadOnlyDictionary< string, byte[]> BioLib.SlideBase.GetExternImages

(

)

        {
            throw new NotImplementedException();
            /*
            Dictionary<string, byte[]> images = new Dictionary<string, byte[]>();
            var r = Math.Max(Schema.Extent.Height, Schema.Extent.Width) / 512;
            images.Add("preview", GetSlice(new SliceInfo { Extent = Schema.Extent, Resolution = r }));
            foreach (var item in SlideImage.GetAssociatedImages())
            {
                var dim = item.Value.Dimensions;
                images.Add(item.Key, ImageUtil.GetJpeg(item.Value.Data, 4, 4 * (int)dim.Width, (int)dim.Width, (int)dim.Height));
            }
            return images;
            */
        }

GetTile()

byte[] BioLib.SlideBase.GetTile	(	TileInfo	tileInfo,
		ZCT	coord )

        {
            try
            {
                if (Schema == null)
                {
                    Console.WriteLine("Schema is null.");
                    return null;
                }
                var r          = Schema.Resolutions[tileInfo.Index.Level].UnitsPerPixel;
                var tileWidth  = Schema.Resolutions[tileInfo.Index.Level].TileWidth;
                var tileHeight = Schema.Resolutions[tileInfo.Index.Level].TileHeight;
 
                // Tile extents are expressed in translated stage/world space, but
                // the underlying Zarr pixels still start at image-local 0,0.
                // Subtract the schema origin here so stage translation affects
                // placement only, not the pixel read offset.
                var schemaExtent = Schema.Extent;
 
                // Tile placement uses translated world-space extents, but the
                // underlying Zarr/OME pixels are still addressed on the tile grid.
                // Derive the read origin from the tile index so translation does
                // not introduce a fractional-pixel bias at the image edge.
                var curLevelOffsetXPixel = tileInfo.Index.Col * tileWidth;
                var curLevelOffsetYPixel = tileInfo.Index.Row * tileHeight;
 
                // Use actual level pixel dimensions from BioImage.
                int lev = tileInfo.Index.Level;
                var levelPixelW = (long)(lev < SlideImage.BioImage.Resolutions.Count
                    ? SlideImage.BioImage.Resolutions[lev].SizeX
                    : Math.Round(Schema.Extent.Width / r));
                var levelPixelH = (long)(lev < SlideImage.BioImage.Resolutions.Count
                    ? SlideImage.BioImage.Resolutions[lev].SizeY
                    : Math.Round(Schema.Extent.Height / r));
 
                long readX = (long)curLevelOffsetXPixel;
                long readY = (long)curLevelOffsetYPixel;
 
                int curTileWidth  = tileWidth;
                int curTileHeight = tileHeight;
 
                // Trim any part of the request that falls outside the image on
                // the left/top instead of asking the Zarr reader to pad with black.
                if (readX < 0)
                {
                    curTileWidth += (int)readX;
                    readX = 0;
                }
                if (readY < 0)
                {
                    curTileHeight += (int)readY;
                    readY = 0;
                }
 
                // Clamp tile read size so we never request pixels past the image boundary.
                curTileWidth  = (int)Math.Max(0, Math.Min(curTileWidth,  levelPixelW - readX));
                curTileHeight = (int)Math.Max(0, Math.Min(curTileHeight, levelPixelH - readY));
 
                // Guard against fully OOB tiles
                if (curTileWidth <= 0 || curTileHeight <= 0)
                {
                    return new byte[tileWidth * tileHeight * 4]; // black padded tile
                }
 
                if (SlideImage == null)
                {
                    Console.WriteLine("SlideImage is null.");
                    return null;
                }
 
                var bgraData = SlideImage.ReadRegion(
                    tileInfo.Index.Level, coord,
                    readX, readY,
                    curTileWidth, curTileHeight);
 
                if (bgraData == null || bgraData.Length == 0)
                    return null;
 
                int expectedSize = tileWidth * tileHeight * 4;
 
                // Full tile — return as-is.
                // Return the raw BGRA data (4 bytes/pixel) so the GL upload path
                // receives a buffer that matches PixelFormat.Bgra / PixelType.UnsignedByte.
                if (bgraData.Length == expectedSize)
                    return bgraData;
 
                // Edge tile: ReadRegion returned fewer pixels than a full tile because
                // this tile hangs off the image boundary. Pad into a full tileWidth x
                // tileHeight RGBA buffer (rows outside the image stay transparent/zeroed)
                // so the GL upload always receives a consistently-sized, correctly-strided
                // buffer and never reads past the end.
                int actualW = Math.Min(curTileWidth,  tileWidth);
                int actualH = Math.Min(curTileHeight, tileHeight);
                int srcStride = actualW * 4;
 
                // If ReadRegion returned even less than expected, derive safe row count
                if (bgraData.Length < actualW * actualH * 4)
                {
                    int safePixels = bgraData.Length / 4;
                    actualH = safePixels / actualW;
                    if (actualH == 0) return null;
                }
 
                byte[] padded = new byte[expectedSize]; // zero-initialised = transparent
                for (int row = 0; row < actualH; row++)
                {
                    int srcOffset = row * srcStride;
                    int dstOffset = row * tileWidth * 4;
                    Buffer.BlockCopy(bgraData, srcOffset, padded, dstOffset, srcStride);
                }
                return padded;
            }
            catch (Exception e)
            {
                Console.WriteLine(e.Message + " " + e.StackTrace);
            }
            return null;
        }

InitResolutions()

void BioLib.SlideBase.InitResolutions ( IDictionary< int, BruTile.Resolution > resolutions, int tileWidth, int tileHeight )

protected

        {
            for (int i = 0; i < SlideImage.LevelCount; i++)
            {
                /*
                bool useInternalWidth = int.TryParse(ExternInfo.TryGetValue($"openslide.level[{i}].tile-width", out var _w) ? (string)_w : null, out var w) && w >= tileWidth;
                bool useInternalHeight = int.TryParse(ExternInfo.TryGetValue($"openslide.level[{i}].tile-height", out var _h) ? (string)_h : null, out var h) && h >= tileHeight;
 
                bool useInternalSize = useInternalHeight && useInternalWidth;
                var tw = useInternalSize ? w : tileWidth;
                var th = useInternalSize ? h : tileHeight;
                resolutions.Add(i, new Resolution(i, MinUnitsPerPixel * SlideImage.GetLevelDownsample(i), tw, th));
                */
                resolutions.Add(i, new BruTile.Resolution(i, SlideImage.BioImage.GetUnitPerPixel(i), tileWidth, tileHeight));
            }
        }

RebuildSchemaForWell()

void BioLib.SlideBase.RebuildSchemaForWell

(

BioImage

b

)

        {
            if (b.ZarrWellLevels == null || b.ZarrWellLevels.Count == 0)
            {
                Log($"[RebuildSchemaForWell] ZarrWellLevels empty — schema not rebuilt");
                return;
            }
            int fi = Math.Clamp(b.WellIndex, 0, b.ZarrWellLevels.Count - 1);
            var fieldLevels = b.ZarrWellLevels[fi];
            if (fieldLevels == null || fieldLevels.Count == 0)
            {
                // Requested field not yet loaded — fall back to first non-null field
                // so the schema matches what TryReadRegionAsync will actually serve.
                fieldLevels = b.ZarrWellLevels.FirstOrDefault(l => l != null && l.Count > 0);
                if (fieldLevels == null)
                {
                    Log($"[RebuildSchemaForWell] no loaded fieldLevels, schema not rebuilt");
                    return;
                }
                Log($"[RebuildSchemaForWell] fi={fi} null, fell back to first loaded field");
            }
 
            int w0 = 1, h0 = 1;
            GetFieldDims(fieldLevels[0], out w0, out h0);
            Log($"[RebuildSchemaForWell] field fi={fi}, level0 w={w0} h={h0}, levels={fieldLevels.Count}");
 
            double stageX = b.Resolutions.Count > 0 ? b.Resolutions[0].StageSizeX : 0;
            double stageY = b.Resolutions.Count > 0 ? b.Resolutions[0].StageSizeY : 0;
 
            var newSchema = new BruTile.TileSchema
            {
                YAxis    = BruTile.YAxis.OSM,
                Format   = "jpg",
                Extent   = new BruTile.Extent(
                    stageX,
                    -(stageY + (h0 * b.PhysicalSizeY)),
                    stageX + (w0 * b.PhysicalSizeX),
                    -stageY),
                OriginX  = stageX,
                OriginY  = stageY,
            };
 
            for (int lev = 0; lev < fieldLevels.Count; lev++)
            {
                GetFieldDims(fieldLevels[lev], out int wL, out int hL);
                double downsample = w0 > 0 ? (double)w0 / Math.Max(1, wL) : Math.Pow(2, lev);
                newSchema.Resolutions[lev] = new BruTile.Resolution(lev, downsample, 256, 256);
                Log($"[RebuildSchemaForWell]   level {lev}: w={wL} h={hL} unitsPerPixel={downsample}");
            }
 
            Schema = newSchema;
        }

Member Data Documentation

SlideImage

readonly SlideImage BioLib.SlideBase.SlideImage

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The documentation for this class was generated from the following file:

• BioLib/Source/Bio/SlideBase.cs