BioLib.SlideBase Class Reference

Inheritance diagram for BioLib.SlideBase:

Public Member Functions
	SlideBase (BioImage source, SlideImage im, bool enableCache=true)
override IReadOnlyDictionary< string, byte[]>	GetExternImages ()
	Extern image.
byte[]	GetTile (TileInfo tileInfo, ZCT coord)
Public Member Functions inherited from BioLib.SlideSourceBase
async Task< byte[]>	GetSlice (SliceInfo sliceInfo)
	Get slice.
byte[]	Get8BitBytes (Image< L8 > image)
byte[]	GetRgb24Bytes (Image< Rgb24 > image)
byte[]	Get16Bytes (Image< L16 > image)
IReadOnlyDictionary< string, byte[]>	GetExternImages ()
	Extern image.
void	Dispose ()
async Task< byte[]>	GetTileAsync (TileInformation tileInfo)
async Task< byte[]>	GetTileAsync (BruTile.TileInfo tileInfo)
Public Member Functions inherited from BioLib.ISliceProvider
Public Member Functions inherited from BioLib.ISlideExternInfo

Static Public Member Functions
static string	DetectVendor (string source)
static byte[]	ConvertRgbaToRgb (byte[] rgbaArray)
Static Public Member Functions inherited from BioLib.SlideSourceBase
static void	Resister (string extensionUpper, Func< string, bool, ISlideSource > factory)
	resister decode for Specific format
static ISlideSource	Create (BioImage source, SlideImage im, bool enableCache=true)
static byte[]	ConvertRgbaToRgb (byte[] rgbaArray)

Public Attributes
readonly SlideImage	SlideImage
Public Attributes inherited from BioLib.SlideSourceBase
TileCache	cache = null

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

Additional Inherited Members
Static Public Attributes inherited from BioLib.SlideSourceBase
static Extent	destExtent
static Extent	sourceExtent
static double	curUnitsPerPixel = 1
static bool	UseVips = true
Properties inherited from BioLib.SlideSourceBase
static bool	UseRealResolution = true [get, set]
double	MinUnitsPerPixel [get, protected set]
	um/pixel
SlideImage	Image [get, set]
ITileSchema	Schema [get, protected set]
string	Name [get, protected set]
Attribution	Attribution [get, protected set]
IReadOnlyDictionary< string, object >	ExternInfo [get, protected set]
	Extern info.
string	Source [get, protected set]
	File path.
Properties inherited from BioLib.ISliceProvider
Properties inherited from BioLib.ISlideExternInfo

Detailed Description

Definition at line 14 of file SlideBase.cs.

Constructor & Destructor Documentation

SlideBase()

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

Definition at line 17 of file SlideBase.cs.

        {
            Source = source.file;
            SlideImage = im;
            Image = im;
            double minUnitsPerPixel;
            if (source.PhysicalSizeX < source.PhysicalSizeY) minUnitsPerPixel = source.PhysicalSizeX; else minUnitsPerPixel = source.PhysicalSizeY;
            MinUnitsPerPixel = UseRealResolution ? minUnitsPerPixel : 1;
            if (MinUnitsPerPixel <= 0) MinUnitsPerPixel = 1;
            var height = SlideImage.Dimensions.Height;
            var width = SlideImage.Dimensions.Width;
            //ExternInfo = GetInfo();
            Schema = new TileSchema
            {
                YAxis = YAxis.OSM,
                Format = "jpg",
                Extent = new Extent(0, -height, width, 0),
                OriginX = 0,
                OriginY = 0,
            };
            InitResolutions(Schema.Resolutions, 256, 256);
        }

Member Function Documentation

ConvertRgbaToRgb()

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

static

Definition at line 97 of file SlideBase.cs.

        {
            // 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

Definition at line 40 of file SlideBase.cs.

        {
            return SlideImage.DetectVendor(source);
        }

Dispose()

override void BioLib.SlideBase.Dispose ( bool disposing )

protectedvirtual

Reimplemented from BioLib.SlideSourceBase.

Definition at line 132 of file SlideBase.cs.

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

GetExternImages()

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

(

)

Extern image.

Returns

Implements BioLib.ISlideExternInfo.

Definition at line 46 of file SlideBase.cs.

        {
            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 )

Definition at line 81 of file SlideBase.cs.

        {
            var r = Schema.Resolutions[tileInfo.Index.Level].UnitsPerPixel;
            var tileWidth = Schema.Resolutions[tileInfo.Index.Level].TileWidth;
            var tileHeight = Schema.Resolutions[tileInfo.Index.Level].TileHeight;
            var curLevelOffsetXPixel = tileInfo.Extent.MinX / MinUnitsPerPixel;
            var curLevelOffsetYPixel = -tileInfo.Extent.MaxY / MinUnitsPerPixel;
            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 = SlideImage.ReadRegion(tileInfo.Index.Level, coord, (long)curLevelOffsetXPixel, (long)curLevelOffsetYPixel, curTileWidth, curTileHeight);
            //We check to see if the data is valid.
            if (bgraData.Length != curTileWidth * curTileHeight * 4)
                return null;
            byte[] bm = ConvertRgbaToRgb(bgraData);
            return bm;
        }

InitResolutions()

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

protected

Definition at line 113 of file SlideBase.cs.

        {
            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));
            }
        }

Member Data Documentation

SlideImage

readonly SlideImage BioLib.SlideBase.SlideImage

Definition at line 16 of file SlideBase.cs.

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

• BioLib/Source/Bio/SlideBase.cs