openslide wrapper More...

Inheritance diagram for BioLib.SlideImage:

Public Member Functions
	SlideImage ()

ImageDimension	GetLevelDimension (int level)
	Get the dimensions of a level.

IEnumerable< ImageDimension >	GetLevelDimensions ()
	Get all level dimensions.

unsafe byte[]	ReadRegion (int level, ZCT zct, long x, long y, long width, long height)
	Copy pre-multiplied BGRA data from a whole slide image.

unsafe bool	TryReadRegion (int level, long x, long y, long width, long height, out byte[] data, ZCT zct)
	Copy pre-multiplied BGRA data from a whole slide image.

void	Close ()

void	Dispose ()

async Task< byte[]>	ReadRegionAsync (int level, long curLevelOffsetXPixel, long curLevelOffsetYPixel, int curTileWidth, int curTileHeight, ZCT coord)

Static Public Member Functions
static string	DetectVendor (string filename)
	Quickly determine whether a whole slide image is recognized.

static void	Initialize (string path=null)
	Add .dll directory to PATH.

static SlideImage	Open (BioImage b)
	Open.

static double	CalculateBaseFactor (int originalResolution, int lastLevelResolution, int totalLevels)
	Calculates the base downsampling factor between two levels of a slide.

static List< double >	GetLevelDownsamples (double baseDownsampleFactor, int totalLevels)
	Calculates the downsample factors for each level of a slide.

Protected Member Functions
virtual void	Dispose (bool disposing)
	Dispose.

Properties
BioImage	BioImage `[get, set]`

int	LevelCount `[get]`
	Get the number of levels in the whole slide image.

ImageDimension	Dimensions `[get]`
	Get the dimensions of level 0 (the largest level). Exactly equivalent to calling GetLevelDimensions(0).

Detailed Description

openslide wrapper

Definition at line 18 of file SlideImage.cs.

Constructor & Destructor Documentation

◆ SlideImage()

BioLib.SlideImage.SlideImage ( )

Parameters

handle
isOwner	close handle when disposed

Exceptions

OpenSlideException

Definition at line 48 of file SlideImage.cs.

        {
            
        }

Member Function Documentation

◆ CalculateBaseFactor()

static double BioLib.SlideImage.CalculateBaseFactor	(	int	originalResolution,
		int	lastLevelResolution,
		int	totalLevels )

static

Calculates the base downsampling factor between two levels of a slide.

Parameters

originalDimension	The dimension (width or height) of the original level.
nextLevelDimension	The dimension (width or height) of the next level.

Returns: The base downsampling factor.

Definition at line 150 of file SlideImage.cs.

        {
            if (totalLevels <= 1)
            {
                throw new ArgumentException("Total levels must be greater than 1 to calculate a base factor.");
            }
            if (lastLevelResolution <= 0 || originalResolution <= 0)
            {
                throw new ArgumentException("Resolutions must be greater than 0.");
            }
 
            // Calculate the base downsampling factor
            double baseFactor = Math.Pow((double)originalResolution / lastLevelResolution, 1.0 / (totalLevels - 1));
            return baseFactor;
        }

◆ Close()

void BioLib.SlideImage.Close ( )

Definition at line 255 of file SlideImage.cs.

        {
           
        }

◆ DetectVendor()

static string BioLib.SlideImage.DetectVendor ( string filename )

static

Quickly determine whether a whole slide image is recognized.

If OpenSlide recognizes the file referenced by filename , return a string identifying the slide format vendor.This is equivalent to the value of the NativeMethods.VENDOR property. Calling Open(string) on this file will return a valid OpenSlide object or an OpenSlide object in error state.

Otherwise, return null.Calling Open(string) on this file will also return null.

Parameters

filename The filename to check. On Windows, this must be in UTF-8.

Returns: An identification of the format vendor for this file, or NULL.

Definition at line 38 of file SlideImage.cs.

        {
            return filename;
        }

◆ Dispose() [1/2]

void BioLib.SlideImage.Dispose ( )

Definition at line 290 of file SlideImage.cs.

        {
            Dispose(disposing: true);
            GC.SuppressFinalize(this);
        }

◆ Dispose() [2/2]

virtual void BioLib.SlideImage.Dispose ( bool disposing )

protectedvirtual

Dispose.

Parameters

disposing

Definition at line 268 of file SlideImage.cs.

        {
            if (!disposedValue)
            {
                if (disposing)
                {
                }
 
                Close();
                disposedValue = true;
            }
        }

◆ GetLevelDimension()

ImageDimension BioLib.SlideImage.GetLevelDimension ( int level )

Get the dimensions of a level.

Parameters

level The desired level.

Exceptions

OpenSlideException

Definition at line 126 of file SlideImage.cs.

        {
            return new ImageDimension(BioImage.Resolutions[level].SizeX, BioImage.Resolutions[level].SizeY);
        }

◆ GetLevelDimensions()

IEnumerable< ImageDimension > BioLib.SlideImage.GetLevelDimensions ( )

Get all level dimensions.

Returns

Exceptions

OpenSlideException

Definition at line 136 of file SlideImage.cs.

        {
            var count = LevelCount;
            for (int i = 0; i < count; i++)
            {
                yield return GetLevelDimension(i);
            }
        }

◆ GetLevelDownsamples()

static List< double > BioLib.SlideImage.GetLevelDownsamples	(	double	baseDownsampleFactor,
		int	totalLevels )

static

Calculates the downsample factors for each level of a slide.

Parameters

baseDownsampleFactor	The downsample factor between each level.
totalLevels	Total number of levels in the slide.

Returns: A list of downsample factors for each level.

Definition at line 172 of file SlideImage.cs.

        {
            var levelDownsamples = new List<double>();
 
            for (int level = 0; level < totalLevels; level++)
            {
                // Calculate the downsample factor for the current level.
                // Math.Pow is used to raise the baseDownsampleFactor to the power of the level.
                double downsampleFactorAtLevel = Math.Pow(baseDownsampleFactor, level);
                levelDownsamples.Add(downsampleFactorAtLevel);
            }
 
            return levelDownsamples;
        }

◆ Initialize()

static void BioLib.SlideImage.Initialize ( string path = null )

static

Add .dll directory to PATH.

Parameters

path

Exceptions

OpenSlideException

Definition at line 58 of file SlideImage.cs.

        {
            
        }

◆ Open()

static SlideImage BioLib.SlideImage.Open ( BioImage b )

static

Open.

Parameters

filename

Returns

Exceptions

OpenSlideException

Definition at line 73 of file SlideImage.cs.

        {
            SlideImage im = new SlideImage();
            im.BioImage = b;
            return im;
        }

◆ ReadRegion()

unsafe byte[] BioLib.SlideImage.ReadRegion	(	int	level,
		ZCT	zct,
		long	x,
		long	y,
		long	width,
		long	height )

Copy pre-multiplied BGRA data from a whole slide image.

Parameters

level	The desired level.
x	The top left x-coordinate, in the level 0 reference frame.
y	The top left y-coordinate, in the level 0 reference frame.
width	The width of the region. Must be non-negative.
height	The height of the region. Must be non-negative.

Returns: The pixel data of this region.

Exceptions

ArgumentOutOfRangeException

Exceptions

OpenSlideException

Definition at line 224 of file SlideImage.cs.

        {
            return BioImage.GetTile(BioImage, BioImage.GetFrameIndex(zct.Z, zct.C, zct.T), level, (int)x, (int)y, (int)width, (int)height).Bytes;
        }

◆ ReadRegionAsync()

async Task< byte[]> BioLib.SlideImage.ReadRegionAsync	(	int	level,
		long	curLevelOffsetXPixel,
		long	curLevelOffsetYPixel,
		int	curTileWidth,
		int	curTileHeight,
		ZCT	coord )

Definition at line 296 of file SlideImage.cs.

        {
            try
            {
                byte[] bts;
                TryReadRegion(level, curLevelOffsetXPixel, curLevelOffsetYPixel, curTileWidth, curTileHeight,out bts,coord);
                return bts;
            }
            catch (Exception e)
            {
                return null;
            }
        }

◆ TryReadRegion()

unsafe bool BioLib.SlideImage.TryReadRegion	(	int	level,
		long	x,
		long	y,
		long	width,
		long	height,
		out byte[]	data,
		ZCT	zct )

Copy pre-multiplied BGRA data from a whole slide image.

Parameters

level	The desired level.
x	The top left x-coordinate, in the level 0 reference frame.
y	The top left y-coordinate, in the level 0 reference frame.
width	The width of the region. Must be non-negative.
height	The height of the region. Must be non-negative.
data	The BGRA pixel data of this region.

Returns

summary> Close an OpenSlide object. /summary> remarks> No other threads may be using the object. After this call returns, the object cannot be used anymore. /remarks>

Definition at line 239 of file SlideImage.cs.

Property Documentation

◆ BioImage

BioImage BioLib.SlideImage.BioImage

getset

Definition at line 20 of file SlideImage.cs.

20{ get; set; }

◆ Dimensions

ImageDimension BioLib.SlideImage.Dimensions

get

Get the dimensions of level 0 (the largest level). Exactly equivalent to calling GetLevelDimensions(0).

Exceptions

OpenSlideException

Definition at line 106 of file SlideImage.cs.

        {
            get
            {
                if (_dimensionsRef == null)
                {
                    lock (_dimensionsSynclock)
                    {
                        if (_dimensionsRef == null)
                            _dimensionsRef = GetLevelDimension(0);
                    }
                }
                return _dimensionsRef.Value;
            }
        }

◆ LevelCount

int BioLib.SlideImage.LevelCount

get

Get the number of levels in the whole slide image.

<return>The number of levels, or -1 if an error occurred.</return>

Exceptions

OpenSlideException

Definition at line 85 of file SlideImage.cs.

        {
            get
            {
                if (BioImage.MacroResolution.HasValue)
                {
                    return BioImage.Resolutions.Count - 2;
                }
                else
                    return BioImage.Resolutions.Count;
            }
        }

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

BioLib/Source/Bio/SlideImage.cs

Public Member Functions

Static Public Member Functions

Protected Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ SlideImage()

Member Function Documentation

◆ CalculateBaseFactor()

◆ Close()

◆ DetectVendor()

◆ Dispose() [1/2]

◆ Dispose() [2/2]

◆ GetLevelDimension()

◆ GetLevelDimensions()

◆ GetLevelDownsamples()

◆ Initialize()

◆ Open()

◆ ReadRegion()

◆ ReadRegionAsync()

◆ TryReadRegion()

Property Documentation

◆ BioImage

◆ Dimensions

◆ LevelCount