Bio.SlideImage Class Reference

openslide wrapper More...

Inheritance diagram for Bio.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, 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

Constructor & Destructor Documentation

SlideImage()

Bio.SlideImage.SlideImage ( )

inline

Parameters

handle
isOwner	close handle when disposed

Exceptions

OpenSlideException

        {
            
        }

Member Function Documentation

CalculateBaseFactor()

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

inlinestatic

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.

        {
            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 Bio.SlideImage.Close ( )

inline

        {
           
        }

DetectVendor()

static string Bio.SlideImage.DetectVendor ( string  filename )

inlinestatic

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.

        {
            return filename;
        }

Dispose() [1/2]

void Bio.SlideImage.Dispose ( )

inline

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

Dispose() [2/2]

virtual void Bio.SlideImage.Dispose ( bool  disposing )

inlineprotectedvirtual

Dispose.

Parameters

disposing

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

GetLevelDimension()

ImageDimension Bio.SlideImage.GetLevelDimension ( int  level )

inline

Get the dimensions of a level.

Parameters

level

The desired level.

Exceptions

OpenSlideException

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

GetLevelDimensions()

IEnumerable< ImageDimension > Bio.SlideImage.GetLevelDimensions ( )

inline

Get all level dimensions.

Returns

Exceptions

OpenSlideException

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

GetLevelDownsamples()

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

inlinestatic

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.

        {
            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 Bio.SlideImage.Initialize ( string  path = null )

inlinestatic

Add .dll directory to PATH.

Parameters

path

Exceptions

OpenSlideException

        {
            
        }

Open()

static SlideImage Bio.SlideImage.Open ( BioImage  b )

inlinestatic

Open.

Parameters

filename

Returns

Exceptions

OpenSlideException

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

ReadRegion()

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

inline

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

        {
            return BioImage.GetTile(BioImage, App.viewer.GetCoordinate(), level, (int)x, (int)y, (int)width, (int)height).Bytes;
        }

ReadRegionAsync()

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

inline

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

TryReadRegion()

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

inline

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>

Property Documentation

BioImage

BioImage Bio.SlideImage.BioImage

getset

{ get; set; }

Dimensions

ImageDimension Bio.SlideImage.Dimensions

get

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

Exceptions

OpenSlideException

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

LevelCount

int Bio.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

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

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

• D:/Kari/repos/BioGTK/Source/Bio/SlideImage.cs