BioLib.QuPath.Image Class Reference

Static Public Member Functions
static Image	FromBioImage (BioImage b, int id)
static List< Image >	FromBioImages (List< BioImage > b, int id)

Properties
ServerBuilder	ServerBuilder [get, set]
int	EntryID [get, set]
string	RandomizedName [get, set]
string	ImageName [get, set]
Dictionary< string, object >	Metadata [get, set]

Member Function Documentation

FromBioImage()

static Image BioLib.QuPath.Image.FromBioImage ( BioImage b, int id )

static

            {
                QuPath.Image im = new QuPath.Image();
                im.EntryID = id;
                im.RandomizedName = Guid.NewGuid().ToString();
                im.ImageName = b.Filename;
                im.ServerBuilder = new QuPath.ServerBuilder();
                im.ServerBuilder.Uri = "file:/" + b.ID.Replace("\\","/");
                im.ServerBuilder.ProviderClassName = "qupath.lib.images.servers.bioformats.BioFormatsServerBuilder";
                im.ServerBuilder.Args = new List<string>();
                im.ServerBuilder.Args.Add("--series");
                im.ServerBuilder.Args.Add(id.ToString());
                im.ServerBuilder.Metadata = new QuPath.Metadata();
                im.ServerBuilder.Metadata.Name = b.Filename;
                im.ServerBuilder.Metadata.Width = b.SizeX;
                im.ServerBuilder.Metadata.Height = b.SizeY;
                im.ServerBuilder.Metadata.Magnification = b.Magnification;
                im.ServerBuilder.Metadata.IsRGB = b.isRGB;
                im.ServerBuilder.Metadata.ChannelType = "DEFAULT";
                im.ServerBuilder.Metadata.PixelCalibration = new PixelCalibration();
                im.ServerBuilder.Metadata.PixelCalibration.PixelWidth = new PixelDimension();
                im.ServerBuilder.Metadata.PixelCalibration.PixelWidth.Value = b.PhysicalSizeX;
                im.ServerBuilder.Metadata.PixelCalibration.PixelWidth.Unit = "µm";
                im.ServerBuilder.Metadata.PixelCalibration.PixelHeight = new PixelDimension();
                im.ServerBuilder.Metadata.PixelCalibration.PixelHeight.Value = b.PhysicalSizeY;
                im.ServerBuilder.Metadata.PixelCalibration.PixelHeight.Unit = "µm";
                im.ServerBuilder.Metadata.PixelCalibration.ZSpacing = new ZSpacing();
                if (b.Resolutions[0].PixelFormat == PixelFormat.Format16bppGrayScale || b.Resolutions[0].PixelFormat == PixelFormat.Format48bppRgb)
                    im.ServerBuilder.Metadata.PixelType = "UINT16";
                else if(b.Resolutions[0].PixelFormat == PixelFormat.Format8bppIndexed || b.Resolutions[0].PixelFormat == PixelFormat.Format24bppRgb)
                    im.ServerBuilder.Metadata.PixelType = "UINT8";
 
                if (b.PhysicalSizeZ != 0 || b.PhysicalSizeZ < 0)
                {
                    im.ServerBuilder.Metadata.PixelCalibration.ZSpacing.Value = b.PhysicalSizeZ;
                    im.ServerBuilder.Metadata.PixelCalibration.ZSpacing.Unit = "µm";
                }
                else
                {
                    im.ServerBuilder.Metadata.PixelCalibration.ZSpacing.Value = 1;
                    im.ServerBuilder.Metadata.PixelCalibration.ZSpacing.Unit = "z-slice";
                }
                im.ServerBuilder.Metadata.PixelCalibration.TimeUnit = "SECONDS";
                im.ServerBuilder.Metadata.PixelCalibration.Timepoints = new List<object>();
                if(b.SizeT > 1)
                for (int i = 0; i < b.SizeT; i++)
                {
                    im.ServerBuilder.Metadata.PixelCalibration.Timepoints.Add(0.0);
                }
                im.ServerBuilder.Metadata.PreferredTileHeight = b.SizeX;
                im.ServerBuilder.Metadata.PreferredTileWidth = b.SizeY;
                im.ServerBuilder.Metadata.SizeT = b.SizeT;
                im.ServerBuilder.Metadata.SizeZ = b.SizeZ;
                im.Metadata = new Dictionary<string, object>();
                double max = Double.MinValue;
                foreach (Bitmap item in b.Buffers)
                {
                    foreach (var s in item.Stats)
                    {
                        if(max < s.Max)
                            max = s.Max;
                    }
                }
                im.ServerBuilder.Metadata.MaxValue = (int)max;
                im.ServerBuilder.Metadata.Levels = new List<Level>();
                int li = 0;
                foreach (var r in b.Resolutions)
                {
                    Level l = new Level();
                    l.Width = r.SizeX;
                    l.Height = r.SizeY;
                    if (b.Type != BioImage.ImageType.stack)
                        l.Downsample = 1;
                    else if (b.Type != BioImage.ImageType.pyramidal)
                        l.Downsample = b.GetLevelDownsample(li);
                    else
                        l.Downsample = 1;
                    im.ServerBuilder.Metadata.Levels.Add(l);
                    li++;
                }
                im.ServerBuilder.Metadata.Channels = new List<Channel>();
                foreach (AForge.Channel c in b.Channels)
                {
                    if(b.isRGB)
                    {
                        QuPath.Channel rr = new QuPath.Channel();
                        QuPath.Channel gg = new QuPath.Channel();
                        QuPath.Channel bb = new QuPath.Channel();
                        rr.Name = c.Name;
                        gg.Name = c.Name;
                        bb.Name = c.Name;
                        int alpha = 255;
                        rr.Color = -65536;
                        gg.Color = -16711936;
                        bb.Color = -16776961;
                        im.ServerBuilder.Metadata.Channels.Add(rr);
                        im.ServerBuilder.Metadata.Channels.Add(gg);
                        im.ServerBuilder.Metadata.Channels.Add(bb);
                    }
                    else
                    {
                        QuPath.Channel rr = new QuPath.Channel();
                        rr.Color = (255 << 24) | (c.EmissionColor.R << 16) | (c.EmissionColor.G << 8) | c.EmissionColor.B;
                        im.ServerBuilder.Metadata.Channels.Add(rr);
                    }
                    
                }
                im.ServerBuilder.BuilderType = "uri";
                return im;
            }

FromBioImages()

static List< Image > BioLib.QuPath.Image.FromBioImages ( List< BioImage > b, int id )

static

            {
                List<Image> images = new List<Image>();
                foreach (var image in b)
                {
                    images.Add(FromBioImage(image,id));
                    id++;
                }
                return images;
            }

Property Documentation

EntryID

int BioLib.QuPath.Image.EntryID

getset

{ get; set; }

ImageName

string BioLib.QuPath.Image.ImageName

getset

{ get; set; }

Metadata

Dictionary<string, object> BioLib.QuPath.Image.Metadata

getset

{ get; set; }

RandomizedName

string BioLib.QuPath.Image.RandomizedName

getset

{ get; set; }

ServerBuilder

ServerBuilder BioLib.QuPath.Image.ServerBuilder

getset

{ get; set; }

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

• BioLib/Source/QuPath.cs