swharden / scitif Goto Github PK

View Code? Open in Web Editor NEW

6.0 6.0 3.0 39.75 MB

A .NET library for working with scientific image data in TIFF files

Home Page: https://www.nuget.org/packages/SciTIF

License: MIT License

C# 98.50% Batchfile 0.18% ImageJ Macro 1.32%

image image-analysis imaging microscopy science tif tiff

scitif's People

Contributors

Stargazers

Watchers

Forkers

koson gheyret uamhforever

scitif's Issues

Image needs Clone()

Image.Crop()

useful for getting stats from rectangular ROIs

ScaleBy() needs ScaledBy() which performs a copy

Support loading other image formats

e.g., 16-bit PNG files

picturebox interpolation mode

interpolation mode is fixed at bilinear. subclass the picturebox class to intercept graphics rendering to control this in the future.

https://www.codeproject.com/Articles/717312/PixelBox-A-PictureBox-with-configurable-Interpolat

XML docs not in nuget package

https://learn.microsoft.com/en-us/dotnet/core/project-sdk/msbuild-props#documentationfile

GetPixel error checking

if X is outside bounds, because of how indexing works it won't throw an exception

Read scale from metadata

using Tiff image = Tiff.Open("demo.tif", "r");

StringBuilder sb = new();

foreach (TiffTag tag in Enum.GetValues(typeof(TiffTag)))
{
    FieldValue[] values = image.GetField(tag);

    if (values is null)
        continue;

    foreach (FieldValue value in values)
        sb.AppendLine($"{tag} = {value}");
}

Console.WriteLine(sb);

SUBFILETYPE = 0
IMAGEWIDTH = 256
IMAGELENGTH = 256
BITSPERSAMPLE = 16
COMPRESSION = NONE
PHOTOMETRIC = MINISBLACK
IMAGEDESCRIPTION = ImageJ=1.53q
images=48
channels=2
frames=24
hyperstack=true
mode=composite
unit=micron
finterval=1
loop=false
min=169.0
max=8191.0
STRIPOFFSETS = System.UInt64[]
SAMPLESPERPIXEL = 1
ROWSPERSTRIP = 16
STRIPBYTECOUNTS = System.UInt64[]
XRESOLUTION = 0.848324
YRESOLUTION = 0.848324
PLANARCONFIG = CONTIG
RESOLUTIONUNIT = NONE
TILEOFFSETS = System.UInt64[]
TILEBYTECOUNTS = System.UInt64[]

public static double GetMicronsPerPixel(string tifFilePath)
{
    using Tiff image = Tiff.Open(tifFilePath, "r");
    return 1.0 / (float)image.GetField(TiffTag.XRESOLUTION).First().Value;
}

metrics of interest:

unit=micron
XRESOLUTION = 0.848324
YRESOLUTION = 0.848324

GetBitmap()

It would be nice if there were simple extension methods for converting images to common bitmap types for System.Drawing and/or SkiaSharp

public static System.Drawing.Bitmap GetBitmap(this SciTIF.ImageRGB img)
{
    byte[] bytes = img.GetBitmapBytes();
    using MemoryStream ms = new(bytes);
    System.Drawing.Bitmap bmp = new(ms);
    return bmp;
}

Image.CollapseHorizontally and Image.CollapseVertically

Something like

public static double[] CollapseHorizontally(SciTIF.Image imgR)
{
    double[] collapsed = new double[imgR.Height];
    for (int y = 0; y < imgR.Height; y++)
    {
        double xSum = 0;
        for (int x = 0; x < imgR.Width; x++)
        {
            int offset = y * imgR.Width + x;
            xSum += imgR.Values[offset];
        }
        double xMean = xSum / imgR.Width;
        collapsed[y] = xMean;
    }
    return collapsed;
}