Skip to content

Commit

Permalink
2.2.0 Well Plates and Multi Pyramid
Browse files Browse the repository at this point in the history 
Further well plate support as well as multi pyramid files.
  • Loading branch information
@BiologyTools
BiologyTools committed Feb 17, 2024
1 parent c03e6ab commit d04067e
Show file tree
Hide file tree
Showing 5 changed files with 232 additions and 43 deletions.
3 changes: 2 additions & 1 deletion .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -360,4 +360,5 @@ MigrationBackup/
.ionide/

# Fody - auto-generated XML schema
FodyWeavers.xsd
FodyWeavers.xsd
*.bin
Binary file modified .vs/ProjectEvaluation/biolib.metadata.v7.bin
View file
Binary file not shown.
Binary file modified .vs/ProjectEvaluation/biolib.projects.v7.bin
View file
Binary file not shown.
8 changes: 4 additions & 4 deletions BioLib.csproj
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,14 @@
<PackageIcon>banner.jpg</PackageIcon>
<PackageReadmeFile>README.md</PackageReadmeFile>
<RepositoryUrl>https://github.com/BiologyTools/BioLib</RepositoryUrl>
<AssemblyVersion>2.1.0</AssemblyVersion>
<FileVersion>2.1.0</FileVersion>
<PackageVersion>2.1.0</PackageVersion>
<AssemblyVersion>2.2.0</AssemblyVersion>
<FileVersion>2.2.0</FileVersion>
<PackageVersion>2.2.0</PackageVersion>
<PackageLicenseExpression>GPL-3.0-only</PackageLicenseExpression>
<PackageRequireLicenseAcceptance>True</PackageRequireLicenseAcceptance>
<PackageProjectUrl>https://biologytools.github.io/</PackageProjectUrl>
<PackageTags>Biology; ImageJ; Bio-Formats; Image-Stacks; Microscopy; Whole-Slide-Image;</PackageTags>
<PackageReleaseNotes>Well plate support and bug fixes.</PackageReleaseNotes>
<PackageReleaseNotes>Further Well Plate Support as well as multi pyramid files.</PackageReleaseNotes>
<Authors>Erik Repo</Authors>
</PropertyGroup>
<ItemGroup>
Expand Down
264 changes: 226 additions & 38 deletions Source/Bio.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2183,6 +2183,76 @@ public ImageInfo Copy()
}
public class BioImage : IDisposable
{
public class WellPlate
{
public class Well
{
public string ID { get; set; }
public int Index { get; set; }
public int Column { get; set; }
public int Row { get; set; }
public System.Drawing.Color Color { get; set; }
public List<Sample> Samples = new List<Sample>();
public class Sample
{
public string ID { get; set; }
public int Index { get; set; }
public PointD Position { get; set; }
public Timestamp Time { get; set; }
}
}
public List<Well> Wells = new List<Well>();

public PointD Origin;
public string ID;
public string Name;
public WellPlate(BioImage b)
{
ID = b.meta.getPlateID(b.series);
Name = b.meta.getPlateName(b.series);
double x, y;
if (b.meta.getPlateWellOriginX(b.series) != null)
x = b.meta.getPlateWellOriginX(b.series).value().doubleValue();
else
x = 0;
if (b.meta.getPlateWellOriginY(b.series) != null)
y = b.meta.getPlateWellOriginY(b.series).value().doubleValue();
else
y = 0;
Origin = new PointD(x, y);
int ws = b.meta.getWellCount(b.series);
for (int i = 0; i < ws; i++)
{
Well w = new Well();
w.ID = b.meta.getWellID(b.series, i);
w.Column = b.meta.getWellColumn(b.series, i).getNumberValue().intValue();
w.Row = b.meta.getWellRow(b.series, i).getNumberValue().intValue();
int wsc = b.meta.getWellSampleCount(b.series, i);
for (int s = 0; s < wsc; s++)
{
Well.Sample sa = new Well.Sample();
sa.Time = b.meta.getWellSampleTimepoint(b.series, i, s);
sa.Index = b.meta.getWellSampleIndex(b.series, i, s).getNumberValue().intValue();
double sx, sy;
if (b.meta.getWellSamplePositionX(b.series, i, s) != null)
sx = b.meta.getWellSamplePositionX(b.series, i, s).value().doubleValue();
else sx = 0;
if (b.meta.getWellSamplePositionY(b.series, i, s) != null)
sy = b.meta.getWellSamplePositionY(b.series, i, s).value().doubleValue();
else sy = 0;
sa.Position = new PointD(sx, sy);
sa.ID = b.meta.getWellSampleID(b.series, i, s);
w.Samples.Add(sa);
}
ome.xml.model.primitives.Color c = b.meta.getWellColor(b.series, i);
if (c != null)
w.Color = System.Drawing.Color.FromArgb(c.getAlpha(), c.getRed(), c.getGreen(), c.getBlue());
Wells.Add(w);
}

}
}
public WellPlate Plate = null;
public int[,,] Coords;
private ZCT coordinate;
public ZCT Coordinate
Expand Down Expand Up @@ -4956,7 +5026,7 @@ public static BioImage OpenFile(string file, int series, bool tab, bool addToIma
int SizeX = image.GetField(TiffTag.IMAGEWIDTH)[0].ToInt();
int SizeY = image.GetField(TiffTag.IMAGELENGTH)[0].ToInt();
b.bitsPerPixel = image.GetField(TiffTag.BITSPERSAMPLE)[0].ToInt();
b.littleEndian = !image.IsBigEndian();
b.littleEndian = image.IsBigEndian();
int RGBChannelCount = image.GetField(TiffTag.SAMPLESPERPIXEL)[0].ToInt();
string desc = "";

Expand Down Expand Up @@ -6194,14 +6264,15 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
if (wells > 0)
{
b.Type = ImageType.well;
b.Plate = new WellPlate(b);
tile = false;
}
}
catch (Exception)
{

}

List<Resolution> rss = new List<Resolution>();
for (int s = 0; s < b.seriesCount; s++)
{
reader.setSeries(s);
Expand All @@ -6215,7 +6286,7 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
PixelFormat px;
try
{
px = GetPixelFormat(rgbc, b.meta.getPixelsType(s));
px = GetPixelFormat(rgbc, b.meta.getPixelsType(r));
}
catch (Exception)
{
Expand All @@ -6224,30 +6295,30 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
res.PixelFormat = px;
res.SizeX = reader.getSizeX();
res.SizeY = reader.getSizeY();
if (b.meta.getPixelsPhysicalSizeX(s) != null)
if (b.meta.getPixelsPhysicalSizeX(r) != null)
{
res.PhysicalSizeX = b.meta.getPixelsPhysicalSizeX(s).value().doubleValue();
res.PhysicalSizeX = b.meta.getPixelsPhysicalSizeX(r).value().doubleValue();
}
else
res.PhysicalSizeX = (96 / 2.54) / 1000;
if (b.meta.getPixelsPhysicalSizeY(s) != null)
if (b.meta.getPixelsPhysicalSizeY(r) != null)
{
res.PhysicalSizeY = b.meta.getPixelsPhysicalSizeY(s).value().doubleValue();
res.PhysicalSizeY = b.meta.getPixelsPhysicalSizeY(r).value().doubleValue();
}
else
res.PhysicalSizeY = (96 / 2.54) / 1000;

if (b.meta.getStageLabelX(s) != null)
res.StageSizeX = b.meta.getStageLabelX(s).value().doubleValue();
if (b.meta.getStageLabelY(s) != null)
res.StageSizeY = b.meta.getStageLabelY(s).value().doubleValue();
if (b.meta.getStageLabelZ(s) != null)
res.StageSizeZ = b.meta.getStageLabelZ(s).value().doubleValue();
if (b.meta.getStageLabelX(r) != null)
res.StageSizeX = b.meta.getStageLabelX(r).value().doubleValue();
if (b.meta.getStageLabelY(r) != null)
res.StageSizeY = b.meta.getStageLabelY(r).value().doubleValue();
if (b.meta.getStageLabelZ(r) != null)
res.StageSizeZ = b.meta.getStageLabelZ(r).value().doubleValue();
else
res.StageSizeZ = 1;
if (b.meta.getPixelsPhysicalSizeZ(s) != null)
if (b.meta.getPixelsPhysicalSizeZ(r) != null)
{
res.PhysicalSizeZ = b.meta.getPixelsPhysicalSizeZ(s).value().doubleValue();
res.PhysicalSizeZ = b.meta.getPixelsPhysicalSizeZ(r).value().doubleValue();
}
else
{
Expand All @@ -6258,19 +6329,61 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
{
Console.WriteLine("No Stage Coordinates. PhysicalSize:(" + res.PhysicalSizeX + "," + res.PhysicalSizeY + "," + res.PhysicalSizeZ + ")");
}
b.Resolutions.Add(res);
rss.Add(res);
}
}
reader.setSeries(serie);


//We need to determine if this image is pyramidal or not.
//We do this by seeing if the resolutions are downsampled or not.
if (b.Resolutions.Count > 1 && b.Type != ImageType.well)
if (b.Resolutions[0].PhysicalSizeX < b.Resolutions[1].PhysicalSizeX)
if (rss.Count > 1 && b.Type != ImageType.well)
{
if (rss[0].SizeX > rss[1].SizeX)
{
b.Type = ImageType.pyramidal;
tile = true;
//We need to determine number of pyramids in this image and which belong to the series we are opening.
List<Tuple<int, int>> ims = new List<Tuple<int, int>>();
int? sr = null;
for (int r = 0; r < rss.Count - 1; r++)
{
if (rss[r].SizeX > rss[r + 1].SizeX)
{
if (sr == null)
{
sr = r;
ims.Add(new Tuple<int, int>(r, 0));
}
}
else
{
ims[ims.Count - 1] = new Tuple<int, int>(ims[ims.Count - 1].Item1, r);
sr = null;
}
}
if (ims[serie].Item2 == 0)
{
ims[serie] = new Tuple<int, int>(ims[serie].Item1, rss.Count);
}
for (int r = ims[serie].Item1; r < ims[serie].Item2; r++)
{
b.Resolutions.Add(rss[r]);
}
if (b.Resolutions.Last().PixelFormat == b.Resolutions.First().PixelFormat && rss.Last().PixelFormat != b.Resolutions.Last().PixelFormat)
{
b.Resolutions.Add(rss.Last());
b.Resolutions.Add(rss[rss.Count - 2]);
}
}
else
{
b.Resolutions.AddRange(rss);
}
}
else
b.Resolutions.AddRange(rss);



b.Volume = new VolumeD(new Point3D(b.StageSizeX, b.StageSizeY, b.StageSizeZ), new Point3D(b.PhysicalSizeX * SizeX, b.PhysicalSizeY * SizeY, b.PhysicalSizeZ * SizeZ));
Expand Down Expand Up @@ -6608,20 +6721,22 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
serFiles.AddRange(reader.getSeriesUsedFiles());

b.Buffers = new List<Bitmap>();
try
{
string st = OpenSlideGTK.OpenSlideImage.DetectVendor(file);
if (st != null)
if (!file.EndsWith("ome.tif"))
try
{
b.openSlideImage = OpenSlideGTK.OpenSlideImage.Open(file);
b.Type = ImageType.pyramidal;
tile = true;
string st = OpenSlideGTK.OpenSlideImage.DetectVendor(file);
if (st != null)
{
b.openSlideImage = OpenSlideGTK.OpenSlideImage.Open(file);
b.openSlideSource = OpenSlideGTK.SlideSourceBase.Create(file);
b.Type = ImageType.pyramidal;
tile = true;
}
}
catch (Exception e)
{
Console.WriteLine(e.Message.ToString());
}
}
catch (Exception e)
{
Console.WriteLine(e.Message.ToString());
}

// read the image data bytes
int pages = reader.getImageCount();
Expand All @@ -6640,8 +6755,11 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
}
else
{
b.Buffers.Add(GetTile(b, new ZCT(z, c, t), serie, tilex, tiley, tileSizeX, tileSizeY));
Statistics.CalcStatistics(b.Buffers.Last());
for (int p = 0; p < pages; p++)
{
b.Buffers.Add(GetTile(b, p, serie, tilex, tiley, tileSizeX, tileSizeY));
Statistics.CalcStatistics(b.Buffers.Last());
}
}
int pls;
try
Expand Down Expand Up @@ -6716,6 +6834,7 @@ public static BioImage OpenOME(string file, int serie, bool tab, bool addToImage
public ImageReader imRead;
public Tiff tifRead;
public OpenSlideGTK.OpenSlideImage openSlideImage;
public OpenSlideGTK.ISlideSource openSlideSource;
static Bitmap bm;
/// It reads a tile from a file, and returns a bitmap
///
Expand All @@ -6737,9 +6856,9 @@ public static Bitmap GetTile(BioImage b, ZCT coord, int serie, int tilex, int ti
return ExtractRegionFromTiledTiff(b, tilex, tiley, tileSizeX, tileSizeY, serie);
}
//We check if we can open this with OpenSlide as this is faster than Bioformats with IKVM.
if (b.openSlideImage != null)
if (b.openSlideImage != null && !b.file.EndsWith("ome.tif"))
{
return new Bitmap(tileSizeX, tileSizeY, AForge.PixelFormat.Format32bppArgb, b.openSlideImage.ReadRegion(serie, tilex, tiley, tileSizeX, tileSizeY), coord, "");
return new Bitmap(tileSizeX, tileSizeY, AForge.PixelFormat.Format32bppArgb, b.openSlideImage.ReadRegion(serie, tilex, tiley, tileSizeX, tileSizeY), new ZCT(), "");
}

string curfile = reader.getCurrentFile();
Expand Down Expand Up @@ -6794,10 +6913,79 @@ public static Bitmap GetTile(BioImage b, ZCT coord, int serie, int tilex, int ti
{
byte[] bytesr = reader.openBytes(b.Coords[coord.Z, coord.C, coord.T], tilex, tiley, sx, sy);
bool interleaved = reader.isInterleaved();
if (bm != null)
bm.Dispose();
bm = new Bitmap(b.file, sx, sy, PixelFormat, bytesr, coord, p, null, littleEndian, interleaved);
return bm;
return new Bitmap(b.file, sx, sy, PixelFormat, bytesr, coord, p, null, littleEndian, interleaved);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
return null;
}
}
public static Bitmap GetTile(BioImage b, int index, int serie, int tilex, int tiley, int tileSizeX, int tileSizeY)
{
if ((b.file.EndsWith("ome.tif") && vips) || (b.file.EndsWith(".tif") && vips))
{
//We can get a tile faster with libvips rather than bioformats.
return ExtractRegionFromTiledTiff(b, tilex, tiley, tileSizeX, tileSizeY, serie);
}
//We check if we can open this with OpenSlide as this is faster than Bioformats with IKVM.
if (b.openSlideImage != null && !b.file.EndsWith("ome.tif"))
{
return new Bitmap(tileSizeX, tileSizeY, AForge.PixelFormat.Format32bppArgb, b.openSlideImage.ReadRegion(serie, tilex, tiley, tileSizeX, tileSizeY), new ZCT(), "");
}

string curfile = reader.getCurrentFile();
if (curfile == null)
{
b.meta = (IMetadata)((OMEXMLService)factory.getInstance(typeof(OMEXMLService))).createOMEXMLMetadata();
reader.close();
reader.setMetadataStore(b.meta);
Console.WriteLine(b.file);
reader.setId(b.file);
}
else
{
string fi = b.file.Replace("\\", "/");
string cf = curfile.Replace("\\", "/");
if (cf != fi)
{
reader.close();
b.meta = (IMetadata)((OMEXMLService)factory.getInstance(typeof(OMEXMLService))).createOMEXMLMetadata();
reader.setMetadataStore(b.meta);
reader.setId(b.file);
}
}
if (reader.getSeries() != serie)
reader.setSeries(serie);
int SizeX = reader.getSizeX();
int SizeY = reader.getSizeY();
bool flat = reader.hasFlattenedResolutions();
bool littleEndian = reader.isLittleEndian();
PixelFormat PixelFormat = b.Resolutions[serie].PixelFormat;
if (tilex < 0)
tilex = 0;
if (tiley < 0)
tiley = 0;
if (tilex >= SizeX)
tilex = SizeX;
if (tiley >= SizeY)
tiley = SizeY;
int sx = tileSizeX;
if (tilex + tileSizeX > SizeX)
sx -= (tilex + tileSizeX) - (SizeX);
int sy = tileSizeY;
if (tiley + tileSizeY > SizeY)
sy -= (tiley + tileSizeY) - (SizeY);
//For some reason calling openBytes with 1x1px area causes an exception.
if (sx <= 1)
return null;
if (sy <= 1)
return null;
try
{
byte[] bytesr = reader.openBytes(index, tilex, tiley, sx, sy);
bool interleaved = reader.isInterleaved();
return new Bitmap(b.file, sx, sy, PixelFormat, bytesr, new ZCT(), index, null, littleEndian, interleaved);
}
catch (Exception e)
{
Expand Down

0 comments on commit d04067e

Please sign in to comment.