private Bitmap ReadRegion(SizeL location, int level, SizeL size)
{
Stopwatch sw = new Stopwatch();
sw.Start();
OpenSlide.TraceMsg("start ReadRegion " + level + "/" + location.Height + "_" + location.Width + ": " + GetBytesReadable(size.Width * size.Height * 3));
Bitmap bmp = new Bitmap((int)size.Width, (int)size.Height);
bmp.SetPixel(0, 0, Color.AliceBlue);
var bmpdata = bmp.LockBits(new Rectangle(0, 0, bmp.Width, bmp.Height), System.Drawing.Imaging.ImageLockMode.ReadWrite, System.Drawing.Imaging.PixelFormat.Format32bppArgb);
OpenSlide.TraceMsg("bmp locked " + level + "/" + location.Height + "_" + location.Width);
unsafe
{
void *p = bmpdata.Scan0.ToPointer();
openslide_read_region(handle, p, location.Width, location.Height, level, size.Width, size.Height);
}
OpenSlide.TraceMsg("read finished " + level + "/" + location.Height + "_" + location.Width + ": " + GetBytesReadable(size.Width * size.Height * 3 / Math.Max(sw.ElapsedMilliseconds, 1)) + "/ms");
bmp.UnlockBits(bmpdata);
OpenSlide.TraceMsg("unlock bits " + level + "/" + location.Height + "_" + location.Width);
if (bmp.GetPixel(0, 0) == Color.Black)
{
var error = CheckForLastError();
if (error != null)
{
throw new ArgumentException($"error reading region loc:{location}, level:{level}, size:{size}" + error);
}
//else just a black image?
}
OpenSlide.TraceMsg("end ReadRegion " + level + "/" + location.Height + "_" + location.Width);
return(bmp);
}
private SKBitmap ReadRegion(SizeL location, int level, SizeL size)
{
Stopwatch sw = new Stopwatch();
sw.Start();
OpenSlide.TraceMsg("start ReadRegion " + level + "/" + location.Height + "_" + location.Width + ": " + GetBytesReadable(size.Width * size.Height * 3));
SKBitmap bmp = new SKBitmap((int)size.Width, (int)size.Height);
bmp.SetPixel(0, 0, SKColors.AliceBlue);
bmp.LockPixels();
var bmpdata = bmp.GetPixels();
OpenSlide.TraceMsg("bmp locked " + level + "/" + location.Height + "_" + location.Width);
unsafe
{
void *p = bmpdata.ToPointer();
Import.openslide_read_region(handle, p, location.Width, location.Height, level, size.Width, size.Height);
}
OpenSlide.TraceMsg("read finished " + level + "/" + location.Height + "_" + location.Width + ": " + GetBytesReadable(size.Width * size.Height * 3 / Math.Max(sw.ElapsedMilliseconds, 1)) + "/ms");
bmp.UnlockPixels();
OpenSlide.TraceMsg("unlock bits " + level + "/" + location.Height + "_" + location.Width);
if (bmp.GetPixel(0, 0) == SKColors.Black)
{
var error = CheckForLastError();
if (error != null)
{
throw new ArgumentException($"error reading region loc:{location}, level:{level}, size:{size}" + error);
}
//else just a black image?
}
OpenSlide.TraceMsg("end ReadRegion " + level + "/" + location.Height + "_" + location.Width);
return(bmp);
}
private IList <SizeL> GetLimitedLevelDimensions()
{
//Slide level dimensions scale factor in each axis
float.TryParse(Osr.Properties[OpenSlide.PROPERTY_NAME_BOUNDS_WIDTH], out float scaledWidth);
float.TryParse(Osr.Properties[OpenSlide.PROPERTY_NAME_BOUNDS_HEIGHT], out float scaledHeight);
var level0Limits = Osr.LevelDimensions[0];
scaledWidth = scaledWidth / level0Limits.Width;
scaledHeight = scaledHeight / level0Limits.Height;
var sizeScale = new SizeF(scaledWidth, scaledHeight);
// Dimensions of active area
var levelDimensions = new List <SizeL>();
foreach (var levelSize in Osr.LevelDimensions)
{
var newScaledWidth = (long)Math.Ceiling((double)levelSize.Width * sizeScale.Width);
var newScaledHeight = (long)Math.Ceiling((double)levelSize.Height * sizeScale.Height);
var scaledLevelSize = new SizeL(newScaledWidth, newScaledHeight);
levelDimensions.Add(scaledLevelSize);
}
return(levelDimensions);
}
public override Image GetThumbnail(SizeL maxSize)
{
var thumbSize = image.GetProportionateResize(maxSize.ToSize());
var callback = new Image.GetThumbnailImageAbort(ThumbnailCallback);
var thumbnail = image.GetThumbnailImage(thumbSize.Width, thumbSize.Height,
callback, new IntPtr());
return(thumbnail);
}
public MemoryStream GetTile(int level, long row, long col)
{
OpenSlide.TraceMsg("start gettile " + level + "/" + col + "_" + row);
if (level < 0 || level >= max_dz_level)
{
throw new ArgumentException($"wrong level level {level}, row {row}, col {col}");
}
if (t_dimensions[level].Width <= col || t_dimensions[level].Height <= row ||
0 > col || 0 > row)
{
throw new ArgumentException($"wrong address level {level}, row {row}, col {col}");
}
var os_level = os_level_for_dz_level[level];
//Calculate top/ left and bottom/ right overlap
var z_overlap_tl = new SizeL(col == 0 ? 0 : 1,
row == 0 ? 0 : 1);
var z_overlap_br = new SizeL(col == t_dimensions[level].Width ? 0 : 1,
row == t_dimensions[level].Height ? 0 : 1);
var z_size = new SizeL(Math.Min(TILE_DOWNSAMPLE, z_dimensions[level].Width - TILE_DOWNSAMPLE * col) + z_overlap_tl.Width + z_overlap_br.Width,
Math.Min(TILE_DOWNSAMPLE, z_dimensions[level].Height - TILE_DOWNSAMPLE * row) + z_overlap_tl.Height + z_overlap_br.Height);
if (z_size.Width < 0 || z_size.Height < 0)
{
throw new ArgumentException($"out of bounds level {level}, row {row}, col {col}");
}
var z_location = new SizeL(TILE_DOWNSAMPLE * col, TILE_DOWNSAMPLE * row);
var l_location = new System.Drawing.SizeF((float)l_z_downsamples[level] * (z_location.Width - z_overlap_tl.Width),
(float)l_z_downsamples[level] * (z_location.Height - z_overlap_tl.Height));
//Round location down and size up, and add offset of active area
var l0_location = new SizeL((long)(downsamples[os_level] * l_location.Width),
(long)(downsamples[os_level] * l_location.Height));
var l_size = new SizeL((long)Math.Min(Math.Ceiling(l_z_downsamples[level] * z_size.Width), dimensions[os_level].Width),
(long)Math.Min(Math.Ceiling(l_z_downsamples[level] * z_size.Height), dimensions[os_level].Height));
OpenSlide.TraceMsg("calcs done " + level + "/" + col + "_" + row);
var bmp = ReadRegion(l0_location, os_level, l_size);
if (l_size.Width != z_size.Width || l_size.Height != z_size.Height)
{ //only resize when necessary
OpenSlide.TraceMsg("resize " + level + "/" + col + "_" + row);
var oldbmp = bmp;
bmp = new SKBitmap((int)z_size.Width, (int)z_size.Height);
oldbmp.Resize(bmp, SKBitmapResizeMethod.Box);
}
OpenSlide.TraceMsg("new bmp " + level + "/" + col + "_" + row);
var stream = new MemoryStream();
//Prints tile coords for testing
//var g = Graphics.FromImage(resizedbmp);
//g.DrawString(level + "/" + col + "_" + row, new Font(FontFamily.GenericSansSerif, 18), new SolidBrush(Color.Black), resizedbmp.Width / 2, resizedbmp.Height / 2);
bmp.Encode(new SKManagedWStream(stream), SKEncodedImageFormat.Jpeg, 80);
OpenSlide.TraceMsg("end gettile " + level + "/" + col + "_" + row);
stream.Position = 0;
return(stream);
}
private void InitZDimensions()
{
///size on a current dz_level
var z_size = dimensions[0];
z_dimensions.Add(z_size);
while (z_size.Width > 1 || z_size.Height > 1)
{
z_size = new SizeL((long)Math.Max(1, Math.Ceiling(z_size.Width / 2.0)),
(long)Math.Max(1, Math.Ceiling(z_size.Height / 2.0)));
z_dimensions.Add(z_size);
}
z_dimensions.Reverse();
}
private void CheckParameters(int level, SizeL adress)
{
var col = adress.Width;
var row = adress.Height;
if (level < 0 || level >= LevelCount)
{
throw new ArgumentException($"wrong level level {level}, row {row}, col {col}");
}
if (TileDimensions[level].Width <= col || TileDimensions[level].Height <= row ||
0 > col || 0 > row)
{
throw new ArgumentException($"wrong address level {level}, row {row}, col {col}");
}
}
public Header(MetafileReader reader)
{
Bounds = new RectL(reader);
Frame = new RectL(reader);
Signature = reader.ReadUInt32();
Version = reader.ReadUInt32();
NumberOfBytes = reader.ReadUInt32();
NumberOfRecords = reader.ReadUInt32();
NumberOfObjects = reader.ReadUInt16();
Reserved = reader.ReadUInt16();
DescriptionLength = reader.ReadUInt32();
DescriptionOffset = reader.ReadUInt32();
NumberOfPaletteEntries = reader.ReadUInt32();
ReferenceDeviceSizePixels = new SizeL(reader);
ReferenceDeviceSizeMillimeters = new SizeL(reader);
}
private IList <SizeL> GetDeepZoomLevels()
{
var deepZoomSize = Level0Dimensions;
var dzLevelDimensions = new List <SizeL> {
deepZoomSize
};
while (deepZoomSize.Width > 1 || deepZoomSize.Height > 1)
{
var width = (long)Math.Max(1, Math.Ceiling(deepZoomSize.Width / 2.0));
var height = (long)Math.Max(1, Math.Ceiling(deepZoomSize.Height / 2.0));
deepZoomSize = new SizeL(width, height);
dzLevelDimensions.Add(deepZoomSize);
}
dzLevelDimensions.Reverse();
return(dzLevelDimensions);
}
/*Returns an image containing the contents of the region.
* location: (x, y) tuple giving the top left pixel in the level 0 reference frame.
* level: the level number.
* maxSize: (width, height) tuple giving the region maxSize.*/
public override Image ReadRegion(SizeL location, int level, SizeL size)
{
if (image == null)
{
throw new ArgumentNullException();
}
if (level != 0)
{
throw new OpenSlideException("Invalid level");
}
if (size.Width < 0 || size.Height < 0)
{
throw new OpenSlideException($"Size {size} must be non-negative");
}
/* Any corner of the requested region may be outside the bounds of
* the image. Create a transparent tile of the correct maxSize and
* paste the valid part of the region into the correct location.*/
var imageTopLeft = new SizeL(Math.Max(0, Math.Min(location.Width, Dimensions.Width)),
Math.Max(0, Math.Min(location.Height, Dimensions.Height)));
var imageBottomRight = new SizeL(Math.Max(0, Math.Min(location.Width + size.Width - 1, Dimensions.Width - 1)),
Math.Max(0, Math.Min(location.Height + size.Height - 1, Dimensions.Height - 1)));
var tile = new Bitmap((int)size.Width, (int)size.Height);
// Crop maxSize is greater than zero in both dimensions.
if (imageBottomRight.Width - imageTopLeft.Width < 0 &&
imageBottomRight.Height - imageTopLeft.Height < 0)
{
return(tile);
}
var crop = new Rectangle((int)imageTopLeft.Width, (int)imageTopLeft.Height,
(int)(imageTopLeft.Width + imageBottomRight.Width + 1),
(int)(imageTopLeft.Height + imageBottomRight.Height + 1));
var g = Graphics.FromImage(tile);
g.DrawImage(image, 0, 0, crop, GraphicsUnit.Pixel);
return(tile);
}
static void Main(string[] args)
{
string filename = "CMU-1-Small-Region";
var openSlide = new OpenSlide();
//var test = openSlide.GetMPP("CMU-1-Small-Region.svs"); //MPP = microns per pixel
SizeL[] levels = openSlide.Levels($"{filename}.svs");
List <SizeL> dimensions = openSlide.Dimensions($"{filename}.svs");
SizeL maxDimensions = dimensions[dimensions.Count - 1];
//Loads DZI file
GetDZI(openSlide, maxDimensions.Width, maxDimensions.Height, $"{filename}.svs", filename);
for (int level = 0; level < levels.Length; level++)
{
Directory.CreateDirectory($"{filename}_files/{level}");
SizeL levelInfo = levels[level];
for (int row = 0; row < levelInfo.Width; row++)
{
for (int col = 0; col < levelInfo.Height; col++)
{
GetJpg(openSlide, level, row, col, $"{filename}.svs", $"{filename}_files/{level}/{row}_{col}");
}
}
}
Console.WriteLine("Done");
Console.ReadLine();
}
public Image GetThumbnail(SizeL size)
{
return(GetThumbnail(size.ToSize()));
}
public abstract Image GetThumbnail(SizeL maxSize);
/*Returns an Image containing the contents of the region. * location: (x, y) tuple giving the top left pixel in the level 0 reference frame. * level: the level number. * maxSize: (width, height) tuple giving the region maxSize.*/ public abstract Image ReadRegion(SizeL location, int level, SizeL size);
public Image GetTile(int level, SizeL address)
{
// Read tile
CheckParameters(level, address);
var col = address.Width;
var row = address.Height;
// Get preferred slide level
var preferedSlideLevel = BestSlideLevelForDeepZoomLevel[level];
// Calculate top left and bottom right overlap
var topLeftOverlap = new SizeL(col == 0 ? 0 : DeepZoomOverlap,
row == 0 ? 0 : DeepZoomOverlap);
var bottomRightOverlap = new SizeL(col == TileDimensions[level].Width - 1 ? 0 : DeepZoomOverlap,
row == TileDimensions[level].Height - 1 ? 0 : DeepZoomOverlap);
// Get final size of the tile
var finalTileWidth = Math.Min(TileSize, DeepZoomLevelDimensions[level].Width - TileSize * col) +
topLeftOverlap.Width + bottomRightOverlap.Width;
var finalTileHeight = Math.Min(TileSize, DeepZoomLevelDimensions[level].Height - TileSize * row) +
topLeftOverlap.Height + bottomRightOverlap.Height;
var finalTileSize = new SizeL(finalTileWidth, finalTileHeight);
if (finalTileSize.Width < 0 || finalTileSize.Height < 0)
{
throw new ArgumentException($"out of bounds level {level}, row {row}, col {col}");
}
// Obtain the region coordinates
var deepZoomLocation = new SizeL(TileSize * col, TileSize * row);
var levelLocation = new SizeF(
(float)DeepZoomLevelDownsamples[level] * (deepZoomLocation.Width - topLeftOverlap.Width),
(float)DeepZoomLevelDownsamples[level] * (deepZoomLocation.Height - topLeftOverlap.Height));
// Round location down and size up, and add offset of active area
var level0Location = new SizeL(
(long)(Osr.LevelDownsamples[preferedSlideLevel] * levelLocation.Width + Level0Offset.Width),
(long)(Osr.LevelDownsamples[preferedSlideLevel] * levelLocation.Height + Level0Offset.Height));
var regionWidth = (long)Math.Min(Math.Ceiling(DeepZoomLevelDownsamples[level] * finalTileSize.Width),
LevelDimensions[preferedSlideLevel].Width - Math.Ceiling(levelLocation.Width));
var regionHeight = (long)Math.Min(Math.Ceiling(DeepZoomLevelDownsamples[level] * finalTileSize.Height),
LevelDimensions[preferedSlideLevel].Height - Math.Ceiling(levelLocation.Height));
var regionSize = new SizeL(regionWidth, regionHeight);
var tileBmp = Osr.ReadRegion(level0Location, preferedSlideLevel, regionSize);
//Apply on background color (composite)
tileBmp = ApplyOnBackgroundColor(tileBmp);
// Scale to the correct size
var deepZoomSize = finalTileSize;
if (regionSize.Width == deepZoomSize.Width &&
regionSize.Height == deepZoomSize.Height)
{
return(tileBmp);
}
tileBmp = new Bitmap(tileBmp, deepZoomSize.ToSize());
return(tileBmp);
}
