private static void InsertSlides(SlideInfoDbContext context)
{
if (context.Slides.Any())
{
return;
}
var dirs = FileFilter.Filter(AppDirectories.SlideStorage, FileFilter.OpenSlideExtensions);
foreach (var path in dirs)
{
var osr = new OpenSlide(path);
var slide = new Slide(osr);
context.Slides.Add(slide);
context.SaveChanges();
var properties = osr.ReadProperties();
foreach (var slideProp in properties)
{
var property = new Property(slide.Id, slideProp.Key, slideProp.Value);
context.Properties.Add(property);
}
}
context.SaveChanges();
}
public IActionResult AssociatedTile(int?id, string imageName, int level, int col, int row)
{
logger.LogInformation("Getting tile of {slug} | lev: {level}, col: {col}, row: {row}", imageName, level, col, row);
try
{
var slide = context.Slides.FirstOrDefault(m => m.Id == id);
if (slide != null)
{
using (var osr = new OpenSlide(slide.FilePath))
{
var associated = osr.AssociatedImages[imageName].ToImageSlide();
var viewModel = new DisplayViewModel(slide.Name, slide.DziUrl, slide.Mpp, associated);
var tile = viewModel.DeepZoomGenerator.GetTile(level, new SizeL(col, row));
using (var stream = new MemoryStream())
{
tile.Save(stream, ImageFormat.Jpeg);
tile.Dispose();
return(File(stream.ToArray(), "image/jpeg"));
}
}
}
}
catch (OpenSlideException)
{
logger.LogError("Error while getting tile | lev: {level}, col: {col}, row: {row}", level, col, row);
HttpContext.Session.SetString(SessionConstants.ALERT, SessionConstants.CANT_LOAD_DATA);
}
return(new FileContentResult(new byte[] { }, ""));
}
// GET: Slides/Display/5
public async Task <IActionResult> Display(int?id)
{
logger.LogInformation("Getting slide {ID} to display...", id);
if (id == null)
{
logger.LogWarning("Slide id was null");
return(NotFound());
}
var slide = await context.Slides.FindAsync(id.Value);
if (slide == null)
{
logger.LogError("GetById({ID}) NOT FOUND", id);
return(NotFound());
}
HttpContext.Session.Set(SessionConstants.CURRENT_SLIDE, slide);
ViewData[SLIDE_ID] = slide.Id.ToString();
HttpContext.Session.SetString(SLIDE_ID, slide.Id.ToString());
ViewData[SLIDE_NAME] = slide.Name;
ViewData[HAS_ASSOCIATED_IMAGES] = slide.HasAssociatedImages;
var comments = context.Comments.Where(c => c.SlideId == id);
ViewData[HAS_COMMENTS] = comments.Any();
var osr = new OpenSlide(slide.FilePath);
var viewModel = new DisplayViewModel(slide.Name, slide.DziUrl, slide.Mpp, osr);
return(View(viewModel));
}
public IActionResult Tile(string slug, int level, int col, int row)
{
try
{
logger.LogInformation("Getting tile: {level}, col: {col}, row: {row}", level, col, row);
var slide = HttpContext.Session.Get <Slide>(SessionConstants.CURRENT_SLIDE) ?? context.Slides.FirstOrDefault(m => m.Url == slug);
if (slide != null)
{
using (var osr = new OpenSlide(slide.FilePath))
{
var viewModel = new DisplayViewModel(slide.Name, slide.DziUrl, slide.Mpp, osr);
var tile = viewModel.DeepZoomGenerator.GetTile(level, new SizeL(col, row));
using (var stream = new MemoryStream())
{
tile.Save(stream, ImageFormat.Jpeg);
tile.Dispose();
return(File(stream.ToArray(), "image/jpeg"));
}
}
}
}
catch (OpenSlideException)
{
logger.LogError("Error while getting tile lev: {level}, col: {col}, row: {row}", level, col, row);
HttpContext.Session.SetString(SessionConstants.ALERT, SessionConstants.CANT_LOAD_DATA);
}
return(new FileContentResult(new byte[] { }, ""));
}
private void GenerateSlideThumbnails(ICollection <Slide> slides)
{
Directory.CreateDirectory(AppDirectories.SlideThumbs);
var existingThumbs = from file in Directory.EnumerateFiles(AppDirectories.SlideThumbs, "*.jpeg")
select file;
var existingThumbsCount = existingThumbs.Count();
if (slides.Count == existingThumbsCount)
{
return;
}
foreach (var slide in slides)
{
var existingSlideThumb = from file in existingThumbs
where file.ToLower().Contains($"{slide.Name.ToUrlSlug()}")
select file;
if (existingSlideThumb.Any())
{
continue;
}
logger.LogInformation("Generating thumbnail of slide {id}: {name}..", slide.Id, slide.Name);
using (var osr = new OpenSlide(slide.FilePath))
{
var thumb = osr.GetThumbnail(new Size(400, 400));
thumb.Save($@"{AppDirectories.SlideThumbs}{slide.Name.ToUrlSlug()}.jpeg", ImageFormat.Jpeg);
}
}
}
public static void UpdateSlides(SlideInfoDbContext context)
{
context.Database.EnsureCreated();
var dirs = FileFilter.Filter(AppDirectories.SlideStorage, FileFilter.OpenSlideExtensions);
foreach (var path in dirs)
{
var osr = new OpenSlide(path);
var newSlide = new Slide(osr);
var existingSlide = context.Slides.FirstOrDefault(s => s.FilePath == path);
if (existingSlide != null)
{
newSlide.Id = existingSlide.Id;
context.Entry(existingSlide).CurrentValues.SetValues(newSlide);
}
else
{
context.Add(newSlide);
var properties = osr.ReadProperties();
foreach (var slideProp in properties)
{
var property = new Property(newSlide.Id, slideProp.Key, slideProp.Value);
context.Add(property);
}
}
}
context.SaveChanges();
}
public void TestDetectFormat()
{
var osr = new OpenSlide();
Assert.IsTrue(osr.DetectFormat("nonExisting") == null);
Assert.IsTrue(osr.DetectFormat("setup.py") == null);
Assert.IsTrue(osr.DetectFormat("tests/boxes.tiff") == "generic-tiff");
}
public void TestReadRegionOnClosedHandle()
{
var osr = new OpenSlide("tests/boxes.tiff");
osr.Close();
osr.ReadRegion(new SizeL(0, 0), 0, new SizeL(100, 100));
}
public AssociatedImagesWriter(string fileName, string outDirectory = "out", string format = "bmp", int quality = 75)
{
this.fileName = fileName;
fileNameWithoutExtension = FileName.GetFileNameWithoutExtension(fileName);
this.outDirectory = outDirectory;
this.format = format;
this.quality = quality;
osr = new OpenSlide(fileName);
pathBuilder = new StringBuilder();
}
static void GetJpg(OpenSlide openSlide, int level, int row, int col, string filename, string outputname)
{
using (var stream = openSlide.GetJpg(filename, $"_files/{level}/{row}_{col}.jpeg"))
{
if (stream.TryGetBuffer(out ArraySegment <byte> buffer))
{
Console.WriteLine($"{outputname}.jpeg successfully created!");
File.WriteAllBytes($"{outputname}.jpeg", buffer.ToArray());
}
else
{
Console.WriteLine($"{outputname}.jpeg failed...");
}
}
}
static void GetDZI(OpenSlide openSlide, long width, long height, string filename, string outputname)
{
using (var stream = openSlide.GetDZI(filename, out width, out height))
{
if (stream.TryGetBuffer(out ArraySegment <byte> buffer))
{
Console.WriteLine($"{outputname}.dzi successfully created!");
File.WriteAllBytes($"{outputname}.dzi", buffer.ToArray());
}
else
{
Console.WriteLine($"{outputname}.dzi failed...");
}
}
}
public DeepZoomTiler(string fileName, string outDirectory = "out", string format = "jpeg", int quality = 75, int tileSize = 254, int overlap = 1, bool limitBounds = true)
{
this.fileName = fileName;
fileNameWithoutExtension = FileName.GetFileNameWithoutExtension(fileName);
this.outDirectory = outDirectory;
this.format = format;
this.quality = quality;
this.tileSize = tileSize;
this.overlap = overlap;
this.limitBounds = limitBounds;
osr = new OpenSlide(fileName);
dz = new DeepZoomGenerator(osr, tileSize, overlap, limitBounds);
pathBuilder = new StringBuilder();
processedTilesCount = 0;
}
// GET: Slides/AssociatedImages/5
public async Task <IActionResult> AssociatedImages(int?id, string imageName)
{
logger.LogInformation("Getting associated images of slide {ID}...", id);
if (id == null)
{
return(NotFound());
}
var slide = await context.Slides.FindAsync(id.Value);
if (slide == null)
{
return(NotFound());
}
ViewData[SLIDE_NAME] = slide.Name;
ViewData[SLIDE_ID] = id.ToString();
HttpContext.Session.SetString(SLIDE_ID, slide.Id.ToString());
ViewData[HAS_ASSOCIATED_IMAGES] = slide.HasAssociatedImages;
var comments = context.Comments.Where(c => c.SlideId == id);
ViewData[HAS_COMMENTS] = comments.Any();
var osr = new OpenSlide(slide.FilePath);
if (!String.IsNullOrEmpty(imageName))
{
logger.LogInformation("Getting associated image {name} of slide {ID}...", imageName, id);
var associatedSlide = osr.AssociatedImages[imageName].ToImageSlide();
var imageUrl = slide.Id + "/" + imageName + ".dzi";
var displayViewModel = new DisplayViewModel(imageName, imageUrl, 0, associatedSlide);
return(View("Display", displayViewModel));
}
var associated = osr.ReadAssociatedImages();
GenerateAssociatedImagesThumbnails(id.Value, associated);
var viewModel = new AssociatedImagesViewModel(slide.Name, associated);
return(View(viewModel));
}
public Slide(OpenSlide osr)
{
FilePath = osr.FilePath;
Name = Path.GetFileName(FilePath);
Url = UrlFormatter.UrlFor(Name);
Vendor = osr.DetectFormat(FilePath);
Width = osr.Dimensions.Width;
Height = osr.Dimensions.Height;
HasAssociatedImages = osr.ReadAssociatedImages().Any();
try
{
double.TryParse(osr.Properties[OpenSlide.PROPERTY_NAME_MPP_X], out double mppX);
double.TryParse(osr.Properties[OpenSlide.PROPERTY_NAME_MPP_Y], out double mppY);
Mpp = (mppX + mppY) / 2;
}
catch (Exception)
{
Mpp = 0;
}
}
public string Dzi(string slug)
{
try
{
logger.LogInformation("Getting {slug}.dzi metadata...", slug);
var slide = HttpContext.Session.Get <Slide>(SessionConstants.CURRENT_SLIDE) ?? context.Slides.FirstOrDefault(m => m.Url == slug);
if (slide != null)
{
using (var osr = new OpenSlide(slide.FilePath))
{
var viewModel = new DisplayViewModel(slide.Name, slide.DziUrl, slide.Mpp, osr);
return(viewModel.DeepZoomGenerator.GetDziMetadataString());
}
}
}
catch (Exception)
{
logger.LogError("Error while getting {slug}.dzi", slug);
HttpContext.Session.SetString(SessionConstants.ALERT, SessionConstants.NO_ACCESS);
}
return("");
}
public string AssociatedDzi(int?id, string imageName)
{
logger.LogInformation("Getting {slug}.dzi metadata...", imageName);
try
{
var slide = context.Slides.FirstOrDefault(m => m.Id == id);
if (slide != null)
{
using (var osr = new OpenSlide(slide.FilePath))
{
var associated = osr.AssociatedImages[imageName].ToImageSlide();
var viewModel = new DisplayViewModel(slide.Name, slide.DziUrl, slide.Mpp, associated);
return(viewModel.DeepZoomGenerator.GetDziMetadataString());
}
}
}
catch (Exception)
{
logger.LogError("Error while getting {slug}.dzi", imageName);
HttpContext.Session.SetString(SessionConstants.ALERT, SessionConstants.NO_ACCESS);
}
return("");
}
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 Slide(string pathToSlide)
{
FilePath = pathToSlide;
Name = Path.GetFileName(pathToSlide);
Url = UrlFormatter.UrlFor(Name);
Vendor = OpenSlide.DetectVendor(pathToSlide);
using (var osr = new OpenSlide(pathToSlide))
{
try
{
double.TryParse(osr.Properties[OpenSlide.PROPERTY_NAME_MPP_X], out double mppX);
double.TryParse(osr.Properties[OpenSlide.PROPERTY_NAME_MPP_Y], out double mppY);
Mpp = (mppX + mppY) / 2;
}
catch (Exception)
{
Mpp = 0;
}
Width = osr.Dimensions.Width;
Height = osr.Dimensions.Height;
HasAssociatedImages = osr.ReadAssociatedImages().Any();
}
}
public void SetUp()
{
osr = new OpenSlide("tests/boxes.tiff");
dz = new DeepZoomGenerator(osr);
}
public void SetUp()
{
osr = new OpenSlide(fileName);
}
public void TestContextManager()
{
var osr = new OpenSlide("tests/boxes.tiff");
Assert.AreEqual(4, osr.LevelCount);
}
