Parasitemia/Parasitemia/GUI/Pia.fs

   1 // ParasitemIA file format.
   2 module Parasitemia.GUI.Pia
   3
   4 open System.Windows
   5 open System.IO
   6 open System.IO.Compression
   7
   8 open FSharp.Data
   9
  10 open Emgu.CV
  11 open Emgu.CV.Structure
  12
  13 open Types
  14
  15 let extension = ".pia"
  16 let filter = "PIA|*.pia"
  17
  18 type FileData = {
  19     sources: SourceImage list
  20     patientID: string }
  21
  22 // The json type associated to a source image.
  23 type JSONSourceImage = JsonProvider<"""
  24     {
  25         "rbcs": [
  26             {
  27                 "num": 1,
  28                 "infected": true,
  29                 "addedManually": false,
  30                 "removed": false,
  31                 "posX" : 42.5,
  32                 "posY" : 42.5,
  33                 "width" : 10.5,
  34                 "height" : 10.5,
  35                 "stainArea" : 10
  36             }
  37         ]
  38     }
  39 """>
  40
  41 // The json type associated to a file.
  42 type JSONMainInformation = JsonProvider<"""
  43     {
  44         "patientID": "1234abcd"
  45     }
  46 """>
  47
  48 let mainFilename = "info.json"
  49 let imageExtension = ".tiff"
  50
  51 let save (filePath: string) (data: FileData) =
  52     use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
  53
  54     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  55         e.Delete()
  56
  57     // Main JSON file.
  58     let mainJSON = JSONMainInformation.Root(data.patientID)
  59     let mainFile = file.CreateEntry(mainFilename, CompressionLevel.Fastest)
  60     use mainFileWriter = new StreamWriter(mainFile.Open())
  61     mainJSON.JsonValue.WriteTo(mainFileWriter, JsonSaveOptions.None)
  62
  63     // Write each images and the associated information.
  64     for imgSrc in data.sources do
  65         let imgFilename = (string imgSrc.num) + imageExtension
  66         let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  67         imgSrc.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
  68
  69         let imgJSON =
  70             JSONSourceImage.Root([| for rbc in imgSrc.rbcs ->
  71                                         JSONSourceImage.Rbc(
  72                                             rbc.num,
  73                                             rbc.infected, rbc.addedManually, rbc.removed,
  74                                             decimal rbc.center.X, decimal rbc.center.Y, decimal rbc.size.Width, decimal rbc.size.Height,
  75                                             rbc.stainArea) |])
  76
  77         let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
  78         use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
  79         imgJSON.JsonValue.WriteTo(imgJSONFileWriter, JsonSaveOptions.None)
  80
  81
  82 let load (filePath: string) : FileData =
  83     use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
  84
  85     let mainFile = file.GetEntry(mainFilename)
  86     let mainJSON = JSONMainInformation.Load(mainFile.Open())
  87
  88     let sources = [
  89         let mutable imgNum = 0
  90         for imgEntry in file.Entries do
  91             let filename = imgEntry.Name
  92             if filename.EndsWith(imageExtension)
  93             then
  94                 let img = new Image<Bgr, byte>(new System.Drawing.Bitmap(imgEntry.Open(), false)) // FIXME: Should we dispose the bitmap?
  95                 imgNum <- imgNum + 1
  96                 let imgJSONEntry = file.GetEntry(filename + ".json")
  97                 let imgJSON = JSONSourceImage.Load(imgJSONEntry.Open())
  98                 yield { num = imgNum; img = img; rbcs = [ for rbc in imgJSON.Rbcs ->
  99                                                             { num = rbc.Num;
 100                                                               infected = rbc.Infected; addedManually = rbc.AddedManually; removed = rbc.Removed;
 101                                                               center = Point(float rbc.PosX, float rbc.PosY); size = Size(float rbc.Width, float rbc.Height);
 102                                                               stainArea = rbc.StainArea } ] } ]
 103     { sources = sources; patientID = mainJSON.PatientId }