Parasitemia/Parasitemia/GUI/PiaZ.fs

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