Parasitemia/Parasitemia/GUI/PiaZ.fs

   1 // ParasitemIA Zipped file format.
   2 module Parasitemia.GUI.PiaZ
   3
   4 open System
   5 open System.Windows
   6 open System.IO
   7 open System.IO.Compression
   8
   9 open FSharp.Data
  10
  11 open Emgu.CV
  12 open Emgu.CV.Structure
  13
  14 open Types
  15
  16 let extension = ".piaz"
  17 let filter = "PIA|*.piaz"
  18
  19 type FileData = {
  20     sources: SourceImage list
  21     patientID: string }
  22
  23 // The json type associated to a source image.
  24 type JSONSourceImage = JsonProvider<"""
  25     {
  26         "RBCRadius" : 32.5,
  27         "dateLastAnalysis" : 1.5,
  28         "rbcs": [
  29             {
  30                 "num": 1,
  31                 "infected": true,
  32                 "setManually": false,
  33                 "posX" : 42.5,
  34                 "posY" : 42.5,
  35                 "width" : 10.5,
  36                 "height" : 10.5,
  37                 "stainArea" : 10
  38             }
  39         ]
  40     }
  41 """>
  42
  43 // The json type associated to a file.
  44 type JSONMainInformation = JsonProvider<"""
  45     {
  46         "patientID": "1234abcd"
  47     }
  48 """>
  49
  50 let mainFilename = "info.json"
  51 let imageExtension = ".tiff"
  52
  53 let save (filePath: string) (data: FileData) =
  54     use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
  55
  56     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  57         e.Delete()
  58
  59     // Main JSON file.
  60     let mainJSON = JSONMainInformation.Root(data.patientID)
  61     let mainFile = file.CreateEntry(mainFilename, CompressionLevel.Fastest)
  62     use mainFileWriter = new StreamWriter(mainFile.Open())
  63     mainJSON.JsonValue.WriteTo(mainFileWriter, JsonSaveOptions.None)
  64
  65     // Write each images and the associated information.
  66     for imgSrc in data.sources do
  67         let imgFilename = (string imgSrc.num) + imageExtension
  68         let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  69         imgSrc.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
  70
  71         let imgJSON =
  72             JSONSourceImage.Root(decimal imgSrc.rbcRadius,
  73                                  decimal <| imgSrc.dateLastAnalysis.ToFileTimeUtc(),
  74                                  [| for rbc in imgSrc.rbcs ->
  75                                        JSONSourceImage.Rbc(
  76                                             rbc.num,
  77                                             rbc.infected, rbc.setManually,
  78                                             decimal rbc.center.X, decimal rbc.center.Y, decimal rbc.size.Width, decimal rbc.size.Height,
  79                                             rbc.infectedArea) |])
  80
  81         let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
  82         use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
  83         imgJSON.JsonValue.WriteTo(imgJSONFileWriter, JsonSaveOptions.None)
  84
  85
  86 let load (filePath: string) : FileData =
  87     use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
  88
  89     let mainFile = file.GetEntry(mainFilename)
  90     let mainJSON = JSONMainInformation.Load(mainFile.Open())
  91
  92     let sources = [
  93         let mutable imgNum = 0
  94         for imgEntry in file.Entries do
  95             let filename = imgEntry.Name
  96             if filename.EndsWith(imageExtension)
  97             then
  98                 let img = new Image<Bgr, byte>(new System.Drawing.Bitmap(imgEntry.Open(), false)) // FIXME: Should we dispose the bitmap?
  99                 imgNum <- imgNum + 1
 100                 let imgJSONEntry = file.GetEntry(filename + ".json")
 101                 let imgJSON = JSONSourceImage.Load(imgJSONEntry.Open())
 102                 yield { num = imgNum
 103                         rbcRadius = float imgJSON.RbcRadius
 104                         dateLastAnalysis = DateTime.FromFileTimeUtc(int64 imgJSON.DateLastAnalysis)
 105                         img = img
 106                         rbcs = [ for rbc in imgJSON.Rbcs ->
 107                                     { num = rbc.Num;
 108                                       infected = rbc.Infected; setManually = rbc.SetManually;
 109                                       center = Point(float rbc.PosX, float rbc.PosY); size = Size(float rbc.Width, float rbc.Height);
 110                                       infectedArea = rbc.StainArea } ] } ]
 111     { sources = sources; patientID = mainJSON.PatientId }