Parasitemia/ParasitemiaUI/PiaZ.fs

   1 // ParasitemIA Zipped document format.
   2 module ParasitemiaUI.PiaZ
   3
   4 open System
   5 open System.Windows
   6 open System.IO
   7 open System.IO.Compression
   8
   9 open Emgu.CV
  10 open Emgu.CV.Structure
  11
  12 open Newtonsoft.Json
  13 open Newtonsoft.Json.Converters
  14
  15 open Types
  16
  17 let extension = ".piaz"
  18 let filter = "PIA|*.piaz"
  19
  20 // Information associated to a document.
  21 type JSONInformation = {
  22     patientID: string
  23 }
  24
  25 // Information associated to each images.
  26 type JSONSourceImage = {
  27     num: int
  28     RBCRadius: float32 // The RBC Radius found by granulometry.
  29     parameters: ParasitemiaCore.Config.Parameters
  30     dateLastAnalysis: DateTime
  31     rbcs: RBC List
  32 }
  33
  34 type DocumentData = {
  35     patientID: string
  36     images: SourceImage list
  37 }
  38
  39 let mainEntryName = "info.json"
  40 let imageExtension = ".tiff"
  41
  42 /// <summary>
  43 /// Save a document in a give file path. The file may already exist.
  44 /// </summary>
  45 /// <param name="filePath"></param>
  46 /// <param name="data"></param>
  47 /// <exception cref="System.IOException">If the file cannot be written</exception>
  48 let save (filePath: string) (data: DocumentData) =
  49     use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
  50
  51     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  52         e.Delete()
  53
  54     // Main JSON file.
  55     let mainEntry = file.CreateEntry(mainEntryName, CompressionLevel.Fastest)
  56     use mainEntryWriter = new StreamWriter(mainEntry.Open())
  57     mainEntryWriter.Write(JsonConvert.SerializeObject({ JSONInformation.patientID = data.patientID }))
  58
  59     // Write each images and the associated information.
  60     for srcImg in data.images do
  61         let imgFilename = (string srcImg.num) + imageExtension
  62         let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  63         srcImg.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
  64
  65         let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
  66         use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
  67         imgJSONFileWriter.Write(JsonConvert.SerializeObject({ num = srcImg.num; RBCRadius = srcImg.config.RBCRadius.Pixel; parameters = srcImg.config.Parameters; dateLastAnalysis = srcImg.dateLastAnalysis; rbcs = srcImg.rbcs }))
  68
  69 /// <summary>
  70 /// Load document from a give file path.
  71 /// </summary>
  72 /// <param name="filePath"></param>
  73 /// <exception cref="System.IOException">If the file cannot be read</exception>
  74 let load (filePath: string) : DocumentData =
  75     use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
  76
  77     let mainEntry = file.GetEntry(mainEntryName)
  78     use mainEntryReader = new StreamReader(mainEntry.Open())
  79     let info = JsonConvert.DeserializeObject<JSONInformation>(mainEntryReader.ReadToEnd())
  80
  81     { patientID = info.patientID
  82       images = [ let mutable imgNum = 0
  83                  for imgEntry in file.Entries do
  84                     if imgEntry.Name.EndsWith(imageExtension)
  85                     then
  86                         let img = new Image<Bgr, byte>(new System.Drawing.Bitmap(imgEntry.Open(), false)) // FIXME: Should we dispose the bitmap?
  87                         imgNum <- imgNum + 1
  88                         let imgEntry = file.GetEntry(imgEntry.Name + ".json")
  89                         use imgEntryFileReader = new StreamReader(imgEntry.Open())
  90                         let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage>(imgEntryFileReader.ReadToEnd())
  91                         let config = ParasitemiaCore.Config.Config(imgInfo.parameters)
  92                         config.SetRBCRadius imgInfo.RBCRadius
  93                         yield { num = imgNum
  94                                 config = config
  95                                 dateLastAnalysis = imgInfo.dateLastAnalysis
  96                                 img = img
  97                                 rbcs = imgInfo.rbcs } ] }