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     fileVersion: int
  24 }
  25
  26 // Information associated to each images.
  27 type JSONSourceImage = {
  28     num: int
  29     name: string
  30
  31     RBCRadius: float32 // The RBC Radius found by granulometry.
  32     parameters: ParasitemiaCore.Config.Parameters
  33     dateLastAnalysis: DateTime
  34     rbcs: RBC List
  35
  36     healthyRBCBrightness: float32 // 0 to 1.
  37     infectedRBCBrightness: float32 // 0 to 1.
  38 }
  39
  40 type DocumentData = {
  41     patientID: string
  42     images: SourceImage list
  43 }
  44
  45 let mainEntryName = "info.json"
  46 let imageExtension = ".tiff"
  47 let currentFileVersion = 2
  48
  49 /// <summary>
  50 /// Save a document in a give file path. The file may already exist.
  51 /// </summary>
  52 /// <param name="filePath"></param>
  53 /// <param name="data"></param>
  54 /// <exception cref="System.IOException">If the file cannot be written</exception>
  55 let save (filePath: string) (data: DocumentData) =
  56     use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
  57
  58     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  59         e.Delete()
  60
  61     // Main JSON file.
  62     let mainEntry = file.CreateEntry(mainEntryName, CompressionLevel.Fastest)
  63     use mainEntryWriter = new StreamWriter(mainEntry.Open())
  64     mainEntryWriter.Write(JsonConvert.SerializeObject({ patientID = data.patientID; fileVersion = currentFileVersion }))
  65
  66     // Write each images and the associated information.
  67     for srcImg in data.images do
  68         let imgFilename = (string srcImg.num) + imageExtension
  69         let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  70         srcImg.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
  71
  72         let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
  73         use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
  74         imgJSONFileWriter.Write(
  75             JsonConvert.SerializeObject(
  76                 { num = srcImg.num
  77                   name = srcImg.name
  78                   RBCRadius = srcImg.config.RBCRadius.Pixel
  79                   parameters = srcImg.config.Parameters
  80                   dateLastAnalysis = srcImg.dateLastAnalysis
  81                   rbcs = srcImg.rbcs
  82                   healthyRBCBrightness = srcImg.healthyRBCBrightness
  83                   infectedRBCBrightness = srcImg.infectedRBCBrightness }))
  84
  85 let updateDocumentData (fromVersion: int) (toVersion: int) (data: DocumentData) : DocumentData =
  86     for v in fromVersion + 1 .. toVersion do
  87         match v with
  88         | 1 -> // Version 0 -> 1 : set initial brightness for rbc.
  89             data.images |> List.iter (fun i -> i.healthyRBCBrightness <- 1.f; i.infectedRBCBrightness <- 1.f)
  90         | _ -> ()
  91     data
  92
  93 /// <summary>
  94 /// Load document from a give file path.
  95 /// </summary>
  96 /// <param name="filePath"></param>
  97 /// <exception cref="System.IOException">If the file cannot be read</exception>
  98 let load (filePath: string) : DocumentData =
  99     use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
 100
 101     let mainEntry = file.GetEntry(mainEntryName)
 102     use mainEntryReader = new StreamReader(mainEntry.Open())
 103     let info = JsonConvert.DeserializeObject<JSONInformation>(mainEntryReader.ReadToEnd())
 104
 105     updateDocumentData info.fileVersion currentFileVersion
 106         { patientID = info.patientID
 107           images = [ let mutable imgNum = 0
 108                      for imgEntry in file.Entries do
 109                         if imgEntry.Name.EndsWith(imageExtension)
 110                         then
 111                             use bitmap = new System.Drawing.Bitmap(imgEntry.Open(), false)
 112                             let img = new Image<Bgr, byte>(bitmap)
 113                             imgNum <- imgNum + 1
 114                             let imgJSONEntry = file.GetEntry(imgEntry.Name + ".json")
 115                             use imgJSONFileReader = new StreamReader(imgJSONEntry.Open())
 116                             let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage>(imgJSONFileReader.ReadToEnd())
 117                             let config = ParasitemiaCore.Config.Config(imgInfo.parameters)
 118                             config.SetRBCRadius imgInfo.RBCRadius
 119                             yield { num = imgNum
 120                                     name = imgInfo.name
 121                                     config = config
 122                                     dateLastAnalysis = imgInfo.dateLastAnalysis
 123                                     img = img
 124                                     rbcs = imgInfo.rbcs
 125                                     healthyRBCBrightness = imgInfo.healthyRBCBrightness
 126                                     infectedRBCBrightness = imgInfo.infectedRBCBrightness } ] }