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