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 // Information associated to each images.
  26 type JSONSourceImage = {
  27     num: int
  28     name: string
  29
  30     RBCRadius: float32 // The RBC Radius found by granulometry.
  31     parameters: ParasitemiaCore.Config.Parameters
  32     dateLastAnalysis: DateTime
  33     rbcs: RBC List
  34
  35     healthyRBCBrightness: float32 // 0 to 1.
  36     infectedRBCBrightness: float32 } // 0 to 1.
  37
  38 type DocumentData = {
  39     patientID: string
  40     images: SourceImage list }
  41
  42 let mainEntryName = "info.json"
  43 let imageExtension = ".tiff"
  44 let currentFileVersion = 2
  45
  46 /// <summary>
  47 /// Save a document in a give file path. The file may already exist.
  48 /// </summary>
  49 /// <param name="filePath"></param>
  50 /// <param name="data"></param>
  51 /// <exception cref="System.IOException">If the file cannot be written</exception>
  52 let save (filePath: string) (data: DocumentData) =
  53     use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
  54
  55     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  56         e.Delete()
  57
  58     // Main JSON file.
  59     let mainEntry = file.CreateEntry(mainEntryName, CompressionLevel.Fastest)
  60     use mainEntryWriter = new StreamWriter(mainEntry.Open())
  61     mainEntryWriter.Write(JsonConvert.SerializeObject({ patientID = data.patientID; fileVersion = currentFileVersion }))
  62
  63     // Write each images and the associated information.
  64     for srcImg in data.images do
  65         let imgFilename = (string srcImg.num) + imageExtension
  66         let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  67         srcImg.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
  68
  69         let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
  70         use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
  71         imgJSONFileWriter.Write(
  72             JsonConvert.SerializeObject(
  73                 { num = srcImg.num
  74                   name = srcImg.name
  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) (defaultConfig: ParasitemiaCore.Config.Config) : 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 imgJSONEntry = file.GetEntry(imgEntry.Name + ".json")
 112                             use imgJSONFileReader = new StreamReader(imgJSONEntry.Open())
 113                             let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage>(imgJSONFileReader.ReadToEnd())
 114
 115                             let config = defaultConfig.Copy()
 116                             config.Parameters <-
 117                                 { ParasitemiaCore.Config.defaultParameters with
 118                                     resolution = imgInfo.parameters.resolution }
 119
 120                             config.SetRBCRadius imgInfo.RBCRadius
 121                             yield { num = imgNum
 122                                     name = imgInfo.name
 123                                     config = config
 124                                     dateLastAnalysis = imgInfo.dateLastAnalysis
 125                                     img = img
 126                                     rbcs = imgInfo.rbcs
 127                                     healthyRBCBrightness = imgInfo.healthyRBCBrightness
 128                                     infectedRBCBrightness = imgInfo.infectedRBCBrightness } ] }