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     {
  23         patientID : string
  24         fileVersion : int
  25     }
  26
  27 // Information associated to each images.
  28 type JSONSourceImage =
  29     {
  30         num : int
  31         name : string
  32
  33         RBCRadius : float32 // The RBC Radius found by granulometry.
  34         parameters : ParasitemiaCore.Config.Parameters
  35         dateLastAnalysis : DateTime
  36         rbcs : RBC List
  37
  38         healthyRBCBrightness : float32 // 0 to 1.
  39         infectedRBCBrightness : float32 // 0 to 1.
  40     }
  41
  42 type DocumentData =
  43     {
  44         patientID : string
  45         images : SourceImage list
  46     }
  47
  48 let mainEntryName = "info.json"
  49 let imageExtension = ".tiff"
  50 let currentFileVersion = 2
  51
  52 /// <summary>
  53 /// Save a document in a give file path. The file may already exist.
  54 /// </summary>
  55 /// <param name="filePath"></param>
  56 /// <param name="data"></param>
  57 /// <exception cref="System.IOException">If the file cannot be written</exception>
  58 let save (filePath : string) (data : DocumentData) =
  59     use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
  60
  61     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  62         e.Delete()
  63
  64     // Main JSON file.
  65     let mainEntry = file.CreateEntry(mainEntryName, CompressionLevel.Fastest)
  66     use mainEntryWriter = new StreamWriter(mainEntry.Open())
  67     mainEntryWriter.Write(JsonConvert.SerializeObject({ patientID = data.patientID; fileVersion = currentFileVersion }))
  68
  69     // Write each images and the associated information.
  70     for srcImg in data.images do
  71         let imgFilename = (string srcImg.num) + imageExtension
  72         let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  73         srcImg.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
  74
  75         let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
  76         use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
  77         imgJSONFileWriter.Write(
  78             JsonConvert.SerializeObject(
  79                 {
  80                     num = srcImg.num
  81                     name = srcImg.name
  82                     RBCRadius = srcImg.config.RBCRadius.Pixel
  83                     parameters = srcImg.config.Parameters
  84                     dateLastAnalysis = srcImg.dateLastAnalysis
  85                     rbcs = srcImg.rbcs
  86                     healthyRBCBrightness = srcImg.healthyRBCBrightness
  87                     infectedRBCBrightness = srcImg.infectedRBCBrightness
  88                 }
  89             )
  90         )
  91
  92 let updateDocumentData (fromVersion : int) (toVersion : int) (data : DocumentData) : DocumentData =
  93     for v in fromVersion + 1 .. toVersion do
  94         match v with
  95         | 1 -> // Version 0 -> 1 : set initial brightness for rbc.
  96             data.images |> List.iter (fun i -> i.healthyRBCBrightness <- 1.f; i.infectedRBCBrightness <- 1.f)
  97         | _ -> ()
  98     data
  99
 100 /// <summary>
 101 /// Load document from a give file path.
 102 /// </summary>
 103 /// <param name="filePath"></param>
 104 /// <exception cref="System.IOException">If the file cannot be read</exception>
 105 let load (filePath : string) (defaultConfig : ParasitemiaCore.Config.Config) : DocumentData =
 106     use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
 107
 108     let mainEntry = file.GetEntry(mainEntryName)
 109     use mainEntryReader = new StreamReader(mainEntry.Open())
 110     let info = JsonConvert.DeserializeObject<JSONInformation>(mainEntryReader.ReadToEnd())
 111
 112     updateDocumentData info.fileVersion currentFileVersion
 113         {
 114             patientID = info.patientID
 115             images =
 116                 [
 117                     let mutable imgNum = 0
 118                     for imgEntry in file.Entries do
 119                         if imgEntry.Name.EndsWith(imageExtension) then
 120                             use bitmap = new System.Drawing.Bitmap(imgEntry.Open(), false)
 121                             let img = new Image<Bgr, byte>(bitmap)
 122                             imgNum <- imgNum + 1
 123                             let imgJSONEntry = file.GetEntry(imgEntry.Name + ".json")
 124                             use imgJSONFileReader = new StreamReader(imgJSONEntry.Open())
 125                             let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage>(imgJSONFileReader.ReadToEnd())
 126
 127                             let config = defaultConfig.Copy()
 128                             config.Parameters <-
 129                                 {
 130                                     ParasitemiaCore.Config.defaultParameters with
 131                                         resolution = imgInfo.parameters.resolution
 132                                 }
 133
 134                             config.SetRBCRadius imgInfo.RBCRadius
 135                             yield
 136                                 {
 137                                     num = imgNum
 138                                     name = imgInfo.name
 139                                     config = config
 140                                     dateLastAnalysis = imgInfo.dateLastAnalysis
 141                                     img = img
 142                                     rbcs = imgInfo.rbcs
 143                                     healthyRBCBrightness = imgInfo.healthyRBCBrightness
 144                                     infectedRBCBrightness = imgInfo.infectedRBCBrightness
 145                                 }
 146                 ]
 147         }