Parasitemia/ParasitemiaUI/PiaZ.fs

   1 // ParasitemIA Zipped document format.
   2 module ParasitemiaUI.PiaZ
   3
   4 open System
   5 open System.IO
   6 open System.IO.Compression
   7
   8 open Emgu.CV
   9 open Emgu.CV.Structure
  10
  11 open Newtonsoft.Json
  12
  13 open Types
  14
  15 let extension = ".piaz"
  16 let filter = "PIA|*.piaz"
  17
  18 // Information associated to a document.
  19 type JSONInformation =
  20     {
  21         patientID : string
  22         fileVersion : int
  23     }
  24
  25 // Information associated to each images.
  26 type JSONSourceImage =
  27     {
  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     {
  42         patientID : string
  43         images : SourceImage list
  44     }
  45
  46 let mainEntryName = "info.json"
  47 let imageExtension = ".tiff"
  48 let currentFileVersion = 2
  49
  50 /// <summary>
  51 /// Save a document in a give file path. The file may already exist.
  52 /// </summary>
  53 /// <param name="filePath"></param>
  54 /// <param name="data"></param>
  55 /// <exception cref="System.IOException">If the file cannot be written</exception>
  56 let save (filePath : string) (data : DocumentData) =
  57     use file = ZipFile.Open (filePath, ZipArchiveMode.Update)
  58
  59     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  60         e.Delete ()
  61
  62     // Main JSON file.
  63     let mainEntry = file.CreateEntry (mainEntryName, CompressionLevel.Fastest)
  64     use mainEntryWriter = new StreamWriter (mainEntry.Open ())
  65     mainEntryWriter.Write (JsonConvert.SerializeObject ({ patientID = data.patientID; fileVersion = currentFileVersion }))
  66
  67     // Write each images and the associated information.
  68     for srcImg in data.images do
  69         let imgFilename = (string srcImg.Num) + imageExtension
  70         let imgEntry = file.CreateEntry (imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
  71         srcImg.Img.ToBitmap().Save (imgEntry.Open (), System.Drawing.Imaging.ImageFormat.Tiff)
  72
  73         let imgJSONEntry = file.CreateEntry (imgFilename + ".json", CompressionLevel.Fastest)
  74         use imgJSONFileWriter = new StreamWriter (imgJSONEntry.Open ())
  75         imgJSONFileWriter.Write (
  76             JsonConvert.SerializeObject (
  77                 {
  78                     num = srcImg.Num
  79                     name = srcImg.Name
  80                     RBCRadius = srcImg.Config.RBCRadius.Pixel
  81                     parameters = srcImg.Config.Parameters
  82                     dateLastAnalysis = srcImg.DateLastAnalysis
  83                     rbcs = srcImg.RBCs
  84                     healthyRBCBrightness = srcImg.HealthyRBCBrightness
  85                     infectedRBCBrightness = srcImg.InfectedRBCBrightness
  86                 }
  87             )
  88         )
  89
  90 let updateDocumentData (fromVersion : int) (toVersion : int) (data : DocumentData) : DocumentData =
  91     for v in fromVersion + 1 .. toVersion do
  92         match v with
  93         | 1 -> // Version 0 -> 1 : set initial brightness for rbc.
  94             data.images |> List.iter (fun i -> i.HealthyRBCBrightness <- 1.f; i.InfectedRBCBrightness <- 1.f)
  95         | _ -> ()
  96     data
  97
  98 /// <summary>
  99 /// Load document from a give file path.
 100 /// </summary>
 101 /// <param name="filePath">Path to the PiaZ file</param>
 102 /// <param name="defaultConfig"></param>
 103 /// <exception cref="System.IOException">If the file cannot be read</exception>
 104 let load (filePath : string) (defaultConfig : ParasitemiaCore.Config.Config) : DocumentData =
 105     use file = ZipFile.Open (filePath, ZipArchiveMode.Read)
 106
 107     let mainEntry = file.GetEntry (mainEntryName)
 108     use mainEntryReader = new StreamReader (mainEntry.Open ())
 109     let info = JsonConvert.DeserializeObject<JSONInformation> (mainEntryReader.ReadToEnd ())
 110
 111     updateDocumentData info.fileVersion currentFileVersion
 112         {
 113             patientID = info.patientID
 114             images =
 115                 [
 116                     let mutable imgNum = 0
 117                     for imgEntry in file.Entries do
 118                         if imgEntry.Name.EndsWith (imageExtension) then
 119                             use bitmap = new System.Drawing.Bitmap (imgEntry.Open (), false)
 120                             let img = bitmap.ToImage<Bgr, byte> ()
 121                             imgNum <- imgNum + 1
 122                             let imgJSONEntry = file.GetEntry (imgEntry.Name + ".json")
 123                             use imgJSONFileReader = new StreamReader (imgJSONEntry.Open ())
 124                             let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage> (imgJSONFileReader.ReadToEnd ())
 125
 126                             let config = defaultConfig.Copy ()
 127                             config.Parameters <-
 128                                 {
 129                                     ParasitemiaCore.Config.defaultParameters with
 130                                         resolution = imgInfo.parameters.resolution
 131                                 }
 132
 133                             config.SetRBCRadius imgInfo.RBCRadius
 134
 135                             SourceImage (imgNum, imgInfo.name, config, imgInfo.dateLastAnalysis, img, imgInfo.rbcs, HealthyRBCBrightness = imgInfo.healthyRBCBrightness, InfectedRBCBrightness = imgInfo.infectedRBCBrightness)
 136                 ]
 137         }