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 MAIN_ENTRY_NAME = "info.json"
  47 let DEFAULT_IMAGE_EXTENSION = ".tiff"
  48 let JSON_EXTENSION = ".json"
  49 let CURRENT_FILE_VERSION = 3
  50
  51 /// <summary>
  52 /// Save a document in a give file path. The file may already exist.
  53 /// </summary>
  54 /// <param name="filePath"></param>
  55 /// <param name="data"></param>
  56 /// <exception cref="System.IOException">If the file cannot be written</exception>
  57 let save (filePath : string) (data : DocumentData) =
  58     use file = ZipFile.Open (filePath, ZipArchiveMode.Update)
  59
  60     // We only delete JSON files and removed images.
  61     for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
  62         if Path.GetExtension e.Name = JSON_EXTENSION || data.images |> List.exists (fun img -> img.OriginalName = e.Name) |> not then
  63             e.Delete ()
  64
  65     // Main JSON file.
  66     let mainEntry = file.CreateEntry (MAIN_ENTRY_NAME, CompressionLevel.Fastest)
  67     use mainEntryWriter = new StreamWriter (mainEntry.Open ())
  68     mainEntryWriter.Write (JsonConvert.SerializeObject ({ patientID = data.patientID; fileVersion = CURRENT_FILE_VERSION }))
  69
  70     // Write each images and the associated information as a JSON file.
  71     for srcImg in data.images do
  72         match srcImg.TempFile with
  73         | Some imgTempFile ->
  74             let imgEntry = file.CreateEntry (srcImg.OriginalName, CompressionLevel.NoCompression)
  75             (File.Open (imgTempFile, FileMode.Open, FileAccess.Read)).CopyTo (imgEntry.Open ())
  76             srcImg.TempFile <- None
  77
  78         | None -> ()
  79
  80         //let imgFilename = (string srcImg.Num) + DEFAULT_IMAGE_EXTENSION
  81         //let imgEntry = file.CreateEntry (imgFilename, CompressionLevel.NoCompression)
  82         //srcImg.Img.ToBitmap().Save (imgEntry.Open (), System.Drawing.Imaging.ImageFormat.Tiff)
  83
  84         let imgJSONEntry = file.CreateEntry (srcImg.OriginalName + JSON_EXTENSION, CompressionLevel.Fastest)
  85         use imgJSONFileWriter = new StreamWriter (imgJSONEntry.Open ())
  86         imgJSONFileWriter.Write (
  87             JsonConvert.SerializeObject (
  88                 {
  89                     num = srcImg.Num
  90                     name = srcImg.Name
  91                     RBCRadius = srcImg.Config.RBCRadius.Pixel
  92                     parameters = srcImg.Config.Parameters
  93                     dateLastAnalysis = srcImg.DateLastAnalysis
  94                     rbcs = srcImg.RBCs
  95                     healthyRBCBrightness = srcImg.HealthyRBCBrightness
  96                     infectedRBCBrightness = srcImg.InfectedRBCBrightness
  97                 }
  98             )
  99         )
 100
 101 let updateDocumentData (fromVersion : int) (toVersion : int) (data : DocumentData) : DocumentData =
 102     for v in fromVersion + 1 .. toVersion do
 103         match v with
 104         | 1 -> // Version 0 -> 1 : set initial brightness for rbc.
 105             data.images |> List.iter (fun i -> i.HealthyRBCBrightness <- 1.f; i.InfectedRBCBrightness <- 1.f)
 106         | _ -> ()
 107     data
 108
 109 exception VersionFileNewerException of int
 110
 111 /// <summary>
 112 /// Load document from a give file path.
 113 /// </summary>
 114 /// <param name="filePath">Path to the PiaZ file</param>
 115 /// <param name="defaultConfig"></param>
 116 /// <exception cref="System.IOException">If the file cannot be read</exception>
 117 /// <exception cref="VersionFileNewerException">If the file version is newer than the current supported version</exception>
 118 let load (filePath : string) (defaultConfig : ParasitemiaCore.Config.Config) : DocumentData =
 119     use file = ZipFile.Open (filePath, ZipArchiveMode.Read)
 120
 121     let mainEntry = file.GetEntry (MAIN_ENTRY_NAME)
 122     use mainEntryReader = new StreamReader (mainEntry.Open ())
 123     let info = JsonConvert.DeserializeObject<JSONInformation> (mainEntryReader.ReadToEnd ())
 124
 125     if info.fileVersion > CURRENT_FILE_VERSION then
 126         raise <| VersionFileNewerException info.fileVersion
 127
 128     updateDocumentData info.fileVersion CURRENT_FILE_VERSION
 129         {
 130             patientID = info.patientID
 131             images =
 132                 [
 133                     for imgEntry in file.Entries do
 134                         if imgEntry.Name.EndsWith JSON_EXTENSION |> not then
 135                             use bitmap = new System.Drawing.Bitmap (imgEntry.Open (), false)
 136                             let img = bitmap.ToImage<Bgr, byte> ()
 137                             let imgJSONEntry = file.GetEntry (imgEntry.Name + JSON_EXTENSION)
 138                             use imgJSONFileReader = new StreamReader (imgJSONEntry.Open ())
 139                             let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage> (imgJSONFileReader.ReadToEnd ())
 140                             let imgNum = imgInfo.num
 141
 142                             let config = defaultConfig.Copy ()
 143                             config.Parameters <-
 144                                 {
 145                                     ParasitemiaCore.Config.defaultParameters with
 146                                         resolution = imgInfo.parameters.resolution
 147                                 }
 148
 149                             config.SetRBCRadius imgInfo.RBCRadius
 150
 151                             SourceImage (imgNum, imgInfo.name, imgEntry.Name, config, imgInfo.dateLastAnalysis, FromMemory img, imgInfo.rbcs, HealthyRBCBrightness = imgInfo.healthyRBCBrightness, InfectedRBCBrightness = imgInfo.infectedRBCBrightness)
 152                 ]
 153                 |> List.sortBy (fun image -> image.Num)
 154         }