222095305e659bf2fc36ac7d3b6e411fabc24392
1
// ParasitemIA Zipped document format.
2 module ParasitemiaUI.PiaZ
7 open System.IO.Compression
10 open Emgu.CV.Structure
13 open Newtonsoft.Json.Converters
17 let extension = ".piaz"
18 let filter = "PIA|*.piaz"
20 // Information associated to a document.
21 type JSONInformation =
27 // Information associated to each images.
28 type JSONSourceImage =
33 RBCRadius : float32
// The RBC Radius found by granulometry.
34 parameters
: ParasitemiaCore.Config.Parameters
35 dateLastAnalysis
: DateTime
38 healthyRBCBrightness
: float32
// 0 to 1.
39 infectedRBCBrightness
: float32
// 0 to 1.
45 images
: SourceImage list
48 let mainEntryName = "info.json"
49 let imageExtension = ".tiff"
50 let currentFileVersion = 2
53 /// Save a document in a give file path. The file may already exist.
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)
61 for e
in List.ofSeq
file.Entries do // 'ofSeq' to not iterate a collection currently modified.
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 }))
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)
75 let imgJSONEntry = file.CreateEntry (imgFilename + ".json", CompressionLevel.Fastest)
76 use imgJSONFileWriter = new StreamWriter (imgJSONEntry.Open ())
77 imgJSONFileWriter.Write (
78 JsonConvert.SerializeObject (
82 RBCRadius = srcImg
.Config.RBCRadius.Pixel
83 parameters
= srcImg
.Config.Parameters
84 dateLastAnalysis
= srcImg
.DateLastAnalysis
86 healthyRBCBrightness
= srcImg
.HealthyRBCBrightness
87 infectedRBCBrightness
= srcImg
.InfectedRBCBrightness
92 let updateDocumentData (fromVersion
: int) (toVersion
: int) (data
: DocumentData) : DocumentData =
93 for v
in fromVersion
+ 1 .. toVersion
do
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
)
101 /// Load document from a give file path.
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)
108 let mainEntry = file.GetEntry (mainEntryName)
109 use mainEntryReader = new StreamReader (mainEntry.Open ())
110 let info = JsonConvert.DeserializeObject<JSONInformation> (mainEntryReader.ReadToEnd ())
112 updateDocumentData info.fileVersion
currentFileVersion
114 patientID
= info.patientID
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)
123 let imgJSONEntry = file.GetEntry (imgEntry.Name + ".json")
124 use imgJSONFileReader = new StreamReader (imgJSONEntry.Open ())
125 let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage> (imgJSONFileReader.ReadToEnd ())
127 let config = defaultConfig
.Copy ()
130 ParasitemiaCore.Config.defaultParameters
with
131 resolution
= imgInfo.parameters
.resolution
134 config.SetRBCRadius imgInfo.RBCRadius
136 SourceImage (imgNum, imgInfo.name
, config, imgInfo.dateLastAnalysis
, img, imgInfo.rbcs
, HealthyRBCBrightness = imgInfo.healthyRBCBrightness
, InfectedRBCBrightness = imgInfo.infectedRBCBrightness
)