let filter = "PIA|*.piaz"
// Information associated to a document.
-type JSONInformation = {
- patientID: string
-}
+type JSONInformation =
+ {
+ patientID : string
+ fileVersion : int
+ }
// Information associated to each images.
-type JSONSourceImage = {
- num: int
- RBCRadius: float32 // The RBC Radius found by granulometry.
- parameters: ParasitemiaCore.Config.Parameters
- dateLastAnalysis: DateTime
- rbcs: RBC List
-}
-
-type DocumentData = {
- patientID: string
- images: SourceImage list
-}
+type JSONSourceImage =
+ {
+ num : int
+ name : string
+
+ RBCRadius : float32 // The RBC Radius found by granulometry.
+ parameters : ParasitemiaCore.Config.Parameters
+ dateLastAnalysis : DateTime
+ rbcs : RBC List
+
+ healthyRBCBrightness : float32 // 0 to 1.
+ infectedRBCBrightness : float32 // 0 to 1.
+ }
+
+type DocumentData =
+ {
+ patientID : string
+ images : SourceImage list
+ }
let mainEntryName = "info.json"
let imageExtension = ".tiff"
+let currentFileVersion = 2
/// <summary>
/// Save a document in a give file path. The file may already exist.
/// <param name="filePath"></param>
/// <param name="data"></param>
/// <exception cref="System.IOException">If the file cannot be written</exception>
-let save (filePath: string) (data: DocumentData) =
- use file = ZipFile.Open(filePath, ZipArchiveMode.Update)
+let save (filePath : string) (data : DocumentData) =
+ use file = ZipFile.Open (filePath, ZipArchiveMode.Update)
for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
- e.Delete()
+ e.Delete ()
// Main JSON file.
- let mainEntry = file.CreateEntry(mainEntryName, CompressionLevel.Fastest)
- use mainEntryWriter = new StreamWriter(mainEntry.Open())
- mainEntryWriter.Write(JsonConvert.SerializeObject({ JSONInformation.patientID = data.patientID }))
+ let mainEntry = file.CreateEntry (mainEntryName, CompressionLevel.Fastest)
+ use mainEntryWriter = new StreamWriter (mainEntry.Open ())
+ mainEntryWriter.Write (JsonConvert.SerializeObject ({ patientID = data.patientID; fileVersion = currentFileVersion }))
// Write each images and the associated information.
for srcImg in data.images do
let imgFilename = (string srcImg.num) + imageExtension
- let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
- srcImg.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
-
- let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
- use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
- imgJSONFileWriter.Write(JsonConvert.SerializeObject({ num = srcImg.num; RBCRadius = srcImg.config.RBCRadius.Pixel; parameters = srcImg.config.Parameters; dateLastAnalysis = srcImg.dateLastAnalysis; rbcs = srcImg.rbcs }))
+ let imgEntry = file.CreateEntry (imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
+ srcImg.img.ToBitmap().Save (imgEntry.Open (), System.Drawing.Imaging.ImageFormat.Tiff)
+
+ let imgJSONEntry = file.CreateEntry (imgFilename + ".json", CompressionLevel.Fastest)
+ use imgJSONFileWriter = new StreamWriter (imgJSONEntry.Open ())
+ imgJSONFileWriter.Write (
+ JsonConvert.SerializeObject (
+ {
+ num = srcImg.num
+ name = srcImg.name
+ RBCRadius = srcImg.config.RBCRadius.Pixel
+ parameters = srcImg.config.Parameters
+ dateLastAnalysis = srcImg.dateLastAnalysis
+ rbcs = srcImg.rbcs
+ healthyRBCBrightness = srcImg.healthyRBCBrightness
+ infectedRBCBrightness = srcImg.infectedRBCBrightness
+ }
+ )
+ )
+
+let updateDocumentData (fromVersion : int) (toVersion : int) (data : DocumentData) : DocumentData =
+ for v in fromVersion + 1 .. toVersion do
+ match v with
+ | 1 -> // Version 0 -> 1 : set initial brightness for rbc.
+ data.images |> List.iter (fun i -> i.healthyRBCBrightness <- 1.f; i.infectedRBCBrightness <- 1.f)
+ | _ -> ()
+ data
/// <summary>
/// Load document from a give file path.
/// </summary>
/// <param name="filePath"></param>
/// <exception cref="System.IOException">If the file cannot be read</exception>
-let load (filePath: string) : DocumentData =
- use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
-
- let mainEntry = file.GetEntry(mainEntryName)
- use mainEntryReader = new StreamReader(mainEntry.Open())
- let info = JsonConvert.DeserializeObject<JSONInformation>(mainEntryReader.ReadToEnd())
-
- { patientID = info.patientID
- images = [ let mutable imgNum = 0
- for imgEntry in file.Entries do
- if imgEntry.Name.EndsWith(imageExtension)
- then
- let img = new Image<Bgr, byte>(new System.Drawing.Bitmap(imgEntry.Open(), false)) // FIXME: Should we dispose the bitmap?
- imgNum <- imgNum + 1
- let imgEntry = file.GetEntry(imgEntry.Name + ".json")
- use imgEntryFileReader = new StreamReader(imgEntry.Open())
- let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage>(imgEntryFileReader.ReadToEnd())
- let config = ParasitemiaCore.Config.Config(imgInfo.parameters)
- config.SetRBCRadius imgInfo.RBCRadius
- yield { num = imgNum
- config = config
- dateLastAnalysis = imgInfo.dateLastAnalysis
- img = img
- rbcs = imgInfo.rbcs } ] }
\ No newline at end of file
+let load (filePath : string) (defaultConfig : ParasitemiaCore.Config.Config) : DocumentData =
+ use file = ZipFile.Open (filePath, ZipArchiveMode.Read)
+
+ let mainEntry = file.GetEntry (mainEntryName)
+ use mainEntryReader = new StreamReader (mainEntry.Open ())
+ let info = JsonConvert.DeserializeObject<JSONInformation> (mainEntryReader.ReadToEnd ())
+
+ updateDocumentData info.fileVersion currentFileVersion
+ {
+ patientID = info.patientID
+ images =
+ [
+ let mutable imgNum = 0
+ for imgEntry in file.Entries do
+ if imgEntry.Name.EndsWith (imageExtension) then
+ use bitmap = new System.Drawing.Bitmap (imgEntry.Open (), false)
+ let img = new Image<Bgr, byte> (bitmap)
+ imgNum <- imgNum + 1
+ let imgJSONEntry = file.GetEntry (imgEntry.Name + ".json")
+ use imgJSONFileReader = new StreamReader (imgJSONEntry.Open ())
+ let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage> (imgJSONFileReader.ReadToEnd ())
+
+ let config = defaultConfig.Copy ()
+ config.Parameters <-
+ {
+ ParasitemiaCore.Config.defaultParameters with
+ resolution = imgInfo.parameters.resolution
+ }
+
+ config.SetRBCRadius imgInfo.RBCRadius
+ yield
+ {
+ num = imgNum
+ name = imgInfo.name
+ config = config
+ dateLastAnalysis = imgInfo.dateLastAnalysis
+ img = img
+ rbcs = imgInfo.rbcs
+ healthyRBCBrightness = imgInfo.healthyRBCBrightness
+ infectedRBCBrightness = imgInfo.infectedRBCBrightness
+ }
+ ]
+ }
\ No newline at end of file
projects / master-thesis.git / blobdiff