module ParasitemiaUI.PiaZ
open System
-open System.Windows
open System.IO
open System.IO.Compression
open Emgu.CV.Structure
open Newtonsoft.Json
-open Newtonsoft.Json.Converters
open Types
let filter = "PIA|*.piaz"
// Information associated to a document.
-type JSONInformation = {
- patientID: string
- fileVersion: int
-}
+type JSONInformation =
+ {
+ patientID : string
+ fileVersion : int
+ }
// Information associated to each images.
-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
+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 MAIN_ENTRY_NAME = "info.json"
+let DEFAULT_IMAGE_EXTENSION = ".tiff"
+let JSON_EXTENSION = ".json"
+let CURRENT_FILE_VERSION = 3
/// <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)
+ // We only delete JSON files and removed images.
for e in List.ofSeq file.Entries do // 'ofSeq' to not iterate a collection currently modified.
- e.Delete()
+ if Path.GetExtension e.Name = JSON_EXTENSION || data.images |> List.exists (fun img -> img.OriginalName = e.Name) |> not then
+ e.Delete ()
// Main JSON file.
- let mainEntry = file.CreateEntry(mainEntryName, CompressionLevel.Fastest)
- use mainEntryWriter = new StreamWriter(mainEntry.Open())
- mainEntryWriter.Write(JsonConvert.SerializeObject({ patientID = data.patientID; fileVersion = currentFileVersion }))
+ let mainEntry = file.CreateEntry (MAIN_ENTRY_NAME, CompressionLevel.Fastest)
+ use mainEntryWriter = new StreamWriter (mainEntry.Open ())
+ mainEntryWriter.Write (JsonConvert.SerializeObject ({ patientID = data.patientID; fileVersion = CURRENT_FILE_VERSION }))
- // Write each images and the associated information.
+ // Write each images and the associated information as a JSON file.
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
- 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 =
+ match srcImg.TempFile with
+ | Some imgTempFile ->
+ let imgEntry = file.CreateEntry (srcImg.OriginalName, CompressionLevel.NoCompression)
+ (File.Open (imgTempFile, FileMode.Open, FileAccess.Read)).CopyTo (imgEntry.Open ())
+ srcImg.TempFile <- None
+
+ | None -> ()
+
+ //let imgFilename = (string srcImg.Num) + DEFAULT_IMAGE_EXTENSION
+ //let imgEntry = file.CreateEntry (imgFilename, CompressionLevel.NoCompression)
+ //srcImg.Img.ToBitmap().Save (imgEntry.Open (), System.Drawing.Imaging.ImageFormat.Tiff)
+
+ let imgJSONEntry = file.CreateEntry (srcImg.OriginalName + JSON_EXTENSION, 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.images |> List.iter (fun i -> i.HealthyRBCBrightness <- 1.f; i.InfectedRBCBrightness <- 1.f)
| _ -> ()
data
+exception VersionFileNewerException of int
+
/// <summary>
/// Load document from a give file path.
/// </summary>
-/// <param name="filePath"></param>
+/// <param name="filePath">Path to the PiaZ file</param>
+/// <param name="defaultConfig"></param>
/// <exception cref="System.IOException">If the file cannot be read</exception>
-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()
+/// <exception cref="VersionFileNewerException">If the file version is newer than the current supported version</exception>
+let load (filePath : string) (defaultConfig : ParasitemiaCore.Config.Config) : DocumentData =
+ use file = ZipFile.Open (filePath, ZipArchiveMode.Read)
+
+ let mainEntry = file.GetEntry (MAIN_ENTRY_NAME)
+ use mainEntryReader = new StreamReader (mainEntry.Open ())
+ let info = JsonConvert.DeserializeObject<JSONInformation> (mainEntryReader.ReadToEnd ())
+
+ if info.fileVersion > CURRENT_FILE_VERSION then
+ raise <| VersionFileNewerException info.fileVersion
+
+ updateDocumentData info.fileVersion CURRENT_FILE_VERSION
+ {
+ patientID = info.patientID
+ images =
+ [
+ for imgEntry in file.Entries do
+ if imgEntry.Name.EndsWith JSON_EXTENSION |> not then
+ use bitmap = new System.Drawing.Bitmap (imgEntry.Open (), false)
+ let img = bitmap.ToImage<Bgr, byte> ()
+ let imgJSONEntry = file.GetEntry (imgEntry.Name + JSON_EXTENSION)
+ use imgJSONFileReader = new StreamReader (imgJSONEntry.Open ())
+ let imgInfo = JsonConvert.DeserializeObject<JSONSourceImage> (imgJSONFileReader.ReadToEnd ())
+ let imgNum = imgInfo.num
+
+ let config = defaultConfig.Copy ()
config.Parameters <-
- { ParasitemiaCore.Config.defaultParameters with
- resolution = imgInfo.parameters.resolution }
+ {
+ 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
+
+ SourceImage (imgNum, imgInfo.name, imgEntry.Name, config, imgInfo.dateLastAnalysis, FromMemory img, imgInfo.rbcs, HealthyRBCBrightness = imgInfo.healthyRBCBrightness, InfectedRBCBrightness = imgInfo.infectedRBCBrightness)
+ ]
+ |> List.sortBy (fun image -> image.Num)
+ }
\ No newline at end of file
projects / master-thesis.git / blobdiff