factorNbPick: float
// Parasites detection.
- darkStainLevel: float
+ darkStainLevel: float // Lower -> more sensitive. Careful about illumination on the borders.
maxDarkStainRatio: float
stainArea: float32 // Factor of a RBC area. 0.5 means the half of RBC area.
open System.Diagnostics
open Microsoft.Win32 // For the common dialogs.
-//open Emgu.CV
-//open Emgu.CV.Structure
open Emgu.CV.WPF
open Config
// Utils.log <- (fun m -> log mainWindow m)
- let colorRBCHealthy = Brushes.Green
- let colorRBCInfected = Brushes.Yellow
+ let colorRBCHealthy = Brushes.YellowGreen
+ let colorRBCInfected = Brushes.Red
let state = State.State()
state.PatientID <- txtPatient.Text
let setCurrentImage (srcImg: SourceImage) =
+ state.CurrentImage <- Some srcImg
+
+ // Highlight the preview.
+ stackPreviews.Children
+ |> Seq.cast<Views.ImageSourcePreview>
+ |> Seq.iter (fun preview -> preview.border.BorderThickness <- Thickness(if preview.lblImageNumber.Content = box srcImg.num then 3. else 0.))
+
canvasCurrentImage.Height <- float srcImg.img.Height
canvasCurrentImage.Width <- float srcImg.img.Width
canvasCurrentImage.Background <- ImageBrush(BitmapSourceConvert.ToBitmapSource(srcImg.img))
// Remove all image canvas children and add the RBC.
canvasCurrentImage.Children.Clear()
- for rbc in (*srcImg.rbcs*) [{ num = 1; infected = true; addedManually = false; removed = false; center = Point(100., 100.); size = Size(40., 40.); stainArea = 10 }] do
+ for rbc in srcImg.rbcs do
let rectangle =
Rectangle(
Height = rbc.size.Height,
Width = rbc.size.Width,
Stroke = (if rbc.infected then colorRBCInfected else colorRBCHealthy),
- StrokeThickness = 1.)
- Canvas.SetLeft(rectangle, rbc.center.X + rbc.size.Width / 2.)
- Canvas.SetTop(rectangle, rbc.center.Y + rbc.size.Height / 2.)
+ StrokeThickness = 1.,
+ Fill = SolidColorBrush(Color.FromArgb(0uy, 0uy, 0uy, 0uy)),
+ Tag = rbc,
+ Opacity = if rbc.infected then 1. else 0.)
+ Canvas.SetLeft(rectangle, rbc.center.X - rbc.size.Width / 2.)
+ Canvas.SetTop(rectangle, rbc.center.Y - rbc.size.Height / 2.)
canvasCurrentImage.Children.Add(rectangle) |> ignore
+ rectangle.MouseEnter.AddHandler(
+ fun obj args -> match obj with
+ | :? Rectangle as r ->
+ r.StrokeThickness <- 3.
+ if not (r.Tag :?> RBC).infected then r.Opacity <- 1.
+ | _ -> ())
+ rectangle.MouseLeave.AddHandler(
+ fun obj args -> match obj with
+ | :? Rectangle as r ->
+ r.StrokeThickness <- 1.
+ if not (r.Tag :?> RBC).infected then r.Opacity <- 0.
+ | _ -> ())
let addPreview (srcImg: SourceImage) =
let imgCtrl = Views.ImageSourcePreview(Margin = Thickness(3.))
let height = srcImg.img.Height * width / srcImg.img.Width
imgCtrl.imagePreview.Source <- BitmapSourceConvert.ToBitmapSource(srcImg.img.Resize(width, height, Emgu.CV.CvEnum.Inter.Cubic))
stackPreviews.Children.Add(imgCtrl) |> ignore
+ imgCtrl.MouseLeftButtonUp.AddHandler(fun obj args -> setCurrentImage (state.SourceImages |> Seq.find (fun i -> box i.num = (obj :?> Views.ImageSourcePreview).lblImageNumber.Content)))
let updatePreviews () =
stackPreviews.Children.Clear ()
synchronizeState ()
if state.FilePath = ""
then
- let dialog = SaveFileDialog(AddExtension = true, DefaultExt = Pia.extension, Filter = Pia.filter);
+ let dialog = SaveFileDialog(AddExtension = true, DefaultExt = PiaZ.extension, Filter = PiaZ.filter);
let res = dialog.ShowDialog()
if res.HasValue && res.Value
then
loadFile.Click.AddHandler(fun obj args ->
// TODO: if current state not saved and not empty, ask to save it.
- let dialog = OpenFileDialog(Filter = Pia.filter)
+ let dialog = OpenFileDialog(Filter = PiaZ.filter)
let res = dialog.ShowDialog()
if res.HasValue && res.Value
then
then
setCurrentImage srcImg)
- butStartAnalysis.Click.AddHandler(fun obj args -> ())
+ butStartAnalysis.Click.AddHandler(fun obj args ->
+ let results = ImageAnalysis.doMultipleAnalysis (state.SourceImages |> Seq.map (fun srcImg -> string srcImg.num, srcImg.img) |> Seq.toList) defaultConfig
+ for id, cells in results do
+ state.SetResult (int id) cells
+ )
// Zoom on the current image.
let adjustCurrentImageBorders (deltaX: float) (deltaY: float) =
scrollViewCurrentImage.ScrollToVerticalOffset(scrollViewCurrentImage.VerticalOffset + deltaY / 8.))
let mutable currentScale = 1.
- let mutable maxScale = 5.
- let mutable minScale = 0.1
+ let mutable maxScale = 4.
+ let mutable minScale = 0.25
let currentImageScaleTransform = ScaleTransform()
canvasCurrentImage.LayoutTransform <- currentImageScaleTransform
borderCurrentImage.PreviewMouseWheel.AddHandler(fun obj args ->
borderCurrentImage.ReleaseMouseCapture()
args.Handled <- true)
- (* let txtPatient: Controls.TextBox = ctrl "txtPatient"
- txtPatient.TextChanged.AddHandler(fun obj args ->
- state.PatientID <- txtPatient.Text) *)
-
- (* saveFileDialog1.Filter = "txt files (*.txt)|*.txt|All files (*.*)|*.*" ;
- saveFileDialog1.FilterIndex = 2 ;
- saveFileDialog1.RestoreDirectory = true ; *)
-
// display mainWindow img
mainWindow.Root.Show()
app.Run()
\ No newline at end of file
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
mc:Ignorable="d" d:DesignWidth="119.223" d:DesignHeight="84.911"
>
- <Grid>
- <Image x:Name="imagePreview" />
- <Label x:Name="lblImageNumber" HorizontalAlignment="Right" VerticalAlignment="Bottom" Background="#4C000000" Foreground="White"/>
- </Grid>
+ <Border x:Name="border" BorderBrush="{DynamicResource {x:Static SystemColors.HighlightBrushKey}}">
+ <Grid>
+ <Image x:Name="imagePreview" />
+ <Label x:Name="lblImageNumber" HorizontalAlignment="Right" VerticalAlignment="Bottom" Background="#4C000000" Foreground="White"/>
+ </Grid>
+ </Border>
</UserControl>
\ No newline at end of file
+++ /dev/null
-// ParasitemIA file format.
-module Parasitemia.GUI.Pia
-
-open System.Windows
-open System.IO
-open System.IO.Compression
-
-open FSharp.Data
-
-open Emgu.CV
-open Emgu.CV.Structure
-
-open Types
-
-let extension = ".pia"
-let filter = "PIA|*.pia"
-
-type FileData = {
- sources: SourceImage list
- patientID: string }
-
-// The json type associated to a source image.
-type JSONSourceImage = JsonProvider<"""
- {
- "rbcs": [
- {
- "num": 1,
- "infected": true,
- "addedManually": false,
- "removed": false,
- "posX" : 42.5,
- "posY" : 42.5,
- "width" : 10.5,
- "height" : 10.5,
- "stainArea" : 10
- }
- ]
- }
-""">
-
-// The json type associated to a file.
-type JSONMainInformation = JsonProvider<"""
- {
- "patientID": "1234abcd"
- }
-""">
-
-let mainFilename = "info.json"
-let imageExtension = ".tiff"
-
-let save (filePath: string) (data: FileData) =
- 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()
-
- // Main JSON file.
- let mainJSON = JSONMainInformation.Root(data.patientID)
- let mainFile = file.CreateEntry(mainFilename, CompressionLevel.Fastest)
- use mainFileWriter = new StreamWriter(mainFile.Open())
- mainJSON.JsonValue.WriteTo(mainFileWriter, JsonSaveOptions.None)
-
- // Write each images and the associated information.
- for imgSrc in data.sources do
- let imgFilename = (string imgSrc.num) + imageExtension
- let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
- imgSrc.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
-
- let imgJSON =
- JSONSourceImage.Root([| for rbc in imgSrc.rbcs ->
- JSONSourceImage.Rbc(
- rbc.num,
- rbc.infected, rbc.addedManually, rbc.removed,
- decimal rbc.center.X, decimal rbc.center.Y, decimal rbc.size.Width, decimal rbc.size.Height,
- rbc.stainArea) |])
-
- let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
- use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
- imgJSON.JsonValue.WriteTo(imgJSONFileWriter, JsonSaveOptions.None)
-
-
-let load (filePath: string) : FileData =
- use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
-
- let mainFile = file.GetEntry(mainFilename)
- let mainJSON = JSONMainInformation.Load(mainFile.Open())
-
- let sources = [
- let mutable imgNum = 0
- for imgEntry in file.Entries do
- let filename = imgEntry.Name
- if filename.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 imgJSONEntry = file.GetEntry(filename + ".json")
- let imgJSON = JSONSourceImage.Load(imgJSONEntry.Open())
- yield { num = imgNum; img = img; rbcs = [ for rbc in imgJSON.Rbcs ->
- { num = rbc.Num;
- infected = rbc.Infected; addedManually = rbc.AddedManually; removed = rbc.Removed;
- center = Point(float rbc.PosX, float rbc.PosY); size = Size(float rbc.Width, float rbc.Height);
- stainArea = rbc.StainArea } ] } ]
- { sources = sources; patientID = mainJSON.PatientId }
\ No newline at end of file
--- /dev/null
+// ParasitemIA Zipped file format.
+module Parasitemia.GUI.PiaZ
+
+open System.Windows
+open System.IO
+open System.IO.Compression
+
+open FSharp.Data
+
+open Emgu.CV
+open Emgu.CV.Structure
+
+open Types
+
+let extension = ".piaz"
+let filter = "PIA|*.piaz"
+
+type FileData = {
+ sources: SourceImage list
+ patientID: string }
+
+// The json type associated to a source image.
+type JSONSourceImage = JsonProvider<"""
+ {
+ "rbcs": [
+ {
+ "num": 1,
+ "infected": true,
+ "setManually": false,
+ "posX" : 42.5,
+ "posY" : 42.5,
+ "width" : 10.5,
+ "height" : 10.5,
+ "stainArea" : 10
+ }
+ ]
+ }
+""">
+
+// The json type associated to a file.
+type JSONMainInformation = JsonProvider<"""
+ {
+ "patientID": "1234abcd"
+ }
+""">
+
+let mainFilename = "info.json"
+let imageExtension = ".tiff"
+
+let save (filePath: string) (data: FileData) =
+ 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()
+
+ // Main JSON file.
+ let mainJSON = JSONMainInformation.Root(data.patientID)
+ let mainFile = file.CreateEntry(mainFilename, CompressionLevel.Fastest)
+ use mainFileWriter = new StreamWriter(mainFile.Open())
+ mainJSON.JsonValue.WriteTo(mainFileWriter, JsonSaveOptions.None)
+
+ // Write each images and the associated information.
+ for imgSrc in data.sources do
+ let imgFilename = (string imgSrc.num) + imageExtension
+ let imgEntry = file.CreateEntry(imgFilename, CompressionLevel.NoCompression) // FIXME: It seems a compression is applied to this file despite of the 'NoCompression' flag.
+ imgSrc.img.ToBitmap().Save(imgEntry.Open(), System.Drawing.Imaging.ImageFormat.Tiff)
+
+ let imgJSON =
+ JSONSourceImage.Root([| for rbc in imgSrc.rbcs ->
+ JSONSourceImage.Rbc(
+ rbc.num,
+ rbc.infected, rbc.setManually,
+ decimal rbc.center.X, decimal rbc.center.Y, decimal rbc.size.Width, decimal rbc.size.Height,
+ rbc.stainArea) |])
+
+ let imgJSONEntry = file.CreateEntry(imgFilename + ".json", CompressionLevel.Fastest)
+ use imgJSONFileWriter = new StreamWriter(imgJSONEntry.Open())
+ imgJSON.JsonValue.WriteTo(imgJSONFileWriter, JsonSaveOptions.None)
+
+
+let load (filePath: string) : FileData =
+ use file = ZipFile.Open(filePath, ZipArchiveMode.Read)
+
+ let mainFile = file.GetEntry(mainFilename)
+ let mainJSON = JSONMainInformation.Load(mainFile.Open())
+
+ let sources = [
+ let mutable imgNum = 0
+ for imgEntry in file.Entries do
+ let filename = imgEntry.Name
+ if filename.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 imgJSONEntry = file.GetEntry(filename + ".json")
+ let imgJSON = JSONSourceImage.Load(imgJSONEntry.Open())
+ yield { num = imgNum; img = img; rbcs = [ for rbc in imgJSON.Rbcs ->
+ { num = rbc.Num;
+ infected = rbc.Infected; setManually = rbc.SetManually;
+ center = Point(float rbc.PosX, float rbc.PosY); size = Size(float rbc.Width, float rbc.Height);
+ stainArea = rbc.StainArea } ] } ]
+ { sources = sources; patientID = mainJSON.PatientId }
\ No newline at end of file
module Parasitemia.GUI.State
open System.Collections.Generic
+open System.Windows
open Emgu.CV
open Emgu.CV.Structure
type State () =
let sourceImages = List<SourceImage>()
- let mutable currentImage = -1
+ member val CurrentImage: SourceImage option = None with get, set
member val FilePath: string = "" with get, set
member val PatientID: string = "" with get, set
member this.Save () =
- let data = { Pia.sources = List.ofSeq sourceImages; Pia.patientID = this.PatientID }
- Pia.save this.FilePath data
+ let data = { PiaZ.sources = List.ofSeq sourceImages; PiaZ.patientID = this.PatientID }
+ PiaZ.save this.FilePath data
member this.Load () =
- let data = Pia.load this.FilePath
+ let data = PiaZ.load this.FilePath
this.PatientID <- data.patientID
sourceImages.Clear()
sourceImages.InsertRange(0, data.sources)
member this.AddSourceImage (filePath: string) : SourceImage =
let srcImg = { num = sourceImages.Count + 1; rbcs = []; img = new Image<Bgr, byte>(filePath) }
sourceImages.Add(srcImg)
- if sourceImages.Count = 1
- then
- currentImage <- 1
srcImg
- member x.SourceImages : SourceImage seq =
+ member this.SetResult (num: int) (cells: Cell list) =
+ let sourceImage = sourceImages.Find(fun srcImg -> srcImg.num = num)
+ sourceImage.rbcs <- cells
+ |> List.filter (fun cell -> match cell.cellClass with HealthyRBC | InfectedRBC -> true | _ -> false )
+ |> List.mapi (fun i cell ->
+ { num = i
+ infected = cell.cellClass = InfectedRBC
+ setManually = false
+ center = Point(float cell.center.X, float cell.center.Y)
+ size = Size(float cell.elements.Width, float cell.elements.Height)
+ stainArea = cell.stainArea })
+
+ member this.SourceImages : SourceImage seq =
sourceImages :> SourceImage seq
member this.Reset () =
num: int
infected: bool
- addedManually: bool
- removed: bool
+ setManually: bool
center: Point
size: Size
type SourceImage = {
num: int
img: Image<Bgr, byte>
- rbcs: RBC list }
\ No newline at end of file
+ mutable rbcs: RBC list }
\ No newline at end of file
open System
open System.Drawing
+open FSharp.Collections.ParallelSeq
+
open Emgu.CV
open Emgu.CV.Structure
| _ -> ()
cells
+
+
+let doMultipleAnalysis (imgs: (string * Image<Bgr, byte>) list) (config : Config) : (string * Cell list) list =
+ let nbConcurrentTaskLimit = 4
+ let n = Environment.ProcessorCount
+
+ imgs
+ |> PSeq.map (fun (id, img) -> id, doAnalysis img id (config.Copy()))
+ |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
+ |> PSeq.toList
\ No newline at end of file
<Resource Include="GUI\MainWindow.xaml" />
<Compile Include="GUI\MainWindow.xaml.fs" />
<Compile Include="GUI\Types.fs" />
- <Compile Include="GUI\Pia.fs" />
+ <Compile Include="GUI\PiaZ.fs" />
<Compile Include="GUI\State.fs" />
<Compile Include="GUI\GUI.fs" />
<Compile Include="Program.fs" />
open System.IO
open System.Threading
-open FSharp.Collections.ParallelSeq
-
open Emgu.CV
open Emgu.CV.Structure
factorNbPick = 1.0
- darkStainLevel = 0.25 // Lower -> more sensitive. 0.3. Careful about illumination on the borders.
+ darkStainLevel = 0.25 // 0.3
maxDarkStainRatio = 0.1 // 10 %
infectionArea = 0.012f // 1.2 %
use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
//try
- let images = seq { for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) }
+ let images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) ]
- let nbConcurrentTaskLimit = 4
- let n = Environment.ProcessorCount
Utils.logTime "Whole analyze" (fun () ->
- let results =
- images
- |> PSeq.map (fun (id, img) -> id, ImageAnalysis.doAnalysis img id (config.Copy()))
- |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
+ let results = ImageAnalysis.doMultipleAnalysis images config
for id, cells in results do
let total, infected = Utils.countCells cells
projects / master-thesis.git / commitdiff