let dimension = Filter.squareCalculator 6.45 2. 20. 2.
+let dimension = Filter.squareCalculator 6.45 2. 20. 2.
-let wvRadius = Filter.cellRadiusCalculator 9.5 6.45 2. 20. 2.
+let wvRadius = Filter.cellRadiusCalculator 9.5 6.45 2. 20. 2.
-let processFolders folderPath height width radius multiplier =
- let subfolders = Directory.GetDirectories folderPath
- let result = subfolders
- |> Array.mapi (fun i folder ->
- printfn "processing folder %i of %i" (i+1) subfolders.Length
- Pipeline.processImages folder height width radius multiplier)
- result
+let processFolders folderPath height width radius multiplier =
+ let subfolders = Directory.GetDirectories folderPath
+ let result = subfolders
+ |> Array.mapi (fun i folder ->
+ printfn "processing folder %i of %i" (i+1) subfolders.Length
+ Pipeline.processImages folder height width radius multiplier)
+ result
-let processAll = processFolders @"...\Dilution\CoulterCounter"
- dimension dimension wvRadius 0.2
+let processAll = processFolders @"...\Dilution\CoulterCounter"
+ dimension dimension wvRadius 0.2
|
The data for the manual counting can be found here, and the Coulter Counter data is here.
A more in depth explanation how to adapt the functions for your use can be found here
-Multiple items
namespace FSharp
--------------------
namespace Microsoft.FSharp
-namespace FSharp.Plotly
-namespace CounterFunctions
-namespace System
-namespace System.IO
-val cellCounter : float []
-val cellCounterStabw : float []
-val manual : float []
-val manualStabw : float []
-val coulterCounter : float []
-val coulterCounterStabw : float []
-val increments : string []
-val xAxis : title:'a -> Axis.LinearAxis
-val title : 'a
-module Axis
from FSharp.Plotly
-Multiple items
type LinearAxis =
inherit DynamicObj
new : unit -> LinearAxis
static member init : ?AxisType:AxisType * ?Title:'a * ?Titlefont:Font * ?Autorange:AutoRange * ?Rangemode:RangeMode * ?Range:Range * ?Fixedrange:'b * ?Tickmode:TickMode * ?nTicks:'c * ?Tick0:'d * ?dTick:'e * ?Tickvals:'f * ?Ticktext:'g * ?Ticks:TickOptions * ?Mirror:Mirror * ?Ticklen:'h * ?Tickwidth:'i * ?Tickcolor:'j * ?Showticklabels:'k * ?Tickfont:Font * ?Tickangle:'l * ?Tickprefix:'m * ?Showtickprefix:ShowTickOption * ?Ticksuffix:'q * ?Showticksuffix:ShowTickOption * ?Showexponent:ShowExponent * ?Exponentformat:ExponentFormat * ?Tickformat:'r * ?Hoverformat:'s * ?Showline:'t * ?Linecolor:'a1 * ?Linewidth:'a2 * ?Showgrid:'a3 * ?Gridcolor:'a4 * ?Gridwidth:'a5 * ?Zeroline:'a6 * ?Zerolinecolor:'a7 * ?Zerolinewidth:'a8 * ?Anchor:AxisAnchorId * ?Side:Side * ?Overlaying:AxisAnchorId * ?Domain:Range * ?Position:float * ?IsSubplotObj:'a9 * ?Tickvalssrc:'a10 * ?Ticktextsrc:'a11 * ?Showspikes:'a12 * ?Spikesides:'a13 * ?Spikethickness:'a14 * ?Spikecolor:'a15 * ?Showbackground:'a16 * ?Backgroundcolor:'a17 * ?Showaxeslabels:'a18 -> LinearAxis
static member style : ?AxisType:AxisType * ?Title:'b * ?Titlefont:Font * ?Autorange:AutoRange * ?Rangemode:RangeMode * ?Range:Range * ?Fixedrange:'c * ?Tickmode:TickMode * ?nTicks:'d * ?Tick0:'e * ?dTick:'f * ?Tickvals:'g * ?Ticktext:'h * ?Ticks:TickOptions * ?Mirror:Mirror * ?Ticklen:'i * ?Tickwidth:'j * ?Tickcolor:'k * ?Showticklabels:'l * ?Tickfont:Font * ?Tickangle:'m * ?Tickprefix:'n * ?Showtickprefix:ShowTickOption * ?Ticksuffix:'o * ?Showticksuffix:ShowTickOption * ?Showexponent:ShowExponent * ?Exponentformat:ExponentFormat * ?Tickformat:'p * ?Hoverformat:'q * ?Showline:'r * ?Linecolor:'s * ?Linewidth:'t * ?Showgrid:'a1 * ?Gridcolor:'a2 * ?Gridwidth:'a3 * ?Zeroline:'a4 * ?Zerolinecolor:'a5 * ?Zerolinewidth:'a6 * ?Anchor:AxisAnchorId * ?Side:Side * ?Overlaying:AxisAnchorId * ?Domain:Range * ?Position:float * ?IsSubplotObj:'a7 * ?Tickvalssrc:'a8 * ?Ticktextsrc:'a9 * ?Showspikes:'a10 * ?Spikesides:'a11 * ?Spikethickness:'a12 * ?Spikecolor:'a13 * ?Showbackground:'a14 * ?Backgroundcolor:'a15 * ?Showaxeslabels:'a16 -> (LinearAxis -> LinearAxis)
--------------------
new : unit -> Axis.LinearAxis
-static member Axis.LinearAxis.init : ?AxisType:StyleParam.AxisType * ?Title:'a * ?Titlefont:Font * ?Autorange:StyleParam.AutoRange * ?Rangemode:StyleParam.RangeMode * ?Range:StyleParam.Range * ?Fixedrange:'b * ?Tickmode:StyleParam.TickMode * ?nTicks:'c * ?Tick0:'d * ?dTick:'e * ?Tickvals:'f * ?Ticktext:'g * ?Ticks:StyleParam.TickOptions * ?Mirror:StyleParam.Mirror * ?Ticklen:'h * ?Tickwidth:'i * ?Tickcolor:'j * ?Showticklabels:'k * ?Tickfont:Font * ?Tickangle:'l * ?Tickprefix:'m * ?Showtickprefix:StyleParam.ShowTickOption * ?Ticksuffix:'q * ?Showticksuffix:StyleParam.ShowTickOption * ?Showexponent:StyleParam.ShowExponent * ?Exponentformat:StyleParam.ExponentFormat * ?Tickformat:'r * ?Hoverformat:'s * ?Showline:'t * ?Linecolor:'a1 * ?Linewidth:'a2 * ?Showgrid:'a3 * ?Gridcolor:'a4 * ?Gridwidth:'a5 * ?Zeroline:'a6 * ?Zerolinecolor:'a7 * ?Zerolinewidth:'a8 * ?Anchor:StyleParam.AxisAnchorId * ?Side:StyleParam.Side * ?Overlaying:StyleParam.AxisAnchorId * ?Domain:StyleParam.Range * ?Position:float * ?IsSubplotObj:'a9 * ?Tickvalssrc:'a10 * ?Ticktextsrc:'a11 * ?Showspikes:'a12 * ?Spikesides:'a13 * ?Spikethickness:'a14 * ?Spikecolor:'a15 * ?Showbackground:'a16 * ?Backgroundcolor:'a17 * ?Showaxeslabels:'a18 -> Axis.LinearAxis
-module StyleParam
from FSharp.Plotly
-type Mirror =
| True
| Ticks
| False
| All
| AllTicks
static member convert : (Mirror -> obj)
static member toString : (Mirror -> string)
-union case StyleParam.Mirror.All: StyleParam.Mirror
-type TickMode =
| Auto
| Linear
| Array
static member convert : (TickMode -> obj)
static member toString : (TickMode -> string)
-union case StyleParam.TickMode.Auto: StyleParam.TickMode
-type TickOptions =
| Outside
| Inside
| Empty
static member convert : (TickOptions -> obj)
static member toString : (TickOptions -> string)
-union case StyleParam.TickOptions.Inside: StyleParam.TickOptions
-Multiple items
type Font =
inherit DynamicObj
new : unit -> Font
static member init : ?Family:FontFamily * ?Size:'b * ?Color:'c * ?Familysrc:'d * ?Sizesrc:'e * ?Colorsrc:'f -> Font
static member style : ?Family:FontFamily * ?Size:'a0 * ?Color:'a1 * ?Familysrc:'a2 * ?Sizesrc:'a3 * ?Colorsrc:'a4 -> (Font -> Font)
--------------------
new : unit -> Font
-static member Font.init : ?Family:StyleParam.FontFamily * ?Size:'b * ?Color:'c * ?Familysrc:'d * ?Sizesrc:'e * ?Colorsrc:'f -> Font
-type FontFamily =
| Arial
| Balto
| Courier_New
| Droid_Sans
| Droid_Serif
| Droid_Sans_Mono
| Gravitas_One
| Old_Standard_TT
| Open_Sans
| Overpass
...
static member convert : (FontFamily -> obj)
static member toString : (FontFamily -> string)
-union case StyleParam.FontFamily.Arial: StyleParam.FontFamily
-val yAxis : title:'a -> Axis.LinearAxis
-val chartCellCounter : GenericChart.GenericChart
-type Chart =
static member Area : xy:seq<#IConvertible * #IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Dash:DrawingStyle * ?Width:'a4 -> GenericChart
static member Area : x:seq<#IConvertible> * y:seq<#IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Dash:DrawingStyle * ?Width:'a4 -> GenericChart
static member Bar : keysvalues:seq<#IConvertible * #IConvertible> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Marker:Marker -> GenericChart
static member Bar : keys:seq<#IConvertible> * values:seq<#IConvertible> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Marker:Marker -> GenericChart
static member BoxPlot : xy:seq<'a0 * 'a1> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Fillcolor:'a3 * ?Opacity:float * ?Whiskerwidth:'a4 * ?Boxpoints:Boxpoints * ?Boxmean:BoxMean * ?Jitter:'a5 * ?Pointpos:'a6 * ?Orientation:Orientation -> GenericChart
static member BoxPlot : ?x:'a0 * ?y:'a1 * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Fillcolor:'a3 * ?Opacity:float * ?Whiskerwidth:'a4 * ?Boxpoints:Boxpoints * ?Boxmean:BoxMean * ?Jitter:'a5 * ?Pointpos:'a6 * ?Orientation:Orientation -> GenericChart
static member Bubble : xysizes:seq<#IConvertible * #IConvertible * #IConvertible> * ?Name:string * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a3 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font -> GenericChart
static member Bubble : x:seq<#IConvertible> * y:seq<#IConvertible> * sizes:seq<#IConvertible> * ?Name:string * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a3 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font -> GenericChart
static member ChoroplethMap : locations:seq<string> * z:seq<#IConvertible> * ?Text:seq<#IConvertible> * ?Locationmode:LocationFormat * ?Autocolorscale:bool * ?Colorscale:Colorscale * ?Colorbar:'a2 * ?Marker:Marker * ?Zmin:'a3 * ?Zmax:'a4 -> GenericChart
static member Column : keysvalues:seq<#IConvertible * #IConvertible> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Marker:Marker -> GenericChart
...
-static member Chart.Line : xy:seq<#System.IConvertible * #System.IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:StyleParam.Symbol * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#System.IConvertible> * ?TextPosition:StyleParam.TextPosition * ?TextFont:Font * ?Dash:'a4 * ?Width:'a5 -> GenericChart.GenericChart
static member Chart.Line : x:seq<#System.IConvertible> * y:seq<#System.IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:StyleParam.Symbol * ?Color:'c * ?Opacity:float * ?Labels:seq<#System.IConvertible> * ?TextPosition:StyleParam.TextPosition * ?TextFont:Font * ?Dash:'e * ?Width:'f -> GenericChart.GenericChart
-static member Chart.withYErrorStyle : ?Array:'a * ?Arrayminus:'b * ?Symmetric:'c * ?Color:'d * ?Thickness:'e * ?Width:'f -> (GenericChart.GenericChart -> GenericChart.GenericChart)
-static member Chart.withTraceName : ?Name:string * ?Showlegend:bool * ?Legendgroup:string * ?Visible:StyleParam.Visible -> (GenericChart.GenericChart -> GenericChart.GenericChart)
-val chartManual : GenericChart.GenericChart
-val chartCoulterCounter : GenericChart.GenericChart
-val combinedChart : GenericChart.GenericChart
-static member Chart.Combine : gCharts:seq<GenericChart.GenericChart> -> GenericChart.GenericChart
-static member Chart.withX_Axis : xAxis:Axis.LinearAxis * ?Id:int -> (GenericChart.GenericChart -> GenericChart.GenericChart)
-static member Chart.withY_Axis : yAxis:Axis.LinearAxis * ?Id:int -> (GenericChart.GenericChart -> GenericChart.GenericChart)
-static member Chart.withSize : width:float * heigth:float -> (GenericChart.GenericChart -> GenericChart.GenericChart)
-val dimension : int
-module Filter
from CounterFunctions
-val squareCalculator : cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> int
-val wvRadius : float
-val cellRadiusCalculator : cellDiameter:float -> cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> float
-val processFolders : folderPath:string -> height:int -> width:int -> radius:float -> multiplier:float -> (int * GenericChart.GenericChart) [] []
-val folderPath : string
-val height : int
-val width : int
-val radius : float
-val multiplier : float
-val subfolders : string []
-type Directory =
static member CreateDirectory : path:string -> DirectoryInfo
static member Delete : path:string -> unit + 1 overload
static member EnumerateDirectories : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFileSystemEntries : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFiles : path:string -> IEnumerable<string> + 2 overloads
static member Exists : path:string -> bool
static member GetCreationTime : path:string -> DateTime
static member GetCreationTimeUtc : path:string -> DateTime
static member GetCurrentDirectory : unit -> string
static member GetDirectories : path:string -> string[] + 2 overloads
...
-Multiple items
Directory.GetDirectories(path: string) : string []
Directory.GetDirectories(path: string, searchPattern: string) : string []
Directory.GetDirectories(path: string, searchPattern: string, searchOption: SearchOption) : string []
--------------------
Directory.GetDirectories(path: string) : string []
Directory.GetDirectories(path: string, searchPattern: string) : string []
Directory.GetDirectories(path: string, searchPattern: string, searchOption: SearchOption) : string []
-val result : (int * GenericChart.GenericChart) [] []
-module Array
from Microsoft.FSharp.Collections
-val mapi : mapping:(int -> 'T -> 'U) -> array:'T [] -> 'U []
-val i : int
-val folder : string
-val printfn : format:Printf.TextWriterFormat<'T> -> 'T
-property System.Array.Length: int
-module Pipeline
from CounterFunctions
-val processImages : folderPath:string -> height:int -> width:int -> radius:float -> multiplier:float -> (int * GenericChart.GenericChart) []
-val processAll : (int * GenericChart.GenericChart) [] []
+namespace Microsoft.FSharp
+namespace System
+namespace System.IO
+val cellCounter : float []
+val cellCounterStabw : float []
+val manual : float []
+val manualStabw : float []
+val coulterCounter : float []
+val coulterCounterStabw : float []
+val increments : string []
+val xAxis : title:'a -> 'b
+val title : 'a
+val yAxis : title:'a -> 'b
+val chartCellCounter : obj
+val chartManual : obj
+val chartCoulterCounter : obj
+val combinedChart : obj
+val dimension : obj
+val wvRadius : obj
+val processFolders : folderPath:string -> height:'a -> width:'b -> radius:'c -> multiplier:'d -> 'e []
+val folderPath : string
+val height : 'a
+val width : 'b
+val radius : 'c
+val multiplier : 'd
+val subfolders : string []
+type Directory =
static member CreateDirectory : path:string -> DirectoryInfo + 1 overload
static member Delete : path:string -> unit + 1 overload
static member EnumerateDirectories : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFileSystemEntries : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFiles : path:string -> IEnumerable<string> + 2 overloads
static member Exists : path:string -> bool
static member GetAccessControl : path:string -> DirectorySecurity + 1 overload
static member GetCreationTime : path:string -> DateTime
static member GetCreationTimeUtc : path:string -> DateTime
static member GetCurrentDirectory : unit -> string
...
+Directory.GetDirectories(path: string) : string []
Directory.GetDirectories(path: string, searchPattern: string) : string []
Directory.GetDirectories(path: string, searchPattern: string, searchOption: SearchOption) : string []
+val result : 'e []
+module Array
from Microsoft.FSharp.Collections
+val mapi : mapping:(int -> 'T -> 'U) -> array:'T [] -> 'U []
+val i : int
+val folder : string
+val printfn : format:Printf.TextWriterFormat<'T> -> 'T
+property System.Array.Length: int
+val processAll : obj []
diff --git a/FunctionExplanation.html b/FunctionExplanation.html
index e322f1b..35fb308 100644
--- a/FunctionExplanation.html
+++ b/FunctionExplanation.html
@@ -40,7 +40,7 @@
1:
|
-Pipeline.processImage filePath height width radius thresholdMultiplier
+Pipeline.processImage filePath height width radius thresholdMultiplier
|
|
filePath is the path of the image. Height and width can be filled with the same result from the Filter.squareCalculator. Radius gets the result from Filter.cellRadiusCalculator.
thresholdMultiplier is a multiplier for the cutoff after the wavelet transformation. It has to be higher the closer in intensity the background to the cells is. The threshold function in the
pipeline contains a boolean for determining whether the cells have a positive or negative value. In all cases so far the intensities were negative. If for some reason they are positive,
-the boolean has to be changed to "true". The chart which is returned in the resulting tuple serves visualization purposes. this functionality can be removed without consequences.
+the boolean has to be changed to "true". The chart which is returned in the resulting tuple serves visualization purposes. This functionality can be removed without consequences. To view the chart
+you have to open FSharp.Plotly and use the command Chart.Show.
1:
|
-Pipeline.processImages folderPath height width radius thresholdMultiplier
+Pipeline.processImages folderPath height width radius thresholdMultiplier
|
|
@@ -85,7 +86,7 @@
1:
|
-Filter.circleSelector pointAXY pointBXY
+Filter.circleSelector pointAXY pointBXY
|
|
@@ -94,7 +95,7 @@
1:
|
-Filter.rectangleSelector upperLeftXY lowerRightBXY
+Filter.rectangleSelector upperLeftXY lowerRightBXY
|
|
@@ -103,17 +104,7 @@
The functions in the modules Maxima and Image are adapted from the BioFSharp library, an open source bioinformatics toolbox written in F#.
The functions were modified to fit the needs of the Cell Counter.
-
Multiple items
namespace FSharp
--------------------
namespace Microsoft.FSharp
-
namespace FSharp.Plotly
-
namespace CounterFunctions
-
module Filter
from CounterFunctions
-
val squareCalculator : cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> int
-
val cellRadiusCalculator : cellDiameter:float -> cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> float
-
module Pipeline
from CounterFunctions
-
val processImage : filePath:string -> height:int -> width:int -> radius:float -> multiplier:float -> int * GenericChart.GenericChart
-
val processImages : folderPath:string -> height:int -> width:int -> radius:float -> multiplier:float -> (int * GenericChart.GenericChart) []
-
val circleSelector : image:float [,] -> float * float -> float * float -> float [] []
-
val rectangleSelector : image:float [,] -> int * int -> int * int -> float [] []
+
namespace Microsoft.FSharp
diff --git a/index.html b/index.html
index f7d98ce..a1488bf 100644
--- a/index.html
+++ b/index.html
@@ -60,13 +60,13 @@
6:
7: