logTime "Finding edges" (fun() -> thin edges)
logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
- (*
- let kmediansResults = KMedians.kmedians filteredGreen 1.0
+ let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
- let radiusRange = config.scale * config.minRBCSize, config.scale * config.maxRBCSize
- let windowSize = roundInt (1.6 * (snd radiusRange))
- let factorNbPick = 1.5
- let ellipses = logTime "Finding ellipses" (fun () ->
- Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick)
+ let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
+ let matchingEllipses = Ellipse.find edges xEdges yEdges config
+ matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
- *)
- let cells = []
// Output pictures if debug flag is set.
match config.debug with
let buildFileName postfix = System.IO.Path.Combine(output, name + postfix)
saveMat (edges * 255.0) (buildFileName " - edges.png")
- (*saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+ saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
saveImg parasites.stain (buildFileName " - parasites - stain.png")
saveImg parasites.infection (buildFileName " - parasites - infection.png")
+ let imgAllEllipses = img.Copy()
+ drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
+ saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+
let imgEllipses = img.Copy()
- drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0))
+ drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
saveImg imgEllipses (buildFileName " - ellipses.png")
saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
let imgCells' = img.Copy()
drawCells imgCells' true cells
- saveImg imgCells' (buildFileName " - cells - full.png")*)
+ saveImg imgCells' (buildFileName " - cells - full.png")
| _ -> ()
cells