diff --git a/app.jl b/app.jl index 09014e9..7718948 100644 --- a/app.jl +++ b/app.jl @@ -248,13 +248,11 @@ include("./julia_imzML_visual.jl") @onbutton btnSearch begin full_route=pick_file(; filterlist="imzML,mzML") if isnothing(full_route) - #println("No file selected") msg="No file selected" warning_msg=true btnStartDisable=true else if endswith(full_route, "imzML") # Case if the file loaded is imzML - #println("Selected file path: ", full_route) btnStartDisable=false btnPlotDisable=false # Splitting the route with regex from imzml to mzml so the plotting can work @@ -297,10 +295,8 @@ include("./julia_imzML_visual.jl") msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient." try spectra=LoadImzml(full_route) - println(typeof(spectra)) msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient." slice=GetMzSliceJl(spectra,Nmass,Tol) - println(typeof(slice)) fig=CairoMakie.Figure(size=(150, 250)) # Container # Append a query string to force the image to refresh timestamp=string(time_ns()) @@ -315,7 +311,6 @@ include("./julia_imzML_visual.jl") try slice=GetMzSliceJl(spectra, Nmass, Tol) sliceTriq=TrIQ(slice, colorLevel, triqProb) - println(typeof(sliceTriq)) if MFilterEnabled # If the Median filter is ON sliceTriq=medianFilterjl(sliceTriq) end @@ -354,12 +349,11 @@ include("./julia_imzML_visual.jl") image_path=joinpath("./public", "MSI_$(text_nmass).bmp") try sliceQuant=IntQuantCl(slice,Int(colorLevel-1)) - println(typeof(sliceQuant)) if MFilterEnabled # If the Median filter is ON sliceQuant=medianFilterjl(sliceQuant) end catch e - println("The error is in the non triq slice: $e") + msg="Warning: $e" end sliceQuant=reverse(sliceQuant, dims=2) SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette) @@ -434,8 +428,7 @@ include("./julia_imzML_visual.jl") try xSpectraMz=mean(spectraMz[1,:]) ySpectraMz=mean(spectraMz[2,:]) - catch e - #println("an error was found: $e") + catch e xSpectraMz=spectraMz[1,1] ySpectraMz=spectraMz[2,1] end @@ -778,8 +771,7 @@ include("./julia_imzML_visual.jl") msg="Plot loaded in $(eTime) seconds" catch e msg="Failed to load and process image: $e" - warning_msg=true - println(msg) + warning_msg=true end else msg="Image could not be 3d plotted" @@ -819,8 +811,7 @@ include("./julia_imzML_visual.jl") msg="Plot loaded in $(eTime) seconds" catch e msg="Failed to load and process image: $e" - warning_msg=true - println(msg) + warning_msg=true end else msg="Image could not be 3d plotted" @@ -863,7 +854,6 @@ include("./julia_imzML_visual.jl") catch e msg="Failed to load and process image: $e" warning_msg=true - println(msg) end else msg="Image could not be 2D plotted" @@ -905,7 +895,6 @@ include("./julia_imzML_visual.jl") catch e msg="Failed to load and process image: $e" warning_msg=true - println(msg) end else msg="Image could not be 2D plotted" diff --git a/julia_imzML_visual.jl b/julia_imzML_visual.jl index 635879b..f35973e 100644 --- a/julia_imzML_visual.jl +++ b/julia_imzML_visual.jl @@ -389,23 +389,19 @@ end # with the close pixels just from the sides to reduce noise. # This one in particular is a midpoint fiter from a 3x3 neighbour area function medianFilterjl(pixMap) - width, height = size(pixMap) + height, width = size(pixMap) target = zeros(eltype(pixMap), height, width) - println("Matrix Dimensions: ", size(pixMap)) - for j in 2:(width-1) for i in 2:(height-1) - println("Current Indices: i = $i, j = $j") neighbors = [] - for dj in max(1, j-1):min(width, j+1) - for di in max(1, i-1):min(height, i+1) + for dj in max(1, j-1):min(j+1, width) + for di in max(1, i-1):min(i+1, height) push!(neighbors, pixMap[di, dj]) end end target[i, j] = median(neighbors) end end + return target +end - return target - -end \ No newline at end of file