Fixed bounding error in the median filter application

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)
@@ -435,7 +429,6 @@ include("./julia_imzML_visual.jl")
                 xSpectraMz=mean(spectraMz[1,:])
                 ySpectraMz=mean(spectraMz[2,:])
             catch e
-                #println("an error was found: $e")
                 xSpectraMz=spectraMz[1,1]
                 ySpectraMz=spectraMz[2,1]
             end
@@ -779,7 +772,6 @@ 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 3d plotted"
@@ -820,7 +812,6 @@ 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 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"

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 dj in max(1, j-1):min(j+1, width)
-                for di in max(1, i-1):min(height, i+1)
+                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
-	return target
-
 end
+