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Fixed bounding error in the median filter application

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This commit is contained in:
Pixelguy14 2025-02-10 18:41:26 -06:00
parent 63c7428214
commit 2b6ec4937f
2 changed files with 9 additions and 24 deletions
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19
app.jl
View File

@ -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"

14
julia_imzML_visual.jl
View File

@ -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