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Implemented an experimental executable for all systems, fixed a few errors, implemented first try for a median filter for the slices in Julia

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This commit is contained in:
Pixelguy14 2025-02-10 15:34:30 -06:00
parent 59630bdd95
commit 63c7428214
5 changed files with 109 additions and 56 deletions
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40
app.jl
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@ -36,6 +36,7 @@ include("./julia_imzML_visual.jl")
# Text field validations
@in triqEnabled=false
@in SpectraEnabled=false
@in MFilterEnabled=false
# Dialogs
@in warning_msg=false
@in CompareDialog=false
@ -97,11 +98,15 @@ include("./julia_imzML_visual.jl")
@in btnOptical=false
@in btnOpticalT=false
@in opticalOverTriq=false
@out imgRoute=""
# Messages to interface variables
@out msg=""
@out msgimg=""
@out msgtriq=""
# Reiteration of the messages under the image to know which spectra is being visualized
@out msgimgComp=""
@out msgtriqComp=""
# Saves the route where imzML and mzML files are located
@out full_route=""
@ -292,12 +297,10 @@ include("./julia_imzML_visual.jl")
msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
try
spectra=LoadImzml(full_route)
msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient."
try
println(typeof(spectra))
msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient."
slice=GetMzSliceJl(spectra,Nmass,Tol)
catch e
println("the error is in the slice: $e")
end
println(typeof(slice))
fig=CairoMakie.Figure(size=(150, 250)) # Container
# Append a query string to force the image to refresh
timestamp=string(time_ns())
@ -312,6 +315,10 @@ include("./julia_imzML_visual.jl")
try
slice=GetMzSliceJl(spectra, Nmass, Tol)
sliceTriq=TrIQ(slice, colorLevel, triqProb)
println(typeof(sliceTriq))
if MFilterEnabled # If the Median filter is ON
sliceTriq=medianFilterjl(sliceTriq)
end
valid_slice=true
catch e
msg="Warning: insufficient tolerance, inputs modified to allow the creation of an image regardless=$Tol: $e"
@ -345,11 +352,14 @@ include("./julia_imzML_visual.jl")
end
else # If we don't use TrIQ
image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
##sliceQuant=IntQuant(slice)
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")
println("The error is in the non triq slice: $e")
end
sliceQuant=reverse(sliceQuant, dims=2)
SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
@ -648,14 +658,14 @@ include("./julia_imzML_visual.jl")
text_nmass=replace(current_msiComp, "MSI_" => "")
text_nmass=replace(text_nmass, ".bmp" => "")
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgComp=[traceImg]
msgimg=""
msgimgComp=""
end
end
@ -676,14 +686,14 @@ include("./julia_imzML_visual.jl")
text_nmass=replace(current_msiComp, "MSI_" => "")
text_nmass=replace(text_nmass, ".bmp" => "")
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgComp=[traceImg]
msgimg=""
msgimgComp=""
end
end
@ -704,14 +714,14 @@ include("./julia_imzML_visual.jl")
text_nmass=replace(current_triqComp, "TrIQ_" => "")
text_nmass=replace(text_nmass, ".bmp" => "")
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgTComp=[traceImg]
msgtriq=""
msgtriqComp=""
end
end
@ -732,14 +742,14 @@ include("./julia_imzML_visual.jl")
text_nmass=replace(current_triqComp, "TrIQ_" => "")
text_nmass=replace(text_nmass, ".bmp" => "")
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgTComp=[traceImg]
msgtriq=""
msgtriqComp=""
end
end

4
app.jl.html
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@ -339,7 +339,7 @@
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarComp"></q-img>
</div>
</div>
<p>{{msgimg}}</p>
<p>{{msgimgComp}}</p>
</q-tab-panel>
<q-tab-panel name="tab1">
@ -359,7 +359,7 @@
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarTComp"></q-img>
</div>
</div>
<p>{{msgtriq}}</p>
<p>{{msgtriqComp}}</p>
</q-tab-panel>
<q-tab-panel name="tab2">
<!-- Content for Tab 2 -->

18
executable.sh Executable file
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@ -0,0 +1,18 @@
#!/bin/bash
command="julia --project=. start_MSI_GUI.jl"
case "$OSTYPE" in
linux*)
$command
;;
darwin*)
$command
;;
cygwin*|msys*|win32)
julia --project=. start_MSI_GUI.jl
;;
*)
echo "Unsupported OS"
;;
esac

25
julia_imzML_visual.jl
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@ -384,3 +384,28 @@ function log_tick_formatter(values::Vector{Float64})
return map((v, e) -> e == 0 ? "$(round(v, sigdigits=2))" : "$(round(v, sigdigits=2))x10" * Makie.UnicodeFun.to_superscript(e), formValues, exponents)
end
# Median filter: an adaptation of the R medianfilter, which averages the matrix
# 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)
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)
push!(neighbors, pixMap[di, dj])
end
end
target[i, j] = median(neighbors)
end
end
return target
end

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