diff --git a/app.jl b/app.jl
index 45f3ecd..09014e9 100644
--- a/app.jl
+++ b/app.jl
@@ -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
@@ -91,17 +92,21 @@ include("./julia_imzML_visual.jl")
@out imgHeight=0
# Optical Image Overlay & Transparency
- @in imgTrans = 1.0
- @in progressOptical = false
- @out btnOpticalDisable = true
- @in btnOptical = false
- @in btnOpticalT = false
- @in opticalOverTriq = false
+ @in imgTrans=1.0
+ @in progressOptical=false
+ @out btnOpticalDisable=true
+ @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
- slice=GetMzSliceJl(spectra,Nmass,Tol)
- catch e
- println("the error is in the slice: $e")
- end
+ println(typeof(spectra))
+ msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient."
+ slice=GetMzSliceJl(spectra,Nmass,Tol)
+ println(typeof(slice))
fig=CairoMakie.Figure(size=(150, 250)) # Container
# Append a query string to force the image to refresh
timestamp=string(time_ns())
@@ -307,14 +310,18 @@ include("./julia_imzML_visual.jl")
warning_msg=true
else
image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp")
- valid_slice = false
+ valid_slice=false
while Tol <= 1.0 && !valid_slice
try
- slice = GetMzSliceJl(spectra, Nmass, Tol)
- sliceTriq = TrIQ(slice, colorLevel, triqProb)
- valid_slice = true
+ 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: $e"
+ msg="Warning: insufficient tolerance, inputs modified to allow the creation of an image regardless=$Tol: $e"
Tol += 0.1
end
end
@@ -327,10 +334,10 @@ include("./julia_imzML_visual.jl")
current_triq="TrIQ_$(text_nmass).bmp"
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Create colorbar
- bound = julia_mzML_imzML.GetOutlierThres(slice, triqProb)
- levels = range(bound[1],stop=bound[2], length=8)
- levels = vcat(levels, 2*levels[end]-levels[end-1])
- Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, bound[2]),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
+ bound =julia_mzML_imzML.GetOutlierThres(slice, triqProb)
+ levels=range(bound[1],stop=bound[2], length=8)
+ levels=vcat(levels, 2*levels[end]-levels[end-1])
+ Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, bound[2]),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size=25)
save("public/colorbar_TrIQ_$(text_nmass).png", fig)
colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
# Get current colorbar
@@ -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)
@@ -361,7 +371,7 @@ include("./julia_imzML_visual.jl")
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Create colorbar
levels=range(0,maximum(slice),length=8)
- Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
+ Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size=25)
save("public/colorbar_MSI_$(text_nmass).png", fig)
colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
# Get current colorbar
@@ -390,7 +400,7 @@ include("./julia_imzML_visual.jl")
end
btnStartDisable=false
btnPlotDisable=false
- btnOpticalDisable = false
+ btnOpticalDisable=false
if isfile(full_routeMz)
# We enable coord search and spectra plot creation
btnSpectraDisable=false
@@ -540,7 +550,7 @@ include("./julia_imzML_visual.jl")
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
- btnOpticalDisable = false
+ btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImg=[traceImg]
@@ -567,7 +577,7 @@ include("./julia_imzML_visual.jl")
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
- btnOpticalDisable = false
+ btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImg=[traceImg]
@@ -595,7 +605,7 @@ include("./julia_imzML_visual.jl")
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
- btnOpticalDisable = false
+ btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgT=[traceImg]
@@ -622,7 +632,7 @@ include("./julia_imzML_visual.jl")
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Process the image in the function
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
- btnOpticalDisable = false
+ btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgT=[traceImg]
@@ -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
+ 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
+ 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
+ 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
+ btnOpticalDisable=false
else
traceImg=PlotlyBase.heatmap(x=[], y=[])
plotdataImgTComp=[traceImg]
- msgtriq=""
+ msgtriqComp=""
end
end
@@ -922,28 +932,28 @@ include("./julia_imzML_visual.jl")
spectracoords=reshape(plotdata, 1, length(plotdata))
# Extract x and y values from data_click
cursor_data=data_click["cursor"]
- x_value = cursor_data["x"]
- y_value = cursor_data["y"]
+ x_value=cursor_data["x"]
+ y_value=cursor_data["y"]
# Find the minimum x-value in spectracoords
- min_x_value = minimum([minimum(val[:x]) for val in spectracoords if !isempty(val[:x])])
+ min_x_value=minimum([minimum(val[:x]) for val in spectracoords if !isempty(val[:x])])
# Adjust x_value and spectracoords x-values to start from 0
- adjusted_x_value = x_value - min_x_value
+ adjusted_x_value=x_value - min_x_value
- closest_distance = Inf
+ closest_distance=Inf
for val in spectracoords
- adjusted_x = val[:x] .- min_x_value
- start_idx = findfirst(x -> x >= adjusted_x_value - 20, adjusted_x)
- end_idx = findlast(x -> x <= adjusted_x_value + 20, adjusted_x)
+ adjusted_x=val[:x] .- min_x_value
+ start_idx=findfirst(x -> x >= adjusted_x_value - 20, adjusted_x)
+ end_idx=findlast(x -> x <= adjusted_x_value + 20, adjusted_x)
if start_idx !== nothing && end_idx !== nothing
for i in start_idx:end_idx
- spectra_x = adjusted_x[i]
- spectra_y = val[:y][i]
- distance = sqrt((spectra_x - adjusted_x_value)^2 + (spectra_y - y_value)^2)
+ spectra_x=adjusted_x[i]
+ spectra_y=val[:y][i]
+ distance=sqrt((spectra_x - adjusted_x_value)^2 + (spectra_y - y_value)^2)
if distance < closest_distance
- closest_distance = distance
- Nmass = round(spectra_x + min_x_value, digits=2)
+ closest_distance=distance
+ Nmass=round(spectra_x + min_x_value, digits=2)
end
end
end
diff --git a/app.jl.html b/app.jl.html
index aa53148..414d971 100644
--- a/app.jl.html
+++ b/app.jl.html
@@ -339,7 +339,7 @@
- {{msgimg}}
+ {{msgimgComp}}
@@ -359,7 +359,7 @@
- {{msgtriq}}
+ {{msgtriqComp}}
diff --git a/executable.sh b/executable.sh
new file mode 100755
index 0000000..934834e
--- /dev/null
+++ b/executable.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+command="julia --project=. start_MSI_GUI.jl"
+
+case "$OSTYPE" in
+ linux*)
+ $command
+ ;;
+ darwin*)
+ $command
+ ;;
+ cygwin*|msys*|win32)
+ julia --project=. start_MSI_GUI.jl
+ ;;
+ *)
+ echo "Unsupported OS"
+ ;;
+esac
diff --git a/julia_imzML_visual.jl b/julia_imzML_visual.jl
index b1fe4a7..635879b 100644
--- a/julia_imzML_visual.jl
+++ b/julia_imzML_visual.jl
@@ -383,4 +383,29 @@ function log_tick_formatter(values::Vector{Float64})
end
return map((v, e) -> e == 0 ? "$(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
\ No newline at end of file
diff --git a/public/css/imgOver.png b/public/css/imgOver.png
deleted file mode 100644
index f167018..0000000
Binary files a/public/css/imgOver.png and /dev/null differ