Implemented an experimental executable for all systems, fixed a few errors, implemented first try for a median filter for the slices in Julia
This commit is contained in:
Pixelguy14
parent
59630bdd95
commit
63c7428214
116
app.jl
116
app.jl
@ -36,6 +36,7 @@ include("./julia_imzML_visual.jl")
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# Text field validations
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@in triqEnabled=false
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@in SpectraEnabled=false
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@in MFilterEnabled=false
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# Dialogs
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@in warning_msg=false
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@in CompareDialog=false
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@ -91,17 +92,21 @@ include("./julia_imzML_visual.jl")
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@out imgHeight=0
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# Optical Image Overlay & Transparency
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@in imgTrans = 1.0
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@in progressOptical = false
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@out btnOpticalDisable = true
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@in btnOptical = false
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@in btnOpticalT = false
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@in opticalOverTriq = false
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@in imgTrans=1.0
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@in progressOptical=false
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@out btnOpticalDisable=true
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@in btnOptical=false
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@in btnOpticalT=false
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@in opticalOverTriq=false
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@out imgRoute=""
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# Messages to interface variables
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@out msg=""
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@out msgimg=""
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@out msgtriq=""
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# Reiteration of the messages under the image to know which spectra is being visualized
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@out msgimgComp=""
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@out msgtriqComp=""
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# Saves the route where imzML and mzML files are located
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@out full_route=""
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@ -292,12 +297,10 @@ include("./julia_imzML_visual.jl")
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msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
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try
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spectra=LoadImzml(full_route)
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msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient."
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try
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println(typeof(spectra))
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msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient."
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slice=GetMzSliceJl(spectra,Nmass,Tol)
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catch e
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println("the error is in the slice: $e")
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end
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println(typeof(slice))
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fig=CairoMakie.Figure(size=(150, 250)) # Container
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# Append a query string to force the image to refresh
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timestamp=string(time_ns())
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@ -307,14 +310,18 @@ include("./julia_imzML_visual.jl")
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warning_msg=true
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else
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image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp")
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valid_slice = false
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valid_slice=false
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while Tol <= 1.0 && !valid_slice
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try
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slice = GetMzSliceJl(spectra, Nmass, Tol)
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sliceTriq = TrIQ(slice, colorLevel, triqProb)
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valid_slice = true
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slice=GetMzSliceJl(spectra, Nmass, Tol)
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sliceTriq=TrIQ(slice, colorLevel, triqProb)
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println(typeof(sliceTriq))
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if MFilterEnabled # If the Median filter is ON
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sliceTriq=medianFilterjl(sliceTriq)
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end
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valid_slice=true
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catch e
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msg="Warning: insufficient tolerance, inputs modified to allow the creation of an image regardless = $Tol: $e"
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msg="Warning: insufficient tolerance, inputs modified to allow the creation of an image regardless=$Tol: $e"
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Tol += 0.1
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end
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end
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@ -327,10 +334,10 @@ include("./julia_imzML_visual.jl")
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current_triq="TrIQ_$(text_nmass).bmp"
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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bound = julia_mzML_imzML.GetOutlierThres(slice, triqProb)
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levels = range(bound[1],stop=bound[2], length=8)
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levels = vcat(levels, 2*levels[end]-levels[end-1])
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, bound[2]),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
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bound =julia_mzML_imzML.GetOutlierThres(slice, triqProb)
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levels=range(bound[1],stop=bound[2], length=8)
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levels=vcat(levels, 2*levels[end]-levels[end-1])
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, bound[2]),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size=25)
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save("public/colorbar_TrIQ_$(text_nmass).png", fig)
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colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
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# Get current colorbar
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@ -345,11 +352,14 @@ include("./julia_imzML_visual.jl")
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end
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else # If we don't use TrIQ
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image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
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##sliceQuant=IntQuant(slice)
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try
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sliceQuant=IntQuantCl(slice,Int(colorLevel-1))
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println(typeof(sliceQuant))
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if MFilterEnabled # If the Median filter is ON
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sliceQuant=medianFilterjl(sliceQuant)
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end
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catch e
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println("the error is in the non triq slice: $e")
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println("The error is in the non triq slice: $e")
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end
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sliceQuant=reverse(sliceQuant, dims=2)
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SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
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@ -361,7 +371,7 @@ include("./julia_imzML_visual.jl")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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levels=range(0,maximum(slice),length=8)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size=25)
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save("public/colorbar_MSI_$(text_nmass).png", fig)
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colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
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# Get current colorbar
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@ -390,7 +400,7 @@ include("./julia_imzML_visual.jl")
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end
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btnStartDisable=false
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btnPlotDisable=false
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btnOpticalDisable = false
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btnOpticalDisable=false
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if isfile(full_routeMz)
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# We enable coord search and spectra plot creation
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btnSpectraDisable=false
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@ -540,7 +550,7 @@ include("./julia_imzML_visual.jl")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImg=[traceImg]
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@ -567,7 +577,7 @@ include("./julia_imzML_visual.jl")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImg=[traceImg]
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@ -595,7 +605,7 @@ include("./julia_imzML_visual.jl")
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgT=[traceImg]
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@ -622,7 +632,7 @@ include("./julia_imzML_visual.jl")
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgT=[traceImg]
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@ -648,14 +658,14 @@ include("./julia_imzML_visual.jl")
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text_nmass=replace(current_msiComp, "MSI_" => "")
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgComp=[traceImg]
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msgimg=""
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msgimgComp=""
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end
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end
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@ -676,14 +686,14 @@ include("./julia_imzML_visual.jl")
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text_nmass=replace(current_msiComp, "MSI_" => "")
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgComp=[traceImg]
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msgimg=""
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msgimgComp=""
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end
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end
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@ -704,14 +714,14 @@ include("./julia_imzML_visual.jl")
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text_nmass=replace(current_triqComp, "TrIQ_" => "")
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgTComp=[traceImg]
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msgtriq=""
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msgtriqComp=""
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end
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end
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@ -732,14 +742,14 @@ include("./julia_imzML_visual.jl")
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text_nmass=replace(current_triqComp, "TrIQ_" => "")
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text_nmass=replace(text_nmass, ".bmp" => "")
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msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Process the image in the function
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plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
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btnOpticalDisable = false
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btnOpticalDisable=false
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else
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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plotdataImgTComp=[traceImg]
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msgtriq=""
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msgtriqComp=""
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end
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end
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@ -922,28 +932,28 @@ include("./julia_imzML_visual.jl")
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spectracoords=reshape(plotdata, 1, length(plotdata))
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# Extract x and y values from data_click
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cursor_data=data_click["cursor"]
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x_value = cursor_data["x"]
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y_value = cursor_data["y"]
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x_value=cursor_data["x"]
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y_value=cursor_data["y"]
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# Find the minimum x-value in spectracoords
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min_x_value = minimum([minimum(val[:x]) for val in spectracoords if !isempty(val[:x])])
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min_x_value=minimum([minimum(val[:x]) for val in spectracoords if !isempty(val[:x])])
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# Adjust x_value and spectracoords x-values to start from 0
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adjusted_x_value = x_value - min_x_value
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adjusted_x_value=x_value - min_x_value
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closest_distance = Inf
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closest_distance=Inf
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for val in spectracoords
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adjusted_x = val[:x] .- min_x_value
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start_idx = findfirst(x -> x >= adjusted_x_value - 20, adjusted_x)
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end_idx = findlast(x -> x <= adjusted_x_value + 20, adjusted_x)
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adjusted_x=val[:x] .- min_x_value
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start_idx=findfirst(x -> x >= adjusted_x_value - 20, adjusted_x)
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end_idx=findlast(x -> x <= adjusted_x_value + 20, adjusted_x)
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if start_idx !== nothing && end_idx !== nothing
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for i in start_idx:end_idx
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spectra_x = adjusted_x[i]
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spectra_y = val[:y][i]
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distance = sqrt((spectra_x - adjusted_x_value)^2 + (spectra_y - y_value)^2)
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spectra_x=adjusted_x[i]
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spectra_y=val[:y][i]
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distance=sqrt((spectra_x - adjusted_x_value)^2 + (spectra_y - y_value)^2)
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if distance < closest_distance
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closest_distance = distance
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Nmass = round(spectra_x + min_x_value, digits=2)
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closest_distance=distance
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Nmass=round(spectra_x + min_x_value, digits=2)
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end
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end
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end
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@ -339,7 +339,7 @@
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarComp"></q-img>
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</div>
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</div>
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<p>{{msgimg}}</p>
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<p>{{msgimgComp}}</p>
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</q-tab-panel>
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<q-tab-panel name="tab1">
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@ -359,7 +359,7 @@
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarTComp"></q-img>
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</div>
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</div>
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<p>{{msgtriq}}</p>
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<p>{{msgtriqComp}}</p>
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</q-tab-panel>
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<q-tab-panel name="tab2">
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<!-- Content for Tab 2 -->
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18
executable.sh
Executable file
18
executable.sh
Executable file
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#!/bin/bash
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command="julia --project=. start_MSI_GUI.jl"
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case "$OSTYPE" in
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linux*)
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$command
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;;
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darwin*)
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$command
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;;
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cygwin*|msys*|win32)
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julia --project=. start_MSI_GUI.jl
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;;
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*)
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echo "Unsupported OS"
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;;
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esac
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@ -384,3 +384,28 @@ function log_tick_formatter(values::Vector{Float64})
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return map((v, e) -> e == 0 ? "$(round(v, sigdigits=2))" : "$(round(v, sigdigits=2))x10" * Makie.UnicodeFun.to_superscript(e), formValues, exponents)
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end
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# Median filter: an adaptation of the R medianfilter, which averages the matrix
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# with the close pixels just from the sides to reduce noise.
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# This one in particular is a midpoint fiter from a 3x3 neighbour area
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function medianFilterjl(pixMap)
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width, height = size(pixMap)
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target = zeros(eltype(pixMap), height, width)
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println("Matrix Dimensions: ", size(pixMap))
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for j in 2:(width-1)
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for i in 2:(height-1)
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println("Current Indices: i = $i, j = $j")
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neighbors = []
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for dj in max(1, j-1):min(width, j+1)
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for di in max(1, i-1):min(height, i+1)
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push!(neighbors, pixMap[di, dj])
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end
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end
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target[i, j] = median(neighbors)
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end
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end
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return target
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end
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