235 lines
9.7 KiB
Julia
235 lines
9.7 KiB
Julia
module App
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# == Packages ==
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using GenieFramework # set up Genie development environment.
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using Pkg
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using Libz
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using PlotlyBase
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using CairoMakie
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using Colors
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using julia_mzML_imzML
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using Statistics
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@genietools
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# == Code import ==
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# add your data analysis code here or in the lib folder. Code in lib/ will be
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# automatically loaded
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rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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# == Reactive code ==
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# reactive code to make the UI interactive
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@app begin
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# == Reactive variables ==
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# reactive variables exist in both the Julia backend and the browser with two-way synchronization
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# @out variables can only be modified by the backend
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# @in variables can be modified by both the backend and the browser
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# variables must be initialized with constant values, or variables defined outside of the @app block
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#@out test = "/test.bmp" #slash means it's getting the info from 'public' folder
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@in file_route = ""
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@in file_name = ""
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@out warning_fr = ""
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@in Nmass = 0.0
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@in Tol = 0.0
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@in triqEnabled = false
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@out Disab_btn = false
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@in triqProb = 0.0
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@in triqColor = 0
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@in Main_Process = false
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@out indeximg = 0
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@out indeximgTriq = 0
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@out lastimg = 0
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@out lastimgTriq = 0
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@in ImgPlus = false
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@in ImgMinus = false
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@out test = "/.bmp"
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@in ImgPlusT = false
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@in ImgMinusT = false
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@out testT = "/.bmp"
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@out msg = ""
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@out msgimg = ""
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@out msgtriq = ""
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@out full_route = ""
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@out full_routeMz = ""
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@out full_routeMz2 = ""
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@out colorbar = "/.png"
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@out colorbarT = "/.png"
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layoutSpectra = PlotlyBase.Layout(
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title = "SUM Spectrum plot",
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xaxis = PlotlyBase.attr(
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title = "<i>m/z</i>",
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showgrid = true
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),
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yaxis = PlotlyBase.attr(
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title = "Intensity",
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showgrid = true
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),
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width = 900,
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height = 500
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)
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traceSpectra = PlotlyBase.scatter(x=[], y=[], mode="lines")
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@out plotdata = [traceSpectra]
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@out plotlayout = layoutSpectra
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# == Reactive handlers ==
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# reactive handlers watch a variable and execute a block of code when
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# its value changes
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@onchange triqEnabled begin
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if !triqEnabled
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#triqProb = 0.0
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#triqColor = 0
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end
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end
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@onchange file_name begin
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msg = ""
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if contains(file_name,".imzML")
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warning_fr = ""
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full_route = joinpath( file_route, file_name )
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if isfile(full_route) # check if the file exists
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full_routeMz = split( full_route, "." )[1] * ".mzML" # Splitting the route from imzml to mzml so the plotting can work
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if isfile(full_routeMz) && (full_routeMz2 == "" || full_routeMz2 != full_routeMz) # check if there is an mzML file around
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Disab_btn = true
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warning_fr = "Loading plot..."
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spectraMz = LoadMzml(full_routeMz)
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# dims = size(spectraMz)
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# scansMax = dims[2] # we get the total of scansMax
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# traceSpectra = PlotlyBase.scatter(x = spectraMz[1, 1], y = spectraMz[2, 1], mode="lines")
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traceSpectra = PlotlyBase.scatter(x = mean(spectraMz[1,:]), y = mean(spectraMz[2,:]), mode="lines")
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plotdata = [traceSpectra] # we add the data of spectra to the plot
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spectraMz = nothing # Important for memory cleaning
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GC.gc() # Trigger garbage collection
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ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
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warning_fr = "Plot loaded."
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Disab_btn = false
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full_routeMz2 = full_routeMz # to avoid creating the plot if its the same file read as before
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end
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else
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warning_fr = "is not an imzML file"
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end
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else
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full_route = "/"
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warning_fr = "is not an imzML file"
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end
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end
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@onchange Nmass begin
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indeximg = floor(Int, Nmass)
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indeximgTriq = floor(Int, Nmass)
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lastimg = floor(Int, Nmass)
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lastimgTriq = floor(Int, Nmass)
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end
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# The onbutton handler will set the variable to false after the block is executed
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@onbutton Main_Process begin
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Disab_btn = true # We disable the button to avoid multiple requests
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indeximg = floor(Int, Nmass)
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full_route = joinpath(file_route, file_name)
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if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <= 1
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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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slice = GetSlice(spectra, Nmass, Tol)
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fig = CairoMakie.Figure(size = (100, 200)) #container
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if triqEnabled # if we have TrIQ
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if triqColor < 1 || triqColor > 256 ||triqProb < 0 || triqProb > 1
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msg = "Incorrect TrIQ values, please adjust accordingly and try again."
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else
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SaveBitmap(joinpath("public", "TrIQ_$(floor(Int, Nmass)).bmp"),TrIQ(slice, Int(triqColor), triqProb),ViridisPalette)
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testT = "/TrIQ_$(floor(Int, Nmass)).bmp" # we define the starting value of the images
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msgtriq = "TrIQ image with the Nmass of $(floor(Int, Nmass))"
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ticks = round.(range(0, stop = maximum(TrIQ(slice, Int(triqColor), triqProb)), length = 10), digits = 2)
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Colorbar(fig[1, 1], colormap = rgb_ViridisPalette, limits = (0, maximum(TrIQ(slice, Int(triqColor), triqProb))),ticks = ticks, label = "Intensity")
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save("public/colorbar_TrIQ_$(floor(Int, Nmass)).png", fig)
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msg = "The file has been created successfully inside the 'public' folder of the app."
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colorbarT = "/colorbar_TrIQ_$(floor(Int, Nmass)).png"
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end
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else # if we don't use TrIQ
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SaveBitmap(joinpath("public", "$(floor(Int, Nmass)).bmp"),IntQuant(slice),ViridisPalette)
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test = "/$(floor(Int, Nmass)).bmp" # we define the starting value of the images
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msgimg = "image with the Nmass of $(floor(Int, Nmass))"
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ticks = round.(range(0, stop = maximum(slice), length = 10), digits = 2)
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Colorbar(fig[1, 1], colormap = rgb_ViridisPalette, limits = (0, maximum(slice)),ticks = ticks, label = "Intensity")
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save("public/colorbar_$(floor(Int, Nmass)).png", fig)
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msg = "The file has been created successfully inside the 'public' folder of the app."
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colorbar = "/colorbar_$(floor(Int, Nmass)).png"
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end
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catch e
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msg = "There was an error loading the ImzML file, please verify the file accordingly and try again. $(e)"
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end
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else
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msg = "File does not exist or a parameter is incorrect, please try again."
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end
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spectra = nothing # Important for memory cleaning
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slice = nothing
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GC.gc() # Trigger garbage collection
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ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
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Disab_btn = false
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end
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@onbutton ImgMinus begin
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indeximg-=1
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while !isfile("public/$(indeximg).bmp") && indeximg > 0
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indeximg -= 1
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end
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if(indeximg <= 0) #if it doesn't find a lower value image
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indeximg = lastimg
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end
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test = "/$(indeximg).bmp"
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colorbar = "/colorbar_$(indeximg).png"
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msgimg = "image with the Nmass of $(indeximg)"
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lastimg = indeximg
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end
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@onbutton ImgPlus begin
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indeximg+=1
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while !isfile("public/$(indeximg).bmp") && indeximg < 2001
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indeximg += 1
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end
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if(indeximg >= 2001)
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indeximg = lastimg
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end
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test = "/$(indeximg).bmp"
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colorbar = "/colorbar_$(indeximg).png"
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msgimg = "image with the Nmass of $(indeximg)"
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lastimg = indeximg
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end
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@onbutton ImgMinusT begin
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indeximgTriq-=1
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while !isfile("public/TrIQ_$(indeximgTriq).bmp") && indeximgTriq > 0
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indeximgTriq -= 1
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end
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if(indeximgTriq <= 0) #if it doesn't find a lower value image
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indeximgTriq = lastimgTriq
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end
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testT = "/TrIQ_$(indeximgTriq).bmp"
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colorbarT = "/colorbar_TrIQ_$(indeximgTriq).png"
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msgtriq = "TrIQ image with the Nmass of $(indeximgTriq)"
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lastimgTriq = indeximgTriq
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end
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@onbutton ImgPlusT begin
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indeximgTriq+=1
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while !isfile("public/TrIQ_$(indeximgTriq).bmp") && indeximgTriq < 2001
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indeximgTriq += 1
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end
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if(indeximgTriq >= 2001)
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indeximgTriq = lastimgTriq
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end
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testT = "/TrIQ_$(indeximgTriq).bmp"
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colorbarT = "/colorbar_TrIQ_$(indeximgTriq).png"
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msgtriq = "TrIQ image with the Nmass of $(indeximgTriq)"
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lastimgTriq = indeximgTriq
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end
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GC.gc() # Trigger garbage collection
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ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
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end
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# == Pages ==
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# register a new route and the page that will be loaded on access
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@page("/", "app.jl.html")
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end
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# == Advanced features ==
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#=
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- The @private macro defines a reactive variable that is not sent to the browser.
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This is useful for storing data that is unique to each user session but is not needed
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in the UI.
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@private table = DataFrame(a = 1:10, b = 10:19, c = 20:29)
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=#
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