Merge pull request #7 from Pixelguy14/Experimental_ColorLevels
Experimental color levels done
This commit is contained in:
José Julián Sierra Álvarez
GitHub
commit
09d680db87
@ -22,7 +22,7 @@ A Graphical User Interface for MSI in Julia: https://github.com/CINVESTAV-LABI/j
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```
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julia --project=. start_MSI_GUI.jl
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```
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3. After the script has finished loading, it should open a page (http://127.0.0.1:1481/) in your browser with the web app running.
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3. After the script has finished loading, You can open a page (http://127.0.0.1:1481/) in your browser with the web app running.
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Additional notes:<br>
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After the first boot initializes the packages in your computer, subsequent uses of the app should not take longer to load.<br>
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121
app.jl
121
app.jl
@ -13,6 +13,7 @@ using Images
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using LinearAlgebra
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using NativeFileDialog # Opens the file explorer depending on the OS
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using StipplePlotly
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include("./julia_imzML_visual.jl")
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@genietools
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# == Code import ==
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@ -54,13 +55,13 @@ function loadImgPlot(interfaceImg::String)
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cleaned_img=lstrip(cleaned_img, '/')
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var=joinpath("./public", cleaned_img)
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img=load(var)
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println("type of img: $(typeof(img))")
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#println("type of img: $(typeof(img))")
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# Convert to grayscale
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img_gray=Gray.(img)
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img_array=Array(img_gray)
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#println(typeof(img_array))
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elevation=Float32.(Array(img_array)) ./ 255.0
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println("type of elevation: $(typeof(elevation))")
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#println("type of elevation: $(typeof(elevation))")
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# Get the X, Y coordinates of the image
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height, width=size(img_array)
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#println("height: $(height), width: $(width)")
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@ -120,7 +121,8 @@ function loadContourPlot(interfaceImg::String)
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img=load(var)
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img_gray=Gray.(img)
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img_array=Array(img_gray)
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elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
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# parse matrix to int32 to closely resemble similarity to original bitmap
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elevation=Float32.(Array(img_array))./ 255.0 # Normalize between 0 and 1
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# Smooth the image
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sigma=3.0
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@ -171,7 +173,7 @@ function loadSurfacePlot(interfaceImg::String)
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img_gray=Gray.(img) # Convert to grayscale
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#println("Grayscale image type:", typeof(img_gray))
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img_array=Array(img_gray)
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elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
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elevation=Float32.(Array(img_array)) ./ 255.0 # Normalize between 0 and 1
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#println("Elevation size:", size(elevation))
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# Smooth the image
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sigma=3.0
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@ -203,10 +205,12 @@ function loadSurfacePlot(interfaceImg::String)
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aspectratio=aspect_ratio
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)
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)
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# Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping
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elevation_smoothed=transpose(elevation_smoothed)
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if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
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# Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping
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elevation_smoothed=transpose(elevation_smoothed)
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Y=-Y
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else
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X=-X
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end
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trace3D=PlotlyBase.surface(
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@ -243,8 +247,42 @@ function crossLinesPlot(x, y, maxwidth, maxheight)
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return trace1, trace2
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end
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function log_tick_formatter(values::Vector{Float64})
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#println("values: $(values) + type: $(typeof(values))")
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# Initialize exponents dictionary
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exponents=zeros(Int, length(values))
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formValues=zeros(Float64, length(values))
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for i in 1:length(values)
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value = values[i]
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#println("value: $(value)")
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if value >= 1000 # positive formatting for notation
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while value >= 1000
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value /= 10
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exponents[i] += 1
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end
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#println("value: $(value) x10^$(exponents[i])")
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elseif value > 0 && value < 1 # negative formatting for notation
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while value < 1
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value *= 10
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exponents[i] -= 1
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end
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#values[i] = round(values[i], digits=2)
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#println("value: $(value) x10^$(exponents[i])")
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end
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#formatted_values[i] = values[i] != 0 ? "$(round(values[i], digits=2))x10" * Makie.UnicodeFun.to_superscript(exponents[i]) : "0"
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formValues[i]=value
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end
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#return formatted_values
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#return map(v -> values * "x10" * Makie.UnicodeFun.to_superscript(round(Int64, v)), exponents)
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#println("formated values: $(formValues) + type: $(typeof(formValues))")
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#println("exponents: $(exponents) + type: $(typeof(exponents))")
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#return map((v, e) -> "$(round(v, digits=2))x10" * Makie.UnicodeFun.to_superscript(e), formValues, exponents)
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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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# == Reactive code ==
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# reactive code to make the UI interactive
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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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@ -476,6 +514,7 @@ end
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end
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@onbutton mainProcess begin
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#@onchange Nmass begin
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progress=true # Start progress button animation
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btnStartDisable=true # We disable the button to avoid multiple requests
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btnPlotDisable=true
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@ -483,44 +522,46 @@ end
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text_nmass=replace(string(Nmass), "." => "_")
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sTime=time()
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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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if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <=1 && colorLevel > 1 && colorLevel < 257
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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=(140, 440)) # Container
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#slice=GetSlice(spectra, Nmass, Tol)
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slice=GetMzSliceJl(spectra,Nmass,Tol)
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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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if triqEnabled # If we have TrIQ
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if colorLevel < 4 || colorLevel > 256 || triqProb < 0.8 || triqProb > 1
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if triqProb < 0.8 || triqProb > 1
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msg="Incorrect TrIQ values, please adjust accordingly and try again."
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warning_msg=true
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else
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image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp")
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SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(colorLevel), triqProb),ViridisPalette)
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# Flip te image vertically then save it again
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img=load(image_path)
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if size(img, 1) > size(img, 2) # fix to taller images
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img=reverse(permutedims(img, (2, 1)), dims=1)
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end
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flipped_img=reverse(img, dims=1)
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imgWidth=size(flipped_img, 2)
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imgHeight=size(flipped_img, 1)
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save(image_path, flipped_img)
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sliceTriq=TrIQ(slice, colorLevel, triqProb)
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#println("slice raw: $(typeof(slice))")
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#println("TriQ matrix: $(typeof(sliceTriq))")
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sliceTriq=reverse(sliceTriq, dims=2)
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##SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),sliceTriq,ViridisPalette)
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SaveBitmapCl(joinpath("public", "TrIQ_$(text_nmass).bmp"),sliceTriq,ViridisPalette)
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# Use timestamp to refresh image interface container
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imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
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plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
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# Get current image
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current_triq="TrIQ_$(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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#ticks=round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3)
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#println("ticks: $(round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3))")
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ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3)
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#println("ticks 2: $(round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3))")
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#Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(colorLevel), triqProb))),ticks=ticks, label="Intensity")
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25)
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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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#println("range of the levels 1: $(levels)")
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levels = vcat(levels, 2*levels[end]-levels[end-1])
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#println("range of the levels 2: $(levels) + $(length(levels))")
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#ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=10), sigdigits=3)
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#ticks=range(0, (stop=maximum(slice)*triqProb), length=5)
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#println("ticks: $(typeof(ticks))")
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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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#Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25)
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#println("Colorbar: $(typeof(fig))")
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save("public/colorbar_TrIQ_$(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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@ -537,16 +578,13 @@ end
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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_$(text_nmass).bmp")
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SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),IntQuant(slice),ViridisPalette)
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# Flip te image vertically then save it again
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img=load(image_path)
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if size(img, 1) > size(img, 2) # fix to taller images
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img=reverse(permutedims(img, (2, 1)), dims=1)
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end
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flipped_img=reverse(img, dims=1)
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imgWidth=size(flipped_img, 2)
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imgHeight=size(flipped_img, 1)
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save(image_path, flipped_img)
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##sliceQuant=IntQuant(slice)
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sliceQuant=IntQuantCl(slice,Int(colorLevel-1))
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#println("slice raw: $(typeof(slice))")
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#println("slice in intQuant: $(typeof(sliceQuant))")
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sliceQuant=reverse(sliceQuant, dims=2)
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##SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
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SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
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# Use timestamp to refresh image interface container
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imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)"
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plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
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@ -554,10 +592,11 @@ end
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current_msi="MSI_$(text_nmass).bmp"
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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levels=range(0,maximum(slice),length=8)
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#ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
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ticks=round.(range(0, stop=maximum(slice), length=15), sigdigits=3)
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#Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(slice)),ticks=ticks, label="Intensity")
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, 256, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
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#ticks=range(0, stop=maximum(slice), length=5)
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#Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
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save("public/colorbar_MSI_$(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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26
app.jl.html
26
app.jl.html
@ -57,21 +57,27 @@
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<p id="lblFullRoute">full route: {{full_route}}</p>
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<!-- Variable Manipulation -->
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<div class="row">
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<div class="st-col col-12 col-sm q-ma-sm">
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<div class="st-col col-4 col-sm q-ma-sm">
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<q-input standout="custom-standout" id="textNmass" step="0.01" v-model="Nmass"
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label="Mass-to-charge ratio of interest" type="number"
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:rules="[ val => !!val || '* Required', val => val >= 0.0 || 'Need positive mass values',]"></q-input>
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:rules="[ val => !!val || '* Required', val => val >= 0.0 || 'Need positive mass values']"></q-input>
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</div>
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<div class="st-col col-12 col-sm q-ma-sm">
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<q-input standout="custom-standout" id="textTol" step="0.05" v-model="Tol"
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<div class="st-col col-4 col-sm q-ma-sm">
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<q-input standout="custom-standout" id="textTol" step="0.005" v-model="Tol"
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label="Mass-to-charge ratio tolerance" type="number"
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:rules="[val => !!val || '* Required', val => val >= 0.0 && val <= 1.0 || 'Needs to be in range between 0 and 1',]"></q-input>
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:rules="[val => !!val || '* Required', val => val >= 0.0 && val <= 1.0 || 'Needs to be in range between 0 and 1']"></q-input>
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</div>
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<div class="st-col col-4 col-sm q-ma-sm">
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<q-input standout="custom-standout" id="textcolorLevel" step="1" v-model="colorLevel"
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label="Color level" type="number" :rules="[ val => !!val || '* Required', val => val >= 2 && val <= 256 || 'Needs to be in range between 2 and 256']"></q-input>
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</div>
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</div>
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<div class="row">
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<!-- Triq Variable Manipulation -->
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<!-- Triq Variable Manipulation and filters-->
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<div class="col-6">
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<div class="st-col col-6 col-sm q-ma-sm">
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<q-toggle id="btnEnableMFilter" v-on:click="MFilterEnabled" v-model="MFilterEnabled" color="green"
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label="Add Median Filter"></q-toggle>
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<q-toggle id="btnEnableTriq" v-on:click="triqEnabled" v-model="triqEnabled" color="blue"
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label="Add Threshold Intensity Quantization (TrIQ)"></q-toggle>
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</div>
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@ -82,12 +88,8 @@
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val => triqEnabled ? ( '* Required', val >= 0.8 && val <= 1 || 'Needs to be in range between 0.8 and 1') : true
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]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
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</div>
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<div class="st-col col-4 col-sm-4 q-ma-sm">
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<q-input standout="custom-standout" id="textcolorLevel" step="1" v-model="colorLevel"
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label="TrIQ color levels" type="number" :rules="[
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val => triqEnabled ? ( '* Required', val >= 4 && val <= 256 || 'Needs to be in range between 2 and 256') : true
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]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
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</div>
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<!--<div class="st-col col-4 col-sm-4 q-ma-sm">
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</div>-->
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</div>
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</div>
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<!-- Spectra Plot Manipulation -->
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80
julia_imzML_visual.jl
Normal file
80
julia_imzML_visual.jl
Normal file
@ -0,0 +1,80 @@
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# IntQuantCl is originally a function of julia mzMl imzML with the adition
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# of altering the scale of the colors according to colorlevel.
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function IntQuantCl( slice , colorLevel)
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# Compute scale factor for amplitude discretization
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lower = minimum( slice )
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scale = colorLevel / maximum( slice )
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dim = size( slice )
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image = zeros( UInt8, dim[1], dim[2] )
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for i in 1:length( slice )
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image[i] = convert( UInt8, floor( slice[i] * scale + 0.5 ) )
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end
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return image
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end
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# SaveBitmap originally a function of the mzML imzML library in julia,
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# This function dinamically adjust the color palete adjusting to the ammount of colors
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# available in pixmap
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function SaveBitmapCl( name, pixMap::Array{UInt8,2}, colorTable::Array{UInt32,1} )
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# Get image dimensions
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dim = size( pixMap )
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if length( dim ) != 2
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return 0
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end
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# Normalize pixel values to get a more accurate reading of the image
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minVal = minimum(pixMap)
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maxVal = maximum(pixMap)
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pixMap = round.(UInt8, 255 * (pixMap .- minVal) ./ (maxVal - minVal))
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# Compute row padding
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padding = ( 4 - dim[1] & 0x3 ) & 0x3
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# Compute file dimensions. Header = 14 + 40 + ( 256 * 4 ) = 1078
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offset = 1078
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imgBytes = dim[2] * ( dim[1] + padding )
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# Create file
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stream = open( name, "w" )
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# Save file header
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write( stream, UInt16( 0x4D42 ) )
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write( stream, UInt32[ offset + imgBytes, 0 , offset ] )
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# Save info header
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write( stream, UInt32[ 40, dim[1], dim[2], 0x80001, 0 ] )
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write( stream, UInt32[ imgBytes, 0, 0, 256, 0 ] )
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# Save color table
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write( stream, colorTable )
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if length( colorTable ) < 256
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fixTable = zeros( UInt32, 256 - length( colorTable ) )
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write( stream, fixTable )
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end
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# Save image pixels
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if padding == 0
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for i = 1:dim[2]
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write( stream, pixMap[:,i] )
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end
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else
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zeroPad = zeros( UInt8, padding )
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for i in 1:dim[2]
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write( stream, pixMap[:,i] )
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write( stream, zeroPad )
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end
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end
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# Close file
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close( stream )
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end
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# SaveBitmap originally a function of the mzML imzML library in julia,
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# now has an adjustment for NaN values in case they exist to mantain data integrity
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function GetMzSliceJl(imzML, mass, tolerance)
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# Alloc space for slice
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width = maximum(imzML[1, :])
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height = maximum(imzML[2, :])
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image = fill(0.0, width, height)
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||||
|
||||
for i in 1:size(imzML)[2]
|
||||
index = julia_mzML_imzML.FindMass(imzML[3, i], mass, tolerance)
|
||||
if index != 0
|
||||
image[imzML[1, i], imzML[2, i]] = imzML[4, i][index]
|
||||
end
|
||||
end
|
||||
# Adjustment for NaN values with 0
|
||||
replace!(image, NaN => 0.0)
|
||||
return image
|
||||
end
|
||||
@ -1,8 +1,10 @@
|
||||
using Pkg
|
||||
sTime=time()
|
||||
Pkg.activate(".")
|
||||
Pkg.instantiate()
|
||||
Pkg.gc()
|
||||
|
||||
"""
|
||||
packages = [
|
||||
"GenieFramework", "Libz", "PlotlyBase", "CairoMakie", "Colors",
|
||||
"Statistics", "NaturalSort", "Genie",
|
||||
@ -20,6 +22,7 @@ end
|
||||
if !("julia_mzML_imzML" in keys(Pkg.dependencies()))
|
||||
Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML")
|
||||
end
|
||||
"""
|
||||
|
||||
using Genie
|
||||
|
||||
@ -29,6 +32,8 @@ Genie.loadapp()
|
||||
# Start the Genie server
|
||||
@async begin
|
||||
up(host="127.0.0.1", port=1481)
|
||||
eTime=round(time()-sTime,digits=3)
|
||||
println("Julia MSI GUI took $(eTime) seconds booting")
|
||||
url = "http://127.0.0.1:1481"
|
||||
# Open the URL in the default web browser based on the OS
|
||||
if Sys.isapple()
|
||||
@ -41,5 +46,4 @@ Genie.loadapp()
|
||||
@async run(`Start-Process $url`) # For Windows
|
||||
end
|
||||
end
|
||||
|
||||
wait()
|
||||
Loading…
x
Reference in New Issue
Block a user