Bitmap is now normalized in creation, which evenly distributes colors of the colorTable better, now IntQuant allows for coloLevel adjustments
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Pixelguy14
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@ -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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31
app.jl
31
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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using Printf
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include("./julia_imzML_visual.jl")
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@genietools
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@ -121,7 +122,8 @@ 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=int32.(Array(img_gray))
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# Smooth the image
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sigma=3.0
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@ -487,7 +489,7 @@ 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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@ -497,12 +499,12 @@ end
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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 < 2 || 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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sliceTriq=TrIQ(slice, Int(colorLevel), triqProb)
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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: $(typeof(sliceTriq))")
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sliceTriq=reverse(sliceTriq, dims=2)
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@ -515,8 +517,19 @@ end
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current_triq="TrIQ_$(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(sliceTriq)*triqProb), length=15), sigdigits=3)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(sliceTriq)*triqProb),ticks=ticks, label="Intensity", size = 25)
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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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"""
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function log_tick_formatter(values)
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return map(v -> "10" * Makie.UnicodeFun.to_superscript(round(Int64, v)), values)
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end
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"""
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println("ticks: $(typeof(ticks))")
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#Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks,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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@ -534,7 +547,7 @@ 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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sliceQuant=IntQuantCl(slice,colorLevel)
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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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@ -548,8 +561,8 @@ end
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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#ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
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ticks=round.(range(0, stop=maximum(sliceQuant), length=15), sigdigits=3)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(sliceQuant)),ticks=ticks, label="Intensity", size = 25)
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ticks=range(0, stop=maximum(slice), length=5)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
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save("public/colorbar_MSI_$(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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10
app.jl.html
10
app.jl.html
@ -60,18 +60,16 @@
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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-4 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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<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="[
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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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]"></q-input>
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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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@ -15,14 +15,16 @@ end
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# SaveBitmap is also 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,
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pixMap::Array{UInt8,2},
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colorTable::Array{UInt32,1} )
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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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min_val = minimum(pixMap)
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max_val = maximum(pixMap)
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pixMap = round.(UInt8, 255 * (pixMap .- min_val) ./ (max_val - min_val))
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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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@ -36,17 +38,12 @@ function SaveBitmapCl( name,
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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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# Get unique colors displayed in pixMap
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unique_colors = unique(vec(pixMap))
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n_colors = length(unique_colors)
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# Color levels can't surpass 256
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levels = min(n_colors, 256)
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extendedColorTable = zeros(UInt32, 256)
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for i in 1:256
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idx = ceil(Int, i * levels / 256)
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extendedColorTable[i] = colorTable[idx]
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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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write(stream, extendedColorTable)
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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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@ -1,4 +1,5 @@
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using Pkg
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sTime=time()
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Pkg.activate(".")
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Pkg.instantiate()
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Pkg.gc()
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@ -31,6 +32,8 @@ Genie.loadapp()
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# Start the Genie server
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@async begin
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up(host="127.0.0.1", port=1481)
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eTime=round(time()-sTime,digits=3)
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println("Julia MSI GUI took $(eTime) seconds booting")
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url = "http://127.0.0.1:1481"
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# Open the URL in the default web browser based on the OS
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if Sys.isapple()
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@ -43,5 +46,4 @@ Genie.loadapp()
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@async run(`Start-Process $url`) # For Windows
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end
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end
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wait()
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