1021 lines
42 KiB
Julia
1021 lines
42 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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using NaturalSort
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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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# == 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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## Interface non Variables
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@out btnStartDisable=true
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@out btnPlotDisable=false
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@out btnSpectraDisable=true
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# Loading animations
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@in progress=false
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@in progressPlot=false
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@in progressSpectraPlot=false
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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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## Interface Variables
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@in file_route=""
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@in file_name=""
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@in Nmass=0.0
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@in Tol=0.1
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@in triqProb=0.98
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@in colorLevel=20
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## Interface Buttons
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@in btnSearch=false # To search for files in your device
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@in mainProcess=false # To generate images
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@in compareBtn=false # To open dialog
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@in createSumPlot=false # To generate sum spectrum plot
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@in createXYPlot=false # To generate an spectrum plot according to the xy values inputed
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@in image3dPlot=false # To generate 3d plot based on current image
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@in triq3dPlot=false # To generate 3d plot based on current triq image
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@in imageCPlot=false # To generate contour plots of current image
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@in triqCPlot=false # To generate contour plots of current triq image
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# Image change buttons
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@in imgPlus=false
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@in imgMinus=false
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@in imgPlusT=false
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@in imgMinusT=false
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# Image change comparative buttons
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@in imgPlusComp=false
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@in imgMinusComp=false
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@in imgPlusTComp=false
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@in imgMinusTComp=false
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## Tabulation variables
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@out tabIDs=["tab0","tab1","tab2","tab3","tab4"]
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@out tabLabels=["Image", "TrIQ", "Spectrum Plot", "Topology Plot","Surface Plot"]
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@in selectedTab="tab0"
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@out CompTabIDs=["tab0","tab1","tab2","tab3","tab4"]
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@out CompTabLabels=["Image", "TrIQ", "Spectrum Plot", "Topology Plot","Surface Plot"]
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@in CompSelectedTab="tab0"
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# Interface Images
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@out imgInt="/.bmp" # image Interface
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@out imgIntT="/.bmp" # image Interface TrIQ
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@out colorbar="/.png"
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@out colorbarT="/.png"
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# Interface controlling for the comparative view
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@out imgIntComp="/.bmp" # image Interface
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@out imgIntTComp="/.bmp" # image Interface TrIQ
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@out colorbarComp="/.png"
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@out colorbarTComp="/.png"
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@out imgWidth=0
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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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@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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@out full_routeMz=""
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@out full_routeMz2=""
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# For the creation of images with a more specific mass charge
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@out text_nmass=""
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# For image search image lists we apply a filter that searches specific type of images into our public folder, then we sort it in a "numerical" order
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@in msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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@in col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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@in triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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@in col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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# Set current image for the list to display
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@out current_msi=""
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@out current_col_msi=""
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@out current_triq=""
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@out current_col_triq=""
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# We reiterate the process to display in the comparative view
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@out current_msiComp=""
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@out current_col_msiComp=""
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@out current_triqComp=""
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@out current_col_triqComp=""
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## Time measurement variables
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@out sTime=time()
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@out fTime=time()
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@out eTime=time()
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## Plots
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# Local image to plot
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layoutImg=PlotlyBase.Layout(
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xaxis=PlotlyBase.attr(
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visible=false,
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scaleanchor="y"
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),
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yaxis=PlotlyBase.attr(
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visible=false
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),
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margin=attr(l=0,r=0,t=0,b=0,pad=0)
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)
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traceImg=PlotlyBase.heatmap(x=[], y=[])
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@out plotdataImg=[traceImg]
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@out plotlayoutImg=layoutImg
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# For the image in the comparative view
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@out plotdataImgComp=[traceImg]
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@out plotlayoutImgComp=layoutImg
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# For triq image
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@out plotdataImgT=[traceImg]
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@out plotlayoutImgT=layoutImg
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# For the triq image in the comparative view
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@out plotdataImgTComp=[traceImg]
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@out plotlayoutImgTComp=layoutImg
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# Interface Plot Spectrum
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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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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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# Dummy 2D scatter plot
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traceSpectra=PlotlyBase.scatter(x=[], y=[], mode="lines")
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# Create conection to frontend
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@out plotdata=[traceSpectra]
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@out plotlayout=layoutSpectra
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@in xCoord=0
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@in yCoord=0
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@out xSpectraMz=Float64[]
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@out ySpectraMz=Float64[]
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# Interactive plot reactions
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@in data_click=Dict{String,Any}()
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#@in data_selected=Dict{String,Any}() # Selected is for areas, this can work for the masks
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#<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" @click="data_selected" class="q-pa-none q-ma-none sync_data"></plotly>
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# Interface Plot Surface
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layoutContour=PlotlyBase.Layout(
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title="2D Topographic Map",
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xaxis=PlotlyBase.attr(
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title="X",
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scaleanchor="y"
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),
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yaxis=PlotlyBase.attr(
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title="Y"
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),
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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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# Dummy 2D surface plot
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traceContour=PlotlyBase.scatter(x=[], y=[], mode="lines")
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# Create conection to frontend
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@out plotdataC=[traceContour]
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@out plotlayoutC=layoutContour
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# Interface Plot 3d
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# Define the layout for the 3D plot
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layout3D=PlotlyBase.Layout(
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title="3D Surface Plot",
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scene=attr(
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xaxis_title="X",
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yaxis_title="Y",
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zaxis_title="Z",
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xaxis_nticks=20,
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yaxis_nticks=20,
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zaxis_nticks=4,
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camera=attr(eye=attr(x=0, y=-1, z=0.5)),
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aspectratio=attr(x=1, y=1, z=0.2)
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),
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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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# Dummy 3D surface plot
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x=1:10
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y=1:10
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z=[sin(i * j / 10) for i in x, j in y]
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trace3D=PlotlyBase.surface(x=[], y=[], z=[],
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contours_z=attr(
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show=true,
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usecolormap=true,
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highlightcolor="limegreen",
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project_z=true
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), colorscale="Viridis")
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# Create conection to frontend
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@out plotdata3d=[trace3D]
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@out plotlayout3d=layout3D
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# == Reactive handlers ==
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# Reactive handlers watch a variable and execute a block of code when its value changes
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# The onbutton handler will set the variable to false after the block is executed
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@onbutton btnSearch begin
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full_route=pick_file(; filterlist="imzML,mzML")
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if full_route==""
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msg="No file selected"
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warning_msg=true
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btnStartDisable=true
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btnSpectraDisable=true
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SpectraEnabled=false
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else
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if endswith(full_route, "imzML") # Case if the file loaded is imzML
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btnStartDisable=false
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btnPlotDisable=false
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# Splitting the route with regex from imzml to mzml so the plotting can work
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full_routeMz=replace(full_route, r"\.[^.]*$" => ".mzML")
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if isfile(full_routeMz)
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# We enable coord search and spectra plot creation
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btnSpectraDisable=false
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SpectraEnabled=true
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else
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# If there's no MzML file, we deny access again
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btnSpectraDisable=true
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SpectraEnabled=false
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end
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else # Case if the file loaded is mzML
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full_routeMz=full_route
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btnSpectraDisable=false
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SpectraEnabled=true
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# Splitting the route the same way
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full_route=replace(full_route, r"\.[^.]*$" => ".imzML")
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if isfile(full_route)
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btnStartDisable=false
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else
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btnStartDisable=true
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full_route=full_routeMz
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end
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progressSpectraPlot=true
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btnPlotDisable=true
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btnStartDisable=true
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msg="Loading SUM spectrum plot..."
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sTime=time()
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plotdata, plotlayout, xSpectraMz, ySpectraMz=sumSpectrumPlot(full_routeMz)
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selectedTab="tab2"
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progressSpectraPlot=false
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btnPlotDisable=false
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if endswith(full_route, "imzML")
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btnStartDisable=false
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end
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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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SpectraEnabled=true
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end
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fTime=time()
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eTime=round(fTime-sTime,digits=3)
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msg="Plot loaded in $(eTime) seconds"
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end
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xCoord=0
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yCoord=0
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end
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end
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@onbutton mainProcess begin
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progress=true # Start progress button animation
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btnStartDisable=true # We disable the button to avoid multiple requests
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btnPlotDisable=true
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btnSpectraDisable=true
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text_nmass=replace(string(Nmass), "." => "_")
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sTime=time()
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if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <=1 && colorLevel > 1 && colorLevel < 257
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msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
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try
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spectra=LoadImzml(full_route)
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msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient."
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slice=GetMzSliceJl(spectra,Nmass,Tol)
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fig=CairoMakie.Figure(size=(150, 250)) # Container
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# Append a query string to force the image to refresh
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timestamp=string(time_ns())
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if triqEnabled # If we have TrIQ
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if triqProb < 0.8 || triqProb > 1
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msg="Incorrect TrIQ values, please adjust accordingly and try again."
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warning_msg=true
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else
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image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp")
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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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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: $e"
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Tol += 0.1
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end
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end
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sliceTriq=reverse(sliceTriq, dims=2)
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SaveBitmapCl(joinpath("public", "TrIQ_$(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 $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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bound=julia_mzML_imzML.GetOutlierThres(slice, triqProb)
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levels=range(bound[1],stop=bound[2], length=8)
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levels=vcat(levels, 2*levels[end]-levels[end-1])
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, bound[2]),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size=25)
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save("public/colorbar_TrIQ_$(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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current_col_triq="colorbar_TrIQ_$(text_nmass).png"
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# We update the directory to include the new placed images.
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triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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fTime=time()
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eTime=round(fTime-sTime,digits=3)
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msg="The file has been created in $(eTime) seconds successfully inside the 'public' folder of the app"
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selectedTab="tab1"
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end
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else # If we don't use TrIQ
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image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
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try
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sliceQuant=IntQuantCl(slice,Int(colorLevel-1))
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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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msg="Warning: $e"
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end
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sliceQuant=reverse(sliceQuant, dims=2)
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SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
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# 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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# Get current image
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current_msi="MSI_$(text_nmass).bmp"
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msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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levels=range(0,maximum(slice),length=8)
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size=25)
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save("public/colorbar_MSI_$(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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current_col_msi="colorbar_MSI_$(text_nmass).png"
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# We update the directory to include the new placed images.
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msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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selectedTab="tab0"
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fTime=time()
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eTime=round(fTime-sTime,digits=3)
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msg="The file has been created in $(eTime) seconds successfully inside the 'public' folder of the app"
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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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warning_msg=true
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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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warning_msg=true
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end
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GC.gc() # Trigger garbage collection
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if Sys.islinux()
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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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btnStartDisable=false
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btnPlotDisable=false
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btnOpticalDisable=false
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progress=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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SpectraEnabled=true
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end
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end
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@onbutton createSumPlot begin
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msg="Sum spectrum plot selected"
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sTime=time()
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if isfile(full_routeMz) # Check if the file exists
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progressSpectraPlot=true
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btnPlotDisable=true
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btnStartDisable=true
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msg="Loading plot..."
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plotdata, plotlayout, xSpectraMz, ySpectraMz=sumSpectrumPlot(full_routeMz)
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GC.gc() # Trigger garbage collection
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if Sys.islinux()
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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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selectedTab="tab2"
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fTime=time()
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eTime=round(fTime-sTime,digits=3)
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msg="Plot loaded in $(eTime) seconds"
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else
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msg="there was an error with the mzML, please try again"
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warning_msg=true
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end
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progressSpectraPlot=false
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btnPlotDisable=false
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if endswith(full_route, "imzML")
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btnStartDisable=false
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end
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if isfile(full_routeMz)
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# We enable coord search and spectra plot creation
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btnSpectraDisable=false
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SpectraEnabled=true
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end
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end
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@onbutton createXYPlot begin
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msg="XY spectrum plot selected"
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sTime=time()
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if isfile(full_routeMz) # Check if the file exists
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progressSpectraPlot=true
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btnStartDisable=true
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btnPlotDisable=true
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btnSpectraDisable=true
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msg="Loading plot..."
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spectraMz=LoadMzml(full_routeMz)
|
|
layoutSpectra=PlotlyBase.Layout(
|
|
title="($xCoord, $yCoord) Specific spectrum plot",
|
|
xaxis=PlotlyBase.attr(
|
|
title="<i>m/z</i>",
|
|
showgrid=true
|
|
),
|
|
yaxis=PlotlyBase.attr(
|
|
title="Intensity",
|
|
showgrid=true
|
|
),
|
|
autosize=false,
|
|
margin=attr(l=0,r=0,t=120,b=0,pad=0)
|
|
)
|
|
if xCoord < 1
|
|
xCoord=1
|
|
elseif xCoord > imgWidth
|
|
xCoord=imgWidth
|
|
end
|
|
if yCoord > -1
|
|
yCoord=-1
|
|
elseif yCoord < -imgHeight
|
|
yCoord=-imgHeight
|
|
end
|
|
xSpectraMz=spectraMz[1,abs(xCoord)]
|
|
ySpectraMz=spectraMz[2,abs(yCoord)]
|
|
traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
|
|
plotdata=[traceSpectra] # We add the data from spectra to the plot
|
|
plotlayout=layoutSpectra
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab2"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
else
|
|
msg="there was an error with the mzML or the coordenates, please try again"
|
|
warning_msg=true
|
|
end
|
|
progressSpectraPlot=false
|
|
btnPlotDisable=false
|
|
if endswith(full_route, "imzML")
|
|
btnStartDisable=false
|
|
end
|
|
if isfile(full_routeMz)
|
|
# We enable coord search and spectra plot creation
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
end
|
|
end
|
|
|
|
# Image loaders based on the position of the current image (increment and decrement for both normal and filter)
|
|
# And a pre-generated list from all image files from /public folder
|
|
@onbutton imgMinus begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images listed in the public folder
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=decrement_image(current_msi, msi_bmp)
|
|
new_col_msi=decrement_image(current_col_msi, col_msi_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_msi=new_msi
|
|
current_col_msi=new_col_msi
|
|
imgInt="/$(current_msi)?t=$(timestamp)"
|
|
colorbar="/$(current_col_msi)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_msi, "MSI_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImg=[traceImg]
|
|
msgimg=""
|
|
end
|
|
end
|
|
@onbutton imgPlus begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images listed in the public folder
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=increment_image(current_msi, msi_bmp)
|
|
new_col_msi=increment_image(current_col_msi, col_msi_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_msi=new_msi
|
|
current_col_msi=new_col_msi
|
|
imgInt="/$(current_msi)?t=$(timestamp)"
|
|
colorbar="/$(current_col_msi)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_msi, "MSI_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImg=[traceImg]
|
|
msgimg=""
|
|
end
|
|
end
|
|
|
|
@onbutton imgMinusT begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images with TrIQ filter listed in the public folder
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=decrement_image(current_triq, triq_bmp)
|
|
new_col_msi=decrement_image(current_col_triq, col_triq_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_triq=new_msi
|
|
current_col_triq=new_col_msi
|
|
imgIntT="/$(current_triq)?t=$(timestamp)"
|
|
colorbarT="/$(current_col_triq)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_triq, "TrIQ_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImgT=[traceImg]
|
|
msgtriq=""
|
|
end
|
|
end
|
|
@onbutton imgPlusT begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images with TrIQ filter listed in the public folder
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=increment_image(current_triq, triq_bmp)
|
|
new_col_msi=increment_image(current_col_triq, col_triq_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_triq=new_msi
|
|
current_col_triq=new_col_msi
|
|
imgIntT="/$(current_triq)?t=$(timestamp)"
|
|
colorbarT="/$(current_col_triq)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_triq, "TrIQ_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImgT=[traceImg]
|
|
msgtriq=""
|
|
end
|
|
end
|
|
|
|
# Image loaders for the comparative view
|
|
@onbutton imgMinusComp begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images listed in the public folder
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=decrement_image(current_msiComp, msi_bmp)
|
|
new_col_msi=decrement_image(current_col_msiComp, col_msi_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_msiComp=new_msi
|
|
current_col_msiComp=new_col_msi
|
|
imgIntComp="/$(current_msiComp)?t=$(timestamp)"
|
|
colorbarComp="/$(current_col_msiComp)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_msiComp, "MSI_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImgComp=[traceImg]
|
|
msgimgComp=""
|
|
end
|
|
end
|
|
|
|
@onbutton imgPlusComp begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images listed in the public folder
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=increment_image(current_msiComp, msi_bmp)
|
|
new_col_msi=increment_image(current_col_msiComp, col_msi_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_msiComp=new_msi
|
|
current_col_msiComp=new_col_msi
|
|
imgIntComp="/$(current_msiComp)?t=$(timestamp)"
|
|
colorbarComp="/$(current_col_msiComp)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_msiComp, "MSI_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImgComp=[traceImg]
|
|
msgimgComp=""
|
|
end
|
|
end
|
|
|
|
@onbutton imgMinusTComp begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images with TrIQ filter listed in the public folder
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=decrement_image(current_triqComp, triq_bmp)
|
|
new_col_msi=decrement_image(current_col_triqComp, col_triq_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_triqComp=new_msi
|
|
current_col_triqComp=new_col_msi
|
|
imgIntTComp="/$(current_triqComp)?t=$(timestamp)"
|
|
colorbarTComp="/$(current_col_triqComp)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_triqComp, "TrIQ_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImgTComp=[traceImg]
|
|
msgtriqComp=""
|
|
end
|
|
end
|
|
|
|
@onbutton imgPlusTComp begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images with TrIQ filter listed in the public folder
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=increment_image(current_triqComp, triq_bmp)
|
|
new_col_msi=increment_image(current_col_triqComp, col_triq_png)
|
|
if new_msi!=nothing || new_col_msi!=nothing
|
|
current_triqComp=new_msi
|
|
current_col_triqComp=new_col_msi
|
|
imgIntTComp="/$(current_triqComp)?t=$(timestamp)"
|
|
colorbarTComp="/$(current_col_triqComp)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_triqComp, "TrIQ_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Process the image in the function
|
|
plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
|
|
btnOpticalDisable=false
|
|
else
|
|
traceImg=PlotlyBase.heatmap(x=[], y=[])
|
|
plotdataImgTComp=[traceImg]
|
|
msgtriqComp=""
|
|
end
|
|
end
|
|
|
|
# 3d plot
|
|
@onbutton image3dPlot begin
|
|
msg="Image 3D plot selected"
|
|
cleaned_imgInt=replace(imgInt, r"\?.*" => "")
|
|
cleaned_imgInt=lstrip(cleaned_imgInt, '/')
|
|
var=joinpath( "./public", cleaned_imgInt )
|
|
sTime=time()
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
btnSpectraDisable=true
|
|
try
|
|
plotdata3d, plotlayout3d=loadSurfacePlot(imgInt)
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab4"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
end
|
|
else
|
|
msg="Image could not be 3d plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
if isfile(full_routeMz)
|
|
# We enable coord search and spectra plot creation
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
end
|
|
end
|
|
# 3d plot for TrIQ
|
|
@onbutton triq3dPlot begin
|
|
msg="TrIQ 3D plot selected"
|
|
cleaned_imgIntT=replace(imgIntT, r"\?.*" => "")
|
|
cleaned_imgIntT=lstrip(cleaned_imgIntT, '/')
|
|
var=joinpath( "./public", cleaned_imgIntT )
|
|
sTime=time()
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
btnSpectraDisable=true
|
|
try
|
|
plotdata3d, plotlayout3d=loadSurfacePlot(imgIntT)
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab4"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
end
|
|
else
|
|
msg="Image could not be 3d plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
if isfile(full_routeMz)
|
|
# We enable coord search and spectra plot creation
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
end
|
|
end
|
|
|
|
# Contour 2d plot
|
|
@onbutton imageCPlot begin
|
|
msg="Image 2D plot selected"
|
|
cleaned_imgInt=replace(imgInt, r"\?.*" => "")
|
|
cleaned_imgInt=lstrip(cleaned_imgInt, '/')
|
|
var=joinpath("./public", cleaned_imgInt)
|
|
sTime=time()
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
btnSpectraDisable=true
|
|
try
|
|
img=load(var)
|
|
plotdataC,plotlayoutC=loadContourPlot(imgInt)
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab3"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
end
|
|
else
|
|
msg="Image could not be 2D plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
if isfile(full_routeMz)
|
|
# We enable coord search and spectra plot creation
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
end
|
|
end
|
|
# Contour 2d plot for TrIQ
|
|
@onbutton triqCPlot begin
|
|
msg="Image 2D plot selected"
|
|
cleaned_imgIntT=replace(imgIntT, r"\?.*" => "")
|
|
cleaned_imgIntT=lstrip(cleaned_imgIntT, '/')
|
|
var=joinpath("./public", cleaned_imgIntT)
|
|
sTime=time()
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
btnSpectraDisable=true
|
|
try
|
|
img=load(var)
|
|
plotdataC,plotlayoutC=loadContourPlot(imgIntT)
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab3"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
end
|
|
else
|
|
msg="Image could not be 2D plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
if isfile(full_routeMz)
|
|
# We enable coord search and spectra plot creation
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
end
|
|
end
|
|
|
|
@onbutton compareBtn begin
|
|
CompareDialog=true
|
|
end
|
|
|
|
# To include a visualization in the spectrum plot indicating where is the selected mass
|
|
@onchange Nmass begin
|
|
if !isempty(xSpectraMz)
|
|
traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines",name="Spectra",showlegend=false)
|
|
trace2=PlotlyBase.scatter(x=[Nmass, Nmass],y=[0, maximum(ySpectraMz)],mode="lines",line=attr(color="red", width=0.5),name="<i>m/z</i> selected",showlegend=false)
|
|
plotdata=[traceSpectra,trace2] # We add the data from spectra and the red line to the plot
|
|
end
|
|
end
|
|
|
|
# Event detection for clicking on the images
|
|
@onchange data_click begin
|
|
if selectedTab == "tab1"
|
|
cursor_data=data_click["cursor"]
|
|
xCoord=Int32(round(cursor_data["x"]))
|
|
yCoord=Int32(round(cursor_data["y"]))
|
|
if xCoord < 1
|
|
xCoord=1
|
|
elseif xCoord > imgWidth
|
|
xCoord=imgWidth
|
|
end
|
|
if yCoord > -1
|
|
yCoord=-1
|
|
elseif yCoord < -imgHeight
|
|
yCoord=-imgHeight
|
|
end # Get the x and y values from the click of the cursor and make sure they don't exceed image proportions
|
|
plotdataImgT=filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y"]), plotdataImgT)
|
|
trace1, trace2=crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
|
|
plotdataImgT=append!(plotdataImgT, [trace1, trace2])
|
|
elseif selectedTab == "tab0"
|
|
cursor_data=data_click["cursor"]
|
|
xCoord=Int32(round(cursor_data["x"]))
|
|
yCoord=Int32(round(cursor_data["y"]))
|
|
if xCoord < 1
|
|
xCoord=1
|
|
elseif xCoord > imgWidth
|
|
xCoord=imgWidth
|
|
end
|
|
if yCoord > -1
|
|
yCoord=-1
|
|
elseif yCoord < -imgHeight
|
|
yCoord=-imgHeight
|
|
end # Get the x and y values from the click of the cursor and make sure they don't exceed image proportions
|
|
plotdataImg=filter(trace -> !(get(trace, :name, "") in ["Line X", "Line Y","Optical"]), plotdataImg)
|
|
trace1, trace2=crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
|
|
plotdataImg=append!(plotdataImg, [trace1, trace2])
|
|
end
|
|
end
|
|
|
|
@onbutton btnOptical begin
|
|
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
|
|
if imgRoute==""
|
|
msg="No optical image selected"
|
|
else
|
|
selectedTab="tab0"
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
|
|
img=load(imgRoute)
|
|
save("./public/css/imgOver.png",img)
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
|
|
end
|
|
|
|
end
|
|
|
|
@onbutton btnOpticalT begin
|
|
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
|
|
if imgRoute==""
|
|
msg="No optical image selected"
|
|
else
|
|
selectedTab="tab1"
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
|
|
img=load(imgRoute)
|
|
save("./public/css/imgOver.png",img)
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
|
|
opticalOverTriq=true
|
|
end
|
|
end
|
|
|
|
@onchange imgTrans begin
|
|
if !opticalOverTriq && imgRoute!=""
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
|
|
elseif opticalOverTriq && imgRoute!=""
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
|
|
end
|
|
end
|
|
|
|
@onchange opticalOverTriq begin
|
|
if !opticalOverTriq && imgRoute!=""
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
|
|
selectedTab="tab0"
|
|
elseif opticalOverTriq && imgRoute!=""
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
|
|
selectedTab="tab1"
|
|
end
|
|
end
|
|
|
|
@mounted watchplots()
|
|
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
end
|
|
# == Pages ==
|
|
# Register a new route and the page that will be loaded on access
|
|
@page("/", "app.jl.html")
|
|
end
|