Fixed some errors to get ready for release
This commit is contained in:
Pixelguy14
parent
455d88cbb7
commit
e3e987f0cd
55
app.jl
55
app.jl
@ -59,7 +59,6 @@ include("./julia_imzML_visual.jl")
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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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@in btnCreateImz=false # To start process for creating imzML and Ibd with mzML and Syncro
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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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@ -281,6 +280,25 @@ include("./julia_imzML_visual.jl")
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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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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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@ -388,9 +406,7 @@ include("./julia_imzML_visual.jl")
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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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spectra=nothing # Important for memory cleaning
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slice=nothing
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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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@ -414,30 +430,7 @@ include("./julia_imzML_visual.jl")
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btnPlotDisable=true
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btnStartDisable=true
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msg="Loading plot..."
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spectraMz=LoadMzml(full_routeMz)
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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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autosize=false,
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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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try
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xSpectraMz=mean(spectraMz[1,:])
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ySpectraMz=mean(spectraMz[2,:])
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catch e
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xSpectraMz=spectraMz[1,1]
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ySpectraMz=spectraMz[2,1]
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end
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traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
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plotdata=[traceSpectra] # We add the data from spectra to the plot
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plotlayout=layoutSpectra
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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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@ -463,7 +456,7 @@ include("./julia_imzML_visual.jl")
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end
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@onbutton createXYPlot begin
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msg="Sum spectrum plot selected"
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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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@ -917,10 +910,6 @@ include("./julia_imzML_visual.jl")
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CompareDialog=true
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end
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@onbutton btnCreateImz begin
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msg="Not yet implemented"
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end
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# To include a visualization in the spectrum plot indicating where is the selected mass
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@onchange Nmass begin
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if !isempty(xSpectraMz)
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@ -90,13 +90,6 @@
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]" :readonly="!SpectraEnabled" :disable="!SpectraEnabled"></q-input>
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</div>
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</div>
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<q-btn id="btnStyle" icon="play_arrow" class="q-ma-sm" v-on:click="btnCreateImz=true" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
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label="Generate imzML">
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<template v-slot:loading>
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<q-spinner-hourglass class="on-left" />
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Loading Plot
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</template>
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</q-btn>
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</div>
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</div>
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<div class="row">
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2
config/env/global.jl
vendored
2
config/env/global.jl
vendored
@ -1 +1 @@
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ENV["GENIE_ENV"] = "dev"
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ENV["GENIE_ENV"] = "prod"
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@ -1,18 +0,0 @@
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#!/bin/bash
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command="julia --project=. start_MSI_GUI.jl"
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case "$OSTYPE" in
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linux*)
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$command
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;;
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darwin*)
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$command
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;;
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cygwin*|msys*|win32)
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julia --project=. start_MSI_GUI.jl
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;;
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*)
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echo "Unsupported OS"
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;;
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esac
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@ -405,3 +405,37 @@ function medianFilterjl(pixMap)
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return target
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end
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# sumSpectrumPlot recieves the local directory of the image as a string,
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# returns the layout and data for the surface plotly plot
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# this function loads the spectra data and makes a mean to display
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# its values in the spectrum plot
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function sumSpectrumPlot(mzmlRoute::String)
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spectraMz=LoadMzml(mzmlRoute)
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xSpectraMz=Float64[]
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ySpectraMz=Float64[]
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layout=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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autosize=false,
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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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try
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xSpectraMz=mean(spectraMz[1,:])
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ySpectraMz=mean(spectraMz[2,:])
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catch e
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xSpectraMz=spectraMz[1,1]
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ySpectraMz=spectraMz[2,1]
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end
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trace=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
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plotdata=[trace] # We add the data from spectra to the plot
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plotlayout=layout
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return plotdata, plotlayout, xSpectraMz, ySpectraMz
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end
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@ -4,26 +4,6 @@ Pkg.activate(".")
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Pkg.instantiate()
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Pkg.gc()
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"""
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packages = [
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"GenieFramework", "Libz", "PlotlyBase", "CairoMakie", "Colors",
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"Statistics", "NaturalSort", "Genie",
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"Images", "LinearAlgebra", "NativeFileDialog", "StipplePlotly"
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]
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# Check for missing packages
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for pkg in packages
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if !(pkg in keys(Pkg.dependencies()))
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Pkg.add(pkg)
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end
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end
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# Add library for mzML imzML from GitHub if missing
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if !("julia_mzML_imzML" in keys(Pkg.dependencies()))
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Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML")
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end
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"""
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using Genie
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# Load and configure Genie
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