Now the file picker allows for mzML choosing, minor changes to the colorbarplots
This commit is contained in:
Pixelguy14
parent
e5e6284d53
commit
4ea5d8e119
55
app.jl
55
app.jl
@ -54,12 +54,13 @@ 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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# 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_gray))
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#println(typeof(elevation))
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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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# 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: $(width)")
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@ -434,22 +435,40 @@ end
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# The onbutton handler will set the variable to false after the block is executed
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@onbutton btnSearch begin
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full_route=pick_file(; filterlist="imzML")
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full_route=pick_file(; filterlist="imzML,mzML")
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if isnothing(full_route)
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#println("No file selected")
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msg="No file selected"
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warning_msg=true
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btnStartDisable=true
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else
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#println("Selected file path: ", full_route)
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btnStartDisable=false
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btnPlotDisable=false
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# Splitting the route with regex from imzml to mzml so the plotting can work
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full_routeMz=replace(full_route, r"\.[^.]*$" => ".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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if endswith(full_route, "imzML") # Case if the file loaded is imzML
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#println("Selected file path: ", full_route)
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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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end
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xCoord=0
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yCoord=0
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@ -470,11 +489,11 @@ end
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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=(120, 220)) # Container
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fig=CairoMakie.Figure(size=(140, 440)) # 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 < 2 || colorLevel > 256 ||triqProb < 0.8 || triqProb > 1
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if colorLevel < 4 || colorLevel > 256 || 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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@ -501,7 +520,7 @@ end
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ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3)
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#println("ticks 2: $(round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3))")
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#Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(colorLevel), triqProb))),ticks=ticks, label="Intensity")
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity")
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Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25)
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save("public/colorbar_TrIQ_$(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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@ -538,7 +557,7 @@ end
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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")
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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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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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@ -620,7 +639,9 @@ end
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end
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progressSpectraPlot=false
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btnPlotDisable=false
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btnStartDisable=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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@ -670,7 +691,9 @@ end
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end
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progressSpectraPlot=false
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btnPlotDisable=false
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btnStartDisable=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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28
app.jl.html
28
app.jl.html
@ -14,9 +14,9 @@
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<!-- Left DIV -->
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<div id="intDivStyle" class="st-col col-12 st-module">
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<!--<q-input id="textRoute" standout="custom-standout" v-model="file_route" label="Insert the route to your imzML file"></q-input>-->
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<h6>Search for your imzML file in your device</h6>
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<h6>Search for the imzML or mzML file in your system</h6>
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<q-btn id="btnStyle" icon="search" class="q-ma-sm" v-on:click="btnSearch=true"
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label="Search in your device for the imzML file"></q-btn>
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label="Select your imzML or mzML file"></q-btn>
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<!--<p>{{full_route}}</p>-->
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<div class="row st-col col-12">
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<!--<q-input id="textName" class="col-9" standout="custom-standout" v-model="file_name" label="Insert the name of your imzML file"></q-input>-->
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@ -85,7 +85,7 @@
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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 >= 2 && val <= 256 || 'Needs to be in range between 2 and 256') : true
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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>
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@ -159,11 +159,11 @@
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</div>
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<!-- Image manager -->
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<div id="image-container" class="row st-col col-12">
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<div class="col-10">
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<div class="col-10 q-pa-none q-ma-none ">
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<plotly id="plotStyle" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none sync_data" @click="data_click"></plotly>
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<!--<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" width="80%"></q-img>-->
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</div>
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<div class="col-2">
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<div class="col-2 q-pa-none q-ma-none ">
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
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</div>
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</div>
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@ -180,11 +180,11 @@
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</div>
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<!-- Triq Image manager -->
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<div id="image-container" class="row st-col col-12">
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<div class="col-10">
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<div class="col-10 q-pa-none q-ma-none ">
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<plotly id="plotStyle" :data="plotdataImgT" :layout="plotlayoutImgT" class="q-pa-none q-ma-none sync_data" @click="data_click"></plotly>
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<!--<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" width="80%"></q-img>-->
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</div>
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<div class="col-2">
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<div class="col-2 q-pa-none q-ma-none ">
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
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</div>
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</div>
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@ -246,10 +246,10 @@
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</div>
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<!-- Image manager -->
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<div id="image-container" class="row st-col col-12">
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<div class="st-col col-10">
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<div class="col-10 q-pa-none q-ma-none ">
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<plotly id="plotStyle" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none"></plotly>
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</div>
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<div class="st-col col-2">
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<div class="col-2">
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
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</div>
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</div>
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@ -265,7 +265,7 @@
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</div>
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<!-- Triq Image manager -->
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<div id="image-container" class="row st-col col-12">
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<div class="col-10">
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<div class="col-10 q-pa-none q-ma-none ">
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<plotly id="plotStyle" :data="plotdataImgT" :layout="plotlayoutImgT" class="q-pa-none q-ma-none"></plotly>
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</div>
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<div class="col-2">
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@ -301,10 +301,10 @@
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</div>
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<!-- Image manager -->
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<div id="image-container" class="row st-col col-12">
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<div class="st-col col-10">
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<div class="col-10 q-pa-none q-ma-none ">
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<plotly id="plotStyle" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none"></plotly>
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</div>
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<div class="st-col col-2">
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<div class="col-2 q-pa-none q-ma-none ">
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
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</div>
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</div>
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@ -320,10 +320,10 @@
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</div>
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<!-- Triq Image manager -->
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<div id="image-container" class="row st-col col-12">
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<div class="col-10">
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<div class="col-10 q-pa-none q-ma-none ">
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<plotly id="plotStyle" :data="plotdataImgT" :layout="plotlayoutImgT" class="q-pa-none q-ma-none"></plotly>
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</div>
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<div class="col-2">
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<div class="col-2 q-pa-none q-ma-none ">
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<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
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</div>
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</div>
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