Julian/JuliaMSI
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Included environment variable to set up production, fixed plot errors and optical image load, started mzML to imzML function

Browse Source
This commit is contained in:
Pixelguy14 2025-02-13 15:34:13 -06:00
parent 2b6ec4937f
commit 455d88cbb7
3 changed files with 50 additions and 65 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

79
app.jl
View File

@ -59,6 +59,7 @@ include("./julia_imzML_visual.jl")
@in triq3dPlot=false # To generate 3d plot based on current triq image
@in imageCPlot=false # To generate contour plots of current image
@in triqCPlot=false # To generate contour plots of current triq image
@in btnCreateImz=false # To start process for creating imzML and Ibd with mzML and Syncro
# Image change buttons
@in imgPlus=false
@in imgMinus=false
@ -83,7 +84,7 @@ include("./julia_imzML_visual.jl")
@out imgIntT="/.bmp" # image Interface TrIQ
@out colorbar="/.png"
@out colorbarT="/.png"
# interface controlling for the comparative view
# Interface controlling for the comparative view
@out imgIntComp="/.bmp" # image Interface
@out imgIntTComp="/.bmp" # image Interface TrIQ
@out colorbarComp="/.png"
@ -247,10 +248,12 @@ include("./julia_imzML_visual.jl")
@onbutton btnSearch begin
full_route=pick_file(; filterlist="imzML,mzML")
if isnothing(full_route)
if full_route==""
msg="No file selected"
warning_msg=true
btnStartDisable=true
btnSpectraDisable=true
SpectraEnabled=false
else
if endswith(full_route, "imzML") # Case if the file loaded is imzML
btnStartDisable=false
@ -914,44 +917,22 @@ include("./julia_imzML_visual.jl")
CompareDialog=true
end
# Event detection for clicking on the spectrum plot
@onbutton btnCreateImz begin
msg="Not yet implemented"
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 == "tab2"
if !isempty(xSpectraMz)
spectracoords=reshape(plotdata, 1, length(plotdata))
# Extract x and y values from data_click
cursor_data=data_click["cursor"]
x_value=cursor_data["x"]
y_value=cursor_data["y"]
# Find the minimum x-value in spectracoords
min_x_value=minimum([minimum(val[:x]) for val in spectracoords if !isempty(val[:x])])
# Adjust x_value and spectracoords x-values to start from 0
adjusted_x_value=x_value - min_x_value
closest_distance=Inf
for val in spectracoords
adjusted_x=val[:x] .- min_x_value
start_idx=findfirst(x -> x >= adjusted_x_value - 20, adjusted_x)
end_idx=findlast(x -> x <= adjusted_x_value + 20, adjusted_x)
if start_idx !== nothing && end_idx !== nothing
for i in start_idx:end_idx
spectra_x=adjusted_x[i]
spectra_y=val[:y][i]
distance=sqrt((spectra_x - adjusted_x_value)^2 + (spectra_y - y_value)^2)
if distance < closest_distance
closest_distance=distance
Nmass=round(spectra_x + min_x_value, digits=2)
end
end
end
end
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
elseif selectedTab == "tab1"
if selectedTab == "tab1"
cursor_data=data_click["cursor"]
xCoord=Int32(round(cursor_data["x"]))
yCoord=Int32(round(cursor_data["y"]))
@ -990,11 +971,11 @@ include("./julia_imzML_visual.jl")
@onbutton btnOptical begin
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
selectedTab="tab0"
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
if isnothing(imgRoute)
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)
@ -1004,11 +985,11 @@ include("./julia_imzML_visual.jl")
@onbutton btnOpticalT begin
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
selectedTab="tab1"
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
if isnothing(imgRoute)
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)
@ -1017,19 +998,19 @@ include("./julia_imzML_visual.jl")
end
@onchange imgTrans begin
if !opticalOverTriq
if !opticalOverTriq && imgRoute!=""
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
else
elseif opticalOverTriq && imgRoute!=""
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
end
end
@onchange opticalOverTriq begin
if !opticalOverTriq
if !opticalOverTriq && imgRoute!=""
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
selectedTab="tab0"
else
elseif opticalOverTriq && imgRoute!=""
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
selectedTab="tab1"

35
app.jl.html
View File

@ -7,22 +7,21 @@
name.</h6>
<h6>It may take a while to generate the image and the plot, please be patient.</h6>
<h6>To generate the contour or surface plots, you have to select the desired image first using the interface.</h6>
<h6>Syncro file is required to create imzML and ibd files.</h6>
</div>
</header>
<div id="extDivStyle" class="row col-12 q-pa-xl">
<div class="row col-6">
<!-- Left DIV -->
<div id="intDivStyle" class="st-col col-12 st-module">
<!--<q-input id="textRoute" standout="custom-standout" v-model="file_route" label="Insert the route to your imzML file"></q-input>-->
<h6>Search for the imzML or mzML file in your system</h6>
<q-btn id="btnStyle" icon="search" class="q-ma-sm" v-on:click="btnSearch=true"
label="Select your imzML or mzML file"></q-btn>
<!--<p>{{full_route}}</p>-->
<p id="lblFullRoute">full route: {{full_route}}</p>
<!-- Variable Manipulation -->
<div class="row">
<div class="st-col col-4 col-sm q-ma-sm">
<q-input standout="custom-standout" id="textNmass" step="0.01" v-model="Nmass"
<q-input standout="custom-standout" id="textNmass" step="0.001" v-model="Nmass"
label="Mass-to-charge ratio of interest" type="number"
:rules="[ val => !!val || '* Required', val => val >= 0.0 || 'Need positive mass values']"></q-input>
</div>
@ -53,8 +52,6 @@
val => triqEnabled ? ( '* Required', val >= 0.8 &amp;&amp; val <= 1 || 'Needs to be in range between 0.8 and 1') : true
]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
</div>
<!--<div class="st-col col-4 col-sm-4 q-ma-sm">
</div>-->
</div>
</div>
<!-- Spectra Plot Manipulation -->
@ -93,6 +90,13 @@
]" :readonly="!SpectraEnabled" :disable="!SpectraEnabled"></q-input>
</div>
</div>
<q-btn id="btnStyle" icon="play_arrow" class="q-ma-sm" v-on:click="btnCreateImz=true" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
label="Generate imzML">
<template v-slot:loading>
<q-spinner-hourglass class="on-left" />
Loading Plot
</template>
</q-btn>
</div>
</div>
<div class="row">
@ -109,7 +113,6 @@
<p>{{msg}}</p>
<div class="row st-col col-12">
<!--<q-input id="textName" class="col-9" standout="custom-standout" v-model="file_name" label="Insert the name of your imzML file"></q-input>-->
<q-btn-dropdown id="btnStyle" class="q-ma-sm" :loading="progressPlot" :disable="btnPlotDisable"
label="Generate Plots" icon="play_arrow">
<template v-slot:loading>
@ -181,7 +184,6 @@
<div class="col-10 q-pa-none q-ma-none">
<plotly id="plotStyle" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none sync_data"
@click="data_click"></plotly>
<!--<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" width="80%"></q-img>-->
</div>
<div class="col-2 q-pa-none q-ma-none">
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
@ -203,7 +205,6 @@
<div class="col-10 q-pa-none q-ma-none ">
<plotly id="plotStyle" :data="plotdataImgT" :layout="plotlayoutImgT"
class="q-pa-none q-ma-none sync_data" @click="data_click"></plotly>
<!--<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" width="80%"></q-img>-->
</div>
<div class="col-2 q-pa-none q-ma-none ">
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
@ -214,9 +215,7 @@
<q-tab-panel name="tab2">
<!-- Content for Tab 2 -->
<!--<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>-->
<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none sync_data"
@click="data_click"></plotly>
<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
</q-tab-panel>
<q-tab-panel name="tab3">
@ -257,7 +256,7 @@
<q-badge style="background-color: #009f90;"> Transparency: {{ imgTrans }}</q-badge>
</div>
<q-toggle id="btnOpticalOver" v-on:click="opticalOverTriq" v-model="opticalOverTriq" color="black"
label="Optical over TrIQ"></q-toggle>
label="Optical over TrIQ"></q-toggle>
</q-card-section>
<q-card-section class="q-pt-none col-12">
@ -327,12 +326,14 @@
<!-- Btn image changer -->
<div>
<q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinusComp=true"></q-btn>
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusComp=true"></q-btn>
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right"
v-on:click="imgPlusComp=true"></q-btn>
</div>
<!-- Image manager -->
<div id="image-container" class="row st-col col-12">
<div class="col-10 q-pa-none q-ma-none ">
<plotly id="plotStyle" :data="plotdataImgComp" :layout="plotlayoutImgComp" class="q-pa-none q-ma-none">
<plotly id="plotStyle" :data="plotdataImgComp" :layout="plotlayoutImgComp"
class="q-pa-none q-ma-none">
</plotly>
</div>
<div class="col-2 q-pa-none q-ma-none ">
@ -347,12 +348,14 @@
<!-- Triq Btn image changer -->
<div>
<q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinusTComp=true"></q-btn>
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusTComp=true"></q-btn>
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right"
v-on:click="imgPlusTComp=true"></q-btn>
</div>
<!-- Triq Image manager -->
<div id="image-container" class="row st-col col-12">
<div class="col-10 q-pa-none q-ma-none ">
<plotly id="plotStyle" :data="plotdataImgTComp" :layout="plotlayoutImgTComp" class="q-pa-none q-ma-none">
<plotly id="plotStyle" :data="plotdataImgTComp" :layout="plotlayoutImgTComp"
class="q-pa-none q-ma-none">
</plotly>
</div>
<div class="col-2 q-pa-none q-ma-none ">

1
config/env/global.jl vendored Normal file
View File

@ -0,0 +1 @@
ENV["GENIE_ENV"] = "dev"