diff --git a/app.jl b/app.jl
index a1c16c0..07ef7d0 100644
--- a/app.jl
+++ b/app.jl
@@ -59,7 +59,6 @@ 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
@@ -274,13 +273,32 @@ include("./julia_imzML_visual.jl")
btnSpectraDisable=false
SpectraEnabled=true
# Splitting the route the same way
- full_route=replace(full_route, r"\.[^.]*$" => ".imzML")
+ full_route=replace(full_route, r"\.[^.]*$" => ".imzML")
if isfile(full_route)
btnStartDisable=false
else
btnStartDisable=true
full_route=full_routeMz
end
+ progressSpectraPlot=true
+ btnPlotDisable=true
+ btnStartDisable=true
+ msg="Loading SUM spectrum plot..."
+ sTime=time()
+ plotdata, plotlayout, xSpectraMz, ySpectraMz=sumSpectrumPlot(full_routeMz)
+ 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
+ fTime=time()
+ eTime=round(fTime-sTime,digits=3)
+ msg="Plot loaded in $(eTime) seconds"
end
xCoord=0
yCoord=0
@@ -388,9 +406,7 @@ include("./julia_imzML_visual.jl")
else
msg="File does not exist or a parameter is incorrect, please try again."
warning_msg=true
- end
- spectra=nothing # Important for memory cleaning
- slice=nothing
+ end|
GC.gc() # Trigger garbage collection
if Sys.islinux()
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
@@ -414,30 +430,7 @@ include("./julia_imzML_visual.jl")
btnPlotDisable=true
btnStartDisable=true
msg="Loading plot..."
- spectraMz=LoadMzml(full_routeMz)
- layoutSpectra=PlotlyBase.Layout(
- title="SUM Spectrum plot",
- xaxis=PlotlyBase.attr(
- title="m/z",
- showgrid=true
- ),
- yaxis=PlotlyBase.attr(
- title="Intensity",
- showgrid=true
- ),
- autosize=false,
- margin=attr(l=0,r=0,t=120,b=0,pad=0)
- )
- try
- xSpectraMz=mean(spectraMz[1,:])
- ySpectraMz=mean(spectraMz[2,:])
- catch e
- xSpectraMz=spectraMz[1,1]
- ySpectraMz=spectraMz[2,1]
- end
- traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
- plotdata=[traceSpectra] # We add the data from spectra to the plot
- plotlayout=layoutSpectra
+ plotdata, plotlayout, xSpectraMz, ySpectraMz=sumSpectrumPlot(full_routeMz)
GC.gc() # Trigger garbage collection
if Sys.islinux()
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
@@ -463,7 +456,7 @@ include("./julia_imzML_visual.jl")
end
@onbutton createXYPlot begin
- msg="Sum spectrum plot selected"
+ msg="XY spectrum plot selected"
sTime=time()
if isfile(full_routeMz) # Check if the file exists
progressSpectraPlot=true
@@ -917,10 +910,6 @@ include("./julia_imzML_visual.jl")
CompareDialog=true
end
- @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)
diff --git a/app.jl.html b/app.jl.html
index ea456c0..e1e6b49 100644
--- a/app.jl.html
+++ b/app.jl.html
@@ -90,13 +90,6 @@
]" :readonly="!SpectraEnabled" :disable="!SpectraEnabled">
-
-
-
- Loading Plot
-
-
diff --git a/config/env/global.jl b/config/env/global.jl
index 5ea3d97..0b24049 100644
--- a/config/env/global.jl
+++ b/config/env/global.jl
@@ -1 +1 @@
-ENV["GENIE_ENV"] = "dev"
+ENV["GENIE_ENV"] = "prod"
diff --git a/executable.sh b/executable.sh
deleted file mode 100755
index 934834e..0000000
--- a/executable.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-command="julia --project=. start_MSI_GUI.jl"
-
-case "$OSTYPE" in
- linux*)
- $command
- ;;
- darwin*)
- $command
- ;;
- cygwin*|msys*|win32)
- julia --project=. start_MSI_GUI.jl
- ;;
- *)
- echo "Unsupported OS"
- ;;
-esac
diff --git a/julia_imzML_visual.jl b/julia_imzML_visual.jl
index f35973e..ef85f57 100644
--- a/julia_imzML_visual.jl
+++ b/julia_imzML_visual.jl
@@ -405,3 +405,37 @@ function medianFilterjl(pixMap)
return target
end
+# sumSpectrumPlot recieves the local directory of the image as a string,
+# returns the layout and data for the surface plotly plot
+# this function loads the spectra data and makes a mean to display
+# its values in the spectrum plot
+function sumSpectrumPlot(mzmlRoute::String)
+ spectraMz=LoadMzml(mzmlRoute)
+ xSpectraMz=Float64[]
+ ySpectraMz=Float64[]
+
+ layout=PlotlyBase.Layout(
+ title="SUM spectrum plot",
+ xaxis=PlotlyBase.attr(
+ title="m/z",
+ showgrid=true
+ ),
+ yaxis=PlotlyBase.attr(
+ title="Intensity",
+ showgrid=true
+ ),
+ autosize=false,
+ margin=attr(l=0,r=0,t=120,b=0,pad=0)
+ )
+ try
+ xSpectraMz=mean(spectraMz[1,:])
+ ySpectraMz=mean(spectraMz[2,:])
+ catch e
+ xSpectraMz=spectraMz[1,1]
+ ySpectraMz=spectraMz[2,1]
+ end
+ trace=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
+ plotdata=[trace] # We add the data from spectra to the plot
+ plotlayout=layout
+ return plotdata, plotlayout, xSpectraMz, ySpectraMz
+end
\ No newline at end of file
diff --git a/start_MSI_GUI.jl b/start_MSI_GUI.jl
index 973cbd6..0d69ef8 100644
--- a/start_MSI_GUI.jl
+++ b/start_MSI_GUI.jl
@@ -4,26 +4,6 @@ Pkg.activate(".")
Pkg.instantiate()
Pkg.gc()
-"""
-packages = [
- "GenieFramework", "Libz", "PlotlyBase", "CairoMakie", "Colors",
- "Statistics", "NaturalSort", "Genie",
- "Images", "LinearAlgebra", "NativeFileDialog", "StipplePlotly"
-]
-
-# Check for missing packages
-for pkg in packages
- if !(pkg in keys(Pkg.dependencies()))
- Pkg.add(pkg)
- end
-end
-
-# Add library for mzML imzML from GitHub if missing
-if !("julia_mzML_imzML" in keys(Pkg.dependencies()))
- Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML")
-end
-"""
-
using Genie
# Load and configure Genie