Fixed some errors to get ready for release

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
@@ -281,6 +280,25 @@ include("./julia_imzML_visual.jl")
                     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
+        end|
-        spectra=nothing # Important for memory cleaning
-        slice=nothing
         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)
+            plotdata, plotlayout, xSpectraMz, ySpectraMz=sumSpectrumPlot(full_routeMz)
-            layoutSpectra=PlotlyBase.Layout(
-                title="SUM 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)
-            )
-            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
             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)

app.jl.html

@@ -90,13 +90,6 @@
                         ]" :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">

config/env/global.jl

@@ -1 +1 @@
-ENV["GENIE_ENV"] = "dev"
+ENV["GENIE_ENV"] = "prod"

executable.sh

@@ -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

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="<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)
+    )
+    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

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