Implemented an experimental executable for all systems, fixed a few errors, implemented first try for a median filter for the slices in Julia

app.jl

@@ -36,6 +36,7 @@ include("./julia_imzML_visual.jl")
     # Text field validations
     @in triqEnabled=false
     @in SpectraEnabled=false
+    @in MFilterEnabled=false
     # Dialogs
     @in warning_msg=false
     @in CompareDialog=false
@@ -97,11 +98,15 @@ include("./julia_imzML_visual.jl")
     @in btnOptical=false
     @in btnOpticalT=false
     @in opticalOverTriq=false
+    @out imgRoute=""
 
     # Messages to interface variables
     @out msg=""
     @out msgimg=""
     @out msgtriq=""
+    # Reiteration of the messages under the image to know which spectra is being visualized
+    @out msgimgComp=""
+    @out msgtriqComp=""
 
     # Saves the route where imzML and mzML files are located
     @out full_route=""
@@ -292,12 +297,10 @@ include("./julia_imzML_visual.jl")
             msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
             try
                 spectra=LoadImzml(full_route)
-                msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient."
+                println(typeof(spectra))
-                try
+                msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient."
                 slice=GetMzSliceJl(spectra,Nmass,Tol)
-                catch e
+                println(typeof(slice))
-                    println("the error is in the slice: $e")
-                end
                 fig=CairoMakie.Figure(size=(150, 250)) # Container
                 # Append a query string to force the image to refresh 
                 timestamp=string(time_ns()) 
@@ -312,6 +315,10 @@ include("./julia_imzML_visual.jl")
                             try
                                 slice=GetMzSliceJl(spectra, Nmass, Tol)
                                 sliceTriq=TrIQ(slice, colorLevel, triqProb)
+                                println(typeof(sliceTriq))
+                                if MFilterEnabled # If the Median filter is ON
+                                    sliceTriq=medianFilterjl(sliceTriq)
+                                end
                                 valid_slice=true
                             catch e
                                 msg="Warning: insufficient tolerance, inputs modified to allow the creation of an image regardless=$Tol: $e"
@@ -345,11 +352,14 @@ include("./julia_imzML_visual.jl")
                     end
                 else # If we don't use TrIQ
                     image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
-                    ##sliceQuant=IntQuant(slice)
                     try
                         sliceQuant=IntQuantCl(slice,Int(colorLevel-1))
+                        println(typeof(sliceQuant))
+                        if MFilterEnabled # If the Median filter is ON
+                            sliceQuant=medianFilterjl(sliceQuant)
+                        end
                     catch e
-                        println("the error is in the non triq slice: $e")
+                        println("The error is in the non triq slice: $e")
                     end
                     sliceQuant=reverse(sliceQuant, dims=2)
                     SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
@@ -648,14 +658,14 @@ include("./julia_imzML_visual.jl")
     
             text_nmass=replace(current_msiComp, "MSI_" => "")
             text_nmass=replace(text_nmass, ".bmp" => "")
-            msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
+            msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
             # Process the image in the function
             plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
             btnOpticalDisable=false
         else
             traceImg=PlotlyBase.heatmap(x=[], y=[])
             plotdataImgComp=[traceImg]
-            msgimg=""
+            msgimgComp=""
         end
     end
     
@@ -676,14 +686,14 @@ include("./julia_imzML_visual.jl")
     
             text_nmass=replace(current_msiComp, "MSI_" => "")
             text_nmass=replace(text_nmass, ".bmp" => "")
-            msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
+            msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
             # Process the image in the function
             plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp)
             btnOpticalDisable=false
         else
             traceImg=PlotlyBase.heatmap(x=[], y=[])
             plotdataImgComp=[traceImg]
-            msgimg=""
+            msgimgComp=""
         end
     end
     
@@ -704,14 +714,14 @@ include("./julia_imzML_visual.jl")
     
             text_nmass=replace(current_triqComp, "TrIQ_" => "")
             text_nmass=replace(text_nmass, ".bmp" => "")
-            msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
+            msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
             # Process the image in the function
             plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
             btnOpticalDisable=false
         else
             traceImg=PlotlyBase.heatmap(x=[], y=[])
             plotdataImgTComp=[traceImg]
-            msgtriq=""
+            msgtriqComp=""
         end
     end
     
@@ -732,14 +742,14 @@ include("./julia_imzML_visual.jl")
     
             text_nmass=replace(current_triqComp, "TrIQ_" => "")
             text_nmass=replace(text_nmass, ".bmp" => "")
-            msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
+            msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
             # Process the image in the function
             plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp)
             btnOpticalDisable=false
         else
             traceImg=PlotlyBase.heatmap(x=[], y=[])
             plotdataImgTComp=[traceImg]
-            msgtriq=""
+            msgtriqComp=""
         end
     end
     

app.jl.html

@@ -339,7 +339,7 @@
                     <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarComp"></q-img>
                   </div>
                 </div>
-                <p>{{msgimg}}</p>
+                <p>{{msgimgComp}}</p>
               </q-tab-panel>
 
               <q-tab-panel name="tab1">
@@ -359,7 +359,7 @@
                     <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarTComp"></q-img>
                   </div>
                 </div>
-                <p>{{msgtriq}}</p>
+                <p>{{msgtriqComp}}</p>
               </q-tab-panel>
               <q-tab-panel name="tab2">
                 <!-- Content for Tab 2 -->

executable.sh

@@ -0,0 +1,18 @@
+#!/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

@@ -384,3 +384,28 @@ function log_tick_formatter(values::Vector{Float64})
     return map((v, e) -> e == 0 ? "$(round(v, sigdigits=2))" : "$(round(v, sigdigits=2))x10" * Makie.UnicodeFun.to_superscript(e), formValues, exponents)
 
 end
+
+# Median filter: an adaptation of the R medianfilter, which averages the matrix
+# with the close pixels just from the sides to reduce noise.
+# This one in particular is a midpoint fiter from a 3x3 neighbour area
+function medianFilterjl(pixMap)
+    width, height = size(pixMap)
+    target = zeros(eltype(pixMap), height, width)
+    println("Matrix Dimensions: ", size(pixMap))
+
+    for j in 2:(width-1)
+        for i in 2:(height-1)
+            println("Current Indices: i = $i, j = $j")
+            neighbors = []
+            for dj in max(1, j-1):min(width, j+1)
+                for di in max(1, i-1):min(height, i+1)
+                    push!(neighbors, pixMap[di, dj])
+                end
+            end
+            target[i, j] = median(neighbors)
+        end
+    end
+
+	return target
+
+end