Bitmap is now normalized in creation, which evenly distributes colors of the colorTable better, now IntQuant allows for coloLevel adjustments

README.md

@@ -22,7 +22,7 @@ A Graphical User Interface for MSI in Julia: https://github.com/CINVESTAV-LABI/j
    ```
    julia --project=. start_MSI_GUI.jl
    ```
-3. After the script has finished loading, it should open a page (http://127.0.0.1:1481/) in your browser with the web app running.
+3. After the script has finished loading, You can open a page (http://127.0.0.1:1481/) in your browser with the web app running.
 
 Additional notes:<br>
 After the first boot initializes the packages in your computer, subsequent uses of the app should not take longer to load.<br>

app.jl

@@ -13,6 +13,7 @@ using Images
 using LinearAlgebra
 using NativeFileDialog # Opens the file explorer depending on the OS
 using StipplePlotly
+using Printf
 include("./julia_imzML_visual.jl")
 @genietools
 
@@ -121,7 +122,8 @@ function loadContourPlot(interfaceImg::String)
     img=load(var)
     img_gray=Gray.(img)
     img_array=Array(img_gray)
-    elevation=Float32.(Array(img_gray)) ./ 255.0  # Normalize between 0 and 1
+    # parse matrix to int32 to closely resemble similarity to original bitmap
+    elevation=int32.(Array(img_gray))  
     
     # Smooth the image
     sigma=3.0
@@ -487,7 +489,7 @@ end
         text_nmass=replace(string(Nmass), "." => "_")
         sTime=time()
         #full_route=joinpath(file_route, file_name)
-        if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <=1
+        if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <=1 && colorLevel > 1 && colorLevel < 257
             msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
             try
                 spectra=LoadImzml(full_route)
@@ -497,12 +499,12 @@ end
                 # Append a query string to force the image to refresh 
                 timestamp=string(time_ns()) 
                 if triqEnabled # If we have TrIQ
-                    if colorLevel < 2 || colorLevel > 256 || triqProb < 0.8 || triqProb > 1
+                    if triqProb < 0.8 || triqProb > 1
                         msg="Incorrect TrIQ values, please adjust accordingly and try again."
                         warning_msg=true
                     else
                         image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp")
-                        sliceTriq=TrIQ(slice, Int(colorLevel), triqProb)
+                        sliceTriq=TrIQ(slice, colorLevel, triqProb)
                         #println("slice raw: $(typeof(slice))")
                         #println("TriQ matrix: $(typeof(sliceTriq))")
                         sliceTriq=reverse(sliceTriq, dims=2)
@@ -515,8 +517,19 @@ end
                         current_triq="TrIQ_$(text_nmass).bmp"
                         msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
                         # Create colorbar
-                        ticks=round.(range(0, (stop=maximum(sliceTriq)*triqProb), length=15), sigdigits=3)
+                        #ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=10), sigdigits=3)
-                        Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(sliceTriq)*triqProb),ticks=ticks, label="Intensity", size = 25)
+                        ticks=range(0, (stop=maximum(slice)*triqProb), length=5)
+
+                        """
+                        function log_tick_formatter(values)
+                            return map(v -> "10" * Makie.UnicodeFun.to_superscript(round(Int64, v)), values)
+                        end
+                        """
+
+                        println("ticks: $(typeof(ticks))")
+                        #Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks,tickformat=log_tick_formatter, label="Intensity", size = 25)
+                        Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25)
+                        println("Colorbar: $(typeof(fig))")
                         save("public/colorbar_TrIQ_$(text_nmass).png", fig)
                         colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
                         # Get current colorbar 
@@ -534,7 +547,7 @@ end
                 else # If we don't use TrIQ
                     image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
                     ##sliceQuant=IntQuant(slice)
-                    sliceQuant=IntQuantCl(slice,colorLevel)
+                    sliceQuant=IntQuantCl(slice,Int(colorLevel-1))
                     #println("slice raw: $(typeof(slice))")
                     #println("slice in intQuant: $(typeof(sliceQuant))")
                     sliceQuant=reverse(sliceQuant, dims=2)
@@ -548,8 +561,8 @@ end
                     msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
                     # Create colorbar 
                     #ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
-                    ticks=round.(range(0, stop=maximum(sliceQuant), length=15), sigdigits=3)
+                    ticks=range(0, stop=maximum(slice), length=5)
-                    Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(sliceQuant)),ticks=ticks, label="Intensity", size = 25)
+                    Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
                     save("public/colorbar_MSI_$(text_nmass).png", fig)
                     colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
                     # Get current colorbar 

app.jl.html

@@ -60,18 +60,16 @@
           <div class="st-col col-4 col-sm q-ma-sm">
             <q-input standout="custom-standout" id="textNmass" step="0.01" 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>
+              :rules="[ val => !!val || '* Required', val => val >= 0.0 || 'Need positive mass values']"></q-input>
           </div>
           <div class="st-col col-4 col-sm q-ma-sm">
-            <q-input standout="custom-standout" id="textTol" step="0.05" v-model="Tol"
+            <q-input standout="custom-standout" id="textTol" step="0.005" v-model="Tol"
               label="Mass-to-charge ratio tolerance" type="number"
-              :rules="[val => !!val || '* Required', val => val >= 0.0 &amp;&amp; val <= 1.0  || 'Needs to be in range between 0 and 1',]"></q-input>
+              :rules="[val => !!val || '* Required', val => val >= 0.0 &amp;&amp; val <= 1.0  || 'Needs to be in range between 0 and 1']"></q-input>
           </div>
           <div class="st-col col-4 col-sm q-ma-sm">
             <q-input standout="custom-standout" id="textcolorLevel" step="1" v-model="colorLevel"
-            label="Color level" type="number" :rules="[
+            label="Color level" type="number" :rules="[ val => !!val || '* Required', val => val >= 2 &amp;&amp; val <= 256 || 'Needs to be in range between 2 and 256']"></q-input>
-                  val => triqEnabled ? ( '* Required', val >= 4 &amp;&amp; val <= 256  || 'Needs to be in range between 2 and 256') : true
-                  ]"></q-input>
           </div>
         </div>
         <div class="row">

julia_imzML_visual.jl

@@ -15,14 +15,16 @@ end
 # SaveBitmap is also originally a function of the mzML imzML library in julia,
 # This function dinamically adjust the color palete adjusting to the ammount of colors
 # available in pixmap
-function SaveBitmapCl( name,
+function SaveBitmapCl( name, pixMap::Array{UInt8,2}, colorTable::Array{UInt32,1} )
-    pixMap::Array{UInt8,2},
-    colorTable::Array{UInt32,1} )
     # Get image dimensions
     dim = size( pixMap )
     if length( dim ) != 2
       return 0
     end
+    # Normalize pixel values to get a more accurate reading of the image
+    min_val = minimum(pixMap)
+    max_val = maximum(pixMap)
+    pixMap = round.(UInt8, 255 * (pixMap .- min_val) ./ (max_val - min_val))
     # Compute row padding
     padding = ( 4 - dim[1] & 0x3 ) & 0x3
     # Compute file dimensions. Header = 14 + 40 + ( 256 * 4 ) = 1078
@@ -36,17 +38,12 @@ function SaveBitmapCl( name,
     # Save info header
     write( stream, UInt32[ 40, dim[1], dim[2], 0x80001, 0 ] )
     write( stream, UInt32[ imgBytes, 0, 0, 256, 0 ] )
-    # Get unique colors displayed in pixMap
+    # Save color table
-    unique_colors = unique(vec(pixMap))
+    write( stream, colorTable )
-    n_colors = length(unique_colors)
+    if length( colorTable ) < 256
-    # Color levels can't surpass 256
+        fixTable = zeros( UInt32, 256 - length( colorTable ) )
-    levels = min(n_colors, 256)
+        write( stream, fixTable )
-    extendedColorTable = zeros(UInt32, 256)
-    for i in 1:256
-      idx = ceil(Int, i * levels / 256)
-      extendedColorTable[i] = colorTable[idx]
     end
-    write(stream, extendedColorTable)
     # Save image pixels
     if padding == 0
         for i = 1:dim[2]

start_MSI_GUI.jl

@@ -1,4 +1,5 @@
 using Pkg
+sTime=time()
 Pkg.activate(".")
 Pkg.instantiate()
 Pkg.gc()
@@ -31,6 +32,8 @@ Genie.loadapp()
 # Start the Genie server
 @async begin
     up(host="127.0.0.1", port=1481)
+    eTime=round(time()-sTime,digits=3)
+    println("Julia MSI GUI took $(eTime) seconds booting")
     url = "http://127.0.0.1:1481"
     # Open the URL in the default web browser based on the OS
     if Sys.isapple()
@@ -43,5 +46,4 @@ Genie.loadapp()
         @async run(`Start-Process $url`) # For Windows
     end
 end
-
 wait()