Merge pull request #7 from Pixelguy14/Experimental_ColorLevels

Experimental color levels done

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
+include("./julia_imzML_visual.jl")
 @genietools
 
 # == Code import ==
@@ -54,13 +55,13 @@ function loadImgPlot(interfaceImg::String)
     cleaned_img=lstrip(cleaned_img, '/')
     var=joinpath("./public", cleaned_img)
     img=load(var)
-    println("type of img: $(typeof(img))")
+    #println("type of img: $(typeof(img))")
     # Convert to grayscale
     img_gray=Gray.(img)
     img_array=Array(img_gray)
     #println(typeof(img_array))
     elevation=Float32.(Array(img_array)) ./ 255.0
-    println("type of elevation: $(typeof(elevation))")
+    #println("type of elevation: $(typeof(elevation))")
     # Get the X, Y coordinates of the image
     height, width=size(img_array)
     #println("height: $(height), width: $(width)")
@@ -120,7 +121,8 @@ 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=Float32.(Array(img_array))./ 255.0 # Normalize between 0 and 1
     
     # Smooth the image
     sigma=3.0
@@ -171,7 +173,7 @@ function loadSurfacePlot(interfaceImg::String)
     img_gray=Gray.(img) # Convert to grayscale
     #println("Grayscale image type:", typeof(img_gray)) 
     img_array=Array(img_gray)
-    elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
+    elevation=Float32.(Array(img_array)) ./ 255.0 # Normalize between 0 and 1
     #println("Elevation size:", size(elevation)) 
     # Smooth the image 
     sigma=3.0
@@ -203,10 +205,12 @@ function loadSurfacePlot(interfaceImg::String)
             aspectratio=aspect_ratio
         )
     )
-    if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
     # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping
     elevation_smoothed=transpose(elevation_smoothed)
+    if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
         Y=-Y
+    else
+        X=-X
     end
 
     trace3D=PlotlyBase.surface(
@@ -243,8 +247,42 @@ function crossLinesPlot(x, y, maxwidth, maxheight)
     return trace1, trace2
 end
 
+function log_tick_formatter(values::Vector{Float64})
+    #println("values: $(values) + type: $(typeof(values))")
+    # Initialize exponents dictionary
+    exponents=zeros(Int, length(values))
+    formValues=zeros(Float64, length(values))
+    for i in 1:length(values)
+        value = values[i]
+        #println("value: $(value)")
+        if value >= 1000  # positive formatting for notation
+            while value >= 1000
+                value /= 10
+                exponents[i] += 1
+            end
+            #println("value: $(value) x10^$(exponents[i])")
+        elseif value > 0 && value < 1  # negative formatting for notation
+            while value < 1
+                value *= 10
+                exponents[i] -= 1
+            end
+            #values[i] = round(values[i], digits=2)
+            #println("value: $(value) x10^$(exponents[i])")
+        end
+        #formatted_values[i] = values[i] != 0 ? "$(round(values[i], digits=2))x10" * Makie.UnicodeFun.to_superscript(exponents[i]) : "0"
+        formValues[i]=value
+    end
+    #return formatted_values
+    #return map(v -> values * "x10" * Makie.UnicodeFun.to_superscript(round(Int64, v)), exponents)
+    #println("formated values: $(formValues) + type: $(typeof(formValues))")
+    #println("exponents: $(exponents) + type: $(typeof(exponents))")
+    #return map((v, e) -> "$(round(v, digits=2))x10" * Makie.UnicodeFun.to_superscript(e), formValues, exponents)
+    return map((v, e) -> e == 0 ? "$(round(v, sigdigits=2))" : "$(round(v, sigdigits=2))x10" * Makie.UnicodeFun.to_superscript(e), formValues, exponents)
+
+end
+
 # == Reactive code ==
-# reactive code to make the UI interactive
+# Reactive code to make the UI interactive
 @app begin
     # == Reactive variables ==
     # reactive variables exist in both the Julia backend and the browser with two-way synchronization
@@ -476,6 +514,7 @@ end
     end
     
     @onbutton mainProcess begin
+    #@onchange Nmass begin
         progress=true # Start progress button animation
         btnStartDisable=true # We disable the button to avoid multiple requests
         btnPlotDisable=true
@@ -483,31 +522,28 @@ 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)
                 msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient."
-                slice=GetSlice(spectra, Nmass, Tol)
+                #slice=GetSlice(spectra, Nmass, Tol)
-                fig=CairoMakie.Figure(size=(140, 440)) # Container
+                slice=GetMzSliceJl(spectra,Nmass,Tol)
+                fig=CairoMakie.Figure(size=(150, 250)) # Container
                 # Append a query string to force the image to refresh 
                 timestamp=string(time_ns()) 
                 if triqEnabled # If we have TrIQ
-                    if colorLevel < 4 || 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_$(text_nmass).bmp")
-                        SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(colorLevel), triqProb),ViridisPalette)
+                        sliceTriq=TrIQ(slice, colorLevel, triqProb)
-                        # Flip te image vertically then save it again
+                        #println("slice raw: $(typeof(slice))")
-                        img=load(image_path)
+                        #println("TriQ matrix: $(typeof(sliceTriq))")
-                        if size(img, 1) > size(img, 2) # fix to taller images 
+                        sliceTriq=reverse(sliceTriq, dims=2)
-                            img=reverse(permutedims(img, (2, 1)), dims=1)
+                        ##SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),sliceTriq,ViridisPalette)
-                        end
+                        SaveBitmapCl(joinpath("public", "TrIQ_$(text_nmass).bmp"),sliceTriq,ViridisPalette)
-                        flipped_img=reverse(img, dims=1)
-                        imgWidth=size(flipped_img, 2)
-                        imgHeight=size(flipped_img, 1)
-                        save(image_path, flipped_img)
                         # Use timestamp to refresh image interface container
                         imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
                         plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
@@ -515,12 +551,17 @@ end
                         current_triq="TrIQ_$(text_nmass).bmp"
                         msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
                         # Create colorbar
-                        #ticks=round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3)
+                        bound  = julia_mzML_imzML.GetOutlierThres(slice, triqProb)
-                        #println("ticks: $(round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3))")
+                        levels = range(bound[1],stop=bound[2], length=8)
-                        ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3)
+                        #println("range of the levels 1: $(levels)")
-                        #println("ticks 2: $(round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3))")
+                        levels = vcat(levels, 2*levels[end]-levels[end-1])
-                        #Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(colorLevel), triqProb))),ticks=ticks, label="Intensity")
+                        #println("range of the levels 2: $(levels) + $(length(levels))")
-                        Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25)
+                        #ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=10), sigdigits=3)
+                        #ticks=range(0, (stop=maximum(slice)*triqProb), length=5)
+                        #println("ticks: $(typeof(ticks))")
+                        Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, bound[2]),ticks=levels,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 
@@ -537,16 +578,13 @@ end
                     end
                 else # If we don't use TrIQ
                     image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
-                    SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),IntQuant(slice),ViridisPalette)
+                    ##sliceQuant=IntQuant(slice)
-                    # Flip te image vertically then save it again
+                    sliceQuant=IntQuantCl(slice,Int(colorLevel-1))
-                    img=load(image_path)
+                    #println("slice raw: $(typeof(slice))")
-                    if size(img, 1) > size(img, 2) # fix to taller images 
+                    #println("slice in intQuant: $(typeof(sliceQuant))")
-                        img=reverse(permutedims(img, (2, 1)), dims=1) 
+                    sliceQuant=reverse(sliceQuant, dims=2)
-                    end
+                    ##SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
-                    flipped_img=reverse(img, dims=1)
+                    SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette)
-                    imgWidth=size(flipped_img, 2)
-                    imgHeight=size(flipped_img, 1)
-                    save(image_path, flipped_img)
                     # Use timestamp to refresh image interface container
                     imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)"
                     plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
@@ -554,10 +592,11 @@ end
                     current_msi="MSI_$(text_nmass).bmp"
                     msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
                     # Create colorbar 
+                    levels=range(0,maximum(slice),length=8)
                     #ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
-                    ticks=round.(range(0, stop=maximum(slice), length=15), sigdigits=3)
+                    #ticks=range(0, stop=maximum(slice), length=5)
-                    #Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(slice)),ticks=ticks, label="Intensity")
+                    #Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
-                    Colorbar(fig[1, 1], colormap=cgrad(:viridis, 256, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
+                    Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
                     save("public/colorbar_MSI_$(text_nmass).png", fig)
                     colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
                     # Get current colorbar 

app.jl.html

@@ -57,21 +57,27 @@
         <p id="lblFullRoute">full route: {{full_route}}</p>
         <!-- Variable Manipulation -->
         <div class="row">
-          <div class="st-col col-12 col-sm q-ma-sm">
+          <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-12 col-sm q-ma-sm">
+          <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="[ val => !!val || '* Required', val => val >= 2 &amp;&amp; val <= 256 || 'Needs to be in range between 2 and 256']"></q-input>
           </div>
         </div>
         <div class="row">
-        <!-- Triq Variable Manipulation -->
+        <!-- Triq Variable Manipulation and filters-->
           <div class="col-6">
             <div class="st-col col-6 col-sm q-ma-sm">
+              <q-toggle id="btnEnableMFilter" v-on:click="MFilterEnabled" v-model="MFilterEnabled" color="green"
+                label="Add Median Filter"></q-toggle>
               <q-toggle id="btnEnableTriq" v-on:click="triqEnabled" v-model="triqEnabled" color="blue"
                 label="Add Threshold Intensity Quantization (TrIQ)"></q-toggle>
             </div>
@@ -82,12 +88,8 @@
                         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 class="st-col col-4 col-sm-4 q-ma-sm">
-                <q-input standout="custom-standout" id="textcolorLevel" step="1" v-model="colorLevel"
+              </div>-->
-                  label="TrIQ color levels" type="number" :rules="[
-                        val => triqEnabled ? ( '* Required', val >= 4 &amp;&amp; val <= 256  || 'Needs to be in range between 2 and 256') : true
-                        ]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
-              </div>
             </div>
           </div>
           <!-- Spectra Plot Manipulation -->

julia_imzML_visual.jl

@@ -0,0 +1,80 @@
+# IntQuantCl is originally a function of julia mzMl imzML with the adition 
+# of altering the scale of the colors according to colorlevel.
+function IntQuantCl( slice , colorLevel)
+    # Compute scale factor for amplitude discretization
+    lower  = minimum( slice )
+    scale  = colorLevel / maximum( slice )
+    dim    = size( slice )
+    image  = zeros( UInt8, dim[1], dim[2] )
+    for i in 1:length( slice )
+        image[i] = convert( UInt8, floor( slice[i] * scale + 0.5 ) )
+    end
+    return image
+end
+
+# SaveBitmap 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, 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
+    minVal = minimum(pixMap)
+    maxVal = maximum(pixMap)
+    pixMap = round.(UInt8, 255 * (pixMap .- minVal) ./ (maxVal - minVal))
+    # Compute row padding
+    padding = ( 4 - dim[1] & 0x3 ) & 0x3
+    # Compute file dimensions. Header = 14 + 40 + ( 256 * 4 ) = 1078
+    offset   = 1078
+    imgBytes = dim[2] * ( dim[1] + padding )
+    # Create file
+    stream = open( name, "w" )
+    # Save file header
+    write( stream, UInt16( 0x4D42 ) )
+    write( stream, UInt32[ offset + imgBytes, 0 , offset ] )
+    # Save info header
+    write( stream, UInt32[ 40, dim[1], dim[2], 0x80001, 0 ] )
+    write( stream, UInt32[ imgBytes, 0, 0, 256, 0 ] )
+    # Save color table
+    write( stream, colorTable )
+    if length( colorTable ) < 256
+        fixTable = zeros( UInt32, 256 - length( colorTable ) )
+        write( stream, fixTable )
+    end
+    # Save image pixels
+    if padding == 0
+        for i = 1:dim[2]
+            write( stream, pixMap[:,i] )
+        end
+    else
+        zeroPad = zeros( UInt8, padding )
+        for i in 1:dim[2]
+            write( stream, pixMap[:,i] )
+            write( stream, zeroPad )
+        end
+    end
+    # Close file
+    close( stream )
+end
+
+# SaveBitmap originally a function of the mzML imzML library in julia,
+# now has an adjustment for NaN values in case they exist to mantain data integrity
+function GetMzSliceJl(imzML, mass, tolerance)
+    # Alloc space for slice
+    width = maximum(imzML[1, :])
+    height = maximum(imzML[2, :])
+    image = fill(0.0, width, height)
+
+    for i in 1:size(imzML)[2]
+        index = julia_mzML_imzML.FindMass(imzML[3, i], mass, tolerance)
+        if index != 0
+            image[imzML[1, i], imzML[2, i]] = imzML[4, i][index]
+        end
+    end
+    # Adjustment for NaN values with 0
+    replace!(image, NaN => 0.0)
+    return image
+end

start_MSI_GUI.jl

@@ -1,8 +1,10 @@
 using Pkg
+sTime=time()
 Pkg.activate(".")
 Pkg.instantiate()
 Pkg.gc()
 
+"""
 packages = [
     "GenieFramework", "Libz", "PlotlyBase", "CairoMakie", "Colors", 
     "Statistics", "NaturalSort",  "Genie", 
@@ -20,6 +22,7 @@ end
 if !("julia_mzML_imzML" in keys(Pkg.dependencies()))
     Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML")
 end
+"""
 
 using Genie
 
@@ -29,6 +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()
@@ -41,5 +46,4 @@ Genie.loadapp()
         @async run(`Start-Process $url`) # For Windows
     end
 end
-
 wait()