diff --git a/app.jl b/app.jl index 47fe52c..b5c155d 100644 --- a/app.jl +++ b/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: $(width)") @@ -203,10 +204,12 @@ function loadSurfacePlot(interfaceImg::String) aspectratio=aspect_ratio ) ) + # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping + elevation_smoothed=transpose(elevation_smoothed) if size(elevation_smoothed, 1) < size(elevation_smoothed, 2) - # Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping - elevation_smoothed=transpose(elevation_smoothed) Y=-Y + else + X=-X end trace3D=PlotlyBase.surface( @@ -244,7 +247,7 @@ function crossLinesPlot(x, y, maxwidth, maxheight) end # == Reactive code == -# reactive code to make the UI interactive +# Reactive code to make the UI interactive @app begin # == Reactive variables == # reactive variables exist in both the Julia backend and the browser with two-way synchronization @@ -476,6 +479,7 @@ end end @onbutton mainProcess begin + #@onchange Nmass begin progress=true # Start progress button animation btnStartDisable=true # We disable the button to avoid multiple requests btnPlotDisable=true @@ -489,25 +493,21 @@ end spectra=LoadImzml(full_route) msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient." slice=GetSlice(spectra, Nmass, Tol) - fig=CairoMakie.Figure(size=(140, 440)) # Container + fig=CairoMakie.Figure(size=(128, 256)) # Container # Append a query string to force the image to refresh timestamp=string(time_ns()) if triqEnabled # If we have TrIQ - if colorLevel < 4 || colorLevel > 256 || triqProb < 0.8 || triqProb > 1 + if colorLevel < 2 || colorLevel > 256 || triqProb < 0.8 || triqProb > 1 msg="Incorrect TrIQ values, please adjust accordingly and try again." warning_msg=true else image_path=joinpath("./public", "TrIQ_$(text_nmass).bmp") - SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(colorLevel), triqProb),ViridisPalette) - # Flip te image vertically then save it again - img=load(image_path) - if size(img, 1) > size(img, 2) # fix to taller images - img=reverse(permutedims(img, (2, 1)), dims=1) - end - flipped_img=reverse(img, dims=1) - imgWidth=size(flipped_img, 2) - imgHeight=size(flipped_img, 1) - save(image_path, flipped_img) + sliceTriq=TrIQ(slice, Int(colorLevel), triqProb) + #println("slice raw: $(typeof(slice))") + #println("TriQ matrix: $(typeof(sliceTriq))") + sliceTriq=reverse(sliceTriq, dims=2) + ##SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),sliceTriq,ViridisPalette) + SaveBitmapCl(joinpath("public", "TrIQ_$(text_nmass).bmp"),sliceTriq,ViridisPalette) # Use timestamp to refresh image interface container imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)" plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT) @@ -515,12 +515,8 @@ end current_triq="TrIQ_$(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) - #println("ticks: $(round.(range(0, stop=maximum(TrIQ(slice, Int(colorLevel), triqProb)), length=10), sigdigits=3))") - ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3) - #println("ticks 2: $(round.(range(0, (stop=maximum(slice)*triqProb), length=15), sigdigits=3))") - #Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(colorLevel), triqProb))),ticks=ticks, label="Intensity") - Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25) + ticks=round.(range(0, (stop=maximum(sliceTriq)*triqProb), length=15), sigdigits=3) + Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(sliceTriq)*triqProb),ticks=ticks, label="Intensity", size = 25) save("public/colorbar_TrIQ_$(text_nmass).png", fig) colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)" # Get current colorbar @@ -537,16 +533,13 @@ 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) - # Flip te image vertically then save it again - img=load(image_path) - if size(img, 1) > size(img, 2) # fix to taller images - img=reverse(permutedims(img, (2, 1)), dims=1) - end - flipped_img=reverse(img, dims=1) - imgWidth=size(flipped_img, 2) - imgHeight=size(flipped_img, 1) - save(image_path, flipped_img) + ##sliceQuant=IntQuant(slice) + sliceQuant=IntQuantCl(slice,colorLevel) + #println("slice raw: $(typeof(slice))") + #println("slice in intQuant: $(typeof(sliceQuant))") + sliceQuant=reverse(sliceQuant, dims=2) + ##SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette) + SaveBitmapCl(joinpath("public", "MSI_$(text_nmass).bmp"),sliceQuant,ViridisPalette) # Use timestamp to refresh image interface container imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)" plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt) @@ -555,9 +548,8 @@ end msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" # Create colorbar #ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3) - ticks=round.(range(0, stop=maximum(slice), length=15), sigdigits=3) - #Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(slice)),ticks=ticks, label="Intensity") - Colorbar(fig[1, 1], colormap=cgrad(:viridis, 256, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25) + ticks=round.(range(0, stop=maximum(sliceQuant), length=15), sigdigits=3) + Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(sliceQuant)),ticks=ticks, label="Intensity", size = 25) save("public/colorbar_MSI_$(text_nmass).png", fig) colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)" # Get current colorbar diff --git a/app.jl.html b/app.jl.html index 34c3478..3d2b22d 100644 --- a/app.jl.html +++ b/app.jl.html @@ -57,21 +57,29 @@

full route: {{full_route}}

-
+
-
+
+
+ +
- +
+
@@ -82,12 +90,8 @@ val => triqEnabled ? ( '* Required', val >= 0.8 && val <= 1 || 'Needs to be in range between 0.8 and 1') : true ]" :readonly="!triqEnabled" :disable="!triqEnabled">
-
- -
+
diff --git a/julia_imzML_visual.jl b/julia_imzML_visual.jl new file mode 100644 index 0000000..a4d5fdb --- /dev/null +++ b/julia_imzML_visual.jl @@ -0,0 +1,64 @@ +# 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 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, + pixMap::Array{UInt8,2}, + colorTable::Array{UInt32,1} ) + # Get image dimensions + dim = size( pixMap ) + if length( dim ) != 2 + return 0 + end + # 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 ] ) + # Get unique colors displayed in pixMap + unique_colors = unique(vec(pixMap)) + n_colors = length(unique_colors) + # Color levels can't surpass 256 + levels = min(n_colors, 256) + 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] + 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 \ No newline at end of file diff --git a/start_MSI_GUI.jl b/start_MSI_GUI.jl index f23f076..35cd8ee 100644 --- a/start_MSI_GUI.jl +++ b/start_MSI_GUI.jl @@ -3,6 +3,7 @@ Pkg.activate(".") Pkg.instantiate() Pkg.gc() +""" packages = [ "GenieFramework", "Libz", "PlotlyBase", "CairoMakie", "Colors", "Statistics", "NaturalSort", "Genie", @@ -20,6 +21,7 @@ end if !("julia_mzML_imzML" in keys(Pkg.dependencies())) Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML") end +""" using Genie