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Alternative versions of SaveBitMap and IntQuant for adjustments to the color level input

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Pixelguy14 2025-01-29 15:55:30 -06:00
parent 4ea5d8e119
commit df0d82910b
4 changed files with 107 additions and 45 deletions
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62
app.jl
View File

@ -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: $(width)")
@ -203,10 +204,12 @@ function loadSurfacePlot(interfaceImg::String)
aspectratio=aspect_ratio
)
)
if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
# Transpose the elevation_smoothed array if Y axis is longer than X axis to fix chopping
elevation_smoothed=transpose(elevation_smoothed)
if size(elevation_smoothed, 1) < size(elevation_smoothed, 2)
Y=-Y
else
X=-X
end
trace3D=PlotlyBase.surface(
@ -244,7 +247,7 @@ function crossLinesPlot(x, y, maxwidth, maxheight)
end
# == Reactive code ==
# reactive code to make the UI interactive
# Reactive code to make the UI interactive
@app begin
# == Reactive variables ==
# reactive variables exist in both the Julia backend and the browser with two-way synchronization
@ -476,6 +479,7 @@ end
end
@onbutton mainProcess begin
#@onchange Nmass begin
progress=true # Start progress button animation
btnStartDisable=true # We disable the button to avoid multiple requests
btnPlotDisable=true
@ -489,25 +493,21 @@ end
spectra=LoadImzml(full_route)
msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient."
slice=GetSlice(spectra, Nmass, Tol)
fig=CairoMakie.Figure(size=(140, 440)) # Container
fig=CairoMakie.Figure(size=(128, 256)) # Container
# Append a query string to force the image to refresh
timestamp=string(time_ns())
if triqEnabled # If we have TrIQ
if colorLevel < 4 || colorLevel > 256 || triqProb < 0.8 || triqProb > 1
if colorLevel < 2 || colorLevel > 256 || triqProb < 0.8 || triqProb > 1
msg="Incorrect TrIQ values, please adjust accordingly and try again."
warning_msg=true
else
image_path=joinpath("./public", "TrIQ_$(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

22
app.jl.html
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@ -57,21 +57,29 @@
<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>
</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"
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>
</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 => 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">
<!-- 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 +90,8 @@
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">
<q-input standout="custom-standout" id="textcolorLevel" step="1" v-model="colorLevel"
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 class="st-col col-4 col-sm-4 q-ma-sm">
</div>-->
</div>
</div>
<!-- Spectra Plot Manipulation -->

64
julia_imzML_visual.jl Normal file
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@ -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

2
start_MSI_GUI.jl
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@ -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