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colorbar scale for both with triq filter and without is finished

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This commit is contained in:
Pixelguy14 2025-01-30 18:17:32 -06:00
parent fdd625d3e0
commit 11349330a4
2 changed files with 77 additions and 24 deletions
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72
app.jl
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@ -13,7 +13,6 @@ using Images
using LinearAlgebra using LinearAlgebra
using NativeFileDialog # Opens the file explorer depending on the OS using NativeFileDialog # Opens the file explorer depending on the OS
using StipplePlotly using StipplePlotly
using Printf
include("./julia_imzML_visual.jl") include("./julia_imzML_visual.jl")
@genietools @genietools
@ -123,7 +122,7 @@ function loadContourPlot(interfaceImg::String)
img_gray=Gray.(img) img_gray=Gray.(img)
img_array=Array(img_gray) img_array=Array(img_gray)
# parse matrix to int32 to closely resemble similarity to original bitmap # parse matrix to int32 to closely resemble similarity to original bitmap
elevation=int32.(Array(img_gray)) elevation=Float32.(Array(img_array))./ 255.0 # Normalize between 0 and 1
# Smooth the image # Smooth the image
sigma=3.0 sigma=3.0
@ -174,7 +173,7 @@ function loadSurfacePlot(interfaceImg::String)
img_gray=Gray.(img) # Convert to grayscale img_gray=Gray.(img) # Convert to grayscale
#println("Grayscale image type:", typeof(img_gray)) #println("Grayscale image type:", typeof(img_gray))
img_array=Array(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)) #println("Elevation size:", size(elevation))
# Smooth the image # Smooth the image
sigma=3.0 sigma=3.0
@ -248,6 +247,40 @@ function crossLinesPlot(x, y, maxwidth, maxheight)
return trace1, trace2 return trace1, trace2
end 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 ==
# Reactive code to make the UI interactive # Reactive code to make the UI interactive
@app begin @app begin
@ -494,8 +527,9 @@ end
try try
spectra=LoadImzml(full_route) spectra=LoadImzml(full_route)
msg="File loaded. Creating Spectra with the specific mass and tolerance, please be patient." 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=(128, 256)) # Container slice=GetMzSliceJl(spectra,Nmass,Tol)
fig=CairoMakie.Figure(size=(150, 250)) # Container
# Append a query string to force the image to refresh # Append a query string to force the image to refresh
timestamp=string(time_ns()) timestamp=string(time_ns())
if triqEnabled # If we have TrIQ if triqEnabled # If we have TrIQ
@ -517,19 +551,17 @@ end
current_triq="TrIQ_$(text_nmass).bmp" current_triq="TrIQ_$(text_nmass).bmp"
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Create colorbar # Create colorbar
bound = julia_mzML_imzML.GetOutlierThres(slice, triqProb)
levels = range(bound[1],stop=bound[2], length=8)
#println("range of the levels 1: $(levels)")
levels = vcat(levels, 2*levels[end]-levels[end-1])
#println("range of the levels 2: $(levels) + $(length(levels))")
#ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=10), sigdigits=3) #ticks=round.(range(0, (stop=maximum(slice)*triqProb), length=10), sigdigits=3)
ticks=range(0, (stop=maximum(slice)*triqProb), length=5) #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)
function log_tick_formatter(values) #Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)*triqProb),ticks=ticks, label="Intensity", size = 25)
return map(v -> "10" * Makie.UnicodeFun.to_superscript(round(Int64, v)), values) #println("Colorbar: $(typeof(fig))")
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) save("public/colorbar_TrIQ_$(text_nmass).png", fig)
colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)" colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
# Get current colorbar # Get current colorbar
@ -560,9 +592,11 @@ end
current_msi="MSI_$(text_nmass).bmp" current_msi="MSI_$(text_nmass).bmp"
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
# Create colorbar # Create colorbar
levels=range(0,maximum(slice),length=8)
#ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3) #ticks=round.(range(0, stop=maximum(slice), length=10), sigdigits=3)
ticks=range(0, stop=maximum(slice), length=5) #ticks=range(0, stop=maximum(slice), length=5)
Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25) #Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=ticks, label="Intensity", size = 25)
Colorbar(fig[1, 1], colormap=cgrad(:viridis, colorLevel, categorical=true), limits=(0, maximum(slice)),ticks=levels,tickformat=log_tick_formatter, label="Intensity", size = 25)
save("public/colorbar_MSI_$(text_nmass).png", fig) save("public/colorbar_MSI_$(text_nmass).png", fig)
colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)" colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
# Get current colorbar # Get current colorbar

29
julia_imzML_visual.jl
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@ -12,7 +12,7 @@ function IntQuantCl( slice , colorLevel)
return image return image
end end
# SaveBitmap is also originally a function of the mzML imzML library in julia, # SaveBitmap originally a function of the mzML imzML library in julia,
# This function dinamically adjust the color palete adjusting to the ammount of colors # This function dinamically adjust the color palete adjusting to the ammount of colors
# available in pixmap # available in pixmap
function SaveBitmapCl( name, pixMap::Array{UInt8,2}, colorTable::Array{UInt32,1} ) function SaveBitmapCl( name, pixMap::Array{UInt8,2}, colorTable::Array{UInt32,1} )
@ -22,9 +22,9 @@ function SaveBitmapCl( name, pixMap::Array{UInt8,2}, colorTable::Array{UInt32,1}
return 0 return 0
end end
# Normalize pixel values to get a more accurate reading of the image # Normalize pixel values to get a more accurate reading of the image
min_val = minimum(pixMap) minVal = minimum(pixMap)
max_val = maximum(pixMap) maxVal = maximum(pixMap)
pixMap = round.(UInt8, 255 * (pixMap .- min_val) ./ (max_val - min_val)) pixMap = round.(UInt8, 255 * (pixMap .- minVal) ./ (maxVal - minVal))
# Compute row padding # Compute row padding
padding = ( 4 - dim[1] & 0x3 ) & 0x3 padding = ( 4 - dim[1] & 0x3 ) & 0x3
# Compute file dimensions. Header = 14 + 40 + ( 256 * 4 ) = 1078 # Compute file dimensions. Header = 14 + 40 + ( 256 * 4 ) = 1078
@ -58,4 +58,23 @@ function SaveBitmapCl( name, pixMap::Array{UInt8,2}, colorTable::Array{UInt32,1}
end end
# Close file # Close file
close( stream ) close( stream )
end 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