782 lines
32 KiB
Julia
782 lines
32 KiB
Julia
module App
|
|
# == Packages ==
|
|
using GenieFramework # Set up Genie development environment.
|
|
using Pkg
|
|
using Libz
|
|
using PlotlyBase
|
|
using CairoMakie
|
|
using Colors
|
|
using julia_mzML_imzML
|
|
using Statistics
|
|
using NaturalSort
|
|
using Images
|
|
using LinearAlgebra
|
|
using NativeFileDialog
|
|
@genietools
|
|
|
|
# == Code import ==
|
|
# add your data analysis code here or in the lib folder. Code in lib/ will be
|
|
# automatically loaded
|
|
rgb_ViridisPalette=reinterpret(ColorTypes.RGB24, ViridisPalette)
|
|
|
|
# == Search functions ==
|
|
function increment_image(current_image, image_list)
|
|
if isempty(image_list)
|
|
return nothing
|
|
end
|
|
current_index=findfirst(isequal(current_image), image_list)
|
|
if current_index == nothing || current_index == length(image_list) || current_image === ""
|
|
return image_list[length(image_list)] # Return the current image if it's the last one or not found
|
|
else
|
|
return image_list[current_index + 1] # Move to the next image
|
|
end
|
|
end
|
|
|
|
function decrement_image(current_image, image_list)
|
|
if isempty(image_list)
|
|
return nothing
|
|
end
|
|
current_index=findfirst(isequal(current_image), image_list)
|
|
if current_index == nothing || current_index == 1 || current_image === ""
|
|
return image_list[1] # Return the current image if it's the first one or not found
|
|
else
|
|
return image_list[current_index - 1] # Move to the previous image
|
|
end
|
|
end
|
|
|
|
# == Reactive code ==
|
|
# 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
|
|
# @out variables can only be modified by the backend
|
|
# @in variables can be modified by both the backend and the browser
|
|
# variables must be initialized with constant values, or variables defined outside of the @app block
|
|
#@out test="/test.bmp" #slash means it's getting the info from 'public' folder
|
|
|
|
# Interface non Variables
|
|
@out warning_fr=""
|
|
@out btnStartDisable=true
|
|
@out btnPlotDisable=false
|
|
@in warning_msg=false
|
|
@in CompareDialog=false
|
|
|
|
# Interface Variables
|
|
@in file_route=""
|
|
@in file_name=""
|
|
@in Nmass=0.0
|
|
@in Tol=0.0
|
|
@in triqProb=0.98
|
|
@in triqColor=256
|
|
|
|
# Interface Buttons
|
|
@in btnSearch=false # To search for files in your device
|
|
@in mainProcess=false # To generate images
|
|
@in CompareBtn=false # to open dialog
|
|
@in createSumPlot=false # To generate sum spectrum plot
|
|
@in image3dPlot=false # To generate 3d plot based on current image
|
|
@in triq3dPlot=false # To generate 3d plot based on current triq image
|
|
@in imageCPlot=false # To generate contour plots of current image
|
|
@in triqCPlot=false # To generate contour plots of current triq image
|
|
@in progress=false
|
|
@in progressPlot=false
|
|
@in triqEnabled=false
|
|
@in ImgPlus=false
|
|
@in ImgMinus=false
|
|
@in ImgPlusT=false
|
|
@in ImgMinusT=false
|
|
|
|
#TABS
|
|
@out tabIDs=["tab0","tab1","tab2","tab3","tab4"]
|
|
@out tabLabels=["Image", "TrIQ", "Spectrum Plot", "Topology Plot","Surface Plot"]
|
|
@in selectedTab= "tab0"
|
|
@out CompTabIDs=["tab0","tab1","tab2","tab3","tab4"]
|
|
@out CompTabLabels=["Image", "TrIQ", "Spectrum Plot", "Topology Plot","Surface Plot"]
|
|
@in CompSelectedTab= "tab0"
|
|
|
|
# Interface Images
|
|
@out imgInt="/.bmp" # image Interface
|
|
@out imgIntT="/.bmp" # image Interface TrIQ
|
|
@out colorbar="/.png"
|
|
@out colorbarT="/.png"
|
|
|
|
@out msg=""
|
|
@out msgimg=""
|
|
@out msgtriq=""
|
|
|
|
@out full_route=""
|
|
@out full_routeMz=""
|
|
@out full_routeMz2=""
|
|
|
|
# For the creation of images with a more specific mass charge
|
|
@out text_nmass=""
|
|
|
|
# For image search
|
|
# Image lists we apply a filter that searches specific type of images into our public folder, then we sort it in a "numerical" order
|
|
@in msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
@in col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
@in triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
@in col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
# Set current image for the list
|
|
@out current_msi=""
|
|
@out current_col_msi=""
|
|
@out current_triq=""
|
|
@out current_col_triq=""
|
|
|
|
@out indeximg=0
|
|
@out indeximgTriq=0
|
|
|
|
@out lastimg=0
|
|
@out lastimgTriq=0
|
|
|
|
# Interface Plot Spectrum
|
|
layoutSpectra=PlotlyBase.Layout(
|
|
title="SUM Spectrum plot",
|
|
xaxis=PlotlyBase.attr(
|
|
title="<i>m/z</i>",
|
|
showgrid=true
|
|
),
|
|
yaxis=PlotlyBase.attr(
|
|
title="Intensity",
|
|
showgrid=true
|
|
)
|
|
)
|
|
# Dummy 2D surface plot
|
|
traceSpectra=PlotlyBase.scatter(x=[], y=[], mode="lines")
|
|
# Create conection to frontend
|
|
@out plotdata=[traceSpectra]
|
|
@out plotlayout=layoutSpectra
|
|
|
|
# Interface Plot Surface
|
|
layoutContour=PlotlyBase.Layout(
|
|
title="2D Topographic Map",
|
|
xaxis=PlotlyBase.attr(
|
|
title="X",
|
|
showgrid=true
|
|
),
|
|
yaxis=PlotlyBase.attr(
|
|
title="Y",
|
|
showgrid=true
|
|
)
|
|
)
|
|
# Dummy 2D surface plot
|
|
traceContour=PlotlyBase.scatter(x=[], y=[], mode="lines")
|
|
# Create conection to frontend
|
|
@out plotdataC=[traceContour]
|
|
@out plotlayoutC=layoutContour
|
|
|
|
# Interface Plot 3d
|
|
# Define the layout for the 3D plot
|
|
layout3D=PlotlyBase.Layout(
|
|
title="3D Surface Plot",
|
|
scene=attr(
|
|
xaxis_title="X",
|
|
yaxis_title="Y",
|
|
zaxis_title="Z",
|
|
xaxis_nticks=20,
|
|
yaxis_nticks=20,
|
|
zaxis_nticks=4,
|
|
camera=attr(eye=attr(x=0, y=-1, z=0.5)),
|
|
aspectratio=attr(x=1, y=1, z=0.2)
|
|
)
|
|
)
|
|
|
|
# Dummy 3D surface plot
|
|
x=1:10
|
|
y=1:10
|
|
z=[sin(i * j / 10) for i in x, j in y]
|
|
trace3D=PlotlyBase.surface(x=[], y=[], z=[],
|
|
contours_z=attr(
|
|
show=true,
|
|
usecolormap=true,
|
|
highlightcolor="limegreen",
|
|
project_z=true
|
|
), colorscale="Viridis")
|
|
# Create conection to frontend
|
|
@out plotdata3d=[trace3D]
|
|
@out plotlayout3d=layout3D
|
|
|
|
# println("3D trace defined: ", trace3D)
|
|
|
|
# == Reactive handlers ==
|
|
# Reactive handlers watch a variable and execute a block of code when its value changes
|
|
# The onbutton handler will set the variable to false after the block is executed
|
|
|
|
@onbutton btnSearch begin
|
|
full_route=pick_file(; filterlist="imzML")
|
|
if isnothing(full_route)
|
|
#println("No file selected")
|
|
msg="No file selected"
|
|
warning_msg=true
|
|
btnStartDisable=true
|
|
else
|
|
#println("Selected file path: ", full_route)
|
|
btnStartDisable=false
|
|
btnPlotDisable=false
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
end
|
|
end
|
|
|
|
"""
|
|
@onchange Nmass begin
|
|
indeximg=floor(Int, Nmass)
|
|
indeximgTriq=floor(Int, Nmass)
|
|
lastimg=floor(Int, Nmass)
|
|
lastimgTriq=floor(Int, Nmass)
|
|
end
|
|
"""
|
|
|
|
@onbutton mainProcess begin
|
|
progress=true # Start progress button animation
|
|
btnStartDisable=true # We disable the button to avoid multiple requests
|
|
btnPlotDisable=true
|
|
indeximg=floor(Int, Nmass)
|
|
text_nmass=replace(string(Nmass), "." => "_")
|
|
#full_route=joinpath(file_route, file_name)
|
|
if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <= 1
|
|
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)
|
|
fig=CairoMakie.Figure(size=(100, 200)) # Container
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
if triqEnabled # If we have TrIQ
|
|
if triqColor < 1 || triqColor > 256 ||triqProb < 0 || 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(triqColor), 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)
|
|
save(image_path, flipped_img)
|
|
# Use timestamp to refresh image interface container
|
|
imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
|
|
# Get current image
|
|
current_triq="TrIQ_$(text_nmass).bmp"
|
|
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Create colorbar
|
|
ticks=round.(range(0, stop=maximum(TrIQ(slice, Int(triqColor), triqProb)), length=10), digits=2)
|
|
Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(TrIQ(slice, Int(triqColor), triqProb))),ticks=ticks, label="Intensity")
|
|
save("public/colorbar_TrIQ_$(text_nmass).png", fig)
|
|
colorbarT="/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
|
|
# Get current colorbar
|
|
current_col_triq="colorbar_TrIQ_$(text_nmass).png"
|
|
# We update the directory to include the new placed images.
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
msg="The file has been created successfully inside the 'public' folder of the app."
|
|
selectedTab="tab1"
|
|
#println("all msi in folder=",triq_bmp)
|
|
#println("all col msi in folder= ",col_triq_png)
|
|
end
|
|
else # If we don't use TrIQ
|
|
image_path=joinpath("./public", "MSI_$(text_nmass).bmp")
|
|
SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),IntQuant(slice),ViridisPalette)
|
|
# Flip te image vertically then save it again
|
|
img=load(image_path)
|
|
if size(img, 1) > size(img, 2) # fix to taller images
|
|
img=reverse(permutedims(img, (2, 1)), dims=1)
|
|
end
|
|
flipped_img=reverse(img, dims=1)
|
|
save(image_path, flipped_img)
|
|
# Use timestamp to refresh image interface container
|
|
imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)"
|
|
# Get current image
|
|
current_msi="MSI_$(text_nmass).bmp"
|
|
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
# Create colorbar
|
|
ticks=round.(range(0, stop=maximum(slice), length=10), digits=2)
|
|
Colorbar(fig[1, 1], colormap=rgb_ViridisPalette, limits=(0, maximum(slice)),ticks=ticks, label="Intensity")
|
|
save("public/colorbar_MSI_$(text_nmass).png", fig)
|
|
colorbar="/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
|
|
# Get current colorbar
|
|
current_col_msi="colorbar_MSI_$(text_nmass).png"
|
|
# We update the directory to include the new placed images.
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
selectedTab="tab0"
|
|
msg="The file has been created successfully inside the 'public' folder of the app."
|
|
#println("all msi in folder=",msi_bmp)
|
|
#println("all col msi in folder= ",col_msi_png)
|
|
end
|
|
catch e
|
|
msg="There was an error loading the ImzML file, please verify the file accordingly and try again. $(e)"
|
|
warning_msg=true
|
|
end
|
|
else
|
|
msg="File does not exist or a parameter is incorrect, please try again."
|
|
warning_msg=true
|
|
end
|
|
spectra=nothing # Important for memory cleaning
|
|
slice=nothing
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
btnStartDisable=false
|
|
btnPlotDisable=false
|
|
progress=false
|
|
end
|
|
|
|
@onbutton createSumPlot begin
|
|
msg="Sum spectrum plot selected"
|
|
#full_route=joinpath( file_route, file_name )
|
|
if isfile(full_route) # Check if the file exists
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
full_routeMz=split( full_route, "." )[1] * ".mzML" # Splitting the route from imzml to mzml so the plotting can work
|
|
if isfile(full_routeMz) && (full_routeMz2 == "" || full_routeMz2 != full_routeMz) # Check if the mzml exists
|
|
println("I'm working as intended")
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
msg="Loading plot..."
|
|
spectraMz=LoadMzml(full_routeMz)
|
|
layoutSpectra=PlotlyBase.Layout(
|
|
title="SUM Spectrum plot",
|
|
xaxis=PlotlyBase.attr(
|
|
title="<i>m/z</i>",
|
|
showgrid=true
|
|
|
|
),
|
|
yaxis=PlotlyBase.attr(
|
|
title="Intensity",
|
|
showgrid=true
|
|
)
|
|
)
|
|
# dims=size(spectraMz)
|
|
# scansMax=dims[2] # we get the total of scansMax
|
|
# traceSpectra=PlotlyBase.scatter(x=spectraMz[1, 1], y=spectraMz[2, 1], mode="lines")
|
|
traceSpectra=PlotlyBase.scatter(x=mean(spectraMz[1,:]), y=mean(spectraMz[2,:]), mode="lines")
|
|
plotdata=[traceSpectra] # We add the data from spectra to the plot
|
|
plotlayout=layoutSpectra
|
|
spectraMz=nothing # Important for memory cleaning
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab2"
|
|
msg="Plot loaded."
|
|
full_routeMz2=full_routeMz # To avoid creating the plot if its the same file read as before
|
|
else
|
|
msg="the mzML file was not found"
|
|
warning_msg=true
|
|
end
|
|
else
|
|
msg="is not an imzML file"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
end
|
|
|
|
# Image loaders based on the position of the current image (increment and decrement for both normal and filter)
|
|
# And a pre-generated list from all image files from /public folder
|
|
@onbutton ImgMinus begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images listed in the public folder
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=decrement_image(current_msi, msi_bmp)
|
|
new_col_msi=decrement_image(current_col_msi, col_msi_png)
|
|
|
|
current_msi=new_msi
|
|
current_col_msi=new_col_msi
|
|
imgInt="/$(current_msi)?t=$(timestamp)"
|
|
colorbar="/$(current_col_msi)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_msi, "MSI_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
end
|
|
@onbutton ImgPlus begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
# Update the array of images listed in the public folder
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
new_msi=increment_image(current_msi, msi_bmp)
|
|
new_col_msi=increment_image(current_col_msi, col_msi_png)
|
|
|
|
current_msi=new_msi
|
|
current_col_msi=new_col_msi
|
|
imgInt="/$(current_msi)?t=$(timestamp)"
|
|
colorbar="/$(current_col_msi)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_msi, "MSI_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
end
|
|
|
|
@onbutton ImgMinusT begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
new_msi=decrement_image(current_triq, triq_bmp)
|
|
new_col_msi=decrement_image(current_col_triq, col_triq_png)
|
|
# Update the array of images with TrIQ filter listed in the public folder
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
current_triq=new_msi
|
|
current_col_triq=new_col_msi
|
|
imgIntT="/$(current_triq)?t=$(timestamp)"
|
|
colorbarT="/$(current_col_triq)?t=$(timestamp)"
|
|
|
|
text_nmass=replace(current_triq, "TrIQ_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
|
|
end
|
|
@onbutton ImgPlusT begin
|
|
# Append a query string to force the image to refresh
|
|
timestamp=string(time_ns())
|
|
new_msi=increment_image(current_triq, triq_bmp)
|
|
new_col_msi=increment_image(current_col_triq, col_triq_png)
|
|
# Update the array of images with TrIQ filter listed in the public folder
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
|
|
|
|
current_triq=new_msi
|
|
current_col_triq=new_col_msi
|
|
imgIntT="/$(current_triq)"
|
|
colorbarT="/$(current_col_triq)"
|
|
|
|
text_nmass=replace(current_triq, "TrIQ_" => "")
|
|
text_nmass=replace(text_nmass, ".bmp" => "")
|
|
msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
|
end
|
|
|
|
# 3d plot
|
|
@onbutton image3dPlot begin
|
|
msg="Image 3D plot selected"
|
|
cleaned_imgInt=replace(imgInt, r"\?.*" => "")
|
|
cleaned_imgInt=lstrip(cleaned_imgInt, '/')
|
|
var=joinpath( "./public", cleaned_imgInt )
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
try
|
|
img=load(var)
|
|
#println("Image type:", typeof(img))
|
|
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
|
|
#println("Elevation size:", size(elevation))
|
|
# Smooth the image
|
|
sigma=3.0
|
|
kernel=Kernel.gaussian(sigma)
|
|
#println(size(kernel))
|
|
elevation_smoothed=imfilter(elevation, kernel)
|
|
#println("Smoothed elevation size:", size(elevation_smoothed))
|
|
# Transpose the elevation_smoothed array
|
|
# Create the X, Y meshgrid coordinates
|
|
x=1:size(elevation_smoothed, 2)
|
|
y=1:size(elevation_smoothed, 1)
|
|
X=repeat(reshape(x, 1, length(x)), length(y), 1)
|
|
#println("Size of X:", size(X))
|
|
Y=repeat(reshape(y, length(y), 1), 1, length(x))
|
|
#println("Size of Y:", size(Y))
|
|
# Calculate the number of ticks and aspect ratio for the 3d plot
|
|
x_nticks=min(20, length(x))
|
|
y_nticks=min(20, length(y))
|
|
z_nticks=5
|
|
aspect_ratio=attr(x=1, y=length(y) / length(x), z=0.5)
|
|
|
|
# Define the layout for the 3D plot
|
|
layout3D=PlotlyBase.Layout(
|
|
title="3D Surface Plot",
|
|
scene=attr(
|
|
xaxis_nticks=x_nticks,
|
|
yaxis_nticks=y_nticks,
|
|
zaxis_nticks=z_nticks,
|
|
camera=attr(eye=attr(x=0, y=-1, z=0.5)),
|
|
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)
|
|
Y=-Y
|
|
end
|
|
|
|
trace3D=PlotlyBase.surface(x=X[1, :], y=Y[:, 1], z=elevation_smoothed,
|
|
contours_z=attr(
|
|
show=true,
|
|
usecolormap=true,
|
|
highlightcolor="limegreen",
|
|
project_z=true
|
|
), colorscale="Viridis")
|
|
plotdata3d=[trace3D] # We add the data from the image to the plot
|
|
plotlayout3d=layout3D # we update the style of the plot to fit the image.
|
|
spectraMz=nothing # Important for memory cleaning
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab4"
|
|
msg="Plot loaded."
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
println(msg)
|
|
end
|
|
else
|
|
msg="Image could not be 3d plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
end
|
|
# 3d plot for TrIQ
|
|
@onbutton triq3dPlot begin
|
|
msg="TrIQ 3D plot selected"
|
|
cleaned_imgIntT=replace(imgIntT, r"\?.*" => "")
|
|
cleaned_imgIntT=lstrip(cleaned_imgIntT, '/')
|
|
var=joinpath( "./public", cleaned_imgIntT )
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
try
|
|
img=load(var)
|
|
img_gray=Gray.(img) # Convert to grayscale
|
|
img_array=Array(img_gray)
|
|
elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
|
|
# Smooth the image
|
|
sigma=3.0
|
|
kernel=Kernel.gaussian(sigma)
|
|
elevation_smoothed=imfilter(elevation, kernel)
|
|
|
|
# Create the X, Y meshgrid coordinates
|
|
x=1:size(elevation_smoothed, 2)
|
|
y=1:size(elevation_smoothed, 1)
|
|
X=repeat(reshape(x, 1, length(x)), length(y), 1)
|
|
Y=repeat(reshape(y, length(y), 1), 1, length(x))
|
|
|
|
# Calculate the number of ticks and aspect ratio for the 3d plot
|
|
x_nticks=min(20, length(x))
|
|
y_nticks=min(20, length(y))
|
|
z_nticks=5
|
|
aspect_ratio=attr(x=1, y=length(y) / length(x), z=0.5)
|
|
|
|
# Define the layout for the 3D plot
|
|
layout3D=PlotlyBase.Layout(
|
|
title="3D Surface Plot",
|
|
scene=attr(
|
|
xaxis_nticks=x_nticks,
|
|
yaxis_nticks=y_nticks,
|
|
zaxis_nticks=z_nticks,
|
|
camera=attr(eye=attr(x=0, y=-1, z=0.5)),
|
|
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)
|
|
Y=-Y
|
|
end
|
|
|
|
trace3D=PlotlyBase.surface(x=X[1, :], y=Y[:, 1], z=elevation_smoothed,
|
|
contours_z=attr(
|
|
show=true,
|
|
usecolormap=true,
|
|
highlightcolor="limegreen",
|
|
project_z=true
|
|
), colorscale="Viridis")
|
|
plotdata3d=[trace3D] # We add the data from the image to the plot
|
|
plotlayout3d=layout3D # we update the style of the plot to fit the image.
|
|
spectraMz=nothing # Important for memory cleaning
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab4"
|
|
msg="Plot loaded."
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
println(msg)
|
|
end
|
|
else
|
|
msg="Image could not be 3d plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
end
|
|
|
|
# Contour 2d plot
|
|
@onbutton imageCPlot begin
|
|
msg="Image 2D plot selected"
|
|
cleaned_imgInt=replace(imgInt, r"\?.*" => "")
|
|
cleaned_imgInt=lstrip(cleaned_imgInt, '/')
|
|
var=joinpath("./public", cleaned_imgInt)
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
try
|
|
img=load(var)
|
|
# Convert to grayscale
|
|
img_gray=Gray.(img)
|
|
img_array=Array(img_gray)
|
|
elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
|
|
|
|
# Smooth the image
|
|
sigma=3.0
|
|
kernel=Kernel.gaussian(sigma)
|
|
elevation_smoothed=imfilter(elevation, kernel)
|
|
|
|
# Create the X, Y meshgrid coordinates
|
|
x=1:size(elevation_smoothed, 2)
|
|
y=1:size(elevation_smoothed, 1)
|
|
X=repeat(reshape(x, 1, length(x)), length(y), 1)
|
|
Y=repeat(reshape(y, length(y), 1), 1, length(x))
|
|
|
|
layoutContour=PlotlyBase.Layout(
|
|
title="2D Topographic Map",
|
|
xaxis_title="X",
|
|
yaxis_title="Y"
|
|
|
|
)
|
|
traceContour=PlotlyBase.contour(
|
|
z=elevation_smoothed,
|
|
x=X[1, :], # Use the first row
|
|
y=-Y[:, 1], # Use the first column
|
|
contours_coloring="Viridis",
|
|
colorscale="Viridis"
|
|
)
|
|
plotdataC=[traceContour]
|
|
plotlayoutC=layoutContour
|
|
|
|
spectraMz=nothing # Important for memory cleaning
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab3"
|
|
msg="Plot loaded."
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
println(msg)
|
|
end
|
|
else
|
|
msg="Image could not be 2D plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
end
|
|
# Contour 2d plot for TrIQ
|
|
@onbutton triqCPlot begin
|
|
msg="Image 2D plot selected"
|
|
cleaned_imgIntT=replace(imgIntT, r"\?.*" => "")
|
|
cleaned_imgIntT=lstrip(cleaned_imgIntT, '/')
|
|
var=joinpath("./public", cleaned_imgIntT)
|
|
|
|
if isfile(var)
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
try
|
|
img=load(var)
|
|
# Convert to grayscale
|
|
img_gray=Gray.(img)
|
|
img_array=Array(img_gray)
|
|
elevation=Float32.(Array(img_gray)) ./ 255.0 # Normalize between 0 and 1
|
|
|
|
# Smooth the image
|
|
sigma=3.0
|
|
kernel=Kernel.gaussian(sigma)
|
|
elevation_smoothed=imfilter(elevation, kernel)
|
|
|
|
# Create the X, Y meshgrid coordinates
|
|
x=1:size(elevation_smoothed, 2)
|
|
y=1:size(elevation_smoothed, 1)
|
|
X=repeat(reshape(x, 1, length(x)), length(y), 1)
|
|
Y=repeat(reshape(y, length(y), 1), 1, length(x))
|
|
|
|
layoutContour=PlotlyBase.Layout(
|
|
title="2D Topographic Map",
|
|
xaxis_title="X",
|
|
yaxis_title="Y",
|
|
|
|
)
|
|
traceContour=PlotlyBase.contour(
|
|
z=elevation_smoothed,
|
|
x=X[1, :], # Use the first row
|
|
y=-Y[:, 1], # Use the first column
|
|
contours_coloring="Viridis",
|
|
colorscale="Viridis"
|
|
)
|
|
plotdataC=[traceContour]
|
|
plotlayoutC=layoutContour
|
|
|
|
spectraMz=nothing # Important for memory cleaning
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab3"
|
|
msg="Plot loaded."
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
println(msg)
|
|
end
|
|
else
|
|
msg="Image could not be 2D plotted"
|
|
warning_msg=true
|
|
end
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
end
|
|
|
|
@onbutton CompareBtn begin
|
|
CompareDialog=true
|
|
end
|
|
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
end
|
|
# == Pages ==
|
|
# Register a new route and the page that will be loaded on access
|
|
@page("/", "app.jl.html")
|
|
end
|
|
|
|
# == Advanced features ==
|
|
#=
|
|
- The @private macro defines a reactive variable that is not sent to the browser.
|
|
This is useful for storing data that is unique to each user session but is not needed
|
|
in the UI.
|
|
@private table=DataFrame(a=1:10, b=10:19, c=20:29)
|
|
|
|
=#
|
|
|