Better image search, 3d images ongoing
This commit is contained in:
Pixelguy14
parent
04f7a107da
commit
e5b796fce0
@ -539,9 +539,9 @@ version = "18.1.7+0"
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[[deps.LZO_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731"
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git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a"
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uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac"
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version = "2.10.2+3"
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version = "2.10.3+0"
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[[deps.LaTeXStrings]]
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git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c"
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@ -630,9 +630,9 @@ version = "1.17.0+1"
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[[deps.Libmount_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0"
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version = "2.40.2+2"
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version = "2.40.3+0"
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[[deps.Libtiff_jll]]
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deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
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@ -642,9 +642,9 @@ version = "4.5.1+1"
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[[deps.Libuuid_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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version = "2.40.2+2"
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version = "2.40.3+0"
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[[deps.Libz]]
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deps = ["BufferedStreams", "Random", "Test"]
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@ -771,9 +771,9 @@ version = "1.0.0"
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[[deps.Nettle_jll]]
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deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl"]
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version = "3.10.0+2"
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version = "3.10.1+0"
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[[deps.NetworkOptions]]
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uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
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@ -1366,9 +1366,9 @@ version = "1.8.6+3"
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[[deps.Xorg_libXau_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a"
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git-tree-sha1 = "e9216fdcd8514b7072b43653874fd688e4c6c003"
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uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec"
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version = "1.0.11+3"
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version = "1.0.12+0"
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[[deps.Xorg_libXcursor_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"]
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@ -1378,9 +1378,9 @@ version = "1.2.3+0"
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[[deps.Xorg_libXdmcp_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "02054ee01980c90297412e4c809c8694d7323af3"
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uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05"
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version = "1.1.4+3"
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version = "1.1.5+0"
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[[deps.Xorg_libXext_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
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@ -1420,9 +1420,9 @@ version = "0.9.11+1"
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[[deps.Xorg_libpthread_stubs_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a"
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git-tree-sha1 = "c57201109a9e4c0585b208bb408bc41d205ac4e9"
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uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74"
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version = "0.1.1+3"
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version = "0.1.2+0"
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[[deps.Xorg_libxcb_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"]
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@ -1486,9 +1486,9 @@ version = "2.39.0+0"
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[[deps.Xorg_xtrans_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e"
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git-tree-sha1 = "6dba04dbfb72ae3ebe5418ba33d087ba8aa8cb00"
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uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
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version = "1.5.0+3"
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version = "1.5.1+0"
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[[deps.YAML]]
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deps = ["Base64", "Dates", "Printf", "StringEncodings"]
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323
app.jl
323
app.jl
@ -8,12 +8,33 @@ using CairoMakie
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using Colors
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using julia_mzML_imzML
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using Statistics
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using NaturalSort
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# using ImageMagick
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@genietools
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# == Code import ==
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# add your data analysis code here or in the lib folder. Code in lib/ will be
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# automatically loaded
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rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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rgb_ViridisPalette = reinterpret(ColorTypes.RGB24, ViridisPalette)
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# == Search functions ==
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function increment_image(current_image, image_list)
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current_index = findfirst(isequal(current_image), image_list)
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if current_index == nothing || current_index == length(image_list) || current_image === ""
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return image_list[length(image_list)] # Return the current image if it's the last one or not found
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else
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return image_list[current_index + 1] # Move to the next image
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end
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end
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function decrement_image(current_image, image_list)
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current_index = findfirst(isequal(current_image), image_list)
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if current_index == nothing || current_index == 1 || current_image === ""
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return image_list[1] # Return the current image if it's the first one or not found
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else
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return image_list[current_index - 1] # Move to the previous image
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end
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end
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# == Reactive code ==
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# reactive code to make the UI interactive
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@ -27,7 +48,7 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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# Interface non Variables
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@out warning_fr = ""
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@out btnStartDisable = false
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@out btnStartDisable = true
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@out btnPlotDisable = true
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@in warning_msg = false
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@ -40,8 +61,10 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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@in triqColor = 0
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# Interface Buttons
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@in Main_Process = false # To generate images
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@in Generate_Plot = false # To generate plot
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@in mainProcess = false # To generate images
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@in createSumPlot = false # To generate sum spectrum plot
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@in image3dPlot = false # To generate 3d plot based on current image
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@in triq3dPlot = false # To generate 3d plot based on current triq image
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@in progress = false
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@in progressPlot = false
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@in triqEnabled = false
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@ -50,12 +73,6 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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@in ImgPlusT = false
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@in ImgMinusT = false
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@out indeximg = 0
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@out indeximgTriq = 0
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@out lastimg = 0
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@out lastimgTriq = 0
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# Interface Images
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@out imgInt = "/.bmp" # image Interface
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@out imgIntT = "/.bmp" # image Interface TrIQ
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@ -70,11 +87,28 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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@out full_routeMz = ""
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@out full_routeMz2 = ""
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# WIP
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@out int_nmass = 0
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@out dec_nmass = 0.0
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# For the creation of images with a more specific mass charge
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@out text_nmass = ""
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# Interface Plot
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# For image search
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# Image lists we apply a filter that searches specific type of images into our public folder, then we sort it in a "numerical" order
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@in msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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@in col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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@in triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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@in col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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# Set current image for the list
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@out current_msi = ""
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@out current_col_msi = ""
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@out current_triq = ""
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@out current_col_triq = ""
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@out indeximg = 0
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@out indeximgTriq = 0
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@out lastimg = 0
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@out lastimgTriq = 0
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# Interface Plot 2d
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layoutSpectra = PlotlyBase.Layout(
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title = "SUM Spectrum plot",
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xaxis = PlotlyBase.attr(
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@ -86,22 +120,42 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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showgrid = true
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)
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)
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# Dummy 2D surface plot
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traceSpectra = PlotlyBase.scatter(x=[], y=[], mode="lines")
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# Create conection to frontend
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@out plotdata = [traceSpectra]
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@out plotlayout = layoutSpectra
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# Interface Plot 3d
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# Define the layout for the 3D plot
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layout3D = PlotlyBase.Layout(
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title = "3D Surface Plot",
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scene = attr(
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xaxis_title = "X",
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yaxis_title = "Y",
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zaxis_title = "Z"
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)
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)
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# Dummy 3D surface plot
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trace3D = PlotlyBase.surface(x=[1:10], y=[1:10], z=[1:10], colorscale="Viridis")
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# Create conection to frontend
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@out plotdata3d = [trace3D]
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@out plotlayout3d = layout3D
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# println("3D trace defined: ", trace3D)
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# == Reactive handlers ==
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# Reactive handlers watch a variable and execute a block of code when its value changes
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# The onbutton handler will set the variable to false after the block is executed
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"""
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@onchange triqEnabled begin
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if !triqEnabled
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#triqProb = 0.0
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#triqColor = 0
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end
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# just in case that they remove an image manually, we use the least intensive button to get all images and re-order them.
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msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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end
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"""
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@onchange file_name begin
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msg = ""
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@ -136,10 +190,11 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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end
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"""
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@onbutton Main_Process begin
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@onbutton mainProcess begin
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progress = true # Start progress button animation
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btnStartDisable = true # We disable the button to avoid multiple requests
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indeximg = floor(Int, Nmass)
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text_nmass = replace(string(Nmass), "." => "_")
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full_route = joinpath(file_route, file_name)
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if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <= 1
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msg = "File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
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@ -155,26 +210,48 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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msg = "Incorrect TrIQ values, please adjust accordingly and try again."
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warning_msg = true
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else
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SaveBitmap(joinpath("public", "TrIQ_$(floor(Int, Nmass)).bmp"),TrIQ(slice, Int(triqColor), triqProb),ViridisPalette)
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SaveBitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"),TrIQ(slice, Int(triqColor), triqProb),ViridisPalette)
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# Use timestamp to refresh image interface container
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imgIntT = "/TrIQ_$(floor(Int, Nmass)).bmp?t=$(timestamp)"
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msgtriq = "TrIQ image with the Nmass of $(floor(Int, Nmass))"
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imgIntT = "/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
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# Get current image
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current_triq = "TrIQ_$(text_nmass).bmp"
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msgtriq = "TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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ticks = round.(range(0, stop = maximum(TrIQ(slice, Int(triqColor), triqProb)), length = 10), digits = 2)
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Colorbar(fig[1, 1], colormap = rgb_ViridisPalette, limits = (0, maximum(TrIQ(slice, Int(triqColor), triqProb))),ticks = ticks, label = "Intensity")
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save("public/colorbar_TrIQ_$(floor(Int, Nmass)).png", fig)
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save("public/colorbar_TrIQ_$(text_nmass).png", fig)
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colorbarT = "/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)"
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# Get current colorbar
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current_col_triq = "colorbar_TrIQ_$(text_nmass).png"
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# We update the directory to include the new placed images.
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triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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msg = "The file has been created successfully inside the 'public' folder of the app."
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colorbarT = "/colorbar_TrIQ_$(floor(Int, Nmass)).png?t=$(timestamp)"
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#println("all msi in folder = ",triq_bmp)
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#println("all col msi in folder= ",col_triq_png)
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end
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else # If we don't use TrIQ
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SaveBitmap(joinpath("public", "MSI_$(floor(Int, Nmass)).bmp"),IntQuant(slice),ViridisPalette)
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SaveBitmap(joinpath("public", "MSI_$(text_nmass).bmp"),IntQuant(slice),ViridisPalette)
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# Use timestamp to refresh image interface container
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imgInt = "/MSI_$(floor(Int, Nmass)).bmp?t=$(timestamp)"
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msgimg = "image with the Nmass of $(floor(Int, Nmass))"
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imgInt = "/MSI_$(text_nmass).bmp?t=$(timestamp)"
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# Get current image
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current_msi = "MSI_$(text_nmass).bmp"
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msgimg = "image with the Nmass of $(replace(text_nmass, "_" => "."))"
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# Create colorbar
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ticks = round.(range(0, stop = maximum(slice), length = 10), digits = 2)
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Colorbar(fig[1, 1], colormap = rgb_ViridisPalette, limits = (0, maximum(slice)),ticks = ticks, label = "Intensity")
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save("public/colorbar_MSI_$(floor(Int, Nmass)).png", fig)
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save("public/colorbar_MSI_$(text_nmass).png", fig)
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colorbar = "/colorbar_MSI_$(text_nmass).png?t=$(timestamp)"
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# Get current colorbar
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current_col_msi = "colorbar_MSI_$(text_nmass).png"
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# We update the directory to include the new placed images.
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msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural)
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col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural)
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msg = "The file has been created successfully inside the 'public' folder of the app."
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colorbar = "/colorbar_MSI_$(floor(Int, Nmass)).png?t=$(timestamp)"
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#println("all msi in folder = ",msi_bmp)
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#println("all col msi in folder= ",col_msi_png)
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end
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catch e
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msg = "There was an error loading the ImzML file, please verify the file accordingly and try again. $(e)"
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@ -194,8 +271,8 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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progress = false
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end
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@onbutton Generate_Plot begin
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msg = ""
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@onbutton createSumPlot begin
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msg = "Sum spectrum plot selected"
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full_route = joinpath( file_route, file_name )
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progressPlot = true
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if isfile(full_route) # Check if the file exists
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@ -203,6 +280,7 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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btnStartDisable = false
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full_routeMz = split( full_route, "." )[1] * ".mzML" # Splitting the route from imzml to mzml so the plotting can work
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if isfile(full_routeMz) && (full_routeMz2 == "" || full_routeMz2 != full_routeMz) # Check if the mzml exists
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println("I'm working as intended")
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btnPlotDisable = true
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msg = "Loading plot..."
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spectraMz = LoadMzml(full_routeMz)
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@ -227,61 +305,146 @@ rgb_ViridisPalette =reinterpret(ColorTypes.RGB24, ViridisPalette)
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progressPlot = false
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end
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# WIP THESE NEED TO CHANGE, A BETTER BLIND SEARCH AND ALLOWANCE FOR DECIMAL IMAGES
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# Also needs to implement timestamp to force reload of image and update if needed.
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# Image loaders based on the position of the current image (increment and decrement for both normal and filter)
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# And a pre-generated list from all image files from /public folder
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@onbutton ImgMinus begin
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indeximg-=1
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||||
while !isfile("public/MSI_$(indeximg).bmp") && indeximg > 0
|
||||
indeximg -= 1
|
||||
end
|
||||
if(indeximg <= 0) # If it doesn't find a lower value image
|
||||
indeximg = lastimg
|
||||
end
|
||||
imgInt = "/MSI_$(indeximg).bmp"
|
||||
colorbar = "/colorbar_MSI_$(indeximg).png"
|
||||
msgimg = "image with the Nmass of $(indeximg)"
|
||||
lastimg = indeximg
|
||||
# Append a query string to force the image to refresh
|
||||
timestamp = string(time_ns())
|
||||
new_msi = decrement_image(current_msi, msi_bmp)
|
||||
new_col_msi = decrement_image(current_col_msi, col_msi_png)
|
||||
|
||||
current_msi = new_msi
|
||||
current_col_msi = new_col_msi
|
||||
imgInt = "/$(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 $(replace(text_nmass, "_" => "."))"
|
||||
end
|
||||
@onbutton ImgPlus begin
|
||||
indeximg+=1
|
||||
while !isfile("public/MSI_$(indeximg).bmp") && indeximg < 2001
|
||||
indeximg += 1
|
||||
end
|
||||
if(indeximg >= 2001)
|
||||
indeximg = lastimg
|
||||
end
|
||||
imgInt = "/MSI_$(indeximg).bmp"
|
||||
colorbar = "/colorbar_MSI_$(indeximg).png"
|
||||
msgimg = "image with the Nmass of $(indeximg)"
|
||||
lastimg = indeximg
|
||||
# Append a query string to force the image to refresh
|
||||
timestamp = string(time_ns())
|
||||
new_msi = increment_image(current_msi, msi_bmp)
|
||||
new_col_msi = increment_image(current_col_msi, col_msi_png)
|
||||
|
||||
current_msi = new_msi
|
||||
current_col_msi = new_col_msi
|
||||
imgInt = "/$(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 $(replace(text_nmass, "_" => "."))"
|
||||
end
|
||||
|
||||
@onbutton ImgMinusT begin
|
||||
indeximgTriq-=1
|
||||
while !isfile("public/TrIQ_$(indeximgTriq).bmp") && indeximgTriq > 0
|
||||
indeximgTriq -= 1
|
||||
end
|
||||
if(indeximgTriq <= 0) # If it doesn't find a lower value image
|
||||
indeximgTriq = lastimgTriq
|
||||
end
|
||||
imgIntT = "/TrIQ_$(indeximgTriq).bmp"
|
||||
colorbarT = "/colorbar_TrIQ_$(indeximgTriq).png"
|
||||
msgtriq = "TrIQ image with the Nmass of $(indeximgTriq)"
|
||||
lastimgTriq = indeximgTriq
|
||||
# Append a query string to force the image to refresh
|
||||
timestamp = string(time_ns())
|
||||
new_msi = decrement_image(current_triq, triq_bmp)
|
||||
new_col_msi = decrement_image(current_col_triq, col_triq_png)
|
||||
|
||||
current_triq = new_msi
|
||||
current_col_triq = new_col_msi
|
||||
imgIntT = "/$(current_triq)?t=$(timestamp)"
|
||||
colorbarT = "/$(current_col_triq)?t=$(timestamp)"
|
||||
|
||||
text_nmass = replace(current_triq, "TrIQ_" => "")
|
||||
text_nmass = replace(text_nmass, ".bmp" => "")
|
||||
msgtriq = "image with the Nmass of $(replace(text_nmass, "_" => "."))"
|
||||
|
||||
end
|
||||
@onbutton ImgPlusT begin
|
||||
indeximgTriq+=1
|
||||
while !isfile("public/TrIQ_$(indeximgTriq).bmp") && indeximgTriq < 2001
|
||||
indeximgTriq += 1
|
||||
end
|
||||
if(indeximgTriq >= 2001)
|
||||
indeximgTriq = lastimgTriq
|
||||
end
|
||||
imgIntT = "/TrIQ_$(indeximgTriq).bmp"
|
||||
colorbarT = "/colorbar_TrIQ_$(indeximgTriq).png"
|
||||
msgtriq = "TrIQ image with the Nmass of $(indeximgTriq)"
|
||||
lastimgTriq = indeximgTriq
|
||||
# Append a query string to force the image to refresh
|
||||
timestamp = string(time_ns())
|
||||
new_msi = increment_image(current_triq, triq_bmp)
|
||||
new_col_msi = increment_image(current_col_triq, col_triq_png)
|
||||
|
||||
current_triq = new_msi
|
||||
current_col_triq = new_col_msi
|
||||
imgIntT = "/$(current_triq)"
|
||||
colorbarT = "/$(current_col_triq)"
|
||||
|
||||
text_nmass = replace(current_triq, "TrIQ_" => "")
|
||||
text_nmass = replace(text_nmass, ".bmp" => "")
|
||||
msgtriq = "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, '/')
|
||||
var1 = joinpath( "public", cleaned_imgInt )
|
||||
if isfile(var1)
|
||||
try
|
||||
img = FileIO.load(File{DataFormat{:BMP}}(var1))
|
||||
img_gray = Gray.(img) # Convert to grayscale
|
||||
img_array = Array(img_gray)
|
||||
catch e
|
||||
msg = "Failed to load and process image: $e"
|
||||
warning_msg = true
|
||||
println(msg)
|
||||
end
|
||||
elevation = img_array / 255.0 # Normalize between 0 and 1
|
||||
# Smooth the image
|
||||
sigma = 4.0
|
||||
elevation_smoothed = imfilter(elevation, Kernel.gaussian(sigma))
|
||||
# Create the X, Y meshgrid coordinates
|
||||
x = 1:size(elevation_smoothed, 2)
|
||||
y = 1:size(elevation_smoothed, 1)
|
||||
X, Y = ndgrid(x, y)
|
||||
trace3D = PlotlyBase.scatter(x = X[1, :], y =Y[:, 1], z=elevation_smoothed, colorscale="Viridis")
|
||||
plotdata3d = [trace3D] # We add the data from the image to the plot
|
||||
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
|
||||
msg = "Plot loaded."
|
||||
else
|
||||
msg = "image could not be 3d plotted"
|
||||
warning_msg = true
|
||||
end
|
||||
end
|
||||
|
||||
@onbutton triq3dPlot begin
|
||||
msg = "TrIQ 3D plot selected"
|
||||
cleaned_imgIntT = replace(imgIntT, r"\?.*" => "")
|
||||
cleaned_imgIntT = lstrip(cleaned_imgIntT, '/')
|
||||
var1 = joinpath( "public", cleaned_imgIntT )
|
||||
if isfile(var1)
|
||||
try
|
||||
img = FileIO.load(File{DataFormat{:BMP}}(var1))
|
||||
img_gray = Gray.(img) # Convert to grayscale
|
||||
img_array = Array(img_gray)
|
||||
catch e
|
||||
msg = "Failed to load and process image: $e"
|
||||
warning_msg = true
|
||||
println(msg)
|
||||
end
|
||||
elevation = img_array / 255.0 # Normalize between 0 and 1
|
||||
# Smooth the image
|
||||
sigma = 4.0
|
||||
elevation_smoothed = imfilter(elevation, Kernel.gaussian(sigma))
|
||||
# Create the X, Y meshgrid coordinates
|
||||
x = 1:size(elevation_smoothed, 2)
|
||||
y = 1:size(elevation_smoothed, 1)
|
||||
X, Y = ndgrid(x, y)
|
||||
trace3D = PlotlyBase.scatter(x = X[1, :], y =Y[:, 1], z=elevation_smoothed, colorscale="Viridis")
|
||||
plotdata3d = [trace3D] # We add the data from the image to the plot
|
||||
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
|
||||
msg = "Plot loaded."
|
||||
else
|
||||
msg = "image could not be 3d plotted"
|
||||
warning_msg = true
|
||||
end
|
||||
end
|
||||
|
||||
GC.gc() # Trigger garbage collection
|
||||
if Sys.islinux()
|
||||
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
||||
|
||||
56
app.jl.html
56
app.jl.html
@ -15,24 +15,50 @@
|
||||
<div id="intDivStyle" class="st-col col-12 col-sm st-module">
|
||||
<!--<q-file v-model="file_route" filled="" label="Select your imzML file" accept=".imzML"></q-file>-->
|
||||
<q-input id="textRoute" standout="custom-standout" v-model="file_route" label="Insert the route to your imzML file"></q-input>
|
||||
<div class="row st-col col-14 col-sm">
|
||||
<q-input id="textName" class="col-8" standout="custom-standout" v-model="file_name" label="Insert the name of your imzML file"></q-input>
|
||||
<q-btn id="btnStyle" class="col-4" :loading="progressPlot" :disabled="btnPlotDisable" icon="play_arrow" v-on:click="Generate_Plot = true">
|
||||
Generate Plot
|
||||
<template v-slot:loading>
|
||||
<q-spinner-hourglass class="on-left" />
|
||||
Loading Plot
|
||||
</template>
|
||||
</q-btn>
|
||||
<div class="row st-col col-12 col-sm">
|
||||
<q-input id="textName" class="col-9" standout="custom-standout" v-model="file_name" label="Insert the name of your imzML file"></q-input>
|
||||
<q-btn-dropdown
|
||||
id="btnStyle"
|
||||
class="col-3"
|
||||
:loading="progressPlot"
|
||||
:disable="btnPlotDisable"
|
||||
label="Generate Plots"
|
||||
icon="play_arrow"
|
||||
>
|
||||
<template v-slot:loading>
|
||||
<q-spinner-hourglass class="on-left" />
|
||||
Loading Plot
|
||||
</template>
|
||||
|
||||
<q-list>
|
||||
<q-item clickable v-close-popup v-on:click="createSumPlot = true">
|
||||
<q-item-section>
|
||||
<q-item-label>Sum Spectrum Plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
|
||||
<q-item clickable v-close-popup v-on:click="image3dPlot = true">
|
||||
<q-item-section>
|
||||
<q-item-label>Image 3D Plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
|
||||
<q-item clickable v-close-popup v-on:click="triq3dPlot = true">
|
||||
<q-item-section>
|
||||
<q-item-label>TrIQ 3D Plot</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
</q-list>
|
||||
</q-btn-dropdown>
|
||||
</div>
|
||||
<p id="lblFullRoute">full route: {{full_route}} {{warning_fr}}</p>
|
||||
<!-- Variable Manipulation -->
|
||||
<div class="row">
|
||||
<div class="st-col col-12 col-sm">
|
||||
<q-input standout="custom-standout" id="textNmass" v-model="Nmass" :dense="true" label="Mass-to-charge ratio of interest" type="number" :rules="[ val => !!val || '* Required', val => val >= 0 && val <= 2000 || 'Need positive mass values',]"></q-input>
|
||||
<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 && val <= 2000.0 || 'Need positive mass values',]"></q-input>
|
||||
</div>
|
||||
<div class="st-col col-12 col-sm">
|
||||
<q-input standout="custom-standout" id="textTol" step="0.01" v-model="Tol" :dense="true" label="Mass-to-charge ratio Tolerance" type="number" :rules="[val => !!val || '* Required', val => val >= 0 && val <= 1 || 'Needs to be in range between 0 and 1',]"></q-input>
|
||||
<q-input standout="custom-standout" id="textTol" step="0.01" v-model="Tol" label="Mass-to-charge ratio Tolerance" type="number" :rules="[val => !!val || '* Required', val => val >= 0.0 && val <= 1.0 || 'Needs to be in range between 0 and 1',]"></q-input>
|
||||
</div>
|
||||
</div>
|
||||
<div class="row">
|
||||
@ -43,17 +69,17 @@
|
||||
<!-- Triq Variable Manipulation -->
|
||||
<div class="row">
|
||||
<div class="st-col col-12 col-sm-8">
|
||||
<q-input standout="custom-standout" id="textTriqProb" step="0.01" v-model="triqProb" :dense="true" label="TrIQ Probability" type="number" :rules="[
|
||||
<q-input standout="custom-standout" id="textTriqProb" step="0.01" v-model="triqProb" label="TrIQ Probability" type="number" :rules="[
|
||||
val => triqEnabled ? ( '* Required', val >= 0 && val <= 1 || 'Needs to be in range between 0 and 1') : true
|
||||
]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
|
||||
</div>
|
||||
<div class="st-col col-12 col-sm-4">
|
||||
<q-input standout="custom-standout" id="textTriqColor" step="1" v-model="triqColor" :dense="true" label="TrIQ Color Levels" type="number" :rules="[
|
||||
<q-input standout="custom-standout" id="textTriqColor" step="1" v-model="triqColor" label="TrIQ Color Levels" type="number" :rules="[
|
||||
val => triqEnabled ? ( '* Required', val >= 0 && val <= 256 || 'Needs to be in range between 1 and 256') : true
|
||||
]" :readonly="!triqEnabled" :disable="!triqEnabled"></q-input>
|
||||
</div>
|
||||
</div>
|
||||
<q-btn id="btnStyle" :loading="progress" :disabled="btnStartDisable" icon="play_arrow" v-on:click="Main_Process = true" padding="lg">
|
||||
<q-btn id="btnStyle" :loading="progress" :disabled="btnStartDisable" icon="play_arrow" v-on:click="mainProcess = true" padding="lg">
|
||||
Start Process
|
||||
<template v-slot:loading>
|
||||
<q-spinner-hourglass class="on-left" />
|
||||
@ -111,7 +137,7 @@
|
||||
</div>
|
||||
<!-- Bottom Right Div -->
|
||||
<div class="st-col col-12 col-sm st-module" >
|
||||
<h1>3d plot goes here</h1>
|
||||
<plotly id="plotStyle3d" :data="plotdata3d" :layout="plotlayout3d" class="st-col col-12 col-sm-12"></plotly>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
@ -1,18 +1,19 @@
|
||||
PENDING
|
||||
|
||||
rmsi julia coherence with image creation
|
||||
Rmsi & julia coherence with image creation and colorbar
|
||||
avoid image enlargement -> CURRENT WIP
|
||||
image rotation?
|
||||
image flip upside down
|
||||
colorbar revamp
|
||||
3d topography for images
|
||||
better blind search for images -> CURRENT WIP
|
||||
multiple plot types?
|
||||
3d topography for images -> CURRENT WIP
|
||||
Multiple plot types
|
||||
|
||||
|
||||
DONE
|
||||
quicker start for julia GUI
|
||||
better UI
|
||||
better style of page
|
||||
more responsiveness
|
||||
Quicker start for julia GUI
|
||||
Better UI
|
||||
refined style of page
|
||||
improved responsiveness
|
||||
UI functionality added
|
||||
code cleaning
|
||||
better code readability
|
||||
Code cleanse
|
||||
better code readability
|
||||
Better blind search for images
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user