Added plot interaction to the UI, improved boot loading, modified UI to accomodate for these changes
This commit is contained in:
Pixelguy14
parent
bf50d0cb0c
commit
09e4a015e0
@ -242,9 +242,9 @@ version = "0.4.1"
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[[deps.ColorSchemes]]
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deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
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git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b"
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git-tree-sha1 = "26ec26c98ae1453c692efded2b17e15125a5bea1"
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uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
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version = "3.27.1"
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version = "3.28.0"
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[[deps.ColorTypes]]
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deps = ["FixedPointNumbers", "Random"]
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@ -525,9 +525,9 @@ version = "0.3.2"
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[[deps.FFTW]]
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deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
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git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d"
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git-tree-sha1 = "7de7c78d681078f027389e067864a8d53bd7c3c9"
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uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
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version = "1.8.0"
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version = "1.8.1"
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[[deps.FFTW_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
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@ -708,15 +708,15 @@ uuid = "5c4fdc26-39e3-47cf-9034-e533e09961c2"
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version = "1.1.0"
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[[deps.GeoFormatTypes]]
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git-tree-sha1 = "ce573eab15760315756de2c82df7406c870c7187"
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git-tree-sha1 = "8e233d5167e63d708d41f87597433f59a0f213fe"
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uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f"
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version = "0.4.3"
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version = "0.4.4"
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[[deps.GeoInterface]]
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deps = ["DataAPI", "Extents", "GeoFormatTypes"]
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git-tree-sha1 = "f4ee66b6b1872a4ca53303fbb51d158af1bf88d4"
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git-tree-sha1 = "294e99f19869d0b0cb71aef92f19d03649d028d5"
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uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
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version = "1.4.0"
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version = "1.4.1"
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[[deps.GeometryBasics]]
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deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "PrecompileTools", "Random", "StaticArrays"]
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@ -814,9 +814,9 @@ version = "0.5.0"
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[[deps.HypergeometricFunctions]]
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deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
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git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9"
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git-tree-sha1 = "2bd56245074fab4015b9174f24ceba8293209053"
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uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
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version = "0.3.25"
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version = "0.3.27"
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[[deps.HypertextLiteral]]
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deps = ["Tricks"]
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@ -933,9 +933,9 @@ version = "0.10.1"
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[[deps.Images]]
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deps = ["Base64", "FileIO", "Graphics", "ImageAxes", "ImageBase", "ImageBinarization", "ImageContrastAdjustment", "ImageCore", "ImageCorners", "ImageDistances", "ImageFiltering", "ImageIO", "ImageMagick", "ImageMetadata", "ImageMorphology", "ImageQualityIndexes", "ImageSegmentation", "ImageShow", "ImageTransformations", "IndirectArrays", "IntegralArrays", "Random", "Reexport", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "TiledIteration"]
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git-tree-sha1 = "12fdd617c7fe25dc4a6cc804d657cc4b2230302b"
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git-tree-sha1 = "a49b96fd4a8d1a9a718dfd9cde34c154fc84fcd5"
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uuid = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
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version = "0.26.1"
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version = "0.26.2"
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[[deps.Imath_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl"]
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@ -980,9 +980,9 @@ version = "0.1.6"
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[[deps.IntelOpenMP_jll]]
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deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"]
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git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e"
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git-tree-sha1 = "0f14a5456bdc6b9731a5682f439a672750a09e48"
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uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
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version = "2024.2.1+0"
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version = "2025.0.4+0"
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[[deps.InteractiveUtils]]
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deps = ["Markdown"]
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@ -1350,9 +1350,9 @@ version = "0.1.4"
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[[deps.MKL_jll]]
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deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"]
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git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f"
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git-tree-sha1 = "5de60bc6cb3899cd318d80d627560fae2e2d99ae"
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uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
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version = "2024.2.0+0"
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version = "2025.0.1+1"
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[[deps.MacroTools]]
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git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472"
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@ -1459,9 +1459,9 @@ version = "1.2.1"
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[[deps.NaNMath]]
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deps = ["OpenLibm_jll"]
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git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71"
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git-tree-sha1 = "fe891aea7ccd23897520db7f16931212454e277e"
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uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
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version = "1.0.3"
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version = "1.1.1"
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[[deps.NativeFileDialog]]
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deps = ["FilePathsBase", "NativeFileDialog_jll"]
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@ -1921,9 +1921,9 @@ version = "1.3.0"
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[[deps.Revise]]
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deps = ["CodeTracking", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "REPL", "Requires", "UUIDs", "Unicode"]
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git-tree-sha1 = "b5e7c125687aa818de948ef8a0b9dc59f043342c"
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git-tree-sha1 = "9bb80533cb9769933954ea4ffbecb3025a783198"
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uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
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version = "3.7.1"
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version = "3.7.2"
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weakdeps = ["Distributed"]
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[deps.Revise.extensions]
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18
README.md
18
README.md
@ -9,20 +9,16 @@ A Graphical User Interface for IMS in Julia: https://github.com/CINVESTAV-LABI/j
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unzip the file in your desired location<br>
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## Load User Interface
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1. Launch Julia in your terminal using:
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1. Set working directory to Julia_msi_GUI (this repository) in your terminal using:
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```
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julia
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cd PathToRepository/Julia_msi_GUI-main
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```
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2. Set working directory to Julia_msi_GUI (this repository) code using:
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2. Launch the Julia project in your terminal using:
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```
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cd("PathToRepository/Julia_msi_GUI-main")
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julia --project=. start_MSI_GUI.jl
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```
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3. With the active directory being Julia_msi_GUI run the next script:
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3. Alternatively, you can open a terminal in the path of the repository and run the command and skip the next step:
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```
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include("start_MSI_GUI.jl")
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julia --project=. start_MSI_GUI.jl
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```
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4. Alternatively, you can open a terminal in the path of the repository and run the command and skip the next step:
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```
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julia start_MSI_GUI.jl
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```
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5. After the script has finished loading, it should open a page in your browser with the web app running.
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4. After the script has finished loading, it should open a page (http://127.0.0.1:1481/) in your browser with the web app running.
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248
app.jl
248
app.jl
@ -55,14 +55,22 @@ end
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# variables must be initialized with constant values, or variables defined outside of the @app block
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#@out test="/test.bmp" #slash means it's getting the info from 'public' folder
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# Interface non Variables
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@out warning_fr=""
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## Interface non Variables
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@out btnStartDisable=true
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@out btnPlotDisable=false
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@out btnSpectraDisable=true
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# Loading animations
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@in progress=false
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@in progressPlot=false
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@in progressSpectraPlot=false
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# Text field validations
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@in triqEnabled=false
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@in SpectraEnabled=false
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# Dialogs
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@in warning_msg=false
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@in CompareDialog=false
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# Interface Variables
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## Interface Variables
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@in file_route=""
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@in file_name=""
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@in Nmass=0.0
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@ -70,24 +78,23 @@ end
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@in triqProb=0.98
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@in triqColor=256
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# Interface Buttons and Validations
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## Interface Buttons
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@in btnSearch=false # To search for files in your device
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@in mainProcess=false # To generate images
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@in compareBtn=false # To open dialog
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@in createSumPlot=false # To generate sum spectrum plot
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@in createXYPlot=false # To generate an spectrum plot according to the xy values inputed
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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 imageCPlot=false # To generate contour plots of current image
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@in triqCPlot=false # To generate contour plots of 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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# Image change buttons
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@in imgPlus=false
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@in imgMinus=false
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@in imgPlusT=false
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@in imgMinusT=false
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# TAB variables
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## Tabulation variables
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@out tabIDs=["tab0","tab1","tab2","tab3","tab4"]
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@out tabLabels=["Image", "TrIQ", "Spectrum Plot", "Topology Plot","Surface Plot"]
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@in selectedTab="tab0"
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@ -100,8 +107,10 @@ end
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@out imgIntT="/.bmp" # image Interface TrIQ
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@out colorbar="/.png"
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@out colorbarT="/.png"
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@out img_width=0
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@out img_height=0
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# Messages to interface Variables
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# Messages to interface variables
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@out msg=""
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@out msgimg=""
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@out msgtriq=""
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@ -126,11 +135,12 @@ end
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@out current_triq=""
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@out current_col_triq=""
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# Starting and finishing times to measure how long it takes for a function to finish in elapse time
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## Time measurement variables
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@out sTime=time()
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@out fTime=time()
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@out eTime=time()
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## Plots
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# Interface Plot Spectrum
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layoutSpectra=PlotlyBase.Layout(
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title="SUM Spectrum plot",
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@ -148,6 +158,10 @@ end
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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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@in xCoord=0
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@in yCoord=0
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@out xSpectraMz=Float64[]
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@out ySpectraMz=Float64[]
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# Interactive plot reactions
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@in data_click=Dict{String,Any}()
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@ -159,12 +173,11 @@ end
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title="2D Topographic Map",
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xaxis=PlotlyBase.attr(
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title="X",
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showgrid=true
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scaleanchor="y"
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),
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yaxis=PlotlyBase.attr(
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title="Y",
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showgrid=true
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)
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title="Y"
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),
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)
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# Dummy 2D surface plot
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traceContour=PlotlyBase.scatter(x=[], y=[], mode="lines")
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@ -218,10 +231,12 @@ end
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#println("Selected file path: ", full_route)
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btnStartDisable=false
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btnPlotDisable=false
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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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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)
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# We enable coord search and spectra plot creation
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btnSpectraDisable=false
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SpectraEnabled=true
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end
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end
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end
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@ -229,6 +244,7 @@ end
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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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btnPlotDisable=true
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btnSpectraDisable=true
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text_nmass=replace(string(Nmass), "." => "_")
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sTime=time()
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#full_route=joinpath(file_route, file_name)
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@ -254,6 +270,8 @@ end
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img=reverse(permutedims(img, (2, 1)), dims=1)
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end
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flipped_img=reverse(img, dims=1)
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img_width=size(flipped_img, 2)
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img_height=size(flipped_img, 1)
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save(image_path, flipped_img)
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# Use timestamp to refresh image interface container
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imgIntT="/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
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@ -286,6 +304,8 @@ end
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img=reverse(permutedims(img, (2, 1)), dims=1)
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end
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flipped_img=reverse(img, dims=1)
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img_width=size(flipped_img, 2)
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img_height=size(flipped_img, 1)
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save(image_path, flipped_img)
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# Use timestamp to refresh image interface container
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imgInt="/MSI_$(text_nmass).bmp?t=$(timestamp)"
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@ -325,6 +345,11 @@ end
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end
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btnStartDisable=false
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btnPlotDisable=false
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if isfile(full_routeMz)
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# We enable coord search and spectra plot creation
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btnSpectraDisable=false
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SpectraEnabled=true
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end
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progress=false
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end
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@ -332,12 +357,8 @@ end
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msg="Sum spectrum plot selected"
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sTime=time()
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#full_route=joinpath( file_route, file_name )
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if isfile(full_route) # Check if the file exists
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btnPlotDisable=false
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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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progressPlot=true
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if isfile(full_routeMz) # Check if the file exists
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progressSpectraPlot=true
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btnPlotDisable=true
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btnStartDisable=true
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msg="Loading plot..."
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@ -347,20 +368,20 @@ end
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xaxis=PlotlyBase.attr(
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title="<i>m/z</i>",
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showgrid=true
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),
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yaxis=PlotlyBase.attr(
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title="Intensity",
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showgrid=true
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)
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),
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autosize=false
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)
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# dims=size(spectraMz)
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# scansMax=dims[2] # we get the total of scansMax
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# traceSpectra=PlotlyBase.scatter(x=spectraMz[1, 1], y=spectraMz[2, 1], mode="lines")
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traceSpectra=PlotlyBase.scatter(x=mean(spectraMz[1,:]), y=mean(spectraMz[2,:]), mode="lines")
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xSpectraMz=mean(spectraMz[1,:])
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ySpectraMz=mean(spectraMz[2,:])
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traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
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plotdata=[traceSpectra] # We add the data from spectra to the plot
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plotlayout=layoutSpectra
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spectraMz=nothing # Important for memory cleaning
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GC.gc() # Trigger garbage collection
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if Sys.islinux()
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ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
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@ -369,18 +390,68 @@ end
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fTime=time()
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eTime=round(fTime-sTime,digits=3)
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msg="Plot loaded in $(eTime) seconds"
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full_routeMz2=full_routeMz # To avoid creating the plot if its the same file read as before
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else
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msg="the mzML file was not found or you're trying to load the same mzML"
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msg="there was an error with the mzML, please try again"
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warning_msg=true
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end
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else
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msg="is not an imzML file"
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warning_msg=true
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end
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progressPlot=false
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progressSpectraPlot=false
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btnPlotDisable=false
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btnStartDisable=false
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if isfile(full_routeMz)
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# We enable coord search and spectra plot creation
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btnSpectraDisable=false
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SpectraEnabled=true
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end
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end
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@onbutton createXYPlot begin
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msg="Sum spectrum plot selected"
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sTime=time()
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#full_route=joinpath( file_route, file_name )
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if isfile(full_routeMz) # Check if the file exists
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progressSpectraPlot=true
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btnStartDisable=true
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btnPlotDisable=true
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btnSpectraDisable=true
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msg="Loading plot..."
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spectraMz=LoadMzml(full_routeMz)
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layoutSpectra=PlotlyBase.Layout(
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title="($xCoord, $yCoord) Specific spectrum plot",
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xaxis=PlotlyBase.attr(
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title="<i>m/z</i>",
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showgrid=true
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),
|
||||
yaxis=PlotlyBase.attr(
|
||||
title="Intensity",
|
||||
showgrid=true
|
||||
),
|
||||
autosize=false
|
||||
)
|
||||
xSpectraMz=spectraMz[1,abs(xCoord)]
|
||||
ySpectraMz=spectraMz[2,abs(yCoord)]
|
||||
traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines")
|
||||
plotdata=[traceSpectra] # We add the data from spectra to the plot
|
||||
plotlayout=layoutSpectra
|
||||
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"
|
||||
fTime=time()
|
||||
eTime=round(fTime-sTime,digits=3)
|
||||
msg="Plot loaded in $(eTime) seconds"
|
||||
else
|
||||
msg="there was an error with the mzML or the coordenates, please try again"
|
||||
warning_msg=true
|
||||
end
|
||||
progressSpectraPlot=false
|
||||
btnPlotDisable=false
|
||||
btnStartDisable=false
|
||||
if isfile(full_routeMz)
|
||||
# We enable coord search and spectra plot creation
|
||||
btnSpectraDisable=false
|
||||
SpectraEnabled=true
|
||||
end
|
||||
end
|
||||
|
||||
# Image loaders based on the position of the current image (increment and decrement for both normal and filter)
|
||||
@ -454,8 +525,8 @@ end
|
||||
|
||||
current_triq=new_msi
|
||||
current_col_triq=new_col_msi
|
||||
imgIntT="/$(current_triq)"
|
||||
colorbarT="/$(current_col_triq)"
|
||||
imgIntT="/$(current_triq)?t=$(timestamp)"
|
||||
colorbarT="/$(current_col_triq)?t=$(timestamp)"
|
||||
|
||||
text_nmass=replace(current_triq, "TrIQ_" => "")
|
||||
text_nmass=replace(text_nmass, ".bmp" => "")
|
||||
@ -474,6 +545,7 @@ end
|
||||
progressPlot=true
|
||||
btnPlotDisable=true
|
||||
btnStartDisable=true
|
||||
btnSpectraDisable=true
|
||||
try
|
||||
img=load(var)
|
||||
#println("Image type:", typeof(img))
|
||||
@ -528,7 +600,6 @@ end
|
||||
), 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
|
||||
@ -549,6 +620,11 @@ end
|
||||
progressPlot=false
|
||||
btnPlotDisable=false
|
||||
btnStartDisable=false
|
||||
if isfile(full_routeMz)
|
||||
# We enable coord search and spectra plot creation
|
||||
btnSpectraDisable=false
|
||||
SpectraEnabled=true
|
||||
end
|
||||
end
|
||||
# 3d plot for TrIQ
|
||||
@onbutton triq3dPlot begin
|
||||
@ -562,6 +638,7 @@ end
|
||||
progressPlot=true
|
||||
btnPlotDisable=true
|
||||
btnStartDisable=true
|
||||
btnSpectraDisable=true
|
||||
try
|
||||
img=load(var)
|
||||
img_gray=Gray.(img) # Convert to grayscale
|
||||
@ -610,7 +687,6 @@ end
|
||||
), 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
|
||||
@ -631,6 +707,11 @@ end
|
||||
progressPlot=false
|
||||
btnPlotDisable=false
|
||||
btnStartDisable=false
|
||||
if isfile(full_routeMz)
|
||||
# We enable coord search and spectra plot creation
|
||||
btnSpectraDisable=false
|
||||
SpectraEnabled=true
|
||||
end
|
||||
end
|
||||
|
||||
# Contour 2d plot
|
||||
@ -645,6 +726,7 @@ end
|
||||
progressPlot=true
|
||||
btnPlotDisable=true
|
||||
btnStartDisable=true
|
||||
btnSpectraDisable=true
|
||||
try
|
||||
img=load(var)
|
||||
# Convert to grayscale
|
||||
@ -665,8 +747,13 @@ end
|
||||
|
||||
layoutContour=PlotlyBase.Layout(
|
||||
title="2D Topographic Map",
|
||||
xaxis_title="X",
|
||||
yaxis_title="Y"
|
||||
xaxis=PlotlyBase.attr(
|
||||
title="X",
|
||||
scaleanchor="y"
|
||||
),
|
||||
yaxis=PlotlyBase.attr(
|
||||
title="Y"
|
||||
),
|
||||
)
|
||||
traceContour=PlotlyBase.contour(
|
||||
z=elevation_smoothed,
|
||||
@ -677,8 +764,6 @@ end
|
||||
)
|
||||
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
|
||||
@ -699,6 +784,11 @@ end
|
||||
progressPlot=false
|
||||
btnPlotDisable=false
|
||||
btnStartDisable=false
|
||||
if isfile(full_routeMz)
|
||||
# We enable coord search and spectra plot creation
|
||||
btnSpectraDisable=false
|
||||
SpectraEnabled=true
|
||||
end
|
||||
end
|
||||
# Contour 2d plot for TrIQ
|
||||
@onbutton triqCPlot begin
|
||||
@ -712,6 +802,7 @@ end
|
||||
progressPlot=true
|
||||
btnPlotDisable=true
|
||||
btnStartDisable=true
|
||||
btnSpectraDisable=true
|
||||
try
|
||||
img=load(var)
|
||||
# Convert to grayscale
|
||||
@ -732,8 +823,13 @@ end
|
||||
|
||||
layoutContour=PlotlyBase.Layout(
|
||||
title="2D Topographic Map",
|
||||
xaxis_title="X",
|
||||
yaxis_title="Y"
|
||||
xaxis=PlotlyBase.attr(
|
||||
title="X",
|
||||
scaleanchor="y"
|
||||
),
|
||||
yaxis=PlotlyBase.attr(
|
||||
title="Y"
|
||||
),
|
||||
)
|
||||
traceContour=PlotlyBase.contour(
|
||||
z=elevation_smoothed,
|
||||
@ -744,8 +840,6 @@ end
|
||||
)
|
||||
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
|
||||
@ -766,19 +860,67 @@ end
|
||||
progressPlot=false
|
||||
btnPlotDisable=false
|
||||
btnStartDisable=false
|
||||
if isfile(full_routeMz)
|
||||
# We enable coord search and spectra plot creation
|
||||
btnSpectraDisable=false
|
||||
SpectraEnabled=true
|
||||
end
|
||||
end
|
||||
|
||||
@onbutton compareBtn begin
|
||||
CompareDialog=true
|
||||
# We remove the red lines
|
||||
traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines",name="Spectra",showlegend=false)
|
||||
plotdata=[traceSpectra]
|
||||
end
|
||||
|
||||
|
||||
# Event detection for clicking on the spectrum plot
|
||||
@onchange data_click begin
|
||||
println("Clicked data on sum spectrum plot : ", data_click)
|
||||
# Now it needs to compare if there is a value from the spectrum close (to make sure it does not select invalid m/z)
|
||||
# and then, add it to the mass-to-charge ratio of interest input to the frontend to ease with inputs
|
||||
# optional: red line signaling which m/z got selected in the spectrum plot
|
||||
if !isempty(xSpectraMz)
|
||||
#println("Clicked data on sum spectrum plot : ", data_click)
|
||||
spectracoords=reshape(plotdata, 1, length(plotdata))
|
||||
#println("Spectra: $(ndims(spectracoords))")
|
||||
# Extract x and y values from data_click
|
||||
cursor_data=data_click["cursor"]
|
||||
x_value = cursor_data["x"]
|
||||
y_value = cursor_data["y"] # Get the x and y values from the click of the cursor
|
||||
closest_distance = Inf
|
||||
|
||||
for val in spectracoords
|
||||
# Find the index where x is within a range
|
||||
start_idx = findfirst(x -> x >= x_value - 10, val[:x])
|
||||
end_idx = findlast(x -> x <= x_value + 10, val[:x])
|
||||
|
||||
# Ensure the index are valid and within range
|
||||
if start_idx !== nothing && end_idx !== nothing
|
||||
for i in start_idx:end_idx
|
||||
spectra_x = val[:x][i]
|
||||
spectra_y = val[:y][i]
|
||||
distance = sqrt((spectra_x - x_value)^2 + (spectra_y - y_value)^2) # Calculate distance
|
||||
if distance < closest_distance
|
||||
closest_distance = distance
|
||||
Nmass = round(spectra_x, digits=2)
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
layoutSpectra=PlotlyBase.Layout(
|
||||
title="SUM Spectrum plot",
|
||||
xaxis=PlotlyBase.attr(
|
||||
title="<i>m/z</i>",
|
||||
showgrid=true
|
||||
),
|
||||
yaxis=PlotlyBase.attr(
|
||||
title="Intensity",
|
||||
showgrid=true
|
||||
),
|
||||
autosize=false
|
||||
)
|
||||
traceSpectra=PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, mode="lines",name="Spectra",showlegend=false)
|
||||
trace2=PlotlyBase.scatter(x=[Nmass, Nmass],y=[0, maximum(ySpectraMz)],mode="lines",line=attr(color="red", width=0.5),name="<i>m/z</i> selected",showlegend=false)
|
||||
plotdata=[traceSpectra,trace2] # We add the data from spectra and the red line to the plot
|
||||
plotlayout=layoutSpectra
|
||||
end
|
||||
end
|
||||
|
||||
# WIP add an x and y input and a plot to select pixels in an image and then calculate a plot (not the sum of plots)
|
||||
|
||||
143
app.jl.html
143
app.jl.html
@ -3,42 +3,31 @@
|
||||
<img src="/css/LABI_logo.jpeg" alt="Labi Logo Icon" id="imgLogo">
|
||||
<div>
|
||||
<h4>Julia mzML imzML analysis GUI </h4>
|
||||
<h6>Please make sure the ibd, the mzML and the imzML files are located in the same directory and have the same name.</h6>
|
||||
<h6>Please make sure the ibd, the mzML and the imzML files are located in the same directory and have the same
|
||||
name.</h6>
|
||||
<h6>It may take a while to generate the image and the plot, please be patient.</h6>
|
||||
<h6>To generate the contour or surface plots, you have to select the desired image first using the interface.</h6>
|
||||
</div>
|
||||
</header>
|
||||
<div id="extDivStyle" class="row col-12 q-pa-xl">
|
||||
<div class="row col-7">
|
||||
<div class="row col-6">
|
||||
<!-- Left DIV -->
|
||||
<div id="intDivStyle" class="st-col col-12 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>-->
|
||||
<h6>Search for your imzML file in your device</h6>
|
||||
<q-btn id="btnStyle" icon="search" class="q-ma-sm" v-on:click="btnSearch=true" label="Search in your device for the imzML file"></q-btn>
|
||||
<q-btn id="btnStyle" icon="search" class="q-ma-sm" v-on:click="btnSearch=true"
|
||||
label="Search in your device for the imzML file"></q-btn>
|
||||
<!--<p>{{full_route}}</p>-->
|
||||
<div class="row st-col col-12">
|
||||
<!--<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="q-ma-sm"
|
||||
:loading="progressPlot"
|
||||
:disable="btnPlotDisable"
|
||||
label="Generate Plots"
|
||||
icon="play_arrow"
|
||||
>
|
||||
<q-btn-dropdown id="btnStyle" class="q-ma-sm" :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="imageCPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Image Contour Plot</q-item-label>
|
||||
@ -65,47 +54,97 @@
|
||||
</q-list>
|
||||
</q-btn-dropdown>
|
||||
</div>
|
||||
<p id="lblFullRoute">full route: {{full_route}} {{warning_fr}}</p>
|
||||
<p id="lblFullRoute">full route: {{full_route}}</p>
|
||||
<!-- Variable Manipulation -->
|
||||
<div class="row">
|
||||
<div class="st-col col-12 col-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 && val <= 2000.0 || 'Need positive mass values',]"></q-input>
|
||||
<div class="st-col col-12 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 && 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" 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 class="st-col col-12 col-sm q-ma-sm">
|
||||
<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">
|
||||
<div class="st-col col-12 col-sm">
|
||||
<q-toggle id="btnEnableTriq" v-on:click="triqEnabled" v-model="triqEnabled" color="blue" label="Add Threshold Intensity Quantization (TrIQ)!"></q-toggle>
|
||||
</div>
|
||||
</div>
|
||||
<!-- Triq Variable Manipulation -->
|
||||
<div class="col-6">
|
||||
<div class="st-col col-6 col-sm q-ma-sm">
|
||||
<q-toggle id="btnEnableTriq" v-on:click="triqEnabled" v-model="triqEnabled" color="blue"
|
||||
label="Add Threshold Intensity Quantization (TrIQ)!"></q-toggle>
|
||||
</div>
|
||||
<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" label="TrIQ probability" type="number" :rules="[
|
||||
<div class="st-col col-4 col-sm-4 q-ma-sm">
|
||||
<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" label="TrIQ color levels" type="number" :rules="[
|
||||
<div class="st-col col-4 col-sm-4 q-ma-sm">
|
||||
<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>
|
||||
</div>
|
||||
<!-- Spectra Plot Manipulation -->
|
||||
<div class="col-6">
|
||||
<div class="st-col col-6 col-sm">
|
||||
<q-btn-dropdown id="btnStyle" class="q-ma-sm" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
|
||||
label="Generate Spectra" 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="createXYPlot=true">
|
||||
<q-item-section>
|
||||
<q-item-label>Spectrum Plot (X,Y)</q-item-label>
|
||||
</q-item-section>
|
||||
</q-item>
|
||||
</q-list>
|
||||
</q-btn-dropdown>
|
||||
</div>
|
||||
<div class="row col-6">
|
||||
<div class="st-col col-4 col-sm-4 q-ma-sm">
|
||||
<q-input standout="custom-standout" step="1" v-model="xCoord" label="X coord"
|
||||
type="number" :rules="[
|
||||
val => SpectraEnabled ? ( '* Required', val >= 0|| 'Needs to be bigger than 0') : true
|
||||
]" :readonly="!SpectraEnabled" :disable="!SpectraEnabled"></q-input>
|
||||
</div>
|
||||
<div class="st-col col-4 col-sm-4 q-ma-sm">
|
||||
<q-input standout="custom-standout" step="1" v-model="yCoord" label="Y coord"
|
||||
type="number" :rules="[
|
||||
val => SpectraEnabled ? ( '* Required', val <= 0|| 'Needs to be lower than 0') : true
|
||||
]" :readonly="!SpectraEnabled" :disable="!SpectraEnabled"></q-input>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="row">
|
||||
<q-btn id="btnStyle" :loading="progress" class="q-ma-sm" :disabled="btnStartDisable" icon="play_arrow" v-on:click="mainProcess=true" padding="lg" label="Main process">
|
||||
<q-btn id="btnStyle" :loading="progress" class="q-ma-sm" :disabled="btnStartDisable" icon="play_arrow"
|
||||
v-on:click="mainProcess=true" padding="lg" label="Main process">
|
||||
<template v-slot:loading>
|
||||
<q-spinner-hourglass class="on-left" />
|
||||
Loading...
|
||||
</template>
|
||||
</q-btn>
|
||||
<q-btn id="btnStyle" icon="zoom_out_map" class="q-ma-sm on-right" v-on:click="compareBtn=true" padding="sm" label="Compare"></q-btn>
|
||||
<q-btn id="btnStyle" icon="zoom_out_map" class="q-ma-sm on-right" v-on:click="compareBtn=true" padding="sm"
|
||||
label="Compare"></q-btn>
|
||||
</div>
|
||||
<p>{{msg}}</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="row col-5">
|
||||
<div class="row col-6">
|
||||
<!-- Right DIV -->
|
||||
<div id="intDivStyle" class="st-col col-12 col-sm st-module">
|
||||
<st-tabs id="tabHeader" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab" no-arrows></st-tabs>
|
||||
@ -119,11 +158,11 @@
|
||||
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlus=true"></q-btn>
|
||||
</div>
|
||||
<!-- Image manager -->
|
||||
<div id="image-container" class="row st-col col-12 items-center">
|
||||
<div class="st-col col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" fit="scale-down"></q-img>
|
||||
<div id="image-container" class="row st-col col-12">
|
||||
<div class="col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" width="80%"></q-img>
|
||||
</div>
|
||||
<div class="st-col col-2">
|
||||
<div class="col-2">
|
||||
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
|
||||
</div>
|
||||
</div>
|
||||
@ -139,9 +178,9 @@
|
||||
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusT=true"></q-btn>
|
||||
</div>
|
||||
<!-- Triq Image manager -->
|
||||
<div id="image-container" class="row st-col col-12 items-center">
|
||||
<div id="image-container" class="row st-col col-12">
|
||||
<div class="col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" fit="scale-down"></q-img>
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" width="80%"></q-img>
|
||||
</div>
|
||||
<div class="col-2">
|
||||
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
|
||||
@ -149,11 +188,14 @@
|
||||
</div>
|
||||
<p>{{msgtriq}}</p>
|
||||
</q-tab-panel>
|
||||
|
||||
<q-tab-panel name="tab2">
|
||||
<!-- Content for Tab 2 -->
|
||||
<!--<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>-->
|
||||
<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" @click="data_click" class="q-pa-none q-ma-none sync_data"></plotly>
|
||||
<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" @click="data_click"
|
||||
class="q-pa-none q-ma-none sync_data"></plotly>
|
||||
</q-tab-panel>
|
||||
|
||||
<q-tab-panel name="tab3">
|
||||
<!-- Content for Tab 3 -->
|
||||
<plotly id="plotStyle" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
|
||||
@ -202,9 +244,9 @@
|
||||
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlus=true"></q-btn>
|
||||
</div>
|
||||
<!-- Image manager -->
|
||||
<div id="image-container" class="row st-col col-12 items-center">
|
||||
<div id="image-container" class="row st-col col-12">
|
||||
<div class="st-col col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" fit="scale-down"></q-img>
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" width="80%"></q-img>
|
||||
</div>
|
||||
<div class="st-col col-2">
|
||||
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
|
||||
@ -221,9 +263,9 @@
|
||||
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusT=true"></q-btn>
|
||||
</div>
|
||||
<!-- Triq Image manager -->
|
||||
<div id="image-container" class="row st-col col-12 items-center">
|
||||
<div id="image-container" class="row st-col col-12">
|
||||
<div class="col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" fit="scale-down"></q-img>
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" width="80%"></q-img>
|
||||
</div>
|
||||
<div class="col-2">
|
||||
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
|
||||
@ -246,7 +288,8 @@
|
||||
</q-tab-panels>
|
||||
</div>
|
||||
<div class="col-6">
|
||||
<st-tabs id="tabHeader" :ids="CompTabIDs" :labels="CompTabLabels" v-model="CompSelectedTab" outside-arrows mobile-arrows></st-tabs>
|
||||
<st-tabs id="tabHeader" :ids="CompTabIDs" :labels="CompTabLabels" v-model="CompSelectedTab" outside-arrows
|
||||
mobile-arrows></st-tabs>
|
||||
<q-tab-panels v-model="CompSelectedTab">
|
||||
<q-tab-panel name="tab0">
|
||||
<!-- Content for Tab 0 -->
|
||||
@ -256,9 +299,9 @@
|
||||
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlus=true"></q-btn>
|
||||
</div>
|
||||
<!-- Image manager -->
|
||||
<div id="image-container" class="row st-col col-12 items-center">
|
||||
<div id="image-container" class="row st-col col-12">
|
||||
<div class="st-col col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" fit="scale-down"></q-img>
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgInt" width="80%"></q-img>
|
||||
</div>
|
||||
<div class="st-col col-2">
|
||||
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
|
||||
@ -275,9 +318,9 @@
|
||||
<q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusT=true"></q-btn>
|
||||
</div>
|
||||
<!-- Triq Image manager -->
|
||||
<div id="image-container" class="row st-col col-12 items-center">
|
||||
<div id="image-container" class="row st-col col-12">
|
||||
<div class="col-10">
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" fit="scale-down"></q-img>
|
||||
<q-img id="imgInt" class="q-ma-none q-pa-none" :src="imgIntT" width="80%"></q-img>
|
||||
</div>
|
||||
<div class="col-2">
|
||||
<q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
|
||||
|
||||
@ -4,8 +4,7 @@ PENDING
|
||||
Create function that makes the imzML from mzML files ?
|
||||
Possibility to add multiple imzML to process at once ?
|
||||
Per pixel of image plot creation for spectra
|
||||
Multiple spectra plot types
|
||||
Even faster initial boot and subsectuential boot
|
||||
Add comparison image (rotate, transform, translate, transparency) CURRENTLY ONGOING
|
||||
|
||||
DONE
|
||||
Quicker start for julia GUI
|
||||
@ -19,8 +18,10 @@ DONE
|
||||
3d topology plots for images
|
||||
2d contour plots for images
|
||||
Image flip upside down
|
||||
Tag for time it takes in creating image and creating plots
|
||||
Measure for the time it takes creating image or plot
|
||||
Rotate vertical images
|
||||
Easier input for files
|
||||
TrIQ default values
|
||||
Comparative for two views
|
||||
Even faster initial boot and subsectuential boot
|
||||
Multiple spectra plot types
|
||||
|
||||
@ -1,13 +1,25 @@
|
||||
using Pkg
|
||||
Pkg.activate(".")
|
||||
Pkg.instantiate()
|
||||
Pkg.update()
|
||||
Pkg.gc()
|
||||
Pkg.add("Libz") ; Pkg.add("PlotlyBase") ; Pkg.add("CairoMakie") ; Pkg.add("Colors") ; Pkg.add("Statistics") ; Pkg.add("NaturalSort") ; Pkg.add("GenieFramework") ;Pkg.add("Genie")
|
||||
Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML") # With this we ensure it uses the latest library iteration
|
||||
Pkg.add("Images") ; Pkg.add("LinearAlgebra")
|
||||
Pkg.add("NativeFileDialog")
|
||||
Pkg.add("StipplePlotly")
|
||||
|
||||
packages = [
|
||||
"GenieFramework", "Libz", "PlotlyBase", "CairoMakie", "Colors",
|
||||
"Statistics", "NaturalSort", "Genie",
|
||||
"Images", "LinearAlgebra", "NativeFileDialog", "StipplePlotly"
|
||||
]
|
||||
|
||||
# Check for missing packages
|
||||
for pkg in packages
|
||||
if !(pkg in keys(Pkg.dependencies()))
|
||||
Pkg.add(pkg)
|
||||
end
|
||||
end
|
||||
|
||||
# Add library for mzML imzML from GitHub if missing
|
||||
if !("julia_mzML_imzML" in keys(Pkg.dependencies()))
|
||||
Pkg.add(url="https://github.com/CINVESTAV-LABI/julia_mzML_imzML")
|
||||
end
|
||||
|
||||
using Genie
|
||||
|
||||
@ -27,3 +39,5 @@ Genie.loadapp()
|
||||
@async run(`start $url`) # For Windows
|
||||
end
|
||||
end
|
||||
|
||||
wait()
|
||||
Loading…
x
Reference in New Issue
Block a user