1971 lines
81 KiB
Julia
1971 lines
81 KiB
Julia
# app.jl
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module App
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# ==Packages ==
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using GenieFramework # Set up Genie development environment.
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using Pkg
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using Libz
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using PlotlyBase
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using CairoMakie
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using Colors
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using MSI_src # Import the new MSIData library
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using Statistics
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using NaturalSort
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using Images
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using LinearAlgebra
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using NativeFileDialog # Opens the file explorer depending on the OS
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using StipplePlotly
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using Base.Filesystem: mv # To rename files in the system
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using Printf # Required for @sprintf macro in colorbar generation
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using JSON
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using Dates
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# Bring MSIData into App module's scope
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using .MSI_src: MSIData, OpenMSIData, process_spectrum, IterateSpectra, ImzMLSource, _iterate_spectra_fast, MzMLSource, find_mass, ViridisPalette, get_mz_slice, get_multiple_mz_slices, quantize_intensity, save_bitmap, median_filter, save_bitmap, downsample_spectrum, TrIQ, precompute_analytics, ImportMzmlFile, generate_colorbar_image, load_and_prepare_mask
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if !@isdefined(increment_image)
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include("./julia_imzML_visual.jl")
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end
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# --- Memory Validation Logging ---
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if get(ENV, "GENIE_ENV", "dev") != "prod"
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function get_rss_mb()
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if !Sys.islinux()
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return 0.0
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end
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try
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pid = getpid()
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cmd = `ps -p $pid -o rss=`
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rss_kb_str = read(cmd, String)
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rss_kb = parse(Int, strip(rss_kb_str))
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return round(rss_kb / 1024, digits=2)
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catch e
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@warn "Could not get RSS via `ps` command. Error: $e"
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return 0.0
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end
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end
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function log_memory_usage(context::String, msi_data_val)
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rss_mb = get_rss_mb()
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msi_data_size_mb = 0
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if msi_data_val !== nothing
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msi_data_size_mb = round(Base.summarysize(msi_data_val) / (1024^2), digits=2)
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end
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gc_time_s = round(GC.time(), digits=3)
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println("--- MEMORY LOG [$(context)] ---")
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println(" Timestamp: $(now())")
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println(" Process RSS: $(rss_mb) MB")
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println(" msi_data size: $(msi_data_size_mb) MB")
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println(" Cumulative GC time: $(gc_time_s) s")
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println("--------------------------")
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end
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else
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log_memory_usage(context::String, msi_data_val) = nothing # No-op for production
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end
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@genietools
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# == Reactive code ==
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# Reactive code to make the UI interactive
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@app begin
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# == Reactive variables ==
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# reactive variables exist in both the Julia backend and the browser with two-way synchronization
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# @out variables can only be modified by the backend
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# @in variables can be modified by both the backend and the browser
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# variables must be initialized with constant values, or variables defined outside of the @app block
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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=false
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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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@in MFilterEnabled=false
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@in maskEnabled=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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@in file_route=""
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@in file_name=""
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@in Nmass="0.0"
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@in Tol=0.1
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@in triqProb=0.98
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@in colorLevel=20
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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 btnAddBatch = false
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@in clear_batch_btn = false
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@out batch_file_count = 0
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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 createMeanPlot=false # To generate mean 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 createSumPlot=false # To generate a sum of all the spectrum plots
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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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# 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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# Image change comparative buttons
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@in imgPlusCompLeft=false
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@in imgMinusCompLeft=false
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@in imgPlusTCompLeft=false
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@in imgMinusTCompLeft=false
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@in imgPlusCompRight=false
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@in imgMinusCompRight=false
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@in imgPlusTCompRight=false
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@in imgMinusTCompRight=false
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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", "Topography Plot","Surface Plot"]
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@in selectedTab="tab0"
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@out CompTabIDsLeft=["tab0","tab1","tab2","tab3","tab4"]
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@out CompTabLabelsLeft=["Image", "TrIQ", "Spectrum Plot", "Topography Plot","Surface Plot"]
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@in CompSelectedTabLeft="tab0"
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@out CompTabIDsRight=["tab0","tab1","tab2","tab3","tab4"]
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@out CompTabLabelsRight=["Image", "TrIQ", "Spectrum Plot", "Topography Plot","Surface Plot"]
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@in CompSelectedTabRight="tab0"
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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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@out colorbar="/.png"
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@out colorbarT="/.png"
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# Interface controlling for the comparative view
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@out imgIntCompLeft="/.bmp"
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@out imgIntTCompLeft="/.bmp"
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@out colorbarCompLeft="/.png"
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@out colorbarTCompLeft="/.png"
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@out imgIntCompRight="/.bmp"
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@out imgIntTCompRight="/.bmp"
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@out colorbarCompRight="/.png"
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@out colorbarTCompRight="/.png"
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@out imgWidth=0
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@out imgHeight=0
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# Optical Image Overlay & Transparency
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@in imgTrans=1.0
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@in progressOptical=false
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@out btnOpticalDisable=true
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@in btnOptical=false
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@in btnOpticalT=false
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@in opticalOverTriq=false
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@out imgRoute=""
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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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# Reiteration of the messages under the image to know which spectra is being visualized
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@out msgimgCompLeft=""
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@out msgtriqCompLeft=""
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@out msgimgCompRight=""
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@out msgtriqCompRight=""
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# Centralized MSIData object
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@out msi_data::Union{MSIData, Nothing} = nothing
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# Metadata table variables
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@in showMetadataDialog = false
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@in showMetadataBtn = false
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@out metadata_columns = []
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@out metadata_rows = []
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@out btnMetadataDisable = false
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@in selected_folder_metadata = ""
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# Saves the route where imzML and mzML files are located
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@out full_route=""
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# == Converter Tab Variables ==
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@in left_tab = "generator"
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@out mzml_full_route = ""
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@out sync_full_route = ""
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@in btnSearchMzml = false
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@in btnSearchSync = false
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@in convert_process = false
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@out progress_conversion = false
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@out msg_conversion = ""
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@out btnConvertDisable = true
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# == Pre Processing Variables ==
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@in pre_tab = "stabilization"
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# == Batch Summary Dialog ==
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@in showBatchSummary = false
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@out batch_summary = ""
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# == Batch Processing & Registry Variables ==
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@private registry_init_done = false
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@in selected_files = String[]
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@in available_folders = String[]
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@in image_available_folders = String[]
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@out registry_path = abspath(joinpath(@__DIR__, "public", "registry.json"))
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# Progress reporting
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@out overall_progress = 0.0
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@out progress_message = ""
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# == Folder-based UI State ==
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@in selected_folder_main = ""
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@in selected_folder_compare_left = ""
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@in selected_folder_compare_right = ""
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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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# For image search image lists we apply a filter that searches specific type of images into our public folder, then we sort it in a "numerical" order
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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 to display
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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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# We reiterate the process to display in the comparative view
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@out current_msiCompLeft=""
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@out current_col_msiCompLeft=""
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@out current_triqCompLeft=""
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@out current_col_triqCompLeft=""
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@out current_msiCompRight=""
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@out current_col_msiCompRight=""
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@out current_triqCompRight=""
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@out current_col_triqCompRight=""
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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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# Local image to plot
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layoutImg=PlotlyBase.Layout(
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title=PlotlyBase.attr(
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text="",
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font=PlotlyBase.attr(
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family="Roboto, Lato, sans-serif",
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size=14,
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color="black"
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)
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),
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xaxis=PlotlyBase.attr(
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visible=false,
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scaleanchor="y",
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range=[0, 0]
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),
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yaxis=PlotlyBase.attr(
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visible=false,
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range=[0, 0]
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),
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margin=attr(l=0,r=0,t=0,b=0,pad=0)
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)
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traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
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@out plotdataImg=[traceImg]
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@out plotlayoutImg=layoutImg
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# For the image in the comparative view
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@out plotdataImgCompLeft=[traceImg]
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@out plotlayoutImgCompLeft=layoutImg
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@out plotdataImgCompRight=[traceImg]
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@out plotlayoutImgCompRight=layoutImg
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# For triq image
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@out plotdataImgT=[traceImg]
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@out plotlayoutImgT=layoutImg
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# For the triq image in the comparative view
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@out plotdataImgTCompLeft=[traceImg]
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@out plotlayoutImgTCompLeft=layoutImg
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@out plotdataImgTCompRight=[traceImg]
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@out plotlayoutImgTCompRight=layoutImg
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# Interface Plot Spectrum
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layoutSpectra=PlotlyBase.Layout(
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title=PlotlyBase.attr(
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text="Spectrum plot",
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font=PlotlyBase.attr(
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family="Roboto, Lato, sans-serif",
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size=18,
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color="black"
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)
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),
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hovermode="closest",
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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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tickformat = ".3g"
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),
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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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# Dummy 2D scatter plot
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traceSpectra=PlotlyBase.scatter(x=Vector{Float64}(), y=Vector{Float64}(), mode="lines", marker=attr(size=1, color="blue", opacity=0.1))
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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 = Vector{Float64}()
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@out ySpectraMz = Vector{Float64}()
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# Interactive plot reactions
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@in data_click=Dict{String,Any}()
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#@in data_selected=Dict{String,Any}() # Selected is for areas, this can work for the masks
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#<plotly id="plotStyle" :data="plotdata" :layout="plotlayout" @click="data_selected" class="q-pa-none q-ma-none sync_data"></plotly>
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# Interface Plot Surface
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layoutContour=PlotlyBase.Layout(
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title=PlotlyBase.attr(
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text="2D Topographic map",
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font=PlotlyBase.attr(
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family="Roboto, Lato, sans-serif",
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size=18,
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color="black"
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)
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),
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xaxis=PlotlyBase.attr(
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visible=false,
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scaleanchor="y"
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),
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yaxis=PlotlyBase.attr(
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visible=false
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),
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margin=attr(l=0,r=0,t=100,b=0,pad=0)
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)
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# Dummy 2D surface plot
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traceContour=PlotlyBase.contour(x=Vector{Float64}(), y=Vector{Float64}(), mode="lines")
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# Create conection to frontend
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@out plotdataC=[traceContour]
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@out plotlayoutC=layoutContour
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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=PlotlyBase.attr(
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text="3D Surface plot",
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font=PlotlyBase.attr(
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family="Roboto, Lato, sans-serif",
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size=18,
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color="black"
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)
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),
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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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xaxis_nticks=20,
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yaxis_nticks=20,
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zaxis_nticks=4,
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camera=attr(eye=attr(x=0, y=-1, z=0.5)),
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aspectratio=attr(x=1, y=1, z=0.2)
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),
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margin=attr(l=0,r=0,t=120,b=0,pad=0)
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)
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# Dummy 3D surface plot
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x=1:10
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y=1:10
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z=[sin(i * j / 10) for i in x, j in y]
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trace3D=PlotlyBase.surface(x=Vector{Float64}(), y=Vector{Float64}(), z=Matrix{Float64}(undef, 0, 0),
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contours_z=attr(
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show=true,
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usecolormap=true,
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highlightcolor="limegreen",
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project_z=true
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), 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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# == 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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# This handler correctly uses pick_file and loads the selected file
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# as the active dataset for the UI.
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@onbutton btnSearch begin
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picked_route = pick_file(; filterlist="imzML,imzml,mzML,mzml")
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if isempty(picked_route)
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return
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end
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progress = true
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msg = "Opening file: $(basename(picked_route))..."
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try
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dataset_name = replace(basename(picked_route), r"(\.(imzML|imzml|mzML|mzml))$"i => "")
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registry = load_registry(registry_path)
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existing_entry = get(registry, dataset_name, nothing)
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# --- Fast Load Path ---
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is_same_file = (existing_entry !== nothing && existing_entry["source_path"] == picked_route)
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if is_same_file && !isempty(get(existing_entry, "metadata", Dict()))
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msg = "Fast loading pre-processed file: $(dataset_name)"
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println(msg)
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full_route = existing_entry["source_path"]
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metadata_rows = existing_entry["metadata"]["summary"]
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dims_str = first(filter(r -> r["parameter"] == "Image Dimensions", metadata_rows))["value"]
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dims = parse.(Int, split(dims_str, " x "))
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imgWidth, imgHeight = dims[1], dims[2]
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msi_data = nothing # Ensure data is not held in memory
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log_memory_usage("Fast Load (msi_data cleared)", msi_data)
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btnMetadataDisable = false
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btnStartDisable = false
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btnPlotDisable = false
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btnSpectraDisable = false
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SpectraEnabled = true
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selected_folder_main = dataset_name
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# Update folder lists in UI
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all_folders = sort(collect(keys(registry)), lt=natural)
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img_folders = filter(folder -> get(get(registry, folder, Dict()), "is_imzML", false), all_folders)
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available_folders = deepcopy(all_folders)
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image_available_folders = deepcopy(img_folders)
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msg = "Successfully loaded pre-processed dataset: $(dataset_name)"
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progress = false
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return
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end
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# --- Full Load Path ---
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msg = "Performing first-time analysis for: $(basename(picked_route))..."
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local local_full_route
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if endswith(picked_route, r"imzml"i)
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local_full_route = replace(picked_route, r"\.imzml$"i => ".imzML")
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if picked_route != local_full_route
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mv(picked_route, local_full_route, force=true)
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end
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else
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local_full_route = picked_route
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end
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full_route = local_full_route
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sTime = time()
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loaded_data = OpenMSIData(local_full_route)
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is_imzML = loaded_data.source isa ImzMLSource
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precompute_analytics(loaded_data)
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metadata_columns = [
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Dict("name" => "parameter", "label" => "Parameter", "field" => "parameter", "align" => "left"),
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Dict("name" => "value", "label" => "Value", "field" => "value", "align" => "left"),
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]
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summary_stats = extract_metadata(loaded_data, local_full_route)
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metadata_rows = summary_stats["summary"]
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btnMetadataDisable = isempty(metadata_rows)
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w, h = loaded_data.image_dims
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imgWidth, imgHeight = w > 0 ? (w, h) : (500, 500)
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update_registry(registry_path, dataset_name, local_full_route, summary_stats, is_imzML)
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# Update folder lists in UI
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registry = load_registry(registry_path)
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all_folders = sort(collect(keys(registry)), lt=natural)
|
|
img_folders = filter(folder -> get(get(registry, folder, Dict()), "is_imzML", false), all_folders)
|
|
available_folders = deepcopy(all_folders)
|
|
image_available_folders = deepcopy(img_folders)
|
|
|
|
selected_folder_main = dataset_name
|
|
msi_data = loaded_data
|
|
log_memory_usage("Full Load", msi_data)
|
|
|
|
eTime = round(time() - sTime, digits=3)
|
|
msg = "Active file loaded in $(eTime) seconds. Dataset '$(dataset_name)' is ready for analysis."
|
|
|
|
btnStartDisable = false
|
|
btnPlotDisable = false
|
|
btnSpectraDisable = false
|
|
SpectraEnabled = true
|
|
|
|
catch e
|
|
msi_data = nothing
|
|
msg = "Error loading active file: $e"
|
|
warning_msg = true
|
|
btnStartDisable = true
|
|
btnSpectraDisable = true
|
|
SpectraEnabled = false
|
|
btnMetadataDisable = true
|
|
@error "File loading failed" exception=(e, catch_backtrace())
|
|
finally
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
progress = false
|
|
progressSpectraPlot = false
|
|
end
|
|
end
|
|
|
|
# This new handler correctly adds the file from full_route to the batch list.
|
|
@onbutton btnAddBatch begin
|
|
if isempty(full_route) || full_route == "unknown (manually added)"
|
|
msg = "No active file selected to add to batch."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
if !(full_route in selected_files)
|
|
push!(selected_files, full_route)
|
|
selected_files = deepcopy(selected_files) # Force reactivity
|
|
batch_file_count = length(selected_files)
|
|
msg = "File added to batch."
|
|
else
|
|
msg = "File is already in the batch list."
|
|
warning_msg = true
|
|
end
|
|
end
|
|
|
|
@onbutton clear_batch_btn begin
|
|
selected_files = String[]
|
|
batch_file_count = 0
|
|
msg = "Batch cleared"
|
|
end
|
|
|
|
@onchange selected_files begin
|
|
batch_file_count = length(selected_files)
|
|
end
|
|
|
|
@onchange full_route begin
|
|
if !isempty(full_route) && !(full_route in selected_files)
|
|
push!(selected_files, full_route)
|
|
selected_files = deepcopy(selected_files) # Force reactivity
|
|
batch_file_count = length(selected_files)
|
|
msg = "File automatically added to batch"
|
|
end
|
|
end
|
|
|
|
@onbutton showMetadataBtn begin
|
|
if !isempty(available_folders)
|
|
if !isempty(selected_folder_main)
|
|
selected_folder_metadata = selected_folder_main
|
|
elseif !isempty(available_folders)
|
|
selected_folder_metadata = first(available_folders)
|
|
end
|
|
showMetadataDialog = true
|
|
else
|
|
msg = "No processed datasets available."
|
|
warning_msg = true
|
|
end
|
|
end
|
|
|
|
@onchange selected_folder_metadata begin
|
|
if !isempty(selected_folder_metadata)
|
|
registry = load_registry(registry_path)
|
|
dataset_info = get(registry, selected_folder_metadata, nothing)
|
|
|
|
if dataset_info !== nothing && haskey(dataset_info, "metadata") && !isempty(get(dataset_info["metadata"], "summary", []))
|
|
metadata_rows = dataset_info["metadata"]["summary"]
|
|
btnMetadataDisable = false
|
|
else
|
|
metadata_rows = []
|
|
btnMetadataDisable = true
|
|
msg = "Metadata not found in registry for $(selected_folder_metadata)."
|
|
end
|
|
end
|
|
end
|
|
|
|
@onchange btnSearchMzml, btnSearchSync begin
|
|
if btnSearchMzml
|
|
picked_route = pick_file(; filterlist="mzML,mzml")
|
|
if !isempty(picked_route)
|
|
mzml_full_route = picked_route
|
|
end
|
|
btnSearchMzml = false # Reset the button
|
|
end
|
|
|
|
if btnSearchSync
|
|
picked_route = pick_file(; filterlist="txt")
|
|
if !isempty(picked_route)
|
|
sync_full_route = picked_route
|
|
end
|
|
btnSearchSync = false # Reset the button
|
|
end
|
|
|
|
# Enable button only if both files are selected
|
|
btnConvertDisable = isempty(mzml_full_route) || isempty(sync_full_route)
|
|
end
|
|
|
|
@onbutton convert_process begin
|
|
if isempty(mzml_full_route) || isempty(sync_full_route)
|
|
msg_conversion = "Please select both an .mzML file and a .txt sync file."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
progress_conversion = true
|
|
btnConvertDisable = true
|
|
msg_conversion = "Starting conversion process..."
|
|
|
|
try
|
|
sTime = time()
|
|
target_imzml = replace(mzml_full_route, r"\.(mzml|mzML)$" => ".imzML")
|
|
|
|
msg_conversion = "Converting $(basename(mzml_full_route)) to $(basename(target_imzml))... This may take a while."
|
|
|
|
success = ImportMzmlFile(mzml_full_route, sync_full_route, target_imzml)
|
|
|
|
fTime = time()
|
|
eTime = round(fTime - sTime, digits=3)
|
|
|
|
if success
|
|
msg_conversion = "Conversion successful in $(eTime) seconds. Output file: $(basename(target_imzml))"
|
|
else
|
|
msg_conversion = "Conversion failed after $(eTime) seconds. Check console for errors."
|
|
warning_msg = true
|
|
end
|
|
|
|
catch e
|
|
msg_conversion = "An error occurred during conversion: $e"
|
|
warning_msg = true
|
|
@error "Conversion failed" exception=(e, catch_backtrace())
|
|
finally
|
|
progress_conversion = false
|
|
# Re-enable button if files are still selected
|
|
btnConvertDisable = isempty(mzml_full_route) || isempty(sync_full_route)
|
|
end
|
|
end
|
|
|
|
@onbutton mainProcess @time begin
|
|
# --- UI State Update ---
|
|
progress = true
|
|
btnStartDisable = true
|
|
btnPlotDisable = true
|
|
btnSpectraDisable = true
|
|
overall_progress = 0.0
|
|
progress_message = "Preparing batch process..."
|
|
|
|
# --- CAPTURE CURRENT VALUES HERE ---
|
|
current_selected_files = selected_files
|
|
current_nmass = Nmass
|
|
current_tol = Tol
|
|
current_color_level = colorLevel
|
|
current_triq_enabled = triqEnabled
|
|
current_triq_prob = triqProb
|
|
current_mfilter_enabled = MFilterEnabled
|
|
current_mask_enabled = maskEnabled
|
|
current_registry_path = registry_path
|
|
|
|
println("starting main process with $(length(current_selected_files)) files")
|
|
total_time_start = time()
|
|
try
|
|
# --- 1. Parameter Validation ---
|
|
if isempty(current_selected_files)
|
|
progress_message = "No .imzML files in batch. Please add files first."
|
|
warning_msg = true
|
|
println(progress_message)
|
|
return
|
|
end
|
|
|
|
masses = Float64[]
|
|
try
|
|
masses = [parse(Float64, strip(m)) for m in split(current_nmass, ',', keepempty=false)]
|
|
catch e
|
|
progress_message = "Invalid m/z value(s). Please provide a comma-separated list of numbers. Error: $e"
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
if isempty(masses)
|
|
progress_message = "No valid m/z values found. Please provide comma-separated positive numbers."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
# --- 2. Batch Processing Loop ---
|
|
num_files = length(current_selected_files)
|
|
total_steps = num_files
|
|
current_step = 0
|
|
errors = Dict("load_errors" => String[], "slice_errors" => String[], "io_errors" => String[])
|
|
newly_created_folders = String[]
|
|
files_without_mask = 0
|
|
|
|
for (file_idx, file_path) in enumerate(current_selected_files)
|
|
progress_message = "Processing file $file_idx/$num_files: $(basename(file_path))"
|
|
overall_progress = current_step / total_steps
|
|
|
|
all_params = (
|
|
tolerance = current_tol,
|
|
colorL = current_color_level,
|
|
triqE = current_triq_enabled,
|
|
triqP = current_triq_prob,
|
|
medianF = current_mfilter_enabled,
|
|
registry = current_registry_path,
|
|
fileIdx = file_idx,
|
|
nFiles = num_files
|
|
)
|
|
|
|
success, error_msg = process_file_safely(file_path, masses, all_params, progress_message, overall_progress, use_mask=current_mask_enabled)
|
|
|
|
if !success
|
|
push!(errors["load_errors"], error_msg)
|
|
else
|
|
push!(newly_created_folders, replace(basename(file_path), r"\.imzML$"i => ""))
|
|
end
|
|
current_step += 1
|
|
end
|
|
|
|
# --- 3. Final Report ---
|
|
total_time_end = round(time() - total_time_start, digits=3)
|
|
|
|
registry = load_registry(current_registry_path)
|
|
all_folders = sort(collect(keys(registry)), lt=natural)
|
|
img_folders = filter(folder -> get(get(registry, folder, Dict()), "is_imzML", false), all_folders)
|
|
available_folders = deepcopy(all_folders)
|
|
image_available_folders = deepcopy(img_folders)
|
|
|
|
if !isempty(newly_created_folders)
|
|
selected_folder_main = first(newly_created_folders)
|
|
end
|
|
|
|
successful_files = length(newly_created_folders)
|
|
total_errors = sum(length, values(errors))
|
|
|
|
if total_errors == 0
|
|
msg = "Successfully processed all $(successful_files) file(s) in $(total_time_end) seconds."
|
|
else
|
|
msg = "Batch completed in $(total_time_end) seconds with $(total_errors) error(s)."
|
|
warning_msg = true
|
|
end
|
|
|
|
mask_summary = current_mask_enabled ? "\nFiles processed without a mask: $(files_without_mask)" : ""
|
|
|
|
batch_summary = """
|
|
Processed $(successful_files)/$(num_files) files successfully.
|
|
$(mask_summary)
|
|
|
|
Errors by category:
|
|
• Load failures: $(length(errors["load_errors"]))
|
|
• Slice generation: $(length(errors["slice_errors"]))
|
|
• I/O issues: $(length(errors["io_errors"]))
|
|
|
|
Detailed errors:
|
|
$(join(vcat(values(errors)...), "\n"))
|
|
"""
|
|
showBatchSummary = true
|
|
|
|
# Update UI to display the last generated image
|
|
if !isempty(newly_created_folders)
|
|
timestamp = string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_main)
|
|
|
|
if current_triq_enabled
|
|
triq_files = filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path))
|
|
col_triq_files = filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path))
|
|
|
|
if !isempty(triq_files)
|
|
latest_triq = triq_files[argmax([mtime(joinpath(folder_path, f)) for f in triq_files])]
|
|
current_triq = latest_triq
|
|
imgIntT = "/$(selected_folder_main)/$(current_triq)?t=$(timestamp)"
|
|
plotdataImgT, plotlayoutImgT, _, _ = loadImgPlot(imgIntT)
|
|
text_nmass = replace(current_triq, r"TrIQ_|.bmp" => "")
|
|
msgtriq = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
|
|
if !isempty(col_triq_files)
|
|
latest_col_triq = col_triq_files[argmax([mtime(joinpath(folder_path, f)) for f in col_triq_files])]
|
|
current_col_triq = latest_col_triq
|
|
colorbarT = "/$(selected_folder_main)/$(current_col_triq)?t=$(timestamp)"
|
|
else
|
|
colorbarT = ""
|
|
end
|
|
selectedTab = "tab1"
|
|
end
|
|
else # Not TrIQ enabled, display regular MSI image
|
|
msi_files = filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path))
|
|
col_msi_files = filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path))
|
|
|
|
if !isempty(msi_files)
|
|
latest_msi = msi_files[argmax([mtime(joinpath(folder_path, f)) for f in msi_files])]
|
|
current_msi = latest_msi
|
|
imgInt = "/$(selected_folder_main)/$(current_msi)?t=$(timestamp)"
|
|
plotdataImg, plotlayoutImg, _, _ = loadImgPlot(imgInt)
|
|
text_nmass = replace(current_msi, r"MSI_|.bmp" => "")
|
|
msgimg = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
|
|
if !isempty(col_msi_files)
|
|
latest_col_msi = col_msi_files[argmax([mtime(joinpath(folder_path, f)) for f in col_msi_files])]
|
|
current_col_msi = latest_col_msi
|
|
colorbar = "/$(selected_folder_main)/$(current_col_msi)?t=$(timestamp)"
|
|
else
|
|
colorbar = ""
|
|
end
|
|
selectedTab = "tab0"
|
|
end
|
|
end
|
|
end
|
|
|
|
catch e
|
|
println("Error in main process: $e")
|
|
msg = "Batch processing failed: $e"
|
|
warning_msg = true
|
|
@error "Main process failed" exception=(e, catch_backtrace())
|
|
finally
|
|
# --- UI State Reset ---
|
|
progress = false
|
|
btnStartDisable = false
|
|
btnPlotDisable = false
|
|
btnOpticalDisable = false
|
|
btnSpectraDisable = false
|
|
SpectraEnabled = true
|
|
overall_progress = 0.0
|
|
println("Done")
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
@onbutton createMeanPlot begin
|
|
if isempty(selected_folder_main)
|
|
msg = "No dataset selected. Please process a file and select a folder first."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
progressSpectraPlot = true
|
|
btnPlotDisable = true
|
|
btnStartDisable = true
|
|
msg = "Loading plot for $(selected_folder_main)..."
|
|
|
|
try
|
|
sTime = time()
|
|
registry = load_registry(registry_path)
|
|
entry = registry[selected_folder_main]
|
|
target_path = entry["source_path"]
|
|
|
|
if target_path == "unknown (manually added)"
|
|
msg = "Dataset selected contained no route."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
if msi_data === nothing || full_route != target_path
|
|
msg = "Reloading $(basename(target_path)) for analysis..."
|
|
full_route = target_path
|
|
msi_data = OpenMSIData(target_path)
|
|
if haskey(get(entry, "metadata", Dict()), "global_min_mz") && entry["metadata"]["global_min_mz"] !== nothing
|
|
msi_data.global_min_mz = entry["metadata"]["global_min_mz"]
|
|
msi_data.global_max_mz = entry["metadata"]["global_max_mz"]
|
|
else
|
|
precompute_analytics(msi_data)
|
|
end
|
|
end
|
|
|
|
local mask_path_for_plot::Union{String, Nothing} = nothing
|
|
if maskEnabled && get(entry, "has_mask", false)
|
|
mask_path_for_plot = get(entry, "mask_path", "")
|
|
if !isfile(mask_path_for_plot)
|
|
@warn "Mask not found for plotting: $(mask_path_for_plot). Plotting without mask."
|
|
mask_path_for_plot = nothing
|
|
end
|
|
end
|
|
|
|
plotdata, plotlayout, xSpectraMz, ySpectraMz = meanSpectrumPlot(msi_data, selected_folder_main, mask_path=mask_path_for_plot)
|
|
selectedTab = "tab2"
|
|
fTime = time()
|
|
eTime = round(fTime - sTime, digits=3)
|
|
msg = "Plot loaded in $(eTime) seconds"
|
|
log_memory_usage("Mean Plot Generated", msi_data)
|
|
catch e
|
|
msg = "Could not generate mean spectrum plot: $e"
|
|
warning_msg = true
|
|
@error "Mean spectrum plotting failed" exception=(e, catch_backtrace())
|
|
finally
|
|
progressSpectraPlot = false
|
|
btnPlotDisable = false
|
|
btnSpectraDisable = false
|
|
btnStartDisable = false
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
@onbutton createSumPlot begin
|
|
if isempty(selected_folder_main)
|
|
msg = "No dataset selected. Please process a file and select a folder first."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
progressSpectraPlot = true
|
|
btnPlotDisable = true
|
|
btnStartDisable = true
|
|
msg = "Loading total spectrum plot for $(selected_folder_main)..."
|
|
|
|
try
|
|
sTime = time()
|
|
registry = load_registry(registry_path)
|
|
entry = registry[selected_folder_main]
|
|
target_path = entry["source_path"]
|
|
|
|
if target_path == "unknown (manually added)"
|
|
msg = "Dataset selected contained no route."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
if msi_data === nothing || full_route != target_path
|
|
msg = "Reloading $(basename(target_path)) for analysis..."
|
|
full_route = target_path
|
|
msi_data = OpenMSIData(target_path)
|
|
if haskey(get(entry, "metadata", Dict()), "global_min_mz") && entry["metadata"]["global_min_mz"] !== nothing
|
|
msi_data.global_min_mz = entry["metadata"]["global_min_mz"]
|
|
msi_data.global_max_mz = entry["metadata"]["global_max_mz"]
|
|
else
|
|
precompute_analytics(msi_data)
|
|
end
|
|
end
|
|
|
|
local mask_path_for_plot::Union{String, Nothing} = nothing
|
|
if maskEnabled && get(entry, "has_mask", false)
|
|
mask_path_for_plot = get(entry, "mask_path", "")
|
|
if !isfile(mask_path_for_plot)
|
|
@warn "Mask not found for plotting: $(mask_path_for_plot). Plotting without mask."
|
|
mask_path_for_plot = nothing
|
|
end
|
|
end
|
|
|
|
plotdata, plotlayout, xSpectraMz, ySpectraMz = sumSpectrumPlot(msi_data, selected_folder_main, mask_path=mask_path_for_plot)
|
|
selectedTab = "tab2"
|
|
fTime = time()
|
|
eTime = round(fTime - sTime, digits=3)
|
|
msg = "Total plot loaded in $(eTime) seconds"
|
|
log_memory_usage("Sum Plot Generated", msi_data)
|
|
catch e
|
|
msg = "Could not generate total spectrum plot: $e"
|
|
warning_msg = true
|
|
@error "Total spectrum plotting failed" exception=(e, catch_backtrace())
|
|
finally
|
|
progressSpectraPlot = false
|
|
btnPlotDisable = false
|
|
btnSpectraDisable = false
|
|
btnStartDisable = false
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
@onbutton createXYPlot begin
|
|
if isempty(selected_folder_main)
|
|
msg = "No dataset selected. Please process a file and select a folder first."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
progressSpectraPlot = true
|
|
btnStartDisable = true
|
|
btnPlotDisable = true
|
|
btnSpectraDisable = true
|
|
msg = "Loading plot for $(selected_folder_main)..."
|
|
|
|
try
|
|
sTime = time()
|
|
registry = load_registry(registry_path)
|
|
|
|
# Add error handling for registry access
|
|
if !haskey(registry, selected_folder_main)
|
|
msg = "Dataset '$selected_folder_main' not found in registry."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
entry = registry[selected_folder_main]
|
|
target_path = entry["source_path"]
|
|
|
|
if target_path == "unknown (manually added)"
|
|
msg = "Dataset selected contained no route."
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
if msi_data === nothing || full_route != target_path
|
|
msg = "Reloading $(basename(target_path)) for analysis..."
|
|
full_route = target_path
|
|
msi_data = OpenMSIData(target_path)
|
|
if haskey(get(entry, "metadata", Dict()), "global_min_mz") && entry["metadata"]["global_min_mz"] !== nothing
|
|
msi_data.global_min_mz = entry["metadata"]["global_min_mz"]
|
|
msi_data.global_max_mz = entry["metadata"]["global_max_mz"]
|
|
else
|
|
precompute_analytics(msi_data)
|
|
end
|
|
end
|
|
|
|
local mask_path_for_plot::Union{String, Nothing} = nothing
|
|
if maskEnabled && get(entry, "has_mask", false)
|
|
mask_path_for_plot = get(entry, "mask_path", "")
|
|
if !isfile(mask_path_for_plot)
|
|
@warn "Mask not found for plotting: $(mask_path_for_plot). Plotting without mask."
|
|
mask_path_for_plot = nothing
|
|
end
|
|
end
|
|
|
|
# Convert to positive coordinates for processing
|
|
y_positive = yCoord < 0 ? abs(yCoord) : yCoord
|
|
plotdata, plotlayout, xSpectraMz, ySpectraMz = xySpectrumPlot(msi_data, xCoord, y_positive, imgWidth, imgHeight, selected_folder_main, mask_path=mask_path_for_plot)
|
|
|
|
# Update coordinates based on actual plot title
|
|
# Extract title text from the Dict safely
|
|
actual_title = if plotlayout.title isa Dict && haskey(plotlayout.title, :text)
|
|
plotlayout.title[:text]
|
|
elseif plotlayout.title isa Dict && haskey(plotlayout.title, "text")
|
|
plotlayout.title["text"]
|
|
else
|
|
string(plotlayout.title) # Fallback
|
|
end
|
|
|
|
if occursin("Masked Spectrum at", actual_title)
|
|
# Extract coordinates from masked spectrum title
|
|
coords_match = match(r"Masked Spectrum at \((\d+), (\d+)\)", actual_title)
|
|
if coords_match !== nothing
|
|
xCoord = parse(Int, coords_match.captures[1])
|
|
yCoord = -parse(Int, coords_match.captures[2]) # Negative for display
|
|
end
|
|
elseif occursin("Spectrum at", actual_title)
|
|
# Extract coordinates from regular spectrum title
|
|
coords_match = match(r"Spectrum at \((\d+), (\d+)\)", actual_title)
|
|
if coords_match !== nothing
|
|
xCoord = parse(Int, coords_match.captures[1])
|
|
yCoord = -parse(Int, coords_match.captures[2]) # Negative for display
|
|
end
|
|
else
|
|
# For non-imaging data or fallback, just clamp the coordinates
|
|
xCoord = clamp(xCoord, 1, imgWidth)
|
|
yCoord = yCoord < 0 ? yCoord : -clamp(yCoord, 1, imgHeight)
|
|
end
|
|
|
|
selectedTab = "tab2"
|
|
fTime = time()
|
|
eTime = round(fTime - sTime, digits=3)
|
|
msg = "Plot loaded in $(eTime) seconds"
|
|
log_memory_usage("XY Plot Generated", msi_data)
|
|
catch e
|
|
msg = "Could not retrieve spectrum: $e"
|
|
warning_msg = true
|
|
@error "Spectrum plotting failed" exception=(e, catch_backtrace())
|
|
finally
|
|
progressSpectraPlot = false
|
|
btnPlotDisable = false
|
|
btnSpectraDisable = false
|
|
btnStartDisable = false
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
# --- Main View Handlers ---
|
|
@onbutton imgMinus begin
|
|
if isempty(selected_folder_main) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_main)
|
|
# Check if folder exists to prevent errors
|
|
if !isdir(folder_path) return end
|
|
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=decrement_image(current_msi, msi_bmp)
|
|
new_col_msi=decrement_image(current_col_msi, col_msi_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_msi = new_msi
|
|
current_col_msi = new_col_msi
|
|
imgInt = "/$(selected_folder_main)/$(current_msi)?t=$(timestamp)"
|
|
colorbar = "/$(selected_folder_main)/$(current_col_msi)?t=$(timestamp)"
|
|
text_nmass = replace(current_msi, r"MSI_|.bmp" => "")
|
|
msgimg = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImg, plotlayoutImg, _, _ = loadImgPlot(imgInt)
|
|
btnOpticalDisable = false
|
|
end
|
|
end
|
|
@onbutton imgPlus begin
|
|
if isempty(selected_folder_main) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_main)
|
|
if !isdir(folder_path) return end
|
|
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=increment_image(current_msi, msi_bmp)
|
|
new_col_msi=increment_image(current_col_msi, col_msi_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_msi = new_msi
|
|
current_col_msi = new_col_msi
|
|
imgInt = "/$(selected_folder_main)/$(current_msi)?t=$(timestamp)"
|
|
colorbar = "/$(selected_folder_main)/$(current_col_msi)?t=$(timestamp)"
|
|
text_nmass = replace(current_msi, r"MSI_|.bmp" => "")
|
|
msgimg = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImg, plotlayoutImg, _, _ = loadImgPlot(imgInt)
|
|
btnOpticalDisable = false
|
|
end
|
|
end
|
|
|
|
@onbutton imgMinusT begin
|
|
if isempty(selected_folder_main) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_main)
|
|
if !isdir(folder_path) return end
|
|
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=decrement_image(current_triq, triq_bmp)
|
|
new_col_msi=decrement_image(current_col_triq, col_triq_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_triq = new_msi
|
|
current_col_triq = new_col_msi
|
|
imgIntT = "/$(selected_folder_main)/$(current_triq)?t=$(timestamp)"
|
|
colorbarT = "/$(selected_folder_main)/$(current_col_triq)?t=$(timestamp)"
|
|
text_nmass = replace(current_triq, r"TrIQ_|.bmp" => "")
|
|
msgtriq = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgT, plotlayoutImgT, _, _ = loadImgPlot(imgIntT)
|
|
btnOpticalDisable = false
|
|
end
|
|
end
|
|
@onbutton imgPlusT begin
|
|
if isempty(selected_folder_main) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_main)
|
|
if !isdir(folder_path) return end
|
|
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=increment_image(current_triq, triq_bmp)
|
|
new_col_msi=increment_image(current_col_triq, col_triq_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_triq = new_msi
|
|
current_col_triq = new_col_msi
|
|
imgIntT = "/$(selected_folder_main)/$(current_triq)?t=$(timestamp)"
|
|
colorbarT = "/$(selected_folder_main)/$(current_col_triq)?t=$(timestamp)"
|
|
text_nmass = replace(current_triq, r"TrIQ_|.bmp" => "")
|
|
msgtriq = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgT, plotlayoutImgT, _, _ = loadImgPlot(imgIntT)
|
|
btnOpticalDisable = false
|
|
end
|
|
end
|
|
|
|
# --- Compare View Handlers ---
|
|
@onbutton imgMinusCompLeft begin
|
|
if isempty(selected_folder_compare_left) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_left)
|
|
if !isdir(folder_path) return end
|
|
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=decrement_image(current_msiCompLeft, msi_bmp)
|
|
new_col_msi=decrement_image(current_col_msiCompLeft, col_msi_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_msiCompLeft = new_msi
|
|
current_col_msiCompLeft = new_col_msi
|
|
imgIntCompLeft = "/$(selected_folder_compare_left)/$(current_msiCompLeft)?t=$(timestamp)"
|
|
colorbarCompLeft = "/$(selected_folder_compare_left)/$(current_col_msiCompLeft)?t=$(timestamp)"
|
|
text_nmass = replace(current_msiCompLeft, r"MSI_|.bmp" => "")
|
|
msgimgCompLeft = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgCompLeft, plotlayoutImgCompLeft, _, _ = loadImgPlot(imgIntCompLeft)
|
|
end
|
|
end
|
|
|
|
@onbutton imgPlusCompLeft begin
|
|
if isempty(selected_folder_compare_left) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_left)
|
|
if !isdir(folder_path) return end
|
|
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=increment_image(current_msiCompLeft, msi_bmp)
|
|
new_col_msi=increment_image(current_col_msiCompLeft, col_msi_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_msiCompLeft = new_msi
|
|
current_col_msiCompLeft = new_col_msi
|
|
imgIntCompLeft = "/$(selected_folder_compare_left)/$(current_msiCompLeft)?t=$(timestamp)"
|
|
colorbarCompLeft = "/$(selected_folder_compare_left)/$(current_col_msiCompLeft)?t=$(timestamp)"
|
|
text_nmass = replace(current_msiCompLeft, r"MSI_|.bmp" => "")
|
|
msgimgCompLeft = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgCompLeft, plotlayoutImgCompLeft, _, _ = loadImgPlot(imgIntCompLeft)
|
|
end
|
|
end
|
|
|
|
@onbutton imgMinusTCompLeft begin
|
|
if isempty(selected_folder_compare_left) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_left)
|
|
if !isdir(folder_path) return end
|
|
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=decrement_image(current_triqCompLeft, triq_bmp)
|
|
new_col_msi=decrement_image(current_col_triqCompLeft, col_triq_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_triqCompLeft = new_msi
|
|
current_col_triqCompLeft = new_col_msi
|
|
imgIntTCompLeft = "/$(selected_folder_compare_left)/$(current_triqCompLeft)?t=$(timestamp)"
|
|
colorbarTCompLeft = "/$(selected_folder_compare_left)/$(current_col_triqCompLeft)?t=$(timestamp)"
|
|
text_nmass = replace(current_triqCompLeft, r"TrIQ_|.bmp" => "")
|
|
msgtriqCompLeft = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgTCompLeft, plotlayoutImgTCompLeft, _, _ = loadImgPlot(imgIntTCompLeft)
|
|
end
|
|
end
|
|
|
|
@onbutton imgPlusTCompLeft begin
|
|
if isempty(selected_folder_compare_left) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_left)
|
|
if !isdir(folder_path) return end
|
|
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=increment_image(current_triqCompLeft, triq_bmp)
|
|
new_col_msi=increment_image(current_col_triqCompLeft, col_triq_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_triqCompLeft = new_msi
|
|
current_col_triqCompLeft = new_col_msi
|
|
imgIntTCompLeft = "/$(selected_folder_compare_left)/$(current_triqCompLeft)?t=$(timestamp)"
|
|
colorbarTCompLeft = "/$(selected_folder_compare_left)/$(current_col_triqCompLeft)?t=$(timestamp)"
|
|
text_nmass = replace(current_triqCompLeft, r"TrIQ_|.bmp" => "")
|
|
msgtriqCompLeft = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgTCompLeft, plotlayoutImgTCompLeft, _, _ = loadImgPlot(imgIntTCompLeft)
|
|
end
|
|
end
|
|
|
|
@onbutton imgMinusCompRight begin
|
|
if isempty(selected_folder_compare_right) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_right)
|
|
if !isdir(folder_path) return end
|
|
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=decrement_image(current_msiCompRight, msi_bmp)
|
|
new_col_msi=decrement_image(current_col_msiCompRight, col_msi_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_msiCompRight = new_msi
|
|
current_col_msiCompRight = new_col_msi
|
|
imgIntCompRight = "/$(selected_folder_compare_right)/$(current_msiCompRight)?t=$(timestamp)"
|
|
colorbarCompRight = "/$(selected_folder_compare_right)/$(current_col_msiCompRight)?t=$(timestamp)"
|
|
text_nmass = replace(current_msiCompRight, r"MSI_|.bmp" => "")
|
|
msgimgCompRight = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgCompRight, plotlayoutImgCompRight, _, _ = loadImgPlot(imgIntCompRight)
|
|
end
|
|
end
|
|
|
|
@onbutton imgPlusCompRight begin
|
|
if isempty(selected_folder_compare_right) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_right)
|
|
if !isdir(folder_path) return end
|
|
|
|
msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=increment_image(current_msiCompRight, msi_bmp)
|
|
new_col_msi=increment_image(current_col_msiCompRight, col_msi_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_msiCompRight = new_msi
|
|
current_col_msiCompRight = new_col_msi
|
|
imgIntCompRight = "/$(selected_folder_compare_right)/$(current_msiCompRight)?t=$(timestamp)"
|
|
colorbarCompRight = "/$(selected_folder_compare_right)/$(current_col_msiCompRight)?t=$(timestamp)"
|
|
text_nmass = replace(current_msiCompRight, r"MSI_|.bmp" => "")
|
|
msgimgCompRight = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgCompRight, plotlayoutImgCompRight, _, _ = loadImgPlot(imgIntCompRight)
|
|
end
|
|
end
|
|
|
|
@onbutton imgMinusTCompRight begin
|
|
if isempty(selected_folder_compare_right) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_right)
|
|
if !isdir(folder_path) return end
|
|
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=decrement_image(current_triqCompRight, triq_bmp)
|
|
new_col_msi=decrement_image(current_col_triqCompRight, col_triq_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_triqCompRight = new_msi
|
|
current_col_triqCompRight = new_col_msi
|
|
imgIntTCompRight = "/$(selected_folder_compare_right)/$(current_triqCompRight)?t=$(timestamp)"
|
|
colorbarTCompRight = "/$(selected_folder_compare_right)/$(current_col_triqCompRight)?t=$(timestamp)"
|
|
text_nmass = replace(current_triqCompRight, r"TrIQ_|.bmp" => "")
|
|
msgtriqCompRight = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgTCompRight, plotlayoutImgTCompRight, _, _ = loadImgPlot(imgIntTCompRight)
|
|
end
|
|
end
|
|
|
|
@onbutton imgPlusTCompRight begin
|
|
if isempty(selected_folder_compare_right) return end
|
|
timestamp=string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_right)
|
|
if !isdir(folder_path) return end
|
|
|
|
triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural)
|
|
col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural)
|
|
|
|
new_msi=increment_image(current_triqCompRight, triq_bmp)
|
|
new_col_msi=increment_image(current_col_triqCompRight, col_triq_png)
|
|
if new_msi !== nothing && new_col_msi !== nothing
|
|
current_triqCompRight = new_msi
|
|
current_col_triqCompRight = new_col_msi
|
|
imgIntTCompRight = "/$(selected_folder_compare_right)/$(current_triqCompRight)?t=$(timestamp)"
|
|
colorbarTCompRight = "/$(selected_folder_compare_right)/$(current_col_triqCompRight)?t=$(timestamp)"
|
|
text_nmass = replace(current_triqCompRight, r"TrIQ_|.bmp" => "")
|
|
msgtriqCompRight = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
plotdataImgTCompRight, plotlayoutImgTCompRight, _, _ = loadImgPlot(imgIntTCompRight)
|
|
end
|
|
end
|
|
|
|
# This handler will now correctly load the first image from the newly selected folder.
|
|
@onchange selected_folder_main begin
|
|
msi_data = nothing
|
|
log_memory_usage("Folder Changed (msi_data cleared)", msi_data)
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
|
|
if !isempty(selected_folder_main)
|
|
folder_path = joinpath("public", selected_folder_main)
|
|
if !isdir(folder_path)
|
|
imgInt = ""
|
|
colorbar = ""
|
|
imgIntT = ""
|
|
colorbarT = ""
|
|
msgimg = "Folder not found."
|
|
msgtriq = "Folder not found."
|
|
plotdataImg = [traceImg]
|
|
plotlayoutImg = layoutImg
|
|
plotdataImgT = [traceImg]
|
|
plotlayoutImgT = layoutImg
|
|
imgWidth, imgHeight = 0, 0
|
|
return
|
|
end
|
|
|
|
# Handle normal images
|
|
msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)), lt=natural)
|
|
col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)), lt=natural)
|
|
|
|
if !isempty(msi_bmp)
|
|
current_msi = first(msi_bmp)
|
|
imgInt = "/$(selected_folder_main)/$(current_msi)"
|
|
plotdataImg, plotlayoutImg, w, h = loadImgPlot(imgInt)
|
|
imgWidth, imgHeight = w, h
|
|
text_nmass = replace(current_msi, r"MSI_|.bmp" => "")
|
|
msgimg = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
if !isempty(col_msi_png)
|
|
current_col_msi = first(col_msi_png)
|
|
colorbar = "/$(selected_folder_main)/$(current_col_msi)"
|
|
else
|
|
colorbar = ""
|
|
end
|
|
else
|
|
imgInt = ""
|
|
colorbar = ""
|
|
msgimg = "No MSI images found in this dataset."
|
|
plotdataImg = [traceImg]
|
|
plotlayoutImg = layoutImg
|
|
end
|
|
|
|
# Handle TrIQ images
|
|
triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)), lt=natural)
|
|
col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)), lt=natural)
|
|
|
|
if !isempty(triq_bmp)
|
|
current_triq = first(triq_bmp)
|
|
imgIntT = "/$(selected_folder_main)/$(current_triq)"
|
|
plotdataImgT, plotlayoutImgT, w, h = loadImgPlot(imgIntT)
|
|
# If no MSI image was loaded, dimensions from TrIQ image are used.
|
|
if isempty(msi_bmp)
|
|
imgWidth, imgHeight = w, h
|
|
end
|
|
text_nmass = replace(current_triq, r"TrIQ_|.bmp" => "")
|
|
msgtriq = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
if !isempty(col_triq_png)
|
|
current_col_triq = first(col_triq_png)
|
|
colorbarT = "/$(selected_folder_main)/$(current_col_triq)"
|
|
else
|
|
colorbarT = ""
|
|
end
|
|
else
|
|
imgIntT = ""
|
|
colorbarT = ""
|
|
msgtriq = "No TrIQ images found in this dataset."
|
|
plotdataImgT = [traceImg]
|
|
plotlayoutImgT = layoutImg
|
|
end
|
|
|
|
if isempty(msi_bmp) && isempty(triq_bmp)
|
|
imgWidth, imgHeight = 0, 0
|
|
end
|
|
end
|
|
end
|
|
|
|
@onchange selected_folder_compare_left begin
|
|
if !isempty(selected_folder_compare_left)
|
|
timestamp = string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_left)
|
|
|
|
if !isdir(folder_path)
|
|
imgIntCompLeft, colorbarCompLeft, imgIntTCompLeft, colorbarTCompLeft = "", "", "", ""
|
|
msgimgCompLeft, msgtriqCompLeft = "Folder not found.", "Folder not found."
|
|
return
|
|
end
|
|
|
|
# Handle normal images
|
|
msi_bmp = sort(filter(f -> startswith(f, "MSI_") && endswith(f, ".bmp"), readdir(folder_path)), lt=natural)
|
|
col_msi_png = sort(filter(f -> startswith(f, "colorbar_MSI_") && endswith(f, ".png"), readdir(folder_path)), lt=natural)
|
|
|
|
if !isempty(msi_bmp)
|
|
current_msiCompLeft = first(msi_bmp)
|
|
imgIntCompLeft = "/$(selected_folder_compare_left)/$(current_msiCompLeft)?t=$(timestamp)"
|
|
plotdataImgCompLeft, plotlayoutImgCompLeft, _, _ = loadImgPlot(imgIntCompLeft)
|
|
text_nmass = replace(current_msiCompLeft, r"MSI_|.bmp" => "")
|
|
msgimgCompLeft = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
|
|
if !isempty(col_msi_png)
|
|
current_col_msiCompLeft = first(col_msi_png)
|
|
colorbarCompLeft = "/$(selected_folder_compare_left)/$(current_col_msiCompLeft)?t=$(timestamp)"
|
|
else
|
|
colorbarCompLeft = ""
|
|
end
|
|
else
|
|
imgIntCompLeft, colorbarCompLeft, msgimgCompLeft = "", "", "No MSI images."
|
|
end
|
|
|
|
# Handle TrIQ images
|
|
triq_bmp = sort(filter(f -> startswith(f, "TrIQ_") && endswith(f, ".bmp"), readdir(folder_path)), lt=natural)
|
|
col_triq_png = sort(filter(f -> startswith(f, "colorbar_TrIQ_") && endswith(f, ".png"), readdir(folder_path)), lt=natural)
|
|
|
|
if !isempty(triq_bmp)
|
|
current_triqCompLeft = first(triq_bmp)
|
|
imgIntTCompLeft = "/$(selected_folder_compare_left)/$(current_triqCompLeft)?t=$(timestamp)"
|
|
plotdataImgTCompLeft, plotlayoutImgTCompLeft, _, _ = loadImgPlot(imgIntTCompLeft)
|
|
text_nmass = replace(current_triqCompLeft, r"TrIQ_|.bmp" => "")
|
|
msgtriqCompLeft = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
|
|
if !isempty(col_triq_png)
|
|
current_col_triqCompLeft = first(col_triq_png)
|
|
colorbarTCompLeft = "/$(selected_folder_compare_left)/$(current_col_triqCompLeft)?t=$(timestamp)"
|
|
else
|
|
colorbarTCompLeft = ""
|
|
end
|
|
else
|
|
imgIntTCompLeft, colorbarTCompLeft, msgtriqCompLeft = "", "", "No TrIQ images."
|
|
end
|
|
end
|
|
end
|
|
|
|
@onchange selected_folder_compare_right begin
|
|
if !isempty(selected_folder_compare_right)
|
|
timestamp = string(time_ns())
|
|
folder_path = joinpath("public", selected_folder_compare_right)
|
|
if !isdir(folder_path)
|
|
imgIntCompRight, colorbarCompRight, imgIntTCompRight, colorbarTCompRight = "", "", "", ""
|
|
msgimgCompRight, msgtriqCompRight = "Folder not found.", "Folder not found."
|
|
return
|
|
end
|
|
|
|
# Handle normal images
|
|
msi_bmp = sort(filter(f -> startswith(f, "MSI_") && endswith(f, ".bmp"), readdir(folder_path)), lt=natural)
|
|
col_msi_png = sort(filter(f -> startswith(f, "colorbar_MSI_") && endswith(f, ".png"), readdir(folder_path)), lt=natural)
|
|
|
|
if !isempty(msi_bmp)
|
|
current_msiCompRight = first(msi_bmp)
|
|
imgIntCompRight = "/$(selected_folder_compare_right)/$(current_msiCompRight)?t=$(timestamp)"
|
|
plotdataImgCompRight, plotlayoutImgCompRight, _, _ = loadImgPlot(imgIntCompRight)
|
|
text_nmass = replace(current_msiCompRight, r"MSI_|.bmp" => "")
|
|
msgimgCompRight = "<i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
|
|
if !isempty(col_msi_png)
|
|
current_col_msiCompRight = first(col_msi_png)
|
|
colorbarCompRight = "/$(selected_folder_compare_right)/$(current_col_msiCompRight)?t=$(timestamp)"
|
|
else
|
|
colorbarCompRight = ""
|
|
end
|
|
else
|
|
imgIntCompRight, colorbarCompRight, msgimgCompRight = "", "", "No MSI images."
|
|
end
|
|
|
|
# Handle TrIQ images
|
|
triq_bmp = sort(filter(f -> startswith(f, "TrIQ_") && endswith(f, ".bmp"), readdir(folder_path)), lt=natural)
|
|
col_triq_png = sort(filter(f -> startswith(f, "colorbar_TrIQ_") && endswith(f, ".png"), readdir(folder_path)), lt=natural)
|
|
|
|
if !isempty(triq_bmp)
|
|
current_triqCompRight = first(triq_bmp)
|
|
imgIntTCompRight = "/$(selected_folder_compare_right)/$(current_triqCompRight)?t=$(timestamp)"
|
|
plotdataImgTCompRight, plotlayoutImgTCompRight, _, _ = loadImgPlot(imgIntTCompRight)
|
|
text_nmass = replace(current_triqCompRight, r"TrIQ_|.bmp" => "")
|
|
msgtriqCompRight = "TrIQ <i>m/z</i>: $(replace(text_nmass, "_" => "."))"
|
|
|
|
if !isempty(col_triq_png)
|
|
current_col_triqCompRight = first(col_triq_png)
|
|
colorbarTCompRight = "/$(selected_folder_compare_right)/$(current_col_triqCompRight)?t=$(timestamp)"
|
|
else
|
|
colorbarTCompRight = ""
|
|
end
|
|
else
|
|
imgIntTCompRight, colorbarTCompRight, msgtriqCompRight = "", "", "No TrIQ images."
|
|
end
|
|
end
|
|
end
|
|
|
|
|
|
# 3d plot
|
|
@onbutton image3dPlot begin
|
|
msg = "Image 3D plot selected"
|
|
cleaned_imgInt = replace(imgInt, r"\?.*" => "")
|
|
cleaned_imgInt = lstrip(cleaned_imgInt, '/')
|
|
var = joinpath("./public", cleaned_imgInt)
|
|
|
|
if !isfile(var)
|
|
msg = "Image could not be 3d plotted"
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
progressPlot = true
|
|
btnPlotDisable = true
|
|
btnStartDisable = true
|
|
btnSpectraDisable = true
|
|
|
|
try
|
|
# --- Get Mask Path ---
|
|
local mask_path_for_plot::Union{String, Nothing} = nothing
|
|
if maskEnabled && !isempty(selected_folder_main)
|
|
registry = load_registry(registry_path)
|
|
entry = get(registry, selected_folder_main, nothing)
|
|
if entry !== nothing && get(entry, "has_mask", false)
|
|
mask_path_candidate = get(entry, "mask_path", "")
|
|
if isfile(mask_path_candidate)
|
|
mask_path_for_plot = mask_path_candidate
|
|
else
|
|
@warn "Mask enabled but file not found: $(mask_path_candidate). Plotting without mask."
|
|
end
|
|
end
|
|
end
|
|
# ---
|
|
|
|
sTime = time()
|
|
if mask_path_for_plot !== nothing
|
|
plotdata3d, plotlayout3d = loadSurfacePlot(imgInt, mask_path_for_plot)
|
|
else
|
|
plotdata3d, plotlayout3d = loadSurfacePlot(imgInt)
|
|
end
|
|
|
|
selectedTab = "tab4"
|
|
fTime = time()
|
|
eTime = round(fTime - sTime, digits=3)
|
|
msg = "Plot loaded in $(eTime) seconds"
|
|
log_memory_usage("Mean Plot Generated", msi_data)
|
|
catch e
|
|
msg = "Failed to load and process image: $e"
|
|
warning_msg = true
|
|
@error "3D plot generation failed" exception=(e, catch_backtrace())
|
|
finally
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
@onbutton triq3dPlot begin
|
|
msg = "TrIQ 3D plot selected"
|
|
cleaned_imgIntT = replace(imgIntT, r"\?.*" => "")
|
|
cleaned_imgIntT = lstrip(cleaned_imgIntT, '/')
|
|
var = joinpath("./public", cleaned_imgIntT)
|
|
|
|
if !isfile(var)
|
|
msg = "Image could not be 3d plotted"
|
|
warning_msg = true
|
|
return
|
|
end
|
|
|
|
progressPlot = true
|
|
btnPlotDisable = true
|
|
btnStartDisable = true
|
|
btnSpectraDisable = true
|
|
|
|
try
|
|
# --- Get Mask Path ---
|
|
local mask_path_for_plot::Union{String, Nothing} = nothing
|
|
if maskEnabled[] && !isempty(selected_folder_main)
|
|
registry = load_registry(registry_path)
|
|
entry = get(registry, selected_folder_main, nothing)
|
|
if entry !== nothing && get(entry, "has_mask", false)
|
|
mask_path_candidate = get(entry, "mask_path", "")
|
|
if isfile(mask_path_candidate)
|
|
mask_path_for_plot = mask_path_candidate
|
|
else
|
|
@warn "Mask enabled but file not found: $(mask_path_candidate). Plotting without mask."
|
|
end
|
|
end
|
|
end
|
|
# ---
|
|
|
|
sTime = time()
|
|
if mask_path_for_plot !== nothing
|
|
plotdata3d, plotlayout3d = loadSurfacePlot(imgIntT, mask_path_for_plot)
|
|
else
|
|
plotdata3d, plotlayout3d = loadSurfacePlot(imgIntT)
|
|
end
|
|
|
|
selectedTab = "tab4"
|
|
fTime = time()
|
|
eTime = round(fTime - sTime, digits=3)
|
|
msg = "Plot loaded in $(eTime) seconds"
|
|
log_memory_usage("Mean Plot Generated", msi_data)
|
|
catch e
|
|
msg = "Failed to load and process image: $e"
|
|
warning_msg = true
|
|
@error "3D TrIQ plot generation failed" exception=(e, catch_backtrace())
|
|
finally
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
# Contour 2d plot
|
|
@onbutton imageCPlot begin
|
|
msg="Image 2D plot selected"
|
|
cleaned_imgInt=replace(imgInt, r"\?.*" => "")
|
|
cleaned_imgInt=lstrip(cleaned_imgInt, '/')
|
|
var=joinpath("./public", cleaned_imgInt)
|
|
|
|
if !isfile(var)
|
|
msg="Image could not be 2D plotted"
|
|
warning_msg=true
|
|
return
|
|
end
|
|
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
btnSpectraDisable=true
|
|
|
|
try
|
|
sTime=time()
|
|
plotdataC,plotlayoutC=loadContourPlot(imgInt)
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab3"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
finally
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
# Contour 2d plot for TrIQ
|
|
@onbutton triqCPlot begin
|
|
msg="Image 2D plot selected"
|
|
cleaned_imgIntT=replace(imgIntT, r"\?.*" => "")
|
|
cleaned_imgIntT=lstrip(cleaned_imgIntT, '/')
|
|
var=joinpath("./public", cleaned_imgIntT)
|
|
|
|
if !isfile(var)
|
|
msg="Image could not be 2D plotted"
|
|
warning_msg=true
|
|
return
|
|
end
|
|
|
|
progressPlot=true
|
|
btnPlotDisable=true
|
|
btnStartDisable=true
|
|
btnSpectraDisable=true
|
|
|
|
try
|
|
sTime=time()
|
|
plotdataC,plotlayoutC=loadContourPlot(imgIntT)
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure Julia returns the freed memory to OS
|
|
end
|
|
selectedTab="tab3"
|
|
fTime=time()
|
|
eTime=round(fTime-sTime,digits=3)
|
|
msg="Plot loaded in $(eTime) seconds"
|
|
catch e
|
|
msg="Failed to load and process image: $e"
|
|
warning_msg=true
|
|
finally
|
|
progressPlot=false
|
|
btnPlotDisable=false
|
|
btnStartDisable=false
|
|
btnSpectraDisable=false
|
|
SpectraEnabled=true
|
|
GC.gc()
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0)
|
|
end
|
|
end
|
|
end
|
|
|
|
@onbutton compareBtn begin
|
|
CompareDialog=true
|
|
end
|
|
|
|
# To include a visualization in the spectrum plot indicating where is the selected mass
|
|
@onchange Nmass begin
|
|
if !isempty(xSpectraMz)
|
|
# Main spectrum trace
|
|
traceSpectra = PlotlyBase.stem(
|
|
x=xSpectraMz,
|
|
y=ySpectraMz,
|
|
marker=attr(size=1, color="blue", opacity=0.5),
|
|
name="Spectrum",
|
|
hoverinfo="x",
|
|
hovertemplate="<b>m/z</b>: %{x:.4f}<extra></extra>",
|
|
showlegend=false
|
|
)
|
|
|
|
# Parse all valid masses from the comma-separated string
|
|
mass_strs = split(Nmass, ',', keepempty=false)
|
|
mass_traces = [traceSpectra] # Start with the main spectrum
|
|
|
|
valid_masses = Float64[]
|
|
for (idx, mass_str) in enumerate(mass_strs)
|
|
try
|
|
mass_val = parse(Float64, strip(mass_str))
|
|
if mass_val > 0 # Only add valid positive masses
|
|
push!(valid_masses, mass_val)
|
|
|
|
# Create a vertical line for this mass (Plotly will auto-assign colors)
|
|
mass_trace = PlotlyBase.scatter(
|
|
x=[mass_val, mass_val],
|
|
y=[0, maximum(ySpectraMz)],
|
|
mode="lines",
|
|
line=attr(width=1.5, dash="dash"),
|
|
name="m/z $(round(mass_val, digits=4))",
|
|
showlegend=false,
|
|
hoverinfo="x+name",
|
|
hovertemplate="<b>%{data.name}</b><extra></extra>"
|
|
)
|
|
push!(mass_traces, mass_trace)
|
|
end
|
|
catch e
|
|
# Skip invalid entries, continue with next
|
|
continue
|
|
end
|
|
end
|
|
|
|
# Update the plot data
|
|
plotdata = mass_traces
|
|
end
|
|
end
|
|
|
|
# Event detection for clicking on the images
|
|
@onchange data_click begin
|
|
if selectedTab == "tab1" || selectedTab == "tab0"
|
|
# This is for the image heatmaps
|
|
cursor_data = get(data_click, "cursor", nothing)
|
|
if cursor_data === nothing
|
|
return
|
|
end
|
|
|
|
x_val = get(cursor_data, "x", nothing)
|
|
y_val = get(cursor_data, "y", nothing)
|
|
|
|
if x_val === nothing || y_val === nothing
|
|
return # Do nothing if coordinates are not provided by the event
|
|
end
|
|
|
|
x = Int32(round(x_val))
|
|
y = Int32(round(y_val)) # y is negative in the UI
|
|
|
|
# Update the reactive coordinates, which will trigger the crosshair update
|
|
xCoord = clamp(x, 1, imgWidth)
|
|
yCoord = clamp(y, -imgHeight, -1)
|
|
end
|
|
end
|
|
|
|
@onchange xCoord, yCoord begin
|
|
if selectedTab == "tab1"
|
|
main_trace = plotdataImgT[1] # The heatmap/image trace
|
|
trace1, trace2 = crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
|
|
plotdataImgT = [main_trace, trace1, trace2] # Fresh array every time
|
|
elseif selectedTab == "tab0"
|
|
main_trace = plotdataImg[1] # The heatmap/image trace
|
|
trace1, trace2 = crossLinesPlot(xCoord, yCoord, imgWidth, -imgHeight)
|
|
plotdataImg = [main_trace, trace1, trace2]
|
|
end
|
|
end
|
|
|
|
@onbutton btnOptical begin
|
|
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
|
|
if imgRoute==""
|
|
msg="No optical image selected"
|
|
else
|
|
selectedTab="tab0"
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
|
|
img=load(imgRoute)
|
|
save("./public/css/imgOver.png",img)
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
|
|
end
|
|
|
|
end
|
|
|
|
@onbutton btnOpticalT begin
|
|
imgRoute=pick_file(; filterlist="png,bmp,jpg,jpeg")
|
|
if imgRoute==""
|
|
msg="No optical image selected"
|
|
else
|
|
selectedTab="tab1"
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
|
|
img=load(imgRoute)
|
|
save("./public/css/imgOver.png",img)
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
|
|
opticalOverTriq=true
|
|
end
|
|
end
|
|
|
|
@onchange imgTrans begin
|
|
if !opticalOverTriq && imgRoute!=""
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
|
|
elseif opticalOverTriq && imgRoute!=""
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
|
|
end
|
|
end
|
|
|
|
@onchange opticalOverTriq begin
|
|
if !opticalOverTriq && imgRoute!=""
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt,"/css/imgOver.png",imgTrans)
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT)
|
|
selectedTab="tab0"
|
|
elseif opticalOverTriq && imgRoute!=""
|
|
plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt)
|
|
plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT,"/css/imgOver.png",imgTrans)
|
|
selectedTab="tab1"
|
|
end
|
|
end
|
|
|
|
@mounted watchplots()
|
|
|
|
@onchange isready begin
|
|
if isready && !registry_init_done
|
|
warmup_init()
|
|
try
|
|
println("Synchronizing registry with filesystem on backend init...")
|
|
reg_path = abspath(joinpath(@__DIR__, "public", "registry.json"))
|
|
registry = isfile(reg_path) ? load_registry(reg_path) : Dict{String, Any}()
|
|
|
|
public_dirs = isdir("public") ? readdir("public") : []
|
|
ignored_dirs = ["css", "masks"]
|
|
|
|
dataset_dirs = filter(d -> isdir(joinpath("public", d)) && !(d in ignored_dirs), public_dirs)
|
|
|
|
registry_keys = Set(keys(registry))
|
|
folder_set = Set(dataset_dirs)
|
|
|
|
new_folders = setdiff(folder_set, registry_keys)
|
|
for folder in new_folders
|
|
println("Found new folder: $folder")
|
|
registry[folder] = Dict(
|
|
"source_path" => "unknown (manually added)",
|
|
"processed_date" => "unknown",
|
|
"metadata" => Dict(),
|
|
"is_imzML" => true # Assume folder contains images if found this way
|
|
)
|
|
end
|
|
|
|
removed_folders = setdiff(registry_keys, folder_set)
|
|
for folder in removed_folders
|
|
delete!(registry, folder)
|
|
end
|
|
|
|
if !isempty(new_folders) || !isempty(removed_folders)
|
|
println("Registry changed, saving...")
|
|
open(reg_path, "w") do f
|
|
JSON.print(f, registry, 4)
|
|
end
|
|
end
|
|
|
|
all_folders = sort(collect(keys(registry)), lt=natural)
|
|
img_folders = filter(folder -> get(get(registry, folder, Dict()), "is_imzML", false), all_folders)
|
|
|
|
available_folders = deepcopy(all_folders)
|
|
image_available_folders = deepcopy(img_folders)
|
|
|
|
println("UI lists updated. All: $(length(available_folders)), Images: $(length(image_available_folders))")
|
|
|
|
catch e
|
|
@warn "Registry synchronization failed: $e"
|
|
available_folders = []
|
|
image_available_folders = []
|
|
selected_files = String[]
|
|
finally
|
|
registry_init_done = true
|
|
end
|
|
end
|
|
log_memory_usage("App Ready", msi_data)
|
|
end
|
|
|
|
GC.gc() # Trigger garbage collection
|
|
if Sys.islinux()
|
|
ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS
|
|
end
|
|
end
|
|
# == Pages ==
|
|
# Register a new route and the page that will be loaded on access
|
|
@page("/", "app.jl.html")
|
|
end
|