diff --git a/.gitignore b/.gitignore index 6f882ee..fcda959 100644 --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,6 @@ public/* public/css/imgOver.png !public/css/ -!public/masks/ -public/masks/* -!public/masks/static.txt log/* R_original_scripts/ test/results/ diff --git a/Manifest.toml b/Manifest.toml index 456263d..40c25fa 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.7" manifest_format = "2.0" -project_hash = "d4aecbadf6a54893101b3b89b57e8ae0ab391000" +project_hash = "b3d73d786a430f468e0f2f1b3b05da6a3addc7fe" [[deps.ATK_jll]] deps = ["Artifacts", "Glib_jll", "JLLWrappers", "Libdl"] diff --git a/Project.toml b/Project.toml index ff9fc31..eed2f9b 100644 --- a/Project.toml +++ b/Project.toml @@ -13,6 +13,7 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" Genie = "c43c736e-a2d1-11e8-161f-af95117fbd1e" GenieFramework = "a59fdf5c-6bf0-4f5d-949c-a137c9e2f353" Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0" +JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Mmap = "a63ad114-7e13-5084-954f-fe012c677804" diff --git a/README.md b/README.md index 489bd0f..df99a18 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ https://codeberg.org/LabABI/JuliaMSI ~/Downloads/JuliaMSI-main/juliamsi 2. Without entering the Julia environment, launch the project in your terminal with the following command (which works for all operating systems): ``` - julia --threads auto --project=. start_MSI_GUI.jl + julia--project=. start_MSI_GUI.jl ``` 3. After the script has finished loading, you can open a [page](http://127.0.0.1:1481/) in your browser with the web app running. diff --git a/app.jl b/app.jl index a62df52..1737fa9 100644 --- a/app.jl +++ b/app.jl @@ -16,12 +16,161 @@ using NativeFileDialog # Opens the file explorer depending on the OS using StipplePlotly using Base.Filesystem: mv # To rename files in the system using Printf # Required for @sprintf macro in colorbar generation +using JSON +using Dates # Bring MSIData into App module's scope -using .MSI_src: MSIData, OpenMSIData, #=GetSpectrum,=# process_spectrum, IterateSpectra, ImzMLSource, _iterate_spectra_fast, MzMLSource, find_mass, ViridisPalette, get_mz_slice, quantize_intensity, save_bitmap, median_filter, save_bitmap, downsample_spectrum, TrIQ, precompute_analytics, ImportMzmlFile +using .MSI_src: MSIData, OpenMSIData, #=GetSpectrum,=# 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 include("./julia_imzML_visual.jl") +function load_registry(registry_path) + if isfile(registry_path) + try + return JSON.parsefile(registry_path, dicttype=Dict{String, Any}) + catch e + @error "Failed to parse registry.json: $e" + return Dict{String, Any}() + end + end + return Dict{String, Any}() +end + +function extract_metadata(msi_data::MSIData, source_path::String) + df = msi_data.spectrum_stats_df + if df === nothing + # This can happen if precompute_analytics hasn't been run + # We can still return basic info + return Dict( + "summary" => [ + Dict("parameter" => "File Name", "value" => basename(source_path)), + Dict("parameter" => "Number of Spectra", "value" => length(msi_data.spectra_metadata)), + Dict("parameter" => "Image Dimensions", "value" => "$(msi_data.image_dims[1]) x $(msi_data.image_dims[2])"), + ], + "global_min_mz" => nothing, + "global_max_mz" => nothing + ) + end + + summary_stats = [ + Dict("parameter" => "File Name", "value" => basename(source_path)), + Dict("parameter" => "Number of Spectra", "value" => length(msi_data.spectra_metadata)), + Dict("parameter" => "Image Dimensions", "value" => "$(msi_data.image_dims[1]) x $(msi_data.image_dims[2])"), + Dict("parameter" => "Global Min m/z", "value" => @sprintf("%.4f", msi_data.global_min_mz)), + Dict("parameter" => "Global Max m/z", "value" => @sprintf("%.4f", msi_data.global_max_mz)), + Dict("parameter" => "Mean TIC", "value" => @sprintf("%.2e", mean(df.TIC))), + Dict("parameter" => "Mean BPI", "value" => @sprintf("%.2e", mean(df.BPI))), + Dict("parameter" => "Mean # Points", "value" => @sprintf("%.1f", mean(df.NumPoints))), + ] + + if hasproperty(df, :Mode) + centroid_count = count(==(MSI_src.CENTROID), df.Mode) + profile_count = count(==(MSI_src.PROFILE), df.Mode) + unknown_count = count(==(MSI_src.UNKNOWN), df.Mode) + + push!(summary_stats, Dict("parameter" => "Centroid Spectra", "value" => string(centroid_count))) + push!(summary_stats, Dict("parameter" => "Profile Spectra", "value" => string(profile_count))) + if unknown_count > 0 + push!(summary_stats, Dict("parameter" => "Unknown Mode Spectra", "value" => string(unknown_count))) + end + end + + return Dict( + "summary" => summary_stats, + "global_min_mz" => msi_data.global_min_mz, + "global_max_mz" => msi_data.global_max_mz + ) +end + +function update_registry(registry_path, dataset_name, source_path, metadata=nothing, is_imzML=false) + registry = load_registry(registry_path) + entry = Dict{String, Any}( # Explicitly type the dictionary to allow mixed value types + "source_path" => source_path, + "processed_date" => string(now()), + "is_imzML" => is_imzML + ) + if metadata !== nothing + entry["metadata"] = metadata + end + registry[dataset_name] = entry + + try + open(registry_path, "w") do f + JSON.print(f, registry, 4) + end + catch e + @error "Failed to write to registry.json: $e" + end +end + +function process_file_safely(file_path, masses, params, progress_message_ref, overall_progress_ref) + local_msi_data = nothing + dataset_name = replace(basename(file_path), r"\.imzML$"i => "") + output_dir = joinpath("public", dataset_name) + println("Processing: $dataset_name -> $output_dir") + + try + # --- Load Data --- + progress_message_ref = "Loading: $(basename(file_path))" + local_msi_data = OpenMSIData(file_path) + if !(local_msi_data.source isa ImzMLSource) + @warn "Skipping non-imzML file: $(basename(file_path))" + return (false, "Skipped: Not an imzML file") + end + + # --- Generate Slices (this will call precompute_analytics if needed) --- + progress_message_ref = "Generating $(length(masses)) slices for $(dataset_name)..." + slice_dict = get_multiple_mz_slices(local_msi_data, masses, params.tolerance) + + # --- Extract metadata *after* it has been computed --- + metadata = extract_metadata(local_msi_data, file_path) + + # --- Save Slices --- + mkpath(output_dir) # Ensure output directory exists + + for (mass_idx, mass) in enumerate(masses) + progress_message_ref = "File $(params.fileIdx)/$(params.nFiles): Saving slice for m/z=$mass" + + slice = slice_dict[mass] + text_nmass = replace(string(mass), "." => "_") + bitmap_filename = params.triqE ? "TrIQ_$(text_nmass).bmp" : "MSI_$(text_nmass).bmp" + colorbar_filename = params.triqE ? "colorbar_TrIQ_$(text_nmass).png" : "colorbar_MSI_$(text_nmass).png" + + if all(iszero, slice) + sliceQuant = zeros(UInt8, size(slice)) + @warn "No intensity data for m/z = $mass in $(dataset_name)" + else + sliceQuant = params.triqE ? TrIQ(slice, params.colorL, params.triqP) : quantize_intensity(slice, params.colorL) + if params.medianF + sliceQuant = round.(UInt8, median_filter(sliceQuant)) + end + end + + save_bitmap(joinpath(output_dir, bitmap_filename), sliceQuant, ViridisPalette) + if !all(iszero, slice) + generate_colorbar_image(slice, params.colorL, joinpath(output_dir, colorbar_filename); use_triq=params.triqE, triq_prob=params.triqP) + end + end + + is_imzML = local_msi_data.source isa ImzMLSource + update_registry(params.registry, dataset_name, file_path, metadata, is_imzML) + return (true, "") + + catch e + @error "File processing failed" file=file_path exception=(e, catch_backtrace()) + return (false, "File: $(basename(file_path)) - $(sprint(showerror, e))") + finally + if local_msi_data !== nothing + # Cleanup + end + local_msi_data = nothing + GC.gc(true) + if Sys.islinux() + ccall(:malloc_trim, Int32, (Int32,), 0) + end + end +end + @genietools # == Reactive code == @@ -36,7 +185,7 @@ include("./julia_imzML_visual.jl") ## Interface non Variables @out btnStartDisable=true @out btnPlotDisable=false - @out btnSpectraDisable=true + @out btnSpectraDisable=false # Loading animations @in progress=false @in progressPlot=false @@ -52,13 +201,16 @@ include("./julia_imzML_visual.jl") ## Interface Variables @in file_route="" @in file_name="" - @in Nmass=0.0 + @in Nmass="0.0" @in Tol=0.1 @in triqProb=0.98 @in colorLevel=20 ## Interface Buttons @in btnSearch=false # To search for files in your device + @in btnAddBatch = false + @in clear_batch_btn = false + @out batch_file_count = 0 @in mainProcess=false # To generate images @in compareBtn=false # To open dialog @in createMeanPlot=false # To generate mean spectrum plot @@ -74,18 +226,25 @@ include("./julia_imzML_visual.jl") @in imgPlusT=false @in imgMinusT=false # Image change comparative buttons - @in imgPlusComp=false - @in imgMinusComp=false - @in imgPlusTComp=false - @in imgMinusTComp=false + @in imgPlusCompLeft=false + @in imgMinusCompLeft=false + @in imgPlusTCompLeft=false + @in imgMinusTCompLeft=false + @in imgPlusCompRight=false + @in imgMinusCompRight=false + @in imgPlusTCompRight=false + @in imgMinusTCompRight=false ## Tabulation variables @out tabIDs=["tab0","tab1","tab2","tab3","tab4"] @out tabLabels=["Image", "TrIQ", "Spectrum Plot", "Topography Plot","Surface Plot"] @in selectedTab="tab0" - @out CompTabIDs=["tab0","tab1","tab2","tab3","tab4"] - @out CompTabLabels=["Image", "TrIQ", "Spectrum Plot", "Topography Plot","Surface Plot"] - @in CompSelectedTab="tab0" + @out CompTabIDsLeft=["tab0","tab1","tab2","tab3","tab4"] + @out CompTabLabelsLeft=["Image", "TrIQ", "Spectrum Plot", "Topography Plot","Surface Plot"] + @in CompSelectedTabLeft="tab0" + @out CompTabIDsRight=["tab0","tab1","tab2","tab3","tab4"] + @out CompTabLabelsRight=["Image", "TrIQ", "Spectrum Plot", "Topography Plot","Surface Plot"] + @in CompSelectedTabRight="tab0" # Interface Images @out imgInt="/.bmp" # image Interface @@ -93,10 +252,14 @@ include("./julia_imzML_visual.jl") @out colorbar="/.png" @out colorbarT="/.png" # Interface controlling for the comparative view - @out imgIntComp="/.bmp" # image Interface - @out imgIntTComp="/.bmp" # image Interface TrIQ - @out colorbarComp="/.png" - @out colorbarTComp="/.png" + @out imgIntCompLeft="/.bmp" + @out imgIntTCompLeft="/.bmp" + @out colorbarCompLeft="/.png" + @out colorbarTCompLeft="/.png" + @out imgIntCompRight="/.bmp" + @out imgIntTCompRight="/.bmp" + @out colorbarCompRight="/.png" + @out colorbarTCompRight="/.png" @out imgWidth=0 @out imgHeight=0 @@ -114,8 +277,10 @@ include("./julia_imzML_visual.jl") @out msgimg="" @out msgtriq="" # Reiteration of the messages under the image to know which spectra is being visualized - @out msgimgComp="" - @out msgtriqComp="" + @out msgimgCompLeft="" + @out msgtriqCompLeft="" + @out msgimgCompRight="" + @out msgtriqCompRight="" # Centralized MSIData object @out msi_data::Union{MSIData, Nothing} = nothing @@ -125,7 +290,8 @@ include("./julia_imzML_visual.jl") @in showMetadataBtn = false @out metadata_columns = [] @out metadata_rows = [] - @out btnMetadataDisable = true + @out btnMetadataDisable = false + @in selected_folder_metadata = "" # Saves the route where imzML and mzML files are located @out full_route="" @@ -141,6 +307,25 @@ include("./julia_imzML_visual.jl") @out msg_conversion = "" @out btnConvertDisable = true + # == Batch Summary Dialog == + @in showBatchSummary = false + @out batch_summary = "" + + # == Batch Processing & Registry Variables == + @private registry_init_done = false + @in selected_files = String[] + @out available_folders = String[] + @out image_available_folders = String[] + @out registry_path = joinpath("public", "registry.json") + # Progress reporting + @out overall_progress = 0.0 + @out progress_message = "" + + # == Folder-based UI State == + @in selected_folder_main = "" + @in selected_folder_compare_left = "" + @in selected_folder_compare_right = "" + # For the creation of images with a more specific mass charge @out text_nmass="" @@ -157,10 +342,14 @@ include("./julia_imzML_visual.jl") @out current_triq="" @out current_col_triq="" # We reiterate the process to display in the comparative view - @out current_msiComp="" - @out current_col_msiComp="" - @out current_triqComp="" - @out current_col_triqComp="" + @out current_msiCompLeft="" + @out current_col_msiCompLeft="" + @out current_triqCompLeft="" + @out current_col_triqCompLeft="" + @out current_msiCompRight="" + @out current_col_msiCompRight="" + @out current_triqCompRight="" + @out current_col_triqCompRight="" ## Time measurement variables @out sTime=time() @@ -193,15 +382,19 @@ include("./julia_imzML_visual.jl") @out plotdataImg=[traceImg] @out plotlayoutImg=layoutImg # For the image in the comparative view - @out plotdataImgComp=[traceImg] - @out plotlayoutImgComp=layoutImg + @out plotdataImgCompLeft=[traceImg] + @out plotlayoutImgCompLeft=layoutImg + @out plotdataImgCompRight=[traceImg] + @out plotlayoutImgCompRight=layoutImg # For triq image @out plotdataImgT=[traceImg] @out plotlayoutImgT=layoutImg # For the triq image in the comparative view - @out plotdataImgTComp=[traceImg] - @out plotlayoutImgTComp=layoutImg + @out plotdataImgTCompLeft=[traceImg] + @out plotlayoutImgTCompLeft=layoutImg + @out plotdataImgTCompRight=[traceImg] + @out plotlayoutImgTCompRight=layoutImg # Interface Plot Spectrum layoutSpectra=PlotlyBase.Layout( title=PlotlyBase.attr( @@ -225,7 +418,7 @@ include("./julia_imzML_visual.jl") margin=attr(l=0,r=0,t=120,b=0,pad=0) ) # Dummy 2D scatter plot - traceSpectra=PlotlyBase.stem(x=Vector{Float64}(), y=Vector{Float64}(),marker=attr(size=1, color="blue", opacity=0.1)) + traceSpectra=PlotlyBase.scatter(x=Vector{Float64}(), y=Vector{Float64}(),marker=attr(size=1, color="blue", opacity=0.1)) # Create conection to frontend @out plotdata=[traceSpectra] @out plotlayout=layoutSpectra @@ -307,82 +500,108 @@ include("./julia_imzML_visual.jl") # Reactive handlers watch a variable and execute a block of code when its value changes # The onbutton handler will set the variable to false after the block is executed + # This handler correctly uses pick_file and loads the selected file + # as the active dataset for the UI. @onbutton btnSearch @time begin - # This part is synchronous and blocking, which is unavoidable picked_route = pick_file(; filterlist="imzML,imzml,mzML,mzml") - if isempty(picked_route) - msg = "No file selected." - warning_msg = true return end - # UI updates immediately progress = true msg = "Opening file: $(basename(picked_route))..." - + @async begin try - # --- Normalize file extension and path --- - if endswith(picked_route, "imzml") - full_route = replace(picked_route, r"\.imzml$"i => ".imzML") - mv(picked_route, full_route, force=true) - elseif endswith(picked_route, "mzml") - full_route = replace(picked_route, r"\.mzml$"i => ".mzML") - mv(picked_route, full_route, force=true) - else - full_route = picked_route - end + dataset_name = replace(basename(picked_route), r"(\.(imzML|imzml|mzML))$"i => "") + registry = load_registry(registry_path) + existing_entry = get(registry, dataset_name, nothing) - # --- Load data using the new MSIData library --- - sTime = time() - msi_data = OpenMSIData(full_route) - - # --- Pre-compute analytics for performance --- - precompute_analytics(msi_data) - - # --- Prepare metadata for display --- - if msi_data.spectrum_stats_df !== nothing - df = msi_data.spectrum_stats_df + # --- Fast Load Path --- + is_same_file = (existing_entry !== nothing && existing_entry["source_path"] == picked_route) + if is_same_file && !isempty(get(existing_entry, "metadata", Dict())) + msg = "Fast loading pre-processed file: $(dataset_name)" + println(msg) - # Define columns for the key-value summary table - metadata_columns = [ - Dict("name" => "parameter", "label" => "Parameter", "field" => "parameter", "align" => "left"), - Dict("name" => "value", "label" => "Value", "field" => "value", "align" => "left"), - ] - - # Calculate summary statistics - summary_stats = [ - Dict("parameter" => "File Name", "value" => basename(full_route)), - Dict("parameter" => "Number of Spectra", "value" => length(msi_data.spectra_metadata)), - Dict("parameter" => "Image Dimensions", "value" => "$(msi_data.image_dims[1]) x $(msi_data.image_dims[2])"), - Dict("parameter" => "Global Min m/z", "value" => @sprintf("%.4f", msi_data.global_min_mz)), - Dict("parameter" => "Global Max m/z", "value" => @sprintf("%.4f", msi_data.global_max_mz)), - Dict("parameter" => "Mean TIC", "value" => @sprintf("%.2e", mean(df.TIC))), - Dict("parameter" => "Mean BPI", "value" => @sprintf("%.2e", mean(df.BPI))), - Dict("parameter" => "Mean # Points", "value" => @sprintf("%.1f", mean(df.NumPoints))), - ] + full_route = existing_entry["source_path"] + metadata_rows = existing_entry["metadata"]["summary"] - metadata_rows = summary_stats + dims_str = first(filter(r -> r["parameter"] == "Image Dimensions", metadata_rows))["value"] + dims = parse.(Int, split(dims_str, " x ")) + imgWidth, imgHeight = dims[1], dims[2] + + msi_data = nothing # Ensure data is not held in memory btnMetadataDisable = false + btnStartDisable = false + btnPlotDisable = false + btnSpectraDisable = false + SpectraEnabled = true + selected_folder_main = dataset_name + + # Update folder lists in UI + 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) + + msg = "Successfully loaded pre-processed dataset: $(dataset_name)" + progress = false + return end - w, h = msi_data.image_dims + # --- Full Load Path --- + msg = "Performing first-time analysis for: $(basename(picked_route))..." + local local_full_route + if endswith(picked_route, r"imzml"i) + local_full_route = replace(picked_route, r"\.imzml$"i => ".imzML") + if picked_route != local_full_route + mv(picked_route, local_full_route, force=true) + end + else + local_full_route = picked_route + end + full_route = local_full_route + + sTime = time() + loaded_data = OpenMSIData(local_full_route) + is_imzML = loaded_data.source isa ImzMLSource + + precompute_analytics(loaded_data) + + metadata_columns = [ + Dict("name" => "parameter", "label" => "Parameter", "field" => "parameter", "align" => "left"), + Dict("name" => "value", "label" => "Value", "field" => "value", "align" => "left"), + ] + summary_stats = extract_metadata(loaded_data, local_full_route) + metadata_rows = summary_stats["summary"] + btnMetadataDisable = isempty(metadata_rows) + + w, h = loaded_data.image_dims imgWidth, imgHeight = w > 0 ? (w, h) : (500, 500) - fTime = time() - eTime = round(fTime - sTime, digits=3) - msg = "File loaded and indexed in $(eTime) seconds." + update_registry(registry_path, dataset_name, local_full_route, summary_stats, is_imzML) + + # Update folder lists in UI + registry = load_registry(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) - # Enable UI controls - btnStartDisable = !(msi_data.source isa ImzMLSource) + selected_folder_main = dataset_name + msi_data = loaded_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 file: $e" + msg = "Error loading active file: $e" warning_msg = true btnStartDisable = true btnSpectraDisable = true @@ -390,7 +609,6 @@ include("./julia_imzML_visual.jl") btnMetadataDisable = true @error "File loading failed" exception=(e, catch_backtrace()) finally - # This block will always run at the end of the async task GC.gc() if Sys.islinux() ccall(:malloc_trim, Int32, (Int32,), 0) @@ -401,8 +619,72 @@ include("./julia_imzML_visual.jl") 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 - showMetadataDialog = true + 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 @@ -469,172 +751,211 @@ include("./julia_imzML_visual.jl") end @onbutton mainProcess @time begin - # UI updates immediately + # --- UI State Update --- progress = true btnStartDisable = true btnPlotDisable = true btnSpectraDisable = true + overall_progress = 0.0 + progress_message = "Preparing batch process..." + + # --- CAPTURE CURRENT VALUES HERE (NO []) --- + 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_registry_path = registry_path + + println("starting main process with $(length(current_selected_files)) files") @async begin + total_time_start = time() try - text_nmass = replace(string(Nmass), "." => "_") - sTime = time() - - if msi_data === nothing || !(msi_data.source isa ImzMLSource) - msg = "No .imzML file loaded or selected file is not an .imzML. Please select a valid file." + # --- 1. Parameter Validation --- + if isempty(current_selected_files) + progress_message = "No .imzML files in batch. Please add files first." warning_msg = true - elseif Nmass > 0 && Tol > 0 && Tol <= 1 && colorLevel > 1 && colorLevel < 257 - msg = "Creating image for m/z=$(Nmass) Tol=$(Tol). Please be patient." - try - # Use the new get_mz_slice with the centralized MSIData object - println("get_mz_slice time:") - slice = @time get_mz_slice(msi_data, Nmass, Tol) + println(progress_message) + return + end - # Failsafe check for empty slice - if all(iszero, slice) - msg = "No intensity data found for m/z = $Nmass with tolerance = $Tol. The resulting image is black. Please consider using a larger tolerance." - warning_msg = true - - # Generate a black image but skip the colorbar that would crash - timestamp = string(time_ns()) - text_nmass = replace(string(Nmass), "." => "_") - sliceQuant = zeros(UInt8, size(slice)) - - if triqEnabled - @time save_bitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"), sliceQuant, ViridisPalette) - imgIntT = "/TrIQ_$(text_nmass).bmp?t=$(timestamp)" - plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT) - current_triq = "TrIQ_$(text_nmass).bmp" - msgtriq = "TrIQ image with the Nmass of $(replace(text_nmass, "_" => ".")) (No data)" - colorbarT = "" # Clear colorbar - current_col_triq = "" - triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")), lt=natural) - selectedTab = "tab1" - else - @time save_bitmap(joinpath("public", "MSI_$(text_nmass).bmp"), sliceQuant, ViridisPalette) - imgInt = "/MSI_$(text_nmass).bmp?t=$(timestamp)" - plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt) - current_msi = "MSI_$(text_nmass).bmp" - msgimg = "Image with the Nmass of $(replace(text_nmass, "_" => ".")) (No data)" - colorbar = "" # Clear colorbar - current_col_msi = "" - msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")), lt=natural) - selectedTab = "tab0" - end - fTime = time() - eTime = round(fTime - sTime, digits=3) - # The warning message is already set above - else - # Original path for when data is found - fig = CairoMakie.Figure(size=(150, 250)) # Container - timestamp = string(time_ns()) + println("Nmass value: '$current_nmass'") + println("Type of current_nmass: $(typeof(current_nmass))") - if triqEnabled # If we have TrIQ - if triqProb < 0.8 || triqProb > 1 - msg = "Incorrect TrIQ values, please adjust accordingly and try again." - warning_msg = true - else - println("TrIQ time:") - sliceTriq = @time TrIQ(slice, colorLevel, triqProb) - if MFilterEnabled - sliceTriq = round.(UInt8, median_filter(sliceTriq)) - end + masses_str = split(current_nmass, ',', keepempty=false) + println("Parsed masses strings: $masses_str") - println("save_bitmap time:") - @time save_bitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"), sliceTriq, ViridisPalette) + masses = Float64[] + try + masses = [parse(Float64, strip(m)) for m in masses_str] + println("Parsed masses: $masses") + catch e + progress_message = "Invalid m/z value(s). Please provide a comma-separated list of numbers. Error: $e" + warning_msg = true + println(progress_message) + return + end - imgIntT = "/TrIQ_$(text_nmass).bmp?t=$(timestamp)" - plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT) - current_triq = "TrIQ_$(text_nmass).bmp" - msgtriq = "TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" + println("Masses array: $masses, type: $(typeof(masses))") - colorbar_path = joinpath("public", "colorbar_TrIQ_$(text_nmass).png") - println("generate_colorbar_image time:") - @time generate_colorbar_image(slice, colorLevel, colorbar_path, use_triq=true, triq_prob=triqProb) - colorbarT = "/colorbar_TrIQ_$(text_nmass).png?t=$(timestamp)" - current_col_triq = "colorbar_TrIQ_$(text_nmass).png" + if !(masses isa AbstractArray) || isempty(masses) + progress_message = "No valid m/z values found. Please provide comma-separated positive numbers." + warning_msg = true + println(progress_message) + return + end - triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")), lt=natural) - col_triq_png = sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")), lt=natural) + # Check other parameters + if !(0 < current_tol <= 1) + progress_message = "Tolerance must be between 0 and 1." + warning_msg = true + println(progress_message) + return + end - fTime = time() - eTime = round(fTime - sTime, digits=3) - msg = "The TrIQ image has been created in $(eTime) seconds successfully inside the 'public' folder of the app" - selectedTab = "tab1" - end - else # If we don't use TrIQ - println("quantize_intensity time:") - sliceQuant = @time quantize_intensity(slice, colorLevel) - if MFilterEnabled - sliceQuant = round.(UInt8, median_filter(sliceQuant)) - end + if !(1 < current_color_level < 257) + progress_message = "Color levels must be between 2 and 256." + warning_msg = true + println(progress_message) + return + end - println("save_bitmap time:") - @time save_bitmap(joinpath("public", "MSI_$(text_nmass).bmp"), sliceQuant, ViridisPalette) + println("entering batch processing loop with masses: $masses") + + # --- 2. Batch Processing Loop --- + num_files = length(current_selected_files) + total_steps = num_files + current_step = 0 + errors = Dict("load_errors" => String[], "slice_errors" => String[], "io_errors" => String[]) + newly_created_folders = String[] - imgInt = "/MSI_$(text_nmass).bmp?t=$(timestamp)" - plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt) - current_msi = "MSI_$(text_nmass).bmp" - msgimg = "Image with the Nmass of $(replace(text_nmass, "_" => "."))" + for (file_idx, file_path) in enumerate(current_selected_files) + # Update progress for current file + progress_message = "Processing file $file_idx/$num_files: $(basename(file_path))" + overall_progress = current_step / total_steps + + # Create parameters for this specific file + all_params = ( + tolerance = current_tol, + colorL = current_color_level, + triqE = current_triq_enabled, + triqP = current_triq_prob, + medianF = current_mfilter_enabled, + registry = current_registry_path, + fileIdx = file_idx, + nFiles = num_files + ) - colorbar_path = joinpath("public", "colorbar_MSI_$(text_nmass).png") - println("generate_colorbar_image time:") - @time generate_colorbar_image(slice, colorLevel, colorbar_path) - colorbar = "/colorbar_MSI_$(text_nmass).png?t=$(timestamp)" - current_col_msi = "colorbar_MSI_$(text_nmass).png" + # Process the file + success, error_msg = process_file_safely(file_path, masses, all_params, progress_message, overall_progress) - msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")), lt=natural) - col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")), lt=natural) - selectedTab = "tab0" - fTime = time() - eTime = round(fTime - sTime, digits=3) - msg = "The image has been created in $(eTime) seconds successfully inside the 'public' folder of the app" - end - end - catch e - msg = "There was an error creating the image: $e" - warning_msg = true - @error "Image creation failed" exception=(e, catch_backtrace()) + if !success + push!(errors["load_errors"], error_msg) + else + dataset_name = replace(basename(file_path), r"\.imzML$"i => "") + push!(newly_created_folders, dataset_name) end + current_step += 1 + end + + # --- 3. Final Report --- + total_time_end = round(time() - total_time_start, digits=3) + + # Update folder lists in UI + 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 = "Invalid parameters. Nmass, Tol, or colorLevel are incorrect." + msg = "Batch completed in $(total_time_end) seconds with $(total_errors) error(s)." warning_msg = true - @error msg end + + batch_summary = """ + Processed $(successful_files)/$(num_files) files successfully. + + 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 + + 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 - # This block will always run at the end of the async task - GC.gc() - if Sys.islinux() - ccall(:malloc_trim, Int32, (Int32,), 0) - end + # --- UI State Reset --- + progress = false btnStartDisable = false btnPlotDisable = false btnOpticalDisable = false - progress = false btnSpectraDisable = false SpectraEnabled = true + overall_progress = 0.0 + println("Done") end end end @onbutton createMeanPlot begin - if msi_data === nothing - msg = "No data loaded. Please select a file first." + if isempty(selected_folder_main) + msg = "No dataset selected. Please process a file and select a folder first." warning_msg = true return end - # UI updates immediately progressSpectraPlot = true btnPlotDisable = true btnStartDisable = true - msg = "Loading plot..." + msg = "Loading plot for $(selected_folder_main)..." @async begin try sTime = time() - plotdata, plotlayout, xSpectraMz, ySpectraMz = meanSpectrumPlot(msi_data) - + registry = load_registry(registry_path) + target_path = registry[selected_folder_main]["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) + + existing_entry = get(registry, selected_folder_main, nothing) + if existing_entry !== nothing && haskey(get(existing_entry, "metadata", Dict()), "global_min_mz") && existing_entry["metadata"]["global_min_mz"] !== nothing + println("Injecting cached m/z range to skip Pass 1...") + msi_data.global_min_mz = existing_entry["metadata"]["global_min_mz"] + msi_data.global_max_mz = existing_entry["metadata"]["global_max_mz"] + else + precompute_analytics(msi_data) + end + end + + plotdata, plotlayout, xSpectraMz, ySpectraMz = meanSpectrumPlot(msi_data, selected_folder_main) selectedTab = "tab2" fTime = time() eTime = round(fTime - sTime, digits=3) @@ -644,35 +965,53 @@ include("./julia_imzML_visual.jl") warning_msg = true @error "Mean spectrum plotting failed" exception=(e, catch_backtrace()) finally - # This runs after the async task is finished progressSpectraPlot = false btnPlotDisable = false btnSpectraDisable = false - if msi_data !== nothing && msi_data.source isa ImzMLSource - btnStartDisable = false - end + btnStartDisable = false end end end @onbutton createSumPlot begin - if msi_data === nothing - msg = "No data loaded. Please select a file first." + if isempty(selected_folder_main) + msg = "No dataset selected. Please process a file and select a folder first." warning_msg = true return end - # UI updates immediately progressSpectraPlot = true btnPlotDisable = true btnStartDisable = true - msg = "Loading total spectrum plot..." + msg = "Loading total spectrum plot for $(selected_folder_main)..." @async begin try sTime = time() - plotdata, plotlayout, xSpectraMz, ySpectraMz = sumSpectrumPlot(msi_data) - + registry = load_registry(registry_path) + target_path = registry[selected_folder_main]["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) + + existing_entry = get(registry, selected_folder_main, nothing) + if existing_entry !== nothing && haskey(get(existing_entry, "metadata", Dict()), "global_min_mz") && existing_entry["metadata"]["global_min_mz"] !== nothing + println("Injecting cached m/z range to skip Pass 1...") + msi_data.global_min_mz = existing_entry["metadata"]["global_min_mz"] + msi_data.global_max_mz = existing_entry["metadata"]["global_max_mz"] + else + precompute_analytics(msi_data) + end + end + + plotdata, plotlayout, xSpectraMz, ySpectraMz = sumSpectrumPlot(msi_data, selected_folder_main) selectedTab = "tab2" fTime = time() eTime = round(fTime - sTime, digits=3) @@ -682,44 +1021,58 @@ include("./julia_imzML_visual.jl") warning_msg = true @error "Total spectrum plotting failed" exception=(e, catch_backtrace()) finally - # This runs after the async task is finished progressSpectraPlot = false btnPlotDisable = false btnSpectraDisable = false - if msi_data !== nothing && msi_data.source isa ImzMLSource - btnStartDisable = false - end + btnStartDisable = false end end end @onbutton createXYPlot begin - if msi_data === nothing - msg = "No data loaded. Please select a file first." + if isempty(selected_folder_main) + msg = "No dataset selected. Please process a file and select a folder first." warning_msg = true return end - # UI updates immediately progressSpectraPlot = true btnStartDisable = true btnPlotDisable = true btnSpectraDisable = true - msg = "Loading plot..." + msg = "Loading plot for $(selected_folder_main)..." @async begin try sTime = time() - # The UI uses negative Y values, so we adjust before calling the plot function + registry = load_registry(registry_path) + target_path = registry[selected_folder_main]["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 $(basename(target_path)) for analysis..." + full_route = target_path + msi_data = OpenMSIData(target_path) + + existing_entry = get(registry, selected_folder_main, nothing) + if existing_entry !== nothing && haskey(get(existing_entry, "metadata", Dict()), "global_min_mz") && existing_entry["metadata"]["global_min_mz"] !== nothing + println("Injecting cached m/z range to skip Pass 1...") + msi_data.global_min_mz = existing_entry["metadata"]["global_min_mz"] + msi_data.global_max_mz = existing_entry["metadata"]["global_max_mz"] + else + precompute_analytics(msi_data) + end + end + y = yCoord < 0 ? abs(yCoord) : yCoord - plotdata, plotlayout, xSpectraMz, ySpectraMz = xySpectrumPlot(msi_data, xCoord, y, imgWidth, imgHeight) - - # Update UI coordinates + plotdata, plotlayout, xSpectraMz, ySpectraMz = xySpectrumPlot(msi_data, xCoord, y, imgWidth, imgHeight, selected_folder_main) xCoord = plotlayout.title == "Spectrum #$(xCoord)" ? xCoord : clamp(xCoord, 1, imgWidth) yCoord = plotlayout.title == "Spectrum #$(xCoord)" ? 0 : -clamp(y, 1, imgHeight) - selectedTab = "tab2" - fTime = time() eTime = round(fTime - sTime, digits=3) msg = "Plot loaded in $(eTime) seconds" @@ -728,249 +1081,460 @@ include("./julia_imzML_visual.jl") warning_msg = true @error "Spectrum plotting failed" exception=(e, catch_backtrace()) finally - # This runs after the async task is finished progressSpectraPlot = false btnPlotDisable = false btnSpectraDisable = false - if msi_data !== nothing && msi_data.source isa ImzMLSource - btnStartDisable = false - end + btnStartDisable = false end end end - # Image loaders based on the position of the current image (increment and decrement for both normal and filter) - # And a pre-generated list from all image files from /public folder + # --- Main View Handlers --- @onbutton imgMinus begin - # Append a query string to force the image to refresh - timestamp=string(time_ns()) - # Update the array of images listed in the public folder - msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural) + if isempty(selected_folder_main) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_main) + # Check if folder exists to prevent errors + if !isdir(folder_path) return end + + msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) new_msi=decrement_image(current_msi, msi_bmp) new_col_msi=decrement_image(current_col_msi, col_msi_png) - if new_msi!=nothing || new_col_msi!=nothing - current_msi=new_msi - current_col_msi=new_col_msi - imgInt="/$(current_msi)?t=$(timestamp)" - colorbar="/$(current_col_msi)?t=$(timestamp)" - - text_nmass=replace(current_msi, "MSI_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImg=[traceImg] - plotlayoutImg=layoutImg - msgimg="" + if new_msi !== nothing && new_col_msi !== nothing + current_msi = new_msi + current_col_msi = new_col_msi + imgInt = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + plotdataImg, plotlayoutImg, _, _ = loadImgPlot(imgInt) + btnOpticalDisable = false end end @onbutton imgPlus begin - # Append a query string to force the image to refresh + if isempty(selected_folder_main) return end timestamp=string(time_ns()) - # Update the array of images listed in the public folder - msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural) + folder_path = joinpath("public", selected_folder_main) + if !isdir(folder_path) return end + + msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) new_msi=increment_image(current_msi, msi_bmp) new_col_msi=increment_image(current_col_msi, col_msi_png) - if new_msi!=nothing || new_col_msi!=nothing - current_msi=new_msi - current_col_msi=new_col_msi - imgInt="/$(current_msi)?t=$(timestamp)" - colorbar="/$(current_col_msi)?t=$(timestamp)" - - text_nmass=replace(current_msi, "MSI_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgimg="Image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImg, plotlayoutImg, imgWidth, imgHeight=loadImgPlot(imgInt) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImg=[traceImg] - plotlayoutImg=layoutImg - msgimg="" + if new_msi !== nothing && new_col_msi !== nothing + current_msi = new_msi + current_col_msi = new_col_msi + imgInt = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + plotdataImg, plotlayoutImg, _, _ = loadImgPlot(imgInt) + btnOpticalDisable = false end end @onbutton imgMinusT begin - # Append a query string to force the image to refresh - timestamp=string(time_ns()) - # Update the array of images with TrIQ filter listed in the public folder - triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural) + if isempty(selected_folder_main) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_main) + if !isdir(folder_path) return end + + triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) new_msi=decrement_image(current_triq, triq_bmp) new_col_msi=decrement_image(current_col_triq, col_triq_png) - if new_msi!=nothing || new_col_msi!=nothing - current_triq=new_msi - current_col_triq=new_col_msi - imgIntT="/$(current_triq)?t=$(timestamp)" - colorbarT="/$(current_col_triq)?t=$(timestamp)" - - text_nmass=replace(current_triq, "TrIQ_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImgT=[traceImg] - plotlayoutImgT=layoutImg - msgtriq="" + if new_msi !== nothing && new_col_msi !== nothing + current_triq = new_msi + current_col_triq = new_col_msi + imgIntT = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgT, plotlayoutImgT, _, _ = loadImgPlot(imgIntT) + btnOpticalDisable = false end end @onbutton imgPlusT begin - # Append a query string to force the image to refresh - timestamp=string(time_ns()) - # Update the array of images with TrIQ filter listed in the public folder - triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural) + if isempty(selected_folder_main) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_main) + if !isdir(folder_path) return end + + triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) new_msi=increment_image(current_triq, triq_bmp) new_col_msi=increment_image(current_col_triq, col_triq_png) - if new_msi!=nothing || new_col_msi!=nothing - current_triq=new_msi - current_col_triq=new_col_msi - imgIntT="/$(current_triq)?t=$(timestamp)" - colorbarT="/$(current_col_triq)?t=$(timestamp)" - - text_nmass=replace(current_triq, "TrIQ_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgtriq="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImgT, plotlayoutImgT, imgWidth, imgHeight=loadImgPlot(imgIntT) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImgT=[traceImg] - plotlayoutImgT=layoutImg - msgtriq="" + if new_msi !== nothing && new_col_msi !== nothing + current_triq = new_msi + current_col_triq = new_col_msi + imgIntT = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgT, plotlayoutImgT, _, _ = loadImgPlot(imgIntT) + btnOpticalDisable = false end end - # Image loaders for the comparative view - @onbutton imgMinusComp begin - # Append a query string to force the image to refresh - timestamp=string(time_ns()) - # Update the array of images listed in the public folder - msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural) - - new_msi=decrement_image(current_msiComp, msi_bmp) - new_col_msi=decrement_image(current_col_msiComp, col_msi_png) - if new_msi!=nothing || new_col_msi!=nothing - current_msiComp=new_msi - current_col_msiComp=new_col_msi - imgIntComp="/$(current_msiComp)?t=$(timestamp)" - colorbarComp="/$(current_col_msiComp)?t=$(timestamp)" - - text_nmass=replace(current_msiComp, "MSI_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImgComp=[traceImg] - plotlayoutImgComp=layoutImg - msgimgComp="" - end - end - - @onbutton imgPlusComp begin - # Append a query string to force the image to refresh + # --- Compare View Handlers --- + @onbutton imgMinusCompLeft begin + if isempty(selected_folder_compare_left) return end timestamp=string(time_ns()) - # Update the array of images listed in the public folder - msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir("public")),lt=natural) + folder_path = joinpath("public", selected_folder_compare_left) + if !isdir(folder_path) return end + + msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=decrement_image(current_msiCompLeft, msi_bmp) + new_col_msi=decrement_image(current_col_msiCompLeft, col_msi_png) + if new_msi !== nothing && new_col_msi !== nothing + current_msiCompLeft = new_msi + current_col_msiCompLeft = new_col_msi + imgIntCompLeft = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgCompLeft, plotlayoutImgCompLeft, _, _ = loadImgPlot(imgIntCompLeft) + end + end + + @onbutton imgPlusCompLeft begin + if isempty(selected_folder_compare_left) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_left) + if !isdir(folder_path) return end + + msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) - new_msi=increment_image(current_msiComp, msi_bmp) - new_col_msi=increment_image(current_col_msiComp, col_msi_png) - if new_msi!=nothing || new_col_msi!=nothing - current_msiComp=new_msi - current_col_msiComp=new_col_msi - imgIntComp="/$(current_msiComp)?t=$(timestamp)" - colorbarComp="/$(current_col_msiComp)?t=$(timestamp)" - - text_nmass=replace(current_msiComp, "MSI_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgimgComp="Image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImgComp, plotlayoutImgComp, _, _=loadImgPlot(imgIntComp) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImgComp=[traceImg] - plotlayoutImgComp=layoutImg - msgimgComp="" + new_msi=increment_image(current_msiCompLeft, msi_bmp) + new_col_msi=increment_image(current_col_msiCompLeft, col_msi_png) + if new_msi !== nothing && new_col_msi !== nothing + current_msiCompLeft = new_msi + current_col_msiCompLeft = new_col_msi + imgIntCompLeft = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgCompLeft, plotlayoutImgCompLeft, _, _ = loadImgPlot(imgIntCompLeft) end end - - @onbutton imgMinusTComp begin - # Append a query string to force the image to refresh - timestamp=string(time_ns()) - # Update the array of images with TrIQ filter listed in the public folder - triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural) - - new_msi=decrement_image(current_triqComp, triq_bmp) - new_col_msi=decrement_image(current_col_triqComp, col_triq_png) - if new_msi!=nothing || new_col_msi!=nothing - current_triqComp=new_msi - current_col_triqComp=new_col_msi - imgIntTComp="/$(current_triqComp)?t=$(timestamp)" - colorbarTComp="/$(current_col_triqComp)?t=$(timestamp)" - - text_nmass=replace(current_triqComp, "TrIQ_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImgTComp=[traceImg] - plotlayoutImgTComp=layoutImg - msgtriqComp="" + + @onbutton imgMinusTCompLeft begin + if isempty(selected_folder_compare_left) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_left) + if !isdir(folder_path) return end + + triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=decrement_image(current_triqCompLeft, triq_bmp) + new_col_msi=decrement_image(current_col_triqCompLeft, col_triq_png) + if new_msi !== nothing && new_col_msi !== nothing + current_triqCompLeft = new_msi + current_col_triqCompLeft = new_col_msi + imgIntTCompLeft = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgTCompLeft, plotlayoutImgTCompLeft, _, _ = loadImgPlot(imgIntTCompLeft) end end - - @onbutton imgPlusTComp begin - # Append a query string to force the image to refresh - timestamp=string(time_ns()) - # Update the array of images with TrIQ filter listed in the public folder - triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")),lt=natural) - col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir("public")),lt=natural) - - new_msi=increment_image(current_triqComp, triq_bmp) - new_col_msi=increment_image(current_col_triqComp, col_triq_png) - if new_msi!=nothing || new_col_msi!=nothing - current_triqComp=new_msi - current_col_triqComp=new_col_msi - imgIntTComp="/$(current_triqComp)?t=$(timestamp)" - colorbarTComp="/$(current_col_triqComp)?t=$(timestamp)" - - text_nmass=replace(current_triqComp, "TrIQ_" => "") - text_nmass=replace(text_nmass, ".bmp" => "") - msgtriqComp="TrIQ image with the Nmass of $(replace(text_nmass, "_" => "."))" - # Process the image in the function - plotdataImgTComp, plotlayoutImgTComp, _, _=loadImgPlot(imgIntTComp) - btnOpticalDisable=false - else - traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}()) - plotdataImgTComp=[traceImg] - plotlayoutImgTComp=layoutImg - msgtriqComp="" + + @onbutton imgPlusTCompLeft begin + if isempty(selected_folder_compare_left) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_left) + if !isdir(folder_path) return end + + triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=increment_image(current_triqCompLeft, triq_bmp) + new_col_msi=increment_image(current_col_triqCompLeft, col_triq_png) + if new_msi !== nothing && new_col_msi !== nothing + current_triqCompLeft = new_msi + current_col_triqCompLeft = new_col_msi + imgIntTCompLeft = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgTCompLeft, plotlayoutImgTCompLeft, _, _ = loadImgPlot(imgIntTCompLeft) end end + + @onbutton imgMinusCompRight begin + if isempty(selected_folder_compare_right) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_right) + if !isdir(folder_path) return end + + msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=decrement_image(current_msiCompRight, msi_bmp) + new_col_msi=decrement_image(current_col_msiCompRight, col_msi_png) + if new_msi !== nothing && new_col_msi !== nothing + current_msiCompRight = new_msi + current_col_msiCompRight = new_col_msi + imgIntCompRight = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgCompRight, plotlayoutImgCompRight, _, _ = loadImgPlot(imgIntCompRight) + end + end + + @onbutton imgPlusCompRight begin + if isempty(selected_folder_compare_right) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_right) + if !isdir(folder_path) return end + + msi_bmp=sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_msi_png=sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=increment_image(current_msiCompRight, msi_bmp) + new_col_msi=increment_image(current_col_msiCompRight, col_msi_png) + if new_msi !== nothing && new_col_msi !== nothing + current_msiCompRight = new_msi + current_col_msiCompRight = new_col_msi + imgIntCompRight = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgCompRight, plotlayoutImgCompRight, _, _ = loadImgPlot(imgIntCompRight) + end + end + + @onbutton imgMinusTCompRight begin + if isempty(selected_folder_compare_right) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_right) + if !isdir(folder_path) return end + + triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=decrement_image(current_triqCompRight, triq_bmp) + new_col_msi=decrement_image(current_col_triqCompRight, col_triq_png) + if new_msi !== nothing && new_col_msi !== nothing + current_triqCompRight = new_msi + current_col_triqCompRight = new_col_msi + imgIntTCompRight = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgTCompRight, plotlayoutImgTCompRight, _, _ = loadImgPlot(imgIntTCompRight) + end + end + + @onbutton imgPlusTCompRight begin + if isempty(selected_folder_compare_right) return end + timestamp=string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_right) + if !isdir(folder_path) return end + + triq_bmp=sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir(folder_path)),lt=natural) + col_triq_png=sort(filter(filename -> startswith(filename, "colorbar_TrIQ_") && endswith(filename, ".png"), readdir(folder_path)),lt=natural) + + new_msi=increment_image(current_triqCompRight, triq_bmp) + new_col_msi=increment_image(current_col_triqCompRight, col_triq_png) + if new_msi !== nothing && new_col_msi !== nothing + current_triqCompRight = new_msi + current_col_triqCompRight = new_col_msi + imgIntTCompRight = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + plotdataImgTCompRight, plotlayoutImgTCompRight, _, _ = loadImgPlot(imgIntTCompRight) + end + end + + # This handler will now correctly load the first image from the newly selected folder. + @onchange selected_folder_main begin + if !isempty(selected_folder_main) + folder_path = joinpath("public", selected_folder_main) + if !isdir(folder_path) + imgInt = "" + colorbar = "" + imgIntT = "" + colorbarT = "" + msgimg = "Folder not found." + msgtriq = "Folder not found." + plotdataImg = [traceImg] + plotlayoutImg = layoutImg + plotdataImgT = [traceImg] + plotlayoutImgT = layoutImg + return + end + + # Handle normal images + msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir(folder_path)), lt=natural) + col_msi_png = sort(filter(filename -> startswith(filename, "colorbar_MSI_") && endswith(filename, ".png"), readdir(folder_path)), lt=natural) + + if !isempty(msi_bmp) + current_msi = first(msi_bmp) + imgInt = "/$(selected_folder_main)/$(current_msi)" + plotdataImg, plotlayoutImg, _, _ = loadImgPlot(imgInt) + text_nmass = replace(current_msi, r"MSI_|.bmp" => "") + msgimg = "m/z: $(replace(text_nmass, "_" => "."))" + if !isempty(col_msi_png) + current_col_msi = first(col_msi_png) + colorbar = "/$(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, _, _ = loadImgPlot(imgIntT) + text_nmass = replace(current_triq, r"TrIQ_|.bmp" => "") + msgtriq = "TrIQ m/z: $(replace(text_nmass, "_" => "."))" + if !isempty(col_triq_png) + current_col_triq = first(col_triq_png) + colorbarT = "/$(selected_folder_main)/$(current_col_triq)" + else + colorbarT = "" + end + else + imgIntT = "" + colorbarT = "" + msgtriq = "No TrIQ images found in this dataset." + plotdataImgT = [traceImg] + plotlayoutImgT = layoutImg + end + end + end + + @onchange selected_folder_compare_left begin + if !isempty(selected_folder_compare_left) + timestamp = string(time_ns()) + folder_path = joinpath("public", selected_folder_compare_left) + + if !isdir(folder_path) + imgIntCompLeft, colorbarCompLeft, imgIntTCompLeft, colorbarTCompLeft = "", "", "", "" + msgimgCompLeft, msgtriqCompLeft = "Folder not found.", "Folder not found." + return + end + + # Handle normal images + msi_bmp = sort(filter(f -> startswith(f, "MSI_") && endswith(f, ".bmp"), readdir(folder_path)), lt=natural) + col_msi_png = sort(filter(f -> startswith(f, "colorbar_MSI_") && endswith(f, ".png"), readdir(folder_path)), lt=natural) + + if !isempty(msi_bmp) + current_msiCompLeft = first(msi_bmp) + imgIntCompLeft = "/$(selected_folder_compare_left)/$(current_msiCompLeft)?t=$(timestamp)" + plotdataImgCompLeft, plotlayoutImgCompLeft, _, _ = loadImgPlot(imgIntCompLeft) + text_nmass = replace(current_msiCompLeft, r"MSI_|.bmp" => "") + msgimgCompLeft = "m/z: $(replace(text_nmass, "_" => "."))" + + if !isempty(col_msi_png) + current_col_msiCompLeft = first(col_msi_png) + colorbarCompLeft = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + + if !isempty(col_triq_png) + current_col_triqCompLeft = first(col_triq_png) + colorbarTCompLeft = "/$(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 = "m/z: $(replace(text_nmass, "_" => "."))" + + if !isempty(col_msi_png) + current_col_msiCompRight = first(col_msi_png) + colorbarCompRight = "/$(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 m/z: $(replace(text_nmass, "_" => "."))" + + if !isempty(col_triq_png) + current_col_triqCompRight = first(col_triq_png) + colorbarTCompRight = "/$(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 @@ -1161,13 +1725,49 @@ include("./julia_imzML_visual.jl") # To include a visualization in the spectrum plot indicating where is the selected mass @onchange Nmass begin if !isempty(xSpectraMz) - # Use a stem plot for the main spectrum for consistency - traceSpectra = PlotlyBase.stem(x=xSpectraMz, y=ySpectraMz, marker=attr(size=1, color="blue", opacity=0.5), name="Spectrum", hoverinfo="x", hovertemplate="m/z: %{x:.4f}", showlegend=false) + # Main spectrum trace + traceSpectra = PlotlyBase.scatter( + x=xSpectraMz, + y=ySpectraMz, + marker=attr(size=1, color="blue", opacity=0.5), + name="Spectrum", + hoverinfo="x", + hovertemplate="m/z: %{x:.4f}", + showlegend=false + ) - # Keep this as a scatter plot to draw the vertical line - trace2 = PlotlyBase.scatter(x=[Nmass, Nmass], y=[0, maximum(ySpectraMz)], mode="lines", line=attr(color="red", width=0.5), name="m/z selected", 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 - plotdata = [traceSpectra, trace2] + 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="%{data.name}" + ) + 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 @@ -1258,6 +1858,67 @@ include("./julia_imzML_visual.jl") @mounted watchplots() + @onchange isready begin + if isready && !registry_init_done + @async begin # Run asynchronously to not block startup + sleep(1.0) # Give frontend time to initialize + try + println("Synchronizing registry with filesystem on backend init...") + reg_path = joinpath("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 + end + warmup_init() + end + GC.gc() # Trigger garbage collection if Sys.islinux() ccall(:malloc_trim, Int32, (Int32,), 0) # Ensure julia returns the freed memory to OS @@ -1267,40 +1928,3 @@ end # Register a new route and the page that will be loaded on access @page("/", "app.jl.html") end - -#= -function __init__() - @async begin - println("Pre-compiling functions at startup...") - - # Create a dummy MSIData object to be used for pre-compilation - dummy_source = ImzMLSource("dummy.ibd", Float32, Float32) - dummy_meta = MSI_src.SpectrumMetadata(0,0,"",MSI_src.UNKNOWN, MSI_src.SpectrumAsset(Float32,false,0,0,:mz), MSI_src.SpectrumAsset(Float32,false,0,0,:intensity)) - dummy_msi_data = MSIData(dummy_source, [dummy_meta], (1,1), zeros(Int,1,1), 0) - - # Pre-compile functions from btnSearch - try OpenMSIData("dummy.imzML") catch end - try precompute_analytics(dummy_msi_data) catch end - - # Pre-compile functions from mainProcess - try get_mz_slice(dummy_msi_data, 1.0, 1.0) catch end - try TrIQ(zeros(10,10), 256, 0.98) catch end - try quantize_intensity(zeros(10,10), 256) catch end - - dummy_bmp_path = joinpath("public", "dummy.bmp") - dummy_png_path = joinpath("public", "dummy.png") - try - save_bitmap(dummy_bmp_path, zeros(UInt8, 10, 10), ViridisPalette) - loadImgPlot("/dummy.bmp") - generate_colorbar_image(zeros(10,10), 256, dummy_png_path) - catch e - @warn "Pre-compilation step failed (this is expected if dummy files can't be created/read)" - finally - rm(dummy_bmp_path, force=true) - rm(dummy_png_path, force=true) - end - - println("Pre-compilation finished.") - end -end -=# diff --git a/app.jl.html b/app.jl.html index 7eb8234..ad97d23 100644 --- a/app.jl.html +++ b/app.jl.html @@ -17,19 +17,42 @@
imzML & mzML Data Processor

Please make sure the ibd and imzML file are located in the same directory and have the same name. -
It may take a while to generate the image and the plot, please be patient. -
To generate the contour or surface plots, you have to select the desired image first using the interface.

- - - - +
It may take a while to generate the slice / spectrum, please be patient. +
To generate the contour or surface plots, you have to select the desired slice first using the interface.

+
+ + + + + +
+ + + + {{ file }} + + + + + + + +
- + +
- - - - - -
-

{{msg}}

- + + + + + + +
+ +
{{ progress_message }}
+
+
+

{{msg}}

@@ -177,13 +204,13 @@ @@ -205,9 +232,10 @@ -
Image visualizer
-
+
+ +
@@ -221,14 +249,15 @@
-

{{msgimg}}

+

-
TrIQ visualizer
-
+
+ +
@@ -242,11 +271,38 @@
-

{{msgtriq}}

+

- +
+ + + + + + + + Mean spectrum plot + + + + + Sum Spectrum plot + + + + + Spectrum plot (X,Y) + + + + +
@@ -281,8 +337,8 @@ - -
Compare two diferent images or plots
+ +
Compare two different images or plots
Transparency: {{ imgTrans }} @@ -294,46 +350,50 @@
- - +
+ + + +
+
- - + +
- +
- +
-

{{msgimg}}

+

- - + +
- +
- +
-

{{msgtriq}}

+

@@ -350,51 +410,54 @@
- - +
+ + + +
+
- + + v-on:click="imgPlusCompRight=true">
-
- +
-

{{msgimgComp}}

+

- + + v-on:click="imgPlusTCompRight=true">
-
- +
-

{{msgtriqComp}}

+

@@ -419,23 +482,53 @@ + + + +
Batch Process Summary
+ + + + 
{{ batch_summary }}
+ + + + + + + + - +
Dataset Summary
+ + - + - {{ row.parameter }} + {{ row.parameter }} - {{ row.value }} + {{ row.value }} +
+ +

No metadata found in registry for this dataset.

+

You may need to process the file first.

+
diff --git a/julia_imzML_visual.jl b/julia_imzML_visual.jl index 2d7fbeb..439cd14 100644 --- a/julia_imzML_visual.jl +++ b/julia_imzML_visual.jl @@ -452,10 +452,11 @@ end # returns the layout and data for the surface plotly plot # this function loads the spectra data and makes a mean to display # its values in the spectrum plot -function meanSpectrumPlot(data::MSIData) +function meanSpectrumPlot(data::MSIData, dataset_name::String="") + title_text = isempty(dataset_name) ? "Average Spectrum Plot" : "Average Spectrum for: $dataset_name" layout = PlotlyBase.Layout( title=PlotlyBase.attr( - text="Average Spectrum Plot", + text=title_text, font=PlotlyBase.attr( family="Roboto, Lato, sans-serif", size=18, @@ -480,9 +481,9 @@ function meanSpectrumPlot(data::MSIData) if isempty(xSpectraMz) @warn "Average spectrum is empty." - trace = PlotlyBase.stem(x=Float64[], y=Float64[]) + trace = PlotlyBase.scatter(x=Float64[], y=Float64[]) else - trace = PlotlyBase.stem(x=xSpectraMz, y=ySpectraMz, marker=attr(size=1, color="blue", opacity=0.5), name="Average", hoverinfo="x",hovertemplate="m/z: %{x:.4f}") + trace = PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, marker=attr(size=1, color="blue", opacity=0.5), name="Average", hoverinfo="x",hovertemplate="m/z: %{x:.4f}") end @@ -491,7 +492,7 @@ function meanSpectrumPlot(data::MSIData) return plotdata, plotlayout, xSpectraMz, ySpectraMz end -function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int, imgHeight::Int) +function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int, imgHeight::Int, dataset_name::String="") local mz::AbstractVector, intensity::AbstractVector local plot_title::String @@ -502,24 +503,24 @@ function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int, x = clamp(xCoord, 1, imgWidth) y = clamp(yCoord, 1, imgHeight) - # mz, intensity = GetSpectrum(data, Int(x), Int(y)) process_spectrum(data, Int(x), Int(y)) do recieved_mz, recieved_intensity mz = recieved_mz intensity = recieved_intensity end - plot_title = "Spectrum at ($x, $y)" + base_title = "Spectrum at ($x, $y)" else # For non-imaging data, treat xCoord as the spectrum index index = clamp(xCoord, 1, length(data.spectra_metadata)) - # mz, intensity = GetSpectrum(data, index) process_spectrum(data, index) do recieved_mz, recieved_intensity mz = recieved_mz intensity = recieved_intensity end - plot_title = "Spectrum #$index" + base_title = "Spectrum #$index" end + plot_title = isempty(dataset_name) ? base_title : "$base_title for: $dataset_name" + layout = PlotlyBase.Layout( title=PlotlyBase.attr( text=plot_title, @@ -545,7 +546,7 @@ function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int, # Downsample for plotting performance mz_down, int_down = MSI_src.downsample_spectrum(mz, intensity) - trace = PlotlyBase.stem(x=mz_down, y=int_down, marker=attr(size=1, color="blue", opacity=0.5), name="Spectrum", hoverinfo="x", hovertemplate="m/z: %{x:.4f}") + trace = PlotlyBase.scatter(x=mz_down, y=int_down, marker=attr(size=1, color="blue", opacity=0.5), name="Spectrum", hoverinfo="x", hovertemplate="m/z: %{x:.4f}") plotdata = [trace] plotlayout = layout @@ -553,10 +554,11 @@ function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int, return plotdata, plotlayout, mz, intensity end -function sumSpectrumPlot(data::MSIData) +function sumSpectrumPlot(data::MSIData, dataset_name::String="") + title_text = isempty(dataset_name) ? "Total Spectrum Plot" : "Total Spectrum for: $dataset_name" layout = PlotlyBase.Layout( title=PlotlyBase.attr( - text="Total Spectrum Plot", + text=title_text, font=PlotlyBase.attr( family="Roboto, Lato, sans-serif", size=18, @@ -581,12 +583,47 @@ function sumSpectrumPlot(data::MSIData) if isempty(xSpectraMz) @warn "Total spectrum is empty." - trace = PlotlyBase.stem(x=Float64[], y=Float64[]) + trace = PlotlyBase.scatter(x=Float64[], y=Float64[]) else - trace = PlotlyBase.stem(x=xSpectraMz, y=ySpectraMz, marker=attr(size=1, color="blue", opacity=0.5), name="Total", hoverinfo="x",hovertemplate="m/z: %{x:.4f}") + trace = PlotlyBase.scatter(x=xSpectraMz, y=ySpectraMz, marker=attr(size=1, color="blue", opacity=0.5), name="Total", hoverinfo="x",hovertemplate="m/z: %{x:.4f}") end plotdata = [trace] plotlayout = layout return plotdata, plotlayout, xSpectraMz, ySpectraMz end + +function warmup_init() + @async begin + println("Pre-compiling functions at startup...") + + # Create a dummy MSIData object to be used for pre-compilation + # dummy_source = ImzMLSource("dummy.ibd", Float32, Float32) + # dummy_meta = MSI_src.SpectrumMetadata(0,0,"",MSI_src.UNKNOWN, MSI_src.SpectrumAsset(Float32,false,0,0,:mz), MSI_src.SpectrumAsset(Float32,false,0,0,:intensity)) + # dummy_msi_data = MSIData(dummy_source, [dummy_meta], (1,1), zeros(Int,1,1), 0) + + # Pre-compile functions from btnSearch + # try OpenMSIData("dummy.imzML") catch end + # try precompute_analytics(dummy_msi_data) catch end + + # Pre-compile functions from mainProcess + # try get_mz_slice(dummy_msi_data, 1.0, 1.0) catch end + try TrIQ(zeros(10,10), 256, 0.98) catch end + try quantize_intensity(zeros(10,10), 256) catch end + + dummy_bmp_path = joinpath("public", "dummy.bmp") + dummy_png_path = joinpath("public", "dummy.png") + try + save_bitmap(dummy_bmp_path, zeros(UInt8, 10, 10), ViridisPalette) + loadImgPlot("/dummy.bmp") + generate_colorbar_image(zeros(10,10), 256, dummy_png_path) + catch e + @warn "Pre-compilation step failed (this is expected if dummy files can't be created/read)" + finally + rm(dummy_bmp_path, force=true) + rm(dummy_png_path, force=true) + end + + println("Pre-compilation finished.") + end +end \ No newline at end of file diff --git a/public/css/genieapp.css b/public/css/genieapp.css index e3779af..f50c1f7 100644 --- a/public/css/genieapp.css +++ b/public/css/genieapp.css @@ -82,7 +82,7 @@ } #intDivStyle-left .q-tab-panels { - height: 670px; /* Set this to accommodate your tallest content */ + height: 700px; /* Set this to accommodate your tallest content */ } #intDivStyle-left .q-tab-panel { diff --git a/public/masks/static.txt b/public/css/masks/static.txt similarity index 100% rename from public/masks/static.txt rename to public/css/masks/static.txt diff --git a/src/MzmlConverter.jl b/src/MzmlConverter.jl index d2997d6..4142c41 100644 --- a/src/MzmlConverter.jl +++ b/src/MzmlConverter.jl @@ -497,7 +497,7 @@ function ConvertMzmlToImzml(source_file::String, target_ibd_file::String, timing open(target_ibd_file, "w") do ibd_stream write(ibd_stream, zeros(UInt8, 16)) # UUID placeholder end - return BinaryMetadata[], Tuple{Int, Int}[], (0, 0) + return BinaryMetadata[], Tuple{Int, Int}[], (0, 0), UNKNOWN end width = maximum(timing_matrix[:, 1]) @@ -505,6 +505,11 @@ function ConvertMzmlToImzml(source_file::String, target_ibd_file::String, timing msi_data = OpenMSIData(source_file) + source_mode = UNKNOWN + if !isempty(msi_data.spectra_metadata) + source_mode = msi_data.spectra_metadata[1].mode + end + scan_time_deltas = zeros(Int64, size(scans, 1)) if size(scans, 1) > 1 for i in 1:(size(scans, 1) - 1) @@ -553,7 +558,7 @@ function ConvertMzmlToImzml(source_file::String, target_ibd_file::String, timing # Write m/z array mz_offset = position(ibd_stream) for val in mz - write(ibd_stream, htol(Float64(val))) + write(ibd_stream, htol(Float32(val))) end mz_length = position(ibd_stream) - mz_offset @@ -569,7 +574,7 @@ function ConvertMzmlToImzml(source_file::String, target_ibd_file::String, timing end @info "Found and processed $empty_pixel_count empty pixels out of $(size(timing_matrix, 1)) total." - return binary_meta_vec, coords_vec, (width, height) + return binary_meta_vec, coords_vec, (width, height), source_mode end """ @@ -589,7 +594,7 @@ experiment and data format. # Returns - `true` on success, `false` on failure. """ -function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, coords::Vector{Tuple{Int, Int}}, dims::Tuple{Int, Int}) +function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, coords::Vector{Tuple{Int, Int}}, dims::Tuple{Int, Int}, mode::SpectrumMode) ibd_file = replace(target_file, r"\.imzML$"i => ".ibd") if isempty(binary_meta) @@ -604,8 +609,7 @@ function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, c open(target_file, "w") do imzml_stream # XML Header write(imzml_stream, """ - - + """) # CV List, File Description, etc. (static parts) @@ -627,13 +631,11 @@ function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, c - - + - @@ -699,13 +701,20 @@ function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, c push!(spectrum_offsets, spectrum_start) # Calculate number of points from byte length - mz_points = meta.mz_length ÷ sizeof(Float64) + mz_points = meta.mz_length ÷ sizeof(Float32) int_points = meta.int_length ÷ sizeof(Float32) write(imzml_stream, """ - - +""") + if mode == CENTROID + write(imzml_stream, """ +""") + else + write(imzml_stream, """ +""") + end + write(imzml_stream, """ @@ -714,16 +723,14 @@ function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, c - - + - - + @@ -734,19 +741,6 @@ function ExportImzml(target_file::String, binary_meta::Vector{BinaryMetadata}, c write(imzml_stream, """ -""") - # Index List - index_list_start = position(imzml_stream) - write(imzml_stream, """ - -""") - for (i, offset) in enumerate(spectrum_offsets) - write(imzml_stream, " $offset\n") - end - write(imzml_stream, """ - - $index_list_start - """) end @@ -784,13 +778,13 @@ function ImportMzmlFile(source_file::String, sync_file::String, target_file::Str println("Step 3: Converting spectra and writing .ibd file...") ibd_file = replace(target_file, r"\.imzML$"i => ".ibd") - binary_meta, coords, (width, height) = ConvertMzmlToImzml(source_file, ibd_file, timing_matrix, scans) + binary_meta, coords, (width, height), source_mode = ConvertMzmlToImzml(source_file, ibd_file, timing_matrix, scans) # Flip image vertically to match R script output flipped_coords = [(x, height - y + 1) for (x, y) in coords] println("Step 4: Exporting .imzML metadata file...") - success = ExportImzml(target_file, binary_meta, flipped_coords, (width, height)) + success = ExportImzml(target_file, binary_meta, flipped_coords, (width, height), source_mode) if success println("Conversion successful: $target_file") diff --git a/src/imzML.jl b/src/imzML.jl index 9b74f63..6c3b48a 100644 --- a/src/imzML.jl +++ b/src/imzML.jl @@ -793,6 +793,84 @@ function get_mz_slice(data::MSIData, mass::Real, tolerance::Real) end +""" + get_multiple_mz_slices(data::MSIData, masses::AbstractVector{<:Real}, tolerance::Real) + +Extracts multiple image slices for a given list of m/z values in a single pass. +This is a highly performant function that iterates through the full dataset only once. + +# Returns +- A `Dict{Real, Matrix{Float64}}` mapping each mass to its intensity slice matrix. +""" +function get_multiple_mz_slices(data::MSIData, masses::AbstractVector{<:Real}, tolerance::Real) + width, height = data.image_dims + + # 1. Initialize a dictionary to hold the output slice matrices + slice_dict = Dict{Real, Matrix{Float64}}() + for mass in masses + slice_dict[mass] = zeros(Float64, height, width) + end + + # 2. Ensure analytics are computed for filtering. + if data.spectrum_stats_df === nothing || !hasproperty(data.spectrum_stats_df, :MinMZ) + println("Per-spectrum metadata not found. Running one-time analytics computation...") + precompute_analytics(data) + end + + println("Filtering candidate spectra for $(length(masses)) m/z values...") + stats_df = data.spectrum_stats_df + candidate_indices = Set{Int}() + + # 3. Find all spectra that could contain *any* of the requested masses. + for mass in masses + target_min = mass - tolerance + target_max = mass + tolerance + for i in 1:length(data.spectra_metadata) + # If already a candidate, no need to check again + if i in candidate_indices + continue + end + spec_min_mz = stats_df.MinMZ[i] + spec_max_mz = stats_df.MaxMZ[i] + if target_max >= spec_min_mz && target_min <= spec_max_mz + push!(candidate_indices, i) + end + end + end + + println("Found $(length(candidate_indices)) total candidate spectra.") + + # 4. Iterate through the data a single time using the optimized iterator. + _iterate_spectra_fast(data) do idx, mz_array, intensity_array + # Process only the spectra that are candidates + if idx in candidate_indices + meta = data.spectra_metadata[idx] + # For this single spectrum, check all masses of interest + for mass in masses + # Check if this spectrum's range actually covers the current mass + # This is a finer-grained check than the initial filtering + if !isempty(mz_array) && (mass + tolerance) >= first(mz_array) && (mass - tolerance) <= last(mz_array) + intensity = find_mass(mz_array, intensity_array, mass, tolerance) + if intensity > 0.0 + if 1 <= meta.x <= width && 1 <= meta.y <= height + slice_dict[mass][meta.y, meta.x] = intensity + end + end + end + end + end + end + + # 5. Clean up and return + for mass in masses + replace!(slice_dict[mass], NaN => 0.0) + end + + println("Finished generating $(length(masses)) slices in a single pass.") + return slice_dict +end + + """ plot_slice(msi_data::MSIData, mass::Float64, tolerance::Float64, output_dir::String; stage_name="slice", bins=256) diff --git a/src/mzML.jl b/src/mzML.jl index 8413845..aac75e9 100644 --- a/src/mzML.jl +++ b/src/mzML.jl @@ -103,9 +103,37 @@ the m/z and intensity array metadata. function parse_spectrum_metadata(stream::IO, offset::Int64) seek(stream, offset) - id_match = find_tag(stream, r"", line) + break + end + end + spectrum_xml = String(take!(spectrum_buffer)) + seek(stream, spectrum_start_pos) # Reset for other parsing + + id_match = match(r"