347 lines
15 KiB
Julia
347 lines
15 KiB
Julia
# test/run_tests.jl
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# ===================================================================
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# Test Environment for JuliaMSI Package
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# ===================================================================
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# This script validates the core functionality of the data processing
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# workflows, including loading, converting, and visualizing mass
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# spectrometry data.
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#
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# Instructions:
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# 1. Fill in the placeholder paths in the "CONFIG" section below.
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# 2. Run the script from the project's root directory:
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# julia --project=. test/run_tests.jl
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# 3. Check the `test/results/` folder for the output images.
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# ===================================================================
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using Printf
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using CairoMakie
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import Pkg
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# --- Load the MSI_src Module ---
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# Activate the project environment at the parent directory of this test script
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Pkg.activate(joinpath(@__DIR__, ".."))
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using MSI_src
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# ===================================================================
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# CONFIG: PLEASE FILL IN YOUR FILE PATHS HERE
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# ===================================================================
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# --- Test Case 1: Standard .mzML file ---
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# A regular, non-imaging mzML file.
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# const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/mzML/T9_A1.mzML"
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const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/CE4_BF_R1/CE4_BF_R1.mzML"
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# const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging_paper_spray/Imaging_paper_spray.mzML"
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# const TEST_MZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging prueba Roya 1/Roya.mzML"
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const SPECTRUM_TO_PLOT = 1 # Which spectrum to plot from the file
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# --- Test Case 2: .mzML + Sync File for Conversion ---
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# The special .mzML file with one spectrum per pixel.
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# const CONVERSION_SOURCE_MZML = "/home/pixel/Documents/Cinvestav_2025/Analisis/CE4_BF_R1/CE4_BF_R1.mzML"
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const CONVERSION_SOURCE_MZML = TEST_MZML_FILE
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# The corresponding synchronization text file.
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const CONVERSION_SYNC_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/CE4_BF_R1/CE4_BF_R1.txt"
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# const CONVERSION_SYNC_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging prueba Roya 1/Synchro.txt"
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# const CONVERSION_SOURCE_MZML = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging_paper_spray/Imaging_paper_spray.mzML"
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# const CONVERSION_SYNC_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging_paper_spray/Imaging_paper_spray.txt"
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# The desired output path for the new .imzML file.
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const CONVERSION_TARGET_IMZML = "test/results/converted_mzml.imzML"
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# --- Test Case 3: Standard .imzML file ---
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# An existing imzML file (can be the one generated from Case 2).
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# const TEST_IMZML_FILE = CONVERSION_TARGET_IMZML # The output from case 2
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# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/imzML_AP_SMALDI/HR2MSImouseurinarybladderS096.imzML"
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# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging_paper_spray/Imaging_paper_spray.imzML" #profile
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# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging prueba Roya 1/royaimg.imzML"
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# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/ltpmsi-chilli.imzML" # centroid aparently?
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# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/Stomach_DHB_compressed.imzML" # centroid compressed
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const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/Stomach_DHB_uncompressed.imzML" # centroid
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# The m/z value to use for creating an image slice.
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# const MZ_VALUE_FOR_SLICE = 309.06 # BF
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# const MZ_VALUE_FOR_SLICE = 896.0 # HR2MSI
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# const MZ_VALUE_FOR_SLICE = 76.03 # I PS
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# const MZ_VALUE_FOR_SLICE = 313 # ROYA
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const MZ_VALUE_FOR_SLICE = 100 # advanced processing
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# const MZ_TOLERANCE = 0.1
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# const MZ_TOLERANCE = 1
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const MZ_TOLERANCE = 0.1
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# Coordinates to plot a specific spectrum from imzML
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const COORDS_TO_PLOT = (50, 50) # Example coordinates (X, Y)
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# --- Output Directory ---
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const RESULTS_DIR = "test/results"
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test1 = false
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test2 = false
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test3 = true
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# ===================================================================
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# DATA VALIDATION UTILITY
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# ===================================================================
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"""
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validate_msi_data(filepath::String)
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Performs a series of checks on a .mzML or .imzML file using the MSIData API.
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"""
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function validate_msi_data(filepath::String)
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println("" * "-"^10 * " Running validation for $filepath " * "-"^10)
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if !isfile(filepath)
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println("SKIPPED VALIDATION: File not found: $filepath")
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return false
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end
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try
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# 1. Basic structure validation
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println("Opening file with OpenMSIData...")
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msi_data = @time OpenMSIData(filepath)
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# 2. Compare spectrum counts
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num_spectra = length(msi_data.spectra_metadata)
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println("Found $num_spectra spectra")
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@assert num_spectra > 0 "No spectra found in file."
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# 3. Test random access
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println("Testing random access to spectra...")
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test_indices = unique([1, max(1, num_spectra ÷ 2), num_spectra])
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println("Testing indices: $test_indices")
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for idx in test_indices
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print("Fetching spectrum #$idx... ")
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@time process_spectrum(msi_data, idx) do mz, intensity
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@assert length(mz) == length(intensity) "Spectrum $idx: mz/intensity length mismatch. Got $(length(mz)) mz values and $(length(intensity)) intensity values."
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println("OK, $(length(mz)) points.")
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end
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end
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# 4. Test iteration
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println("Testing iteration over all spectra...")
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count = 0
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iter_time = @elapsed for (idx, (mz, intensity)) in IterateSpectra(msi_data)
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count += 1
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# Basic data validation
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@assert all(isfinite, mz) "Non-finite mz values in spectrum $idx"
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@assert all(>=(0), intensity) "Negative intensities in spectrum $idx"
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end
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println("Iterated over $count spectra in $iter_time seconds.")
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@assert count == num_spectra "Iteration count mismatch: expected $num_spectra, got $count."
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println("VALIDATION SUCCESSFUL for $filepath")
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return true
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catch e
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println("VALIDATION FAILED for $filepath.")
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showerror(stdout, e, catch_backtrace())
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println()
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return false
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end
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end
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function debug_xml_parsing(file_path::String)
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println("=== DEBUG XML PARSING ===")
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stream = open(file_path, "r")
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# Find and print the first spectrum
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while !eof(stream)
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line = readline(stream)
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if occursin("<spectrum", line)
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println("FOUND FIRST SPECTRUM:")
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spectrum_xml = line
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# Read until end of spectrum
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while !eof(stream) && !occursin("</spectrum>", line)
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line = readline(stream)
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spectrum_xml *= line
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end
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println("SPECTRUM XML:")
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println(spectrum_xml)
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break
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end
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end
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close(stream)
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println("=== END DEBUG ===")
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end
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# ===================================================================
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# TEST RUNNER
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# ===================================================================
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function run_test()
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println("Starting MSI_src Test Suite...")
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# --- Test Case 1: Process a standard .mzML file ---
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println("" * "="^20 * " Test Case 1: Processing .mzML " * "="^20)
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if test1 == true
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# Run new, stronger validation
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validate_msi_data(TEST_MZML_FILE)
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# Also run original plotting test to ensure visualization still works
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if isfile(TEST_MZML_FILE)
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try
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println("Plotting a sample spectrum from $TEST_MZML_FILE...")
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msi_data = @time OpenMSIData(TEST_MZML_FILE)
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process_spectrum(msi_data, SPECTRUM_TO_PLOT) do mz, intensity
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fig = Figure(size = (800, 600))
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ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Intensity", title="Spectrum #$SPECTRUM_TO_PLOT from $(basename(TEST_MZML_FILE))")
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lines!(ax, mz, intensity)
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output_path = joinpath(RESULTS_DIR, "test_mzml_spectrum.png")
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save(output_path, fig)
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println("SUCCESS: Spectrum plot saved to $output_path")
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end
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# Get the summed spectrum data
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mz, intensity = get_total_spectrum(msi_data)
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# Plot the data
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println("Plotting total spectrum...")
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fig = Figure(size = (800, 600))
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ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Total Intensity", title="Total Spectrum from $(basename(TEST_MZML_FILE))")
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lines!(ax, mz, intensity)
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# Saving the output
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output_path = joinpath(RESULTS_DIR, "test_mzml_total_spectrum.png")
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save(output_path, fig)
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println("SUCCESS: Total spectrum plot saved to $output_path")
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# Get the averaged spectrum data
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mz, intensity = get_average_spectrum(msi_data)
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# Plot the data
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println("Plotting averaged spectrum...")
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fig = Figure(size = (800, 600))
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ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Average Intensity", title="Average Spectrum from $(basename(TEST_MZML_FILE))")
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lines!(ax, mz, intensity)
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# Saving the output
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output_path = joinpath(RESULTS_DIR, "test_mzml_average_spectrum.png")
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save(output_path, fig)
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println("SUCCESS: Total spectrum plot saved to $output_path")
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catch e
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println("ERROR during plotting in Test Case 1: $e")
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end
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end
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else
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println("SKIPPED Test Case 1.")
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end
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# --- Test Case 2: Convert .mzML + .txt to .imzML ---
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println("" * "="^20 * " Test Case 2: Converting to .imzML " * "="^20)
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if isfile(CONVERSION_SOURCE_MZML) && isfile(CONVERSION_SYNC_FILE) && test2 == true
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try
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println("Running conversion process (with profiling)...")
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success = @time ImportMzmlFile(CONVERSION_SOURCE_MZML, CONVERSION_SYNC_FILE, CONVERSION_TARGET_IMZML)
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if success
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println("SUCCESS: Conversion process completed.")
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# Validate the newly created imzML file
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validate_msi_data(CONVERSION_TARGET_IMZML)
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else
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println("FAILURE: Conversion process failed.")
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end
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catch e
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println("ERROR in Test Case 2: $e")
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end
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else
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println("SKIPPED: Files not found for Test Case 2.")
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println(" - mzML: $CONVERSION_SOURCE_MZML")
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println(" - Sync: $CONVERSION_SYNC_FILE")
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end
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# --- Test Case 3: Process an existing .imzML file ---
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println("" * "="^20 * " Test Case 3: Processing .imzML " * "="^20)
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if test3 == true
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# Run new, stronger validation for imzML
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validate_msi_data(TEST_IMZML_FILE)
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# Also run tests for plotting spectrum and image slice
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if isfile(TEST_IMZML_FILE)
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debug_xml_parsing(TEST_IMZML_FILE)
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msi_data = @time OpenMSIData(TEST_IMZML_FILE)
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precompute_analytics(msi_data)
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# Add spectrum plotting for imzML to match Test Case 1
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try
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# Get the msi data from the imzml
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println("Plotting a sample spectrum from $TEST_IMZML_FILE...")
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# Use coordinates from the first spectrum in the metadata
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first_spectrum_meta = msi_data.spectra_metadata[1]
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x_coord = first_spectrum_meta.x
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y_coord = first_spectrum_meta.y
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println("DIAGNOSTIC_READ: Reading from coordinate_map[$x_coord, $y_coord]. Value is $(msi_data.coordinate_map[x_coord, y_coord]).")
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# Get the x y coordinate spectrum data and plot it using the function barrier
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process_spectrum(msi_data, Int(x_coord), Int(y_coord)) do mz, intensity
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# Plot the data
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fig = Figure(size = (800, 600))
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ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Intensity", title="Spectrum at ($x_coord, $y_coord) from $(basename(TEST_IMZML_FILE))")
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lines!(ax, mz, intensity)
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# Saving the output
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output_path = joinpath(RESULTS_DIR, "test_imzml_spectrum.png")
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save(output_path, fig)
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println("SUCCESS: Spectrum plot saved to $output_path")
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end
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# Get the summed spectrum data
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mz, intensity = get_total_spectrum(msi_data)
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# Plot the data
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println("Plotting total spectrum...")
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fig = Figure(size = (800, 600))
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ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Total Intensity", title="Total Spectrum from $(basename(TEST_IMZML_FILE))")
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lines!(ax, mz, intensity)
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# Saving the output
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output_path = joinpath(RESULTS_DIR, "test_imzml_total_spectrum.png")
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save(output_path, fig)
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println("SUCCESS: Total spectrum plot saved to $output_path")
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# Get the averaged spectrum data
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mz, intensity = get_average_spectrum(msi_data)
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# Plot the data
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println("Plotting averaged spectrum...")
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fig = Figure(size = (800, 600))
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ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Average Intensity", title="Average Spectrum from $(basename(TEST_IMZML_FILE))")
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lines!(ax, mz, intensity)
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# Saving the output
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output_path = joinpath(RESULTS_DIR, "test_imzml_average_spectrum.png")
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save(output_path, fig)
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println("SUCCESS: Total spectrum plot saved to $output_path")
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# println("No spectrums tested on this try.")
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catch e
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println("ERROR during spectrum plotting in Test Case 3: $e")
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end
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# Test the plot_slice function
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try
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println("Testing plot_slice function on $TEST_IMZML_FILE...")
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# Use the base peak m/z from the first spectrum for the slice
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# Or a more general approach: use the global max intensity m/z
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# For now, let's use the base peak m/z of the first spectrum
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slice_mz_value = msi_data.spectrum_stats_df.BasePeakMZ[1]
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@time plot_slice(msi_data, slice_mz_value, MZ_TOLERANCE, RESULTS_DIR, stage_name="test_imzml_single_slice")
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# The success message is now inside plot_slice
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catch e
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println("ERROR during plot_slice test in Test Case 3: $e")
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end
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end
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else
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println("SKIPPED Test Case 3.")
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end
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println("Tests for all 3 cases is finished.")
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end
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# --- Execute ---
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# Ensure the results directory exists
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mkpath(RESULTS_DIR)
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@time run_test() |