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finished test script, included instructions in test/readme.md, the test performs mzml, imzml and conversion tests, along with throwing reference plots and images which result from the files

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This commit is contained in:
Pixelguy14 2025-09-29 10:57:11 -06:00
parent b1d7838a60
commit cd1115368f
17 changed files with 2145 additions and 2084 deletions
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1
.gitignore vendored
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@ -5,3 +5,4 @@ public/css/imgOver.png
!public/css/LABI_logo.png !public/css/LABI_logo.png
log/* log/*
R_original_scripts/ R_original_scripts/
test/results/

1109
Manifest.toml
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File diff suppressed because it is too large Load Diff

10
Project.toml
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@ -1,6 +1,15 @@
name = "MSI_src"
authors = ["JJSA"]
version = "0.1.0"
[deps] [deps]
Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
Genie = "c43c736e-a2d1-11e8-161f-af95117fbd1e" Genie = "c43c736e-a2d1-11e8-161f-af95117fbd1e"
GenieFramework = "a59fdf5c-6bf0-4f5d-949c-a137c9e2f353" GenieFramework = "a59fdf5c-6bf0-4f5d-949c-a137c9e2f353"
Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0" Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
@ -9,6 +18,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
NativeFileDialog = "e1fe445b-aa65-4df4-81c1-2041507f0fd4" NativeFileDialog = "e1fe445b-aa65-4df4-81c1-2041507f0fd4"
NaturalSort = "c020b1a1-e9b0-503a-9c33-f039bfc54a85" NaturalSort = "c020b1a1-e9b0-503a-9c33-f039bfc54a85"
PlotlyBase = "a03496cd-edff-5a9b-9e67-9cda94a718b5" PlotlyBase = "a03496cd-edff-5a9b-9e67-9cda94a718b5"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
StipplePlotly = "ec984513-233d-481d-95b0-a3b58b97af2b" StipplePlotly = "ec984513-233d-481d-95b0-a3b58b97af2b"
julia_mzML_imzML = "38eb50d3-2fb6-4afa-992a-964ed8562ed9" julia_mzML_imzML = "38eb50d3-2fb6-4afa-992a-964ed8562ed9"

6
app.jl
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@ -6,7 +6,7 @@ using Libz
using PlotlyBase using PlotlyBase
using CairoMakie using CairoMakie
using Colors using Colors
# using julia_mzML_imzML using julia_mzML_imzML
using Statistics using Statistics
using NaturalSort using NaturalSort
using Images using Images
@ -15,7 +15,7 @@ using NativeFileDialog # Opens the file explorer depending on the OS
using StipplePlotly using StipplePlotly
using Base.Filesystem: mv # To rename files in the system using Base.Filesystem: mv # To rename files in the system
include("./julia_imzML_visual.jl") include("./julia_imzML_visual.jl")
include("./src/imzML.jl")
@genietools @genietools
# == Reactive code == # == Reactive code ==
@ -363,7 +363,7 @@ include("./src/imzML.jl")
if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <=1 && colorLevel > 1 && colorLevel < 257 if isfile(full_route) && Nmass > 0 && Tol > 0 && Tol <=1 && colorLevel > 1 && colorLevel < 257
msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient." msg="File exists, Nmass=$(Nmass) Tol=$(Tol). Loading file will begin, please be patient."
try try
spectra=load_imzml(full_route) spectra=LoadImzml(full_route)
msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient." msg="File loaded. Creating spectra with the specific mass and tolerance, please be patient."
slice=GetMzSliceJl(spectra,Nmass,Tol) slice=GetMzSliceJl(spectra,Nmass,Tol)
fig=CairoMakie.Figure(size=(150, 250)) # Container fig=CairoMakie.Figure(size=(150, 250)) # Container

399
src/Bitmap.jl
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@ -1,399 +0,0 @@
# ********************************************************************
# SaveBitmap
# ********************************************************************
"""
SaveBitmap( name, pixMap, colorTable )
Save a discretized imzML slice as a bitmap file
# Arguments
* ` name`: Full path name of target bitmap
* ` pixMap`: [UInt8] Bidimensional matrix with image info
* `colorTable`: [UInt32] Vector with RGB colors for each gray level
# Examples
```julia
# Saves a bitmap with black and white alternate image squares
img = zeros(UInt8, 32, 32)
img[17:32,1:16] .= 1
img[1:16,17:32] .= 1
SaveBitmap( "test.bmp", img, UInt32[0, 0x00FFFFFF] )
```
The following image will be created on your hard disk
![](./Test.bmp)
"""
function SaveBitmap( name,
pixMap::Array{UInt8,2},
colorTable::Array{UInt32,1} )
# Get image dimensions
dim = size( pixMap )
if length( dim ) != 2
return 0
end
# Compute row padding
padding = ( 4 - dim[1] & 0x3 ) & 0x3
# Compute file dimensions. Header = 14 + 40 + ( 256 * 4 ) = 1078
offset = 1078
imgBytes = dim[2] * ( dim[1] + padding )
# Create file
stream = open( name, "w" )
# Save file header
write( stream, UInt16( 0x4D42 ) )
write( stream, UInt32[ offset + imgBytes, 0 , offset ] )
# Save info header
write( stream, UInt32[ 40, dim[1], dim[2], 0x80001, 0 ] )
write( stream, UInt32[ imgBytes, 0, 0, 256, 0 ] )
# Save color table
write( stream, colorTable )
if length( colorTable ) < 256
fixTable = zeros( UInt32, 256 - length( colorTable ) )
write( stream, fixTable )
end
# Save image pixels
if padding == 0
for i = 1:dim[2]
write( stream, pixMap[:,i] )
end
else
zeroPad = zeros( UInt8, padding )
for i in 1:dim[2]
write( stream, pixMap[:,i] )
write( stream, zeroPad )
end
end
# Close file
close( stream )
end
# ********************************************************************
# FindMass
# massVector: mz Vector sorted in ascending order
# mass: target mz value
# tolerance: bi-axial tolerance to find mass
# ********************************************************************
function FindMass( massVector, mass, tolerance )
index = Int( 0 )
lower = Int( 1 )
higher = Int( length( massVector ) )
while lower <= higher
# Compute mid element
index = ( lower + higher ) ÷ 2
# Go to lower portion ?
if massVector[ index ] > ( mass + tolerance )
higher = index - 1
continue
end
# Go to Higher portion?
if massVector[ index ] < ( mass - tolerance )
lower = index + 1
continue
end
# mass was found
return index
end
# mass was not found
return 0
end
# ********************************************************************
# GetSlice
# imzML: imzML data
# mass: mz target value
# tolerance: bi-axial tolerance to find mass
# ********************************************************************
"""
GetSlice( imzML, mass, tolerance )
Extract a mz-image from an imzML image data array loaded with
`LoadImzml` function. The resulting image array preserves the same
data type of the y-axis vectors in the file.
# Arguments
* ` imzML`: Image array loaded with `LoadImzml` function
* ` mass`: mz value for image extraction
* `tolerance`: Maximum lateral tolerance for a valid mz search
# Examples
```julia
# Load DESI MSI Carcinoma 885.55 mz slice
spectra = LoadImzml( "80TopL, 50TopR, 70BottomL, 60BottomR-centroid.imzML" )
slice = GetSlice( spectra, 885.55, 0.005 )
```
"""
function GetSlice( imzML, mass, tolerance )
# Alloc space for slice
width = maximum( imzML[1,:] )
height = maximum( imzML[2,:] )
image = zeros( Float64, width, height )
for i in 1:size( imzML )[2]
index = FindMass( imzML[3,i], mass, tolerance )
if index != 0
image[ imzML[1,i], imzML[2,i] ] = imzML[4,i][index]
end
end
return image
end
# ********************************************************************
# IntQuant, Discretize image amplitude in 0:255 range
# slice: Image matriz in measured arbitrary units
# ********************************************************************
"""
IntQuant( slice )
Zero Memory intensity quantizer. Discretize the image?s continuos
intensity range in discrete bins from 0 to 255 gray levels.
Returns a UInt8 bidimensional matrix
# Arguments
* `slice`: slice returned by the `GetSlice` function
# Examples
```julia
# Save DESI MSI Carcinoma 885.55 mz slice as a bitmap file
spectra = LoadImzml( "80TopL, 50TopR, 70BottomL, 60BottomR-centroid.imzML" )
slice = GetSlice( spectra, 885.55, 0.005
SaveBitmap( "Slice.bmp", IntQuant( slice ), ViridisPalette )
```
The following image will be created on your hard disk
![](./Slice.bmp)
"""
function IntQuant( slice )
# Compute scale factor for amplitude discretization
lower = minimum( slice )
scale = 255 / maximum( slice )
dim = size( slice )
image = zeros( UInt8, dim[1], dim[2] )
for i in 1:length( slice )
image[i] = convert( UInt8, floor( slice[i] * scale + 0.5 ) )
end
return image
end
# ********************************************************************
# TrIQ, Discretize image amplitude in 0:255 range, grouping outliers
# in the highest bin
# slice: Image matrix in measured arbitrary units
# ********************************************************************
function GetOutlierThres( slice, prob )
# Get bin width
low = minimum( slice )
upp = maximum( slice )
# Compute histogram's bin count & separation
if ( upp - low + 1 ) >= 100
bins = convert( Int32, 100 )
step = ( upp + (upp-low)/(bins-1) - low ) / bins
else
bins = convert( Int32, ceil( upp ) - floor( low ) + 1 )
step = 1
end
# Compute histogram
histCount = zeros( bins, 1 )
for k in slice
index = convert( Int64, floor( ( k - low ) / step ) + 1 )
histCount[ index ] += 1
end
# Get bin index, that accounts for desired probability
prob = 0.95
delta = cumsum( histCount, dims=1 ) / sum( histCount ) .- prob
index = findmin( broadcast( abs, delta ) )[2][1]
# Find max intensity image value
key = low + step * index
upp = -1
for k in slice[:]
if key > k && k > upp
upp = k
end
end
return [ low, upp ]
end
# ********************************************************************
# Discretize image's intensity using a given intensity range
# slice: Image matrix in measured arbitrary units
# bounds: max and min intensity discretizing range
# depth: number of intensity discrete steps in final image
# ********************************************************************
function SetPixelDepth( slice, bounds, depth )
# Compute intensity bins
bins = depth - 1
limits = collect(
range( bounds[1], stop = bounds[2], length = depth ) )
# Reserve memory for output image
imgBytes = zeros( UInt8, size( slice ) )
nPixels = length( slice )
step = limits[2] - limits[1]
# Set intensity depth
for k in 1:nPixels
# Find bin
i::Int64 = floor( ( slice[k] - limits[1] ) / step ) + 1
if i < bins
imgBytes[k] = i + ( slice[k] > limits[i] ) - 1
else
imgBytes[k] = bins
end
end
return imgBytes
end
# ********************************************************************
# Discretize image's intensity removing intensity outliers
# slice: Image matrix in measured arbitrary units
# depth: Number of intensity discrete steps in final image
# prob: Proportion of pixesl to take into account in discretization
# ********************************************************************
"""
TrIQ( slice, depth, prob = 0.98 )
TrIQ intensity quantizer as described in _DOI 10.7717/peerj-cs.585_.
Discretize the image?s continuos intensity range in discrete bins
from 0 to 255 gray levels, groupping intensity outiers in the
highehst bin. Returns a UInt8 bidimensional matrix
# Arguments
* `slice`: slice returned by the `GetSlice` function
* `depth`: Number ob discrete bins for intensity quantization
* ` prob`: Cummulative distribute function cutting value
# Examples
```julia
# Save DESI MSI Carcinoma 885.55 mz slice as a bitmap file
spectra = LoadImzml( "80TopL, 50TopR, 70BottomL, 60BottomR-centroid.imzML" )
slice = GetSlice( spectra, 885.55, 0.005 )
SaveBitmap( "TrIQ.bmp", TrIQ( slice, 256, 0.95 ), ViridisPalette )
```
The following image will be created on your hard disk
![](./TrIQ.bmp)
"""
function TrIQ( slice, depth, prob )
return SetPixelDepth(
slice,
GetOutlierThres( slice, prob ),
depth
)
end
# ********************************************************************
# Viridis color palette 256 color levels
# ********************************************************************
ViridisPalette = UInt32[
0x440154, 0x440256, 0x450457, 0x450559,
0x46075A, 0x46085C, 0x460A5D, 0x460B5E,
0x470D60, 0x470E61, 0x471063, 0x471164,
0x471365, 0x481467, 0x481668, 0x481769,
0x48186A, 0x481A6C, 0x481B6D, 0x481C6E,
0x481D6F, 0x481F70, 0x482071, 0x482173,
0x482374, 0x482475, 0x482576, 0x482677,
0x482878, 0x482979, 0x472A7A, 0x472C7A,
0x472D7B, 0x472E7C, 0x472F7D, 0x46307E,
0x46327E, 0x46337F, 0x463480, 0x453581,
0x453781, 0x453882, 0x443983, 0x443A83,
0x443B84, 0x433D84, 0x433E85, 0x423F85,
0x424086, 0x424186, 0x414287, 0x414487,
0x404588, 0x404688, 0x3F4788, 0x3F4889,
0x3E4989, 0x3E4A89, 0x3E4C8A, 0x3D4D8A,
0x3D4E8A, 0x3C4F8A, 0x3C508B, 0x3B518B,
0x3B528B, 0x3A538B, 0x3A548C, 0x39558C,
0x39568C, 0x38588C, 0x38598C, 0x375A8C,
0x375B8D, 0x365C8D, 0x365D8D, 0x355E8D,
0x355F8D, 0x34608D, 0x34618D, 0x33628D,
0x33638D, 0x32648E, 0x32658E, 0x31668E,
0x31678E, 0x31688E, 0x30698E, 0x306A8E,
0x2F6B8E, 0x2F6C8E, 0x2E6D8E, 0x2E6E8E,
0x2E6F8E, 0x2D708E, 0x2D718E, 0x2C718E,
0x2C728E, 0x2C738E, 0x2B748E, 0x2B758E,
0x2A768E, 0x2A778E, 0x2A788E, 0x29798E,
0x297A8E, 0x297B8E, 0x287C8E, 0x287D8E,
0x277E8E, 0x277F8E, 0x27808E, 0x26818E,
0x26828E, 0x26828E, 0x25838E, 0x25848E,
0x25858E, 0x24868E, 0x24878E, 0x23888E,
0x23898E, 0x238A8D, 0x228B8D, 0x228C8D,
0x228D8D, 0x218E8D, 0x218F8D, 0x21908D,
0x21918C, 0x20928C, 0x20928C, 0x20938C,
0x1F948C, 0x1F958B, 0x1F968B, 0x1F978B,
0x1F988B, 0x1F998A, 0x1F9A8A, 0x1E9B8A,
0x1E9C89, 0x1E9D89, 0x1F9E89, 0x1F9F88,
0x1FA088, 0x1FA188, 0x1FA187, 0x1FA287,
0x20A386, 0x20A486, 0x21A585, 0x21A685,
0x22A785, 0x22A884, 0x23A983, 0x24AA83,
0x25AB82, 0x25AC82, 0x26AD81, 0x27AD81,
0x28AE80, 0x29AF7F, 0x2AB07F, 0x2CB17E,
0x2DB27D, 0x2EB37C, 0x2FB47C, 0x31B57B,
0x32B67A, 0x34B679, 0x35B779, 0x37B878,
0x38B977, 0x3ABA76, 0x3BBB75, 0x3DBC74,
0x3FBC73, 0x40BD72, 0x42BE71, 0x44BF70,
0x46C06F, 0x48C16E, 0x4AC16D, 0x4CC26C,
0x4EC36B, 0x50C46A, 0x52C569, 0x54C568,
0x56C667, 0x58C765, 0x5AC864, 0x5CC863,
0x5EC962, 0x60CA60, 0x63CB5F, 0x65CB5E,
0x67CC5C, 0x69CD5B, 0x6CCD5A, 0x6ECE58,
0x70CF57, 0x73D056, 0x75D054, 0x77D153,
0x7AD151, 0x7CD250, 0x7FD34E, 0x81D34D,
0x84D44B, 0x86D549, 0x89D548, 0x8BD646,
0x8ED645, 0x90D743, 0x93D741, 0x95D840,
0x98D83E, 0x9BD93C, 0x9DD93B, 0xA0DA39,
0xA2DA37, 0xA5DB36, 0xA8DB34, 0xAADC32,
0xADDC30, 0xB0DD2F, 0xB2DD2D, 0xB5DE2B,
0xB8DE29, 0xBADE28, 0xBDDF26, 0xC0DF25,
0xC2DF23, 0xC5E021, 0xC8E020, 0xCAE11F,
0xCDE11D, 0xD0E11C, 0xD2E21B, 0xD5E21A,
0xD8E219, 0xDAE319, 0xDDE318, 0xDFE318,
0xE2E418, 0xE5E419, 0xE7E419, 0xEAE51A,
0xECE51B, 0xEFE51C, 0xF1E51D, 0xF4E61E,
0xF6E620, 0xF8E621, 0xFBE723, 0xFDE725 ]

94
src/Common.jl
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@ -1,94 +0,0 @@
# *******************************************************************
# VectorConfig, structure with axis decoding instructions
# *******************************************************************
mutable struct SpecDim
Format::DataType # Float32, Float64
Packed::Bool # 0: none 1: zlib compression
Axis::Int32 # 1: m/z 2: Amplitude
Skip::Int64 # Bytes to skip
end
# *******************************************************************
# Fill VectorConfig fields from "cvParam" tags
# *******************************************************************
function ConfigureSpecDim( stream )
# Vector configuration
axis = SpecDim( Float64, false, 1, 0 )
# Initial values
offset = position( stream )
currLine = ""
matchInfo = RegexMatch
while true
# Next field
currLine = readline( stream )
matchInfo = match( r"^\s*<(cvParam)", currLine )
if matchInfo === nothing
matchInfo = match( r"^\s*", currLine )
axis.Skip = position( stream ) - offset -
length( currLine ) + length( matchInfo.match )
return axis
end
index = length( matchInfo.captures[1] )
matchInfo = GetAttribute( currLine[index:end], "accession" )
if matchInfo.captures[1] == "MS:1000515" # intensity array
axis.Axis = 2
continue
elseif matchInfo.captures[1] == "MS:1000519" # 32-bit integer
axis.Format = Int32
continue
elseif matchInfo.captures[1] == "MS:1000521" # 32-bit float
axis.Format = Float32
continue
elseif matchInfo.captures[1] == "MS:1000522" # 64-bit integer
axis.Format = Int64
continue
elseif matchInfo.captures[1] == "MS:1000574" # zlib compresion
axis.Packed = true
continue
end
end
end
# *******************************************************************
# Read lines in file until regex match
# stream: Source file stream
# regex: target tag e.g. "binaryDataArray"
# *******************************************************************
function FindTag( stream, regex )
while true
isTag = match( regex, readline( stream ) )
if isTag !== nothing
return isTag
end
end
end
# *******************************************************************
# Retrieve attribute/value pair
# source: String with atr="value" pairs
# tag: Optional attribute, e.g. "\\spectrum"
# *******************************************************************
function GetAttribute( source, tag = "([^=]+)" )
# Build regex and retrieve attribute/value pair
regStr = Regex( "\\s" * tag * "=\"([^\"]*)\"" )
return( match( regStr, source ) )
end

82
src/DataAccess.jl
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@ -1,82 +0,0 @@
# src/DataAccess.jl
"""
load_spectra(fileName::String)
Eagerly loads all spectra from a .mzML or .imzML file into a 2xN matrix.
This function follows the eager-loading pattern of the original `LoadMzml`
for backward compatibility and for analyses that require all data in memory.
Each column in the returned matrix represents a single spectrum:
- Row 1: m/z array
- Row 2: Intensity array
For .imzML files, the (x,y) spatial coordinates are discarded.
# Arguments
* `fileName`: Full path to the .mzML or .imzML file.
# Returns
- An `Array{Any, 2}` containing all spectra.
"""
function load_spectra(fileName::String)
if endswith(lowercase(fileName), ".mzml")
# Detected .mzML file. Using the existing eager loader.
return LoadMzml(fileName)
elseif endswith(lowercase(fileName), ".imzml")
# Detected .imzML file. Eagerly loading all spectra from .ibd.
# Lazily load metadata to get offsets and counts
imzml_data = load_imzml(fileName)
try
num_spectra = length(imzml_data.spectra_metadata)
if num_spectra == 0
return Array{Any}(undef, (2, 0))
end
spectra_matrix = Array{Any}(undef, (2, num_spectra))
hIbd = imzml_data.ibd_handle
mz_format = imzml_data.mz_format
int_format = imzml_data.intensity_format
# For performance, pre-allocate one large buffer for reading.
# This avoids re-allocating memory for each spectrum inside the loop.
max_points = maximum(meta.mz_count for meta in imzml_data.spectra_metadata)
mz_array_buffer = Array{mz_format}(undef, max_points)
intensity_array_buffer = Array{int_format}(undef, max_points)
for i in 1:num_spectra
meta = imzml_data.spectra_metadata[i]
# Create a view into the buffer with the correct size for this spectrum
current_mz_array = view(mz_array_buffer, 1:meta.mz_count)
current_int_array = view(intensity_array_buffer, 1:meta.intensity_count)
# Read binary data directly into the sized views
seek(hIbd, meta.mz_offset)
read!(hIbd, current_mz_array)
seek(hIbd, meta.intensity_offset)
read!(hIbd, current_int_array)
# Store a copy in the final matrix. A copy is necessary because
# the buffer is overwritten in the next iteration.
spectra_matrix[1, i] = copy(current_mz_array)
spectra_matrix[2, i] = copy(current_int_array)
end
return spectra_matrix
finally
# Ensure the .ibd file handle is closed, as this is an eager load.
if isopen(imzml_data.ibd_handle)
close(imzml_data.ibd_handle)
end
end
else
error("Unsupported file type. Please provide a .mzML or .imzML file.")
end
end

369
src/MSIData.jl Normal file
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@ -0,0 +1,369 @@
# src/MSIData.jl
"""
This file defines the unified MSIData object and the associated data access layer,
including caching and iteration logic, for handling large mzML and imzML datasets
efficiently.
"""
using Base64, Libz # For reading binary data
# Abstract type for different data sources (e.g., mzML, imzML)
# This allows dispatching to the correct binary reading logic.
abstract type MSDataSource end
# Concrete type for imzML data sources
struct ImzMLSource <: MSDataSource
ibd_handle::IO
mz_format::Type
intensity_format::Type
end
# Concrete type for mzML data sources
struct MzMLSource <: MSDataSource
file_handle::IO
mz_format::Type
intensity_format::Type
end
# Struct to hold info about a binary data array (mz or intensity)
struct SpectrumAsset
format::Type
is_compressed::Bool
offset::Int64
encoded_length::Int32
# For mzML, axis_type is needed to distinguish mz from intensity.
# For imzML, this can be ignored as the order is fixed.
axis_type::Symbol
end
# Metadata for a single spectrum, common to both formats
struct SpectrumMetadata
# For imzML
x::Int32
y::Int32
# For mzML
id::String
# Common binary data info
mz_asset::SpectrumAsset
int_asset::SpectrumAsset
end
# The main unified data object
mutable struct MSIData
source::MSDataSource
spectra_metadata::Vector{SpectrumMetadata}
image_dims::Tuple{Int, Int} # (width, height) for imaging data
coordinate_map::Union{Matrix{Int}, Nothing} # Maps (x,y) to linear index for imzML
# LRU Cache implementation
cache::Dict{Int, Tuple{Vector, Vector}}
cache_order::Vector{Int} # Stores indices, with most recently used at the end
cache_size::Int # Max number of spectra in cache
function MSIData(source, metadata, dims, coordinate_map, cache_size)
obj = new(source, metadata, dims, coordinate_map, Dict(), [], cache_size)
# Ensure file handles are closed when the object is garbage collected
finalizer(obj) do o
if o.source isa ImzMLSource && isopen(o.source.ibd_handle)
close(o.source.ibd_handle)
elseif o.source isa MzMLSource && isopen(o.source.file_handle)
close(o.source.file_handle)
end
end
return obj
end
end
# --- Internal function for reading binary data --- #
function read_binary_vector(io::IO, asset::SpectrumAsset)
seek(io, asset.offset)
raw_b64 = read(io, asset.encoded_length)
decoded_bytes = base64decode(strip(String(raw_b64)))
bytes_io = IOBuffer(asset.is_compressed ? Libz.inflate(decoded_bytes) : decoded_bytes)
n_elements = Int(bytes_io.size / sizeof(asset.format))
out_array = Array{asset.format}(undef, n_elements)
read!(bytes_io, out_array)
return out_array
end
# Overload for different source types
function read_spectrum_from_disk(source::ImzMLSource, meta::SpectrumMetadata)
# For imzML, the binary data is raw, not base64 encoded.
# The `encoded_length` field in this case holds the number of points.
mz = Array{source.mz_format}(undef, meta.mz_asset.encoded_length)
intensity = Array{source.intensity_format}(undef, meta.int_asset.encoded_length)
seek(source.ibd_handle, meta.mz_asset.offset)
read!(source.ibd_handle, mz)
seek(source.ibd_handle, meta.int_asset.offset)
read!(source.ibd_handle, intensity)
return mz, intensity
end
function read_spectrum_from_disk(source::MzMLSource, meta::SpectrumMetadata)
# For mzML, data is Base64 encoded within the XML
mz = read_binary_vector(source.file_handle, meta.mz_asset)
intensity = read_binary_vector(source.file_handle, meta.int_asset)
return mz, intensity
end
# --- Public API --- #
"""
GetSpectrum(data::MSIData, index::Int)
Retrieves a single spectrum by its index, utilizing a cache for performance.
This function is the core of the "Indexed" and "Cache" access patterns.
"""
function GetSpectrum(data::MSIData, index::Int)
if index < 1 || index > length(data.spectra_metadata)
error("Spectrum index $index out of bounds.")
end
# Phase 1: Check the cache
if haskey(data.cache, index)
# Cache Hit: Move item to the end of the LRU list and return from cache
filter!(x -> x != index, data.cache_order)
push!(data.cache_order, index)
return data.cache[index]
end
# Phase 2: Cache Miss - Read from disk
meta = data.spectra_metadata[index]
spectrum = read_spectrum_from_disk(data.source, meta)
# Phase 3: Update cache
if data.cache_size > 0
if length(data.cache) >= data.cache_size
# Evict the least recently used item (at the front of the list)
lru_index = popfirst!(data.cache_order)
delete!(data.cache, lru_index)
end
data.cache[index] = spectrum
push!(data.cache_order, index)
end
return spectrum
end
"""
GetSpectrum(data::MSIData, x::Int, y::Int)
Retrieves a single spectrum by its (x, y) coordinates for imaging data.
Utilizes a coordinate map for efficient lookup and then the cache.
"""
function GetSpectrum(data::MSIData, x::Int, y::Int)
if data.coordinate_map === nothing
error("Coordinate map not available. This method is only for imaging data loaded from .imzML files.")
end
width, height = data.image_dims
if x < 1 || x > width || y < 1 || y > height
error("Coordinates ($x, $y) out of bounds for image dimensions ($width, $height).")
end
index = data.coordinate_map[x, y]
if index == 0
error("No spectrum found at coordinates ($x, $y).")
end
return GetSpectrum(data, index) # Call the existing method
end
"""
get_total_spectrum(msi_data::MSIData; num_bins::Int=20000) -> Tuple{Vector{Float64}, Vector{Float64}}
Calculates the sum of all spectra in the dataset by binning.
The m/z range is determined dynamically by finding the global min/max m/z values
across the entire dataset.
Returns a tuple containing two vectors: the binned m/z axis and the summed intensities.
"""
function get_total_spectrum(msi_data::MSIData; num_bins::Int=20000)
println("Calculating total spectrum...")
# 1. First Pass: Find the global m/z range
println(" Pass 1: Finding global m/z range...")
global_min_mz = Inf
global_max_mz = -Inf
_iterate_spectra_fast(msi_data) do idx, mz, _
if !isempty(mz)
local_min, local_max = extrema(mz)
global_min_mz = min(global_min_mz, local_min)
global_max_mz = max(global_max_mz, local_max)
end
end
if !isfinite(global_min_mz)
@warn "Could not determine a valid m/z range. All spectra might be empty."
return (Float64[], Float64[])
end
println(" Global m/z range found: [$(global_min_mz), $(global_max_mz)]")
# 2. Define Bins
mz_bins = range(global_min_mz, stop=global_max_mz, length=num_bins)
intensity_sum = zeros(Float64, num_bins)
bin_step = step(mz_bins)
# 3. Second Pass: Sum intensities into bins
println(" Pass 2: Summing intensities into $num_bins bins...")
_iterate_spectra_fast(msi_data) do idx, mz, intensity
if isempty(mz)
return # continue equivalent
end
for i in eachindex(mz)
# Find the correct bin for the current m/z value
bin_index = clamp(round(Int, (mz[i] - global_min_mz) / bin_step) + 1, 1, num_bins)
intensity_sum[bin_index] += intensity[i]
end
end
println("Total spectrum calculation complete.")
return (collect(mz_bins), intensity_sum)
end
"""
get_average_spectrum(msi_data::MSIData; num_bins::Int=20000) -> Tuple{Vector{Float64}, Vector{Float64}}
Calculates the average of all spectra in the dataset by binning.
This is effectively the total ion chromatogram (TIC) divided by the number of spectra.
Returns a tuple containing two vectors: the binned m/z axis and the averaged intensities.
"""
function get_average_spectrum(msi_data::MSIData; num_bins::Int=20000)
# This function uses the exact same logic as get_total_spectrum...
mz_bins, intensity_sum = get_total_spectrum(msi_data, num_bins=num_bins)
if isempty(intensity_sum)
return (mz_bins, intensity_sum)
end
# ...with one final step: dividing by the number of spectra to get the average.
println("Averaging spectrum...")
num_spectra = length(msi_data.spectra_metadata)
average_intensity = intensity_sum ./ num_spectra
return (mz_bins, average_intensity)
end
# --- Iterator Implementation --- #
struct MSIDataIterator
data::MSIData
end
"""
IterateSpectra(data::MSIData)
Returns an iterator that yields each spectrum, processing the file sequentially
with minimal memory overhead.
This function is the core of the "Event-driven" access pattern.
"""
function IterateSpectra(data::MSIData)
return MSIDataIterator(data)
end
# Define the iteration interface for the custom iterator
Base.length(it::MSIDataIterator) = length(it.data.spectra_metadata)
Base.eltype(it::MSIDataIterator) = Tuple{Int, Tuple{Vector, Vector}} # Index, (mz, intensity)
function Base.iterate(it::MSIDataIterator, state=1)
if state > length(it.data.spectra_metadata)
return nothing # End of iteration
end
# GetSpectrum uses the cache, so iteration is also cached
spectrum = GetSpectrum(it.data, state)
# Yield the index and the spectrum
return ((state, spectrum), state + 1)
end
# --- High-performance Internal Iterator --- #
"""
_iterate_spectra_fast(f::Function, data::MSIData)
An internal, high-performance iterator for bulk processing.
It avoids the overhead of `GetSpectrum` by reading directly from the file stream
and reusing pre-allocated buffers.
- `f`: A function to call for each spectrum, with signature `f(index, mz, intensity)`.
- `data`: The `MSIData` object.
"""
function _iterate_spectra_fast_impl(f::Function, data::MSIData, source::ImzMLSource)
# This implementation is for imzML and is optimized for performance by
# using pre-allocated buffers.
max_points = 0
for meta in data.spectra_metadata
# For imzML, encoded_length is the number of points
max_points = max(max_points, meta.mz_asset.encoded_length)
end
# If all spectra are empty, just call f with empty arrays
if max_points == 0 && !isempty(data.spectra_metadata)
for i in 1:length(data.spectra_metadata)
f(i, source.mz_format[], source.intensity_format[])
end
return
end
mz_buffer = Vector{source.mz_format}(undef, max_points)
int_buffer = Vector{source.intensity_format}(undef, max_points)
for i in 1:length(data.spectra_metadata)
meta = data.spectra_metadata[i]
nPoints = meta.mz_asset.encoded_length
if nPoints == 0
f(i, source.mz_format[], source.intensity_format[])
continue
end
mz_view = view(mz_buffer, 1:nPoints)
int_view = view(int_buffer, 1:nPoints)
seek(source.ibd_handle, meta.mz_asset.offset)
read!(source.ibd_handle, mz_view)
seek(source.ibd_handle, meta.int_asset.offset)
read!(source.ibd_handle, int_view)
f(i, mz_view, int_view)
end
end
function _iterate_spectra_fast_impl(f::Function, data::MSIData, source::MzMLSource)
# This implementation is for mzML. It iterates through each spectrum,
# decodes it, and then calls the function `f`. It's less performant than
# the imzML version because we cannot pre-allocate buffers of a known size,
# but it is correct and still faster than using GetSpectrum due to bypassing the cache.
for i in 1:length(data.spectra_metadata)
meta = data.spectra_metadata[i]
mz = read_binary_vector(source.file_handle, meta.mz_asset)
intensity = read_binary_vector(source.file_handle, meta.int_asset)
f(i, mz, intensity)
end
end
function _iterate_spectra_fast(f::Function, data::MSIData)
# Dispatch to the correct implementation based on the source type
_iterate_spectra_fast_impl(f, data, data.source)
end

33
src/MSI_src.jl Normal file
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@ -0,0 +1,33 @@
module MSI_src
# Export the public API
export OpenMSIData, GetSpectrum, IterateSpectra, ImportMzmlFile, load_slices, plot_slices, plot_slice, get_total_spectrum, get_average_spectrum, LoadMzml, LoadSpectra
# Include all source files directly into the main module
include("MSIData.jl")
include("ParserHelpers.jl")
include("mzML.jl")
include("imzML.jl")
include("MzmlConverter.jl")
# --- Main Entry Point --- #
"""
OpenMSIData(filepath::String; cache_size=100)
Opens a .mzML or .imzML file and prepares it for data access.
This is the main entry point for the new data access API.
"""
function OpenMSIData(filepath::String; cache_size=100)
if endswith(lowercase(filepath), ".mzml")
return load_mzml_lazy(filepath, cache_size=cache_size)
elseif endswith(lowercase(filepath), ".imzml")
return load_imzml_lazy(filepath, cache_size=cache_size)
else
error("Unsupported file type: $filepath. Please provide a .mzML or .imzML file.")
end
end
end # module MSI_src

605
src/MzmlConverter.jl
View File

@ -1,16 +1,14 @@
# src/MzmlConverter.jl
""" """
This file contains the workflow for converting .mzML files (with one spectrum per pixel) This file contains the workflow for converting .mzML files (with one spectrum per pixel)
into a proper .imzML/.ibd file pair, using a separate synchronization file. into a proper .imzML/.ibd file pair, using a separate synchronization file.
It replicates the functionality of the project's original R scripts that use MALDIquant. It replicates the functionality of the original R scripts that use MALDIquant.
""" """
using CSV, DataFrames using DataFrames, Printf, CSV
# This file assumes that the main application file (e.g., app.jl) has already included
# the necessary source files: MSIData.jl, mzML.jl, imzML.jl
# Note: This file assumes that `LoadSpectra` from DataAccess.jl and the necessary
# structs/functions from ParserHelpers.jl, mzML.jl, and imzML.jl are available
# in the execution context (e.g., included in the main app.jl).
# A struct to hold the processed pixel data before exporting # A struct to hold the processed pixel data before exporting
struct ProcessedPixel struct ProcessedPixel
@ -19,11 +17,18 @@ struct ProcessedPixel
intensity::Vector{Float32} intensity::Vector{Float32}
end end
# This struct will hold the metadata needed for the XML file
struct BinaryMetadata
mz_offset::UInt64
mz_length::UInt64
int_offset::UInt64
int_length::UInt64
end
""" """
GetMzmlScanTime(fileName::String) GetMzmlScanTime(fileName::String)
Parses a .mzML file to extract the scan start time for each spectrum. Parses a .mzML file to extract the scan start time for each spectrum.
This is a Julia implementation of the `GetMzmlScanTime` function from the R scripts.
# Arguments # Arguments
* `fileName`: Path to the .mzML file. * `fileName`: Path to the .mzML file.
@ -32,48 +37,75 @@ This is a Julia implementation of the `GetMzmlScanTime` function from the R scri
- A `Matrix{Int64}` where each row is `[spectrum_index, time_in_milliseconds]`. - A `Matrix{Int64}` where each row is `[spectrum_index, time_in_milliseconds]`.
""" """
function GetMzmlScanTime(fileName::String) function GetMzmlScanTime(fileName::String)
spec_count = 0
times = Tuple{Int64, Int64}[] times = Tuple{Int64, Int64}[]
# Pre-allocate based on an estimate to reduce re-allocations
try
file_size = filesize(fileName)
estimated_spectra = max(1000, file_size ÷ 10000) # Heuristic
sizehint!(times, estimated_spectra)
catch
# Ignore if filesize fails, sizehint! is just an optimization
end
open(fileName, "r") do stream open(fileName, "r") do stream
file_content = read(stream, String) state = :outside_spectrum
current_index = 0
current_time = nothing
# First, find the total number of spectra to pre-allocate for line in eachline(stream)
spectrum_list_match = match(r"<spectrumList count=\"(\d+)\"", file_content) if state == :outside_spectrum
if spectrum_list_match === nothing if occursin("<spectrum ", line)
error("Could not find <spectrumList> tag or count attribute.") state = :in_spectrum
current_index = 0
current_time = nothing
# Process index from the start tag itself
idx_match = match(r"index=\"(\d+)\"", line)
if idx_match !== nothing
current_index = parse(Int, idx_match.captures[1]) + 1
end end
total_spectra = parse(Int, spectrum_list_match.captures[1]) end
sizehint!(times, total_spectra) elseif state == :in_spectrum
# Look for time cvParam
# Iterate over each spectrum block if occursin("<cvParam", line)
for spectrum_match in eachmatch(r"<spectrum index=\"(\d+)\"[^>]*>.*?<\/spectrum>", file_content, overlay=true) if occursin("MS:1000016", line) || occursin("MS:1000015", line)
spec_block = spectrum_match.match time_match = match(r"value=\"([\d\.]+)\"", line)
# The R script appears to treat the 0-based mzML index as 1-based, so we add 1.
spec_index = parse(Int, spectrum_match.captures[1]) + 1
# Find the scan start time within the spectrum block
time_match = match(r"<cvParam accession=\"MS:1000016\".*?value=\"([\d\.]+)\"", spec_block)
if time_match !== nothing if time_match !== nothing
# The value is in minutes. Convert to milliseconds and round. time_val = parse(Float64, time_match.captures[1])
time_in_minutes = parse(Float64, time_match.captures[1]) # MS:1000016 is minutes, MS:1000015 is seconds
time_in_ms = round(Int64, time_in_minutes * 60000) unit_scale = occursin("MS:1000016", line) ? 60000 : 1000
push!(times, (spec_index, time_in_ms)) current_time = round(Int64, time_val * unit_scale)
end
end end
end end
# Normalize times so the first scan is at t=0 # Check for end of spectrum
if occursin("</spectrum>", line)
state = :outside_spectrum
if current_index > 0 && current_time !== nothing
push!(times, (current_index, current_time))
end
end
end
end
end
# Sort by spectrum index to ensure correct order before normalization
sort!(times, by = x -> x[1])
# Normalize times relative to the first scan
if !isempty(times) if !isempty(times)
sort!(times, by = x -> x[1]) # Ensure scans are sorted by index
first_time = times[1][2] first_time = times[1][2]
for i in eachindex(times) for i in eachindex(times)
times[i] = (times[i][1], times[i][2] - first_time) times[i] = (times[i][1], times[i][2] - first_time)
end end
end end
end # open
# Convert vector of tuples to a matrix # Convert vector of tuples to a matrix
if isempty(times)
return Matrix{Int64}(undef, 0, 2)
end
return permutedims(hcat(collect.(times)...)) return permutedims(hcat(collect.(times)...))
end end
@ -92,144 +124,491 @@ This is a Julia implementation of the `MatchAcquireTime` function from the R scr
# Returns # Returns
- A `Matrix{Int64}` where each row is `[pixel_index, pixel_time_ms, first_scan_index, last_scan_index]`. - A `Matrix{Int64}` where each row is `[pixel_index, pixel_time_ms, first_scan_index, last_scan_index]`.
""" """
function MatchAcquireTime(sync_file_path::String, scans::Matrix{Int64}) function MatchAcquireTime(sync_file_path::String, scans::Matrix{Int64}; img_width::Int=0, img_height::Int=0)
if !isfile(sync_file_path) if !isfile(sync_file_path)
error("Synchronization file not found: $sync_file_path") error("Synchronization file not found: $sync_file_path")
end end
# Load xyz stage pixel delays from the sync file, skipping the first 2 header lines.
pixel_df = CSV.read(sync_file_path, DataFrame, header=false, skipto=3) pixel_df = CSV.read(sync_file_path, DataFrame, header=false, skipto=3)
pixel = Matrix(pixel_df) pixel_matrix = Matrix(pixel_df)
# Normalize pixel times so the first is at t=0 num_pixels_original = size(pixel_matrix, 1)
pixel[:, 2] .-= pixel[1, 2] if num_pixels_original == 0
return zeros(Int64, 0, 5)
num_pixels = size(pixel, 1)
num_scans = size(scans, 1)
index_matrix = zeros(Int64, num_pixels, 2)
scan_row = 1
for pixel_row in 1:(num_pixels - 1)
start_scan = scan_row
# Find the scan that ends after the *next* pixel starts
while scan_row <= num_scans && scans[scan_row, 2] < pixel[pixel_row + 1, 2]
scan_row += 1
end end
index_matrix[pixel_row, 1] = start_scan # Determine image dimensions and generate coordinates
index_matrix[pixel_row, 2] = scan_row - 1 current_img_width = img_width
current_img_height = img_height
# The next pixel's scans start from the one that crossed the boundary if current_img_width == 0 || current_img_height == 0
scan_row = max(1, scan_row - 1) if size(pixel_matrix, 2) >= 3
@info "Sync file contains X, Y coordinates"
coordinates = convert(Matrix{Int}, pixel_matrix[:, 1:2])
pixel_times = convert(Vector{Int64}, pixel_matrix[:, 3])
current_img_width = maximum(coordinates[:, 1])
current_img_height = maximum(coordinates[:, 2])
# Apply R's pixel truncation logic
num_pixels = (floor(Int, (num_pixels_original - 1) / current_img_width)) * current_img_width
if num_pixels <= 0
error("Calculated num_pixels to process is zero or negative: $num_pixels")
end end
# Assign scans for the last pixel # Truncate arrays
index_matrix[num_pixels, 1] = scan_row final_coordinates = coordinates[1:num_pixels, :]
index_matrix[num_pixels, 2] = num_scans final_pixel_times = pixel_times[1:num_pixels]
else
@info "Sync file contains Index and Time; generating coordinates"
pixel_times = convert(Vector{Int64}, pixel_matrix[:, 2])
# R's width detection logic
diffs = pixel_matrix[2:end, 1] .- pixel_matrix[1:end-1, 1]
width_indices = findall(x -> x != 1, diffs)
if !isempty(width_indices)
current_img_width = width_indices[1]
else
current_img_width = num_pixels_original
end
current_img_height = num_pixels_original ÷ current_img_width
# R's pixel truncation logic
num_pixels = (floor(Int, (num_pixels_original - 1) / current_img_width)) * current_img_width
if num_pixels <= 0
error("Calculated num_pixels to process is zero or negative: $num_pixels")
end
# Generate coordinates for truncated pixels
final_coordinates = zeros(Int, num_pixels, 2)
final_pixel_times = zeros(Int64, num_pixels)
# Handle cases where some pixels have no scans by creating an empty range
for i in 1:num_pixels for i in 1:num_pixels
if index_matrix[i, 2] < index_matrix[i, 1] idx = pixel_matrix[i, 1]
index_matrix[i, 2] = index_matrix[i, 1] - 1 final_coordinates[i, 1] = ((idx - 1) % current_img_width) + 1
final_coordinates[i, 2] = fld(idx - 1, current_img_width) + 1
final_pixel_times[i] = pixel_times[i]
end
end
else
@info "Using provided dimensions: $(current_img_width)x$(current_img_height)"
pixel_times = convert(Vector{Int64}, pixel_matrix[:, 2])
# R's pixel truncation logic (FIXED: consistent formula)
num_pixels = (floor(Int, (num_pixels_original - 1) / current_img_width)) * current_img_width
if num_pixels <= 0
error("Calculated num_pixels to process is zero or negative: $num_pixels")
end
# Generate coordinates
final_coordinates = zeros(Int, num_pixels, 2)
final_pixel_times = zeros(Int64, num_pixels)
for i in 1:num_pixels
idx = pixel_matrix[i, 1]
final_coordinates[i, 1] = ((idx - 1) % current_img_width) + 1
final_coordinates[i, 2] = fld(idx - 1, current_img_width) + 1
final_pixel_times[i] = pixel_times[i]
end end
end end
return hcat(pixel, index_matrix) # Normalize pixel times
if !isempty(final_pixel_times)
min_pixel_time = minimum(final_pixel_times)
final_pixel_times .-= min_pixel_time
end
num_scans = size(scans, 1)
if num_scans == 0
return hcat(final_coordinates, final_pixel_times, zeros(Int64, num_pixels, 2))
end
# FIXED R's time matching algorithm with bounds checking
first_idx = 1
last_idx = 1
index_matrix = zeros(Int, num_pixels, 2)
for i_pixel in 1:num_pixels
pixel_time = final_pixel_times[i_pixel]
# Find the first scan that reaches or exceeds pixel time
while last_idx <= num_scans && scans[last_idx, 2] < pixel_time
last_idx += 1
end
# Ensure valid indices
if last_idx > num_scans
# No more scans available for remaining pixels
index_matrix[i_pixel:end, 1] .= num_scans + 1 # Invalid index
index_matrix[i_pixel:end, 2] .= num_scans # Invalid index
break
end
# Assign scan indices with bounds checking
start_scan = max(1, first_idx)
end_scan = max(1, last_idx - 1)
# Ensure start_scan <= end_scan
if start_scan > end_scan
start_scan = end_scan
end
index_matrix[i_pixel, 1] = start_scan
index_matrix[i_pixel, 2] = end_scan
# Update for next iteration (R's algorithm)
first_idx = last_idx - 1
last_idx = first_idx
# Ensure first_idx doesn't go below 1
if first_idx < 1
first_idx = 1
last_idx = 1
end
end
return hcat(final_coordinates, final_pixel_times, index_matrix)
end end
function RenderPixel(pixel_info, scans, spectra, scan_time_deltas, pixel_time_deltas) function RenderPixel(pixel_info, scans, msi_data::MSIData, scan_time_deltas, pixel_time_deltas)
first_scan = pixel_info[3] pixel_time = pixel_info[3]
last_scan = pixel_info[4] first_scan = pixel_info[4]
last_scan = pixel_info[5]
num_actions = last_scan - first_scan num_actions = last_scan - first_scan
# Use the m/z array of the first scan as the reference # Get reference m/z array from the first scan involved
mz_array = spectra[1, first_scan] mz_array, _ = GetSpectrum(msi_data, first_scan)
new_intensity = zeros(Float32, length(mz_array)) new_intensity = zeros(Float32, length(mz_array))
# SAFETY: Ensure we have valid scan indices
if first_scan < 1 || last_scan > size(scans, 1) || first_scan > last_scan
return (mz_array, new_intensity) # Return zero intensity for invalid ranges
end
if num_actions == 0 # Single scan contributes to the pixel if num_actions == 0 # Single scan contributes to the pixel
scale = pixel_time_deltas[pixel_info[1]] / scan_time_deltas[first_scan] _, intensity = GetSpectrum(msi_data, first_scan)
new_intensity .+= spectra[2, first_scan] .* scale # SAFETY: Ensure positive scaling
scale = max(pixel_time_deltas[first_scan] / scan_time_deltas[first_scan], 0.0f0)
new_intensity .= intensity .* scale
elseif num_actions == 1 # Two partial scans contribute elseif num_actions == 1 # Two partial scans contribute
# First partial scan # First partial scan
scale1 = (scans[last_scan, 2] - pixel_info[2]) / scan_time_deltas[first_scan] _, intensity1 = GetSpectrum(msi_data, first_scan)
new_intensity .+= spectra[2, first_scan] .* scale1 scale1 = max((scans[last_scan, 2] - pixel_time) / scan_time_deltas[first_scan], 0.0f0)
new_intensity .+= intensity1 .* scale1
# Second partial scan # Second partial scan
next_pixel_time = pixel_info[2] + pixel_time_deltas[pixel_info[1]] _, intensity2 = GetSpectrum(msi_data, last_scan)
scale2 = (next_pixel_time - scans[last_scan, 2]) / scan_time_deltas[last_scan] next_pixel_time = pixel_time + pixel_time_deltas[first_scan]
new_intensity .+= spectra[2, last_scan] .* scale2 scale2 = max((next_pixel_time - scans[last_scan, 2]) / scan_time_deltas[last_scan], 0.0f0)
new_intensity .+= intensity2 .* scale2
elseif num_actions > 1 # Multiple scans contribute elseif num_actions > 1 # Multiple scans contribute
# First partial scan # First partial scan
scale1 = (scans[first_scan + 1, 2] - pixel_info[2]) / scan_time_deltas[first_scan] _, intensity1 = GetSpectrum(msi_data, first_scan)
new_intensity .+= spectra[2, first_scan] .* scale1 scale1 = max((scans[first_scan + 1, 2] - pixel_time) / scan_time_deltas[first_scan], 0.0f0)
new_intensity .+= intensity1 .* scale1
# Full scans in the middle # Full scans in the middle
for i in (first_scan + 1):(last_scan - 1) for i in (first_scan + 1):(last_scan - 1)
new_intensity .+= spectra[2, i] _, intensity_middle = GetSpectrum(msi_data, i)
new_intensity .+= intensity_middle
end end
# Last partial scan # Last partial scan
next_pixel_time = pixel_info[2] + pixel_time_deltas[pixel_info[1]] _, intensity2 = GetSpectrum(msi_data, last_scan)
scale2 = (next_pixel_time - scans[last_scan, 2]) / scan_time_deltas[last_scan] next_pixel_time = pixel_time + pixel_time_deltas[first_scan]
new_intensity .+= spectra[2, last_scan] .* scale2 scale2 = max((next_pixel_time - scans[last_scan, 2]) / scan_time_deltas[last_scan], 0.0f0)
new_intensity .+= intensity2 .* scale2
end end
# FINAL SAFETY: Clamp any negative values to zero
new_intensity = max.(new_intensity, 0.0f0)
return (mz_array, new_intensity) return (mz_array, new_intensity)
end end
function ConvertMzmlToImzml(source_file::String, timing_matrix::Matrix{Int64}, scans::Matrix{Int64}) function ConvertMzmlToImzml(source_file::String, timing_matrix::Matrix{Int64}, scans::Matrix{Int64})
# Get image width from timing info if size(timing_matrix, 1) == 0
width = findfirst(i -> timing_matrix[i, 1] - timing_matrix[i-1, 1] != 1, 2:size(timing_matrix, 1)) return ProcessedPixel[], (0, 0)
height = size(timing_matrix, 1) ÷ width end
# Load the full mzML data # Get image dimensions from timing_matrix (assuming columns 1 and 2 are X and Y)
spectra = LoadSpectra(source_file) width = maximum(timing_matrix[:, 1])
height = maximum(timing_matrix[:, 2])
# Pre-calculate time deltas # Open the mzML file using the new memory-efficient API
scan_time_deltas = diff(scans[:, 2]) msi_data = OpenMSIData(source_file)
pixel_time_deltas = diff(timing_matrix[:, 2])
# Append a final delta for the last element # Pre-calculate time deltas robustly
push!(scan_time_deltas, scan_time_deltas[end]) scan_time_deltas = zeros(Int64, size(scans, 1))
push!(pixel_time_deltas, pixel_time_deltas[end]) if size(scans, 1) > 1
for i in 1:(size(scans, 1) - 1)
delta = scans[i+1, 2] - scans[i, 2]
scan_time_deltas[i] = max(1, delta) # Ensure delta is at least 1
end
scan_time_deltas[end] = max(1, scan_time_deltas[end-1]) # Use previous delta for last scan, ensure at least 1
end
pixel_time_deltas = zeros(Int64, size(timing_matrix, 1))
if size(timing_matrix, 1) > 1
for i in 1:(size(timing_matrix, 1) - 1)
# Assumes time is in the 3rd column of the timing_matrix
delta = timing_matrix[i+1, 3] - timing_matrix[i, 3]
pixel_time_deltas[i] = max(1, delta) # Ensure delta is at least 1
end
pixel_time_deltas[end] = max(1, pixel_time_deltas[end-1]) # Use previous delta for last pixel, ensure at least 1
end
processed_pixels = ProcessedPixel[] processed_pixels = ProcessedPixel[]
sizehint!(processed_pixels, size(timing_matrix, 1)) sizehint!(processed_pixels, size(timing_matrix, 1))
empty_pixel_count = 0
# DEBUG: Scan coverage analysis
println("DEBUG: Scan coverage analysis:")
covered_pixels_count = 0
for i in 1:size(timing_matrix, 1)
first_scan = timing_matrix[i, 4]
last_scan = timing_matrix[i, 5]
if first_scan <= last_scan && first_scan >= 1 && last_scan <= size(scans, 1)
covered_pixels_count += 1
end
end
println(" Pixels with potential scans: $covered_pixels_count/$(size(timing_matrix, 1))")
println(" Total scans available: $(size(scans, 1))")
for i in 1:size(timing_matrix, 1) for i in 1:size(timing_matrix, 1)
pixel_info = timing_matrix[i, :] pixel_info = timing_matrix[i, :]
first_scan = pixel_info[3] x = pixel_info[1]
last_scan = pixel_info[4] y = pixel_info[2]
first_scan = pixel_info[4]
last_scan = pixel_info[5]
# Skip if there are no scans for this pixel if first_scan > last_scan || first_scan < 1 || last_scan > size(scans, 1)
(first_scan > last_scan) && continue empty_pixel_count += 1
push!(processed_pixels, ProcessedPixel((x, y), Float64[], Float32[]))
continue
end
# Calculate coordinates mz, intensity = RenderPixel(pixel_info, scans, msi_data, scan_time_deltas, pixel_time_deltas)
x = ((pixel_info[1] - 1) % width) + 1
y = fld(pixel_info[1] - 1, width) + 1
mz, intensity = RenderPixel(pixel_info, scans, spectra, scan_time_deltas, pixel_time_deltas)
push!(processed_pixels, ProcessedPixel((x, y), mz, intensity)) push!(processed_pixels, ProcessedPixel((x, y), mz, intensity))
end end
@info "Found and created $empty_pixel_count empty pixels out of $(size(timing_matrix, 1)) total."
return processed_pixels, (width, height) return processed_pixels, (width, height)
end end
function ExportImzml(target_file::String, pixels::Vector{ProcessedPixel}, dims::Tuple{Int, Int}) function ExportImzml(target_file::String, pixels::Vector{ProcessedPixel}, dims::Tuple{Int, Int})
@warn "ExportImzml is not yet implemented. The processed pixel data has been generated but not saved to .imzML/.ibd files." ibd_file = replace(target_file, r"\.imzML$"i => ".ibd")
# TODO: Implement the logic to write the .imzML (XML) and .ibd (binary) files.
# 1. Open target_file.imzML and target_file.ibd for writing. # Ensure we have valid pixels
# 2. Write all m/z and intensity arrays sequentially to the .ibd file, tracking offsets and lengths. if isempty(pixels)
# 3. Write the .imzML XML structure, including: @error "No pixels to export"
# - Boilerplate headers
# - <fileDescription>, <referenceableParamGroupList>, <scanSettingsList>
# - A <spectrumList> with a <spectrum> for each pixel.
# - Each <spectrum> must contain cvParams for x/y coords and external data pointers to the .ibd file.
return false return false
end
binary_meta = BinaryMetadata[]
sizehint!(binary_meta, length(pixels))
try
# Step 1: Write .ibd file with proper binary format
open(ibd_file, "w") do ibd_stream
# Write UUID as first 16 bytes (placeholder)
write(ibd_stream, zeros(UInt8, 16))
# Write in little-endian format (standard for imzML)
for pixel in pixels
# Write m/z array as 64-bit little-endian floats
mz_offset = position(ibd_stream)
for val in pixel.mz
write(ibd_stream, htol(Float64(val))) # Host to little-endian
end
mz_length = position(ibd_stream) - mz_offset
# Write intensity array as 32-bit little-endian floats
int_offset = position(ibd_stream)
for val in pixel.intensity
write(ibd_stream, htol(Float32(val))) # Host to little-endian
end
int_length = position(ibd_stream) - int_offset
push!(binary_meta, BinaryMetadata(mz_offset, mz_length, int_offset, int_length))
end
end
# Step 2: Write proper .imzML XML file
open(target_file, "w") do imzml_stream
# Use indexedmzML wrapper
write(imzml_stream, """<?xml version="1.0" encoding="ISO-8859-1"?>
<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
<mzML version="1.1" id="$(splitext(basename(target_file))[1])">
""")
# CV List
write(imzml_stream, """ <cvList count="3">
<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>
<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>
</cvList>
""")
# File Description
write(imzml_stream, """ <fileDescription>
<fileContent>
<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
<cvParam cvRef="IMS" accession="IMS:1000080" name="mass spectrum"/>
<cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
</fileContent>
</fileDescription>
""")
# Referenceable Param Groups
write(imzml_stream, """ <referenceableParamGroupList count="2">
<referenceableParamGroup id="mzArray">
<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float"/>
</referenceableParamGroup>
<referenceableParamGroup id="intensityArray">
<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
</referenceableParamGroup>
</referenceableParamGroupList>
""")
# Sample List
write(imzml_stream, """ <sampleList count="1">
<sample id="sample1" name="ImagingSample">
<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
</sample>
</sampleList>
""")
# Software List - OPEN SOURCE
write(imzml_stream, """ <softwareList count="1">
<software id="MSIConverter" version="1.0">
<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="mzML to imzML converter"/>
</software>
</softwareList>
""")
# Scan Settings IMAGING
write(imzml_stream, """ <scanSettingsList count="1">
<scanSettings id="scanSettings1">
<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="$(dims[1])"/>
<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="$(dims[2])"/>
<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
</scanSettings>
</scanSettingsList>
""")
# Instrument Configuration MALDI/TOF
write(imzml_stream, """ <instrumentConfigurationList count="1">
<instrumentConfiguration id="instrument1">
<componentList count="3">
<source order="1">
<cvParam cvRef="MS" accession="MS:1000075" name="MALDI source"/>
</source>
<analyzer order="2">
<cvParam cvRef="MS" accession="MS:1000084" name="time-of-flight"/>
</analyzer>
<detector order="3">
<cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier"/>
</detector>
</componentList>
<softwareRef ref="MSIConverter"/>
</instrumentConfiguration>
</instrumentConfigurationList>
""")
# Data Processing
write(imzml_stream, """ <dataProcessingList count="1">
<dataProcessing id="conversionProcessing">
<processingMethod order="1" softwareRef="MSIConverter">
<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to imzML"/>
</processingMethod>
</dataProcessing>
</dataProcessingList>
""")
# Run and Spectrum List
spectrum_offsets = UInt64[]
write(imzml_stream, """ <run defaultInstrumentConfigurationRef="instrument1" id="run1" sampleRef="sample1">
<spectrumList count="$(length(pixels))" defaultDataProcessingRef="conversionProcessing">
""")
# Write each spectrum
for (i, pixel) in enumerate(pixels)
meta = binary_meta[i]
x, y = pixel.coords
spectrum_start = position(imzml_stream)
push!(spectrum_offsets, spectrum_start)
write(imzml_stream, """ <spectrum id="Scan=$(i)" defaultArrayLength="$(length(pixel.mz))" index="$(i-1)">
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
<scanList count="1">
<scan instrumentConfigurationRef="instrument1">
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="$(x)"/>
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="$(y)"/>
</scan>
</scanList>
<binaryDataArrayList count="2">
<binaryDataArray encodedLength="0">
<referenceableParamGroupRef ref="mzArray"/>
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="$(meta.mz_offset)"/>
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="$(length(pixel.mz))"/>
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="$(meta.mz_length)"/>
<binary/>
</binaryDataArray>
<binaryDataArray encodedLength="0">
<referenceableParamGroupRef ref="intensityArray"/>
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="$(meta.int_offset)"/>
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="$(length(pixel.intensity))"/>
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="$(meta.int_length)"/>
<binary/>
</binaryDataArray>
</binaryDataArrayList>
</spectrum>
""")
end
write(imzml_stream, """ </spectrumList>
</run>
</mzML>
""")
# Index List
index_list_start = position(imzml_stream)
write(imzml_stream, """ <indexList count="1">
<index name="spectrum">
""")
for (i, offset) in enumerate(spectrum_offsets)
write(imzml_stream, " <offset idRef=\"Scan=$(i)\">$offset</offset>\n")
end
write(imzml_stream, """ </index>
</indexList>
<indexListOffset>$index_list_start</indexListOffset>
</indexedmzML>
""")
end
println("Successfully created: $target_file")
println("Successfully created: $ibd_file")
return true
catch e
@error "Failed to export imzML files" exception=(e, catch_backtrace())
# Clean up partial files
isfile(ibd_file) && rm(ibd_file, force=true)
isfile(target_file) && rm(target_file, force=true)
return false
end
end end
""" """
@ -241,13 +620,15 @@ Main workflow function to convert a .mzML file to an .imzML file.
* `source_file`: Path to the input .mzML file. * `source_file`: Path to the input .mzML file.
* `sync_file`: Path to the synchronization text file. * `sync_file`: Path to the synchronization text file.
* `target_file`: Path for the output .imzML file (the .ibd will be named accordingly). * `target_file`: Path for the output .imzML file (the .ibd will be named accordingly).
* `img_width`: width dimention for the creation of the x axis
* `img_height`: height dimention for the creation of the y axis
""" """
function ImportMzmlFile(source_file::String, sync_file::String, target_file::String) function ImportMzmlFile(source_file::String, sync_file::String, target_file::String; img_width::Int=0, img_height::Int=0)
println("Step 1: Getting scan times from .mzML file...") println("Step 1: Getting scan times from .mzML file...")
scans = GetMzmlScanTime(source_file) scans = GetMzmlScanTime(source_file)
println("Step 2: Matching acquisition times...") println("Step 2: Matching acquisition times...")
timing_matrix = MatchAcquireTime(sync_file, scans) timing_matrix = MatchAcquireTime(sync_file, scans; img_width=img_width, img_height=img_height)
println("Step 3: Converting spectra...") println("Step 3: Converting spectra...")
processed_pixels, (width, height) = ConvertMzmlToImzml(source_file, timing_matrix, scans) processed_pixels, (width, height) = ConvertMzmlToImzml(source_file, timing_matrix, scans)
@ -264,7 +645,7 @@ function ImportMzmlFile(source_file::String, sync_file::String, target_file::Str
if success if success
println("Conversion successful: $target_file") println("Conversion successful: $target_file")
else else
println("Conversion failed. Exporting is not yet implemented.") println("Conversion failed.")
end end
return success return success
end end

15
src/ParserHelpers.jl
View File

@ -51,7 +51,7 @@ Retrieves an attribute's value from an XML tag string.
""" """
function get_attribute(source::AbstractString, tag::String = "([^=]+)") function get_attribute(source::AbstractString, tag::String = "([^=]+)")
# Construct the regex pattern string # Construct the regex pattern string
pattern_str = "\s" * tag * "=\"([^"]*)\"" pattern_str = "\\s" * tag * "=\"([^\"]*)\""
regStr = Regex(pattern_str) regStr = Regex(pattern_str)
return match(regStr, source) return match(regStr, source)
end end
@ -107,16 +107,3 @@ mutable struct CVParams
is_compressed::Bool is_compressed::Bool
axis_type::Symbol axis_type::Symbol
end end
function update_cv_params!(params::CVParams, acc::String)
if acc == "MS:1000514"; params.axis_type = :mz;
elseif acc == "MS:1000515"; params.axis_type = :intensity;
elseif acc == "MS:1000519"; params.format = Int32;
elseif acc == "MS:1000521"; params.format = Float32;
elseif acc == "MS:1000522"; params.format = Int64;
elseif acc == "MS:1000523"; params.format = Float64;
elseif acc == "MS:1000574"; params.is_compressed = true;
end
end

281
src/imzML.jl
View File

@ -1,40 +1,4 @@
using Images, Statistics, CairoMakie, DataFrames, Printf, ColorSchemes
using Images, ImageFiltering, StatsBase, Statistics, CairoMakie, ColorSchemes, DataFrames, CSV, Printf, Dates
include("ParserHelpers.jl")
# --- Lazy Loading Data Structures ---
# Struct to hold metadata for a single spectrum, for lazy loading.
struct SpectrumMetadata
x::Int32
y::Int32
mz_offset::Int64
intensity_offset::Int64
mz_count::Int32
intensity_count::Int32
end
# Struct to hold the parsed imzML metadata and the handle to the .ibd file.
mutable struct ImzMLData
ibd_handle::IO
mz_format::Type
intensity_format::Type
spectra_metadata::Vector{SpectrumMetadata}
width::Int
height::Int
mz_is_first::Bool # To know the order in the ibd file
function ImzMLData(ibd_handle::IO, mz_format::Type, intensity_format::Type, spectra_metadata::Vector{SpectrumMetadata}, width::Int, height::Int, mz_is_first::Bool)
obj = new(ibd_handle, mz_format, intensity_format, spectra_metadata, width, height, mz_is_first)
finalizer(obj) do o
if isopen(o.ibd_handle)
close(o.ibd_handle)
end
end
return obj
end
end
# --- Extracted from imzML.jl --- # --- Extracted from imzML.jl ---
@ -43,7 +7,7 @@ This file provides a library for parsing `.imzML` and `.ibd` files in pure Julia
It is intended to be included by a parent script. It is intended to be included by a parent script.
Core Functions: Core Functions:
- `load_imzml`: The main function that orchestrates the parsing. - `load_imzml_lazy`: The main function that orchestrates the parsing.
- Helper functions for reading XML metadata and binary spectral data. - Helper functions for reading XML metadata and binary spectral data.
""" """
@ -174,70 +138,66 @@ end
""" """
load_imzml(file_path::String) load_imzml_lazy(file_path::String; cache_size=100)
Main function to parse an `.imzML`/.ibd file pair and prepare for lazy loading.
It parses the metadata from the `.imzML` file, including spectrum coordinates and
byte offsets for data in the `.ibd` file, but does not load the spectral data itself.
# Returns Main function to parse an `.imzML`/.ibd file pair and prepare for lazy loading.
- An `ImzMLData` struct containing the open `.ibd` file handle and all necessary metadata It now returns a unified MSIData object.
for on-demand data loading.
""" """
function load_imzml(file_path::String) function load_imzml_lazy(file_path::String; cache_size=100)
println("DEBUG: Checking for .imzML file at $file_path")
if !isfile(file_path) if !isfile(file_path)
error("Provided path is not a file: $(file_path)") error("Provided path is not a file: $(file_path)")
end end
ibd_path = replace(file_path, ".imzML" => ".ibd") ibd_path = replace(file_path, r"\.(imzML|mzML)"i => ".ibd")
println("DEBUG: Checking for .ibd file at $ibd_path")
if !isfile(ibd_path) if !isfile(ibd_path)
error("Corresponding .ibd file not found for: $(file_path)") error("Corresponding .ibd file not found for: $(file_path)")
end end
stream = open(file_path) println("DEBUG: Opening file streams for .imzML and .ibd")
hIbd = open(ibd_path) stream = open(file_path, "r")
hIbd = open(ibd_path, "r")
# We don't use a try/finally block because we need to return the open hIbd handle.
# The finalizer on the ImzMLData struct will be responsible for closing it.
try
println("DEBUG: Configuring axes...")
axis = axes_config_img(stream) axis = axes_config_img(stream)
println("DEBUG: Getting image dimensions...")
imgDim = get_img_dimensions(stream) imgDim = get_img_dimensions(stream)
width, height, num_spectra = imgDim width, height, num_spectra = imgDim
println("DEBUG: Image dimensions: $(width)x$(height), $num_spectra spectra.")
# Determine which format is for m/z and which for intensity from the referenceableParamGroups
mz_config_idx = findfirst(a -> a.Axis == 1, axis) mz_config_idx = findfirst(a -> a.Axis == 1, axis)
int_config_idx = findfirst(a -> a.Axis == 2, axis) int_config_idx = findfirst(a -> a.Axis == 2, axis)
mz_format = axis[mz_config_idx].Format mz_format = axis[mz_config_idx].Format
intensity_format = axis[int_config_idx].Format intensity_format = axis[int_config_idx].Format
println("DEBUG: m/z format: $mz_format, Intensity format: $intensity_format")
# The original parsing logic is highly optimized and relies on fixed offsets within the XML structure. # --- NEW PARSING LOGIC based on the old, working code ---
# We reuse it to get the initial .ibd file offset and the structural attributes of the <spectrum> tags. println("DEBUG: Learning file structure from first spectrum...")
start_of_spectra_xml = position(stream) start_of_spectra_xml = position(stream)
attr = get_spectrum_attributes(stream, hIbd) attr = get_spectrum_attributes(stream, hIbd)
# get_spectrum_attributes moves the hIbd pointer to the start of the first spectrum's binary data.
current_ibd_offset = position(hIbd) current_ibd_offset = position(hIbd)
# We need to re-scan the spectra list from the beginning to get metadata for each spectrum.
seek(stream, start_of_spectra_xml) seek(stream, start_of_spectra_xml)
println("DEBUG: Initial IBD offset: $current_ibd_offset")
spectra_metadata = Vector{SpectrumMetadata}(undef, num_spectra) spectra_metadata = Vector{SpectrumMetadata}(undef, num_spectra)
# attr[3] is 4 if the first binary data array is intensity, 3 if it's m/z.
mz_is_first = attr[3] == 3 mz_is_first = attr[3] == 3
println("DEBUG: Parsing metadata for $num_spectra spectra using skip-based method...")
for k in 1:num_spectra for k in 1:num_spectra
# These skips are based on the structure of the first spectrum tag, assuming all are identical. # Use skip values learned from the first spectrum, assuming all are identical.
skip(stream, attr[5]) # Skip to X coordinate value skip(stream, attr[5]) # Skip to X coordinate value
val_tag = find_tag(stream, r"value=\"(\d+)\"") val_tag_x = find_tag(stream, r"value=\"(\d+)\"")
x = parse(Int32, val_tag.captures[1]) x = parse(Int32, val_tag_x.captures[1])
skip(stream, attr[6]) # Skip to Y coordinate value skip(stream, attr[6]) # Skip to Y coordinate value
val_tag = find_tag(stream, r"value=\"(\d+)\"") val_tag_y = find_tag(stream, r"value=\"(\d+)\"")
y = parse(Int32, val_tag.captures[1]) y = parse(Int32, val_tag_y.captures[1])
skip(stream, attr[7]) # Skip to array length value skip(stream, attr[7]) # Skip to array length value
val_tag = find_tag(stream, r"value=\"(\d+)\"") val_tag_len = find_tag(stream, r"value=\"(\d+)\"")
nPoints = parse(Int32, val_tag.captures[1]) nPoints = parse(Int32, val_tag_len.captures[1])
mz_len_bytes = nPoints * sizeof(mz_format) mz_len_bytes = nPoints * sizeof(mz_format)
int_len_bytes = nPoints * sizeof(intensity_format) int_len_bytes = nPoints * sizeof(intensity_format)
@ -251,18 +211,42 @@ function load_imzml(file_path::String)
mz_offset = int_offset + int_len_bytes mz_offset = int_offset + int_len_bytes
end end
spectra_metadata[k] = SpectrumMetadata(x, y, mz_offset, int_offset, nPoints, nPoints) # Create modern SpectrumAsset objects
mz_asset = SpectrumAsset(mz_format, false, mz_offset, nPoints, :mz)
int_asset = SpectrumAsset(intensity_format, false, int_offset, nPoints, :intensity)
spectra_metadata[k] = SpectrumMetadata(x, y, "", mz_asset, int_asset)
# Advance the offset for the next spectrum's data. # Advance the offset for the next spectrum's data.
current_ibd_offset += mz_len_bytes + int_len_bytes current_ibd_offset += mz_len_bytes + int_len_bytes
skip(stream, attr[8]) # Skip to the end of the spectrum tag skip(stream, attr[8]) # Skip to the end of the spectrum tag
end end
# --- END OF NEW PARSING LOGIC ---
println("DEBUG: Metadata parsing complete.")
# Build coordinate map for imzML files
println("DEBUG: Building coordinate map...")
coordinate_map = zeros(Int, width, height)
for (idx, meta) in enumerate(spectra_metadata)
if 1 <= meta.x <= width && 1 <= meta.y <= height
coordinate_map[meta.x, meta.y] = idx
end
end
println("DEBUG: Coordinate map built.")
# Close the .imzML file stream, but leave the .ibd stream open for lazy reading.
close(stream) close(stream)
return ImzMLData(hIbd, mz_format, intensity_format, spectra_metadata, width, height, mz_is_first) source = ImzMLSource(hIbd, mz_format, intensity_format)
println("DEBUG: Creating MSIData object.")
return MSIData(source, spectra_metadata, (width, height), coordinate_map, cache_size)
catch e
close(stream)
close(hIbd)
rethrow(e)
end
end end
# --- End of content from imzML.jl --- # --- End of content from imzML.jl ---
@ -310,9 +294,8 @@ end
load_slices(folder, masses, tolerance) load_slices(folder, masses, tolerance)
Loads image slices for multiple masses from all `.imzML` files in a directory. Loads image slices for multiple masses from all `.imzML` files in a directory.
This function is optimized to read the binary data file (`.ibd`) only once per file. This function is now refactored to use the new MSIData architecture and its
It iterates through each spectrum, reads its data, and finds all target masses caching capabilities.
before proceeding to the next spectrum, minimizing disk I/O.
""" """
function load_slices(folder, masses, tolerance) function load_slices(folder, masses, tolerance)
files = filter(f -> endswith(f, ".imzML"), readdir(folder, join=true)) files = filter(f -> endswith(f, ".imzML"), readdir(folder, join=true))
@ -331,43 +314,27 @@ function load_slices(folder, masses, tolerance)
push!(names, name) push!(names, name)
@info "Processing $(i)/$(n_files): $(name)" @info "Processing $(i)/$(n_files): $(name)"
imzML_data = @time load_imzml(file) # This is fast, it's fine. # Load data using the new lazy loader, returning an MSIData object
msi_data = @time load_imzml_lazy(file)
# Create empty images for all slices for the current file # Create empty images for all slices for the current file
current_file_slices = [zeros(Float64, imzML_data.width, imzML_data.height) for _ in 1:n_slices] width, height = msi_data.image_dims
current_file_slices = [zeros(Float64, width, height) for _ in 1:n_slices]
hIbd = imzML_data.ibd_handle # Use the high-performance iterator to process all spectra
mz_format = imzML_data.mz_format _iterate_spectra_fast(msi_data) do spec_idx, mz_array, intensity_array
int_format = imzML_data.intensity_format meta = msi_data.spectra_metadata[spec_idx]
# Pre-allocate arrays to be reused for each spectrum
mz_array = Array{mz_format}(undef, 0)
intensity_array = Array{int_format}(undef, 0)
# Iterate through each spectrum ONCE
for meta in imzML_data.spectra_metadata
# Resize arrays if the number of points in the spectrum has changed
if length(mz_array) != meta.mz_count
resize!(mz_array, meta.mz_count)
resize!(intensity_array, meta.intensity_count)
end
# Read spectrum data ONCE from the .ibd file
seek(hIbd, meta.mz_offset)
read!(hIbd, mz_array)
seek(hIbd, meta.intensity_offset)
read!(hIbd, intensity_array)
# Now, check for all masses of interest in this single spectrum # Now, check for all masses of interest in this single spectrum
for (j, mass) in enumerate(masses) for (j, mass) in enumerate(masses)
intensity = find_mass(mz_array, intensity_array, mass, tolerance) intensity = find_mass(mz_array, intensity_array, mass, tolerance)
if intensity > 0.0 if intensity > 0.0
if 1 <= meta.x <= imzML_data.width && 1 <= meta.y <= imzML_data.height if 1 <= meta.x <= width && 1 <= meta.y <= height
current_file_slices[j][meta.x, meta.y] = intensity current_file_slices[j][meta.y, meta.x] = intensity
end end
end end
end end
end # end of spectra loop end # end of fast iterator
# Assign the generated images to the main list # Assign the generated images to the main list
for j in 1:n_slices for j in 1:n_slices
@ -379,6 +346,70 @@ function load_slices(folder, masses, tolerance)
return (img_list, names) return (img_list, names)
end end
"""
plot_slice(msi_data::MSIData, mass::Float64, tolerance::Float64, output_dir::String; stage_name="slice", bins=256)
Generates and saves a plot of a single image slice for a given m/z value.
This function closely imitates the logic of the original `GetSlice` but uses
the modern `MSIData` access patterns and robust peak finding.
"""
function plot_slice(msi_data::MSIData, mass::Real, tolerance::Real, output_dir::String; stage_name="slice_mz_$(mass)", bins=256)
# 1. Create an empty image for the slice, with dimensions matching plotting expectations
width, height = msi_data.image_dims
slice_matrix = zeros(Float64, height, width)
# 2. Iterate through each spectrum to build the slice
println("Generating slice for m/z $mass...")
_iterate_spectra_fast(msi_data) do spec_idx, mz_array, intensity_array
meta = msi_data.spectra_metadata[spec_idx]
# Find the peak intensity using the modern, robust find_mass
intensity = find_mass(mz_array, intensity_array, mass, tolerance)
if intensity > 0.0
# Populate the matrix using (y, x) indexing
if 1 <= meta.x <= width && 1 <= meta.y <= height
slice_matrix[meta.y, meta.x] = intensity
end
end
end
println("Slice generation complete.")
# 3. Plot the resulting slice matrix using CairoMakie
println("Plotting slice...")
fig = Figure(size = (600, 500))
ax = CairoMakie.Axis(fig[1, 1],
aspect=DataAspect(),
title=@sprintf("Slice for m/z: %.2f", mass)
)
hidedecorations!(ax)
# Use mass-specific bounds for colorrange, ensuring a valid range
min_val, max_val = extrema(slice_matrix)
if min_val == max_val
max_val = min_val + 1.0 # Ensure the color range has a non-zero width
end
hm = heatmap!(ax, slice_matrix,
colormap=cgrad(ColorSchemes.viridis, bins),
colorrange=(min_val, max_val)
)
Colorbar(fig[1, 2], hm, label="Intensity")
colgap!(fig.layout, 5)
# 4. Save the plot
mkpath(output_dir)
filename = "$(stage_name).png"
save_path = joinpath(output_dir, filename)
save(save_path, fig)
@info "Saved slice plot to $save_path"
return fig
end
# ============================================================================ # ============================================================================
# #
# #
@ -647,53 +678,3 @@ function plot_slices(slices, names, masses, output_dir; stage_name, bins=256, dp
end end
return fig return fig
end end
# =============================================================================
#
#
# Main Workflow
#
# ============================================================================
function load_config(path)
config = Dict{String, Any}()
if !isfile(path)
@warn "Config file not found at $(path). Using default parameters."
# Define defaults here in case the file is missing
config["masses"] = [100]
config["tolerance"] = 0.1
config["color_depth"] = 255
config["outlier_prob"] = 0.98
return config
end
for line in eachline(path)
line = strip(line)
if isempty(line) || startswith(line, "#")
continue # Skip empty lines and comments
end
parts = split(line, '=', limit=2)
if length(parts) != 2
@warn "Skipping malformed line in config: $(line)"
continue
end
key = strip(parts[1])
value_str = strip(parts[2])
try
if key == "masses"
values = [parse(Float64, s) for s in split(value_str, ',')]
config[key] = values
elseif key == "tolerance"
config[key] = parse(Float64, value_str)
elseif key == "color_depth"
config[key] = parse(Int, value_str)
elseif key == "outlier_prob"
config[key] = parse(Float64, value_str)
end
catch e
@error "Could not parse value for key '$(key)': $(value_str)"
end
end
return config
end

246
src/imzML_old.jl
View File

@ -1,246 +0,0 @@
# include( "Common.jl" );
# *******************************************************************
# Load Spectra and return a matrix
# fileName: Full name path
# *******************************************************************
"""
LoadImzml( fileName )
Load an imzML file as a matrix. Each column stores x-pixel position,
y-pixel position, x-axis data and y-axis data.
# Arguments
* `fileName`: Full path name of the imzML file
# Examples
```julia
# Load DESI MSI Carcinoma image data
spectra = LoadImzml( "80TopL, 50TopR, 70BottomL, 60BottomR-centroid.imzML" )
size( spectra )
(4, 18632)
```
"""
function LoadImzml( fileName )
# Open file handles
if !isfile(fileName)
error("provided path is not a file")
end
if endswith(fileName, ".imzML")
stream = open(fileName)
hIbd = open(replace(fileName, ".imzML" => ".ibd"))
else
stream = open(fileName * ".imzML")
hIbd = open(fileName * ".ibd")
end
# Get axes types and image dimensions
axis = AxesConfigImg( stream )
imgDim = GetImgDimensions( stream )
format = [ axis[1].Format, axis[2].Format ]
# Locate spectrum attributes
start = position( stream )
attr = GetSpectrumAttributes( stream, hIbd )
# Load spectra
seek( stream, start )
spectra = LoadImgData( stream, hIbd, attr, imgDim[3], format )
close( stream )
close( hIbd )
return spectra
end
# *******************************************************************
# Get axes value type
# *******************************************************************
function AxesConfigImg( stream )
# Locate which axis is defined at first
tag = FindTag( stream, r"^\s*<(referenceableParamGroup )" )
value = GetAttribute( tag.captures[1], "intensityArray" )
order = 1 + ( value !== nothing )
# Read first axis configuration
axis = Array{ SpecDim, 1 }( undef, 2 )
axis[ order ] = ConfigureSpecDim( stream )
# Read second axis configuration
FindTag( stream, r"^\s*<(referenceableParamGroup )" )
axis[ xor( order,3 ) ] = ConfigureSpecDim( stream )
return axis
end
# *******************************************************************
# Get vector's storage options and image dimensions
# *******************************************************************
function GetImgDimensions( stream )
# Looks for "scanSettings" tag
# FindImgTag( stream, "scanSettings" )
FindTag( stream, r"^\s*<(scanSettings )" )
# Initial values for dimension retrieve
n = 2
dim = [ 0, 0, 0 ]
currLine = ""
matchInfo = RegexMatch
while( n > 0 )
# Next field
currLine = readline( stream )
matchInfo = match( r"^\s*<(cvParam)", currLine )
index = length( matchInfo.captures[1] )
matchInfo = GetAttribute( currLine[index:end], "accession" )
# Get axis identity
if( matchInfo.captures[1] == "IMS:1000042" # max X
|| matchInfo.captures[1] == "IMS:1000043" ) # max Y
# Read dimension's pixels
axis = matchInfo.captures[1][end] - '1'
index += matchInfo.offsets[1] + length( matchInfo.captures[1] )
matchInfo = GetAttribute( currLine[index:end], "value" )
dim[axis] = parse( Int32, matchInfo.captures[1] )
n -= 1
end
end
# Load stored spectra counter
matchInfo = FindTag( stream, r"^\s*<spectrumList(.+)" )
matchInfo = GetAttribute( matchInfo.captures[1], "count" )
dim[ 3 ] = parse( Int32, matchInfo.captures[1] )
return dim
end
# *******************************************************************
# Length of "spectrum" tag without attribute values
# *******************************************************************
function GetSpectrumTag( stream )
offset = position( stream )
tag = FindTag( stream, r"^\s*<spectrum (.+)" )
first = 1
while true
value = match( r"[^=]+=\"([^\"]+)\"", tag.captures[1][first:end] )
if value === nothing
break
end
first += value.offsets[1] + length( value.captures[1] )
offset += length( value.captures[1] )
end
return offset
end
# seek( stream, 7141 )
# *******************************************************************
# Locate spectrum attribute's
# [1] 1: x position stored first 2: y position stored first
# [2] Second stored position
# [3] 1: mzArray stored first 2: intensityArray stored first
# [4] Second stored axis
# [5] skip chars to find first dimension
# [6] skip chars to find second dimension
# [7] skip chars to find vector length
# [8] skip chars to find next spectrum
# *******************************************************************
function GetSpectrumAttributes( stream, hIbd )
# Reserve memory for vector configuration
skip = Vector{ UInt32 }( undef, 8 )
offset = GetSpectrumTag( stream )
# Get axis order and position of pixel coordinate values
tag = FindTag( stream, r" accession=\"IMS:100005(\d)\"(.+)" )
skip[1] = tag.captures[1][1] + 1 - '0'
skip[2] = xor( skip[1], 3 )
value = match( r" value=\"(\d+)\".+", tag.captures[2] )
skip[5] = position( stream ) - offset - length( value.match ) - 2
value = match( r" value=\"\d+\".+", readline( stream ) )
skip[6] = value.offset
# Get axis order
offset = position( stream )
tag = FindTag( stream, r"^\s*<referenceableParamGroupRef(.+)" )
value = GetAttribute( tag.captures[1], "ref" )
skip[3] = ( value.captures[1] == "intensityArray" ) + 3
skip[4] = xor( skip[3], 7 )
k = 2
while k != 0
tag = FindTag( stream, r" accession=\"IMS:100010(\d)\"(.+)" )
# Set IBD offset for first spectrum
if tag.captures[1][1] == '2'
value = GetAttribute( tag.match, "value" )
seek( hIbd, parse( Int32, value.captures[1] ) )
k -= 1
continue
elseif tag.captures[1][1] == '3'
skip[7] = position( stream ) - offset - length( tag.match )
offset = position( stream )
k -= 1
end
end
# Compute characters to skip
FindTag( stream, r"^\s*</spectrum" )
skip[8] = position( stream ) - offset
return skip
end
# *******************************************************************
# Read spectral data
# *******************************************************************
function LoadImgData( stream, hIbd, attr, imgDim, format )
# Reserve spectra memory & update IBD seek offset
spectra = Array{Any}( undef, ( 4, imgDim ) )
contador = 0;
for k in 1:imgDim
# Load image coordinates
skip( stream, attr[5] )
value = FindTag( stream, r"value=\"(\d+)\"" )
spectra[ attr[1],k ] = parse( Int32, value.captures[1] )
skip( stream, attr[6] )
value = FindTag( stream, r"value=\"(\d+)\"" )
spectra[ attr[2],k ] = parse( Int32, value.captures[1] )
# Get vector length
skip( stream, attr[7] )
value = FindTag( stream, r"value=\"(\d+)\"" )
nPoints = parse( Int32, value.captures[1] )
# Reserve memory and read spectrum
spectra[ 3,k ] = Array{ format[1] }( undef, nPoints )
spectra[ 4,k ] = Array{ format[2] }( undef, nPoints )
read!( hIbd, spectra[ attr[3],k ] )
read!( hIbd, spectra[ attr[4],k ] )
skip( stream, attr[8] )
end
return spectra
end

219
src/mzML.jl
View File

@ -1,78 +1,89 @@
# /home/pixel/Documents/Cinvestav_2025/JuliaMSI/src/mzML_lazy.jl # /home/pixel/Documents/Cinvestav_2025/JuliaMSI/src/mzML.jl
using Base64, Libz # This file is responsible for parsing metadata from .mzML files.
include("ParserHelpers.jl") # It has been refactored to produce a unified MSIData object.
# ============================================================================
# Data Structures for Lazy Loading
# ============================================================================
struct SpectrumAsset
format::Type
is_compressed::Bool
offset::Int64
encoded_length::Int32
axis_type::Symbol # :mz or :intensity
end
struct MzMLSpectrumMetadata
id::String
mz_asset::SpectrumAsset
intensity_asset::SpectrumAsset
end
mutable struct MzMLData
file_handle::IO
spectra_metadata::Vector{MzMLSpectrumMetadata}
function MzMLData(file_handle::IO, spectra_metadata::Vector{MzMLSpectrumMetadata})
obj = new(file_handle, spectra_metadata)
finalizer(obj) do o
if isopen(o.file_handle)
close(o.file_handle)
end
end
return obj
end
end
# ============================================================================
# mzML Parser Implementation
# ============================================================================
# This function is kept internal to the mzML parsing process
function get_spectrum_asset_metadata(stream) function get_spectrum_asset_metadata(stream)
start_pos = position(stream) start_pos = position(stream)
bda_tag = find_tag(stream, r"<binaryDataArray\s+encodedLength=\"(\d+)\"") bda_tag = find_tag(stream, r"<binaryDataArray\s+encodedLength=\"(\d+)\"" )
if bda_tag === nothing; error("Cannot find binaryDataArray"); end if bda_tag === nothing
error("Cannot find binaryDataArray")
end
encoded_length = parse(Int32, bda_tag.captures[1]) encoded_length = parse(Int32, bda_tag.captures[1])
params = CVParams(Float64, false, :mz) # Initialize parameters as separate variables
data_format = Float64
compression_flag = false
axis = :mz
while true while true
line = readline(stream) line = readline(stream)
if occursin("</binaryDataArray>", line); break; end if occursin("</binaryDataArray>", line)
break
end
if occursin("<cvParam", line) if occursin("<cvParam", line)
accession = get_attribute(line, "accession") accession = get_attribute(line, "accession")
if accession === nothing; continue; end if accession === nothing
update_cv_params!(params, accession.captures[1]) continue
end
acc_str = accession.captures[1]
# println("DEBUG: Processing accession: $acc_str")
# Direct inline logic - NO FUNCTION CALLS
if acc_str == "MS:1000514"
axis = :mz
# println("DEBUG: Set axis_type to :mz")
elseif acc_str == "MS:1000515"
axis = :intensity
# println("DEBUG: Set axis_type to :intensity")
elseif acc_str == "MS:1000518"
data_format = Int16
# println("DEBUG: Set format to Int16")
elseif acc_str == "MS:1000519"
data_format = Int32
# println("DEBUG: Set format to Int32")
elseif acc_str == "MS:1000520"
data_format = Float64
# println("DEBUG: Set format to Float64")
elseif acc_str == "MS:1000521"
data_format = Float32
# println("DEBUG: Set format to Float32")
elseif acc_str == "MS:1000522"
data_format = Int64
# println("DEBUG: Set format to Int64")
elseif acc_str == "MS:1000523"
data_format = Float64
# println("DEBUG: Set format to Float64")
elseif acc_str == "MS:1000574"
compression_flag = true
# println("DEBUG: Set is_compressed to true")
elseif acc_str == "MS:1000576"
compression_flag = false
# println("DEBUG: Set is_compressed to false")
else
# println("DEBUG: Unknown accession: $acc_str")
end
end end
end end
seek(stream, start_pos) seek(stream, start_pos)
binary_tag = find_tag(stream, r"<binary>") readuntil(stream, "<binary>")
if binary_tag === nothing; error("Cannot find binary tag"); end
binary_offset = position(stream) binary_offset = position(stream)
find_tag(stream, r"</binaryDataArray>") # Position for next call # Move stream to the end of the binary data array for the next iteration
readuntil(stream, "</binaryDataArray>")
return SpectrumAsset(params.format, params.is_compressed, binary_offset, encoded_length, params.axis_type) # Create SpectrumAsset directly from the variables
return SpectrumAsset(data_format, compression_flag, binary_offset, encoded_length, axis)
end end
# This function is updated to return the generic SpectrumMetadata struct
function parse_spectrum_metadata(stream, offset::Int64) function parse_spectrum_metadata(stream, offset::Int64)
seek(stream, offset) seek(stream, offset)
id_match = find_tag(stream, r"<spectrum\s+index=\"\d+\"\s+id=\"([^"]+)\"") id_match = find_tag(stream, r"<spectrum\s+index=\"\d+\"\s+id=\"([^\"]+)" )
id = id_match === nothing ? "" : id_match.captures[1] id = id_match === nothing ? "" : id_match.captures[1]
asset1 = get_spectrum_asset_metadata(stream) asset1 = get_spectrum_asset_metadata(stream)
@ -81,111 +92,113 @@ function parse_spectrum_metadata(stream, offset::Int64)
mz_asset = asset1.axis_type == :mz ? asset1 : asset2 mz_asset = asset1.axis_type == :mz ? asset1 : asset2
int_asset = asset1.axis_type == :intensity ? asset1 : asset2 int_asset = asset1.axis_type == :intensity ? asset1 : asset2
return MzMLSpectrumMetadata(id, mz_asset, int_asset) # Create the new unified metadata object
# For mzML, x and y coordinates are not applicable, so we use 0.
return SpectrumMetadata(0, 0, id, mz_asset, int_asset)
end end
function parse_offset_list(stream) function parse_offset_list(stream)
offsets = Int64[] offsets = Int64[]
while true offset_regex = r"<offset[^>]*>(\d+)</offset>"
# Actively search for offset tags, ignoring other lines until the end of the index is found.
while !eof(stream)
line = readline(stream) line = readline(stream)
m = match(r"<offset\s+idRef=\"\S+\">(\d+)</offset>", line)
if m !== nothing # First, check for the end condition.
push!(offsets, parse(Int64, m.captures[1])) if occursin("</index>", line) || occursin("</indexedmzML>", line)
elseif occursin("</index>", line) || occursin("</indexedmzML>", line)
break break
end end
# If it's not the end, see if it's an offset tag.
m = match(offset_regex, line)
if m !== nothing
push!(offsets, parse(Int64, m.captures[1]))
end
# If it's neither, ignore the line and continue the loop.
end end
return offsets return offsets
end end
function load_mzml_lazy(file_path::String) # This is the main lazy-loading function for mzML, now returning an MSIData object.
stream = open(file_path) function load_mzml_lazy(file_path::String; cache_size::Int=100)
println("DEBUG: Opening file stream for $file_path")
stream = open(file_path, "r")
try try
println("DEBUG: Seeking to end of file.")
seekend(stream) seekend(stream)
skip(stream, -4096) # Read last 4KB println("DEBUG: Skipping back to read footer.")
skip(stream, -4096)
footer = read(stream, String) footer = read(stream, String)
println("DEBUG: Footer read successfully.")
index_offset_match = match(r"<indexListOffset>(\d+)</indexListOffset>", footer) index_offset_match = match(r"<indexListOffset>(\d+)</indexListOffset>", footer)
if index_offset_match === nothing if index_offset_match === nothing
close(stream)
error("Could not find <indexListOffset>. File may not be an indexed mzML.") error("Could not find <indexListOffset>. File may not be an indexed mzML.")
end end
println("DEBUG: Found indexListOffset.")
index_offset = parse(Int64, index_offset_match.captures[1]) index_offset = parse(Int64, index_offset_match.captures[1])
println("DEBUG: Seeking to index list at offset $index_offset.")
seek(stream, index_offset) seek(stream, index_offset)
println("DEBUG: Searching for '<index name=\"spectrum\">'.")
if find_tag(stream, r"<index\s+name=\"spectrum\"") === nothing if find_tag(stream, r"<index\s+name=\"spectrum\"") === nothing
close(stream)
error("Could not find spectrum index.") error("Could not find spectrum index.")
end end
println("DEBUG: Found spectrum index tag. ")
println("DEBUG: Parsing spectrum offsets...")
spectrum_offsets = parse_offset_list(stream) spectrum_offsets = parse_offset_list(stream)
if isempty(spectrum_offsets) if isempty(spectrum_offsets)
close(stream)
error("No spectrum offsets found.") error("No spectrum offsets found.")
end end
println("DEBUG: Found $(length(spectrum_offsets)) spectrum offsets.")
println("DEBUG: Parsing metadata for each spectrum...")
spectra_metadata = [parse_spectrum_metadata(stream, offset) for offset in spectrum_offsets] spectra_metadata = [parse_spectrum_metadata(stream, offset) for offset in spectrum_offsets]
println("DEBUG: Metadata parsing complete.")
# We return the stream inside MzMLData, so we don't close it here. # Assuming uniform data formats, take from the first spectrum
# The finalizer on MzMLData will handle it. first_meta = spectra_metadata[1]
return MzMLData(stream, spectra_metadata) mz_format = first_meta.mz_asset.format
intensity_format = first_meta.int_asset.format
source = MzMLSource(stream, mz_format, intensity_format)
println("DEBUG: Creating MSIData object.")
return MSIData(source, spectra_metadata, (0, 0), nothing, cache_size)
catch e catch e
close(stream) # Close file on error close(stream) # Ensure stream is closed on error
rethrow(e) rethrow(e)
end end
end end
# ============================================================================
# Data Access Functions
# ============================================================================
function read_binary_vector(io::IO, asset::SpectrumAsset)
seek(io, asset.offset)
# Read the raw base64 data. The regex is slow. Reading bytes is better.
# The old code did `Vector{UInt8}(base64Vec.captures[1])`. This implies ASCII.
raw_b64 = read(io, asset.encoded_length)
decoded_bytes = base64decode(String(raw_b64))
bytes_io = IOBuffer(asset.is_compressed ? Libz.inflate(decoded_bytes) : decoded_bytes)
n_elements = Int(bytes_io.size / sizeof(asset.format))
out_array = Array{asset.format}(undef, n_elements)
read!(bytes_io, out_array)
return out_array
end
function get_spectrum(data::MzMLData, index::Int)
meta = data.spectra_metadata[index]
mz_array = read_binary_vector(data.file_handle, meta.mz_asset)
intensity_array = read_binary_vector(data.file_handle, meta.intensity_asset)
return (id=meta.id, mz=mz_array, intensity=intensity_array)
end
""" """
LoadMzml(fileName::String) LoadMzml(fileName::String)
Eagerly loads all spectra from a .mzML file. Eagerly loads all spectra from a .mzML file.
Provided for backward compatibility. Provided for backward compatibility. Now uses the new MSIData architecture.
""" """
function LoadMzml(fileName::String) function LoadMzml(fileName::String)
mzml_data = load_mzml_lazy(fileName) # Use the lazy loader to get the MSIData object
msi_data = load_mzml_lazy(fileName, cache_size=0) # No need to cache if we load all
num_spectra = length(mzml_data.spectra_metadata) num_spectra = length(msi_data.spectra_metadata)
spectra_matrix = Array{Any}(undef, (2, num_spectra)) spectra_matrix = Array{Any}(undef, (2, num_spectra))
for i in 1:num_spectra for i in 1:num_spectra
spectrum = get_spectrum(mzml_data, i) # Use the new GetSpectrum API
spectra_matrix[1, i] = spectrum.mz mz, intensity = GetSpectrum(msi_data, i)
spectra_matrix[2, i] = spectrum.intensity spectra_matrix[1, i] = mz
spectra_matrix[2, i] = intensity
end end
# Eager load, so we can close the handle now. # The finalizer on MSIData will close the handle, so no need to close it here.
close(mzml_data.file_handle)
return spectra_matrix return spectra_matrix
end end

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@ -1,350 +0,0 @@
# *******************************************************************
# Load scans from mzML file
# fileName: Full name path
# *******************************************************************
"""
`LoadMzml( fileName )`
Load the mzML file as a Matrix. Each column stores a single scan,
x-axis and y-axis scan data are stored in the first and second
row respectively.
# Arguments
* `fileName`: Full path name of the mzML file
# Examples
```julia
spectra = LoadMzml( "T9_A1.mzML" )
size( spectra )
(2, 10)
using Plots
plot( spectra[1,4], spectra[2,4] )
```
The following image will appear in an auxiliary window
![](./Plots.bmp)
"""
function LoadMzml( fileName )
# Open file hFile = open( joinpath( data_dir, "Col_1.mzML" ), "r+" )
stream = open( fileName, "r+" )
intensity = []
# Load footer
seekend( stream )
skip( stream, -160 )
raw = read( stream, 160 )
footer = String( raw )
# Search "indexListOffset" tag
index = match( r"<indexListOffset>(?<Ofst>\d+)</indexListOffset>", footer )
if index !== nothing
# Jump to index table
seek( stream, parse( Int64, index.captures[1] ) )
# Find first "index" tag
index = FindTag( stream, r"<index +name=\"spectrum" )
# Load offset list and load spectra
if index !== nothing
intensity = LoadSpectra( stream, ParseOffsetList( stream ) )
end
end
# Close file handle
close( stream )
# Return spectral matrix
return intensity
end
# *******************************************************************
# Parse indexList offsets
# stream: Source file stream
# *******************************************************************
function ParseOffsetList( stream )
# List of 8 elements
entry = zeros( Int64, 8 )
used = 0
unused = 8
while true
# Get offset string
raw = readline( stream )
index = match( r">(?<Ofst>\d+)<", String( raw ) )
# Exit condition
if index === nothing
break
end
# Save index
used += 1
unused -= 1
entry[used] = parse( Int64, index.captures[1] )
# Grow list when needed
if unused == 0
append!( entry, zeros( Int64, 8 ) )
unused = 8
end
end
return entry[1:used]
end
# *******************************************************************
# Read vector data
# stream: Source file stream
# *******************************************************************
function ReadVector( stream, axis )
# Read base64 vector
base64Vec = FindTag( stream, r"<binary>([^<]+)<" )
base64Vec = Vector{ UInt8 }( base64Vec.captures[1] )
# Fill a IO stream with decoded data
if axis.Packed == 1
io = IOBuffer( Libz.inflate( Decode64( base64Vec ) ) )
else
io = IOBuffer( Decode64( base64Vec ) )
end
# Convert IO stream content as dataType vector
nElem = Int32( io.size / sizeof( axis.Format ) )
out = Array{ axis.Format }( undef, nElem )
read!( io, out )
return out
end
# *******************************************************************
# Get the decoding options for the first vector in spectrum
# stream: Valid file stream
# lastTag: Last tag to skip i.e. "binaryDataArray"
# *******************************************************************
function AxisConfig( stream )
offset = position( stream )
skip = 0
while true
# Load line
raw = readline( stream )
tag = match( r"^\s*<([^\s]+)", raw )
start = length( tag.match ) + 1
# Is a "cvParam" tag?
if tag.captures[1] == "cvParam"
# Get accesion field value
attribute = GetAttribute( raw[ start:end ], "accession" )
# Subtract file name length from skip field
if attribute.captures[1] != "MS:1000796"
continue
else
start += attribute.offset + length( attribute.match )
value = GetAttribute( raw[ start:end ], "value" )
skip += length( value.captures[1] )
continue
end
# Exit condition
elseif tag.captures[1] == "binaryDataArray"
value = GetAttribute( raw[ start:end ], "encodedLength" )
offset = position( stream ) - offset
front = ConfigureSpecDim( stream )
front.Skip += offset - length( value.captures[1] ) - skip
return ( front )
end
end
end
# *******************************************************************
# Load Spectra and return a matrix
# stream: Source file stream
# *******************************************************************
function LoadSpectra( stream, offset )
# Move file pointer towards first spectrum tag
seek( stream, offset[1] )
# Decodes axis information and skip counter
firstAxis = AxisConfig( stream )
secondAxis = AxisConfig( stream )
# Allocates memory for spectra storage
specCount = length( offset )
spectrum = Array{ Any }( undef, ( 2, specCount ) )
index = 1
order = 1 + ( firstAxis.Axis == 2 )
for i in 1:specCount
# Load first vector
seek( stream, offset[ i ] )
skip( stream, firstAxis.Skip )
spectrum[ order, i ] = ReadVector( stream, firstAxis )
# Load second vector
skip( stream, secondAxis.Skip )
spectrum[ xor( order,3 ), i ] = ReadVector( stream, secondAxis )
end
return( spectrum )
end
# *******************************************************************
# Decoding base64 blocks
# *******************************************************************
# Decoding exchange table
base64dec = Vector{UInt8}( [
62, # (01) + -> 43d, 0x2B
0, # (02) ,
0, # (03) -
0, # (04) .
63, # (05) /
52, # (06) 0
53, # (07) 1
54, # (08) 2
55, # (09) 3
56, # (10) 4
57, # (11) 5
58, # (12) 6
59, # (13) 7
60, # (14) 8
61, # (15) 9
0, # (16) :
0, # (17) ;
0, # (18) <
0, # (19) =
0, # (20) >
0, # (21) ?
0, # (22) @
0, # (23) A
1, # (24) B
2, # (25) C
3, # (26) D
4, # (27) E
5, # (28) F
6, # (29) G
7, # (40) H
8, # (41) I
9, # (42) J
10, # (43) K
11, # (44) L
12, # (45) M
13, # (46) N
14, # (47) O
15, # (48) P
16, # (49) Q
17, # (40) R
18, # (41) S
19, # (42) T
20, # (43) U
21, # (44) V
22, # (45) W
23, # (46) X
24, # (47) Y
25, # (48) Z
0, # (49) [
0, # (50) \
0, # (51) ]
0, # (52) ^
0, # (53) _
0, # (54) `
26, # (55) a
27, # (56) b
28, # (57) c
29, # (58) d
30, # (59) e
31, # (60) f
32, # (61) g
33, # (62) h
34, # (63) i
35, # (64) j
36, # (65) k
37, # (66) l
38, # (67) m
39, # (68) n
40, # (69) o
41, # (70) p
42, # (71) q
43, # (72) r
44, # (73) s
45, # (74) t
46, # (75) u
47, # (76) v
48, # (77) w
49, # (78) x
50, # (79) y
51, # (80) z
] )
# base64 decoding
function DecodeTriplet( data, base64 )
# Character to binary equivalent
data = data .- 0x2A
data[1] = base64[ data[1] ]
data[2] = base64[ data[2] ]
data[3] = base64[ data[3] ]
data[4] = base64[ data[4] ]
# Get Triplet
decode = Array{UInt8}( undef,3 )
decode[1] = data[1] << 2 + data[2] >> 4
decode[2] = data[2] << 4 + data[3] >> 2
decode[3] = data[3] << 6 + data[4]
return decode
end
function Decode64( data )
# Reserve uninitialized memory
block = divrem( sizeof( data ), 4 )
decode = Array{UInt8}( undef, 3*block[1] )
# Recover binary from Chars
index = 1
first = 1
last = 3
for i in 1:block[1]
decode[first:last] = DecodeTriplet( data[index:index+3], base64dec )
index += 4
first += 3
last += 3
end
# Adjust block size
if data[end-1] == 0x3D
decode = decode[1:end-2]
elseif data[end] == 0x3D
decode = decode[1:end-1]
end
return decode
end

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to run the tests:
time julia --project=. test/run_tests.jl
to enable the different test cases, there are boolean variables
test1 = true
test2 = true
test3 = true
set them to true to perform that specific test.
test 1 consists in mzml validation and spectrum plotting
test 2 consists in imzml conversion and validation
test 3 consists in imzml validation and spectrum and slice plotting
use the global variables:
TEST_MZML_FILE, SPECTRUM_TO_PLOT, CONVERSION_SOURCE_MZML, CONVERSION_SYNC_FILE, CONVERSION_TARGET_IMZML, TEST_IMZML_FILE, MZ_VALUE_FOR_SLICE, MZ_TOLERANCE, COORDS_TO_PLOT, RESULTS_DIR
to modify input that the test script will recieve.

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