seascape

Read functions for analysis of Waters *.raw files.

Turner Seascape from tate.org.uk

Scope

There are a range of functions for reading and processing Waters .raw files. The workflow for 1D pre-processing can be found in Workflow1D.m which details the stages from:

Import raw data
Determine average spectrum for each file
Peak picking with FT noise reduction
Peak extraction

Statistical analysis, and processing of 2D imaging files, is not performed in this repository. For the former, see maml and the latter see imzmlProc.

WatersRaw

This is a MATLAB class for easier import of Waters .raw files. To initiate an object w = WatersRaw(filePath,fileName) which initially gets the required informaiton from the file, namely:

Pointers
w.numS - the number of scans
w.grid - the grid in raw coordinates
w.xy - the grid that sized as [1:numR,1:numC]
w.sz - the size of the grid, being [numR numC]

There are two methods; the first is readFullGrid() which runs on initiation (it can be slow) as all scan coordinates need to be read. The second method allows a single spectrum to be read from the raw file:

[mz,sp,gridXY] = w.readSpectrum(i)

i takes values from 1:w.numS. Note that to construct an image, reference needs to be made to w.xy, where w.xy(1,1) provides the index i for the top left pixel and w.xy(w.sz(1),w.sz(2)) the index i for the bottom right pixel. The values of gridXY are raw coordinates as found in w.grid.

Thus to read in an image in sequential format (i.e. from the top of each row downwards, then across to the next row, moving left to right), employ the following code:

g = reshape(w.xy,[w.sz(1)*w.sz(2) 1]);
tot = zeros(w.sz(1)*w.sz(2),1);

for n = 1:w.numS

    [mz,sp,~] = w.readSpectrum(g(n));
    tot(n) = sum(sp);

end

tot = reshape(tot,w.sz);

Dependencies

The following code/repositories/packages are required to successfully run this code.

ftpeakpeak